Linker-mediated assembly of gold nanoparticles into multimeric motifs

Energy Technology Data Exchange (ETDEWEB)

Sikora, Mateusz; Cieplak, Marek [Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, 02-668 Warsaw (Poland); Szymczak, Piotr [Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, ulica Hoza 69, 00-681 Warsaw (Poland); Thompson, Damien, E-mail: mc@ifpan.edu.pl [Tyndall National Institute, Lee Maltings, University College Cork, Cork (Ireland)

2011-11-04

We present a theoretical description of linker-mediated self-assembly of gold nanoparticles (Au-NP). Using mesoscale simulations with a coarse-grained model for the Au NPs and dirhenium-based linker molecules, we investigate the conditions under which large clusters can grow and construct a phase diagram that identifies favorable growth conditions in terms of floating and bound linker concentrations. The findings can be considered as generic, as we expect other NP-linker systems to behave in a qualitatively similar way. In particular, we also discuss the case of antibody-functionalised Au NPs connected by the C-reactive proteins (CRPs). We extract some general rules for NP linking that may aid the production of size- and shape-specific NP clusters for technology applications.

Morphological changes of plasma membrane and protein assembly during clathrin-mediated endocytosis

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Yoshida, Aiko; Sakai, Nobuaki; Uekusa, Yoshitsugu; Imaoka, Yuka; Itagaki, Yoshitsuna; Suzuki, Yuki

2018-01-01

Clathrin-mediated endocytosis (CME) proceeds through a series of morphological changes of the plasma membrane induced by a number of protein components. Although the spatiotemporal assembly of these proteins has been elucidated by fluorescence-based techniques, the protein-induced morphological changes of the plasma membrane have not been fully clarified in living cells. Here, we visualize membrane morphology together with protein localizations during CME by utilizing high-speed atomic force microscopy (HS-AFM) combined with a confocal laser scanning unit. The plasma membrane starts to invaginate approximately 30 s after clathrin starts to assemble, and the aperture diameter increases as clathrin accumulates. Actin rapidly accumulates around the pit and induces a small membrane swelling, which, within 30 s, rapidly covers the pit irreversibly. Inhibition of actin turnover abolishes the swelling and induces a reversible open–close motion of the pit, indicating that actin dynamics are necessary for efficient and irreversible pit closure at the end of CME. PMID:29723197

Assembly of spikes into coronavirus particles is mediated by the carboxy-terminal domain of the spike protein

NARCIS (Netherlands)

Godeke, G J; de Haan, Cornelis A M; Rossen, J W; Vennema, H; Rottier, P J

The type I glycoprotein S of coronavirus, trimers of which constitute the typical viral spikes, is assembled into virions through noncovalent interactions with the M protein. Here we demonstrate that incorporation is mediated by the short carboxy-terminal segment comprising the transmembrane and

A biomimetic colorimetric logic gate system based on multi-functional peptide-mediated gold nanoparticle assembly.

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Li, Yong; Li, Wang; He, Kai-Yu; Li, Pei; Huang, Yan; Nie, Zhou; Yao, Shou-Zhuo

2016-04-28

In natural biological systems, proteins exploit various functional peptide motifs to exert target response and activity switch, providing a functional and logic basis for complex cellular activities. Building biomimetic peptide-based bio-logic systems is highly intriguing but remains relatively unexplored due to limited logic recognition elements and complex signal outputs. In this proof-of-principle work, we attempted to address these problems by utilizing multi-functional peptide probes and the peptide-mediated nanoparticle assembly system. Here, the rationally designed peptide probes function as the dual-target responsive element specifically responsive to metal ions and enzymes as well as the mediator regulating the assembly of gold nanoparticles (AuNPs). Taking advantage of Zn2+ ions and chymotrypsin as the model inputs of metal ions and enzymes, respectively, we constructed the peptide logic system computed by the multi-functional peptide probes and outputted by the readable colour change of AuNPs. In this way, the representative binary basic logic gates (AND, OR, INHIBIT, NAND, IMPLICATION) have been achieved by delicately coding the peptide sequence, demonstrating the versatility of our logic system. Additionally, we demonstrated that the three-input combinational logic gate (INHIBIT-OR) could also be successfully integrated and applied as a multi-tasking biosensor for colorimetric detection of dual targets. This nanoparticle-based peptide logic system presents a valid strategy to illustrate peptide information processing and provides a practical platform for executing peptide computing or peptide-related multiplexing sensing, implying that the controllable nanomaterial assembly is a promising and potent methodology for the advancement of biomimetic bio-logic computation.

Cooperative effects of fibronectin matrix assembly and initial cell-substrate adhesion strength in cellular self-assembly.

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Brennan, James R; Hocking, Denise C

2016-03-01

The cell-dependent polymerization of intercellular fibronectin fibrils can stimulate cells to self-assemble into multicellular structures. The local physical cues that support fibronectin-mediated cellular self-assembly are largely unknown. Here, fibronectin matrix analogs were used as synthetic adhesive substrates to model cell-matrix fibronectin fibrils having different integrin-binding specificity, affinity, and/or density. We utilized this model to quantitatively assess the relationship between adhesive forces derived from cell-substrate interactions and the ability of fibronectin fibril assembly to induce cellular self-assembly. Results indicate that the strength of initial, rather than mature, cell-substrate attachments correlates with the ability of substrates to support fibronectin-mediated cellular self-assembly. The cellular response to soluble fibronectin was bimodal and independent of the integrin-binding specificity of the substrate; increasing soluble fibronectin levels above a critical threshold increased aggregate cohesion on permissive substrates. Once aggregates formed, continuous fibronectin polymerization was necessary to maintain cohesion. During self-assembly, soluble fibronectin decreased cell-substrate adhesion strength and induced aggregate cohesion via a Rho-dependent mechanism, suggesting that the balance of contractile forces derived from fibronectin fibrils within cell-cell versus cell-substrate adhesions controls self-assembly and aggregate cohesion. Thus, initial cell-substrate attachment strength may provide a quantitative basis with which to build predictive models of fibronectin-mediated microtissue fabrication on a variety of substrates. Cellular self-assembly is a process by which cells and extracellular matrix (ECM) proteins spontaneously organize into three-dimensional (3D) tissues in the absence of external forces. Cellular self-assembly can be initiated in vitro, and represents a potential tool for tissue engineers to

Fluid-Mediated Stochastic Self-Assembly at Centimetric and Sub-Millimetric Scales: Design, Modeling, and Control

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Bahar Haghighat

2016-08-01

Full Text Available Stochastic self-assembly provides promising means for building micro-/nano-structures with a variety of properties and functionalities. Numerous studies have been conducted on the control and modeling of the process in engineered self-assembling systems constituted of modules with varied capabilities ranging from completely reactive nano-/micro-particles to intelligent miniaturized robots. Depending on the capabilities of the constituting modules, different approaches have been utilized for controlling and modeling these systems. In the quest of a unifying control and modeling framework and within the broader perspective of investigating how stochastic control strategies can be adapted from the centimeter-scale down to the (sub-millimeter-scale, as well as from mechatronic to MEMS-based technology, this work presents the outcomes of our research on self-assembly during the past few years. As the first step, we leverage an experimental platform to study self-assembly of water-floating passive modules at the centimeter scale. A dedicated computational framework is developed for real-time tracking, modeling and control of the formation of specific structures. Using a similar approach, we then demonstrate controlled self-assembly of microparticles into clusters of a preset dimension in a microfluidic chamber, where the control loop is closed again through real-time tracking customized for a much faster system dynamics. Finally, with the aim of distributing the intelligence and realizing programmable self-assembly, we present a novel experimental system for fluid-mediated programmable stochastic self-assembly of active modules at the centimeter scale. The system is built around the water-floating 3-cm-sized Lily robots specifically designed to be operative in large swarms and allows for exploring the whole range of fully-centralized to fully-distributed control strategies. The outcomes of our research efforts extend the state-of-the-art methodologies

Hydrazine-mediated construction of nanocrystal self-assembly materials.

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Zhou, Ding; Liu, Min; Lin, Min; Bu, Xinyuan; Luo, Xintao; Zhang, Hao; Yang, Bai

2014-10-28

Self-assembly is the basic feature of supramolecular chemistry, which permits to integrate and enhance the functionalities of nano-objects. However, the conversion of self-assembled structures to practical materials is still laborious. In this work, on the basis of studying one-pot synthesis, spontaneous assembly, and in situ polymerization of aqueous semiconductor nanocrystals (NCs), NC self-assembly materials are produced and applied to design high performance white light-emitting diode (WLED). In producing self-assembly materials, the additive hydrazine (N2H4) is curial, which acts as the promoter to achieve room-temperature synthesis of aqueous NCs by favoring a reaction-controlled growth, as the polyelectrolyte to weaken inter-NC electrostatic repulsion and therewith facilitate the one-dimensional self-assembly, and in particular as the bifunctional monomers to polymerize with mercapto carboxylic acid-modified NCs via in situ amidation reaction. This strategy is versatile for mercapto carboxylic acid-modified aqueous NCs, for example CdS, CdSe, CdTe, CdSe(x)Te(1-x), and Cd(y)Hg(1-y)Te. Because of the multisite modification with carboxyl, the NCs act as macromonomers, thus producing cross-linked self-assembly materials with excellent thermal, solvent, and photostability. The assembled NCs preserve strong luminescence and avoid unpredictable fluorescent resonance energy transfer, the main problem in design WLED from multiple NC components. These advantages allow the fabrication of NC-based WLED with high color rendering index (86), high luminous efficacy (41 lm/W), and controllable color temperature.

Surface mediated assembly of small, metastable gold nanoclusters

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Pettibone, John M.; Osborn, William A.; Rykaczewski, Konrad; Talin, A. Alec; Bonevich, John E.; Hudgens, Jeffrey W.; Allendorf, Mark D.

2013-06-01

The unique properties of metallic nanoclusters are attractive for numerous commercial and industrial applications but are generally less stable than nanocrystals. Thus, developing methodologies for stabilizing nanoclusters and retaining their enhanced functionality is of great interest. We report the assembly of PPh3-protected Au9 clusters from a heterogeneous mixture into films consisting of sub 3 nm nanocluster assemblies. The depositing nanoclusters are metastable in solution, but the resulting nanocluster assemblies are stabilized indefinitely in air or fresh solvent. The films exhibit distinct structure from Au nanoparticles observed by X-ray diffraction, and film dissolution data support the preservation of small nanoclusters. UV-Vis spectroscopy, electrospray ionization mass spectrometry, X-ray photoelectron spectroscopy and electron microscopy are used to elucidate information regarding the nanocluster formation and assembly mechanism. Preferential deposition of nanocluster assemblies can be achieved on multiple substrates, including polymer, Cr, Si, SiO2, SiNx, and metal-organic frameworks (MOFs). Unlike other vapor phase coating processes, nanocluster assembly on the MIL-68(In) MOF crystal is capable of preferentially coating the external surface and stabilizing the crystal structure in hydrothermal conditions, which should enhance their storage, separation and delivery capabilities.The unique properties of metallic nanoclusters are attractive for numerous commercial and industrial applications but are generally less stable than nanocrystals. Thus, developing methodologies for stabilizing nanoclusters and retaining their enhanced functionality is of great interest. We report the assembly of PPh3-protected Au9 clusters from a heterogeneous mixture into films consisting of sub 3 nm nanocluster assemblies. The depositing nanoclusters are metastable in solution, but the resulting nanocluster assemblies are stabilized indefinitely in air or fresh solvent. The

Simple method for assembly of CRISPR synergistic activation mediator gRNA expression array.

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Vad-Nielsen, Johan; Nielsen, Anders Lade; Luo, Yonglun

2018-05-20

When studying complex interconnected regulatory networks, effective methods for simultaneously manipulating multiple genes expression are paramount. Previously, we have developed a simple method for generation of an all-in-one CRISPR gRNA expression array. We here present a Golden Gate Assembly-based system of synergistic activation mediator (SAM) compatible CRISPR/dCas9 gRNA expression array for the simultaneous activation of multiple genes. Using this system, we demonstrated the simultaneous activation of the transcription factors, TWIST, SNAIL, SLUG, and ZEB1 a human breast cancer cell line. Copyright © 2018 Elsevier B.V. All rights reserved.

Cytosolic chaperones mediate quality control of higher-order septin assembly in budding yeast.

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Johnson, Courtney R; Weems, Andrew D; Brewer, Jennifer M; Thorner, Jeremy; McMurray, Michael A

2015-04-01

Septin hetero-oligomers polymerize into cytoskeletal filaments with essential functions in many eukaryotic cell types. Mutations within the oligomerization interface that encompasses the GTP-binding pocket of a septin (its "G interface") cause thermoinstability of yeast septin hetero-oligomer assembly, and human disease. When coexpressed with its wild-type counterpart, a G interface mutant is excluded from septin filaments, even at moderate temperatures. We show that this quality control mechanism is specific to G interface mutants, operates during de novo septin hetero-oligomer assembly, and requires specific cytosolic chaperones. Chaperone overexpression lowers the temperature permissive for proliferation of cells expressing a G interface mutant as the sole source of a given septin. Mutations that perturb the septin G interface retard release from these chaperones, imposing a kinetic delay on the availability of nascent septin molecules for higher-order assembly. Un-expectedly, the disaggregase Hsp104 contributes to this delay in a manner that does not require its "unfoldase" activity, indicating a latent "holdase" activity toward mutant septins. These findings provide new roles for chaperone-mediated kinetic partitioning of non-native proteins and may help explain the etiology of septin-linked human diseases. © 2015 Johnson et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Influence of wetting-layer wave functions on phonon-mediated carrier capture into self-assembled quantum dots

DEFF Research Database (Denmark)

Markussen, Troels; Kristensen, Philip Trøst; Tromborg, Bjarne

2006-01-01

Models of carrier dynamics in quantum dots rely strongly on adequate descriptions of the carrier wave functions. In this work we numerically solve the one-band effective mass Schrodinger equation to calculate the capture times of phonon-mediated carrier capture into self-assembled quantum dots. C....... Comparing with results obtained using approximate carrier wave functions, we demonstrate that the capture times are strongly influenced by properties of the wetting layer wave functions not accounted for by earlier theoretical analyses....

IGD motifs, which are required for migration stimulatory activity of fibronectin type I modules, do not mediate binding in matrix assembly.

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Lisa M Maurer

Full Text Available Picomolar concentrations of proteins comprising only the N-terminal 70-kDa region (70K of fibronectin (FN stimulate cell migration into collagen gels. The Ile-Gly-Asp (IGD motifs in four of the nine FN type 1 (FNI modules in 70K are important for such migratory stimulating activity. The 70K region mediates binding of nanomolar concentrations of intact FN to cell-surface sites where FN is assembled. Using baculovirus, we expressed wildtype 70K and 70K with Ile-to-Ala mutations in (3FNI and (5FNI; (7FNI and (9FNI; or (3FNI, (5FNI, (7FNI, and (9FNI. Wildtype 70K and 70K with Ile-to-Ala mutations were equally active in binding to assembly sites of FN-null fibroblasts. This finding indicates that IGD motifs do not mediate the interaction between 70K and the cell-surface that is important for FN assembly. Further, FN fragment N-(3FNIII, which does not stimulate migration, binds to assembly sites on FN-null fibroblast. The Ile-to-Ala mutations had effects on the structure of FNI modules as evidenced by decreases in abilities of 70K with Ile-to-Ala mutations to bind to monoclonal antibody 5C3, which recognizes an epitope in (9FNI, or to bind to FUD, a polypeptide based on the F1 adhesin of Streptococcus pyogenes that interacts with 70K by the β-zipper mechanism. These results suggest that the picomolar interactions of 70K with cells that stimulate cell migration require different conformations of FNI modules than the nanomolar interactions required for assembly.

Highly selective and sensitive method for Cu2 + detection based on chiroptical activity of L-Cysteine mediated Au nanorod assemblies

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Abbasi, Shahryar; Khani, Hamzeh

2017-11-01

Herein, we demonstrated a simple and efficient method to detect Cu2 + based on amplified optical activity in the chiral nanoassemblies of gold nanorods (Au NRs). L-Cysteine can induce side-by-side or end-to-end assembly of Au NRs with an evident plasmonic circular dichroism (PCD) response due to coupling between surface plasmon resonances (SPR) of Au NRs and the chiral signal of L-Cys. Because of the obvious stronger plasmonic circular dichrosim (CD) response of the side-by-side assembly compared with the end-to-end assemblies, SS assembled Au NRs was selected as a sensitive platform and used for Cu2 + detection. In the presence of Cu2 +, Cu2 + can catalyze O2 oxidation of cysteine to cystine. With an increase in Cu2 + concentration, the L-Cysteine-mediated assembly of Au NRs decreased because of decrease in the free cysteine thiol groups, and the PCD signal decreased. Taking advantage of this method, Cu2 + could be detected in the concentration range of 20 pM-5 nM. Under optimal conditions, the calculated detection limit was found to be 7 pM.

NSF- and SNARE-mediated membrane fusion is required for nuclear envelope formation and completion of nuclear pore complex assembly in Xenopus laevis egg extracts.

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Baur, Tina; Ramadan, Kristijan; Schlundt, Andreas; Kartenbeck, Jürgen; Meyer, Hemmo H

2007-08-15

Despite the progress in understanding nuclear envelope (NE) reformation after mitosis, it has remained unclear what drives the required membrane fusion and how exactly this is coordinated with nuclear pore complex (NPC) assembly. Here, we show that, like other intracellular fusion reactions, NE fusion in Xenopus laevis egg extracts is mediated by SNARE proteins that require activation by NSF. Antibodies against Xenopus NSF, depletion of NSF or the dominant-negative NSF(E329Q) variant specifically inhibited NE formation. Staging experiments further revealed that NSF was required until sealing of the envelope was completed. Moreover, excess exogenous alpha-SNAP that blocks SNARE function prevented membrane fusion and caused accumulation of non-flattened vesicles on the chromatin surface. Under these conditions, the nucleoporins Nup107 and gp210 were fully recruited, whereas assembly of FxFG-repeat-containing nucleoporins was blocked. Together, we define NSF- and SNARE-mediated membrane fusion events as essential steps during NE formation downstream of Nup107 recruitment, and upstream of membrane flattening and completion of NPC assembly.

Assembly of tobacco mosaic virus into fibrous and macroscopic bundled arrays mediated by surface aniline polymerization.

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Niu, Zhongwei; Bruckman, Michael A; Li, Siqi; Lee, L Andrew; Lee, Byeongdu; Pingali, Sai Venkatesh; Thiyagarajan, P; Wang, Qian

2007-06-05

One-dimensional (1D) polyaniline/tobacco mosaic virus (TMV) composite nanofibers and macroscopic bundles of such fibers were generated via a self-assembly process of TMV assisted by in-situ polymerization of polyaniline on the surface of TMV. At near-neutral reaction pH, branched polyaniline formed on the surface of TMV preventing lateral association. Therefore, long 1D nanofibers were observed with high aspect ratios and excellent processibility. At a lower pH, transmission electron microscopy (TEM) analysis revealed that initially long nanofibers were formed which resulted in bundled structures upon long-time reaction, presumably mediated by the hydrophobic interaction because of the polyaniline on the surface of TMV. In-situ time-resolved small-angle X-ray scattering study of TMV at different reaction conditions supported this mechanism. This novel strategy to assemble TMV into 1D and 3D supramolecular composites could be utilized in the fabrication of advanced materials for potential applications including electronics, optics, sensing, and biomedical engineering.

The convergence of quantum-dot-mediated fluorescence resonance energy transfer and microfluidics for monitoring DNA polyplex self-assembly in real time

International Nuclear Information System (INIS)

Ho Yiping; Wang, T-H; Chen, Hunter H; Leong, Kam W

2009-01-01

We present a novel convergence of quantum-dot-mediated fluorescence resonance energy transfer (QD-FRET) and microfluidics, through which molecular interactions were precisely controlled and monitored using highly sensitive quantum-dot-mediated FRET. We demonstrate its potential in studying the kinetics of self-assembly of DNA polyplexes under laminar flow in real time with millisecond resolution. The integration of nanophotonics and microfluidics offers a powerful tool for elucidating the formation of polyelectrolyte polyplexes, which is expected to provide better control and synthesis of uniform and customizable polyplexes for future nucleic acid-based therapeutics.

Scanning Tunneling Microscopic Observation of Adatom-Mediated Motifs on Gold-Thiol Self-assembled Monolayers at High Coverage

DEFF Research Database (Denmark)

Wang, Yun; Chi, Qijin; Hush, Noel S.

2009-01-01

the structural motifs observed on surfaces at low coverage and on gold nanoparticles to the observed spectroscopic properties of high-coverage SAMs formed by methanethiol. However, the significant role attributed to intermolecular steric packing effects suggests a lack of generality for the adatom-mediated motif......Self-assembled monolayers (SAMs) formed by chemisorption of a branched-chain alkanethiol, 2-methyl-1-propanethiol, on Au(111) surfaces were studied by in situ scanning tunneling microscopy (STM) under electrochemical potential control and analyzed using extensive density functional theory (DFT...... two R−S−Au−S−R adatom-mediated motifs per surface cell, with steric-induced variations in the adsorbate alignment inducing the observed STM image contrasts. Observed pits covering 5.6 ± 0.5% of the SAM surface are consistent with this structure. These results provide the missing link from...

Surface Mediated Self-Assembly of Amyloid Peptides

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Fakhraai, Zahra

2015-03-01

Amyloid fibrils have been considered as causative agents in many neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, type II diabetes and amyloidosis. Amyloid fibrils form when proteins or peptides misfold into one dimensional crystals of stacked beta-sheets. In solution, amyloid fibrils form through a nucleation and growth mechanism. The rate limiting nucleation step requires a critical concentration much larger than those measured in physiological conditions. As such the exact origins of the seeds or oligomers that result in the formation of fully mature fibrils in the body remain topic intense studies. It has been suggested that surfaces and interfaces can enhance the fibrillization rate. However, studies of the mechanism and kinetics of the surface-mediated fibrillization are technologically challenging due to the small size of the oligomer and protofibril species. Using smart sample preparation technique to dry the samples after various incubation times we are able to study the kinetics of fibril formation both in solution and in the vicinity of various surfaces using high-resolution atomic force microscopy. These studies elucidate the role of surfaces in catalyzing amyloid peptide formation through a nucleation-free process. The nucleation free self-assembly is rapid and requires much smaller concentrations of peptides or proteins. We show that this process resembles diffusion limited aggregation and is governed by the peptide adhesion rate, two -dimensional diffusion of the peptides on the surface, and preferential interactions between the peptides. These studies suggest an alternative pathway for amyloid formation may exist, which could lead to new criteria for disease prevention and alternative therapies. Research was partially supported by a seed grant from the National Institute of Aging of the National Institutes of Health (NIH) under Award Number P30AG010124 (PI: John Trojanowski) and the University of Pennsylvania.

Chemical reactions directed Peptide self-assembly.

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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.

Mediator binds to boundaries of chromosomal interaction domains and to proteins involved in DNA looping, RNA metabolism, chromatin remodeling, and actin assembly.

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Chereji, Razvan V; Bharatula, Vasudha; Elfving, Nils; Blomberg, Jeanette; Larsson, Miriam; Morozov, Alexandre V; Broach, James R; Björklund, Stefan

2017-09-06

Mediator is a multi-unit molecular complex that plays a key role in transferring signals from transcriptional regulators to RNA polymerase II in eukaryotes. We have combined biochemical purification of the Saccharomyces cerevisiae Mediator from chromatin with chromatin immunoprecipitation in order to reveal Mediator occupancy on DNA genome-wide, and to identify proteins interacting specifically with Mediator on the chromatin template. Tandem mass spectrometry of proteins in immunoprecipitates of mediator complexes revealed specific interactions between Mediator and the RSC, Arp2/Arp3, CPF, CF 1A and Lsm complexes in chromatin. These factors are primarily involved in chromatin remodeling, actin assembly, mRNA 3'-end processing, gene looping and mRNA decay, but they have also been shown to enter the nucleus and participate in Pol II transcription. Moreover, we have found that Mediator, in addition to binding Pol II promoters, occupies chromosomal interacting domain (CID) boundaries and that Mediator in chromatin associates with proteins that have been shown to interact with CID boundaries, such as Sth1, Ssu72 and histone H4. This suggests that Mediator plays a significant role in higher-order genome organization. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Opto-electronic devices with nanoparticles and their assemblies

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Nguyen, Chieu Van

Nanotechnology is a fast growing field; engineering matters at the nano-meter scale. A key nanomaterial is nanoparticles (NPs). These sub-wavelength (background noise. The second device is based on a one-dimensional (1-D) self-directed self-assembly of Au NPs mediated by dielectric materials. Depending on the coverage density of the Au NPs assembly deposited on the device, electronic emission was observed at ultra-low bias of 40V, leading to low-power plasma generation in air at atmospheric pressure. Light emitted from the plasma is apparent to the naked eyes. Similarly, 1-D self-assembly of Au NPs mediated by iron oxide was fabricated and exhibits ferro-magnetic behavior. The multi-functional 1-D self-assembly of Au NPs has great potential in modern electronics such as solid state lighting, plasma-based nanoelectronics, and memory devices.

Solvent-mediated self-assembly of hexadecanethiol on GaAs (0 0 1)

International Nuclear Information System (INIS)

Huang, Xiaohuan; Dubowski, Jan J.

2014-01-01

Graphical abstract: - Highlights: • Outstanding quality hexadecanethiol self-assembled monolayers (HDT SAM) produced on GaAs (0 0 1) due to the mediated role of water in an alcoholic environment. • HDT SAM formed in chloroform exhibit excellent electronic passivation properties in contrast to their structural characteristics. • Low dielectric constant solvents do not necessary provide conditions advantageous for the formation of high quality alkanethiol SAM. • Photoluminescence emitting materials allow to investigate the mechanisms of both electronic and chemical passivation and, thus, they are an excellent platform for studying the mechanisms of SAM formation on solid substrates. - Abstract: We have investigated the influence of solvents on the quality of hexadecanethiol (HDT) self-assembled monolayers (SAM) formed on GaAs (0 0 1) in chloroform, ethanol and ethanol/water 1:1 characterized by their increasing dielectric constants from 4.8 (chloroform) to 24.5 (ethanol) and water (80.1). Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) data show that the incubation in ethanol/water 1:1 solution creates conditions favouring inter-molecular interaction leading to the formation of an outstanding quality HDT SAM on GaAs (0 0 1). Incubation in low-dielectric constant solvents is not offering advantageous conditions for growing HDT SAM on GaAs. The chloroform environment, while weakening the thiol–thiol interaction, induces the oxidation of the GaAs surface and, in particular, formation of Ga 2 O 3 . This reduces the concentration of surface defects responsible for non-radiative recombination and leads to an enhanced photoluminescence emission, despite the fact that HDT SAM formed in chloroform are highly disordered, exhibiting the worst chemical passivation among the investigated samples

Mitochondria mediate septin cage assembly to promote autophagy of Shigella.

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Sirianni, Andrea; Krokowski, Sina; Lobato-Márquez, Damián; Buranyi, Stephen; Pfanzelter, Julia; Galea, Dieter; Willis, Alexandra; Culley, Siân; Henriques, Ricardo; Larrouy-Maumus, Gerald; Hollinshead, Michael; Sancho-Shimizu, Vanessa; Way, Michael; Mostowy, Serge

2016-07-01

Septins, cytoskeletal proteins with well-characterised roles in cytokinesis, form cage-like structures around cytosolic Shigella flexneri and promote their targeting to autophagosomes. However, the processes underlying septin cage assembly, and whether they influence S. flexneri proliferation, remain to be established. Using single-cell analysis, we show that the septin cages inhibit S. flexneri proliferation. To study mechanisms of septin cage assembly, we used proteomics and found mitochondrial proteins associate with septins in S. flexneri-infected cells. Strikingly, mitochondria associated with S. flexneri promote septin assembly into cages that entrap bacteria for autophagy. We demonstrate that the cytosolic GTPase dynamin-related protein 1 (Drp1) interacts with septins to enhance mitochondrial fission. To avoid autophagy, actin-polymerising Shigella fragment mitochondria to escape from septin caging. Our results demonstrate a role for mitochondria in anti-Shigella autophagy and uncover a fundamental link between septin assembly and mitochondria. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

ULtiMATE system for rapid assembly of customized TAL effectors.

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Junjiao Yang

Full Text Available Engineered TAL-effector nucleases (TALENs and TALE-based constructs have become powerful tools for eukaryotic genome editing. Although many methods have been reported, it remains a challenge for the assembly of designer-based TALE repeats in a fast, precise and cost-effective manner. We present an ULtiMATE (USER-based Ligation Mediated Assembly of TAL Effector system for speedy and accurate assembly of customized TALE constructs. This method takes advantage of uracil-specific excision reagent (USER to create multiple distinct sticky ends between any neighboring DNA fragments for specific ligation. With pre-assembled templates, multiple TALE DNA-binding domains could be efficiently assembled in order within hours with minimal manual operation. This system has been demonstrated to produce both functional TALENs for effective gene knockout and TALE-mediated gene-specific transcription activation (TALE-TA. The feature of both ease-of-operation and high efficiency of ULtiMATE system makes it not only an ideal method for biologic labs, but also an approach well suited for large-scale assembly of TALENs and any other TALE-based constructions.

RISC assembly: Coordination between small RNAs and Argonaute proteins.

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Kobayashi, Hotaka; Tomari, Yukihide

2016-01-01

Non-coding RNAs generally form ribonucleoprotein (RNP) complexes with their partner proteins to exert their functions. Small RNAs, including microRNAs, small interfering RNAs, and PIWI-interacting RNAs, assemble with Argonaute (Ago) family proteins into the effector complex called RNA-induced silencing complex (RISC), which mediates sequence-specific target gene silencing. RISC assembly is not a simple binding between a small RNA and Ago; rather, it follows an ordered multi-step pathway that requires specific accessory factors. Some steps of RISC assembly and RISC-mediated gene silencing are dependent on or facilitated by particular intracellular platforms, suggesting their spatial regulation. In this review, we summarize the currently known mechanisms for RISC assembly of each small RNA class and propose a revised model for the role of the chaperone machinery in the duplex-initiated RISC assembly pathway. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa. Copyright © 2015 Elsevier B.V. All rights reserved.

Dewetting-mediated pattern formation in nanoparticle assemblies

International Nuclear Information System (INIS)

Stannard, Andrew

2011-01-01

The deposition of nanoparticles from solution onto solid substrates is a diverse subfield of current nanoscience research. Complex physical and chemical processes underpin the self-assembly and self-organization of colloidal nanoparticles at two-phase (solid-liquid, liquid-air) interfaces and three-phase (solid-liquid-air) contact lines. This review discusses key recent advances made in the understanding of nonequilibrium dewetting processes of nanoparticle-containing solutions, detailing how such an apparently simple experimental system can give rise to such a strikingly varied palette of two-dimensional self-organized nanoparticle array morphologies. Patterns discussed include worm-like domains, cellular networks, microscale rings, and fractal-like fingering structures. There remain many unresolved issues regarding the role of the solvent dewetting dynamics in assembly processes of this type, with a significant focus on how dewetting can be coerced to produce nanoparticle arrays with desirable characteristics such as long-range order. In addition to these topics, methods developed to control nanofluid dewetting through routes such as confining the geometries of drying solutions, depositing onto pre-patterned heterogeneous substrates, and post-dewetting pattern evolution via local or global manipulation are covered. (topical review)

Dewetting-mediated pattern formation in nanoparticle assemblies.

Science.gov (United States)

Stannard, Andrew

2011-03-02

The deposition of nanoparticles from solution onto solid substrates is a diverse subfield of current nanoscience research. Complex physical and chemical processes underpin the self-assembly and self-organization of colloidal nanoparticles at two-phase (solid-liquid, liquid-air) interfaces and three-phase (solid-liquid-air) contact lines. This review discusses key recent advances made in the understanding of nonequilibrium dewetting processes of nanoparticle-containing solutions, detailing how such an apparently simple experimental system can give rise to such a strikingly varied palette of two-dimensional self-organized nanoparticle array morphologies. Patterns discussed include worm-like domains, cellular networks, microscale rings, and fractal-like fingering structures. There remain many unresolved issues regarding the role of the solvent dewetting dynamics in assembly processes of this type, with a significant focus on how dewetting can be coerced to produce nanoparticle arrays with desirable characteristics such as long-range order. In addition to these topics, methods developed to control nanofluid dewetting through routes such as confining the geometries of drying solutions, depositing onto pre-patterned heterogeneous substrates, and post-dewetting pattern evolution via local or global manipulation are covered.

Molecular lego for the assembly of biosensing layers.

Science.gov (United States)

Mano, N; Kuhn, A

2005-03-31

We propose a procedure to assemble monolayers of redox mediator, coenzyme, enzyme and stabilizing polyelectrolyte on an electrode surface using essentially electrostatic and complexing interactions. In a first step a monolayer of redox mediator, substituted nitrofluorenones, is adsorbed. In a second step, a layer of calcium cations is immobilized at the interface. It establishes a bridge between the redox mediator and the subsequently adsorbed coenzyme NAD(+). In the next step we use the intrinsic affinity of the NAD(+) monolayer for dehydrogenases to build up a multilayer composed of mediator/Ca(2+)/NAD(+)/dehydrogenase. The so obtained modified electrode can be used as a biosensor. Quartz crystal microbalance measurements allowed us to better understand the different parameters responsible for the adsorption. A more detailed investigation of the system made it possible to finally stabilize the assembly sufficiently by the adsorption of a polyelectrolyte layer in order to perform rotating disk electrode measurements with the whole supramolecular architecture on the electrode surface.

The nucleosome assembly activity of NAP1 is enhanced by Alien.

Science.gov (United States)

Eckey, Maren; Hong, Wei; Papaioannou, Maria; Baniahmad, Aria

2007-05-01

The assembly of nucleosomes into chromatin is essential for the compaction of DNA and inactivation of the DNA template to modulate and repress gene expression. The nucleosome assembly protein 1, NAP1, assembles nucleosomes independent of DNA synthesis and was shown to enhance coactivator-mediated gene expression, suggesting a role for NAP1 in transcriptional regulation. Here, we show that Alien, known to harbor characteristics of a corepressor of nuclear hormone receptors such as of the vitamin D receptor (VDR), binds in vivo and in vitro to NAP1 and modulates its activity by enhancing NAP1-mediated nucleosome assembly on DNA. Furthermore, Alien reduces the accessibility of the histones H3 and H4 for NAP1-promoted assembly reaction. This indicates that Alien sustains and reinforces the formation of nucleosomes. Employing deletion mutants of Alien suggests that different regions of Alien are involved in enhancement of NAP1-mediated nucleosome assembly and in inhibiting the accessibility of the histones H3 and H4. In addition, we provide evidence that Alien is associated with chromatin and with micrococcus nuclease-prepared nucleosome fractions and interacts with the histones H3 and H4. Furthermore, chromatin immunoprecipitation and reimmunoprecipitation experiments suggest that NAP1 and Alien localize to the endogenous CYP24 promoter in vivo, a VDR target gene. Based on these findings, we present here a novel pathway linking corepressor function with nucleosome assembly activity.

Proton Mediated Chemistry and Catalysis in a Self-Assembled Supramolecular Host

Energy Technology Data Exchange (ETDEWEB)

Pluth, Michael; Bergman, Robert; Raymond, Kenneth

2009-04-10

Synthetic supramolecular host assemblies can impart unique reactivity to encapsulated guest molecules. Synthetic host molecules have been developed to carry out complex reactions within their cavities, despite the fact that they lack the type of specifically tailored functional groups normally located in the analogous active sites of enzymes. Over the past decade, the Raymond group has developed a series of self-assembled supramolecules and the Bergman group has developed and studied a number of catalytic transformations. In this Account, we detail recent collaborative work between these two groups, focusing on chemical catalysis stemming from the encapsulation of protonated guests and expanding to acid catalysis in basic solution. We initially investigated the ability of a water-soluble, self-assembled supramolecular host molecule to encapsulate protonated guests in its hydrophobic core. Our study of encapsulated protonated amines revealed rich host-guest chemistry. We established that self-exchange (that is, in-out guest movement) rates of protonated amines were dependent on the steric bulk of the amine rather than its basicity. The host molecule has purely rotational tetrahedral (T) symmetry, so guests with geminal N-methyl groups (and their attendant mirror plane) were effectively desymmetrized; this allowed for the observation and quantification of the barriers for nitrogen inversion followed by bond rotation. Furthermore, small nitrogen heterocycles, such as N-alkylaziridines, N-alkylazetidines, and N-alkylpyrrolidines, were found to be encapsulated as proton-bound homodimers or homotrimers. We further investigated the thermodynamic stabilization of protonated amines, showing that encapsulation makes the amines more basic in the cavity. Encapsulation raises the effective basicity of protonated amines by up to 4.5 pK{sub a} units, a difference almost as large as that between the moderate and strong bases carbonate and hydroxide. The thermodynamic stabilization

Proton-Mediated Chemistry and Catalysis in a Self-Assembled Supramolecular Host

International Nuclear Information System (INIS)

Pluth, Michael; Bergman, Robert; Raymond, Kenneth

2009-01-01

Synthetic supramolecular host assemblies can impart unique reactivity to encapsulated guest molecules. Synthetic host molecules have been developed to carry out complex reactions within their cavities, despite the fact that they lack the type of specifically tailored functional groups normally located in the analogous active sites of enzymes. Over the past decade, the Raymond group has developed a series of self-assembled supramolecules and the Bergman group has developed and studied a number of catalytic transformations. In this Account, we detail recent collaborative work between these two groups, focusing on chemical catalysis stemming from the encapsulation of protonated guests and expanding to acid catalysis in basic solution. We initially investigated the ability of a water-soluble, self-assembled supramolecular host molecule to encapsulate protonated guests in its hydrophobic core. Our study of encapsulated protonated amines revealed rich host-guest chemistry. We established that self-exchange (that is, in-out guest movement) rates of protonated amines were dependent on the steric bulk of the amine rather than its basicity. The host molecule has purely rotational tetrahedral (T) symmetry, so guests with geminal N-methyl groups (and their attendant mirror plane) were effectively desymmetrized; this allowed for the observation and quantification of the barriers for nitrogen inversion followed by bond rotation. Furthermore, small nitrogen heterocycles, such as N-alkylaziridines, N-alkylazetidines, and N-alkylpyrrolidines, were found to be encapsulated as proton-bound homodimers or homotrimers. We further investigated the thermodynamic stabilization of protonated amines, showing that encapsulation makes the amines more basic in the cavity. Encapsulation raises the effective basicity of protonated amines by up to 4.5 pK a units, a difference almost as large as that between the moderate and strong bases carbonate and hydroxide. The thermodynamic stabilization of

Reactive oxygen species promote heat shock protein 90-mediated HBV capsid assembly

International Nuclear Information System (INIS)

Kim, Yoon Sik; Seo, Hyun Wook; Jung, Guhung

2015-01-01

Hepatitis B virus (HBV) infection induces reactive oxygen species (ROS) production and has been associated with the development of hepatocellular carcinoma (HCC). ROS are also an important factor in HCC because the accumulated ROS leads to abnormal cell proliferation and chromosome mutation. In oxidative stress, heat shock protein 90 (Hsp90) and glutathione (GSH) function as part of the defense mechanism. Hsp90 prevents cellular component from oxidative stress, and GSH acts as antioxidants scavenging ROS in the cell. However, it is not known whether molecules regulated by oxidative stress are involved in HBV capsid assembly. Based on the previous study that Hsp90 facilitates HBV capsid assembly, which is an important step for the packing of viral particles, here, we show that ROS enrich Hsp90-driven HBV capsid formation. In cell-free system, HBV capsid assembly was facilitated by ROS with Hsp90, whereas it was decreased without Hsp90. In addition, GSH inhibited the function of Hsp90 to decrease HBV capsid assembly. Consistent with the result of cell-free system, ROS and buthionine sulfoximine (BS), an inhibitor of GSH synthesis, increased HBV capsid formation in HepG2.2.15 cells. Thus, our study uncovers the interplay between ROS and Hsp90 during HBV capsid assembly. - Highlights: • We examined H 2 O 2 and GSH modulate HBV capsid assembly. • H 2 O 2 facilitates HBV capsid assembly in the presence of Hsp90. • GSH inhibits function of Hsp90 in facilitating HBV capsid assembly. • H 2 O 2 and GSH induce conformation change of Hsp90

Reactive oxygen species promote heat shock protein 90-mediated HBV capsid assembly

Energy Technology Data Exchange (ETDEWEB)

Kim, Yoon Sik, E-mail: yumshak@naver.com; Seo, Hyun Wook, E-mail: suruk@naver.com; Jung, Guhung, E-mail: drjung@snu.ac.kr

2015-02-13

Hepatitis B virus (HBV) infection induces reactive oxygen species (ROS) production and has been associated with the development of hepatocellular carcinoma (HCC). ROS are also an important factor in HCC because the accumulated ROS leads to abnormal cell proliferation and chromosome mutation. In oxidative stress, heat shock protein 90 (Hsp90) and glutathione (GSH) function as part of the defense mechanism. Hsp90 prevents cellular component from oxidative stress, and GSH acts as antioxidants scavenging ROS in the cell. However, it is not known whether molecules regulated by oxidative stress are involved in HBV capsid assembly. Based on the previous study that Hsp90 facilitates HBV capsid assembly, which is an important step for the packing of viral particles, here, we show that ROS enrich Hsp90-driven HBV capsid formation. In cell-free system, HBV capsid assembly was facilitated by ROS with Hsp90, whereas it was decreased without Hsp90. In addition, GSH inhibited the function of Hsp90 to decrease HBV capsid assembly. Consistent with the result of cell-free system, ROS and buthionine sulfoximine (BS), an inhibitor of GSH synthesis, increased HBV capsid formation in HepG2.2.15 cells. Thus, our study uncovers the interplay between ROS and Hsp90 during HBV capsid assembly. - Highlights: • We examined H{sub 2}O{sub 2} and GSH modulate HBV capsid assembly. • H{sub 2}O{sub 2} facilitates HBV capsid assembly in the presence of Hsp90. • GSH inhibits function of Hsp90 in facilitating HBV capsid assembly. • H{sub 2}O{sub 2} and GSH induce conformation change of Hsp90.

Transcription regulation by the Mediator complex.

Science.gov (United States)

Soutourina, Julie

2018-04-01

Alterations in the regulation of gene expression are frequently associated with developmental diseases or cancer. Transcription activation is a key phenomenon in the regulation of gene expression. In all eukaryotes, mediator of RNA polymerase II transcription (Mediator), a large complex with modular organization, is generally required for transcription by RNA polymerase II, and it regulates various steps of this process. The main function of Mediator is to transduce signals from the transcription activators bound to enhancer regions to the transcription machinery, which is assembled at promoters as the preinitiation complex (PIC) to control transcription initiation. Recent functional studies of Mediator with the use of structural biology approaches and functional genomics have revealed new insights into Mediator activity and its regulation during transcription initiation, including how Mediator is recruited to transcription regulatory regions and how it interacts and cooperates with PIC components to assist in PIC assembly. Novel roles of Mediator in the control of gene expression have also been revealed by showing its connection to the nuclear pore and linking Mediator to the regulation of gene positioning in the nuclear space. Clear links between Mediator subunits and disease have also encouraged studies to explore targeting of this complex as a potential therapeutic approach in cancer and fungal infections.

Biologic Constraints on Modelling Virus Assembly

Directory of Open Access Journals (Sweden)

Robert L. Garcea

2008-01-01

Full Text Available The mathematic modelling of icosahedral virus assembly has drawn increasing interest because of the symmetric geometry of the outer shell structures. Many models involve equilibrium expressions of subunit binding, with reversible subunit additions forming various intermediate structures. The underlying assumption is that a final lowest energy state drives the equilibrium toward assembly. In their simplest forms, these models have explained why high subunit protein concentrations and strong subunit association constants can result in kinetic traps forming off pathway partial and aberrant structures. However, the cell biology of virus assembly is exceedingly complex. The biochemistry and biology of polyoma and papillomavirus assembly described here illustrates many of these specific issues. Variables include the use of cellular ‘chaperone’ proteins as mediators of assembly fidelity, the coupling of assembly to encapsidation of a specific nucleic acid genome, the use of cellular structures as ‘workbenches’ upon which assembly occurs, and the underlying problem of making a capsid structure that is metastable and capable of rapid disassembly upon infection. Although formidable to model, incorporating these considerations could advance the relevance of mathematical models of virus assembly to the real world.

DNA-mediated self-assembly of tetrahedral plasmonic clusters for metafluids

Science.gov (United States)

Schade, Nicholas; Sun, Li; Lee, You-Jin; Fan, Jonathan; Capasso, Federico; Yi, Gi-Ra; Manoharan, Vinothan

2014-03-01

We direct the self-assembly of clusters of gold nanospheres with the goal of creating a bulk, isotropic, optical metafluid. We use spherical gold nanoparticles that are exceptionally smooth, monocrystalline, and monodisperse. These particles exhibit highly reproducible scattering spectra compared with commercially available gold colloids. We label them with DNA sequences and mix them together to self-assemble small clusters. By controlling the particle sizes and the interactions between them, we maximize the yield of tetrahedral clusters, the ideal structures for isotropic metamaterials.

Ultrasensitive electrochemical biosensor based on the oligonucleotide self-assembled monolayer-mediated immunosensing interface

Energy Technology Data Exchange (ETDEWEB)

Liu, Dengyou; Luo, Qimei [Science College of Hunan Agricultural University, Changsha 410128 (China); Deng, Fawen [The Fourth Hospital of Chansha, Changsha 410006 (China); Li, Zhen [Science College of Hunan Agricultural University, Changsha 410128 (China); Li, Benxiang, E-mail: 172170960@qq.com [Science College of Hunan Agricultural University, Changsha 410128 (China); Shen, Zhifa, E-mail: shenzhifa@wmu.edu.cn [Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035 (China)

2017-06-08

Highly sensitive and selective quantitation of a variety of proteins over a wide concentration range is highly desirable for increased accuracy of biomarker detection or for multidisease diagnostics. In the present contribution, using human immunoglobulin G (HIgG) as the model target protein, an electrochemical ultrasensitive immunosensing platform was developed based on the oligonucleotide self-assembled monolayer-mediated (OSAM) sensing interface. For this immunosensor, the “signal-on” signaling mechanism and enzymatic signal amplification effect were integrated into one sensing architecture. Moreover, the thiolated flexible single-stranded DNAs immobilized onto gold electrode surface not only performs the wobbling motion to facilitate the electron transfer between the electrode surface and biosensing layer but also fundamentally prohibiting the direct interaction of proteins with gold substrate. Thus, the electrochemical signal could be efficiently enhanced and the unspecific adsorption or cross-reaction might be eliminated. As a result, utilizing the newly-proposed immunosensor, the HIgG can be detected down to 0.5 ng/mL, and the high detection specificity is offered. The successful design of OSAM and the highly desirable detection capability of new immunosensor are expected to provide a perspective for fabricating new robust immunosensing platform and for promising potential of oligonucleotide probe in biological research and biomedical diagnosis. - Highlights: • An electrochemical ultrasensitive immunosensing platform was developed based on the oligonucleotide self-assembled monolayer (OASM). • OASM severs as a flexible monolayer to promote electron transfer and prohibits the direct interaction of proteins with gold substrate. • The electrochemical signal is efficiently enhanced and the unspecific adsorption or cross-reaction is eliminated. • Target protein can be detected down to 0.5 ng/mL, and the high detection specificity can be obtained. �

Light-activated control of protein channel assembly mediated by membrane mechanics

Science.gov (United States)

Miller, David M.; Findlay, Heather E.; Ces, Oscar; Templer, Richard H.; Booth, Paula J.

2016-12-01

Photochemical processes provide versatile triggers of chemical reactions. Here, we use a photoactivated lipid switch to modulate the folding and assembly of a protein channel within a model biological membrane. In contrast to the information rich field of water-soluble protein folding, there is only a limited understanding of the assembly of proteins that are integral to biological membranes. It is however possible to exploit the foreboding hydrophobic lipid environment and control membrane protein folding via lipid bilayer mechanics. Mechanical properties such as lipid chain lateral pressure influence the insertion and folding of proteins in membranes, with different stages of folding having contrasting sensitivities to the bilayer properties. Studies to date have relied on altering bilayer properties through lipid compositional changes made at equilibrium, and thus can only be made before or after folding. We show that light-activation of photoisomerisable di-(5-[[4-(4-butylphenyl)azo]phenoxy]pentyl)phosphate (4-Azo-5P) lipids influences the folding and assembly of the pentameric bacterial mechanosensitive channel MscL. The use of a photochemical reaction enables the bilayer properties to be altered during folding, which is unprecedented. This mechanical manipulation during folding, allows for optimisation of different stages of the component insertion, folding and assembly steps within the same lipid system. The photochemical approach offers the potential to control channel assembly when generating synthetic devices that exploit the mechanosensitive protein as a nanovalve.

Building superlattices from individual nanoparticles via template-confined DNA-mediated assembly

Energy Technology Data Exchange (ETDEWEB)

Lin, Qing-Yuan; Mason, Jarad A.; Li, Zhongyang; Zhou, Wenjie; O’Brien, Matthew N.; Brown, Keith A.; Jones, Matthew R.; Butun, Serkan; Lee, Byeongdu; Dravid, Vinayak P.; Aydin, Koray; Mirkin, Chad A.

2018-01-18

DNA programmable assembly has been combined with top-down lithography to construct superlattices of discrete, reconfigurable nanoparticle architectures on a gold surface over large areas. Specifically, individual colloidal plasmonic nanoparticles with different shapes and sizes are assembled with ‘locked” nucleic acids in polymer pores into oriented architectures that feature tunable arrangements and independently controllable distances at both nanometer and micrometer length scales. These structures, which would be difficult to construct via other common assembly methods, provide a platform to systematically study and control light-matter interactions in nanoparticle-based optical materials. The generality and potential of this approach is explored by identifying a broadband absorber with a solvent polarity response that allows dynamic tuning of the wavelength response and amplitude of visible light absorption.

Aerosolized droplet mediated self-assembly of photosynthetic pigment analogues and deposition onto substrates.

Science.gov (United States)

Shah, Vivek B; Biswas, Pratim

2014-02-25

Self-assembled photosynthetic molecules have a high extinction coefficient and a broad absorption in the infrared region, and these properties can be used to improve the efficiency of solar cells. We have developed a single-step method for the self-assembly of synthetic chlorin molecules (analogues of native bacteriochlorophylls) in aerosolized droplets, containing a single solvent and two solvents, to synthesize biomimetic light-harvesting structures. In the single-solvent approach, assembly is promoted by a concentration-driven process due to evaporation of the solvent. The peak absorbance of Zn(II) 3-(1-hydroxyethyl)-10-phenyl-13(1)-oxophorbine (1) in methanol shifted from 646 nm to 725 nm (∼ 80 nm shift) after assembly, which is comparable to the shift observed in the naturally occurring assembly of bacteriochlorophyll c. Although assembly is thermodynamically favorable, the kinetics of self-assembly play an important role, and this was demonstrated by varying the initial concentration of the pigment monomer. To overcome kinetic limitations, a two-solvent approach using a volatile solvent (tetrahydrofuran) in which the dye is soluble and a less volatile solvent (ethanol) in which the dye is sparingly soluble was demonstrated to be effective. The effect of molecular structure is demonstrated by spraying the sterically hindered Zn(II) 3-(1-hydroxyethyl)-10-mesityl-13(1)-oxophorbine (2), which is an analogue of 1, under similar conditions. The results illustrate a valuable and facile aerosol-based method for the formation of films of supramolecular assemblies.

Characterization of tetratricopeptide repeat-containing proteins critical for cilia formation and function.

Directory of Open Access Journals (Sweden)

Yanan Xu

Full Text Available Cilia formation and function require a special set of trafficking machinery termed intraflagellar transport (IFT, consisting mainly of protein complexes IFT-A, IFT-B, BBSome, and microtubule-dependent molecular motors. Tetratricopeptide repeat-containing (TTC proteins are widely involved in protein complex formation. Nine of them are known to serve as components of the IFT or BBSome complexes. How many TTC proteins are cilia-related and how they function, however, remain unclear. Here we show that twenty TTC genes were upregulated by at least 2-fold during the differentiation of cultured mouse tracheal epithelial cells (MTECs into multiciliated cells. Our systematic screen in zebrafish identified four novel TTC genes, ttc4, -9c, -36, and -39c, that are critical for cilia formation and motility. Accordingly, their zebrafish morphants displayed typical ciliopathy-related phenotypes, including curved body, abnormal otolith, hydrocephalus, and defective left-right patterning. The morphants of ttc4 and ttc25, a known cilia-related gene, additionally showed pronephric cyst formation. Immunoprecipitation indicated associations of TTC4, -9c, -25, -36, and -39c with components or entire complexes of IFT-A, IFT-B, or BBSome, implying their participations in IFT or IFT-related activities. Our results provide a global view for the relationship between TTC proteins and cilia.

ATP-dependent human RISC assembly pathways.

Science.gov (United States)

Yoda, Mayuko; Kawamata, Tomoko; Paroo, Zain; Ye, Xuecheng; Iwasaki, Shintaro; Liu, Qinghua; Tomari, Yukihide

2010-01-01

The assembly of RNA-induced silencing complex (RISC) is a key process in small RNA-mediated gene silencing. In humans, small interfering RNAs (siRNAs) and microRNAs (miRNAs) are incorporated into RISCs containing the Argonaute (AGO) subfamily proteins Ago1-4. Previous studies have proposed that, unlike Drosophila melanogaster RISC assembly pathways, human RISC assembly is coupled with dicing and is independent of ATP. Here we show by careful reexamination that, in humans, RISC assembly and dicing are uncoupled, and ATP greatly facilitates RISC loading of small-RNA duplexes. Moreover, all four human AGO proteins show remarkably similar structural preferences for small-RNA duplexes: central mismatches promote RISC loading, and seed or 3'-mid (guide position 12-15) mismatches facilitate unwinding. All these features of human AGO proteins are highly reminiscent of fly Ago1 but not fly Ago2.

Building superlattices from individual nanoparticles via template-confined DNA-mediated assembly

Science.gov (United States)

Lin, Qing-Yuan; Mason, Jarad A.; Li, Zhongyang; Zhou, Wenjie; O’Brien, Matthew N.; Brown, Keith A.; Jones, Matthew R.; Butun, Serkan; Lee, Byeongdu; Dravid, Vinayak P.; Aydin, Koray; Mirkin, Chad A.

2018-02-01

DNA programmable assembly has been combined with top-down lithography to construct superlattices of discrete, reconfigurable nanoparticle architectures on a gold surface over large areas. Specifically, the assembly of individual colloidal plasmonic nanoparticles with different shapes and sizes is controlled by oligonucleotides containing “locked” nucleic acids and confined environments provided by polymer pores to yield oriented architectures that feature tunable arrangements and independently controllable distances at both nanometer- and micrometer-length scales. These structures, which would be difficult to construct by other common assembly methods, provide a platform to systematically study and control light-matter interactions in nanoparticle-based optical materials. The generality and potential of this approach are explored by identifying a broadband absorber with a solvent polarity response that allows dynamic tuning of visible light absorption.

The structure of the COPII transport-vesicle coat assembled on membranes.

Science.gov (United States)

Zanetti, Giulia; Prinz, Simone; Daum, Sebastian; Meister, Annette; Schekman, Randy; Bacia, Kirsten; Briggs, John A G

2013-09-17

Coat protein complex II (COPII) mediates formation of the membrane vesicles that export newly synthesised proteins from the endoplasmic reticulum. The inner COPII proteins bind to cargo and membrane, linking them to the outer COPII components that form a cage around the vesicle. Regulated flexibility in coat architecture is essential for transport of a variety of differently sized cargoes, but structural data on the assembled coat has not been available. We have used cryo-electron tomography and subtomogram averaging to determine the structure of the complete, membrane-assembled COPII coat. We describe a novel arrangement of the outer coat and find that the inner coat can assemble into regular lattices. The data reveal how coat subunits interact with one another and with the membrane, suggesting how coordinated assembly of inner and outer coats can mediate and regulate packaging of vesicles ranging from small spheres to large tubular carriers. DOI:http://dx.doi.org/10.7554/eLife.00951.001.

Silver-mediated base pairings: towards dynamic DNA nanostructures with enhanced chemical and thermal stability

International Nuclear Information System (INIS)

Swasey, Steven M; Gwinn, Elisabeth G

2016-01-01

The thermal and chemical fragility of DNA nanomaterials assembled by Watson–Crick (WC) pairing constrain the settings in which these materials can be used and how they can be functionalized. Here we investigate use of the silver cation, Ag + , as an agent for more robust, metal-mediated self-assembly, focusing on the simplest duplex building blocks that would be required for more elaborate Ag + –DNA nanostructures. Our studies of Ag + -induced assembly of non-complementary DNA oligomers employ strands of 2–24 bases, with varied base compositions, and use electrospray ionization mass spectrometry to determine product compositions. High yields of duplex products containing narrowly distributed numbers of Ag + can be achieved by optimizing solution conditions. These Ag + -mediated duplexes are stable to at least 60 mM Mg 2+ , higher than is necessary for WC nanotechnology schemes such as tile assemblies and DNA origami, indicating that sequential stages of Ag + -mediated and WC-mediated assembly may be feasible. Circular dichroism spectroscopy suggests simple helical structures for Ag + -mediated duplexes with lengths to at least 20 base pairs, and further indicates that the structure of cytosine-rich duplexes is preserved at high urea concentrations. We therefore propose an approach towards dynamic DNA nanomaterials with enhanced thermal and chemical stability through designs that combine sturdy silver-mediated ‘frames’ with WC paired ‘pictures’. (paper)

DNA mediated assembly of lipid particles and uses therefor

DEFF Research Database (Denmark)

2007-01-01

The present invention relates to detection of target nucleic acids by targetnucleic acid induced liposome assembly. The invention provides oligonucleotides for use in detection and a method of detecting target nucleic acids.Other aspects of the invention are use of the oligonucleotide of the inve...

Molecular Architecture of the Human Mediator–RNA Polymerase II–TFIIF Assembly

Science.gov (United States)

Bernecky, Carrie; Grob, Patricia; Ebmeier, Christopher C.; Nogales, Eva; Taatjes, Dylan J.

2011-01-01

The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator–pol II interface is not well-characterized, whereas attempts to structurally define the Mediator–pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator–pol II–TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator–pol II–TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator–pol II–TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator–CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator–pol II complexes lacking TFIIF reveal that TFIIF plays a key role in

Multiligand Metal-Phenolic Assembly from Green Tea Infusions.

Science.gov (United States)

Rahim, Md Arifur; Björnmalm, Mattias; Bertleff-Zieschang, Nadja; Ju, Yi; Mettu, Srinivas; Leeming, Michael G; Caruso, Frank

2018-03-07

The synthesis of hybrid functional materials using the coordination-driven assembly of metal-phenolic networks (MPNs) is of interest in diverse areas of materials science. To date, MPN assembly has been explored as monoligand systems (i.e., containing a single type of phenolic ligand) where the phenolic components are primarily obtained from natural sources via extraction, isolation, and purification processes. Herein, we demonstrate the fabrication of MPNs from a readily available, crude phenolic source-green tea (GT) infusions. We employ our recently introduced rust-mediated continuous assembly strategy to prepare these GT MPN systems. The resulting hollow MPN capsules contain multiple phenolic ligands and have a shell thickness that can be controlled through the reaction time. These multiligand MPN systems have different properties compared to the analogous MPN systems reported previously. For example, the Young's modulus (as determined using colloidal-probe atomic force microscopy) of the GT MPN system presented herein is less than half that of MPN systems prepared using tannic acid and iron salt solutions, and the disassembly kinetics are faster (∼50%) than other, comparable MPN systems under identical disassembly conditions. Additionally, the use of rust-mediated assembly enables the formation of stable capsules under conditions where the conventional approach (i.e., using iron salt solutions) results in colloidally unstable dispersions. These differences highlight how the choice of phenolic ligand and its source, as well as the assembly protocol (e.g., using solution-based or solid-state iron sources), can be used to tune the properties of MPNs. The strategy presented herein expands the toolbox of MPN assembly while also providing new insights into the nature and robustness of metal-phenolic interfacial assembly when using solution-based or solid-state metal sources.

Folate mediated self-assembled phytosterol-alginate nanoparticles for targeted intracellular anticancer drug delivery.

Science.gov (United States)

Wang, Jianting; Wang, Ming; Zheng, Mingming; Guo, Qiong; Wang, Yafan; Wang, Heqing; Xie, Xiangrong; Huang, Fenghong; Gong, Renmin

2015-05-01

Self-assembled core/shell nanoparticles (NPs) were synthesized from water-soluble alginate substituted by hydrophobic phytosterols. Folate, a cancer-cell-specific ligand, was conjugated to the phytosterol-alginate (PA) NPs for targeting folate-receptor-overexpressing cancer cells. The physicochemical properties of folate-phytosterol-alginate (FPA) NPs were characterized by nuclear magnetic resonance, transmission electron microscopy, dynamic light scattering, electrophoretic light scattering, and fluorescence spectroscopy. Doxorubicin (DOX), an anticancer drug, was entrapped inside prepared NPs by dialysis method. The identification of prepared FPA NPs to folate-receptor-overexpressing cancer cells (KB cells) was confirmed by cytotoxicity and folate competition assays. Compared to the pure DOX and DOX/PA NPs, the DOX/FPA NPs had lower IC50 value to KB cells because of folate-receptor-mediated endocytosis process and the cytotoxicity of DOX/FPA NPs to KB cells could be competitively inhibited by free folate. The cellular uptake and internalization of pure DOX and DOX/FPA NPs was confirmed by confocal laser scanning microscopy image and the higher intracellular uptake of drug for DOX/FPA NPs over pure DOX was observed. The FPA NPs had the potential as a promising carrier to target drugs to cancer cells overexpressing folate receptors and avoid cytotoxicity to normal tissues. Copyright © 2015 Elsevier B.V. All rights reserved.

The Nucleosome Assembly Activity of NAP1 Is Enhanced by Alien▿

OpenAIRE

Eckey, Maren; Hong, Wei; Papaioannou, Maria; Baniahmad, Aria

2007-01-01

The assembly of nucleosomes into chromatin is essential for the compaction of DNA and inactivation of the DNA template to modulate and repress gene expression. The nucleosome assembly protein 1, NAP1, assembles nucleosomes independent of DNA synthesis and was shown to enhance coactivator-mediated gene expression, suggesting a role for NAP1 in transcriptional regulation. Here, we show that Alien, known to harbor characteristics of a corepressor of nuclear hormone receptors such as of the vitam...

Overall Architecture of the Intraflagellar Transport (IFT)-B Complex Containing Cluap1/IFT38 as an Essential Component of the IFT-B Peripheral Subcomplex*

Science.gov (United States)

Katoh, Yohei; Terada, Masaya; Nishijima, Yuya; Takei, Ryota; Nozaki, Shohei; Hamada, Hiroshi; Nakayama, Kazuhisa

2016-01-01

Intraflagellar transport (IFT) is essential for assembly and maintenance of cilia and flagella as well as ciliary motility and signaling. IFT is mediated by multisubunit complexes, including IFT-A, IFT-B, and the BBSome, in concert with kinesin and dynein motors. Under high salt conditions, purified IFT-B complex dissociates into a core subcomplex composed of at least nine subunits and at least five peripherally associated proteins. Using the visible immunoprecipitation assay, which we recently developed as a convenient protein-protein interaction assay, we determined the overall architecture of the IFT-B complex, which can be divided into core and peripheral subcomplexes composed of 10 and 6 subunits, respectively. In particular, we identified TTC26/IFT56 and Cluap1/IFT38, neither of which was included with certainty in previous models of the IFT-B complex, as integral components of the core and peripheral subcomplexes, respectively. Consistent with this, a ciliogenesis defect of Cluap1-deficient mouse embryonic fibroblasts was rescued by exogenous expression of wild-type Cluap1 but not by mutant Cluap1 lacking the binding ability to other IFT-B components. The detailed interaction map as well as comparison of subcellular localization of IFT-B components between wild-type and Cluap1-deficient cells provides insights into the functional relevance of the architecture of the IFT-B complex. PMID:26980730

Superlattices assembled through shape-induced directional binding

Science.gov (United States)

Lu, Fang; Yager, Kevin G.; Zhang, Yugang; Xin, Huolin; Gang, Oleg

2015-04-01

Organization of spherical particles into lattices is typically driven by packing considerations. Although the addition of directional binding can significantly broaden structural diversity, nanoscale implementation remains challenging. Here we investigate the assembly of clusters and lattices in which anisotropic polyhedral blocks coordinate isotropic spherical nanoparticles via shape-induced directional interactions facilitated by DNA recognition. We show that these polyhedral blocks--cubes and octahedrons--when mixed with spheres, promote the assembly of clusters with architecture determined by polyhedron symmetry. Moreover, three-dimensional binary superlattices are formed when DNA shells accommodate the shape disparity between nanoparticle interfaces. The crystallographic symmetry of assembled lattices is determined by the spatial symmetry of the block's facets, while structural order depends on DNA-tuned interactions and particle size ratio. The presented lattice assembly strategy, exploiting shape for defining the global structure and DNA-mediation locally, opens novel possibilities for by-design fabrication of binary lattices.

Green-fuel-mediated synthesis of self-assembled NiO nano-sticks for dual applications—photocatalytic activity on Rose Bengal dye and antimicrobial action on bacterial strains

Science.gov (United States)

Iyyappa Rajan, P.; Vijaya, J. Judith; Jesudoss, S. K.; Kaviyarasu, K.; Kennedy, L. John; Jothiramalingam, R.; Al-Lohedan, Hamad A.; Vaali-Mohammed, Mansoor-Ali

2017-08-01

With aim of promoting the employability of green fuels in the synthesis of nano-scaled materials with new kinds of morphologies for multiple applications, successful synthesis of self-assembled NiO nano-sticks was achieved through a 100% green-fuel-mediated hot-plate combustion reaction. The synthesized NiO nano-sticks show excellent photocatalytic activity on Rose Bengal dye and superior antibacterial potential towards both Gram-positive and Gram-negative bacteria.

Template mediated protein self-assembly as a valuable tool in regenerative therapy.

Science.gov (United States)

Kundu, B; Eltohamy, M; Yadavalli, V K; Reis, R L; Kim, H W

2018-04-11

The assembly of natural proteinaceous biopolymers into macro-scale architectures is of great importance in synthetic biology, soft-material science and regenerative therapy. The self-assembly of protein tends to be limited due to anisotropic interactions among protein molecules, poor solubility and stability. Here, we introduce a unique platform to self-immobilize diverse proteins (fibrous and globular, positively and negatively charged, low and high molecular weight) using silicon surfaces with pendant -NH 2 groups via a facile one step diffusion limited aggregation (DLA) method. All the experimental proteins (type I collagen, bovine serum albumin and cytochrome C) self-assemble into seaweed-like branched dendritic architectures via classical DLA in the absence of any electrolytes. The notable differences in branching architectures are due to dissimilarities in protein colloidal sub-units, which is typical for each protein type, along with the heterogeneous distribution of surface -NH 2 groups. Fractal analysis of assembled structures is used to explain the underlying route of fractal deposition; which concludes how proteins with different functionality can yield similar assembly. Further, the nano-micro-structured surfaces can be used to provide functional topographical cues to study cellular responses, as demonstrated using rat bone marrow stem cells. The results indicate that the immobilization of proteins via DLA does not affect functionality, instead serving as topographical cues to guide cell morphology. This indicates a promising design strategy at the tissue-material interface and is anticipated to guide future surface modifications. A cost-effective standard templating strategy is therefore proposed for fundamental and applied particle aggregation studies, which can be used at multiple length scales for biomaterial design and surface reformation.

Defined DNA-mediated assemblies of gene-expressing giant unilamellar vesicles

DEFF Research Database (Denmark)

Hadorn, M.; Boenzli, E.; Sørensen, Kristian T.

2013-01-01

The technological aspects of artificial vesicles as prominent cell mimics are evolving toward higher-order assemblies of functional vesicles with tissuelike architectures. Here, we demonstrate the spatially controlled DNA-directed bottom-up synthesis of complex microassemblies and macroassemblies...

Molecular determinants in TRPV5 channel assembly.

NARCIS (Netherlands)

Chang, Q.; Gyftogianni, E.; Graaf, K.F.J. van de; Hoefs, S.J.G.; Weidema, A.F.; Bindels, R.J.M.; Hoenderop, J.G.J.

2004-01-01

The epithelial Ca(2+) channels TRPV5 and TRPV6 mediate the Ca(2+) influx in 1,25-dihydroxyvitamin D(3)-responsive epithelia and are therefore essential in the maintenance of the body Ca(2+) balance. These Ca(2+) channels assemble in (hetero)tetrameric channel complexes with different functional

Molecular determinants in TRPV5 channel assembly

NARCIS (Netherlands)

Chang, Qing; Gyftogianni, Emmanouela; van de Graaf, Stan F. J.; Hoefs, Susan; Weidema, Freek A.; Bindels, René J. M.; Hoenderop, Joost G. J.

2004-01-01

The epithelial Ca(2+) channels TRPV5 and TRPV6 mediate the Ca(2+) influx in 1,25-dihydroxyvitamin D(3)-responsive epithelia and are therefore essential in the maintenance of the body Ca(2+) balance. These Ca(2+) channels assemble in (hetero)tetrameric channel complexes with different functional

Mediator independently orchestrates multiple steps of preinitiation complex assembly in vivo

OpenAIRE

Eyboulet, Fanny; Wydau-Dematteis, Sandra; Eychenne, Thomas; Alibert, Olivier; Neil, Helen; Boschiero, Claire; Nevers, Marie-Claire; Volland, Herv?; Cornu, David; Redeker, Virginie; Werner, Michel; Soutourina, Julie

2015-01-01

Mediator is a large multiprotein complex conserved in all eukaryotes, which has a crucial coregulator function in transcription by RNA polymerase II (Pol II). However, the molecular mechanisms of its action in vivo remain to be understood. Med17 is an essential and central component of the Mediator head module. In this work, we utilised our large collection of conditional temperature-sensitive med17 mutants to investigate Mediator's role in coordinating preinitiation complex (PIC) formation i...

Kinase-Mediated Regulation of 40S Ribosome Assembly in Human Breast Cancer

Science.gov (United States)

2017-02-01

and will assess if this resistance involves gain-of-function mutations in Ltv1, and if resistance can be overcome with drugs that direct...ribosome assembly factor Ltv1 in both yeast and TNBC cells, and that selective knockdown or silencing of CK1δ, or forced expression of Ltv1 mutant that...cannot be phosphorylated by CK1δ, blocks ribosome assembly in yeast and compromises the growth and survival of TNBC cells. Further, we have shown that

Alzheimer’s disease Aβ assemblies mediating rapid disruption of synaptic plasticity and memory

Directory of Open Access Journals (Sweden)

Klyubin Igor

2012-07-01

Full Text Available Abstract Alzheimer’s disease (AD is characterized by episodic memory impairment that often precedes clinical diagnosis by many years. Probing the mechanisms of such impairment may provide much needed means of diagnosis and therapeutic intervention at an early, pre-dementia, stage. Prior to the onset of significant neurodegeneration, the structural and functional integrity of synapses in mnemonic circuitry is severely compromised in the presence of amyloidosis. This review examines recent evidence evaluating the role of amyloid-ß protein (Aβ in causing rapid disruption of synaptic plasticity and memory impairment. We evaluate the relative importance of different sizes and conformations of Aβ, including monomer, oligomer, protofibril and fibril. We pay particular attention to recent controversies over the relevance to the pathophysiology of AD of different water soluble Aβ aggregates and the importance of cellular prion protein in mediating their effects. Current data are consistent with the view that both low-n oligomers and larger soluble assemblies present in AD brain, some of them via a direct interaction with cellular prion protein, cause synaptic memory failure. At the two extremes of aggregation, monomers and fibrils appear to act in vivo both as sources and sinks of certain metastable conformations of soluble aggregates that powerfully disrupt synaptic plasticity. The same principle appears to apply to other synaptotoxic amyloidogenic proteins including tau, α-synuclein and prion protein.

Human serum albumin mediated self-assembly of gold nanoparticles into hollow spheres

Energy Technology Data Exchange (ETDEWEB)

Nayak, Nimai C [Singapore-MIT Alliance, Manufacturing Systems and Technology Programme, Nanyang Technological University, 65 Nanyang Drive, 637460 (Singapore); Shin, Kwanwoo [Interdisciplinary Program of Integrated Biotechnology, Sogang University, Shinsoo-dong, Mapo-gu, Seoul 121-742 (Korea, Republic of)], E-mail: ncnayak@gmail.com

2008-07-02

The assembly of nanoparticles in topologically predefined superstructures is an important area in nanoscale architecture. In this paper, we report an unusual aggregation phenomenon involving L-lysine capped gold nanoparticles and human serum albumin into hollow nanospheres. The electrostatic interaction between positively charged L-lysine capped gold nanoparticles and negatively charged human serum albumin at physiological pH led to the assembly of the gold nanoparticles into hollow spheres. The phenomenon can be explained by the dry hole opening mechanism.

Human serum albumin mediated self-assembly of gold nanoparticles into hollow spheres

International Nuclear Information System (INIS)

Nayak, Nimai C; Shin, Kwanwoo

2008-01-01

The assembly of nanoparticles in topologically predefined superstructures is an important area in nanoscale architecture. In this paper, we report an unusual aggregation phenomenon involving L-lysine capped gold nanoparticles and human serum albumin into hollow nanospheres. The electrostatic interaction between positively charged L-lysine capped gold nanoparticles and negatively charged human serum albumin at physiological pH led to the assembly of the gold nanoparticles into hollow spheres. The phenomenon can be explained by the dry hole opening mechanism

Experience with construction and assembly of V-1 nuclear power plant

International Nuclear Information System (INIS)

Prochazka, J.; Stepanek, S.; Drahy, J.

1981-01-01

The model is discussed of the constructions of the V-1 nuclear power plant at Jaslovske Bohunice with SKODA Trust fulfilling the role of the general supplier of the secondary part technology and the chief and special assembly contractor. The SKODA Trust mediated the Soviet supplies of technology, Soviet assembly and special assembly, and the mounting of the primary part according to Soviet projects. Plant start-up was safeguarded by the investor through Bohunice power plant staff and Soviet experts. The assembly of the primary circuit and the test assembly of reactor parts are described and the experience gained is discussed. The technological requirements are illustrated by the most important characteristics of the individual parts of the primary circuit. Also described are the design specifications of the 220 MW saturated steam turbine and the experience with its assembly and start-up. (B.S.)

Dynamic colloidal assembly pathways via low dimensional models

Energy Technology Data Exchange (ETDEWEB)

Yang, Yuguang; Bevan, Michael A., E-mail: mabevan@jhu.edu [Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Thyagarajan, Raghuram; Ford, David M. [Chemical Engineering, University of Massachusetts, Amherst, Massachusetts 01003 (United States)

2016-05-28

Here we construct a low-dimensional Smoluchowski model for electric field mediated colloidal crystallization using Brownian dynamic simulations, which were previously matched to experiments. Diffusion mapping is used to infer dimensionality and confirm the use of two order parameters, one for degree of condensation and one for global crystallinity. Free energy and diffusivity landscapes are obtained as the coefficients of a low-dimensional Smoluchowski equation to capture the thermodynamics and kinetics of microstructure evolution. The resulting low-dimensional model quantitatively captures the dynamics of different assembly pathways between fluid, polycrystal, and single crystals states, in agreement with the full N-dimensional data as characterized by first passage time distributions. Numerical solution of the low-dimensional Smoluchowski equation reveals statistical properties of the dynamic evolution of states vs. applied field amplitude and system size. The low-dimensional Smoluchowski equation and associated landscapes calculated here can serve as models for predictive control of electric field mediated assembly of colloidal ensembles into two-dimensional crystalline objects.

Cytoplasmic Actin: Purification and Single Molecule Assembly Assays

Science.gov (United States)

Hansen, Scott D.; Zuchero, J. Bradley; Mullins, R. Dyche

2014-01-01

The actin cytoskeleton is essential to all eukaryotic cells. In addition to playing important structural roles, assembly of actin into filaments powers diverse cellular processes, including cell motility, cytokinesis, and endocytosis. Actin polymerization is tightly regulated by its numerous cofactors, which control spatial and temporal assembly of actin as well as the physical properties of these filaments. Development of an in vitro model of actin polymerization from purified components has allowed for great advances in determining the effects of these proteins on the actin cytoskeleton. Here we describe how to use the pyrene actin assembly assay to determine the effect of a protein on the kinetics of actin assembly, either directly or as mediated by proteins such as nucleation or capping factors. Secondly, we show how fluorescently labeled phalloidin can be used to visualize the filaments that are created in vitro to give insight into how proteins regulate actin filament structure. Finally, we describe a method for visualizing dynamic assembly and disassembly of single actin filaments and fluorescently labeled actin binding proteins using total internal reflection fluorescence (TIRF) microscopy. PMID:23868587

Self-Assembly of DNA-Coated Particles: Experiment, Simulation and Theory

Science.gov (United States)

Song, Minseok

The bottom-up assembly of material architectures with tunable complexity, function, composition, and structure is a long sought goal in rational materials design. One promising approach aims to harnesses the programmability and specificity of DNA hybridization in order to direct the assembly of oligonucleotide-functionalized nano- and micro-particles by tailoring, in part, interparticle interactions. DNA-programmable assembly into three-dimensionally ordered structures has attracted extensive research interest owing to emergent applications in photonics, plasmonics and catalysis and potentially many other areas. Progress on the rational design of DNA-mediated interactions to create useful two-dimensional structures (e.g., structured films), on the other hand, has been rather slow. In this thesis, we establish strategies to engineer a diversity of 2D crystalline arrangements by designing and exploiting DNA-programmable interparticle interactions. We employ a combination of simulation, theory and experiments to predict and confirm accessibility of 2D structural diversity in an effort to establish a rational approach to 2D DNA-mediated particle assembly. We start with the experimental realization of 2D DNA-mediated assembly by decorating micron-sized silica particles with covalently attached single-stranded DNA through a two-step reaction. Subsequently, we elucidate sensitivity and ultimate controllability of DNA-mediated assembly---specifically the melting transition from dispersed singlet particles to aggregated or assembled structures---through control of the concentration of commonly employed nonionic surfactants. We relate the observed tunability to an apparent coupling with the critical micelle temperature in these systems. Also, both square and hexagonal 2D ordered particle arrangements are shown to evolve from disordered aggregates under appropriate annealing conditions defined based upon pre-established melting profiles. Subsequently, the controlled mixing of

The LINKS motif zippers trans-acyltransferase polyketide synthase assembly lines into a biosynthetic megacomplex.

Science.gov (United States)

Gay, Darren C; Wagner, Drew T; Meinke, Jessica L; Zogzas, Charles E; Gay, Glen R; Keatinge-Clay, Adrian T

2016-03-01

Polyketides such as the clinically-valuable antibacterial agent mupirocin are constructed by architecturally-sophisticated assembly lines known as trans-acyltransferase polyketide synthases. Organelle-sized megacomplexes composed of several copies of trans-acyltransferase polyketide synthase assembly lines have been observed by others through transmission electron microscopy to be located at the Bacillus subtilis plasma membrane, where the synthesis and export of the antibacterial polyketide bacillaene takes place. In this work we analyze ten crystal structures of trans-acyltransferase polyketide synthases ketosynthase domains, seven of which are reported here for the first time, to characterize a motif capable of zippering assembly lines into a megacomplex. While each of the three-helix LINKS (Laterally-INteracting Ketosynthase Sequence) motifs is observed to similarly dock with a spatially-reversed copy of itself through hydrophobic and ionic interactions, the amino acid sequences of this motif are not conserved. Such a code is appropriate for mediating homotypic contacts between assembly lines to ensure the ordered self-assembly of a noncovalent, yet tightly-knit, enzymatic network. LINKS-mediated lateral interactions would also have the effect of bolstering the vertical association of the polypeptides that comprise a polyketide synthase assembly line. Copyright © 2015 Elsevier Inc. All rights reserved.

Self-assembled fluorescent organic nanoparticles for live cell imaging

NARCIS (Netherlands)

Fischer, I.; Petkau, K.; Dorland, Y.L.; Schenning, A.P.H.J.; Brunsveld, L.

2013-01-01

Fluorescent, cell-permeable, organic nanoparticles based on self-assembled p-conjugated oligomers with high absorption cross-sections and high quantum yields have been developed. The nanoparticles are generated with a tuneable density of amino groups for charge-mediated cellular uptake by a

Fragile X mental retardation protein stimulates ribonucleoprotein assembly of influenza A virus

Science.gov (United States)

Zhou, Zhuo; Cao, Mengmeng; Guo, Yang; Zhao, Lili; Wang, Jingfeng; Jia, Xue; Li, Jianguo; Wang, Conghui; Gabriel, Gülsah; Xue, Qinghua; Yi, Yonghong; Cui, Sheng; Jin, Qi; Wang, Jianwei; Deng, Tao

2014-02-01

The ribonucleoprotein (RNP) of the influenza A virus is responsible for the transcription and replication of viral RNA in the nucleus. These processes require interplay between host factors and RNP components. Here, we report that the Fragile X mental retardation protein (FMRP) targets influenza virus RNA synthesis machinery and facilitates virus replication both in cell culture and in mice. We demonstrate that FMRP transiently associates with viral RNP and stimulates viral RNP assembly through RNA-mediated interaction with the nucleoprotein. Furthermore, the KH2 domain of FMRP mediates its association with the nucleoprotein. A point mutation (I304N) in the KH2 domain, identified from a Fragile X syndrome patient, disrupts the FMRP-nucleoprotein association and abolishes the ability of FMRP to participate in viral RNP assembly. We conclude that FMRP is a critical host factor used by influenza viruses to facilitate viral RNP assembly. Our observation reveals a mechanism of influenza virus RNA synthesis and provides insights into FMRP functions.

Cilium transition zone proteome reveals compartmentalization and differential dynamics of ciliopathy complexes

Czech Academy of Sciences Publication Activity Database

Dean, S.; Moreira-Leite, F.; Varga, Vladimír; Gull, K.

2016-01-01

Roč. 113, č. 35 (2016), E5135-E5143 ISSN 0027-8424 Institutional support: RVO:68378050 Keywords : transition zone * cilium/flagellum * BBSome * MKS/B9 complex * trypanosome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.661, year: 2016

Massively Parallel Nanostructure Assembly Strategies for Sensing and Information Technology. Phase 2

Science.gov (United States)

2013-05-25

Mirkin In order to remove the nanoparticle thin-film superlattices from the saline environment necessary to preserve Watson - Crick base-pairing and...polypyrroles and motor proteins. Functionalizing carbon nanotube bridged wires with biological receptors allowed fabrication of biosensors that could detect DNA ...the application of electrical stimuli. From an assembly perspective, we report on two major advances: (1) the utilization of DNA -mediated assembly to

ATR- and ATM-Mediated DNA Damage Response Is Dependent on Excision Repair Assembly during G1 but Not in S Phase of Cell Cycle.

Science.gov (United States)

Ray, Alo; Blevins, Chessica; Wani, Gulzar; Wani, Altaf A

2016-01-01

Cell cycle checkpoint is mediated by ATR and ATM kinases, as a prompt early response to a variety of DNA insults, and culminates in a highly orchestrated signal transduction cascade. Previously, we defined the regulatory role of nucleotide excision repair (NER) factors, DDB2 and XPC, in checkpoint and ATR/ATM-dependent repair pathway via ATR and ATM phosphorylation and recruitment to ultraviolet radiation (UVR)-induced damage sites. Here, we have dissected the molecular mechanisms of DDB2- and XPC- mediated regulation of ATR and ATM recruitment and activation upon UVR exposures. We show that the ATR and ATM activation and accumulation to UVR-induced damage not only depends on DDB2 and XPC, but also on the NER protein XPA, suggesting that the assembly of an active NER complex is essential for ATR and ATM recruitment. ATR and ATM localization and H2AX phosphorylation at the lesion sites occur as early as ten minutes in asynchronous as well as G1 arrested cells, showing that repair and checkpoint-mediated by ATR and ATM starts early upon UV irradiation. Moreover, our results demonstrated that ATR and ATM recruitment and H2AX phosphorylation are dependent on NER proteins in G1 phase, but not in S phase. We reasoned that in G1 the UVR-induced ssDNA gaps or processed ssDNA, and the bound NER complex promote ATR and ATM recruitment. In S phase, when the UV lesions result in stalled replication forks with long single-stranded DNA, ATR and ATM recruitment to these sites is regulated by different sets of proteins. Taken together, these results provide evidence that UVR-induced ATR and ATM recruitment and activation differ in G1 and S phases due to the existence of distinct types of DNA lesions, which promote assembly of different proteins involved in the process of DNA repair and checkpoint activation.

Interface-defect-mediated photocatalysis of mesocrystalline ZnO assembly synthesized in-situ via a template-free hydrothermal approach

Science.gov (United States)

Wang, Hui; Wang, Cuicui; Chen, Qifeng; Ren, Baosheng; Guan, Ruifang; Cao, Xiaofeng; Yang, Xiaopeng; Duan, Ran

2017-08-01

Both architecture construction and defects engineering of photocatalysts are highly vital in the photocatalytic activity. We report herein that the interface-defect-mediated photocatalytic activity of pompon-like ZnO (P-ZnO) mesocrystal photocatalyst synthesized via an aqueous approach, in the presence of sodium citrate without any other organic templates. The microstructure and defects of the diverse ZnO photocatalysts were examined with various techniques. The results indicated that the P-ZnO assemblies were composed of mesocrystal nanosheets exposed high energy (002) facet with high crystallinity. More importantly, the defects located at the interfaces among the nanocrystals in ZnO mesocrystals played an important role in the photocatalytic activity than that of interstitial zinc vacancies in bulk, which was confirmed by photocatalytic degradation of organic pollutants, such as methylene blue (MB) and 2,4,6-trichlorophenol (2,4,6-TCP). The results showed that the P-ZnO exhibited higher photocatalytic activity than that of the nanosized ZnO (N-ZnO), which could be attributed to not only the unique mesocrystal structure and high energy (002) facet exposed, but also the defects located at interfaces among nanocrystals in ZnO mesocrystals. In addition, the formation mechanism of the P-ZnO was investigated via a time-dependent method. It was found that the formation of P-ZnO hierarchical architecture assembled with ZnO mesocrystals involved a nonclassical crystallization growth and Ostwald Ripening process. This study provides a perspective on the improvement in photocatalytic activity via adjusting the bulk and interface defects and construction of hierarchical architectures of semiconductors.

An unusual dimeric structure and assembly for TLR4 regulator RP105-MD-1

Energy Technology Data Exchange (ETDEWEB)

Yoon, Sung-il; Hong, Minsun; Wilson, Ian A [Scripps

2011-11-16

RP105-MD-1 modulates the TLR4-MD-2-mediated, innate immune response against bacterial lipopolysaccharide (LPS). The crystal structure of the bovine 1:1 RP105-MD-1 complex bound to a putative endogenous lipid at 2.9 Å resolution shares a similar overall architecture to its homolog TLR4-MD-2 but assembles into an unusual 2:2 homodimer that differs from any other known TLR-ligand assembly. The homodimer is assembled in a head-to-head orientation that juxtaposes the N-terminal leucine-rich repeats (LRRs) of the two RP105 chains, rather than the usual tail-to-tail configuration of C-terminal LRRs in ligand-activated TLR dimers, such as TLR1-TRL2, TLR2-TLR6, TLR3-TLR3 and TLR4-TLR4. Another unusual interaction is mediated by an RP105-specific asparagine-linked glycan, which wedges MD-1 into the co-receptor binding concavity on RP105. This unique mode of assembly represents a new paradigm for TLR complexes and suggests a molecular mechanism for regulating LPS responses.

Multiphonon capture processes in self-assembled quantum dots

DEFF Research Database (Denmark)

Magnúsdóttir, Ingibjörg; Uskov, A.; Bischoff, Svend

2001-01-01

We investigate capture of carriers from states in the continuous part of the energy spectrum into the discrete states of self-assembled InAs/GaAs QDs via emission of one or two phonons. We are not aware of any other investigations of two-phonon mediated capture processes in QDs, but we show...

Mediator-dependent Nuclear Receptor Functions

Science.gov (United States)

Chen, Wei; Roeder, Robert

2011-01-01

As gene-specific transcription factors, nuclear hormone receptors are broadly involved in many important biological processes. Their function on target genes requires the stepwise assembly of different coactivator complexes that facilitate chromatin remodeling and subsequent preinitiation complex (PIC) formation and function. Mediator has proved to be a crucial, and general, nuclear receptor-interacting coactivator, with demonstrated functions in transcription steps ranging from chromatin remodeling to subsequent PIC formation and function. Here we discuss (i) our current understanding of pathways that nuclear receptors and other interacting cofactors employ to recruit Mediator to target gene enhancers and promoters, including conditional requirements for the strong NR-Mediator interactions mediated by the NR AF2 domain and the MED1 LXXLLL motifs and (ii) mechanisms by which Mediator acts to transmit signals from enhancer-bound nuclear receptors to the general transcription machinery at core promoters to effect PIC formation and function. PMID:21854863

Diblock-copolymer-mediated self-assembly of protein-stabilized iron oxide nanoparticle clusters for magnetic resonance imaging.

Science.gov (United States)

Tähkä, Sari; Laiho, Ari; Kostiainen, Mauri A

2014-03-03

Superparamagnetic iron oxide nanoparticles (SPIONs) can be used as efficient transverse relaxivity (T2 ) contrast agents in magnetic resonance imaging (MRI). Organizing small (Doxide) diblock copolymer (P2QVP-b-PEO) to mediate the self-assembly of protein-cage-encapsulated iron oxide (γ-Fe2 O3 ) nanoparticles (magnetoferritin) into stable PEO-coated clusters. This approach relies on electrostatic interactions between the cationic N-methyl-2-vinylpyridinium iodide block and magnetoferritin protein cage surface (pI≈4.5) to form a dense core, whereas the neutral ethylene oxide block provides a stabilizing biocompatible shell. Formation of the complexes was studied in aqueous solvent medium with dynamic light scattering (DLS) and cryogenic transmission electron microcopy (cryo-TEM). DLS results indicated that the hydrodynamic diameter (Dh ) of the clusters is approximately 200 nm, and cryo-TEM showed that the clusters have an anisotropic stringlike morphology. MRI studies showed that in the clusters the longitudinal relaxivity (r1 ) is decreased and the transverse relaxivity (r2 ) is increased relative to free magnetoferritin (MF), thus indicating that clusters can provide considerable contrast enhancement. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Overall Architecture of the Intraflagellar Transport (IFT)-B Complex Containing Cluap1/IFT38 as an Essential Component of the IFT-B Peripheral Subcomplex.

Science.gov (United States)

Katoh, Yohei; Terada, Masaya; Nishijima, Yuya; Takei, Ryota; Nozaki, Shohei; Hamada, Hiroshi; Nakayama, Kazuhisa

2016-05-20

Intraflagellar transport (IFT) is essential for assembly and maintenance of cilia and flagella as well as ciliary motility and signaling. IFT is mediated by multisubunit complexes, including IFT-A, IFT-B, and the BBSome, in concert with kinesin and dynein motors. Under high salt conditions, purified IFT-B complex dissociates into a core subcomplex composed of at least nine subunits and at least five peripherally associated proteins. Using the visible immunoprecipitation assay, which we recently developed as a convenient protein-protein interaction assay, we determined the overall architecture of the IFT-B complex, which can be divided into core and peripheral subcomplexes composed of 10 and 6 subunits, respectively. In particular, we identified TTC26/IFT56 and Cluap1/IFT38, neither of which was included with certainty in previous models of the IFT-B complex, as integral components of the core and peripheral subcomplexes, respectively. Consistent with this, a ciliogenesis defect of Cluap1-deficient mouse embryonic fibroblasts was rescued by exogenous expression of wild-type Cluap1 but not by mutant Cluap1 lacking the binding ability to other IFT-B components. The detailed interaction map as well as comparison of subcellular localization of IFT-B components between wild-type and Cluap1-deficient cells provides insights into the functional relevance of the architecture of the IFT-B complex. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Long-range energy transfer in self-assembled quantum dot-DNA cascades

Science.gov (United States)

Goodman, Samuel M.; Siu, Albert; Singh, Vivek; Nagpal, Prashant

2015-11-01

The size-dependent energy bandgaps of semiconductor nanocrystals or quantum dots (QDs) can be utilized in converting broadband incident radiation efficiently into electric current by cascade energy transfer (ET) between layers of different sized quantum dots, followed by charge dissociation and transport in the bottom layer. Self-assembling such cascade structures with angstrom-scale spatial precision is important for building realistic devices, and DNA-based QD self-assembly can provide an important alternative. Here we show long-range Dexter energy transfer in QD-DNA self-assembled single constructs and ensemble devices. Using photoluminescence, scanning tunneling spectroscopy, current-sensing AFM measurements in single QD-DNA cascade constructs, and temperature-dependent ensemble devices using TiO2 nanotubes, we show that Dexter energy transfer, likely mediated by the exciton-shelves formed in these QD-DNA self-assembled structures, can be used for efficient transport of energy across QD-DNA thin films.The size-dependent energy bandgaps of semiconductor nanocrystals or quantum dots (QDs) can be utilized in converting broadband incident radiation efficiently into electric current by cascade energy transfer (ET) between layers of different sized quantum dots, followed by charge dissociation and transport in the bottom layer. Self-assembling such cascade structures with angstrom-scale spatial precision is important for building realistic devices, and DNA-based QD self-assembly can provide an important alternative. Here we show long-range Dexter energy transfer in QD-DNA self-assembled single constructs and ensemble devices. Using photoluminescence, scanning tunneling spectroscopy, current-sensing AFM measurements in single QD-DNA cascade constructs, and temperature-dependent ensemble devices using TiO2 nanotubes, we show that Dexter energy transfer, likely mediated by the exciton-shelves formed in these QD-DNA self-assembled structures, can be used for efficient

Classification of coordination polygons and polyhedra according to their mode of self-assembly.

Science.gov (United States)

Swiegers, G F; Malefetse, T J

2001-09-03

This work extends techniques for the controlled formation of synthetic molecular containers by metal-mediated self-assembly. A new classification system based on the self-assembly of such species is proposed. The system: 1) allows a systematic identification of suitable acceptor-donor combinations, 2) widens the variety of design possibilities available, 3) allows a ready comparison of the self-assembly of different compounds, 4) reveals useful commonalities between different compounds, 5) aids in the development of novel architectures, and 6) permits identification of systems capable of being switched back-and-forth between architectures.

Self-recognition in the coordination driven self-assembly of 2-D polygons.

Science.gov (United States)

Addicott, Chris; Das, Neeladri; Stang, Peter J

2004-08-23

Self-recognition in the transition-metal-mediated self-assembly of some 2-D polygons is presented. Prolonged heating of two or three organoplatinum reagents with 4,4'-dipyridyl in aqueous acetone results in the predominant formation of a rectangle, triangle, and/or square. All mixtures are characterized with NMR and electrospray ionization mass spectrometry (ESIMS). Despite the potential for ill-defined oligomeric products, these mixed ligand systems prefer to self-assemble into discrete species.

Modification and Assembly of a Versatile Lactonase for Bacterial Quorum Quenching

Directory of Open Access Journals (Sweden)

Melissa K. Rhoads

2018-02-01

Full Text Available This work sets out to provide a self-assembled biopolymer capsule activated with a multi-functional enzyme for localized delivery. This enzyme, SsoPox, which is a lactonase and phosphotriesterase, provides a means of interrupting bacterial communication pathways that have been shown to mediate pathogenicity. Here we demonstrate the capability to express, purify and attach SsoPox to the natural biopolymer chitosan, preserving its activity to “neutralize” long-chain autoinducer-1 (AI-1 communication molecules. Attachment is shown via non-specific binding and by engineering tyrosine and glutamine affinity ‘tags’ at the C-terminus for covalent linkage. Subsequent degradation of AI-1, in this case N-(3-oxododecanoyl-l-homoserine lactone (OdDHL, serves to “quench” bacterial quorum sensing (QS, silencing intraspecies communication. By attaching enzymes to pH-responsive chitosan that, in turn, can be assembled into various forms, we demonstrate device-based flexibility for enzyme delivery. Specifically, we have assembled quorum-quenching capsules consisting of an alginate inner core and an enzyme “decorated” chitosan shell that are shown to preclude bacterial QS crosstalk, minimizing QS mediated behaviors.

Rigid Biopolymer Nanocrystal Systems for Controlling Multicomponent Nanoparticle Assembly and Orientation in Thin Film Solar Cells

Energy Technology Data Exchange (ETDEWEB)

Cha, Jennifer [Univ. of Colorado, Boulder, CO (United States)

2016-10-31

We have discovered techniques to synthesize well-defined DN conjugated nanostructures that are stable in a wide variety of conditions needed for DNA mediated assembly. Starting from this, we have shown that DNA can be used to control the assembly and integration of semiconductor nanocrystals into thin film devices that show photovoltaic effects.

Stoichiometry-Controlled Inversion of Supramolecular Chirality in Nanostructures Co-assembled with Bipyridines.

Science.gov (United States)

Wang, Fang; Feng, Chuan-Liang

2018-02-01

To control supramolecular chirality of the co-assembled nanostructures, one of the remaining issues is how stoichiometry of the different molecules involved in co-assembly influence chiral transformation. Through co-assembly of achiral 1,4-bis(pyrid-4-yl)benzene and chiral phenylalanine-glycine derivative hydrogelators, stoichiometry is found to be an effective tool for controlling supramolecular chirality inversion processes. This inversion is mainly mediated by a delicate balance between intermolecular hydrogen bonding interactions and π-π stacking of the two components, which may subtly change the stacking of the molecules, in turn, the self-assembled nanostructures. This study exemplifies a simplistic way to invert the handedness of chiral nanostructures and provide fundamental understanding of the inherent principles of supramolecular chirality. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

DEFF Research Database (Denmark)

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

2015-01-01

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

Missing Links in Antibody Assembly Control

Directory of Open Access Journals (Sweden)

Tiziana Anelli

2013-01-01

Full Text Available Fidelity of the humoral immune response requires that quiescent B lymphocytes display membrane bound immunoglobulin M (IgM on B lymphocytes surface as part of the B cell receptor, whose function is to recognize an antigen. At the same time B lymphocytes should not secrete IgM until recognition of the antigen has occurred. The heavy chains of the secretory IgM have a C-terminal tail with a cysteine instead of a membrane anchor, which serves to covalently link the IgM subunits by disulfide bonds to form “pentamers” or “hexamers.” By virtue of the same cysteine, unassembled secretory IgM subunits are recognized and retained (via mixed disulfide bonds by members of the protein disulfide isomerase family, in particular ERp44. This so-called “thiol-mediated retention” bars assembly intermediates from prematurely leaving the cell and thereby exerts quality control on the humoral immune response. In this essay we discuss recent findings on how ERp44 governs such assembly control in a pH-dependent manner, shuttling between the cisGolgi and endoplasmic reticulum, and finally on how pERp1/MZB1, possibly as a co-chaperone of GRP94, may help to overrule the thiol-mediated retention in the activated B cell to give way to antibody secretion.

Interfacial assembly structures and nanotribological properties of saccharic acids.

Science.gov (United States)

Shi, Hongyu; Liu, Yuhong; Zeng, Qingdao; Yang, Yanlian; Wang, Chen; Lu, Xinchun

2017-01-04

Saccharides have been recognized as potential bio-lubricants because of their good hydration ability. However, the interfacial structures of saccharides and their derivatives are rarely studied and the molecular details of interaction mechanisms have not been well understood. In this paper, the supramolecular assembly structures of saccharic acids (including galactaric acid and lactobionic acid), mediated by hydrogen bonds O-HN and O-HO, were successfully constructed on a highly oriented pyrolytic graphite (HOPG) surface by introducing pyridine modulators and were explicitly revealed by using scanning tunneling microscopy (STM). Furthermore, friction forces were measured in the saccharic acid/pyridine co-assembled system by atomic force microscopy (AFM), revealing a larger value than a pristine saccharic acid system, which could be attributed to the stronger tip-assembled molecule interactions that lead to the higher potential energy barrier needed to overcome. The effort on saccharide-related supramolecular self-assembly and nanotribological behavior could provide a novel and promising pathway to explore the interaction mechanisms underlying friction and reveal the structure-property relationship at the molecular level.

Bioengineering towards self-assembly of particulate vaccines.

Science.gov (United States)

Rehm, Bernd H A

2017-12-01

There is an unmet demand for safe and efficient vaccines for prevention of various infectious diseases. Subunit vaccines comprise selected pathogen specific antigens are a safe alternative to whole organism vaccines. However they often lack immunogenicity. Natural and synthetic self-assembling polymers and proteins will be reviewed in view their use to encapsulate and/or display antigens to serve as immunogenic antigen carriers for induction of protective immunity. Recent advances made in in vivo assembly of antigen-displaying polyester inclusions will be a focus. Particulate vaccines are inherently immunogenic due to enhanced uptake by antigen presenting cells which process antigens mediating adaptive immune responses. Bioengineering approaches enable the design of tailor-made particulate vaccines to fine tune immune responses towards protective immunity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Flexible Connectors between Capsomer Subunits that Regulate Capsid Assembly.

Science.gov (United States)

Hasek, Mary L; Maurer, Joshua B; Hendrix, Roger W; Duda, Robert L

2017-08-04

Viruses build icosahedral capsids of specific size and shape by regulating the spatial arrangement of the hexameric and pentameric protein capsomers in the growing shell during assembly. In the T=7 capsids of Escherichia coli bacteriophage HK97 and other phages, 60 capsomers are hexons, while the rest are pentons that are correctly positioned during assembly. Assembly of the HK97 capsid to the correct size and shape has been shown to depend on specific ionic contacts between capsomers. We now describe additional ionic interactions within capsomers that also regulate assembly. Each is between the long hairpin, the "E-loop," that extends from one subunit to the adjacent subunit within the same capsomer. Glutamate E153 on the E-loop and arginine R210 on the adjacent subunit's backbone alpha-helix form salt bridges in hexamers and pentamers. Mutations that disrupt these salt bridges were lethal for virus production, because the mutant proteins assembled into tubes or sheets instead of capsids. X-ray structures show that the E153-R210 links are flexible and maintained during maturation despite radical changes in capsomer shape. The E153-R210 links appear to form early in assembly to enable capsomers to make programmed changes in their shape during assembly. The links also prevent flattening of capsomers and premature maturation. Mutant phenotypes and modeling support an assembly model in which flexible E153-R210 links mediate capsomer shape changes that control where pentons are placed to create normal-sized capsids. The E-loop may be conserved in other systems in order to play similar roles in regulating assembly. Copyright © 2017 Elsevier Ltd. All rights reserved.

Stepwise Assembly and Characterization of DNA Linked Two-Color Quantum Dot Clusters.

Science.gov (United States)

Coopersmith, Kaitlin; Han, Hyunjoo; Maye, Mathew M

2015-07-14

The DNA-mediated self-assembly of multicolor quantum dot (QD) clusters via a stepwise approach is described. The CdSe/ZnS QDs were synthesized and functionalized with an amphiphilic copolymer, followed by ssDNA conjugation. At each functionalization step, the QDs were purified via gradient ultracentrifugation, which was found to remove excess polymer and QD aggregates, allowing for improved conjugation yields and assembly reactivity. The QDs were then assembled and disassembled in a stepwise manner at a ssDNA functionalized magnetic colloid, which provided a convenient way to remove unreacted QDs and ssDNA impurities. After assembly/disassembly, the clusters' optical characteristics were studied by fluorescence spectroscopy and the assembly morphology and stoichiometry was imaged via electron microscopy. The results indicate that a significant amount of QD-to-QD energy transfer occurred in the clusters, which was studied as a function of increasing acceptor-to-donor ratios, resulting in increased QD acceptor emission intensities compared to controls.

Single-Molecule Analysis for RISC Assembly and Target Cleavage.

Science.gov (United States)

Sasaki, Hiroshi M; Tadakuma, Hisashi; Tomari, Yukihide

2018-01-01

RNA-induced silencing complex (RISC) is a small RNA-protein complex that mediates silencing of complementary target RNAs. Biochemistry has been successfully used to characterize the molecular mechanism of RISC assembly and function for nearly two decades. However, further dissection of intermediate states during the reactions has been warranted to fill in the gaps in our understanding of RNA silencing mechanisms. Single-molecule analysis with total internal reflection fluorescence (TIRF) microscopy is a powerful imaging-based approach to interrogate complex formation and dynamics at the individual molecule level with high sensitivity. Combining this technique with our recently established in vitro reconstitution system of fly Ago2-RISC, we have developed a single-molecule observation system for RISC assembly. In this chapter, we summarize the detailed protocol for single-molecule analysis of chaperone-assisted assembly of fly Ago2-RISC as well as its target cleavage reaction.

Assembly of dynamic P450-mediated metabolons - order versus chaos

DEFF Research Database (Denmark)

Bassard, Jean-Étienne André; Møller, Birger Lindberg; Laursen, Tomas

2017-01-01

PURPOSE OF REVIEW: We provide an overview of the current knowledge on cytochrome P450-mediated metabolism organized as metabolons and factors that facilitate their stabilization. Essential parameters will be discussed including those that are commonly disregarded using the dhurrin metabolon from ...

Microfluidic Droplet-Facilitated Hierarchical Assembly for Dual Cargo Loading and Synergistic Delivery.

Science.gov (United States)

Yu, Ziyi; Zheng, Yu; Parker, Richard M; Lan, Yang; Wu, Yuchao; Coulston, Roger J; Zhang, Jing; Scherman, Oren A; Abell, Chris

2016-04-06

Bottom-up hierarchical assembly has emerged as an elaborate and energy-efficient strategy for the fabrication of smart materials. Herein, we present a hierarchical assembly process, whereby linear amphiphilic block copolymers are self-assembled into micelles, which in turn are accommodated at the interface of microfluidic droplets via cucurbit[8]uril-mediated host-guest chemistry to form supramolecular microcapsules. The monodisperse microcapsules can be used for simultaneous carriage of both organic (Nile Red) and aqueous-soluble (fluorescein isothiocyanate-dextran) cargo. Furthermore, the well-defined compartmentalized structure benefits from the dynamic nature of the supramolecular interaction and offers synergistic delivery of cargos with triggered release or through photocontrolled porosity. This demonstration of premeditated hierarchical assembly, where interactions from the molecular to microscale are designed, illustrates the power of this route toward accessing the next generation of functional materials and encapsulation strategies.

Structural Polymorphism in a Self-Assembled Tri-Aromatic Peptide System.

Science.gov (United States)

Brown, Noam; Lei, Jiangtao; Zhan, Chendi; Shimon, Linda J W; Adler-Abramovich, Lihi; Wei, Guanghong; Gazit, Ehud

2018-04-24

Self-assembly is a process of key importance in natural systems and in nanotechnology. Peptides are attractive building blocks due to their relative facile synthesis, biocompatibility, and other unique properties. Diphenylalanine (FF) and its derivatives are known to form nanostructures of various architectures and interesting and varied characteristics. The larger triphenylalanine peptide (FFF) was found to self-assemble as efficiently as FF, forming related but distinct architectures of plate-like and spherical nanostructures. Here, to understand the effect of triaromatic systems on the self-assembly process, we examined carboxybenzyl-protected diphenylalanine (z-FF) as a minimal model for such an arrangement. We explored different self-assembly conditions by changing solvent compositions and peptide concentrations, generating a phase diagram for the assemblies. We discovered that z-FF can form a variety of structures, including nanowires, fibers, nanospheres, and nanotoroids, the latter were previously observed only in considerably larger or co-assembly systems. Secondary structure analysis revealed that all assemblies possessed a β-sheet conformation. Additionally, in solvent combinations with high water ratios, z-FF formed rigid and self-healing hydrogels. X-ray crystallography revealed a "wishbone" structure, in which z-FF dimers are linked by hydrogen bonds mediated by methanol molecules, with a 2-fold screw symmetry along the c-axis. All-atom molecular dynamics (MD) simulations revealed conformations similar to the crystal structure. Coarse-grained MD simulated the assembly of the peptide into either fibers or spheres in different solvent systems, consistent with the experimental results. This work thus expands the building block library for the fabrication of nanostructures by peptide self-assembly.

DNA-mediated self-assembly of carbon nanotubes on gold

International Nuclear Information System (INIS)

Sanchez-Pomales, Germarie; Rivera-Velez, Nelson E; Cabrera, Carlos R

2007-01-01

This report presents the use of disulfide-modified single-stranded DNA (ssDNA) to form DNA self-assembled monolayers (SAMs) and mixed DNA-carbon nanotube (CNT) hybrids SAMs on gold substrates. Mixed DNA-CNT SAMs are composed of DNA, mercaptohexanol (MCH) and DNA-CNT aggregates. Both, DNA-CNT and DNA areas of the mixed SAMs were analyzed and compared to traditional DNA SAMs. The results suggest the formation of a more compact and densely packed monolayer of DNA-CNT in comparison with DNA. The use of DNA-CNT hybrids to form SAMs on gold substrates might represent a new approach to improve the immobilization of DNA strands on gold, and might therefore help with the development of enhanced DNA sensors

A Critical Appraisal of RAFT-Mediated Polymerization-Induced Self-Assembly

Science.gov (United States)

2016-01-01

Recently, polymerization-induced self-assembly (PISA) has become widely recognized as a robust and efficient route to produce block copolymer nanoparticles of controlled size, morphology, and surface chemistry. Several reviews of this field have been published since 2012, but a substantial number of new papers have been published in the last three years. In this Perspective, we provide a critical appraisal of the various advantages offered by this approach, while also pointing out some of its current drawbacks. Promising future research directions as well as remaining technical challenges and unresolved problems are briefly highlighted. PMID:27019522

Desmosome Assembly and Disassembly Are Membrane Raft-Dependent

Science.gov (United States)

Faundez, Victor; Koval, Michael; Mattheyses, Alexa L.; Kowalczyk, Andrew P.

2014-01-01

Strong intercellular adhesion is critical for tissues that experience mechanical stress, such as the skin and heart. Desmosomes provide adhesive strength to tissues by anchoring desmosomal cadherins of neighboring cells to the intermediate filament cytoskeleton. Alterations in assembly and disassembly compromise desmosome function and may contribute to human diseases, such as the autoimmune skin blistering disease pemphigus vulgaris (PV). We previously demonstrated that PV auto-antibodies directed against the desmosomal cadherin desmoglein 3 (Dsg3) cause loss of adhesion by triggering membrane raft-mediated Dsg3 endocytosis. We hypothesized that raft membrane microdomains play a broader role in desmosome homeostasis by regulating the dynamics of desmosome assembly and disassembly. In human keratinocytes, Dsg3 is raft associated as determined by biochemical and super resolution immunofluorescence microscopy methods. Cholesterol depletion, which disrupts rafts, prevented desmosome assembly and adhesion, thus functionally linking rafts to desmosome formation. Interestingly, Dsg3 did not associate with rafts in cells lacking desmosomal proteins. Additionally, PV IgG-induced desmosome disassembly occurred by redistribution of Dsg3 into raft-containing endocytic membrane domains, resulting in cholesterol-dependent loss of adhesion. These findings demonstrate that membrane rafts are required for desmosome assembly and disassembly dynamics, suggesting therapeutic potential for raft targeting agents in desmosomal diseases such as PV. PMID:24498201

Molecular anatomy of the recombination mediator function of Saccharomyces cerevisiae Rad52

DEFF Research Database (Denmark)

Seong, C.; Sehorn, M.G.; Plate, Iben

2008-01-01

A helical filament of Rad51 on single-strand DNA (ssDNA), called the presynaptic filament, catalyzes DNA joint formation during homologous recombination. Rad52 facilitates presynaptic filament assembly, and this recombination mediator activity is thought to rely on the interactions of Rad52...... with Rad51, the ssDNA-binding protein RPA, and ssDNA. The N-terminal region of Rad52, which has DNA binding activity and an oligomeric structure, is thought to be crucial for mediator activity and recombination. Unexpectedly, we find that the C-terminal region of Rad52 also harbors a DNA binding function....... Importantly, the Rad52 C-terminal portion alone can promote Rad51 presynaptic filament assembly. The middle portion of Rad52 associates with DNA-bound RPA and contributes to the recombination mediator activity. Accordingly, expression of a protein species that harbors the middle and C-terminal regions of Rad...

Mediator: A key regulator of plant development.

Science.gov (United States)

Buendía-Monreal, Manuel; Gillmor, C Stewart

2016-11-01

Mediator is a multiprotein complex that regulates transcription at the level of RNA pol II assembly, as well as through regulation of chromatin architecture, RNA processing and recruitment of epigenetic marks. Though its modular structure is conserved in eukaryotes, its subunit composition has diverged during evolution and varies in response to environmental and tissue-specific inputs, suggesting different functions for each subunit and/or Mediator conformation. In animals, Mediator has been implicated in the control of differentiation and morphogenesis through modulation of numerous signaling pathways. In plants, studies have revealed roles for Mediator in regulation of cell division, cell fate and organogenesis, as well as developmental timing and hormone responses. We begin this review with an overview of biochemical mechanisms of yeast and animal Mediator that are likely to be conserved in all eukaryotes, as well as a brief discussion of the role of Mediator in animal development. We then present a comprehensive review of studies of the role of Mediator in plant development. Finally, we point to important questions for future research on the role of Mediator as a master coordinator of development. Copyright © 2016 Elsevier Inc. All rights reserved.

DNA-Mediated Electrochemistry

Science.gov (United States)

Gorodetsky, Alon A.; Buzzeo, Marisa C.

2009-01-01

The base pair stack of DNA has been demonstrated as a medium for long range charge transport chemistry both in solution and at DNA-modified surfaces. This chemistry is exquisitely sensitive to structural perturbations in the base pair stack as occur with lesions, single base mismatches, and protein binding. We have exploited this sensitivity for the development of reliable electrochemical assays based on DNA charge transport at self-assembled DNA monolayers. Here we discuss the characteristic features, applications, and advantages of DNA-mediated electrochemistry. PMID:18980370

Self-assembled M2L4 coordination cages : Synthesis and potential applications

NARCIS (Netherlands)

Schmidt, Andrea; Casini, Angela; Kuehn, Fritz E.

2014-01-01

Metal-mediated self-assemblies of the general formula MxLy (M = metal ion, L = ligand) have emerged as a promising research area of supramolecular chemistry because of their applicability in various fields such as molecular recognition, catalysis and drug delivery. The focus of this review is on

Noncanonical self-assembly of multifunctional DNA nanoflowers for biomedical applications.

Science.gov (United States)

Zhu, Guizhi; Hu, Rong; Zhao, Zilong; Chen, Zhuo; Zhang, Xiaobing; Tan, Weihong

2013-11-06

DNA nanotechnology has been extensively explored to assemble various functional nanostructures for versatile applications. Mediated by Watson-Crick base-pairing, these DNA nanostructures have been conventionally assembled through hybridization of many short DNA building blocks. Here we report the noncanonical self-assembly of multifunctional DNA nanostructures, termed as nanoflowers (NFs), and the versatile biomedical applications. These NFs were assembled from long DNA building blocks generated via rolling circle replication (RCR) of a designer template. NF assembly was driven by liquid crystallization and dense packaging of building blocks, without relying on Watson-Crick base-pairing between DNA strands, thereby avoiding the otherwise conventional complicated DNA sequence design. NF sizes were readily tunable in a wide range, by simply adjusting such parameters as assembly time and template sequences. NFs were exceptionally resistant to nuclease degradation, denaturation, or dissociation at extremely low concentration, presumably resulting from the dense DNA packaging in NFs. The exceptional biostability is critical for biomedical applications. By rational design, NFs can be readily incorporated with myriad functional moieties. All these properties make NFs promising for versatile applications. As a proof-of-principle demonstration, in this study, NFs were integrated with aptamers, bioimaging agents, and drug loading sites, and the resultant multifunctional NFs were demonstrated for selective cancer cell recognition, bioimaging, and targeted anticancer drug delivery.

Competitive chiral induction in a 2D molecular assembly: Intrinsic chirality versus coadsorber-induced chirality.

Science.gov (United States)

Chen, Ting; Li, Shu-Ying; Wang, Dong; Wan, Li-Jun

2017-11-01

Noncovalently introducing stereogenic information is a promising approach to embed chirality in achiral molecular systems. However, the interplay of the noncovalently introduced chirality with the intrinsic chirality of molecules or molecular aggregations has rarely been addressed. We report a competitive chiral expression of the noncovalent interaction-mediated chirality induction and the intrinsic stereogenic center-controlled chirality induction in a two-dimensional (2D) molecular assembly at the liquid/solid interface. Two enantiomorphous honeycomb networks are formed by the coassembly of an achiral 5-(benzyloxy)isophthalic acid (BIC) derivative and 1-octanol at the liquid/solid interface. The preferential formation of the globally homochiral assembly can be achieved either by using the chiral analog of 1-octanol, ( S )-6-methyl-1-octanol, as a chiral coadsorber to induce chirality to the BIC assembly via noncovalent hydrogen bonding or by covalently linking a chiral center in the side chain of BIC. Both the chiral coadsorber and the intrinsically chiral BIC derivative can act as a chiral seeds to induce a preferred handedness in the assembly of the achiral BIC derivatives. Furthermore, the noncovalent interaction-mediated chirality induction can restrain or even overrule the manifestation of the intrinsic chirality of the BIC molecule and dominate the handedness of the 2D molecular coassembly. This study provides insight into the interplay of intrinsically chiral centers and external chiral coadsorbers in the chiral induction, transfer, and amplification processes of 2D molecular assembly.

Interactions within the yeast t-SNARE Sso1p that control SNARE complex assembly.

Science.gov (United States)

Munson, M; Chen, X; Cocina, A E; Schultz, S M; Hughson, F M

2000-10-01

In the eukaryotic secretory and endocytic pathways, transport vesicles shuttle cargo among intracellular organelles and to and from the plasma membrane. Cargo delivery entails fusion of the transport vesicle with its target, a process thought to be mediated by membrane bridging SNARE protein complexes. Temporal and spatial control of intracellular trafficking depends in part on regulating the assembly of these complexes. In vitro, SNARE assembly is inhibited by the closed conformation adopted by the syntaxin family of SNAREs. To visualize this closed conformation directly, the X-ray crystal structure of a yeast syntaxin, Sso1p, has been determined and refined to 2.1 A resolution. Mutants designed to destabilize the closed conformation exhibit accelerated rates of SNARE assembly. Our results provide insight into the mechanism of SNARE assembly and its intramolecular and intermolecular regulation.

Malleable machines in transcription regulation: the mediator complex.

Directory of Open Access Journals (Sweden)

Agnes Tóth-Petróczy

2008-12-01

Full Text Available The Mediator complex provides an interface between gene-specific regulatory proteins and the general transcription machinery including RNA polymerase II (RNAP II. The complex has a modular architecture (Head, Middle, and Tail and cryoelectron microscopy analysis suggested that it undergoes dramatic conformational changes upon interactions with activators and RNAP II. These rearrangements have been proposed to play a role in the assembly of the preinitiation complex and also to contribute to the regulatory mechanism of Mediator. In analogy to many regulatory and transcriptional proteins, we reasoned that Mediator might also utilize intrinsically disordered regions (IDRs to facilitate structural transitions and transmit transcriptional signals. Indeed, a high prevalence of IDRs was found in various subunits of Mediator from both Saccharomyces cerevisiae and Homo sapiens, especially in the Tail and the Middle modules. The level of disorder increases from yeast to man, although in both organisms it significantly exceeds that of multiprotein complexes of a similar size. IDRs can contribute to Mediator's function in three different ways: they can individually serve as target sites for multiple partners having distinctive structures; they can act as malleable linkers connecting globular domains that impart modular functionality on the complex; and they can also facilitate assembly and disassembly of complexes in response to regulatory signals. Short segments of IDRs, termed molecular recognition features (MoRFs distinguished by a high protein-protein interaction propensity, were identified in 16 and 19 subunits of the yeast and human Mediator, respectively. In Saccharomyces cerevisiae, the functional roles of 11 MoRFs have been experimentally verified, and those in the Med8/Med18/Med20 and Med7/Med21 complexes were structurally confirmed. Although the Saccharomyces cerevisiae and Homo sapiens Mediator sequences are only weakly conserved, the

Interactions of p60, a mediator of progesterone receptor assembly, with heat shock proteins hsp90 and hsp70

DEFF Research Database (Denmark)

Chen, S; Prapapanich, V; Rimerman, R A

1996-01-01

Previous studies on the assembly of progesterone receptor (PR) complexes in vitro have suggested that PR assembly is a dynamic, ordered process involving at least eight nonreceptor proteins. One of these proteins, p60, appears transiently during assembly and is not a component of functionally...

Bioorthogonal cyclization-mediated in situ self-assembly of small-molecule probes for imaging caspase activity in vivo

Science.gov (United States)

Ye, Deju; Shuhendler, Adam J.; Cui, Lina; Tong, Ling; Tee, Sui Seng; Tikhomirov, Grigory; Felsher, Dean W.; Rao, Jianghong

2014-06-01

Directed self-assembly of small molecules in living systems could enable a myriad of applications in biology and medicine, and already this has been used widely to synthesize supramolecules and nano/microstructures in solution and in living cells. However, controlling the self-assembly of synthetic small molecules in living animals is challenging because of the complex and dynamic in vivo physiological environment. Here we employ an optimized first-order bioorthogonal cyclization reaction to control the self-assembly of a fluorescent small molecule, and demonstrate its in vivo applicability by imaging caspase-3/7 activity in human tumour xenograft mouse models of chemotherapy. The fluorescent nanoparticles assembled in situ were imaged successfully in both apoptotic cells and tumour tissues using three-dimensional structured illumination microscopy. This strategy combines the advantages offered by small molecules with those of nanomaterials and should find widespread use for non-invasive imaging of enzyme activity in vivo.

ICK is essential for cell type-specific ciliogenesis and the regulation of ciliary transport.

Science.gov (United States)

Chaya, Taro; Omori, Yoshihiro; Kuwahara, Ryusuke; Furukawa, Takahisa

2014-06-02

Cilia and flagella are formed and maintained by intraflagellar transport (IFT) and play important roles in sensing and moving across species. At the distal tip of the cilia/flagella, IFT complexes turn around to switch from anterograde to retrograde transport; however, the underlying regulatory mechanism is unclear. Here, we identified ICK localization at the tip of cilia as a regulator of ciliary transport. In ICK-deficient mice, we found ciliary defects in neuronal progenitor cells with Hedgehog signal defects. ICK-deficient cells formed cilia with mislocalized Hedgehog signaling components. Loss of ICK caused the accumulation of IFT-A, IFT-B, and BBSome components at the ciliary tips. In contrast, overexpression of ICK induced the strong accumulation of IFT-B, but not IFT-A or BBSome components at ciliary tips. In addition, ICK directly phosphorylated Kif3a, while inhibition of this Kif3a phosphorylation affected ciliary formation. Our results suggest that ICK is a Kif3a kinase and essential for proper ciliogenesis in development by regulating ciliary transport at the tip of cilia. © 2014 The Authors.

Achieving 3-D Nanoparticle Assembly in Nanocomposite Thin Films via Kinetic Control

Energy Technology Data Exchange (ETDEWEB)

Huang, Jingyu; Xiao, Yihan; Xu, Ting [UCB

2017-02-20

Nanocomposite thin films containing well-ordered nanoparticle (NP) assemblies are ideal candidates for the fabrication of metamaterials. Achieving 3-D assembly of NPs in nanocomposite thin films is thermodynamically challenging as the particle size gets similar to that of a single polymer chain. The entropic penalties of polymeric matrix upon NP incorporation leads to NP aggregation on the film surface or within the defects in the film. Controlling the kinetic pathways of assembly process provides an alternative path forward by arresting the system in nonequilibrium states. Here, we report the thin film 3-D hierarchical assembly of 20 nm NPs in supramolecules with a 30 nm periodicity. By mediating the NP diffusion kinetics in the supramolecular matrix, surface aggregation of NPs was suppressed and NPs coassemble with supramolecules to form new 3-D morphologies in thin films. The present studies opened a viable route to achieve designer functional composite thin films via kinetic control.

Novel apigenin-loaded sodium hyaluronate nano-assemblies for targeting tumor cells.

Science.gov (United States)

Zhao, Ting; He, Yue; Chen, Huali; Bai, Yan; Hu, Wenjing; Zhang, Liangke

2017-12-01

We aimed to construct a novel nano-assembly carrying apigenin (APG), a hydrophobic drug, and to evaluate its in vitro targeting ability for A549 cells overexpressing CD44 receptors. The apigenin-loaded sodium hyaluronate nano-assemblies (APG/SH-NAs) were assembled by multiple non-covalent interactions between sodium hyaluronate (SH) and APG. The prepared APG/SH-NAs exhibited a small average size and narrow particle size distribution. In addition, satisfactory encapsulation efficiency and drug loading were obtained. The drug release curves indicated that APG/SH-NAs achieved a sustainable drug-release effect due to the presence of hydrophilic materials. The in vitro cytotoxicity of APG/SH-NAs against A549 cells and HepG2 cells was evaluated, and the results indicated that the prepared APG/SH-NA showed higher cytotoxicity compared to apigenin suspensions. When CD44 receptors on the surface of A549 cells were blocked by the addition of excess SH, the cytotoxicity of APG/SH-NA was significantly reduced. However, similar phenomena were not observed in HepG2 cells with relatively low CD44 receptor expression. The resulting APG/SH-NAs could efficiently facilitate the internalization of APG into A549 cells, which might be due to their high affinity for CD44 receptors. Moreover, the apoptotic rate of APG/SH-NAs through receptor-mediated endocytosis mechanism was higher than that of the other groups in A549 cells. Thus, such nano-assemblies were considered to be an effective transport system with excellent affinity for CD44 receptors to allow the SH-mediated targeted delivery of APG. Copyright © 2017. Published by Elsevier Ltd.

The Mediator complex and transcription regulation

Science.gov (United States)

Poss, Zachary C.; Ebmeier, Christopher C.

2013-01-01

The Mediator complex is a multi-subunit assembly that appears to be required for regulating expression of most RNA polymerase II (pol II) transcripts, which include protein-coding and most non-coding RNA genes. Mediator and pol II function within the pre-initiation complex (PIC), which consists of Mediator, pol II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH and is approximately 4.0 MDa in size. Mediator serves as a central scaffold within the PIC and helps regulate pol II activity in ways that remain poorly understood. Mediator is also generally targeted by sequence-specific, DNA-binding transcription factors (TFs) that work to control gene expression programs in response to developmental or environmental cues. At a basic level, Mediator functions by relaying signals from TFs directly to the pol II enzyme, thereby facilitating TF-dependent regulation of gene expression. Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression). In this review, we summarize an expansive body of research on the Mediator complex, with an emphasis on yeast and mammalian complexes. We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing. We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module. PMID:24088064

Weak Molecular Interactions in Clathrin-Mediated Endocytosis

Directory of Open Access Journals (Sweden)

Sarah M. Smith

2017-11-01

Full Text Available Clathrin-mediated endocytosis is a process by which specific molecules are internalized from the cell periphery for delivery to early endosomes. The key stages in this step-wise process, from the starting point of cargo recognition, to the later stage of assembly of the clathrin coat, are dependent on weak interactions between a large network of proteins. This review discusses the structural and functional data that have improved our knowledge and understanding of the main weak molecular interactions implicated in clathrin-mediated endocytosis, with a particular focus on the two key proteins: AP2 and clathrin.

Cloning Should Be Simple: Escherichia coli DH5α-Mediated Assembly of Multiple DNA Fragments with Short End Homologies

Science.gov (United States)

Richardson, Ruth E.; Suzuki, Yo

2015-01-01

Numerous DNA assembly technologies exist for generating plasmids for biological studies. Many procedures require complex in vitro or in vivo assembly reactions followed by plasmid propagation in recombination-impaired Escherichia coli strains such as DH5α, which are optimal for stable amplification of the DNA materials. Here we show that despite its utility as a cloning strain, DH5α retains sufficient recombinase activity to assemble up to six double-stranded DNA fragments ranging in size from 150 bp to at least 7 kb into plasmids in vivo. This process also requires surprisingly small amounts of DNA, potentially obviating the need for upstream assembly processes associated with most common applications of DNA assembly. We demonstrate the application of this process in cloning of various DNA fragments including synthetic genes, preparation of knockout constructs, and incorporation of guide RNA sequences in constructs for clustered regularly interspaced short palindromic repeats (CRISPR) genome editing. This consolidated process for assembly and amplification in a widely available strain of E. coli may enable productivity gain across disciplines involving recombinant DNA work. PMID:26348330

Liquid Crystal Mediated Nano-assembled Gold Micro-shells

Science.gov (United States)

Quint, Makiko; Sarang, Som; Quint, David; Huang, Kerwyn; Gopinathan, Ajay; Hirst, Linda; Ghosh, Sayantani

We have created 3D nano-assenbled micro-shell by using thermotropic liquid crystal (LC), 4-Cyano-4'-pentylbiphenyl (5CB), doped with mesogen-functionalized gold nanoparticles (AuNPs). The assembly process is driven by the isotropic-nematic phase transition dynamics. We uniformly disperse the functionalized AuNPs into isotropic liquid crystal matrix and the mixture is cooled from the isotropic to the nematic phase. During the phase transition, the separation of LC-AuNP rich isotropic and ordered 5CB rich domains cause the functionalized AuNPs to move into the shrinking isotropic regions. The mesogenic ligands are locally crystalized during this process, which leads to the formation of a spherical shell with a densely packed wall of AuNPs. These micro-shells are capable of encapsulating fluorescence dye without visible leakages for several months. Additionally, they demonstrate strong localized surface plasmon resonance, which leads to localized heating on optical excitation. This photothermal effect disrupts the structure, releasing contents within seconds. Our results exhibiting the capture and optically regulated release of encapsulated substances is a novel platform that combines drug-delivery and photothermal therapy in one versatile and multifunctional unit. This work is supported by the NSF Grants No. DMR-1056860, ECC-1227034, and a University of California Merced Faculty Mentor Fellowship.

NMR derived model of GTPase effector domain (GED self association: relevance to dynamin assembly.

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Swagata Chakraborty

Full Text Available Self-association of dynamin to form spiral structures around lipidic vesicles during endocytosis is largely mediated by its 'coiled coil' GTPase Effector Domain (GED, which, in vitro, self-associates into huge helical assemblies. Residue-level structural characterizations of these assemblies and understanding the process of association have remained a challenge. It is also impossible to get folded monomers in the solution phase. In this context, we have developed here a strategy to probe the self-association of GED by first dissociating the assembly using Dimethyl Sulfoxide (DMSO and then systematically monitoring the refolding into helix and concomitant re-association using NMR spectroscopy, as DMSO concentration is progressively reduced. The short segment, Arg109 - Met116, acts as the nucleation site for helix formation and self-association. Hydrophobic and complementary charge interactions on the surfaces drive self-association, as the helices elongate in both the directions resulting in an antiparallel stack. A small N-terminal segment remains floppy in the assembly. Following these and other published results on inter-domain interactions, we have proposed a plausible mode of dynamin self assembly.

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

Science.gov (United States)

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

2017-01-01

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

Sequence assembly

DEFF Research Database (Denmark)

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

2009-01-01

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

Identification of a tetrameric assembly domain in the C terminus of heat-activated TRPV1 channels.

Science.gov (United States)

Zhang, Feng; Liu, Shuang; Yang, Fan; Zheng, Jie; Wang, KeWei

2011-04-29

Transient receptor potential (TRP) channels as cellular sensors are thought to function as tetramers. Yet, the molecular determinants governing channel multimerization remain largely elusive. Here we report the identification of a segment comprising 21 amino acids (residues 752-772 of mouse TRPV1) after the known TRP-like domain in the channel C terminus that functions as a tetrameric assembly domain (TAD). Purified recombinant C-terminal proteins of TRPV1-4, but not the N terminus, mediated the protein-protein interaction in an in vitro pulldown assay. Western blot analysis combined with electrophysiology and calcium imaging demonstrated that TAD exerted a robust dominant-negative effect on wild-type TRPV1. When fused with the membrane-tethered peptide Gap43, the TAD blocked the formation of stable homomultimers. Calcium imaging and current recordings showed that deletion of the TAD in a poreless TRPV1 mutant subunit suppressed its dominant-negative phenotype, confirming the involvement of the TAD in assembly of functional channels. Our findings suggest that the C-terminal TAD in TRPV1 channels functions as a domain that is conserved among TRPV1-4 and mediates a direct subunit-subunit interaction for tetrameric assembly.

Calcium-dependent regulation of SNARE-mediated membrane fusion by calmodulin.

Science.gov (United States)

Di Giovanni, Jerome; Iborra, Cécile; Maulet, Yves; Lévêque, Christian; El Far, Oussama; Seagar, Michael

2010-07-30

Neuroexocytosis requires SNARE proteins, which assemble into trans complexes at the synaptic vesicle/plasma membrane interface and mediate bilayer fusion. Ca(2+) sensitivity is thought to be conferred by synaptotagmin, although the ubiquitous Ca(2+)-effector calmodulin has also been implicated in SNARE-dependent membrane fusion. To examine the molecular mechanisms involved, we examined the direct action of calmodulin and synaptotagmin in vitro, using fluorescence resonance energy transfer to assay lipid mixing between target- and vesicle-SNARE liposomes. Ca(2+)/calmodulin inhibited SNARE assembly and membrane fusion by binding to two distinct motifs located in the membrane-proximal regions of VAMP2 (K(D) = 500 nm) and syntaxin 1 (K(D) = 2 microm). In contrast, fusion was increased by full-length synaptotagmin 1 anchored in vesicle-SNARE liposomes. When synaptotagmin and calmodulin were combined, synaptotagmin overcame the inhibitory effects of calmodulin. Furthermore, synaptotagmin displaced calmodulin binding to target-SNAREs. These findings suggest that two distinct Ca(2+) sensors act antagonistically in SNARE-mediated fusion.

Bacteriophage Assembly

Directory of Open Access Journals (Sweden)

Anastasia A. Aksyuk

2011-02-01

Full Text Available 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.

A surface-mediated siRNA delivery system developed with chitosan/hyaluronic acid-siRNA multilayer films through layer-by-layer self-assembly

Energy Technology Data Exchange (ETDEWEB)

Wu, Lijuan [Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062 (China); Suzhou Novovita Bio-products Co., Ltd., Suzhou 215300 (China); Wu, Changlin, E-mail: Ph.Dclwu1314@sina.cn [Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062 (China); Suzhou Novovita Bio-products Co., Ltd., Suzhou 215300 (China); Liu, Guangwan [Suzhou Novovita Bio-products Co., Ltd., Suzhou 215300 (China); Liao, Nannan [Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062 (China); Suzhou Novovita Bio-products Co., Ltd., Suzhou 215300 (China); Zhao, Fang; Yang, Xuxia; Qu, Hongyuan [Suzhou Novovita Bio-products Co., Ltd., Suzhou 215300 (China); Peng, Bo [Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062 (China); Chen, Li [Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062 (China); Suzhou Novovita Bio-products Co., Ltd., Suzhou 215300 (China); Yang, Guang [Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062 (China)

2016-12-15

Highlights: • We prepared Chitosan/Hyaluronic acid-siRNA multilayer as carrier to effectively load and protect siRNAs. • The stability and integrity of the siRNA was verified in the siRNA-loaded films. • The siRNA-loaded films showed good cells adhesion and gene silencing effect in eGFP-HEK 293T cells. • This is a new type of surface-mediated non-viral multilayer films. - Abstract: siRNA delivery remains highly challenging because of its hydrophilic and anionic nature and its sensitivity to nuclease degradation. Effective siRNA loading and improved transfection efficiency into cells represents a key problem. In our study, we prepared Chitosan/Hyaluronic acid-siRNA multilayer films through layer-by-layer self-assembly, in which siRNAs can be effectively loaded and protected. The construction process was characterized by FTIR, {sup 13}C NMR (CP/MAS), UV–vis spectroscopy, and atomic force microscopy (AFM). We presented the controlled-release performance of the films during incubation in 1 M NaCl solution for several days through UV–vis spectroscopy and polyacrylamide gel electrophoresis (PAGE). Additionally, we verified the stability and integrity of the siRNA loaded on multilayer films. Finally, the biological efficacy of the siRNA delivery system was evaluated via cells adhesion and gene silencing analyses in eGFP-HEK 293T cells. This new type of surface-mediated non-viral multilayer films may have considerable potential in the localized and controlled-release delivery of siRNA in mucosal tissues, and tissue engineering application.

Intraflagellar Transport (IFT) Role in Ciliary Assembly, Resorption and Signalling

DEFF Research Database (Denmark)

Pedersen, Lotte B; Rosenbaum, Joel L

2008-01-01

Cilia and flagella have attracted tremendous attention in recent years as research demonstrated crucial roles for these organelles in coordinating a number of physiologically and developmentally important signaling pathways, including the platelet-derived growth factor receptor (PDGFR) alpha, Sonic...... hedgehog, polycystin, and Wnt pathways. In addition, the realization that defective assembly or function of cilia can cause a plethora of diseases and developmental defects ("ciliopathies") has increased focus on the mechanisms by which these antenna-like, microtubular structures assemble. Ciliogenesis...... mechanisms and functions of IFT. In addition to a general, up-to-date description of IFT, we discuss mechanisms by which proteins are selectively targeted to the ciliary compartment, with special focus on the ciliary transition zone. Finally, we briefly review the role of IFT in cilia-mediated signaling...

Optimizing Transcriptome Assemblies for Eleusine indica Leaf and Seedling by Combining Multiple Assemblies from Three De Novo Assemblers

Directory of Open Access Journals (Sweden)

Shu Chen

2015-03-01

Full Text Available Due to rapid advances in sequencing technology, increasing amounts of genomic and transcriptomic data are available for plant species, presenting enormous challenges for biocomputing analysis. A crucial first step for a successful transcriptomics-based study is the building of a high-quality assembly. Here, we utilized three different de novo assemblers (Trinity, Velvet, and CLC and the EvidentialGene pipeline tr2aacds to assemble two optimized transcript sets for the notorious weed species, . Two RNA sequencing (RNA-seq datasets from leaf and aboveground seedlings were processed using three assemblers, which resulted in 20 assemblies for each dataset. The contig numbers and N50 values of each assembly were compared to study the effect of read number, k-mer size, and in silico normalization on assembly output. The 20 assemblies were then processed through the tr2aacds pipeline to remove redundant transcripts and to select the transcript set with the best coding potential. Each assembly contributed a considerable proportion to the final transcript combination with the exception of the CLC-k14. Thus each assembler and parameter set did assemble better contigs for certain transcripts. The redundancy, total contig number, N50, fully assembled contig number, and transcripts related to target-site herbicide resistance were evaluated for the EvidentialGene and Trinity assemblies. Comparing the EvidentialGene set with the Trinity assembly revealed improved quality and reduced redundancy in both leaf and seedling EvidentialGene sets. The optimized transcriptome references will be useful for studying herbicide resistance in and the evolutionary process in the three allotetraploid offspring.

Off-pathway assembly of fimbria subunits is prevented by chaperone CfaA of CFA/I fimbriae from enterotoxigenic E. coli.

Science.gov (United States)

Bao, Rui; Liu, Yang; Savarino, Stephen J; Xia, Di

2016-12-01

The assembly of the class 5 colonization factor antigen I (CFA/I) fimbriae of enterotoxigenic E. coli was proposed to proceed via the alternate chaperone-usher pathway. Here, we show that in the absence of the chaperone CfaA, CfaB, the major pilin subunit of CFA/I fimbriae, is able to spontaneously refold and polymerize into cyclic trimers. CfaA kinetically traps CfaB to form a metastable complex that can be stabilized by mutations. Crystal structure of the stabilized complex reveals distinctive interactions provided by CfaA to trap CfaB in an assembly competent state through donor-strand complementation (DSC) and cleft-mediated anchorage. Mutagenesis indicated that DSC controls the stability of the chaperone-subunit complex and the cleft-mediated anchorage of the subunit C-terminus additionally assist in subunit refolding. Surprisingly, over-stabilization of the chaperone-subunit complex led to delayed fimbria assembly, whereas destabilizing the complex resulted in no fimbriation. Thus, CfaA acts predominantly as a kinetic trap by stabilizing subunit to avoid its off-pathway self-polymerization that results in energetically favorable trimers and could serve as a driving force for CFA/I pilus assembly, representing an energetic landscape unique to class 5 fimbria assembly. Published 2016. This article is a U.S. Government work and is in the public domain in the USA. Molecular Microbiology published by John Wiley & Sons Ltd.

Self-Assembly of Telechelic Tyrosine End-Capped PEO Star Polymers in Aqueous Solution.

Science.gov (United States)

Edwards-Gayle, Charlotte J C; Greco, Francesca; Hamley, Ian W; Rambo, Robert P; Reza, Mehedi; Ruokolainen, Janne; Skoulas, Dimitrios; Iatrou, Hermis

2018-01-08

We investigate the self-assembly of two telechelic star polymer-peptide conjugates based on poly(ethylene oxide) (PEO) four-arm star polymers capped with oligotyrosine. The conjugates were prepared via N-carboxy anhydride-mediated ring-opening polymerization from PEO star polymer macroinitiators. Self-assembly occurs above a critical aggregation concentration determined via fluorescence probe assays. Peptide conformation was examined using circular dichroism spectroscopy. The structure of self-assembled aggregates was probed using small-angle X-ray scattering and cryogenic transmission electron microscopy. In contrast to previous studies on linear telechelic PEO-oligotyrosine conjugates that show self-assembly into β-sheet fibrils, the star architecture suppresses fibril formation and micelles are generally observed instead, a small population of fibrils only being observed upon pH adjustment. Hydrogelation is also suppressed by the polymer star architecture. These peptide-functionalized star polymer solutions are cytocompatible at sufficiently low concentration. These systems present tyrosine at high density and may be useful in the development of future enzyme or pH-responsive biomaterials.

Seasonal changes in the assembly mechanisms structuring tropical fish communities.

Science.gov (United States)

Fitzgerald, Daniel B; Winemiller, Kirk O; Sabaj Pérez, Mark H; Sousa, Leandro M

2017-01-01

Despite growing interest in trait-based approaches to community assembly, little attention has been given to seasonal variation in trait distribution patterns. Mobile animals can rapidly mediate influences of environmental factors and species interactions through dispersal, suggesting that the relative importance of different assembly mechanisms can vary over short time scales. This study analyzes seasonal changes in functional trait distributions of tropical fishes in the Xingu River, a major tributary of the Amazon with large predictable temporal variation in hydrologic conditions and species density. Comparison of observed functional diversity revealed that species within wet-season assemblages were more functionally similar than those in dry-season assemblages. Further, species within wet-season assemblages were more similar than random expectations based on null model predictions. Higher functional richness within dry season communities is consistent with increased niche complementarity during the period when fish densities are highest and biotic interactions should be stronger; however, null model tests suggest that stochastic factors or a combination of assembly mechanisms influence dry-season assemblages. These results demonstrate that the relative influence of community assembly mechanisms can vary seasonally in response to changing abiotic conditions, and suggest that studies attempting to infer a single dominant mechanism from functional patterns may overlook important aspects of the assembly process. During the prolonged flood pulse of the wet season, expanded habitat and lower densities of aquatic organisms likely reduce the influence of competition and predation. This temporal shift in the influence of different assembly mechanisms, rather than any single mechanism, may play a large role in maintaining the structure and diversity of tropical rivers and perhaps other dynamic and biodiverse systems. © 2016 by the Ecological Society of America.

Energetics, kinetics, and pathway of SNARE folding and assembly revealed by optical tweezers.

Science.gov (United States)

Zhang, Yongli

2017-07-01

Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are universal molecular engines that drive membrane fusion. Particularly, synaptic SNAREs mediate fast calcium-triggered fusion of neurotransmitter-containing vesicles with plasma membranes for synaptic transmission, the basis of all thought and action. During membrane fusion, complementary SNAREs located on two apposed membranes (often called t- and v-SNAREs) join together to assemble into a parallel four-helix bundle, releasing the energy to overcome the energy barrier for fusion. A long-standing hypothesis suggests that SNAREs act like a zipper to draw the two membranes into proximity and thereby force them to fuse. However, a quantitative test of this SNARE zippering hypothesis was hindered by difficulties to determine the energetics and kinetics of SNARE assembly and to identify the relevant folding intermediates. Here, we first review different approaches that have been applied to study SNARE assembly and then focus on high-resolution optical tweezers. We summarize the folding energies, kinetics, and pathways of both wild-type and mutant SNARE complexes derived from this new approach. These results show that synaptic SNAREs assemble in four distinct stages with different functions: slow N-terminal domain association initiates SNARE assembly; a middle domain suspends and controls SNARE assembly; and rapid sequential zippering of the C-terminal domain and the linker domain directly drive membrane fusion. In addition, the kinetics and pathway of the stagewise assembly are shared by other SNARE complexes. These measurements prove the SNARE zippering hypothesis and suggest new mechanisms for SNARE assembly regulated by other proteins. © 2017 The Protein Society.

Fuel assemblies

International Nuclear Information System (INIS)

Nakatsuka, Masafumi.

1979-01-01

Purpose: To prevent scattering of gaseous fission products released from fuel assemblies stored in an fbr type reactor. Constitution; A cap provided with means capable of storing gas is adapted to amount to the assembly handling head, for example, by way of threading in a storage rack of spent fuel assemblies consisting of a bottom plate, a top plate and an assembly support mechanism. By previously eliminating the gas inside of the assembly and the cap in the storage rack, gaseous fission products upon loading, if released from fuel rods during storage, are stored in the cap and do not scatter in the storage rack. (Horiuchi, T.)

Dynamic release of nuclear RanGTP triggers TPX2-dependent microtubule assembly during the apoptotic execution phase.

Science.gov (United States)

Moss, David K; Wilde, Andrew; Lane, Jon D

2009-03-01

During apoptosis, the interphase microtubule network is dismantled then later replaced by a novel, non-centrosomal microtubule array. These microtubules assist in the peripheral redistribution of nuclear fragments in the apoptotic cell; however, the regulation of apoptotic microtubule assembly is not understood. Here, we demonstrate that microtubule assembly depends upon the release of nuclear RanGTP into the apoptotic cytoplasm because this process is blocked in apoptotic cells overexpressing dominant-negative GDP-locked Ran (T24N). Actin-myosin-II contractility provides the impetus for Ran release and, consequently, microtubule assembly is blocked in blebbistatin- and Y27632-treated apoptotic cells. Importantly, the spindle-assembly factor TPX2 (targeting protein for Xklp2), colocalises with apoptotic microtubules, and siRNA silencing of TPX2, but not of the microtubule motors Mklp1 and Kid, abrogates apoptotic microtubule assembly. These data provide a molecular explanation for the assembly of the apoptotic microtubule network, and suggest important similarities with the process of RanGTP- and TPX2-mediated mitotic spindle formation.

FET immunosensor for hemoglobin A1c using a gold nanofilm grown by a seed-mediated technique and covered with mixed self-assembled monolayers

International Nuclear Information System (INIS)

Xue, Q.; Bian, C.; Tong, J.; Sun, J.; Zhang, H.; Xia, S.

2012-01-01

A micro FET-based immunosensor was developed for the determination of hemoglobin-A1c (HbA1c). The HbA1c/hemoglobin ratio is an important index in diabetes control. The sensor was fabricated by Complementary Metal-Oxide-Semiconductor Transistor (CMOS) and Micro Electronic Mechanical System (MEMS) techniques. The antibodies were immobilized via mixed self-assembled monolayers (SAMs) on a gold nanofilm. The nanofilm was deposited on a gold electrode by seed-mediated growth and gave a uniform and well distributed coverage. Nonspecific sites and interferences by noise were eliminated by covering the AuNPs with mixed SAMs. Compared to the immunosensor fabricated via the mixed SAMs method without gold nanofilm, the immunosensor displays a more than 2-fold sensitivity. The immunosensor is capable of detecting HbA1c and hemoglobin in hemolyzed and diluted whole blood, and results showed good agreement with the established clinical method. (author)

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

Science.gov (United States)

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

PIC Activation through Functional Interplay between Mediator and TFIIH.

Science.gov (United States)

Malik, Sohail; Molina, Henrik; Xue, Zhu

2017-01-06

The multiprotein Mediator coactivator complex functions in large part by controlling the formation and function of the promoter-bound preinitiation complex (PIC), which consists of RNA polymerase II and general transcription factors. However, precisely how Mediator impacts the PIC, especially post-recruitment, has remained unclear. Here, we have studied Mediator effects on basal transcription in an in vitro transcription system reconstituted from purified components. Our results reveal a close functional interplay between Mediator and TFIIH in the early stages of PIC development. We find that under conditions when TFIIH is not normally required for transcription, Mediator actually represses transcription. TFIIH, whose recruitment to the PIC is known to be facilitated by the Mediator, then acts to relieve Mediator-induced repression to generate an active form of the PIC. Gel mobility shift analyses of PICs and characterization of TFIIH preparations carrying mutant XPB translocase subunit further indicate that this relief of repression is achieved through expending energy via ATP hydrolysis, suggesting that it is coupled to TFIIH's established promoter melting activity. Our interpretation of these results is that Mediator functions as an assembly factor that facilitates PIC maturation through its various stages. Whereas the overall effect of the Mediator is to stimulate basal transcription, its initial engagement with the PIC generates a transcriptionally inert PIC intermediate, which necessitates energy expenditure to complete the process. Copyright © 2016 Elsevier Ltd. All rights reserved.

Sensor mount assemblies and sensor assemblies

Science.gov (United States)

Miller, David H [Redondo Beach, CA

2012-04-10

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

Ferritin Assembly in Enterocytes of Drosophila melanogaster

Directory of Open Access Journals (Sweden)

Abraham Rosas-Arellano

2016-02-01

Full Text Available Ferritins are protein nanocages that accumulate inside their cavity thousands of oxidized iron atoms bound to oxygen and phosphates. Both characteristic types of eukaryotic ferritin subunits are present in secreted ferritins from insects, but here dimers between Ferritin 1 Heavy Chain Homolog (Fer1HCH and Ferritin 2 Light Chain Homolog (Fer2LCH are further stabilized by disulfide-bridge in the 24-subunit complex. We addressed ferritin assembly and iron loading in vivo using novel transgenic strains of Drosophila melanogaster. We concentrated on the intestine, where the ferritin induction process can be controlled experimentally by dietary iron manipulation. We showed that the expression pattern of Fer2LCH-Gal4 lines recapitulated iron-dependent endogenous expression of the ferritin subunits and used these lines to drive expression from UAS-mCherry-Fer2LCH transgenes. We found that the Gal4-mediated induction of mCherry-Fer2LCH subunits was too slow to effectively introduce them into newly formed ferritin complexes. Endogenous Fer2LCH and Fer1HCH assembled and stored excess dietary iron, instead. In contrast, when flies were genetically manipulated to co-express Fer2LCH and mCherry-Fer2LCH simultaneously, both subunits were incorporated with Fer1HCH in iron-loaded ferritin complexes. Our study provides fresh evidence that, in insects, ferritin assembly and iron loading in vivo are tightly regulated.

Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex.

Science.gov (United States)

Robinson, Philip J; Trnka, Michael J; Bushnell, David A; Davis, Ralph E; Mattei, Pierre-Jean; Burlingame, Alma L; Kornberg, Roger D

2016-09-08

A complete, 52-protein, 2.5 million dalton, Mediator-RNA polymerase II pre-initiation complex (Med-PIC) was assembled and analyzed by cryo-electron microscopy and by chemical cross-linking and mass spectrometry. The resulting complete Med-PIC structure reveals two components of functional significance, absent from previous structures, a protein kinase complex and the Mediator-activator interaction region. It thereby shows how the kinase and its target, the C-terminal domain of the polymerase, control Med-PIC interaction and transcription. Copyright © 2016 Elsevier Inc. All rights reserved.

Self-assembly of multiferroic core-shell particulate nanocomposites through DNA-DNA hybridization and magnetic field directed assembly of superstructures

Energy Technology Data Exchange (ETDEWEB)

Sreenivasulu, Gollapudi; Srinivasan, Gopalan, E-mail: srinivas@oakland.edu, E-mail: chavez@oakland.edu [Department of Physics, Oakland University, Rochester, MI 48309-4401 (United States); Lochbiler, Thomas A.; Panda, Manashi; Chavez, Ferman A., E-mail: srinivas@oakland.edu, E-mail: chavez@oakland.edu [Department of Chemistry, Oakland University, Rochester, MI 48309-4401 (United States)

2016-04-15

Multiferroic composites of ferromagnetic and ferroelectric phases are of importance for studies on mechanical strain mediated coupling between the magnetic and electric subsystems. This work is on DNA-assisted self-assembly of superstructures of such composites with nanometer periodicity. The synthesis involved oligomeric DNA-functionalized ferroelectric and ferromagnetic nanoparticles, 600 nm BaTiO{sub 3} (BTO) and 200 nm NiFe{sub 2}O{sub 4} (NFO), respectively. Mixing BTO and NFO particles, possessing complementary DNA sequences, resulted in the formation of ordered core-shell heteronanocomposites held together by DNA hybridization. The composites were imaged by scanning electron microscopy and scanning microwave microscopy. The presence of heteroassemblies along with core-shell architecture is clearly observed. The reversible nature of the DNA hybridization allows for restructuring the composites into mm-long linear chains and 2D-arrays in the presence of a static magnetic field and ring-like structures in a rotating-magnetic field. Strong magneto-electric (ME) coupling in as-assembled composites is evident from static magnetic field H induced polarization and low-frequency magnetoelectric voltage coefficient measurements. Upon annealing the nanocomposites at high temperatures, evidence for the formation of bulk composites with excellent cross-coupling between the electric and magnetic subsystems is obtained by H-induced polarization and low-frequency ME voltage coefficient. The ME coupling strength in the self-assembled composites is measured to be much stronger than in bulk composites with randomly distributed NFO and BTO prepared by direct mixing and sintering.

Protein adsorption and biomimetic mineralization behaviors of PLL-DNA multilayered films assembled onto titanium

Energy Technology Data Exchange (ETDEWEB)

Gao Wenli [Key Laboratory of Advanced Technologies of Materials, Ministry of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031 (China); Feng Bo, E-mail: fengbo@swjtu.edu.cn [Key Laboratory of Advanced Technologies of Materials, Ministry of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031 (China); Ni Yuxiang [Key Laboratory of Advanced Technologies of Materials, Ministry of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031 (China); Yang Yongli [College of Material Science and Engineering, Sichuan University, Chengdu 610054 (China); Lu Xiong; Weng Jie [Key Laboratory of Advanced Technologies of Materials, Ministry of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031 (China)

2010-11-01

Titanium and its alloys are frequently used as surgical implants in load bearing situations, such as hip prostheses and dental implants, owing to their biocompatibility, mechanical and physical properties. In this paper, a layer-by-layer (LBL) self-assembly technique, based on the polyelectrolyte-mediated electrostatic adsorption of poly-L-lysine (PLL) and DNA, was used to the formation of multilayer on titanium surfaces. Then bovine serum albumin (BSA) adsorption and biomimetic mineralization of modified surfaces were studied. The chemical composition and wettability of assembled substrates were investigated by X-ray photoelectron spectroscopy (XPS), fluorescence microscopy and water contact angle measurement, respectively. The XPS analysis indicated that the layers were assembled successfully through electrostatic attractions. The measurement with ultraviolet (UV) spectrophotometer revealed that the LBL films enhanced ability of BSA adsorption onto titanium. The adsorption quantity of BSA on the surface terminated with PLL was higher than that of the surface terminated with DNA, and the samples of TiOH/P/D/P absorbed BSA most. Scanning electron microscopy (SEM) and X-ray diffraction (XRD) showed that samples of assembled PLL or/and DNA had better bioactivity in inducing HA formation. Thus the assembling of PLL and DNA onto the surface of titanium in turn via a layer-by-layer self-assembly technology can improve the bioactivity of titanium.

GTPase activity, structure, and mechanical properties of filaments assembled from bacterial cytoskeleton protein MreB.

Science.gov (United States)

Esue, Osigwe; Wirtz, Denis; Tseng, Yiider

2006-02-01

MreB, a major component of the recently discovered bacterial cytoskeleton, displays a structure homologous to its eukaryotic counterpart actin. Here, we study the assembly and mechanical properties of Thermotoga maritima MreB in the presence of different nucleotides in vitro. We found that GTP, not ADP or GDP, can mediate MreB assembly into filamentous structures as effectively as ATP. Upon MreB assembly, both GTP and ATP release the gamma phosphate at similar rates. Therefore, MreB is an equally effective ATPase and GTPase. Electron microscopy and quantitative rheology suggest that the morphologies and micromechanical properties of filamentous ATP-MreB and GTP-MreB are similar. In contrast, mammalian actin assembly is favored in the presence of ATP over GTP. These results indicate that, despite high structural homology of their monomers, T. maritima MreB and actin filaments display different assembly, morphology, micromechanics, and nucleotide-binding specificity. Furthermore, the biophysical properties of T. maritima MreB filaments, including high rigidity and propensity to form bundles, suggest a mechanism by which MreB helical structure may be involved in imposing a cylindrical architecture on rod-shaped bacterial cells.

Si-doping bone composite based on protein template-mediated assembly for enhancing bone regeneration

Science.gov (United States)

Yang, Qin; Du, Yingying; Wang, Yifan; Wang, Zhiying; Ma, Jun; Wang, Jianglin; Zhang, Shengmin

2017-06-01

Bio-inspired hybrid materials that contain organic and inorganic networks interpenetration at the molecular level have been a particular focus of interest on designing novel nanoscale composites. Here we firstly synthesized a series of hybrid bone composites, silicon-hydroxyapatites/silk fibroin/collagen, based on a specific molecular assembled strategy. Results of material characterization confirmed that silicate had been successfully doped into nano-hydroxyapatite lattice. In vitro evaluation at the cellular level clearly showed that these Si-doped composites were capable of promoting the adhesion and proliferation of rat mesenchymal stem cells (rMSCs), extremely enhancing osteoblastic differentiation of rMSCs compared with silicon-free composite. More interestingly, we found there was a critical point of silicon content in the composition on regulating multiple cell behaviors. In vivo animal evaluation further demonstrated that Si-doped composites enabled to significantly improve the repair of cranial bone defect. Consequently, our current work not only suggests fabricating a potential bone repair materials by integrating element-doping and molecular assembled strategy in one system, but also paves a new way for constructing multi-functional composite materials in the future.

Si-doping bone composite based on protein template-mediated assembly for enhancing bone regeneration

Institute of Scientific and Technical Information of China (English)

Qin YANG; Yingying DU; Yifan WANG; Zhiying WANG; Jun MA; Jianglin WANG; Shengmin ZHANG

2017-01-01

Bio-inspired hybrid materials that contain organic and inorganic networks interpenetration at the molecular level have been a particular focus of interest on designing novel nanoscale composites.Here we firstly synthesized a series of hybrid bone composites,silicon-hydroxyapatites/silk fibroin/collagen,based on a specific molecular assembled strategy.Results of material characterization confirmed that silicate had been successfully doped into nano-hydroxyapatite lattice.In vitro evaluation at the cellular level clearly showed that these Si-doped composites were capable of promoting the adhesion and proliferation of rat mesenchymal stem cells (rMSCs),extremely enhancing osteoblastic differentiation of rMSCs compared with silicon-free composite.More interestingly,we found there was a critical point of silicon content in the composition on regulating multiple cell behaviors.In vivo animal evaluation further demonstrated that Si-doped composites enabled to significantly improve the repair of cranial bone defect.Consequently,our current work not only suggests fabricating a potential bone repair materials by integrating element-doping and molecular assembled strategy in one system,but also paves a new way for constructing multi-functional composite materials in the future.

Assembly-history dynamics of a pitcher-plant protozoan community in experimental microcosms.

Directory of Open Access Journals (Sweden)

Kohmei Kadowaki

Full Text Available History drives community assembly through differences both in density (density effects and in the sequence in which species arrive (sequence effects. Density effects arise from predictable population dynamics, which are free of history, but sequence effects are due to a density-free mechanism, arising solely from the order and timing of immigration events. Few studies have determined how components of immigration history (timing, number of individuals, frequency alter local dynamics to determine community assembly, beyond addressing when immigration history produces historically contingent assembly.We varied density and sequence effects independently in a two-way factorial design to follow community assembly in a three-species aquatic protozoan community. A superior competitor, Colpoda steinii, mediated alternative community states; early arrival or high introduction density allowed this species to outcompete or suppress the other competitors (Poterioochromonas malhamensis and Eimeriidae gen. sp.. Multivariate analysis showed that density effects caused greater variation in community states, whereas sequence effects altered the mean community composition.A significant interaction between density and sequence effects suggests that we should refine our understanding of priority effects. These results highlight a practical need to understand not only the "ingredients" (species in ecological communities but their "recipes" as well.

When lithography meets self-assembly: a review of recent advances in the directed assembly of complex metal nanostructures on planar and textured surfaces

Science.gov (United States)

Hughes, Robert A.; Menumerov, Eredzhep; Neretina, Svetlana

2017-07-01

One of the foremost challenges in nanofabrication is the establishment of a processing science that integrates wafer-based materials, techniques, and devices with the extraordinary physicochemical properties accessible when materials are reduced to nanoscale dimensions. Such a merger would allow for exacting controls on nanostructure positioning, promote cooperative phenomenon between adjacent nanostructures and/or substrate materials, and allow for electrical contact to individual or groups of nanostructures. With neither self-assembly nor top-down lithographic processes being able to adequately meet this challenge, advancements have often relied on a hybrid strategy that utilizes lithographically-defined features to direct the assembly of nanostructures into organized patterns. While these so-called directed assembly techniques have proven viable, much of this effort has focused on the assembly of periodic arrays of spherical or near-spherical nanostructures comprised of a single element. Work directed toward the fabrication of more complex nanostructures, while still at a nascent stage, has nevertheless demonstrated the possibility of forming arrays of nanocubes, nanorods, nanoprisms, nanoshells, nanocages, nanoframes, core-shell structures, Janus structures, and various alloys on the substrate surface. In this topical review, we describe the progress made in the directed assembly of periodic arrays of these complex metal nanostructures on planar and textured substrates. The review is divided into three broad strategies reliant on: (i) the deterministic positioning of colloidal structures, (ii) the reorganization of deposited metal films at elevated temperatures, and (iii) liquid-phase chemistry practiced directly on the substrate surface. These strategies collectively utilize a broad range of techniques including capillary assembly, microcontact printing, chemical surface modulation, templated dewetting, nanoimprint lithography, and dip-pen nanolithography and

Mobius Assembly: A versatile Golden-Gate framework towards universal DNA assembly.

Directory of Open Access Journals (Sweden)

Andreas I Andreou

Full Text Available Synthetic biology builds upon the foundation of engineering principles, prompting innovation and improvement in biotechnology via a design-build-test-learn cycle. A community-wide standard in DNA assembly would enable bio-molecular engineering at the levels of predictivity and universality in design and construction that are comparable to other engineering fields. Golden Gate Assembly technology, with its robust capability to unidirectionally assemble numerous DNA fragments in a one-tube reaction, has the potential to deliver a universal standard framework for DNA assembly. While current Golden Gate Assembly frameworks (e.g. MoClo and Golden Braid render either high cloning capacity or vector toolkit simplicity, the technology can be made more versatile-simple, streamlined, and cost/labor-efficient, without compromising capacity. Here we report the development of a new Golden Gate Assembly framework named Mobius Assembly, which combines vector toolkit simplicity with high cloning capacity. It is based on a two-level, hierarchical approach and utilizes a low-frequency cutter to reduce domestication requirements. Mobius Assembly embraces the standard overhang designs designated by MoClo, Golden Braid, and Phytobricks and is largely compatible with already available Golden Gate part libraries. In addition, dropout cassettes encoding chromogenic proteins were implemented for cost-free visible cloning screening that color-code different cloning levels. As proofs of concept, we have successfully assembled up to 16 transcriptional units of various pigmentation genes in both operon and multigene arrangements. Taken together, Mobius Assembly delivers enhanced versatility and efficiency in DNA assembly, facilitating improved standardization and automation.

Nonequilibrium carrier dynamics in self-assembled InGaAs quantum dots

International Nuclear Information System (INIS)

Wesseli, M.; Ruppert, C.; Trumm, S.; Betz, M.; Krenner, H.J.; Finley, J.J.

2006-01-01

Carrier dynamics in InGaAs/GaAs quantum dots is analyzed with highly sensitive femtosecond transmission spectroscopy. In a first step, measurements on a large ensemble of nanoislands reveal the dynamical electronic filling of quantum dots from the surrounding wetting layer. Most interestingly, we find a spin-preserving phonon mediated scattering into fully localized states within a few picoseconds. Then, individual artificial atoms are isolated with metallic shadow masks. For the first time, a single self-assembled quantum dot is addressed in an ultrafast transmission experiment. We find bleaching signals in the order of 10 -5 that arise from individual interband transitions of one quantum dot. As a result, we have developed an ultrafast optical tool for both manipulation and read-out of a single self-assembled quantum dot. (copyright 2006 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Programmed Nanomaterial Assemblies in Large Scales: Applications of Synthetic and Genetically- Engineered Peptides to Bridge Nano-Assemblies and Macro-Assemblies

Energy Technology Data Exchange (ETDEWEB)

Matsui, Hiroshi

2014-09-09

Work is reported in these areas: Large-scale & reconfigurable 3D structures of precise nanoparticle assemblies in self-assembled collagen peptide grids; Binary QD-Au NP 3D superlattices assembled with collagen-like peptides and energy transfer between QD and Au NP in 3D peptide frameworks; Catalytic peptides discovered by new hydrogel-based combinatorial phage display approach and their enzyme-mimicking 2D assembly; New autonomous motors of metal-organic frameworks (MOFs) powered by reorganization of self-assembled peptides at interfaces; Biomimetic assembly of proteins into microcapsules on oil-in-water droplets with structural reinforcement via biomolecular recognition-based cross-linking of surface peptides; and Biomimetic fabrication of strong freestanding genetically-engineered collagen peptide films reinforced by quantum dot joints. We gained the broad knowledge about biomimetic material assembly from nanoscale to microscale ranges by coassembling peptides and NPs via biomolecular recognition. We discovered: Genetically-engineered collagen-like peptides can be self-assembled with Au NPs to generate 3D superlattices in large volumes (> μm{sup 3}); The assembly of the 3D peptide-Au NP superstructures is dynamic and the interparticle distance changes with assembly time as the reconfiguration of structure is triggered by pH change; QDs/NPs can be assembled with the peptide frameworks to generate 3D superlattices and these QDs/NPs can be electronically coupled for the efficient energy transfer; The controlled assembly of catalytic peptides mimicking the catalytic pocket of enzymes can catalyze chemical reactions with high selectivity; and, For the bacteria-mimicking swimmer fabrication, peptide-MOF superlattices can power translational and propellant motions by the reconfiguration of peptide assembly at the MOF-liquid interface.

Controlled self-assembly of multiferroic core-shell nanoparticles exhibiting strong magneto-electric effects

Energy Technology Data Exchange (ETDEWEB)

Sreenivasulu, Gollapudi; Hamilton, Sean L.; Lehto, Piper R.; Srinivasan, Gopalan, E-mail: srinivas@oakland.edu [Physics Department, Oakland University, Rochester, Michigan 48309-4401 (United States); Popov, Maksym [Physics Department, Oakland University, Rochester, Michigan 48309-4401 (United States); Radiophysics Department, Taras Shevchenko National University of Kyiv, Kyiv 01601 (Ukraine); Chavez, Ferman A. [Chemistry Department, Oakland University, Rochester, Michigan 48309-4401 (United States)

2014-02-03

Ferromagnetic-ferroelectric composites show strain mediated coupling between the magnetic and electric sub-systems due to magnetostriction and piezoelectric effects associated with the ferroic phases. We have synthesized core-shell multiferroic nano-composites by functionalizing 10–100 nm barium titanate and nickel ferrite nanoparticles with complementary coupling groups and allowing them to self-assemble in the presence of a catalyst. The core-shell structure was confirmed by electron microscopy and magnetic force microscopy. Evidence for strong strain mediated magneto-electric coupling was obtained by static magnetic field induced variations in the permittivity over 16–18 GHz and polarization and by electric field induced by low-frequency ac magnetic fields.

Self-assembly of self-assembled molecular triangles

Indian Academy of Sciences (India)

While the solution state structure of 1 can be best described as a trinuclear complex, in the solidstate well-fashioned intermolecular - and CH- interactions are observed. Thus, in the solid-state further self-assembly of already self-assembled molecular triangle is witnessed. The triangular panels are arranged in a linear ...

Evaluation of nine popular de novo assemblers in microbial genome assembly.

Science.gov (United States)

Forouzan, Esmaeil; Maleki, Masoumeh Sadat Mousavi; Karkhane, Ali Asghar; Yakhchali, Bagher

2017-12-01

Next generation sequencing (NGS) technologies are revolutionizing biology, with Illumina being the most popular NGS platform. Short read assembly is a critical part of most genome studies using NGS. Hence, in this study, the performance of nine well-known assemblers was evaluated in the assembly of seven different microbial genomes. Effect of different read coverage and k-mer parameters on the quality of the assembly were also evaluated on both simulated and actual read datasets. Our results show that the performance of assemblers on real and simulated datasets could be significantly different, mainly because of coverage bias. According to outputs on actual read datasets, for all studied read coverages (of 7×, 25× and 100×), SPAdes and IDBA-UD clearly outperformed other assemblers based on NGA50 and accuracy metrics. Velvet is the most conservative assembler with the lowest NGA50 and error rate. Copyright © 2017. Published by Elsevier B.V.

A conceptual design of assembly strategy and dedicated tools for assembly of 40o sector

International Nuclear Information System (INIS)

Park, H.K.; Nam, K.O.; Kim, D.J.; Ahn, H.J.; Lee, J.H.; Im, K.; Shaw, R.

2010-01-01

The International Thermanuclear Experimental Reactor (ITER) tokamak device is composed of 9 vacuum vessel (VV)/toroidal field coils (TFCs)/vacuum vessel thermal shields (VVTS) 40 o sectors. Each VV/TFCs/VVTS 40 o sector is made up of one 40 o VV, two 20 o TFCs and associated VVTS segments. The 40 o sectors are sub-assembled at assembly hall respectively and then nine 40 o sectors sub-assembled at assembly hall are finally assembled at tokamak in-pit hall. The assembly strategy and tools for the 40 o sector sub-assembly and final assembly should be developed to satisfy the basic assembly requirements of the ITER tokamak device. Accordingly, the purpose-built assembly tools should be designed and manufactured considering assembly plan, available space, cost, safety, easy operation, efficient maintenance, and so on. The 40 o sector assembly tools are classified into 2 groups. One group is the sub-assembly tools including upending tool, lifting tool, sub-assembly tool, VV supports and bracing tools used at assembly hall and the other group is the in-pit assembly tools including lifting tool, central column, radial beams and their supports. This paper describes the current status of the assembly strategy and major tools for the VV/TFCs/VVTS 40 o sector assembly at in-pit hall and assembly hall. The conceptual design of the major assembly tools and assembly process at assembly hall and tokamak in-pit hall are presented also.

Paramecium tetraurelia chromatin assembly factor-1-like protein PtCAF-1 is involved in RNA-mediated control of DNA elimination.

Science.gov (United States)

Ignarski, Michael; Singh, Aditi; Swart, Estienne C; Arambasic, Miroslav; Sandoval, Pamela Y; Nowacki, Mariusz

2014-10-29

Genome-wide DNA remodelling in the ciliate Paramecium is ensured by RNA-mediated trans-nuclear crosstalk between the germline and the somatic genomes during sexual development. The rearrangements include elimination of transposable elements, minisatellites and tens of thousands non-coding elements called internally eliminated sequences (IESs). The trans-nuclear genome comparison process employs a distinct class of germline small RNAs (scnRNAs) that are compared against the parental somatic genome to select the germline-specific subset of scnRNAs that subsequently target DNA elimination in the progeny genome. Only a handful of proteins involved in this process have been identified so far and the mechanism of DNA targeting is unknown. Here we describe chromatin assembly factor-1-like protein (PtCAF-1), which we show is required for the survival of sexual progeny and localizes first in the parental and later in the newly developing macronucleus. Gene silencing shows that PtCAF-1 is required for the elimination of transposable elements and a subset of IESs. PTCAF-1 depletion also impairs the selection of germline-specific scnRNAs during development. We identify specific histone modifications appearing during Paramecium development which are strongly reduced in PTCAF-1 depleted cells. Our results demonstrate the importance of PtCAF-1 for the epigenetic trans-nuclear cross-talk mechanism. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Hierarchically assembled DNA origami tubules with reconfigurable chirality

International Nuclear Information System (INIS)

Chen, Haorong; Cha, Tae-Gon; Pan, Jing; Choi, Jong Hyun

2013-01-01

The dynamic reconfiguration of a hierarchically assembled tubular structure is demonstrated using the DNA origami technique. Short cylindrical DNA origami monomers are synthesized and linked into elongated tubules, which can then be disassembled via toehold-mediated strand displacement. The disassembled subunits are subsequently linked into tubules of a different chirality. The reconfiguration is performed with the subunits carrying dumbbell hairpin DNA oligonucleotides or gold nanoparticles (AuNPs). The reconfiguration of higher order origami structures presented here is useful for constructing dynamic nanostructures that exceed the size limit of single DNA origami and may facilitate the study of molecular or particle interactions by tuning their relative distance and organization. (paper)

Fuel injection assembly for use in turbine engines and method of assembling same

Science.gov (United States)

Berry, Jonathan Dwight; Johnson, Thomas Edward; York, William David; Uhm, Jong Ho

2015-12-15

A fuel injection assembly for use in a turbine engine is provided. The fuel injection assembly includes an end cover, an endcap assembly, a fluid supply chamber, and a plurality of tube assemblies positioned at the endcap assembly. Each of the tube assemblies includes housing having a fuel plenum and a cooling fluid plenum. The cooling fluid plenum is positioned downstream from the fuel plenum and separated from the fuel plenum by an intermediate wall. The plurality of tube assemblies also include a plurality of tubes that extends through the housing. Each of the plurality of tubes is coupled in flow communication with the fluid supply chamber and a combustion chamber positioned downstream from the tube assembly. The plurality of tube assemblies further includes an aft plate at a downstream end of the cooling fluid plenum. The plate includes at least one aperture.

Melting and related precursor cooperative phenomena in chemically bonded assemblies

International Nuclear Information System (INIS)

March, N.H.

2004-09-01

A number of experimental studies of condensed matter assemblies with different types of chemical bonding will provide the focus of this work. Condensed compounds X(CH 3 ) 4 , with X = C,Si or Ge, are the first of such assemblies; two phase boundaries in the pressure temperature plane being studied: melting and a solid phase boundary heralding orientational disordering of molecules still however on a lattice. Secondly, directionally bonded d-electron transition metals such as Ni, Pd and Nb will be treated. Here, melting is the main focus, but the precursor transition is now the separation of a high-temperature ductile solid from a lower temperature mechanically brittle phase. A dislocation-mediated model of these transitions is discussed, leading into the third area of covalently bonded solids graphite and silicon. Here topological defect models again provide the focus; both dislocations and rotation-dislocations now being invoked. Some qualitative suggestions are made to interpret the melting curve of graphite subjected to high pressure. (author)

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

Science.gov (United States)

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.

Effect of Dendritic Polymer Architecture on Biological Behaviors of Self-Assembled Nanocarriers

Science.gov (United States)

Hsu, Hao-Jui

Polymeric self-assembled nanocarriers represent one of the most versatile platforms for drug delivery. Through tailoring the physiochemical properties of amphiphilic block copolymers, self-assembled nanocarriers with great thermodynamic stability and desired biological properties could be achieved. The PEGylated dendron-based copolymers (PDCs) are one of the novel amphiphilic copolymers that have attracted a great deal of scientific interest due to their unique dendritic structure and properties. While the dendritic polymer architecture of PDC has been shown to enhance the thermodynamic stability of the self-assembling PDCs, dendron micelles, the effect of this polymer architecture on the biological properties of dendron micelles has not yet been studied. Therefore, this dissertation research is focused on understanding the role of dendritic polymer structure on moderating the biological properties of various self-assembled nanocarriers. To systematically investigate this, three studies have been designed and performed. First, we studied whether the dendritic structure of PDC allows dendron micelles to behave non-specific cellular interactions in a similar way that dendrimers would do. Second, cell-specific interactions of dendron micelles mediated by conjugated ligands were investigated. Third, we investigated the influence of dendritic PEG outer shell on micelle-serum protein interactions and its subsequent implication. Our results revealed that both non-specific and specific cellular interactions of dendron micelles were controllable through modulation of the PEG corona length. While the non-specific charge-dependent cellular interactions of dendron micelles were tunable through controlling the length of PEG corona, the use of long PEG tether was found to enhance the ligand-mediated cellular interactions of dendron micelles. With the ligand tethers, a 27-fold enhancement in ligand-mediated cellular interactions can be achieved, compared to non-targeted dendron

Substrate mediated enzyme prodrug therapy.

Directory of Open Access Journals (Sweden)

Betina Fejerskov

Full Text Available In this report, we detail Substrate Mediated Enzyme Prodrug Therapy (SMEPT as a novel approach in drug delivery which relies on enzyme-functionalized cell culture substrates to achieve a localized conversion of benign prodrug(s into active therapeutics with subsequent delivery to adhering cells or adjacent tissues. For proof-of-concept SMEPT, we use surface adhered micro-structured physical hydrogels based on poly(vinyl alcohol, β-glucuronidase enzyme and glucuronide prodrugs. We demonstrate enzymatic activity mediated by the assembled hydrogel samples and illustrate arms of control over rate of release of model fluorescent cargo. SMEPT was not impaired by adhering cells and afforded facile time - and dose - dependent uptake of the in situ generated fluorescent cargo by hepatic cells, HepG2. With the use of a glucuronide derivative of an anticancer drug, SN-38, SMEPT afforded a decrease in cell viability to a level similar to that achieved using parent drug. Finally, dose response was achieved using SMEPT and administration of judiciously chosen concentration of SN-38 glucuronide prodrug thus revealing external control over drug delivery using drug eluting surface. We believe that this highly adaptable concept will find use in diverse biomedical applications, specifically surface mediated drug delivery and tissue engineering.

Assembly, alignment and test of the Transiting Exoplanet Survey Satellite (TESS) optical assemblies

Science.gov (United States)

Balonek, Gregory; Brown, Joshua J.; Andre, James E.; Chesbrough, Christian D.; Chrisp, Michael P.; Dalpiaz, Michael; Lennon, Joseph; Richards, B. C.; Clark, Kristin E.

2017-08-01

The Transiting Exoplanet Survey Satellite (TESS) will carry four visible waveband, seven-element, refractive F/1.4 lenses, each with a 34 degree diagonal field of view. This paper describes the methods used for the assembly, alignment and test of the four flight optical assemblies. Prior to commencing the build of the four flight optical assemblies, a Risk Reduction Unit (RRU) was successfully assembled and tested [1]. The lessons learned from the RRU were applied to the build of the flight assemblies. The main modifications to the flight assemblies include the inking of the third lens element stray light mitigation, tighter alignment tolerances, and diamond turning for critical mechanical surfaces. Each of the optical assemblies was tested interferometrically and measured with a low coherence distance measuring interferometer (DMI) to predict the optimal shim thickness between the lens assembly and detector before -75°C environmental testing. In addition to individual test data, environmental test results from prior assemblies allow for the exploration of marginal performance differences between each of the optical assemblies.

SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores.

Science.gov (United States)

Meng, Jintao; Wang, Bingqiang; Wei, Yanjie; Feng, Shengzhong; Balaji, Pavan

2014-01-01

There is a widening gap between the throughput of massive parallel sequencing machines and the ability to analyze these sequencing data. Traditional assembly methods requiring long execution time and large amount of memory on a single workstation limit their use on these massive data. This paper presents a highly scalable assembler named as SWAP-Assembler for processing massive sequencing data using thousands of cores, where SWAP is an acronym for Small World Asynchronous Parallel model. In the paper, a mathematical description of multi-step bi-directed graph (MSG) is provided to resolve the computational interdependence on merging edges, and a highly scalable computational framework for SWAP is developed to automatically preform the parallel computation of all operations. Graph cleaning and contig extension are also included for generating contigs with high quality. Experimental results show that SWAP-Assembler scales up to 2048 cores on Yanhuang dataset using only 26 minutes, which is better than several other parallel assemblers, such as ABySS, Ray, and PASHA. Results also show that SWAP-Assembler can generate high quality contigs with good N50 size and low error rate, especially it generated the longest N50 contig sizes for Fish and Yanhuang datasets. In this paper, we presented a highly scalable and efficient genome assembly software, SWAP-Assembler. Compared with several other assemblers, it showed very good performance in terms of scalability and contig quality. This software is available at: https://sourceforge.net/projects/swapassembler.

Assembly tool design

International Nuclear Information System (INIS)

Kanamori, Naokazu; Nakahira, Masataka; Ohkawa, Yoshinao; Tada, Eisuke; Seki, Masahiro

1996-06-01

The reactor core of the International Thermonuclear Experimental Reactor (ITER) is assembled with a number of large and asymmetric components within a tight tolerance in order to assure the structural integrity for various loads and to provide the tritium confinement. In addition, the assembly procedure should be compatible with remote operation since the core structures will be activated by 14-MeV neutrons once it starts operation and thus personal access will be prohibited. Accordingly, the assembly procedure and tool design are quite essential and should be designed from the beginning to facilitate remote operation. According to the ITER Design Task Agreement, the Japan Atomic Energy Research Institute (JAERI) has performed design study to develop the assembly procedures and associated tool design for the ITER tokamak assembly. This report describes outlines of the assembly tools and the remaining issues obtained in this design study. (author)

Kinetics of cellular uptake of viruses and nanoparticles via clathrin-mediated endocytosis

Science.gov (United States)

Banerjee, Anand; Berezhkovskii, Alexander; Nossal, Ralph

2016-02-01

Several viruses exploit clathrin-mediated endocytosis to gain entry into host cells. This process is also used extensively in biomedical applications to deliver nanoparticles (NPs) to diseased cells. The internalization of these nano-objects is controlled by the assembly of a clathrin-containing protein coat on the cytoplasmic side of the plasma membrane, which drives the invagination of the membrane and the formation of a cargo-containing endocytic vesicle. Current theoretical models of receptor-mediated endocytosis of viruses and NPs do not explicitly take coat assembly into consideration. In this paper we study cellular uptake of viruses and NPs with a focus on coat assembly. We characterize the internalization process by the mean time between the binding of a particle to the membrane and its entry into the cell. Using a coarse-grained model which maps the stochastic dynamics of coat formation onto a one-dimensional random walk, we derive an analytical formula for this quantity. A study of the dependence of the mean internalization time on NP size shows that there is an upper bound above which this time becomes extremely large, and an optimal size at which it attains a minimum. Our estimates of these sizes compare well with experimental data. We also study the sensitivity of the obtained results on coat parameters to identify factors which significantly affect the internalization kinetics.

Drive piston assembly for a valve actuator assembly

Science.gov (United States)

Sun, Zongxuan

2010-02-23

A drive piston assembly is provided that is operable to selectively open a poppet valve. The drive piston assembly includes a cartridge defining a generally stepped bore. A drive piston is movable within the generally stepped bore and a boost sleeve is coaxially disposed with respect to the drive piston. A main fluid chamber is at least partially defined by the generally stepped bore, drive piston, and boost sleeve. First and second feedback chambers are at least partially defined by the drive piston and each are disposed at opposite ends of the drive piston. At least one of the drive piston and the boost sleeve is sufficiently configured to move within the generally stepped bore in response to fluid pressure within the main fluid chamber to selectively open the poppet valve. A valve actuator assembly and engine are also provided incorporating the disclosed drive piston assembly.

The Cac2 subunit is essential for productive histone binding and nucleosome assembly in CAF-1

Energy Technology Data Exchange (ETDEWEB)

Mattiroli, Francesca; Gu, Yajie; Balsbaugh, Jeremy L.; Ahn, Natalie G.; Luger, Karolin

2017-04-18

Nucleosome assembly following DNA replication controls epigenome maintenance and genome integrity. Chromatin assembly factor 1 (CAF-1) is the histone chaperone responsible for histone (H3-H4)2 deposition following DNA synthesis. Structural and functional details for this chaperone complex and its interaction with histones are slowly emerging. Using hydrogen-deuterium exchange coupled to mass spectrometry, combined with in vitro and in vivo mutagenesis studies, we identified the regions involved in the direct interaction between the yeast CAF-1 subunits, and mapped the CAF-1 domains responsible for H3-H4 binding. The large subunit, Cac1 organizes the assembly of CAF-1. Strikingly, H3-H4 binding is mediated by a composite interface, shaped by Cac1-bound Cac2 and the Cac1 acidic region. Cac2 is indispensable for productive histone binding, while deletion of Cac3 has only moderate effects on H3-H4 binding and nucleosome assembly. These results define direct structural roles for yeast CAF-1 subunits and uncover a previously unknown critical function of the middle subunit in CAF-1.

Assembly and enlargement of the primary cell wall in plants

Science.gov (United States)

Cosgrove, D. J.

1997-01-01

Growing plant cells are shaped by an extensible wall that is a complex amalgam of cellulose microfibrils bonded noncovalently to a matrix of hemicelluloses, pectins, and structural proteins. Cellulose is synthesized by complexes in the plasma membrane and is extruded as a self-assembling microfibril, whereas the matrix polymers are secreted by the Golgi apparatus and become integrated into the wall network by poorly understood mechanisms. The growing wall is under high tensile stress from cell turgor and is able to enlarge by a combination of stress relaxation and polymer creep. A pH-dependent mechanism of wall loosening, known as acid growth, is characteristic of growing walls and is mediated by a group of unusual wall proteins called expansins. Expansins appear to disrupt the noncovalent bonding of matrix hemicelluloses to the microfibril, thereby allowing the wall to yield to the mechanical forces generated by cell turgor. Other wall enzymes, such as (1-->4) beta-glucanases and pectinases, may make the wall more responsive to expansin-mediated wall creep whereas pectin methylesterases and peroxidases may alter the wall so as to make it resistant to expansin-mediated creep.

Assembly of a biocompatible triazole-linked gene by one-pot click-DNA ligation

Science.gov (United States)

Kukwikila, Mikiembo; Gale, Nittaya; El-Sagheer, Afaf H.; Brown, Tom; Tavassoli, Ali

2017-11-01

The chemical synthesis of oligonucleotides and their enzyme-mediated assembly into genes and genomes has significantly advanced multiple scientific disciplines. However, these approaches are not without their shortcomings; enzymatic amplification and ligation of oligonucleotides into genes and genomes makes automation challenging, and site-specific incorporation of epigenetic information and/or modified bases into large constructs is not feasible. Here we present a fully chemical one-pot method for the assembly of oligonucleotides into a gene by click-DNA ligation. We synthesize the 335 base-pair gene that encodes the green fluorescent protein iLOV from ten functionalized oligonucleotides that contain 5ʹ-azide and 3ʹ-alkyne units. The resulting click-linked iLOV gene contains eight triazoles at the sites of chemical ligation, and yet is fully biocompatible; it is replicated by DNA polymerases in vitro and encodes a functional iLOV protein in Escherichia coli. We demonstrate the power and potential of our one-pot gene-assembly method by preparing an epigenetically modified variant of the iLOV gene.

Managing lifelike behavior in a dynamic self-assembled system

Science.gov (United States)

Ropp, Chad; Bachelard, Nicolas; Wang, Yuan; Zhang, Xiang

Self-organization can arise outside of thermodynamic equilibrium in a process of dynamic self-assembly. This is observed in nature, for example in flocking birds, but can also be created artificially with non-living entities. Such dynamic systems often display lifelike properties, including the ability to self-heal and adapt to environmental changes, which arise due to the collective and often complex interactions between the many individual elements. Such interactions are inherently difficult to predict and control, and limit the development of artificial systems. Here, we report a fundamentally new method to manage dynamic self-assembly through the direct external control of collective phenomena. Our system consists of a waveguide filled with mobile scattering particles. These particles spontaneously self-organize when driven by a coherent field, self-heal when mechanically perturbed, and adapt to changes in the drive wavelength. This behavior is governed by particle interactions that are completely mediated by coherent wave scattering. Compared to hydrodynamic interactions which lead to compact ordered structures, our system displays sinusoidal degeneracy and many different steady-state geometries that can be adjusted using the external field.

Silver nanoprisms self-assembly on differently functionalized silica surface

International Nuclear Information System (INIS)

Pilipavicius, J; Chodosovskaja, A; Beganskiene, A; Kareiva, A

2015-01-01

In this work colloidal silica/silver nanoprisms (NPRs) composite coatings were made. Firstly colloidal silica sols were synthesized by sol-gel method and produced coatings on glass by dip-coating technique. Next coatings were silanized by (3-Aminopropyl)triethoxysilane (APTES), N-[3-(Trimethoxysilyl)propyl]ethylenediamine (AEAPTMS), (3- Mercaptopropyl)trimethoxysilane (MPTMS). Silver NPRs where synthesized via seed-mediated method and high yield of 94±15 nm average edge length silver NPRs were obtained with surface plasmon resonance peak at 921 nm. Silica-Silver NPRs composite coatings obtained by selfassembly on silica coated-functionalized surface. In order to find the most appropriate silanization way for Silver NPRs self-assembly, the composite coatings were characterized by scanning electron microscopy (SEM), dynamic light scattering (DLS), water contact angle (CA) and surface free energy (SFE) methods. Results have showed that surface functionalization is necessary to achieve self-assembled Ag NPRs layer. MPTMS silanized coatings resulted sparse distribution of Ag NPRs. Most homogeneous, even distribution composite coatings obtained on APTES functionalized silica coatings, while AEAPTMS induced strong aggregation of Silver NPRs

The retrograde IFT machinery of C. elegans cilia: two IFT dynein complexes?

Directory of Open Access Journals (Sweden)

Limin Hao

Full Text Available We analyzed the relatively poorly understood IFT-dynein (class DYNC2-driven retrograde IFT pathway in C. elegans cilia, which yielded results that are surprising in the context of current models of IFT. Assays of C. elegans dynein gene expression and intraflagellar transport (IFT suggest that conventional IFT-dynein contains essential heavy (CHE-3, light-intermediate (XBX-1, plus three light polypeptide chains that participate in IFT, but no "essential" intermediate chain. IFT assays of XBX-1::YFP suggest that IFT-dynein is transported as cargo to the distal tip of the cilium by kinesin-2 motors, but independent of the IFT-particle/BBSome complexes. Finally, we were surprised to find that the subset of cilia present on the OLQ (outer labial quadrant neurons assemble independently of conventional "CHE-3" IFT-dynein, implying that there is a second IFT-dynein acting in these cilia. We have found a novel gene encoding a dynein heavy chain, DHC-3, and two light chains, in OLQ neurons, which could constitute an IFT-dynein complex in OLQ neuronal cilia. Our results underscore several surprising features of retrograde IFT that require clarification.

Nanocomposite hydrogels stabilized by self-assembled multivalent bisphosphonate-magnesium nanoparticles mediate sustained release of magnesium ion and promote in-situ bone regeneration.

Science.gov (United States)

Zhang, Kunyu; Lin, Sien; Feng, Qian; Dong, Chaoqun; Yang, Yanhua; Li, Gang; Bian, Liming

2017-12-01

Hydrogels are appealing biomaterials for applications in regenerative medicine due to their tunable physical and bioactive properties. Meanwhile, therapeutic metal ions, such as magnesium ion (Mg 2+ ), not only regulate the cellular behaviors but also stimulate local bone formation and healing. However, the effective delivery and tailored release of Mg 2+ remains a challenge, with few reports on hydrogels being used for Mg 2+ delivery. Bisphosphonate exhibits a variety of specific bioactivities and excellent binding affinity to multivalent cations such as Mg 2+ . Herein, we describe a nanocomposite hydrogel based on hyaluronic acid and self-assembled bisphosphonate-magnesium (BP-Mg) nanoparticles. These nanoparticles bearing acrylate groups on the surface not only function as effective multivalent crosslinkers to strengthen the hydrogel network structure, but also promote the mineralization of hydrogels and mediate sustained release of Mg 2+ . The released Mg 2+ ions facilitate stem cell adhesion and spreading on the hydrogel substrates in the absence of cell adhesion ligands, and promote osteogenesis of the seeded hMSCs in vitro. Furthermore, the acellular porous hydrogels alone can support in situ bone regeneration without using exogenous cells and inductive agents, thereby greatly simplifying the approaches of bone regeneration therapy. In this study, we developed a novel bioactive nanocomposite hydrogel based on hyaluronic acid and self-assembled bisphosphonate-magnesium (BP-Mg) nanoparticles. Such hydrogels are stabilized by the multivalent crosslinking domains formed by the aggregation of Ac-BP-Mg NPs, and therefore show enhanced mechanical properties, improved capacity for mineralization, and controlled release kinetics of Mg 2+ . Moreover, the released Mg 2+ can enhance cell adhesion and spreading, and further promote the osteogenic differentiation of hMSCs. Owing to these unique properties, these acellular hydrogels alone can well facilitate the in vivo

Force and time-dependent self-assembly, disruption and recovery of supramolecular peptide amphiphile nanofibers.

Science.gov (United States)

Dikecoglu, F Begum; Topal, Ahmet E; Ozkan, Alper D; Tekin, E Deniz; Tekinay, Ayse B; Guler, Mustafa O; Dana, Aykutlu

2018-07-13

Biological feedback mechanisms exert precise control over the initiation and termination of molecular self-assembly in response to environmental stimuli, while minimizing the formation and propagation of defects through self-repair processes. Peptide amphiphile (PA) molecules can self-assemble at physiological conditions to form supramolecular nanostructures that structurally and functionally resemble the nanofibrous proteins of the extracellular matrix, and their ability to reconfigure themselves in response to external stimuli is crucial for the design of intelligent biomaterials systems. Here, we investigated real-time self-assembly, deformation, and recovery of PA nanofibers in aqueous solution by using a force-stabilizing double-pass scanning atomic force microscopy imaging method to disrupt the self-assembled peptide nanofibers in a force-dependent manner. We demonstrate that nanofiber damage occurs at tip-sample interaction forces exceeding 1 nN, and the damaged fibers subsequently recover when the tip pressure is reduced. Nanofiber ends occasionally fail to reconnect following breakage and continue to grow as two individual nanofibers. Energy minimization calculations of nanofibers with increasing cross-sectional ellipticity (corresponding to varying levels of tip-induced fiber deformation) support our observations, with high-ellipticity nanofibers exhibiting lower stability compared to their non-deformed counterparts. Consequently, tip-mediated mechanical forces can provide an effective means of altering nanofiber integrity and visualizing the self-recovery of PA assemblies.

Assembly and Multiplex Genome Integration of Metabolic Pathways in Yeast Using CasEMBLR

DEFF Research Database (Denmark)

Jakočiūnas, Tadas; Jensen, Emil D.; Jensen, Michael Krogh

2018-01-01

and marker-free integration of the carotenoid pathway from 15 exogenously supplied DNA parts into three targeted genomic loci. As a second proof-of-principle, a total of ten DNA parts were assembled and integrated in two genomic loci to construct a tyrosine production strain, and at the same time knocking......Genome integration is a vital step for implementing large biochemical pathways to build a stable microbial cell factory. Although traditional strain construction strategies are well established for the model organism Saccharomyces cerevisiae, recent advances in CRISPR/Cas9-mediated genome...... engineering allow much higher throughput and robustness in terms of strain construction. In this chapter, we describe CasEMBLR, a highly efficient and marker-free genome engineering method for one-step integration of in vivo assembled expression cassettes in multiple genomic sites simultaneously. Cas...

Structural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9).

Science.gov (United States)

Fu, Qinqin; Yuan, Y Adam

2013-03-01

Intensive research interest has focused on small RNA-processing machinery and the RNA-induced silencing complex (RISC), key cellular machines in RNAi pathways. However, the structural mechanism regarding RISC assembly, the primary step linking small RNA processing and RNA-mediated gene silencing, is largely unknown. Human RNA helicase A (DHX9) was reported to function as an RISC-loading factor, and such function is mediated mainly by its dsRNA-binding domains (dsRBDs). Here, we report the crystal structures of human RNA helicase A (RHA) dsRBD1 and dsRBD2 domains in complex with dsRNAs, respectively. Structural analysis not only reveals higher siRNA duplex-binding affinity displayed by dsRBD1, but also identifies a crystallographic dsRBD1 pair of physiological significance in cooperatively recognizing dsRNAs. Structural observations are further validated by isothermal titration calorimetric (ITC) assay. Moreover, co-immunoprecipitation (co-IP) assay coupled with mutagenesis demonstrated that both dsRBDs are required for RISC association, and such association is mediated by dsRNA. Hence, our structural and functional efforts have revealed a potential working model for siRNA recognition by RHA tandem dsRBDs, and together they provide direct structural insights into RISC assembly facilitated by RHA.

RNA processing and ribonucleoprotein assembly studied in vivo by RNA transfection

International Nuclear Information System (INIS)

Kleinschmidt, A.M.; Pederson, T.

1990-01-01

The authors present a method for studying RNA processing and ribonucleoprotein assembly in vivo, by using RNA synthesized in vitro. SP6-transcribed 32 P-labeled U2 small nuclear RNA precursor molecules were introduced into cultured human 293 cells by calcium phosphate-mediated uptake, as in standard DNA transfection experiments. RNase protection mapping demonstrated that the introduced pre-U2 RNA underwent accurate 3' end processing. The introduced U2 RNA was assembled into ribonucleoprotein particles that reacted with an antibody specific for proteins known to be associated with the U2 small nuclear ribonucleoprotein particle. The 3' end-processed, ribonucleoprotein-assembled U2 RNA accumulated in the nuclear fraction. When pre-U2 RNA with a 7-methylguanosine group at the 5' end was introduced into cells, it underwent conversion to a 2,2,7-trimethylguanosine cap structure, a characteristic feature of the U-small nuclear RNAs. Pre-U2 RNA introduced with an adenosine cap (Ap-ppG) also underwent processing, small nuclear ribonucleoprotein assembly, and nuclear accumulation, establishing that a methylated guanosine cap structure is not required for these steps in U2 small nuclear ribonucleprotein biosynthesis. Beyond its demonstrated usefulness in the study of small nuclear ribonucleoprotein biosynthesis, RNA transfection may be of general applicability to the investigation of eukaryotic RNA processing in vivo and may also offer opportunities for introducing therapeutically targeted RNAs (ribozymes or antisense RNA) into cells

Self-assembled nanostructures

CERN Document Server

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

2003-01-01

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

Mediating Discourses of Transnational Adoption on the Internet

DEFF Research Database (Denmark)

McIlvenny, Paul; Raudaskoski, Pirkko Liisa

2005-01-01

Transnational (or intercountry) adoption is a global phenomenon with a diverse range of practices which are increasingly under scrutiny. Notable differences are found in practices across both ‘sending’ countries (such as China, Columbia, India, South Africa and South Korea, and ‘receiving...... prior to their first contact with the adopted child. Research studies of transnational adoption are increasingly common, but come predominantly from psychological, psycho-social or social welfare perspectives. In contrast, we take a discourse studies approach that develops a theoretical...... and methodological bridge between mediated discourse analysis (MDA) and other approaches to mediation, agency and action. With this approach we trace a host of discourses and contingent practices that are heterogeneously assembled to ‘translate’ a child from one familial ‘place’ or nexus of practice in the world...

Assembly of the Arp5 (Actin-related Protein) Subunit Involved in Distinct INO80 Chromatin Remodeling Activities*

Science.gov (United States)

Yao, Wei; Beckwith, Sean L.; Zheng, Tina; Young, Thomas; Dinh, Van T.; Ranjan, Anand; Morrison, Ashby J.

2015-01-01

ATP-dependent chromatin remodeling, which repositions and restructures nucleosomes, is essential to all DNA-templated processes. The INO80 chromatin remodeling complex is an evolutionarily conserved complex involved in diverse cellular processes, including transcription, DNA repair, and replication. The functional diversity of the INO80 complex can, in part, be attributed to specialized activities of distinct subunits that compose the complex. Furthermore, structural analyses have identified biochemically discrete subunit modules that assemble along the Ino80 ATPase scaffold. Of particular interest is the Saccharomyces cerevisiae Arp5-Ies6 module located proximal to the Ino80 ATPase and the Rvb1-Rvb2 helicase module needed for INO80-mediated in vitro activity. In this study we demonstrate that the previously uncharacterized Ies2 subunit is required for Arp5-Ies6 association with the catalytic components of the INO80 complex. In addition, Arp5-Ies6 module assembly with the INO80 complex is dependent on distinct conserved domains within Arp5, Ies6, and Ino80, including the spacer region within the Ino80 ATPase domain. Arp5-Ies6 interacts with chromatin via assembly with the INO80 complex, as IES2 and INO80 deletion results in loss of Arp5-Ies6 chromatin association. Interestingly, ectopic addition of the wild-type Arp5-Ies6 module stimulates INO80-mediated ATP hydrolysis and nucleosome sliding in vitro. However, the addition of mutant Arp5 lacking unique insertion domains facilitates ATP hydrolysis in the absence of nucleosome sliding. Collectively, these results define the requirements of Arp5-Ies6 assembly, which are needed to couple ATP hydrolysis to productive nucleosome movement. PMID:26306040

Newnes electronics assembly handbook

CERN Document Server

Brindley, Keith

2013-01-01

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

Structures of transcription pre-initiation complex with TFIIH and Mediator.

Science.gov (United States)

Schilbach, S; Hantsche, M; Tegunov, D; Dienemann, C; Wigge, C; Urlaub, H; Cramer, P

2017-11-09

For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron microscopy structures of the Saccharomyces cerevisiae PIC and PIC-core Mediator complex at nominal resolutions of 4.7 Å and 5.8 Å, respectively. The structures reveal transcription factor IIH (TFIIH), and suggest how the core and kinase TFIIH modules function in the opening of promoter DNA and the phosphorylation of Pol II, respectively. The TFIIH core subunit Ssl2 (a homologue of human XPB) is positioned on downstream DNA by the 'E-bridge' helix in TFIIE, consistent with TFIIE-stimulated DNA opening. The TFIIH kinase module subunit Tfb3 (MAT1 in human) anchors the kinase Kin28 (CDK7), which is mobile in the PIC but preferentially located between the Mediator hook and shoulder in the PIC-core Mediator complex. Open spaces between the Mediator head and middle modules may allow access of the kinase to its substrate, the C-terminal domain of Pol II.

Filamentous phages as building blocks for reconfigurable and hierarchical self-assembly

Science.gov (United States)

Gibaud, Thomas

2017-12-01

Filamentous bacteriophages such as fd-like viruses are monodisperse rod-like colloids that have well defined properties of diameter, length, rigidity, charge and chirality. Engineering these viruses leads to a library of colloidal rods, which can be used as building blocks for reconfigurable and hierarchical self-assembly. Their condensation in an aqueous solution with additive polymers, which act as depletants to induce attraction between the rods, leads to a myriad of fluid-like micronic structures ranging from isotropic/nematic droplets, colloid membranes, achiral membrane seeds, twisted ribbons, π-wall, pores, colloidal skyrmions, Möbius anchors, scallop membranes to membrane rafts. These structures, and the way that they shape-shift, not only shed light on the role of entropy, chiral frustration and topology in soft matter, but also mimic many structures encountered in different fields of science. On the one hand, filamentous phages being an experimental realization of colloidal hard rods, their condensation mediated by depletion interactions constitutes a blueprint for the self-assembly of rod-like particles and provides a fundamental foundation for bio- or material-oriented applications. On the other hand, the chiral properties of the viruses restrict the generalities of some results but vastly broaden the self-assembly possibilities.

Fuel Assembly Damping Summary

Energy Technology Data Exchange (ETDEWEB)

Lee, Kanghee; Kang, Heungseok; Oh, Dongseok; Yoon, Kyungho; Kim, Hyungkyu; Kim, Jaeyong [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2013-10-15

This paper summary the fuel assembly damping data in air/in still water/under flow, released from foreign fuel vendors, compared our data with the published data. Some technical issues in fuel assembly damping measurement testing are also briefly discussed. Understanding of each fuel assembly damping mechanisms according to the surrounding medium and flow velocity can support the fuel design improvement in fuel assembly dynamics and structural integrity aspect. Because the upgraded requirements of the newly-developed advanced reactor system will demands to minimize fuel design margin in integrity evaluation, reduction in conservatism of fuel assembly damping can contribute to alleviate the fuel design margin for sure. Damping is an energy dissipation mechanism in a vibrating mechanical structure and prevents a resonant structure from having infinite vibration amplitudes. The sources of fuel assembly damping are various from support friction to flow contribution, and it can be increased by the viscosity or drag of surrounding fluid medium or the average velocity of water flowing. Fuel licensing requires fuel design evaluation in transient or accidental condition. Dynamic response analysis of fuel assembly is to show fuel integrity and requires information on assembly-wise damping in dry condition and under wet or water flowing condition. However, damping measurement test for the full-scale fuel assembly prototype is not easy to carry out because of the scale (fuel prototype, test facility), unsteadiness of test data (scattering, random sampling and processing), instrumentation under water flowing (water-proof response measurement), and noise. LWR fuel technology division in KAERI is preparing the infra structure for damping measurement test of full-scale fuel assembly, to support fuel industries and related research activities. Here is a preliminary summary of fuel assembly damping, published in the literature. Some technical issues in fuel assembly damping

Protein Self-Assembly and Protein-Induced DNA Morphologies

Science.gov (United States)

Mawhinney, Matthew T.

The ability of biomolecules to associate into various structural configurations has a substantial impact on human physiology. The synthesis of protein polypeptide chains using the information encoded by DNA is mediated through the use of regulatory proteins, known as transcription factors. Some transcription factors perform function by inducing local curvature in deoxyribonucleic acid (DNA) strands, the mechanisms of which are not entirely known. An important architectural protein, eleven zinc finger CTCF (11 ZF CTCF) is involved in genome organization and hypothesized to mediate DNA loop formation. Direct evidence for these CTCF-induced DNA loops has yet to be observed. In this thesis, the effect of 11 ZF CTCF on DNA morphology is examined using atomic force microscopy, a powerful technique for visualizing biomolecules with nanometer resolution. The presence of CTCF is revealed to induce a variety of morphologies deviating from the relaxed state of control DNA samples, including compact circular complexes, meshes, and networks. Images reveal quasi-circular DNA/CTCF complexes consistent with a single DNA molecule twice wrapped around the protein. The structures of DNA and proteins are highly important for operations in the cell. Structural irregularities may lead to a variety of issues, including more than twenty human pathologies resulting from aberrant protein misfolding into amyloid aggregates of elongated fibrils. Insulin deficiency and resistance characterizing type 2 diabetes often requires administration of insulin. Injectable and inhalable delivery methods have been documented to result in the deposition of amyloid fibrils. Oligomers, soluble multiprotein assemblies, are believed to play an important role in this process. Insulin aggregation under physiological conditions is not well understood and oligomers have not yet been fully characterized. In this thesis, in vitro insulin aggregation at acidic and neutral pH is explored using a variety of techniques

Fuel assembly

International Nuclear Information System (INIS)

Abe, Hideaki; Sakai, Takao; Ishida, Tomio; Yokota, Norikatsu.

1992-01-01

The lower ends of a plurality of plate-like shape memory alloys are secured at the periphery of the upper inside of the handling head of a fuel assembly. As the shape memory alloy, a Cu-Zn alloy, a Ti-Pd alloy or a Fe-Ni alloy is used. When high temperature coolants flow out to the handling head, the shape memory alloy deforms by warping to the outer side more greatly toward the upper portion thereof with the temperature increase of the coolants. As the result, the shape of the flow channel of the coolants is changed so as to enlarge at the exit of the upper end of the fuel assembly. Then, the pressure loss of the coolants in the fuel assembly is decreased by the enlargement. Accordingly, the flow rate of the coolants in the fuel assembly is increased to lower the temperature of the coolants. Further, high temperature coolants and low temperature coolants are mixed sufficiently just above the fuel assembly. This can suppress the temperature fluctuation of the mixed coolants in the upper portion of the reactor core, thereby enabling to decrease a fatigue and failures of the structural components in the upper portion of the reactor core. (I.N.)

Soldering in electronics assembly

CERN Document Server

Judd, Mike

2013-01-01

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

Multivalent protein assembly using monovalent self-assembling building blocks

NARCIS (Netherlands)

Petkau - Milroy, K.; Sonntag, M.H.; Colditz, A.; Brunsveld, L.

2013-01-01

Discotic molecules, which self-assemble in water into columnar supramolecular polymers, emerged as an alternative platform for the organization of proteins. Here, a monovalent discotic decorated with one single biotin was synthesized to study the self-assembling multivalency of this system in regard

Bearing assemblies, apparatuses, and motor assemblies using the same

Science.gov (United States)

Sexton, Timothy N.; Cooley, Craig H.; Knuteson, Cody W.

2015-12-29

Various embodiments of the invention relate to bearing assemblies, apparatuses and motor assemblies that include geometric features configured to impart a selected amount of heat transfer and/or hydrodynamic film formation. In an embodiment, a bearing assembly may include a plurality of superhard bearing pads distributed circumferentially about an axis. At least some of the plurality of superhard bearing pads may include a plurality of sub-superhard bearing elements defining a bearing surface. At least some of the plurality of sub-superhard bearing elements may be spaced from one another by one or more voids to impart a selected amount of heat transfer and hydrodynamic film formation thereon during operation. The bearing assembly may also include a support ring that carries the plurality of superhard bearing pads. In addition, at least a portion of the sub-superhard bearing elements may extend beyond the support ring.

Fuel assembly

International Nuclear Information System (INIS)

Gjertsen, R.K.; Bassler, E.A.; Huckestein, E.A.; Salton, R.B.; Tower, S.N.

1988-01-01

A fuel assembly adapted for use with a pressurized water nuclear reactor having capabilities for fluid moderator spectral shift control is described comprising: parallel arranged elongated nuclear fuel elements; means for providing for axial support of the fuel elements and for arranging the fuel elements in a spaced array; thimbles interspersed among the fuel elements adapted for insertion of a rod control cluster therewithin; means for structurally joining the fuel elements and the guide thimbles; fluid moderator control means for providing a volume of low neutron absorbing fluid within the fuel assembly and for removing a substantially equivalent volume of reactor coolant water therefrom, a first flow manifold at one end of the fuel assembly sealingly connected to a first end of the moderator control tubes whereby the first ends are commonly flow connected; and a second flow manifold, having an inlet passage and an outlet passage therein, sealingly connected to a second end of the moderator control tubes at a second end of the fuel assembly

Self assembly of organic nanostructures and dielectrophoretic assembly of inorganic nanowires.

Science.gov (United States)

Dholakia, Geetha; Kuo, Steven; Allen, E. L.

2007-03-01

Self assembly techniques enable the organization of organic molecules into nanostructures. Currently engineering strategies for efficient assembly and routine integration of inorganic nanoscale objects into functional devices is very limited. AC Dielectrophoresis is an efficient technique to manipulate inorganic nanomaterials into higher dimensional structures. We used an alumina template based sol-gel synthesis method for the growth of various metal oxide nanowires with typical diameters of 100-150 nm, ranging in length from 3-10 μm. Here we report the dielectrophoretic assembly of TiO2 nanowires, an important material for photocatalysis and photovoltaics, onto interdigitated devices. Self assembly in organic nanostructures and its dependence on structure and stereochemistry of the molecule and dielectrophoretic field dependence in the assembly of inorganic nanowires will be compared and contrasted. Tunneling spectroscopy and DOS of these nanoscale systems will also be discussed.

HOIP Deficiency Causes Embryonic Lethality by Aberrant TNFR1-Mediated Endothelial Cell Death

Directory of Open Access Journals (Sweden)

Nieves Peltzer

2014-10-01

Full Text Available Summary: Linear ubiquitination is crucial for innate and adaptive immunity. The linear ubiquitin chain assembly complex (LUBAC, consisting of HOIL-1, HOIP, and SHARPIN, is the only known ubiquitin ligase that generates linear ubiquitin linkages. HOIP is the catalytically active LUBAC component. Here, we show that both constitutive and Tie2-Cre-driven HOIP deletion lead to aberrant endothelial cell death, resulting in defective vascularization and embryonic lethality at midgestation. Ablation of tumor necrosis factor receptor 1 (TNFR1 prevents cell death, vascularization defects, and death at midgestation. HOIP-deficient cells are more sensitive to death induction by both tumor necrosis factor (TNF and lymphotoxin-α (LT-α, and aberrant complex-II formation is responsible for sensitization to TNFR1-mediated cell death in the absence of HOIP. Finally, we show that HOIP’s catalytic activity is necessary for preventing TNF-induced cell death. Hence, LUBAC and its linear-ubiquitin-forming activity are required for maintaining vascular integrity during embryogenesis by preventing TNFR1-mediated endothelial cell death. : HOIP is the main catalytic subunit of the linear ubiquitin chain assembly complex (LUBAC, a crucial regulator of TNF and other immune signaling pathways. Peltzer et al. find that HOIP deficiency results in embryonic lethality at midgestation due to endothelial cell death mediated by TNFR1. Aberrant formation of a TNF-mediated cell-death-inducing complex in HOIP-deficient (but not -proficient cells underlies the phenotype, with the catalytic activity of HOIP required for the control of cell death in response to TNF.

Fire resistant PV shingle assembly

Science.gov (United States)

Lenox, Carl J.

2012-10-02

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

Endocytic pathways mediating oligomeric Aβ42 neurotoxicity

Directory of Open Access Journals (Sweden)

Laxton Kevin

2010-05-01

Full Text Available Abstract Background One pathological hallmark of Alzheimer's disease (AD is amyloid plaques, composed primarily of amyloid-β peptide (Aβ. Over-production or diminished clearance of the 42 amino acid form of Aβ (Aβ42 in the brain leads to accumulation of soluble Aβ and plaque formation. Soluble oligomeric Aβ (oAβ has recently emerged to be as a likely proximal cause of AD. Results Here we demonstrate that endocytosis is critical in mediating oAβ42-induced neurotoxicity and intraneuronal accumulation of Aβ. Inhibition of clathrin function either with a pharmacological inhibitor, knock-down of clathrin heavy chain expression, or expression of the dominant-negative mutant of clathrin-assembly protein AP180 did not block oAβ42-induced neurotoxicity or intraneuronal accumulation of Aβ. However, inhibition of dynamin and RhoA by expression of dominant negative mutants reduced neurotoxicity and intraneuronal Aβ accumulation. Pharmacologic inhibition of the dynamin-mediated endocytic pathway by genistein also reduced neurotoxicity. Conclusions These data suggest that dynamin-mediated and RhoA-regulated endocytosis are integral steps for oligomeric Aβ42-induced neurotoxicity and intraneuronal Aβ accumulation.

Nuclear reactor fuel assembly

International Nuclear Information System (INIS)

Marmonier, Pierre; Mesnage, Bernard; Nervi, J.C.

1975-01-01

This invention refers to fuel assemblies for a liquid metal cooled fast neutron reactor. Each assembly is composed of a hollow vertical casing, of regular polygonal section, containing a bundle of clad pins filled with a fissile or fertile substance. The casing is open at its upper end and has a cylindrical foot at its lower end for positioning the assembly in a housing provided in the horizontal diagrid, on which the core assembly rests. A set of flat bars located on the external surface of the casing enables it to be correctly orientated in its housing among the other core assemblies [fr

Modulating the forces between self-assembling molecules to control the shape of vesicles and the mechanics and alignment of nanofiber networks

Science.gov (United States)

Greenfield, Megan Ann

One of the great challenges in supramolecular chemistry is the design of molecules that can self-assemble into functional aggregates with well-defined three-dimensional structures and bulk material properties. Since the self-assembly of nanostructures is greatly influenced by both the nature of the self-assembling components and the environmental conditions in which the components assemble, this work explores how changes in the molecular design and the environment affect the properties of self-assembled structures. We first explore how to control the mechanical properties of self-assembled fibrillar networks by changing environmental conditions. We report here on how changing pH, screening ions, and solution temperature affect the gelation, stiffness, and response to deformation of peptide amphiphile gels. Although the morphology of PA gels formed by charge neutralization and salt-mediated charge screening are similar by electron microscopy, rheological measurements indicate that the calcium-mediated ionic bridges in CaCl2-PA gels form stronger intra- and inter-fiber crosslinks than the hydrogen bonds formed by the protonated carboxylic acid residues in HCl-PA gels. In contrast, the structure of PA gels changes drastically when the PA solution is annealed prior to gel formation. Annealed PA solutions are birefringent and can form viscoelastic strings of aligned nanofibers when manually dragged across a thin film of CaCl2. These aligned arrays of PA nanofibers hold great promise in controlling the orientation of cells in three-dimensions. Separately, we applied the principles of molecular design to create buckled membrane nanostructures that mimic the shape of viruses. When oppositely charged amphiphilic molecules are mixed they can form vesicles with a periodic two-dimensional ionic lattice that opposes the membrane's natural curvature and can result in vesicle buckling. Our results demonstrate that a large +3 to -1 charge imbalance between the cationic and anionic

Development of short and highly potent self-assembling elastin-derived pentapeptide repeats containing aromatic amino acid residues.

Science.gov (United States)

Taniguchi, Suguru; Watanabe, Noriko; Nose, Takeru; Maeda, Iori

2016-01-01

Tropoelastin is the primary component of elastin, which forms the elastic fibers that make up connective tissues. The hydrophobic domains of tropoelastin are thought to mediate the self-assembly of elastin into fibers, and the temperature-mediated self-assembly (coacervation) of one such repetitive peptide sequence (VPGVG) has been utilized in various bio-applications. To elucidate a mechanism for coacervation activity enhancement and to develop more potent coacervatable elastin-derived peptides, we synthesized two series of peptide analogs containing an aromatic amino acid, Trp or Tyr, in addition to Phe-containing analogs and tested their functional characteristics. Thus, position 1 of the hydrophobic pentapeptide repeat of elastin (X(1)P(2)G(3)V(4)G(5)) was substituted by Trp or Tyr. Eventually, we acquired a novel, short Trp-containing elastin-derived peptide analog (WPGVG)3 with potent coacervation ability. From the results obtained during this process, we determined the importance of aromaticity and hydrophobicity for the coacervation potency of elastin-derived peptide analogs. Generally, however, the production of long-chain synthetic polypeptides in quantities sufficient for commercial use remain cost-prohibitive. Therefore, the identification of (WPGVG)3, which is a 15-mer short peptide consisting simply of five natural amino acids and shows temperature-dependent self-assembly activity, might serve as a foundation for the development of various kinds of biomaterials. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.

Seed size and provenance mediate the joint effects of disturbance and seed predation on community assembly

Science.gov (United States)

John L. Maron; Dean E. Pearson; Teal Potter; Yvette K. Ortega

2012-01-01

Local plant community assembly is influenced by a series of filters that affect the recruitment and establishment of species. These filters include regional factors that limit seeds of any given species from reaching a local site as well as local interactions such as post-dispersal seed predation and disturbance, which dictate what species actually establish. How these...

Self assembly of rectangular shapes on concentration programming and probabilistic tile assembly models.

Science.gov (United States)

Kundeti, Vamsi; Rajasekaran, Sanguthevar

2012-06-01

Efficient tile sets for self assembling rectilinear shapes is of critical importance in algorithmic self assembly. A lower bound on the tile complexity of any deterministic self assembly system for an n × n square is [Formula: see text] (inferred from the Kolmogrov complexity). Deterministic self assembly systems with an optimal tile complexity have been designed for squares and related shapes in the past. However designing [Formula: see text] unique tiles specific to a shape is still an intensive task in the laboratory. On the other hand copies of a tile can be made rapidly using PCR (polymerase chain reaction) experiments. This led to the study of self assembly on tile concentration programming models. We present two major results in this paper on the concentration programming model. First we show how to self assemble rectangles with a fixed aspect ratio ( α:β ), with high probability, using Θ( α + β ) tiles. This result is much stronger than the existing results by Kao et al. (Randomized self-assembly for approximate shapes, LNCS, vol 5125. Springer, Heidelberg, 2008) and Doty (Randomized self-assembly for exact shapes. In: proceedings of the 50th annual IEEE symposium on foundations of computer science (FOCS), IEEE, Atlanta. pp 85-94, 2009)-which can only self assembly squares and rely on tiles which perform binary arithmetic. On the other hand, our result is based on a technique called staircase sampling . This technique eliminates the need for sub-tiles which perform binary arithmetic, reduces the constant in the asymptotic bound, and eliminates the need for approximate frames (Kao et al. Randomized self-assembly for approximate shapes, LNCS, vol 5125. Springer, Heidelberg, 2008). Our second result applies staircase sampling on the equimolar concentration programming model (The tile complexity of linear assemblies. In: proceedings of the 36th international colloquium automata, languages and programming: Part I on ICALP '09, Springer-Verlag, pp 235

Characterization of self-assembled redox polymer and antibody molecules on thiolated gold electrodes.

Science.gov (United States)

Calvo, E J; Danilowicz, C; Lagier, C M; Manrique, J; Otero, M

2004-05-15

Multilayer immobilization of antibody and redox polymer molecules on a gold electrode was achieved, as a strategy for the potential development of an amperometric immunosensor. The step-by-step assembly of antibiotin IgG on Os(bpy)(2)ClPyCH(2)NH poly(allylamine) redox polymer (PAH-Os) adsorbed on thiolated gold electrodes was proved by quartz crystal microbalance (QCM) and atomic force microscopy (AFM) experiments, confirming the electrochemical evidence. The increase of redox charge during the layer-by-layer deposition demonstrated that charge propagation within the layers is feasible. The multilayer structure proved to be effective for the molecular recognition of horseradish peroxidase-biotin conjugate (HRP-biotin), as confirmed by the QCM measurements and the electrocatalytic reduction current obtained upon H(2)O(2) addition. The catalytic current resulting from PAH-Os mediation was shown to increase with the number of assembled layers. Furthermore, the inventory of IgG molecules on the supramolecular self-assembled structure and the specific and non-specific binding of HRP-biotin conjugate were confirmed by the QCM transient studies, giving information on the kinetics of IgG deposition and HRP-biotin conjugate binding to the IgG.

Assembling large, complex environmental metagenomes

Energy Technology Data Exchange (ETDEWEB)

Howe, A. C. [Michigan State Univ., East Lansing, MI (United States). Microbiology and Molecular Genetics, Plant Soil and Microbial Sciences; Jansson, J. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division; Malfatti, S. A. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Tringe, S. G. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Tiedje, J. M. [Michigan State Univ., East Lansing, MI (United States). Microbiology and Molecular Genetics, Plant Soil and Microbial Sciences; Brown, C. T. [Michigan State Univ., East Lansing, MI (United States). Microbiology and Molecular Genetics, Computer Science and Engineering

2012-12-28

The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources. We apply two pre-assembly filtering approaches, digital normalization and partitioning, to make large metagenome assemblies more computationaly tractable. Using a human gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes from matched Iowa corn and native prairie soils. The predicted functional content and phylogenetic origin of the assembled contigs indicate significant taxonomic differences despite similar function. The assembly strategies presented are generic and can be extended to any metagenome; full source code is freely available under a BSD license.

Nuclear fuel string assembly

International Nuclear Information System (INIS)

Ip, A.K.; Koyanagi, K.; Tarasuk, W.R.

1976-01-01

A method of fabricating rodded fuels suitable for use in pressure tube type reactors and in pressure vessel type reactors is described. Fuel rods are secured as an inner and an outer sub-assembly, each rod attached between mounting rings secured to the rod ends. The two sub-assemblies are telescoped together and positioned by spaced thimbles located between them to provide precise positioning while permittng differential axial movement between the sub-assemblies. Such sub-assemblies are particularly suited for mounting as bundle strings. The method provides particular advantages in the assembly of annular-section fuel pins, which includes booster fuel containing enriched fuel material. (LL)

Fuel assembly reconstitution

International Nuclear Information System (INIS)

Morgado, Mario M.; Oliveira, Monica G.N.; Ferreira Junior, Decio B.M.; Santos, Barbara O. dos; Santos, Jorge E. dos

2009-01-01

Fuel failures have been happened in Nuclear Power Plants worldwide, without lost of integrity and safety, mainly for the public, environment and power plants workers. The most common causes of these events are corrosion (CRUD), fretting and pellet cladding interaction. These failures are identified by increasing the activity of fission products, verified by chemical analyses of reactor coolant. Through these analyses, during the fourth operation cycle of Angra 2 Nuclear Power Plant, was possible to observe fuel failure indication. This indication was confirmed in the end of the cycle during the unloading of reactor core through leakage tests of fuel assembly, using the equipment called 'In Mast Sipping' and 'Box Sipping'. After confirmed, the fuel assembly reconstitution was scheduled, and happened in April, 2007, where was identified the cause and the fuel rod failure, which was substitute by dummy rods (zircaloy). The cause was fretting by 'debris'. The actions to avoid and prevent fuel assemblies failures are important. The goals of this work are to describe the methodology of fuel assembly reconstitution using the FARE (Fuel Assembly Reconstitution Equipment) system, to describe the results of this task in economic and security factors of the company and show how the fuel assembly failures are identified during operation and during the outage. (author)

Assembly and activation of neurotrophic factor receptor complexes.

Science.gov (United States)

Simi, Anastasia; Ibáñez, Carlos F

2010-04-01

Neurotrophic factors play important roles in the development and function of both neuronal and glial elements of the central and peripheral nervous systems. Their functional diversity is in part based on their ability to interact with alternative complexes of receptor molecules. This review focuses on our current understanding of the mechanisms that govern the assembly and activation of neurotrophic factor receptor complexes. The realization that many, if not the majority, of these complexes exist in a preassembled form at the plasma membrane has forced the revision of classical ligand-mediated oligomerization models, and led to the discovery of novel mechanisms of receptor activation and generation of signaling diversity which are likely to be shared by many different classes of receptors.

Reflector-moderated critical assemblies

International Nuclear Information System (INIS)

Paxton, H.C.; Jarvis, G.A.; Byers, C.C.

1975-07-01

Experiments with reflector-moderated critical assemblies were part of the Rover Program at the Los Alamos Scientific Laboratory (LASL). These assemblies were characterized by thick D 2 O or beryllium reflectors surrounding large cavities that contained highly enriched uranium at low average densities. Because interest in this type of system has been revived by LASL Plasma Cavity Assembly studies, more detailed descriptions of the early assemblies than had been available in the unclassified literature are provided. (U.S.)

SWAP-Assembler 2: Optimization of De Novo Genome Assembler at Large Scale

Energy Technology Data Exchange (ETDEWEB)

Meng, Jintao; Seo, Sangmin; Balaji, Pavan; Wei, Yanjie; Wang, Bingqiang; Feng, Shengzhong

2016-08-16

In this paper, we analyze and optimize the most time-consuming steps of the SWAP-Assembler, a parallel genome assembler, so that it can scale to a large number of cores for huge genomes with the size of sequencing data ranging from terabyes to petabytes. According to the performance analysis results, the most time-consuming steps are input parallelization, k-mer graph construction, and graph simplification (edge merging). For the input parallelization, the input data is divided into virtual fragments with nearly equal size, and the start position and end position of each fragment are automatically separated at the beginning of the reads. In k-mer graph construction, in order to improve the communication efficiency, the message size is kept constant between any two processes by proportionally increasing the number of nucleotides to the number of processes in the input parallelization step for each round. The memory usage is also decreased because only a small part of the input data is processed in each round. With graph simplification, the communication protocol reduces the number of communication loops from four to two loops and decreases the idle communication time. The optimized assembler is denoted as SWAP-Assembler 2 (SWAP2). In our experiments using a 1000 Genomes project dataset of 4 terabytes (the largest dataset ever used for assembling) on the supercomputer Mira, the results show that SWAP2 scales to 131,072 cores with an efficiency of 40%. We also compared our work with both the HipMER assembler and the SWAP-Assembler. On the Yanhuang dataset of 300 gigabytes, SWAP2 shows a 3X speedup and 4X better scalability compared with the HipMer assembler and is 45 times faster than the SWAP-Assembler. The SWAP2 software is available at https://sourceforge.net/projects/swapassembler.

One-step self-assembled nanomicelles for improving the oral bioavailability of nimodipine.

Science.gov (United States)

Luo, Jing-Wen; Zhang, Zhi-Rong; Gong, Tao; Fu, Yao

2016-01-01

Our study aimed to develop a self-assembled nanomicelle for oral administration of nimodipine (NIM) with poor water solubility. Using Solutol(®) HS15, the NIM-loaded self-assembled nanomicelles displayed a near-spherical morphology with a narrow size distribution of 12.57 ± 0.21 nm (polydispersity index =0.071 ± 0.011). Compared with Nimotop(®) (NIM tablets), the intestinal absorption of NIM from NIM nanomicelle in rats was improved by 3.13- and 2.25-fold in duodenum and jejunum at 1 hour after oral administration. The cellular transport of NIM nanomicelle in Caco-2 cell monolayers was significantly enhanced compared to that of Nimotop(®). Regarding the transport pathways, clathrin, lipid raft/caveolae, and macropinocytosis mediated the cell uptake of NIM nanomicelles, while P-glycoprotein and endoplasmic reticulum/Golgi complex (ER/Golgi) pathways were involved in exocytosis. Pharmacokinetic studies in our research laboratory have showed that the area under the plasma concentration-time curve (AUC0-∞) of NIM nanomicelles was 3.72-fold that of Nimotop(®) via oral administration in rats. Moreover, the NIM concentration in the brain from NIM nanomicelles was dramatically improved. Therefore, Solutol(®) HS15-based self-assembled nanomicelles represent a promising delivery system to enhance the oral bioavailability of NIM.

Construction of photoelectrochemical thrombin aptasensor via assembling multilayer of graphene-CdS nanocomposites.

Science.gov (United States)

Shangguan, Li; Zhu, Wei; Xue, Yanchun; Liu, Songqin

2015-02-15

A photoelectrochemical (PEC) aptasensor for highly sensitive and specific detection of thrombin was developed by using graphene–CdS nanocomposites multilayer as photoactive species and electroactive mediator hexaammineruthenium(III) chloride (Ru(NH(3))(6)(3+)) as signal enhancer. Graphene–CdS nanocomposites (G–CdS) were synthesized by one-pot reduction of oxide graphene and CdCl2 with thioacetamide. The photoactive multilayer was prepared by alternative assembly of the negatively charged 3-mercaptopropionic acid modified graphene–CdS nanocomposites (MPA-G–CdS) and the positively charged polyethylenimine (PEI) on ITO electrode. This layer-by-layer assembly method enhanced the stability and homogeneity of the photocurrent readout of G–CdS. Thrombin aptamer was covalently bound to the multilayer by using glutaraldehyde as cross-linking. Electroactive mediator (Ru(NH(3))(6)(3+)) could interact with the DNA phosphate backbone and thus facilitated the electron transfer between G–CdS multilayer and electrode and enhanced the photocurrent. Hybridizing of a long complementary DNA with thrombin aptamer could increase the adsorption amount of (Ru(NH(3))(6)(3+)), which in turn boosted the signal readout. In the presence of target thrombin, the affinity interaction between thrombin and its aptamer resulted in the long complementary DNA releasing from the G–CdS multilayer and decreasing of photocurrent signal. On the basis of G–CdS multilayer as the photoactive species, (Ru (NH(3))(6)(3+)) as an electroactive mediator, and aptamer as a recognition module, a high sensitive PEC aptasensor for thrombin detection was proposed. The thrombin aptasensor displayed a linear range from 2.0 pM to 600.0 pM and a detection limit of 1.0 pM. The present strategy provided a promising ideology for the future development of PEC biosensor. Copyright © 2014 Elsevier B.V. All rights reserved.

Polymer Directed Protein Assemblies

NARCIS (Netherlands)

van Rijn, Patrick

2013-01-01

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

Core/coil assembly for use in superconducting magnets and method for assembling the same

Science.gov (United States)

Kassner, David A.

1979-01-01

A core/coil assembly for use in a superconducting magnet of the focusing or bending type used in syncronous particle accelerators comprising a coil assembly contained within an axial bore of the stacked, washer type, carbon steel laminations which comprise the magnet core assembly, and forming an interference fit with said laminations at the operating temperature of said magnet. Also a method for making such core/coil assemblies comprising the steps of cooling the coil assembly to cryogenic temperatures and drawing it rapidly upwards into the bore of said stacked laminations.

Improved enzyme-mediated synthesis and supramolecular self-assembly of naturally occurring conjugates of beta-sitosterol

Czech Academy of Sciences Publication Activity Database

Wimmerová, Martina; Siglerová, Věra; Šaman, David; Šlouf, Miroslav; Kaletová, Eva; Wimmer, Zdeněk

2017-01-01

Roč. 117, JAN (2017), s. 38-43 ISSN 0039-128X R&D Projects: GA MŠk LD15012; GA MŠk(CZ) LO1507 Institutional support: RVO:61389030 ; RVO:61388963 ; RVO:61389013 Keywords : glycosides * esterification * resolution * sterols * esters * foods * l. * beta-Sitosterol * Acylated steryl glycoside * Lipase * Ionic liquid * Supramolecular self-assembly * Pharmacological activity Subject RIV: CC - Organic Chemistry; CD - Macromolecular Chemistry (UMCH-V) OBOR OECD: Organic chemistry; Polymer science (UMCH-V); Organic chemistry (UOCHB-X) Impact factor: 2.282, year: 2016

Assembly mechanism of FCT region type 1 pili in serotype M6 Streptococcus pyogenes.

Science.gov (United States)

Nakata, Masanobu; Kimura, Keiji Richard; Sumitomo, Tomoko; Wada, Satoshi; Sugauchi, Akinari; Oiki, Eiji; Higashino, Miharu; Kreikemeyer, Bernd; Podbielski, Andreas; Okahashi, Nobuo; Hamada, Shigeyuki; Isoda, Ryutaro; Terao, Yutaka; Kawabata, Shigetada

2011-10-28

The human pathogen Streptococcus pyogenes produces diverse pili depending on the serotype. We investigated the assembly mechanism of FCT type 1 pili in a serotype M6 strain. The pili were found to be assembled from two precursor proteins, the backbone protein T6 and ancillary protein FctX, and anchored to the cell wall in a manner that requires both a housekeeping sortase enzyme (SrtA) and pilus-associated sortase enzyme (SrtB). SrtB is primarily required for efficient formation of the T6 and FctX complex and subsequent polymerization of T6, whereas proper anchoring of the pili to the cell wall is mainly mediated by SrtA. Because motifs essential for polymerization of pilus backbone proteins in other Gram-positive bacteria are not present in T6, we sought to identify the functional residues involved in this process. Our results showed that T6 encompasses the novel VAKS pilin motif conserved in streptococcal T6 homologues and that the lysine residue (Lys-175) within the motif and cell wall sorting signal of T6 are prerequisites for isopeptide linkage of T6 molecules. Because Lys-175 and the cell wall sorting signal of FctX are indispensable for substantial incorporation of FctX into the T6 pilus shaft, FctX is suggested to be located at the pilus tip, which was also implied by immunogold electron microscopy findings. Thus, the elaborate assembly of FCT type 1 pili is potentially organized by sortase-mediated cross-linking between sorting signals and the amino group of Lys-175 positioned in the VAKS motif of T6, thereby displaying T6 and FctX in a temporospatial manner.

Nuclear fuel assemblies and fuel pins usable in such assemblies

International Nuclear Information System (INIS)

Jolly, R.

1982-01-01

A novel end cap for a nuclear fuel assembly is described in detail. It consists of a trisection arrangement which is received within a cell of a cellular grid. The cell contains abutment means with which the trisection comes into abutment. The grid also contains an abutment means for preventing the trisections from being inserted into the cell in an incorrect orientation. The present design allows fuel pins to be securely held in a hold-down grid of a sub-assembly. The design also allows easier dis-assembly of the swollen and embrittled fuel pins prior to reprocessing. (U.K.)

Lymphocytes accelerate epithelial tight junction assembly: role of AMP-activated protein kinase (AMPK.

Directory of Open Access Journals (Sweden)

Xiao Xiao Tang

2010-08-01

Full Text Available The tight junctions (TJs, characteristically located at the apicolateral borders of adjacent epithelial cells, are required for the proper formation of epithelial cell polarity as well as for sustaining the mucosal barrier to the external environment. The observation that lymphocytes are recruited by epithelial cells to the sites of infection [1] suggests that they may play a role in the modulation of epithelial barrier function and thus contribute to host defense. To test the ability of lymphocytes to modulate tight junction assembly in epithelial cells, we set up a lymphocyte-epithelial cell co-culture system, in which Madin-Darby canine kidney (MDCK cells, a well-established model cell line for studying epithelial TJ assembly [2], were co-cultured with mouse lymphocytes to mimic an infection state. In a typical calcium switch experiment, the TJ assembly in co-culture was found to be accelerated compared to that in MDCK cells alone. This accelaration was found to be mediated by AMP-activated protein kinase (AMPK. AMPK activation was independent of changes in cellular ATP levels but it was found to be activated by the pro-inflammatory cytokine TNF-alpha. Forced suppression of AMPK, either with a chemical inhibitor or by knockdown, abrogated the accelerating effect of lymphocytes on TJ formation. Similar results were also observed in a co-culture with lymphocytes and Calu-3 human airway epithelial cells, suggesting that the activation of AMPK may be a general mechanism underlying lymphocyte-accelerated TJ assembly in different epithelia. These results suggest that signals from lymphocytes, such as cytokines, facilitate TJ assembly in epithelial cells via the activation of AMPK.

Self-assembly of coiled coil peptides into nanoparticles vs 2-d plates: effects of assembly pathway

Science.gov (United States)

Kim, Kyunghee; Pochan, Darrin

Molecular solution assembly, or self-assembly, is a process by which ordered nanostructures or patterns are formed by non-covalent interactions during assembly. Biomimicry, the use of bioinspired molecules or biologically relevant materials, is an important area of self-assembly research with peptides serving a critical role as molecular tools. The morphology of peptide assemblies can be controlled by adjusting solution conditions such as the concentration of peptides, the temperature, and pH. Herein, spherical nanostructures, which have potential for creating an encapsulation system, are formed by self-assembly when coiled coil peptides are combined in solution. These peptides are homotrimeric and heterodimeric coiled-coil bundles and the homotrimer is connected with each of heterodimer through their external surfaces via disulfide bonds. The resultant covalent constructs could co-assemble into complementary trimeric hubs, respectively. The two peptide constructs are directly mixed and assembled in solution in order to produce either spherical particles or 2-d plates depending on the solution conditions and kinetic pathway of assembly. In particular, structural changes of the self-assembled peptides are explored by control of the thermal history of the assembly solution.

The co-chaperones Fkbp4/5 control Argonaute2 expression and facilitate RISC assembly.

Science.gov (United States)

Martinez, Natalia J; Chang, Hao-Ming; Borrajo, Jacob de Riba; Gregory, Richard I

2013-11-01

Argonaute2 (Ago2) protein and associated microRNAs (miRNAs) or small interfering RNAs (siRNAs) form the RNA-induced silencing complex (RISC) for target messenger RNA cleavage and post-transcriptional gene silencing. Although Ago2 is essential for RISC activity, the mechanism of RISC assembly is not well understood, and factors controlling Ago2 protein expression are largely unknown. A role for the Hsc70/Hsp90 chaperone complex in loading small RNA duplexes into the RISC has been demonstrated in cell extracts, and unloaded Ago2 is unstable and degraded by the lysosome in mammalian cells. Here we identify the co-chaperones Fkbp4 and Fkbp5 as Ago2-associated proteins in mouse embryonic stem cells. Pharmacological inhibition of this interaction using FK506 or siRNA-mediated Fkbp4/5 depletion leads to decreased Ago2 protein levels. We find FK506 treatment inhibits, whereas Fkbp4/5 overexpression promotes, miRNA-mediated stabilization of Ago2 expression. Simultaneous treatment with a lysosome inhibitor revealed the accumulation of unloaded Ago2 complexes in FK506-treated cells. We find that, consistent with unloaded miRNAs being unstable, FK506 treatment also affects miRNA abundance, particularly nascent miRNAs. Our results support a role for Fkbp4/5 in RISC assembly.

Rapid centriole assembly in Naegleria reveals conserved roles for both de novo and mentored assembly.

Science.gov (United States)

Fritz-Laylin, Lillian K; Levy, Yaron Y; Levitan, Edward; Chen, Sean; Cande, W Zacheus; Lai, Elaine Y; Fulton, Chandler

2016-03-01

Centrioles are eukaryotic organelles whose number and position are critical for cilia formation and mitosis. Many cell types assemble new centrioles next to existing ones ("templated" or mentored assembly). Under certain conditions, centrioles also form without pre-existing centrioles (de novo). The synchronous differentiation of Naegleria amoebae to flagellates represents a unique opportunity to study centriole assembly, as nearly 100% of the population transitions from having no centrioles to having two within minutes. Here, we find that Naegleria forms its first centriole de novo, immediately followed by mentored assembly of the second. We also find both de novo and mentored assembly distributed among all major eukaryote lineages. We therefore propose that both modes are ancestral and have been conserved because they serve complementary roles, with de novo assembly as the default when no pre-existing centriole is available, and mentored assembly allowing precise regulation of number, timing, and location of centriole assembly. © 2016 Wiley Periodicals, Inc.

Structural dissection of Ebola virus and its assembly determinants using cryo-electron tomography.

Science.gov (United States)

Bharat, Tanmay A M; Noda, Takeshi; Riches, James D; Kraehling, Verena; Kolesnikova, Larissa; Becker, Stephan; Kawaoka, Yoshihiro; Briggs, John A G

2012-03-13

Ebola virus is a highly pathogenic filovirus causing severe hemorrhagic fever with high mortality rates. It assembles heterogenous, filamentous, enveloped virus particles containing a negative-sense, single-stranded RNA genome packaged within a helical nucleocapsid (NC). We have used cryo-electron microscopy and tomography to visualize Ebola virus particles, as well as Ebola virus-like particles, in three dimensions in a near-native state. The NC within the virion forms a left-handed helix with an inner nucleoprotein layer decorated with protruding arms composed of VP24 and VP35. A comparison with the closely related Marburg virus shows that the N-terminal region of nucleoprotein defines the inner diameter of the Ebola virus NC, whereas the RNA genome defines its length. Binding of the nucleoprotein to RNA can assemble a loosely coiled NC-like structure; the loose coil can be condensed by binding of the viral matrix protein VP40 to the C terminus of the nucleoprotein, and rigidified by binding of VP24 and VP35 to alternate copies of the nucleoprotein. Four proteins (NP, VP24, VP35, and VP40) are necessary and sufficient to mediate assembly of an NC with structure, symmetry, variability, and flexibility indistinguishable from that in Ebola virus particles released from infected cells. Together these data provide a structural and architectural description of Ebola virus and define the roles of viral proteins in its structure and assembly.

Next-generation transcriptome assembly

Energy Technology Data Exchange (ETDEWEB)

Martin, Jeffrey A.; Wang, Zhong

2011-09-01

Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalog of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches - reference-based, de novo and combined strategies-along with some perspectives on transcriptome assembly in the near future.

Human Assisted Assembly Processes

Energy Technology Data Exchange (ETDEWEB)

CALTON,TERRI L.; PETERS,RALPH R.

2000-01-01

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

Nanoparticle assembled microcapsules for application as pH and ammonia sensor

International Nuclear Information System (INIS)

Amali, Arlin Jose; Awwad, Nour H.; Rana, Rohit Kumar; Patra, Digambara

2011-01-01

Graphical abstract: HPTS encapsulated nanoparticle assembled microcapsule is exploited as dual excitations ratiometic pH sensor. This nanoparticle assembled microcapsule based fluorescence sensor can determine ammonia and offers a robust, simple and fast sensing material. Highlights: ► A novel HPTS encapsulated nanoparticle assembled microcapsule is developed. ► Its dual excitation facilitates a ratiometic pH sensor. ► It is successfully applied for the determination of ammonia. ► It provides a robust, simple and fast sensing material. - Abstract: The encapsulation of molecular probes in a suitable nanostructured matrix can be exploited to alter their optical properties and robustness for fabricating efficient chemical sensors. Despite high sensitivity, simplicity, selectivity and cost effectiveness, the photo-destruction and photo-bleaching are the serious concerns while utilizing molecular probes. Herein we demonstrate that hydroxy pyrene trisulfonate (HPTS), a pH sensitive molecular probe, when encapsulated in a microcapsule structure prepared via the assembly of silica nanoparticles mediated by poly-L-lysine and trisodium citrate, provides a robust sensing material for pH sensing under the physiological conditions. The temporal evolution under continuous irradiation indicates that the fluorophore inside the silica microcapsule is extraordinarily photostable. The fluorescence intensity alternation at dual excitation facilitates for a ratiometic sensing of the pH, however, the fluorescence lifetime is insensitive to hydrogen ion concentration. The sensing scheme is found to be robust, fast and simple for the measurement of pH in the range 5.8–8.0, and can be successfully applied for the determination of ammonia in the concentration range 0–1.2 mM, which is important for aquatic life and the environment.

Self-Assembly of Infinite Structures

Directory of Open Access Journals (Sweden)

Scott M. Summers

2009-06-01

Full Text Available We review some recent results related to the self-assembly of infinite structures in the Tile Assembly Model. These results include impossibility results, as well as novel tile assembly systems in which shapes and patterns that represent various notions of computation self-assemble. Several open questions are also presented and motivated.

Nuclear fuel assembly

International Nuclear Information System (INIS)

Anthony, A.J.

1980-01-01

A bimetallic spacer means is cooperatively associated with a nuclear fuel assembly and operative to resist the occurrence of in-reactor bowing of the nuclear fuel assembly. The bimetallic spacer means in one embodiment of the invention includes a space grid formed, at least principally, of zircaloy to the external surface of which are attached a plurality of stainless steel strips. In another embodiment the strips are attached to fuel pins. In each of the embodiments, the stainless steel strips during power production expand outwardly to a greater extent than do the members to which the stainless steel strips are attached, thereby forming stiff springs which abut against like bimetallic spacer means with which the other nuclear fuel assemblies are provided in a given nuclear reactor core to thus prevent the occurrence of in-reactor bowing of the nuclear fuel assemblies. (author)

Nuclear fuel assembly

International Nuclear Information System (INIS)

Betten, P.R.

1976-01-01

Under the invention the fuel assembly is particularly suitable for liquid metal cooled fast neutron breeder reactors. Hence, according to the invention a fuel assembly cladding includes inward corrugations with respect to the remainder of the cladding according to a recurring pattern determined by the pitch of the metal wire helically wound round the fuel rods of the assembly. The parts of the cladding pressed inwards correspond to the areas in which the wire encircling the peripheral fuel rods is generally located apart from the cladding, thereby reducing the play between the cladding and the peripheral fuel rods situated in these areas. The reduction in the play in turn improves the coolant flow in the internal secondary channels of the fuel assembly to the detriment of the flow in the peripheral secondary channels and thereby establishes a better coolant fluid temperature profile [fr

Method and apparatus for assembling a permanent magnet pole assembly

Science.gov (United States)

Carl, Jr., Ralph James; Bagepalli, Bharat Sampathkumaran [Niskayuna, NY; Jansen, Patrick Lee [Scotia, NY; Dawson, Richard Nils [Voorheesville, NY; Qu, Ronghai [Clifton Park, NY; Avanesov, Mikhail Avramovich [Moscow, RU

2009-08-11

A pole assembly for a rotor, the pole assembly includes a permanent magnet pole including at least one permanent magnet block, a plurality of laminations including a pole cap mechanically coupled to the pole, and a plurality of laminations including a base plate mechanically coupled to the pole.

TPX assembly plan

International Nuclear Information System (INIS)

Knutson, D.

1993-01-01

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

Assembly Modulated by Particle Position and Shape: A New Concept in Self-Assembly

DEFF Research Database (Denmark)

Tavacoli, Joe W; Heuvingh, Julien; Du Roure, Olivia

2017-01-01

In this communication we outline how the bespoke arrangements and design of micron-sized superparamagnetic shapes provide levers to modulate their assembly under homogeneous magnetic fields. We label this new approach, 'assembly modulated by particle position and shape' (APPS). Specifically, using...... rectangular lattices of superparamagnetic micron-sized cuboids, we construct distinct microstructures by adjusting lattice pitch and angle of array with respect to a magnetic field. Broadly, we find two modes of assembly: (1) immediate 2D jamming of the cuboids as they rotate to align with the applied field...... (rotation-induced jamming) and (2) aggregation via translation after their full alignment (dipole-dipole assembly). The boundary between these two assembly pathways is independent on field strength being solely a function of the cuboid's dimensions, lattice pitch, and array angle with respect to field...

Dynamic behaviour of diagnostic assemblies

International Nuclear Information System (INIS)

Pecinka, L.

1980-01-01

The methodology is shown of calculating the frequency spectrum of a diagnostic assembly. The oscillations of the assembly as a whole, of a fuel rod bundle, the assembly jacket and of the individual rods in the bundle were considered. The manufacture is suggested of a model assembly which would be used for testing forced vibrations using an experimental water loop. (M.S.)

Selecting Operations for Assembler Encoding

Directory of Open Access Journals (Sweden)

Tomasz Praczyk

2010-04-01

Full Text Available Assembler Encoding is a neuro-evolutionary method in which a neural network is represented in the form of a simple program called Assembler Encoding Program. The task of the program is to create the so-called Network Definition Matrix which maintains all the information necessary to construct the network. To generate Assembler Encoding Programs and the subsequent neural networks evolutionary techniques are used.
The performance of Assembler Encoding strongly depends on operations used in Assembler Encoding Programs. To select the most effective operations, experiments in the optimization and the predator-prey problem were carried out. In the experiments, Assembler Encoding Programs equipped with different types of operations were tested. The results of the tests are presented at the end of the paper.

Mediation Analysis with Multiple Mediators.

Science.gov (United States)

VanderWeele, T J; Vansteelandt, S

2014-01-01

Recent advances in the causal inference literature on mediation have extended traditional approaches to direct and indirect effects to settings that allow for interactions and non-linearities. In this paper, these approaches from causal inference are further extended to settings in which multiple mediators may be of interest. Two analytic approaches, one based on regression and one based on weighting are proposed to estimate the effect mediated through multiple mediators and the effects through other pathways. The approaches proposed here accommodate exposure-mediator interactions and, to a certain extent, mediator-mediator interactions as well. The methods handle binary or continuous mediators and binary, continuous or count outcomes. When the mediators affect one another, the strategy of trying to assess direct and indirect effects one mediator at a time will in general fail; the approach given in this paper can still be used. A characterization is moreover given as to when the sum of the mediated effects for multiple mediators considered separately will be equal to the mediated effect of all of the mediators considered jointly. The approach proposed in this paper is robust to unmeasured common causes of two or more mediators.

Flashback resistant pre-mixer assembly

Science.gov (United States)

Laster, Walter R [Oviedo, FL; Gambacorta, Domenico [Oviedo, FL

2012-02-14

A pre-mixer assembly associated with a fuel supply system for mixing of air and fuel upstream from a main combustion zone in a gas turbine engine. The pre-mixer assembly includes a swirler assembly disposed about a fuel injector of the fuel supply system and a pre-mixer transition member. The swirler assembly includes a forward end defining an air inlet and an opposed aft end. The pre-mixer transition member has a forward end affixed to the aft end of the swirler assembly and an opposed aft end defining an outlet of the pre-mixer assembly. The aft end of the pre-mixer transition member is spaced from a base plate such that a gap is formed between the aft end of the pre-mixer transition member and the base plate for permitting a flow of purge air therethrough to increase a velocity of the air/fuel mixture exiting the pre-mixer assembly.

Vectorial electron transfer for improved hydrogen evolution by mercaptopropionic-acid-regulated CdSe quantum-dots-TiO2 -Ni(OH)2 assembly.

Science.gov (United States)

Yu, Shan; Li, Zhi-Jun; Fan, Xiang-Bing; Li, Jia-Xin; Zhan, Fei; Li, Xu-Bing; Tao, Ye; Tung, Chen-Ho; Wu, Li-Zhu

2015-02-01

A visible-light-induced hydrogen evolution system based on a CdSe quantum dots (QDs)-TiO2 -Ni(OH)2 ternary assembly has been constructed under an ambient environment, and a bifunctional molecular linker, mercaptopropionic acid, is used to facilitate the interaction between CdSe QDs and TiO2 . This hydrogen evolution system works effectively in a basic aqueous solution (pH 11.0) to achieve a hydrogen evolution rate of 10.1 mmol g(-1)  h(-1) for the assembly and a turnover frequency of 5140 h(-1) with respect to CdSe QDs (10 h); the latter is comparable with the highest value reported for QD systems in an acidic environment. X-ray photoelectron spectroscopy, X-ray absorption spectroscopy, and control experiments demonstrate that Ni(OH)2 is an efficient hydrogen evolution catalyst. In addition, inductively coupled plasma optical emission spectroscopy and the emission decay of the assembly combined with the hydrogen evolution experiments show that TiO2 functions mainly as the electron mediator; the vectorial electron transfer from CdSe QDs to TiO2 and then from TiO2 to Ni(OH)2 enhances the efficiency for hydrogen evolution. The assembly comprises light antenna CdSe QDs, electron mediator TiO2 , and catalytic Ni(OH)2 , which mimics the strategy of photosynthesis exploited in nature and takes us a step further towards artificial photosynthesis. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Assembly and Multiplex Genome Integration of Metabolic Pathways in Yeast Using CasEMBLR.

Science.gov (United States)

Jakočiūnas, Tadas; Jensen, Emil D; Jensen, Michael K; Keasling, Jay D

2018-01-01

Genome integration is a vital step for implementing large biochemical pathways to build a stable microbial cell factory. Although traditional strain construction strategies are well established for the model organism Saccharomyces cerevisiae, recent advances in CRISPR/Cas9-mediated genome engineering allow much higher throughput and robustness in terms of strain construction. In this chapter, we describe CasEMBLR, a highly efficient and marker-free genome engineering method for one-step integration of in vivo assembled expression cassettes in multiple genomic sites simultaneously. CasEMBLR capitalizes on the CRISPR/Cas9 technology to generate double-strand breaks in genomic loci, thus prompting native homologous recombination (HR) machinery to integrate exogenously derived homology templates. As proof-of-principle for microbial cell factory development, CasEMBLR was used for one-step assembly and marker-free integration of the carotenoid pathway from 15 exogenously supplied DNA parts into three targeted genomic loci. As a second proof-of-principle, a total of ten DNA parts were assembled and integrated in two genomic loci to construct a tyrosine production strain, and at the same time knocking out two genes. This new method complements and improves the field of genome engineering in S. cerevisiae by providing a more flexible platform for rapid and precise strain building.

Nuclear reactor fuel assembly

International Nuclear Information System (INIS)

Sasaki, Y.; Tashima, J.

1975-01-01

A description is given of nuclear reactor fuel assemblies arranged in the form of a lattice wherein there is attached to the interface of one of two adjacent fuel assemblies a plate spring having a concave portion curved toward said interface and to the interface of the other fuel assembly a plate spring having a convex portion curved away from said interface

Design of the ITER Tokamak Assembly Tools

International Nuclear Information System (INIS)

Park, Hyunki; Her, Namil; Kim, Byungchul; Im, Kihak; Jung, Kijung; Lee, Jaehyuk; Im, Kisuk

2006-01-01

ITER (International Thermonuclear Experimental Reactor) Procurement allocation among the seven Parties, EU, JA, CN, IN , KO, RF and US had been decided in Dec. 2005. ITER Tokamak assembly tools is one of the nine components allocated to Korea for the construction of the ITER. Assembly tools except measurement and common tools are supplied to assemble the ITER Tokamak and classified into 9 groups according to components to be assembled. Among the 9 groups of assembly tools, large-sized Sector Sub-assembly Tools and Sector Assembly Tools are used at the first stage of ITER Tokamak construction and need to be designed faster than seven other assembly tools. ITER IT (International Team) proposed Korea to accomplish ITA (ITER Transitional Arrangements) Task on detailed design, manufacturing feasibility and contract specification of specific, large sized tools such as Upending Tool, Lifting Tool, Sector Sub-assembly Tool and Sector Assembly Tool in Oct. 2004. Based on the concept design by ITER IT, Korea carried out ITA Task on detailed design of large-sized and specific Sector Sub-assembly and Sector Assembly Tools until Mar. 2006. The Sector Sub-assembly Tools mainly consist of the Upending, Lifting, Vacuum Vessel Support and Bracing, and Sector Sub-assembly Tool, among which the design of three tools are herein. The Sector Assembly Tools mainly consist of the Toroidal Field (TF) Gravity Support Assembly, Sector In-pit Assembly, TF Coil Assembly, Vacuum Vessel (VV) Welding and Vacuum Vessel Thermal Shield (TS) Assembly Tool, among which the design of Sector In-pit Assembly Tool is described herein

Judgement on the data for fuel assembly outlet temperatures of WWER fuel assemblies in power reactors based on measurements with experimental fuel assemblies

International Nuclear Information System (INIS)

Krause, F.

1986-01-01

In the period from 1980 to 1985, in the Rheinsberg nuclear power plant experimental fuel assemblies were used on lattices at the periphery of the core. These particular fuel assemblies dispose of an extensive in-core instrumentation with different sensors. Besides this, they are fit out with a device to systematically thottle the coolant flow. The large power gradient present at the core position of the experimental fuel assembly causes a temperature profile along the fuel assemblies which is well provable at the measuring points of the outlet temperature. Along the direction of flow this temperature profile in the coolant degrades only slowly. This effect is to be taken into account when measuring the fuel assembly outlet temperature of WWER fuel assemblies. Besides this, the results of the measurements hinted both at a γ-heating of the temperature measuring points and at tolerances in the calculation of the micro power density distribution. (author)

Interplay of adsorbate-adsorbate and adsorbate-substrate interactions in self-assembled molecular surface nanostructures

DEFF Research Database (Denmark)

Schnadt, Joachim; Xu, Wei; Vang, Ronnie Thorbjørn

2010-01-01

a large tolerance to monatomic surface steps on the Ag(110) surface. The observed behaviour is explained in terms of strong intermolecular hydrogen bonding and a strong surface-mediated directionality, assisted by a sufficient degree of molecular backbone flexibility. In contrast, the same kind of step......-edge crossing is not observed when the molecules are adsorbed on the isotropic Ag(111) or more reactive Cu(110) surfaces. On Ag(111), similar 1-D assemblies are formed to those on Ag(110), but they are oriented along the step edges. On Cu(110), the carboxylic groups of NDCA are deprotonated and form covalent...... bonds to the surface, a situation which is also achieved on Ag(110) by annealing to 200 degrees C. These results show that the formation of particular self-assembled molecular nanostructures depends significantly on a subtle balance between the adsorbate-adsorbate and adsorbate-substrate interactions...

Fuel assemblies

International Nuclear Information System (INIS)

Nagano, Mamoru; Yoshioka, Ritsuo

1983-01-01

Purpose: To effectively utilize nuclear fuels by increasing the reactivity of a fuel assembly and reduce the concentration at the central region thereof upon completion of the burning. Constitution: A fuel assembly is bisected into a central region and a peripheral region by disposing an inner channel box within a channel box. The flow rate of coolants passing through the central region is made greater than that in the peripheral region. The concentration of uranium 235 of the fuel rods in the central region is made higher. In such a structure, since the moderating effect in the central region is improved, the reactivity of the fuel assembly is increased and the uranium concentration in the central region upon completion of the burning can be reduced, fuel economy and effective utilization of uranium can be attained. (Kamimura, M.)

Fuel assembly

International Nuclear Information System (INIS)

Nakatsuka, Masafumi; Matsuzuka, Ryuji.

1976-01-01

Object: To provide a fuel assembly which can decrease pressure loss of coolant to uniform temperature. Structure: A sectional area of a flow passage in the vicinity of an inner peripheral surface of a wrapper tube is limited over the entire length to prevent the temperature of a fuel element in the outermost peripheral portion from being excessively decreased to thereby flatten temperature distribution. To this end, a plurality of pincture-frame-like sheet metals constituting a spacer for supporting a fuel assembly, which has a plurality of fuel elements planted lengthwise and in given spaced relation within the wrapper tube, is disposed in longitudinal grooves and in stacked fashion to form a substantially honeycomb-like space in cross section. The fuel elements are inserted and supported in the space to form a fuel assembly. (Kamimura, M.)

Halobenzoquinone-mediated assembly of amino acid modified Mn-doped ZnS quantum dots for halobenzoquinones detection in drinking water.

Science.gov (United States)

Jiao, Zhe; Zhang, Pengfei; Chen, Hongwei; Li, Jingwen; Zhong, Zhengquan; Fan, Hongbo; Cheng, Faliang

2018-10-05

Halobenzoquinones (HBQs) were reported as disinfection byproducts (DBPs) which had potential risk of bladder cancer. In this paper, a highly selective analytical method for HBQs was developed by HBQs-mediated assembly of amino acid modified Mn-doped ZnS/Quantum Dots (Mn: ZnS QDs). In the presence HBQs, a charge-transfer complex (CTC) was formed between aromatic rings of HBQs and the primary amino groups on the surface of the QDs. The formation of CTC led to the aggregation of QDs, as a result fluorescence decreasing occurred. The decrease was correlated with the concentration of HBQs. Then a fluorescence sensor array for discrimination of three kinds of HBQs including 2,6-Dichloro-1,4-benzoquinone (DCBQ), 2,6-Dibromo-1,4-benzoquinone (DBBQ) and 2,3,6-trichloro-1,4-benzoquinone (TCBQ) was developed. Four kinds of amino acids including cysteine, threonine, tyrosine and tryptophan were embellished on the Mn: ZnS QDs. The different extents of aggregation led to different fluorescence decreasing effect, thus distinct fluorescence patterns were created. It showed that three kinds of HBQs could be discriminated successfully by fluorescence sensor array at a range of concentrations through principal component analysis (PCA). The unknown samples were predicted by with a stepwise linear discriminant analysis (SLDA) using Mahalanobis distance as a selection criterion with accuracy of 100%. Remarkably, the practicability of the proposed sensor array was further validated by identification of three kinds of HBQs at different concentrations in real drinking water samples. Compared to LC/MS/MS, this fluorescent sensor array-based method was proved to be more convenient since the nanoparticles can be prepared flexibly according to the property of the target. Copyright © 2018 Elsevier B.V. All rights reserved.

Welding facilities for NPP assembling

International Nuclear Information System (INIS)

Rojtenberg, S.S.

1987-01-01

Recommendations concerning the choice of equipment for welding in pre-assembling work shops, in the enlarging assembling shops and at the assembling site, are given. Advanced production automatic welders and semiautomatic machines, applied during the NPP equipment assembling as well as automatic machines specially produced for welding the main reactor components and pipelines are described. Automatic and semiautomatic machine and manual welding post supply sources are considered

RACK1-mediated translation control promotes liver fibrogenesis

Energy Technology Data Exchange (ETDEWEB)

Liu, Min; Peng, Peike; Wang, Jiajun [Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032 (China); Wang, Lan; Duan, Fangfang [Institute of Biomedical Science, Fudan University, Shanghai 200032 (China); Jia, Dongwei, E-mail: jiadongwei@fudan.edu.cn [Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032 (China); Ruan, Yuanyuan, E-mail: yuanyuanruan@fudan.edu.cn [Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032 (China); Gu, Jianxin [Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032 (China); Institute of Biomedical Science, Fudan University, Shanghai 200032 (China)

2015-07-31

Activation of quiescent hepatic stellate cells (HSCs) is the central event of liver fibrosis. The translational machinery is an optimized molecular network that affects cellular homoeostasis and diseases, whereas the role of protein translation in HSCs activation and liver fibrosis is little defined. Our previous report suggests that up-regulation of receptor for activated C-kinase 1(RACK1) in HSCs is critical for liver fibrogenesis. In this study, we found that RACK1 promoted macrophage conditioned medium (MCM)-induced assembly of eIF4F and phosphorylation of eIF4E in primary HSCs. RACK1 enhanced the translation and expression of pro-fibrogenic factors collagen 1α1, snail and cyclin E1 induced by MCM. Administration of PP242 or knock-down of eIF4E suppressed RACK1-stimulated collagen 1α1 production, proliferation and migration in primary HSCs. In addition, depletion of eIF4E attenuated thioacetamide (TAA)-induced liver fibrosis in vivo. Our data suggest that RACK1-mediated stimulation of cap-dependent translation plays crucial roles in HSCs activation and liver fibrogenesis, and targeting translation initiation could be a promising strategy for the treatment of liver fibrosis. - Highlights: • RACK1 induces the assembly of eIF4F and phosphorylation of eIF4E in primary HSCs. • RACK1 stimulates the translation of collagen 1α1, snail and cyclin E1 in HSCs. • RACK1 promotes HSCs activation via cap-mediated translation. • Depletion of eIF4E suppresses liver fibrogenesis in vivo.

RACK1-mediated translation control promotes liver fibrogenesis

International Nuclear Information System (INIS)

Liu, Min; Peng, Peike; Wang, Jiajun; Wang, Lan; Duan, Fangfang; Jia, Dongwei; Ruan, Yuanyuan; Gu, Jianxin

2015-01-01

Activation of quiescent hepatic stellate cells (HSCs) is the central event of liver fibrosis. The translational machinery is an optimized molecular network that affects cellular homoeostasis and diseases, whereas the role of protein translation in HSCs activation and liver fibrosis is little defined. Our previous report suggests that up-regulation of receptor for activated C-kinase 1(RACK1) in HSCs is critical for liver fibrogenesis. In this study, we found that RACK1 promoted macrophage conditioned medium (MCM)-induced assembly of eIF4F and phosphorylation of eIF4E in primary HSCs. RACK1 enhanced the translation and expression of pro-fibrogenic factors collagen 1α1, snail and cyclin E1 induced by MCM. Administration of PP242 or knock-down of eIF4E suppressed RACK1-stimulated collagen 1α1 production, proliferation and migration in primary HSCs. In addition, depletion of eIF4E attenuated thioacetamide (TAA)-induced liver fibrosis in vivo. Our data suggest that RACK1-mediated stimulation of cap-dependent translation plays crucial roles in HSCs activation and liver fibrogenesis, and targeting translation initiation could be a promising strategy for the treatment of liver fibrosis. - Highlights: • RACK1 induces the assembly of eIF4F and phosphorylation of eIF4E in primary HSCs. • RACK1 stimulates the translation of collagen 1α1, snail and cyclin E1 in HSCs. • RACK1 promotes HSCs activation via cap-mediated translation. • Depletion of eIF4E suppresses liver fibrogenesis in vivo

Composite turbine bucket assembly

Science.gov (United States)

Liotta, Gary Charles; Garcia-Crespo, Andres

2014-05-20

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

Self-Assembling Multifunctional Peptide Dimers for Gene Delivery Systems

Directory of Open Access Journals (Sweden)

Kitae Ryu

2015-01-01

Full Text Available Self-assembling multifunctional peptide was designed for gene delivery systems. The multifunctional peptide (MP consists of cellular penetrating peptide moiety (R8, matrix metalloproteinase-2 (MMP-2 specific sequence (GPLGV, pH-responsive moiety (H5, and hydrophobic moiety (palmitic acid (CR8GPLGVH5-Pal. MP was oxidized to form multifunctional peptide dimer (MPD by DMSO oxidation of thiols in terminal cysteine residues. MPD could condense pDNA successfully at a weight ratio of 5. MPD itself could self-assemble into submicron micelle particles via hydrophobic interaction, of which critical micelle concentration is about 0.01 mM. MPD showed concentration-dependent but low cytotoxicity in comparison with PEI25k. MPD polyplexes showed low transfection efficiency in HEK293 cells expressing low level of MMP-2 but high transfection efficiency in A549 and C2C12 cells expressing high level of MMP-2, meaning the enhanced transfection efficiency probably due to MMP-induced structural change of polyplexes. Bafilomycin A1-treated transfection results suggest that the transfection of MPD is mediated via endosomal escape by endosome buffering ability. These results show the potential of MPD for MMP-2 targeted gene delivery systems due to its multifunctionality.

TOOL ASSEMBLY WITH BI-DIRECTIONAL BEARING

Science.gov (United States)

Longhurst, G.E.

1961-07-11

A two-direction motion bearing which is incorporated in a refueling nuclear fuel element trsnsfer tool assembly is described. A plurality of bi- directional bearing assembliesare fixed equi-distantly about the circumference of the transfer tool assembly to provide the tool assembly with a bearing surface- for both axial and rotational motion. Each bi-directional bearing assembly contains a plurality of circumferentially bulged rollers mounted in a unique arrangement which will provide a bearing surface for rotational movement of the tool assembly within a bore. The bi-direc tional bearing assembly itself is capable of rational motion and thus provides for longitudinal movement of the tool assembly.

Nanorod mediated collagen scaffolds as extra cellular matrix mimics

International Nuclear Information System (INIS)

Vedhanayagam, Mohan; Nair, Balachandran Unni; Sreeram, Kalarical Janardhanan; Mohan, Ranganathan

2015-01-01

Creating collagen scaffolds that mimic extracellular matrices without using toxic exogenous materials remains a big challenge. A new strategy to create scaffolds through end-to-end crosslinking through functionalized nanorods leading to well-designed architecture is presented here. Self-assembled scaffolds with a denaturation temperature of 110 °C, porosity of 70%, pore size of 0.32 μm and Young’s modulus of 231 MPa were developed largely driven by imine bonding between 3-mercapto-1-propanal (MPA) functionalized ZnO nanorods and collagen. The mechanical properties obtained were much higher than that of native collagen, collagen—MPA, collagen—3-mercapto-1-propanol (3MPOH) or collagen- 3-MPOH-ZnO, clearly bringing out the relevance of nanorod mediated assembly of fibrous networks. This new strategy has led to scaffolds with mechanical properties much higher than earlier reports and can provide support for cell growth and facilitation of cell attachment. (paper)

Fuel assembly spacer

International Nuclear Information System (INIS)

Shirakawa, Ken-etsu.

1988-01-01

Purpose: To reduce the pressure loss of coolants by fuel assembly spacers. Constitution: Spacers for supporting a fuel assembly are attached by means of a plurality of wires to an outer frame. The outer frame is made of shape memory alloy such that the wires are caused to slacken at normal temperature and the slacking of the wires is eliminated in excess of the transition temperature. Since the wires slacken at the normal temperature, fuel rods can be inserted easily. After the insertion of the fuel rods, when the entire portion or the outer frame is heated by water or gas at a predetermined temperature, the outer frame resumes its previously memorized shape to tighten the wires and, accordingly, the fuel rods can be supported firmly. In this way, since the fuel rods are inserted in the slacken state of the wires and, after the assembling, the outer frame resumes its memorized shape, the assembling work can be conducted efficiently. (Kamimura, M.)

Ordinary General Assembly

CERN Multimedia

Staff Association

2011-01-01

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

Ordinary General Assembly

CERN Multimedia

Staff Association

2011-01-01

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

Ordinary General Assembly

CERN Multimedia

Staff Association

2010-01-01

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

Self-Assembly of pH-Responsive Microspheres for Intestinal Delivery of Diverse Lipophilic Therapeutics.

Science.gov (United States)

Zhou, Xing; Zhao, Yang; Chen, Siyu; Han, Songling; Xu, Xiaoqiu; Guo, Jiawei; Liu, Mengyu; Che, Ling; Li, Xiaohui; Zhang, Jianxiang

2016-08-08

Targeted delivery of therapeutics to the intestine is preferred for the management of many diseases due to its diverse advantages. Currently, there are still challenges in creating cost-effective and translational pH-responsive microspheres for intestinal delivery of various hydrophobic drugs. Herein we report a multiple noncovalent interactions-mediated assembly strategy in which carboxyl-bearing compounds (CBCs) are guest molecules, while poly(N-isopropylacrylamide) (PNIPAm) serves as a host polymer. Formation of microparticles and therapeutic packaging can be achieved simultaneously by this assembly approach, leading to well-shaped microspheres with extremely higher drug loading capacity as compared to microspheres based on two FDA-approved materials of poly(d,l-lactide-co-glycolide) (PLGA) and an enteric coating polymer EudragitS 100 (S100). Also, carboxyl-deficient hydrophobic drugs can be effectively entrapped. These assembled microspheres, with excellent reconstitution capability as well as desirable scalability, could selectively release drug molecules under intestinal conditions. By significantly enhancing drug dissolution/release in the intestine, these pH-responsive assemblies may notably improve the oral bioavailability of loaded therapeutics. Moreover, the assembled microspheres possessed superior therapeutic performance in rodent models of inflammation and tumor over the control microspheres derived from PLGA and S100. Therapy with newly developed microspheres did not cause undesirable side effects. Furthermore, in vivo evaluation in mice revealed the carrier material PNIPAm was safe for oral delivery at doses as high as 10 g/kg. Collectively, our findings demonstrated that this type of pH-responsive microsphere may function as superior and translational intestine-directed delivery systems for a diverse array of therapeutics.

Manipulating cluster size of polyanion-stabilized Fe3O4 magnetic nanoparticle clusters via electrostatic-mediated assembly for tunable magnetophoresis behavior

International Nuclear Information System (INIS)

Yeap, Swee Pin; Ahmad, Abdul Latif; Ooi, Boon Seng; Lim, JitKang

2015-01-01

We report in this article an approach for manipulating the size of magnetic nanoparticle clusters (MNCs) via electrostatic-mediated assembly technique using an electrolyte as a clustering agent. The clusters were surface-tethered with poly(sodium 4-styrenesulfonate) (PSS) through electrostatic compensation to enhance their colloidal stability. Dynamic light scattering was employed to trace the evolution of cluster size. Simultaneously, electrophoretic mobility and Fourier transform infrared spectroscopy analyses were conducted to investigate the possible schemes involved in both cluster formation and PSS grafting. Results showed that the average hydrodynamic cluster size of the PSS/MNCs and their corresponding size distributions were successfully shifted by means of manipulating the suspension pH, the ionic nature of the electrolyte, and the electrolyte concentration. More specifically, the electrokinetic behavior of the particles upon interaction with the electrolyte plays a profound role in the formation of the PSS/MNCs. Nonetheless, the solubility of the polymer in electrolyte solution and the purification of the particles from residual ions should not be omitted in determining the effectiveness of this clustering approach. The PSS adlayer makes the resultant entities highly water-dispersible and provides electrosteric stabilization to shield the PSS/MNCs from aggregation. In this study, the experimental observations were analyzed and discussed on the basis of existing fundamental colloidal theories. The strategy of cluster size manipulation proposed here is simple and convenient to implement. Furthermore, manipulating the size of the MNCs also facilitates the tuning of magnetophoresis kinetics on exposure to low magnetic field gradient, which makes this nano-entity useful for engineering applications, specifically in separation processes.

Preliminary High-Throughput Metagenome Assembly

Energy Technology Data Exchange (ETDEWEB)

Dusheyko, Serge; Furman, Craig; Pangilinan, Jasmyn; Shapiro, Harris; Tu, Hank

2007-03-26

Metagenome data sets present a qualitatively different assembly problem than traditional single-organism whole-genome shotgun (WGS) assembly. The unique aspects of such projects include the presence of a potentially large number of distinct organisms and their representation in the data set at widely different fractions. In addition, multiple closely related strains could be present, which would be difficult to assemble separately. Failure to take these issues into account can result in poor assemblies that either jumble together different strains or which fail to yield useful results. The DOE Joint Genome Institute has sequenced a number of metagenomic projects and plans to considerably increase this number in the coming year. As a result, the JGI has a need for high-throughput tools and techniques for handling metagenome projects. We present the techniques developed to handle metagenome assemblies in a high-throughput environment. This includes a streamlined assembly wrapper, based on the JGI?s in-house WGS assembler, Jazz. It also includes the selection of sensible defaults targeted for metagenome data sets, as well as quality control automation for cleaning up the raw results. While analysis is ongoing, we will discuss preliminary assessments of the quality of the assembly results (http://fames.jgi-psf.org).

Functional analysis of the accessory protein TapA in Bacillus subtilis amyloid fiber assembly.

Science.gov (United States)

Romero, Diego; Vlamakis, Hera; Losick, Richard; Kolter, Roberto

2014-04-01

Bacillus subtilis biofilm formation relies on the assembly of a fibrous scaffold formed by the protein TasA. TasA polymerizes into highly stable fibers with biochemical and morphological features of functional amyloids. Previously, we showed that assembly of TasA fibers requires the auxiliary protein TapA. In this study, we investigated the roles of TapA sequences from the C-terminal and N-terminal ends and TapA cysteine residues in its ability to promote the assembly of TasA amyloid-like fibers. We found that the cysteine residues are not essential for the formation of TasA fibers, as their replacement by alanine residues resulted in only minor defects in biofilm formation. Mutating sequences in the C-terminal half had no effect on biofilm formation. However, we identified a sequence of 8 amino acids in the N terminus that is key for TasA fiber formation. Strains expressing TapA lacking these 8 residues were completely defective in biofilm formation. In addition, this TapA mutant protein exhibited a dominant negative effect on TasA fiber formation. Even in the presence of wild-type TapA, the mutant protein inhibited fiber assembly in vitro and delayed biofilm formation in vivo. We propose that this 8-residue sequence is crucial for the formation of amyloid-like fibers on the cell surface, perhaps by mediating the interaction between TapA or TapA and TasA molecules.

Assembling Transgender Moments

Science.gov (United States)

Greteman, Adam J.

2017-01-01

In this article, the author seeks to assemble moments--scholarly, popular, and aesthetic--in order to explore the possibilities that emerge as moments collect in education's encounters with the needs, struggles, and possibilities of transgender lives and practices. Assembling moments, the author argues, illustrates the value of "moments"…

Centrioles: some self-assembly required.

Science.gov (United States)

Song, Mi Hye; Miliaras, Nicholas B; Peel, Nina; O'Connell, Kevin F

2008-12-01

Centrioles play an important role in organizing microtubules and are precisely duplicated once per cell cycle. New (daughter) centrioles typically arise in association with existing (mother) centrioles (canonical assembly), suggesting that mother centrioles direct the formation of daughter centrioles. However, under certain circumstances, centrioles can also selfassemble free of an existing centriole (de novo assembly). Recent work indicates that the canonical and de novo pathways utilize a common mechanism and that a mother centriole spatially constrains the self-assembly process to occur within its immediate vicinity. Other recently identified mechanisms further regulate canonical assembly so that during each cell cycle, one and only one daughter centriole is assembled per mother centriole.

Fuel assembly storage pool

International Nuclear Information System (INIS)

Hiranuma, Hiroshi.

1976-01-01

Object: To remove limitation of the number of storage of fuel assemblies to increase the number of storage thereof so as to relatively reduce the water depth required for shielding radioactive rays. Structure: Fuel assembly storage rack containers for receiving a plurality of spent fuel assembly racks are stacked in multi-layer fashion within a storage pool filled with water for shielding radioactive rays and removing heat. (Furukawa, Y.)

Polymer Directed Protein Assemblies

Directory of Open Access Journals (Sweden)

Patrick van Rijn

2013-05-01

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

Ag(I)-mediated homo and hetero pairs of guanosine and cytidine: monitoring by circular dichroism spectroscopy.

Science.gov (United States)

Goncharova, Iryna

2014-01-24

Ag(I)-containing compounds are attractive as antibacterial and antifungal agents. The renewed interest in the application of silver(I) compounds has led to the need for detailed knowledge of the mechanism of their action. One of the possible ways is the coordination of Ag(I) to G-C pairs of DNA, where Ag(+) ions form Ag(I)-mediated base pairs and inhibit the transcription. Herein, a systematic chiroptical study on silver(I)-mediated homo and mixed pairs of the C-G complementary-base derivatives cytidine(C) and 5'-guanosine monophosphate(G) in water is presented. Ag(I)-mediated homo and hetero pairs of G and C and their self-assembled species were studied under two pH levels (7.0 and 10.0) by vibrational (VCD) and electronic circular dichroism(ECD). VCD was used for the first time in this field and showed itself to be a powerful method for obtaining specific structural information in solution. Based on results of the VCD experiments, the different geometries of the homo pairs were proposed under pH 7.0 and 10.0. ECD was used as a diagnostic tool to characterize the studied systems and as a contact point between the previously defined structures of the metal or proton mediated pairs of nucleobases and the systems studied here. On the basis of the obtained data, the formation of the self-assembled species of cytidine with a structure similar to the i-motif structure in DNA was proposed at pH 10.0. Copyright © 2013 Elsevier B.V. All rights reserved.

Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly

Science.gov (United States)

Fonseca, Pedro; Romano, Flavio; Schreck, John S.; Ouldridge, Thomas E.; Doye, Jonathan P. K.; Louis, Ard A.

2018-04-01

Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.

Mouse zygote-specific proteasome assembly chaperone important for maternal-to-zygotic transition

Directory of Open Access Journals (Sweden)

Seung-Wook Shin

2012-11-01

During the maternal-to-zygotic transition (MZT, maternal proteins in oocytes are degraded by the ubiquitin–proteasome system (UPS, and new proteins are synthesized from the zygotic genome. However, the specific mechanisms underlying the UPS at the MZT are not well understood. We identified a molecule named zygote-specific proteasome assembly chaperone (ZPAC that is specifically expressed in mouse gonads, and expression of ZPAC was transiently increased at the mouse MZT. ZPAC formed a complex with Ump1 and associated with precursor forms of 20S proteasomes. Transcription of ZPAC genes was also under the control of an autoregulatory feedback mechanism for the compensation of reduced proteasome activity similar to Ump1 and 20S proteasome subunit gene expression. Knockdown of ZPAC in early embryos caused a significant reduction of proteasome activity and decrease in Ump1 and mature proteasomes, leading to accumulation of proteins that need to be degraded at the MZT and early developmental arrest. Therefore, a unique proteasome assembly pathway mediated by ZPAC is important for progression of the mouse MZT.

Dynamic Multi-Component Hemiaminal Assembly

Science.gov (United States)

You, Lei; Long, S. Reid; Lynch, Vincent M.

2012-01-01

A simple approach to generating in situ metal templated tris-(2-picolyl)amine-like multi-component assemblies with potential applications in molecular recognition and sensing is reported. The assembly is based on the reversible covalent association between di-(2-picolyl)amine and aldehydes. Zinc ion is the best for inducing assembly among the metal salts investigated, while 2-picolinaldehyde is the best among the heterocyclic aldehydes studied. Although an equilibrium constant of 6.6 * 103 M-1 was measured for the assembly formed by 2-picolinaldehdye, di-(2-picolyl)amine, and zinc triflate, the equilibrium constants for other systems are in the 102 M-1 range. X-ray structural analysis revealed that zinc adopts a trigonal bipyramidal geometry within the assembled ligand. The diversity and equilibrium of the assemblies are readily altered by simply changing concentrations, varying components, or adding counter anions. PMID:21919095

Advanced gray rod control assembly

Science.gov (United States)

Drudy, Keith J; Carlson, William R; Conner, Michael E; Goldenfield, Mark; Hone, Michael J; Long, Jr., Carroll J; Parkinson, Jerod; Pomirleanu, Radu O

2013-09-17

An advanced gray rod control assembly (GRCA) for a nuclear reactor. The GRCA provides controlled insertion of gray rod assemblies into the reactor, thereby controlling the rate of power produced by the reactor and providing reactivity control at full power. Each gray rod assembly includes an elongated tubular member, a primary neutron-absorber disposed within the tubular member said neutron-absorber comprising an absorber material, preferably tungsten, having a 2200 m/s neutron absorption microscopic capture cross-section of from 10 to 30 barns. An internal support tube can be positioned between the primary absorber and the tubular member as a secondary absorber to enhance neutron absorption, absorber depletion, assembly weight, and assembly heat transfer characteristics.

Multi-Robot Assembly Strategies and Metrics

Science.gov (United States)

MARVEL, JEREMY A.; BOSTELMAN, ROGER; FALCO, JOE

2018-01-01

We present a survey of multi-robot assembly applications and methods and describe trends and general insights into the multi-robot assembly problem for industrial applications. We focus on fixtureless assembly strategies featuring two or more robotic systems. Such robotic systems include industrial robot arms, dexterous robotic hands, and autonomous mobile platforms, such as automated guided vehicles. In this survey, we identify the types of assemblies that are enabled by utilizing multiple robots, the algorithms that synchronize the motions of the robots to complete the assembly operations, and the metrics used to assess the quality and performance of the assemblies. PMID:29497234

Multi-Robot Assembly Strategies and Metrics.

Science.gov (United States)

Marvel, Jeremy A; Bostelman, Roger; Falco, Joe

2018-02-01

We present a survey of multi-robot assembly applications and methods and describe trends and general insights into the multi-robot assembly problem for industrial applications. We focus on fixtureless assembly strategies featuring two or more robotic systems. Such robotic systems include industrial robot arms, dexterous robotic hands, and autonomous mobile platforms, such as automated guided vehicles. In this survey, we identify the types of assemblies that are enabled by utilizing multiple robots, the algorithms that synchronize the motions of the robots to complete the assembly operations, and the metrics used to assess the quality and performance of the assemblies.

Bistability and oscillations in gene regulation mediated by small noncoding RNAs.

Directory of Open Access Journals (Sweden)

Dengyu Liu

Full Text Available The interplay of small noncoding RNAs (sRNAs, mRNAs, and proteins has been shown to play crucial roles in almost all cellular processes. As key post-transcriptional regulators of gene expression, the mechanisms and roles of sRNAs in various cellular processes still need to be fully understood. When participating in cellular processes, sRNAs mainly mediate mRNA degradation or translational repression. Here, we show how the dynamics of two minimal architectures is drastically affected by these two mechanisms. A comparison is also given to reveal the implication of the fundamental differences. This study may help us to analyze complex networks assembled by simple modules more easily. A better knowledge of the sRNA-mediated motifs is also of interest for bio-engineering and artificial control.

Soft-template mediated synthesis of GaOOH nanorod-shelled microspheres and thermal conversion to beta-Ga2O3.

Science.gov (United States)

Wang, Jian; Li, Qi; Qiu, Xiaohui; He, Yujian; Liu, Wei

2010-07-01

Micrometer-scale hollow spheres self-assembled by GaOOH nanorods were synthesized under hydrothermal conditions using gallium nitrate and sodium hydroxide as starting materials. The structures and morphologies of the products were studied by X-ray diffraction and scanning electron microscopy. Time-dependent experiments revealed three stages involved in the process of reaction including the initial stage of formation of surfactant vesicles which can be considered as soft templates, followed by the nucleation of GaOOH nanoclusters, and the assembling and growth of nanorods under the modulation of the spherical vesicles. The growth kinetics of the GaOOH nanorods was systematically investigated. Based on the experimental observation, a template-mediated assembling mechanism was proposed. We further demonstrated that the GaOOH nanorods could be converted to gallium oxide (beta-Ga2O3) nanorods by calcination without changing the spherical morphology of the assemblies.

Dissection of β-barrel Outer Membrane Protein Assembly Pathways through Characterizing BamA POTRA 1 Mutants of Escherichia coli

Science.gov (United States)

Bennion, Drew; Charlson, Emily S.; Coon, Eric; Misra, Rajeev

2010-01-01

Summary BamA of Escherichia coli is an essential component of the hetero-oligomeric machinery that mediates β-barrel outer membrane protein (OMP) assembly. The C- and N-termini of BamA fold into trans-membrane β-barrel and five soluble POTRA domains, respectively. Detailed characterization of BamA POTRA 1 missense and deletion mutants revealed two competing OMP assembly pathways, one of which is followed by the archetypal trimeric β-barrel OMPs, OmpF and LamB, and is dependent on POTRA 1. Interestingly, our data suggest that BamA also requires its POTRA 1 domain for proper assembly. The second pathway is independent of POTRA 1 and is exemplified by TolC. Site-specific cross-linking analysis revealed that the POTRA 1 domain of BamA interacts with SurA, a periplasmic chaperone required for the assembly of OmpF and LamB, but not that of TolC and BamA. The data suggest that SurA and BamA POTRA 1 domain function in concert to assist folding and assembly of most β-barrel OMPs except for TolC, which folds into a unique soluble α-helical barrel and an OM-anchored β-barrel. The two assembly pathways finally merge at some step beyond POTRA 1 but presumably before membrane insertion, which is thought to be catalyzed by the trans-membrane β-barrel domain of Bam A. PMID:20598079

ASSEMBLY TRANSFER SYSTEM DESCRIPTION DOCUMENT

International Nuclear Information System (INIS)

Gorpani, B.

2000-01-01

The Assembly Transfer System (ATS) receives, cools, and opens rail and truck transportation casks from the Carrier/Cask Handling System (CCHS). The system unloads transportation casks consisting of bare Spent Nuclear Fuel (SNF) assemblies, single element canisters, and Dual Purpose Canisters (DPCs). For casks containing DPCs, the system opens the DPCs and unloads the SNF. The system stages the assemblies, transfer assemblies to and from fuel-blending inventory pools, loads them into Disposal Containers (DCs), temporarily seals and inerts the DC, decontaminates the DC and transfers it to the Disposal Container Handling System. The system also prepares empty casks and DPCs for off-site shipment. Two identical Assembly Transfer System lines are provided in the Waste Handling Building (WHB). Each line operates independently to handle the waste transfer throughput and to support maintenance operations. Each system line primarily consists of wet and dry handling areas. The wet handling area includes a cask transport system, cask and DPC preparation system, and a wet assembly handling system. The basket transport system forms the transition between the wet and dry handling areas. The dry handling area includes the dry assembly handling system, assembly drying system, DC preparation system, and DC transport system. Both the wet and dry handling areas are controlled by the control and tracking system. The system operating sequence begins with moving transportation casks to the cask preparation area. The cask preparation operations consist of cask cavity gas sampling, cask venting, cask cool-down, outer lid removal, and inner shield plug lifting fixture attachment. Casks containing bare SNF (no DPC) are filled with water and placed in the cask unloading pool. The inner shield plugs are removed underwater. For casks containing a DPC, the cask lid(s) is removed, and the DPC is penetrated, sampled, vented, and cooled. A DPC lifting fixture is attached and the cask is placed

Storage method for spent fuel assembly

International Nuclear Information System (INIS)

Tajiri, Hiroshi.

1992-01-01

In the present invention, spent fuel assemblies are arranged at a dense pitch in a storage rack by suppressing the reactivity of the assemblies, to increase storage capacity for the spent fuel assemblies. That is, neutron absorbers are filled in the cladding tube of an absorbing rod, and the diameter thereof is substantially equal with that of a fuel rod. A great amount of the absorbing rods are arranged at the outer circumference of the fuel assembly. Then, they are fixed integrally to the fuel assembly and stored in a storage rack. In this case, the storage rack may be constituted only with angle materials which are inexpensive and installed simply. With such a constitution, in the fuel assembly having absorbing rods wound therearound, neutrons are absorbed by absorbing rods and the reactivity is lowered. Accordingly, the assembly arrangement pitch in the storage rack can be made dense. As a result, the storage capacity for the assemblies is increased. (I.S.)

Nuclear reactor fuel assembly

International Nuclear Information System (INIS)

Vikhorev, Yu.V.; Biryukov, G.I.; Kirilyuk, N.A.; Lobanov, V.N.

1977-01-01

A fuel assembly is proposed for nuclear reactors allowing remote replacement of control rod bundles or their shifting from one assembly to another, i.e., their multipurpose use. This leads to a significant increase in fuel assembly usability. In the fuel assembly the control rod bundle is placed in guide tube channels to which baffles are attached for fuel element spacing. The remote handling of control rods is provided by a hollow cylinder with openings in its lower bottom through which the control rods pass. All control rods in a bundle are mounted to a cross beam which in turn is mounted in the cylinder and is designed for grasping the whole rod bundle by a remotely controlled telescopic mechanism in bundle replacement or shifting. (Z.M.)

Nuclear fuel assembly

International Nuclear Information System (INIS)

Delafosse, Jacques.

1977-01-01

This invention relates to a nuclear fuel assembly for a light or heavy water reactor, or for a fast reactor of the kind with a bundle of cladded pins, maintained parallel to each other in a regular network by an assembly of separate supporting grids, fitted with elastic bearing surfaces on these pins [fr

Blade attachment assembly

Science.gov (United States)

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

2016-05-03

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

Magnetic nanoparticle assemblies

CERN Document Server

Trohidou, Kalliopi N

2014-01-01

Magnetic nanoparticles with diameters in the range of a few nanometers are today at the cutting edge of modern technology and innovation because of their use in numerous applications ranging from engineering to biomedicine. A great deal of scientific interest has been focused on the functionalization of magnetic nanoparticle assemblies. The understanding of interparticle interactions is necessary to clarify the physics of these assemblies and their use in the development of high-performance magnetic materials. This book reviews prominent research studies on the static and dynamic magnetic properties of nanoparticle assemblies, gathering together experimental and computational techniques in an effort to reveal their optimized magnetic properties for biomedical use and as ultra-high magnetic recording media.

Nuclear fuel assembly

International Nuclear Information System (INIS)

Hayashi, Hiroshi; Watari, Yoshio; Hizahara, Hiroshi; Masuoka, Ryuzo.

1970-01-01

When exchanging nuclear fuel assemblies during the operation of a nuclear reactor, melting of fuel bodies, and severence of tubular claddings is halted at the time of insertion by furnishing a neutron absorbing material such as B 10 , Cd, Gd or the like at the forward end of the fuel assembly to thereby lower the power peak at the forward ends of the fuel elements to within tolerable levels and thus prevent both fuel liquification and excessive expansion. The neutron absorbing material may be attached in the form of a plate to the fuel assembly forward tie plate, or may be inserted as a pellet into the front end of the tubular cladding. (Owens, K.J.)

Reactor fuel assembly

International Nuclear Information System (INIS)

Anthony, A.J.; Groves, M.D.

1980-01-01

A nuclear reactor fuel assembly having a lower end fitting and actuating means interacting therewith for holding the assembly down on the core support stand against the upward flow of coolant. Locking means for interacting with projections on the support stand are carried by the lower end fitting and are actuated by the movement of an actuating rod operated from above the top of the assembly. In one embodiment of the invention the downward movement of the actuating rod forces a latched spring to move outward into locking engagement with a shoulder on the support stand projections. In another embodiment, the actuating rod is rotated to effect the locking between the end fitting and the projection. (author)

Fuel assembly inspection device

International Nuclear Information System (INIS)

Yaginuma, Yoshitaka

1998-01-01

The present invention provides a device suitable to inspect appearance of fuel assemblies by photographing the appearance of fuel assemblies. Namely, the inspection device of the present invention measures bowing of fuel assembly or each of fuel rods or both of them based on the partially photographed images of fuel assembly. In this case, there is disposed a means which flashily projects images in the form of horizontal line from a direction intersecting obliquely relative to a horizontal cross section of the fuel assembly. A first image processing means separates the projected image pictures including projected images and calculates bowing. A second image processing means replaces the projected image pictures of the projected images based on projected images just before and after the photographing. Then, images for the measurement of bowing and images for inspection can be obtained simultaneously. As a result, the time required for the photographing can be shortened, the time for inspection can be shortened and an effect of preventing deterioration of photographing means by radiation rays can be provided. (I.S.)

Vertical pump assembly

International Nuclear Information System (INIS)

Dohnal, M.; Rosel, J.; Skarka, V.

1988-01-01

The mounting is described of the drive assembly of a vertical pump for nuclear power plants in areas with seismic risk. The assembly is attached to the building floor using flexible and damping elements. The design allows producing seismically resistant pumps without major design changes in the existing types of vertical pumps. (E.S.). 1 fig

Tunneling nanotube (TNT)-mediated neuron-to neuron transfer of pathological Tau protein assemblies.

Science.gov (United States)

Tardivel, Meryem; Bégard, Séverine; Bousset, Luc; Dujardin, Simon; Coens, Audrey; Melki, Ronald; Buée, Luc; Colin, Morvane

2016-11-04

A given cell makes exchanges with its neighbors through a variety of means ranging from diffusible factors to vesicles. Cells use also tunneling nanotubes (TNTs), filamentous-actin-containing membranous structures that bridge and connect cells. First described in immune cells, TNTs facilitate HIV-1 transfer and are found in various cell types, including neurons. We show that the microtubule-associated protein Tau, a key player in Alzheimer's disease, is a bona fide constituent of TNTs. This is important because Tau appears beside filamentous actin and myosin 10 as a specific marker of these fine protrusions of membranes and cytosol that are difficult to visualize. Furthermore, we observed that exogenous Tau species increase the number of TNTs established between primary neurons, thereby facilitating the intercellular transfer of Tau fibrils. In conclusion, Tau may contribute to the formation and function of the highly dynamic TNTs that may be involved in the prion-like propagation of Tau assemblies.

Nanoparticle mediated micromotor motion

Science.gov (United States)

Liu, Mei; Liu, Limei; Gao, Wenlong; Su, Miaoda; Ge, Ya; Shi, Lili; Zhang, Hui; Dong, Bin; Li, Christopher Y.

2015-03-01

In this paper, we report the utilization of nanoparticles to mediate the motion of a polymer single crystal catalytic micromotor. Micromotors have been fabricated by directly self-assembling functional nanoparticles (platinum and iron oxide nanoparticles) onto one or both sides of two-dimensional polymer single crystals. We show that the moving velocity of these micromotors in fluids can be readily tuned by controlling the nanoparticles' surface wettability and catalytic activity. A 3 times velocity increase has been achieved for a hydrophobic micromotor as opposed to the hydrophilic ones. Furthermore, we demonstrate that the catalytic activity of platinum nanoparticles inside the micromotor can be enhanced by their synergetic interactions with iron oxide nanoparticles and an electric field. Both strategies lead to dramatically increased moving velocities, with the highest value reaching ~200 μm s-1. By decreasing the nanoparticles' surface wettability and increasing their catalytic activity, a maximum of a ~10-fold increase in the moving speed of the nanoparticle based micromotor can be achieved. Our results demonstrate the advantages of using nanoparticles in micromotor systems.In this paper, we report the utilization of nanoparticles to mediate the motion of a polymer single crystal catalytic micromotor. Micromotors have been fabricated by directly self-assembling functional nanoparticles (platinum and iron oxide nanoparticles) onto one or both sides of two-dimensional polymer single crystals. We show that the moving velocity of these micromotors in fluids can be readily tuned by controlling the nanoparticles' surface wettability and catalytic activity. A 3 times velocity increase has been achieved for a hydrophobic micromotor as opposed to the hydrophilic ones. Furthermore, we demonstrate that the catalytic activity of platinum nanoparticles inside the micromotor can be enhanced by their synergetic interactions with iron oxide nanoparticles and an electric

Technology for assembling and welding of top and bottom nozzles in fuel assembly

International Nuclear Information System (INIS)

Xia Chenglie; Wan Longfu

1989-10-01

The construction character, technology and sequence of assembling and welding, assembling jig used for preventing from deformation, and acceptance test of welding technology for top and bottom nozzles are presented

RNA Packing Specificity and Folding during Assembly of the Bacteriophage MS2

Directory of Open Access Journals (Sweden)

Ottar Rolfsson

2008-01-01

Full Text Available Using a combination of biochemistry, mass spectrometry, NMR spectroscopy and cryo-electron microscopy (cryo-EM, we have been able to show that quasi-equivalent conformer switching in the coat protein (CP of an RNA bacteriophage (MS2 is controlled by a sequence-specific RNA–protein interaction. The RNA component of this complex is an RNA stem-loop encompassing just 19 nts from the phage genomic RNA, which is 3569 nts in length. This binding results in the conversion of a CP dimer from a symmetrical conformation to an asymmetric one. Only when both symmetrical and asymmetrical dimers are present in solution is assembly of the T = 3 phage capsid efficient. This implies that the conformers, we have characterized by NMR correspond to the two distinct quasi-equivalent conformers seen in the 3D structure of the virion. An icosahedrally-averaged single particle cryo-EM reconstruction of the wild-type phage (to ∼9 Å resolution has revealed icosahedrally ordered density encompassing up to 90% of the single-stranded RNA genome. The RNA is seen with a novel arrangement of two concentric shells, with connections between them along the 5-fold symmetry axes. RNA in the outer shell interacts with each of the 90 CP dimers in the T = 3 capsid and although the density is icosahedrally averaged, there appears to be a different average contact at the different quasi-equivalent protein dimers: precisely the result that would be expected if protein conformer switching is RNA-mediated throughout the assembly pathway. This unprecedented RNA structure provides new constraints for models of viral assembly and we describe experiments aimed at probing these. Together, these results suggest that viral genomic RNA folding is an important factor in efficient assembly, and further suggest that RNAs that could sequester viral CPs but not fold appropriately could act as potent inhibitors of viral assembly.

X-Ray Assembler Data

Data.gov (United States)

U.S. Department of Health & Human Services — Federal regulations require that an assembler who installs one or more certified components of a diagnostic x-ray system submit a report of assembly. This database...

Mutation Detection with Next-Generation Resequencing through a Mediator Genome

Energy Technology Data Exchange (ETDEWEB)

Wurtzel, Omri; Dori-Bachash, Mally; Pietrokovski, Shmuel; Jurkevitch, Edouard; Sorek, Rotem; Ben-Jacob, Eshel

2010-12-31

The affordability of next generation sequencing (NGS) is transforming the field of mutation analysis in bacteria. The genetic basis for phenotype alteration can be identified directly by sequencing the entire genome of the mutant and comparing it to the wild-type (WT) genome, thus identifying acquired mutations. A major limitation for this approach is the need for an a-priori sequenced reference genome for the WT organism, as the short reads of most current NGS approaches usually prohibit de-novo genome assembly. To overcome this limitation we propose a general framework that utilizes the genome of relative organisms as mediators for comparing WT and mutant bacteria. Under this framework, both mutant and WT genomes are sequenced with NGS, and the short sequencing reads are mapped to the mediator genome. Variations between the mutant and the mediator that recur in the WT are ignored, thus pinpointing the differences between the mutant and the WT. To validate this approach we sequenced the genome of Bdellovibrio bacteriovorus 109J, an obligatory bacterial predator, and its prey-independent mutant, and compared both to the mediator species Bdellovibrio bacteriovorus HD100. Although the mutant and the mediator sequences differed in more than 28,000 nucleotide positions, our approach enabled pinpointing the single causative mutation. Experimental validation in 53 additional mutants further established the implicated gene. Our approach extends the applicability of NGS-based mutant analyses beyond the domain of available reference genomes.

Nuclear fuel assembly seismic amplitude limiter

International Nuclear Information System (INIS)

Anthony, A.J.

1977-01-01

The ability of a nuclear reactor to withstand high seismic loading is enhanced by including, on each fuel assembly, at least one seismic grid which reduces the magnitude of the possible lateral deflection of the individual fuel elements and the entire fuel assembly. The reduction in possible deflection minimizes the possibility of impact of the spacer grids of one fuel assembly on those of an adjacent fuel assembly and reduces the magnitude of forces associated with any such impact thereby minimizing the possibility of fuel assembly damage as a result of high seismic loading. The seismic grid is mounted from the fuel assembly guide tubes, has greater external dimensions when compared to the fuel assembly spacer grids and normally does not support or otherwise contact the fuel elements. The reduction in possible deflection is achieved through reduction of the clearance between adjacent fuel assemblies made possible by the use in the seismic grid of a high strength material characterized by favorable thermal expansion characteristics and minimal irradiation induced expansion

Benchmark assemblies of the Los Alamos critical assemblies facility

International Nuclear Information System (INIS)

Dowdy, E.J.

1986-01-01

Several critical assemblies of precisely known materials composition and easily calculated and reproducible geometries have been constructed at the Los Alamos National Laboratory. Some of these machines, notably Jezebel, Flattop, Big Ten, and Godiva, have been used as benchmark assemblies for the comparison of the results of experimental measurements and computation of certain nuclear reaction parameters. These experiments are used to validate both the input nuclear data and the computational methods. The machines and the applications of these machines for integral nuclear data checks are described. (author)

Benchmark assemblies of the Los Alamos Critical Assemblies Facility

International Nuclear Information System (INIS)

Dowdy, E.J.

1985-01-01

Several critical assemblies of precisely known materials composition and easily calculated and reproducible geometries have been constructed at the Los Alamos National Laboratory. Some of these machines, notably Jezebel, Flattop, Big Ten, and Godiva, have been used as benchmark assemblies for the comparison of the results of experimental measurements and computation of certain nuclear reaction parameters. These experiments are used to validate both the input nuclear data and the computational methods. The machines and the applications of these machines for integral nuclear data checks are described

Benchmark assemblies of the Los Alamos critical assemblies facility

International Nuclear Information System (INIS)

Dowdy, E.J.

1985-01-01

Several critical assemblies of precisely known materials composition and easily calculated and reproducible geometries have been constructed at the Los Alamos National Laboratory. Some of these machines, notably Jezebel, Flattop, Big Ten, and Godiva, have been used as benchmark assemblies for the comparison of the results of experimental measurements and computation of certain nuclear reaction parameters. These experiments are used to validate both the input nuclear data and the computational methods. The machines and the applications of these machines for integral nuclear data checks are described

An unprecedented two-fold nested super-polyrotaxane: sulfate-directed hierarchical polythreading assembly of uranyl polyrotaxane moieties

Energy Technology Data Exchange (ETDEWEB)

Mei, Lei; Wu, Qun-yan; Yuan, Li-yong; Wang, Lin; An, Shu-wen; Xie, Zhen-ni; Hu, Kong-qiu; Shi, Wei-qun [Laboratory of Nuclear Energy Chemistry and Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing (China); Chai, Zhi-fang [Laboratory of Nuclear Energy Chemistry and Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing (China); School of Radiological and Interdisciplinary Sciences and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou (China); Burns, Peter C. [Department of Chemistry and Biochemistry, University of Notre Dame, IN (United States)

2016-08-01

The hierarchical assembly of well-organized submoieties could lead to more complicated superstructures with intriguing properties. We describe herein an unprecedented polyrotaxane polythreading framework containing a two-fold nested super-polyrotaxane substructure, which was synthesized through a uranyl-directed hierarchical polythreading assembly of one-dimensional polyrotaxane chains and two-dimensional polyrotaxane networks. This special assembly mode actually affords a new way of supramolecular chemistry instead of covalently linked bulky stoppers to construct stable interlocked rotaxane moieties. An investigation of the synthesis condition shows that sulfate can assume a vital role in mediating the formation of different uranyl species, especially the unique trinuclear uranyl moiety [(UO{sub 2}){sub 3}O(OH){sub 2}]{sup 2+}, involving a notable bent [O=U=O] bond with a bond angle of 172.0(9) . Detailed analysis of the coordination features, the thermal stability as well as a fluorescence, and electrochemical characterization demonstrate that the uniqueness of this super-polyrotaxane structure is mainly closely related to the trinuclear uranyl moiety, which is confirmed by quantum chemical calculations. (copyright 2016 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Molecular self-assembly advances and applications

CERN Document Server

Dequan, Alex Li

2012-01-01

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

SP-100 nuclear assembly test: Test assembly functional requirements and system arrangement

International Nuclear Information System (INIS)

Fallas, T.T.; Gluck, R.; Motwani, K.; Clay, H.; O'Neill, G.

1991-01-01

This paper describes the functional requirements and the system that will be tested to validate the reactor, flight shield, and flight controller of the SP-100 Generic Flight System (GFS). The Nuclear Assembly Test (NAT) consists of the test article (SP-100 reactor with control devices and the flight shield) and its supporting systems. The NAT test assembly is being designed by GE. Westinghouse Hanford Company (WHC) is designing the test cell and vacuum vessel system that will contain the NAT test assembly (Renkey et al. 1989). Preliminary design reviews have been completed and the final design is under way

Fuel assembly guide tube

International Nuclear Information System (INIS)

Jabsen, F.S.

1979-01-01

This invention is directed toward a nuclear fuel assembly guide tube arrangement which restrains spacer grid movement due to coolant flow and which offers secondary means for supporting a fuel assembly during handling and transfer operations

Magnetic self-assembly of small parts

Science.gov (United States)

Shetye, Sheetal B.

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

Mechanical Self-Assembly Science and Applications

CERN Document Server

2013-01-01

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

Directed Self-Assembly of Nanodispersions

Energy Technology Data Exchange (ETDEWEB)

Furst, Eric M [University of Delaware

2013-11-15

Directed self-assembly promises to be the technologically and economically optimal approach to industrial-scale nanotechnology, and will enable the realization of inexpensive, reproducible and active nanostructured materials with tailored photonic, transport and mechanical properties. These new nanomaterials will play a critical role in meeting the 21st century grand challenges of the US, including energy diversity and sustainability, national security and economic competitiveness. The goal of this work was to develop and fundamentally validate methods of directed selfassembly of nanomaterials and nanodispersion processing. The specific aims were: 1. Nanocolloid self-assembly and interactions in AC electric fields. In an effort to reduce the particle sizes used in AC electric field self-assembly to lengthscales, we propose detailed characterizations of field-driven structures and studies of the fundamental underlying particle interactions. We will utilize microscopy and light scattering to assess order-disorder transitions and self-assembled structures under a variety of field and physicochemical conditions. Optical trapping will be used to measure particle interactions. These experiments will be synergetic with calculations of the particle polarizability, enabling us to both validate interactions and predict the order-disorder transition for nanocolloids. 2. Assembly of anisotropic nanocolloids. Particle shape has profound effects on structure and flow behavior of dispersions, and greatly complicates their processing and self-assembly. The methods developed to study the self-assembled structures and underlying particle interactions for dispersions of isotropic nanocolloids will be extended to systems composed of anisotropic particles. This report reviews several key advances that have been made during this project, including, (1) advances in the measurement of particle polarization mechanisms underlying field-directed self-assembly, and (2) progress in the

Inverse Problem in Self-assembly

Science.gov (United States)

Tkachenko, Alexei

2012-02-01

By decorating colloids and nanoparticles with DNA, one can introduce highly selective key-lock interactions between them. This leads to a new class of systems and problems in soft condensed matter physics. In particular, this opens a possibility to solve inverse problem in self-assembly: how to build an arbitrary desired structure with the bottom-up approach? I will present a theoretical and computational analysis of the hierarchical strategy in attacking this problem. It involves self-assembly of particular building blocks (``octopus particles''), that in turn would assemble into the target structure. On a conceptual level, our approach combines elements of three different brands of programmable self assembly: DNA nanotechnology, nanoparticle-DNA assemblies and patchy colloids. I will discuss the general design principles, theoretical and practical limitations of this approach, and illustrate them with our simulation results. Our crucial result is that not only it is possible to design a system that has a given nanostructure as a ground state, but one can also program and optimize the kinetic pathway for its self-assembly.

Microbial community assembly and metabolic function during mammalian corpse decomposition

Energy Technology Data Exchange (ETDEWEB)

Metcalf, J. L.; Xu, Z. Z.; Weiss, S.; Lax, S.; Van Treuren, W.; Hyde, E. R.; Song, S. J.; Amir, A.; Larsen, P.; Sangwan, N.; Haarmann, D.; Humphrey, G. C.; Ackermann, G.; Thompson, L. R.; Lauber, C.; Bibat, A.; Nicholas, C.; Gebert, M. J.; Petrosino, J. F.; Reed, S. C.; Gilbert, J. A.; Lynne, A. M.; Bucheli, S. R.; Carter, D. O.; Knight, R.

2015-12-10

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

Microbial community assembly and metabolic function during mammalian corpse decomposition

Science.gov (United States)

Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R.; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C.; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob

2016-01-01

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

Robust, directed assembly of fluorescent nanodiamonds.

Science.gov (United States)

Kianinia, Mehran; Shimoni, Olga; Bendavid, Avi; Schell, Andreas W; Randolph, Steven J; Toth, Milos; Aharonovich, Igor; Lobo, Charlene J

2016-10-27

Arrays of fluorescent nanoparticles are highly sought after for applications in sensing, nanophotonics and quantum communications. Here we present a simple and robust method of assembling fluorescent nanodiamonds into macroscopic arrays. Remarkably, the yield of this directed assembly process is greater than 90% and the assembled patterns withstand ultra-sonication for more than three hours. The assembly process is based on covalent bonding of carboxyl to amine functional carbon seeds and is applicable to any material, and to non-planar surfaces. Our results pave the way to directed assembly of sensors and nanophotonics devices.

WHO: World Health Assembly.

Science.gov (United States)

McGregor, A

1992-05-23

1200 delegates from 175 member countries attended the 45th World Health Assembly in Geneva. Everyone at the Assembly ratified measures to prevent and control AIDS. 12 countries intended to do long term planning for community based care for AIDS patients. Further the Assembly denounced instances where countries and individuals denied the gravity of the AIDS pandemic. In fact, it expressed the importance for urgent and intensive action against HIV/AIDS. The assembly backed proposals to prevent and control sexually transmitted diseases that affect AIDS patients, especially hepatitis B. For example, in countries with hepatitis B prevalence 8% (many countries in Sub-Sahara Africa, Asia, the Pacific region, and South America), health officials should introduce hepatitis B vaccine into their existing immunization programs by 1995. By 1997, this vaccine should be part of all immunization programs. The Assembly was aware of the obstacles of establishing reliable cold chains for nationwide distribution, however. Delegates in Committee A objected to the fact that 50% of the populations of developing countries continued to have limited access to essential drugs. They also expressed disapproval in implementation of WHO's 1988 ethical criteria for promotion of drugs which WHO entrusted to the Council for International Organisations of Medical Sciences (CIOMS). CIOMS lacked WHO's status and thus could not effectively monitor drug advertising. In fact, the pharmaceutical industry as well as WHO provided the funds for a meeting of 25 experts to discuss principles included in the ethical criteria. At least 4 countries insisted that WHO have the ultimate authority in monitoring drug advertising. Delegates did adopt a compromise resolution on this topic which required that industry promotion methods be reported to the 1994 Assembly via the Executive Board. The Assembly requested WHO to establish an international advisory committee on nursing and midwifery and to improve the network of

A repeatedly refuelable mediated biofuel cell based on a hierarchical porous carbon electrode

Science.gov (United States)

Fujita, Shuji; Yamanoi, Shun; Murata, Kenichi; Mita, Hiroki; Samukawa, Tsunetoshi; Nakagawa, Takaaki; Sakai, Hideki; Tokita, Yuichi

2014-05-01

Biofuel cells that generate electricity from renewable fuels, such as carbohydrates, must be reusable through repeated refuelling, should these devices be used in consumer electronics. We demonstrate the stable generation of electricity from a glucose-powered mediated biofuel cell through multiple refuelling cycles. This refuelability is achieved by immobilizing nicotinamide adenine dinucleotide (NAD), an electron-transfer mediator, and redox enzymes in high concentrations on porous carbon particles constituting an anode while maintaining their electrochemical and enzymatic activities after the immobilization. This bioanode can be refuelled continuously for more than 60 cycles at 1.5 mA cm-2 without significant potential drop. Cells assembled with these bioanodes and bilirubin-oxidase-based biocathodes can be repeatedly used to power a portable music player at 1 mW cm-3 through 10 refuelling cycles. This study suggests that the refuelability within consumer electronics should facilitate the development of long and repeated use of the mediated biofuel cells as well as of NAD-based biosensors, bioreactors, and clinical applications.

Self-Assembly of Gold Nanoparticles at the Liquid/Liquid Interface

International Nuclear Information System (INIS)

Lee, Kang Yeol; Han, Sang Woo

2005-01-01

We have shown that the crown ether derivative can mediate the transfer of gold nanoparticles in water solution to water/oil interface, results in directing the self-assembly of nanoparticles in the form of a novel nanocomposite film. The interfacial film of nanoparticles could be transferred to various solid substrates. The experimental results indicate the formation of nanoparticles monolayers at water/oil interfaces. Our work is an important step towards interfacial entrapment and self-assembly of nanoparticles for efficient creation of 2D nanostructures. These types of materials may be used in developing catalysts, sensors, and nanoelectronic devices. Currently, we are attempting to synthesize other composite films by using specific interactions between suitable organic or inorganic ligands and various nanoparticles. The intense research activity in the field of nanoparticles is motivated by the search for new materials in order to further miniaturize electronic devices, as well as by the fundamental question of how molecular electronic properties evolve with increasing size in this intermediate region between molecular and solid-state physics. In this respect, molecularly bridged nanoparticle aggregates have been attracting growing interest. The properties of two-dimensional assemblies of metal nanoparticles are controlled by the composition, geometry, and spatial arrangement of the nanoparticle building blocks. Such structures have been used for a variety of important applications in catalysis, photonics, electronics, and biological sensing. The 2D/3D control over the spatial arrangement of nanoparticles is primarily based on the thiolamphilic nature of metal nanoparticles, hydrogenbonding interactions, the highly specific recognition interaction of antigens/antibodies, and specific base-pairing interactions between DNA and its complementary strand

Tetraspanin Assemblies in Virus Infection

Directory of Open Access Journals (Sweden)

Luise Florin

2018-05-01

Full Text Available Tetraspanins (Tspans are a family of four-span transmembrane proteins, known as plasma membrane “master organizers.” They form Tspan-enriched microdomains (TEMs or TERMs through lateral association with one another and other membrane proteins. If multiple microdomains associate with each other, larger platforms can form. For infection, viruses interact with multiple cell surface components, including receptors, activating proteases, and signaling molecules. It appears that Tspans, such as CD151, CD82, CD81, CD63, CD9, Tspan9, and Tspan7, coordinate these associations by concentrating the interacting partners into Tspan platforms. In addition to mediating viral attachment and entry, these platforms may also be involved in intracellular trafficking of internalized viruses and assist in defining virus assembly and exit sites. In conclusion, Tspans play a role in viral infection at different stages of the virus replication cycle. The present review highlights recently published data on this topic, with a focus on events at the plasma membrane. In light of these findings, we propose a model for how Tspan interactions may organize cofactors for viral infection into distinct molecular platforms.

General Assembly

CERN Multimedia

Staff Association

2016-01-01

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

Light-driven self-assembly of hetero-shaped gold nanorods

Science.gov (United States)

Liaw, Jiunn-Woei; Chao, Hsueh-Yu; Huang, Cheng-Wei; Kuo, Mao-Kuen

2018-01-01

Light-driven self-assembly and coalescence of two nearby hetero-shaped gold nanorods (GNRs) with different lengths are studied theoretically. The optical forces and torques, in terms of Maxwell's stress tensor, upon these GNRs provided by a linearly polarized (LP) plane wave are analyzed using the multiple multipole (MMP) method. Numerical results show that the optical torque dominates their alignments and the optical force their attraction. The most likely outcome of the plasmon-mediated light-matter interaction is wavelength dependent. Three different coalescences of the two GNRs could be induced by a LP light in three different wavelength regimes, respectively. For example, the side-by-side coalescence of two GNRs with radius of 15 nm and different lengths (120 and 240 nm) is induced in water as irradiated by a LP light at 633 nm, the T-shaped one at 1064 nm, and the end-to-end one at 1700 nm. The plasmonic attractive force and heating power densities inside GNRs with different gaps are also studied; the smaller the gap, the larger the attractive force and heating power. The results imply that the plasmonic coalescence and heating of two discrete GNRs may cause the local fusion at the junction of the assembly and the subsequent annealing (even recrystallization). Because the heating makes the two discrete GNRs fused to become a new nanostructure, the plasmonic coalescence of optical manipulation is irreversible.

Nuclear reactor control assembly

International Nuclear Information System (INIS)

Negron, S.B.

1991-01-01

This patent describes an assembly for providing global power control in a nuclear reactor having the core split into two halves. It comprises a disk assembly formed from at least two disks each machined with an identical surface hole pattern such that rotation of one disk relative to the other causes the hole pattern to open or close, the disk assembly being positioned substantially at the longitudinal center of and coaxial with the core halves; and means for rotating at least one of the disks relative to the other

Apparatus for lifting spent fuel assembly

International Nuclear Information System (INIS)

Hirasawa, Yoshinari; Sato, Isao; Yoneda, Yoshiyuki.

1976-01-01

Object: To increase the efficiency of cooling of a used fuel assembly being moved within a guide tube in the axial direction thereof by directly cooling the assembly with cooling gas fed into the guide tube, thus facilitating the handling of the spent fuel assembly. Structure: An end of a lock portion is inserted into the top portion of a spent fuel assembly, the assembly being hooked on the lock portion. The lock portion is provided on its outer periphery with a seal member and a centering member and at its tip with a pawl capable of being projected and retracted in the radial direction. Thus, when the lock portion is moved along the guide tube, the used fuel assembly can be moved along the guide tube by maintaining the concentric relation thereto. Meanwhile, when cooling gas is fed into the guide tube, it is blown into the used fuel assembly to directly cool the same. Thus, the cooling efficiency can be increased. (Moriyama, M.)

Chemical similarity and local community assembly in the species rich tropical genus Piper.

Science.gov (United States)

Salazar, Diego; Jaramillo, M Alejandra; Marquis, Robert J

2016-11-01

Community ecologists have strived to find mechanisms that mediate the assembly of natural communities. Recent evidence suggests that natural enemies could play an important role in the assembly of hyper-diverse tropical plant systems. Classic ecological theory predicts that in order for coexistence to occur, species differences must be maximized across biologically important niche dimensions. For plant-herbivore interactions, it has been recently suggested that, within a particular community, plant species that maximize the difference in chemical defense profiles compared to neighboring taxa will have a relative competitive advantage. Here we tested the hypothesis that plant chemical diversity can affect local community composition in the hyper-diverse genus Piper at a lowland wet forest location in Costa Rica. We first characterized the chemical composition of 27 of the most locally abundant species of Piper. We then tested whether species with different chemical compositions were more likely to coexist. Finally, we assessed the degree to which Piper phylogenetic relationships are related to differences in secondary chemical composition and community assembly. We found that, on average, co-occurring species were more likely to differ in chemical composition than expected by chance. Contrary to expectations, there was no phylogenetic signal for overall secondary chemical composition. In addition we found that species in local communities were, on average, more phylogenetically closely related than expected by chance, suggesting that functional traits other than those measured here also influence local assembly. We propose that selection by herbivores for divergent chemistries between closely related species facilitates the coexistence of a high diversity of congeneric taxa via apparent competition. © 2016 by the Ecological Society of America.

Self-assembled nanomaterials for photoacoustic imaging

Science.gov (United States)

Wang, Lei; Yang, Pei-Pei; Zhao, Xiao-Xiao; Wang, Hao

2016-01-01

In recent years, extensive endeavors have been paid to construct functional self-assembled nanomaterials for various applications such as catalysis, separation, energy and biomedicines. To date, different strategies have been developed for preparing nanomaterials with diversified structures and functionalities via fine tuning of self-assembled building blocks. In terms of biomedical applications, bioimaging technologies are urgently calling for high-efficient probes/contrast agents for high-performance bioimaging. Photoacoustic (PA) imaging is an emerging whole-body imaging modality offering high spatial resolution, deep penetration and high contrast in vivo. The self-assembled nanomaterials show high stability in vivo, specific tolerance to sterilization and prolonged half-life stability and desirable targeting properties, which is a kind of promising PA contrast agents for biomedical imaging. Herein, we focus on summarizing recent advances in smart self-assembled nanomaterials with NIR absorption as PA contrast agents for biomedical imaging. According to the preparation strategy of the contrast agents, the self-assembled nanomaterials are categorized into two groups, i.e., the ex situ and in situ self-assembled nanomaterials. The driving forces, assembly modes and regulation of PA properties of self-assembled nanomaterials and their applications for long-term imaging, enzyme activity detection and aggregation-induced retention (AIR) effect for diagnosis and therapy are emphasized. Finally, we conclude with an outlook towards future developments of self-assembled nanomaterials for PA imaging.

Self-assembled nanomaterials for photoacoustic imaging.

Science.gov (United States)

Wang, Lei; Yang, Pei-Pei; Zhao, Xiao-Xiao; Wang, Hao

2016-02-07

In recent years, extensive endeavors have been paid to construct functional self-assembled nanomaterials for various applications such as catalysis, separation, energy and biomedicines. To date, different strategies have been developed for preparing nanomaterials with diversified structures and functionalities via fine tuning of self-assembled building blocks. In terms of biomedical applications, bioimaging technologies are urgently calling for high-efficient probes/contrast agents for high-performance bioimaging. Photoacoustic (PA) imaging is an emerging whole-body imaging modality offering high spatial resolution, deep penetration and high contrast in vivo. The self-assembled nanomaterials show high stability in vivo, specific tolerance to sterilization and prolonged half-life stability and desirable targeting properties, which is a kind of promising PA contrast agents for biomedical imaging. Herein, we focus on summarizing recent advances in smart self-assembled nanomaterials with NIR absorption as PA contrast agents for biomedical imaging. According to the preparation strategy of the contrast agents, the self-assembled nanomaterials are categorized into two groups, i.e., the ex situ and in situ self-assembled nanomaterials. The driving forces, assembly modes and regulation of PA properties of self-assembled nanomaterials and their applications for long-term imaging, enzyme activity detection and aggregation-induced retention (AIR) effect for diagnosis and therapy are emphasized. Finally, we conclude with an outlook towards future developments of self-assembled nanomaterials for PA imaging.

Fuel cell sub-assembly

Science.gov (United States)

Chi, Chang V.

1983-01-01

A fuel cell sub-assembly comprising a plurality of fuel cells, a first section of a cooling means disposed at an end of the assembly and means for connecting the fuel cells and first section together to form a unitary structure.

Stochastic modeling of virus capsid assembly pathways

Science.gov (United States)

Schwartz, Russell

2009-03-01

Virus capsids have become a key model system for understanding self-assembly due to their high complexity, robust and efficient assembly processes, and experimental tractability. Our ability to directly examine and manipulate capsid assembly kinetics in detail nonetheless remains limited, creating a need for computer models that can infer experimentally inaccessible features of the assembly process and explore the effects of hypothetical manipulations on assembly trajectories. We have developed novel algorithms for stochastic simulation of capsid assembly [1,2] that allow us to model capsid assembly over broad parameter spaces [3]. We apply these methods to study the nature of assembly pathway control in virus capsids as well as their sensitivity to assembly conditions and possible experimental interventions. [4pt] [1] F. Jamalyaria, R. Rohlfs, and R. Schwartz. J Comp Phys 204, 100 (2005). [0pt] [2] N. Misra and R. Schwartz. J Chem Phys 129, in press (2008). [0pt] [3] B. Sweeney, T. Zhang, and R. Schwartz. Biophys J 94, 772 (2008).

Faucet: streaming de novo assembly graph construction.

Science.gov (United States)

Rozov, Roye; Goldshlager, Gil; Halperin, Eran; Shamir, Ron

2018-01-01

We present Faucet, a two-pass streaming algorithm for assembly graph construction. Faucet builds an assembly graph incrementally as each read is processed. Thus, reads need not be stored locally, as they can be processed while downloading data and then discarded. We demonstrate this functionality by performing streaming graph assembly of publicly available data, and observe that the ratio of disk use to raw data size decreases as coverage is increased. Faucet pairs the de Bruijn graph obtained from the reads with additional meta-data derived from them. We show these metadata-coverage counts collected at junction k-mers and connections bridging between junction pairs-contain most salient information needed for assembly, and demonstrate they enable cleaning of metagenome assembly graphs, greatly improving contiguity while maintaining accuracy. We compared Fauceted resource use and assembly quality to state of the art metagenome assemblers, as well as leading resource-efficient genome assemblers. Faucet used orders of magnitude less time and disk space than the specialized metagenome assemblers MetaSPAdes and Megahit, while also improving on their memory use; this broadly matched performance of other assemblers optimizing resource efficiency-namely, Minia and LightAssembler. However, on metagenomes tested, Faucet,o outputs had 14-110% higher mean NGA50 lengths compared with Minia, and 2- to 11-fold higher mean NGA50 lengths compared with LightAssembler, the only other streaming assembler available. Faucet is available at https://github.com/Shamir-Lab/Faucet. rshamir@tau.ac.il or eranhalperin@gmail.com. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Essential Assembly Factor Rpf2 Forms Novel Interactions within the 5S RNP in Trypanosoma brucei.

Science.gov (United States)

Kamina, Anyango D; Jaremko, Daniel; Christen, Linda; Williams, Noreen

2017-01-01

Ribosome biogenesis is a highly complex and conserved cellular process that is responsible for making ribosomes. During this process, there are several assembly steps that function as regulators to ensure proper ribosome formation. One of these steps is the assembly of the 5S ribonucleoprotein particle (5S RNP) in the central protuberance of the 60S ribosomal subunit. In eukaryotes, the 5S RNP is composed of 5S rRNA, ribosomal proteins L5 and L11, and assembly factors Rpf2 and Rrs1. Our laboratory previously showed that in Trypanosoma brucei , the 5S RNP is composed of 5S rRNA, L5, and trypanosome-specific RNA binding proteins P34 and P37. In this study, we characterize an additional component of the 5S RNP, the T. brucei homolog of Rpf2. This is the first study to functionally characterize interactions mediated by Rpf2 in an organism other than fungi. T . brucei Rpf2 (TbRpf2) was identified from tandem affinity purification using extracts prepared from protein A-tobacco etch virus (TEV)-protein C (PTP)-tagged L5, P34, and P37 cell lines, followed by mass spectrometry analysis. We characterized the binding interactions between TbRpf2 and the previously characterized members of the T. brucei 5S RNP. Our studies show that TbRpf2 mediates conserved binding interactions with 5S rRNA and L5 and that TbRpf2 also interacts with trypanosome-specific proteins P34 and P37. We performed RNA interference (RNAi) knockdown of TbRpf2 and showed that this protein is essential for the survival of the parasites and is critical for proper ribosome formation. These studies provide new insights into a critical checkpoint in the ribosome biogenesis pathway in T. brucei . IMPORTANCE Trypanosoma brucei is the parasitic protozoan that causes African sleeping sickness. Ribosome assembly is essential for the survival of this parasite through the different host environments it encounters during its life cycle. The assembly of the 5S ribonucleoprotein particle (5S RNP) functions as one of

Nuclear reactor fuel assembly

International Nuclear Information System (INIS)

Sakurai, Shungo; Ogiya, Shunsuke.

1990-01-01

In a fuel assembly, if the entire fuels comprise mixed oxide fuels, reactivity change in cold temperature-power operation is increased to worsen the reactor shutdown margin. The reactor shutdown margin has been improved by increasing the burnable poison concentration thereby reducing the reactivity of the fuel assembly. However, since unburnt poisons are present at the completion of the reactor operation, the reactivity can not be utilized effectively to bring about economical disadvantage. In view of the above, the reactivity change between lower temperature-power operations is reduced by providing a non-boiling range with more than 9.1% of cross sectional area at the inside of a channel at the central portion of the fuel assembly. As a result, the amount of the unburnt burnable poisons is decreased, the economy of fuel assembly is improved and the reactor shutdown margin can be increase. (N.H.)

On the Role of the SP1 Domain in HIV-1 Particle Assembly: a Molecular Switch?▿

Science.gov (United States)

Datta, Siddhartha A. K.; Temeselew, Lakew G.; Crist, Rachael M.; Soheilian, Ferri; Kamata, Anne; Mirro, Jane; Harvin, Demetria; Nagashima, Kunio; Cachau, Raul E.; Rein, Alan

2011-01-01

Expression of a retroviral protein, Gag, in mammalian cells is sufficient for assembly of immature virus-like particles (VLPs). VLP assembly is mediated largely by interactions between the capsid (CA) domains of Gag molecules but is facilitated by binding of the nucleocapsid (NC) domain to nucleic acid. We have investigated the role of SP1, a spacer between CA and NC in HIV-1 Gag, in VLP assembly. Mutational analysis showed that even subtle changes in the first 4 residues of SP1 destroy the ability of Gag to assemble correctly, frequently leading to formation of tubes or other misassembled structures rather than proper VLPs. We also studied the conformation of the CA-SP1 junction region in solution, using both molecular dynamics simulations and circular dichroism. Consonant with nuclear magnetic resonance (NMR) studies from other laboratories, we found that SP1 is nearly unstructured in aqueous solution but undergoes a concerted change to an α-helical conformation when the polarity of the environment is reduced by addition of dimethyl sulfoxide (DMSO), trifluoroethanol, or ethanol. Remarkably, such a coil-to-helix transition is also recapitulated in an aqueous medium at high peptide concentrations. The exquisite sensitivity of SP1 to mutational changes and its ability to undergo a concentration-dependent structural transition raise the possibility that SP1 could act as a molecular switch to prime HIV-1 Gag for VLP assembly. We suggest that changes in the local environment of SP1 when Gag oligomerizes on nucleic acid might trigger this switch. PMID:21325421

Liquid-liquid interfacial nanoparticle assemblies

Science.gov (United States)

Emrick, Todd S [South Deerfield, MA; Russell, Thomas P [Amherst, MA; Dinsmore, Anthony [Amherst, MA; Skaff, Habib [Amherst, MA; Lin, Yao [Amherst, MA

2008-12-30

Self-assembly of nanoparticles at the interface between two fluids, and methods to control such self-assembly process, e.g., the surface density of particles assembling at the interface; to utilize the assembled nanoparticles and their ligands in fabrication of capsules, where the elastic properties of the capsules can be varied from soft to tough; to develop capsules with well-defined porosities for ultimate use as delivery systems; and to develop chemistries whereby multiple ligands or ligands with multiple functionalities can be attached to the nanoparticles to promote the interfacial segregation and assembly of the nanoparticles. Certain embodiments use cadmium selenide (CdSe) nanoparticles, since the photoluminescence of the particles provides a convenient means by which the spatial location and organization of the particles can be probed. However, the systems and methodologies presented here are general and can, with suitable modification of the chemistries, be adapted to any type of nanoparticle.

Circulating levels of the angiogenesis mediators endoglin, HB-EGF, BMP-9 and FGF-2 in patients with severe sepsis and septic shock

NARCIS (Netherlands)

Faiotto, Vanessa Boury; Franci, Daniel; Enz Hubert, Rodolfo Monteiro; de Souza, Gleice Regina; Fiusa, Maiara Marx Luz; Hounkpe, Bidossessi Wilfried; Santos, Thiago Martins; Carvalho-Filho, Marco Antonio; De Paula, Erich Vinicius

2017-01-01

PURPOSE: Endothelial barrier dysfunction is a hallmark of sepsis, and is at least partially mediated by pathways that regulate endothelial barrier assembly during angiogenesis. Not surprisingly, increased levels of key angiogenic proteins such as VEGF-A and Angiopoietin-2 have been described in

SolidWorks 2011 Assemblies Bible

CERN Document Server

Lombard, Matt

2011-01-01

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

Seismic behaviour of fuel assembly

Energy Technology Data Exchange (ETDEWEB)

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

1993-11-01

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

Airfoil nozzle and shroud assembly

Science.gov (United States)

Shaffer, J.E.; Norton, P.F.

1997-06-03

An airfoil and nozzle assembly are disclosed including an outer shroud having a plurality of vane members attached to an inner surface and having a cantilevered end. The assembly further includes a inner shroud being formed by a plurality of segments. Each of the segments having a first end and a second end and having a recess positioned in each of the ends. The cantilevered end of the vane member being positioned in the recess. The airfoil and nozzle assembly being made from a material having a lower rate of thermal expansion than that of the components to which the airfoil and nozzle assembly is attached. 5 figs.

Capacitor assembly and related method of forming

Science.gov (United States)

Zhang, Lili; Tan, Daniel Qi; Sullivan, Jeffrey S.

2017-12-19

A capacitor assembly is disclosed. The capacitor assembly includes a housing. The capacitor assembly further includes a plurality of capacitors disposed within the housing. Furthermore, the capacitor assembly includes a thermally conductive article disposed about at least a portion of a capacitor body of the capacitors, and in thermal contact with the capacitor body. Moreover, the capacitor assembly also includes a heat sink disposed within the housing and in thermal contact with at least a portion of the housing and the thermally conductive article such that the heat sink is configured to remove heat from the capacitor in a radial direction of the capacitor assembly. Further, a method of forming the capacitor assembly is also presented.

Gas separation membrane module assembly

Science.gov (United States)

Wynn, Nicholas P [Palo Alto, CA; Fulton, Donald A [Fairfield, CA

2009-03-31

A gas-separation membrane module assembly and a gas-separation process using the assembly. The assembly includes a set of tubes, each containing gas-separation membranes, arranged within a housing. The housing contains a tube sheet that divides the space within the housing into two gas-tight spaces. A permeate collection system within the housing gathers permeate gas from the tubes for discharge from the housing.

Comparing de novo assemblers for 454 transcriptome data.

Science.gov (United States)

Kumar, Sujai; Blaxter, Mark L

2010-10-16

Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base) reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC) to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis. Although no single assembler performed best on all our criteria, Newbler 2.5 gave longer contigs, better alignments to some reference sequences, and was fast and easy to use. SeqMan assemblies performed best on the criterion of recapitulating known transcripts, and had more novel sequence than the other assemblers, but generated an excess of small, redundant contigs. The remaining assemblers all performed almost as well, with the exception of Newbler 2.3 (the version currently used by most assembly projects), which generated assemblies that had significantly lower total length. As different assemblers use different underlying algorithms to generate contigs, we also explored merging of assemblies and found that the merged datasets not only aligned better to reference sequences than individual assemblies, but were also more consistent in the number and size of contigs. Transcriptome assemblies are smaller than genome assemblies and thus should be more computationally tractable, but are often harder because individual contigs can have highly variable read coverage. Comparing single assemblers, Newbler 2.5 performed best on our trial data set, but other assemblers were closely comparable. Combining differently optimal assemblies from different programs however gave a more credible

3D Programmable Micro Self Assembly

National Research Council Canada - National Science Library

Bohringer, Karl F; Parviz, Babak A; Klavins, Eric

2005-01-01

.... We have developed a "self assembly tool box" consisting of a range of methods for micro-scale self-assembly in 2D and 3D We have shown physical demonstrations of simple 3D self-assemblies which lead...

A comparative evaluation of genome assembly reconciliation tools.

Science.gov (United States)

Alhakami, Hind; Mirebrahim, Hamid; Lonardi, Stefano

2017-05-18

The majority of eukaryotic genomes are unfinished due to the algorithmic challenges of assembling them. A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or parameters to use for a specific genome size and complexity. It is, therefore, common practice to produce multiple assemblies using different assemblers and parameters, then select the best one for public release. A more compelling approach would allow one to merge multiple assemblies with the intent of producing a higher quality consensus assembly, which is the objective of assembly reconciliation. Several assembly reconciliation tools have been proposed in the literature, but their strengths and weaknesses have never been compared on a common dataset. We fill this need with this work, in which we report on an extensive comparative evaluation of several tools. Specifically, we evaluate contiguity, correctness, coverage, and the duplication ratio of the merged assembly compared to the individual assemblies provided as input. None of the tools we tested consistently improved the quality of the input GAGE and synthetic assemblies. Our experiments show an increase in contiguity in the consensus assembly when the original assemblies already have high quality. In terms of correctness, the quality of the results depends on the specific tool, as well as on the quality and the ranking of the input assemblies. In general, the number of misassemblies ranges from being comparable to the best of the input assembly to being comparable to the worst of the input assembly.

Matrix development in self-assembly of articular cartilage.

Directory of Open Access Journals (Sweden)

Gidon Ofek

2008-07-01

Full Text Available Articular cartilage is a highly functional tissue which covers the ends of long bones and serves to ensure proper joint movement. A tissue engineering approach that recapitulates the developmental characteristics of articular cartilage can be used to examine the maturation and degeneration of cartilage and produce fully functional neotissue replacements for diseased tissue.This study examined the development of articular cartilage neotissue within a self-assembling process in two phases. In the first phase, articular cartilage constructs were examined at 1, 4, 7, 10, 14, 28, 42, and 56 days immunohistochemically, histologically, and through biochemical analysis for total collagen and glycosaminoglycan (GAG content. Based on statistical changes in GAG and collagen levels, four time points from the first phase (7, 14, 28, and 56 days were chosen to carry into the second phase, where the constructs were studied in terms of their mechanical characteristics, relative amounts of collagen types II and VI, and specific GAG types (chondroitin 4-sulfate, chondroitin 6-sulfate, dermatan sulfate, and hyaluronan. Collagen type VI was present in initial abundance and then localized to a pericellular distribution at 4 wks. N-cadherin activity also spiked at early stages of neotissue development, suggesting that self-assembly is mediated through a minimization of free energy. The percentage of collagen type II to total collagen significantly increased over time, while the proportion of collagen type VI to total collagen decreased between 1 and 2 wks. The chondroitin 6- to 4- sulfate ratio decreased steadily during construct maturation. In addition, the compressive properties reached a plateau and tensile characteristics peaked at 4 wks.The indices of cartilage formation examined in this study suggest that tissue maturation in self-assembled articular cartilage mirrors known developmental processes for native tissue. In terms of tissue engineering, it is

Magnetic scanning of LWR fuel assemblies

International Nuclear Information System (INIS)

Fiarman, S.; Moodenbaugh, A.

1980-01-01

Nondestructive assay (NDA) techniques are available both for fresh and spent fuel, but generally are too time consuming and do not uniquely identify an assembly. A new method is reported to obtain a signature from a magnetic scan of each assembly. This scan is an NDA technique that detects magnetic inclusions. It is potentially fast (5 min/assembly), and may provide a unique signature from the magnetic properties of each fuel assembly

QUAST: quality assessment tool for genome assemblies.

Science.gov (United States)

Gurevich, Alexey; Saveliev, Vladislav; Vyahhi, Nikolay; Tesler, Glenn

2013-04-15

Limitations of genome sequencing techniques have led to dozens of assembly algorithms, none of which is perfect. A number of methods for comparing assemblers have been developed, but none is yet a recognized benchmark. Further, most existing methods for comparing assemblies are only applicable to new assemblies of finished genomes; the problem of evaluating assemblies of previously unsequenced species has not been adequately considered. Here, we present QUAST-a quality assessment tool for evaluating and comparing genome assemblies. This tool improves on leading assembly comparison software with new ideas and quality metrics. QUAST can evaluate assemblies both with a reference genome, as well as without a reference. QUAST produces many reports, summary tables and plots to help scientists in their research and in their publications. In this study, we used QUAST to compare several genome assemblers on three datasets. QUAST tables and plots for all of them are available in the Supplementary Material, and interactive versions of these reports are on the QUAST website. http://bioinf.spbau.ru/quast . Supplementary data are available at Bioinformatics online.

Power module assembly

Science.gov (United States)

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

2011-11-15

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

A key centriole assembly interaction interface between human PLK4 and STIL appears to not be conserved in flies

Directory of Open Access Journals (Sweden)

Matthew A. Cottee

2017-03-01

Full Text Available A small number of proteins form a conserved pathway of centriole duplication. In humans and flies, the binding of PLK4/Sak to STIL/Ana2 initiates daughter centriole assembly. In humans, this interaction is mediated by an interaction between the Polo-Box-3 (PB3 domain of PLK4 and the coiled-coil domain of STIL (HsCCD. We showed previously that the Drosophila Ana2 coiled-coil domain (DmCCD is essential for centriole assembly, but it forms a tight parallel tetramer in vitro that likely precludes an interaction with PB3. Here, we show that the isolated HsCCD and HsPB3 domains form a mixture of homo-multimers in vitro, but these readily dissociate when mixed to form the previously described 1:1 HsCCD:HsPB3 complex. In contrast, although Drosophila PB3 (DmPB3 adopts a canonical polo-box fold, it does not detectably interact with DmCCD in vitro. Thus, surprisingly, a key centriole assembly interaction interface appears to differ between humans and flies.

Method of transporting fuel assemblies

International Nuclear Information System (INIS)

Okada, Katsutoshi.

1979-01-01

Purpose: To enable safety transportation of fuel assemblies for FBR type reactors by surrounding each of fuel elements in a wrapper tube by a rubbery, hollow cylindrical container and by sealing medium such as air to the inside of the container. Method: A fuel element is contained in a hollow cylindrical rubber-like tube. The fuel element has an upper end plug, a lower end plug and a wire spirally wound around the outer periphery. Upon transportation of the fuel assemblies, each of the fuel elements is covered with the container and arranged in the wrapper tube and then the fuel assemblies are assembled. Then, medium such as air is sealed for each of the fuel elements by way of an opening and then the opening is tightly closed. Before loading the transported fuel assemblies in the reactor, the medium is discharged through the opening and the container is completely extracted and removed from the inside of the wrapper tube. (Seki, T.)

Modular fuel-cell stack assembly

Science.gov (United States)

Patel, Pinakin

2010-07-13

A fuel cell assembly having a plurality of fuel cells arranged in a stack. An end plate assembly abuts the fuel cell at an end of said stack. The end plate assembly has an inlet area adapted to receive an exhaust gas from the stack, an outlet area and a passage connecting the inlet area and outlet area and adapted to carry the exhaust gas received at the inlet area from the inlet area to the outlet area. A further end plate assembly abuts the fuel cell at a further opposing end of the stack. The further end plate assembly has a further inlet area adapted to receive a further exhaust gas from the stack, a further outlet area and a further passage connecting the further inlet area and further outlet area and adapted to carry the further exhaust gas received at the further inlet area from the further inlet area to the further outlet area.

Nuclear reactor spacer assembly

International Nuclear Information System (INIS)

Anthony, A.J.; Groves, M.D.

1979-01-01

A fuel assembly for a nuclear reactor is disclosed wherein the fuel element receiving and supporting grid is comprised of a first metal, the guide tubes which pass through the grid assembly are comprised of a second metal and the grid is supported on the guide tubes by means of expanded sleeves located intermediate the grid and guide tubes. The fuel assembly is fabricated by inserting the sleeves, of initial outer diameter commensurate with the guide tube outer diameters, through the holes in the grid assembly provided for the guide tubes and thereafter expanding the sleeves radially outwardly along their entire length such that the guide tubes can subsequently be passed through the sleeves. The step of radial expansion, as a result of windows provided in the sleeves having dimensions commensurate with the geometry of the grid, mechanically captures the grid and simultaneously preloads the sleeve against the grid whereby relative motion between the grid and guide tube will be precluded

Automated ensemble assembly and validation of microbial genomes

Science.gov (United States)

2014-01-01

Background The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to sequence the majority of new genomes, it is important to establish best practices for genome assembly. However, recent evaluations such as GAGE and the Assemblathon have concluded that there is no single best approach to genome assembly. Instead, it is preferable to generate multiple assemblies and validate them to determine which is most useful for the desired analysis; this is a labor-intensive process that is often impossible or unfeasible. Results To encourage best practices supported by the community, we present iMetAMOS, an automated ensemble assembly pipeline; iMetAMOS encapsulates the process of running, validating, and selecting a single assembly from multiple assemblies. iMetAMOS packages several leading open-source tools into a single binary that automates parameter selection and execution of multiple assemblers, scores the resulting assemblies based on multiple validation metrics, and annotates the assemblies for genes and contaminants. We demonstrate the utility of the ensemble process on 225 previously unassembled Mycobacterium tuberculosis genomes as well as a Rhodobacter sphaeroides benchmark dataset. On these real data, iMetAMOS reliably produces validated assemblies and identifies potential contamination without user intervention. In addition, intelligent parameter selection produces assemblies of R. sphaeroides comparable to or exceeding the quality of those from the GAGE-B evaluation, affecting the relative ranking of some assemblers. Conclusions Ensemble assembly with iMetAMOS provides users with multiple, validated assemblies for each genome. Although computationally limited to small or mid-sized genomes, this approach is the most effective and reproducible means for generating high-quality assemblies and enables users to

Storage arrangement for nuclear reactor fuel assemblies

International Nuclear Information System (INIS)

Wade, E.E.

1977-01-01

Said invention is intended for providing an arrangement of spent fuel assembly storage inside which the space is efficiently used without accumulating a critical mass. The storage is provided for long fuel assemblies having along their longitudinal axis an active part containing the fuel and an inactive part empty of fuel. Said storage arrangement comprises a framework constituting some long-shaped cells designed so as each of them can receive a fuel assembly. Means of axial positioning of said assembly in a cell make it possible to support the fuel assemblies inside the framework according to a spacing ratio, along the cell axis, such as the active part of an assembly is adjacent to the inactive part of the adjacent assemblies [fr

Integral nuclear fuel element assembly

International Nuclear Information System (INIS)

Schluderberg, D. C.

1985-01-01

An integral nuclear fuel element assembly utilizes longitudinally finned fuel pins. The continuous or interrupted fins of the fuel pins are brazed to fins of juxtaposed fuel pins or directly to the juxtaposed fuel pins or both. The integrally brazed fuel assembly is designed to satisfy the thermal and hydraulic requirements of a fuel assembly lattice having moderator to fuel atom ratios required to achieve high conversion and breeding ratios

Centrioles: Some Self-Assembly Required

OpenAIRE

Song, Mi Hye; Miliaras, Nicholas B.; Peel, Nina; O'Connell, Kevin F.

2008-01-01

Centrioles play an important role in organizing microtubules and are precisely duplicated once per cell cycle. New (daughter) centrioles typically arise in association with existing (mother) centrioles (canonical assembly), suggesting that mother centrioles direct the formation of daughter centrioles. However, under certain circumstances, centrioles can also self-assemble free of an existing centriole (de novo assembly). Recent work indicates that the canonical and de novo pathways utilize a ...

Vegetation Dynamics and Community Assembly in Post-Agricultural Heathland

DEFF Research Database (Denmark)

Kepfer Rojas, Sebastian

that land-use legacies are still present in the soil and were important determinants of vegetation dynamics and community assembly. However, the effects of land-use legacies were mostly mediated by the understory vegetation and differed according to the functional groups. The distance to the edge, a proxy...... for the proximity to external seed sources, was an important factor affecting different components of the structure of the vegetation, demonstrating the importance of dispersal in the development of the community. My results indicate that the effect of the biotic interactions varies along abiotic gradients (e......Summary This PhD study aims at understanding how biotic, abiotic and stochastic factors interact to structure a heathland vegetation community managed under different traditional land-use practices for centuries prior to abandonment ca. 120 years ago. This study is part of one of the longest...

Structure of an APC3-APC16 complex: Insights into assembly of the Anaphase Promoting Complex/Cyclosome

OpenAIRE

Yamaguchi, Masaya; Yu, Shanshan; Qiao, Renping; Weissmann, Florian; Miller, Darcie J.; VanderLinden, Ryan; Brown, Nicholas G.; Frye, Jeremiah J.; Peters, Jan-Michael; Schulman, Brenda A.

2014-01-01

The Anaphase Promoting Complex/Cyclosome (APC/C) is a massive E3 ligase that controls mitosis by catalyzing ubiquitination of key cell cycle regulatory proteins. The APC/C assembly contains two subcomplexes: the “Platform” centers around a cullin-RING-like E3 ligase catalytic core; the “Arc Lamp” is a hub that mediates transient association with regulators and ubiquitination substrates. The Arc Lamp contains the small subunits APC16, CDC26, and APC13, and tetratricopeptide repeat (TPR) protei...

Assembly of the PLT device

International Nuclear Information System (INIS)

Marino, R.

1975-11-01

The assembly of the PLT device began in June 1974 with a preassembly of the mechanical structure at a remote site. The preassembly sequence incorporated final fabrication procedures with an initial staging operation. This successful staging/fabrication procedure proved to be an invaluable asset when the final assembly was started in August 1974. The assembly continued with the initial reassembly of the previously tested structural components at the final machine site. Construction was interrupted at several points to allow for toroidal field coil, vacuum vessel, and poloidal coil installation. Two phases of toroidal field coil power tests were included in the assembly sequence prior to, and just after the vacuum vessel insertion

PAVE: Program for assembling and viewing ESTs

Directory of Open Access Journals (Sweden)

Bomhoff Matthew

2009-08-01

Full Text Available Abstract Background New sequencing technologies are rapidly emerging. Many laboratories are simultaneously working with the traditional Sanger ESTs and experimenting with ESTs generated by the 454 Life Science sequencers. Though Sanger ESTs have been used to generate contigs for many years, no program takes full advantage of the 5' and 3' mate-pair information, hence, many tentative transcripts are assembled into two separate contigs. The new 454 technology has the benefit of high-throughput expression profiling, but introduces time and space problems for assembling large contigs. Results The PAVE (Program for Assembling and Viewing ESTs assembler takes advantage of the 5' and 3' mate-pair information by requiring that the mate-pairs be assembled into the same contig and joined by n's if the two sub-contigs do not overlap. It handles the depth of 454 data sets by "burying" similar ESTs during assembly, which retains the expression level information while circumventing time and space problems. PAVE uses MegaBLAST for the clustering step and CAP3 for assembly, however it assembles incrementally to enforce the mate-pair constraint, bury ESTs, and reduce incorrect joins and splits. The PAVE data management system uses a MySQL database to store multiple libraries of ESTs along with their metadata; the management system allows multiple assemblies with variations on libraries and parameters. Analysis routines provide standard annotation for the contigs including a measure of differentially expressed genes across the libraries. A Java viewer program is provided for display and analysis of the results. Our results clearly show the benefit of using the PAVE assembler to explicitly use mate-pair information and bury ESTs for large contigs. Conclusion The PAVE assembler provides a software package for assembling Sanger and/or 454 ESTs. The assembly software, data management software, Java viewer and user's guide are freely available.

PAVE: program for assembling and viewing ESTs.

Science.gov (United States)

Soderlund, Carol; Johnson, Eric; Bomhoff, Matthew; Descour, Anne

2009-08-26

New sequencing technologies are rapidly emerging. Many laboratories are simultaneously working with the traditional Sanger ESTs and experimenting with ESTs generated by the 454 Life Science sequencers. Though Sanger ESTs have been used to generate contigs for many years, no program takes full advantage of the 5' and 3' mate-pair information, hence, many tentative transcripts are assembled into two separate contigs. The new 454 technology has the benefit of high-throughput expression profiling, but introduces time and space problems for assembling large contigs. The PAVE (Program for Assembling and Viewing ESTs) assembler takes advantage of the 5' and 3' mate-pair information by requiring that the mate-pairs be assembled into the same contig and joined by n's if the two sub-contigs do not overlap. It handles the depth of 454 data sets by "burying" similar ESTs during assembly, which retains the expression level information while circumventing time and space problems. PAVE uses MegaBLAST for the clustering step and CAP3 for assembly, however it assembles incrementally to enforce the mate-pair constraint, bury ESTs, and reduce incorrect joins and splits. The PAVE data management system uses a MySQL database to store multiple libraries of ESTs along with their metadata; the management system allows multiple assemblies with variations on libraries and parameters. Analysis routines provide standard annotation for the contigs including a measure of differentially expressed genes across the libraries. A Java viewer program is provided for display and analysis of the results. Our results clearly show the benefit of using the PAVE assembler to explicitly use mate-pair information and bury ESTs for large contigs. The PAVE assembler provides a software package for assembling Sanger and/or 454 ESTs. The assembly software, data management software, Java viewer and user's guide are freely available.

Structure-based analysis of CysZ-mediated cellular uptake of sulfate

Science.gov (United States)

Assur Sanghai, Zahra; Liu, Qun; Clarke, Oliver B; Belcher-Dufrisne, Meagan; Wiriyasermkul, Pattama; Giese, M Hunter; Leal-Pinto, Edgar; Kloss, Brian; Tabuso, Shantelle; Love, James; Punta, Marco; Banerjee, Surajit; Rajashankar, Kanagalaghatta R; Rost, Burkhard; Logothetis, Diomedes; Quick, Matthias; Hendrickson, Wayne A

2018-01-01

Sulfur, most abundantly found in the environment as sulfate (SO42-), is an essential element in metabolites required by all living cells, including amino acids, co-factors and vitamins. However, current understanding of the cellular delivery of SO42- at the molecular level is limited. CysZ has been described as a SO42- permease, but its sequence family is without known structural precedent. Based on crystallographic structure information, SO42- binding and flux experiments, we provide insight into the molecular mechanism of CysZ-mediated translocation of SO42- across membranes. CysZ structures from three different bacterial species display a hitherto unknown fold and have subunits organized with inverted transmembrane topology. CysZ from Pseudomonas denitrificans assembles as a trimer of antiparallel dimers and the CysZ structures from two other species recapitulate dimers from this assembly. Mutational studies highlight the functional relevance of conserved CysZ residues. PMID:29792261

Technical operations procedure for assembly and emplacement of the soil temperature test--test assembly

International Nuclear Information System (INIS)

Weber, A.P.

1978-01-01

A description is given of the plan for assembly, instrumentation, emplacement, and operational checkout of the soil temperature test assembly and dry well liner. The activities described cover all operations necessary to accomplish the receiving inspection, instrumentation and pre-construction handling of the dry well liner, plus all operations performed with the test article. Actual details of construction work are not covered by this procedure. Each part and/or section of this procedure is a separate function to be accomplished as required by the nature of the operation. The organization of the procedure is not intended to imply a special operational sequence or schedular requirement. Specific procedure operational sections include: receiving inspection; liner assembly operations; construction operations (by others); prepare shield plug; test article assembly and installation; and operational checkout

Comparing de novo assemblers for 454 transcriptome data

Directory of Open Access Journals (Sweden)

Blaxter Mark L

2010-10-01

Full Text Available Abstract Background Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis. Results Although no single assembler performed best on all our criteria, Newbler 2.5 gave longer contigs, better alignments to some reference sequences, and was fast and easy to use. SeqMan assemblies performed best on the criterion of recapitulating known transcripts, and had more novel sequence than the other assemblers, but generated an excess of small, redundant contigs. The remaining assemblers all performed almost as well, with the exception of Newbler 2.3 (the version currently used by most assembly projects, which generated assemblies that had significantly lower total length. As different assemblers use different underlying algorithms to generate contigs, we also explored merging of assemblies and found that the merged datasets not only aligned better to reference sequences than individual assemblies, but were also more consistent in the number and size of contigs. Conclusions Transcriptome assemblies are smaller than genome assemblies and thus should be more computationally tractable, but are often harder because individual contigs can have highly variable read coverage. Comparing single assemblers, Newbler 2.5 performed best on our trial data set, but other assemblers were closely comparable. Combining differently optimal assemblies

Self-assembled nanogaps via seed-mediated growth of end-to-end linked gold nanorods

DEFF Research Database (Denmark)

Jain, Titoo; Westerlund, Axel Rune Fredrik; Johnson, Erik

2009-01-01

Gold nanorods (AuNRs) are of interest for a wide range of applications, ranging from imaging to molecular electronics, and they have been studied extensively for the past decade. An important issue in AuNR applications is the ability to self-assemble the rods in predictable structures...... on the nanoscale. We here present a new way to end-to-end link AuNRs with a single or few linker molecules. Whereas methods reported in the literature so far rely on modification of the AuNRs after the synthesis, we here dimerize gold nanoparticle seeds with a water-soluble dithiol-functionalized polyethylene...... that a large fraction of the rods are flexible around the hinging molecule in solution, as expected for a molecularly linked nanogap. By using excess of gold nanoparticles relative to the linking dithiol molecule, this method can provide a high probability that a single molecule is connecting the two rods...

Transfer of fuel assemblies

International Nuclear Information System (INIS)

Vuckovich, M.; Burkett, J. P.; Sallustio, J.

1984-01-01

Fuel assemblies of a nuclear reactor are transferred during fueling or refueling or the like by a crane. The work-engaging fixture of the crane picks up an assembly, removes it from this slot, transfers it to the deposit site and deposits it in its slot at the deposit site. The control for the crane includes a strain gauge connected to the crane line which raises and lowers the load. The strain gauge senses the load on the crane. The signal from the strain gauge is compared with setpoints; a high-level setpoint, a low-level setpoint and a slack-line setpoint. If the strain gauge signal exceeds the high-level setpoint, the line drive is disabled. This event may occur during raising of a fuel assembly which encounters resistance. The high-level setpoint may be overridden under proper precautions. The line drive is also disabled if the strain gauge signal is less than the low-level setpoint. This event occurs when a fuel assembly being deposited contacts the bottom of its slot or an obstruction in, or at the entry to the slot. To preclude lateral movement and possible damage to a fuel assembly suspended from the crane line, the traverse drive of the crane is disabled once the strain-gauge exceets the lov-level setpoint. The traverse drive can only be enabled after the strain-gauge signal is less than the slack-line set-point. This occurs when the lines has been set in slack-line setting. When the line is tensioned after slack-li ne setting, the traverse drive remains enabled only if the line has been disconnected from the fuel assembly

Improvements in nuclear fuel assembly sleeves

International Nuclear Information System (INIS)

Eaton, C.W.; Seeley, T.A.; Ince, G.; Speakman, W.T.

1986-01-01

The graphite sleeve of a nuclear fuel assembly or reflector element for a stringer mounts a number of grids via mounting assemblies installed in grooves formed in the interior wall surface of the sleeve. The bore of the sleeve is of reduced cross-section between two successive grooves such that the internal diameter of the sleeve is substantially the same as the inner diameter of the radially innermost extremity of the mounting assemblies whereby the coolant pressure loss at each transition between the reduced diameter bore section and the mounting assemblies is reduced. Each mounting assembly may be of radially contractable split ring construction to permit its placement in the groove and may carry burnable poison material. (author)

Improvements in nuclear fuel assembly sleeves

Energy Technology Data Exchange (ETDEWEB)

Eaton, C.W.; Seeley, T.A.; Ince, G.; Speakman, W.T.

1986-02-26

The graphite sleeve of a nuclear fuel assembly or reflector element for a stringer mounts a number of grids via mounting assemblies installed in grooves formed in the interior wall surface of the sleeve. The bore of the sleeve is of reduced cross-section between two successive grooves such that the internal diameter of the sleeve is substantially the same as the inner diameter of the radially innermost extremity of the mounting assemblies whereby the coolant pressure loss at each transition between the reduced diameter bore section and the mounting assemblies is reduced. Each mounting assembly may be of radially contractable split ring construction to permit its placement in the groove and may carry burnable poison material.

Physical principles for DNA tile self-assembly.

Science.gov (United States)

Evans, Constantine G; Winfree, Erik

2017-06-19

DNA tiles provide a promising technique for assembling structures with nanoscale resolution through self-assembly by basic interactions rather than top-down assembly of individual structures. Tile systems can be programmed to grow based on logical rules, allowing for a small number of tile types to assemble large, complex assemblies that can retain nanoscale resolution. Such algorithmic systems can even assemble different structures using the same tiles, based on inputs that seed the growth. While programming and theoretical analysis of tile self-assembly often makes use of abstract logical models of growth, experimentally implemented systems are governed by nanoscale physical processes that can lead to very different behavior, more accurately modeled by taking into account the thermodynamics and kinetics of tile attachment and detachment in solution. This review discusses the relationships between more abstract and more physically realistic tile assembly models. A central concern is how consideration of model differences enables the design of tile systems that robustly exhibit the desired abstract behavior in realistic physical models and in experimental implementations. Conversely, we identify situations where self-assembly in abstract models can not be well-approximated by physically realistic models, putting constraints on physical relevance of the abstract models. To facilitate the discussion, we introduce a unified model of tile self-assembly that clarifies the relationships between several well-studied models in the literature. Throughout, we highlight open questions regarding the physical principles for DNA tile self-assembly.

System for assembling nuclear fuel elements

International Nuclear Information System (INIS)

1980-01-01

An automatic system is described for assembling nuclear fuel elements, in particular those employing mixed oxide fuels. The system includes a sealing mechanism which allows movement during the assembling of the fuel element along the assembly stations without excessive release of contaminants. (U.K.)

Assembly study for JT-60SA tokamak

Energy Technology Data Exchange (ETDEWEB)

Shibanuma, K., E-mail: shibanuma.kiyoshi@jaea.go.jp [Japan Atomic Energy Agency, Naka, Ibaraki-ken 311-0193 (Japan); Arai, T.; Hasegawa, K.; Hoshi, R.; Kamiya, K.; Kawashima, H.; Kubo, H.; Masaki, K.; Saeki, H.; Sakurai, S.; Sakata, S.; Sakasai, A.; Sawai, H.; Shibama, Y.K.; Tsuchiya, K.; Tsukao, N.; Yagyu, J.; Yoshida, K.; Kamada, Y. [Japan Atomic Energy Agency, Naka, Ibaraki-ken 311-0193 (Japan); Mizumaki, S. [Toshiba Corporation, Minato-ku, Tokyo 105-8001 (Japan); and others

2013-10-15

The assembly scenarios and assembly tools of the major tokamak components for JT-60SA are studied in the following. (1) The assembly frame (with a dedicated 30-tonne crane), which is located around the JT-60SA tokamak, is adopted for effective assembly works in the torus hall and the temporary support of the components during assembly. (2) Metrology for precise positioning of the components is also studied by defining the metrology points on the components. (3) The sector segmentation for weld joints and positioning of the vacuum vessel (VV), the assembly scenario and tools for VV thermal shield (TS), the connection of the outer intercoil structure (OIS) and the installation of the final toroidal field coil (TFC) are studied, as typical examples of the assembly scenarios and tools for JT-60SA.

Gag induces the coalescence of clustered lipid rafts and tetraspanin-enriched microdomains at HIV-1 assembly sites on the plasma membrane.

Science.gov (United States)

Hogue, Ian B; Grover, Jonathan R; Soheilian, Ferri; Nagashima, Kunio; Ono, Akira

2011-10-01

The HIV-1 structural protein Gag associates with two types of plasma membrane microdomains, lipid rafts and tetraspanin-enriched microdomains (TEMs), both of which have been proposed to be platforms for HIV-1 assembly. However, a variety of studies have demonstrated that lipid rafts and TEMs are distinct microdomains in the absence of HIV-1 infection. To measure the impact of Gag on microdomain behaviors, we took advantage of two assays: an antibody-mediated copatching assay and a Förster resonance energy transfer (FRET) assay that measures the clustering of microdomain markers in live cells without antibody-mediated patching. We found that lipid rafts and TEMs copatched and clustered to a greater extent in the presence of membrane-bound Gag in both assays, suggesting that Gag induces the coalescence of lipid rafts and TEMs. Substitutions in membrane binding motifs of Gag revealed that, while Gag membrane binding is necessary to induce coalescence of lipid rafts and TEMs, either acylation of Gag or binding of phosphatidylinositol-(4,5)-bisphosphate is sufficient. Finally, a Gag derivative that is defective in inducing membrane curvature appeared less able to induce lipid raft and TEM coalescence. A higher-resolution analysis of assembly sites by correlative fluorescence and scanning electron microscopy showed that coalescence of clustered lipid rafts and TEMs occurs predominantly at completed cell surface virus-like particles, whereas a transmembrane raft marker protein appeared to associate with punctate Gag fluorescence even in the absence of cell surface particles. Together, these results suggest that different membrane microdomain components are recruited in a stepwise manner during assembly.

Assemble-to-order systems: a review

NARCIS (Netherlands)

Atan, Z.; Ahmadi, T.; Stegehuis, C.; de Kok, A.G.; Adan, I.J.B.F.

2017-01-01

In this paper, we review the recent literature on assemble-to-order systems. Each assemble-to-order system consists of multiple components and end-products. The components are assembled into the end-products after information on customer demand is received but the decision on what components to

A conceptual design and structural stabilities of in-pit assembly tools for the completion of final sector assembly at tokamak hall

International Nuclear Information System (INIS)

Nam, K.O.; Park, H.K.; Kim, D.J.; Ahn, H.J.; Kim, K.K.; Im, K.; Shaw, R.

2010-01-01

The final assembly of main components of the International Thermonuclear Experimental Reactor (ITER) tokamak, Vacuum Vessel (VV) and Toroidal Field Coils (TFCs), is achieved by the sequential assembly of the nine sub-assembled 40 o sectors in tokamak pit. Each sub-assembled 40 o sector is composed of one VV 40 o sector, two TFCs, and in-between Vacuum Vessel Thermal Shield (VVTS) segments. Sub-assembly is carried out in the assembly building and then the sub-assembled sectors are transferred into tokamak pit, in sequence, to complete sector assembly. The role of in-pit assembly tool is to support and align the sub-assembled sectors in tokamak pit. It also plays the role of reference datum during assembly until the completion of main components assembly. Korea Domestic Agency (KO DA) has developed the conceptual design of most ITER purpose-built assembly tools under the collaboration with the ITER Organization. Among the conceptual designs carried out, this paper describes the function, the structure, the selected material and the design results of the in-pit assembly tools comprising central column, radial beams and their supports, TF inner supports and in-pit working floor. The results of structural analysis using ANSYS for the various loading cases are given as well. The resultant stresses and deflections turned out to fall within the allowable ranges.

Quantifying quality in DNA self-assembly

Science.gov (United States)

Wagenbauer, Klaus F.; Wachauf, Christian H.; Dietz, Hendrik

2014-01-01

Molecular self-assembly with DNA is an attractive route for building nanoscale devices. The development of sophisticated and precise objects with this technique requires detailed experimental feedback on the structure and composition of assembled objects. Here we report a sensitive assay for the quality of assembly. The method relies on measuring the content of unpaired DNA bases in self-assembled DNA objects using a fluorescent de-Bruijn probe for three-base ‘codons’, which enables a comparison with the designed content of unpaired DNA. We use the assay to measure the quality of assembly of several multilayer DNA origami objects and illustrate the use of the assay for the rational refinement of assembly protocols. Our data suggests that large and complex objects like multilayer DNA origami can be made with high strand integration quality up to 99%. Beyond DNA nanotechnology, we speculate that the ability to discriminate unpaired from paired nucleic acids in the same macromolecule may also be useful for analysing cellular nucleic acids. PMID:24751596

The MARVEL assembly for neutron multiplication

Energy Technology Data Exchange (ETDEWEB)

David L. Chichester; Mathew T. Kinlaw

2013-10-01

A new multiplying test assembly is under development at Idaho National Laboratory to support research, validation, evaluation, and learning. The item is comprised of three stacked, highly-enriched uranium (HEU) cylinders, each 11.4 cm in diameter and having a combined height of up to 11.7 cm. The combined mass of all three cylinders is 20.3 kg of HEU. Calculations for the bare configuration of the assembly indicate a multiplication level of >3.5 (keff=0.72). Reflected configurations of the assembly, using either polyethylene or tungsten, are possible and have the capability of raising the assembly's multiplication level to greater than 10. This paper describes simulations performed to assess the assembly's multiplication level under different conditions and describes the resources available at INL to support the use of these materials. We also describe some preliminary calculations and test activities using the assembly to study neutron multiplication.

The MARVEL assembly for neutron multiplication.

Science.gov (United States)

Chichester, David L; Kinlaw, Mathew T

2013-10-01

A new multiplying test assembly is under development at Idaho National Laboratory to support research, validation, evaluation, and learning. The item is comprised of three stacked, highly-enriched uranium (HEU) cylinders, each 11.4 cm in diameter and having a combined height of up to 11.7 cm. The combined mass of all three cylinders is 20.3 kg of HEU. Calculations for the bare configuration of the assembly indicate a multiplication level of >3.5 (k(eff)=0.72). Reflected configurations of the assembly, using either polyethylene or tungsten, are possible and have the capability of raising the assembly's multiplication level to greater than 10. This paper describes simulations performed to assess the assembly's multiplication level under different conditions and describes the resources available at INL to support the use of these materials. We also describe some preliminary calculations and test activities using the assembly to study neutron multiplication. Copyright © 2013 Elsevier Ltd. All rights reserved.

Characterization of Semiconductor Nanocrystal Assemblies as Components of Optoelectronic Devices

Science.gov (United States)

Malfavon-Ochoa, Mario

This dissertation presents new insight into the ability of small molecule passivated NCs to achieve intimate approach distances, despite being well passivated, while developing guiding principles in the area of ligand mediated microstructure control and the resulting macroscopic optical and electronic properties that close packing of high quality NCs enables. NC ligand coverage will be characterized quantitatively through thermogravimetric analysis (TGA), and qualitatively by photoluminescence and electroluminescence, in the case of functional devices; illustrating the importance of practitioner dependent control of ligand coverage through variations in the dispersion precipitation purification procedure. A unique examination of the relative contribution of energy and charge transfer in NC LEDs will demonstrate the ability to achieve charge transfer, at a level competitive with energy transfer, to well passivated NCs at various wt% loading in a polymer matrix. The observation of potential dependent recombination zones within an active layer further suggest novel, NC surface passivation mediated control of blend microstructure during solution processing towards the development of a bi-continuous network. Next, NC self-assembly and resulting microstructure dependent optical and electronic properties will be examined through electroluminescence and high-resolution transmission electron microscopy (TEM) micrographs of functional NC/polymer bulk heterojunction LEDs. The joint characterization of NC optical properties, and self-assembly microstructure provide a deeper understanding of the significant and inseparable effects of minimal changes in NC surface passivation on structure and function, and emphasize the potential to rely on strongly passivating ligands to control physical properties and processing parameters concurrently towards higher efficiency devices via low cost processing. Finally, micro-contact printing of blazed transmission gratings, using stable

Directed self-assembly of large scaffold-free multi-cellular honeycomb structures

International Nuclear Information System (INIS)

Tejavibulya, Nalin; Youssef, Jacquelyn; Bao, Brian; Ferruccio, Toni-Marie; Morgan, Jeffrey R

2011-01-01

A significant challenge to the field of biofabrication is the rapid construction of large three-dimensional (3D) living tissues and organs. Multi-cellular spheroids have been used as building blocks. In this paper, we create large multi-cellular honeycomb building blocks using directed self-assembly, whereby cell-to-cell adhesion, in the context of the shape and obstacles of a micro-mold, drives the formation of a 3D structure. Computer-aided design, rapid prototyping and replica molding were used to fabricate honeycomb-shaped micro-molds. Nonadhesive hydrogels cast from these micro-molds were equilibrated in the cell culture medium and seeded with two types of mammalian cells. The cells settled into the honeycomb recess were unable to attach to the nonadhesive hydrogel and so cell-to-cell adhesion drove the self-assembly of a large multi-cellular honeycomb within 24 h. Distinct morphological changes occurred to the honeycomb and its cells indicating the presence of significant cell-mediated tension. Unlike the spheroid, whose size is constrained by a critical diffusion distance needed to maintain cell viability, the overall size of the honeycomb is not limited. The rapid production of the honeycomb building unit, with its multiple rings of high-density cells and open lumen spaces, offers interesting new possibilities for biofabrication strategies.

School Assemblies: The Lost Art.

Science.gov (United States)

Beach, Daniel R.

1979-01-01

Guidelines and suggestions are offered for successful school assemblies. The school assembly should be a positive event; an occasion for developing unity, group loyalty, and desirable audience habits. (Author/MLF)

Analysis of PWR assembly bow

International Nuclear Information System (INIS)

Fetterman, Robert J.; Franceschini, Fausto

2008-01-01

Excessive out of core assembly bow has been observed during refueling outages of certain PWRs. Assembly bow can take on a rather complex S-shape, and in other cases C-shape bow is prevalent. Concerns have been raised regarding the impact of the observed assembly bow on the in-core power distribution and the safety analyses supporting the plant operations. In response to these concerns, Westinghouse has developed a comprehensive analysis process for determining the effects of assembly bow on core power distributions and plant operating margins. This methodology has been applied to a particular reactor as part of an overall safety reanalysis completed in support of plant modifications. This paper provides a brief description of the methods used and a summary of the pertinent results. (authors)

Analysis of PWR assembly bow

Energy Technology Data Exchange (ETDEWEB)

Fetterman, Robert J.; Franceschini, Fausto [Westinghouse Electric Company LLC, Pittsburgh, PA (United States)

2008-07-01

Excessive out of core assembly bow has been observed during refueling outages of certain PWRs. Assembly bow can take on a rather complex S-shape, and in other cases C-shape bow is prevalent. Concerns have been raised regarding the impact of the observed assembly bow on the in-core power distribution and the safety analyses supporting the plant operations. In response to these concerns, Westinghouse has developed a comprehensive analysis process for determining the effects of assembly bow on core power distributions and plant operating margins. This methodology has been applied to a particular reactor as part of an overall safety reanalysis completed in support of plant modifications. This paper provides a brief description of the methods used and a summary of the pertinent results. (authors)

Impact analysis of spent fuel jacket assemblies

International Nuclear Information System (INIS)

Aramayo, G.A.

1994-01-01

As part of the analyses performed in support of the reracking of the High Flux Isotope Reactor pool, it became necessary to prove the structural integrity of the spent fuel jacket assemblies subjected to gravity drop that result from postulated accidents associated with the handling of these assemblies while submerged in the pool. The spent fuel jacket assemblies are an integral part of the reracking project, and serve to house fuel assemblies. The structure integrity of the jacket assemblies from loads that result from impact from a height of 10 feet onto specified targets has been performed analytically using the computer program LS-DYNA3D. Nine attitudes of the assembly at the time of impact have been considered. Results of the analyses show that there is no failure of the assemblies as a result of the impact scenarios considered

One-step self-assembled nanomicelles for improving the oral bioavailability of nimodipine

Directory of Open Access Journals (Sweden)

Luo JW

2016-03-01

Full Text Available Jing-Wen Luo, Zhi-Rong Zhang, Tao Gong, Yao Fu Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, People’s Republic of China Abstract: Our study aimed to develop a self-assembled nanomicelle for oral administration of nimodipine (NIM with poor water solubility. Using Solutol® HS15, the NIM-loaded self-assembled nanomicelles displayed a near-spherical morphology with a narrow size distribution of 12.57±0.21 nm (polydispersity index =0.071±0.011. Compared with Nimotop® (NIM tablets, the intestinal absorption of NIM from NIM nanomicelle in rats was improved by 3.13- and 2.25-fold in duodenum and jejunum at 1 hour after oral administration. The cellular transport of NIM nanomicelle in Caco-2 cell monolayers was significantly enhanced compared to that of Nimotop®. Regarding the transport pathways, clathrin, lipid raft/caveolae, and macropinocytosis mediated the cell uptake of NIM nanomicelles, while P-glycoprotein and endoplasmic reticulum/Golgi complex (ER/Golgi pathways were involved in exocytosis. Pharmacokinetic studies in our research laboratory have showed that the area under the plasma concentration–time curve (AUC0–∞ of NIM nanomicelles was 3.72-fold that of Nimotop® via oral administration in rats. Moreover, the NIM concentration in the brain from NIM nanomicelles was dramatically improved. Therefore, Solutol® HS15-based self-assembled nanomicelles represent a promising delivery system to enhance the oral bioavailability of NIM. Keywords: nanomicelles, stability, nimodipine, oral bioavailability, transport mechanism 

Deacetylation of H4-K16Ac and heterochromatin assembly in senescence

Directory of Open Access Journals (Sweden)

Contrepois Kévin

2012-08-01

Full Text Available Abstract Background Cellular senescence is a stress response of mammalian cells leading to a durable arrest of cell proliferation that has been implicated in tumor suppression, wound healing, and aging. The proliferative arrest is mediated by transcriptional repression of genes essential for cell division by the retinoblastoma protein family. This repression is accompanied by varying degrees of heterochromatin assembly, but little is known regarding the molecular mechanisms involved. Results We found that both deacetylation of H4-K16Ac and expression of HMGA1/2 can contribute to DNA compaction during senescence. SIRT2, an NAD-dependent class III histone deacetylase, contributes to H4-K16Ac deacetylation and DNA compaction in human fibroblast cell lines that assemble striking senescence-associated heterochromatin foci (SAHFs. Decreased H4-K16Ac was observed in both replicative and oncogene-induced senescence of these cells. In contrast, this mechanism was inoperative in a fibroblast cell line that did not assemble extensive heterochromatin during senescence. Treatment of senescent cells with trichostatin A, a class I/II histone deacetylase inhibitor, also induced rapid and reversible decondensation of SAHFs. Inhibition of DNA compaction did not significantly affect the stability of the senescent state. Conclusions Variable DNA compaction observed during senescence is explained in part by cell-type specific regulation of H4 deacetylation and HMGA1/2 expression. Deacetylation of H4-K16Ac during senescence may explain reported decreases in this mark during mammalian aging and in cancer cells.

Genome Sequence Databases (Overview): Sequencing and Assembly

Energy Technology Data Exchange (ETDEWEB)

Lapidus, Alla L.

2009-01-01

From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

Human Contamination in Public Genome Assemblies.

Science.gov (United States)

Kryukov, Kirill; Imanishi, Tadashi

2016-01-01

Contamination in genome assembly can lead to wrong or confusing results when using such genome as reference in sequence comparison. Although bacterial contamination is well known, the problem of human-originated contamination received little attention. In this study we surveyed 45,735 available genome assemblies for evidence of human contamination. We used lineage specificity to distinguish between contamination and conservation. We found that 154 genome assemblies contain fragments that with high confidence originate as contamination from human DNA. Majority of contaminating human sequences were present in the reference human genome assembly for over a decade. We recommend that existing contaminated genomes should be revised to remove contaminated sequence, and that new assemblies should be thoroughly checked for presence of human DNA before submitting them to public databases.

Manipulating cluster size of polyanion-stabilized Fe{sub 3}O{sub 4} magnetic nanoparticle clusters via electrostatic-mediated assembly for tunable magnetophoresis behavior

Energy Technology Data Exchange (ETDEWEB)

Yeap, Swee Pin, E-mail: sweepin0727@hotmail.com; Ahmad, Abdul Latif; Ooi, Boon Seng; Lim, JitKang, E-mail: chjitkangl@usm.my [Universiti Sains Malaysia, School of Chemical Engineering (Malaysia)

2015-10-15

We report in this article an approach for manipulating the size of magnetic nanoparticle clusters (MNCs) via electrostatic-mediated assembly technique using an electrolyte as a clustering agent. The clusters were surface-tethered with poly(sodium 4-styrenesulfonate) (PSS) through electrostatic compensation to enhance their colloidal stability. Dynamic light scattering was employed to trace the evolution of cluster size. Simultaneously, electrophoretic mobility and Fourier transform infrared spectroscopy analyses were conducted to investigate the possible schemes involved in both cluster formation and PSS grafting. Results showed that the average hydrodynamic cluster size of the PSS/MNCs and their corresponding size distributions were successfully shifted by means of manipulating the suspension pH, the ionic nature of the electrolyte, and the electrolyte concentration. More specifically, the electrokinetic behavior of the particles upon interaction with the electrolyte plays a profound role in the formation of the PSS/MNCs. Nonetheless, the solubility of the polymer in electrolyte solution and the purification of the particles from residual ions should not be omitted in determining the effectiveness of this clustering approach. The PSS adlayer makes the resultant entities highly water-dispersible and provides electrosteric stabilization to shield the PSS/MNCs from aggregation. In this study, the experimental observations were analyzed and discussed on the basis of existing fundamental colloidal theories. The strategy of cluster size manipulation proposed here is simple and convenient to implement. Furthermore, manipulating the size of the MNCs also facilitates the tuning of magnetophoresis kinetics on exposure to low magnetic field gradient, which makes this nano-entity useful for engineering applications, specifically in separation processes.

A divide-and-conquer algorithm for large-scale de novo transcriptome assembly through combining small assemblies from existing algorithms.

Science.gov (United States)

Sze, Sing-Hoi; Parrott, Jonathan J; Tarone, Aaron M

2017-12-06

While the continued development of high-throughput sequencing has facilitated studies of entire transcriptomes in non-model organisms, the incorporation of an increasing amount of RNA-Seq libraries has made de novo transcriptome assembly difficult. Although algorithms that can assemble a large amount of RNA-Seq data are available, they are generally very memory-intensive and can only be used to construct small assemblies. We develop a divide-and-conquer strategy that allows these algorithms to be utilized, by subdividing a large RNA-Seq data set into small libraries. Each individual library is assembled independently by an existing algorithm, and a merging algorithm is developed to combine these assemblies by picking a subset of high quality transcripts to form a large transcriptome. When compared to existing algorithms that return a single assembly directly, this strategy achieves comparable or increased accuracy as memory-efficient algorithms that can be used to process a large amount of RNA-Seq data, and comparable or decreased accuracy as memory-intensive algorithms that can only be used to construct small assemblies. Our divide-and-conquer strategy allows memory-intensive de novo transcriptome assembly algorithms to be utilized to construct large assemblies.

Fuel assembly and reactor core

International Nuclear Information System (INIS)

Aoyama, Motoo; Koyama, Jun-ichi; Uchikawa, Sadao; Bessho, Yasunori; Nakajima, Akiyoshi; Maruyama, Hiromi; Ozawa, Michihiro; Nakamura, Mitsuya.

1990-01-01

The present invention concerns fuel assemblies charged in a BWR type reactor and the reactor core. The fuel assembly comprises fuel rods containing burnable poisons and fuel rods not containing burnable poisons. Both of the highest and the lowest gadolinia concentrations of the fuel rods containing gadolinia as burnable poisons are present in the lower region of the fuel assembly. This can increase the spectral shift effect without increasing the maximum linear power density. (I.N.)

Cleaning device for fuel assemblies

International Nuclear Information System (INIS)

Kita, Kaoru.

1986-01-01

Purpose: To completely remove obstacles deposited to the lower sides of supporting lattices for fuel assemblies by utilizing water within a pit before reloading of the fuel assemblies. Constitution: A cylindrical can, to which a fuel assembly is inserted through the upper end opening thereof, is vertically disposed within water of a pit and the bottom of the can is communicated with a pump by way of a suction pipe and a filter device disposed out of the pit. While on the other hand, a fuel assembly is suspended downwardly by a crane and inserted to the inside of the can through the upper end of the opening thereof and supported therein followed by starting the pump. As a result, water in the pit is circulated through the inside of the can, suction pipe, filtering device, pump, discharge pipe and to the inside of the pit thereby enabling to completely eliminate obstacles deposited to the lower surface, etc. of supporting lattices for the fuel assembly supported within the can. (Takahashi, M.)

Inverse design of multicomponent assemblies

Science.gov (United States)

Piñeros, William D.; Lindquist, Beth A.; Jadrich, Ryan B.; Truskett, Thomas M.

2018-03-01

Inverse design can be a useful strategy for discovering interactions that drive particles to spontaneously self-assemble into a desired structure. Here, we extend an inverse design methodology—relative entropy optimization—to determine isotropic interactions that promote assembly of targeted multicomponent phases, and we apply this extension to design interactions for a variety of binary crystals ranging from compact triangular and square architectures to highly open structures with dodecagonal and octadecagonal motifs. We compare the resulting optimized (self- and cross) interactions for the binary assemblies to those obtained from optimization of analogous single-component systems. This comparison reveals that self-interactions act as a "primer" to position particles at approximately correct coordination shell distances, while cross interactions act as the "binder" that refines and locks the system into the desired configuration. For simpler binary targets, it is possible to successfully design self-assembling systems while restricting one of these interaction types to be a hard-core-like potential. However, optimization of both self- and cross interaction types appears necessary to design for assembly of more complex or open structures.

DEHP exposure impairs mouse oocyte cyst breakdown and primordial follicle assembly through estrogen receptor-dependent and independent mechanisms

Energy Technology Data Exchange (ETDEWEB)

Mu, Xinyi [Laboratory of Reproductive Biology, Chongqing Medical University, Chongqing 400016 (China); Department of Histology and Embryology, College of Basic Medicine, Chongqing Medical University, Chongqing 400016 (China); Liao, Xinggui; Chen, Xuemei; Li, Yanli; Wang, Meirong; Shen, Cha; Zhang, Xue; Wang, Yingxiong; Liu, Xueqing [Laboratory of Reproductive Biology, Chongqing Medical University, Chongqing 400016 (China); He, Junlin, E-mail: hejunlin_11@aliyun.com [Laboratory of Reproductive Biology, Chongqing Medical University, Chongqing 400016 (China)

2015-11-15

Highlights: • DEHP inhibits primordial folliculogenesis in vivo and in vitro. • Estrogen receptors participate in the effect of DEHP on early ovarian development. • DEHP exposure impairs the expression of Notch2 signaling components. • DEHP exposure disrupts the proliferation of pregranulosa precursor cells. - Abstract: Estrogen plays an essential role in the development of mammalian oocytes, and recent studies suggest that it also regulates primordial follicle assembly in the neonatal ovaries. During the last decade, potential exposure of humans and animals to estrogen-like endocrine disrupting chemicals has become a growing concern. In the present study, we focused on the effect of diethylhexyl phthalate (DEHP), a widespread plasticizer with estrogen-like activity, on germ-cell cyst breakdown and primordial follicle assembly in the early ovarian development of mouse. Neonatal mice injected with DEHP displayed impaired cyst breakdown. Using ovary organ cultures, we revealed that impairment was mediated through estrogen receptors (ERs), as ICI 182,780, an efficient antagonist of ER, reversed this DEHP-mediated effect. DEHP exposure reduced the expression of ERβ, progesterone receptor (PR), and Notch2 signaling components. Finally, DEHP reduced proliferation of pregranulosa precursor cells during the process of primordial folliculogenesis. Together, our results indicate that DEHP influences oocyte cyst breakdown and primordial follicle formation through several mechanisms. Therefore, exposure to estrogen-like chemicals during fetal or neonatal development may adversely influence early ovarian development.

Structural analysis of ITER sub-assembly tools

International Nuclear Information System (INIS)

Nam, K.O.; Park, H.K.; Kim, D.J.; Ahn, H.J.; Lee, J.H.; Kim, K.K.; Im, K.; Shaw, R.

2011-01-01

The ITER Tokamak assembly tools are purpose-built assembly tools to complete the ITER Tokamak machine which includes the cryostat and the components contained therein. The sector sub-assembly tools descried in this paper are main assembly tools to assemble vacuum vessel, thermal shield and toroidal filed coils into a complete 40 o sector. The 40 o sector sub-assembly tools are composed of sector sub-assembly tool, including radial beam, vacuum vessel supports and mid-plane brace tools. These tools shall have sufficient strength to transport and handle heavy weight of the ITER Tokamak machine reached several hundred tons. Therefore these tools should be designed and analyzed to confirm both the strength and structural stability even in the case of conservative assumptions. To verify structural stabilities of the sector sub-assembly tools in terms of strength and deflection, ANSYS code was used for linear static analysis. The results of the analysis show that these tools are designed with sufficient strength and stiffness. The conceptual designs of these tools are briefly described in this paper also.

Shock buffer for nuclear control assembly

International Nuclear Information System (INIS)

Bevilacqua, F.

1977-01-01

A shock buffer is provided for the gradual deceleration of a rapidly descending control element assembly in a nuclear reactor. The interactive buffer components are associated respectively with the movable control element assembly and part of the upper guide structure independent of and spaced from the fuel assemblies of the reactor

Community Assembly Processes of the Microbial Rare Biosphere.

Science.gov (United States)

Jia, Xiu; Dini-Andreote, Francisco; Falcão Salles, Joana

2018-03-14

Our planet teems with microorganisms that often present a skewed abundance distribution in a local community, with relatively few dominant species coexisting alongside a high number of rare species. Recent studies have demonstrated that these rare taxa serve as limitless reservoirs of genetic diversity, and perform disproportionate types of functions despite their low abundances. However, relatively little is known about the mechanisms controlling rarity and the processes promoting the development of the rare biosphere. Here, we propose the use of multivariate cut-offs to estimate rare species and phylogenetic null models applied to predefined rare taxa to disentangle the relative influences of ecoevolutionary processes mediating the assembly of the rare biosphere. Importantly, the identification of the factors controlling rare species assemblages is critical for understanding the types of rarity, how the rare biosphere is established, and how rare microorganisms fluctuate over spatiotemporal scales, thus enabling prospective predictions of ecosystem responses. Copyright © 2018 Elsevier Ltd. All rights reserved.

Bola-amphiphile self-assembly

DEFF Research Database (Denmark)

Svaneborg, Carsten

2012-01-01

Bola-amphiphiles are rod-like molecules where both ends of the molecule likes contact with water, while the central part of the molecule dislikes contact with water. What do such molecules do when they are dissolved in water? They self-assemble into micelles. This is a Dissipartive particle...... dynamics simulation of this self-assembly behaviour....

Assembling RNA Nanoparticles.

Science.gov (United States)

Xiao, Shou-Jun

2017-01-01

RNA nanoparticles are designed and self-assembled according to noncanonical interactions of naturally conserved RNA motifs and/or canonical Watson-Crick base-pairing interactions, which have potential applications in gene therapy and nanomedicine. These artificially engineered nanoparticles are mainly synthesized from in vitro transcribed RNAs, purified by denaturing and native polyacrylamide gel electrophoresis (PAGE), and characterized with native PAGE, AFM, and TEM technologies. The protocols of in vitro transcription, denaturing and native PAGE, and RNA nanoparticle self-assembly are described in detail.

A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: Assembly of the duck (Anas platyrhynchos transcriptome.

Directory of Open Access Journals (Sweden)

Joanna eMoreton

2014-06-01

Full Text Available For vertebrate organisms where a reference genome is not available, de novo transcriptome assembly enables a cost effective insight into the identification of tissue specific or differentially expressed genes and variation of the coding part of the genome. However, since there are a number of different tools and parameters that can be used to reconstruct transcripts, it is difficult to determine an optimal method. Here we suggest a pipeline based on (1 assessing the performance of three different assembly tools (2 using both single and multiple k-mer approaches (3 examining the influence of the number of reads used in the assembly (4 merging assemblies from different tools. We use an example dataset from the vertebrate Anas platyrhynchos domestica (Pekin duck. We find that taking a subset of data enables a robust assembly to be produced by multiple methods without the need for very high memory capacity. The use of reads mapped back to transcripts (RMBT and CEGMA (Core Eukaryotic Genes Mapping Approach provides useful metrics to determine the completeness of assembly obtained. For this dataset the use of multiple k-mers in the assembly generated a more complete assembly as measured by greater number of RMBT and CEGMA score. Merged single k-mer assemblies are generally smaller but consist of longer transcripts, suggesting an assembly consisting of fewer fragmented transcripts. We suggest that the use of a subset of reads during assembly allows the relatively rapid investigation of assembly characteristics and can guide the user to the most appropriate transcriptome for particular downstream use. Transcriptomes generated by the compared assembly methods and the final merged assembly are freely available for download at http://dx.doi.org/10.6084/m9.figshare.1032613.

Design of the ITER tokamak assembly tools

Energy Technology Data Exchange (ETDEWEB)

Park, Hyunki [National Fusion Research Institute, 52 Eoeun-Dong, Yuseong-Gu, Daejon 305-333 (Korea, Republic of)], E-mail: hkpark@nfri.re.kr; Lee, Jaehyuk; Kim, Taehyung [SFA Engineering Corp., 42-7 Palyong-dong, Changwon-si, Gyeongsangnam-do 641-847 (Korea, Republic of); Song, Yunju [National Fusion Research Institute, 52 Eoeun-Dong, Yuseong-Gu, Daejon 305-333 (Korea, Republic of); Im, Kihak [ITER Organization, CEA Cadarasche, 13108 Saint Paul-lez-Durance (France); Kim, Byungchul; Lee, Hyeongon; Jung, Ki-Jung [National Fusion Research Institute, 52 Eoeun-Dong, Yuseong-Gu, Daejon 305-333 (Korea, Republic of)

2008-12-15

ITER tokamak assembly is mainly composed of lower cryostat activities, sector sub-assembly, sector assembly, in-vessel activities and ex-vessel activities. The main tools for sector sub-assembly procedures consists of upending tool, sector lifting tool, vacuum vessel support and bracing tool and sector sub-assembly tool. Conceptual design of assembly tools for sector sub-assembly procedures is described herein. The basic structure for upending tool has been developed under the assumption that upending is performed with crane which will be installed in Tokamak building. Sector lifting tool is designed to adjust the position of a sector to minimize the difference between the center of the tokamak building crane and the center of gravity of the sector. Sector sub-assembly tool is composed of special frame for the fine adjustment of position control with 6 degrees of freedom. The design of VV support and bracing tool for four kinds of VV 40 deg. sectors has been developed. Also, structural analysis for upending tool, sector sub-assembly tool has been studied using ANSYS for the situation of an applied load with the same dead weight multiplied by 3/4. The results of structural analyses for these tools were below the allowable values.

Fuel assembly for a nuclear reactor

International Nuclear Information System (INIS)

Gjertsen, R.K.

1982-01-01

A fuel assembly in a nuclear reactor comprises a locking mechanism that is capable of locking the fuel assembly to the core plate of a nuclear reactor to prevent inadvertent movement of the fuel assembly. The locking mechanism comprises a ratchet mechanism 108 that allows the fuel assembly to be easily locked to the core plate but prevents unlocking except when the ratchet is disengaged. The ratchet mechanism is coupled to the locking mechanism by a rotatable guide tube for a control rod or water displacer rod. (author)

Design configuration of GCFR core assemblies

International Nuclear Information System (INIS)

LaBar, M.P.; Lee, G.E.; Meyer, R.J.

1980-05-01

The current design configurations of the core assemblies for the gas-cooled fast reactor (GCFR) demonstration plant reactor core conceptual design are described. Primary emphasis is placed upon the design innovations that have been incorporated in the design of the core assemblies since the establishment of the initial design of an upflow GCFR core. A major feature of the design configurations is that they are prototypical of core assemblies for use in commercial plants; a larger number of the same assemblies would be used in a commercial plant

Mediation Analysis with Multiple Mediators

OpenAIRE

VanderWeele, T.J.; Vansteelandt, S.

2014-01-01

Recent advances in the causal inference literature on mediation have extended traditional approaches to direct and indirect effects to settings that allow for interactions and non-linearities. In this paper, these approaches from causal inference are further extended to settings in which multiple mediators may be of interest. Two analytic approaches, one based on regression and one based on weighting are proposed to estimate the effect mediated through multiple mediators and the effects throu...

Deterministic nanoparticle assemblies: from substrate to solution

International Nuclear Information System (INIS)

Barcelo, Steven J; Gibson, Gary A; Yamakawa, Mineo; Li, Zhiyong; Kim, Ansoon; Norris, Kate J

2014-01-01

The deterministic assembly of metallic nanoparticles is an exciting field with many potential benefits. Many promising techniques have been developed, but challenges remain, particularly for the assembly of larger nanoparticles which often have more interesting plasmonic properties. Here we present a scalable process combining the strengths of top down and bottom up fabrication to generate deterministic 2D assemblies of metallic nanoparticles and demonstrate their stable transfer to solution. Scanning electron and high-resolution transmission electron microscopy studies of these assemblies suggested the formation of nanobridges between touching nanoparticles that hold them together so as to maintain the integrity of the assembly throughout the transfer process. The application of these nanoparticle assemblies as solution-based surface-enhanced Raman scattering (SERS) materials is demonstrated by trapping analyte molecules in the nanoparticle gaps during assembly, yielding uniformly high enhancement factors at all stages of the fabrication process. (paper)

SAGE: String-overlap Assembly of GEnomes.

Science.gov (United States)

Ilie, Lucian; Haider, Bahlul; Molnar, Michael; Solis-Oba, Roberto

2014-09-15

De novo genome assembly of next-generation sequencing data is one of the most important current problems in bioinformatics, essential in many biological applications. In spite of significant amount of work in this area, better solutions are still very much needed. We present a new program, SAGE, for de novo genome assembly. As opposed to most assemblers, which are de Bruijn graph based, SAGE uses the string-overlap graph. SAGE builds upon great existing work on string-overlap graph and maximum likelihood assembly, bringing an important number of new ideas, such as the efficient computation of the transitive reduction of the string overlap graph, the use of (generalized) edge multiplicity statistics for more accurate estimation of read copy counts, and the improved use of mate pairs and min-cost flow for supporting edge merging. The assemblies produced by SAGE for several short and medium-size genomes compared favourably with those of existing leading assemblers. SAGE benefits from innovations in almost every aspect of the assembly process: error correction of input reads, string-overlap graph construction, read copy counts estimation, overlap graph analysis and reduction, contig extraction, and scaffolding. We hope that these new ideas will help advance the current state-of-the-art in an essential area of research in genomics.

Research on Outfitting Virtual Assembly based on Ergonomics

Directory of Open Access Journals (Sweden)

Jiang Zuhua

2018-01-01

Full Text Available To improve the present situation where the assembly work of ship outfitting depends on manual experiential operation, the thesis, taking outfitting assembly operation as the research object and optimal assembly path as the target, puts forward the simulation method and procedure of outfitting virtual assembly considering operational posture, operational load, reachability and visibility and other ergonomic factors, taking pipe assembly operation of ship section as the application example. The results show that the method can obtain better assembly operation path, avoid interference of workers’ operation process and improve the efficiency of assembly operation.

Ordinary General Assembly

CERN Multimedia

Association du personnel

2010-01-01

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

Fuel assembly

International Nuclear Information System (INIS)

Ueda, Sei; Ando, Ryohei; Mitsutake, Toru.

1995-01-01

The present invention concerns a fuel assembly suitable to a BWR-type reactor and improved especially with the nuclear characteristic, heat performance, hydraulic performance, dismantling or assembling performance and economical property. A part of poison rods are formed as a large-diameter/multi-region poison rods having a larger diameter than a fuel rod. A large number of fuel rods are disposed surrounding a large diameter water rod and a group of the large-diameter/multi-region poison rods in adjacent with the water rod. The large-diameter water rod has a burnable poison at the tube wall portion. At least a portion of the large-diameter poison rods has a coolant circulation portion allowing coolants to circulate therethrough. Since the large-diameter poison rods are disposed at a position of high neutron fluxes, a large neutron multiplication factor suppression effect can be provided, thereby enabling to reduce the number of burnable poison rods relative to fuels. As a result, power peaking in the fuel assembly is moderated and a greater amount of plutonium can be loaded. In addition the flow of cooling water which tends to gather around the large diameter water rod can be controlled to improve cooling performance of fuels. (N.H.)

Self-assembled biomimetic nanoreactors I: Polymeric template

Science.gov (United States)

McTaggart, Matt; Malardier-Jugroot, Cecile; Jugroot, Manish

2015-09-01

The variety of nanoarchitectures made feasible by the self-assembly of alternating copolymers opens new avenues for biomimicry. Indeed, self-assembled structures allow the development of nanoreactors which combine the efficiency of high surface area metal active centres to the effect of confinement due to the very small cavities generated by the self-assembly process. A novel self-assembly of high molecular weight alternating copolymers is characterized in the present study. The self-assembly is shown to organize into nanosheets, providing a 2 nm hydrophobic cavity with a 1D confinement.

Self-Controlling Rig for Jaw Crusher Assembly

OpenAIRE

Saurabh Jadhav; Anup Pawar

2017-01-01

The aim of the work is to develop a method for easy assembly of the bearing in the housing by standardized way. The assembly of bearing should take place on the atomized set up. Based on this method a assembly setup was constructed which enables to assembly of the shaft with bearing of different models of jaw crusher. First tests were done with manual alignment and it shows that with proper alignment shaft assembly is very easy operation and also safe. Results of those tests show that the dev...

Novel Chiral Bis-Phosphoramides as Organocatalysts for Tetrachlorosilane-Mediated Reactions

Directory of Open Access Journals (Sweden)

Sergio Rossi

2017-12-01

Full Text Available The formation of novel chiral bidentate phosphoroamides structures able to promote Lewis base-catalyzed Lewis acid-mediated reactions was investigated. Two different classes of phosphoroamides were synthetized: the first class presents a phthalic acid/primary diamine moiety, designed with the aim to perform a self-assembly recognition process through hydrogen bonds; the second one is characterized by the presence of two phosphoroamides as side arms connected to a central pyridine unit, able to chelate SiCl4 in a 2:1 adduct. These species were tested as organocatalysts in the stereoselective allylation of benzaldehyde and a few other aromatic aldehydes with allyl tributyltin in the presence of SiCl4 with good results. NMR studies confirm that only pyridine-based phosphoroamides effectively coordinate tetrachlorosilane and may lead to the generation of a self-assembled entity that would act as a promoter of the reaction. Although further work is necessary to clarify and confirm the formation of the hypothesized adduct, the study lays the foundation for the design and the synthesis of chiral supramolecular organocatalysts.

Dual personality of Mad1: regulation of nuclear import by a spindle assembly checkpoint protein.

Science.gov (United States)

Cairo, Lucas V; Ptak, Christopher; Wozniak, Richard W

2013-01-01

Nuclear transport is a dynamic process that can be modulated in response to changes in cellular physiology. We recently reported that the transport activity of yeast nuclear pore complexes (NPCs) is altered in response to kinetochore-microtubule (KT-MT) interaction defects. Specifically, KT detachment from MTs activates a signaling pathway that prevents the nuclear import of cargos by the nuclear transport factor Kap121p. This loss of Kap121p-mediated import is thought to influence the nuclear environment, including the phosphorylation state of nuclear proteins. A key regulator of this process is the spindle assembly checkpoint protein Mad1p. In response to unattached KTs, Mad1p dynamically cycles between NPCs and KTs. This cycling appears to induce NPC molecular rearrangements that prevent the nuclear import of Kap121p-cargo complexes. Here, we discuss the underlying mechanisms and the physiological relevance of Mad1p cycling and the inhibition of Kap121p-mediated nuclear import, focusing on outstanding questions within the pathway.

Gigadalton-scale shape-programmable DNA assemblies

Science.gov (United States)

Wagenbauer, Klaus F.; Sigl, Christian; Dietz, Hendrik

2017-12-01

Natural biomolecular assemblies such as molecular motors, enzymes, viruses and subcellular structures often form by self-limiting hierarchical oligomerization of multiple subunits. Large structures can also assemble efficiently from a few components by combining hierarchical assembly and symmetry, a strategy exemplified by viral capsids. De novo protein design and RNA and DNA nanotechnology aim to mimic these capabilities, but the bottom-up construction of artificial structures with the dimensions and complexity of viruses and other subcellular components remains challenging. Here we show that natural assembly principles can be combined with the methods of DNA origami to produce gigadalton-scale structures with controlled sizes. DNA sequence information is used to encode the shapes of individual DNA origami building blocks, and the geometry and details of the interactions between these building blocks then control their copy numbers, positions and orientations within higher-order assemblies. We illustrate this strategy by creating planar rings of up to 350 nanometres in diameter and with atomic masses of up to 330 megadaltons, micrometre-long, thick tubes commensurate in size to some bacilli, and three-dimensional polyhedral assemblies with sizes of up to 1.2 gigadaltons and 450 nanometres in diameter. We achieve efficient assembly, with yields of up to 90 per cent, by using building blocks with validated structure and sufficient rigidity, and an accurate design with interaction motifs that ensure that hierarchical assembly is self-limiting and able to proceed in equilibrium to allow for error correction. We expect that our method, which enables the self-assembly of structures with sizes approaching that of viruses and cellular organelles, can readily be used to create a range of other complex structures with well defined sizes, by exploiting the modularity and high degree of addressability of the DNA origami building blocks used.

Three-dimensional assemblies of graphene prepared by a novel chemical reduction-induced self-assembly method

KAUST Repository

Zhang, Lianbin

2012-01-01

In this study, three-dimensional (3D) graphene assemblies are prepared from graphene oxide (GO) by a facile in situ reduction-assembly method, using a novel, low-cost, and environment-friendly reducing medium which is a combination of oxalic acid (OA) and sodium iodide (NaI). It is demonstrated that the combination of a reducing acid, OA, and NaI is indispensable for effective reduction of GO in the current study and this unique combination (1) allows for tunable control over the volume of the thus-prepared graphene assemblies and (2) enables 3D graphene assemblies to be prepared from the GO suspension with a wide range of concentrations (0.1 to 4.5 mg mL-1). To the best of our knowledge, the GO concentration of 0.1 mg mL-1 is the lowest GO concentration ever reported for preparation of 3D graphene assemblies. The thus-prepared 3D graphene assemblies exhibit low density, highly porous structures, and electrically conducting properties. As a proof of concept, we show that by infiltrating a responsive polymer of polydimethylsiloxane (PDMS) into the as-resulted 3D conducting network of graphene, a conducting composite is obtained, which can be used as a sensing device for differentiating organic solvents with different polarity. © 2012 The Royal Society of Chemistry.

Spontaneous Assembly of Exopolymers from Phytoplankton

Directory of Open Access Journals (Sweden)

Yong-Xue Ding

2009-01-01

Full Text Available Phytoplankton exopolymeric substances (EPS contribute significantly to the dissolved organic car bon (DOC pool in the ocean, playing crucial roles in the surface ocean car bon cycle. Recent studies have demonstrated that ~10% of marine DOC can self-assemble as microgels through electro static Ca bonds providing hotspots of enriched microbial substrate. How ever, the question whether EPS can self-assemble and the formation mechanisms for EPS microgels have not been examined. Here were port that EPS from three representative phytoplankton species, Synechococcus, Emiliania huxleyi, and Skeletonema costatum can spontaneously self assemble in artificial sea water (ASW, forming microscopic gels of ~ 3 - 4 __m in diameter. Different from the marine DOC polymers assembly, these EPS samples can self-assemble in Ca2+-free ASW. Further experiments from fluorescence enhancement and chemical composition analysis confirmed the existence of fair amounts of hydrophobic domains in these EPS samples. These results suggest that hydrophobic interactions play a key role in the assembly of EPS from these three species of marine phytoplankton.

Gag Induces the Coalescence of Clustered Lipid Rafts and Tetraspanin-Enriched Microdomains at HIV-1 Assembly Sites on the Plasma Membrane ▿

Science.gov (United States)

Hogue, Ian B.; Grover, Jonathan R.; Soheilian, Ferri; Nagashima, Kunio; Ono, Akira

2011-01-01

The HIV-1 structural protein Gag associates with two types of plasma membrane microdomains, lipid rafts and tetraspanin-enriched microdomains (TEMs), both of which have been proposed to be platforms for HIV-1 assembly. However, a variety of studies have demonstrated that lipid rafts and TEMs are distinct microdomains in the absence of HIV-1 infection. To measure the impact of Gag on microdomain behaviors, we took advantage of two assays: an antibody-mediated copatching assay and a Förster resonance energy transfer (FRET) assay that measures the clustering of microdomain markers in live cells without antibody-mediated patching. We found that lipid rafts and TEMs copatched and clustered to a greater extent in the presence of membrane-bound Gag in both assays, suggesting that Gag induces the coalescence of lipid rafts and TEMs. Substitutions in membrane binding motifs of Gag revealed that, while Gag membrane binding is necessary to induce coalescence of lipid rafts and TEMs, either acylation of Gag or binding of phosphatidylinositol-(4,5)-bisphosphate is sufficient. Finally, a Gag derivative that is defective in inducing membrane curvature appeared less able to induce lipid raft and TEM coalescence. A higher-resolution analysis of assembly sites by correlative fluorescence and scanning electron microscopy showed that coalescence of clustered lipid rafts and TEMs occurs predominately at completed cell surface virus-like particles, whereas a transmembrane raft marker protein appeared to associate with punctate Gag fluorescence even in the absence of cell surface particles. Together, these results suggest that different membrane microdomain components are recruited in a stepwise manner during assembly. PMID:21813604

The Effect of Intermolecular Halogen Bond on 19F DNP Enhancement in 1, 4-Diiodotetrafluorobenzene/4-OH-TEMPO Supramolecular Assembly

Directory of Open Access Journals (Sweden)

GAO Shan

2017-12-01

Full Text Available Halogen bond, as hydrogen bond, is a non-covalent bond. Dynamic nuclear polarization (DNP technique has been used previously to study hydrogen bonds-mediated intermolecular interactions. However, no study has been carried out so far to study the halogen bond-mediated intermolecular interactions with DNP. In this work, 19F DNP polarization efficiency of the halogen bonds existing in supramolecular assembling by 4-OH-TEMPO and 1,4-diiodotetrafluorobenzene (DITFB was studied on a home-made DNP system. The formation of intermolecular halogen bonds appeared to increase 19F DNP polarization efficiency, suggesting that the spin-spin interactions among electrons were weakened by the halogen bonds, resulting in an increased T2e and a larger saturation factor.

Structure and assembly of the essential RNA ring component of a viral DNA packaging motor.

Science.gov (United States)

Ding, Fang; Lu, Changrui; Zhao, Wei; Rajashankar, Kanagalaghatta R; Anderson, Dwight L; Jardine, Paul J; Grimes, Shelley; Ke, Ailong

2011-05-03

Prohead RNA (pRNA) is an essential component in the assembly and operation of the powerful bacteriophage 29 DNA packaging motor. The pRNA forms a multimeric ring via intermolecular base-pairing interactions between protomers that serves to guide the assembly of the ring ATPase that drives DNA packaging. Here we report the quaternary structure of this rare multimeric RNA at 3.5 Å resolution, crystallized as tetrameric rings. Strong quaternary interactions and the inherent flexibility helped rationalize how free pRNA is able to adopt multiple oligomerization states in solution. These characteristics also allowed excellent fitting of the crystallographic pRNA protomers into previous prohead/pRNA cryo-EM reconstructions, supporting the presence of a pentameric, but not hexameric, pRNA ring in the context of the DNA packaging motor. The pentameric pRNA ring anchors itself directly to the phage prohead by interacting specifically with the fivefold symmetric capsid structures that surround the head-tail connector portal. From these contacts, five RNA superhelices project from the pRNA ring, where they serve as scaffolds for binding and assembly of the ring ATPase, and possibly mediate communication between motor components. Construction of structure-based designer pRNAs with little sequence similarity to the wild-type pRNA were shown to fully support the packaging of 29 DNA.

Stable assembly of HIV-1 export complexes occurs cotranscriptionally

DEFF Research Database (Denmark)

Nawroth, Isabel; Mueller, Florian; Basyuk, Eugenia

2014-01-01

The HIV-1 Rev protein mediates export of unspliced and singly spliced viral transcripts by binding to the Rev response element (RRE) and recruiting the cellular export factor CRM1. Here, we investigated the recruitment of Rev to the transcription sites of HIV-1 reporters that splice either post......- or cotranscriptionally. In both cases, we observed that Rev localized to the transcription sites of the reporters and recruited CRM1. Rev and CRM1 remained at the reporter transcription sites when cells were treated with the splicing inhibitor Spliceostatin A (SSA), showing that the proteins associate with RNA prior...... to or during early spliceosome assembly. Fluorescence recovery after photobleaching (FRAP) revealed that Rev and CRM1 have similar kinetics as the HIV-1 RNA, indicating that Rev, CRM1, and RRE-containing RNAs are released from the site of transcription in one single export complex. These results suggest...

DNA-Directed Assembly of Capture Tools for Constitutional Studies of Large Protein Complexes.

Science.gov (United States)

Meyer, Rebecca; Faesen, Alex; Vogel, Katrin; Jeganathan, Sadasivam; Musacchio, Andrea; Niemeyer, Christof M

2015-06-10

Large supramolecular protein complexes, such as the molecular machinery involved in gene regulation, cell signaling, or cell division, are key in all fundamental processes of life. Detailed elucidation of structure and dynamics of such complexes can be achieved by reverse-engineering parts of the complexes in order to probe their interactions with distinctive binding partners in vitro. The exploitation of DNA nanostructures to mimic partially assembled supramolecular protein complexes in which the presence and state of two or more proteins are decisive for binding of additional building blocks is reported here. To this end, four-way DNA Holliday junction motifs bearing a fluorescein and a biotin tag, for tracking and affinity capture, respectively, are site-specifically functionalized with centromeric protein (CENP) C and CENP-T. The latter serves as baits for binding of the so-called KMN component, thereby mimicking early stages of the assembly of kinetochores, structures that mediate and control the attachment of microtubules to chromosomes in the spindle apparatus. Results from pull-down experiments are consistent with the hypothesis that CENP-C and CENP-T may bind cooperatively to the KMN network. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Surface coating of siRNA-peptidomimetic nano-self-assemblies with anionic lipid bilayers: enhanced gene silencing and reduced adverse effects in vitro

Science.gov (United States)

Zeng, Xianghui; de Groot, Anne Marit; Sijts, Alice J. A. M.; Broere, Femke; Oude Blenke, Erik; Colombo, Stefano; van Eden, Willem; Franzyk, Henrik; Nielsen, Hanne Mørck; Foged, Camilla

2015-11-01

Cationic vectors have demonstrated the potential to facilitate intracellular delivery of therapeutic oligonucleotides. However, enhanced transfection efficiency is usually associated with adverse effects, which also proves to be a challenge for vectors based on cationic peptides. In this study a series of proteolytically stable palmitoylated α-peptide/β-peptoid peptidomimetics with a systematically varied number of repeating lysine and homoarginine residues was shown to self-assemble with small interfering RNA (siRNA). The resulting well-defined nanocomplexes were coated with anionic lipids giving rise to net anionic liposomes. These complexes and the corresponding liposomes were optimized towards efficient gene silencing and low adverse effects. The optimal anionic liposomes mediated a high silencing effect, which was comparable to that of the control (cationic Lipofectamine 2000), and did not display any noticeable cytotoxicity and immunogenicity in vitro. In contrast, the corresponding nanocomplexes mediated a reduced silencing effect with a more narrow safety window. The surface coating with anionic lipid bilayers led to partial decomplexation of the siRNA-peptidomimetic nanocomplex core of the liposomes, which facilitated siRNA release. Additionally, the optimal anionic liposomes showed efficient intracellular uptake and endosomal escape. Therefore, these findings suggest that a more efficacious and safe formulation can be achieved by surface coating of the siRNA-peptidomimetic nano-self-assemblies with anionic lipid bilayers.Cationic vectors have demonstrated the potential to facilitate intracellular delivery of therapeutic oligonucleotides. However, enhanced transfection efficiency is usually associated with adverse effects, which also proves to be a challenge for vectors based on cationic peptides. In this study a series of proteolytically stable palmitoylated α-peptide/β-peptoid peptidomimetics with a systematically varied number of repeating lysine

Subcritical assemblies, use and their feasibility assessment

International Nuclear Information System (INIS)

Haroon, M.R.

1982-03-01

In developing countries, subcritical assemblies can be a useful tool for training and research in the field of nuclear technology with minimum cost. The historical development of subcritical assemblies and the reactor physics experiments which can be carried out using this facility are outlined. The different types of subcritical assemblies have been described and material requirements for each assembly have been pointed out. (author)

Virtual Reality and Haptics for Product Assembly

Directory of Open Access Journals (Sweden)

Maria Teresa Restivo

2012-01-01

Full Text Available Haptics can significantly enhance the user's sense of immersion and interactivity. An industrial application of virtual reality and haptics for product assembly is described in this paper, which provides a new and low-cost approach for product assembly design, assembly task planning and assembly operation training. A demonstration of the system with haptics device interaction was available at the session of exp.at'11.

Electrode assembly for a lithium ion battery, process for the production of such electrode assembly, and lithium ion battery comprising such electrode assemblies

NARCIS (Netherlands)

Mulder, F.M.; Wagemaker, M.

2013-01-01

The invention provides an electrode assembly for a lithium ion battery, the electrode assembly comprising a lithium storage electrode layer on a current collector, wherein the lithium storage electrode layer is a porous layer having a porosity in the range of -35 %, with pores having pore widths in

Effect of assembled time on the corrosion behaviors of SAMs film on the AM60B alloy and its assembled mechanism

Energy Technology Data Exchange (ETDEWEB)

Liu, Xianbin, E-mail: xbliu@imr.ac.cn; Shan, Dayong; Song, Yingwei; Han, En-hou

2015-01-15

The influence of assembled time on the corrosion behaviors of SAMs film on the AM60B alloy and its assembled mechanism have been investigated by electrochemical measurements, scanning electron microscopy (SEM) observation and X-ray photoelectron spectroscopy (XPS) analysis. The self-assembled experiment on the AM60B magnesium alloy indicates that the corrosion susceptibility decreases with increasing assembled time until 24 h on cast AM60B alloy and then increases with increase of the assembled time proved by EIS measurement and potentiodynamic curves. The self-assembled experiments on pure magnesium and various heat treated cast AM60B magnesium alloy illuminate that the dissolved aluminum in magnesium solid solution is the key factor for assembled efficiency and is hard to self-assemble on the pure magnesium without aluminum. The corrosion resistance of self-assembled film on AM60B magnesium alloy is monotonically increasing with the dissolved aluminum. The results of XPS analysis reveal the assembled mechanism on AM60B and corroborate the function of Al element. - Highlights: • It is hard to self-assemble on the pure magnesium. • 24 h assembled film has the low corrosion susceptibility by EIS and polarization. • The corrosion susceptibility of SAMs film lie on the Al atom state in AM60B. • The corrosion susceptibility of SAMs film is decreasing with the dissolved Al.

Effect of assembled time on the corrosion behaviors of SAMs film on the AM60B alloy and its assembled mechanism

International Nuclear Information System (INIS)

Liu, Xianbin; Shan, Dayong; Song, Yingwei; Han, En-hou

2015-01-01

The influence of assembled time on the corrosion behaviors of SAMs film on the AM60B alloy and its assembled mechanism have been investigated by electrochemical measurements, scanning electron microscopy (SEM) observation and X-ray photoelectron spectroscopy (XPS) analysis. The self-assembled experiment on the AM60B magnesium alloy indicates that the corrosion susceptibility decreases with increasing assembled time until 24 h on cast AM60B alloy and then increases with increase of the assembled time proved by EIS measurement and potentiodynamic curves. The self-assembled experiments on pure magnesium and various heat treated cast AM60B magnesium alloy illuminate that the dissolved aluminum in magnesium solid solution is the key factor for assembled efficiency and is hard to self-assemble on the pure magnesium without aluminum. The corrosion resistance of self-assembled film on AM60B magnesium alloy is monotonically increasing with the dissolved aluminum. The results of XPS analysis reveal the assembled mechanism on AM60B and corroborate the function of Al element. - Highlights: • It is hard to self-assemble on the pure magnesium. • 24 h assembled film has the low corrosion susceptibility by EIS and polarization. • The corrosion susceptibility of SAMs film lie on the Al atom state in AM60B. • The corrosion susceptibility of SAMs film is decreasing with the dissolved Al

Neuregulin 3 Mediates Cortical Plate Invasion and Laminar Allocation of GABAergic Interneurons

Directory of Open Access Journals (Sweden)

Giorgia Bartolini

2017-01-01

Full Text Available Neural circuits in the cerebral cortex consist of excitatory pyramidal cells and inhibitory interneurons. These two main classes of cortical neurons follow largely different genetic programs, yet they assemble into highly specialized circuits during development following a very precise choreography. Previous studies have shown that signals produced by pyramidal cells influence the migration of cortical interneurons, but the molecular nature of these factors has remained elusive. Here, we identified Neuregulin 3 (Nrg3 as a chemoattractive factor expressed by developing pyramidal cells that guides the allocation of cortical interneurons in the developing cortical plate. Gain- and loss-of-function approaches reveal that Nrg3 modulates the migration of interneurons into the cortical plate in a process that is dependent on the tyrosine kinase receptor ErbB4. Perturbation of Nrg3 signaling in conditional mutants leads to abnormal lamination of cortical interneurons. Nrg3 is therefore a critical mediator in the assembly of cortical inhibitory circuits.

TracWorks - global fuel assembly data management

International Nuclear Information System (INIS)

Cooney, B.F.

1997-01-01

The TracWorks Data Management System is a workstation-based software product that provides a utility with a single, broadly available, regularly updated source for virtually every data item available for a fuel assembly or core component. TracWorks is designed to collect, maintain and provide information about assembly and component locations and movements during the refuelling process and operation, assembly burnup and isotopic inventory (both in-core and out-of-core), pin burnup and isotopics for pins that have been removed from their original assemblies, assembly and component inspection results (including video) and manufacturing data provided by the fabrication plant. (UK)

Network spandrels reflect ecological assembly.

Science.gov (United States)

Maynard, Daniel S; Serván, Carlos A; Allesina, Stefano

2018-03-01

Ecological networks that exhibit stable dynamics should theoretically persist longer than those that fluctuate wildly. Thus, network structures which are over-represented in natural systems are often hypothesised to be either a cause or consequence of ecological stability. Rarely considered, however, is that these network structures can also be by-products of the processes that determine how new species attempt to join the community. Using a simulation approach in tandem with key results from random matrix theory, we illustrate how historical assembly mechanisms alter the structure of ecological networks. We demonstrate that different community assembly scenarios can lead to the emergence of structures that are often interpreted as evidence of 'selection for stability'. However, by controlling for the underlying selection pressures, we show that these assembly artefacts-or spandrels-are completely unrelated to stability or selection, and are instead by-products of how new species are introduced into the system. We propose that these network-assembly spandrels are critically overlooked aspects of network theory and stability analysis, and we illustrate how a failure to adequately account for historical assembly can lead to incorrect inference about the causes and consequences of ecological stability. © 2018 John Wiley & Sons Ltd/CNRS.

Probabilistic reasoning for assembly-based 3D modeling

KAUST Repository

Chaudhuri, Siddhartha; Kalogerakis, Evangelos; Guibas, Leonidas; Koltun, Vladlen

2011-01-01

Assembly-based modeling is a promising approach to broadening the accessibility of 3D modeling. In assembly-based modeling, new models are assembled from shape components extracted from a database. A key challenge in assembly-based modeling

NEDDylation promotes stress granule assembly.

Science.gov (United States)

Jayabalan, Aravinth Kumar; Sanchez, Anthony; Park, Ra Young; Yoon, Sang Pil; Kang, Gum-Yong; Baek, Je-Hyun; Anderson, Paul; Kee, Younghoon; Ohn, Takbum

2016-07-06

Stress granules (SGs) harbour translationally stalled messenger ribonucleoproteins and play important roles in regulating gene expression and cell fate. Here we show that neddylation promotes SG assembly in response to arsenite-induced oxidative stress. Inhibition or depletion of key components of the neddylation machinery concomitantly inhibits stress-induced polysome disassembly and SG assembly. Affinity purification and subsequent mass-spectrometric analysis of Nedd8-conjugated proteins from translationally stalled ribosomal fractions identified ribosomal proteins, translation factors and RNA-binding proteins (RBPs), including SRSF3, a previously known SG regulator. We show that SRSF3 is selectively neddylated at Lys85 in response to arsenite. A non-neddylatable SRSF3 (K85R) mutant do not prevent arsenite-induced polysome disassembly, but fails to support the SG assembly, suggesting that the neddylation pathway plays an important role in SG assembly.

Lateral loadings on snubber assemblies

International Nuclear Information System (INIS)

Raphael, L.S.

1981-01-01

This paper examines the installation of snubber assemblies in power plants with respect to transverse or lateral loads as well as axial loads. Evaluation of the effects of low level, lateral loads was performed by analytical means. At higher loadings, the snubber assembly could no longer be treated as a column; therefore, the effects of lateral loadings was determined by test. The test consisted of applying both lateral and axial loads simultaneously. Results of both the analysis and the test showed that the application of lateral loads had a considerable effect on the snubber assemblies

Directed Assembly of Gold Nanoparticles

DEFF Research Database (Denmark)

Westerlund, Axel Rune Fredrik; Bjørnholm, Thomas

2009-01-01

As a complement to common "top-down" lithography techniques, "bottom-up" assembly techniques are emerging as promising tools to build nanoscale structures in a predictable way. Gold nanoparticles that are stable and relatively easy to synthesize are important building blocks in many such structures...... due to their useful optical and electronic properties. Programmed assembly of gold nanoparticles in one, two, and three dimensions is therefore of large interest. This review focuses on the progress from the last three years in the field of directed gold nanoparticle and nanorod assembly using...

Surface plasmon resonance spectroscopic study of UV-addressable phenylalanine sensing based on a self-assembled spirooxazine derivative monolayer

International Nuclear Information System (INIS)

Suk, Shinae; Suh, Hee-Jung; Gun An, Won; Kim, Jae-Ho; Jin, Sung-Ho; Kim, Sung-Hoon; Gal, Yeong-Soon; Koh, Kwangnak

2004-01-01

Light-addressable compounds are very interesting due to the possibilities of their practical use such as optical switches and memories or variable transmission materials. For example, transportation of phenylalanine across liposomal bilayers mediated by a photoresponsive carrier like spirooxazine through electrostatic interaction between phenylalanine and spirooxazine derivative. Thus, the spirooxazine is expected to form a UV-addressable phenylalanine sensing interface. In this study, we prepared phenylalanine sensing interface of a spirooxazine derivative by self-assembly technique and evaluated interaction between a spirooxazine moiety and phenylalanine with a surface plasmon resonance (SPR). The refractive index change of monolayer caused by interaction between a spirooxazine derivative and phenylalanine led to the SPR angle shifts upon UV irradiation. The SPR angle shift increased with increasing the concentration of phenylalanine solution. These results indicated that the spirooxazine derivative self-assembled monolayer (SAM) has an application potential for UV-addressable phenylalanine sensing

The immitigable nature of assembly bias: the impact of halo definition on assembly bias

Science.gov (United States)

Villarreal, Antonio S.; Zentner, Andrew R.; Mao, Yao-Yuan; Purcell, Chris W.; van den Bosch, Frank C.; Diemer, Benedikt; Lange, Johannes U.; Wang, Kuan; Campbell, Duncan

2017-11-01

Dark matter halo clustering depends not only on halo mass, but also on other properties such as concentration and shape. This phenomenon is known broadly as assembly bias. We explore the dependence of assembly bias on halo definition, parametrized by spherical overdensity parameter, Δ. We summarize the strength of concentration-, shape-, and spin-dependent halo clustering as a function of halo mass and halo definition. Concentration-dependent clustering depends strongly on mass at all Δ. For conventional halo definitions (Δ ∼ 200 - 600 m), concentration-dependent clustering at low mass is driven by a population of haloes that is altered through interactions with neighbouring haloes. Concentration-dependent clustering can be greatly reduced through a mass-dependent halo definition with Δ ∼ 20 - 40 m for haloes with M200 m ≲ 1012 h-1M⊙. Smaller Δ implies larger radii and mitigates assembly bias at low mass by subsuming altered, so-called backsplash haloes into now larger host haloes. At higher masses (M200 m ≳ 1013 h-1M⊙) larger overdensities, Δ ≳ 600 m, are necessary. Shape- and spin-dependent clustering are significant for all halo definitions that we explore and exhibit a relatively weaker mass dependence. Generally, both the strength and the sense of assembly bias depend on halo definition, varying significantly even among common definitions. We identify no halo definition that mitigates all manifestations of assembly bias. A halo definition that mitigates assembly bias based on one halo property (e.g. concentration) must be mass dependent. The halo definitions that best mitigate concentration-dependent halo clustering do not coincide with the expected average splashback radii at fixed halo mass.

Self-assembled DNA Structures for Nanoconstruction

Science.gov (United States)

Yan, Hao; Yin, Peng; Park, Sung Ha; Li, Hanying; Feng, Liping; Guan, Xiaoju; Liu, Dage; Reif, John H.; LaBean, Thomas H.

2004-09-01

In recent years, a number of research groups have begun developing nanofabrication methods based on DNA self-assembly. Here we review our recent experimental progress to utilize novel DNA nanostructures for self-assembly as well as for templates in the fabrication of functional nano-patterned materials. We have prototyped a new DNA nanostructure known as a cross structure. This nanostructure has a 4-fold symmetry which promotes its self-assembly into tetragonal 2D lattices. We have utilized the tetragonal 2D lattices as templates for highly conductive metallic nanowires and periodic 2D protein nano-arrays. We have constructed and characterized a DNA nanotube, a new self-assembling superstructure composed of DNA tiles. We have also demonstrated an aperiodic DNA lattice composed of DNA tiles assembled around a long scaffold strand; the system translates information encoded in the scaffold strand into a specific and reprogrammable barcode pattern. We have achieved metallic nanoparticle linear arrays templated on self-assembled 1D DNA arrays. We have designed and demonstrated a 2-state DNA lattice, which displays expand/contract motion switched by DNA nanoactuators. We have also achieved an autonomous DNA motor executing unidirectional motion along a linear DNA track.

Improvements in nuclear fuel assembly cages

Energy Technology Data Exchange (ETDEWEB)

Eaton, C.W.; Seeley, T.A.; Ince, G.; Speakman, W.T.

1986-03-12

The fuel pin/guide tube supporting grids of an assembly cage for a multi pin fuel element or a reflector element for a stringer are mounted in the moderator sleeve by way of mounting assemblies engaged in grooves machined into the interior surface of the sleeve, each mounting assembly including a split ring which is assembled into its groove by being radially contracted, pushed along the sleeve into registry with the groove and allowed to radially expand. The split ring may carry burnable neutron absorber. The region of the sleeve between two adjacent grids may be of smaller internal diameter than the remainder of the sleeve.

Mediation analysis with time varying exposures and mediators.

Science.gov (United States)

VanderWeele, Tyler J; Tchetgen Tchetgen, Eric J

2017-06-01

In this paper we consider causal mediation analysis when exposures and mediators vary over time. We give non-parametric identification results, discuss parametric implementation, and also provide a weighting approach to direct and indirect effects based on combining the results of two marginal structural models. We also discuss how our results give rise to a causal interpretation of the effect estimates produced from longitudinal structural equation models. When there are time-varying confounders affected by prior exposure and mediator, natural direct and indirect effects are not identified. However, we define a randomized interventional analogue of natural direct and indirect effects that are identified in this setting. The formula that identifies these effects we refer to as the "mediational g-formula." When there is no mediation, the mediational g-formula reduces to Robins' regular g-formula for longitudinal data. When there are no time-varying confounders affected by prior exposure and mediator values, then the mediational g-formula reduces to a longitudinal version of Pearl's mediation formula. However, the mediational g-formula itself can accommodate both mediation and time-varying confounders and constitutes a general approach to mediation analysis with time-varying exposures and mediators.

Precision polymers and 3D DNA nanostructures: emergent assemblies from new parameter space.

Science.gov (United States)

Serpell, Christopher J; Edwardson, Thomas G W; Chidchob, Pongphak; Carneiro, Karina M M; Sleiman, Hanadi F

2014-11-05

Polymer self-assembly and DNA nanotechnology have both proved to be powerful nanoscale techniques. To date, most attempts to merge the fields have been limited to placing linear DNA segments within a polydisperse block copolymer. Here we show that, by using hydrophobic polymers of a precisely predetermined length conjugated to DNA strands, and addressable 3D DNA prisms, we are able to effect the formation of unprecedented monodisperse quantized superstructures. The structure and properties of larger micelles-of-prisms were probed in depth, revealing their ability to participate in controlled release of their constituent nanostructures, and template light-harvesting energy transfer cascades, mediated through both the addressability of DNA and the controlled aggregation of the polymers.

Peripheral pin alignment system for fuel assemblies

International Nuclear Information System (INIS)

Anthony, A.J.

1981-01-01

An alignment system is provided for nuclear fuel assemblies in a nuclear core. The core support structure of the nuclear reactor includes upwardly pointing alignment pins arranged in a square grid and engage peripheral depressions formed in the lateral periphery of the lower ends of each of the fuel assemblies of the core. In a preferred embodiment, the depressions are located at the corners of the fuel assemblies so that each depression includes one-quarter of a cylindrical void. Accordingly, each fuel assembly is positioned and aligned by one-quarter of four separate alignment pins which engage the fuel assemblies at their lower exterior corners. (author)

Ultrasensitive SERS detection of mercury based on the assembled gold nanochains.

Science.gov (United States)

Xu, Liguang; Yin, Honghong; Ma, Wei; Kuang, Hua; Wang, Libing; Xu, Chuanlai

2015-05-15

Mercuric ions (Hg(2+)) mediate the transformation of single-stranded DNA to form double helical DNA by T-Hg(2+)-T interaction between base pairs. With this strategy, DNA modified gold nanoparticles (Au NPs) were assembled into chains which were displayed remarkable surface-enhanced Raman scattering (SERS) signal. Under optimized conditions, the length of gold nanochains was directly proportional to the mercuric ions concentrations over 0.001-0.5 ng mL(-1) and the limit of detection (LOD) in drinking water was as low as 0.45 pg mL(-1). With ultrasensitivity and excellent selectivity, this feasible and simple method is potentially as a promising tool for monitoring of mercury ions in food safety and environmental applications. Copyright © 2014 Elsevier B.V. All rights reserved.

CAD Parts-Based Assembly Modeling by Probabilistic Reasoning

KAUST Repository

Zhang, Kai-Ke

2016-04-11

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

CAD Parts-Based Assembly Modeling by Probabilistic Reasoning

KAUST Repository

Zhang, Kai-Ke; Hu, Kai-Mo; Yin, Li-Cheng; Yan, Dongming; Wang, Bin

2016-01-01

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

Shaft seal assembly and method

Science.gov (United States)

Keba, John E. (Inventor)

2007-01-01

A pressure-actuated shaft seal assembly and associated method for controlling the flow of fluid adjacent a rotatable shaft are provided. The seal assembly includes one or more seal members that can be adjusted between open and closed positions, for example, according to the rotational speed of the shaft. For example, the seal member can be configured to be adjusted according to a radial pressure differential in a fluid that varies with the rotational speed of the shaft. In addition, in the closed position, each seal member can contact a rotatable member connected to the shaft to form a seal with the rotatable member and prevent fluid from flowing through the assembly. Thus, the seal can be closed at low speeds of operation and opened at high speeds of operation, thereby reducing the heat and wear in the seal assembly while maintaining a sufficient seal during all speeds of operation.

WHAMM links actin assembly via the Arp2/3 complex to autophagy.

Science.gov (United States)

Kast, David J; Dominguez, Roberto

2015-01-01

Macroautophagy (hereafter autophagy) is the process by which cytosolic material destined for degradation is enclosed inside a double-membrane cisterna known as the autophagosome and processed for secretion and/or recycling. This process requires a large collection of proteins that converge on certain sites of the ER membrane to generate the autophagosome membrane. Recently, it was shown that actin accumulates around autophagosome precursors and could play a role in this process, but the mechanism and role of actin polymerization in autophagy were unknown. Here, we discuss our recent finding that the nucleation-promoting factor (NPF) WHAMM recruits and activates the Arp2/3 complex for actin assembly at sites of autophagosome formation on the ER. Using high-resolution, live-cell imaging, we showed that WHAMM forms dynamic puncta on the ER that comigrate with several autophagy markers, and propels the spiral movement of these puncta by an Arp2/3 complex-dependent actin comet tail mechanism. In starved cells, WHAMM accumulates at the interface between neighboring autophagosomes, whose number and size increases with WHAMM expression. Conversely, knocking down WHAMM, inhibiting the Arp2/3 complex or interfering with actin polymerization reduces the size and number of autophagosomes. These findings establish a link between Arp2/3 complex-mediated actin assembly and autophagy.

Step-wise assembly, maturation and dynamic behavior of the human CENP-P/O/R/Q/U kinetochore sub-complex.

Directory of Open Access Journals (Sweden)

Anja Eskat

Full Text Available Kinetochores are multi-protein megadalton assemblies that are required for attachment of microtubules to centromeres and, in turn, the segregation of chromosomes in mitosis. Kinetochore assembly is a cell cycle regulated multi-step process. The initial step occurs during interphase and involves loading of the 15-subunit constitutive centromere associated complex (CCAN, which contains a 5-subunit (CENP-P/O/R/Q/U sub-complex. Here we show using a fluorescent three-hybrid (F3H assay and fluorescence resonance energy transfer (FRET in living mammalian cells that CENP-P/O/R/Q/U subunits exist in a tightly packed arrangement that involves multifold protein-protein interactions. This sub-complex is, however, not pre-assembled in the cytoplasm, but rather assembled on kinetochores through the step-wise recruitment of CENP-O/P heterodimers and the CENP-P, -O, -R, -Q and -U single protein units. SNAP-tag experiments and immuno-staining indicate that these loading events occur during S-phase in a manner similar to the nucleosome binding components of the CCAN, CENP-T/W/N. Furthermore, CENP-P/O/R/Q/U binding to the CCAN is largely mediated through interactions with the CENP-N binding protein CENP-L as well as CENP-K. Once assembled, CENP-P/O/R/Q/U exchanges slowly with the free nucleoplasmic pool indicating a low off-rate for individual CENP-P/O/R/Q/U subunits. Surprisingly, we then find that during late S-phase, following the kinetochore-binding step, both CENP-Q and -U but not -R undergo oligomerization. We propose that CENP-P/O/R/Q/U self-assembles on kinetochores with varying stoichiometry and undergoes a pre-mitotic maturation step that could be important for kinetochores switching into the correct conformation necessary for microtubule-attachment.

Three-dimensional assemblies of graphene prepared by a novel chemical reduction-induced self-assembly method

KAUST Repository

Zhang, Lianbin; Chen, Guoying; Hedhili, Mohamed N.; Zhang, Hongnan; Wang, Peng

2012-01-01

In this study, three-dimensional (3D) graphene assemblies are prepared from graphene oxide (GO) by a facile in situ reduction-assembly method, using a novel, low-cost, and environment-friendly reducing medium which is a combination of oxalic acid

Self-assembling peptide semiconductors

Science.gov (United States)

Tao, Kai; Makam, Pandeeswar; Aizen, Ruth; Gazit, Ehud

2017-01-01

Semiconductors are central to the modern electronics and optics industries. Conventional semiconductive materials bear inherent limitations, especially in emerging fields such as interfacing with biological systems and bottom-up fabrication. A promising candidate for bioinspired and durable nanoscale semiconductors is the family of self-assembled nanostructures comprising short peptides. The highly ordered and directional intermolecular π-π interactions and hydrogen-bonding network allow the formation of quantum confined structures within the peptide self-assemblies, thus decreasing the band gaps of the superstructures into semiconductor regions. As a result of the diverse architectures and ease of modification of peptide self-assemblies, their semiconductivity can be readily tuned, doped, and functionalized. Therefore, this family of electroactive supramolecular materials may bridge the gap between the inorganic semiconductor world and biological systems. PMID:29146781

Integrated magnetic transformer assembly

DEFF Research Database (Denmark)

2014-01-01

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

Molecular assembly of recombinant chicken type II collagen in the yeast Pichia pastoris.

Science.gov (United States)

Xi, Caixia; Liu, Nan; Liang, Fei; Zhao, Xiao; Long, Juan; Yuan, Fang; Yun, Song; Sun, Yuying; Xi, Yongzhi

2018-01-09

Effective treatment of rheumatoid arthritis can be mediated by native chicken type II collagen (nCCII), recombinant peptide containing nCCII tolerogenic epitopes (CTEs), or a therapeutic DNA vaccine encoding the full-length CCOL2A1 cDNA. As recombinant CCII (rCCII) might avoid potential pathogenic virus contamination during nCCII preparation or chromosomal integration and oncogene activation associated with DNA vaccines, here we evaluated the importance of propeptide and telopeptide domains on rCCII triple helix molecular assembly. We constructed pC- and pN-procollagen (without N- or Cpropeptides, respectively) as well as CTEs located in the triple helical domain lacking both propeptides and telopeptides, and expressed these in yeast Pichia pastoris host strain GS115 (his4, Mut + ) simultaneously with recombinant chicken prolyl-4-hydroxylase α and β subunits. Both pC- and pN-procollagen monomers accumulated inside P. pastoris cells, whereas CTE was assembled into homotrimers with stable conformation and secreted into the supernatants, suggesting that the large molecular weight pC-or pN-procollagens were retained within the endoplasmic reticulum whereas the smaller CTEs proceeded through the secretory pathway. Furthermore, resulting recombinant chicken type II collagen pCα1(II) can induced collagen-induced arthritis (CIA) rat model, which seems to be as effective as the current standard nCCII. Notably, protease digestion assays showed that rCCII could assemble in the absence of C- and N-propeptides or telopeptides. These findings provide new insights into the minimal structural requirements for rCCII expression and folding.

Crops: a green approach toward self-assembled soft materials.

Science.gov (United States)

Vemula, Praveen Kumar; John, George

2008-06-01

To date, a wide range of industrial materials such as solvents, fuels, synthetic fibers, and chemical products are being manufactured from petroleum resources. However, rapid depletion of fossil and petroleum resources is encouraging current and future chemists to orient their research toward designing safer chemicals, products, and processes from renewable feedstock with an increased awareness of environmental and industrial impact. Advances in genetics, biotechnology, process chemistry, and engineering are leading to a new manufacturing concept for converting renewable biomass to valuable fuels and products, generally known as the biorefinery concept. The swift integration of crop-based materials synthesis and biorefinery manufacturing technologies offers the potential for new advances in sustainable energy alternatives and biomaterials that will lead to a new manufacturing paradigm. This Account presents a novel and emerging concept of generating various forms of soft materials from crops (an alternate feedstock). In future research, developing biobased soft materials will be a fascinating yet demanding practice, which will have direct impact on industrial applications as an economically viable alternative. Here we discuss some remarkable examples of glycolipids generated from industrial byproducts such as cashew nut shell liquid, which upon self-assembly produced soft nanoarchitectures including lipid nanotubes, twisted/helical nanofibers, low-molecular-weight gels, and liquid crystals. Synthetic methods applied to a "chiral pool" of carbohydrates using the selectivity of enzyme catalysis yield amphiphilic products derived from biobased feedstock including amygdalin, trehalose, and vitamin C. This has been achieved with a lipase-mediated regioselective synthetic procedure to obtain such amphiphiles in quantitative yields. Amygdalin amphiphiles showed unique gelation behavior in a broad range of solvents such as nonpolar hexanes to polar aqueous solutions

Targeted assembly of short sequence reads.

Directory of Open Access Journals (Sweden)

René L Warren

Full Text Available As next-generation sequence (NGS production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole genome data sets in their entirety. Rather, NGS data sets can be mined for the presence of sequence variants of interest by localized assembly, which is a faster, easier, and more accurate approach. We present TASR, a streamlined assembler that interrogates very large NGS data sets for the presence of specific variants by only considering reads within the sequence space of input target sequences provided by the user. The NGS data set is searched for reads with an exact match to all possible short words within the target sequence, and these reads are then assembled stringently to generate a consensus of the target and flanking sequence. Typically, variants of a particular locus are provided as different target sequences, and the presence of the variant in the data set being interrogated is revealed by a successful assembly outcome. However, TASR can also be used to find unknown sequences that flank a given target. We demonstrate that TASR has utility in finding or confirming genomic mutations, polymorphisms, fusions and integration events. Targeted assembly is a powerful method for interrogating large data sets for the presence of sequence variants of interest. TASR is a fast, flexible and easy to use tool for targeted assembly.

Moisture Research - Optimizing Wall Assemblies

Energy Technology Data Exchange (ETDEWEB)

Arena, L.; Mantha, P.

2013-05-01

The Consortium for Advanced Residential Buildings (CARB) evaluated several different configurations of wall assemblies to determine the accuracy of moisture modeling and make recommendations to ensure durable, efficient assemblies. WUFI and THERM were used to model the hygrothermal and heat transfer characteristics of these walls.

Equilibrium polymerization models of re-entrant self-assembly

Science.gov (United States)

Dudowicz, Jacek; Douglas, Jack F.; Freed, Karl F.

2009-04-01

As is well known, liquid-liquid phase separation can occur either upon heating or cooling, corresponding to lower and upper critical solution phase boundaries, respectively. Likewise, self-assembly transitions from a monomeric state to an organized polymeric state can proceed either upon increasing or decreasing temperature, and the concentration dependent ordering temperature is correspondingly called the "floor" or "ceiling" temperature. Motivated by the fact that some phase separating systems exhibit closed loop phase boundaries with two critical points, the present paper analyzes self-assembly analogs of re-entrant phase separation, i.e., re-entrant self-assembly. In particular, re-entrant self-assembly transitions are demonstrated to arise in thermally activated equilibrium self-assembling systems, when thermal activation is more favorable than chain propagation, and in equilibrium self-assembly near an adsorbing boundary where strong competition exists between adsorption and self-assembly. Apparently, the competition between interactions or equilibria generally underlies re-entrant behavior in both liquid-liquid phase separation and self-assembly transitions.

Illustrating how mechanical assemblies work

KAUST Repository

Mitra, Niloy J.; Yang, Yongliang; Yan, Dongming; Li, Wilmot; Agrawala, Maneesh

2010-01-01

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

Fuel assembly in a reactor

International Nuclear Information System (INIS)

Saito, Shozo; Kawahara, Akira.

1975-01-01

Object: To provide a fuel assembly in a reactor which can effectively prevent damage of the clad tube caused by mutual interference between pellets and the clad tube. Structure: A clad tube for a fuel element, which is located in the outer peripheral portion, among the fuel elements constituting fuel assemblies arranged in assembled and lattice fashion within a channel box, is increased in thickness by reducing the inside diameter thereof to be smaller than that of fuel elements internally located, thereby preventing damage of the clad tube resulting from rapid rise in output produced when control rods are removed. (Kamimura, M.)

Illustrating how mechanical assemblies work

KAUST Repository

Mitra, Niloy J.

2010-07-26

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

Loop-mediated isothermal amplification (LAMP) shield for Arduino DNA detection.

Science.gov (United States)

Velders, Aldrik H; Schoen, Cor; Saggiomo, Vittorio

2018-02-01

Loop-mediated isothermal amplification (LAMP) of DNA is gaining relevance as a method to detect nucleic acids, as it is easier, faster, and more powerful than conventional Polymerase Chain Reaction. However, LAMP is still mostly used in laboratory settings, because of the lack of a cheap and easy, one-button device that can perform LAMP experiments. Here we show how to build and program an Arduino shield for a LAMP and detection of DNA. The here described Arduino Shield is cheap, easy to assemble, to program and use, it is battery operated and the detection of DNA is done by naked-eye so that it can be used in field.

Assembly considerations for large reflectors

Science.gov (United States)

Bush, H.

1988-01-01

The technologies developed at LaRC in the area of erectable instructures are discussed. The information is of direct value to the Large Deployable Reflector (LDR) because an option for the LDR backup structure is to assemble it in space. The efforts in this area, which include development of joints, underwater assembly simulation tests, flight assembly/disassembly tests, and fabrication of 5-meter trusses, led to the use of the LaRC concept as the baseline configuration for the Space Station Structure. The Space Station joint is linear in the load and displacement range of interest to Space Station; the ability to manually assemble and disassemble a 45-foot truss structure was demonstrated by astronauts in space as part of the ACCESS Shuttle Flight Experiment. The structure was built in 26 minutes 46 seconds, and involved a total of 500 manipulations of untethered hardware. Also, the correlation of the space experience with the neutral buoyancy simulation was very good. Sections of the proposed 5-meter bay Space Station truss have been built on the ground. Activities at LaRC have included the development of mobile remote manipulator systems (which can traverse the Space Station 5-meter structure), preliminary LDR sun shield concepts, LDR construction scenarios, and activities in robotic assembly of truss-type structures.

Hierarchical Self Assembly of Patterns from the Robinson Tilings: DNA Tile Design in an Enhanced Tile Assembly Model.

Science.gov (United States)

Padilla, Jennifer E; Liu, Wenyan; Seeman, Nadrian C

2012-06-01

We introduce a hierarchical self assembly algorithm that produces the quasiperiodic patterns found in the Robinson tilings and suggest a practical implementation of this algorithm using DNA origami tiles. We modify the abstract Tile Assembly Model, (aTAM), to include active signaling and glue activation in response to signals to coordinate the hierarchical assembly of Robinson patterns of arbitrary size from a small set of tiles according to the tile substitution algorithm that generates them. Enabling coordinated hierarchical assembly in the aTAM makes possible the efficient encoding of the recursive process of tile substitution.

Viral capsid assembly as a model for protein aggregation diseases: Active processes catalyzed by cellular assembly machines comprising novel drug targets.

Science.gov (United States)

Marreiros, Rita; Müller-Schiffmann, Andreas; Bader, Verian; Selvarajah, Suganya; Dey, Debendranath; Lingappa, Vishwanath R; Korth, Carsten

2015-09-02

Viruses can be conceptualized as self-replicating multiprotein assemblies, containing coding nucleic acids. Viruses have evolved to exploit host cellular components including enzymes to ensure their replicative life cycle. New findings indicate that also viral capsid proteins recruit host factors to accelerate their assembly. These assembly machines are RNA-containing multiprotein complexes whose composition is governed by allosteric sites. In the event of viral infection, the assembly machines are recruited to support the virus over the host and are modified to achieve that goal. Stress granules and processing bodies may represent collections of such assembly machines, readily visible by microscopy but biochemically labile and difficult to isolate by fractionation. We hypothesize that the assembly of protein multimers such as encountered in neurodegenerative or other protein conformational diseases, is also catalyzed by assembly machines. In the case of viral infection, the assembly machines have been modified by the virus to meet the virus' need for rapid capsid assembly rather than host homeostasis. In the case of the neurodegenerative diseases, it is the monomers and/or low n oligomers of the so-called aggregated proteins that are substrates of assembly machines. Examples for substrates are amyloid β peptide (Aβ) and tau in Alzheimer's disease, α-synuclein in Parkinson's disease, prions in the prion diseases, Disrupted-in-schizophrenia 1 (DISC1) in subsets of chronic mental illnesses, and others. A likely continuum between virus capsid assembly and cell-to-cell transmissibility of aggregated proteins is remarkable. Protein aggregation diseases may represent dysfunction and dysregulation of these assembly machines analogous to the aberrations induced by viral infection in which cellular homeostasis is pathologically reprogrammed. In this view, as for viral infection, reset of assembly machines to normal homeostasis should be the goal of protein aggregation

Self-assembling triblock proteins for biofunctional surface modification

Science.gov (United States)

Fischer, Stephen E.

Despite the tremendous promise of cell/tissue engineering, significant challenges remain in engineering functional scaffolds to precisely regulate the complex processes of tissue growth and development. As the point of contact between the cells and the scaffold, the scaffold surface plays a major role in mediating cellular behaviors. In this dissertation, the development and utility of self-assembling, artificial protein hydrogels as biofunctional surface modifiers is described. The design of these recombinant proteins is based on a telechelic triblock motif, in which a disordered polyelectrolyte central domain containing embedded bioactive ligands is flanked by two leucine zipper domains. Under moderate conditions of temperature and pH, the leucine zipper end domains form amphiphilic alpha-helices that reversibly associate into homo-trimeric aggregates, driving hydrogel formation. Moreover, the amphiphilic nature of these helical domains enables surface adsorption to a variety of scaffold materials to form biofunctional protein coatings. The nature and stability of these coatings in various solution conditions, and their interaction with mammalian cells is the primary focus of this dissertation. In particular, triblock protein coatings functionalized with cell recognition sequences are shown to produce well-defined surfaces with precise control over ligand density. The impact of this is demonstrated in multiple cell types through ligand density-dependent cell-substrate interactions. To improve the stability of these physically self-assembled coatings, two covalent crosslinking strategies are described---one in which a zero-length chemical crosslinker (EDC) is utilized and a second in which disulfide bonds are engineered into the recombinant proteins. These targeted crosslinking approaches are shown to increase the stability of surface adsorbed protein layers with minimal effect on the presentation of many bioactive ligands. Finally, to demonstrate the versatility