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Sample records for binding mrnp assembly

  1. Nuclear surveillance of mRNP formation

    DEFF Research Database (Denmark)

    Jensen, Torben Heick

    and biochemical data now show that a defective THO complex negatively impacts mRNA 3’-end processing. We are currently trying to understand the relationship between this phenomenon and mRNP quality control. Retention of mRNP in THO mutants is dependent on the nuclear exosome component Rrp6p. Using the solved......Proper formation of mRNP requires co-transcriptional loading of proteins onto nascent transcripts. Mutations in several genes involved in mRNA processing, mRNP assembly and nuclear export lead to production of aberrant mRNPs that are retained in transcription site-associated foci. Retention...... and degradation of transcripts depend on the nuclear exosome of 3’-5’ exonucleases.We have studied connections between mRNP assembly and quality control in the yeast S. cerevisiae using mutants of the THO complex. THO is implicated in co-transcriptional mRNP assembly, but its precise role is not known. Genetic...

  2. Insights into mRNP biogenesis provided by new genetic interactions among export and transcription factors

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    Estruch Francisco

    2012-09-01

    Full Text Available Abstract Background The various steps of mRNP biogenesis (transcription, processing and export are interconnected. It has been shown that the transcription machinery plays a pivotal role in mRNP assembly, since several mRNA export factors are recruited during transcription and physically interact with components of the transcription machinery. Although the shuttling DEAD-box protein Dbp5p is concentrated on the cytoplasmic fibrils of the NPC, previous studies demonstrated that it interacts physically and genetically with factors involved in transcription initiation. Results We investigated the effect of mutations affecting various components of the transcription initiation apparatus on the phenotypes of mRNA export mutant strains. Our results show that growth and mRNA export defects of dbp5 and mex67 mutant strains can be suppressed by mutation of specific transcription initiation components, but suppression was not observed for mutants acting in the very first steps of the pre-initiation complex (PIC formation. Conclusions Our results indicate that mere reduction in the amount of mRNP produced is not sufficient to suppress the defects caused by a defective mRNA export factor. Suppression occurs only with mutants affecting events within a narrow window of the mRNP biogenesis process. We propose that reducing the speed with which transcription converts from initiation and promoter clearance to elongation may have a positive effect on mRNP formation by permitting more effective recruitment of partially-functional mRNP proteins to the nascent mRNP.

  3. Xp54, the Xenopus homologue of human RNA helicase p54, is an integral component of stored mRNP particles in oocytes.

    Science.gov (United States)

    Ladomery, M; Wade, E; Sommerville, J

    1997-01-01

    In investigating the composition of stored (maternal) mRNP particles in Xenopus oocytes, attention has focussed primarily on the phosphoproteins pp60/56, which are Y-box proteins involved in a general packaging of mRNA. We now identify a third, abundant, integral component of stored mRNP particles, Xp54, which belongs to the family of DEAD-box RNA helicases. Xp54 was first detected by its ability to photocrosslink ATP. Subsequent sequence analysis identifies Xp54 as a member of a helicase subfamily which includes: human p54, encoded at a chromosomal breakpoint in the B-cell lymphoma cell line, RC-K8; Drosophila ME31B, encoded by a maternally-expressed gene, and Saccharomyces pombe Ste13, cloned by complementation of the sterility mutant ste13. Expression studies reveal that the gene encoding Xp54 is transcribed maximally at early oogenesis: no transcripts are detected in adult tissues, other than ovary. Using a monospecific antibody raised against native Xp54, its presence in mRNP particles is confirmed by immunoblotting fractions bound to oligo(dT)-cellulose and separated by rate sedimentation and buoyant density. On isolating Xp54 from mRNP particles, it is shown to possess an ATP-dependent RNA helicase activity. Possible functions of Xp54 are discussed in relation to the assembly and utilization of mRNP particles. PMID:9023105

  4. Differential expression of THOC1 and ALY mRNP biogenesis/export factors in human cancers

    International Nuclear Information System (INIS)

    One key step in gene expression is the biogenesis of mRNA ribonucleoparticle complexes (mRNPs). Formation of the mRNP requires the participation of a number of conserved factors such as the THO complex. THO interacts physically and functionally with the Sub2/UAP56 RNA-dependent ATPase, and the Yra1/REF1/ALY RNA-binding protein linking transcription, mRNA export and genome integrity. Given the link between genome instability and cancer, we have performed a comparative analysis of the expression patterns of THOC1, a THO complex subunit, and ALY in tumor samples. The mRNA levels were measured by quantitative real-time PCR and hybridization of a tumor tissue cDNA array; and the protein levels and distribution by immunostaining of a custom tissue array containing a set of paraffin-embedded samples of different tumor and normal tissues followed by statistical analysis. We show that the expression of two mRNP factors, THOC1 and ALY are altered in several tumor tissues. THOC1 mRNA and protein levels are up-regulated in ovarian and lung tumors and down-regulated in those of testis and skin, whereas ALY is altered in a wide variety of tumors. In contrast to THOC1, ALY protein is highly detected in normal proliferative cells, but poorly in high-grade cancers. These results suggest a differential connection between tumorogenesis and the expression levels of human THO and ALY. This study opens the possibility of defining mRNP biogenesis factors as putative players in cell proliferation that could contribute to tumor development

  5. Superlattices assembled through shape-induced directional binding.

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

    2015-01-01

    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.

  6. Characterization of transcription site-associated mRNP retention in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Jensen, Torben Heick

    In a variety of S. cerevisiae mutants with defective mRNP maturation and/or export, heat shock (hs) mRNPs are retained at or near their sites of transcription. For example, mutants of the THO complex display an intense hs-mRNA FISH signal, which co-localizes with the hs-gene after transcriptional...... underrepresented in recovered fractions from mutant cells. This bias is abolished when a THO mutation is combined with a second site mutation alleviating the mRNA export block. Thus, the bias parallels transcription-site retention of the mRNP and suggests the existence of a complex specifically formed at the 3...

  7. Drosophila glutamate receptor mRNA expression and mRNP particles.

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    Ganesan, Subhashree; Karr, Julie E; Featherstone, David E

    2011-01-01

    The processes controlling glutamate receptor expression early in synaptogenesis are poorly understood. Here, we examine glutamate receptor (GluR) subunit mRNA expression and localization in Drosophila embryonic/larval neuromuscular junctions (NMJs). We show that postsynaptic GluR subunit gene expression is triggered by contact from the presynaptic nerve, approximately halfway through embryogenesis. After contact, GluRIIA and GluRIIB mRNA abundance rises quickly approximately 20-fold, then falls within a few hours back to very low levels. Protein abundance, however, gradually increases throughout development. At the same time that mRNA levels decrease following their initial spike, GluRIIA, GluRIIB, and GluRIIC subunit mRNA aggregates become visible in the cytoplasm of postsynaptic muscle cells. These mRNA aggregates do not colocalize with eIF4E, but nevertheless presumably represent mRNP particles of unknown function. Multiplex FISH shows that different GluR subunit mRNAs are found in different mRNPs. GluRIIC mRNPs are most common, followed by GluRIIA and then GluRIIB mRNPs. GluR mRNP density is not increased near NMJs, for any subunit; if anything, GluR mRNP density is highest away from NMJs and near nuclei. These results reveal some of the earliest events in postsynaptic development and provide a foundation for future studies of GluR mRNA biology.

  8. Stable MCC binding to the APC/C is required for a functional spindle assembly checkpoint

    DEFF Research Database (Denmark)

    Hein, Jamin B; Nilsson, Jakob

    2014-01-01

    The spindle assembly checkpoint (SAC) delays progression into anaphase until all chromosomes have aligned on the metaphase plate by inhibiting Cdc20, the mitotic co-activator of the APC/C. Mad2 and BubR1 bind and inhibit Cdc20, thereby forming the mitotic checkpoint complex (MCC), which can bind...

  9. Filament assembly by Spire: key residues and concerted actin binding.

    Science.gov (United States)

    Rasson, Amy S; Bois, Justin S; Pham, Duy Stephen L; Yoo, Haneul; Quinlan, Margot E

    2015-02-27

    The most recently identified class of actin nucleators, WASp homology domain 2 (WH2) nucleators, use tandem repeats of monomeric actin-binding WH2 domains to facilitate actin nucleation. WH2 domains are involved in a wide variety of actin regulatory activities. Structurally, they are expected to clash with interprotomer contacts within the actin filament. Thus, the discovery of their role in nucleation was surprising. Here we use Drosophila Spire (Spir) as a model system to investigate both how tandem WH2 domains can nucleate actin and what differentiates nucleating WH2-containing proteins from their non-nucleating counterparts. We found that the third WH2 domain in Spir (Spir-C or SC) plays a unique role. In the context of a short nucleation construct (containing only two WH2 domains), placement of SC in the N-terminal position was required for the most potent nucleation. We found that the native organization of the WH2 domains with respect to each other is necessary for binding to actin with positive cooperativity. We identified two residues within SC that are critical for its activity. Using this information, we were able to convert a weak synthetic nucleator into one with activity equal to a native Spir construct. Lastly, we found evidence that SC binds actin filaments, in addition to monomers.

  10. Engineered Bacterial Metal-binding Proteins for Nanoscale Self-assembly and heavy Metal Tolerance

    Science.gov (United States)

    Hall Sedlak, Ruth Amanda

    Implementing biological principles in material synthesis and assembly is one way to expand our abilities to efficiently assemble nanoscale materials and devices. Specifically, recent advances in identifying peptides that bind inorganic materials with high affinity and specificity has spurred investigation of protein models for nanoscale inorganic assembly. This dissertation presents the results of my studies of several E. coli proteins engineered to bind inorganic materials through simple peptide motifs. I demonstrate that these proteins modulate the self-assembly of DNA-based nanostructures and can introduce heavy metal tolerance into metal-sensitive bacteria. Chapter 2 explores use of the engineered F plasmid DNA relaxase/helicase TraI for the self-assembly of complex DNA-protein-gold nanostructures. The full-length protein is engineered with a gold binding motif at an internal permissive site (TraI369GBP1-7x), while a truncated version of TraI is engineered with the same gold binding motif at the C-terminus (TraI361GBP1-7x). Both constructs bind gold nanoparticles while maintaining their DNA binding activity, and transmission electron microscopy reveals TraI369GBP1-7x utilizes its non-specific DNA binding activity to decorate single-stranded and double-stranded DNA with gold nanoparticles. The self assembly principles demonstrated in this work will be fundamental to constructing higher ordered hybrid nanostructures through DNA-protein-nanoparticle interactions. Chapter 3 studies the effects of expressing inorganic binding peptides within cells. I identified a silver binding peptide that, when fused to the periplasmic maltose binding protein, protects E. coli from silver toxicity in batch culture and reduces silver ions to silver nanoparticles within the bacterial periplasm. Engineered metal-ion tolerant microorganisms such as this E. coli could potentially be used in applications ranging from remediation to interrogation of biomolecule-metal interactions in vivo

  11. Self-assembled cardanol azo derivatives as antifungal agent with chitin-binding ability.

    Science.gov (United States)

    Mahata, Denial; Mandal, Santi M; Bharti, Rashmi; Gupta, Vinay Krishna; Mandal, Mahitosh; Nag, Ahindra; Nando, Golok B

    2014-08-01

    Cardanol is a non-isoprenoic phenolic lipid-mixture of distilled cashew nut shell liquid obtained from Anacardium occidentale. Herein, cardanol is purified from cashew nut shell liquid (CNSL) and synthesized to new compounds with different azo amphiphiles. These synthesized compounds are allowed to self-assembled in hydrophobic environment and checked antifungal activity against Candida albicans. Self-assembled structure of CABA showed higher antifungal activity (16μg/mL) and chitin-binding ability in comparison to CAP and CANB. Furthermore, the self-assembled azo amphiphiles are immobilized with silver ions to prepare hydrogel which showed eight folds enhanced antifungal activity. Toxicity is reduced by several folds of self-assembled or hydrogel structure in comparison to pure compounds. Thus, the self-assembled structure of amphiphiles and their hydrogels have been found to be new macromolecules of interest with potential use as antifungal drugs. PMID:24836571

  12. Binding of the Covalent Flavin Assembly Factor to the Flavoprotein Subunit of Complex II.

    Science.gov (United States)

    Maklashina, Elena; Rajagukguk, Sany; Starbird, Chrystal A; McDonald, W Hayes; Koganitsky, Anna; Eisenbach, Michael; Iverson, Tina M; Cecchini, Gary

    2016-02-01

    Escherichia coli harbors two highly conserved homologs of the essential mitochondrial respiratory complex II (succinate:ubiquinone oxidoreductase). Aerobically the bacterium synthesizes succinate:quinone reductase as part of its respiratory chain, whereas under microaerophilic conditions, the quinol:fumarate reductase can be utilized. All complex II enzymes harbor a covalently bound FAD co-factor that is essential for their ability to oxidize succinate. In eukaryotes and many bacteria, assembly of the covalent flavin linkage is facilitated by a small protein assembly factor, termed SdhE in E. coli. How SdhE assists with formation of the covalent flavin bond and how it binds the flavoprotein subunit of complex II remain unknown. Using photo-cross-linking, we report the interaction site between the flavoprotein of complex II and the SdhE assembly factor. These data indicate that SdhE binds to the flavoprotein between two independently folded domains and that this binding mode likely influences the interdomain orientation. In so doing, SdhE likely orients amino acid residues near the dicarboxylate and FAD binding site, which facilitates formation of the covalent flavin linkage. These studies identify how the conserved SdhE assembly factor and its homologs participate in complex II maturation.

  13. Self-Assembly of Protein Monolayers Engineered for Improved Monoclonal Immunoglobulin G Binding

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    Jeremy H. Lakey

    2011-08-01

    Full Text Available Bacterial outer membrane proteins, along with a filling lipid molecule can be modified to form stable self-assembled monolayers on gold. The transmembrane domain of Escherichia coli outer membrane protein A has been engineered to create a scaffold protein to which functional motifs can be fused. In earlier work we described the assembly and structure of an antibody-binding array where the Z domain of Staphylococcus aureus protein A was fused to the scaffold protein. Whilst the binding of rabbit polyclonal immunoglobulin G (IgG to the array is very strong, mouse monoclonal IgG dissociates from the array easily. This is a problem since many immunodiagnostic tests rely upon the use of mouse monoclonal antibodies. Here we describe a strategy to develop an antibody-binding array that will bind mouse monoclonal IgG with lowered dissociation from the array. A novel protein consisting of the scaffold protein fused to two pairs of Z domains separated by a long flexible linker was manufactured. Using surface plasmon resonance the self-assembly of the new protein on gold and the improved binding of mouse monoclonal IgG were demonstrated.

  14. Assembly of custom TALE-type DNA binding domains by modular cloning.

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    Morbitzer, Robert; Elsaesser, Janett; Hausner, Jens; Lahaye, Thomas

    2011-07-01

    Transcription activator-like effector (TALE) DNA binding proteins show tremendous potential as molecular tools for targeted binding to any desired DNA sequence. Their DNA binding domain consists of tandem arranged repeats, and due to this repetitive structure it is challenging to generate designer TALEs (dTALEs) with user-defined specificity. We present a cloning approach that facilitates the assembly of multiple repeat-encoding DNA fragments that translate into dTALEs with pre-defined DNA binding specificity. This method makes use of type IIS restriction enzymes in two sequential cut-ligase reactions to build dTALE repeat arrays. We employed this modular approach for generation of a dTALE that differentiates between two highly similar DNA sequences that are both targeted by the Xanthomonas TALE, AvrBs3. These data show that this modular assembly system allows rapid generation of highly specific TALE-type DNA binding domains that target binding sites of predefined length and sequence. This approach enables the rapid and flexible production of dTALEs for gene regulation and genome editing in routine and high-throughput applications.

  15. Creating Prebiotic Sanctuary: Self-Assembling Supramolecular Peptide Structures Bind and Stabilize RNA

    Science.gov (United States)

    Carny, Ohad; Gazit, Ehud

    2011-04-01

    Any attempt to uncover the origins of life must tackle the known `blind watchmaker problem'. That is to demonstrate the likelihood of the emergence of a prebiotic system simple enough to be formed spontaneously and yet complex enough to allow natural selection that will lead to Darwinistic evolution. Studies of short aromatic peptides revealed their ability to self-assemble into ordered and stable structures. The unique physical and chemical characteristics of these peptide assemblies point out to their possible role in the origins of life. We have explored mechanisms by which self-assembling short peptides and RNA fragments could interact together and go through a molecular co-evolution, using diphenylalanine supramolecular assemblies as a model system. The spontaneous formation of these self-assembling peptides under prebiotic conditions, through the salt-induced peptide formation (SIPF) pathway was demonstrated. These peptide assemblies possess the ability to bind and stabilize ribonucleotides in a sequence-depended manner, thus increase their relative fitness. The formation of these peptide assemblies is dependent on the homochirality of the peptide monomers: while homochiral peptides (L-Phe-L-Phe and D-Phe-D-Phe) self-assemble rapidly in aqueous environment, heterochiral diastereoisomers (L-Phe-D-Phe and D-Phe-L-Phe) do not tend to self-assemble. This characteristic consists with the homochirality of all living matter. Finally, based on these findings, we propose a model for the role of short self-assembling peptides in the prebiotic molecular evolution and the origin of life.

  16. Characterization of engineered actin binding proteins that control filament assembly and structure.

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    Crista M Brawley

    Full Text Available BACKGROUND: Eukaryotic cells strictly regulate the structure and assembly of their actin filament networks in response to various stimuli. The actin binding proteins that control filament assembly are therefore attractive targets for those who wish to reorganize actin filaments and reengineer the cytoskeleton. Unfortunately, the naturally occurring actin binding proteins include only a limited set of pointed-end cappers, or proteins that will block polymerization from the slow-growing end of actin filaments. Of the few that are known, most are part of large multimeric complexes that are challenging to manipulate. METHODOLOGY/PRINCIPAL FINDINGS: We describe here the use of phage display mutagenesis to generate of a new class of binding protein that can be targeted to the pointed-end of actin. These proteins, called synthetic antigen binders (sABs, are based on an antibody-like scaffold where sequence diversity is introduced into the binding loops using a novel "reduced genetic code" phage display library. We describe effective strategies to select and screen for sABs that ensure the generated sABs bind to the pointed-end surface of actin exclusively. CONCLUSIONS/SIGNIFICANCE: From our set of pointed-end binders, we identify three sABs with particularly useful properties to systematically probe actin dynamics: one protein that caps the pointed end, a second that crosslinks actin filaments, and a third that severs actin filaments and promotes disassembly.

  17. WAVE binds Ena/VASP for enhanced Arp2/3 complex-based actin assembly.

    Science.gov (United States)

    Havrylenko, Svitlana; Noguera, Philippe; Abou-Ghali, Majdouline; Manzi, John; Faqir, Fahima; Lamora, Audrey; Guérin, Christophe; Blanchoin, Laurent; Plastino, Julie

    2015-01-01

    The WAVE complex is the main activator of the Arp2/3 complex for actin filament nucleation and assembly in the lamellipodia of moving cells. Other important players in lamellipodial protrusion are Ena/VASP proteins, which enhance actin filament elongation. Here we examine the molecular coordination between the nucleating activity of the Arp2/3 complex and the elongating activity of Ena/VASP proteins for the formation of actin networks. Using an in vitro bead motility assay, we show that WAVE directly binds VASP, resulting in an increase in Arp2/3 complex-based actin assembly. We show that this interaction is important in vivo as well, for the formation of lamellipodia during the ventral enclosure event of Caenorhabditis elegans embryogenesis. Ena/VASP's ability to bind F-actin and profilin-complexed G-actin are important for its effect, whereas Ena/VASP tetramerization is not necessary. Our data are consistent with the idea that binding of Ena/VASP to WAVE potentiates Arp2/3 complex activity and lamellipodial actin assembly.

  18. Tubulin assembly, taxoid site binding, and cellular effects of the microtubule-stabilizing agent dictyostatin.

    Science.gov (United States)

    Madiraju, Charitha; Edler, Michael C; Hamel, Ernest; Raccor, Brianne S; Balachandran, Raghavan; Zhu, Guangyu; Giuliano, Kenneth A; Vogt, Andreas; Shin, Youseung; Fournier, Jean-Hugues; Fukui, Yoshikazu; Brückner, Arndt M; Curran, Dennis P; Day, Billy W

    2005-11-15

    (-)-Dictyostatin is a sponge-derived, 22-member macrolactone natural product shown to cause cells to accumulate in the G2/M phase of the cell cycle, with changes in intracellular microtubules analogous to those observed with paclitaxel treatment. Dictyostatin also induces assembly of purified tubulin more rapidly than does paclitaxel, and nearly as vigorously as does dictyostatin's close structural congener, (+)-discodermolide (Isbrucker et al. (2003), Biochem. Pharmacol. 65, 75-82). We used synthetic (-)-dictyostatin to study its biochemical and cytological activities in greater detail. The antiproliferative activity of dictyostatin did not differ greatly from that of paclitaxel or discodermolide. Like discodermolide, dictyostatin retained antiproliferative activity against human ovarian carcinoma cells resistant to paclitaxel due to beta-tubulin mutations and caused conversion of cellular soluble tubulin pools to microtubules. Detailed comparison of the abilities of dictyostatin and discodermolide to induce tubulin assembly demonstrated that the compounds had similar potencies. Dictyostatin inhibited the binding of radiolabeled discodermolide to microtubules more potently than any other compound examined, and dictyostatin and discodermolide had equivalent activity as inhibitors of the binding of both radiolabeled epothilone B and paclitaxel to microtubules. These results are consistent with the idea that the macrocyclic structure of dictyostatin represents the template for the bioactive conformation of discodermolide.

  19. Molecular Dynamics Simulation of the Binding Interaction between Hormone Glucagon Protein and Self-Assembled Monolayer Molecules

    Institute of Scientific and Technical Information of China (English)

    WANG,Yeng-Tseng; CHENG,Cheng-Lung; SHIH,Yu-Ching; KAN,Heng-Chuan; CHEN,Chang-Hung; HU,Jeu-Jiun; SU,Zhi-Yuan

    2007-01-01

    Restrained molecular dynamics simulations were performed to study the binding affinity of the peptide with alkanethiols of different tail-groups, S(CH2)7CH3, S(CH2)7OH and S(CH2)7COOH, which self-assembled on Au(111)surface in the presence of water molecules. The curves of binding affinity were calculated by fixing the center of mass of the peptide at various distances from the assembling surface. Simulation results show that the binding affinity is in the order as COOH-SAMs>OH-SAMs>CH3-SAMs, while 100% COOH-SAMs>5% COOH-SAMs in concentration. The effects on binding affinity by different tail-groups were also studied. Results show that the binding affinity between COOH-SAMs and the peptide is bigger than those of the others and increasing the acidity of COOH-SAMs will result in stronger attractive power.

  20. Brittle Culm1, a COBRA-like protein, functions in cellulose assembly through binding cellulose microfibrils.

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    Lifeng Liu

    Full Text Available Cellulose represents the most abundant biopolymer in nature and has great economic importance. Cellulose chains pack laterally into crystalline forms, stacking into a complicated crystallographic structure. However, the mechanism of cellulose crystallization is poorly understood. Here, via functional characterization, we report that Brittle Culm1 (BC1, a COBRA-like protein in rice, modifies cellulose crystallinity. BC1 was demonstrated to be a glycosylphosphatidylinositol (GPI anchored protein and can be released into cell walls by removal of the GPI anchor. BC1 possesses a carbohydrate-binding module (CBM at its N-terminus. In vitro binding assays showed that this CBM interacts specifically with crystalline cellulose, and several aromatic residues in this domain are essential for binding. It was further demonstrated that cell wall-localized BC1 via the CBM and GPI anchor is one functional form of BC1. X-ray diffraction (XRD assays revealed that mutations in BC1 and knockdown of BC1 expression decrease the crystallite width of cellulose; overexpression of BC1 and the CBM-mutated BC1s caused varied crystallinity with results that were consistent with the in vitro binding assay. Moreover, interaction between the CBM and cellulose microfibrils was largely repressed when the cell wall residues were pre-stained with two cellulose dyes. Treating wild-type and bc1 seedlings with the dyes resulted in insensitive root growth responses in bc1 plants. Combined with the evidence that BC1 and three secondary wall cellulose synthases (CESAs function in different steps of cellulose production as revealed by genetic analysis, we conclude that BC1 modulates cellulose assembly by interacting with cellulose and affecting microfibril crystallinity.

  1. Calcium-binding capacity of centrin2 is required for linear POC5 assembly but not for nucleotide excision repair.

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    Tiago J Dantas

    Full Text Available Centrosomes, the principal microtubule-organising centres in animal cells, contain centrins, small, conserved calcium-binding proteins unique to eukaryotes. Centrin2 binds to xeroderma pigmentosum group C protein (XPC, stabilising it, and its presence slightly increases nucleotide excision repair (NER activity in vitro. In previous work, we deleted all three centrin isoforms present in chicken DT40 cells and observed delayed repair of UV-induced DNA lesions, but no centrosome abnormalities. Here, we explore how centrin2 controls NER. In the centrin null cells, we expressed centrin2 mutants that cannot bind calcium or that lack sites for phosphorylation by regulatory kinases. Expression of any of these mutants restored the UV sensitivity of centrin null cells to normal as effectively as expression of wild-type centrin. However, calcium-binding-deficient and T118A mutants showed greatly compromised localisation to centrosomes. XPC recruitment to laser-induced UV-like lesions was only slightly slower in centrin-deficient cells than in controls, and levels of XPC and its partner HRAD23B were unaffected by centrin deficiency. Interestingly, we found that overexpression of the centrin interactor POC5 leads to the assembly of linear, centrin-dependent structures that recruit other centrosomal proteins such as PCM-1 and NEDD1. Together, these observations suggest that assembly of centrins into complex structures requires calcium binding capacity, but that such assembly is not required for centrin activity in NER.

  2. Rapid dynamics of general transcription factor TFIIB binding during preinitiation complex assembly revealed by single-molecule analysis

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    Zhang, Zhengjian; English, Brian P.; Grimm, Jonathan B.; Kazane, Stephanie A.; Hu, Wenxin; Tsai, Albert; Inouye, Carla; You, Changjiang; Piehler, Jacob; Schultz, Peter G.; Lavis, Luke D.; Revyakin, Andrey; Tjian, Robert

    2016-01-01

    Transcription of protein-encoding genes in eukaryotic cells requires the coordinated action of multiple general transcription factors (GTFs) and RNA polymerase II (Pol II). A “step-wise” preinitiation complex (PIC) assembly model has been suggested based on conventional ensemble biochemical measurements, in which protein factors bind stably to the promoter DNA sequentially to build a functional PIC. However, recent dynamic measurements in live cells suggest that transcription factors mostly interact with chromatin DNA rather transiently. To gain a clearer dynamic picture of PIC assembly, we established an integrated in vitro single-molecule transcription platform reconstituted from highly purified human transcription factors and complemented it by live-cell imaging. Here we performed real-time measurements of the hierarchal promoter-specific binding of TFIID, TFIIA, and TFIIB. Surprisingly, we found that while promoter binding of TFIID and TFIIA is stable, promoter binding by TFIIB is highly transient and dynamic (with an average residence time of 1.5 sec). Stable TFIIB–promoter association and progression beyond this apparent PIC assembly checkpoint control occurs only in the presence of Pol II–TFIIF. This transient-to-stable transition of TFIIB-binding dynamics has gone undetected previously and underscores the advantages of single-molecule assays for revealing the dynamic nature of complex biological reactions. PMID:27798851

  3. Xp54 and related (DDX6-like) RNA helicases: roles in messenger RNP assembly, translation regulation and RNA degradation

    Science.gov (United States)

    Weston, Andrew; Sommerville, John

    2006-01-01

    The DEAD-box RNA helicase Xp54 is an integral component of the messenger ribonucleoprotein (mRNP) particles of Xenopus oocytes. In oocytes, several abundant proteins bind pre-mRNA transcripts to modulate nuclear export, RNA stability and translational fate. Of these, Xp54, the mRNA-masking protein FRGY2 and its activating protein kinase CK2α, bind to nascent transcripts on chromosome loops, whereas an Xp54-associated factor, RapA/B, binds to the mRNP complex in the cytoplasm. Over-expression, mutation and knockdown experiments indicate that Xp54 functions to change the conformation of mRNP complexes, displacing one subset of proteins to accommodate another. The sequence of Xp54 is highly conserved in a wide spectrum of organisms. Like Xp54, Drosophila Me31B and Caenorhabditis CGH-1 are required for proper meiotic development, apparently by regulating the translational activation of stored mRNPs and also for sorting certain mRNPs into germplasm-containing structures. Studies on yeast Dhh1 and mammalian rck/p54 have revealed a key role for these helicases in mRNA degradation and in earlier remodelling of mRNP for entry into translation, storage or decay pathways. The versatility of Xp54 and related helicases in modulating the metabolism of mRNAs at all stages of their lifetimes marks them out as key regulators of post-transcriptional gene expression. PMID:16769775

  4. Optimized modification of gold nanoparticles with a self-assembled monolayer for suppression of nonspecific binding in DNA assays

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    Esashika, Keiko; Saiki, Toshiharu

    2016-10-01

    Homogeneous DNA assays using gold nanoparticles (AuNPs) require the reduction of nonspecific binding between AuNPs to improve sensitivity in detecting the target molecule. In this study, we employed alkanethiol self-assembled monolayers (SAMs) for modifying the AuNP surface to attain both good dispersability and high hybridization efficiency. The alkanethiol SAMs enhance the repulsive interaction between AuNPs, reducing nonspecific binding and promoting the extension of surface-immobilized ssDNA into the solvent, thus enhancing the hybridization process. Introduction of oligoethylene glycol into the alkanethiol prevented nonspecific binding caused by the entanglement of alkane chains. Finally, the conditions were optimized by controlling the surface charge density through the introduction of a COOH group at the alkanethiol terminus, resulting in the complete blocking of nonspecific binding and the maintenance of high hybridization efficiency.

  5. The internal Cdc20 binding site in BubR1 facilitates both spindle assembly checkpoint signalling and silencing

    DEFF Research Database (Denmark)

    Lischetti, Tiziana; Zhang, Gang; Sedgwick, Garry G;

    2014-01-01

    Improperly attached kinetochores activate the spindle assembly checkpoint (SAC) and by an unknown mechanism catalyse the binding of two checkpoint proteins, Mad2 and BubR1, to Cdc20 forming the mitotic checkpoint complex (MCC). Here, to address the functional role of Cdc20 kinetochore localization...... on the SAC because the IC20BD is also required for efficient SAC silencing. Indeed, the IC20BD can disrupt the MCC providing a mechanism for its role in SAC silencing. We thus uncover an unexpected dual function of the second Cdc20 binding site in BubR1 in promoting both efficient SAC signalling and SAC...

  6. RNA-binding Domain of the Key Structural Protein P7 for the Rice dwarf virus Particle Assembly

    Institute of Scientific and Technical Information of China (English)

    Bo-Xiong ZHONG; Yan-Wei SHEN; Toshihiro OMURA

    2005-01-01

    The Rice dwarf virus (RDV) P7 structural protein is the key protein in the RDV particle assembly. The P7 protein was digested partially or completely by Staphylococcus aureus V8 protease and/or Pseudomonas fragi Asp-N protease. The molecular mass and the N-terminal amino acid sequence of the polypeptide fragments of the P7 protein were determined by SDS-PAGE and the Edman degradation method,respectively. Then the polypeptides were located in the deduced amino acid sequence of the RDV P7 protein based on the nucleotide sequence information, with the knowledge of the specific cleavage sites of the Staphylococcus aureus V8 and Pseudomonasfragi Asp-N protease, and the two RNA-binding domains in the P7 protein were identified. Domain 1 was located in the residue 128-249 containing 122 amino acids and domain 2 was located in the residue 325-355 containing 31 amino acids. Thus, these two domains may play an important role in the virus particle assembly by contributing to the packaging of viral dsRNAs inside the particles. The two domains may be novel RNA-binding domains, because no amino acid sequences highly similar to the conservative sequences of known dsRNA-binding domains reported so far. The similarity between the motif of domain 1 and the motif of the DNA-binding protein suggests that the DNA-binding activity of the RDV P7 protein may be due to this sequence. The similarity between the motif of domain 1 and the motif of the RNA polymerase domain suggests that the P7 protein may also play a role in RNA synthesis,besides its function in the assembly and subsequent packaging of viral dsRNA into core particles.

  7. The role of the poly(A) binding protein in the assembly of the Cap-binding complex during translation initiation in plants

    OpenAIRE

    Gallie, Daniel R.

    2014-01-01

    Translation initiation in eukaryotes requires the involvement of multiple initiation factors (eIFs) that facilitate the binding of the 40 S ribosomal subunit to an mRNA and assemble the 80 S ribosome at the correct initiation codon. eIF4F, composed of eIF4E, eIF4A, and eIF4G, binds to the 5′-cap structure of an mRNA and prepares an mRNA for recruitment of a 40 S subunit. eIF4B promotes the ATP-dependent RNA helicase activity of eIF4A and eIF4F needed to unwind secondary structure present in a...

  8. Repetitive N-WASP-binding elements of the enterohemorrhagic Escherichia coli effector EspF(U synergistically activate actin assembly.

    Directory of Open Access Journals (Sweden)

    Kenneth G Campellone

    2008-10-01

    Full Text Available Enterohemorrhagic Escherichia coli (EHEC generate F-actin-rich adhesion pedestals by delivering effector proteins into mammalian cells. These effectors include the translocated receptor Tir, along with EspF(U, a protein that associates indirectly with Tir and contains multiple peptide repeats that stimulate actin polymerization. In vitro, the EspF(U repeat region is capable of binding and activating recombinant derivatives of N-WASP, a host actin nucleation-promoting factor. In spite of the identification of these important bacterial and host factors, the underlying mechanisms of how EHEC so potently exploits the native actin assembly machinery have not been clearly defined. Here we show that Tir and EspF(U are sufficient for actin pedestal formation in cultured cells. Experimental clustering of Tir-EspF(U fusion proteins indicates that the central role of the cytoplasmic portion of Tir is to promote clustering of the repeat region of EspF(U. Whereas clustering of a single EspF(U repeat is sufficient to bind N-WASP and generate pedestals on cultured cells, multi-repeat EspF(U derivatives promote actin assembly more efficiently. Moreover, the EspF(U repeats activate a protein complex containing N-WASP and the actin-binding protein WIP in a synergistic fashion in vitro, further suggesting that the repeats cooperate to stimulate actin polymerization in vivo. One explanation for repeat synergy is that simultaneous engagement of multiple N-WASP molecules can enhance its ability to interact with the actin nucleating Arp2/3 complex. These findings define the minimal set of bacterial effectors required for pedestal formation and the elements within those effectors that contribute to actin assembly via N-WASP-Arp2/3-mediated signaling pathways.

  9. A yeast glycolipid biosurfactant, mannosylerythritol lipid, shows high binding affinity towards lectins on a self-assembled monolayer system.

    Science.gov (United States)

    Konishi, Masaaki; Imura, Tomohiro; Fukuoka, Tokuma; Morita, Tomotake; Kitamoto, Dai

    2007-03-01

    Mannosylerythritol lipids (MEL), which are glycolipid biosurfactants secreted by the Pseudozyma yeasts, show not only excellent surface-active properties but also versatile biochemical actions including antitumor and cell-differentiation activities. In order to address the biochemical actions, interactions between MEL-A, the major component of MEL, and different lectins were investigated using the surface plasmon resonance spectroscopy. The monolayer of MEL-A showed high binding affinity to concanavalin A (ConA) and Maackia amurensis lectin-I (MAL-I). The observed affinity constants for ConA and MAL-I were estimated to be 9.48 +/- 1.31 x 10(6) and 3.13 +/- 0.274 x 10(6) M(-1), respectively; the value was comparable to that of Manalpha1-6(Manalpha1-3)Man, which is one of the most specific probe to ConA. Significantly, alpha-methyl-D-mannopyranoside (1 mM) exhibited no binding inhibition between MEL-A and ConA. MEL-A is thus likely to self-assemble to give a high affinity surface, where ConA binds to the hydrophilic headgroup in a different manner from that generally observed in lectin-saccharide interactions. The binding manner should be related with the biochemical actions of MEL toward mammalian cells via protein-carbohydrate interactions. PMID:17205206

  10. Direct Biomolecules Binding on Nonfouling Surface via Newly Discovered Supramolecular Self-assembly of Lysozyme under Physiological Condition

    Science.gov (United States)

    Yang, Peng

    2013-01-01

    A major challenge in the development of low cost and practical strategies for biomolecules immobilization on solid supports is that the multi-step chemical/physical activating and following deactivating procedures on nonfouling substrates often increase the cost and complexity of surface functional group types as well as deteriorate the surface integrity. Herein, we show a novel phase transition of lysozyme could be used to constitute a major step to address the above problem. It is found that when lysozyme is dissolved in a neutral buffer solution of 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES, pH 7.4) with 1–50 mM tris(2-carboxyethyl)phosphine (TCEP) added, a fast phase transition process occurs and the resulting novel fibra-like hierarchical supramolecular assemblies made by primary spherical particles aggregation would function as a “superglue” that strongly and quickly bind onto non-fouling coatings. This binding is highly selective towards lysozyme, and excludes completely tedious synthetical, chemical/physical activation/deactivation (blocking) steps. When biotin is conjugated with lysozyme, such phase transition quickly constructs a perfect biotinylated surface on nonfouling surface for avidin binding, showing great potential for the development of low-cost and practical biochips. PMID:22707360

  11. Assembly of the central domain of the 30S ribosomal subunit: roles for the primary binding ribosomal proteins S15 and S8.

    Science.gov (United States)

    Jagannathan, Indu; Culver, Gloria M

    2003-07-01

    Assembly of the 30S ribosomal subunit occurs in a highly ordered and sequential manner. The ordered addition of ribosomal proteins to the growing ribonucleoprotein particle is initiated by the association of primary binding proteins. These proteins bind specifically and independently to 16S ribosomal RNA (rRNA). Two primary binding proteins, S8 and S15, interact exclusively with the central domain of 16S rRNA. Binding of S15 to the central domain results in a conformational change in the RNA and is followed by the ordered assembly of the S6/S18 dimer, S11 and finally S21 to form the platform of the 30S subunit. In contrast, S8 is not part of this major platform assembly branch. Of the remaining central domain binding proteins, only S21 association is slightly dependent on S8. Thus, although S8 is a primary binding protein that extensively contacts the central domain, its role in assembly of this domain remains unclear. Here, we used directed hydroxyl radical probing from four unique positions on S15 to assess organization of the central domain of 16S rRNA as a consequence of S8 association. Hydroxyl radical probing of Fe(II)-S15/16S rRNA and Fe(II)-S15/S8/16S rRNA ribonucleoprotein particles reveal changes in the 16S rRNA environment of S15 upon addition of S8. These changes occur predominantly in helices 24 and 26 near previously identified S8 binding sites. These S8-dependent conformational changes are consistent with 16S rRNA folding in complete 30S subunits. Thus, while S8 binding is not absolutely required for assembly of the platform, it appears to affect significantly the 16S rRNA environment of S15 by influencing central domain organization.

  12. Ku80 binds to human replication origins prior to the assembly of the ORC complex.

    Science.gov (United States)

    Sibani, Sahar; Price, Gerald B; Zannis-Hadjopoulos, Maria

    2005-05-31

    The Ku heterodimer, an abundant nuclear protein, binds DNA replication origins in a sequence-specific manner and promotes initiation. In this study, using HCT116 Ku80+/- haplo-insufficient and Orc2(delta/-) hypomorphic cells, the order of binding of Ku and the human origin recognition complex (HsORC) was determined. The nuclear expression of Ku80 was found to be decreased by 60% in Ku80+/- cells, while its general association with chromatin was decreased by 33%. Coimmunoprecipitation studies indicated that the Ku heterodimer associates specifically with the human HsOrc-2, -3, -4, and -6 subunits. Chromatin immunoprecipitation (ChIP) experiments, using cells synchronized to late G1, showed that the association of Ku80 with the lamin B2, beta-globin, and c-myc origins in vivo was decreased by 1.5-, 2.3-, and 2.5-fold, respectively, in Ku80+/- cells. The association of HsOrc-3, -4, and -6 was consistently decreased in all three origins examined in Ku80+/- cells, while that of HsOrc-2 showed no significant variation, indicating that the HsOrc-3, -4, and -6 subunits bind to the origins after Ku80. In Orc2(delta/-) cells, the association of HsOrc-2 with the lamin B2, beta-globin, and c-myc origins was decreased by 2.8-, 4.9-, and 2.8-fold, respectively, relative to wild-type HCT116 cells. Furthermore, nascent strand abundance at these three origins was decreased by 4.5-, 2.3-, and 2.6-fold in Orc2(delta/-) relative to HCT116 cells, respectively. Interestingly, the association of Ku80 with these origins was not affected in this hypomorphic cell line, indicating that Ku and HsOrc-2 bind to origins independently of each other.

  13. C11orf83, a Mitochondrial Cardiolipin-Binding Protein Involved in bc1 Complex Assembly and Supercomplex Stabilization

    Science.gov (United States)

    Foti, Michelangelo; Raemy, Etienne; Vaz, Frédéric Maxime; Martinou, Jean-Claude; Bairoch, Amos

    2015-01-01

    Mammalian mitochondria may contain up to 1,500 different proteins, and many of them have neither been confidently identified nor characterized. In this study, we demonstrated that C11orf83, which was lacking experimental characterization, is a mitochondrial inner membrane protein facing the intermembrane space. This protein is specifically associated with the bc1 complex of the electron transport chain and involved in the early stages of its assembly by stabilizing the bc1 core complex. C11orf83 displays some overlapping functions with Cbp4p, a yeast bc1 complex assembly factor. Therefore, we suggest that C11orf83, now called UQCC3, is the functional human equivalent of Cbp4p. In addition, C11orf83 depletion in HeLa cells caused abnormal crista morphology, higher sensitivity to apoptosis, a decreased ATP level due to impaired respiration and subtle, but significant, changes in cardiolipin composition. We showed that C11orf83 binds to cardiolipin by its α-helices 2 and 3 and is involved in the stabilization of bc1 complex-containing supercomplexes, especially the III2/IV supercomplex. We also demonstrated that the OMA1 metalloprotease cleaves C11orf83 in response to mitochondrial depolarization, suggesting a role in the selection of cells with damaged mitochondria for their subsequent elimination by apoptosis, as previously described for OPA1. PMID:25605331

  14. Transcriptional modulation of hepatic lipoprotein assembly and secretion : coordinate regulation of the liver-fatty acid binding protein and microsomal triglyceride transfer protein genes

    OpenAIRE

    Spann, Nathanael J.

    2006-01-01

    Hepatic production of apolipoprotein (apo) B-containing lipoproteins provides a means to transport essential lipids and fat-soluble nutrients to peripheral tissues for utilization and storage. Liver-fatty acid binding protein (L-FABP) and microsomal triglyceride transfer protein (MTP) bind fatty acids and glycerolipids, respectively and facilitate their transfer into the VLDL assembly and secretion pathway. Sequence analysis reveals that the proximal promoter regions of L-FABP and MTP contain...

  15. MspA Porin-Gold Nanoparticle Assemblies: Enhanced Binding through a Controlled Cysteine Mutation.

    Science.gov (United States)

    Dani, Raj Kumar; Kang, Myungshim; Kalita, Mausam; Smith, Paul E; Bossmann, Stefan H; Chikan, Viktor

    2008-04-01

    In this study, the interactions of two gold nanoparticles of different sizes (average diameters of 3.7 +/- 2.6 and 17 +/- 3 nm) with octameric mycobacterial porin A from Mycobacterium smegmatis (MspA) and a mutant of MspA featuring a cysteine mutation in position 126 (Q126C) are investigated. From the observation of enhanced photoluminescence quenching, it is inferred that the presence of eight cysteines in the MspA Q126C mutant significantly enhances the binding of selected small gold nanoparticles within the inner pore of MspA. The large gold nanoparticle/porin complex shows photoluminescence enhancement, which is expected since the larger nanoparticles cannot dock within the homopore of MspA due to size exclusion. In addition to the fluorescence experiments, observation of energy transfer from the small gold nanoparticles to the MspA shows the close proximity of the small gold nanoparticles with the porin. Interestingly, the energy transfer of the large nanoparticle/MspA complex is completely missing. From high-performance liquid chromatography data, the estimated binding constants for small Au@MspA, large Au@MspA, small Au@MspAcys, and large Au@MspAcys are 1.3 x 10 (9), 2.22 x 10 (10), > 10 (12) (irreversible), and 1.7 x 10 (10), respectively. PMID:18318505

  16. Molecule-binding dependent assembly of split aptamer and γ-cyclodextrin: A sensitive excimer signaling approach for aptamer biosensors

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Fen [State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (China); Hubei Key Laboratory of Mine Environmental Pollution Control and Remediation, Environmental Science and Engineering College, Hubei Polytechnic University, Huangshi 435003 (China); Lian, Yan; Li, Jishan; Zheng, Jing; Hu, Yaping; Liu, Jinhua; Huang, Jin [State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (China); Yang, Ronghua, E-mail: Yangrh@pku.edu.cn [State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (China)

    2013-10-17

    Graphical abstract: Adenosine-binding aptamer was splitted into two fragments P2 and P3 which labeled pyrene molecules, mainly produce monomer signal. γ-CD cavity brings P2 and P3 in close proximity, allowing for weak excimer emission. In the presence of target, P2 and P3 are expected to bind ATP and form an aptamer/target complex, leads to large increase of the pyrene excimer fluorescence. -- Highlights: •We assembled split aptamer and γ-cyclodextrin fluorescence biosensors for ATP detection. •The biosensor increased quantum yield and emission lifetime of the excimer. •Time-resolved fluorescence is effective for ATP assay in complicated environment. -- Abstract: A highly sensitive and selective fluorescence aptamer biosensors for the determination of adenosine triphosphate (ATP) was developed. Binding of a target with splitting aptamers labeled with pyrene molecules form stable pyrene dimer in the γ-cyclodextrin (γ-CD) cavity, yielding a strong excimer emission. We have found that inclusion of pyrene dimer in γ-cyclodextrin cavity not only exhibits additive increases in quantum yield and emission lifetime of the excimer, but also facilitates target-induced fusion of the splitting aptamers to form the aptamer/target complex. As proof-of-principle, the approach was applied to fluorescence detection of adenosine triphosphate. With an anti-ATP aptamer, the approach exhibits excimer fluorescence response toward ATP with a maximum signal-to-background ratio of 32.1 and remarkably low detection limit of 80 nM ATP in buffer solution. Moreover, due to the additive fluorescence lifetime of excimer induced by γ-cyclodextrin, time-resolved measurements could be conveniently used to detect as low as 0.5 μM ATP in blood serum quantitatively.

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

    Directory of Open Access Journals (Sweden)

    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.

  18. Modulation of microtubule assembly by the HIV-1 Tat protein is strongly dependent on zinc binding to Tat

    Directory of Open Access Journals (Sweden)

    Muller Sylviane

    2008-07-01

    Full Text Available Abstract Background During HIV-1 infection, the Tat protein plays a key role by transactivating the transcription of the HIV-1 proviral DNA. In addition, Tat induces apoptosis of non-infected T lymphocytes, leading to a massive loss of immune competence. This apoptosis is notably mediated by the interaction of Tat with microtubules, which are dynamic components essential for cell structure and division. Tat binds two Zn2+ ions through its conserved cysteine-rich region in vitro, but the role of zinc in the structure and properties of Tat is still controversial. Results To investigate the role of zinc, we first characterized Tat apo- and holo-forms by fluorescence correlation spectroscopy and time-resolved fluorescence spectroscopy. Both of the Tat forms are monomeric and poorly folded but differ by local conformational changes in the vicinity of the cysteine-rich region. The interaction of the two Tat forms with tubulin dimers and microtubules was monitored by analytical ultracentrifugation, turbidity measurements and electron microscopy. At 20°C, both of the Tat forms bind tubulin dimers, but only the holo-Tat was found to form discrete complexes. At 37°C, both forms promoted the nucleation and increased the elongation rates of tubulin assembly. However, only the holo-Tat increased the amount of microtubules, decreased the tubulin critical concentration, and stabilized the microtubules. In contrast, apo-Tat induced a large amount of tubulin aggregates. Conclusion Our data suggest that holo-Tat corresponds to the active form, responsible for the Tat-mediated apoptosis.

  19. On sulfur core level binding energies in thiol self-assembly and alternative adsorption sites: An experimental and theoretical study

    International Nuclear Information System (INIS)

    Characteristic core level binding energies (CLBEs) are regularly used to infer the modes of molecular adsorption: orientation, organization, and dissociation processes. Here, we focus on a largely debated situation regarding CLBEs in the case of chalcogen atom bearing molecules. For a thiol, this concerns the case when the CLBE of a thiolate sulfur at an adsorption site can be interpreted alternatively as due to atomic adsorption of a S atom, resulting from dissociation. Results of an investigation of the characteristics of thiol self-assembled monolayers (SAMs) obtained by vacuum evaporative adsorption are presented along with core level binding energy calculations. Thiol ended SAMs of 1,4-benzenedimethanethiol (BDMT) obtained by evaporation on Au display an unconventional CLBE structure at about 161.25 eV, which is close to a known CLBE of a S atom on Au. Adsorption and CLBE calculations for sulfur atoms and BDMT molecules are reported and allow delineating trends as a function of chemisorption on hollow, bridge, and atop sites and including the presence of adatoms. These calculations suggest that the 161.25 eV peak is due to an alternative adsorption site, which could be associated to an atop configuration. Therefore, this may be an alternative interpretation, different from the one involving the adsorption of atomic sulfur resulting from the dissociation process of the S–C bond. Calculated differences in S(2p) CLBEs for free BDMT molecules, SH group sulfur on top of the SAM, and disulfide are also reported to clarify possible errors in assignments

  20. On sulfur core level binding energies in thiol self-assembly and alternative adsorption sites: An experimental and theoretical study

    Energy Technology Data Exchange (ETDEWEB)

    Jia, Juanjuan [Institut des Sciences Moléculaires d’Orsay, Université-Paris Sud, 91405 Orsay (France); CNRS, UMR 8214, Institut des Sciences Moléculaires d’Orsay, Orsay ISMO, Bâtiment 351, Université Paris Sud, 91405 Orsay (France); Kara, Abdelkader, E-mail: abdelkader.kara@ucf.edu, E-mail: vladimir.esaulov@u-psud.fr [Department of Physics, University of Central Florida, Orlando, Florida 32816 (United States); Pasquali, Luca [Dipartimento di Ingegneria “E. Ferrari,” Università di Modena e Reggio Emilia, Via Vignolese 905, 41125 Modena (Italy); IOM-CNR, s.s. 14, Km. 163.5 in AREA Science Park, 34149 Basovizza, Trieste (Italy); Department of Physics, University of Johannesburg, P.O. Box 524, Auckland Park 2006 (South Africa); Bendounan, Azzedine; Sirotti, Fausto [Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, BP 48, F-91192 Gif-sur-Yvette Cedex (France); Esaulov, Vladimir A., E-mail: abdelkader.kara@ucf.edu, E-mail: vladimir.esaulov@u-psud.fr [Institut des Sciences Moléculaires d’Orsay, Université-Paris Sud, 91405 Orsay (France); CNRS, UMR 8214, Institut des Sciences Moléculaires d’Orsay, Orsay ISMO, Bâtiment 351, Université Paris Sud, 91405 Orsay (France); IOM-CNR, s.s. 14, Km. 163.5 in AREA Science Park, 34149 Basovizza, Trieste (Italy)

    2015-09-14

    Characteristic core level binding energies (CLBEs) are regularly used to infer the modes of molecular adsorption: orientation, organization, and dissociation processes. Here, we focus on a largely debated situation regarding CLBEs in the case of chalcogen atom bearing molecules. For a thiol, this concerns the case when the CLBE of a thiolate sulfur at an adsorption site can be interpreted alternatively as due to atomic adsorption of a S atom, resulting from dissociation. Results of an investigation of the characteristics of thiol self-assembled monolayers (SAMs) obtained by vacuum evaporative adsorption are presented along with core level binding energy calculations. Thiol ended SAMs of 1,4-benzenedimethanethiol (BDMT) obtained by evaporation on Au display an unconventional CLBE structure at about 161.25 eV, which is close to a known CLBE of a S atom on Au. Adsorption and CLBE calculations for sulfur atoms and BDMT molecules are reported and allow delineating trends as a function of chemisorption on hollow, bridge, and atop sites and including the presence of adatoms. These calculations suggest that the 161.25 eV peak is due to an alternative adsorption site, which could be associated to an atop configuration. Therefore, this may be an alternative interpretation, different from the one involving the adsorption of atomic sulfur resulting from the dissociation process of the S–C bond. Calculated differences in S(2p) CLBEs for free BDMT molecules, SH group sulfur on top of the SAM, and disulfide are also reported to clarify possible errors in assignments.

  1. Reversible supramolecular assembly at specific DNA sites: nickel-promoted bivalent DNA binding with designed peptide and bipyridyl-bis(benzamidine) components.

    Science.gov (United States)

    Sánchez, Mateo I; Mosquera, Jesús; Vázquez, M Eugenio; Mascareñas, José L

    2014-09-01

    At specific DNA sites, nickel(II) salts promote the assembly of designed components, namely a bis(histidine)-modified peptide that is derived from a bZIP transcription factor and a bis(benzamidine) unit that is equipped with a bipyridine. This programmed supramolecular system with emergent properties reproduces some key characteristics of naturally occurring DNA-binding proteins, such as bivalence, selectivity, responsiveness to external agents, and reversibility.

  2. Structure-Function Analysis of Friedreich's Ataxia Mutants Reveals Determinants of Frataxin Binding and Activation of the Fe-S Assembly Complex

    Energy Technology Data Exchange (ETDEWEB)

    Bridwell-Rabb, Jennifer; Winn, Andrew M; Barondeau, David P [TAM

    2012-08-01

    Friedreich's ataxia (FRDA) is a progressive neurodegenerative disease associated with the loss of function of the protein frataxin (FXN) that results from low FXN levels due to a GAA triplet repeat expansion or, occasionally, from missense mutations in the FXN gene. Here biochemical and structural properties of FXN variants, including three FRDA missense mutations (N146K, Q148R, and R165C) and three related mutants (N146A, Q148G, and Q153A), were determined in an effort to understand the structural basis for the loss of function. In vitro assays revealed that although the three FRDA missense mutations exhibited similar losses of cysteine desulfurase and Fe-S cluster assembly activities, the causes for these activation defects were distinct. The R165C variant exhibited a kcat/KM higher than that of native FXN but weak binding to the NFS1, ISD11, and ISCU2 (SDU) complex, whereas the Q148R variant exhibited the lowest kcat/KM of the six tested FXN variants and only a modest binding deficiency. The order of the FXN binding affinities for the SDU Fe-S assembly complex was as follows: FXN > Q148R > N146A > Q148G > N146K > Q153A > R165C. Four different classes of FXN variants were identified on the basis of their biochemical properties. Together, these structure-function studies reveal determinants for the binding and allosteric activation of the Fe-S assembly complex and provide insight into how FRDA missense mutations are functionally compromised.

  3. Assembly sequence generation for hierarchical structure product based on virtual assembly binding%基于虚拟装配体绑定的产品层次化装配序列生成

    Institute of Scientific and Technical Information of China (English)

    宋泾舸; 查建中; 陆一平

    2011-01-01

    装配是产品制造中的重要环节之一计算机辅助装配顺序的生成为实施快速、灵活、优化的装配,提高装配质量和效率提供有力的支持.任务层次与分解方法的设计是层次任务网规划方法应用的关键技术.文中提出了一种基于虚拟装配体绑定的底层装配操作实施机制,在此基拙上建立了产品装配序列生成的任务分解策略.装配实例表明,该方法在产品装配序列生成中具有建模层次清晰、任务分解策略易于制定、装配序列生成比较灵活的特点.%Assembly is one of the important procedures during product manufacturing. Computer assistant assembly sequence generation could provide positive support for carrying out fast, flexible and optimal assembling, and improving the quality and efficiency of manufacturing. Designing task hierarchy and decomposition strategies is regarded as key technique in hierarchical task network (HTN) planning approach. A mechanism for carrying out assembling behavior is proposed based on virtual assembly binding. Then, based on this mcchanism, strategies for assembling task decomposition are presented.Examples show that the proposed model has clear hierarchy, task decomposition strategy is easy to design, and the sequence generation process is flexible.

  4. Orc1 Binding to Mitotic Chromosomes Precedes Spatial Patterning during G1 Phase and Assembly of the Origin Recognition Complex in Human Cells.

    Science.gov (United States)

    Kara, Nihan; Hossain, Manzar; Prasanth, Supriya G; Stillman, Bruce

    2015-05-01

    Replication of eukaryotic chromosomes occurs once every cell division cycle in normal cells and is a tightly controlled process that ensures complete genome duplication. The origin recognition complex (ORC) plays a key role during the initiation of DNA replication. In human cells, the level of Orc1, the largest subunit of ORC, is regulated during the cell division cycle, and thus ORC is a dynamic complex. Upon S phase entry, Orc1 is ubiquitinated and targeted for destruction, with subsequent dissociation of ORC from chromosomes. Time lapse and live cell images of human cells expressing fluorescently tagged Orc1 show that Orc1 re-localizes to condensing chromatin during early mitosis and then displays different nuclear localization patterns at different times during G1 phase, remaining associated with late replicating regions of the genome in late G1 phase. The initial binding of Orc1 to mitotic chromosomes requires C-terminal amino acid sequences that are similar to mitotic chromosome-binding sequences in the transcriptional pioneer protein FOXA1. Depletion of Orc1 causes concomitant loss of the mini-chromosome maintenance (Mcm2-7) helicase proteins on chromatin. The data suggest that Orc1 acts as a nucleating center for ORC assembly and then pre-replication complex assembly by binding to mitotic chromosomes, followed by gradual removal from chromatin during the G1 phase. PMID:25784553

  5. Design of a minimal polypeptide unit for bacteriochlorophyll binding and self-assembly based on photosynthetic bacterial light-harvesting proteins.

    Science.gov (United States)

    Noy, Dror; Dutton, P Leslie

    2006-02-21

    We introduce LH1beta24, a minimal 24 amino acid polypeptide that binds and assembles bacteriochlorophylls (BChls) in micelles of octyl beta-glucoside (OG) into complexes with spectral properties that resemble those of B820, a universal intermediate in the assembly of native purple bacterial light-harvesting complexes (LHs). LH1beta24 was designed by a survey of sequences and crystal structures of bacterial LH proteins from different organisms combined with currently available information from in vitro reconstitution studies and genetically modified LHs in vivo. We took as a template for the design sphbeta31, a truncated 31 amino acid analogue of the native beta-apoprotein from the core LH complex of Rhodobacter sphaeroides. This peptide self-assembles with BChls to form B820 and, upon cooling and lowering OG concentration, forms red-shifted B850 spectral species that are considered analogous to native LH complexes. We find that LH1beta24 self-assembles with BChl in OG to form homodimeric B820-type subunits comprising two LH1beta24 and two BChl molecules per subunit. We demonstrate, by modeling the structure using the highly homologous structure of LH2 from Rhodospirillum molischianum, that it has the minimal size for BChl binding. Additionally, we have compared the self-assembly of sphbeta31 and LH1beta24 with BChls and discovered that the association enthalpies and entropies of both species are similar to those measured for native LH1 from Rhodospirillum rubrum. However, sphbeta31 readily aggregates into intermediate higher oligomeric species and further to form B850 species; moreover, the assembly process of these oligomers is not reversible, and they are apparently large nonspecific BChl-peptide coaggregates rather than well-defined nativelike LH complexes. Similar aggregates were observed during LH1beta24 assembly, but these were formed less readily and required lower temperatures than sphbeta31. In view of these results, we reevaluate previous in vitro

  6. Fabrication of Thermo-Responsive Molecular Layers from Self-Assembling Elastin-Like Oligopeptides Containing Cell-Binding Domain for Tissue Engineering

    Directory of Open Access Journals (Sweden)

    Tomoyuki Koga

    2015-01-01

    Full Text Available Novel thermo-responsive elastin-like oligopeptides containing cell-binding epitope (Arg-Gly-Asp-Ser sequence; arginine-glycine-aspartic acid-serine (RGDS-elastin-like peptides (ELP and RGDS-deg-ELP; were newly prepared as building blocks of self-assembled molecular layer for artificial extra cellular matrix. A detailed analysis of the conformation of the oligo(ELPs in water and their self-assembling behavior onto hydrophobic surfaces were performed by using circular dichroism, Fourier transform infrared spectroscopy (FTIR, atomic force microscopy and water contact angle measurements. The experimental results revealed that both oligo(ELPs self-assembled onto hydrophobic surfaces and formed molecular layers based on their thermo-responsive conformational change from hydrous random coil to dehydrated β-turn structure. Effective cell adhesion and spreading behaviors were observed on these self-assembled oligo(ELP layers. In addition, attached cells were found to be recovered successfully as a cell-sheet by temperature-induced disassembly of oligo(ELP layer. This achievement provides an important insight to construct novel oligopeptide-based nano-surfaces for the design of smart artificial extra-cellular matrix.

  7. Influence of “Glow Discharge Plasma” as an External Stimulus on the Self-Assembly, Morphology and Binding Affinity of Gold Nanoparticle-Streptavidin Conjugates

    Directory of Open Access Journals (Sweden)

    Chang-Jun Liu

    2012-05-01

    Full Text Available In this study, we investigate the influence of glow discharge plasma (GDP on the self-assembly, morphology and binding affinity of streptavidin coated gold nanoparticles (Au-NP-SV and biotinylated antibody (bAb adsorbed on a highly oriented pyrolytic graphite (HOPG substrate. Atomic force microscope (AFM was used to image the pre- and post-GDP treated samples. The analysis of the AFM images showed a considerable change in the aggregation and morphology of Au-NP-conjugates after treatment with GDP. To our knowledge, this is the first report on using GDP to enhance and speed-up the aggregation (sintering of adsorbed NP biomolecular conjugates. These results show a promising route that could be generalized for other NPs and their conjugates. It can also be considered as an alternative and cheap aggregation method for controlling the binding affinity of biomolecular species on different surfaces with interesting applications.

  8. The cholesterol-dependent cytolysin signature motif: a critical element in the allosteric pathway that couples membrane binding to pore assembly.

    Directory of Open Access Journals (Sweden)

    Kelley J Dowd

    Full Text Available The cholesterol-dependent cytolysins (CDCs constitute a family of pore-forming toxins that contribute to the pathogenesis of a large number of Gram-positive bacterial pathogens.The most highly conserved region in the primary structure of the CDCs is the signature undecapeptide sequence (ECTGLAWEWWR. The CDC pore forming mechanism is highly sensitive to changes in its structure, yet its contribution to the molecular mechanism of the CDCs has remained enigmatic. Using a combination of fluorescence spectroscopic methods we provide evidence that shows the undecapeptide motif of the archetype CDC, perfringolysin O (PFO, is a key structural element in the allosteric coupling of the cholesterol-mediated membrane binding in domain 4 (D4 to distal structural changes in domain 3 (D3 that are required for the formation of the oligomeric pore complex. Loss of the undecapeptide function prevents all measurable D3 structural transitions, the intermolecular interaction of membrane bound monomers and the assembly of the oligomeric pore complex. We further show that this pathway does not exist in intermedilysin (ILY, a CDC that exhibits a divergent undecapeptide and that has evolved to use human CD59 rather than cholesterol as its receptor. These studies show for the first time that the undecapeptide of the cholesterol-binding CDCs forms a critical element of the allosteric pathway that controls the assembly of the pore complex.

  9. Tankyrase Inhibitors Stimulate the Ability of Tankyrases to Bind Axin and Drive Assembly of β-Catenin Degradation-Competent Axin Puncta.

    Directory of Open Access Journals (Sweden)

    Estefania Martino-Echarri

    Full Text Available Activation of the wnt signaling pathway is a major cause of colon cancer development. Tankyrase inhibitors (TNKSi have recently been developed to block the wnt pathway by increasing axin levels to promote degradation of the wnt-regulator β-catenin. TNKSi bind to the PARP (poly(ADPribose polymerase catalytic region of tankyrases (TNKS, preventing the PARylation of TNKS and axin that normally control axin levels through ubiquitination and degradation. TNKSi treatment of APC-mutant SW480 colorectal cancer cells can induce axin puncta which act as sites for assembly of β-catenin degradation complexes, however this process is poorly understood. Using this model system, we found that siRNA knockdown of TNKSs 1 and 2 actually blocked the ability of TNKSi drugs to induce axin puncta, revealing that puncta formation requires both the expression and the inactivation of TNKS. Immunoprecipitation assays showed that treatment of cells with TNKSi caused a strong increase in the formation of axin-TNKS complexes, correlating with an increase in insoluble or aggregated forms of TNKS/axin. The efficacy of TNKSi was antagonized by proteasome inhibitors, which stabilized the PARylated form of TNKS1 and reduced TNKSi-mediated assembly of axin-TNKS complexes and puncta. We hypothesise that TNKSi act to stimulate TNKS oligomerization and assembly of the TNKS-axin scaffold that form puncta. These new insights may help in optimising the future application of TNKSi in anticancer drug design.

  10. Solid-state capture and real-time analysis of individual T cell activation via self-assembly of binding multimeric proteins on functionalized materials surfaces.

    Science.gov (United States)

    Diener, Kerrilyn R; Christo, Susan N; Griesser, Stefani S; Sarvestani, Ghafar T; Vasilev, Krasimir; Griesser, Hans J; Hayball, John D

    2012-01-01

    Polyfunctional T cell responses are increasingly underpinning new and improved vaccination regimens. Studies of the nature and extent of these T cell responses may be facilitated if specific T cell populations can be assessed from mixed populations by ligand-mediated capture in a solid-state assay format. Accordingly, we report here the development of a novel strategy for the solid-state capture and real-time activation analyses of individual cognate T cells which utilizes a spontaneous self-assembly process for generating multimers of biotinylated class I major histocompatibility-peptide complex (MHCp) directly on the solid-state assay surface while also ensuring stability by covalent interfacial binding. The capture surface was constructed by the fabrication of multilayer coatings onto standard slides. The first layer was a thin polymer coating with surface aldehyde groups, onto which streptavidin was covalently immobilized, followed by the docking of multimers of biotinylated MHCp or biotinylated anti-CD45.1 monoclonal antibody. The high binding strength at each step of this immobilization sequence aims to ensure that artefacts such as (partial) detachment, or displacement by proteins from solution, would not interfere with the intended biological assays. The multilayer coating steps were monitored by X-ray photoelectron spectroscopy; data indicated that the MHCp proteins self-assembled in a multimeric form onto the streptavidin surface. Immobilized multimeric MHCp demonstrated the capacity to bind and retain antigen-specific T cells from mixed populations of cells onto the solid carrier. Furthermore, real-time confocal microscopic detection and quantification of subsequent calcium flux using paired fluorescent ratiometric probes facilitated the analysis of individual T cell response profiles, as well as population analyses using a combination of individual T cell events. PMID:21945827

  11. Enantioselective binding of amino acids and amino alcohols by self-assembled chiral basket-shaped receptors

    NARCIS (Netherlands)

    Escuder, B.; Rowan, A.E.; Feiters, M.C.; Nolte, R.J.M.

    2004-01-01

    Amino acid appended diphenylglycoluril-based chiral molecular receptors 2 and 3 have been prepared and their aggregation has been studied in water at various pH's and in chloroform. The binding of several biologically relevant guests with aromatic moieties to these aggregates has been studied with U

  12. Asymmetric Assembly of Merkel Cell Polyomavirus Large T-Antigen Origin Binding Domains at the Viral Origin

    Energy Technology Data Exchange (ETDEWEB)

    C Harrison; G Meinke; H Kwun; H Rogalin; P Phelan; P Bullock; Y Chang; P Moore; A Bohm

    2011-12-31

    The double-stranded DNA polyomavirus Merkel cell polyomavirus (MCV) causes Merkel cell carcinoma, an aggressive but rare human skin cancer that most often affects immunosuppressed and elderly persons. As in other polyomaviruses, the large T-antigen of MCV recognizes the viral origin of replication by binding repeating G(A/G)GGC pentamers. The spacing, number, orientation, and necessity of repeats for viral replication differ, however, from other family members such as SV40 and murine polyomavirus. We report here the 2.9 {angstrom} crystal structure of the MCV large T-antigen origin binding domain (OBD) in complex with a DNA fragment from the MCV origin of replication. Consistent with replication data showing that three of the G(A/G)GGC-like binding sites near the center of the origin are required for replication, the crystal structure contains three copies of the OBD. This stoichiometry was verified using isothermal titration calorimetry. The affinity for G(A/G)GGC-containing double-stranded DNA was found to be {approx} 740 nM, approximately 8-fold weaker than the equivalent domain in SV40 for the analogous region of the SV40 origin. The difference in affinity is partially attributable to DNA-binding residue Lys331 (Arg154 in SV40). In contrast to SV40, a small protein-protein interface is observed between MCV OBDs when bound to the central region of the origin. This protein-protein interface is reminiscent of that seen in bovine papilloma virus E1 protein. Mutational analysis indicates, however, that this interface contributes little to DNA binding energy.

  13. Protein-DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies.

    Science.gov (United States)

    Zakrzewska, Krystyna; Bouvier, Benjamin; Michon, Alexis; Blanchet, Christophe; Lavery, Richard

    2009-12-01

    We use a physics-based approach termed ADAPT to analyse the sequence-specific interactions of three proteins which bind to DNA on the side of the minor groove. The analysis is able to estimate the binding energy for all potential sequences, overcoming the combinatorial problem via a divide-and-conquer approach which breaks the protein-DNA interface down into a series of overlapping oligomeric fragments. All possible base sequences are studied for each fragment. Energy minimisation with an all-atom representation and a conventional force field allows for conformational adaptation of the DNA and of the protein side chains for each new sequence. As a result, the analysis depends linearly on the length of the binding site and complexes as large as the nucleosome can be treated, although this requires access to grid computing facilities. The results on the three complexes studied are in good agreement with experiment. Although they all involve significant DNA deformation, it is found that this does not necessarily imply that the recognition will be dominated by the sequence-dependent mechanical properties of DNA.

  14. Structure of the hepatitis E virus-like particle suggests mechanisms for virus assembly and receptor binding

    Energy Technology Data Exchange (ETDEWEB)

    Guu, Tom S.Y.; Liu, Zheng; Ye, Qiaozhen; Mata, Douglas A.; Li, Kunpeng; Yin, Changcheng; Zhang, Jingqiang; Tao, Yizhi Jane; (Sun Yat-Sen); (Rice); (Peking)

    2009-08-25

    Hepatitis E virus (HEV), a small, non-enveloped RNA virus in the family Hepeviridae, is associated with endemic and epidemic acute viral hepatitis in developing countries. Our 3.5-{angstrom} structure of a HEV-like particle (VLP) shows that each capsid protein contains 3 linear domains that form distinct structural elements: S, the continuous capsid; P1, 3-fold protrusions; and P2, 2-fold spikes. The S domain adopts a jelly-roll fold commonly observed in small RNA viruses. The P1 and P2 domains both adopt {beta}-barrel folds. Each domain possesses a potential polysaccharide-binding site that may function in cell-receptor binding. Sugar binding to P1 at the capsid protein interface may lead to capsid disassembly and cell entry. Structural modeling indicates that native T = 3 capsid contains flat dimers, with less curvature than those of T = 1 VLP. Our findings significantly advance the understanding of HEV molecular biology and have application to the development of vaccines and antiviral medications.

  15. The Oligomeric Outer Dynein Arm Assembly Factor CCDC103 Is Tightly Integrated within the Ciliary Axoneme and Exhibits Periodic Binding to Microtubules*

    Science.gov (United States)

    King, Stephen M.; Patel-King, Ramila S.

    2015-01-01

    CCDC103 is an ∼29-kDa protein consisting of a central RPAP3_C domain flanked by N- and C-terminal coiled coils. Defects in CCDC103 lead to primary ciliary dyskinesia caused by the loss of outer dynein arms. This protein is present along the entire length of the ciliary axoneme and does not require other dynein or docking complex components for its integration. Unlike other known dynein assembly factors within the axoneme, CCDC103 is not solubilized by 0.6 m NaCl and requires more chaotropic conditions, such as 0.5 m KI. Alternatively, it can be extracted using 0.3% sarkosyl. CCDC103 forms stable dimers and other oligomers in solution through interactions involving the central domain. The smallest particle observed by dynamic light scattering has a hydrodynamic diameter of ∼25 nm. Furthermore, CCDC103 binds microtubules directly, forming ∼9-nm diameter particles that exhibit a 12-nm spacing on the microtubule lattice, suggesting that there may be two CCDC103 units per outer arm dynein repeat. Although the outer dynein arm docking complex is necessary to form arrays of dyneins along microtubules, it is not sufficient to set up a single array in a precise location on each axonemal doublet. We propose that CCDC103 helps generate a high-affinity site on the doublets for outer arm assembly, either through direct interactions or indirectly, perhaps by modifying the underlying microtubule lattice. PMID:25572396

  16. The TPR domain in the host Cyp40-like cyclophilin binds to the viral replication protein and inhibits the assembly of the tombusviral replicase.

    Science.gov (United States)

    Lin, Jing-Yi; Mendu, Venugopal; Pogany, Judit; Qin, Jun; Nagy, Peter D

    2012-02-01

    Replication of plus-stranded RNA viruses is greatly affected by numerous host-coded proteins acting either as susceptibility or resistance factors. Previous genome-wide screens and global proteomics approaches with Tomato bushy stunt tombusvirus (TBSV) in a yeast model host revealed the involvement of cyclophilins, which are a large family of host prolyl isomerases, in TBSV replication. In this paper, we identified those members of the large cyclophilin family that interacted with the viral replication proteins and inhibited TBSV replication. Further characterization of the most effective cyclophilin, the Cyp40-like Cpr7p, revealed that it strongly inhibits many steps during TBSV replication in a cell-free replication assay. These steps include viral RNA recruitment inhibited via binding of Cpr7p to the RNA-binding region of the viral replication protein; the assembly of the viral replicase complex and viral RNA synthesis. Since the TPR (tetratricopeptide repeats) domain, but not the catalytic domain of Cpr7p is needed for the inhibitory effect on TBSV replication, it seems that the chaperone activity of Cpr7p provides the negative regulatory function. We also show that three Cyp40-like proteins from plants can inhibit TBSV replication in vitro and Cpr7p is also effective against Nodamura virus, an insect pathogen. Overall, the current work revealed a role for Cyp40-like proteins and their TPR domains as regulators of RNA virus replication.

  17. Ha83, a Chitin Binding Domain Encoding Gene, Is Important to Helicoverpa armigera Nucleopolyhedrovirus Budded Virus Production and Occlusion Body Assembling.

    Science.gov (United States)

    Yu, Huan; Xu, Jian; Liu, Qiang; Liu, Tong-Xian; Wang, Dun

    2015-01-01

    Helicoerpa armigera nucleopolyhedrovirus (HearNPV) ha83 is a late expressed gene that encodes a chitin binding protein. Chitin domain truncation studies revealed that the cysteine at the 128 amino acid position probably played an important role in both chitin binding ability and protein transmission of Ha83. In order to study the function of ha83 in the HearNPV infection cycle, an ha83 knockout HearNPV (Ha83KO) was constructed via homologous recombination. Viral growth and viral DNA replication curves showed that fewer budded virions were produced in Ha83KO transfected cells, while viral DNA replication was increased. Electron microscopy revealed that fewer nucleocapsids were transmitted from virogenic stroma in the Ha83KO transfected cell nucleus, and the morphology of occlusion bodies was prominently larger and cube-shaped. Furthermore, DNA quantity in occlusion bodies of Ha83KO was significantly lower than the occlusion bodies of HaWT. The transcription analysis indicated that these changes may be due to the decreased expression level of viral structural associated genes, such as polyhedrin, p10, pif-2, or cg30 in Ha83KO infected cells. Above results demonstrated that the cysteine at the 128 amino acid position in Ha83 might be the key amino acid, and Ha83 plays an important role in BVs production and OBs assembling. PMID:26057202

  18. Dynein Light Chain LC8 Is Required for RNA Polymerase I-Mediated Transcription in Trypanosoma brucei, Facilitating Assembly and Promoter Binding of Class I Transcription Factor A.

    Science.gov (United States)

    Kirkham, Justin K; Park, Sung Hee; Nguyen, Tu N; Lee, Ju Huck; Günzl, Arthur

    2016-01-01

    Dynein light chain LC8 is highly conserved among eukaryotes and has both dynein-dependent and dynein-independent functions. Interestingly, LC8 was identified as a subunit of the class I transcription factor A (CITFA), which is essential for transcription by RNA polymerase I (Pol I) in the parasite Trypanosoma brucei. Given that LC8 has never been identified with a basal transcription factor and that T. brucei relies on RNA Pol I for expressing the variant surface glycoprotein (VSG), the key protein in antigenic variation, we investigated the CITFA-specific role of LC8. Depletion of LC8 from mammalian-infective bloodstream trypanosomes affected cell cycle progression, reduced the abundances of rRNA and VSG mRNA, and resulted in rapid cell death. Sedimentation analysis, coimmunoprecipitation of recombinant proteins, and bioinformatic analysis revealed an LC8 binding site near the N terminus of the subunit CITFA2. Mutation of this site prevented the formation of a CITFA2-LC8 heterotetramer and, in vivo, was lethal, affecting assembly of a functional CITFA complex. Gel shift assays and UV cross-linking experiments identified CITFA2 as a promoter-binding CITFA subunit. Accordingly, silencing of LC8 or CITFA2 resulted in a loss of CITFA from RNA Pol I promoters. Hence, we discovered an LC8 interaction that, unprecedentedly, has a basal function in transcription.

  19. Protein self-assembly and lipid binding in the folding of the potassium channel KcsA.

    Science.gov (United States)

    Barrera, Francisco N; Renart, M Lourdes; Poveda, José A; de Kruijff, Ben; Killian, J Antoinette; González-Ros, José M

    2008-02-19

    Moderate concentrations of the alcohol 2,2,2-trifluoroethanol (TFE) cause the coupled unfolding and dissociation into subunits of the homotetrameric potassium channel KcsA, in a process that is partially irreversible when the protein is solubilized in plain dodecyl beta-d-maltoside (DDM) micelles [Barrera et al. (2005) Biochemistry 44, 14344-52]. Here we report that the transition from the folded tetramer to the unfolded monomer becomes completely reversible when KcsA is solubilized in mixed micelles composed of the detergent DDM and the lipids DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) and DOPG (1,2-dioleoyl-sn-glycero-3-[phospho-rac-(1-glycerol)]). This result suggests that lipids may act as effectors in the tetramerization of KcsA. The observed reversibility allowed the determination of the standard free energy of the folding reaction of KcsA: DeltaG = 30.5 +/- 3.1 kcal x mol-1. We also observed that, prior to the unfolding of the tetramer, the presence of lower TFE concentrations causes the disassembly of supramolecular clusters of KcsA into the individual tetrameric molecules. Within the limits of experimental resolution, this is also a reversible process, but unlike the tetramer to monomer transition from above, the level of clustering is not influenced by the presence of solubilized lipids. These observations suggest a distinct role of the lipids in the different in vitro assembly steps (folding/tetramerization and clustering) of KcsA. PMID:18205389

  20. Microplate-based assay for identifying small molecules that bind a specific intersubunit interface within the assembled HIV-1 capsid.

    Science.gov (United States)

    Halambage, Upul D; Wong, Jason P; Melancon, Bruce J; Lindsley, Craig W; Aiken, Christopher

    2015-09-01

    Despite the availability of >30 effective drugs for managing HIV-1 infection, no current therapy is curative, and long-term management is challenging owing to the emergence and spread of drug-resistant mutants. Identification of drugs against novel HIV-1 targets would expand the current treatment options and help to control resistance. The highly conserved HIV-1 capsid protein represents an attractive target because of its multiple roles in replication of the virus. However, the low antiviral potencies of the reported HIV-1 capsid-targeting inhibitors render them unattractive for therapeutic development. To facilitate the identification of more-potent HIV-1 capsid inhibitors, we developed a scintillation proximity assay to screen for small molecules that target a biologically active and specific intersubunit interface in the HIV-1 capsid. The assay, which is based on competitive displacement of a known capsid-binding small-molecule inhibitor, exhibited a signal-to-noise ratio of >9 and a Z factor of >0.8. In a pilot screen of a chemical library containing 2,400 druglike compounds, we obtained a hit rate of 1.8%. This assay has properties that are suitable for screening large compound libraries to identify novel HIV-1 capsid ligands with antiviral activity. PMID:26077250

  1. Mac-2 binding protein is a cell-adhesive protein of the extracellular matrix which self-assembles into ring-like structures and binds beta1 integrins, collagens and fibronectin

    DEFF Research Database (Denmark)

    Sasaki, T; Brakebusch, C; Engel, J;

    1998-01-01

    Human Mac-2 binding protein (M2BP) was prepared in recombinant form from the culture medium of 293 kidney cells and consisted of a 92 kDa subunit. The protein was obtained in a native state as indicated by CD spectroscopy, demonstrating alpha-helical and beta-type structure, and by protease resis...

  2. The structure of tubulin-binding cofactor A from Leishmania major infers a mode of association during the early stages of microtubule assembly

    Energy Technology Data Exchange (ETDEWEB)

    Barrack, Keri L.; Fyfe, Paul K.; Hunter, William N., E-mail: w.n.hunter@dundee.ac.uk [University of Dundee, Dow Street, Dundee DD1 5EH, Scotland (United Kingdom)

    2015-04-21

    The structure of a tubulin-binding cofactor from L. major is reported and compared with yeast, plant and human orthologues. Tubulin-binding cofactor A (TBCA) participates in microtubule formation, a key process in eukaryotic biology to create the cytoskeleton. There is little information on how TBCA might interact with β-tubulin en route to microtubule biogenesis. To address this, the protozoan Leishmania major was targeted as a model system. The crystal structure of TBCA and comparisons with three orthologous proteins are presented. The presence of conserved features infers that electrostatic interactions that are likely to involve the C-terminal tail of β-tubulin are key to association. This study provides a reagent and template to support further work in this area.

  3. The PASTA domain of penicillin-binding protein SpoVD is dispensable for endospore cortex peptidoglycan assembly in Bacillus subtilis.

    Science.gov (United States)

    Bukowska-Faniband, Ewa; Hederstedt, Lars

    2015-02-01

    Peptidoglycan is the major structural component of the bacterial cell wall. Penicillin-binding proteins (PBPs), located at the exterior of the cytoplasmic membrane, play a major role in peptidoglycan synthesis and remodelling. A PASTA domain (penicillin-binding protein and serine/threonine kinase associated domain) of about 65 residues is found at the C-terminal end of some PBPs and eukaryotic-like protein serine/threonine kinases in a variety of bacteria. The function of PASTA domains is not understood, but some of them are thought to bind uncross linked peptidoglycan. Bacillus subtilis has 16 different PBPs, but only 2 of them, Pbp2b and SpoVD, contain a PASTA domain. SpoVD is specific for sporulation and essential for endospore cortex peptidoglycan synthesis. We have studied the role of the PASTA domain in SpoVD by deleting this domain and analysing the effects on endospore formation and subcellular localization of SpoVD. Our results demonstrate that the PASTA domain in SpoVD is not essential for cortex synthesis and not important for targeting SpoVD to the forespore outer membrane during sporulation.

  4. The acidic C-terminus of vaccinia virus I3 single-strand binding protein promotes proper assembly of DNA-protein complexes.

    Science.gov (United States)

    Harrison, Melissa L; Desaulniers, Megan A; Noyce, Ryan S; Evans, David H

    2016-02-01

    The vaccinia virus I3L gene encodes a single-stranded DNA binding protein (SSB) that is essential for virus DNA replication and is conserved in all Chordopoxviruses. The I3 protein contains a negatively charged C-terminal tail that is a common feature of SSBs. Such acidic tails are critical for SSB-dependent replication, recombination and repair. We cloned and purified variants of the I3 protein, along with a homolog from molluscum contagiosum virus, and tested how the acidic tail affected DNA-protein interactions. Deleting the C terminus of I3 enhanced the affinity for single-stranded DNA cellulose and gel shift analyses showed that it also altered the migration of I3-DNA complexes in agarose gels. Microinjecting an antibody against I3 into vaccinia-infected cells also selectively inhibited virus replication. We suggest that this domain promotes cooperative binding of I3 to DNA in a way that would maintain an open DNA configuration around a replication site.

  5. Crystal Structure of the VapBC Toxin–Antitoxin Complex from Shigella flexneri Reveals a Hetero-Octameric DNA-Binding Assembly

    DEFF Research Database (Denmark)

    Dienemann, Christian; Bøggild, Andreas; Winther, Kristoffer S.;

    2011-01-01

    Toxin–antitoxin (TA) loci are common in archaea and prokaryotes and allow cells to rapidly adapt to changing environmental conditions through release of active regulators of metabolism. Many toxins are endonucleases that target cellular mRNA and tRNAs, while the antitoxins tightly wrap around...... the toxins to inhibit them under normal circumstances. The antitoxins also bind to operators in the promoter regions of the cognate TA operon and thereby regulate transcription. For enteric vapBC TA loci, the VapC toxins specifically cleave tRNAfMet and thus down-regulate protein synthesis. Here, we describe...... molecular mass of about 100 kDa. The structure gives new insights into the inhibition of VapC toxins by VapB and provides the molecular basis for understanding transcriptional regulation through VapB dimerization....

  6. A combinatorial approach for directing the amount of fibronectin fibrils assembled by cells that uses surfaces derivatized with mixtures of fibronectin and cell binding domains.

    Science.gov (United States)

    Kshatriya, Pradnya P; Karuri, Stella W; Chiang, Chunyi; Karuri, Nancy W

    2012-01-01

    Fibrillar fibronectin (FN) has the crucial role of attracting and attaching cells as well as molecules that mediate tissue repair during wound healing. A previous study demonstrated higher extracellular staining of FN fibrils in cells cultured on surfaces tethered with an equimolar mixture of a FN binding domain and FN's cell binding domain, III1-2 and III9-10 respectively, than on surfaces with III9-10 alone. The effect of varying surface amounts of III1-2 and III9-10 on the quantity of FN fibrils formed by NIH-3T3 fibroblasts was examined. GST tagged III1-2 and III9-10 were conjugated to polyurethane surfaces and ELISAs were used to identify the experimental design space or the range of concentrations of GST-III1-2 and GST-III9-10 that demarcated the limits of protein loading on the surface. When GST-III1-2 was fixed and GST-III9-10 varied within the design space, the amount of FN fibrils measured by immunoblotting detergent insoluble cell lysates was dependent on the ratio of III9-10 to III1-2. When the total protein concentration was fixed and the mixture composition of GST-III1-2 and GST-III9-10 varied such that it optimally covered the design space, a parabolic relationship between FN fibril amount and the ratio of III9-10 to III1-2 was obtained. This relationship had a maximum value when the surface was bonded to equal amounts of III1-2 and III9-10 (P<0.05). Thus the ratio of III9-10 to III1-2 can be utilized to direct the quantity of FN fibrils formed on surfaces.

  7. The inhibition of assembly of HIV-1 virus-like particles by 3-O-(3',3'-dimethylsuccinyl betulinic acid (DSB is counteracted by Vif and requires its Zinc-binding domain

    Directory of Open Access Journals (Sweden)

    Bouaziz Serge

    2008-12-01

    Full Text Available Abstract Background DSB, the 3-O-(3',3'dimethylsuccinyl derivative of betulinic acid, blocks the last step of protease-mediated processing of HIV-1 Gag precursor (Pr55Gag, which leads to immature, noninfectious virions. When administered to Pr55Gag-expressing insect cells (Sf9, DSB inhibits the assembly and budding of membrane-enveloped virus-like particles (VLP. In order to explore the possibility that viral factors could modulate the susceptibility to DSB of the VLP assembly process, several viral proteins were coexpressed individually with Pr55Gag in DSB-treated cells, and VLP yields assayed in the extracellular medium. Results Wild-type Vif (Vifwt restored the VLP production in DSB-treated cells to levels observed in control, untreated cells. DSB-counteracting effect was also observed with Vif mutants defective in encapsidation into VLP, suggesting that packaging and anti-DSB effect were separate functions in Vif. The anti-DSB effect was abolished for VifC133S and VifS116V, two mutants which lacked the zinc binding domain (ZBD formed by the four H108C114C133H139 coordinates with a Zn atom. Electron microscopic analysis of cells coexpressing Pr55Gag and Vifwt showed that a large proportion of VLP budded into cytoplasmic vesicles and were released from Sf9 cells by exocytosis. However, in the presence of mutant VifC133S or VifS116V, most of the VLP assembled and budded at the plasma membrane, as in control cells expressing Pr55Gag alone. Conclusion The function of HIV-1 Vif protein which negated the DSB inhibition of VLP assembly was independent of its packaging capability, but depended on the integrity of ZBD. In the presence of Vifwt, but not with ZBD mutants VifC133S and VifS116V, VLP were redirected to a vesicular compartment and egressed via the exocytic pathway.

  8. Assembling different antennas of the gp120 high mannose-type glycans on gold nanoparticles provides superior binding to the anti-HIV antibody 2G12 than the individual antennas.

    Science.gov (United States)

    Chiodo, Fabrizio; Enríquez-Navas, Pedro M; Angulo, Jesús; Marradi, Marco; Penadés, Soledad

    2015-03-20

    In order to re-build Man9GlcNAc2 clusters of the HIV gp120 glycoprotein, ∼2 nm gold glyconanoparticles (GNPs) were coated with the synthetic partial structures of Man9, the tetramannoside Manα1-2Manα1-2Manα1-3Manα1- and the pentamannoside Manα1-2Manα1-3[Manα1-2Manα1-6]Manα1-. Their interactions with the anti-HIV broadly neutralizing antibody 2G12 were studied by surface plasmon resonance (SPR)-based biosensors and saturation transfer difference (STD)-NMR spectroscopy. A synergistic effect of the tetra- and pentamannosides multimerized on a same GNP was observed. The assembly of these antennas of the gp120 high-mannose type glycan on GNPs provided superior binding to the anti-HIV antibody 2G12 with respect to GNPs carrying only the individual oligomannosides. The results presented in this work provide new molecular information on the interactions between clusters of oligomannosides and 2G12 that could help in the design of a carbohydrate-based vaccine against HIV.

  9. Photovoltaic self-assembly.

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-10-01

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

  10. Sequence assembly

    DEFF Research Database (Denmark)

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

    2009-01-01

    and plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences...

  11. The Box H/ACA snoRNP Assembly Factor Shq1p is a Chaperone Protein Homologous to Hsp90 Cochaperones that Binds to the Cbf5p Enzyme

    Energy Technology Data Exchange (ETDEWEB)

    Godin, Katherine S.; Walbott, Helene; Leulliot, Nicolas; van Tilbeurgh, Herman; Varani, Gabriele

    2009-05-06

    Box H/ACA small nucleolar (sno) ribonucleoproteins (RNPs) are responsible for the formation of pseudouridine in a variety of RNAs and are essential for ribosome biogenesis, modification of spliceosomal RNAs, and telomerase stability. A mature snoRNP has been reconstituted in vitro and is composed of a single RNA and four proteins. However, snoRNP biogenesis in vivo requires multiple factors to coordinate a complex and poorly understood assembly and maturation process. Among the factors required for snoRNP biogenesis in yeast is Shq1p, an essential protein necessary for stable expression of box H/ACA snoRNAs. We have found that Shq1p consists of two independent domains that contain casein kinase 1 phosphorylation sites. We also demonstrate that Shq1p binds the pseudourydilating enzyme Cbf5p through the C-terminal domain, in synergy with the N-terminal domain. The NMR solution structure of the N-terminal domain has striking homology to the ‘Chord and Sgt1’ domain of known Hsp90 cochaperones, yet Shq1p does not interact with the yeast Hsp90 homologue in vitro. Surprisingly, Shq1p has stand-alone chaperone activity in vitro. This activity is harbored by the C-terminal domain, but it is increased by the presence of the N-terminal domain. These results provide the first evidence of a specific biochemical activity for Shq1p and a direct link to the H/ACA snoRNP.

  12. Dynamic pathways for viral capsid assembly

    Energy Technology Data Exchange (ETDEWEB)

    Hagan, Michael F.; Chandler, David

    2006-02-09

    We develop a class of models with which we simulate the assembly of particles into T1 capsid-like objects using Newtonian dynamics. By simulating assembly for many different values of system parameters, we vary the forces that drive assembly. For some ranges of parameters, assembly is facile, while for others, assembly is dynamically frustrated by kinetic traps corresponding to malformed or incompletely formed capsids. Our simulations sample many independent trajectories at various capsomer concentrations, allowing for statistically meaningful conclusions. Depending on subunit (i.e., capsomer) geometries, successful assembly proceeds by several mechanisms involving binding of intermediates of various sizes. We discuss the relationship between these mechanisms and experimental evaluations of capsid assembly processes.

  13. Furnace assembly

    Science.gov (United States)

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

    1985-01-01

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

  14. 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...

  15. Triazatriangulene as binding group for molecular electronics

    DEFF Research Database (Denmark)

    Wei, Zhongming; Wang, Xintai; Borges, Anders;

    2014-01-01

    The triazatriangulene (TATA) ring system was investigated as a binding group for tunnel junctions of molecular wires on gold surfaces. Self-assembled monolayers (SAMs) of TATA platforms with three different lengths of phenylene wires were fabricated, and their electrical conductance was recorded ...... with its high stability and directionality make this binding group very attractive for molecular electronic measurements and devices. (Figure Presented)....

  16. Binding Procurement

    Science.gov (United States)

    Rao, Gopalakrishna M.; Vaidyanathan, Hari

    2007-01-01

    This viewgraph presentation reviews the use of the binding procurement process in purchasing Aerospace Flight Battery Systems. NASA Engineering and Safety Center (NESC) requested NASA Aerospace Flight Battery Systems Working Group to develop a set of guideline requirements document for Binding Procurement Contracts.

  17. Assembling consumption

    DEFF Research Database (Denmark)

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

  18. Heater assembly

    International Nuclear Information System (INIS)

    An electrical resistance heater, installed in the H1 borehole, is used to thermally perturb the rock mass through a controlled heating and cooling cycle. Heater power levels are controlled by a Variac power transformer and are measured by wattmeters. Temperatures are measured by thermocouples on the borehole wall and on the heater assembly. Power and temperature values are recorded by the DAS described in Chapter 12. The heater assembly consists of a 3.55-m (11.6-ft) long by 20.3-cm (8-in.) O.D., Type 304 stainless steel pipe, containing a tubular hairpin heating element. The element has a heated length of 3 m (9.84 ft). The power rating of the element is 10 kW; however, we plan to operate the unit at a maximum power of only 3 kW. The heater is positioned with its midpoint directly below the axis of the P2 borehole, as shown in the borehole configuration diagram. This heater midpoint position corresponds to a distance of approximately 8.5 m (27.9 ft) from the H1 borehole collar. A schematic of the heater assembly in the borehole is shown. The distance from the borehole collar to the closest point on the assembly (the front end) is 6.5 m (21.3 ft). A high-temperature inflatable packer, used to seal the borehole for moisture collection, is positioned 50 cm (19.7 in.) ahead of the heater front end. The heater is supported and centralized within the borehole by two skids, fabricated from 25-mm (1-in.) O.D. stainless steel pipe. Thermocouples are installed at a number of locations in the H1 borehole. Four thermocouples that are attached to the heater skin monitor temperatures on the outer surface of the can, while three thermocouples that are held in place by rock sections monitor borehole wall temperatures beneath the heater. Temperatures are also monitored at the heater terminal and on the packer hardware

  19. General Assembly

    CERN Multimedia

    Staff Association

    2015-01-01

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

  20. General assembly

    CERN Multimedia

    Staff Association

    2015-01-01

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

  1. General Assembly

    CERN Multimedia

    Staff Association

    2016-01-01

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

  2. Mapping interactions between mRNA export factors in living cells.

    Directory of Open Access Journals (Sweden)

    I-Fang Teng

    Full Text Available The TREX complex couples nuclear mRNA processing events with subsequent export to the cytoplasm. TREX also acts as a binding platform for the mRNA export receptor Nxf1. The sites of mRNA transcription and processing within the nucleus have been studied extensively. However, little is known about where TREX assembly takes place and where Nxf1 is recruited to TREX to form the export competent mRNP. Here we have used sensitized emission Förster resonance energy transfer (FRET and fluorescence lifetime imaging (FLIM-FRET, to produce a spatial map in living cells of the sites for the interaction of two TREX subunits, Alyref and Chtop, with Nxf1. Prominent assembly sites for export factors are found in the vicinity of nuclear speckles in regions known to be involved in transcription, splicing and exon junction complex formation highlighting the close coupling of mRNA export with mRNP biogenesis.

  3. ULTRASONIC ASSEMBLY [REVIEW

    Directory of Open Access Journals (Sweden)

    PORAV Viorica

    2015-05-01

    Full Text Available The paper exposes the possibility of machine producesers to optimize the costs of clothes assembling. Ultrasonic systems being frequently utilized have many advantages on semi products of synthetic textile and technical textile. First of all, sewing – cutting process can be accomplished under high speeds and rate of losses can be minimized. Cutting seal applications are frequently used for underwear and sportswear. Slicing and unit cutting machines, as well as portable sealing machines are available for labeling sector. Products such as bag, pocket and cover can be sewed in a seamless manner for promotion purposes. All objects in terms of accessories are obtained in same standard. Our quilting machines are preferred in worldwide due to its threadless, high quality sealing. An alternative to the classic sewing assembly, with thread and needles is ultrasonic seaming. In ultrasonic welding, there are no connective bolts, nails, soldering materials, or adhesives necessary to bind the materials together. Ultrasonic is defined as acoustic frequencies above the range audible to the human ear. Ultrasonic frequencies are administered to the fabric from the sonotrode of bonding machine. The high frequency and powerful energy produced, when is release in one special environment, the ultrasound heating this environment. The ability to ultrasonic weld textiles and films depend on their thermoplastic contents and the desired end results. The paper defines the weld ability of more common textiles and films. The welding refers to all types of bonding and sealing, as in point bonding of fabric, or continuous sealing of film.

  4. Fuel assembly

    International Nuclear Information System (INIS)

    Since the neutron flux distribution and the power distribution of a fuel assembly in which short fuel rods vary greatly in the vicinity of a boundary where the distribution of uranium amount is different, the reading value of local power range monitors, having the detectors positioned in the vicinity of the boundary is varied. Then in the present invention, the upper end of the effective axial length of fuel rod is so made as not approaching with the detection position of the local power range monitor in a reactor core. Further, the upper end of the effective axial length of fuel rods in a 4 x 4 fuel rod lattice positioned at the corner on the side of the local power range monitor is so made as not approaching the detection position of the local power range monitor. As a result, the change of the neutron flux distribution and power distribution in the vicinity of the position where the detector of the local power range monitor is situated can be extremely reduced. Accordingly, there is no scattering and fluctuation for the reading value by the local power range monitor, to improve the monitoring performance for thermal characteristics in the reactor core. (N.H.)

  5. Fuel assembly

    International Nuclear Information System (INIS)

    Purpose: To reconstruct a BWR type reactor into a high conversion reactor with no substantial changes for the reactor inner structure such as control rod structure. Constitution: The horizontal cross sectional shape of a channel box is reformed into a square configuration and the arrangement of fuel rods is formed as a trigonal lattice-like configuration. As a method of improving the conversion ratio, there is considered to use a dense lattice by narrowing the distance between fuel rods and trigonal lattice arrangement for fuel rod is advantageous therefor. A square shape cross sectional configuration having equal length both in the lateral and longitudinal directions is suitable for the channel box as a guide upon movement of the control rod. Fuel rods can be arranged with no loss by the trigonal lattice configuration, by which it is possible to improve the neutron moderation, increase the reactor core reactivity and conduct effective fuel combustion. In this way, it is possible to attain the object by inserting the follower portion of the control rod at the earier half and extracting the same at the latter half during the operation period in the reactor core comprising fuel assemblies suitable to a high conversion BWR type reactor having average conversion ratio of about 0.8. (Kamimura, M.)

  6. A self-assembled ionophore

    Science.gov (United States)

    Tirumala, Sampath K.

    1997-11-01

    Ionophores are compounds that bind and transport ions. Ion binding and transport are fundamental to many biological and chemical processes. In this thesis we detail the structural characterization and cation binding properties of a self-assembled ionophore built from an isoguanosine (isoG) derivative, 5sp'-t-butyldimethylsilyl-2sp',3sp'-isopropylidene isoG 30. We begin with a summary of the themes that facilitate ionophore design and the definitions of "self-assembly" and "self-assembled ionophore" in Chapter 1. In Chapter 2, we describe the structural characterization of the isoG 30 self-assembly. IsoG possesses complementary hydrogen bond donor and acceptor sites suitable to form a Csb4-symmetric tetramer, (isoG)sb4 51, that is stable even in high dielectric organic solvents such as CDsb3CN and dsb6-acetone. The isoG tetramer 51 has been characterized by vapor phase osmometry, UV spectroscopy, and by 1D and 2D NMR spectroscopy. The isoG tetramer 51 organizes by hydrogen bonding between the Watson-Crick face of one isoG base and the complementary bottom edge of another purine. The tetramer 51 is stabilized by an inner and outer ring of hydrogen bonds. The inner ring forms between the imino NH1 proton of one monomer and the C2 carbonyl oxygen of an adjacent monomer, while the outer ring is made up of four NH6-N3 hydrogen bonds. The isoG tetramer 51 is thermodynamically stable, with an equilibrium constant (Ksba) of ca. 10sp9-10sp{10} Msp{-3} at room temperature, and a DeltaGsp° of tetramer formation of -12.5 kcal molsp{-1} in dsb6-acetone at 25sp°C. The van't Hoff plots indicated that the thermodynamic parameters for tetramer formation were DeltaHsp° = -18.2 ± 0.87 kcal molsp{-1} and DeltaSsp°sb{298} = -19.1 ± 5.45 eu. In Chapter 3, we describe the cation binding properties of isoG tetramer 51. The isoG tetramer 51 has a central cavity, containing four oxygen atoms, that is suitable for cation coordination. Depending on the cation, the resulting iso

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-09-12

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

  9. Probe tip heating assembly

    Energy Technology Data Exchange (ETDEWEB)

    Schmitz, Roger William; Oh, Yunje

    2016-10-25

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

  10. 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

  11. Inlet nozzle assembly

    Science.gov (United States)

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

    1987-01-01

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

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

    Science.gov (United States)

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

    2017-01-01

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

  13. Tilt assembly for tracking solar collector assembly

    Science.gov (United States)

    Almy, Charles; Peurach, John; Sandler, Reuben

    2012-01-24

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

  14. Hermes RNA-binding protein targets RNAs-encoding proteins involved in meiotic maturation, early cleavage, and germline development.

    Science.gov (United States)

    Song, Hye-Won; Cauffman, Karen; Chan, Agnes P; Zhou, Yi; King, Mary Lou; Etkin, Laurence D; Kloc, Malgorzata

    2007-07-01

    The early development of metazoans is mainly regulated by differential translation and localization of maternal mRNAs in the embryo. In general, these processes are orchestrated by RNA-binding proteins interacting with specific sequence motifs in the 3'-untranslated region (UTR) of their target RNAs. Hermes is an RNA-binding protein, which contains a single RNA recognition motif (RRM) and is found in various vertebrate species from fish to human. In Xenopus laevis, Hermes mRNA and protein are localized in the vegetal region of oocytes. A subpopulation of Hermes protein is concentrated in a specific structure in the vegetal cortex, called the germ plasm (believed to contain determinants of the germ cell fate) where Hermes protein co-localizes with Xcat2 and RINGO/Spy mRNAs. The level of total Hermes protein decreases during maturation. The precocious depletion of Hermes protein by injection of Hermes antisense morpholino oligonucleotide (HE-MO) accelerates the process of maturation and results in cleavage defects in vegetal blastomeres of the embryo. It is known that several maternal mRNAs including RINGO/Spy and Mos are regulated at the translational level during meiotic maturation and early cleavage in Xenopus. The ectopic expression of RINGO/Spy or Mos causes resumption of meiotic maturation and cleavage arrests, which resemble the loss of Hermes phenotypes. We found that the injection of HE-MO enhances the acceleration of maturation caused by the injection of RINGO/Spy mRNA, and that Hermes protein is present as mRNP complex containing RINGO/Spy, Mos, and Xcat2 mRNAs in vivo. We propose that as an RNA-binding protein, Hermes may be involved in maturation, cleavage events at the vegetal pole and germ cell development by negatively regulating the expression of RINGO/Spy, Mos, and Xcat2 mRNAs. PMID:17309605

  15. Transcription-associated quality control of mRNP

    DEFF Research Database (Denmark)

    Schmid, Manfred; Jensen, Torben Heick

    2013-01-01

    Although a prime purpose of transcription is to produce RNA, a substantial amount of transcript is nevertheless turned over very early in its lifetime. During transcription RNAs are matured by nucleases from longer precursors and activities are also employed to exert quality control over the RNA ...

  16. Carbohydrate nanotechnology: hierarchical assembly using nature's other information carrying biopolymers.

    Science.gov (United States)

    Han, Xu; Zheng, Yeting; Munro, Catherine J; Ji, Yiwen; Braunschweig, Adam B

    2015-08-01

    Despite their central role in directing some of the most complex biological processes, carbohydrates--nature's other information carrying biopolymer--have been largely ignored as building blocks for synthetic hierarchical assemblies. The non-stoichiometric binding and astronomical diversity characteristic of carbohydrates could lead to tantalizingly complex assembly algorithms, but these attributes simultaneously increase the difficulty of preparing carbohydrate assemblies and anticipating their behavior. Convergences in biotechnology, nanotechnology, polymer chemistry, surface science, and supramolecular chemistry have led to many recent important breakthroughs in glycan microarrays and synthetic carbohydrate receptors, where the idiosyncrasies of carbohydrate structure and binding are increasingly considered. We hope to inspire more researchers to consider carbohydrate structure, diversity, and binding as attractive tools for constructing synthetic hierarchical assemblies.

  17. Assembly plans for ITER

    International Nuclear Information System (INIS)

    The assembly of ITER represents an extrapolation of a factor of two or more in size over existing large tokamaks. An assembly plan has been developed based on the ITER Outline Design. This plan was reviewed by technical experts and critical issues were identified. Alternate designs are being developed to address the most serious concerns and to minimize cost and assembly schedule. Because ITER has many characteristics of a full-scale nuclear reactor its assembly has challenges not faced previously by the fusion community. Careful assembly planning and well-designed tooling are required to insure success in the assembly of ITER

  18. Firearm trigger assembly

    Science.gov (United States)

    Crandall, David L.; Watson, Richard W.

    2010-02-16

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

  19. Autonomous electrochromic assembly

    Science.gov (United States)

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

    2015-03-10

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

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

    Science.gov (United States)

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

    2016-01-01

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

  1. Material Binding Peptides for Nanotechnology

    Directory of Open Access Journals (Sweden)

    Urartu Ozgur Safak Seker

    2011-02-01

    Full Text Available Remarkable progress has been made to date in the discovery of material binding peptides and their utilization in nanotechnology, which has brought new challenges and opportunities. Nowadays phage display is a versatile tool, important for the selection of ligands for proteins and peptides. This combinatorial approach has also been adapted over the past decade to select material-specific peptides. Screening and selection of such phage displayed material binding peptides has attracted great interest, in particular because of their use in nanotechnology. Phage display selected peptides are either synthesized independently or expressed on phage coat protein. Selected phage particles are subsequently utilized in the synthesis of nanoparticles, in the assembly of nanostructures on inorganic surfaces, and oriented protein immobilization as fusion partners of proteins. In this paper, we present an overview on the research conducted on this area. In this review we not only focus on the selection process, but also on molecular binding characterization and utilization of peptides as molecular linkers, molecular assemblers and material synthesizers.

  2. 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

  3. Sensor mount assemblies and sensor assemblies

    Science.gov (United States)

    Miller, David H.

    2012-04-10

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

  4. Soldering in electronics assembly

    CERN Document Server

    Judd, Mike

    2013-01-01

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

  5. Ternary self-assemblies in water

    DEFF Research Database (Denmark)

    Hill, Leila R.; Blackburn, Octavia A.; Jones, Michael W.;

    2013-01-01

    The self-assembly of higher order structures in water is realised by using the association of 1,3-biscarboxylates to binuclear meta-xylyl bridged DO3A complexes. Two dinicotinate binding sites are placed at a right-angle in a rhenium complex, which is shown to form a 1 : 2 complex with α,α'-bis(E......The self-assembly of higher order structures in water is realised by using the association of 1,3-biscarboxylates to binuclear meta-xylyl bridged DO3A complexes. Two dinicotinate binding sites are placed at a right-angle in a rhenium complex, which is shown to form a 1 : 2 complex with α...

  6. Rasputin, more promiscuous than ever: a review of G3BP.

    Science.gov (United States)

    Irvine, Katharine; Stirling, Renee; Hume, David; Kennedy, Derek

    2004-12-01

    In this review, we highlight what G3BP's domain structure initially suggested; that G3BPs are "scaffolding" proteins linking signal transduction to RNA metabolism. Whilst it is most attractive to hypothesise about G3BP's role in signalling to mRNA metabolism, it is not known whether all G3BP functions impinge on their RNA-binding activities, so any theories are naturally subject to this qualification. It is hypothesised that, in coordination with an array of other proteins, G3BP, in a phosphorylation-dependent manner, is involved in the post-transcriptional regulation of a subset of mRNAs, at least some of which are in common with those regulated by Hu proteins. These transcripts, partially controlled at the post-transcriptional level by G3BPs, code for proteins important in transcription (e.g. c-Myc) and cytoskeletal arrangement (e.g. Tau), amongst other as yet undetermined pathways. The subtle differences between G3BP family members could dictate binding to a variety of signalling proteins, so each of the G3BPs may participate in different, though possibly related mRNPs, which are assembled in response to different stimuli. The combinatorial nature of the mRNP complex offers a powerful means of regulating gene expression, beyond that provided by a simple mRNA sequence. The ways in which mRNP flexibility and specificity may be harnessed to coordinate gene expression of functionally or structurally related mRNAs are not yet fully appreciated. Characterising mRNP composition and the function/s of mRNP components, such as the G3BPs, will aid in the understanding of how post-transcriptional mechanisms contribute to the global regulation of gene expression.

  7. Data on the kinetics of in vitro assembled chromatin.

    Science.gov (United States)

    Völker-Albert, Moritz Carl; Pusch, Miriam Caroline; Schmidt, Andreas; Imhof, Axel

    2016-09-01

    Here, we use LC-MS/MS and SWATH-MS to describe the kinetics of in vitro assembled chromatin supported by an embryo extract prepared from preblastoderm Drosophila melanogaster embryos (DREX). This system allows easy manipulation of distinct aspects of chromatin assembly such as post-translational histone modifications, the levels of histone chaperones and the concentration of distinct DNA binding factors. In total, 480 proteins have been quantified as chromatin enriched factors and their binding kinetics have been monitored in the time course of 15 min, 1 h and 4 h of chromatin assembly. The data accompanying the manuscript on this approach, Völker-Albert et al., 2016 "A quantitative proteomic analysis of in vitro assembled chromatin" [1], has been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository with the dataset identifier submission number PRIDE: PXD002537 and PRIDE: PXD003445. PMID:27331114

  8. Analyzing binding data.

    Science.gov (United States)

    Motulsky, Harvey J; Neubig, Richard R

    2010-07-01

    Measuring the rate and extent of radioligand binding provides information on the number of binding sites, and their affinity and accessibility of these binding sites for various drugs. This unit explains how to design and analyze such experiments.

  9. Target Assembly Facility

    Data.gov (United States)

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

  10. Assembly of ISX

    Energy Technology Data Exchange (ETDEWEB)

    Durfee, N.W.

    1977-01-01

    The Impurity Study Experiment, a moderate size tokamak, was recently assembled at ORNL. Demountable toroidal field coils allowed for the assembly of major components at remote locations and rapid installation into ISX. A discharge cleaning plasma was generated in ISX six weeks after the arrival of the final toroidal field coil. A chronological summary of the assembly is presented, emphasizing features designed to aid in assembly and maintenance. A cross-section of the machine showing the major mechanical components to be discussed is given.

  11. 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.

  12. Self assembly of interlocked architectures

    CERN Document Server

    Schergna, S

    2002-01-01

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

  13. A parameter estimation technique for stochastic self-assembly systems and its application to human papillomavirus self-assembly

    International Nuclear Information System (INIS)

    Virus capsid assembly has been a key model system for studies of complex self-assembly but it does pose some significant challenges for modeling studies. One important limitation is the difficulty of determining accurate rate parameters. The large size and rapid assembly of typical viruses make it infeasible to directly measure coat protein binding rates or deduce them from the relatively indirect experimental measures available. In this work, we develop a computational strategy to deduce coat–coat binding rate parameters for viral capsid assembly systems by fitting stochastic simulation trajectories to experimental measures of assembly progress. Our method combines quadratic response surface and quasi-gradient descent approximations to deal with the high computational cost of simulations, stochastic noise in simulation trajectories and limitations of the available experimental data. The approach is demonstrated on a light scattering trajectory for a human papillomavirus (HPV) in vitro assembly system, showing that the method can provide rate parameters that produce accurate curve fits and are in good concordance with prior analysis of the data. These fits provide an insight into potential assembly mechanisms of the in vitro system and give a basis for exploring how these mechanisms might vary between in vitro and in vivo assembly conditions

  14. Assembly of the Respiratory Mucin MUC5B

    OpenAIRE

    Ridley, C.; Kouvatsos, Nikos; Thornton, David J.; Raynal, Bertrand D; Howard, Marj; Collins, Richard F.; Desseyn, Jean-Luc; Jowitt, Thomas A.; Baldock, Clair; Davis, C. William; Timothy E. Hardingham

    2014-01-01

    Mucins are essential components in mucus gels that form protective barriers at all epithelial surfaces, but much remains unknown about their assembly, intragranular organization, and post-secretion unfurling to form mucus. MUC5B is a major polymeric mucin expressed by respiratory epithelia, and we investigated the molecular mechanisms involved during its assembly. Studies of intact polymeric MUC5B revealed a single high affinity calcium-binding site, distinct from multiple low affinity sites ...

  15. Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach.

    Science.gov (United States)

    Trylska, Joanna; McCammon, J Andrew; Brooks Iii, Charles L

    2005-08-10

    To explore the relationship between the assembly of the 30S ribosomal subunit and interactions among the constituent components, 16S RNA and proteins, relative binding free energies of the T. thermophilus 30S proteins to the 16S RNA were studied based on an implicit solvent model of electrostatic, nonpolar, and entropic contributions. The late binding proteins in our assembly map were found not to bind to the naked 16S RNA. The 5' domain early kinetic class proteins, on average, carry the highest positive charge, get buried the most upon binding to 16S RNA, and show the most favorable binding. Some proteins (S10/S14, S6/S18, S13/S19) have more stabilizing interactions while binding as dimers. Our computed assembly map resembles that of E. coli; however, the central domain path is more similar to that of A. aeolicus, a hyperthermophilic bacteria.

  16. Sequential programmable self-assembly: Role of cooperative interactions

    Science.gov (United States)

    Halverson, Jonathan D.; Tkachenko, Alexei V.

    2016-03-01

    We propose a general strategy of "sequential programmable self-assembly" that enables a bottom-up design of arbitrary multi-particle architectures on nano- and microscales. We show that a naive realization of this scheme, based on the pairwise additive interactions between particles, has fundamental limitations that lead to a relatively high error rate. This can be overcome by using cooperative interparticle binding. The cooperativity is a well known feature of many biochemical processes, responsible, e.g., for signaling and regulations in living systems. Here we propose to utilize a similar strategy for high precision self-assembly, and show that DNA-mediated interactions provide a convenient platform for its implementation. In particular, we outline a specific design of a DNA-based complex which we call "DNA spider," that acts as a smart interparticle linker and provides a built-in cooperativity of binding. We demonstrate versatility of the sequential self-assembly based on spider-functionalized particles by designing several mesostructures of increasing complexity and simulating their assembly process. This includes a number of finite and repeating structures, in particular, the so-called tetrahelix and its several derivatives. Due to its generality, this approach allows one to design and successfully self-assemble virtually any structure made of a "GEOMAG" magnetic construction toy, out of nanoparticles. According to our results, once the binding cooperativity is strong enough, the sequential self-assembly becomes essentially error-free.

  17. Self-assembly of smallest magnetic particles.

    Science.gov (United States)

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

    2015-11-24

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

  18. Extending reference assembly models

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  19. Assembly of primary cilia

    DEFF Research Database (Denmark)

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

    2008-01-01

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

  20. Perspective: Geometrically frustrated assemblies

    Science.gov (United States)

    Grason, Gregory M.

    2016-09-01

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

  1. Fuel Assembly Damping Summary

    International Nuclear Information System (INIS)

    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

  2. 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.

  3. Constrained space camera assembly

    Science.gov (United States)

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

    1999-01-01

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

  4. Discodermolide interferes with the binding of tau protein to microtubules.

    Science.gov (United States)

    Kar, Santwana; Florence, Gordon J; Paterson, Ian; Amos, Linda A

    2003-03-27

    We investigated whether discodermolide, a novel antimitotic agent, affects the binding to microtubules of tau protein repeat motifs. Like taxol, the new drug reduces the proportion of tau that pellets with microtubules. Despite their differing structures, discodermolide, taxol and tau repeats all bind to a site on beta-tubulin that lies within the microtubule lumen and is crucial in controlling microtubule assembly. Low concentrations of tau still bind strongly to the outer surfaces of preformed microtubules when the acidic C-terminal regions of at least six tubulin dimers are available for interaction with each tau molecule; otherwise binding is very weak.

  5. The Actin Binding Protein Adseverin Regulates Osteoclastogenesis

    OpenAIRE

    Hassanpour, Siavash; Jiang, Hongwei; Wang, Yongqiang; Kuiper, Johannes W. P.; Glogauer, Michael

    2014-01-01

    Adseverin (Ads), a member of the Gelsolin superfamily of actin binding proteins, regulates the actin cytoskeleton architecture by severing and capping existing filamentous actin (F-actin) strands and nucleating the assembly of new F-actin filaments. Ads has been implicated in cellular secretion, exocytosis and has also been shown to regulate chondrogenesis and megakaryoblastic leukemia cell differentiation. Here we report for the first time that Ads is involved in regulating osteoclastogenesi...

  6. DC source assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Campbell, Jeremy B; Newson, Steve

    2013-02-26

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

  7. Steam separator latch assembly

    Science.gov (United States)

    Challberg, Roy C.; Kobsa, Irvin R.

    1994-01-01

    A latch assembly removably joins a steam separator assembly to a support flange disposed at a top end of a tubular shroud in a nuclear reactor pressure vessel. The assembly includes an annular head having a central portion for supporting the steam separator assembly thereon, and an annular head flange extending around a perimeter thereof for supporting the head to the support flange. A plurality of latches are circumferentially spaced apart around the head flange with each latch having a top end, a latch hook at a bottom end thereof, and a pivot support disposed at an intermediate portion therebetween and pivotally joined to the head flange. The latches are pivoted about the pivot supports for selectively engaging and disengaging the latch hooks with the support flange for fixedly joining the head to the shroud or for allowing removal thereof.

  8. Nuclear reactor spacer assembly

    International Nuclear Information System (INIS)

    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

  9. Spent fuel assembly hardware

    International Nuclear Information System (INIS)

    When spent nuclear fuel is disposed of in a repository, the waste package will include the spent fuel assembly hardware, the structural portion of the fuel assembly, and the fuel pins. The spent fuel assembly hardware is the subject of this paper. The basic constituent parts of the fuel assembly will be described with particular attention on the materials used in their construction. The results of laboratory analyses performed to determine radionuclide inventories and trace impurities also will be described. Much of this work has been incorporated into a US Department of Energy (DOE) database maintained by Oak Ridge National Laboratory (ORNL). This database is documented in DOE/RW-0184 and can be obtained from Karl Notz at ORNL. The database provides a single source for information regarding wastes that may be sent to the repository

  10. High speed door assembly

    Energy Technology Data Exchange (ETDEWEB)

    Shapiro, C.

    1991-12-31

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

  11. Assemblies of gold icosahedra

    OpenAIRE

    Bilalbegovic, G.

    2004-01-01

    Low-dimensional free-standing aggregates of bare gold clusters are studied by the molecular dynamics simulation. Icosahedra of 55 and 147 atoms are equilibrated at T=300 K. Then, their one- and two-dimensional assemblies are investigated. It is found that icosahedra do not coalescence into large drops, but stable amorphous nanostructures are formed: nanowires for one-dimensional and nanofilms for two-dimensional assemblies. The high-temperature stability of these nanostructures is also invest...

  12. Phase behavior and selectivity of DNA-linked nanoparticle assemblies

    NARCIS (Netherlands)

    Lukatsky, D.B.; Frenkel, D.

    2004-01-01

    We propose a model that can account for the experimentally observed phase behavior of DNA-nanoparticle assemblies [R. Jin et al., J. Am. Chem. Soc. 125, 1643 (2003); T. A. Taton et al., Science 289, 1757 (2000)]. The binding of DNA-coated nanoparticles by dissolved DNA linkers can be described by ex

  13. 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

  14. RNA-binding region of Macrobrachium rosenbergii nodavirus capsid protein.

    Science.gov (United States)

    Goh, Zee Hong; Mohd, Nur Azmina Syakirin; Tan, Soon Guan; Bhassu, Subha; Tan, Wen Siang

    2014-09-01

    White tail disease (WTD) kills prawn larvae and causes drastic losses to the freshwater prawn (Macrobrachium rosenbergii) industry. The main causative agent of WTD is Macrobrachium rosenbergii nodavirus (MrNV). The N-terminal end of the MrNV capsid protein is very rich in positively charged amino acids and is postulated to interact with RNA molecules. N-terminal and internal deletion mutagenesis revealed that the RNA-binding region is located at positions 20-29, where 80 % of amino acids are positively charged. Substitution of all these positively charged residues with alanine abolished the RNA binding. Mutants without the RNA-binding region still assembled into virus-like particles, suggesting that this region is not a part of the capsid assembly domain. This paper is, to the best of our knowledge, the first to report the specific RNA-binding region of MrNV capsid protein.

  15. Cyclodextrin nanoaggregates and their assembly with protein: a spectroscopic investigation

    Science.gov (United States)

    Micali, N.; Villari, V.; Mazzaglia, A.; Monsú Scolaro, L.; Valerio, A.; Rencurosi, A.; Lay, L.

    2006-07-01

    Light scattering and time-resolved fluorescence spectroscopy results showed that specially designed amphiphilic cyclodextrins are able to bind a specific protein, PA-I lectin. When containing a galactosyl group, the self-assembled cyclodextrins interact with the protein affecting the dynamical properties of the system and the fluorescence lifetimes (as well as the fluorescence anisotropy) of the protein itself. The self-assembled cyclodextrins containing a glucosyl group, on the other hand, do not induce any change in these measured quantities, suggesting no interaction with protein. This binding capability of galactosyl-modified cyclodextrins offers perspectives on exploiting self-assembled supramolecular structures as nano-carriers to deliver drugs to target tissues.

  16. Cyclodextrin nanoaggregates and their assembly with protein: a spectroscopic investigation

    Energy Technology Data Exchange (ETDEWEB)

    Micali, N [CNR-Istituto per i Processi Chimico-Fisici, Via La Farina 237, I-98123, Messina (Italy); Villari, V [CNR-Istituto per i Processi Chimico-Fisici, Via La Farina 237, I-98123, Messina (Italy); Mazzaglia, A [CNR-Istituto per lo Studio dei Materiali Nanostrutturati, c/o Dipartimento di Chimica Inorganica, Chimica Analitica e Chimica Fisica, Universita di Messina, Contrada Papardo Salita Sperone 31, 98166, Messina (Italy); Scolaro, L Monsu [Dipartimento di Chimica Inorganica, Chimica Analitica e Chimica Fisica and CIRCMSB, Universita di Messina, Contrada Papardo Salita Sperone 31, 98166, Messina (Italy); Valerio, A [Dipartimento di Chimica Organica ed Industriale, Universita di Milano, Via G Venezian 21, 20133, Milan (Italy); Rencurosi, A [CNR-Istituto di Scienze e Tecnologie Molecolari, Via C Golgi 19, 20133 Milan (Italy); Lay, L [Dipartimento di Chimica Organica ed Industriale, Universita di Milano, Via G Venezian 21, 20133, Milan (Italy)

    2006-07-14

    Light scattering and time-resolved fluorescence spectroscopy results showed that specially designed amphiphilic cyclodextrins are able to bind a specific protein, PA-I lectin. When containing a galactosyl group, the self-assembled cyclodextrins interact with the protein affecting the dynamical properties of the system and the fluorescence lifetimes (as well as the fluorescence anisotropy) of the protein itself. The self-assembled cyclodextrins containing a glucosyl group, on the other hand, do not induce any change in these measured quantities, suggesting no interaction with protein. This binding capability of galactosyl-modified cyclodextrins offers perspectives on exploiting self-assembled supramolecular structures as nano-carriers to deliver drugs to target tissues.

  17. Protein-directed self-assembly of a fullerene crystal

    Science.gov (United States)

    Kim, Kook-Han; Ko, Dong-Kyun; Kim, Yong-Tae; Kim, Nam Hyeong; Paul, Jaydeep; Zhang, Shao-Qing; Murray, Christopher B.; Acharya, Rudresh; Degrado, William F.; Kim, Yong Ho; Grigoryan, Gevorg

    2016-04-01

    Learning to engineer self-assembly would enable the precise organization of molecules by design to create matter with tailored properties. Here we demonstrate that proteins can direct the self-assembly of buckminsterfullerene (C60) into ordered superstructures. A previously engineered tetrameric helical bundle binds C60 in solution, rendering it water soluble. Two tetramers associate with one C60, promoting further organization revealed in a 1.67-Å crystal structure. Fullerene groups occupy periodic lattice sites, sandwiched between two Tyr residues from adjacent tetramers. Strikingly, the assembly exhibits high charge conductance, whereas both the protein-alone crystal and amorphous C60 are electrically insulating. The affinity of C60 for its crystal-binding site is estimated to be in the nanomolar range, with lattices of known protein crystals geometrically compatible with incorporating the motif. Taken together, these findings suggest a new means of organizing fullerene molecules into a rich variety of lattices to generate new properties by design.

  18. An update on complex I assembly: the assembly of players

    OpenAIRE

    Vartak, Rasika S.; Semwal, Manpreet Kaur; Bai, Yidong

    2014-01-01

    Defects in Complex I assembly is one of the emerging underlying causes of severe mitochondrial disorders. The assembly of Complex I has been difficult to understand due to its large size, dual genetic control and the number of proteins involved. Mutations in Complex I subunits as well as assembly factors have been reported to hinder its assembly and give rise to a range of mitochondria disorders. In this review, we summarize the recent progress made in understanding the Complex I assembly pat...

  19. Total iron binding capacity

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003489.htm Total iron binding capacity To use the sharing features on this page, please enable JavaScript. Total iron binding capacity (TIBC) is a blood test to ...

  20. Assembly of the 30S ribosomal subunit: positioning ribosomal protein S13 in the S7 assembly branch.

    Science.gov (United States)

    Grondek, Joel F; Culver, Gloria M

    2004-12-01

    Studies of Escherichia coli 30S ribosomal subunit assembly have revealed a hierarchical and cooperative association of ribosomal proteins with 16S ribosomal RNA; these results have been used to compile an in vitro 30S subunit assembly map. In single protein addition and omission studies, ribosomal protein S13 was shown to be dependent on the prior association of ribosomal protein S20 for binding to the ribonucleoprotein particle. While the overwhelming majority of interactions revealed in the assembly map are consistent with additional data, the dependency of S13 on S20 is not. Structural studies position S13 in the head of the 30S subunit > 100 A away from S20, which resides near the bottom of the body of the 30S subunit. All of the proteins that reside in the head of the 30S subunit, except S13, have been shown to be part of the S7 assembly branch, that is, they all depend on S7 for association with the assembling 30S subunit. Given these observations, the assembly requirements for S13 were investigated using base-specific chemical footprinting and primer extension analysis. These studies reveal that S13 can bind to 16S rRNA in the presence of S7, but not S20. Additionally, interaction between S13 and other members of the S7 assembly branch have been observed. These results link S13 to the 3' major domain family of proteins, and the S7 assembly branch, placing S13 in a new location in the 30S subunit assembly map where its position is in accordance with much biochemical and structural data.

  1. Plant Hormone Binding Sites

    OpenAIRE

    Napier, Richard

    2004-01-01

    • Aims Receptors for plant hormones are becoming identified with increasing rapidity, although a frustrating number remain unknown. There have also been many more hormone‐binding proteins described than receptors. This Botanical Briefing summarizes what has been discovered about hormone binding sites, their discovery and descriptions, and will not dwell on receptor functions or activities except where these are relevant to understand binding.

  2. Analysis of binding heterogeneity.

    NARCIS (Netherlands)

    Nederlof, M.M.

    1992-01-01

    Binding heterogeneity, due to different functional groups on a reactive surface, plays an important role in the binding of small molecules or ions to many adsorbents, both in industrial processes and in natural environments. The binding heterogeneity is described by a distribution of affinity consta

  3. Colloidal self-assembly at an interface

    Directory of Open Access Journals (Sweden)

    Ryan McGorty

    2010-06-01

    Full Text Available Mix a drop of water into a vial of oil. With some surfactant and a vigorous shake, that one droplet has become thousands, and the total interfacial area has increased by an order of magnitude or more. Like the folded membranes in our mitochondria, the alveoli in our lungs, and the catalytic converters in our cars, oil-water emulsions contain a vast reservoir of interfacial area that can be used to control and transform the things that encounter it. The oil-water interface is especially well-suited to directing the assembly of colloidal particles, which bind to it rapidly and often irreversibly.

  4. Modular Fixture Assembly Model for Virtual Assembly Design

    Institute of Scientific and Technical Information of China (English)

    PENG Gao-liang; CHEN Guang-feng; LIU Xin-hua

    2009-01-01

    To support modular fixture assembly design in virtual environment, a multi-view based modular fixture virtual assembly model is proposed. Instead of squeezing all assembly related information into a single model, three complementary views of assembly model, element information, function and structure, and assembly relationship are proposed to be used. The first view contains the detailed element information, while the other two explicitly capture the hierarchical function relationships and mating relationships respectively. These views are complementary in the sense that each view only contains a specific aspect of assembly related information while together they include required assembly related information. The proposed assembly model is specialized to accommodate the features of modular fixture virtual assembly design and applied in our developed prototype system.

  5. Analyzing radioligand binding data.

    Science.gov (United States)

    Motulsky, Harvey; Neubig, Richard

    2002-08-01

    Radioligand binding experiments are easy to perform, and provide useful data in many fields. They can be used to study receptor regulation, discover new drugs by screening for compounds that compete with high affinity for radioligand binding to a particular receptor, investigate receptor localization in different organs or regions using autoradiography, categorize receptor subtypes, and probe mechanisms of receptor signaling, via measurements of agonist binding and its regulation by ions, nucleotides, and other allosteric modulators. This unit reviews the theory of receptor binding and explains how to analyze experimental data. Since binding data are usually best analyzed using nonlinear regression, this unit also explains the principles of curve fitting with nonlinear regression.

  6. Power module assembly

    Science.gov (United States)

    Campbell, Jeremy B.; Newson, Steve

    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.

  7. 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.

  8. In vitro kinetochore assembly

    Science.gov (United States)

    Miell, Matthew D D; Straight, Aaron F

    2016-01-01

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

  9. Assembling Sustainable Territories

    DEFF Research Database (Denmark)

    Vandergeest, Peter; Ponte, Stefano; Bush, Simon

    2015-01-01

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

  10. 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...

  11. Transfer of fuel assemblies

    International Nuclear Information System (INIS)

    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

  12. Low inductance connector assembly

    Science.gov (United States)

    Holbrook, Meghan Ann; Carlson, Douglas S

    2013-07-09

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

  13. 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.

  14. An Interactive Assembly Process Planner

    Institute of Scientific and Technical Information of China (English)

    廖华飞; 张林鍹; 肖田元; 曾理; 古月

    2004-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Yi Zhang

    2012-01-01

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

  16. Self-assembly drugs: from micelles to nanomedicine.

    Science.gov (United States)

    Messina, Paula V; Besada-Porto, Jose Miguel; Ruso, Juan M

    2014-03-01

    Self-assembly has fascinated many scientists over the past few decades. Rapid advances and widespread interest in the study of this subject has led to the synthesis of an ever-increasing number of elegant and intricate functional structures with sizes that approach nano- and mesoscopic dimensions. Today, it has grown into a mature field of modern science whose interfaces with many disciplines have provided invaluable opportunities for crossing boundaries for scientists seeking to design novel molecular materials exhibiting unusual properties, and for researchers investigating the structure and function of biomolecules. Consequently, self-assembly transcends the traditional divisional boundaries of science and represents a highly interdisciplinary field including nanotechnology and nanomedicine. Basically, self-assembly focuses on a wide range of discrete molecules or molecular assemblies and uses physical transformations to achieve its goals. In this Review, we present a comprehensive overview of the advances in the field of drug self-assembly and discuss in detail the synthesis, self-assembly behavior, and physical properties as well as applications. We refer the reader to past reviews dealing with colloidal molecules and colloidal self-assembly. In the first part, we will discuss, compare, and link the various bioinformatic procedures: Molecular Dynamics and Quantitative Structure Activity Relationship. The second section deals with the self-assembly behavior in more detail, in which we focus on several experimental techniques, selected according to the depth of knowledge obtained. The last part will review the advances in drug-protein assembly. Nature provides many examples of proteins that form their substrate binding sites by bringing together the component pieces in a process of self-assembly. We will focus in the understanding of physical properties and applications developing thereof. PMID:24444168

  17. Self-assembly drugs: from micelles to nanomedicine.

    Science.gov (United States)

    Messina, Paula V; Besada-Porto, Jose Miguel; Ruso, Juan M

    2014-03-01

    Self-assembly has fascinated many scientists over the past few decades. Rapid advances and widespread interest in the study of this subject has led to the synthesis of an ever-increasing number of elegant and intricate functional structures with sizes that approach nano- and mesoscopic dimensions. Today, it has grown into a mature field of modern science whose interfaces with many disciplines have provided invaluable opportunities for crossing boundaries for scientists seeking to design novel molecular materials exhibiting unusual properties, and for researchers investigating the structure and function of biomolecules. Consequently, self-assembly transcends the traditional divisional boundaries of science and represents a highly interdisciplinary field including nanotechnology and nanomedicine. Basically, self-assembly focuses on a wide range of discrete molecules or molecular assemblies and uses physical transformations to achieve its goals. In this Review, we present a comprehensive overview of the advances in the field of drug self-assembly and discuss in detail the synthesis, self-assembly behavior, and physical properties as well as applications. We refer the reader to past reviews dealing with colloidal molecules and colloidal self-assembly. In the first part, we will discuss, compare, and link the various bioinformatic procedures: Molecular Dynamics and Quantitative Structure Activity Relationship. The second section deals with the self-assembly behavior in more detail, in which we focus on several experimental techniques, selected according to the depth of knowledge obtained. The last part will review the advances in drug-protein assembly. Nature provides many examples of proteins that form their substrate binding sites by bringing together the component pieces in a process of self-assembly. We will focus in the understanding of physical properties and applications developing thereof.

  18. 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...

  19. 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...

  20. 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...

  1. Rotary shaft sealing assembly

    Science.gov (United States)

    Dietle, Lannie L.; Schroeder, John E.; Kalsi, Manmohan S.; Alvarez, Patricio D.

    2010-09-21

    A rotary shaft sealing assembly in which a first fluid is partitioned from a second fluid in a housing assembly having a rotary shaft located at least partially within. In one embodiment a lip seal is lubricated and flushed with a pressure-generating seal ring preferably having an angled diverting feature. The pressure-generating seal ring and a hydrodynamic seal may be used to define a lubricant-filled region with each of the seals having hydrodynamic inlets facing the lubricant-filled region. Another aspect of the sealing assembly is having a seal to contain pressurized lubricant while withstanding high rotary speeds. Another rotary shaft sealing assembly embodiment includes a lubricant supply providing a lubricant at an elevated pressure to a region between a lip seal and a hydrodynamic seal with a flow control regulating the flow of lubricant past the lip seal. The hydrodynamic seal may include an energizer element having a modulus of elasticity greater than the modulus of elasticity of a sealing lip of the hydrodynamic seal.

  2. Corium protection assembly

    Science.gov (United States)

    Gou, Perng-Fei; Townsend, Harold E.; Barbanti, Giancarlo

    1994-01-01

    A corium protection assembly includes a perforated base grid disposed below a pressure vessel containing a nuclear reactor core and spaced vertically above a containment vessel floor to define a sump therebetween. A plurality of layers of protective blocks are disposed on the grid for protecting the containment vessel floor from the corium.

  3. Spool assembly support analysis

    International Nuclear Information System (INIS)

    This document provides the wind/seismic analysis and evaluation for the pump pit spool assemblies. Hand calculations were used for the analysis. UBC, AISC, and load factors were used in this evaluation. The results show that the actual loads are under the allowable loads and all requirements are met

  4. Turbomachine blade assembly

    Energy Technology Data Exchange (ETDEWEB)

    Garcia Crespo, Andres Jose

    2016-11-01

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

  5. Assembly of citrate gold nanoparticles on hydrophilic monolayers

    Science.gov (United States)

    Vikholm-Lundin, Inger; Rosqvist, Emil; Ihalainen, Petri; Munter, Tony; Honkimaa, Anni; Marjomäki, Varpu; Albers, Willem M.; Peltonen, Jouko

    2016-08-01

    Self-assembled monolayers (SAMs) as model surfaces were linked onto planar gold films thorough lipoic acid or disulfide groups. The molecules used were polyethylene glycol (EG-S-S), N-[tris-(hydroxymethyl)methyl]acrylamide polymers with and without lipoic acid (Lipa-pTHMMAA and pTHMMAA) and a lipoic acid triazine derivative (Lipa-MF). All the layers, but Lipa-MF with a primary amino group were hydroxyl terminated. The layers were characterized by contact angle measurements and atomic force microscopy, AFM. Citrate stabilized nanoparticles, AuNPs in water and phosphate buffer were allowed to assemble on the layers for 10 min and the binding was followed in real-time with surface plasmon resonance, SPR. The SPR resonance curves were observed to shift to higher angles and become increasingly damped, while also the peaks strongly broaden when large nanoparticles assembled on the surface. Both the angular shift and the damping of the curve was largest for nanoparticles assembling on the EG-S-S monolayer. High amounts of particles were also assembled on the pTHMMAA layer without the lipoic acid group, but the damping of the curve was considerably lower with a more even distribution of the particles. Topographical images confirmed that the highest number of particles were assembled on the polyethylene glycol monolayer. By increasing the interaction time more particles could be assembled on the surface.

  6. 1.15 Å resolution structure of the proteasome-assembly chaperone Nas2 PDZ domain

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Chingakham R. [Kansas State University, 338 Ackert Hall, Manhattan, KS 66506 (United States); Lovell, Scott; Mehzabeen, Nurjahan [University of Kansas, Del Shankel Structural Biology Center, Lawrence, KS 66047 (United States); Chowdhury, Wasimul Q.; Geanes, Eric S. [Kansas State University, 338 Ackert Hall, Manhattan, KS 66506 (United States); Battaile, Kevin P. [IMCA-CAT Hauptman–Woodward Medical Research Institute, 9700 South Cass Avenue, Building 435A, Argonne, IL 60439 (United States); Roelofs, Jeroen, E-mail: jroelofs@ksu.edu [Kansas State University, 338 Ackert Hall, Manhattan, KS 66506 (United States)

    2014-03-25

    The proteasome-assembly chaperone Nas2 binds to the proteasome subunit Rpt5 using its PDZ domain. The structure of the Nas2 PDZ domain has been determined. The 26S proteasome is a 2.5 MDa protease dedicated to the degradation of ubiquitinated proteins in eukaryotes. The assembly of this complex containing 66 polypeptides is assisted by at least nine proteasome-specific chaperones. One of these, Nas2, binds to the proteasomal AAA-ATPase subunit Rpt5. The PDZ domain of Nas2 binds to the C-terminal tail of Rpt5; however, it does not require the C-terminus of Rpt5 for binding. Here, the 1.15 Å resolution structure of the PDZ domain of Nas2 is reported. This structure will provide a basis for further insights regarding the structure and function of Nas2 in proteasome assembly.

  7. Top-down assembly design using assembly features

    Institute of Scientific and Technical Information of China (English)

    石万凯; DENEUX; Dominique; 等

    2002-01-01

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

  8. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7.

    Science.gov (United States)

    Nowotny, V; Nierhaus, K H

    1988-09-01

    A protein which initiates assembly of ribosomes is defined as a protein which binds to the respective rRNA without cooperativity (i.e., without the help of other proteins) during the onset of assembly and is essential for the formation of active ribosomal subunits. The number of proteins binding without cooperativity was determined by monitoring the reconstitution output of active particles at various inputs of 16S rRNA, in the presence of constant amounts of 30S-derived proteins (TP30): This showed that only two of the proteins of the 30S subunit are assembly-initiator proteins. These two proteins are still present on a LiCl core particle comprising 16S rRNA and 12 proteins (including minor proteins). The 12 proteins were isolated, and a series of reconstitution experiments at various levels of rRNA excess demonstrated that S4 and S7 are the initiator proteins. Pulse-chase experiments performed during the early assembly with 14C- and 3H-labeled TP30 and the determination of the 14C/3H ratio of the individual proteins within the assembled particles revealed a bilobal structure of the 30S assembly: A group of six proteins headed by S4 (namely, S4, S20, S16, S15, S6, and S18) resisted the chasing most efficiently (S4 assembly domain). None of the proteins depending on S7 during assembly were found in this group but rather in a second group with intermediate chasing stability [S7 assembly domain; consisting of S7, S9, (S8), S19, and S3]. A number of proteins could be fully chased during the early assembly and therefore represent "late assembly proteins" (S10, S5, S13, S2, S21, S1). These findings fit well with the 30S assembly map.(ABSTRACT TRUNCATED AT 250 WORDS)

  9. Python bindings for libcloudph++

    OpenAIRE

    Jarecka, Dorota; Arabas, Sylwester; Del Vento, Davide

    2015-01-01

    This technical note introduces the Python bindings for libcloudph++. The libcloudph++ is a C++ library of algorithms for representing atmospheric cloud microphysics in numerical models. The bindings expose the complete functionality of the library to the Python users. The bindings are implemented using the Boost.Python C++ library and use NumPy arrays. This note includes listings with Python scripts exemplifying the use of selected library components. An example solution for using the Python ...

  10. DNS & Bind Cookbook

    CERN Document Server

    Liu, Cricket

    2011-01-01

    The DNS & BIND Cookbook presents solutions to the many problems faced by network administrators responsible for a name server. Following O'Reilly's popular problem-and-solution cookbook format, this title is an indispensable companion to DNS & BIND, 4th Edition, the definitive guide to the critical task of name server administration. The cookbook contains dozens of code recipes showing solutions to everyday problems, ranging from simple questions, like, "How do I get BIND?" to more advanced topics like providing name service for IPv6 addresses. It's full of BIND configuration files that yo

  11. Python bindings for libcloudph++

    CERN Document Server

    Jarecka, Dorota; Del Vento, Davide

    2015-01-01

    This technical note introduces the Python bindings for libcloudph++. The libcloudph++ is a C++ library of algorithms for representing atmospheric cloud microphysics in numerical models. The bindings expose the complete functionality of the library to the Python users. The bindings are implemented using the Boost.Python C++ library and use NumPy arrays. This note includes listings with Python scripts exemplifying the use of selected library components. An example solution for using the Python bindings to access libcloudph++ from Fortran is presented.

  12. Optical Space Telescope Assembly Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The Optical Space Telescope Assembly (OSTA) task is to demonstrate the technology readiness of assembling large space telescopes on orbit in 2015. This task is an...

  13. 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)

  14. 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...

  15. The decorin sequence SYIRIADTNIT binds collagen type I

    DEFF Research Database (Denmark)

    Kalamajski, Sebastian; Aspberg, Anders; Oldberg, Ake

    2007-01-01

    Decorin belongs to the small leucine-rich repeat proteoglycan family, interacts with fibrillar collagens, and regulates the assembly, structure, and biomechanical properties of connective tissues. The decorin-collagen type I-binding region is located in leucine-rich repeats 5-6. Site......-directed mutagenesis of this 54-residue-long collagen-binding sequence identifies Arg-207 and Asp-210 in leucine-rich repeat 6 as crucial for the binding to collagen. The synthetic peptide SYIRIADTNIT, which includes Arg-207 and Asp-210, inhibits the binding of full-length recombinant decorin to collagen in vitro....... These collagen-binding amino acids are exposed on the exterior of the beta-sheet-loop structure of the leucine-rich repeat. This resembles the location of interacting residues in other leucine-rich repeat proteins....

  16. Reflector-moderated critical assemblies

    International Nuclear Information System (INIS)

    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 D2O 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.)

  17. Measurement Technology for Engine Assembly

    Institute of Scientific and Technical Information of China (English)

    GAO Li; ZHENG Zeyu; DAI Shangping

    2006-01-01

    In many industrial, it is often necessary to analyze the engine assembly. This paper introduces three kinds of new technologies on the assembly line of engine in recent years, it have played the positive role in improving the quality of assembling.

  18. Low inductance busbar assembly

    Science.gov (United States)

    Holbrook, Meghan Ann

    2010-09-21

    A busbar assembly for electrically coupling first and second busbars to first and second contacts, respectively, on a power module is provided. The assembly comprises a first terminal integrally formed with the first busbar, a second terminal integrally formed with the second busbar and overlapping the first terminal, a first bridge electrode having a first tab electrically coupled to the first terminal and overlapping the first and second terminals, and a second tab electrically coupled to the first contact, a second bridge electrode having a third tab electrically coupled to the second terminal, and overlapping the first and second terminals and the first tab, and a fourth tab electrically coupled to the second contact, and a fastener configured to couple the first tab to the first terminal, and the third tab to the second terminal.

  19. Fuel assemblies chemical cleaning

    International Nuclear Information System (INIS)

    NPP Paks found a thermal-hydraulic anomaly in the reactor core during cycle 14 that was caused by corrosion product deposits on fuel assemblies (FAs) that increased the hydraulic resistance of the FAs. Consequently, the coolant flow through the FAs was insufficient resulting in a temperature asymmetry inside the reactor core. Based on this fact NPP Paks performed differential pressure measurements of all fuel assemblies in order to determine the hydraulic resistance and subsequently the limit values for the hydraulic acceptance of FAs to be used. Based on the hydraulic investigations a total number of 170 FAs was selected for cleaning. The necessity for cleaning the FAs was explained by the fact that the FAs were subjected to a short term usage in the reactor core only maximum of 1,5 years and had still a capacity for additional 2 fuel cycles. (authors)

  20. Nuclear fuel assembly

    International Nuclear Information System (INIS)

    Purpose: To increase the fuel assembly rigidity while making balance in view of the dimension thereby improving the earthquake proofness. Constitution: In a nuclear fuel assembly having a control rod guide thimble tube, the gap between the thimble tube and fuel insert (inner diameter of the guiding thimble tube-outer diameter of the fuel insert) is made greater than 1.0 mm. Further, the wall thickness of the thimble tube is made to about 4 - 5 % of the outer diameter, while the flowing fluid pore cross section S in the thimble tube is set as: S = S0 x A0/A where S0: cross section of the present flowing fluid pore, A: effective cross section after improvement, = Π/4(d2 - D2) in which d is the thimble tube inner diameter and the D is the fuel insert outer diameter. A0: present effective cross section. (Seki, T.)

  1. Fuel nozzle assembly

    Science.gov (United States)

    Johnson, Thomas Edward; Ziminsky, Willy Steve; Lacey, Benjamin Paul; York, William David; Stevenson, Christian Xavier

    2011-08-30

    A fuel nozzle assembly is provided. The assembly includes an outer nozzle body having a first end and a second end and at least one inner nozzle tube having a first end and a second end. One of the nozzle body or nozzle tube includes a fuel plenum and a fuel passage extending therefrom, while the other of the nozzle body or nozzle tube includes a fuel injection hole slidably aligned with the fuel passage to form a fuel flow path therebetween at an interface between the body and the tube. The nozzle body and the nozzle tube are fixed against relative movement at the first ends of the nozzle body and nozzle tube, enabling the fuel flow path to close at the interface due to thermal growth after a flame enters the nozzle tube.

  2. Uniform Test Assembly

    Science.gov (United States)

    Belov, Dmitry I.

    2008-01-01

    In educational practice, a test assembly problem is formulated as a system of inequalities induced by test specifications. Each solution to the system is a test, represented by a 0-1 vector, where each element corresponds to an item included (1) or not included (0) into the test. Therefore, the size of a 0-1 vector equals the number of items "n"…

  3. REACTOR NOZZLE ASSEMBLY

    Science.gov (United States)

    Capuder, F.C.; Dearwater, J.R.

    1959-02-10

    An improved nozzle assembly useful in a process for the direct reduction of uranium hexafluoride to uranium tetrafluoride by means of dissociated ammonia in a heated reaction vessel is descrlbed. The nozzle design provides for intimate mixing of the two reactants and at the same time furnishes a layer of dissociated ammonia adjacent to the interior wall of the reaction vessel, thus preventing build-up of the reaction product on the vessel wall.

  4. Fourth Doctoral Student Assembly

    CERN Multimedia

    Ingrid Haug

    2016-01-01

    On 10 May, over 130 PhD students and their supervisors, from both CERN and partner universities, gathered for the 4th Doctoral Student Assembly in the Council Chamber.   The assembly was followed by a poster session, at which eighteen doctoral students presented the outcome of their scientific work. The CERN Doctoral Student Programme currently hosts just over 200 students in applied physics, engineering, computing and science communication/education. The programme has been in place since 1985. It enables students to do their research at CERN for a maximum of three years and to work on a PhD thesis, which they defend at their University. The programme is steered by the TSC committee, which holds two selection committees per year, in June and December. The Doctoral Student Assembly was opened by the Director-General, Fabiola Gianotti, who stressed the importance of the programme in the scientific environment at CERN, emphasising that there is no more rewarding activity than lear...

  5. IAHS Third Scientific Assembly

    Science.gov (United States)

    The International Association of Hydrological Sciences (IAHS) convened its Third Scientific Assembly in Baltimore, Md., May 10-19, 1989. The Assembly was attended by about 450 scientists and engineers. The attendance was highest from the U.S., as could be expected; 37 were from Canada; 22 each, Netherlands and United Kingdom; 14, Italy; 12, China; 10, Federal Republic of Germany; 8 each from France, the Republic of South Africa, and Switzerland; 7, Austria; 6 each, Finland and Japan; others were scattered among the remainder of 48 countries total.one of the cosponsors and also handled business matters for the Assembly. Other cosponsors included the International Association of Meteorology and Atmospheric Physics (IAMAP), United Nations Environmental Program (UNEP), United Nations Educational, Scientific, and Cultural Organization (UNESCO), World Meteorological Organization (WMO), and U.K. Overseas Development Authority (ODA). U.S. federal agencies serving as cosponsors included the Environmental Protection Agency, National Aeronautics and Space Administration, National Science Foundation, National Weather Service, Department of Agriculture, Department of State, and U.S. Geological Survey.

  6. 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...

  7. SCT Barrel Assembly Complete

    CERN Multimedia

    L. Batchelor

    As reported in the April 2005 issue of the ATLAS eNews, the first of the four Semiconductor Tracker (SCT) barrels, complete with modules and services, arrived safely at CERN in January of 2005. In the months since January, the other three completed barrels arrived as well, and integration of the four barrels into the entire barrel assembly commenced at CERN, in the SR1 building on the ATLAS experimental site, in July. Assembly was completed on schedule in September, with the addition of the innermost layer to the 4-barrel assembly. Work is now underway to seal the barrel thermal enclosure. This is necessary in order to enclose the silicon tracker in a nitrogen atmosphere and provide it with faraday-cage protection, and is a delicate and complicated task: 352 silicon module powertapes, 352 readout-fibre bundles, and over 400 Detector Control System sensors must be carefully sealed into the thermal enclosure bulkhead. The team is currently verifying the integrity of the low mass cooling system, which must be d...

  8. Melanin-binding radiopharmaceuticals

    Energy Technology Data Exchange (ETDEWEB)

    Packer, S; Fairchild, R G; Watts, K P; Greenberg, D; Hannon, S J

    1980-01-01

    The scope of this paper is limited to an analysis of the factors that are important to the relationship of radiopharmaceuticals to melanin. While the authors do not attempt to deal with differences between melanin-binding vs. melanoma-binding, a notable variance is assumed. (PSB)

  9. DNS BIND Server Configuration

    Directory of Open Access Journals (Sweden)

    Radu MARSANU

    2011-01-01

    Full Text Available After a brief presentation of the DNS and BIND standard for Unix platforms, the paper presents an application which has a principal objective, the configuring of the DNS BIND 9 server. The general objectives of the application are presented, follow by the description of the details of designing the program.

  10. Assembly of pericellular matrices by COS-7 cells transfected with CD44 lymphocyte-homing receptor genes.

    OpenAIRE

    Knudson, W.; Bartnik, E; Knudson, C B

    1993-01-01

    The capacity to assemble and retain a pericellular matrix is correlated with the expression of the cell surface binding sites specific for the extracellular matrix macromolecule hyaluronan. These binding proteins have been termed hyaluronan receptors. The lymphocyte-homing receptor CD44 may have identity with these hyaluronan receptors. To determine whether hyaluronan receptors function independently in this capacity for matrix assembly, mammalian cells were transfected with cDNA encoding the...

  11. Cooperative assembly in targeted drug delivery

    Science.gov (United States)

    Auguste, Debra

    2012-02-01

    Described as cell analogues, liposomes are self-assembled lipid bilayer spheres that encapsulate aqueous volumes. Liposomes offer several drug delivery advantages due to their structural versatility related to size, composition, bilayer fluidity, and ability to encapsulate a large variety of compounds non-covalently. However, liposomes lack the structural information embedded within cell membranes. Partitioning of unsaturated and saturated lipids into liquid crystalline (Lα) and gel phase (Lβ) domains, respectively, affects local molecular diffusion and elasticity. Liposome microdomains may be used to pattern molecules, such as antibodies, on the liposome surface to create concentrated, segregated binding regions. We have synthesized, characterized, and evaluated a series of homogeneous and heterogeneous liposomal vehicles that target inflamed endothelium. These drug delivery vehicles are designed to complement the heterogeneous presentation of lipids and receptors on endothelial cells (ECs). EC surfaces are dynamic; they segregate receptors within saturated lipid microdomains on the cell surface to regulate binding and signaling events. We have demonstrated that cooperative binding of two antibodies enhances targeting by multiple fold. Further, we have shown that organization of these antibodies on the surface can further enhance cell uptake. The data suggest that EC targeting may be enhanced by designing liposomes that mirror the segregated structure of lipid and receptor molecules involved in neutrophil-EC adhesion. This strategy is employed in an atherosclerotic mouse model in vivo.

  12. PNA Directed Sequence Addressed Self-Assembly of DNA Nanostructures

    DEFF Research Database (Denmark)

    Nielsen, Peter E.

    2008-01-01

    Peptide nucleic acids (PNA) can be designed to target duplex DNA with very high sequence specificity and efficiency via various binding modes. We have designed three domain PNA clamps, that bind stably to predefined decameric homopurine targets in large dsDNA mols. and via a third PNA domain...... sequence specifically recognize another PNA oligomer. We describe how such three domain PNAs have utility for assembling dsDNA grid and clover leaf structures, and in combination with SNAP-tag technol. of protein dsDNA structures. (c) 2008 American Institute of Physics. [on SciFinder (R)] Udgivelsesdato...

  13. PNA Directed Sequence Addressed Self-Assembly of DNA Nanostructures

    Science.gov (United States)

    Nielsen, Peter E.

    2008-10-01

    Peptide nucleic acids (PNA) can be designed to target duplex DNA with very high sequence specificity and efficiency via various binding modes. We have designed three domain PNA clamps, that bind stably to predefined decameric homopurine targets in large dsDNA molecules and via a third PNA domain sequence specifically recognize another PNA oligomer. We describe how such three domain PNAs have utility for assembling dsDNA grid and clover leaf structures, and in combination with SNAP-tag technology of protein dsDNA structures.

  14. Self assembly of interlocked architectures

    International Nuclear Information System (INIS)

    An area of great interest is the synthesis and characterisation of molecules possessing moving parts, with the goal that they can act as 'molecular machine' carrying out tasks that molecules with fixed conventional architectures cannot do. Rotaxanes and catenanes (mechanically interlocked architectures) represent one approach toward achieving these aims as their component wheels and / or threads are connected together but can still move, in certain, controlled directions. This thesis focused on the study of structural rigidity and the preorganisation of thread binding sites as factors of major influence on template efficiency in the synthesis of hydrogen bond assembled supramolecular structures (rotaxanes and catenanes). Chapter One gives a brief outline of the common synthetic approaches to interlocked architectures (catenanes and rotaxanes) that are now being developed to address the problems outlined above. Chapter Two and Chapter Three concerns the synthesis of novel amide-based rotaxanes containing various saturated and unsaturated skeletons in their templating core. These new amide-based rotaxanes (muconic, hydromuconic and glutaconic) were synthesised by a clipping strategy in high yields. Chapter Four concerns the synthesis of a novel class of rotaxanes containing a naphthalene tetramide macrocycle that has a larger cavity (102). Several rotaxanation experiments based on macrocycle 102 precursors and threads containing several possible templating motifs were examined. Chapter Five report on the use of rotaxane wheels as a non-covalent protecting group able to influence the chemical behaviour of the functional groups in the central part of the axle. Chapter Six several heterocircuit [2]catenanes functionalised with various sulphide groups were synthesised and their monolayer forming capability on a gold surface studied. Another approach involving covalent attachment of macrocycles and catenanes on a pre-formed monolayer was also investigated. (author)

  15. Fractal dimension of microbead assemblies used for protein detection

    Science.gov (United States)

    Hecht, Ariel; Commiskey, Patrick; Lazaridis, Filippos; Argyrakis, Panos

    2014-01-01

    We use fractal analysis to calculate the protein concentration in a rotating magnetic assembly of microbeads of size 1μm, which has optimized parameters of sedimentation, binding sites and magnetic volume. We utilize the original Forrest-Witten method, but due to the relatively small number of bead particles, which is of the order of 500, we use a large number of origins and also a large number of algorithm iterations. We find a value of the fractal dimension in the range 1.70–1.90, as a function of the thrombin concentration, which plays the role of binding the microbeads together. This is in good agreement with previous results from magnetorotation studies. The calculation of the fractal dimension using multiple points of reference can be used for any assembly with a relatively small number of particles. PMID:25195559

  16. RNA binding to APOBEC3G induces the disassembly of functional deaminase complexes by displacing single-stranded DNA substrates

    OpenAIRE

    Polevoda, Bogdan; McDougall, William M.; Tun, Bradley N.; Cheung, Michael; Salter, Jason D.; Friedman, Alan E.; Smith, Harold C.

    2015-01-01

    APOBEC3G (A3G) DNA deaminase activity requires a holoenzyme complex whose assembly on nascent viral reverse transcripts initiates with A3G dimers binding to ssDNA followed by formation of higher-order A3G homo oligomers. Catalytic activity is inhibited when A3G binds to RNA. Our prior studies suggested that RNA inhibited A3G binding to ssDNA. In this report, near equilibrium binding and gel shift analyses showed that A3G assembly and disassembly on ssDNA was an ordered process involving A3G d...

  17. Molecular basis for oligomeric-DNA binding and episome maintenance by KSHV LANA.

    Directory of Open Access Journals (Sweden)

    John F Domsic

    Full Text Available LANA is the KSHV-encoded terminal repeat binding protein essential for viral replication and episome maintenance during latency. We have determined the X-ray crystal structure of LANA C-terminal DNA binding domain (LANADBD to reveal its capacity to form a decameric ring with an exterior DNA binding surface. The dimeric core is structurally similar to EBV EBNA1 with an N-terminal arm that regulates DNA binding and is required for replication function. The oligomeric interface between LANA dimers is dispensable for single site DNA binding, but is required for cooperative DNA binding, replication function, and episome maintenance. We also identify a basic patch opposite of the DNA binding surface that is responsible for the interaction with BRD proteins and contributes to episome maintenance function. The structural features of LANADBD suggest a novel mechanism of episome maintenance through DNA-binding induced oligomeric assembly.

  18. Spatially confined assembly of nanoparticles.

    Science.gov (United States)

    Jiang, Lin; Chen, Xiaodong; Lu, Nan; Chi, Lifeng

    2014-10-21

    The ability to assemble NPs into ordered structures that are expected to yield collective physical or chemical properties has afforded new and exciting opportunities in the field of nanotechnology. Among the various configurations of nanoparticle assemblies, two-dimensional (2D) NP patterns and one-dimensional (1D) NP arrays on surfaces are regarded as the ideal assembly configurations for many technological devices, for example, solar cells, magnetic memory, switching devices, and sensing devices, due to their unique transport phenomena and the cooperative properties of NPs in assemblies. To realize the potential applications of NP assemblies, especially in nanodevice-related applications, certain key issues must still be resolved, for example, ordering and alignment, manipulating and positioning in nanodevices, and multicomponent or hierarchical structures of NP assemblies for device integration. Additionally, the assembly of NPs with high precision and high levels of integration and uniformity for devices with scaled-down dimensions has become a key and challenging issue. Two-dimensional NP patterns and 1D NP arrays are obtained using traditional lithography techniques (top-down strategies) or interfacial assembly techniques (bottom-up strategies). However, a formidable challenge that persists is the controllable assembly of NPs in desired locations over large areas with high precision and high levels of integration. The difficulty of this assembly is due to the low efficiency of small features over large areas in lithography techniques or the inevitable structural defects that occur during the assembly process. The combination of self-assembly strategies with existing nanofabrication techniques could potentially provide effective and distinctive solutions for fabricating NPs with precise position control and high resolution. Furthermore, the synergistic combination of spatially mediated interactions between nanoparticles and prestructures on surfaces may play

  19. Robotic Thumb Assembly

    Science.gov (United States)

    Ihrke, Chris A. (Inventor); Bridgwater, Lyndon (Inventor); Platt, Robert (Inventor); Wampler, II, Charles W. (Inventor); Goza, S. Michael (Inventor)

    2013-01-01

    An improved robotic thumb for a robotic hand assembly is provided. According to one aspect of the disclosure, improved tendon routing in the robotic thumb provides control of four degrees of freedom with only five tendons. According to another aspect of the disclosure, one of the five degrees of freedom of a human thumb is replaced in the robotic thumb with a permanent twist in the shape of a phalange. According to yet another aspect of the disclosure, a position sensor includes a magnet having two portions shaped as circle segments with different center points. The magnet provides a linearized output from a Hall effect sensor.

  20. Assembly and characterization of supramolecular architectures for biosensor applications

    OpenAIRE

    Xu, Fei

    2005-01-01

    The research has included the efforts in designing, assembling and structurally and functionally characterizing supramolecular biofunctional architectures for optical biosensing applications. In the first part of the study, a class of interfaces based on the biotin-NeutrAvidin binding matrix for the quantitative control of enzyme surface coverage and activity was developed. Genetically modified ß-lactamase was chosen as a model enzyme and attached to five different types of NeutrAvidi...

  1. Reversible Guest Exchange Mechanisms in Supramolecular Host-GuestAssemblies

    Energy Technology Data Exchange (ETDEWEB)

    Pluth, Michael D.; Raymond, Kenneth N.

    2006-09-01

    Synthetic chemists have provided a wide array of supramolecular assemblies able to encapsulate guest molecules. The scope of this tutorial review focuses on supramolecular host molecules capable of reversibly encapsulating polyatomic guests. Much work has been done to determine the mechanism of guest encapsulation and guest release. This review covers common methods of monitoring and characterizing guest exchange such as NMR, UV-VIS, mass spectroscopy, electrochemistry, and calorimetry and also presents representative examples of guest exchange mechanisms. The guest exchange mechanisms of hemicarcerands, cucurbiturils, hydrogen-bonded assemblies, and metal-ligand assemblies are discussed. Special attention is given to systems which exhibit constrictive binding, a motif common in supramolecular guest exchange systems.

  2. Actinide sequestration using self-assembled monolayers on mesoporous supports.

    Science.gov (United States)

    Fryxell, Glen E; Lin, Yuehe; Fiskum, Sandy; Birnbaum, Jerome C; Wu, Hong; Kemner, Ken; Kelly, Shelley

    2005-03-01

    Surfactant templated synthesis of mesoporous ceramics provides a versatile foundation upon which to create high efficiency environmental sorbents. These nanoporous ceramic oxides condense a huge amount of surface area into a very small volume. The ceramic oxide interface is receptive to surface functionalization through molecular self-assembly. The marriage of mesoporous ceramics with self-assembled monolayer chemistry creates a powerful new class of environmental sorbent materials called self-assembled monolayers on mesoporous supports (SAMMS). These SAMMS materials are highly efficient sorbents whose interfacial chemistry can be fine-tuned to selectively sequester a specific target species, such as heavy metals, tetrahedral oxometalate anions, and radionuclides. Details addressing the design, synthesis, and characterization of SAMMS materials specifically designed to sequester actinides, of central importance to the environmental cleanup necessary after 40 years of weapons-grade plutonium production, as well as evaluation of their binding affinities and kinetics are presented. PMID:15787373

  3. Dynamics of nucleosome assembly and effects of DNA methylation.

    Science.gov (United States)

    Lee, Ju Yeon; Lee, Jaehyoun; Yue, Hongjun; Lee, Tae-Hee

    2015-02-13

    The nucleosome is the fundamental packing unit of the eukaryotic genome, and CpG methylation is an epigenetic modification associated with gene repression and silencing. We investigated nucleosome assembly mediated by histone chaperone Nap1 and the effects of CpG methylation based on three-color single molecule FRET measurements, which enabled direct monitoring of histone binding in the context of DNA wrapping. According to our observation, (H3-H4)2 tetramer incorporation must precede H2A-H2B dimer binding, which is independent of DNA termini wrapping. Upon CpG methylation, (H3-H4)2 tetramer incorporation and DNA termini wrapping are facilitated, whereas proper incorporation of H2A-H2B dimers is inhibited. We suggest that these changes are due to rigidified DNA and increased random binding of histones to DNA. According to the results, CpG methylation expedites nucleosome assembly in the presence of abundant DNA and histones, which may help facilitate gene packaging in chromatin. The results also indicate that the slowest steps in nucleosome assembly are DNA termini wrapping and tetramer positioning, both of which are affected heavily by changes in the physical properties of DNA.

  4. SHBG (Sex Hormone Binding Globulin)

    Science.gov (United States)

    ... as: Testosterone-estrogen Binding Globulin; TeBG Formal name: Sex Hormone Binding Globulin Related tests: Testosterone , Free Testosterone, ... I should know? How is it used? The sex hormone binding globulin (SHBG) test may be used ...

  5. Progress of EMBarrel assembly

    CERN Multimedia

    Chalifour, M

    2002-01-01

    The assembly of the sixteen "M" modules into a vertical axis cylinder has been achieved last Friday, completing the first wheel of the Electromagnetic Barrel Calorimeter (see picture). With this, an important milestone in the construction of the ATLAS detector has been reached. Future steps are the rotation of the cylinder axis into horizontal position, in order to integrate the presamplers and heat exchangers by the end of October. The transportation of the wheel and its insertion into the cryostat is the next major milestone, and is planned for the beginning of 2003. The construction of the modules (the so-called "P" modules) of the second wheel is ongoing at Saclay, Annecy and CERN, and will be completed in the coming months. The assembly of the second wheel should start at CERN in February, and its insertion in the cryostat is scheduled for June 2003. This achievement is the result of a successful collaboration of all institutes involved in the construction of the EM Barrel, namely Annecy, Saclay and CE...

  6. ANNUAL GENERAL ASSEMBLY

    CERN Multimedia

    2001-01-01

    All members and beneficiaries of the Pension Fund are invited to attend the Annual General Asssembly to be held in the CERN Auditorium on Wednesday 3 October 2001 at 14.30 hrs The Agenda comprises:   Opening Remarks (P. Levaux) Some aspects of risk in a pension fund (C. Cuénoud) Annual Report 2000: Presentation and results (C. Cuénoud) Copies of the Report are available from divisional secretariats. Results of the actuarial reviews (G. Maurin) Questions from members and beneficiaries Persons wishing to ask questions are encouraged to submit them, where possible, in writing in advance, addressed to Mr C. Cuénoud, Administrator of the Fund. Conclusions (P. Levaux) As usual, participants are invited to drinks after the assembly. NB The minutes of the 2000 General Assembly are available from the Administration of the Fund (tel. + 41 22 767 91 94; e-mail Graziella.Praire@cern.ch) The English version will be published next week.

  7. Fuel assembly supporting structure

    International Nuclear Information System (INIS)

    For use in forming the core of a pressurized-water reactor, a fuel assembly supporting structure for holding a bundle of interspaced fuel rods, is formed by interspaced end pieces having holes in which the end portions of control rod guide tubes are inserted, fuel rod spacer grids being positioned by these guide tubes between the end pieces. The end pieces are fastened to the end portions of the guide tubes, to integrate the supporting structure, and in the case of at least one of the end pieces, this is done by means which releases that end piece from the guide tubes when the end pieces receive an abnormal thrust force directed towards each other and which would otherwise place the guide tubes under a compressive stress that would cause them to buckle. The spacer grids normally hold the fuel rods interspaced by distances determined by nuclear physics, and buckling of the control rod guide tubes can distort the fuel rod spacer grids with consequent dearrangement of the fuel rod interspacing. A sudden loss of pressure in a pressurized-water reactor pressure vessel can result in the pressurized coolant in the vessel discharging from the vessel at such high velocity as to result in the abnormal thrust force on the end pieces of each fuel assembly, which could cause buckling of the control rod guide tubes when the end pieces are fixed to them in the normal rigid and unyielding manner

  8. Computational design of co-assembling protein-DNA nanowires

    Science.gov (United States)

    Mou, Yun; Yu, Jiun-Yann; Wannier, Timothy M.; Guo, Chin-Lin; Mayo, Stephen L.

    2015-09-01

    Biomolecular self-assemblies are of great interest to nanotechnologists because of their functional versatility and their biocompatibility. Over the past decade, sophisticated single-component nanostructures composed exclusively of nucleic acids, peptides and proteins have been reported, and these nanostructures have been used in a wide range of applications, from drug delivery to molecular computing. Despite these successes, the development of hybrid co-assemblies of nucleic acids and proteins has remained elusive. Here we use computational protein design to create a protein-DNA co-assembling nanomaterial whose assembly is driven via non-covalent interactions. To achieve this, a homodimerization interface is engineered onto the Drosophila Engrailed homeodomain (ENH), allowing the dimerized protein complex to bind to two double-stranded DNA (dsDNA) molecules. By varying the arrangement of protein-binding sites on the dsDNA, an irregular bulk nanoparticle or a nanowire with single-molecule width can be spontaneously formed by mixing the protein and dsDNA building blocks. We characterize the protein-DNA nanowire using fluorescence microscopy, atomic force microscopy and X-ray crystallography, confirming that the nanowire is formed via the proposed mechanism. This work lays the foundation for the development of new classes of protein-DNA hybrid materials. Further applications can be explored by incorporating DNA origami, DNA aptamers and/or peptide epitopes into the protein-DNA framework presented here.

  9. Biodiscovery of aluminum binding peptides

    Science.gov (United States)

    Adams, Bryn L.; Sarkes, Deborah A.; Finch, Amethist S.; Hurley, Margaret M.; Stratis-Cullum, Dimitra

    2013-05-01

    Cell surface peptide display systems are large and diverse libraries of peptides (7-15 amino acids) which are presented by a display scaffold hosted by a phage (virus), bacteria, or yeast cell. This allows the selfsustaining peptide libraries to be rapidly screened for high affinity binders to a given target of interest, and those binders quickly identified. Peptide display systems have traditionally been utilized in conjunction with organic-based targets, such as protein toxins or carbon nanotubes. However, this technology has been expanded for use with inorganic targets, such as metals, for biofabrication, hybrid material assembly and corrosion prevention. While most current peptide display systems employ viruses to host the display scaffold, we have recently shown that a bacterial host, Escherichia coli, displaying peptides in the ubiquitous, membrane protein scaffold eCPX can also provide specific peptide binders to an organic target. We have, for the first time, extended the use of this bacterial peptide display system for the biodiscovery of aluminum binding 15mer peptides. We will present the process of biopanning with macroscopic inorganic targets, binder enrichment, and binder isolation and discovery.

  10. 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.

  11. Ribosome Assembly as Antimicrobial Target.

    Science.gov (United States)

    Nikolay, Rainer; Schmidt, Sabine; Schlömer, Renate; Deuerling, Elke; Nierhaus, Knud H

    2016-01-01

    Many antibiotics target the ribosome and interfere with its translation cycle. Since translation is the source of all cellular proteins including ribosomal proteins, protein synthesis and ribosome assembly are interdependent. As a consequence, the activity of translation inhibitors might indirectly cause defective ribosome assembly. Due to the difficulty in distinguishing between direct and indirect effects, and because assembly is probably a target in its own right, concepts are needed to identify small molecules that directly inhibit ribosome assembly. Here, we summarize the basic facts of ribosome targeting antibiotics. Furthermore, we present an in vivo screening strategy that focuses on ribosome assembly by a direct fluorescence based read-out that aims to identify and characterize small molecules acting as primary assembly inhibitors. PMID:27240412

  12. Self-assembly via microfluidics

    OpenAIRE

    Wang, Lei; Sánchez, Samuel

    2015-01-01

    The self-assembly of amphiphilic building blocks has attracted extensive interest in myriad fields in recent years, due to their great potential in the nanoscale design of functional hybrid materials. Microfluidic techniques provide an intriguing method to control kinetic aspects of the self-assembly of molecular amphiphiles by the facile adjustment of the hydrodynamics of the fluids. Up to now, there have been several reports about one-step direct self-assembly of different building blocks w...

  13. Coded nanoscale self-assembly

    Indian Academy of Sciences (India)

    Prathyush Samineni; Debabrata Goswami

    2008-12-01

    We demonstrate coded self-assembly in nanostructures using the code seeded at the component level through computer simulations. Defects or cavities occur in all natural assembly processes including crystallization and our simulations capture this essential aspect under surface minimization constraints for self-assembly. Our bottom-up approach to nanostructures would provide a new dimension towards nanofabrication and better understanding of defects and crystallization process.

  14. Thermodynamic Studies of Electrostatic Self-assembly of Poly Diallyldimethylammonium Chloride on Proton Exchange Membrane

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The electrostatic self-assembly of polymer on proton exchange membrane was studied by calorimetric tech-nique. The titration of poly diallyldimethylammonium chloride (PDDA) into Nation membrane was designed and performed to determine the thermodynamic parameters. The enthalpy change △rH(○)m and binding constant K in the process of self-assembly were obtained from data analysis with the help of Origin. According to the calculated thermodynamic parameters, the electrostatic self-assembly of PDDA on the proton exchange membrane is an "en-thalpy-driven" reaction. The released heat indicates decrease of energy, which is helpful for the occurrence of the self-assembly process, and the degree of disorder is reduced, which went against the adsorption process. As to everyion bond, the value of △rH(○)m of DDA is beyond PDDA because a small molecule can bind itself to the membranewithout steric hindrance.

  15. Seismic behaviour of fuel assembly

    International Nuclear Information System (INIS)

    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

  16. 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.

  17. Methanation assembly using multiple reactors

    Science.gov (United States)

    Jahnke, Fred C.; Parab, Sanjay C.

    2007-07-24

    A methanation assembly for use with a water supply and a gas supply containing gas to be methanated in which a reactor assembly has a plurality of methanation reactors each for methanating gas input to the assembly and a gas delivery and cooling assembly adapted to deliver gas from the gas supply to each of said methanation reactors and to combine water from the water supply with the output of each methanation reactor being conveyed to a next methanation reactor and carry the mixture to such next methanation reactor.

  18. JWST NIRCam flight mirror assemblies

    Science.gov (United States)

    Mammini, Paul V.; Holmes, Howard C.; Huff, Lynn; Jacoby, Mike S.; Lopez, Frank

    2011-10-01

    The Near Infrared Camera (NIRCam) instrument for NASA's James Webb Space Telescope (JWST) has an optical prescription which includes numerous fold mirror assemblies. The instrument will operate at 35K after experiencing launch loads at ~293K. The optic mounts must accommodate all associated thermal and mechanical stresses, plus maintain exceptional optical quality during operation. Lockheed Martin Space Systems Company (LMSSC) conceived, designed, analyzed, assembled, tested, and integrated the mirror assemblies for the NIRCam instrument. This paper covers the design, analysis, assembly, and test of two of the instruments key fold mirrors.

  19. Geometric reasoning about assembly tools

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, R.H.

    1997-01-01

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

  20. Rocket Assembly and Checkout Facility

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Integrates, tests, and calibrates scientific instruments flown on sounding rocket payloads. The scientific instruments are assembled on an optical bench;...

  1. Moisture Research - Optimizing Wall Assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Arena, Lois [Consortium for Advanced Residential Buildings (CARB), Norwalk, CT (United States); Mantha, Pallavi [Consortium for Advanced Residential Buildings (CARB), Norwalk, CT (United States)

    2013-05-01

    In this project, the Consortium for Advanced Residential Buildings (CARB) team evaluated several different configurations of wall assemblies to determine the accuracy of moisture modeling and make recommendations to ensure durable, efficient assemblies. WUFI and THERM were used to model the hygrothermal and heat transfer characteristics of these walls. Wall assemblies evaluated included code minimum walls using spray foam insulation and fiberglass batts, high R-value walls at least 12 in. thick (R-40 and R-60 assemblies), and brick walls with interior insulation.

  2. Airfoil nozzle and shroud assembly

    Science.gov (United States)

    Shaffer, James E.; Norton, Paul F.

    1997-01-01

    An airfoil and nozzle assembly 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.

  3. 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.

  4. Multilayers Assembly of DNA Probe for Biosensor

    Institute of Scientific and Technical Information of China (English)

    谢文章; 路英杰; 隋森芳

    2002-01-01

    Surface plasmon resonance (SPR) was a sensitive method to study molecular interactions. Based on the specific binding, this paper presented the molecular assembly of protein-nucleic acid multilayers on the surface of a gold film. The first layer was a biotin-lipid (B-DMPE/DMPE) containing a monolayer prepared using the Langmuir-Blodgett (LB) technique. The second and third layers were avidin and DNA labeled biotin, respectively. The fourth layer was anti-DNA antibody extracted from the serum of patients with systemic lupus erythematosus (SLE). These interactions provide stability in the multilayer films of the complexes. The multilayer formation process was detected by SPR spectroscopy. The results show that the chip-based sensor system can be used for functional characterization of protein-protein and protein-DNA interactions.

  5. Quantum dot-polypeptide hybrid assemblies: Synthesis, fundamental properties, and application

    Science.gov (United States)

    Thedjoisworo, Bayu Atmaja

    We report the development of a multifunctional system that has the capability to target cancer cells, as well as simultaneously image and deliver therapeutics to these targeted cells. Such a "three-in-one" technology that has integrated targeting, imaging, and drug delivery capabilities is highly desirable in the field of cancer therapy. The material that we have developed for this application is a quantum dot (QD)-polypeptide hybrid assembly system that is spontaneously formed through the self-assembly of carboxyl-functionalized QDs and poly(diethylene glycol L-lysine)-poly(L-lysine) (PEGLL-PLL) diblock copolypeptide molecules. The hybrid assemblies could be modified to target a great variety of cancer biomarkers and have potential ability to carry therapeutic agents with diverse chemical and physical properties. In addition, the QD-polypeptide assemblies have the advantage of extensive tunability and versatility that allow their properties to be tailored and optimized for a broad range of applications. Cancer targeting can be achieved by modifying the QD-polypeptide hybrid assemblies with ligands that have affinity for certain biomarkers, which are overexpressed on cancer cells. Upon binding and uptake by the target cells through specific ligand-receptor mediated interactions, the assemblies could then allow for the simultaneous imaging of the cells and delivery of therapeutic agents to these cells. Imaging of the cells is done through detection of the QD fluorescence, and drug-delivery can be effected by loading the assembly with therapeutic agents and releasing them by means that disrupt the self-assembly. When compared to other dual imaging and drug-delivery systems, our QD-polypeptide hybrid assemblies have the advantage of extensive tunability and versatility. To showcase the tunability of the assembly, we demonstrated how its tumor-cell binding characteristics could be modulated and optimized by changing the PEGLL x-PLLy, architecture and the self-assembly

  6. Identical linkage and cooperativity of oxygen and carbon monoxide binding to Octopus dofleini hemocyanin

    Energy Technology Data Exchange (ETDEWEB)

    Connelly, P.R.; Gill, S.J.; Miller, K.I.; Zhou, G.; van Holde, K.E. (Univ. of Colorado, Boulder (USA))

    1989-02-21

    Employment of high-precision thin-layer methods has enabled detailed functional characterization of oxygen and carbon monoxide binding for (1) the fully assembled form with 70 binding sites and (2) the isolated chains with 7 binding sites of octopus dofleini hemocyanin. The striking difference in the cooperativities of the two ligands for the assembled decamer is revealed through an examination of the binding capacities and the partition coefficient, determined as functions of the activities of both ligands. A global analysis of the data sets supported by a two-state allosteric model assuming an allosteric unit of 7. Higher level allosteric interactions were not indicated. This contrasts to results obtained for arthropod hemocyanins. Oxygen and carbon monoxide experiments performed on the isolated subunit chain confirmed the presence of functional heterogeneity reported previously. The analysis shows two types of binding sites in the ratio of 4:3.

  7. Identical linkage and cooperativity of oxygen and carbon monoxide binding to Octopus dofleini hemocyanin.

    Science.gov (United States)

    Connelly, P R; Gill, S J; Miller, K I; Zhou, G; van Holde, K E

    1989-02-21

    Employment of high-precision thin-layer methods has enabled detailed functional characterization of oxygen and carbon monoxide binding for (1) the fully assembled form with 70 binding sites and (2) the isolated chains with 7 binding sites of Octopus dofleini hemocyanin. The striking difference in the cooperativities of the two ligands for the assembled decamer is revealed through an examination of the binding capacities and the partition coefficient, determined as functions of the activities of both ligands. A global analysis of the data sets supported a two-state allosteric model assuming an allosteric unit of 7. Higher level allosteric interactions were not indicated. This contrasts to results obtained for arthropod hemocyanins. Oxygen and carbon monoxide experiments performed on the isolated subunit chain confirmed the presence of functional heterogeneity reported previously [Miller, K. (1985) Biochemistry 24, 4582-4586]. The analysis shows two types of binding sites in the ratio of 4:3. PMID:2719937

  8. GTP hydrolysis is required for vesicle fusion during nuclear envelope assembly in vitro

    OpenAIRE

    1992-01-01

    Nuclear envelope assembly was studied in vitro using extracts from Xenopus eggs. Nuclear-specific vesicles bound to demembranated sperm chromatin but did not fuse in the absence of cytosol. Addition of cytosol stimulated vesicle fusion, pore complex assembly, and eventual nuclear envelope growth. Vesicle binding and fusion were assayed by light and electron microscopy. Addition of ATP and GTP to bound vesicles caused limited vesicle fusion, but enclosure of the chromatin was not observed. Thi...

  9. Gold Nanoparticle Assembly Microfluidic Reactor for Efficient On-line Proteolysis

    OpenAIRE

    Liu, Y; Xue, Y.; Ji, J; Chen, X; Kong, J.; Yang, P.; Girault, H H

    2007-01-01

    A microchip reactor coated with a gold nanoparticle network entrapping trypsin was designed for the efficient on-line proteolysis of low level proteins and complex extracts originating from mouse macrophages. The nanostructured surface coating was assembled via a layer-bylayer electrostatic binding of poly(diallyldimethylammonium chloride) and gold nanoparticles. The assembly process was monitored by UV-visible spectroscopy, atomic force microscopy, and quartz crystal microbalance. The contro...

  10. Assembly of single wall carbon nanotube-metal nanohybrids using biomolecular components

    Science.gov (United States)

    Kim, Sang Nyon; Slocik, Joseph M.; Naik, Rajesh R.

    2010-08-01

    Biomaterials such as nucleic acids and proteins can be exploited to create higher order structures. The biomolecular components such as DNA and peptides have been used to assemble nanoparticles with high fidelity. Here, we use DNA and peptides, and their preferential interaction with inorganic and carbon nanomaterials to form homogeneous hybrids. The enhanced binding of Pt ions to both DNA and peptide functionalized nanoparticles mediates the assembly of carbon nanotubes functionalized with DNA with peptide coated gold nanoparticles.

  11. Conduit coupling assembly

    International Nuclear Information System (INIS)

    A conduit coupling assembly for coupling pipes with an interposed seal has a first part for receiving a pipe and is in splined engagement with a bush fixed to a pipe. A second part having radial fingers so that it can be turned by a manipulator, has a threaded engagement with the first part which is the same hand but different pitch to a threaded engagement between the second part and the bush. Pitches of 8:7 for couplings will give a mechanical advantage of 56:1 thus reducing the force needed to obtain a given axial movement of the bush and thus of the pipe and compression of the seal. (author)

  12. Subcritical nuclear assembly

    International Nuclear Information System (INIS)

    A Subcritical Nuclear Assembly is a device where the nuclear-fission chain reaction is initiated and maintained using an external neutron source. It is a valuable educational and research tool where in a safe way many reactor parameters can be measured. Here, we have used the Wigner-Seitz method in the six-factor formula to calculate the effective multiplication factor of a subcritical nuclear reactor Nuclear Chicago model 9000. This reactor has approximately 2500 kg of natural uranium heterogeneously distributed in slugs. The reactor uses a 239PuBe neutron source that is located in the center of an hexagonal array. Using Monte Carlo methods, with the MCNP5 code, a three-dimensional model of the subcritical reactor was designed to estimate the effective multiplication factor, the neutron spectra, the total and thermal neutron fluences along the radial and axial axis. With the neutron spectra in two locations outside the reactor the ambient dose equivalent were estimated. (Author)

  13. Cilium assembly and disassembly

    Science.gov (United States)

    2016-01-01

    The primary cilium is an antenna-like, immotile organelle present on most types of mammalian cells, which interprets extracellular signals that regulate growth and development. Although once considered a vestigial organelle, the primary cilium is now the focus of considerable interest. We now know that ciliary defects lead to a panoply of human diseases, termed ciliopathies, and the loss of this organelle may be an early signature event during oncogenic transformation. Ciliopathies include numerous seemingly unrelated developmental syndromes, with involvement of the retina, kidney, liver, pancreas, skeletal system and brain. Recent studies have begun to clarify the key mechanisms that link cilium assembly and disassembly to the cell cycle, and suggest new possibilities for therapeutic intervention. PMID:27350441

  14. Photovoltaic cell assembly

    Science.gov (United States)

    Beavis, Leonard C.; Panitz, Janda K. G.; Sharp, Donald J.

    1990-01-01

    A photovoltaic assembly for converting high intensity solar radiation into lectrical energy in which a solar cell is separated from a heat sink by a thin layer of a composite material which has excellent dielectric properties and good thermal conductivity. This composite material is a thin film of porous Al.sub.2 O.sub.3 in which the pores have been substantially filled with an electrophoretically-deposited layer of a styrene-acrylate resin. This composite provides electrical breakdown strengths greater than that of a layer consisting essentially of Al.sub.2 O.sub.3 and has a higher thermal conductivity than a layer of styrene-acrylate alone.

  15. Fluid cooled electrical assembly

    Science.gov (United States)

    Rinehart, Lawrence E.; Romero, Guillermo L.

    2007-02-06

    A heat producing, fluid cooled assembly that includes a housing made of liquid-impermeable material, which defines a fluid inlet and a fluid outlet and an opening. Also included is an electrical package having a set of semiconductor electrical devices supported on a substrate and the second major surface is a heat sink adapted to express heat generated from the electrical apparatus and wherein the second major surface defines a rim that is fit to the opening. Further, the housing is constructed so that as fluid travels from the fluid inlet to the fluid outlet it is constrained to flow past the opening thereby placing the fluid in contact with the heat sink.

  16. Curcumin Binding to Beta Amyloid: A Computational Study.

    Science.gov (United States)

    Rao, Praveen P N; Mohamed, Tarek; Teckwani, Karan; Tin, Gary

    2015-10-01

    Curcumin, a chemical constituent present in the spice turmeric, is known to prevent the aggregation of amyloid peptide implicated in the pathophysiology of Alzheimer's disease. While curcumin is known to bind directly to various amyloid aggregates, no systematic investigations have been carried out to understand its ability to bind to the amyloid aggregates including oligomers and fibrils. In this study, we constructed computational models of (i) Aβ hexapeptide (16) KLVFFA(21) octamer steric-zipper β-sheet assembly and (ii) full-length Aβ fibril β-sheet assembly. Curcumin binding in these models was evaluated by molecular docking and molecular dynamics (MD) simulation studies. In both the models, curcumin was oriented in a linear extended conformation parallel to fiber axis and exhibited better stability in the Aβ hexapeptide (16) KLVFFA(21) octamer steric-zipper model (Ebinding  = -10.05 kcal/mol) compared to full-length Aβ fibril model (Ebinding  = -3.47 kcal/mol). Analysis of MD trajectories of curcumin bound to full-length Aβ fibril shows good stability with minimum Cα-atom RMSD shifts. Interestingly, curcumin binding led to marked fluctuations in the (14) HQKLVFFA(21) region that constitute the fibril spine with RMSF values ranging from 1.4 to 3.6 Å. These results show that curcumin binding to Aβ shifts the equilibrium in the aggregation pathway by promoting the formation of non-toxic aggregates.

  17. Molecular interactions of ribosomal components. IV: Cooperative interactions during assembly in vitro.

    Science.gov (United States)

    Green, M; Kurland, C G

    1973-08-01

    Cooperative interactions between different 30S ribosomal proteins during assembly in vitro are described. The site specific binding of S7 to 16S RNA is enhanced by S20; that of S16 requires S4 and S20; and S7 is required for the maximum binding of S9, S13 and S19. Some of these interactions are reflected in the protein neighborhoods of the functional ribosome, but this may not be a general rule. Finally, we suggest that the assembly cooperativety observed may not be a consequence of direct-protein interactions.

  18. Higher-order assemblies of BAR domain proteins for shaping membranes.

    Science.gov (United States)

    Suetsugu, Shiro

    2016-06-01

    Most cellular organelles contain lipid bilayer membranes. The earliest characterization of cellular organelles was performed by electron microscopy observation of such membranes. However, the precise mechanisms for shaping the membrane in particular subcellular organelles is poorly understood. Classically, the overall cellular shape, i.e. the shape of the plasma membrane, was thought to be governed by the reorganization of cytoskeletal components such as actin and microtubules. The plasma membrane contains various submicron structures such as clathrin-coated pits, caveolae, filopodia and lamellipodia. These subcellular structures are either invaginations or protrusions and are associated with the cytoskeleton. Therefore, it could be hypothesized that there are membrane-binding proteins that cooperates with cytoskeleton in shaping of plasma membrane organelles. Proteins with the Bin-Amphiphysin-Rvs (BAR) domain connect a variety of membrane shapes to actin filaments. The BAR domains themselves bend the membranes by their rigidity and then mold the membranes into tubules through their assembly as spiral polymers, which are thought to be involved in the various submicron structures. Membrane tubulation by polymeric assembly of the BAR domains is supposed to be regulated by binding proteins, binding lipids and the mechanical properties of the membrane. This review gives an overview of BAR protein assembly, describes the significance of the assembly and discusses how to study the assembly in the context of membrane and cellular morphology. The technical problems encountered in microscopic observation of BAR domain assembly are also discussed. PMID:26884618

  19. Higher-order assemblies of BAR domain proteins for shaping membranes.

    Science.gov (United States)

    Suetsugu, Shiro

    2016-06-01

    Most cellular organelles contain lipid bilayer membranes. The earliest characterization of cellular organelles was performed by electron microscopy observation of such membranes. However, the precise mechanisms for shaping the membrane in particular subcellular organelles is poorly understood. Classically, the overall cellular shape, i.e. the shape of the plasma membrane, was thought to be governed by the reorganization of cytoskeletal components such as actin and microtubules. The plasma membrane contains various submicron structures such as clathrin-coated pits, caveolae, filopodia and lamellipodia. These subcellular structures are either invaginations or protrusions and are associated with the cytoskeleton. Therefore, it could be hypothesized that there are membrane-binding proteins that cooperates with cytoskeleton in shaping of plasma membrane organelles. Proteins with the Bin-Amphiphysin-Rvs (BAR) domain connect a variety of membrane shapes to actin filaments. The BAR domains themselves bend the membranes by their rigidity and then mold the membranes into tubules through their assembly as spiral polymers, which are thought to be involved in the various submicron structures. Membrane tubulation by polymeric assembly of the BAR domains is supposed to be regulated by binding proteins, binding lipids and the mechanical properties of the membrane. This review gives an overview of BAR protein assembly, describes the significance of the assembly and discusses how to study the assembly in the context of membrane and cellular morphology. The technical problems encountered in microscopic observation of BAR domain assembly are also discussed.

  20. Direct Simulation of the Self-Assembly of a Small DNA Origami.

    Science.gov (United States)

    Snodin, Benedict E K; Romano, Flavio; Rovigatti, Lorenzo; Ouldridge, Thomas E; Louis, Ard A; Doye, Jonathan P K

    2016-02-23

    By using oxDNA, a coarse-grained nucleotide-level model of DNA, we are able to directly simulate the self-assembly of a small 384-base-pair origami from single-stranded scaffold and staple strands in solution. In general, we see attachment of new staple strands occurring in parallel, but with cooperativity evident for the binding of the second domain of a staple if the adjacent junction is already partially formed. For a system with exactly one copy of each staple strand, we observe a complete assembly pathway in an intermediate temperature window; at low temperatures successful assembly is prevented by misbonding while at higher temperature the free-energy barriers to assembly become too large for assembly on our simulation time scales. For high-concentration systems involving a large staple strand excess, we never see complete assembly because there are invariably instances where two copies of the same staple both bind to the scaffold, creating a kinetic trap that prevents the complete binding of either staple. This mutual staple blocking could also lead to aggregates of partially formed origamis in real systems, and helps to rationalize certain successful origami design strategies. PMID:26766072

  1. Two distinct domains of protein 4.1 critical for assembly offunctional nuclei in Vitro

    Energy Technology Data Exchange (ETDEWEB)

    Krauss, Sharon Wald; Heald, Rebecca; Lee, Gloria; Nunomura, Wataru; Gimm,J. Aura; Mohandas, Narla; Chasis, Joel AnneJ. Aura; Mohandas, Narla; Chasis, Joel Anne

    2002-11-15

    Protein 4.1R, a multifunctional structural protein, acts asan adaptor in mature red cell membrane skeletons linking spectrin-actincomplexes to plasma membrane-associated proteins. In nucleated cellsprotein 4.1 is not associated exclusively with plasma membrane but isalso detected at several important subcellular locations crucial for celldivision. To identify 4.1 domains having critical functions in nuclearassembly, 4.1 domain peptides were added to Xenopus egg extract nuclearreconstitution reactions. Morphologically disorganized, replicationdeficient nuclei assembled when spectrin-actin binding domain orNuMA-binding C-terminal domain peptides were present. However, controlvariant spectrin-actin binding domain peptides incapable of bindingactin, or mutant C-terminal domain peptides with reduced NuMA binding,had no deleterious effects on nuclear reconstitution. To test if 4.1 isrequired for proper nuclear assembly, 4.1 isoforms were depleted withspectrin-actin binding or C-terminal domain-specific antibodies. Nucleiassembled in depleted extracts ha d deranged phenotypes. However, nuclearassembly could be rescued by addition of recombinant 4.1R. Our dataestablishes that protein 4.1 is essential for nuclear assembly andidentifies two distinct 4.1 domains, initially characterized incytoskeletal interactions, that have crucial and versatile functions innuclear assembly.

  2. Assembly sequencing with toleranced parts

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-02-21

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

  3. The Bicycle Assembly Line Game

    Science.gov (United States)

    Klotz, Dorothy

    2011-01-01

    "The Bicycle Assembly Line Game" is a team-based, in-class activity that helps students develop a basic understanding of continuously operating processes. Each team of 7-10 students selects one of seven prefigured bicycle assembly lines to operate. The lines are run in real-time, and the team that operates the line that yields the…

  4. WHATS IN A CELL ASSEMBLY

    NARCIS (Netherlands)

    DALENOORT, GJ; DEVRIES, PH

    1995-01-01

    The cell assembly as a simple attractor cannot explain many cognitive phenomena. It must be a highly structured network that can sustain highly structured excitation patterns. Moreover, a cell assembly must be more widely distributed in space than on a square millimeter.

  5. What was the Assembly Line?

    DEFF Research Database (Denmark)

    Nye, David

    2010-01-01

    The assembly line is still evolving a century after its invention, and it was not a distinct historical stage, nor was it part of an inevitable sequence that followed "Taylorism."......The assembly line is still evolving a century after its invention, and it was not a distinct historical stage, nor was it part of an inevitable sequence that followed "Taylorism."...

  6. Newnes electronics assembly pocket book

    CERN Document Server

    Brindley, Keith

    2013-01-01

    Produced in association with the Engineering Training Authority with contributions from dozens of people in the electronics industry. The material covers common skills in electrical and electronic engineering and concentrates mainly on wiring and assembly. 'Newnes Electronics Assembly Pocket Book' is for electronics technicians, students and apprentices.

  7. 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.

  8. 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.

  9. Intrinsic universality and the computational power of self-assembly.

    Science.gov (United States)

    Woods, Damien

    2015-07-28

    Molecular self-assembly, the formation of large structures by small pieces of matter sticking together according to simple local interactions, is a ubiquitous phenomenon. A challenging engineering goal is to design a few molecules so that large numbers of them can self-assemble into desired complicated target objects. Indeed, we would like to understand the ultimate capabilities and limitations of this bottom-up fabrication process. We look to theoretical models of algorithmic self-assembly, where small square tiles stick together according to simple local rules in order to carry out a crystal growth process. In this survey, we focus on the use of simulation between such models to classify and separate their computational and expressive powers. Roughly speaking, one model simulates another if they grow the same structures, via the same dynamical growth processes. Our journey begins with the result that there is a single intrinsically universal tile set that, with appropriate initialization and spatial scaling, simulates any instance of Winfree's abstract Tile Assembly Model. This universal tile set exhibits something stronger than Turing universality: it captures the geometry and dynamics of any simulated system in a very direct way. From there we find that there is no such tile set in the more restrictive non-cooperative model, proving it weaker than the full Tile Assembly Model. In the two-handed model, where large structures can bind together in one step, we encounter an infinite set of infinite hierarchies of strictly increasing simulation power. Towards the end of our trip, we find one tile to rule them all: a single rotatable flipable polygonal tile that simulates any tile assembly system. We find another tile that aperiodically tiles the plane (but with small gaps). These and other recent results show that simulation is giving rise to a kind of computational complexity theory for self-assembly. It seems this could be the beginning of a much longer journey

  10. Goodpasture Antigen-binding Protein (GPBP) Directs Myofibril Formation

    Science.gov (United States)

    Revert-Ros, Francisco; López-Pascual, Ernesto; Granero-Moltó, Froilán; Macías, Jesús; Breyer, Richard; Zent, Roy; Hudson, Billy G.; Saadeddin, Anas; Revert, Fernando; Blasco, Raül; Navarro, Carmen; Burks, Deborah; Saus, Juan

    2011-01-01

    Goodpasture antigen-binding protein-1 (GPBP-1) is an exportable non-conventional Ser/Thr kinase that regulates glomerular basement membrane collagen organization. Here we provide evidence that GPBP-1 accumulates in the cytoplasm of differentiating mouse myoblasts prior to myosin synthesis. Myoblasts deficient in GPBP-1 display defective myofibril formation, whereas myofibrils assemble with enhanced efficiency in those overexpressing GPBP-1. We also show that GPBP-1 targets the previously unidentified GIP130 (GPBP-interacting protein of 130 kDa), which binds to myosin and promotes its myofibrillar assembly. This report reveals that GPBP-1 directs myofibril formation, an observation that expands its reported role in supramolecular organization of structural proteins to the intracellular compartment. PMID:21832087

  11. Fluorescently Sensing of DNA Triplex Assembly Using an Isoquinoline Alkaloid as Selector, Stabilizer, Inducer, and Switch-On Emitter.

    Science.gov (United States)

    Hu, Yuehua; Lin, Fan; Wu, Tao; Wang, Ying; Zhou, Xiao-Shun; Shao, Yong

    2016-07-20

    DNA triplex assembly has attracted a variety of interest in the regulation of genetic expression, drug screening, molecular switches, and sensors. However, these achievements are essentially dependent on the formation and stability of the triplex assembly. Herein, the recognition of DNA triplex assembly with various isoquinoline alkaloids was investigated. We found that natural chelerythrine (CHE) exhibits the highest selectivity in recognizing the triplex structure. The DNA triplex stability is substantially increased upon CHE binding, as opposed to the invariance in the stability of the duplex counterpart. CHE also favors the assembly of the triplex-forming oligonucleotide (TFO) with its duplex counterpart. The triplex binding switches CHE to a strong fluorescent emitter, which suggests CHE as a useful probe in following triplex assembly. As a unique triplex selector, inducer, and emitter, CHE successfully reports the wide pH- and metal-ion-dependent tunability of the triplex nanoswitch in a label-free manner. PMID:27252050

  12. An NMR-Based Structural Rationale for Contrasting Stoichiometry and Ligand Binding Site(s) in Fatty Acid-binding Proteins†

    OpenAIRE

    He, Yan; Estephan, Rima; Yang, Xiaomin; Vela, Adriana; Wang, Hsin; Bernard, Cédric; Stark, Ruth E.

    2011-01-01

    Liver fatty acid-binding protein (LFABP) is a 14-kDa cytosolic polypeptide, differing from other family members in number of ligand binding sites, diversity of bound ligands, and transfer of fatty acid(s) to membranes primarily via aqueous diffusion rather than direct collisional interactions. Distinct two-dimensional 1H-15N NMR signals indicative of slowly exchanging LFABP assemblies formed during stepwise ligand titration were exploited, without solving the protein-ligand complex structures...

  13. ASSEMBLY TRANSFER SYSTEM DESCRIPTION DOCUMENT

    Energy Technology Data Exchange (ETDEWEB)

    B. Gorpani

    2000-06-26

    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

  14. Ile-phe dipeptide self-assembly: clues to amyloid formation.

    Science.gov (United States)

    de Groot, Natalia Sánchez; Parella, Teodor; Aviles, Francesc X; Vendrell, Josep; Ventura, Salvador

    2007-03-01

    Peptidic self-assembled nanostructures are said to have a wide range of applications in nanotechnology, yet the mechanistic details of hierarchical self-assembly are still poorly understood. The Phe-Phe recognition motif of the Alzheimer's Abeta peptide is the smallest peptide able to assemble into higher-order structures. Here, we show that the Ile-Phe dipeptide analog is also able to self-associate in aqueous solution as a transparent, thermoreversible gel formed by a network of fibrillar nanostructures that exhibit strong birefringence upon Congo red binding. Besides, a second dipeptide Val-Phe, differing only in a methyl group from the former, is unable to self-assemble. The detailed analysis of the differential polymeric behavior of these closely related molecules provides insight into the forces triggering the first steps in self-assembly processes such as amyloid formation. PMID:17172307

  15. Analyzing Intracellular Binding and Diffusion with Continuous Fluorescence Photobleaching

    OpenAIRE

    Wachsmuth, Malte; Weidemann, Thomas; Müller, Gabriele; Hoffmann-Rohrer, Urs W.; Knoch, Tobias A.; Waldeck, Waldemar; Langowski, Jörg

    2003-01-01

    Transport and binding of molecules to specific sites are necessary for the assembly and function of ordered supramolecular structures in cells. For analyzing these processes in vivo, we have developed a confocal fluorescence fluctuation microscope that allows both imaging of the spatial distribution of fluorescent molecules with confocal laser scanning microscopy and probing their mobility at specific positions in the cell with fluorescence correlation spectroscopy and continuous fluorescence...

  16. Determination of stoichiometry and conformational changes in the first step of the P22 tail assembly.

    Science.gov (United States)

    Lorenzen, Kristina; Olia, Adam S; Uetrecht, Charlotte; Cingolani, Gino; Heck, Albert J R

    2008-05-30

    Large oligomeric portal assemblies have a central role in the life-cycles of bacteriophages and herpesviruses. The stoichiometry of in vitro assembled portal proteins has been a subject of debate for several years. The intrinsic polymorphic oligomerization of ectopically expressed portal proteins makes it possible to form rings of diverse stoichiometry (e.g., 11-mer, 12-mer, 13-mer, etc.) in solution. In this study, we have investigated the stoichiometry of the in vitro-assembled portal protein of bacteriophage P22 and characterized its association with the tail factor gp4. Using native mass spectrometry, we show for the first time that the reconstituted portal protein (assembled in vitro using a modified purification and assembly protocol) is exclusively dodecameric. Under the conditions used here, 12 copies of tail factor gp4 bind to the portal ring, in a cooperative fashion, to form a 12:12 complex of 1.050 MDa. We applied tandem mass spectrometry to the complete assembly and found an unusual dimeric dissociation pattern of gp4, suggesting a dimeric sub-organization of gp4 when assembled with the portal ring. Furthermore, native and ion mobility mass spectrometry reveal a major conformational change in the portal upon binding of gp4. We propose that the gp4-induced conformational change in the portal ring initiates a cascade of events assisting in the stabilization of newly filled P22 particles, which marks the end of phage morphogenesis. PMID:18448123

  17. Detection of Intermediates And Kinetic Control During Assembly of Bacteriophage P22 Procapsid

    Energy Technology Data Exchange (ETDEWEB)

    Tuma, R.; Tsuruta, H.; French, K.H.; Prevelige, P.

    2009-05-26

    Bacteriophage P22 serves as a model for the assembly and maturation of other icosahedral double-stranded DNA viruses. P22 coat and scaffolding proteins assemble in vitro into an icosahedral procapsid, which then expands during DNA packaging (maturation). Efficient in vitro assembly makes this system suitable for design and production of monodisperse spherical nanoparticles (diameter {approx} 50 nm). In this work, we explore the possibility of controlling the outcome of assembly by scaffolding protein engineering. The scaffolding protein exists in monomer-dimer-tetramer equilibrium. We address the role of monomers and dimers in assembly by using three different scaffolding proteins with altered monomer-dimer equilibrium (weak dimer, covalent dimer, monomer). The progress and outcome of assembly was monitored by time-resolved X-ray scattering, which allowed us to distinguish between closed shells and incomplete assembly intermediates. Binding of scaffolding monomer activates the coat protein for assembly. Excess dimeric scaffolding protein resulted in rapid nucleation and kinetic trapping yielding incomplete shells. Addition of monomeric wild-type scaffold with excess coat protein completed these metastable shells. Thus, the monomeric scaffolding protein plays an essential role in the elongation phase by activating the coat and effectively lowering its critical concentration for assembly.

  18. Development of a tuneable test problem generator for assembly sequence planning and assembly line balancing

    OpenAIRE

    Ab Rashid, Mohd Fadzil Faisae; Hutabarat, Windo; Tiwari, Ashutosh

    2012-01-01

    Assembly optimisation activities that involve assembly sequence planning and assembly line balancing have been extensively studied because of the importance of optimal assembly efficiency to manufacturing competitiveness. Numerous research works in assembly sequence planning and assembly line balancing mainly focus on developing algorithms to solve problems and to optimise assembly sequence planning and assembly line balancing. However, there is a scarcity in works that focus on developing pr...

  19. Structure of the RNA-Binding Domain of Telomerase: Implications For RNA Recognition and Binding

    Energy Technology Data Exchange (ETDEWEB)

    Rouda,S.; Skordalakes, E.

    2007-01-01

    Telomerase, a ribonucleoprotein complex, replicates the linear ends of eukaryotic chromosomes, thus taking care of the 'end of replication problem.' TERT contains an essential and universally conserved domain (TRBD) that makes extensive contacts with the RNA (TER) component of the holoenzyme, and this interaction is thought to facilitate TERT/TER assembly and repeat-addition processivity. Here, we present a high-resolution structure of TRBD from Tetrahymena thermophila. The nearly all-helical structure comprises a nucleic acid-binding fold suitable for TER binding. An extended pocket on the surface of the protein, formed by two conserved motifs (CP and T motifs) comprises TRBD's RNA-binding pocket. The width and the chemical nature of this pocket suggest that it binds both single- and double-stranded RNA, possibly stem I, and the template boundary element (TBE). Moreover, the structure provides clues into the role of this domain in TERT/TER stabilization and telomerase repeat-addition processivity.

  20. Subcritical nuclear assembly

    Energy Technology Data Exchange (ETDEWEB)

    Vega C, H. R., E-mail: fermineutron@yahoo.com [Universidad Autonoma de Zacatecas, Unidad Academica de Estudios Nucleares, Cipres No. 10, Fracc. La Penuela, 98068 Zacatecas (Mexico)

    2014-08-15

    A Subcritical Nuclear Assembly is a device where the nuclear-fission chain reaction is initiated and maintained using an external neutron source. It is a valuable educational and research tool where in a safe way many reactor parameters can be measured. Here, we have used the Wigner-Seitz method in the six-factor formula to calculate the effective multiplication factor of a subcritical nuclear reactor Nuclear Chicago model 9000. This reactor has approximately 2500 kg of natural uranium heterogeneously distributed in slugs. The reactor uses a {sup 239}PuBe neutron source that is located in the center of an hexagonal array. Using Monte Carlo methods, with the MCNP5 code, a three-dimensional model of the subcritical reactor was designed to estimate the effective multiplication factor, the neutron spectra, the total and thermal neutron fluences along the radial and axial axis. With the neutron spectra in two locations outside the reactor the ambient dose equivalent were estimated. (Author)

  1. ITER assembly and maintenance

    International Nuclear Information System (INIS)

    This document is intended to describe the work conducted by the ITER Assembly and Maintenance (A and M) Design Unit and the supporting home teams during the ITER Conceptual Design Activities, carried out from 1988 through 1990. Its content consists of two main sections, i.e., Chapter III, which describes the identified tasks to be performed by the A and M system and a general description of the required equipment; and Chapter IV, which provides a more detailed description of the equipment proposed to perform the assigned tasks. A two-stage R and D program is now planned, i.e., (1) a prototype equipment functional tests using full scale mock-ups and (2) a full scale integration demonstration test facility with real components (vacuum vessel with ports, blanket modules, divertor modules, armor tiles, etc.). Crucial in-vessel and ex-vessel operations and the associated remote handling equipment, including handling of divertor plates and blanket modules will be demonstrated in the first phase, whereby the database needed to proceed with the engineering phase will be acquired. The second phase will demonstrate the ability of the overall system to execute the required maintenance procedures and evaluate the performance of the prototype equipment

  2. Flexible Foot Test Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Kurita, C.H.; /Fermilab

    1987-04-27

    A test model of the flexible foot support was constructed early in the design stages to check its reactions to applied loads. The prototype was made of SS 304 and contained four vertical plates as opposed to the fourteen Inconel 718 plates which comprise the actual structure. Due to the fact that the prototype was built before the design of the support was finalized, the plate dimensions are different from those of the actual proposed design (i.e. model plate thickness is approximately one-half that of the actual plates). See DWG. 3740.210-MC-222376 for assembly details of the test model and DWG. 3740.210-MB-222377 for plate dimensions. This stanchion will be required to not only support the load of the inner vessel of the cryostat and its contents, but it must also allow for the movement of the vessel due to thermal contraction. Assuming that each vertical plate acts as a column, then the following formula from the Manual of Steel Construction (American Institute of Steel Construction, Inc., Eigth edition, 1980) can be applied to determine whether or not such columns undergoing simultaneous axial compression and transverse loading are considered safe for the given loading. The first term is representative of the axially compressive stress, and the second term, the bending stress. If the actual compressive stress is greater than 15% of the allowable compressive stress, then there are additional considerations which must be accounted for in the bending stress term.

  3. Cellulose binding domain proteins

    Energy Technology Data Exchange (ETDEWEB)

    Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc (Davis, CA); Doi, Roy (Davis, CA)

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  4. Sequential memory: Binding dynamics

    Science.gov (United States)

    Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

    2015-10-01

    Temporal order memories are critical for everyday animal and human functioning. Experiments and our own experience show that the binding or association of various features of an event together and the maintaining of multimodality events in sequential order are the key components of any sequential memories—episodic, semantic, working, etc. We study a robustness of binding sequential dynamics based on our previously introduced model in the form of generalized Lotka-Volterra equations. In the phase space of the model, there exists a multi-dimensional binding heteroclinic network consisting of saddle equilibrium points and heteroclinic trajectories joining them. We prove here the robustness of the binding sequential dynamics, i.e., the feasibility phenomenon for coupled heteroclinic networks: for each collection of successive heteroclinic trajectories inside the unified networks, there is an open set of initial points such that the trajectory going through each of them follows the prescribed collection staying in a small neighborhood of it. We show also that the symbolic complexity function of the system restricted to this neighborhood is a polynomial of degree L - 1, where L is the number of modalities.

  5. Lectin binding in meningiomas.

    Science.gov (United States)

    Kleinert, R; Radner, H

    1987-01-01

    Forty-two meningiomas of different morphological sub-type were examined to determine their pattern of binding to 11 different lectins which characterize cell surface components such as carbohydrate residues. Histiocytic and xanthoma cells within meningiomas could be demonstrated with six different lectins: wheat germ agglutinin (WGA), peanut agglutinin (PNA) Bauhinia purpurea agglutinin (BPA), Helix pomatia agglutinin (HPA), Vicia fava agglutinin (VFA) and Soyabean agglutinin (SBA). Vascular elements including endothelial cells and intimal cells, bound Ulex europaeus agglutinin type 1 (UEA 1), WGA and HPA. The fibrous stroma in fibrous and fibroblastic meningiomas bound PNA, Laburnum alpinum agglutinin (LAA) and SBA. Tumour cells in meningotheliomatous meningiomas and some areas of anaplastic meningiomas bound Concanavalin A, PNA, LAA and VFA whereas tumour cells in fibrous and fibroblastic meningiomas bound BPA, LAA and VFA. Lectin binding has proved to be of value in detecting histiocytic and xanthoma cells together with vascular elements within meningiomas. In addition, the different lectin binding patterns allow different histological sub-types of meningioma to be distinguished although the biological significance of the binding patterns is unclear. PMID:3658105

  6. 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.

  7. 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.

  8. Illustrating how mechanical assemblies work

    KAUST Repository

    Mitra, Niloy J.

    2013-01-01

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

  9. 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.

  10. Spider Silk-CBD-Cellulose Nanocrystal Composites: Mechanism of Assembly

    Science.gov (United States)

    Meirovitch, Sigal; Shtein, Zvi; Ben-Shalom, Tal; Lapidot, Shaul; Tamburu, Carmen; Hu, Xiao; Kluge, Jonathan A.; Raviv, Uri; Kaplan, David L.; Shoseyov, Oded

    2016-01-01

    The fabrication of cellulose-spider silk bio-nanocomposites comprised of cellulose nanocrystals (CNCs) and recombinant spider silk protein fused to a cellulose binding domain (CBD) is described. Silk-CBD successfully binds cellulose, and unlike recombinant silk alone, silk-CBD self-assembles into microfibrils even in the absence of CNCs. Silk-CBD-CNC composite sponges and films show changes in internal structure and CNC alignment related to the addition of silk-CBD. The silk-CBD sponges exhibit improved thermal and structural characteristics in comparison to control recombinant spider silk sponges. The glass transition temperature (Tg) of the silk-CBD sponge was higher than the control silk sponge and similar to native dragline spider silk fibers. Gel filtration analysis, dynamic light scattering (DLS), small angle X-ray scattering (SAXS) and cryo-transmission electron microscopy (TEM) indicated that silk-CBD, but not the recombinant silk control, formed a nematic liquid crystalline phase similar to that observed in native spider silk during the silk spinning process. Silk-CBD microfibrils spontaneously formed in solution upon ultrasonication. We suggest a model for silk-CBD assembly that implicates CBD in the central role of driving the dimerization of spider silk monomers, a process essential to the molecular assembly of spider-silk nanofibers and silk-CNC composites. PMID:27649169

  11. Spider Silk-CBD-Cellulose Nanocrystal Composites: Mechanism of Assembly.

    Science.gov (United States)

    Meirovitch, Sigal; Shtein, Zvi; Ben-Shalom, Tal; Lapidot, Shaul; Tamburu, Carmen; Hu, Xiao; Kluge, Jonathan A; Raviv, Uri; Kaplan, David L; Shoseyov, Oded

    2016-01-01

    The fabrication of cellulose-spider silk bio-nanocomposites comprised of cellulose nanocrystals (CNCs) and recombinant spider silk protein fused to a cellulose binding domain (CBD) is described. Silk-CBD successfully binds cellulose, and unlike recombinant silk alone, silk-CBD self-assembles into microfibrils even in the absence of CNCs. Silk-CBD-CNC composite sponges and films show changes in internal structure and CNC alignment related to the addition of silk-CBD. The silk-CBD sponges exhibit improved thermal and structural characteristics in comparison to control recombinant spider silk sponges. The glass transition temperature (Tg) of the silk-CBD sponge was higher than the control silk sponge and similar to native dragline spider silk fibers. Gel filtration analysis, dynamic light scattering (DLS), small angle X-ray scattering (SAXS) and cryo-transmission electron microscopy (TEM) indicated that silk-CBD, but not the recombinant silk control, formed a nematic liquid crystalline phase similar to that observed in native spider silk during the silk spinning process. Silk-CBD microfibrils spontaneously formed in solution upon ultrasonication. We suggest a model for silk-CBD assembly that implicates CBD in the central role of driving the dimerization of spider silk monomers, a process essential to the molecular assembly of spider-silk nanofibers and silk-CNC composites. PMID:27649169

  12. Spider Silk-CBD-Cellulose Nanocrystal Composites: Mechanism of Assembly

    Directory of Open Access Journals (Sweden)

    Sigal Meirovitch

    2016-09-01

    Full Text Available The fabrication of cellulose-spider silk bio-nanocomposites comprised of cellulose nanocrystals (CNCs and recombinant spider silk protein fused to a cellulose binding domain (CBD is described. Silk-CBD successfully binds cellulose, and unlike recombinant silk alone, silk-CBD self-assembles into microfibrils even in the absence of CNCs. Silk-CBD-CNC composite sponges and films show changes in internal structure and CNC alignment related to the addition of silk-CBD. The silk-CBD sponges exhibit improved thermal and structural characteristics in comparison to control recombinant spider silk sponges. The glass transition temperature (Tg of the silk-CBD sponge was higher than the control silk sponge and similar to native dragline spider silk fibers. Gel filtration analysis, dynamic light scattering (DLS, small angle X-ray scattering (SAXS and cryo-transmission electron microscopy (TEM indicated that silk-CBD, but not the recombinant silk control, formed a nematic liquid crystalline phase similar to that observed in native spider silk during the silk spinning process. Silk-CBD microfibrils spontaneously formed in solution upon ultrasonication. We suggest a model for silk-CBD assembly that implicates CBD in the central role of driving the dimerization of spider silk monomers, a process essential to the molecular assembly of spider-silk nanofibers and silk-CNC composites.

  13. Spider Silk-CBD-Cellulose Nanocrystal Composites: Mechanism of Assembly.

    Science.gov (United States)

    Meirovitch, Sigal; Shtein, Zvi; Ben-Shalom, Tal; Lapidot, Shaul; Tamburu, Carmen; Hu, Xiao; Kluge, Jonathan A; Raviv, Uri; Kaplan, David L; Shoseyov, Oded

    2016-09-18

    The fabrication of cellulose-spider silk bio-nanocomposites comprised of cellulose nanocrystals (CNCs) and recombinant spider silk protein fused to a cellulose binding domain (CBD) is described. Silk-CBD successfully binds cellulose, and unlike recombinant silk alone, silk-CBD self-assembles into microfibrils even in the absence of CNCs. Silk-CBD-CNC composite sponges and films show changes in internal structure and CNC alignment related to the addition of silk-CBD. The silk-CBD sponges exhibit improved thermal and structural characteristics in comparison to control recombinant spider silk sponges. The glass transition temperature (Tg) of the silk-CBD sponge was higher than the control silk sponge and similar to native dragline spider silk fibers. Gel filtration analysis, dynamic light scattering (DLS), small angle X-ray scattering (SAXS) and cryo-transmission electron microscopy (TEM) indicated that silk-CBD, but not the recombinant silk control, formed a nematic liquid crystalline phase similar to that observed in native spider silk during the silk spinning process. Silk-CBD microfibrils spontaneously formed in solution upon ultrasonication. We suggest a model for silk-CBD assembly that implicates CBD in the central role of driving the dimerization of spider silk monomers, a process essential to the molecular assembly of spider-silk nanofibers and silk-CNC composites.

  14. Binding of NF1 to the MMTV promoter in nucleosomes: influence of rotational phasing, translational positioning and histone H1.

    OpenAIRE

    Eisfeld, K; Candau, R; Truss, M; Beato, M

    1997-01-01

    To analyse the role of rotational orientation and translational positioning of nucleosomal DNA on transcription factor binding we have generated a series of mutant MMTV promoters containing insertions of various lengths between the hormone-responsive region and the binding site for NF1. These various MMTV promoter fragments were assembled in mononucleosomes and used for structural studies and binding experiments. We show that the insertions change the rotational phase and translational positi...

  15. Multiple complementary gas distribution assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Ng, Tuoh-Bin; Melnik, Yuriy; Pang, Lily L; Tuncel, Eda; Nguyen, Son T; Chen, Lu

    2016-04-05

    In one embodiment, an apparatus includes a first gas distribution assembly that includes a first gas passage for introducing a first process gas into a second gas passage that introduces the first process gas into a processing chamber and a second gas distribution assembly that includes a third gas passage for introducing a second process gas into a fourth gas passage that introduces the second process gas into the processing chamber. The first and second gas distribution assemblies are each adapted to be coupled to at least one chamber wall of the processing chamber. The first gas passage is shaped as a first ring positioned within the processing chamber above the second gas passage that is shaped as a second ring positioned within the processing chamber. The gas distribution assemblies may be designed to have complementary characteristic radial film growth rate profiles.

  16. Direct hierarchical assembly of nanoparticles

    Science.gov (United States)

    Xu, Ting; Zhao, Yue; Thorkelsson, Kari

    2014-07-22

    The present invention provides hierarchical assemblies of a block copolymer, a bifunctional linking compound and a nanoparticle. The block copolymers form one micro-domain and the nanoparticles another micro-domain.

  17. Chromatin assembly using Drosophila systems.

    Science.gov (United States)

    Fyodorov, Dmitry V; Levenstein, Mark E

    2002-05-01

    To successfully study chromatin structure and activity in vitro, it is essential to have a chromatin assembly system that will prepare extended nucleosome arrays with highly defined protein content that resemble bulk chromatin isolated from living cell nuclei in terms of periodicity and nucleosome positioning. The Drosophila ATP-dependent chromatin assembly system described in this unit meets these requirements. The end product of the reaction described here has highly periodic extended arrays with physiologic spacing and positioning of the nucleosomes.

  18. Another successful Doctoral Student Assembly

    CERN Multimedia

    Katarina Anthony

    2014-01-01

    On Wednesday 2 April, CERN hosted its third Doctoral Student Assembly in the Council Chamber.   CERN PhD students show off their posters in CERN's Main Building. Speaking to a packed house, Director-General Rolf Heuer gave the assembly's opening speech and introduced the poster session that followed. Seventeen CERN PhD students presented posters on their work, and were greeted by their CERN and University supervisors. It was a very successful event!

  19. Assembly delay line pulse generators

    CERN Multimedia

    1971-01-01

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

  20. DNA controlled assembly of liposomes

    DEFF Research Database (Denmark)

    Vogel, Stefan; Jakobsen, Ulla; Simonsen, Adam Cohen

    2009-01-01

    DNA-encoding of solid nanoparticles requires surfacechemistry, which is often tedious and not generally applicable. In the present study non-covalently attached DNA are used to assemble soft nanoparticles (liposomes) in solution. This process displays remarkably sharp thermal transitions from...... assembled to disassembled state for which reason this method allows easy and fast detection of polynucleotides (e.g. DNA or RNA), including single nucleotide polymorphisms as well as insertions and deletions....

  1. Los Alamos Critical Assemblies Facility

    International Nuclear Information System (INIS)

    The Critical Assemblies Facility of the Los Alamos National Laboratory has been in existence for thirty-five years. In that period, many thousands of measurements have been made on assemblies of 235U, 233U, and 239Pu in various configurations, including the nitrate, sulfate, fluoride, carbide, and oxide chemical compositions and the solid, liquid, and gaseous states. The present complex of eleven operating machines is described, and typical applications are presented

  2. Arabidopsis chloroplast chaperonin 10 is a calmodulin-binding protein

    Science.gov (United States)

    Yang, T.; Poovaiah, B. W.

    2000-01-01

    Calcium regulates diverse cellular activities in plants through the action of calmodulin (CaM). By using (35)S-labeled CaM to screen an Arabidopsis seedling cDNA expression library, a cDNA designated as AtCh-CPN10 (Arabidopsis thaliana chloroplast chaperonin 10) was cloned. Chloroplast CPN10, a nuclear-encoded protein, is a functional homolog of E. coli GroES. It is believed that CPN60 and CPN10 are involved in the assembly of Rubisco, a key enzyme involved in the photosynthetic pathway. Northern analysis revealed that AtCh-CPN10 is highly expressed in green tissues. The recombinant AtCh-CPN10 binds to CaM in a calcium-dependent manner. Deletion mutants revealed that there is only one CaM-binding site in the last 31 amino acids of the AtCh-CPN10 at the C-terminal end. The CaM-binding region in AtCh-CPN10 has higher homology to other chloroplast CPN10s in comparison to GroES and mitochondrial CPN10s, suggesting that CaM may only bind to chloroplast CPN10s. Furthermore, the results also suggest that the calcium/CaM messenger system is involved in regulating Rubisco assembly in the chloroplast, thereby influencing photosynthesis. Copyright 2000 Academic Press.

  3. Flexibility of PCNA-protein interface accommodates differential binding partners.

    Directory of Open Access Journals (Sweden)

    Anthony M Pedley

    Full Text Available The expanding roles of PCNA in functional assembly of DNA replication and repair complexes motivated investigation of the structural and dynamic properties guiding specificity of PCNA-protein interactions. A series of biochemical and computational analyses were combined to evaluate the PIP Box recognition features impacting complex formation. The results indicate subtle differences in topological and molecular descriptors distinguishing both affinity and stoichiometry of binding among PCNA-peptide complexes through cooperative effects. These features were validated using peptide mimics of p85α and Akt, two previously unreported PCNA binding partners. This study characterizes for the first time a reverse PIP Box interaction with PCNA. Small molecule ligand binding at the PIP Box interaction site confirmed the adaptive nature of the protein in dictating overall shape and implicates allosterism in transmitting biological effects.

  4. The Fundamental Role of Flexibility on the Strength of Molecular Binding

    OpenAIRE

    Forrey, Christopher; Douglas, Jack F.; Gilson, Michael K.

    2012-01-01

    Non-covalent molecular association underlies a diverse set of biologically and technologically relevant phenomena, including the action of drugs on their biomolecular targets and self- and supra-molecular assembly processes. Computer models employed to model binding frequently use interaction potentials with atomistic detail while neglecting the thermal molecular motions of the binding species. However, errors introduced by this simplification and, more broadly, the thermodynamic consequences...

  5. Multiple GTP-binding proteins participate in clathrin-coated vesicle- mediated endocytosis

    OpenAIRE

    1993-01-01

    We have examined the effects of various agonists and antagonists of GTP- binding proteins on receptor-mediated endocytosis in vitro. Stage- specific assays which distinguish coated pit assembly, invagination, and coat vesicle budding have been used to demonstrate requirements for GTP-binding protein(s) in each of these events. Coated pit invagination and coated vesicle budding are both stimulated by addition of GTP and inhibited by GDP beta S. Although coated pit invagination is resistant to ...

  6. Interaction between microtubules and the Drosophila formin Cappuccino and its effect on actin assembly.

    Science.gov (United States)

    Roth-Johnson, Elizabeth A; Vizcarra, Christina L; Bois, Justin S; Quinlan, Margot E

    2014-02-14

    Formin family actin nucleators are potential coordinators of the actin and microtubule cytoskeletons, as they can both nucleate actin filaments and bind microtubules in vitro. To gain a more detailed mechanistic understanding of formin-microtubule interactions and formin-mediated actin-microtubule cross-talk, we studied microtubule binding by Cappuccino (Capu), a formin involved in regulating actin and microtubule organization during Drosophila oogenesis. We found that two distinct domains within Capu, FH2 and tail, work together to promote high-affinity microtubule binding. The tail domain appears to bind microtubules through nonspecific charge-based interactions. In contrast, distinct residues within the FH2 domain are important for microtubule binding. We also report the first visualization of a formin polymerizing actin filaments in the presence of microtubules. Interestingly, microtubules are potent inhibitors of the actin nucleation activity of Capu but appear to have little effect on Capu once it is bound to the barbed end of an elongating filament. Because Capu does not simultaneously bind microtubules and assemble actin filaments in vitro, its actin assembly and microtubule binding activities likely require spatial and/or temporal regulation within the Drosophila oocyte.

  7. The BBSome controls IFT assembly and turnaround in cilia.

    Science.gov (United States)

    Wei, Qing; Zhang, Yuxia; Li, Yujie; Zhang, Qing; Ling, Kun; Hu, Jinghua

    2012-09-01

    The bidirectional movement of intraflagellar transport (IFT) particles, which are composed of motors, IFT-A and IFT-B subcomplexes, and cargoes, is required for the biogenesis and signalling of cilia(1,2). A successful IFT cycle depends on the proper assembly of the massive IFT particle at the ciliary base and its turnaround from anterograde to retrograde transport at the ciliary tip. However, how IFT assembly and turnaround are regulated in vivo remains elusive. From a whole-genome mutagenesis screen in Caenorhabditis elegans, we identified two hypomorphic mutations in dyf-2 and bbs-1 as the only mutants showing normal anterograde IFT transport but defective IFT turnaround at the ciliary tip. Further analyses revealed that the BBSome (refs 3, 4), a group of conserved proteins affected in human Bardet-Biedl syndrome(5) (BBS), assembles IFT complexes at the ciliary base, then binds to the anterograde IFT particle in a DYF-2- (an orthologue of human WDR19) and BBS-1-dependent manner, and lastly reaches the ciliary tip to regulate proper IFT recycling. Our results identify the BBSome as the key player regulating IFT assembly and turnaround in cilia. PMID:22922713

  8. Thermodynamics and Kinetics of DNA Tile-Based Self-Assembly

    Science.gov (United States)

    Jiang, Shuoxing

    Deoxyribonucleic acid (DNA) has emerged as an attractive building material for creating complex architectures at the nanometer scale that simultaneously affords versatility and modularity. Particularly, the programmability of DNA enables the assembly of basic building units into increasingly complex, arbitrary shapes or patterns. With the expanding complexity and functionality of DNA toolboxes, a quantitative understanding of DNA self-assembly in terms of thermodynamics and kinetics, will provide researchers with more subtle design guidelines that facilitate more precise spatial and temporal control. This dissertation focuses on studying the physicochemical properties of DNA tile-based self-assembly process by recapitulating representative scenarios and intermediate states with unique assembly pathways. First, DNA double-helical tiles with increasing flexibility were designed to investigate the dimerization kinetics. The higher dimerization rates of more rigid tiles result from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. Next, the thermodynamics and kinetics of single tile attachment to preformed "multitile" arrays were investigated to test the fundamental assumptions of tile assembly models. The results offer experimental evidences that double crossover tile attachment is determined by the electrostatic environment and the steric hindrance at the binding site. Finally, the assembly of double crossover tiles within a rhombic DNA origami frame was employed as the model system to investigate the competition between unseeded, facet and seeded nucleation. The results revealed that preference of nucleation types can be tuned by controlling the rate-limiting nucleation step. The works presented in this dissertation will be helpful for refining the DNA tile assembly model for future designs and simulations. Moreover, The works presented here could also be

  9. Megalin binds and mediates cellular internalization of folate binding protein

    DEFF Research Database (Denmark)

    Birn, Henrik; Zhai, Xiaoyue; Holm, Jan;

    2005-01-01

    Folate is an essential vitamin involved in a number of biological processes. High affinity folate binding proteins (FBPs) exist both as glycosylphosphatidylinositol-linked, membrane associated folate binding proteins and as soluble FBPs in plasma and some secretory fluids such as milk, saliva...... to bind and mediate cellular uptake of FBP. Surface plasmon resonance analysis shows binding of bovine and human milk FBP to immobilized megalin, but not to low density lipoprotein receptor related protein. Binding of (125)I-labeled folate binding protein (FBP) to sections of kidney proximal tubule, known...... to express high levels of megalin, is inhibitable by excess unlabeled FBP and by receptor associated protein, a known inhibitor of binding to megalin. Immortalized rat yolk sac cells, representing an established model for studying megalin-mediated uptake, reveal (125)I-labeled FBP uptake which is inhibited...

  10. 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

  11. 49 CFR 572.186 - Abdomen assembly.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Abdomen assembly. 572.186 Section 572.186... Dummy, 50th Percentile Adult Male § 572.186 Abdomen assembly. (a) The abdomen assembly (175-5000) is part of the dummy assembly shown in drawing 175-0000 including load sensors specified in §...

  12. 49 CFR 572.113 - Neck assembly.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Neck assembly. 572.113 Section 572.113... 50th Percentile Male § 572.113 Neck assembly. The head/neck assembly consists of the parts 78051-61X...) Test procedure. (1) Soak the head and neck assembly in a test environment at any temperature between...

  13. 48 CFR 239.7409 - Special assembly.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 3 2010-10-01 2010-10-01 false Special assembly. 239.7409... Services 239.7409 Special assembly. (a) Special assembly is the designing, manufacturing, arranging... general use equipment. (b) Special assembly rates and charges shall be based on estimated costs....

  14. 49 CFR 572.112 - Head assembly.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Head assembly. 572.112 Section 572.112... 50th Percentile Male § 572.112 Head assembly. The head assembly consists of the head (drawing 78051-61X...) accelerometers that are mounted in conformance to § 572.36 (c). (a) Test procedure. (1) Soak the head assembly...

  15. A lightweight suction gripper for micro assembly

    NARCIS (Netherlands)

    Bos, E.J.C.; Bullema, J.E.; Delbressine, F.L.M.; Schellekens, P.H.J.; Dietzel, A.H.

    2008-01-01

    Assembly is a crucial part in the realization of a product. Compared to assembly in the macro world, assembly in the micro world is influenced by scaling effects. These include surface forces, high requirements on placement uncertainty and small product dimensions. Conventional high-speed assembly i

  16. Bioinspired matrices assembled by polysaccharide-protein interactions

    Science.gov (United States)

    Zhang, Le

    Bioinspired matrices assembled on the basis of noncovalent interactions between proteins and polysaccharides have been proved suitable to deliver therapeutically relevant proteins or DNAs. Our initial efforts were dedicated to the relationship between mechanical properties of hydrogels assembled based on specific interactions between low molecular weight heparin (LMWH) and heparin binding peptides (HBPs) such as HIP, ATIII, and PF4ZIP peptides. The measured differences in affinity and kinetics for LMWH-HBP binding likely lead to observed differences in the phase separation behavior of the poly (ethylene glycol) (PEG)-LMWH/PEG-HIP hydrogels versus the PEG-LMWH/PEG-ATIII hydrogels. More attention has been given to the PF4ZIP peptide employed for the noncovalent assembly of heparinized hydrogels. Multifunctional star PEG-PF4ZIP bioconjugates complexed with star PEG-LMWH form hydrogels that exhibit increasing elastic moduli with increasing mole ratio of PEG-PF4ZIP. The viscoelastic properties of the hydrogels can be controlled via alterations in the ratio between LMWH and PF4ZIP peptide, and comparisons with other PEG-LMWH/PEG-HBP hydrogels suggest the importance of both LMWH/HBP binding kinetics and the binding capacity of LMWH in determining rheological properties in these hydrogels. Characterization of the PEG-LMWH/PEG-PF4ZIP hydrogels suggests that useful moduli for soft tissue engineering applications are obtained at physiological temperatures and after applying high shear. Furthermore, in the basic fibroblast growth factor (bFGF) release, bFGF/vascular endothelial growth factor (VEGF) co-release, and hydrogel erosion results, the combination of growth factor (GF) release profiles and hydrogel erosion profiles suggests that GF delivery from the assembled hydrogels is mainly an erosion-controlled process that may permit co-release of GF with PEG-LMWH and may therefore also improve the bioactivity of GF delivered from these matrices. Hydrogels with such engineered

  17. Anastral spindle assembly and γ-tubulin in Drosophila oocytes

    Directory of Open Access Journals (Sweden)

    Hallen Mark A

    2011-01-01

    Full Text Available Abstract Background Anastral spindles assemble by a mechanism that involves microtubule nucleation and growth from chromatin. It is still uncertain whether γ-tubulin, a microtubule nucleator essential for mitotic spindle assembly and maintenance, plays a role. Not only is the requirement for γ-tubulin to form anastral Drosophila oocyte meiosis I spindles controversial, but its presence in oocyte meiosis I spindles has not been demonstrated and is uncertain. Results We show, for the first time, using a bright GFP fusion protein and live imaging, that the Drosophila maternally-expressed γTub37C is present at low levels in oocyte meiosis I spindles. Despite this, we find that formation of bipolar meiosis I spindles does not require functional γTub37C, extending previous findings by others. Fluorescence photobleaching assays show rapid recovery of γTub37C in the meiosis I spindle, similar to the cytoplasm, indicating weak binding by γTub37C to spindles, and fits of a new, potentially more accurate model for fluorescence recovery yield kinetic parameters consistent with transient, diffusional binding. Conclusions The FRAP results, together with its mutant effects late in meiosis I, indicate that γTub37C may perform a role subsequent to metaphase I, rather than nucleating microtubules for meiosis I spindle formation. Weak binding to the meiosis I spindle could stabilize pre-existing microtubules or position γ-tubulin for function during meiosis II spindle assembly, which follows rapidly upon oocyte activation and completion of the meiosis I division.

  18. Product lifecycle-oriented virtual assembly technology

    Institute of Scientific and Technical Information of China (English)

    LIU Jian-hua; NING Ru-xin; YAO Jun; WAN Bi-le

    2006-01-01

    VA (virtual assembly) provides a more efficient,intuitive and convenient method for assembly process modeling,simulation and analysis.Previous researches about VA are almost isolated and dispersive,and have not established the understanding and definition of VA from a macroscopical and integrated view.Based on the analysis of the connotations of VA,a PLO-VATA (product lifecycle-oriented virtual assembly technology architecture) is proposed,in this architecture,VA is decomposed into four basic elements:principles and methodology of DFA (design for assembly),assembly analysis and evaluation,virtual assembly model and virtual assembly toolkits.Immersion,concurrence,integration and collaboration are the four main characteristics of VA being put forward.The key techniques of VA including virtual assembly model,virtual assembly analysis and evaluation,and virtual assembly process planning are discussed.Finally,a prototype system is built to validate the feasibility of the proposed method.

  19. Carboplatin binding to histidine

    Energy Technology Data Exchange (ETDEWEB)

    Tanley, Simon W. M. [University of Manchester, Brunswick Street, Manchester M13 9PL (United Kingdom); Diederichs, Kay [University of Konstanz, D-78457 Konstanz (Germany); Kroon-Batenburg, Loes M. J. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Levy, Colin [University of Manchester, 131 Princess Street, Manchester M1 7DN (United Kingdom); Schreurs, Antoine M. M. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Helliwell, John R., E-mail: john.helliwell@manchester.ac.uk [University of Manchester, Brunswick Street, Manchester M13 9PL (United Kingdom)

    2014-08-29

    An X-ray crystal structure showing the binding of purely carboplatin to histidine in a model protein has finally been obtained. This required extensive crystallization trials and various novel crystal structure analyses. Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the bromine form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.

  20. Photogenerated Exciton Dissociation in Highly Coupled Lead Salt Nanocrystal Assemblies

    KAUST Repository

    Choi, Joshua J.

    2010-05-12

    Internanocrystal coupling induced excitons dissociation in lead salt nanocrystal assemblies is investigated. By combining transient photoluminescence spectroscopy, grazing incidence small-angle X-ray scattering, and time-resolved electric force microscopy, we show that excitons can dissociate, without the aid of an external bias or chemical potential gradient, via tunneling through a potential barrier when the coupling energy is comparable to the exciton binding energy. Our results have important implications for the design of nanocrystal-based optoelectronic devices. © 2010 American Chemical Society.

  1. Assembly and testing of microparticle and microcapsule smart tattoo materials

    Science.gov (United States)

    McShane, Michael J.

    2007-01-01

    Microscale biochemical sensors are attractive for in vitro diagnostics and disease management, as well as medical and biological research applications. Fluorescent sensors, coupling specific glucose-binding proteins with fluorescent readout methods, have been developed for this purpose. Our work has focused on the development of assembly and packaging systems for producing micro- and nanoscale sensing components that can be used as implants, intracellular reporters, or as elements in larger systems. Both hybrid organic/inorganic particles and hollow microshells have been developed to physically couple the sensing materials together in biocompatible, semipermeable packages. Fabrication details and sensor characterization are used to demonstrate the potential of these sensor concepts.

  2. Directed Formation of DNA Nanoarrays through Orthogonal Self-Assembly

    Directory of Open Access Journals (Sweden)

    Eugen Stulz

    2011-06-01

    Full Text Available We describe the synthesis of terpyridine modified DNA strands which selectively form DNA nanotubes through orthogonal hydrogen bonding and metal complexation interactions. The short DNA strands are designed to self-assemble into long duplexes through a sticky-end approach. Addition of weakly binding metals such as Zn(II and Ni(II induces the formation of tubular arrays consisting of DNA bundles which are 50-200 nm wide and 2-50 nm high. TEM shows additional long distance ordering of the terpy-DNA complexes into fibers.

  3. Assembly of lamins in vitro

    Institute of Scientific and Technical Information of China (English)

    MINGUNGWEI; XIANGJUNTONG; 等

    1996-01-01

    After lamins A,B and C were isolated and purified from rat liver,their assembly properties were examined by electron microscopy and scanning tunneling microscopy by electron microscopy and scanning tunneling microscopy using negative staining and the glycerol coating method,respectively.By varying the assembly time or the ionic conditions under which polymerization takes place,we have observed different stages of lamin assembly,which may provide clues on the structure of the 10 nm lamin filaments.At the first level of structural organization,two lamin polypeptides associate laterally into dimers with the two domains being parallel and in register.At the second level of structural organization,two dimers associate in a half-staggered and antiparallel fashion to form a tetramer 75 nm in length.At the third level of structural organization,4-10 lamin tetramers associate laterally in register to form 75 nm long 10nm filaments,which in turn combine head to head into long,fully assembled lamin filaments.The assembled lamin filaments are nonpolar.

  4. Molecular Details of the Yeast Frataxin-Isu1 Interaction during Mitochondrial Fe-S Cluster Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Cook, J.; Kondapalli, K; Rawat, S; Childs, W; Murugesan, Y; Dancis, A; Stemmler, T

    2010-01-01

    Frataxin, a conserved nuclear-encoded mitochondrial protein, plays a direct role in iron-sulfur cluster biosynthesis within the ISC assembly pathway. Humans with frataxin deficiency have Friedreich's ataxia, a neurodegenerative disorder characterized by mitochondrial iron overload and disruption in Fe-S cluster synthesis. Biochemical and genetic studies have shown frataxin interacts with the iron-sulfur cluster assembly scaffold protein (in yeast, there are two, Isu1 and Isu2), indicating frataxin plays a direct role in cluster assembly, possibly by serving as an iron chaperone in the assembly pathway. Here we provide molecular details of how yeast frataxin (Yfh1) interacts with Isu1 as a structural module to improve our understanding of the multiprotein complex assembly that completes Fe-S cluster assembly; this complex also includes the cysteine desulfurase (Nfs1 in yeast) and the accessory protein (Isd11), together in the mitochondria. Thermodynamic binding parameters for protein partner and iron binding were measured for the yeast orthologs using isothermal titration calorimetry. Nuclear magnetic resonance spectroscopy was used to provide the molecular details to understand how Yfh1 interacts with Isu1. X-ray absorption studies were used to electronically and structurally characterize how iron is transferred to Isu1 and then incorporated into an Fe-S cluster. These results were combined with previously published data to generate a structural model for how the Fe-S cluster protein assembly complex can come together to accomplish Fe-S cluster assembly.

  5. Simulation of water cluster assembly on a graphite surface.

    Science.gov (United States)

    Lin, C S; Zhang, R Q; Lee, S T; Elstner, M; Frauenheim, Th; Wan, L J

    2005-07-28

    The assembly of small water clusters (H2O)n, n = 1-6, on a graphite surface is studied using a density functional tight-binding method complemented with an empirical van der Waals force correction, with confirmation using second-order Møller-Plesset perturbation theory. It is shown that the optimized geometry of the water hexamer may change its original structure to an isoenergy one when interacting with a graphite surface in some specific orientation, while the smaller water cluster will maintain its cyclic or linear configurations (for the water dimer). The binding energy of water clusters interacting with graphite is dependent on the number of water molecules that form hydrogen bonds, but is independent of the water cluster size. These physically adsorbed water clusters show little change in their IR peak position and leave an almost perfect graphite surface.

  6. Dynamics of assembly production flow

    CERN Document Server

    Ezaki, Takahiro; Nishinari, Katsuhiro

    2015-01-01

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

  7. FUEL ASSEMBLY SHAKER TEST SIMULATION

    Energy Technology Data Exchange (ETDEWEB)

    Klymyshyn, Nicholas A.; Sanborn, Scott E.; Adkins, Harold E.; Hanson, Brady D.

    2013-05-30

    This report describes the modeling of a PWR fuel assembly under dynamic shock loading in support of the Sandia National Laboratories (SNL) shaker test campaign. The focus of the test campaign is on evaluating the response of used fuel to shock and vibration loads that a can occur during highway transport. Modeling began in 2012 using an LS-DYNA fuel assembly model that was first created for modeling impact scenarios. SNL’s proposed test scenario was simulated through analysis and the calculated results helped guide the instrumentation and other aspects of the testing. During FY 2013, the fuel assembly model was refined to better represent the test surrogate. Analysis of the proposed loads suggested the frequency band needed to be lowered to attempt to excite the lower natural frequencies of the fuel assembly. Despite SNL’s expansion of lower frequency components in their five shock realizations, pretest predictions suggested a very mild dynamic response to the test loading. After testing was completed, one specific shock case was modeled, using recorded accelerometer data to excite the model. Direct comparison of predicted strain in the cladding was made to the recorded strain gauge data. The magnitude of both sets of strain (calculated and recorded) are very low, compared to the expected yield strength of the Zircaloy-4 material. The model was accurate enough to predict that no yielding of the cladding was expected, but its precision at predicting micro strains is questionable. The SNL test data offers some opportunity for validation of the finite element model, but the specific loading conditions of the testing only excite the fuel assembly to respond in a limited manner. For example, the test accelerations were not strong enough to substantially drive the fuel assembly out of contact with the basket. Under this test scenario, the fuel assembly model does a reasonable job of approximating actual fuel assembly response, a claim that can be verified through

  8. Workload analyse of assembling process

    Science.gov (United States)

    Ghenghea, L. D.

    2015-11-01

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

  9. Assembly of Aditya upgrade tokamak

    International Nuclear Information System (INIS)

    The existing Aditya tokamak, a medium sized tokamak with limiter configuration is being upgraded to a tokamak with divertor configuration. At present the existing ADITYA tokamak has been dismantled up to bottom plinth on which the whole assembly of toroidal field (TF) coils and vacuum vessel rested. The major components of ADITYA machine includes 20 TF coils and its structural components, 9 Ohmic coils and its clamps, 4 BV coils and its clamps as well as their busbar connections, vacuum vessel and its supports and buckling cylinder, which are all being dismantled. The re-assembly of the ADITYA Upgrade tokamak started with installation and positioning of new buckling cylinder and central solenoid (TR1) coil. After that the inner sections of TF coils are placed following which in-situ winding, installation, positioning and support mounting of two pairs of new inner divertor coils have been carried out. After securing the TF coils with top I-beams the new torus shaped vacuum vessel with circular cross-section in 2 halves have been installed. The assembly of TF structural components such as top and bottom guiding wedges, driving wedges, top and bottom compression ring, inner and outer fish plates and top inverted triangle has been carried out in an appropriate sequence. The assembly of outer sections of TF coils along with the proper placements of top auxiliary TR and vertical field coils with proper alignment and positioning with the optical metrology instrument mainly completes the reassembly. Detailed re-assembly steps and challenges faced during re-assembly will be discussed in this paper. (author)

  10. Self-Assembly of Micro-Parts onto Si Substrates at Liquid-Liquid Interface

    Institute of Scientific and Technical Information of China (English)

    LIU Mei; ZHANG Jian-Gang; LV Yao; XIA Shan-Hong

    2006-01-01

    We report a new approach for the self-assembly of cuboid micro-parts onto Si substrates to construct threedimensional microstructures.To perform assembly,the Si substrates are prepared with a deep cavity array as binding sites.An aggregate composed of hundreds of uniformly aligned micro-parts is formed at the C10F18-H2O interface.The micro-parts are arranged by passing the substrate through the aggregate of micro-parts,thus the micro-parts are left on the substrate,and then the substrate is vibrated ultrasonically in the solution,making it possible for the micro-parts to fall into the cavities on the substrate.Finally the substrate is pulled out of the solution after assembly.This technique could give a high yield of up to 70%,providing a ilew method for micro-assembly.

  11. ALIX is recruited temporarily into HIV-1 budding sites at the end of gag assembly.

    Directory of Open Access Journals (Sweden)

    Pei-I Ku

    Full Text Available Polymerization of Gag on the inner leaflet of the plasma membrane drives the assembly of Human Immunodeficiency Virus 1 (HIV-1. Gag recruits components of the endosomal sorting complexes required for transport (ESCRT to facilitate membrane fission and virion release. ESCRT assembly is initiated by recruitment of ALIX and TSG101/ESCRT-I, which bind directly to the viral Gag protein and then recruit the downstream ESCRT-III and VPS4 factors to complete the budding process. In contrast to previous models, we show that ALIX is recruited transiently at the end of Gag assembly, and that most ALIX molecules are recycled into the cytosol as the virus buds, although a subset remains within the virion. Our experiments imply that ALIX is recruited to the neck of the assembling virion and is mostly recycled after virion release.

  12. Significance of respirasomes for the assembly/stability of human respiratory chain complex I.

    Science.gov (United States)

    Schägger, Hermann; de Coo, René; Bauer, Matthias F; Hofmann, Sabine; Godinot, Catherine; Brandt, Ulrich

    2004-08-27

    We showed that the human respiratory chain is organized in supramolecular assemblies of respiratory chain complexes, the respirasomes. The mitochondrial complexes I (NADH dehydrogenase) and III (cytochrome c reductase) form a stable core respirasome to which complex IV (cytochrome c oxidase) can also bind. An analysis of the state of respirasomes in patients with an isolated deficiency of single complexes provided evidence that the formation of respirasomes is essential for the assembly/stability of complex I, the major entry point of respiratory chain substrates. Genetic alterations leading to a loss of complex III prevented respirasome formation and led to the secondary loss of complex I. Therefore, primary complex III assembly deficiencies presented as combined complex III/I defects. This dependence of complex I assembly/stability on respirasome formation has important implications for the diagnosis of mitochondrial respiratory chain disorders.

  13. DNA-guided nanoparticle assemblies

    Science.gov (United States)

    Gang, Oleg; Nykypanchuk, Dmytro; Maye, Mathew; van der Lelie, Daniel

    2013-07-16

    In some embodiments, DNA-capped nanoparticles are used to define a degree of crystalline order in assemblies thereof. In some embodiments, thermodynamically reversible and stable body-centered cubic (bcc) structures, with particles occupying <.about.10% of the unit cell, are formed. Designs and pathways amenable to the crystallization of particle assemblies are identified. In some embodiments, a plasmonic crystal is provided. In some aspects, a method for controlling the properties of particle assemblages is provided. In some embodiments a catalyst is formed from nanoparticles linked by nucleic acid sequences and forming an open crystal structure with catalytically active agents attached to the crystal on its surface or in interstices.

  14. Oscillations in molecular motor assemblies

    CERN Document Server

    Vilfan, A; Vilfan, Andrej; Frey, Erwin

    2005-01-01

    Autonomous oscillations in biological systems may have a biochemical origin or result from an interplay between force-generating and visco-elastic elements. In molecular motor assemblies the force-generating elements are molecular engines and the visco-elastic elements are stiff cytoskeletal polymers. The physical mechanism leading to oscillations depends on the particular architecture of the assembly. Existing models can be grouped into two distinct categories: systems with a {\\em delayed force activation} and {\\em anomalous force-velocity relations}. We discuss these systems within phase plane analysis known from the theory of dynamic systems and by adopting methods from control theory, the Nyquist criterion.

  15. A generalized macro-assembler

    International Nuclear Information System (INIS)

    The objective of this research is to study existing macro assemblers, and to create a generalized macro assembler, MAG-I, which is a system independent of a source language, and provides the following possibilities: development of any existing language, translation from a language to another, and creation of a new language. The user can choose his own notations to define macros. The system is implemented on an IBM 360/91 computer. Programs are written in symbolic language and the input/output software is written in Fortran

  16. Self-Assembly Dynamics of Linear Virus-Like Particles: Theory and Experiment.

    Science.gov (United States)

    Punter, Melle T J J M; Hernandez-Garcia, Armando; Kraft, Daniela J; de Vries, Renko; van der Schoot, Paul

    2016-07-01

    We experimentally and theoretically studied the self-assembly kinetics of linear virus-like particles (VLPs) consisting of double-stranded DNA and virus-like coat proteins. The polynucleotide acts as a self-assembly template for our proteins with engineered attractive protein-DNA and protein-protein interactions that imitate the physicochemical functionality of virus coat proteins. Inspired by our experimental observations, where we found that VLPs grow from one point onward, our model presumes a nucleation step before subsequent sequential cooperative binding from one of the ends of the polynucleotide. By numerically solving the pertinent reaction rate equations, we investigated the assembly dynamics as a function of the ratio between the number of available binding sites and proteins in the solution, i.e., the stoichiometry of the molecular building blocks. Depending on the stoichiometry, we found monotonic or nonmonotonic assembly kinetics. If the proteins in the solution vastly outnumber the binding sites on all of the polynucleotides, then the assembly kinetics were strictly monotonic and the assembled fraction increases steadily with time. However, if the concentration of proteins and binding sites is equal, then we found an overshoot in the concentration of fully covered polynucleotides. We compared our model with length distributions of two types of VLPs measured by atomic force microscopy imaging and found satisfactory agreement, suggesting that a relatively simple model may be useful in describing the assembly kinetics of chemically complex systems. We furthermore re-evaluated data by Hernandez-Garcia et al. (Nat. Nanotechnol. 2014, 9, 698-702) to include the effect of a finite protein concentration previously ignored. By fitting our model to the experimental data, we were able to pinpoint the sum of the protein-protein and protein-DNA interaction free energies, the binding rate of a protein to the DNA, and the nucleation free energy associated with

  17. CENP-C recruits M18BP1 to centromeres to promote CENP-A chromatin assembly

    OpenAIRE

    Moree, Ben; Meyer, Corey B.; Fuller, Colin J.; Straight, Aaron F.

    2011-01-01

    Eukaryotic chromosomes segregate by attaching to microtubules of the mitotic spindle through a chromosomal microtubule binding site called the kinetochore. Kinetochores assemble on a specialized chromosomal locus termed the centromere, which is characterized by the replacement of histone H3 in centromeric nucleosomes with the essential histone H3 variant CENP-A (centromere protein A). Understanding how CENP-A chromatin is assembled and maintained is central to understanding chromosome segrega...

  18. Lysine-specific molecular tweezers are broad-spectrum inhibitors of assembly and toxicity of amyloid proteins

    OpenAIRE

    Sinha, Sharmistha; Lopes, Dahabada H. J.; Du, Zhenming; Pang, Eric S.; Shanmugam, Akila; Lomakin, Aleksey; Talbiersky, Peter; Tennstaedt, Annette; McDaniel, Kirsten; Bakshi, Reena; Kuo, Pei-Yi; Ehrmann, Michael; Benedek, George B.; Loo, Joseph A.; Klärner, Frank-Gerrit

    2011-01-01

    Amyloidoses are diseases characterized by abnormal protein folding and self-assembly, for which no cure is available. Inhibition or modulation of abnormal protein self-assembly therefore is an attractive strategy for prevention and treatment of amyloidoses. We examined Lys-specific molecular tweezers and discovered a lead compound termed CLR01, which is capable of inhibiting the aggregation and toxicity of multiple amyloidogenic proteins by binding to Lys residues and disrupting hydrophobic a...

  19. Self-assembly of silver nanoparticles and bacteriophage

    Directory of Open Access Journals (Sweden)

    Santi Scibilia

    2016-03-01

    Full Text Available Biohybrid nanostructured materials, composed of both inorganic nanoparticles and biomolecules, offer prospects for many new applications in extremely diverse fields such as chemistry, physics, engineering, medicine and nanobiotechnology. In the recent years, Phage display technique has been extensively used to generate phage clones displaying surface peptides with functionality towards organic materials. Screening and selection of phage displayed material binding peptides has attracted great interest because of their use for development of hybrid materials with multiple functionalities. Here, we present a self-assembly approach for the construction of hybrid nanostructured networks consisting of M13 P9b phage clone, specific for Pseudomonas aeruginosa, selected by Phage display technology, directly assembled with silver nanoparticles (AgNPs, previously prepared by pulsed laser ablation. These networks are characterized by UV–vis optical spectroscopy, scanning/transmission electron microscopies and Raman spectroscopy. We investigated the influence of different ions and medium pH on self-assembly by evaluating different phage suspension buffers. The assembly of these networks is controlled by electrostatic interactions between the phage pVIII major capsid proteins and the AgNPs. The formation of the AgNPs-phage networks was obtained only in two types of tested buffers at a pH value near the isoelectric point of each pVIII proteins displayed on the surface of the clone. This systematic study allowed to optimize the synthesis procedure to assembly AgNPs and bacteriophage. Such networks find application in the biomedical field of advanced biosensing and targeted gene and drug delivery.

  20. Focal Plane Image Assembly of Subpixel

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    This paper describes the scanning assembly principle and construction of scanning assembly sample.The factors that affect assembly accuracy are analyzed.There are two steps in CCD focal plane scanning assembly.The first is rough assembly,and the second is accurate assembly.In this paper,the moiré fringe is introduced in judging assembly accuracy directly and accurately.The equation for optical transmission characteristics of CCD Moiré fringes is presented.The measurement of Moiré fringes can be completed when some conditions are satisfied.2D-assembly error can be obtained by using digital correlation filtering technique.Finally,the result of focal plane scanning assembly is presented.The result is in good accordance with theory.

  1. Assembly Sequence Planning for Mechanical Products

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

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

  2. Exploiting anthracene photodimerization within peptides: light induced sequence-selective DNA binding.

    Science.gov (United States)

    Bullen, Gemma A; Tucker, James H R; Peacock, Anna F A

    2015-05-11

    The unprecedented use of anthracene photodimerization within a protein or peptide system is explored through its incorporation into a DNA-binding peptide, derived from the GCN4 transcription factor. This study demonstrates an effective and dynamic interplay between a photoreaction and a peptide-DNA assembly, with each process able to exert control over the other.

  3. Chemotaxis receptor complexes: from signaling to assembly.

    Directory of Open Access Journals (Sweden)

    Robert G Endres

    2007-07-01

    Full Text Available Complexes of chemoreceptors in the bacterial cytoplasmic membrane allow for the sensing of ligands with remarkable sensitivity. Despite the excellent characterization of the chemotaxis signaling network, very little is known about what controls receptor complex size. Here we use in vitro signaling data to model the distribution of complex sizes. In particular, we model Tar receptors in membranes as an ensemble of different sized oligomer complexes, i.e., receptor dimers, dimers of dimers, and trimers of dimers, where the relative free energies, including receptor modification, ligand binding, and interaction with the kinase CheA determine the size distribution. Our model compares favorably with a variety of signaling data, including dose-response curves of receptor activity and the dependence of activity on receptor density in the membrane. We propose that the kinetics of complex assembly can be measured in vitro from the temporal response to a perturbation of the complex free energies, e.g., by addition of ligand.

  4. Analyzing Intracellular Binding and Diffusion with Continuous Fluorescence Photobleaching

    Science.gov (United States)

    Wachsmuth, Malte; Weidemann, Thomas; Müller, Gabriele; Hoffmann-Rohrer, Urs W.; Knoch, Tobias A.; Waldeck, Waldemar; Langowski, Jörg

    2003-01-01

    Transport and binding of molecules to specific sites are necessary for the assembly and function of ordered supramolecular structures in cells. For analyzing these processes in vivo, we have developed a confocal fluorescence fluctuation microscope that allows both imaging of the spatial distribution of fluorescent molecules with confocal laser scanning microscopy and probing their mobility at specific positions in the cell with fluorescence correlation spectroscopy and continuous fluorescence photobleaching (CP). Because fluorescence correlation spectroscopy is restricted to rapidly diffusing particles and CP to slower processes, these two methods complement each other. For the analysis of binding-related contributions to mobility we have derived analytical expressions for the temporal behavior of CP curves from which the bound fraction and/or the dissociation rate or residence time at binding sites, respectively, can be obtained. In experiments, we investigated HeLa cells expressing different fluorescent proteins: Although enhanced green fluorescent protein (EGFP) shows high mobility, fusions of histone H2B with the yellow fluorescent protein are incorporated into chromatin, and these nuclei exhibit the presence of a stably bound and a freely diffusing species. Nonpermanent binding was found for mTTF-I, a transcription termination factor for RNA polymerase I, fused with EGFP. The cells show fluorescent nucleoli, and binding is transient. CP yields residence times for mTTF-I-EGFP of ∼13 s. PMID:12719264

  5. SlmA Antagonism of FtsZ Assembly Employs a Two-pronged Mechanism like MinCD

    OpenAIRE

    Shishen Du; Joe Lutkenhaus

    2014-01-01

    Assembly of the Z-ring over unsegregated nucleoids is prevented by a process called nucleoid occlusion (NO), which in Escherichia coli is partially mediated by SlmA. SlmA is a Z ring antagonist that is spatially regulated and activated by binding to specific DNA sequences (SlmA binding sites, SBSs) more abundant in the origin proximal region of the chromosome. However, the mechanism by which SBS bound SlmA (activated form) antagonizes Z ring assembly is controversial. Here, we report the isol...

  6. Arginine methylation and citrullination of splicing factor proline- and glutamine-rich (SFPQ/PSF) regulates its association with mRNA.

    Science.gov (United States)

    Snijders, Ambrosius P; Hautbergue, Guillaume M; Bloom, Alex; Williamson, James C; Minshull, Thomas C; Phillips, Helen L; Mihaylov, Simeon R; Gjerde, Douglas T; Hornby, David P; Wilson, Stuart A; Hurd, Paul J; Dickman, Mark J

    2015-03-01

    Splicing factor proline- and glutamine-rich (SFPQ) also commonly known as polypyrimidine tract-binding protein-associated-splicing factor (PSF) and its binding partner non-POU domain-containing octamer-binding protein (NONO/p54nrb), are highly abundant, multifunctional nuclear proteins. However, the exact role of this complex is yet to be determined. Following purification of the endogeneous SFPQ/NONO complex, mass spectrometry analysis identified a wide range of interacting proteins, including those involved in RNA processing, RNA splicing, and transcriptional regulation, consistent with a multifunctional role for SFPQ/NONO. In addition, we have identified several sites of arginine methylation in SFPQ/PSF using mass spectrometry and found that several arginines in the N-terminal domain of SFPQ/PSF are asymmetrically dimethylated. Furthermore, we find that the protein arginine N-methyltransferase, PRMT1, catalyzes this methylation in vitro and that this is antagonized by citrullination of SFPQ. Arginine methylation and citrullination of SFPQ/PSF does not affect complex formation with NONO. However, arginine methylation was shown to increase the association with mRNA in mRNP complexes in mammalian cells. Finally we show that the biochemical properties of the endogenous complex from cell lysates are significantly influenced by the ionic strength during purification. At low ionic strength, the SFPQ/NONO complex forms large heterogeneous protein assemblies or aggregates, preventing the purification of the SFPQ/NONO complex. The ability of the SFPQ/NONO complex to form varying protein assemblies, in conjunction with the effect of post-translational modifications of SFPQ modulating mRNA binding, suggests key roles affecting mRNP dynamics within the cell.

  7. Association of DNA with nuclear matrix in in vitro assembled nuclei induced by rDNA from Tetrahymena shanghaiensis in Xenopus egg extracts

    Institute of Scientific and Technical Information of China (English)

    CHENYING; BOZHANG; 等

    1997-01-01

    The nuclei assembled from exogenous DNA or chromatin in egg extracts resemble their in vivo counterparts in many aspects.However,the distribution pattern of DNA in these nuclei remains unknown.We introduced rDNA from the macronuclei of Tetrahymena into Xenopus cellfree extracts to examine the association of specific DNA sequences with nuclear matrix(NM) in the nuclei assembled in vitro.Our previous works showed the 5'NTS(nontranscription sequences) of the rDNA specifically bind to the NM system in the macronuclei.We show now the rDNA could induce chromatin assembly and nuclear formation in Xenopus cell-free system.When we extracted the NM system and compared the binding affinity of different regions of rDNA with the NM system,we found that the 5'NTS still hold their binding affinity with insoluble structure of the assembled nuclei in the estracts of Xenopus eggs.

  8. Analytic QCD Binding Potentials

    CERN Document Server

    Fried, H M; Grandou, T; Sheu, Y -M

    2011-01-01

    This paper applies the analytic forms of a recent non-perturbative, manifestly gauge- and Lorentz-invariant description (of the exchange of all possible virtual gluons between quarks ($Q$) and/or anti-quarks ($\\bar{Q}$) in a quenched, eikonal approximation) to extract analytic forms for the binding potentials generating a model $Q$-$\\bar{Q}$ "pion", and a model $QQQ$ "nucleon". Other, more complicated $Q$, $\\bar{Q}$ contributions to such color-singlet states may also be identified analytically. An elementary minimization technique, relevant to the ground states of such bound systems, is adopted to approximate the solutions to a more proper, but far more complicated Schroedinger/Dirac equation; the existence of possible contributions to the pion and nucleon masses due to spin, angular momentum, and "deformation" degrees of freedom is noted but not pursued. Neglecting electromagnetic and weak interactions, this analysis illustrates how the one new parameter making its appearance in this exact, realistic formali...

  9. Chromatin-bound NLS proteins recruit membrane vesicles and nucleoporins for nuclear envelope assembly via importin-α/β

    Institute of Scientific and Technical Information of China (English)

    Quanlong Lu; Zhigang Lu; Qinying Liu; Li Guo; He Ren; Jingyan Fu; Qing Jiang; Paul R Clarke; Chuanmao Zhang

    2012-01-01

    The mechanism for nuclear envelope (NE) assembly is not fully understood.Importin-β and the small GTPase Ran have been implicated in the spatial regulation of NE assembly process.Here we report that chromatin-bound NLS (nuclear localization sequence) proteins provide docking sites for the NE precursor membrane vesicles and nucleoporins via importin-α and -β during NE assembly in Xenopus egg extracts.We show that along with the fast recruitment of the abundant NLS proteins such as nucleoplasmin and histones to the demembranated sperm chromatin in the extracts,importin-α binds the chromatin NLS proteins rapidly.Meanwhile,importin-β binds cytoplasmic NE precursor membrane vesicles and nucleoporins.Through interacting with importin-α on the chromatin NLS proteins,importin-β targets the membrane vesicles and nucleoporins to the chromatin surface.Once encountering RanGTP on the chromatin generated by RCC1,importin-β preferentially binds Ran-GTP and releases the membrane vesicles and nucleoporins for NE assembly.NE assembly is disrupted by blocking the interaction between importin-α and NLS proteins with excess soluble NLS proteins or by depletion of importin-β from the extract.Our findings reveal a novel molecular mechanism for NE assembly in Xenopus egg extracts.

  10. Quantum magnetism through atomic assembly

    NARCIS (Netherlands)

    Spinelli, A.

    2015-01-01

    This thesis presents an experimental study of magnetic structures, composed of only a few atoms. Those structures are first built atom-by-atom and then locally probed, both with a low-temperature STM. The technique that we use to assemble them is vertical atom manipulation, while to study their phy

  11. 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...

  12. Self-assembly of cyclodextrins

    DEFF Research Database (Denmark)

    Fülöp, Z.; Kurkov, S.V.; Nielsen, T.T.;

    2012-01-01

    The design of functional cyclodextrin (CD) nanoparticles is a developing area in the field of nanomedicine. CDs can not only help in the formation of drug carriers but also increase the local concentration of drugs at the site of action. CD monomers form aggregates by self-assembly, a tendency...

  13. Monolithic fiber optic sensor assembly

    Energy Technology Data Exchange (ETDEWEB)

    Sanders, Scott

    2015-02-10

    A remote sensor element for spectrographic measurements employs a monolithic assembly of one or two fiber optics to two optical elements separated by a supporting structure to allow the flow of gases or particulates therebetween. In a preferred embodiment, the sensor element components are fused ceramic to resist high temperatures and failure from large temperature changes.

  14. In vitro assembly of catalase.

    Science.gov (United States)

    Baureder, Michael; Barane, Elisabeth; Hederstedt, Lars

    2014-10-10

    Most aerobic organisms contain catalase, which functions to decompose hydrogen peroxide. Typical catalases are structurally complex homo-tetrameric enzymes with one heme prosthetic group buried in each subunit. It is not known how catalase in the cell is assembled from its constituents. The bacterium Enterococcus faecalis cannot synthesize heme but can acquire it from the environment to form a cytoplasmic catalase. We have in E. faecalis monitored production of the enzyme polypeptide (KatA) depending on the availability of heme and used our findings to devise a procedure for the purification of preparative amounts of in vivo-synthesized apocatalase. We show that fully active catalase can be obtained in vitro by incubating isolated apoprotein with hemin. We have characterized features of the assembly process and describe a temperature-trapped hemylated intermediate of the enzyme maturation process. Hemylation of apocatalase does not require auxiliary cell components, but rapid assembly of active enzyme seemingly is assisted in the cell. Our findings provide insight about catalase assembly and offer new experimental possibilities for detailed studies of this process.

  15. Pattern formation in centrosome assembly.

    Science.gov (United States)

    Mahen, Robert; Venkitaraman, Ashok R

    2012-02-01

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

  16. TWOWS Assembly Convenes in Beijing

    Institute of Scientific and Technical Information of China (English)

    SONG Jianlan

    2010-01-01

    @@ "Women are still under-represented in the fields of science and technology,"remarked HE Naledi Pandor,minister of science and technology of South Africa,at her invited speech heralding the opening of the Fourth General Assembly and International Conference of the Third World Organization for Women in Science(TWOWS)on the morning of June 27 in Beijing.

  17. ATLAS Assembly Hall Open Day

    CERN Multimedia

    Patrice Loiez

    2004-01-01

    To mark the 50th Anniversary of the founding of CERN, a day of tours, displays and presentations was held in October 2004. The assembly halls for the experiments that were waiting to be installed on the LHC, such as ATLAS shown here, were transformed into display areas and cafés.

  18. Engineering Metal Ion Coordination to Regulate Amyloid Fibril Assembly And Toxicity

    Energy Technology Data Exchange (ETDEWEB)

    Dong, J.; Canfield, J.M.; Mehta, A.K.; Shokes, J.E.; Tian, B.; Childers, W.S.; Simmons, J.A.; Mao, Z.; Scott, R.A.; Warncke, K.; Lynn, D.G.

    2009-06-02

    Protein and peptide assembly into amyloid has been implicated in functions that range from beneficial epigenetic controls to pathological etiologies. However, the exact structures of the assemblies that regulate biological activity remain poorly defined. We have previously used Zn{sup 2+} to modulate the assembly kinetics and morphology of congeners of the amyloid {beta} peptide (A{beta}) associated with Alzheimer's disease. We now reveal a correlation among A{beta}-Cu{sup 2+} coordination, peptide self-assembly, and neuronal viability. By using the central segment of A{beta}, HHQKLVFFA or A{beta}(13-21), which contains residues H13 and H14 implicated in A{beta}-metal ion binding, we show that Cu{sup 2+} forms complexes with A{beta}(13-21) and its K16A mutant and that the complexes, which do not self-assemble into fibrils, have structures similar to those found for the human prion protein, PrP. N-terminal acetylation and H14A substitution, Ac-A{beta}(13-21)H14A, alters metal coordination, allowing Cu{sup 2+} to accelerate assembly into neurotoxic fibrils. These results establish that the N-terminal region of A{beta} can access different metal-ion-coordination environments and that different complexes can lead to profound changes in A{beta} self-assembly kinetics, morphology, and toxicity. Related metal-ion coordination may be critical to the etiology of other neurodegenerative diseases.

  19. Cell-cycle regulation of formin-mediated actin cable assembly.

    Science.gov (United States)

    Miao, Yansong; Wong, Catherine C L; Mennella, Vito; Michelot, Alphée; Agard, David A; Holt, Liam J; Yates, John R; Drubin, David G

    2013-11-19

    Assembly of appropriately oriented actin cables nucleated by formin proteins is necessary for many biological processes in diverse eukaryotes. However, compared with knowledge of how nucleation of dendritic actin filament arrays by the actin-related protein-2/3 complex is regulated, the in vivo regulatory mechanisms for actin cable formation are less clear. To gain insights into mechanisms for regulating actin cable assembly, we reconstituted the assembly process in vitro by introducing microspheres functionalized with the C terminus of the budding yeast formin Bni1 into extracts prepared from yeast cells at different cell-cycle stages. EM studies showed that unbranched actin filament bundles were reconstituted successfully in the yeast extracts. Only extracts enriched in the mitotic cyclin Clb2 were competent for actin cable assembly, and cyclin-dependent kinase 1 activity was indispensible. Cyclin-dependent kinase 1 activity also was found to regulate cable assembly in vivo. Here we present evidence that formin cell-cycle regulation is conserved in vertebrates. The use of the cable-reconstitution system to test roles for the key actin-binding proteins tropomyosin, capping protein, and cofilin provided important insights into assembly regulation. Furthermore, using mass spectrometry, we identified components of the actin cables formed in yeast extracts, providing the basis for comprehensive understanding of cable assembly and regulation.

  20. Size-Selective Nanoparticle Assembly on Substrates by DNA Density Patterning.

    Science.gov (United States)

    Myers, Benjamin D; Lin, Qing-Yuan; Wu, Huanxin; Luijten, Erik; Mirkin, Chad A; Dravid, Vinayak P

    2016-06-28

    The vision of nanoscale self-assembly research is the programmable synthesis of macroscale structures with controlled long and short-range order that exhibit a desired set of properties and functionality. However, strategies to reliably isolate and manipulate the nanoscale building blocks based on their size, shape, or chemistry are still in their infancy. Among the promising candidates, DNA-mediated self-assembly has enabled the programmable assembly of nanoparticles into complex architectures. In particular, two-dimensional assembly on substrates has potential for the development of integrated functional devices and analytical systems. Here, we combine the high-resolution patterning capabilities afforded by electron-beam lithography with the DNA-mediated assembly process to enable direct-write grayscale DNA density patterning. This method allows modulation of the functionally active DNA surface density to control the thermodynamics of interactions between nanoparticles and the substrate. We demonstrate that size-selective directed assembly of nanoparticle films from solutions containing a bimodal distribution of particles can be realized by exploiting the cooperativity of DNA binding in this system. To support this result, we study the temperature-dependence of nanoparticle assembly, analyze the DNA damage by X-ray photoelectron spectroscopy and fluorescence microscopy, and employ molecular dynamics simulations to explore the size-selection behavior. PMID:27192324

  1. Quarkonium Binding and Entropic Force

    CERN Document Server

    Satz, Helmut

    2015-01-01

    A Q-Qbar bound state represents a balance between repulsive kinetic and attractive potential energy. In a hot quark-gluon plasma, the interaction potential experiences medium effects. Color screening modifies the attractive binding force between the quarks, while the increase of entropy with Q-Qbar separation gives rise to a growing repulsion. We study the role of these phenomena for in-medium Q-Qbar binding and dissociation. It is found that the relevant potential for Q-Qbar binding is the free energy F; with increasing Q-Qbar separation, further binding through the internal energy U is compensated by repulsive entropic effects.

  2. Self-Assembling Peptide Amphiphiles for Targeted Drug Delivery

    Science.gov (United States)

    Moyer, Tyson

    The systemic delivery of therapeutics is currently limited by off-target side effects and poor drug uptake into the cells that need to be treated. One way to circumvent these issues is to target the delivery and release of therapeutics to the desired location while limiting systemic toxicity. Using self-assembling peptide amphiphiles (PAs), this work has investigated supramolecular nanostructures for the development of targeted therapies. Specifically, the research has focused on the interrelationships between presentation of targeting moeities and the control of nanostructure morphology in the context of systemic delivery for targeting cancer and vascular injuries. The self-assembly region of the PA was systematically altered to achieve control of nanostructure widths, from 100 nm to 10 nm, by the addition of valine-glutamic acid dimers into the chemical structure, subsequently increasing the degree of nanostructure twist. For the targeting of tumors, a homing PA was synthesized to include a dimeric, cyclic peptide sequence known to target the cancer-specific, death receptor 5 (DR5) and initiate apoptosis through the oligomerization of DR5. This PA presented a multivalent display of DR5-binding peptides, resulting in improved binding affinity measured by surface plasmon resonance. The DR5-targeting PA also showed enhanced efficacy in both in vitro and in vivo tumor models relative to non-targeted controls. Alternative modifications to the PA-based antitumor therapies included the use of a cytotoxic, membrane-lytic PA coassembled with a pegylated PA, which showed enhanced biodistribution and in vivo activity after coassembly. The functionalization of the hydrophobic core was also accomplished through the encapsulation of the chemotherapy camptothecin, which was shown to be an effective treatment in vivo. Additionally, a targeted PA nanostructure was designed to bind to the site of vascular intervention by targeting collagen IV. Following balloon angioplasty

  3. Identification of a DNA binding protein that recognizes the nonamer recombinational signal sequence of immunoglobulin genes.

    Science.gov (United States)

    Halligan, B D; Desiderio, S V

    1987-10-01

    Extracts of nuclei from B- and T-lymphoid cells contain a protein that binds specifically to the conserved nonamer DNA sequence within the recombinational signals of immunoglobulin genes. Complexes with DNA fragments from four kappa light-chain joining (J) segments have the same electrophoretic mobility. Nonamer-containing DNA fragments from heavy-chain and light-chain genes compete for binding. Within the 5'-flanking DNA of the J kappa 4 gene segment, the binding site has been localized to a 27-base-pair interval spanning the nonamer region. The binding activity is recovered as a single peak after ion-exchange chromatography. The site of binding of the protein and its presence in nuclei of lymphoid cells suggest that it may function in the assembly of immunoglobulin genes.

  4. DESIGN REUSE METHOD FOR ASSEMBLIES IN CONCEPT DESIGN

    Institute of Scientific and Technical Information of China (English)

    Dong Yan; Tan Jianrong; Xu Jing

    2005-01-01

    Aiming at difficult sorting and retrieving complicated structure assemblies in assembly lib,a method for compartmentalizing assembly design resource by conceptual product structure model is presented. The similar assembly retrieval mechanisms of symbol assembly relation graph matching and symbol assembly relation graph similarity are discussed. The method is validated by taking valve rod assemblies as example.

  5. Peptide binding landscapes: Specificity and homophilicity across sequence space in a lattice model

    Science.gov (United States)

    Jeon, Joohyun; Shell, M. Scott

    2016-10-01

    Peptide aggregation frequently involves sequences with strong homophilic binding character, i.e., sequences that self-assemble with like species in a crowded cellular environment, in the face of a multitude of other peptides or proteins as potential heterophilic binding partners. What kinds of sequences display a strong tendency towards homophilic binding and self-assembly, and what are the origins of this behavior? Here, we consider how sequence specificity in oligomerization processes plays out in a simple two-dimensional (2D) lattice statistical-thermodynamic peptide model that permits exhaustive examination of the entire sequence and configurational landscapes. We find that sequences with strong self-specificities have either alternating hydrophobic and hydrophilic residues or short patches of hydrophobic residues, both which minimize intramolecular hydrophobic interactions in part due to the constraints of the 2D lattice. We also find that these specificities are highly sensitive to entropic and free energetic features of the unbound conformational state, such that direct binding interaction energies alone do not capture the complete behavior. These results suggest that the ability of particular peptide sequences to self-assemble and aggregate in a many-protein environment reflects a precise balance of direct binding interactions and behavior in the unbound (monomeric) state.

  6. Minimus: a fast, lightweight genome assembler

    Directory of Open Access Journals (Sweden)

    Salzberg Steven L

    2007-02-01

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

  7. Metal selective co-ordinative self-assembly of -donors

    Indian Academy of Sciences (India)

    Ankit Jain; K Venkata Rao; Ankita Goswami; Subi J George

    2011-11-01

    Metal selective co-ordinative nanostructures were constructed by the supramolecular co-assembly of pyridine appended TTF (TTF-Py) and pyrene (PYR-Py) derivatives in appropriate solvent composition mixtures with metal ions.Microscopic analyses show that TTF-Py shows distinctive morphology with either of these metal ions, forming I-D tapes with 1:1 Pb2+ complex and 2-D sheets with 1:2 Zn2+ complex. A rationale has been provided from molecular level packing for such hierarchical changes. In case of Cu2+, we have observed an anomalous binding of metal ion to the core sulphur groups causing redox changes in the TTF core. PYR-Py on the other hand is shown to be a fluorescent sensor for Pb2+, Zn2+, Hg2+ and Ag+. With different fluorescent response for metal complexes, we essentially obtained similar 1-D assemblies suggesting similar binding modes for all of them. Supramolecular approach through which morphology of an electron donor moiety can be engineered by metal ions can be a new tool in nanoelectronics.

  8. Thermodynamics of Rev-RNA interactions in HIV-1 Rev-RRE assembly.

    Science.gov (United States)

    Jayaraman, Bhargavi; Mavor, David; Gross, John D; Frankel, Alan D

    2015-10-27

    The HIV-1 protein Rev facilitates the nuclear export of intron-containing viral mRNAs by recognizing a structured RNA site, the Rev-response-element (RRE), contained in an intron. Rev assembles as a homo-oligomer on the RRE using its α-helical arginine-rich-motif (ARM) for RNA recognition. One unique feature of this assembly is the repeated use of the ARM from individual Rev subunits to contact distinct parts of the RRE in different binding modes. How the individual interactions differ and how they contribute toward forming a functional complex is poorly understood. Here we examine the thermodynamics of Rev-ARM peptide binding to two sites, RRE stem IIB, the high-affinity site that nucleates Rev assembly, and stem IA, a potential intermediate site during assembly, using NMR spectroscopy and isothermal titration calorimetry (ITC). NMR data indicate that the Rev-IIB complex forms a stable interface, whereas the Rev-IA interface is highly dynamic. ITC studies show that both interactions are enthalpy-driven, with binding to IIB being 20-30 fold tighter than to IA. Salt-dependent decreases in affinity were similar at both sites and predominantly enthalpic in nature, reflecting the roles of electrostatic interactions with arginines. However, the two interactions display strikingly different partitioning between enthalpy and entropy components, correlating well with the NMR observations. Our results illustrate how the variation in binding modes to different RRE target sites may influence the stability or order of Rev-RRE assembly and disassembly, and consequently its function.

  9. Hydraulic Experiment for Simulative Assemblies of Blanket Assembly and Np Transmutation Assembly of China Experimental Fast Reactor

    Institute of Scientific and Technical Information of China (English)

    CHENG; Dao-xi; QI; Xiao-guang; ZHAI; Wei-ming; YANG; Bing; ZHOU; Ping

    2013-01-01

    The out-of reactor hydraulic experiment of fast reactor assembly is one of the important experiments in the process of the development of the fast reactor assembly.In this experiment,the size of the throttling element in the foot of the assembly is decided which is fit for the flow division in the reactor and the

  10. Self-assembly of self-assembled molecular triangles

    Indian Academy of Sciences (India)

    Mili C Naranthatta; V Ramkumar; Dillip Kumar Chand

    2014-09-01

    A rare variety of self-assembledmolecular triangle [Pd3(bpy)3(imidazolate)3](NO3)3, 1 is prepared by the combination of Pd(bpy)(NO3)2 with imidazole, at 1:1 ratio, in acetonitrile-water. Deprotonation of imidazole happened during the course of the complexation reaction where upon the metallomacrocycle is formed. The bowl-shaped trinuclear architecture of 1 is crafted with three peripheral bpy units capable of - stacking interactions. 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 manner utilizing intermolecular - interactions where upon two out of three bpy units of each molecule participated in the chain formation.

  11. Alcohol Binding to the Odorant Binding Protein LUSH: Multiple Factors Affecting Binding Affinities

    OpenAIRE

    Ader, Lauren; Jones, David N. M.; Lin, Hai

    2010-01-01

    Density function theory (DFT) calculations have been carried out to investigate the binding of alcohols to the odorant binding protein LUSH from Drosophila melanogaster. LUSH is one of the few proteins known to bind to ethanol at physiologically relevant concentrations and where high-resolution structural information is available for the protein bound to alcohol at these concentrations. The structures of the LUSH–alcohol complexes identify a set of specific hydrogen-bonding interactions as cr...

  12. Compact MCP assemblies for mass spectrometers

    Energy Technology Data Exchange (ETDEWEB)

    Matsuura, S. [Hamamatsu Photonics K.K., Shizuoka (Japan). Electron Tube Div.; Umebayashi, S. [Hamamatsu Photonics K.K., Shizuoka (Japan). Electron Tube Div.; Kusuyama, Y. [Hamamatsu Photonics K.K., Shizuoka (Japan). Electron Tube Div.; Natsume, Y. [Hamamatsu Photonics K.K., Shizuoka (Japan). Electron Tube Div.; Oba, K. [Hamamatsu Photonics K.K., Shizuoka (Japan). Electron Tube Div.

    1995-09-01

    We have developed compact microchannel plate (MCP) assemblies which have a high gain, good pulse height resolution and a fast response for MS applications. In this paper, these new assemblies are described referring to their structures, functions and characteristics. (orig.).

  13. The Procedure for Assembling the EAST Tokamak

    Institute of Scientific and Technical Information of China (English)

    Wu Songtao

    2005-01-01

    Due to the complicated constitution and high precision requirements of the EAST superconducting tokamak, a meticulous assembling procedure and measurement scheme must be established. The big size and mass of the EAST machine's components and complicated configuration with tight installation tolerances call for a highly careful assembling procedure. The assembling procedure consists of three main sub-procedures for the assembling of the base, of the tori of the VV, the vacuum vessel TS and the TF, and of the peripheral parts respectively. Before the assembly, a reference framework has been set up by means of an industrial measurement system with reference fiducial targets fixed on the wall of the test hall. In this paper, the assembling procedure is described in detail, the survey control system of the assembly is discussed, and progress in the assembly work is also reported.

  14. Assembly of a Notch transcriptional activation complex requires multimerization.

    Science.gov (United States)

    Vasquez-Del Carpio, Rodrigo; Kaplan, Fred M; Weaver, Kelly L; VanWye, Jeffrey D; Alves-Guerra, Marie-Clotilde; Robbins, David J; Capobianco, Anthony J

    2011-04-01

    Notch transmembrane receptors direct essential cellular processes, such as proliferation and differentiation, through direct cell-to-cell interactions. Inappropriate release of the intracellular domain of Notch (N(ICD)) from the plasma membrane results in the accumulation of deregulated nuclear N(ICD) that has been linked to human cancers, notably T-cell acute lymphoblastic leukemia (T-ALL). Nuclear N(ICD) forms a transcriptional activation complex by interacting with the coactivator protein Mastermind-like 1 and the DNA binding protein CSL (for CBF-1/Suppressor of Hairless/Lag-1) to regulate target gene expression. Although it is well understood that N(ICD) forms a transcriptional activation complex, little is known about how the complex is assembled. In this study, we demonstrate that N(ICD) multimerizes and that these multimers function as precursors for the stepwise assembly of the Notch activation complex. Importantly, we demonstrate that the assembly is mediated by N(ICD) multimers interacting with Skip and Mastermind. These interactions form a preactivation complex that is then resolved by CSL to form the Notch transcriptional activation complex on DNA.

  15. Predictive energy landscapes for folding membrane protein assemblies.

    Science.gov (United States)

    Truong, Ha H; Kim, Bobby L; Schafer, Nicholas P; Wolynes, Peter G

    2015-12-28

    We study the energy landscapes for membrane protein oligomerization using the Associative memory, Water mediated, Structure and Energy Model with an implicit membrane potential (AWSEM-membrane), a coarse-grained molecular dynamics model previously optimized under the assumption that the energy landscapes for folding α-helical membrane protein monomers are funneled once their native topology within the membrane is established. In this study we show that the AWSEM-membrane force field is able to sample near native binding interfaces of several oligomeric systems. By predicting candidate structures using simulated annealing, we further show that degeneracies in predicting structures of membrane protein monomers are generally resolved in the folding of the higher order assemblies as is the case in the assemblies of both nicotinic acetylcholine receptor and V-type Na(+)-ATPase dimers. The physics of the phenomenon resembles domain swapping, which is consistent with the landscape following the principle of minimal frustration. We revisit also the classic Khorana study of the reconstitution of bacteriorhodopsin from its fragments, which is the close analogue of the early Anfinsen experiment on globular proteins. Here, we show the retinal cofactor likely plays a major role in selecting the final functional assembly. PMID:26723586

  16. An assembly model of Rift Valley fever virus

    Directory of Open Access Journals (Sweden)

    Mirabela eRusu

    2012-07-01

    Full Text Available Rift Valley fever virus (RVFV is a bunyavirus endemic to Africa and the Arabian Peninsula that infects humans and livestock. The virus encodes two glycoproteins, Gn and Gc, which represent the major structural antigens and are responsible for host cell receptor binding and fusion. Both glycoproteins are organized on the virus surface as cylindrical hollow spikes that cluster into distinct capsomers with the overall assembly exhibiting an icosahedral symmetry. Currently, no experimental three-dimensional structure for any entire bunyavirus glycoprotein is available. Using fold recognition, we generated molecular models for both RVFV glycoproteins and found significant structural matches between the RVFV Gn protein and the influenza virus hemagglutinin protein and a separate match between RVFV Gc protein and Sindbis virus envelope protein E1. Using these models, the potential interaction and arrangement of both glycoproteins in the RVFV particle was analyzed, by modeling their placement within the cryo-electron microscopy density map of RVFV. We identified four possible arrangements of the glycoproteins in the virion envelope. Each assembly model proposes that the ectodomain of Gn forms the majority of the protruding capsomer and that Gc is involved in formation of the capsomer base. Furthermore, Gc is suggested to facilitate intercapsomer connections. The proposed arrangement of the two glycoproteins on the RVFV surface is similar to that described for the alphavirus E1-E2 proteins. Our models will provide guidance to better understand the assembly process of phleboviruses and such structural studies can also contribute to the design of targeted antivirals.

  17. Predictive energy landscapes for folding membrane protein assemblies

    Science.gov (United States)

    Truong, Ha H.; Kim, Bobby L.; Schafer, Nicholas P.; Wolynes, Peter G.

    2015-12-01

    We study the energy landscapes for membrane protein oligomerization using the Associative memory, Water mediated, Structure and Energy Model with an implicit membrane potential (AWSEM-membrane), a coarse-grained molecular dynamics model previously optimized under the assumption that the energy landscapes for folding α-helical membrane protein monomers are funneled once their native topology within the membrane is established. In this study we show that the AWSEM-membrane force field is able to sample near native binding interfaces of several oligomeric systems. By predicting candidate structures using simulated annealing, we further show that degeneracies in predicting structures of membrane protein monomers are generally resolved in the folding of the higher order assemblies as is the case in the assemblies of both nicotinic acetylcholine receptor and V-type Na+-ATPase dimers. The physics of the phenomenon resembles domain swapping, which is consistent with the landscape following the principle of minimal frustration. We revisit also the classic Khorana study of the reconstitution of bacteriorhodopsin from its fragments, which is the close analogue of the early Anfinsen experiment on globular proteins. Here, we show the retinal cofactor likely plays a major role in selecting the final functional assembly.

  18. United assembly algorithm for optical burst switching

    Institute of Scientific and Technical Information of China (English)

    Jinhui Yu(于金辉); Yijun Yang(杨教军); Yuehua Chen(陈月华); Ge Fan(范戈)

    2003-01-01

    Optical burst switching (OBS) is a promising optical switching technology. The burst assembly algorithm controls burst assembly, which significantly impacts performance of OBS network. This paper provides a new assembly algorithm, united assembly algorithm, which has more practicability than conventional algorithms. In addition, some factors impacting selections of parameters of this algorithm are discussed and the performance of this algorithm is studied by computer simulation.

  19. 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.

  20. Hybrid Assembly for Ultra-Precise Manufacturing

    OpenAIRE

    Steinecker, Alexander

    2010-01-01

    International audience This paper presents a European integrated project in the domain of innovative hybrid assembly - the combination of self-assembly and robotics. Robotics allows for high precision and flexibility with full control of the assembly process. Self-assembly, on the other hand, offers massively parallel, unsupervised processing and thus provides high throughputs that cannot be reached with simple robotics alone. The combination of these approaches thus offers robust, high-sp...

  1. Multiple Roles of the τ131 Subunit of Yeast Transcription Factor IIIC (TFIIIC) in TFIIIB Assembly

    OpenAIRE

    Dumay-Odelot, Hélène; Acker, Joël; Arrebola, Rosalia; Sentenac, André; Marck, Christian

    2002-01-01

    Yeast transcription factor IIIC (TFIIIC) plays a key role in assembling the transcription initiation factor TFIIIB on class III genes after TFIIIC-DNA binding. The second largest subunit of TFIIIC, τ131, is thought to initiate TFIIIB assembly by interacting with Brf1/TFIIIB70. In this work, we have analyzed a TFIIIC mutant (τ131-ΔTPR2) harboring a deletion in τ131 removing the second of its 11 tetratricopeptide repeats. Remarkably, this thermosensitive mutation was selectively suppressed in v...

  2. Binding Energy and Enzymatic Catalysis.

    Science.gov (United States)

    Hansen, David E.; Raines, Ronald T.

    1990-01-01

    Discussed is the fundamental role that the favorable free energy of binding of the rate-determining transition state plays in catalysis. The principle that all of the catalytic factors discussed are realized by the use of this binding energy is reviewed. (CW)

  3. Simultaneous Assembly of Multiple Test Forms

    NARCIS (Netherlands)

    Linden, van der Wim J.; Adema, Jos J.

    1998-01-01

    An algorithm for the assembly of multiple test forms is proposed in which the multiple-form problem is reduced to a series of computationally less intensive two-form problems. At each step, one form is assembled to its true specifications; the other form is a dummy assembled only to maintain a balan

  4. 24 CFR 3285.601 - Field assembly.

    Science.gov (United States)

    2010-04-01

    ... 24 Housing and Urban Development 5 2010-04-01 2010-04-01 false Field assembly. 3285.601 Section... § 3285.601 Field assembly. Home manufacturers must provide specific installation instructions for the proper field assembly of manufacturer-supplied and shipped loose ducts, plumbing, and fuel supply...

  5. 49 CFR 572.182 - Head assembly.

    Science.gov (United States)

    2010-10-01

    .... The head shall be tested per procedure specified in 49 CFR § 572.112(a). (c) Performance criteria. (1... 49 Transportation 7 2010-10-01 2010-10-01 false Head assembly. 572.182 Section 572.182... Dummy, 50th Percentile Adult Male § 572.182 Head assembly. (a) The head assembly consists of the...

  6. 49 CFR 572.184 - Shoulder assembly.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Shoulder assembly. 572.184 Section 572.184... Dummy, 50th Percentile Adult Male § 572.184 Shoulder assembly. (a) The shoulder (175-3000) is part of the body assembly shown in drawing 175-0000. When subjected to impact tests specified in paragraph...

  7. 49 CFR 572.183 - Neck assembly.

    Science.gov (United States)

    2010-10-01

    ... CFR 572.33) at the time the pendulum makes contact with the decelerating mechanism. The velocity-time... 49 Transportation 7 2010-10-01 2010-10-01 false Neck assembly. 572.183 Section 572.183... Dummy, 50th Percentile Adult Male § 572.183 Neck assembly. (a) The neck assembly consists of parts...

  8. Snowball: Strain aware gene assembly of Metagenomes

    NARCIS (Netherlands)

    Gregor, I.; Schoenhuth, A.; McHardy, A.C.

    2015-01-01

    Gene assembly is an important step in functional analysis of shotgun metagenomic data. Nonetheless, strain aware assembly remains a challenging task, as current assembly tools often fail to distinguish among strain variants or require closely related reference genomes of the studied species to be av

  9. Shock buffer for nuclear control assembly

    International Nuclear Information System (INIS)

    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

  10. LHC Magnet Assembly Facility in building 181

    CERN Multimedia

    CERN Video Productions

    2005-01-01

    Hall 181 activities for the LHC machine * Reception of the American magnets : quadrupoles and separation dipoles * Assembly of the string Low-Beta Triplet -Q2-Q3-DFBX-D1 * Insertion quadrupoles cold masses assembly * Magnets reception type MQM, MQY, MCBC et MCBY * Assembly in the shell * Longitudinal welding under the press * Equipment with end covers in the finishing area

  11. Regenerator cross arm seal assembly

    Science.gov (United States)

    Jackman, Anthony V.

    1988-01-01

    A seal assembly for disposition between a cross arm on a gas turbine engine block and a regenerator disc, the seal assembly including a platform coextensive with the cross arm, a seal and wear layer sealingly and slidingly engaging the regenerator disc, a porous and compliant support layer between the platform and the seal and wear layer porous enough to permit flow of cooling air therethrough and compliant to accommodate relative thermal growth and distortion, a dike between the seal and wear layer and the platform for preventing cross flow through the support layer between engine exhaust and pressurized air passages, and air diversion passages for directing unregenerated pressurized air through the support layer to cool the seal and wear layer and then back into the flow of regenerated pressurized air.

  12. Combinatorial pathway assembly in yeast

    Directory of Open Access Journals (Sweden)

    Khalil Essani

    2015-10-01

    Full Text Available With the emergence of synthetic biology and the vast knowledge about individual biocatalytic reactions, the challenge nowadays is to implement whole natural or synthetic pathways into microorganisms. For this purpose balanced enzyme activities throughout the pathway need to be achieved in addition to simple functional gene expression to avoid bottlenecks and to obtain high titers of the desired product. As the optimization of pathways in a specific biological context is often hard to achieve by rational design, combinatorial approaches have been developed to address this issue. Here, current strategies and proof of concepts for combinatorial pathway assembly in yeasts are reviewed. By exploiting its ability to join multiple DNA fragments in a very efficient and easy manner, the yeast Saccharomyces cerevisiae does not only constitute an attractive host for heterologous pathway expression, but also for assembling pathways by recombination in vivo.

  13. Reversibly assembled cellular composite materials.

    Science.gov (United States)

    Cheung, Kenneth C; Gershenfeld, Neil

    2013-09-13

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

  14. A novel lipid transfer protein from the pea Pisum sativum: isolation, recombinant expression, solution structure, antifungal activity, lipid binding, and allergenic properties

    OpenAIRE

    Bogdanov, Ivan V.; Shenkarev, Zakhar O.; Finkina, Ekaterina I.; Melnikova, Daria N.; Rumynskiy, Eugene I.; Arseniev, Alexander S.; Ovchinnikova, Tatiana V.

    2016-01-01

    Background Plant lipid transfer proteins (LTPs) assemble a family of small (7–9 kDa) ubiquitous cationic proteins with an ability to bind and transport lipids as well as participate in various physiological processes including defense against phytopathogens. They also form one of the most clinically relevant classes of plant allergens. Nothing is known to date about correlation between lipid-binding and IgE-binding properties of LTPs. The garden pea Pisum sativum is widely consumed crop and i...

  15. Alignment Pins for Assembling and Disassembling Structures

    Science.gov (United States)

    Campbell, Oliver C.

    2008-01-01

    Simple, easy-to-use, highly effective tooling has been devised for maintaining alignment of bolt holes in mating structures during assembly and disassembly of the structures. The tooling was originally used during removal of a body flap from the space shuttle Atlantis, in which misalignments during removal of the last few bolts could cause the bolts to bind in their holes. By suitably modifying the dimensions of the tooling components, the basic design of the tooling can readily be adapted to other structures that must be maintained in alignment. The tooling includes tapered, internally threaded alignment pins designed to fit in the bolt holes in one of the mating structures, plus a draw bolt and a cup that are used to install or remove each alignment pin. In preparation for disassembly of two mating structures, external supports are provided to prevent unintended movement of the structures. During disassembly of the structures, as each bolt that joins the structures is removed, an alignment pin is installed in its place. Once all the bolts have been removed and replaced with pins, the pins maintain alignment as the structures are gently pushed or pulled apart on the supports. In assembling the two structures, one reverses the procedure described above: pins are installed in the bolt holes, the structures are pulled or pushed together on the supports, then the pins are removed and replaced with bolts. The figure depicts the tooling and its use. To install an alignment pin in a bolt hole in a structural panel, the tapered end of the pin is inserted from one side of the panel, the cup is placed over the pin on the opposite side of the panel, the draw bolt is inserted through the cup and threaded into the pin, the draw bolt is tightened to pull the pin until the pin is seated firmly in the hole, then the draw bolt and cup are removed, leaving the pin in place. To remove an alignment pin, the cup is placed over the pin on the first-mentioned side of the panel, the draw

  16. Multifunctional self-assembled monolayers

    Energy Technology Data Exchange (ETDEWEB)

    Zawodzinski, T.; Bar, G.; Rubin, S.; Uribe, F. [Los Alamos National Lab., NM (United States); Ferrais, J. [Texas Univ., Dallas, TX (United States)

    1996-06-01

    This is the final report of at three year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The specific goals of this research project were threefold: to develop multifunctional self-assembled monolayers, to understand the role of monolayer structure on the functioning of such systems, and to apply this knowledge to the development of electrochemical enzyme sensors. An array of molecules that can be used to attach electrochemically active biomolecules to gold surfaces has been synthesized. Several members of a class of electroactive compounds have been characterized and the factors controlling surface modification are beginning to be characterized. Enzymes have been attached to self-assembled molecules arranged on the gold surface, a critical step toward the ultimate goal of this project. Several alternative enzyme attachment strategies to achieve robust enzyme- modified surfaces have been explored. Several means of juxtaposing enzymes and mediators, electroactive compounds through which the enzyme can exchange electrons with the electrode surface, have also been investigated. Finally, the development of sensitive biosensors based on films loaded with nanoscale-supported gold particles that have surface modified with the self-assembled enzyme and mediator have been explored.

  17. Self-assembled plasmonic metamaterials

    Science.gov (United States)

    Mühlig, Stefan; Cunningham, Alastair; Dintinger, José; Scharf, Toralf; Bürgi, Thomas; Lederer, Falk; Rockstuhl, Carsten

    2013-07-01

    Nowadays for the sake of convenience most plasmonic nanostructures are fabricated by top-down nanofabrication technologies. This offers great degrees of freedom to tailor the geometry with unprecedented precision. However, it often causes disadvantages as well. The structures available are usually planar and periodically arranged. Therefore, bulk plasmonic structures are difficult to fabricate and the periodic arrangement causes undesired effects, e.g., strong spatial dispersion is observed in metamaterials. These limitations can be mitigated by relying on bottom-up nanofabrication technologies. There, self-assembly methods and techniques from the field of colloidal nanochemistry are used to build complex functional unit cells in solution from an ensemble of simple building blocks, i.e., in most cases plasmonic nanoparticles. Achievable structures are characterized by a high degree of nominal order only on a short-range scale. The precise spatial arrangement across larger dimensions is not possible in most cases; leading essentially to amorphous structures. Such self-assembled nanostructures require novel analytical means to describe their properties, innovative designs of functional elements that possess a desired near- and far-field response, and entail genuine nanofabrication and characterization techniques. Eventually, novel applications have to be perceived that are adapted to the specifics of the self-assembled nanostructures. This review shall document recent progress in this field of research. Emphasis is put on bottom-up amorphous metamaterials. We document the state-of-the-art but also critically assess the problems that have to be overcome.

  18. MYBPH inhibits NM IIA assembly via direct interaction with NMHC IIA and reduces cell motility

    Energy Technology Data Exchange (ETDEWEB)

    Hosono, Yasuyuki [Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya 466-8550 (Japan); Usukura, Jiro [Division of Integrated Project, EcoTopia Science Institute, Nagoya University, Chikusa-ku, Nagoya 464-8603 (Japan); Yamaguchi, Tomoya; Yanagisawa, Kiyoshi; Suzuki, Motoshi [Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya 466-8550 (Japan); Takahashi, Takashi, E-mail: tak@med.nagoya-u.ac.jp [Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya 466-8550 (Japan)

    2012-11-09

    Highlights: Black-Right-Pointing-Pointer MYBPH inhibits NMHC IIA assembly and cell motility. Black-Right-Pointing-Pointer MYBPH interacts to assembly-competent NM IIA. Black-Right-Pointing-Pointer MYBPH inhibits RLC and NMHC IIA, independent components of NM IIA. -- Abstract: Actomyosin filament assembly is a critical step in tumor cell migration. We previously found that myosin binding protein H (MYBPH) is directly transactivated by the TTF-1 lineage-survival oncogene in lung adenocarcinomas and inhibits phosphorylation of the myosin regulatory light chain (RLC) of non-muscle myosin IIA (NM IIA) via direct interaction with Rho kinase 1 (ROCK1). Here, we report that MYBPH also directly interacts with an additional molecule, non-muscle myosin heavy chain IIA (NMHC IIA), which was found to occur between MYBPH and the rod portion of NMHC IIA. MYBPH inhibited NMHC IIA assembly and reduced cell motility. Conversely, siMYBPH-induced increased motility was partially, yet significantly, suppressed by blebbistatin, a non-muscle myosin II inhibitor, while more profound effects were attained by combined treatment with siROCK1 and blebbistatin. Electron microscopy observations showed well-ordered paracrystals of NMHC IIA reflecting an assembled state, which were significantly less frequently observed in the presence of MYBPH. Furthermore, an in vitro sedimentation assay showed that a greater amount of NMHC IIA was in an unassembled state in the presence of MYBPH. Interestingly, treatment with a ROCK inhibitor that impairs transition of NM IIA from an assembly-incompetent to assembly-competent state reduced the interaction between MYBPH and NMHC IIA, suggesting that MYBPH has higher affinity to assembly-competent NM IIA. These results suggest that MYBPH inhibits RLC and NMHC IIA, independent components of NM IIA, and negatively regulates actomyosin organization at 2 distinct steps, resulting in firm inhibition of NM IIA assembly.

  19. MYBPH inhibits NM IIA assembly via direct interaction with NMHC IIA and reduces cell motility

    International Nuclear Information System (INIS)

    Highlights: ► MYBPH inhibits NMHC IIA assembly and cell motility. ► MYBPH interacts to assembly-competent NM IIA. ► MYBPH inhibits RLC and NMHC IIA, independent components of NM IIA. -- Abstract: Actomyosin filament assembly is a critical step in tumor cell migration. We previously found that myosin binding protein H (MYBPH) is directly transactivated by the TTF-1 lineage-survival oncogene in lung adenocarcinomas and inhibits phosphorylation of the myosin regulatory light chain (RLC) of non-muscle myosin IIA (NM IIA) via direct interaction with Rho kinase 1 (ROCK1). Here, we report that MYBPH also directly interacts with an additional molecule, non-muscle myosin heavy chain IIA (NMHC IIA), which was found to occur between MYBPH and the rod portion of NMHC IIA. MYBPH inhibited NMHC IIA assembly and reduced cell motility. Conversely, siMYBPH-induced increased motility was partially, yet significantly, suppressed by blebbistatin, a non-muscle myosin II inhibitor, while more profound effects were attained by combined treatment with siROCK1 and blebbistatin. Electron microscopy observations showed well-ordered paracrystals of NMHC IIA reflecting an assembled state, which were significantly less frequently observed in the presence of MYBPH. Furthermore, an in vitro sedimentation assay showed that a greater amount of NMHC IIA was in an unassembled state in the presence of MYBPH. Interestingly, treatment with a ROCK inhibitor that impairs transition of NM IIA from an assembly-incompetent to assembly-competent state reduced the interaction between MYBPH and NMHC IIA, suggesting that MYBPH has higher affinity to assembly-competent NM IIA. These results suggest that MYBPH inhibits RLC and NMHC IIA, independent components of NM IIA, and negatively regulates actomyosin organization at 2 distinct steps, resulting in firm inhibition of NM IIA assembly.

  20. AGORA: Assembly Guided by Optical Restriction Alignment

    Directory of Open Access Journals (Sweden)

    Lin Henry C

    2012-08-01

    Full Text Available Abstract Background Genome assembly is difficult due to repeated sequences within the genome, which create ambiguities and cause the final assembly to be broken up into many separate sequences (contigs. Long range linking information, such as mate-pairs or mapping data, is necessary to help assembly software resolve repeats, thereby leading to a more complete reconstruction of genomes. Prior work has used optical maps for validating assemblies and scaffolding contigs, after an initial assembly has been produced. However, optical maps have not previously been used within the genome assembly process. Here, we use optical map information within the popular de Bruijn graph assembly paradigm to eliminate paths in the de Bruijn graph which are not consistent with the optical map and help determine the correct reconstruction of the genome. Results We developed a new algorithm called AGORA: Assembly Guided by Optical Restriction Alignment. AGORA is the first algorithm to use optical map information directly within the de Bruijn graph framework to help produce an accurate assembly of a genome that is consistent with the optical map information provided. Our simulations on bacterial genomes show that AGORA is effective at producing assemblies closely matching the reference sequences. Additionally, we show that noise in the optical map can have a strong impact on the final assembly quality for some complex genomes, and we also measure how various characteristics of the starting de Bruijn graph may impact the quality of the final assembly. Lastly, we show that a proper choice of restriction enzyme for the optical map may substantially improve the quality of the final assembly. Conclusions Our work shows that optical maps can be used effectively to assemble genomes within the de Bruijn graph assembly framework. Our experiments also provide insights into the characteristics of the mapping data that most affect the performance of our algorithm, indicating the

  1. Robust, directed assembly of fluorescent nanodiamonds

    CERN Document Server

    Kianinia, Mehran; Shimoni, Olga; Randolph, Steven J; Toth, Milos; Aharonovich, Igor; Lobo, Charlene J

    2016-01-01

    Arrays of fluorescent nanoparticles are highly sought after for applications in sensing and nanophotonics. 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 sensing and nanophotonics devices.

  2. Nuclear fuel assembly identification using computer vision

    International Nuclear Information System (INIS)

    This report describes an improved method of remotely identifying irradiated nuclear fuel assemblies. The method uses existing in-cell TV cameras to input an image of the notch-coded top of the fuel assemblies into a computer vision system, which then produces the identifying number for that assembly. This system replaces systems that use either a mechanical mechanism to feel the notches or use human operators to locate notches visually. The system was developed for identifying fuel assemblies from the Fast Flux Test Facility (FFTF) and the Clinch River Breeder Reactor, but could be used for other reactor assembly identification, as appropriate

  3. Sugared biomaterial binding lectins: achievements and perspectives.

    Science.gov (United States)

    Bojarová, P; Křen, V

    2016-07-19

    Lectins, a distinct group of glycan-binding proteins, play a prominent role in the immune system ranging from pathogen recognition and tuning of inflammation to cell adhesion or cellular signalling. The possibilities of their detailed study expanded along with the rapid development of biomaterials in the last decade. The immense knowledge of all aspects of glycan-lectin interactions both in vitro and in vivo may be efficiently used in bioimaging, targeted drug delivery, diagnostic and analytic biological methods. Practically applicable examples comprise photoluminescence and optical biosensors, ingenious three-dimensional carbohydrate microarrays for high-throughput screening, matrices for magnetic resonance imaging, targeted hyperthermal treatment of cancer tissues, selective inhibitors of bacterial toxins and pathogen-recognising lectin receptors, and many others. This review aims to present an up-to-date systematic overview of glycan-decorated biomaterials promising for interactions with lectins, especially those applicable in biology, biotechnology or medicine. The lectins of interest include galectin-1, -3 and -7 participating in tumour progression, bacterial lectins from Pseudomonas aeruginosa (PA-IL), E. coli (Fim-H) and Clostridium botulinum (HA33) or DC-SIGN, receptors of macrophages and dendritic cells. The spectrum of lectin-binding biomaterials covered herein ranges from glycosylated organic structures, calixarene and fullerene cores over glycopeptides and glycoproteins, functionalised carbohydrate scaffolds of cyclodextrin or chitin to self-assembling glycopolymer clusters, gels, micelles and liposomes. Glyconanoparticles, glycan arrays, and other biomaterials with a solid core are described in detail, including inorganic matrices like hydroxyapatite or stainless steel for bioimplants. PMID:27075026

  4. Trapping of Hepatitis B Virus capsid assembly intermediates by phenylpropenamide assembly accelerators

    OpenAIRE

    Katen, Sarah P.; Chirapu, Srinivas Reddy; Finn, M.G.; Zlotnick, Adam

    2010-01-01

    Understanding the biological self-assembly process of virus capsids is key to understanding the viral life cycle, as well as serving as a platform for the design of assembly-based antiviral drugs. Here we identify and characterize the phenylpropenamide family of small molecules, known to have antiviral activity in vivo, as assembly effectors of the Hepatitis B Virus (HBV) capsid. We have found two representative phenylpropenamides to be assembly accelerators, increasing the rate of assembly w...

  5. Cooperative binding: a multiple personality.

    Science.gov (United States)

    Martini, Johannes W R; Diambra, Luis; Habeck, Michael

    2016-06-01

    Cooperative binding has been described in many publications and has been related to or defined by several different properties of the binding behavior of the ligand to the target molecule. In addition to the commonly used Hill coefficient, other characteristics such as a sigmoidal shape of the overall titration curve in a linear plot, a change of ligand affinity of the other binding sites when a site of the target molecule becomes occupied, or complex roots of the binding polynomial have been used to define or to quantify cooperative binding. In this work, we analyze how the different properties are related in the most general model for binding curves based on the grand canonical partition function and present several examples which highlight differences between the cooperativity characterizing properties which are discussed. Our results mainly show that among the presented definitions there are not two which fully coincide. Moreover, this work poses the question whether it can make sense to distinguish between positive and negative cooperativity based on the macroscopic binding isotherm only. This article shall emphasize that scientists who investigate cooperative effects in biological systems could help avoiding misunderstandings by stating clearly which kind of cooperativity they discuss.

  6. Control of actin-based motility through localized actin binding

    International Nuclear Information System (INIS)

    A wide variety of cell biological and biomimetic systems use actin polymerization to drive motility. It has been suggested that an object such as a bacterium can propel itself by self-assembling a high concentration of actin behind it, if it is repelled by actin. However, it is also known that it is essential for the moving object to bind actin. Therefore, a key question is how the actin tail can propel an object when it both binds and repels the object. We present a physically consistent Brownian dynamics model for actin-based motility that includes the minimal components of the dendritic nucleation model and allows for both attractive and repulsive interactions between actin and a moveable disc. We find that the concentration gradient of filamentous actin generated by polymerization is sufficient to propel the object, even with moderately strong binding interactions. Additionally, actin binding can act as a biophysical cap, and may directly control motility through modulation of network growth. Overall, this mechanism is robust in that it can drive motility against a load up to a stall pressure that depends on the Young’s modulus of the actin network and can explain several aspects of actin-based motility. (paper)

  7. Capacitance-modulated transistor detects odorant binding protein chiral interactions

    Science.gov (United States)

    Mulla, Mohammad Yusuf; Tuccori, Elena; Magliulo, Maria; Lattanzi, Gianluca; Palazzo, Gerardo; Persaud, Krishna; Torsi, Luisa

    2015-01-01

    Peripheral events in olfaction involve odorant binding proteins (OBPs) whose role in the recognition of different volatile chemicals is yet unclear. Here we report on the sensitive and quantitative measurement of the weak interactions associated with neutral enantiomers differentially binding to OBPs immobilized through a self-assembled monolayer to the gate of an organic bio-electronic transistor. The transduction is remarkably sensitive as the transistor output current is governed by the small capacitance of the protein layer undergoing minute changes as the ligand-protein complex is formed. Accurate determination of the free-energy balances and of the capacitance changes associated with the binding process allows derivation of the free-energy components as well as of the occurrence of conformational events associated with OBP ligand binding. Capacitance-modulated transistors open a new pathway for the study of ultra-weak molecular interactions in surface-bound protein-ligand complexes through an approach that combines bio-chemical and electronic thermodynamic parameters.

  8. RNA-protein binding kinetics in an automated microfluidic reactor.

    Science.gov (United States)

    Ridgeway, William K; Seitaridou, Effrosyni; Phillips, Rob; Williamson, James R

    2009-11-01

    Microfluidic chips can automate biochemical assays on the nanoliter scale, which is of considerable utility for RNA-protein binding reactions that would otherwise require large quantities of proteins. Unfortunately, complex reactions involving multiple reactants cannot be prepared in current microfluidic mixer designs, nor is investigation of long-time scale reactions possible. Here, a microfluidic 'Riboreactor' has been designed and constructed to facilitate the study of kinetics of RNA-protein complex formation over long time scales. With computer automation, the reactor can prepare binding reactions from any combination of eight reagents, and is optimized to monitor long reaction times. By integrating a two-photon microscope into the microfluidic platform, 5-nl reactions can be observed for longer than 1000 s with single-molecule sensitivity and negligible photobleaching. Using the Riboreactor, RNA-protein binding reactions with a fragment of the bacterial 30S ribosome were prepared in a fully automated fashion and binding rates were consistent with rates obtained from conventional assays. The microfluidic chip successfully combines automation, low sample consumption, ultra-sensitive fluorescence detection and a high degree of reproducibility. The chip should be able to probe complex reaction networks describing the assembly of large multicomponent RNPs such as the ribosome.

  9. An assembly model of Rice dwarf virus particle

    Institute of Scientific and Technical Information of China (English)

    ZHONG; Boxiong; Don; Allen; Roth; ZHU; Yafeng; Toshihiro

    2004-01-01

    The Phytoreovirus rice dwarf virus (RDV) has a complex nucleocapsid architecture composed of multiple proteins and RNAs. However, specific RNA-protein and protein-protein interactions involved in virion packaging have not been entirely elucidated. In order to define mechanisms governing RDV particle assembly, interactions between individual components were analyzed both in vivo and in vitro. The P7 core protein binds specifically and with high affinity to all 12 genomic RDV dsRNAs. P1, a putative RNA polymerase, P5, a putative guanyltransferase and P7 are encapsidated within the virion and also bind viral transcripts based upon in vitro binding assays. P1, P5, P7 and genomic dsRNAs were lacking in empty particles purified from infected tissues that also yielded fractions containing intact, infectious particles. In addition, P7 forms complexes with P1 and P3, a core capsid protein, in viral particles. These results indicate the possibility that core proteins and dsRNAs interact as one unit suggesting a mechanism for assortment of viral RNAs and subsequent packaging into core particles.

  10. Cooperative Assembly of a Protein-DNA Filament for Nonhomologous End Joining*

    OpenAIRE

    Tsai, Chun J.; Chu, Gilbert

    2013-01-01

    Nonhomologous end joining repairs DNA double-strand breaks created by ionizing radiation and V(D)J recombination. Ku, XRCC4/Ligase IV (XL), and XLF have a remarkable mismatched end (MEnd) ligase activity, particularly for ends with mismatched 3′ overhangs, but the mechanism has remained obscure. Here, we showed XL required Ku to bind DNA, whereas XLF required both Ku and XL to bind DNA. We detected cooperative assembly of one or two Ku molecules and up to five molecules each of XL and XLF int...

  11. Self-Assembled Mercaptan on Mesoporous Silica (SAMMS) technology of mercury removal and stabilization

    International Nuclear Information System (INIS)

    This paper explains the technology developed to produce Self-Assembled Mercaptan on Mesoporous Silica (SAMMS) for mercury removal from aqueous wastewater and from organic wastes. The characteristics of SAMMS materials, including physical characteristics and mercury loading, and its application for mercury removal and stabilization are discussed. Binding kinetics and binding speciations are reported. Preliminary cost estimates are provided for producing SAMMS materials and for mercury removal from wastewater. The characteristics of SAMMS in mercury separation were studied at PNNL using simulated aqueous tank wastes and actual tritiated pump oil wastes from Savannah River Site; preliminary results are outlined. 47 refs., 16 figs., 16 tabs

  12. High-density display of protein ligands on self-assembled capsules via noncovalent fluorous interactions.

    Science.gov (United States)

    Harano, Koji; Yamada, Junya; Mizuno, Shinichiro; Nakamura, Eiichi

    2015-01-01

    Ligand display on self-assembled nanostructures is an important tool in generating bioactive materials. Here, we demonstrate the display of sugar and biotin molecules on sub-100 nm-sized capsules with a high surface coverage, which was achieved by the use of noncovalent fluorous interactions between a fluorous-tagged ligand molecule and a fullerene vesicle covered with fluorous chains. Even after the high-density ligand display and protein binding, the vesicle stably maintains its spherical structure because the fluorous binding of the sugar does not affect the structural integrity of the vesicle that originates from strong fullerene-fullerene interactions. PMID:25404018

  13. Self-Assembled Mercaptan on Mesoporous Silica (SAMMS) technology of mercury removal and stabilization

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Xiangdong; Liu, Jun; Fryxell, G.E. [and others

    1997-09-01

    This paper explains the technology developed to produce Self-Assembled Mercaptan on Mesoporous Silica (SAMMS) for mercury removal from aqueous wastewater and from organic wastes. The characteristics of SAMMS materials, including physical characteristics and mercury loading, and its application for mercury removal and stabilization are discussed. Binding kinetics and binding speciations are reported. Preliminary cost estimates are provided for producing SAMMS materials and for mercury removal from wastewater. The characteristics of SAMMS in mercury separation were studied at PNNL using simulated aqueous tank wastes and actual tritiated pump oil wastes from Savannah River Site; preliminary results are outlined. 47 refs., 16 figs., 16 tabs.

  14. 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.

  15. [3]tetrahydrotrazodone binding. Association with serotonin binding sites

    International Nuclear Information System (INIS)

    High (17 nM) and low (603 nM) affinity binding sites for [3]tetrahydrotrazodone ([3] THT), a biologically active analogue of trazodone, have been identified in rat brain membranes. The substrate specificity, concentration, and subcellular and regional distributions of these sites suggest that they may represent a component of the serotonin transmitter system. Pharmacological analysis of [3]THT binding, coupled with brain lesion and drug treatment experiments, revealed that, unlike other antidepressants, [3] THT does not attach to either a biogenic amine transporter or serotonin binding sites. Rather, it would appear that [3]THT may be an antagonist ligand for the serotonin binding site. This probe may prove of value in defining the mechanism of action of trazodone and in further characterizing serotonin receptors

  16. Interactions of Brf1 Peptides with the Tetratricopeptide Repeat-Containing Subunit of TFIIIC Inhibit and Promote Preinitiation Complex Assembly

    OpenAIRE

    Liao, Yanling; Moir, Robyn D.; Willis, Ian M.

    2006-01-01

    The binding of Brf1 to the tetratricopeptide repeat (TPR)-containing transcription factor IIIC (TFIIIC) subunit (Tfc4) represents a rate-limiting step in the ordered assembly of the RNA polymerase III initiation factor TFIIIB. Tfc4 contains multiple binding sites for Brf1 within its amino terminus and adjacent TPR arrays, but the access of Brf1 to these sites is limited by autoinhibition. Moreover, the Brf1 binding sites in Tfc4 overlap with sites important for the subsequent recruitment of a...

  17. Design, Synthesis, Assembly, and Engineering of Peptoid Nanosheets.

    Science.gov (United States)

    Robertson, Ellen J; Battigelli, Alessia; Proulx, Caroline; Mannige, Ranjan V; Haxton, Thomas K; Yun, Lisa; Whitelam, Stephen; Zuckermann, Ronald N

    2016-03-15

    chains first assemble into a monolayer at either an air-water or oil-water interface, on which peptoid chains extend, order, and pack into a brick-like pattern. Upon mechanical compression of the interface, the monolayer buckles into stable bilayer structures. Recent work has focused on the design of nanosheets with tunable properties and functionality. They are readily engineerable, as functional monomers can be readily incorporated onto the nanosheet surface or into the interior. For example, functional hydrophilic "loops" have been displayed on the surfaces of nanosheets. These loops can interact with specific protein targets, serving as a potentially general platform for molecular recognition. Nanosheets can also bind metal ions and serve as 2D templates for mineral growth. Through our understanding of the formation mechanism, along with predicted features ascertained from molecular modeling, we aim to further design and synthesize nanosheets as robust protein mimetics with the potential for unprecedented functionality and stability. PMID:26741294

  18. Design, Synthesis, Assembly, and Engineering of Peptoid Nanosheets.

    Science.gov (United States)

    Robertson, Ellen J; Battigelli, Alessia; Proulx, Caroline; Mannige, Ranjan V; Haxton, Thomas K; Yun, Lisa; Whitelam, Stephen; Zuckermann, Ronald N

    2016-03-15

    chains first assemble into a monolayer at either an air-water or oil-water interface, on which peptoid chains extend, order, and pack into a brick-like pattern. Upon mechanical compression of the interface, the monolayer buckles into stable bilayer structures. Recent work has focused on the design of nanosheets with tunable properties and functionality. They are readily engineerable, as functional monomers can be readily incorporated onto the nanosheet surface or into the interior. For example, functional hydrophilic "loops" have been displayed on the surfaces of nanosheets. These loops can interact with specific protein targets, serving as a potentially general platform for molecular recognition. Nanosheets can also bind metal ions and serve as 2D templates for mineral growth. Through our understanding of the formation mechanism, along with predicted features ascertained from molecular modeling, we aim to further design and synthesize nanosheets as robust protein mimetics with the potential for unprecedented functionality and stability.

  19. Genome-wide prediction, display and refinement of binding sites with information theory-based models

    Directory of Open Access Journals (Sweden)

    Leeder J Steven

    2003-09-01

    Full Text Available Abstract Background We present Delila-genome, a software system for identification, visualization and analysis of protein binding sites in complete genome sequences. Binding sites are predicted by scanning genomic sequences with information theory-based (or user-defined weight matrices. Matrices are refined by adding experimentally-defined binding sites to published binding sites. Delila-Genome was used to examine the accuracy of individual information contents of binding sites detected with refined matrices as a measure of the strengths of the corresponding protein-nucleic acid interactions. The software can then be used to predict novel sites by rescanning the genome with the refined matrices. Results Parameters for genome scans are entered using a Java-based GUI interface and backend scripts in Perl. Multi-processor CPU load-sharing minimized the average response time for scans of different chromosomes. Scans of human genome assemblies required 4–6 hours for transcription factor binding sites and 10–19 hours for splice sites, respectively, on 24- and 3-node Mosix and Beowulf clusters. Individual binding sites are displayed either as high-resolution sequence walkers or in low-resolution custom tracks in the UCSC genome browser. For large datasets, we applied a data reduction strategy that limited displays of binding sites exceeding a threshold information content to specific chromosomal regions within or adjacent to genes. An HTML document is produced listing binding sites ranked by binding site strength or chromosomal location hyperlinked to the UCSC custom track, other annotation databases and binding site sequences. Post-genome scan tools parse binding site annotations of selected chromosome intervals and compare the results of genome scans using different weight matrices. Comparisons of multiple genome scans can display binding sites that are unique to each scan and identify sites with significantly altered binding strengths

  20. Integrated Virtual Assembly Process Planning System

    Institute of Scientific and Technical Information of China (English)

    LIU Jianhua; HOU Weiwei; HOU Weiwei; SHANG Wei; SHANG Wei; NING Ruxin; NING Ruxin

    2009-01-01

    Assembly process planning(APP) for complicated products is a time-consuming and difficult work with conventional method. Virtual assembly process planning(VAPP) provides engineers a new and efficiency way. Previous studies in VAPP are almost isolated and dispersive, and have not established a whole understanding and discussed key realization techniques of VAPP from a systemic and integrated view. The integrated virtual assembly process planning(IVAPP) system is a new virtual reality based engineering application, which offers engineers an efficient, intuitive, immersive and integrated method for assembly process planning in a virtual environment. Based on analysis the information integration requirement of VAPP, the architecture of IVAPP is proposed. Through the integrated structure, IVAPP system can realize information integration and workflow controlling. In order to model the assembly process in IVAPP, a hierarchical assembly task list(HATL) is presented, in which different assembly tasks for assembling different components are organized into a hierarchical list. A process-oriented automatic geometrical constraint recognition algorithm(AGCR) is proposed, so that geometrical constraints between components can be automatically recognized during the process of interactive assembling. At the same time, a progressive hierarchical reasoning(PHR) model is discussed. AGCR and PHR will greatly reduce the interactive workload. A discrete control node model(DCNM) for cable harness assembly planning in IVAPP is detailed. DCNM converts a cable harness into continuous flexed line segments connected by a series of section center points, and designs can realize cable harness planning through controlling those control nodes. Mechanical assemblies (such as transmission case and engine of automobile) are used to illustrate the feasibility of the proposed method and algorithms. The application of IVAPP system reveals advantages over the traditional assembly process planning method

  1. Stepwise and dynamic assembly of the earliest precursors of small ribosomal subunits in yeast.

    Science.gov (United States)

    Zhang, Liman; Wu, Chen; Cai, Gaihong; Chen, She; Ye, Keqiong

    2016-03-15

    The eukaryotic ribosomal RNA (rRNA) is associated cotranscriptionally with numerous factors into an enormous 90S preribosomal particle that conducts early processing of small ribosomal subunits. The assembly pathway and structure of the 90S particle is poorly understood. Here, we affinity-purified and analyzed the constituents of yeast 90S particles that were assembled on a series of plasmid-encoded 3'-truncated pre-18S RNAs. We determined the assembly point of 65 proteins and the U3, U14, and snR30 small nucleolar RNAs (snoRNAs), revealing a stepwise and dynamic assembly map. The 5' external transcribed spacer (ETS) alone can nucleate a large complex. When the 18S rRNA is nearly complete, the 90S structure undergoes a dramatic reorganization, releasing U14, snR30, and 14 protein factors that bind earlier. We also identified a reference state of 90S that is fully assembled yet has not undergone 5'ETS processing. The assembly map present here provides a new framework to understand small subunit biogenesis.

  2. ULtiMATE system for rapid assembly of customized TAL effectors.

    Directory of Open Access Journals (Sweden)

    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.

  3. Supramolecular Assembly of an Evolved Miniprotein Host and Fluorogenic Guest Pair.

    Science.gov (United States)

    Xu, Bi; Zhou, Xinqi; Stains, Cliff I

    2015-11-18

    Small-molecule-induced assembly of defined protein structures could have broad implications for the fabrication of new materials as well as biological signaling pathways. However, the design of new host-guest pairs capable of small-molecule-induced assembly in a biologically relevant context remains a significant challenge. Herein, we report a series of miniprotein hosts, evolved from the tenth type III domain of fibronectin (Fn3), that display remarkable binding affinity toward a red-shifted environment-sensitive merocyanine derivative, termed sI-Pht. Importantly, the consensus binder isolated from directed evolution experiments (6.2.18) forms a higher order assembly in response to addition of sI-Pht, as assessed by analytical ultracentrifugation. sI-Pht-induced assembly of 6.2.18 results in a 570-fold increase in fluorescence compared to free dye. This property enables the direct visualization of host-guest assemblies by fluorescence microscopy. As a demonstration, we show that supramolecular assembly of the 6.2.18-sI-Pht system can be visualized on the surface of living yeast cells. This new host-guest pair provides a tool for the potential development of new materials as well as pathway engineering. In a broader context, this work details a new design paradigm for the discovery of host-guest systems that function in the context of living cells. PMID:26523606

  4. Self-assembly of microcapsules via colloidal bond hybridization and anisotropy

    Science.gov (United States)

    Evers, Chris H. J.; Luiken, Jurriaan A.; Bolhuis, Peter G.; Kegel, Willem K.

    2016-06-01

    Particles with directional interactions are promising building blocks for new functional materials and may serve as models for biological structures. Mutually attractive nanoparticles that are deformable owing to flexible surface groups, for example, may spontaneously order themselves into strings, sheets and large vesicles. Furthermore, anisotropic colloids with attractive patches can self-assemble into open lattices and the colloidal equivalents of molecules and micelles. However, model systems that combine mutual attraction, anisotropy and deformability have not yet been realized. Here we synthesize colloidal particles that combine these three characteristics and obtain self-assembled microcapsules. We propose that mutual attraction and deformability induce directional interactions via colloidal bond hybridization. Our particles contain both mutually attractive and repulsive surface groups that are flexible. Analogously to the simplest chemical bond—in which two isotropic orbitals hybridize into the molecular orbital of H2—these flexible groups redistribute on binding. Via colloidal bond hybridization, isotropic spheres self-assemble into planar monolayers, whereas anisotropic snowman-shaped particles self-assemble into hollow monolayer microcapsules. A modest change in the building blocks thus results in much greater complexity of the self-assembled structures. In other words, these relatively simple building blocks self-assemble into markedly more complex structures than do similar particles that are isotropic or non-deformable.

  5. Self-assembly of microcapsules via colloidal bond hybridization and anisotropy.

    Science.gov (United States)

    Evers, Chris H J; Luiken, Jurriaan A; Bolhuis, Peter G; Kegel, Willem K

    2016-06-16

    Particles with directional interactions are promising building blocks for new functional materials and may serve as models for biological structures. Mutually attractive nanoparticles that are deformable owing to flexible surface groups, for example, may spontaneously order themselves into strings, sheets and large vesicles. Furthermore, anisotropic colloids with attractive patches can self-assemble into open lattices and the colloidal equivalents of molecules and micelles. However, model systems that combine mutual attraction, anisotropy and deformability have not yet been realized. Here we synthesize colloidal particles that combine these three characteristics and obtain self-assembled microcapsules. We propose that mutual attraction and deformability induce directional interactions via colloidal bond hybridization. Our particles contain both mutually attractive and repulsive surface groups that are flexible. Analogously to the simplest chemical bond--in which two isotropic orbitals hybridize into the molecular orbital of H2--these flexible groups redistribute on binding. Via colloidal bond hybridization, isotropic spheres self-assemble into planar monolayers, whereas anisotropic snowman-shaped particles self-assemble into hollow monolayer microcapsules. A modest change in the building blocks thus results in much greater complexity of the self-assembled structures. In other words, these relatively simple building blocks self-assemble into markedly more complex structures than do similar particles that are isotropic or non-deformable. PMID:27281213

  6. Chikungunya Virus nsP3 Blocks Stress Granule Assembly by Recruitment of G3BP into Cytoplasmic Foci

    NARCIS (Netherlands)

    Fros, J.J.; Domeradzka, N.E.; Baggen, J.; Geertsema, C.; Flipse, J.; Vlak, J.M.; Pijlman, G.P.

    2012-01-01

    Chikungunya virus nonstructural protein nsP3 has an essential but unknown role in alphavirus replication and interacts with Ras-GAP SH3 domain-binding protein (G3BP). Here we describe the first known function of nsP3, to inhibit stress granule assembly by recruiting G3BP into cytoplasmic foci. A con

  7. Non-enzymatic glycation of type I collagen diminishes collagen-proteoglycan binding and weakens cell adhesion

    OpenAIRE

    Reigle, Kristin L.; Di Lullo, Gloria; Turner, Kevin R.; Last, Jerold A; Chervoneva, Inna; Birk, David E.; Funderburgh, James L.; Elrod, Elizabeth; Markus W. Germann; Surber, Charles; Sanderson, Ralph D.; San Antonio, James D.

    2008-01-01

    Non-enzymatic glycation of type I collagen occurs in aging and diabetes, and may affect collagen solubility, charge, polymerization, and intermolecular interactions. Proteoglycans1(PGs) bind type I collagen and are proposed to regulate fibril assembly, function, and cell-collagen interactions. Moreover, on the collagen fibril a keratan sulfate (KS) PG binding region overlaps with preferred collagen glycation sites. Thus, we examined the effect of collagen modified by simple glycation on PG-co...

  8. Graphene–cyclodextrin–cytochrome c layered assembly with improved electron transfer rate and high supramolecular recognition capability

    Energy Technology Data Exchange (ETDEWEB)

    Gong, Cheng-Bin; Guo, Cong-Cong; Jiang, Dan; Tang, Qian, E-mail: qiantang@swu.edu.cn; Liu, Chang-Hua; Ma, Xue-Bing

    2014-06-01

    This study aimed to develop a new graphene-based layered assembly, named graphene–cyclodextrin–cytochrome c with improved electron transfer rate. This assembly has combined high conductivity of graphene nanosheets (GNs), selectively binding properties and electronegativity of cyclodextrins (CDs), as well as electropositivity of cytochrome c (Cyt c). This assembly can also mimic the confined environments of the intermembrane space of mitochondria. A β-cyclodextrin (β-CD) functionalized GN (GN–CD) assembly was initially prepared by a simple wet-chemical strategy, i.e., in situ thermal reduction of graphene oxide with hydrazine hydrate in the presence of β-CD. Cyt c was then intercalated to the GN–CD assembly to form a layered self-assembled structure, GN–CD–Cyt c, through electrostatic interaction. Compared with GNs and GN–CD, GN–CD–Cyt c assembly displayed improved electron transfer rate and high supramolecular recognition capability toward six probe molecules. - Highlights: • A new tertiary layered assembly named GN–CD–Cyt c was prepared. • Compared with GNs and GN–CD, GN–CD–Cyt c shows improved electron transfer rate. • GN–CD–Cyt c displays high supramolecular recognition capability.

  9. Piston and connecting rod assembly

    Science.gov (United States)

    Brogdon, James William (Inventor); Gill, David Keith (Inventor); Chatten, John K. (Inventor)

    2001-01-01

    A piston and connecting rod assembly includes a piston crown, a piston skirt, a connecting rod, and a bearing insert. The piston skirt is a component separate from the piston crown and is connected to the piston crown to provide a piston body. The bearing insert is a component separate from the piston crown and the piston skirt and is fixedly disposed within the piston body. A bearing surface of a connecting rod contacts the bearing insert to thereby movably associate the connecting rod and the piston body.

  10. Computer-aided lens assembly.

    Science.gov (United States)

    Tomlinson, Richard; Alcock, Rob; Petzing, Jon; Coupland, Jeremy

    2004-01-20

    We propose a computer-aided method of lens manufacture that allows assembly, adjustment, and test phases to be run concurrently until an acceptable level of optical performance is reached. Misalignment of elements within a compound lens is determined by a comparison of the results of physical ray tracing by use of an array of Gaussian laser beams with numerically obtained geometric ray traces. An estimate of misalignment errors is made, and individual elements are adjusted in an iterative manner until performance criteria are achieved. The method is illustrated for the alignment of an air-spaced doublet. PMID:14765916

  11. Chemoselective approaches to glycoprotein assembly

    International Nuclear Information System (INIS)

    Oligosaccharides on proteins and lipids play central roles in human health and disease. The molecular analysis of glycoconjugate function has benefited tremendously from new methods for their chemical synthesis, which provides homogeneous material not attainable from biosynthetic systems. Still, glycoconjugate synthesis requires the manipulation of multiple stereocenters and protecting groups and remains the domain of a few expert laboratories around the world. This account summarizes chemoselective approaches for assembling homogeneous glycoconjugates that attempt to reduce the barriers to their synthesis. The objective of these methods is to make glycoconjugate synthesis accessible to a broader community, thereby accelerating progress in glycobiology

  12. Nanoengineered membrane electrode assembly interface

    Science.gov (United States)

    Song, Yujiang; Shelnutt, John A

    2013-08-06

    A membrane electrode structure suitable for use in a membrane electrode assembly (MEA) that comprises membrane-affixed metal nanoparticles whose formation is controlled by a photochemical process that controls deposition of the metal nanoparticles using a photocatalyst integrated with a polymer electrolyte membrane, such as an ionomer membrane. Impregnation of the polymer membrane with the photocatalyst prior to metal deposition greatly reduces the required amount of metal precursor in the deposition reaction solution by restricting metal reduction substantially to the formation of metal nanoparticles affixed on or near the surface of the polymer membrane with minimal formation of metallic particles not directly associated with the membrane.

  13. Experimental Binding Energies in Supramolecular Complexes.

    Science.gov (United States)

    Biedermann, Frank; Schneider, Hans-Jörg

    2016-05-11

    On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information. PMID:27136957

  14. Nanoscale Ordering at the Liquid-Solid Interface using Self-Assembly Principles

    OpenAIRE

    Kampschulte, Lorenz

    2007-01-01

    The focus of this work is on the investigation and the understanding of molecular adsorption at the liquid-solid interface. Unlike ultra high vacuum conditions, this highly dynamic environment gives room for multiple ways controlling the structure formation, through adapting external parameters. In order to achieve self-assembled networks with a high degree of flexibility it was important to choose systems with weak to moderately strong binding behavior, both between molecule and substrate...

  15. The AAA-ATPase NVL2 is a telomerase component essential for holoenzyme assembly

    Energy Technology Data Exchange (ETDEWEB)

    Her, Joonyoung [Departments of Biology and Integrated Omics for Biomedical Science, Yonsei University, Seoul 120-749 (Korea, Republic of); Chung, In Kwon, E-mail: topoviro@yonsei.ac.kr [Departments of Biology and Integrated Omics for Biomedical Science, Yonsei University, Seoul 120-749 (Korea, Republic of)

    2012-01-20

    Highlights: Black-Right-Pointing-Pointer Identification of the AAA-ATPase NVL2 as a novel hTERT-interacting protein. Black-Right-Pointing-Pointer NVL2 associates with catalytically active telomerase via an interaction with hTERT. Black-Right-Pointing-Pointer NVL2 is a telomerase component essential for holoenzyme assembly. Black-Right-Pointing-Pointer ATP-binding activity of NVL2 is required for hTERT binding and telomerase assembly. -- Abstract: Continued cell proliferation requires telomerase to maintain functional telomeres that are essential for chromosome integrity. Although the core enzyme includes a telomerase reverse transcriptase (TERT) and a telomerase RNA component (TERC), a number of auxiliary proteins have been identified to regulate telomerase assembly, localization, and enzymatic activity. Here we describe the characterization of the AAA-ATPase NVL2 as a novel hTERT-interacting protein. NVL2 interacts and co-localizes with hTERT in the nucleolus. NLV2 is also found in association with catalytically competent telomerase in cell lysates through an interaction with hTERT. Depletion of endogenous NVL2 by small interfering RNA led to a decrease in hTERT without affecting the steady-state levels of hTERT mRNA, thereby reducing telomerase activity, suggesting that NVL2 is an essential component of the telomerase holoenzyme. We also found that ATP-binding activity of NVL2 is required for hTERT binding as well as telomerase assembly. Our findings suggest that NVL2, in addition to its role in ribosome biosynthesis, is essential for telomerase biogenesis and provides an alternative approach for inhibiting telomerase activity in cancer.

  16. Stress induces the assembly of RNA granules in the chloroplast of Chlamydomonas reinhardtii

    OpenAIRE

    Uniacke, James; Zerges, William

    2008-01-01

    Eukaryotic cells under stress repress translation and localize these messenger RNAs (mRNAs) to cytoplasmic RNA granules. We show that specific stress stimuli induce the assembly of RNA granules in an organelle with bacterial ancestry, the chloroplast of Chlamydomonas reinhardtii. These chloroplast stress granules (cpSGs) form during oxidative stress and disassemble during recovery from stress. Like mammalian stress granules, cpSGs contain poly(A)-binding protein and the small, but not the lar...

  17. The impact of conformational fluctuations on self-assembly: Cooperative aggregation of archaeal chaperonin proteins

    Science.gov (United States)

    Whitelam, Stephen; Rogers, Carl; Pasqua, Andrea; Paavola, Chad; Trent, Jonathan; Geissler, Phillip L.

    2009-01-01

    Protein complexes called rosettasomes self-assemble in solution to form large-scale filamentous and planar structures. The relative abundance of these aggregates varies abruptly with environmental conditions and sample composition. Our simulations of a model of patchy nanoparticles can reproduce this sharp crossover, but only if particles are allowed to switch between two internal states favoring different geometries of local binding. These results demonstrate how local conformational adaptivity can fundamentally influence the cooperativity of pattern-forming dynamics. PMID:19072304

  18. Characterization and DNA-binding specificities of Ralstonia TAL-like effectors

    KAUST Repository

    Li, Lixin

    2013-07-01

    Transcription activator-like effectors (TALEs) from Xanthomonas sp. have been used as customizable DNA-binding modules for genome-engineering applications. Ralstonia solanacearum TALE-like proteins (RTLs) exhibit similar structural features to TALEs, including a central DNA-binding domain composed of 35 amino acid-long repeats. Here, we characterize the RTLs and show that they localize in the plant cell nucleus, mediate DNA binding, and might function as transcriptional activators. RTLs have a unique DNA-binding architecture and are enriched in repeat variable di-residues (RVDs), which determine repeat DNA-binding specificities. We determined the DNA-binding specificities for the RVD sequences ND, HN, NP, and NT. The RVD ND mediates highly specific interactions with C nucleotide, HN interacts specifically with A and G nucleotides, and NP binds to C, A, and G nucleotides. Moreover, we developed a highly efficient repeat assembly approach for engineering RTL effectors. Taken together, our data demonstrate that RTLs are unique DNA-targeting modules that are excellent alternatives to be tailored to bind to user-selected DNA sequences for targeted genomic and epigenomic modifications. These findings will facilitate research concerning RTL molecular biology and RTL roles in the pathogenicity of Ralstonia spp. © 2013 The Author.

  19. Structural studies of sugar binding proteins

    OpenAIRE

    Sooriyaarachchi, Sanjeewani

    2010-01-01

    Binding proteins, which are themselves non-enzymatic, play an important role in enzymatic reactions as well as non-enzymatic processes by providing a binding platform for the specific recognition of particular molecules. For example, periplasmic binding proteins play a vital role in nutrient uptake in Gram-negative bacteria. In the present study, three sugar binding proteins, including two periplasmic binding proteins and a β-glucan binding protein, are described. The glucose/galactose bindin...

  20. 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.

  1. CENP-C recruits M18BP1 to centromeres to promote CENP-A chromatin assembly.

    Science.gov (United States)

    Moree, Ben; Meyer, Corey B; Fuller, Colin J; Straight, Aaron F

    2011-09-19

    Eukaryotic chromosomes segregate by attaching to microtubules of the mitotic spindle through a chromosomal microtubule binding site called the kinetochore. Kinetochores assemble on a specialized chromosomal locus termed the centromere, which is characterized by the replacement of histone H3 in centromeric nucleosomes with the essential histone H3 variant CENP-A (centromere protein A). Understanding how CENP-A chromatin is assembled and maintained is central to understanding chromosome segregation mechanisms. CENP-A nucleosome assembly requires the Mis18 complex and the CENP-A chaperone HJURP. These factors localize to centromeres in telophase/G1, when new CENP-A chromatin is assembled. The mechanisms that control their targeting are unknown. In this paper, we identify a mechanism for recruiting the Mis18 complex protein M18BP1 to centromeres. We show that depletion of CENP-C prevents M18BP1 targeting to metaphase centromeres and inhibits CENP-A chromatin assembly. We find that M18BP1 directly binds CENP-C through conserved domains in the CENP-C protein. Thus, CENP-C provides a link between existing CENP-A chromatin and the proteins required for new CENP-A nucleosome assembly. PMID:21911481

  2. Structural basis for proteasome formation controlled by an assembly chaperone nas2.

    Science.gov (United States)

    Satoh, Tadashi; Saeki, Yasushi; Hiromoto, Takeshi; Wang, Ying-Hui; Uekusa, Yoshinori; Yagi, Hirokazu; Yoshihara, Hidehito; Yagi-Utsumi, Maho; Mizushima, Tsunehiro; Tanaka, Keiji; Kato, Koichi

    2014-05-01

    Proteasome formation does not occur due to spontaneous self-organization but results from a highly ordered process assisted by several assembly chaperones. The assembly of the proteasome ATPase subunits is assisted by four client-specific chaperones, of which three have been structurally resolved. Here, we provide the structural basis for the working mechanisms of the last, hereto structurally uncharacterized assembly chaperone, Nas2. We revealed that Nas2 binds to the Rpt5 subunit in a bivalent mode: the N-terminal helical domain of Nas2 masks the Rpt1-interacting surface of Rpt5, whereas its C-terminal PDZ domain caps the C-terminal proteasome-activating motif. Thus, Nas2 operates as a proteasome activation blocker, offering a checkpoint during the formation of the 19S ATPase prior to its docking onto the proteolytic 20S core particle. PMID:24685148

  3. Structure of Hepatitis E Virion-Sized Particle Reveals an RNA-Dependent Viral Assembly Pathway

    Energy Technology Data Exchange (ETDEWEB)

    Xing, L.; Wall, J.; Li, T.-C.; Mayazaki, N.; Simon, M. N.; Moore, M.; Wang, C.-Y.; Takeda, N.; Wakita, T.; Miyamura, T.; Cheng, R. H.

    2010-10-22

    Hepatitis E virus (HEV) induces acute hepatitis in humans with a high fatality rate in pregnant women. There is a need for anti-HEV research to understand the assembly process of HEV native capsid. Here, we produced a large virion-sized and a small T=1 capsid by expressing the HEV capsid protein in insect cells with and without the N-terminal 111 residues, respectively, for comparative structural analysis. The virion-sized capsid demonstrates a T=3 icosahedral lattice and contains RNA fragment in contrast to the RNA-free T=1 capsid. However, both capsids shared common decameric organization. The in vitro assembly further demonstrated that HEV capsid protein had the intrinsic ability to form decameric intermediate. Our data suggest that RNA binding is the extrinsic factor essential for the assembly of HEV native capsids.

  4. Anisotropic magnetic porous assemblies of oxide nanoparticles interconnected via silica bridges for catalytic application.

    Science.gov (United States)

    Wacker, Josias B; Parashar, Virendra K; Gijs, Martin A M

    2011-04-19

    We report the microfluidic chip-based assembly of colloidal silanol-functionalized silica nanoparticles using monodisperse water-in-oil droplets as templates. The nanoparticles are linked via silica bridges, thereby forming superstructures that range from doublets to porous spherical or rod-like micro-objects. Adding magnetite nanoparticles to the colloid generates micro-objects that can be magnetically manipulated. We functionalized such magnetic porous assemblies with horseradish peroxidase and demonstrate the catalytic binding of fluorescent dye-labeled tyramide over the complete effective surface of the superstructure. Such nanoparticle assemblies permit easy manipulation and recovery after a heterogeneous catalytic process while providing a large surface similar to that of the individual nanoparticles. PMID:21417232

  5. Protein-responsive assemblies from catechol-metal ion supramolecular coordination.

    Science.gov (United States)

    Yuan, C; Chen, J; Yu, S; Chang, Y; Mao, J; Xu, Y; Luo, W; Zeng, B; Dai, L

    2015-03-21

    Supramolecular self-assembly driven by catechol-metal ion coordination has gained great success in the fabrication of functional materials including adhesives, capsules, coatings and hydrogels. However, this route has encountered a great challenge in the construction of nanoarchitectures in the absence of removable templates, because of the uncontrollable crosslinking of catechol-metal ion coordination. Herein, we show that a supramolecular approach, combining both catechol-metal ion coordination and polymer self-assembly together, can organize polymers into hybrid nanoassemblies ranging from solid particles, homogeneous vesicles to Janus vesicles. Without the introduction of a specific binding ligand or complicated molecular design, these assemblies can totally disassemble in response to proteins. UV/vis absorption, fluorescence quenching and recovery investigations have confirmed that proteins can seize metal ions from the hybrid nanoassemblies, thus causing the degradation of catechol-metal ion coordination networks.

  6. DNA brick self-assembly with an off-lattice potential

    CERN Document Server

    Reinhardt, Aleks

    2016-01-01

    We report Monte Carlo simulations of a simple off-lattice patchy-particle model for DNA `bricks'. We relate the parameters that characterise this model with the binding free energy of pairs of single-stranded DNA molecules. We verify that an off-lattice potential parameterised in this way reproduces much of the behaviour seen with a simpler lattice model we introduced previously, although the relaxation of the geometric constraints leads to a more error-prone self-assembly pathway. We investigate the self-assembly process as a function of the strength of the non-specific interactions. We show that our off-lattice model for DNA bricks results in robust self-assembly into a variety of target structures.

  7. The myosin-binding UCS domain but not the Hsp90-binding TPR domain of the UNC-45 chaperone is essential for function in Caenorhabditis elegans.

    Science.gov (United States)

    Ni, Weiming; Hutagalung, Alex H; Li, Shumin; Epstein, Henry F

    2011-09-15

    The UNC-45 family of molecular chaperones is expressed in metazoan organisms from Caenorhabditis elegans to humans. The UNC-45 protein is essential in C. elegans for early body-wall muscle cell development and A-band assembly. We show that the myosin-binding UCS domain of UNC-45 alone is sufficient to rescue lethal unc-45 null mutants arrested in embryonic muscle development and temperature-sensitive loss-of-function unc-45 mutants defective in worm A-band assembly. Removal of the Hsp90-binding TPR domain of UNC-45 does not affect rescue. Similar results were obtained with overexpression of the same fragments in wild-type nematodes when assayed for diminution of myosin accumulation and assembly. Titration experiments show that, on a per molecule basis, UCS has greater activity in C. elegans muscle in vivo than full-length UNC-45 protein, suggesting that UNC-45 is inhibited by either the TPR domain or its interaction with the general chaperone Hsp90. In vitro experiments with purified recombinant C. elegans Hsp90 and UNC-45 proteins show that they compete for binding to C. elegans myosin. Our in vivo genetic and in vitro biochemical experiments are consistent with a novel inhibitory role for Hsp90 with respect to UNC-45 action.

  8. Multivalent IDP assemblies: Unique properties of LC8-associated, IDP duplex scaffolds.

    Science.gov (United States)

    Clark, Sarah A; Jespersen, Nathan; Woodward, Clare; Barbar, Elisar

    2015-09-14

    A wide variety of subcellular complexes are composed of one or more intrinsically disordered proteins (IDPs) that are multivalent, flexible, and characterized by dynamic binding of diverse partner proteins. These multivalent IDP assemblies, of broad functional diversity, are classified here into five categories distinguished by the number of IDP chains and the arrangement of partner proteins in the functional complex. Examples of each category are summarized in the context of the exceptional molecular and biological properties of IDPs. One type - IDP duplex scaffolds - is considered in detail. Its unique features include parallel alignment of two IDP chains, formation of new self-associated domains, enhanced affinity for additional bivalent ligands, and ubiquitous binding of the hub protein LC8. For two IDP duplex scaffolds, dynein intermediate chain IC and nucleoporin Nup159, these duplex features, together with the inherent flexibility of IDPs, are central to their assembly and function. A new type of IDP-LC8 interaction, distributed binding of LC8 among multiple IDP recognition sites, is described for Nup159 assembly. PMID:26226419

  9. Nuclear actin and protein 4.1: Essential interactions during nuclear assembly in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Krauss, Sharon Wald; Chen, Cynthia; Penman, Sheldon; Heald, Rebecca

    2003-06-11

    Structural protein 4.1, which has crucial interactions within the spectin-actin lattice of the human red cell membrane skeleton, also is widely distributed at diverse intracellular sites in nucleated cells. We previously showed that 4.1 is essential for assembly of functional nuclei in vitro and that the capacity of 4.1 to bind actin is required. Here we report that 4.1 and actin colocalize in mammalian cell nuclei using fluorescence microscopy and, by higher resolution cell whole mount electron microscopy, are associated on nuclear filaments. We also devised a cell-free assay using Xenopus egg extract containing fluorescent actin to follow actin during nuclear assembly. By directly imaging actin under non-perturbing conditions, the total nuclear actin population is retained and is visualized in situ relative to intact chromatin. We detected actin initially when chromatin and nuclear pores began assembling. As the nuclear lamina assembled, but preceding DNA synthesis, a discrete actin network formed throughout the nucleus. Protein 4.1 epitopes also were detected when actin began to accumulate in nuclei, producing a diffuse coincident pattern. As nuclei matured, actin was detected both coincident with and also independent of 4.1 epitopes. To test whether acquisition of nuclear actin is required for nuclear assembly, the actin inhibitor latrunculin A was added to Xenopus egg extracts during nuclear assembly. Latrunculin A strongly perturbed nuclear assembly and produced distorted nuclear structures containing neither actin nor protein 4.1. Our results suggest that actin as well as 4.1 is necessary for nuclear assembly and that 4.1-actin interactions may be critical.

  10. Tank binding kinase 1 is a centrosome-associated kinase necessary for microtubule dynamics and mitosis.

    Science.gov (United States)

    Pillai, Smitha; Nguyen, Jonathan; Johnson, Joseph; Haura, Eric; Coppola, Domenico; Chellappan, Srikumar

    2015-01-01

    TANK Binding Kinase 1 (TBK1) is a non-canonical IκB kinase that contributes to KRAS-driven lung cancer. Here we report that TBK1 plays essential roles in mammalian cell division. Specifically, levels of active phospho-TBK1 increase during mitosis and localize to centrosomes, mitotic spindles and midbody, and selective inhibition or silencing of TBK1 triggers defects in spindle assembly and prevents mitotic progression. TBK1 binds to the centrosomal protein CEP170 and to the mitotic apparatus protein NuMA, and both CEP170 and NuMA are TBK1 substrates. Further, TBK1 is necessary for CEP170 centrosomal localization and binding to the microtubule depolymerase Kif2b, and for NuMA binding to dynein. Finally, selective disruption of the TBK1-CEP170 complex augments microtubule stability and triggers defects in mitosis, suggesting that TBK1 functions as a mitotic kinase necessary for microtubule dynamics and mitosis.

  11. Ephemeral protein binding to DNA shapes stable nuclear bodies and chromatin domains

    CERN Document Server

    Brackley, C A; Michieletto, D; Mouvet, F; Cook, P R; Marenduzzo, D

    2016-01-01

    Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To shed light on this, we perform large-scale Brownian dynamics simulations of a chromatin fiber interacting with an ensemble of (multivalent) DNA-binding proteins; these proteins switch between two states -- active (binding) and inactive (non-binding). This system provides a model for any DNA-binding protein that can be modified post-translationally to change its affinity for DNA (e.g., like the phosphorylation of a transcription factor). Due to this out-of-equilibrium process, proteins spontaneously assemble into clusters of self-limiting size, as individual proteins in a cluster exchange with the soluble pool with kinetics like those seen in photo-bleaching experiments. This behavior contrasts sharply with that exhibited by "equilibrium", or non-switching, proteins that exis...

  12. Plasma Pyrolysis Assembly Regeneration Evaluation

    Science.gov (United States)

    Medlen, Amber; Abney, Morgan B.; Miller, Lee A.

    2011-01-01

    In April 2010 the Carbon Dioxide Reduction Assembly (CRA) was delivered to the International Space Station (ISS). This technology requires hydrogen to recover oxygen from carbon dioxide. This results in the production of water and methane. Water is electrolyzed to provide oxygen to the crew. Methane is vented to space resulting in a loss of valuable hydrogen and unreduced carbon dioxide. This is not critical for ISS because of the water resupply from Earth. However, in order to have enough oxygen for long-term missions, it will be necessary to recover the hydrogen to maximize oxygen recovery. Thus, the Plasma Pyrolysis Assembly (PPA) was designed to recover hydrogen from methane. During operation, the PPA produces small amounts of carbon that can ultimately reduce performance by forming on the walls and windows of the reactor chamber. The carbon must be removed, although mechanical methods are highly inefficient, thus chemical methods are of greater interest. The purpose of this effort was to determine the feasibility of chemically removing the carbon from the walls and windows of a PPA reactor using a pure carbon dioxide stream.

  13. Types for DSP Assembler Programs

    DEFF Research Database (Denmark)

    Larsen, Ken

    2006-01-01

    In this dissertation I present my thesis: A high-level type system is a good aid for developing signal processing programs in handwritten Digital Signal Processor (DSP) assembler code. The problem behind the thesis is that it if often necessary to programing software for embedded systems in assem......In this dissertation I present my thesis: A high-level type system is a good aid for developing signal processing programs in handwritten Digital Signal Processor (DSP) assembler code. The problem behind the thesis is that it if often necessary to programing software for embedded systems...... hearing aids. I present a baseline type system which is the type system of DTAL adapted to Featherweight DSP. I then explain two classes of programs that uncovers some shortcomings of the baseline type systesm. The classes of problematic programs are exemplified by a procedure that initialises an array...... for reuse, and a procedure that computes point-wise vector multiplication. The latter uses a common idiom of prefetching memory resulting in out-of-bounds reading from memory. I present two extensions to the baseline type system: The first extension is a simple modification of some type rules to allow out...

  14. Nanoparticle Assemblies at Fluid Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Russell, Thomas P.

    2015-03-10

    A systematic study of the structure and dynamics of nanoparticles (NP) and NP-surfactants was performed. The ligands attached to both the NPs and NP-surfactants dictate the manner in which the nanoscopic materials assemble at fluid interfaces. Studies have shown that a single layer of the nanoscpic materials form at the interface to reduce the interactions between the two immiscible fluids. The shape of the NP is, also, important, where for spherical particles, a disordered, liquid-like monolayer forms, and, for nanorods, ordered domains at the interface is found and, if the monolayers are compressed, the orientation of the nanorods with respect to the interface can change. By associating end-functionalized polymers to the NPs assembled at the interface, NP-surfactants are formed that increase the energetic gain in segregating each NP at the interface which allows the NP-surfactants to jam at the interface when compressed. This has opened the possibility of structuring the two liquids by freezing in shape changes of the liquids.

  15. Size-dependent self-assembly of submicron/nano beads-protein conjugates for construction of a protein nanoarray

    International Nuclear Information System (INIS)

    A protein nanoarray is created when submicro and nano beads, varying in their size and each conjugated with different proteins, self-assemble to specific locations depending on the diameter matching the surface electron beam patterns created. Protein binding is confirmed from the fluorescence attenuation of the beads upon antigen-antibody binding on the bead surface. This method, called size-dependent self-assembly, allows control of the location of each type of bead, and thus, control of the location of multiple proteins. It provides fast multi-component patterning with a high binding resolution, which can be detected using a fluorescent light microscope. This method is developed to be a simple stand-alone tool for analysis of protein interactions. In addition, it has the potential to be used in conjunction with other protein analysis methods, such as enzyme-linked immunosorbent assay (ELISA) and atomic force microscopy (AFM).

  16. Dynamic-Model Assembly Line Scheduling

    Directory of Open Access Journals (Sweden)

    Aaima Najam

    2013-07-01

    Full Text Available The assembly line scheduling solution is restricted to two assembly lines that fulfill the requirement of small manufacturing industry by identifying the least cost path. Problem arises when large manufacturing industry comes under discussion where more than two assembly lines say three to fulfill the job, In this case two types of assembly line cost are involve: switching from one assembly line to another; switching from one station to the next. This study considers a solution for above mentioned scenario by least cost path identification, path cost calculation through back tracking, and a derived solution formula in order to reduce the computational complexity of scheduling at latter stages for n station. That provides the understanding for m number of assembly lines at the same time.

  17. Biochemical characterization and molecular dynamic simulation of β-sitosterol as a tubulin-binding anticancer agent.

    Science.gov (United States)

    Mahaddalkar, Tejashree; Suri, Charu; Naik, Pradeep Kumar; Lopus, Manu

    2015-08-01

    Βeta-sitosterol (β-SITO), a phytosterol present in pomegranate, peanut, corn oil, almond, and avocado, has been recognized to offer health benefits and potential clinical uses. β-SITO is orally bioavailable and, as a constituent of edible natural products, is considered to have no undesired side effects. It has also been considered as a potent anticancer agent. However, the molecular mechanism of action of β-SITO as a tubulin-binding anticancer agent and its binding site on tubulin are poorly understood. Using a combination of biochemical analyses and molecular dynamic simulation, we investigated the molecular details of the binding interactions of β-SITO with tubulin. A polymer mass assay comparing the effects of β-SITO and of taxol and vinblastine on tubulin assembly showed that this phytosterol stabilized microtubule assembly in a manner similar to taxol. An 8-anilino-1-naphthalenesulfonic acid assay confirmed the direct interaction of β-SITO with tubulin. Although β-SITO did not show direct binding to the colchicine site on tubulin, it stabilized the colchicine binding. Interestingly, no sulfhydryl groups of tubulin were involved in the binding interaction of β-SITO with tubulin. Based on the results from the biochemical assays, we computationally modeled the binding of β-SITO with tubulin. Using molecular docking followed by molecular dynamic simulations, we found that β-SITO binds tubulin at a novel site (which we call the 'SITO site') adjacent to the colchicine and noscapine sites. Our data suggest that β-SITO is a potent anticancer compound that interferes with microtubule assembly dynamics by binding to a novel site on tubulin. PMID:25912799

  18. Attomolar DNA detection with chiral nanorod assemblies

    OpenAIRE

    Ma, Wei; Kuang, Hua; Xu, Liguang; Ding, Li; Xu, Chuanlai; Wang, Libing; Kotov, Nicholas A.

    2013-01-01

    Nanoscale plasmonic assemblies display exceptionally strong chiral optical activity. So far, their structural design was primarily driven by challenges related to metamaterials whose practical applications are remote. Here we demonstrate that gold nanorods assembled by the polymerase chain reaction into DNA-bridged chiral systems have promising analytical applications. The chiroplasmonic activity of side-by-side assembled patterns is attributed to a 7–9 degree twist between the nanorod axes. ...

  19. Optics assembly for high power laser tools

    Science.gov (United States)

    Fraze, Jason D.; Faircloth, Brian O.; Zediker, Mark S.

    2016-06-07

    There is provided a high power laser rotational optical assembly for use with, or in high power laser tools for performing high power laser operations. In particular, the optical assembly finds applications in performing high power laser operations on, and in, remote and difficult to access locations. The optical assembly has rotational seals and bearing configurations to avoid contamination of the laser beam path and optics.

  20. Control model for reconfigurable assembly systems

    Institute of Scientific and Technical Information of China (English)

    Yu Jianfeng; Yin Yuehong; Chen Zhaoneng

    2005-01-01

    This paper proposes knowledge based object-oriented timed colored Petri net, a modeling method for reconfigurable assembly systems. Combining knowledge and object-oriented method into timed colored Petri net, a comprehensive and powerful representation model for control of RAS is obtained. With object-oriented method the whole system can be decomposed into concrete objects explicitly, and their relationships are constructed according to the system assembly requirements. Finally, a simple assembly system modeled by the KTCOPN is presented.

  1. Morphological Analysis of Forest Tractor Assemblies

    OpenAIRE

    Šušnjar, Marijan; Horvat, Dubravko; Kristić, Andrija; Pandur, Zdravko

    2008-01-01

    The results of this paper present the morphological analysis of nine different types of tractor assemblies used in forestry practice in timber forwarding from thinning operations of lowland forests. Among these tractor assemblies 4 types are older, equipped mechanical cranes. The remaining 5 tractor assemblies, manufactured more recently, are equipped with hydraulic cranes, and two of them are additionally equipped with double-drum winches. According to the research results, older tractor ass...

  2. Design for Un-heterogeneous Critical Assembly

    Institute of Scientific and Technical Information of China (English)

    WANG; Fan; ZHOU; Qi

    2013-01-01

    In order to study the nuclear criticality issues in the dissolving process,a new critical assembly is designed by theoretical calculation to satisfy the heterogeneous critical experimental demands based on the existed YSR assembly(Fig.1).The experiment plans,geometry structure of the assembly,solution contents and fuel rods arrangements are determined.The parameters for each scheme are listed in Table 1.

  3. Efficient synergistic single-cell genome assembly

    Directory of Open Access Journals (Sweden)

    Narjes S. Movahedi

    2016-05-01

    Full Text Available As the vast majority of all microbes are unculturable, single-cell sequencing has become a significant method to gain insight into microbial physiology. Single-cell sequencing methods, currently powered by multiple displacement genome amplification (MDA, have passed important milestones such as finishing and closing the genome of a prokaryote. However, the quality and reliability of genome assemblies from single cells are still unsatisfactory due to uneven coverage depth and the absence of scattered chunks of the genome in the final collection of reads caused by MDA bias. In this work, our new algorithm Hybrid De novo Assembler (HyDA demonstrates the power of co-assembly of multiple single-cell genomic data sets through significant improvement of the assembly quality in terms of predicted functional elements and length statistics. Co-assemblies contain significantly more base pairs and protein coding genes, cover more subsystems, and consist of longer contigs compared to individual assemblies by the same algorithm as well as state-of-the-art single-cell assemblers SPAdes and IDBA-UD. Hybrid emph{De novo} Assembler (HyDA is also able to avoid chimeric assemblies by detecting and separating shared and exclusive pieces of sequence for input data sets. By replacing one deep single-cell sequencing experiment with a few single-cell sequencing experiments of lower depth, the co-assembly method can hedge against the risk of failure and loss of the sample, without significantly increasing sequencing cost. Application of the single-cell co-assembler HyDA to the study of three uncultured members of an alkane-degrading methanogenic community validated the usefulness of the co-assembly concept. HyDA is open source and publicly available at http://chitsazlab.org/software.html and the raw reads are available at http://chitsazlab.org/research.html.

  4. Hierarchical assembly of diphenylalanine into dendritic nanoarchitectures.

    Science.gov (United States)

    Han, Tae Hee; Oh, Jun Kyun; Lee, Gyoung-Ja; Pyun, Su-Il; Kim, Sang Ouk

    2010-09-01

    Highly ordered, multi-dimensional dendritic nanoarchitectures were created via self-assembly of diphenylalanine from an acidic buffer solution. The self-similarity of dendritic structures was characterized by examining their fractal dimensions with the box-counting method. The fractal dimension was determined to be 1.7, which demonstrates the fractal dimension of structures generated by diffusion limited aggregation on a two-dimensional substrate surface. By confining the dendritic assembly of diphenylalanine within PDMS microchannels, the self-similar dendritic growth could be hierarchically directed to create linearly assembled nanoarchitectures. Our approach offers a novel pathway for creating and directing hierarchical nanoarchitecture from biomolecular assembly. PMID:20605423

  5. 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.

  6. Metagenomic Assembly: Overview, Challenges and Applications

    Science.gov (United States)

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

    2016-01-01

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

  7. Assembly and Calcium Binding Properties of Quantum Dot-Calmodulin Calcium Sensor.

    Science.gov (United States)

    Eun, Su-yong; Nguyen-ta, Kim; Yoo, Hoon; Silva, Gabriel A; Kim, Soon-jong

    2016-02-01

    We have developed the first nanoengineered quantum dot molecular complex designed to measure changes of calcium ion (Ca2+) concentration at high spatial and temporal resolutions in real time. The sensor is ratiometric and composed of three components: a quantum dot (QD) emitting at 620 nm as a fluorescence donor, an organic dye (Alexa Fluor 647) as a fluorescence acceptor, and a calmodulin-M13 (CaM-M13) protein part as a calcium sensing component. In this work, we have determined the maximal number of CaM-M13 required for saturating a single QD particle to be approximately 16. The dissociation constant, Kd of the QD-based calcium ion sensor was also estimated to be around 30 microM. PMID:27433729

  8. 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...

  9. Ultrasound transducer assembly and method for manufacturing an ultrasound transducer assembly

    NARCIS (Netherlands)

    Dekker, R.; Henneken, V.A.; Louwerse, M.C.; Raganato, M.F.

    2015-01-01

    The present invention relates to an ultrasound transducer assembly (10), in particular for intravascular ultrasound systems. The ultrasound transducer assembly comprises at least one silicon substrate element (30) including an ultrasound transducer element (14) for emitting and receiving ultrasound

  10. A new Fe[superscript II] quaterpyridyl M[subscript 4]L[subscript 6] tetrahedron exhibiting selective anion binding

    Energy Technology Data Exchange (ETDEWEB)

    Glasson, Christopher R.K.; Meehan, George V.; Clegg, Jack K.; Lindoy, Leonard F.; Turner, Peter; Duriska, Martin B.; Willis, Rick (Sydney); (James Cook U.); (Monash); (AIMS)

    2008-11-03

    A rigid linear bis-bidentate quaterpyridine undergoes metal directed self-assembly with iron(II) salts yielding M{sub 4}L{sub 6} host-guest complexes; selective anion binding for PF{sub 6}{sup -} over BR{sub 4}{sup -} is observed.

  11. Fibrillin assemblies: extracellular determinants of tissue formation and fibrosis

    Directory of Open Access Journals (Sweden)

    Olivieri Jacopo

    2010-12-01

    Full Text Available Abstract The extracellular matrix (ECM plays a key role in tissue formation, homeostasis and repair, mutations in ECM components have catastrophic consequences for organ function and therefore, for the fitness and survival of the organism. Collagen, fibrillin and elastin polymers represent the architectural scaffolds that impart specific mechanic properties to tissues and organs. Fibrillin assemblies (microfibrils have the additional function of distributing, concentrating and modulating local transforming growth factor (TGF-β and bone morphogenetic protein (BMP signals that regulate a plethora of cellular activities, including ECM formation and remodeling. Fibrillins also contain binding sites for integrin receptors, which induce adaptive responses to changes in the extracellular microenvironment by reorganizing the cytoskeleton, controlling gene expression, and releasing and activating matrix-bound latent TGF-β complexes. Genetic evidence has indicated that fibrillin-1 and fibrillin-2 contribute differently to the organization and structural properties of non-collagenous architectural scaffolds, which in turn translate into discrete regulatory outcomes of locally released TGF-β and BMP signals. Additionally, the study of congenital dysfunctions of fibrillin-1 has yielded insights into the pathogenesis of acquired connective tissue disorders of the connective tissue, such as scleroderma. On the one hand, mutations that affect the structure or expression of fibrillin-1 perturb microfibril biogenesis, stimulate improper latent TGF-β activation, and give rise to the pleiotropic manifestations in Marfan syndrome (MFS. On the other hand, mutations located around the integrin-binding site of fibrillin-1 perturb cell matrix interactions, architectural matrix assembly and extracellular distribution of latent TGF-β complexes, and lead to the highly restricted fibrotic phenotype of Stiff Skin syndrome. Understanding the molecular similarities and

  12. Recognition of glycoprotein peroxidase via Con A-carrying self-assembly layer on gold.

    Science.gov (United States)

    Liu, Songqin; Wang, Kewei; Du, Dan; Sun, Yueming; He, Lin

    2007-07-01

    We have successfully fabricated a self-assembled layer of concanavalin A (Con A) on a gold surface for recognition of glycoproteins. The type IV Con A is covalently bound to 11-mercaptoundecanoic acid (MUA) on gold with a 2-(5-norbornene-2,3-dicarboximido)-1,1,3,3-tetramethyluronium tetrafluoroborate (TNTU) linkage. The binding interaction between glycoproteins and self-assembled Con A is studied using horseradish peroxidase (HRP) as a model glycoprotein. Voltammetric, electrochemical impedance studies, and photometric activity measurements show the presence of both specific and nonspecific bindings of HRP to the Con A interface. The specific binding is attributed to the Con A-sugar interaction where Con A selectively recognizes the glycosylation sites of HRP. The catalytic current of the HRP-loaded electrode, because of catalytic oxidation of thionine in the presence of hydrogen peroxide (H2O2), is found to be proportional to the HRP concentrations in the incubation solution. A linear correlation coefficient of 0.993 was obtained over a wide HRP concentration range of 12.5 microg/mL to 1 mg/mL. The approach described in this study provides a simple yet selective means to immobilize glycoproteins on a solid support. The specific binding achieved is desirable in biosensor fabrication, glycoprotein separation, recognition, and purification as well as in drug-releasing systems.

  13. Low inductance power electronics assembly

    Science.gov (United States)

    Herron, Nicholas Hayden; Mann, Brooks S.; Korich, Mark D.; Chou, Cindy; Tang, David; Carlson, Douglas S.; Barry, Alan L.

    2012-10-02

    A power electronics assembly is provided. A first support member includes a first plurality of conductors. A first plurality of power switching devices are coupled to the first support member. A first capacitor is coupled to the first support member. A second support member includes a second plurality of conductors. A second plurality of power switching devices are coupled to the second support member. A second capacitor is coupled to the second support member. The first and second pluralities of conductors, the first and second pluralities of power switching devices, and the first and second capacitors are electrically connected such that the first plurality of power switching devices is connected in parallel with the first capacitor and the second capacitor and the second plurality of power switching devices is connected in parallel with the second capacitor and the first capacitor.

  14. Reconfigurable optical assembly of nanostructures.

    Science.gov (United States)

    Montelongo, Yunuen; Yetisen, Ali K; Butt, Haider; Yun, Seok-Hyun

    2016-01-01

    Arrangements of nanostructures in well-defined patterns are the basis of photonic crystals, metamaterials and holograms. Furthermore, rewritable optical materials can be achieved by dynamically manipulating nanoassemblies. Here we demonstrate a mechanism to configure plasmonic nanoparticles (NPs) in polymer media using nanosecond laser pulses. The mechanism relies on optical forces produced by the interference of laser beams, which allow NPs to migrate to lower-energy configurations. The resulting NP arrangements are stable without any external energy source, but erasable and rewritable by additional recording pulses. We demonstrate reconfigurable optical elements including multilayer Bragg diffraction gratings, volumetric photonic crystals and lenses, as well as dynamic holograms of three-dimensional virtual objects. We aim to expand the applications of optical forces, which have been mostly restricted to optical tweezers. Holographic assemblies of nanoparticles will allow a new generation of programmable composites for tunable metamaterials, data storage devices, sensors and displays. PMID:27337216

  15. Dual contact pogo pin assembly

    Energy Technology Data Exchange (ETDEWEB)

    Hatch, Stephen McGarry

    2016-06-21

    A contact assembly includes a base and a pair of electrical contacts supported by the base. A first end of the first electrical contact corresponds to a first end of the base and is configured to engage a first external conductive circuit element. A first end of the second electrical contact also corresponds to the first end of the base and is configured to engage a second external conductive circuit element. The first contact and the second contact are electrically isolated from one another and configured to compress when engaging an external connector element. The base includes an aperture positioned on a second end of the base outboard of a second end of the first and second electrical contacts. The aperture presents a narrowing shape with a wide mouth distal the electrical contacts and a narrow internal through-hole proximate the electrical contacts.

  16. Reconfigurable optical assembly of nanostructures

    Science.gov (United States)

    Montelongo, Yunuen; Yetisen, Ali K.; Butt, Haider; Yun, Seok-Hyun

    2016-01-01

    Arrangements of nanostructures in well-defined patterns are the basis of photonic crystals, metamaterials and holograms. Furthermore, rewritable optical materials can be achieved by dynamically manipulating nanoassemblies. Here we demonstrate a mechanism to configure plasmonic nanoparticles (NPs) in polymer media using nanosecond laser pulses. The mechanism relies on optical forces produced by the interference of laser beams, which allow NPs to migrate to lower-energy configurations. The resulting NP arrangements are stable without any external energy source, but erasable and rewritable by additional recording pulses. We demonstrate reconfigurable optical elements including multilayer Bragg diffraction gratings, volumetric photonic crystals and lenses, as well as dynamic holograms of three-dimensional virtual objects. We aim to expand the applications of optical forces, which have been mostly restricted to optical tweezers. Holographic assemblies of nanoparticles will allow a new generation of programmable composites for tunable metamaterials, data storage devices, sensors and displays. PMID:27337216

  17. Nanocrystal assembly for tandem catalysis

    Science.gov (United States)

    Yang, Peidong; Somorjai, Gabor; Yamada, Yusuke; Tsung, Chia-Kuang; Huang, Wenyu

    2014-10-14

    The present invention provides a nanocrystal tandem catalyst comprising at least two metal-metal oxide interfaces for the catalysis of sequential reactions. One embodiment utilizes a nanocrystal bilayer structure formed by assembling sub-10 nm platinum and cerium oxide nanocube monolayers on a silica substrate. The two distinct metal-metal oxide interfaces, CeO.sub.2--Pt and Pt--SiO.sub.2, can be used to catalyze two distinct sequential reactions. The CeO.sub.2--Pt interface catalyzed methanol decomposition to produce CO and H.sub.2, which were then subsequently used for ethylene hydroformylation catalyzed by the nearby Pt--SiO.sub.2 interface. Consequently, propanal was selectively produced on this nanocrystal bilayer tandem catalyst.

  18. The APOLLO assembly spectrum code

    International Nuclear Information System (INIS)

    The APOLLO code was originally developed as a design tool for HTR's, later it was aimed at the calculation of PWR lattices. APOLLO is a general purpose assembly spectrum code based on the multigroup integral transport equation; refined collision probability modules allow the computation of 1D geometries with linearly anisotropic scattering and two term flux expansion. In 2D geometries modules based on the substructure method provide fast and accurate design calculations and a module based on a direct discretization is devoted to reference calculations. The SPH homogenization technique provides corrected cross sections performing an equivalence between coarse and refined calculations. The post processing module of APOLLO generate either APOLLIB to be used by APOLLO or NEPLIB for reactor diffusion calculation. The cross section library of APOLLO contains data and self-shielding data for more than 400 isotopes. APOLLO is able to compute the depletion of any medium accounting for any heavy isotope or fission product chain. 21 refs

  19. Photonic-powered cable assembly

    Science.gov (United States)

    Sanderson, Stephen N.; Appel, Titus James; Wrye, IV, Walter C.

    2013-01-22

    A photonic-cable assembly includes a power source cable connector ("PSCC") coupled to a power receive cable connector ("PRCC") via a fiber cable. The PSCC electrically connects to a first electronic device and houses a photonic power source and an optical data transmitter. The fiber cable includes an optical transmit data path coupled to the optical data transmitter, an optical power path coupled to the photonic power source, and an optical feedback path coupled to provide feedback control to the photonic power source. The PRCC electrically connects to a second electronic device and houses an optical data receiver coupled to the optical transmit data path, a feedback controller coupled to the optical feedback path to control the photonic power source, and a photonic power converter coupled to the optical power path to convert photonic energy received over the optical power path to electrical energy to power components of the PRCC.

  20. Reconfigurable optical assembly of nanostructures

    Science.gov (United States)

    Montelongo, Yunuen; Yetisen, Ali K.; Butt, Haider; Yun, Seok-Hyun

    2016-06-01

    Arrangements of nanostructures in well-defined patterns are the basis of photonic crystals, metamaterials and holograms. Furthermore, rewritable optical materials can be achieved by dynamically manipulating nanoassemblies. Here we demonstrate a mechanism to configure plasmonic nanoparticles (NPs) in polymer media using nanosecond laser pulses. The mechanism relies on optical forces produced by the interference of laser beams, which allow NPs to migrate to lower-energy configurations. The resulting NP arrangements are stable without any external energy source, but erasable and rewritable by additional recording pulses. We demonstrate reconfigurable optical elements including multilayer Bragg diffraction gratings, volumetric photonic crystals and lenses, as well as dynamic holograms of three-dimensional virtual objects. We aim to expand the applications of optical forces, which have been mostly restricted to optical tweezers. Holographic assemblies of nanoparticles will allow a new generation of programmable composites for tunable metamaterials, data storage devices, sensors and displays.

  1. Snubber assembly for turbine blades

    Science.gov (United States)

    Marra, John J

    2013-09-03

    A snubber associated with a rotatable turbine blade in a turbine engine, the turbine blade including a pressure sidewall and a suction sidewall opposed from the pressure wall. The snubber assembly includes a first snubber structure associated with the pressure sidewall of the turbine blade, a second snubber structure associated with the suction sidewall of the turbine blade, and a support structure. The support structure extends through the blade and is rigidly coupled at a first end portion thereof to the first snubber structure and at a second end portion thereof to the second snubber structure. Centrifugal loads exerted by the first and second snubber structures caused by rotation thereof during operation of the engine are at least partially transferred to the support structure, such that centrifugal loads exerted on the pressure and suctions sidewalls of the turbine blade by the first and second snubber structures are reduced.

  2. Product-internal assembly functions: a novel micro-assembly concept applied to optical interconnects

    OpenAIRE

    Henneken, V.A.

    2008-01-01

    In this project, the technical feasibility of a novel assembly concept was explored, in which microsystem-based self-assembly functionality is added to an existing product. The case considered is the accurate alignment of an optical fibre relative to a telecommunication laser source. In the most demanding cases this requires alignment accuracies down to 0.1 µm to achieve adequate optical coupling. This is very difficult to achieve using conventional assembly, making the assembly cost up ...

  3. Unification of the a priori inconsistencies checking among assembly constraints in assembly sequence planning.

    OpenAIRE

    Perrard, Christophe; Bonjour, Eric

    2013-01-01

    International audience Sequence planning generation is an important problem in assembly line design. A good assembly sequence can help to reduce the cost and time of the manufacturing process. This paper focuses on assembly sequence planning (ASP) known as a hard combinatorial optimization problem. Although the ASP problem has been tackled via even more sophisticated optimization techniques, these techniques are often inefficient for proposing feasible assembly sequences that satisfy the a...

  4. Hierarchical Self-Assembly of Peptide Amphiphiles: Form and Function at Multiple Length Scales

    Science.gov (United States)

    Zha, Runye Helen

    Hierarchical self-assembly, the organization of molecules into supramolecular structures of increasing size and complexity, is a potent tool for materials synthesis and requires understanding the connections of structure across multiple length scales. Herein, self-assembly of peptide amphiphiles (PAs) into nanoscopic and macroscopic materials is explored, and their anti-cancer applications are investigated. First, nanoscale assembly is examined in the context of an anti-angiogenic PA bearing the G-helix motif of maspin, a tumor suppressor protein. Assembly of this maspin-mimetic PA (MMPA) stabilizes the native G-helix conformation and improves binding to endothelial cells. Furthermore, PA nanostructures significantly increase cell adhesion to fibronectin as compared to G-helix peptide alone. Combined with its inhibitory effect on cell migration, MMPA nanostructures thus show anti-angiogenic activity on par with maspin protein in vitro and in vivo. Second, assembly of cationic PAs with hyaluronic acid (HA), an anionic polyelectrolyte, into macroscopic membranes is explored using PAs with identical formal charge but systematically varied self-assembly domains. Results suggest that membrane formation is dictated by the initial moments of component aggregation and is highly sensitive to PA molecular structure via nanoscale assembly. Specifically, PAs with beta-sheet forming residues are nanofibrous and have high surface charge density, leading to robust membranes with aligned-fiber microstructure. PAs without beta-sheet forming residues are nanospherical and have low surface charge density, leading to weak membranes with non-fibrous finger-like microstructure. Lastly, the principles of PA-HA membrane assembly are applied towards development of anti-cancer therapeutic biomaterials. Here, cytotoxic PAs bearing the epitope (KLAKLAKbeta)2 are co-assembled with non-bioactive cationic PA in order to achieve varying nanoscale morphology. These nanostructures are then

  5. Probing protein phosphatase substrate binding

    DEFF Research Database (Denmark)

    Højlys-Larsen, Kim B.; Sørensen, Kasper Kildegaard; Jensen, Knud Jørgen;

    2012-01-01

    profile of the integrin-linked kinase associated phosphatase (ILKAP), a member of the protein phosphatase 2C (PP2C) family. Phosphatases can potentially dephosphorylate these phosphopeptide substrates but, interestingly, performing the binding studies at 4 °C allowed efficient binding to phosphopeptides...... around the phosphorylated residue are important for the binding affinity of ILKAP. We conclude that solid-phase affinity pull-down of proteins from complex mixtures can be applied in phosphoproteomics and systems biology.......Proteomics and high throughput analysis for systems biology can benefit significantly from solid-phase chemical tools for affinity pull-down of proteins from complex mixtures. Here we report the application of solid-phase synthesis of phosphopeptides for pull-down and analysis of the affinity...

  6. Water binding in legume seeds

    Science.gov (United States)

    Vertucci, C. W.; Leopold, A. C.

    1987-01-01

    The physical status of water in seeds has a pivotal role in determining the physiological reactions that can take place in the dry state. Using water sorption isotherms from cotyledon and axis tissue of five leguminous seeds, the strength of water binding and the numbers of binding sites have been estimated using van't Hoff analyses and the D'Arcy/Watt equation. These parameters of water sorption are calculated for each of the three regions of water binding and for a range of temperatures. Water sorption characteristics are reflective of the chemical composition of the biological materials as well as the temperature at which hydration takes place. Changes in the sorption characteristics with temperature and hydration level may suggest hydration-induced structural changes in cellular components.

  7. Self-assembly of azide containing dipeptides.

    Science.gov (United States)

    Yuran, Sivan; Razvag, Yair; Das, Priyadip; Reches, Meital

    2014-07-01

    Functional structures and materials are formed spontaneously in nature through the process of self-assembly. Mimicking this process in vitro will lead to the formation of new substances that would impact many areas including energy production and storage, biomaterials and implants, and drug delivery. The considerable structural diversity of peptides makes them appealing building blocks for self-assembly in vitro. This paper describes the self-assembly of three aromatic dipeptides containing an azide moiety: H-Phe(4-azido)-Phe(4-azido)-OH, H-Phe(4-azido)-Phe-OH, and H-Phe-Phe(4-azido)-OH. The peptide H-Phe(4-azido)-Phe(4-azido)-OH self-assembled into porous spherical structures, whereas the peptides H-Phe(4-azido)-Phe-OH and H-Phe-Phe(4-azido)-OH did not form any ordered structures under the examined experimental conditions. The azido group of the peptide can serve as a photo cross-linking agent upon irradiation with UV light. To examine the effect of this group and its activity on the self-assembled structures, we irradiated the assemblies in solution for different time periods. Using electron microscopy, we determined that the porous spherical assemblies formed by the peptide H-Phe(4-azido)-Phe(4-azido)-OH underwent a structural change upon irradiation. In addition, using FT-IR, we detected the chemical change of the peptide azido group. Moreover, using indentation experiments with atomic force microscopy, we showed that the Young's modulus of the spherical assemblies increased after 20 min of irradiation with UV light. Overall, irradiating the solution of the peptide assemblies containing the azido group resulted in a change both in the morphology and mechanical properties of the peptide-based structures. These ordered assemblies or their peptide monomer building blocks can potentially be incorporated into other peptide assemblies to generate stiffer and more stable materials. PMID:24889029

  8. Prion protein inhibits microtubule assembly by inducing tubulin oligomerization

    International Nuclear Information System (INIS)

    A growing body of evidence points to an association of prion protein (PrP) with microtubular cytoskeleton. Recently, direct binding of PrP to tubulin has also been found. In this work, using standard light scattering measurements, sedimentation experiments, and electron microscopy, we show for First time the effect of a direct interaction between these proteins on tubulin polymerization. We demonstrate that full-length recombinant PrP induces a rapid increase in the turbidity of tubulin diluted below the critical concentration for microtubule assembly. This effect requires magnesium ions and is weakened by NaCl. Moreover, the PrP-induced light scattering structures of tubulin are cold-stable. In preparations of diluted tubulin incubated with PrP, electron microscopy revealed the presence of ∼50 nm disc-shaped structures not reported so far. These unique tubulin oligomers may form large aggregates. The effect of PrP is more pronounced under the conditions promoting microtubule formation. In these tubulin samples, PrP induces formation of the above oligomers associated with short protofilaments and sheets of protofilaments into aggregates. Noticeably, this is accompanied by a significant reduction of the number and length of microtubules. Hence, we postulate that prion protein may act as an inhibitor of microtubule assembly by inducing formation of stable tubulin oligomers

  9. Physical controls on directed virus assembly at nanoscale chemical templates

    Energy Technology Data Exchange (ETDEWEB)

    Cheung, C L; Chung, S; Chatterji, A; Lin, T; Johnson, J E; Hok, S; Perkins, J; De Yoreo, J

    2006-05-10

    Viruses are attractive building blocks for nanoscale heterostructures, but little is understood about the physical principles governing their directed assembly. In-situ force microscopy was used to investigate organization of Cowpea Mosaic Virus engineered to bind specifically and reversibly at nanoscale chemical templates with sub-30nm features. Morphological evolution and assembly kinetics were measured as virus flux and inter-viral potential were varied. The resulting morphologies were similar to those of atomic-scale epitaxial systems, but the underlying thermodynamics was analogous to that of colloidal systems in confined geometries. The 1D templates biased the location of initial cluster formation, introduced asymmetric sticking probabilities, and drove 1D and 2D condensation at subcritical volume fractions. The growth kinetics followed a t{sup 1/2} law controlled by the slow diffusion of viruses. The lateral expansion of virus clusters that initially form on the 1D templates following introduction of polyethylene glycol (PEG) into the solution suggests a significant role for weak interaction.

  10. Assembly and stability of nisin-lipid II pores.

    Science.gov (United States)

    Hasper, Hester Emilie; de Kruijff, Ben; Breukink, Eefjan

    2004-09-14

    The peptide antibiotic nisin was the first reported example of an antibiotic that kills bacteria via targeted pore formation. The specific target of nisin is Lipid II, an essential intermediate in the bacterial cell-wall synthesis. High-affinity binding of the antibiotic to Lipid II is followed by rapid permeabilization of the membrane. Here, we investigated the assembly and stability of nisin-Lipid II pore complexes by means of pyrene fluorescence and circular dichroism. We demonstrated that nisin uses all available Lipid II molecules in the membrane to form pore complexes. The pore complexes have a uniform structure and consist of 8 nisin and 4 Lipid II molecules. Moreover, the pores displayed a remarkable stability, because they were able to resist the solubilization of the membrane environment by mild detergents. Similar experiments with [N20P/M21P]nisin showed that the hinge region is essential for the assembly into stable pore complexes. The new insights were used to propose a refined model for nisin pore formation. PMID:15350143

  11. Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe.

    Science.gov (United States)

    Brown, William R A; Thomas, Geraint; Lee, Nicholas C O; Blythe, Martin; Liti, Gianni; Warringer, Jonas; Loose, Matthew W

    2014-02-01

    Kinetochores in multicellular eukaryotes are usually associated with heterochromatin. Whether this heterochromatin simply promotes the cohesion necessary for accurate chromosome segregation at cell division or whether it also has a role in kinetochore assembly is unclear. Schizosaccharomyces pombe is an important experimental system for investigating centromere function, but all of the previous work with this species has exploited a single strain or its derivatives. The laboratory strain and most other S. pombe strains contain three chromosomes, but one recently discovered strain, CBS 2777, contains four. We show that the genome of CBS 2777 is related to that of the laboratory strain by a complex chromosome rearrangement. As a result, two of the kinetochores in CBS 2777 contain the central core sequences present in the laboratory strain centromeres, but lack adjacent heterochromatin. The closest block of heterochromatin to these rearranged kinetochores is ∼100 kb away at new telomeres. Despite lacking large amounts of adjacent heterochromatin, the rearranged kinetochores bind CENP-A(Cnp1) and CENP-C(Cnp3) in similar quantities and with similar specificities as those of the laboratory strain. The simplest interpretation of this result is that constitutive kinetochore assembly and heterochromatin formation occur autonomously. PMID:24449889

  12. Self-Assembly of Emulsion Droplets into Polymer Chains

    Science.gov (United States)

    Bargteil, Dylan; McMullen, Angus; Brujic, Jasna

    We experimentally investigate `beads-on-a-string' models of polymers using the spontaneous assembly of emulsion droplets into linear chains. Droplets functionalized with surface-mobile DNA allow for programmable 'monomers' through which we can influence the three-dimensional structure of the assembled 'polymer'. Such model polymers can be used to study conformational changes of polypeptides and the principles governing protein folding. In our system, we find that droplets bind via complementary DNA strands that are recruited into adhesion patches. Recruitment is driven by the DNA hybridization energy, and is limited by the energy cost of surface deformation and the entropy loss of the mobile linkers, yielding adhesion patches of a characteristic size with a given number of linkers. By tuning the initial surface coverage of linkers, we control valency between the droplets to create linear or branched polymer chains. We additionally control the flexibility of the model polymers by varying the salt concentration and study their dynamics between extended and collapsed states. This system opens the possibility of programming stable three-dimensional structures, such as those found within folded proteins.

  13. A thermodynamic model of microtubule assembly and disassembly.

    Directory of Open Access Journals (Sweden)

    Bernard M A G Piette

    Full Text Available Microtubules are self-assembling polymers whose dynamics are essential for the normal function of cellular processes including chromosome separation and cytokinesis. Therefore understanding what factors effect microtubule growth is fundamental to our understanding of the control of microtubule based processes. An important factor that determines the status of a microtubule, whether it is growing or shrinking, is the length of the GTP tubulin microtubule cap. Here, we derive a Monte Carlo model of the assembly and disassembly of microtubules. We use thermodynamic laws to reduce the number of parameters of our model and, in particular, we take into account the contribution of water to the entropy of the system. We fit all parameters of the model from published experimental data using the GTP tubulin dimer attachment rate and the lateral and longitudinal binding energies of GTP and GDP tubulin dimers at both ends. Also we calculate and incorporate the GTP hydrolysis rate. We have applied our model and can mimic published experimental data, which formerly suggested a single layer GTP tubulin dimer microtubule cap, to show that these data demonstrate that the GTP cap can fluctuate and can be several microns long.

  14. The assembly of kinesin-based nanotransport systems

    Science.gov (United States)

    Oliveira, D.; Kim, D.-M.; Umetsu, M.; Kumagai, I.; Adschiri, T.; Teizer, W.

    2012-12-01

    At the nano-scale many proteins act as biological actuators for rotation or translation. Among these proteins, the building blocks of self-assembled, highly efficient natural motors, kinesin is considered a promising tool in the development of synthetic nanorobots. Conversion of chemical energy into mechanical work, harnessed by the hydrolysis of adenosine triphosphate, propels kinesin along a cytoplasmic system of fibers, known as a microtubule. Even though recent efforts were made to engineer tailor-made artificial nanotransport systems using kinesin, no systematic study investigated how these systems can be organized from the bottom up using the surface plasmon resonance technique. Here, we show that it is possible to quantitatively evaluate how each component of such nanoscopic machines is sequentially assembled by monitoring the individual association of its components, focusing specifically on the kinesin association to microtubules as well as the cargo-kinesin association. Furthermore, the kinetic parameters reported here for the microtubules and recombinant biotinylated kinesin binding process properties are of utmost importance due to the current widespread use of biotinylated kinesin in the construction of synthetic nano-machines.

  15. Structural Mechanisms in NLR Inflammasome Assembly and Signaling.

    Science.gov (United States)

    Hu, Zehan; Chai, Jijie

    2016-01-01

    Inflammasomes are multimeric protein complexes that mediate the activation of inflammatory caspases. One central component of inflammasomes is nucleotide-binding domain (NBD)- and leucine-rich repeat (LRR)-containing proteins (NLRs) that can function as pattern recognition receptors (PRRs). In resting cells, NLR proteins exist in an auto-inhibited, monomeric, and ADP-bound state. Perception of microbial or damage-associated signals results in NLR oligomerization, thus recruiting inflammatory caspases directly or through the adaptor molecule apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC). The assembled NLR inflammasomes serve as dedicated machinery to facilitate the activation of the inflammatory caspases. Here, we review current understanding of the structures of NLR inflammasomes with an emphasis on the molecular mechanisms of their assembly and activation. We also discuss implications of the self-propagation model derived from the NAIP-NLRC4 inflammasomes for the activation of other NLR inflammasomes and a potential role of the C-terminal LRR domain in the activation of an NLR protein. PMID:27460803

  16. Dendrimers in Layer-by-Layer Assemblies: Synthesis and Applications

    Directory of Open Access Journals (Sweden)

    Katsuhiko Sato

    2013-07-01

    Full Text Available We review the synthesis of dendrimer-containing layer-by-layer (LbL assemblies and their applications, including biosensing, controlled drug release, and bio-imaging. Dendrimers can be built into LbL films and microcapsules by alternating deposition of dendrimers and counter polymers on the surface of flat substrates and colloidal microparticles through electrostatic bonding, hydrogen bonding, covalent bonding, and biological affinity. Dendrimer-containing LbL assemblies have been used to construct biosensors, in which electron transfer mediators and metal nanoparticles are often coupled with dendrimers. Enzymes have been successfully immobilized on the surface of electrochemical and optical transducers by forming enzyme/dendrimer LbL multilayers. In this way, high-performance enzyme sensors are fabricated. In addition, dendrimer LbL films and microcapsules are useful for constructing drug delivery systems because dendrimers bind drugs to form inclusion complexes or the dendrimer surface is covalently modified with drugs. Magnetic resonance imaging of cancer cells by iron oxide nanoparticles coated with dendrimer LbL film is also discussed.

  17. Mechanical Properties of Nanoworm Assembled by DNA and Nanoparticle Conjugates.

    Science.gov (United States)

    Zhou, Yihua; Sohrabi, Salman; Tan, Jifu; Liu, Yaling

    2016-06-01

    Recently, DNA-nanoparticle conjugates have been widely used as building blocks for assembling complex nanostructures, due to their programmable recognitions, high cellular uptake and enhanced binding capabilities. In this study, a nanoworm structure, which can be applied in fields of drug targeting, image probing and thermal therapies, has been assembled by DNA-nanoparticle conjugates. Subsequently, its mechanical properties have been investigated due to their importance on the structural stability, transport and circulations of the nanoworm. Stiffness and strengths of the nanoworm under different deformation types are studied by coarse-grained molecular dynamics simulations. Effects of temperature, DNA coating density and particle size on mechanical properties of nanoworms are also thoroughly investigated. Results show that both resistance and strength of the nanoworm are the weakest along the axial direction, indicating it is more prone to be ruptured by a stretching force. i addition, DNA strands are found to be more important than nanoparticles in determining mechanical properties of the nanoworm. Moreover, both strength and resistance in regardless of directions are proved to be enhanced by decreasing the temperature, raising the DNA coating density and enlarging the particle size. This study is capable of serving as guidance for designing nanoworms with optimal mechanical strengths for applications. PMID:27427583

  18. Computational Prediction of RNA-Binding Proteins and Binding Sites.

    Science.gov (United States)

    Si, Jingna; Cui, Jing; Cheng, Jin; Wu, Rongling

    2015-01-01

    Proteins and RNA interaction have vital roles in many cellular processes such as protein synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and post-transcriptional levels. Approximately 6%-8% of all proteins are RNA-binding proteins (RBPs). Distinguishing these RBPs or their binding residues is a major aim of structural biology. Previously, a number of experimental methods were developed for the determination of protein-RNA interactions. However, these experimental methods are expensive, time-consuming, and labor-intensive. Alternatively, researchers have developed many computational approaches to predict RBPs and protein-RNA binding sites, by combining various machine learning methods and abundant sequence and/or structural features. There are three kinds of computational approaches, which are prediction from protein sequence, prediction from protein structure, and protein-RNA docking. In this paper, we review all existing studies of predictions of RNA-binding sites and RBPs and complexes, including data sets used in different approaches, sequence and structural features used in several predictors, prediction method classifications, performance comparisons, evaluation methods, and future directions.

  19. Computational Prediction of RNA-Binding Proteins and Binding Sites

    Directory of Open Access Journals (Sweden)

    Jingna Si

    2015-11-01

    Full Text Available Proteins and RNA interaction have vital roles in many cellular processes such as protein synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and post-transcriptional levels. Approximately 6%–8% of all proteins are RNA-binding proteins (RBPs. Distinguishing these RBPs or their binding residues is a major aim of structural biology. Previously, a number of experimental methods were developed for the determination of protein–RNA interactions. However, these experimental methods are expensive, time-consuming, and labor-intensive. Alternatively, researchers have developed many computational approaches to predict RBPs and protein–RNA binding sites, by combining various machine learning methods and abundant sequence and/or structural features. There are three kinds of computational approaches, which are prediction from protein sequence, prediction from protein structure, and protein-RNA docking. In this paper, we review all existing studies of predictions of RNA-binding sites and RBPs and complexes, including data sets used in different approaches, sequence and structural features used in several predictors, prediction method classifications, performance comparisons, evaluation methods, and future directions.

  20. Skyrmions with low binding energies

    Directory of Open Access Journals (Sweden)

    Mike Gillard

    2015-06-01

    Full Text Available Nuclear binding energies are investigated in two variants of the Skyrme model: the first replaces the usual Skyrme term with a term that is sixth order in derivatives, and the second includes a potential that is quartic in the pion fields. Solitons in the first model are shown to deviate significantly from ansätze previously assumed in the literature. The binding energies obtained in both models are lower than those obtained from the standard Skyrme model, and those obtained in the second model are close to the experimental values.

  1. Skyrmions with low binding energies

    Energy Technology Data Exchange (ETDEWEB)

    Gillard, Mike, E-mail: m.n.gillard@leeds.ac.uk; Harland, Derek, E-mail: d.g.harland@leeds.ac.uk; Speight, Martin, E-mail: speight@maths.leeds.ac.uk

    2015-06-15

    Nuclear binding energies are investigated in two variants of the Skyrme model: the first replaces the usual Skyrme term with a term that is sixth order in derivatives, and the second includes a potential that is quartic in the pion fields. Solitons in the first model are shown to deviate significantly from ansätze previously assumed in the literature. The binding energies obtained in both models are lower than those obtained from the standard Skyrme model, and those obtained in the second model are close to the experimental values.

  2. Structural and dynamic properties of linker histone H1 binding to DNA

    CERN Document Server

    Dootz, Rolf; Pfohl, Thomas

    2010-01-01

    Found in all eukaryotic cells, linker histones H1 are known to bind to and rearrange nucleosomal linker DNA. In vitro, the fundamental nature of H1/DNA interactions has attracted wide interest among research communities - for biologists from a chromatin organization deciphering point of view, and for physicists from the study of polyelectrolyte interactions point of view. Hence, H1/DNA binding processes, structural and dynamical information about these self-assemblies is of broad importance. Targeting a quantitative understanding of H1 induced DNA compaction mechanisms our strategy is based on using small angle X-ray microdiffraction in combination with microfluidics. The usage of microfluidic hydrodynamic focusing devices facilitate a microscale control of these self-assembly processes. In addition, the method enables time-resolved access to structure formation in situ, in particular to transient intermediate states. The observed time dependent structure evolution shows that the interaction of H1 with DNA ca...

  3. Pre-replication assembly of E. coli replisome components.

    Science.gov (United States)

    den Blaauwen, Tanneke; Aarsman, Mirjam E G; Wheeler, Linda J; Nanninga, Nanne

    2006-11-01

    The localization of SeqA, thymidylate synthase, DnaB (helicase) and the DNA polymerase components alpha and tau, has been studied by immunofluorescence microscopy. The origin has been labelled through GFP-LacI bound near oriC. SeqA was located in the cell centre for one replication factory (RF) and at 1/4 and 3/4 positions in pre-divisional cells harbouring two RFs. The transition of central to 1/4 and 3/4 positions of SeqA appeared abrupt. Labelled thymidylate synthetase was found all over the cell, thus not supporting the notion of a dNTP-synthesizing complex exclusively localized near the RF. More DnaB, alpha and tau foci were found than expected. We have hypothesized that extra foci arise at pre-replication assembly sites, where the number of sites equals the number of origins, i.e. the number of future RFs. A reasonable agreement was found between predicted and found foci. In the case of multifork replication the number of foci appeared consistent with the assumption that three RFs are grouped into a higher-order structure. The RF is probably separate from the foci containing SeqA and the hemi-methylated SeqA binding sites because these foci did not coincide significantly with DnaB as marker of the RF. Co-labelling of DnaB and oriC revealed limited colocalization, indicating that DnaB did not yet become associated with oriC at a pre-replication assembly site. DnaB and tau co-labelled in the cell centre, though not at presumed pre-replication assembly sites. By contrast, alpha and tau co-labelled consistently suggesting that they are already associated before replication starts.

  4. Pre-replication assembly of E. coli replisome components.

    Science.gov (United States)

    den Blaauwen, Tanneke; Aarsman, Mirjam E G; Wheeler, Linda J; Nanninga, Nanne

    2006-11-01

    The localization of SeqA, thymidylate synthase, DnaB (helicase) and the DNA polymerase components alpha and tau, has been studied by immunofluorescence microscopy. The origin has been labelled through GFP-LacI bound near oriC. SeqA was located in the cell centre for one replication factory (RF) and at 1/4 and 3/4 positions in pre-divisional cells harbouring two RFs. The transition of central to 1/4 and 3/4 positions of SeqA appeared abrupt. Labelled thymidylate synthetase was found all over the cell, thus not supporting the notion of a dNTP-synthesizing complex exclusively localized near the RF. More DnaB, alpha and tau foci were found than expected. We have hypothesized that extra foci arise at pre-replication assembly sites, where the number of sites equals the number of origins, i.e. the number of future RFs. A reasonable agreement was found between predicted and found foci. In the case of multifork replication the number of foci appeared consistent with the assumption that three RFs are grouped into a higher-order structure. The RF is probably separate from the foci containing SeqA and the hemi-methylated SeqA binding sites because these foci did not coincide significantly with DnaB as marker of the RF. Co-labelling of DnaB and oriC revealed limited colocalization, indicating that DnaB did not yet become associated with oriC at a pre-replication assembly site. DnaB and tau co-labelled in the cell centre, though not at presumed pre-replication assembly sites. By contrast, alpha and tau co-labelled consistently suggesting that they are already associated before replication starts. PMID:16999830

  5. MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning

    OpenAIRE

    , Afiahayati; Sato, Kengo; Sakakibara, Yasubumi

    2014-01-01

    The assembly of multiple genomes from mixed sequence reads is a bottleneck in metagenomic analysis. A single-genome assembly program (assembler) is not capable of resolving metagenome sequences, so assemblers designed specifically for metagenomics have been developed. MetaVelvet is an extension of the single-genome assembler Velvet. It has been proved to generate assemblies with higher N50 scores and higher quality than single-genome assemblers such as Velvet and SOAPdenovo when applied to me...

  6. Peptide Arrays for Binding Studies of E3 Ubiquitin Ligases.

    Science.gov (United States)

    Klecker, Maria; Dissmeyer, Nico

    2016-01-01

    The automated SPOT (synthetic peptide arrays on membrane support technique) synthesis technology has entrenched as a rapid and robust method to generate peptide libraries on cellulose membrane supports. The synthesis method is based on conventional Fmoc chemistry building up peptides with free N-terminal amino acids starting at their cellulose-coupled C-termini. Several hundreds of peptide sequences can be assembled with this technique on one membrane comprising a strong binding potential due to high local peptide concentrations. Peptide orientation on SPOT membranes qualifies this array type for assaying substrate specificities of N-recognins, the recognition elements of the N-end rule pathway of targeted protein degradation (NERD). Pioneer studies described binding capability of mammalian and yeast enzymes depending on a peptide's N-terminus. SPOT arrays have been successfully used to describe substrate specificity of N-recognins which are the recognition elements of the N-end rule pathway of targeted protein degradation (NERD). Here, we describe the implementation of SPOT binding assays with focus on the identification of N-recognin substrates, applicable also for plant NERD enzymes. PMID:27424747

  7. Early fibrillin-1 assembly monitored through a modifiable recombinant cell approach

    Science.gov (United States)

    Hubmacher, Dirk; Bergeron, Eric; Fagotto-Kaufmann, Christine; Sakai, Lynn Y.; Reinhardt, Dieter P.

    2016-01-01

    Fibrillin proteins constitute the backbone of extracellular macromolecular microfibrils. Mutations in fibrillins cause heritable connective tissue disorders, including Marfan syndrome, dominant Weill-Marchesani syndrome, and stiff skin syndrome. Fibronectin provides a critical scaffold for microfibril assembly in cell culture models. Full length recombinant fibrillin-1 was expressed by HEK 293 cells, which deposited the secreted protein in a punctate pattern on the cell surface. Co-cultured fibroblasts consistently triggered assembly of recombinant fibrillin-1, which was dependent on a fibronectin network formed by the fibroblasts. Deposition of recombinant fibrillin-1 on fibronectin fibers occurred first in discrete packages that subsequently extended along fibronectin fibers. Mutant fibrillin-1 harboring either a cysteine 204 to serine mutation or a RGD to RGA mutation which prevents integrin binding, did not affect fibrillin-1 assembly. In conclusion, we developed a modifiable recombinant full-length fibrillin-1 assembly system that allows for rapid analysis of critical roles in fibrillin assembly and functionality. This system can be used to study the contributions of specific residues, domains or regions of fibrillin-1 to the biogenesis and functionality of microfibrils. It provides also a method to evaluate disease-causing mutations, and to produce microfibril-containing matrices for tissue engineering applications for example in designing novel vascular grafts or stents. PMID:24559401

  8. Unique self-assembly properties of a bridge-shaped protein dimer with quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jianhao; Jiang, Pengju [Changzhou University, School of Pharmaceutical Engineering and Life Science (China); Gao, Liqian; Yu, Yongsheng; Lu, Yao [The Chinese University of Hong Kong, Department of Chemistry (Hong Kong, China) (China); Qiu, Lin; Wang, Cheli [Changzhou University, School of Pharmaceutical Engineering and Life Science (China); Xia, Jiang, E-mail: jiangxia@cuhk.edu.hk [The Chinese University of Hong Kong, Department of Chemistry (Hong Kong, China) (China)

    2013-09-15

    How protein-protein interaction affects protein-nanoparticle self-assembly is the key to the understanding of biomolecular coating of nanoparticle in biological fluids. However, the relationship between protein shape and its interaction with nanoparticles is still under-exploited because of lack of a well-conceived binding system and a method to detect the subtle change in the protein-nanoparticle assemblies. Noticing this unresolved need, we cloned and expressed a His-tagged SpeA protein that adopts a bridge-shaped dimer structure, and utilized a high-resolution capillary electrophoresis method to monitor assembly formation between the protein and quantum dots (QDs, 5 nm in diameter). We observed that the bridge-shaped structure rendered a low SpeA:QD stoichiometry at saturation. Also, close monitoring of imidazole (Im) displacement of surface-bound protein revealed a unique two-step process. High-concentration Im could displace surface-bound SpeA protein and form a transient QD-protein intermediate, through a kinetically controlled displacement process. An affinity-driven equilibrium step then followed, resulting in re-assembling of the QD-protein complex in about 1 h. Through a temporarily formed intermediate, Im causes a rearrangement of His-tagged proteins on the surface. Thus, our work showcases that the synergistic interplay between QD-His-tag interaction and protein-protein interaction can result in unique properties of protein-nanoparticle assembly for the first time.

  9. Synthesis of self-assembly plasmonic silver nanoparticles with tunable luminescence color

    Energy Technology Data Exchange (ETDEWEB)

    Al-Ghamdi, Haifa S.; Mahmoud, Waleed E., E-mail: w_e_mahmoud@yahoo.com

    2014-01-15

    Assembly is an elegant and effective bottom-up approach to prepare arrays of nanoparticles from nobel metals. Noble metal nanoparticles are perfect building blocks because they can be prepared with an adequate functionalization to allow their assembly and with controlled sizes. Herein, we report a novel recipe for the synthesis of self-assembled silver nanoparticles with tunable optical properties and sizes. The synthetic route followed here based on the covalent binding among silver nanoparticles by means of poly vinyl alcohol for the first time. The size of silver nanoparticle is governed by varying the amount of sodium borohydride. The as-synthesized nanoparticles were characterized by transmission electron microscopy, x-ray diffraction, energy dispersive x-ray spectroscopy, selected area electron diffraction and UV–vis spectroscopy. Results depicted that self-assembly of mono-dispersed silver nanoparticles with different sizes have been achieved. The silver nanostructure has a single crystalline faced centered cubic structure with growth orientation along (1 1 1) facet. These nanoparticles exhibited localized surface plasmon resonance at 403 nm. The luminescence peaks were red-sifted from violet to green due to the increase of the particle sizes. -- Highlights: • Self-assembled silver nanoparticles based PVA were synthesized. • NaBH{sub 4} amount was found particle size dependent. • Silver nanoparticles strongly affected the surface plasmon resonance. • Highly symmetric luminescence emission band narrow width is obtained. • Dark field image showed a tunable color change from violet to green.

  10. Synthetic heparin-binding growth factor analogs

    Science.gov (United States)

    Pena, Louis A.; Zamora, Paul; Lin, Xinhua; Glass, John D.

    2007-01-23

    The invention provides synthetic heparin-binding growth factor analogs having at least one peptide chain that binds a heparin-binding growth factor receptor, covalently bound to a hydrophobic linker, which is in turn covalently bound to a non-signaling peptide that includes a heparin-binding domain. The synthetic heparin-binding growth factor analogs are useful as soluble biologics or as surface coatings for medical devices.

  11. Formal Verification of Self-Assembling Systems

    CERN Document Server

    Sterling, Aaron

    2010-01-01

    This paper introduces the theory and practice of formal verification of self-assembling systems. We interpret a well-studied abstraction of nanomolecular self assembly, the Abstract Tile Assembly Model (aTAM), into Computation Tree Logic (CTL), a temporal logic often used in model checking. We then consider the class of "rectilinear" tile assembly systems. This class includes most aTAM systems studied in the theoretical literature, and all (algorithmic) DNA tile self-assembling systems that have been realized in laboratories to date. We present a polynomial-time algorithm that, given a tile assembly system T as input, either provides a counterexample to T's rectilinearity or verifies whether T has a unique terminal assembly. Using partial order reductions, the verification search space for this algorithm is reduced from exponential size to O(n^2), where n x n is the size of the assembly surface. That reduction is asymptotically the best possible. We report on experimental results obtained by translating tile ...

  12. Uracil Excision for Assembly of Complex Pathways

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  13. Assembly of the CMS hadronic calorimeter

    CERN Multimedia

    Maximilien Brice

    2004-01-01

    The hadronic calorimeter is assembled on the end-cap of the CMS detector in the assembly hall. Hadronic calorimeters measure the energy of particles that interact via the strong force, called hadrons. The detectors are made in a sandwich-like structure where these scintillator tiles are placed between metal sheets.

  14. 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).

  15. 49 CFR 570.63 - Wheel assemblies.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 6 2010-10-01 2010-10-01 false Wheel assemblies. 570.63 Section 570.63 Transportation Other Regulations Relating to Transportation (Continued) NATIONAL HIGHWAY TRAFFIC SAFETY... 10,000 Pounds § 570.63 Wheel assemblies. (a) Wheel integrity. A tire rim, wheel disc or spider...

  16. Fibril assembly in whey protein mixtures

    NARCIS (Netherlands)

    Bolder, S.G.

    2007-01-01

    The objective of this thesis was to study fibril assembly in mixtures of whey proteins. The effect of the composition of the protein mixture on the structures and the resulting phase behaviour was investigated. The current work has shown that beta-lactoglobulin is responsible for the fibril assembly

  17. Microfabricated field calibration assembly for analytical instruments

    Science.gov (United States)

    Robinson, Alex L.; Manginell, Ronald P.; Moorman, Matthew W.; Rodacy, Philip J.; Simonson, Robert J.

    2011-03-29

    A microfabricated field calibration assembly for use in calibrating analytical instruments and sensor systems. The assembly comprises a circuit board comprising one or more resistively heatable microbridge elements, an interface device that enables addressable heating of the microbridge elements, and, in some embodiments, a means for positioning the circuit board within an inlet structure of an analytical instrument or sensor system.

  18. Aerodynamic seal assemblies for turbo-machinery

    Energy Technology Data Exchange (ETDEWEB)

    Bidkar, Rahul Anil; Wolfe, Christopher; Fang, Biao

    2015-09-29

    The present application provides an aerodynamic seal assembly for use with a turbo-machine. The aerodynamic seal assembly may include a number of springs, a shoe connected to the springs, and a secondary seal positioned about the springs and the shoe.

  19. Self-assembled nanogaps for molecular electronics

    DEFF Research Database (Denmark)

    Tang, Qingxin; Tong, Yanhong; Jain, Titoo;

    2009-01-01

    A nanogap for molecular devices was realized using solution-based self-assembly. Gold nanorods were assembled to gold nanoparticle-coated conducting SnO2:Sb nanowires via thiol end-capped oligo(phenylenevinylene)s (OPVs). The molecular gap was easily created by the rigid molecule itself during se...

  20. 49 CFR 572.192 - Head assembly.

    Science.gov (United States)

    2010-10-01

    ... CFR 572.112(a). (c) Performance criteria. (1) When the head assembly is dropped from either the right...) and a set of three (3) accelerometers in conformance with specifications in 49 CFR 572.200(d) and... 49 Transportation 7 2010-10-01 2010-10-01 false Head assembly. 572.192 Section...