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Sample records for binding mrnp assembly

  1. Nuclear surveillance of mRNP formation

    DEFF Research Database (Denmark)

    Jensen, Torben Heick

    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...... 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...

  2. A Y-box protein/RNA helicase complex links mRNP assembly on the gene to mRNA translation

    OpenAIRE

    Nashchekin, Dmitri

    2006-01-01

    Immediately upon transcription, messenger RNA molecules become associated with proteins to form ribonucleoprotein (RNP) complexes, usually called mRNP particles. The mRNPs are the actual targets for regulation and dictate the fate of an mRNA in the gene expression pathway. To understand the molecular basis of mRNP formation on the gene, export and translation the behaviour of the mRNP proteins have to be investigated. In the salivary glands of the dipteran Chironomus tentans...

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

    Directory of Open Access Journals (Sweden)

    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.

  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. 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...

  6. 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

  7. 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

    stably to the APC/C. Whether MCC formation per se is sufficient for a functional SAC or MCC association with the APC/C is required remains unclear. Here, we analyze the role of two conserved motifs in Cdc20, IR and C-Box, in binding of the MCC to the APC/C. Mutants in both motifs assemble the MCC...

  8. A BPTTF-based self-assembled electron-donating triangle capable of C60 binding.

    Science.gov (United States)

    Goeb, Sébastien; Bivaud, Sébastien; Dron, Paul Ionut; Balandier, Jean-Yves; Chas, Marcos; Sallé, Marc

    2012-03-25

    A kinetically stable self-assembled redox-active triangle is isolated. The resulting electron-donating cavity, which incorporates three BPTTF units, exhibits a remarkable binding ability for electron-deficient C(60), supported by a favorable combination of structural and electronic features. PMID:22344044

  9. 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.

  10. 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.

  11. 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.

  12. Monomeric myosin V uses two binding regions for the assembly of stable translocation complexes

    OpenAIRE

    Heuck, Alexander; Du, Tung-Gia; Jellbauer, Stephan; Richter, Klaus; Kruse, Claudia; Jaklin, Sigrun; Müller, Marisa; Buchner, Johannes; Jansen, Ralf-Peter; Niessing, Dierk

    2007-01-01

    Myosin-motors are conserved from yeast to human and transport a great variety of cargoes. Most plus-end directed myosins, which constitute the vast majority of all myosin motors, form stable dimers and interact constitutively with their cargo complexes. To date, little is known about regulatory mechanisms for cargo-complex assembly. In this study, we show that the type V myosin Myo4p binds to its cargo via two distinct binding regions, the C-terminal tail and a coiled-coil domain-containing f...

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

    OpenAIRE

    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 sub...

  14. Entropy driven binding of the alkaloid chelerythrine to polyadenylic acid leads to spontaneous self-assembled structure formation

    International Nuclear Information System (INIS)

    Highlights: • The interaction of chelerythrine to polyadenylic acid has been characterized. • The strongly positive entropy change is due to structural reorganization. • The binding was cooperative with affinity of the order of 107 M−1. • The binding was enhanced with [Na+]. • Self-assembled structure induction in poly(A) occurred spontaneously. - Abstract: The binding thermodynamics and interaction of the putative anticancer alkaloid chelerythrine with polyadenylic acid were investigated by isothermal titration calorimetry, absorption and fluorescence spectroscopy, circular dichroism, differential scanning calorimetry and thermal melting experiments. The equilibrium binding constant was evaluated to be of the order of 107 M−1. Strong positive entropic and favorable enthalpic contributions to the binding were revealed. The binding affinity was enhanced within (10 to 100) mM Na+ concentration. Circular dichroism spectra confirmed that the increase in entropy change was caused by a strong conformational change in the RNA polynucleotide. Absorption and circular dichroism melting studies revealed that chelerythrine binding induced self-assembled duplex structure formation in poly(A) molecules resulting in a cooperative melting profile. This was further confirmed from differential scanning calorimetry data. The intercalation binding of the alkaloid involved strong energy transfer from the polynucleotide bases to the bound alkaloid molecules. The remarkably high entropy driven binding of the alkaloid induced spontaneous self-assembled structure formation in poly(A) and the associated binding affinity is the highest so far reported for a small molecule binding to poly(A)

  15. 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.

  16. Interdomain allostery promotes assembly of the poly(A) mRNA complex with PABP and eIF4G.

    Science.gov (United States)

    Safaee, Nozhat; Kozlov, Guennadi; Noronha, Anne M; Xie, Jingwei; Wilds, Christopher J; Gehring, Kalle

    2012-11-01

    Many RNA-binding proteins contain multiple single-strand nucleic acid-binding domains and assemble into large multiprotein messenger ribonucleic acid protein (mRNP) complexes. The mechanisms underlying the self-assembly of these complexes are largely unknown. In eukaryotes, the association of the translation factors polyadenylate-binding protein-1 (PABP) and eIF4G is essential for high-level expression of polyadenylated mRNAs. Here, we report the crystal structure of the ternary complex poly(A)(11)·PABP(1-190)·eIF4G(178-203) at 2.0 Å resolution. Our NMR and crystallographic data show that eIF4G interacts with the RRM2 domain of PABP. Analysis of the interaction by small-angle X-ray scattering, isothermal titration calorimetry, and electromobility shift assays reveals that this interaction is allosterically regulated by poly(A) binding to PABP. Furthermore, we have confirmed the importance of poly(A) for the endogenous PABP and eIF4G interaction in immunoprecipitation experiments using HeLa cell extracts. Our findings reveal interdomain allostery as a mechanism for cooperative assembly of RNP complexes. PMID:23041282

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

    Directory of Open Access Journals (Sweden)

    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.

  18. Conserved SMP domains of the ERMES complex bind phospholipids and mediate tether assembly

    Science.gov (United States)

    AhYoung, Andrew P.; Jiang, Jiansen; Zhang, Jiang; Khoi Dang, Xuan; Loo, Joseph A.; Zhou, Z. Hong; Egea, Pascal F.

    2015-01-01

    Membrane contact sites (MCS) between organelles are proposed as nexuses for the exchange of lipids, small molecules, and other signals crucial to cellular function and homeostasis. Various protein complexes, such as the endoplasmic reticulum-mitochondrial encounter structure (ERMES), function as dynamic molecular tethers between organelles. Here, we report the reconstitution and characterization of subcomplexes formed by the cytoplasm-exposed synaptotagmin-like mitochondrial lipid-binding protein (SMP) domains present in three of the five ERMES subunits—the soluble protein Mdm12, the endoplasmic reticulum (ER)-resident membrane protein Mmm1, and the mitochondrial membrane protein Mdm34. SMP domains are conserved lipid-binding domains found exclusively in proteins at MCS. We show that the SMP domains of Mdm12 and Mmm1 associate into a tight heterotetramer with equimolecular stoichiometry. Our 17-Å-resolution EM structure of the complex reveals an elongated crescent-shaped particle in which two Mdm12 subunits occupy symmetric but distal positions at the opposite ends of a central ER-anchored Mmm1 homodimer. Rigid body fitting of homology models of these SMP domains in the density maps reveals a distinctive extended tubular structure likely traversed by a hydrophobic tunnel. Furthermore, these two SMP domains bind phospholipids and display a strong preference for phosphatidylcholines, a class of phospholipids whose exchange between the ER and mitochondria is essential. Last, we show that the three SMP-containing ERMES subunits form a ternary complex in which Mdm12 bridges Mmm1 to Mdm34. Our findings highlight roles for SMP domains in ERMES assembly and phospholipid binding and suggest a structure-based mechanism for the facilitated transport of phospholipids between organelles. PMID:26056272

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

    Directory of Open Access Journals (Sweden)

    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.

  20. Calcium-Binding Capacity of Centrin2 Is Required for Linear POC5 Assembly but Not for Nucleotide Excision Repair

    Science.gov (United States)

    Dantas, Tiago J.; Daly, Owen M.; Conroy, Pauline C.; Tomas, Martin; Wang, Yifan; Lalor, Pierce; Dockery, Peter; Ferrando-May, Elisa; Morrison, Ciaran G.

    2013-01-01

    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. PMID:23844208

  1. The actin-binding ERM protein Moesin directly regulates spindle assembly and function during mitosis.

    Science.gov (United States)

    Vilmos, Péter; Kristó, Ildikó; Szikora, Szilárd; Jankovics, Ferenc; Lukácsovich, Tamás; Kari, Beáta; Erdélyi, Miklós

    2016-06-01

    Ezrin-Radixin-Moesin proteins are highly conserved, actin-binding cytoskeletal proteins that play an essential role in microvilli formation, T-cell activation, and tumor metastasis by linking actin filaments to the plasma membrane. Recent studies demonstrated that the only Ezrin-Radixin-Moesin protein of Drosophila melanogaster, Moesin, is involved in mitotic spindle function through stabilizing cell shape and microtubules at the cell cortex. We previously observed that Moesin localizes to the mitotic spindle; hence, we tested for the biological significance of this surprising localization and investigated whether it plays a direct role in spindle function. To separate the cortical and spindle functions of Moesin during mitosis we combined cell biological and genetic methods. We used early Drosophila embryos, in which mitosis occurs in the absence of a cell cortex, and found in vivo evidence for the direct requirement of Moesin in mitotic spindle assembly and function. We also found that the accumulation of Moesin precedes the construction of the microtubule spindle, and the fusiform structure formed by Moesin persists even after the microtubules have disassembled. PMID:27006187

  2. Selective Binding, Self-Assembly and Nanopatterning of the Creutz-Taube Ion on Surfaces

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    Qingling Hang

    2009-02-01

    Full Text Available The surface attachment properties of the Creutz-Taube ion, i.e., [(NH35Ru(pyrazineRu(NH35]5+, on both hydrophilic and hydrophobic types of surfaces were investigated using X-ray photoelectron spectroscopy (XPS. The results indicated that the Creutz-Taube ions only bound to hydrophilic surfaces, such as SiO2 and –OH terminated organic SAMs on gold substrates. No attachment of the ions on hydrophobic surfaces such as –CH3 terminated organic SAMs and poly(methylmethacrylate (PMMA thin films covered gold or SiO2 substrates was observed. Further ellipsometric, atomic force microscopy (AFM and time-dependent XPS studies suggested that the attached cations could form an inorganic analog of the self-assembled monolayer on SiO2 substrate with a “lying-down” orientation. The strong electrostatic interaction between the highly charged cations and the anionic SiO2 surface was believed to account for these observations. Based on its selective binding property, patterning of wide (~200 nm and narrow (~35 nm lines of the Creutz-Taube ions on SiO2 surface were demonstrated through PMMA electron resist masks written by electron beam lithography (EBL.

  3. Discovery of a chlorophyll binding protein complex involved in the early steps of photosystem II assembly in Synechocystis.

    Science.gov (United States)

    Knoppová, Jana; Sobotka, Roman; Tichy, Martin; Yu, Jianfeng; Konik, Peter; Halada, Petr; Nixon, Peter J; Komenda, Josef

    2014-03-01

    Efficient assembly and repair of the oxygen-evolving photosystem II (PSII) complex is vital for maintaining photosynthetic activity in plants, algae, and cyanobacteria. How chlorophyll is delivered to PSII during assembly and how vulnerable assembly complexes are protected from photodamage are unknown. Here, we identify a chlorophyll and β-carotene binding protein complex in the cyanobacterium Synechocystis PCC 6803 important for formation of the D1/D2 reaction center assembly complex. It is composed of putative short-chain dehydrogenase/reductase Ycf39, encoded by the slr0399 gene, and two members of the high-light-inducible protein (Hlip) family, HliC and HliD, which are small membrane proteins related to the light-harvesting chlorophyll binding complexes found in plants. Perturbed chlorophyll recycling in a Ycf39-null mutant and copurification of chlorophyll synthase and unassembled D1 with the Ycf39-Hlip complex indicate a role in the delivery of chlorophyll to newly synthesized D1. Sequence similarities suggest the presence of a related complex in chloroplasts. PMID:24681620

  4. 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.

  5. 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...

  6. Fibronectin Binding to the Treponema pallidum Adhesin Protein Fragment rTp0483 on Functionalized Self-Assembled Monolayers

    Science.gov (United States)

    Dickerson, Matthew T.; Abney, Morgan B.; Cameron, Caroline E.; Knecht, Marc; Bachas, Leonidas G.; Anderson, Kimberly W.

    2012-01-01

    Past work has shown that Treponema pallidum, the causative agent of syphilis, binds host fibronectin (FN). FN and other host proteins are believed to bind to rare outer membrane proteins (OMPs) of T. pallidum, and it is postulated that this interaction may facilitate cell attachment and mask antigenic targets on the surface. This research seeks to prepare a surface capable of mimicking the FN binding ability of T. pallidum in order to investigate the impact of FN binding with adsorbed Tp0483 on the host response to the surface. By understanding this interaction it may be possible to develop more effective treatments for infection and possibly mimic the stealth properties of the bacteria. Functionalized self-assembled monolayers (SAMs) on0 gold were used to investigate rTp0483 and FN adsorption. Using a quartz crystal microbalance (QCM) rTp0483 adsorption and subsequent FN adsorption onto rTp0483 was determined to be higher on negatively charged carboxylate-terminated self-assembled monolayers (−COO− SAMs) compared to the other surfaces analyzed. Kinetic analysis of rTp0483 adsorption using surface plasmon resonance (SPR) supported this finding. Kinetic analysis of FN adsorption using SPR revealed a multi-step event, where the concentration of immobilized rTp0483 plays a role in FN binding. An examination of relative QCM dissipation energy compared to the shift in frequency showed a correlation between the physical properties of adsorbed rTp0483 and SAM surface chemistry. In addition, AFM images of rTp0483 on selected SAMs illustrated a preference of rTp0483 to bind as aggregates. Adsorption on −COO− SAMs was more uniform across the surface, which may help further explain why FN bound more strongly. rTp0483 antibody studies suggested the involvement of amino acids 274–289 and 316–333 in binding between rTp0483 to FN, while a peptide blocking study only showed inhibition of binding with amino acids 316–333. Finally, surface adsorbed rTp0483 with FN

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

    Science.gov (United States)

    Gallie, Daniel R

    2014-09-01

    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 5'-leader that would otherwise impede scanning of the 40 S subunit during initiation. The poly(A) binding protein (PABP), which binds the poly(A) tail, interacts with eIF4G and eIF4B to promote circularization of an mRNA and stimulates translation by promoting 40 S subunit recruitment. Thus, these factors serve essential functions in the early steps of protein synthesis. Their assembly and function requires multiple interactions that are competitive in nature and determine the nature of interactions between the termini of an mRNA. In this review, the domain organization and partner protein interactions are presented for the factors in plants which share similarities with those in animals and yeast but differ in several important respects. The functional consequences of their interactions on factor activity are also discussed. PMID:26779409

  8. Assembly and iron-binding properties of human frataxin, the protein deficient in Friedreich ataxia

    Czech Academy of Sciences Publication Activity Database

    Cavadini, P.; ONeill, H.; Benada, Oldřich; Isaya, G.

    2002-01-01

    Roč. 11, č. 3 (2002), s. 217-227. ISSN 0964-6906 Institutional research plan: CEZ:AV0Z5020903 Keywords : assembly * human * frataxin Subject RIV: EE - Microbiology, Virology Impact factor: 8.726, year: 2002

  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. Poly(A) binding protein abundance regulates eukaryotic translation initiation factor 4F assembly in human cytomegalovirus-infected cells.

    Science.gov (United States)

    McKinney, Caleb; Perez, Cesar; Mohr, Ian

    2012-04-10

    By commandeering cellular translation initiation factors, or destroying those dispensable for viral mRNA translation, viruses often suppress host protein synthesis. In contrast, cellular protein synthesis proceeds in human cytomegalovirus (HCMV)-infected cells, forcing viral and cellular mRNAs to compete for limiting translation initiation factors. Curiously, inactivating the host translational repressor 4E-BP1 in HCMV-infected cells stimulates synthesis of the cellular poly(A) binding protein (PABP), significantly increasing PABP abundance. Here, we establish that new PABP synthesis is translationally controlled by the HCMV-encoded UL38 mammalian target of rapamycin complex 1-activator. The 5' UTR within the mRNA encoding PABP contains a terminal oligopyrimidine (TOP) element found in mRNAs, the translation of which is stimulated in response to mitogenic, growth, and nutritional stimuli, and proteins encoded by TOP-containing mRNAs accumulated in HCMV-infected cells. Furthermore, UL38 expression was necessary and sufficient to regulate expression of a PABP TOP-containing reporter. Remarkably, preventing the rise in PABP abundance by RNAi impaired eIF4E binding to eIF4G, thereby reducing assembly of the multisubunit initiation factor eIF4F, viral protein production, and replication. This finding demonstrates that viruses can increase host translation initiation factor concentration to foster their replication and defines a unique mechanism whereby control of PABP abundance regulates eIF4F assembly. PMID:22431630

  11. 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

  12. Assembly of an antiparallel homo-adenine DNA duplex by small-molecule binding.

    Science.gov (United States)

    Persil, Ozgül; Santai, Catherine T; Jain, Swapan S; Hud, Nicholas V

    2004-07-21

    Molecules that reversibly bind DNA and trigger the formation of non-Watson-Crick secondary structures would be useful in the design of dynamic DNA nanostructures and as potential leads for new therapeutic agents. We demonstrate that coralyne, a small crescent-shaped molecule, promotes the formation of a duplex secondary structure from homo-adenine oligonucleotides. AFM studies reveal that the staggered alignment of homo-adenine oligonucleotides upon coralyne binding produces polymers of micrometers in length, but only 2 nm in height. A DNA duplex was also studied that contained eight A.A mismatches between two flanking 7-bp Watson-Crick helices. CD spectra confirm that the multiple A.A mismatches of this duplex bind coralyne in manner similar to that of homo-adenine oligonucleotides. Furthermore, the melting temperature of this hybrid duplex increases by 13 degrees C upon coralyne binding. These observations illustrate that the helical structure of the homo-adenine-coralyne duplex is compatible with the B-form DNA helix. PMID:15250704

  13. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo

    OpenAIRE

    Bestman, Jennifer E.; Cline, Hollis T.

    2008-01-01

    Visual system development requires experience-dependent mechanisms that regulate neuronal structure and function, including dendritic arbor growth, synapse formation, and stabilization. Although RNA binding proteins have been shown to affect some forms of synaptic plasticity in adult animals, their role in the development of neuronal structure and functional circuitry is not clear. Using two-photon time-lapse in vivo imaging and electrophysiology combined with morpholino-mediated knockdown an...

  14. Role of Rck-Pat1b binding in assembly of processing-bodies

    OpenAIRE

    Ozgur, Sevim; Stoecklin, Georg

    2013-01-01

    The DEAD box RNA helicase Rck and the scaffold protein Pat1b participate in controlling gene expression at the post-transcriptional level by suppressing mRNA translation and promoting mRNA decapping. In addition, both proteins are required for the assembly of processing (P)-bodies, cytoplasmic foci that contain stalled mRNAs and numerous components of the mRNA decay machinery. The C-terminal RecA-like domain of Rck interacts with the N-terminal acidic domain of Pat1b. Here, we identified poin...

  15. A spectroscopic method to estimate the binding potency of amphiphile assemblies

    Czech Academy of Sciences Publication Activity Database

    Gauger, D. R.; Andrushchenko, Valery; Bouř, Petr; Pohle, W.

    2010-01-01

    Roč. 398, č. 2 (2010), s. 1109-1123. ISSN 1618-2642 R&D Projects: GA ČR GA203/06/0420; GA ČR GA202/07/0732; GA ČR GAP208/10/0559; GA AV ČR IAA400550702; GA AV ČR IAA400550701 Institutional research plan: CEZ:AV0Z40550506 Keywords : miccels * amphiphile assemblies * molecular dynamics * infrared spectroscopy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.841, year: 2010

  16. Assembly, molecular organization, and membrane-binding properties of development-specific septins.

    Science.gov (United States)

    Garcia, Galo; Finnigan, Gregory C; Heasley, Lydia R; Sterling, Sarah M; Aggarwal, Adeeti; Pearson, Chad G; Nogales, Eva; McMurray, Michael A; Thorner, Jeremy

    2016-02-29

    Septin complexes display remarkable plasticity in subunit composition, yet how a new subunit assembled into higher-order structures confers different functions is not fully understood. Here, this question is addressed in budding yeast, where during meiosis Spr3 and Spr28 replace the mitotic septin subunits Cdc12 and Cdc11 (and Shs1), respectively. In vitro, the sole stable complex that contains both meiosis-specific septins is a linear Spr28-Spr3-Cdc3-Cdc10-Cdc10-Cdc3-Spr3-Spr28 hetero-octamer. Only coexpressed Spr3 and Spr28 colocalize with Cdc3 and Cdc10 in mitotic cells, indicating that incorporation requires a Spr28-Spr3 protomer. Unlike their mitotic counterparts, Spr28-Spr3-capped rods are unable to form higher-order structures in solution but assemble to form long paired filaments on lipid monolayers containing phosphatidylinositol-4,5-bisphosphate, mimicking presence of this phosphoinositide in the prospore membrane. Spr28 and Spr3 fail to rescue the lethality of a cdc11Δ cdc12Δ mutant, and Cdc11 and Cdc12 fail to restore sporulation proficiency to spr3Δ/spr3Δ spr28Δ/spr28Δ diploids. Thus, specific meiotic and mitotic subunits endow septin complexes with functionally distinct properties. PMID:26929450

  17. C11orf83, a mitochondrial cardiolipin-binding protein involved in bc1 complex assembly and supercomplex stabilization.

    Science.gov (United States)

    Desmurs, Marjorie; Foti, Michelangelo; Raemy, Etienne; Vaz, Frédéric Maxime; Martinou, Jean-Claude; Bairoch, Amos; Lane, Lydie

    2015-04-01

    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

  18. Regulation of spindle pole body assembly and cytokinesis by the centrin-binding protein Sfi1 in fission yeast.

    Science.gov (United States)

    Lee, I-Ju; Wang, Ning; Hu, Wen; Schott, Kersey; Bähler, Jürg; Giddings, Thomas H; Pringle, John R; Du, Li-Lin; Wu, Jian-Qiu

    2014-09-15

    Centrosomes play critical roles in the cell division cycle and ciliogenesis. Sfi1 is a centrin-binding protein conserved from yeast to humans. Budding yeast Sfi1 is essential for the initiation of spindle pole body (SPB; yeast centrosome) duplication. However, the recruitment and partitioning of Sfi1 to centrosomal structures have never been fully investigated in any organism, and the presumed importance of the conserved tryptophans in the internal repeats of Sfi1 remains untested. Here we report that in fission yeast, instead of doubling abruptly at the initiation of SPB duplication and remaining at a constant level thereafter, Sfi1 is gradually recruited to SPBs throughout the cell cycle. Like an sfi1Δ mutant, a Trp-to-Arg mutant (sfi1-M46) forms monopolar spindles and exhibits mitosis and cytokinesis defects. Sfi1-M46 protein associates preferentially with one of the two daughter SPBs during mitosis, resulting in a failure of new SPB assembly in the SPB receiving insufficient Sfi1. Although all five conserved tryptophans tested are involved in Sfi1 partitioning, the importance of the individual repeats in Sfi1 differs. In summary, our results reveal a link between the conserved tryptophans and Sfi1 partitioning and suggest a revision of the model for SPB assembly. PMID:25031431

  19. 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

  20. 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...

  1. 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

  2. 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.

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

    International Nuclear Information System (INIS)

    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

  4. 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.; Gerdes, Kenn; Brodersen, Ditlev

    2011-01-01

    the crystal structure of the intact Shigella flexneri VapBC TA complex, determined to 2.7 Å resolution. Both in solution and in the crystal structure, four molecules of each protein combine to form a large and globular hetero-octameric assembly with SpoVT/AbrB-type DNA-binding domains at each end and...

  5. Characterization of the myosin light chain kinase from smooth muscle as an actin-binding protein that assembles actin filaments in vitro.

    Science.gov (United States)

    Hayakawa, K; Okagaki, T; Ye, L H; Samizo, K; Higashi-Fujime, S; Takagi, T; Kohama, K

    1999-05-01

    In addition to its kinase activity, myosin light chain kinase has an actin-binding activity, which results in bundling of actin filaments [Hayakawa et al., Biochem. Biophys. Res. Commun. 199, 786-791, 1994]. There are two actin-binding sites on the kinase: calcium- and calmodulin-sensitive and insensitive sites [Ye et al., J. Biol. Chem. 272, 32182-32189, 1997]. The calcium/calmodulin-sensitive, actin-binding site is located at Asp2-Pro41 and the insensitive site is at Ser138-Met213. The cyanogen bromide fragment, consisting of Asp2-Met213, is furnished with both sites and is the actin-binding core of myosin light chain kinase. Cross-linking between the two sites assembles actin filaments into bundles. Breaking of actin-binding at the calcium/calmodulin-sensitive site by calcium/calmodulin disassembles the bundles. PMID:10231551

  6. 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.

  7. 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

  8. 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.

  9. Assembling of Holotrichia parallela (dark black chafer) midgut tissue transcriptome and identification of midgut proteins that bind to Cry8Ea toxin from Bacillus thuringiensis.

    Science.gov (United States)

    Shu, Changlong; Tan, Shuqian; Yin, Jiao; Soberón, Mario; Bravo, Alejandra; Liu, Chunqing; Geng, Lili; Song, Fuping; Li, Kebin; Zhang, Jie

    2015-09-01

    Holotrichia parallela is one of the most severe crop pests in China, affecting peanut, soybean, and sweet potato crops. Previous work showed that Cry8Ea toxin is highly effective against this insect. In order to identify Cry8Ea-binding proteins in the midgut cells of H. parallela larvae, we assembled a midgut tissue transcriptome by high-throughput sequencing and used this assembled transcriptome to identify Cry8Ea-binding proteins by liquid chromatography-tandem mass spectrometry (LC-MS/MS). First, we obtained de novo sequences of cDNAs from midgut tissue of H. parallela larvae and used available cDNA data in the GenBank. In a parallel assay, we obtained 11 Cry8Ea-binding proteins by pull-down assays performed with midgut brush border membrane vesicles. Peptide sequences from these proteins were matched to the H. parallela newly assembled midgut transcriptome, and 10 proteins were identified. Some of the proteins were shown to be intracellular proteins forming part of the cell cytoskeleton and/or vesicle transport such as actin, myosin, clathrin, dynein, and tubulin among others. In addition, an apolipophorin, which is a protein involved in lipid metabolism, and a novel membrane-bound alanyl aminopeptidase were identified. Our results suggest that Cry8Ea-binding proteins could be different from those characterized for Cry1A toxins in lepidopteran insects. PMID:26135984

  10. Stark effect of donor binding energy in a self-assembled GaAs quantum dot subjected to a tilted electric field

    International Nuclear Information System (INIS)

    We theoretically investigated the donor binding energy distribution with respect to the dopant positions in a self-assembled GaAs/AlGaAs quantum dot (QD) in the presence of a tilted electric field. It is found that there is a critical line in a doping plane, corresponding to zero Stark shift of the donor binding energy. At low electric fields, our work reveals that Stark shift of an on-center donor binding energy is a “purely” quadratic function of the electric field strength, irrespective of QD dimensions and field orientations. This scaling law permits us to indirectly estimate the impurity polarizability in a self-assembled QD. -- Highlights: ► There is a critical line corresponding to zero shift of the donor binding energy. ► Dot dimensions and applied electric field affect significantly the critical line. ► Stark shift of on center donor binding energy is a quadratic function of the field. ► An indirect way to estimate the impurity polarizability has been reported.

  11. Stark effect of donor binding energy in a self-assembled GaAs quantum dot subjected to a tilted electric field

    Energy Technology Data Exchange (ETDEWEB)

    Zeng, Zaiping [Materials Science Department, University of Patras, Rio 26504 (Greece); Garoufalis, Christos S. [Materials Science Department, University of Patras, Rio 26504 (Greece); Department of Environment Technology and Ecology, Technological Institute of Ionian Islands, 2 Kalvou Sq, 29100 Zakynthos (Greece); Baskoutas, Sotirios, E-mail: bask@upatras.gr [Materials Science Department, University of Patras, Rio 26504 (Greece); Terzis, Andreas F. [Physics Department, University of Patras, 26504 Patras (Greece)

    2012-09-03

    We theoretically investigated the donor binding energy distribution with respect to the dopant positions in a self-assembled GaAs/AlGaAs quantum dot (QD) in the presence of a tilted electric field. It is found that there is a critical line in a doping plane, corresponding to zero Stark shift of the donor binding energy. At low electric fields, our work reveals that Stark shift of an on-center donor binding energy is a “purely” quadratic function of the electric field strength, irrespective of QD dimensions and field orientations. This scaling law permits us to indirectly estimate the impurity polarizability in a self-assembled QD. -- Highlights: ► There is a critical line corresponding to zero shift of the donor binding energy. ► Dot dimensions and applied electric field affect significantly the critical line. ► Stark shift of on center donor binding energy is a quadratic function of the field. ► An indirect way to estimate the impurity polarizability has been reported.

  12. 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.

  13. Structure and Mechanism of Dimer-Monomer Transition of a Plant Poly(A)-Binding Protein upon RNA Interaction: Insights into Its Poly(A) Tail Assembly.

    Science.gov (United States)

    Domingues, Mariane Noronha; Sforça, Mauricio Luis; Soprano, Adriana Santos; Lee, Jack; Souza, Tatiana de Arruda Campos Brasil de; Cassago, Alexandre; Portugal, Rodrigo Villares; Zeri, Ana Carolina de Mattos; Murakami, Mario Tyago; Sadanandom, Ari; Oliveira, Paulo Sergio Lopes de; Benedetti, Celso Eduardo

    2015-07-31

    Poly(A)-binding proteins (PABPs) play crucial roles in mRNA biogenesis, stability, transport and translational control in most eukaryotic cells. Although animal PABPs are well-studied proteins, the biological role, three-dimensional structure and RNA-binding mode of plant PABPs remain largely uncharacterized. Here, we report the structural features and RNA-binding mode of a Citrus sinensis PABP (CsPABPN1). CsPABPN1 has a domain architecture of nuclear PABPs (PABPNs) with a single RNA recognition motif (RRM) flanked by an acidic N-terminus and a GRPF-rich C-terminus. The RRM domain of CsPABPN1 displays virtually the same three-dimensional structure and poly(A)-binding mode of animal PABPNs. However, while the CsPABPN1 RRM domain specifically binds poly(A), the full-length protein also binds poly(U). CsPABPN1 localizes to the nucleus of plant cells and undergoes a dimer-monomer transition upon poly(A) interaction. We show that poly(A) binding by CsPABPN1 begins with the recognition of the RNA-binding sites RNP1 and RNP2, followed by interactions with residues of the β2 strands, which stabilize the dimer, thus leading to dimer dissociation. Like human PABPN1, CsPABPN1 also seems to form filaments in the presence of poly(A). Based on these data, we propose a structural model in which contiguous CsPABPN1 RRM monomers wrap around the RNA molecule creating a superhelical structure that could not only shield the poly(A) tail but also serve as a scaffold for the assembly of additional mRNA processing factors. PMID:26013164

  14. 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

  15. 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

  16. The conserved core domain of the human TATA binding protein is sufficient to assemble the multisubunit RNA polymerase I-specific transcription factor SL1.

    OpenAIRE

    Rudloff, U; Eberhard, D; Grummt, I

    1994-01-01

    The human ribosomal RNA polymerase (Pol) I promoter selectivity factor SL1 is a complex consisting of the TATA binding protein (TBP) and three TBP-associated factors (TAFs). We have investigated which elements of TBP are involved in the assembly of Pol I-specific TBP-TAF complexes by comparing SL1 isolated from two human cell lines, one expressing epitope-tagged full-length TBP and another expressing a deletion of nearly the entire N-terminal domain (e delta NTBP). We have immunopurified epit...

  17. Direct Binding of SAS-6 to ZYG-1 Recruits SAS-6 to the Mother Centriole for Cartwheel Assembly

    OpenAIRE

    Lettman, Molly M; Wong, Yao Liang; Viscardi, Valeria; Niessen, Sherry; Chen, Sheng-hong; Shiau, Andrew K.; Zhou, Huilin; Desai, Arshad; Oegema, Karen

    2013-01-01

    Assembly of SAS-6 dimers to form the centriolar cartwheel requires the ZYG-1/Plk4 kinase. Here we show that ZYG-1 recruits SAS-6 to the mother centriole independently of its kinase activity; kinase activity is subsequently required for cartwheel assembly. We identify a direct interaction between ZYG-1 and the SAS-6 coiled-coil that explains its kinase activity-independent function in SAS-6 recruitment. Perturbing this interaction, or the interaction between an adjacent segment of the SAS-6 co...

  18. 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.

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

    Science.gov (United States)

    Martino-Echarri, Estefania; Brocardo, Mariana G.; Mills, Kate M.; Henderson, Beric R.

    2016-01-01

    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(ADP)ribose 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. PMID:26930278

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

    Science.gov (United States)

    Martino-Echarri, Estefania; Brocardo, Mariana G; Mills, Kate M; Henderson, Beric R

    2016-01-01

    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(ADP)ribose 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. PMID:26930278

  1. Impaired Elastogenesis in Hurler Disease : Dermatan Sulfate Accumulation Linked to Deficiency in Elastin-Binding Protein and Elastic Fiber Assembly

    OpenAIRE

    Hinek, Aleksander; Wilson, Sarah E.

    2000-01-01

    Hurler disease resulting from a deficiency in α-l-iduronidase, which causes an accumulation of dermatan sulfate and heparan sulfate glycosaminoglycans, is characterized by connective tissue and skeletal deformations, cardiomyopathy, cardiac valve defects, and progressive coronary artery stenosis. In this report, we present evidence that accumulation of dermatan sulfate but not heparan sulfate moieties is linked to impaired elastic fiber assembly that, in turn, contributes substantially to the...

  2. Detection and characterization of agarose-binding, capsid-like particles produced during assembly of a bacteriophage T7 procapsid.

    OpenAIRE

    Serwer, P; Watson, R H; Hayes, S J

    1982-01-01

    It has previously been shown that: (i) during infection of its host, the DNA bacteriophage T7 assembles a DNA-free procapsid (capsid I), a capsid with an envelope differing physically and chemically from the capsid of the mature bacteriophage, and (ii) capsid I converts to a capsid (capsid II) with a bacteriophage-like envelope as it packages DNA. Lysates of phage T7-infected Escherichia coli contained a particle (AG particle) which copurified with capsid II during buoyant density sedimentati...

  3. 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; Bolanos-Garcia, Victor M; Nilsson, Jakob

    2014-01-01

    in the SAC, we delineate the molecular details of its interaction with kinetochores. We find that BubR1 recruits the bulk of Cdc20 to kinetochores through its internal Cdc20 binding domain (IC20BD). We show that preventing Cdc20 kinetochore localization by removal of the IC20BD has a limited effect...

  4. 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.

  5. Investigation of the binding properties of a multi-modular GH45 cellulase using bioinspired model assemblies

    OpenAIRE

    Fong, Monica; Berrin, Jean-Guy

    2016-01-01

    Background Enzymes degrading plant biomass polymers are widely used in biotechnological applications. Their efficiency can be limited by non-specific interactions occurring with some chemical motifs. In particular, the lignin component is known to bind enzymes irreversibly. In order to determine interactions of enzymes with their substrates, experiments are usually performed on isolated simple polymers which are not representative of plant cell wall complexity. But when using natural plant su...

  6. Self-assembled nanospheres with multiple endohedral binding sites pre-organize catalysts and substrates for highly efficient reactions.

    Science.gov (United States)

    Wang, Qi-Qiang; Gonell, Sergio; Leenders, Stefan H A M; Dürr, Maximilian; Ivanović-Burmazović, Ivana; Reek, Joost N H

    2016-03-01

    Tuning reagent and catalyst concentrations is crucial in the development of efficient catalytic transformations. In enzyme-catalysed reactions the substrate is bound-often by multiple non-covalent interactions-in a well-defined pocket close to the active site of the enzyme; this pre-organization facilitates highly efficient transformations. Here we report an artificial system that co-encapsulates multiple catalysts and substrates within the confined space defined by an M12L24 nanosphere that contains 24 endohedral guanidinium-binding sites. Cooperative binding means that sulfonate guests are bound much more strongly than carboxylates. This difference has been used to fix gold-based catalysts firmly, with the remaining binding sites left to pre-organize substrates. This strategy was applied to a Au(I)-catalysed cyclization of acetylenic acid to enol lactone in which the pre-organization resulted in much higher reaction rates. We also found that the encapsulated sulfonate-containing Au(I) catalysts did not convert neutral (acid) substrates, and so could have potential in the development of substrate-selective catalysis and base-triggered on/off switching of catalysis. PMID:26892553

  7. 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.

  8. Discovery of a Chllorophyll Binding Protein Complex Involved in the Early Steps of Photosystem II Assembly in Synechocystis

    Czech Academy of Sciences Publication Activity Database

    Knoppová, Jana; Sobotka, Roman; Tichý, Martin; Jianfeng, Yu; Koník, P.; Halada, Petr; Nixon, P. J.; Komenda, Josef

    2014-01-01

    Roč. 26, č. 4 (2014), s. 1200-1212. ISSN 1040-4651 R&D Projects: GA ČR P501/11/0377; GA MŠk ED2.1.00/03.0110 Grant ostatní: UK Biotechnology and Biological Sciences Research Council(GB) BB/F020554/1; UK Biotechnology and Biological Sciences Research Council(GB) BB/L003260/1; Magistrát hl. m. Prahy(CZ) CZ.2.16/3.1.00/24023 Institutional support: RVO:61388971 Keywords : Synechocystis * photosystem II * assembly * proteins Subject RIV: EE - Microbiology, Virology Impact factor: 9.338, year: 2014

  9. 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

  10. 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

  11. 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

  12. Mutation in the loop C-terminal to the cyclophilin A binding site of HIV-1 capsid protein disrupts proper virus assembly and infectivity

    Directory of Open Access Journals (Sweden)

    Höglund Anders

    2007-03-01

    Full Text Available Abstract We have studied the effects associated with two single amino acid substitution mutations in HIV-1 capsid (CA, the E98A and E187G. Both amino acids are well conserved among all major HIV-1 subtypes. HIV-1 infectivity is critically dependent on proper CA cone formation and mutations in CA are lethal when they inhibit CA assembly by destabilizing the intra and/or inter molecular CA contacts, which ultimately abrogate viral replication. Glu98, which is located on a surface of a flexible cyclophilin A binding loop is not involved in any intra-molecular contacts with other CA residues. In contrast, Glu187 has extensive intra-molecular contacts with eight other CA residues. Additionally, Glu187 has been shown to form a salt-bridge with Arg18 of another N-terminal CA monomer in a N-C dimer. However, despite proper virus release, glycoprotein incorporation and Gag processing, electron microscopy analysis revealed that, in contrast to the E187G mutant, only the E98A particles had aberrant core morphology that resulted in loss of infectivity.

  13. Specific Inhibitors of HIV Capsid Assembly Binding to the C-Terminal Domain of the Capsid Protein: Evaluation of 2-Arylquinazolines as Potential Antiviral Compounds

    Czech Academy of Sciences Publication Activity Database

    Machara, A.; Lux, V.; Kožíšek, Milan; Grantz Šašková, Klára; Štěpánek, O.; Kotora, M.; Parkan, Kamil; Pávová, Marcela; Glass, B.; Sehr, P.; Lewis, J.; Müller, B.; Kräusslich, H. G.; Konvalinka, Jan

    2016-01-01

    Roč. 59, č. 2 (2016), s. 545-558. ISSN 0022-2623 R&D Projects: GA ČR GA13-19561S EU Projects: European Commission(XE) 201095 - HIV ACE Institutional support: RVO:61388963 Keywords : HIV-1 assembly * capsid * high-throughput screening * AlphaScreen assay Subject RIV: CE - Biochemistry Impact factor: 5.447, year: 2014

  14. 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.

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

    OpenAIRE

    Martino-Echarri, Estefania; Brocardo, Mariana G.; Mills, Kate M.; Henderson, Beric R.

    2016-01-01

    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(ADP)ribose 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 col...

  16. Studies of metal ion binding by apo-metallothioneins attached onto preformed self-assembled monolayers using a highly sensitive surface plasmon resonance spectrometer

    OpenAIRE

    Zhang, Yintang; Xu, Maotian; Wang, Yanju; Toledo, Freddy; Zhou, Feimeng

    2007-01-01

    The use of a flow-injection surface plasmon resonance (FI-SPR) spectrometer equipped with a bicell detector or a position-sensitive device for determining coordination of heavy metal ions (Cd2+ and Hg2+) by surface-confined apo-metallothionein (apo-MT) molecules is described. To facilitate the formation of a compact MT adsorbate layer with a uniform surface orientation, MT molecules were attached onto a preformed alkanethiol self-assembled monolayer. The method resorts to the generation of ap...

  17. The nuclear pore complex–associated protein, Mlp2p, binds to the yeast spindle pole body and promotes its efficient assembly

    OpenAIRE

    Niepel, Mario; Strambio-De-Castillia, Caterina; Fasolo, Joseph; Chait, Brian T.; Rout, Michael P

    2005-01-01

    The two yeast proteins Mlp1p and Mlp2p (homologues of the vertebrate protein Tpr) are filamentous proteins attached to the nuclear face of nuclear pore complexes. Here we perform a proteomic analysis, which reveals that the two Mlps have strikingly different interacting partners, testifying to their different roles within the cell. We find that Mlp2p binds directly to Spc110p, Spc42p, and Spc29p, which are three core components of the spindle pole body (SPB), the nuclear envelope–associated y...

  18. 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.

  19. A conserved KIN17 curved DNA-binding domain protein assembles with SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE7 to adapt Arabidopsis growth and development to limiting copper availability.

    Science.gov (United States)

    Garcia-Molina, Antoni; Xing, Shuping; Huijser, Peter

    2014-02-01

    Proper copper (Cu) homeostasis is required by living organisms to maintain essential cellular functions. In the model plant Arabidopsis (Arabidopsis thaliana), the SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE7 (SPL7) transcription factor participates in reprogramming global gene expression during Cu insufficiency in order to improve the metal uptake and prioritize its distribution to Cu proteins of major importance. As a consequence, spl7 null mutants show morphological and physiological disorders during Cu-limited growth, resulting in lower fresh weight, reduced root elongation, and chlorosis. On the other hand, the Arabidopsis KIN17 homolog belongs to a well-conserved family of essential eukaryotic nuclear proteins known to be stress activated and involved in DNA and possibly RNA metabolism in mammals. In the study presented here, we uncovered that Arabidopsis KIN17 participates in promoting the Cu deficiency response by means of a direct interaction with SPL7. Moreover, the double mutant kin17-1 spl7-2 displays an enhanced Cu-dependent phenotype involving growth arrest, oxidative stress, floral bud abortion, and pollen inviability. Taken together, the data presented here provide evidence for SPL7 and KIN17 protein interaction as a point of convergence in response to both Cu deficiency and oxidative stress. PMID:24335506

  20. Sequence assembly

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  1. 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.

  2. 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.

  3. Fuel assembly

    International Nuclear Information System (INIS)

    Purpose: To improve the thermal and mechanical safety of fuel rods and structural components by making the local power coefficient of jointed fuel rods greater than that of other fuel rods in a fuel assembly. Constitution: In a fuel assembly comprising a plurality of fuel rods bundled by a spacer and held at the upper and the lower positions with tie plates for insertion into a channel, the degree of enrichment of uranium 235 for uranium dioxide fuel pellets charged in jointed fuel rods is adjusted such that the local power coefficient of the jointed fuel rods is made greater than that of the other fuel rods. In the case if the upper tie plate is moved upwardly by the extension of the jointed fuel rods, other fuel rods axially free from the upper tie plate receives no tension, whereby the safety of the fuel assembly can be improved. (Moriyama, K.)

  4. 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.

  5. The LIM-only protein Lmo2 is a bridging molecule assembling an erythroid, DNA-binding complex which includes the TAL1, E47, GATA-1 and Ldb1/NLI proteins.

    OpenAIRE

    Wadman, I A; Osada, H; Grütz, G G; Agulnick, A D; Westphal, H; Forster, A.; Rabbitts, T H

    1997-01-01

    The LIM-only protein Lmo2, activated by chromosomal translocations in T-cell leukaemias, is normally expressed in haematopoiesis. It interacts with TAL1 and GATA-1 proteins, but the function of the interaction is unexplained. We now show that in erythroid cells Lmo2 forms a novel DNA-binding complex, with GATA-1, TAL1 and E2A, and the recently identified LIM-binding protein Ldb1/NLI. This oligomeric complex binds to a unique, bipartite DNA motif comprising an E-box, CAGGTG, followed approxima...

  6. Fuel assembly

    International Nuclear Information System (INIS)

    A fuel assembly is composed of a fuel bundle surrounded by a channel box. The fuel bundle comprises a large number of fuel rods and a water rod secured to upper and lower tie plate by way of a plurality of fuel spacers. Grooves (libretti) are formed in the direction along the flowing direction of coolants to at least one of the surface of the fuel rods, the inner surface of the channel box, the surface of the water rod and spacer constituting components. In this case, the lateral width of the libretto in the flowing direction is determined as the minimum thickness of the bottom layer of a layered flow determined by a coolant flow rate. With such a constitution, abrasion resistance relative to coolants is reduced to reduce the pressure loss of fuel assemblies. (I.N.)

  7. 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...

  8. 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.

  9. 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

  10. 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 i...... societies. This is an essential reading for both seasoned scholars and advanced students of markets, economies and social forms of consumption....... 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...

  11. 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...

  12. 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...

  13. 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...

  14. Fuel assembly

    International Nuclear Information System (INIS)

    The cross section of a fuel assembly is divided to a first region containing corner portions at which channel fasteners are situated and a second region not containing corner portions. The average enrichment degree of plutonium in the first region is decreased than that of the second region, and the number of fuel rods containing burnable poisons is increased at the first region than that of the second region. In the first region of the fuel assembly, the effect of moderating neutrons is enhanced since the cross section of a moderator flow channel at the outer side of the channel box is large. Therefore, local power peaking is increased in the first region while it is decreased in the second region that opposes to a narrow gap. The average enrichment degree of plutonium in the first region is decreased and that in the second region is increased by so much, to flatten the power distribution. Then, the reduction of the reactivity worth of gadolinia, as burnable poisons, can be suppressed. (N.H.)

  15. Hatch assembly

    International Nuclear Information System (INIS)

    This patent describes a nuclear reactor installation including means defining a fuel handling area and means defining a containment area separated from the fuel handling area and including a refuelling cavity; the improvement comprising: (a) a fuel transfer tube connecting the refuelling cavity with the fuel handling area; the fuel transfer tube having a first end in the fuel handling area and a second end in the refueling cavity; (b) valve means for opening and closing the first end; and (c) a hatch assembly mounted on the second end; the hatch assembly including (1) a hatch ring affixed to the fuel transfer tube at the second end the hatch ring has an integral annular seat surrounded by the hatch ring and defines a hatch opening in the second end of the fuel transfer tube; (2) a hatch cover adapts to be positioned on the annular seat for covering the hatch opening; (3) latching units are supported on the hatch ring about the hatch opening, each latching unit

  16. Fuel assembly

    International Nuclear Information System (INIS)

    The present invention concerns a fuel assembly of a BWR type reactor, and prevents aging change of flow rate of coolants leaked from a gap between a lower tie plate and a channel box. That is, in the fuel assembly, a great number of fuel rods and a plurality of water rods are bundled by a plurality of spacers, the upper and the lower ends thereof are supported by upper and lower tie plates, and they are contained in a channel box. Plate-like protrusions are disposed rotatably to the lower tie plate at a position corresponding to the lower end of the channel box. In addition, through holes are disposed on the side wall of the lower tie plate. With such a constitution, the protrusions rotate at a connection portion by hydraulic pressure of leaking coolants, and urge the channel box by the other end to control leakage of coolants. Further, since the through holes are disposed on the side wall of the lower tie plate, pressure difference is caused between the upper and the lower surfaces of the plate of the protrusion, to rotate the protrusions at the connection portion, and the other end of the protrusions presses the channel box to obtain the same effect. (I.S.)

  17. Impaired elastin fiber assembly related to reduced 67-kD elastin-binding protein in fetal lamb ductus arteriosus and in cultured aortic smooth muscle cells treated with chondroitin sulfate.

    OpenAIRE

    Hinek, A; Mecham, R. P.; Keeley, F; M. Rabinovitch

    1991-01-01

    In the fetal ductus arteriosus (DA) disruption in the assembly of elastin fibers is associated with intimal thickening and we previously reported that fetal lamb DA smooth muscle cells incubated with endothelial conditioned medium produce two-fold more chondroitin sulfate (CS) compared with aorta (Ao) cells (Boudreau, N., and M. Rabinovitch. 1991. Lab. Invest. 64:187-199). We hypothesized that CS or dermatan sulfate (DS), both N-acetylgalactosamine glycosaminoglycans (GAGs), may be similar to...

  18. Fuel assembly

    International Nuclear Information System (INIS)

    A fuel assembly of a BWR type reactor comprises a rectangular parallelopiped channel box and fuel bundles contained in the channel box. The fuel bundle comprises an upper tie plate, a lower tie plate, a plurality of spacers a plurality of fuel rods and a water rod. In each fuel rod, the amount of fission products is reduced at upper and lower end regions of an effective fuel portion than that in other regions of the effective fuel region. In a portion of the fuel rods, fuel pellets containing burnable poisons are disposed at the upper and lower end regions. In addition, the upper and lower portions are constituted with natural uranium. Each of the upper and lower end regions is not greater than 15% of the effective fuel length. Since this can enhance reactivity control effect without worsening fuel economy, the control amount for excess reactivity upon long-term cycle operation can be increased. (I.N.)

  19. 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.)

  20. 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.)

  1. Fuel assembly

    International Nuclear Information System (INIS)

    Fuel rods are arranged in a lattice-like structure by way of a plurality of spacers and the lower ends thereof are fixed to a lower tie plate for assembling a fuel rod bundle. The outer circumference is surrounded by a basket having a plurality of openings and the basket is surrounded by a channel box. The basket is connected to a handle at the upper end and to a lower tie plate at the lower end and, further, defined with a scraper at each of openings. Coolants flown from the lower tie plate to the channel box flow the channels between the channel box and the basket and a fuel rod bundle, uprise while forming a two-phase flow and flow out from the upper end of the channel box. Since no upper tie plate is present, pressure loss of coolants flow is reduced, and liquid membranes of coolants are peeled off by the scraper disposed at the opening of the basket, which contributes to the improvement of the limit power. In addition, fuel rods are inspected and cleaned easily. (N.H.)

  2. Fuel assembly

    International Nuclear Information System (INIS)

    The object of the present invention is to improve the hydrodynamic stability in the fuel channels of BWR type reactors and effectively utilize the coolant driving power corresponding to the reduction due to pressure loss. That is, in a fuel assembly having usual fuel rods and, in addition, water rods and short fuel rods, the structures of water rods, upper tie plates and the spacers are designed from a hydrodynamic point of view, to reduce the pressure loss. On the other hand, a lattice-like flow channel resistance member is disposed to a lower tie plate. The bundle flow rate is made uniform by the flow channel resistance member, and the pressure loss of the tie plate is increased by the reduction of the pressure loss by the arrangement of the short fuel rod and the reduction of the pressure loss described above. Since this increases the ratio of the single phase stream pressure loss in the total reactor core pressure loss, the hydrodynamic stability in the fuel channel is improved. (I.J.)

  3. Nuclear reactor fuel assembly

    International Nuclear Information System (INIS)

    A fuel assembly construction for liquid metal cooled fast breeder reactors is described in which the sub-assemblies carry a smaller proportion of parasitic material than do conventional sub-assemblies. (U.K.)

  4. 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 ...

  5. 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

  6. Using lateral capillary forces to compute by self-assembly

    OpenAIRE

    Rothemund, Paul W. K.

    2000-01-01

    Investigations of DNA computing have highlighted a fundamental connection between self-assembly (SA) and computation: in principle, any computation can be performed by a suitable self-assembling system. In practice, exploration of this connection is limited by our ability to control the geometry and specificity of binding interactions. Recently, a system has been developed that uses surface tension to assemble plastic tiles according to shape complementarity and likeness of wetting [Bowden, N...

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. Structural assembly demonstration experiment

    Science.gov (United States)

    Stokes, J. W.

    1982-01-01

    The experiment is of an operational variety, designed to assess crew capability in Large Space System (LSS) assembly. The six Structural Assembly Demonstration Experiment objectives include: (1) the establishment of a quantitative correlation between LSS neutral buoyancy simulation and on-orbit assembly operations in order to enhance the validity of those assembly simulations; (2) the quantitative study of the capabilities and mechanics of human assembly in an Extravehicular Activity environment; (3) the further corroboration of the LSS Assembly Analysis cost algorithm through the obtainment of hard data base information; (4) the verification of LSS assembly techniques and timeless, as well as the identification of crew imposed loads and assembly aid requirements and concepts; (5) verification of a Launch/Assembly Platform structure concept for other LSS missions; and (6) lastly, to advance thermal control concepts through a flexible heat pipe.

  12. 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.

  13. 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

  14. 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.

  15. Rrp6p controls mRNA poly(A) tail length and its decoration with poly(A) binding proteins.

    Science.gov (United States)

    Schmid, Manfred; Poulsen, Mathias Bach; Olszewski, Pawel; Pelechano, Vicent; Saguez, Cyril; Gupta, Ishaan; Steinmetz, Lars M; Moore, Claire; Jensen, Torben Heick

    2012-07-27

    Poly(A) (pA) tail binding proteins (PABPs) control mRNA polyadenylation, stability, and translation. In a purified system, S. cerevisiae PABPs, Pab1p and Nab2p, are individually sufficient to provide normal pA tail length. However, it is unknown how this occurs in more complex environments. Here we find that the nuclear exosome subunit Rrp6p counteracts the in vitro and in vivo extension of mature pA tails by the noncanonical pA polymerase Trf4p. Moreover, PABP loading onto nascent pA tails is controlled by Rrp6p; while Pab1p is the major PABP, Nab2p only associates in the absence of Rrp6p. This is because Rrp6p can interact with Nab2p and displace it from pA tails, potentially leading to RNA turnover, as evidenced for certain pre-mRNAs. We suggest that a nuclear mRNP surveillance step involves targeting of Rrp6p by Nab2p-bound pA-tailed RNPs and that pre-mRNA abundance is regulated at this level. PMID:22683267

  16. 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.

  17. 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

  18. 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...

  19. Assembler for de novo assembly of large genomes

    OpenAIRE

    Chu, Te-Chin; Lu, Chen-Hua; Liu, Tsunglin; Lee, Greg C.; Li, Wen-Hsiung; Shih, Arthur Chun-Chieh

    2013-01-01

    Assembling a large genome faces three challenges: assembly quality, computer memory requirement, and execution time. Our developed assembler, JR-Assembler, uses (a) a strategy that selects good seeds for contig construction, (b) an extension strategy that uses whole sequencing reads to increase the chance to jump over repeats and to expedite extension, and (c) detecting misassemblies by remapping reads to assembled sequences. Compared with current assemblers, JR-Assembler achieves a better ov...

  20. 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

  1. Assembly tool design

    International Nuclear Information System (INIS)

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

  2. 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

  3. 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...

  4. 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...

  5. 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.

  6. 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.

  7. 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 ...

  8. Method of assembling nuclear fuel assembly

    International Nuclear Information System (INIS)

    Thin films are formed to the surface of a fuel rod for preventing the occurrence of injuries at the surface of the fuel rod. That is, in a method of assembling a nuclear fuel assembly by inserting fuel rods into lattice cells of a support lattice, thin films of polyvinyl alcohol are formed to a predetermined thickness at the surface of each of the fuel rods and, after insertion of the fuel rods into the lattice cells, the nuclear fuel assemblies are dipped into water or steams to dissolve and remove the thin films. Since polyvinyl alcohol is noncombustible and not containing nuclear inhibitive material as the ingredient, they cause no undesired effects on plant facilities even if not completely removed from the fuel rods. The polyvinyl alcohol thin films have high strength and can sufficiently protect the fuel rod. Further, scraping damages caused by support members of the support lattice upon insertion can also be prevented. (T.M.)

  9. 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.

  10. Double-degradable responsive self-assembled multivalent arrays-temporary nanoscale recognition between dendrons and DNA

    OpenAIRE

    Barnard, A.; Posocco, P.; Fermeglia, M.; Tschiche, A.; Calderon, Marcelo; Pricl, S.; Smith, D. K.

    2014-01-01

    This article reports self-assembling dendrons which bind DNA in a multivalent manner. The molecular design directly impacts on self-assembly which subsequently controls the way these multivalent nanostructures bind DNA-this can be simulated by multiscale modelling. Incorporation of an S-S linkage between the multivalent hydrophilic dendron and the hydrophobic units responsible for self-assembly allows these structures to undergo triggered reductive cleavage, with dithiothreitol (DTT) inducing...

  11. Reactor fuel assemblies

    International Nuclear Information System (INIS)

    A description is given of an improved spacer grid for a nuclear fuel assembly comprising fuel rods in a matrix wherein each rod is adapted to be enclosed by a spacer ''cell'' for positioning thereof relative to adjacent rods in the fuel assembly. 7 claims, 12 drawing figures

  12. 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...

  13. Laser bottom hole assembly

    Science.gov (United States)

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

    2014-01-14

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

  14. 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

  15. 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.

  16. 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...

  17. Nuclear fuel assembly

    International Nuclear Information System (INIS)

    A nuclear fuel assembly includes and upper yoke, a base, an elongated, outer flow channel disposed substantially along the entire length of the fuel assembly and an elongated, internal, central water cross, formed by four, elongated metal angles, that divides the nuclear fuel assembly into four, separate, elongated fuel sections and that provides a centrally disposed path for the flow of subcooled neutron moderator along the length of the fuel assembly. A separate fuel bundle is located in each of the four fuel sections and includes an upper tie plate, a lower tie plate and a plurality of elongated fuel rods disposed therebetween. Preferably, each upper tie plate is formed from a plurality of interconnected thin metal bars and includes an elongated, axially extending pin that is received by the upper yoke of the fuel assembly for restraining lateral motion of the fuel bundle while permitting axial movement of the fuel bundle with respect to the outer flow channel. The outer flow channel is fixedly secured at its opposite longitudinal ends to the upper yoke and to the base to permit the fuel assembly to be lifted and handled in a vertical position without placing lifting loads or stresses on the fuel rods. The yoke, removably attached at the upper end of the fuel assembly to four structural ribs secured to the inner walls of the outer flow channel, includes, as integrally formed components, a lifting bail or handle, laterally extending bumpers, a mounting post for a spring assembly, four elongated apertures for receiving with a slip fit the axially extending pins mounted on the upper tie plates and slots for receiving the structural ribs secured to the outer flow channel. Locking pins securely attach the yoke to the structural ribs enabling the fuel assembly to be lifted as an entity

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. 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...

  3. 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.

  4. 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 ...

  5. Fuel assembly reconstitution

    International Nuclear Information System (INIS)

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

  6. Polymer Directed Protein Assemblies

    Directory of Open Access Journals (Sweden)

    Patrick van Rijn

    2013-05-01

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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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...

  13. Method of loading fuel assembly

    International Nuclear Information System (INIS)

    Purpose: To shorten the fuel assembly loading time by loading fuel assembly group as one body into the reactor core. Method: A fuel assembly is fed from an auxiliary reactor building via a pit crane into the reactor container, and is stood from lateral position to vertical position. Further, the fuel assemblies are moved laterallyiin a pool of the container, and every four assembly groups are formed by an aligning jig. These assembly groups are associated into one body and loaded into the container. Thus, the round trip time of the crane in the fuel assembly loading work can be shortened. (Yoshihara, H.)

  14. 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.

  15. 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.

  16. Nuclear fuel assembly

    International Nuclear Information System (INIS)

    A fuel assembly of PWR comprises a fuel bundle portion supported by a plurality of support lattices and an upper and lower nozzles each secured to the upper and lower portions. Leaf springs are attached to the four sides of the upper nozzle for preventing rising of the fuel assembly by streams of cooling water by the contact with an upper reactor core plate. The leaf springs are attached to the upper nozzle so that four leaf springs are laminated. The uppermost leaf spring is bent slightly upwardly from the mounted portion and the other leaf springs are extended linearly from the mounted portion without being bent. The mounted portions of the leaf springs are stacked and secured to the upper nozzle by a bolt obliquely relative to the axial line of the fuel assembly. (I.N.)

  17. Blade attachment assembly

    Energy Technology Data Exchange (ETDEWEB)

    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.

  18. 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.

  19. Lead Test Assembly program

    International Nuclear Information System (INIS)

    Implementation of the new/alternative fuel requires addressing all aspects of the fuel assembly design basis (mechanical, fuel handling, thermal-hydraulic, nuclear design, chemistry, safety analysis and licensing and including mix core effects. The scope of the work is minimized by implementing a Lead Test Assembly (LTA) program with a limited number of assemblies (6 or more), using approved designed features, and placing the LTAs in a unlimited core power location. The topics discussed in the contribution include plant licensing basis and regulatory requirements, plant interface review, compatibility with resident fuel and reactor environment, safety analysis, and post radiation examination. It is concluded that the LTA program is a prudent means of introducing new core designs into existing cores. (P.A.)

  20. Optical interconnect assembly

    Science.gov (United States)

    Laughlin, Daric; Abel, Philip

    2015-06-09

    An optical assembly includes a substrate with a first row of apertures and a second row of apertures. A first optical die includes a first plurality of optical transducer elements and is mounted on the substrate such that an optical signal interface of each transducer element is aligned with an aperture of the first row of optical apertures. A second optical die includes a second plurality of optical transducer elements and is mounted on the substrate such that an optical signal interface of each of the second plurality of optical transducer elements is aligned with an aperture of the second row of optical apertures. A connector configured to mate with the optical assembly supports a plurality of optical fibers. A terminal end of each optical fiber protrudes from the connector and extends into one of the apertures when the connector is coupled with the optical assembly.

  1. 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

  2. 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...... 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 their...

  3. 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.

  4. 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.

  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. 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 ...

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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...

  12. 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...

  13. Assembly of primary cilia

    DEFF Research Database (Denmark)

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

    2008-01-01

    our current knowledge about IFT is based on studies performed in Chlamydomonas and Caenorhabditis elegans. Therefore, our review of the IFT literature includes studies performed in these two model organisms. The role of several non-IFT proteins (e.g., centrosomal proteins) in the ciliary assembly...

  14. 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...

  15. Nuclear fuel assembly spacer

    International Nuclear Information System (INIS)

    In a fuel assembly for a nuclear reactor a fuel element spacer formed of an array of laterally positioned cojoined tubular ferrules each providing a passage for one of the fuel elements, the elements being laterally supported in the ferrules between slender spring members and laterally oriented rigid stops

  16. Turneri preemia 2015: Assemble

    Index Scriptorium Estoniae

    2015-01-01

    Turneri 2015. aasta preemia pälvis radikaalne noorte arhitektide kollektiiv Assemble. Rühmitus on 18-liikmeline ja baseerub Ida-Londonis ning selle tegevust võib üldistatult nimetada hüljatud ruumide taaselustamiseks kogukondlike aktsioonide kaudu

  17. High resolution characterization of myosin IIC protein tailpiece and its effect on filament assembly.

    Science.gov (United States)

    Rosenberg, Masha M; Ronen, Daniel; Lahav, Noa; Nazirov, Elvira; Ravid, Shoshana; Friedler, Assaf

    2013-04-01

    The motor protein nonmuscle myosin II (NMII) must undergo dynamic oligomerization into filaments to perform its cellular functions. A small nonhelical region at the tail of the long coiled-coil region (tailpiece) is a common feature of all dynamically assembling myosin II proteins. This tailpiece is a key regulatory domain affecting NMII filament assembly properties and is subject to phosphorylation in vivo. We previously demonstrated that the positively charged region of the tailpiece binds to assembly-incompetent NMII-C fragments, inducing filament assembly. In the current study, we investigated the molecular mechanisms by which the tailpiece regulates NMII-C self-assembly. Using alanine scan, we found that specific positive and aromatic residues within the positively charged region of the tailpiece are important for inducing NMII-C filament assembly and for filament elongation. Combining peptide arrays with deletion studies allowed us to identify the tailpiece binding sites in the coiled-coil rod. Elucidation of the mechanism by which the tailpiece induces filament assembly permitted us further investigation into the role of tailpiece phosphorylation. Sedimentation and CD spectroscopy identified that phosphorylation of Thr(1957) or Thr(1960) inhibited the ability of the tailpiece to bind the coiled-coil rod and to induce NMII-C filament formation. This study provides molecular insight into the role of specific residues within the NMII-C tailpiece that are responsible for shifting the oligomeric equilibrium of NMII-C toward filament assembly and determining its morphology. PMID:23426373

  18. 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

  19. 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.

  20. 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....

  1. Characterization and DNA-Binding Specificities of Ralstonia TAL-Like Effectors

    OpenAIRE

    Li, LiXin; Atef, Ahmed; Piatek, Agnieszka; Ali, Zahir; Piatek, Marek; Aouida, Mustapha; Sharakuu, Altanbadralt; Mahjoub, Ali; Wang, Guangchao; Khan, Suhail; Fedoroff, Nina V.; Zhu, Jian-Kang; Mahfouz, Magdy M

    2013-01-01

    We report the characterization of three Ralstonia TAL-like effectors, which mediate DNA binding and can be used as customizable architectures for DNA targeting. We determined DNA-binding specificities of novel repeat variable di-residues (RVDs) and devised a repeat assembly approach for engineering Ralstonia solanacearum TALE-like proteins (RTLs).

  2. Self-assembled magnetic nanospheres with three-dimensional magnetic vortex

    International Nuclear Information System (INIS)

    We report the electron holography images of spin configurations in peculiar assemblies of soft magnetic nanoparticles in single-, double-, triple-, or quadruple-sphere geometrical arrangements, in which each particle has a three-dimensional (3D) magnetic-vortex structure. Micromagnetic numerical calculations reveal that the uniqueness of the nanoparticles' 3D vortex structure plays a crucial role in their assembly, especially in terms of the contrasting contributions of the exchange and dipolar interactions to their binding energies. The results represent physical insights into the assembly of 3D-vortex-structure magnetic nanoparticles in different geometrical configurations and offer a practical means of controlling those assemblies

  3. Engineering colloidal assembly via biological adhesion

    Science.gov (United States)

    Hiddessen, Amy Lynn

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

  4. 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.

  5. [Transcript assembly and quality assessment].

    Science.gov (United States)

    Deng, Feilong; Jia, Xianbo; Lai, Songjia; Liu, Yiping; Chen, Shiyi

    2015-09-01

    The transcript assembly is essential for transcriptome studies trom next-generation sequencing data. However, there are still many faults of algorithms in the present assemblers, which should be largely improved in the future. According to the requirement of reference genome or not, the transcript assembly could be classified into the genome-guided and de novo methods. The two methods have different algorithms and implementation processes. The quality of assembled transcripts depends on a large number of factors, such as the PCR amplification, sequencing techniques, assembly algorithm and genome character. Here, we reviewed the present tools of transcript assembly and various indexes for assessing the quality of assembled transcripts, which would help biologists to determine which assembler should be used in their studies. PMID:26955705

  6. 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)

  7. 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...

  8. 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...

  9. 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)

  10. Melanin-binding radiopharmaceuticals

    International Nuclear Information System (INIS)

    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

  11. 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.

  12. 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.)

  13. 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 by...... platform displays a contact resistance only slightly larger than the thiols. This surprising finding has not been reported before and was analyzed by theoretical computations of the transmission functions of the TATA anchored molecular wires. The relatively low contact resistance of the TATA platform along...

  14. 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.

  15. 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...... inductor winding comprising series coupled first and second half-windings wherein the first half-winding is wound around a second predetermined segment of the first magnetically permeable core and the second half-winding is wound around a second predetermined segment of the second magnetically permeable...

  16. 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)

  17. Ingestion resistant seal assembly

    Science.gov (United States)

    Little, David A.

    2011-12-13

    A seal assembly limits gas leakage from a hot gas path to one or more disc cavities in a gas turbine engine. The seal assembly includes a seal apparatus associated with a blade structure including a row of airfoils. The seal apparatus includes an annular inner shroud associated with adjacent stationary components, a wing member, and a first wing flange. The wing member extends axially from the blade structure toward the annular inner shroud. The first wing flange extends radially outwardly from the wing member toward the annular inner shroud. A plurality of regions including one or more recirculation zones are defined between the blade structure and the annular inner shroud that recirculate working gas therein back toward the hot gas path.

  18. Turbine seal assembly

    Science.gov (United States)

    Little, David A.

    2013-04-16

    A seal assembly that limits gas leakage from a hot gas path to one or more disc cavities in a turbine engine. The seal assembly includes a seal apparatus that limits gas leakage from the hot gas path to a respective one of the disc cavities. The seal apparatus comprises a plurality of blade members rotatable with a blade structure. The blade members are associated with the blade structure and extend toward adjacent stationary components. Each blade member includes a leading edge and a trailing edge, the leading edge of each blade member being located circumferentially in front of the blade member's corresponding trailing edge in a direction of rotation of the turbine rotor. The blade members are arranged such that a space having a component in a circumferential direction is defined between adjacent circumferentially spaced blade members.

  19. 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.

  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. 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...

  2. Composite airfoil assembly

    Science.gov (United States)

    Garcia-Crespo, Andres Jose

    2015-03-03

    A composite blade assembly for mounting on a turbine wheel includes a ceramic airfoil and an airfoil platform. The ceramic airfoil is formed with an airfoil portion, a blade shank portion and a blade dovetail tang. The metal platform includes a platform shank and a radially inner platform dovetail. The ceramic airfoil is captured within the metal platform, such that in use, the ceramic airfoil is held within the turbine wheel independent of the metal platform.

  3. 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"…

  4. Nuclear fuel assembly

    International Nuclear Information System (INIS)

    A nuclear fuel assembly comprises a cluster of elongated fuel, retained parallel and at the nodal points of a square network by a bottom supporting plate and by spacing grids. The supporting plate is connected to a top end plate via tie-rods which replace fuel pins at certain of the nodal points of the network. The diameter of the tie-rods is equal to that of the pins and both are slidably received in the grids

  5. Nuclear fuel assembly spacer

    International Nuclear Information System (INIS)

    A spacer for use in a fuel assembly of a nuclear reactor having thin, full-height divider members, slender spring members and laterally oriented rigid stops and wherein the total amount of spacer material, the amount of high neutron cross section material, the projected area of the spacer structure and changes in cross section area of the spacer structure are minimized whereby neutron absorption by the spacer and coolant flow resistance through the spacer are minimized

  6. 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.

  7. Assembling Toyota in Portugal

    OpenAIRE

    Machado, Tiago; Moniz, António

    2003-01-01

    A lot has been written over the last decade with regard to Toyota and the productive model associated to it (toyota-ism). And more specifically concerning the "(…) best-seller that changed the... sociological world" (Castillo, 1998: 31). But the case of Salvador Caetano’s Ovar Industrial Division (OID), that assembles Toyota light commercial vehicles in Portugal, allows us to put forward a sub-hypothesis that fits into the analysis schema proposed in the First GERPISA International Program – ...

  8. 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...

  9. 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...

  10. Gas sealed assembly

    International Nuclear Information System (INIS)

    A gas sealed assembly is disposed to a reactor core of an LMFBR type reactor. The gas sealed assembly has a cylindrical duct, and an entrance nozzle having a coolant flowing hole is connected to the lower portion of the duct. Sodium coolants and a sealed gas comprising inert gases such as argon are contained in the duct. A black material is disposed on the inner surface of the duct. Chromium carbide, for example, is used as the black material. Since the black material is disposed to the inner surface of the duct, heat from sodium at the circumference is transferred to the sealed gas by radiation by way of the duct, the gas expands sufficiently. Therefore, when the pressure of coolants is lowered and the temperature of coolants is elevated upon occurrence of an accident such as of stoppage of pumps, the liquid level of the coolants in the gas sealed assembly can be lowered reliably. Accordingly, the reactor shut down can be conducted safely. (I.N.)

  11. 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...

  12. Structural Insights into KCTD Protein Assembly and Cullin3 Recognition.

    Science.gov (United States)

    Ji, Alan X; Chu, Anh; Nielsen, Tine Kragh; Benlekbir, Samir; Rubinstein, John L; Privé, Gilbert G

    2016-01-16

    Cullin3 (Cul3)-based ubiquitin E3 ligase complexes catalyze the transfer of ubiquitin from an E2 enzyme to target substrate proteins. In these assemblies, the C-terminal region of Cul3 binds Rbx1/E2-ubiquitin, while the N-terminal region interacts with various BTB (bric-à-brac, tramtrack, broad complex) domain proteins that serve as substrate adaptors. Previous crystal structures of the homodimeric BTB proteins KLHL3, KLHL11 and SPOP in complex with the N-terminal domain of Cul3 revealed the features required for Cul3 recognition in these proteins. A second class of BTB-domain-containing proteins, the KCTD proteins, is also Cul3 substrate adaptors, but these do not share many of the previously identified determinants for Cul3 binding. We report the pentameric crystal structures of the KCTD1 and KCTD9 BTB domains and identify plasticity in the KCTD1 rings. We find that the KCTD proteins 5, 6, 9 and 17 bind to Cul3 with high affinity, while the KCTD proteins 1 and 16 do not have detectable binding. Finally, we confirm the 5:5 assembly of KCTD9/Cul3 complexes by cryo-electron microscopy and provide a molecular rationale for BTB-mediated Cul3 binding specificity in the KCTD family. PMID:26334369

  13. 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...

  14. Orientational nanoparticle assemblies and biosensors.

    Science.gov (United States)

    Ma, Wei; Xu, Liguang; Wang, Libing; Kuang, Hua; Xu, Chuanlai

    2016-05-15

    Assemblies of nanoparticles (NPs) have regional correlated properties with new features compared to individual NPs or random aggregates. The orientational NP assembly contributes greatly to the collective interaction of individual NPs with geometrical dependence. Therefore, orientational NPs assembly techniques have emerged as promising tools for controlling inorganic NPs spatial structures with enhanced interesting properties. The research fields of orientational NP assembly have developed rapidly with characteristics related to the different methods used, including chemical, physical and biological techniques. The current and potential applications, important challenges remain to be investigated. An overview of recent developments in orientational NPs assemblies, the multiple strategies, biosensors and challenges will be discussed in this review. PMID:26708241

  15. 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.

  16. 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

  17. 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)

  18. 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 ...

  19. 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...

  20. Dielectrophoresis and electrohydrodynamics-mediated fluidic assembly of silicon resistors

    OpenAIRE

    Lee, S. W.; Bashir, Rashid

    2003-01-01

    In this letter, we present techniques, utilizing dielectrophoresis and electrohydrodynamics, which can be used for assembling single-crystal silicon devices suspended in a solution onto a binding site on a heterogeneous substrate. Silicon resistors with gold/chromium layers located at the end of the resistors and silicon blocks without metal were fabricated on bonded and etched-backed silicon-on-insulator wafers and successfully released into deionized water. The devices were subsequently ass...

  1. Multivalent Protein Assembly Using Monovalent Self-Assembling Building Blocks

    Directory of Open Access Journals (Sweden)

    Katja Petkau-Milroy

    2013-10-01

    Full Text Available Discotic molecules, which self-assemble in water into columnar supramolecular polymers, emerged as an alternative platform for the organization of proteins. Here, a monovalent discotic decorated with one single biotin was synthesized to study the self-assembling multivalency of this system in regard to streptavidin. Next to tetravalent streptavidin, monovalent streptavidin was used to study the protein assembly along the supramolecular polymer in detail without the interference of cross-linking. Upon self-assembly of the monovalent biotinylated discotics, multivalent proteins can be assembled along the supramolecular polymer. The concentration of discotics, which influences the length of the final polymers at the same time dictates the amount of assembled proteins.

  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. 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.

  4. FORTRAN and ASSEMBLER programs

    International Nuclear Information System (INIS)

    A collection of programs written in FORTRAN and ASSEMBLER programming languages used in DOS-IBM is presented. The problems solved are of different sorts: linear programming, integration, matrix calculus, computation of absorbed doses in teletherapy, data sets (files) on magnetic tapes and disks, completion of DOS operating system etc. For reasons of space no details are given on the numerical methods or supplements and devices developed in order to achieve superior programs as to computation time and accuracy of result, although these might have been of use. All the programs in the collection have been checked up on an IBM 370/135 computer. (author)

  5. Nuclear fuel assembly

    International Nuclear Information System (INIS)

    Purpose: To obtain a nuclear fuel assembly having a function of eliminating corrosion products exfoliating from the surface of a fuel can, thereby reduce the radioactive crud in primary sodium coolant during operation of a FBR type reactor. Constitution: Nickel plates or grids made of metal plate with a nickel coated on the surface thereof are inserted in the upper blanket of a nuclear fuel element and between nuclear fuel element corresponding to the gas plenum. The nickel becomes helpful at high temperature in adsorbing Mn-54 which accounts for a major portion of the corrosion products. (J.P.N.)

  6. 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.

  7. Phylogenetic comparative assembly

    Directory of Open Access Journals (Sweden)

    Husemann Peter

    2010-01-01

    Full Text Available Abstract Background Recent high throughput sequencing technologies are capable of generating a huge amount of data for bacterial genome sequencing projects. Although current sequence assemblers successfully merge the overlapping reads, often several contigs remain which cannot be assembled any further. It is still costly and time consuming to close all the gaps in order to acquire the whole genomic sequence. Results Here we propose an algorithm that takes several related genomes and their phylogenetic relationships into account to create a graph that contains the likelihood for each pair of contigs to be adjacent. Subsequently, this graph can be used to compute a layout graph that shows the most promising contig adjacencies in order to aid biologists in finishing the complete genomic sequence. The layout graph shows unique contig orderings where possible, and the best alternatives where necessary. Conclusions Our new algorithm for contig ordering uses sequence similarity as well as phylogenetic information to estimate adjacencies of contigs. An evaluation of our implementation shows that it performs better than recent approaches while being much faster at the same time.

  8. 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.

  9. 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...

  10. 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

  11. Assembly of oriented zeolite monolayers and thin films on polymeric surfaces via hydrogen bonding.

    Science.gov (United States)

    Zhou, Ming; Liu, Xiufeng; Zhang, Baoquan; Zhu, Huiming

    2008-10-21

    The b-oriented monolayers of microsized silicalite-1 crystals have been manually assembled on glass plate supported poly(ethylene oxide) (PEO), poly(vinyl alcohol) (PVA), chitosan, and poly(methyl methacrylate) (PMMA) thin films via hydrogen bonding with much enhanced binding strength and satisfactory degrees of coverage and close packing. The exerted pressure and rubbing time in the manual assembly do not affect the binding strength of the silicalite-1 monolayer on the glass plate supported polymeric film. This manual assembly has been further applied to fabricate zeolite monolayers on commercially available Plexiglas surfaces and b-oriented multilayered films of silicalite-1 crystals on glass plates. The assembly method established in this study provides a feasible way to produce zeolite monolayers on polymer-modified solid substrates and Plexiglas and to fabricate zeolite-polymer composite membranes by means of the layer-by-layer technique. PMID:18785711

  12. 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.

  13. THE ROLES OF LIPIDS AND NUCLEIC ACIDS IN HIV-1 ASSEMBLY

    Directory of Open Access Journals (Sweden)

    AynaAlfadhli

    2014-05-01

    Full Text Available During HIV-1 assembly, precursor Gag (PrGag proteins are delivered to plasma membrane (PM assembly sites, where they are triggered to oligomerize and bud from cells as immature virus particles. The delivery and triggering processes are coordinated by the PrGag matrix (MA and nucleocapsid (NC domains. Targeting of PrGag proteins to membranes enriched in cholesterol and phosphatidylinositol-4,5-bisphosphate (PI[4,5]P2 is mediated by the MA domain, which also has been shown to bind both RNA and DNA. Evidence suggests that the nucleic acid-binding function of MA serves to inhibit PrGag binding to inappropriate intracellular membranes, prior to delivery to the PM. At the PM, MA domains putatively trade RNA ligands for PI(4,5P2 ligands, fostering high affinity membrane binding. Triggering of oligomerization, budding and virus particle release results when NC domains on adjacent PrGag proteins bind to viral RNA, leading to capsid (CA domain oligomerization. This process leads to the assembly of immature virus shells in which hexamers of membrane-bound MA trimers appear to organize above interlinked CA hexamers. Here we review the functions of retroviral MA proteins, with an emphasis on the nucleic acid binding capability of the HIV-1 MA protein, and its effects on membrane binding.

  14. 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

  15. Reference-assisted chromosome assembly

    OpenAIRE

    Kim, Jaebum; Larkin, Denis M; Cai, Qingle; Asan,; Zhang, Yongfen; Ge, Ri-Li; Auvil, Loretta; Capitanu, Boris; Zhang, Guojie; Lewin, Harris A.; Ma, Jian

    2013-01-01

    One of the most difficult problems in modern genomics is the assembly of full-length chromosomes using next generation sequencing (NGS) data. To address this problem, we developed “reference-assisted chromosome assembly” (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads. Evaluation of results using simulated and real genome assemblies indicates that ou...

  16. 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...

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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;...

  9. 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...

  10. 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...

  11. Double-degradable responsive self-assembled multivalent arrays--temporary nanoscale recognition between dendrons and DNA.

    Science.gov (United States)

    Barnard, Anna; Posocco, Paola; Fermeglia, Maurizio; Tschiche, Ariane; Calderon, Marcelo; Pricl, Sabrina; Smith, David K

    2014-01-21

    This article reports self-assembling dendrons which bind DNA in a multivalent manner. The molecular design directly impacts on self-assembly which subsequently controls the way these multivalent nanostructures bind DNA--this can be simulated by multiscale modelling. Incorporation of an S-S linkage between the multivalent hydrophilic dendron and the hydrophobic units responsible for self-assembly allows these structures to undergo triggered reductive cleavage, with dithiothreitol (DTT) inducing controlled breakdown, enabling the release of bound DNA. As such, the high-affinity self-assembled multivalent binding is temporary. Furthermore, because the multivalent dendrons are constructed from esters, a second slow degradation step causes further breakdown of these structures. This two-step double-degradation mechanism converts a large self-assembling unit with high affinity for DNA into small units with no measurable binding affinity--demonstrating the advantage of self-assembled multivalency (SAMul) in achieving highly responsive nanoscale binding of biological targets. PMID:24263553

  12. Assembly of the Ebola Virus Nucleoprotein from a Chaperoned VP35 Complex

    OpenAIRE

    Robert N. Kirchdoerfer; Dafna M. Abelson; Sheng Li; Malcolm R. Wood; Erica Ollmann Saphire

    2015-01-01

    Ebolavirus NP oligomerizes into helical filaments found at the core of the virion, encapsidates the viral RNA genome, and serves as a scaffold for additional viral proteins within the viral nucleocapsid. We identified a portion of the phosphoprotein homolog VP35 that binds with high affinity to nascent NP and regulates NP assembly and viral genome binding. Removal of the VP35 peptide leads to NP self-assembly via its N-terminal oligomerization arm. NP oligomerization likely causes a conformat...

  13. Nuclear reactor fuel assembly

    International Nuclear Information System (INIS)

    The description is given of a nuclear reactor fuel assembly comprising fuel elements arranged in a supporting frame composed of two end pieces, one at the top and the other at the bottom, on which are secured the ends of a number of vertical tubes, each end piece comprising a plane bottom on which two series of holes are made for holding the tubes and for the passage of the coolant. According to the invention, the bottom of each end piece is fixed to an internal plate fitted with the same series of holes for holding the tubes and for the fluid to pass through. These holes are of oblong section and are fitted with fixing elements cooperating with corresponding elements for securing these tubes by transversal movement of the inside plate

  14. 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)

  15. 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)

  16. 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.

  17. Fuel assembly supports

    International Nuclear Information System (INIS)

    Purpose: To prevent fuel assembly from lifting by forming through holes in the entrance nozzle and the connection pipe respectively opposed to each other and forming an expanded portion and inserting therein a stopper member at the position where the two holes are joined. Constitution: A through hole is formed in a connection tube slanted upwardly and inwardly from a high pressure plenum to the inside of the connection tube. While on the other hand, another through hole slanted with same angle is also formed to the reduced diameter portion of an entrance nozzle at the position corresponding to the above hole in the connection tube. Further, an expanded diameter section is formed to the inside of the connection tube and the outside of the reduced diameter section of the entrance nozzle, and a steel ball is mounted therein. (Kawakami, Y.)

  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. 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

  20. Inhibition of selectin binding

    Energy Technology Data Exchange (ETDEWEB)

    Nagy, Jon O. (Rodeo, CA); Spevak, Wayne R. (Albany, CA); Dasgupta, Falguni (New Delhi, IN); Bertozzi, Caroline (Albany, CA)

    2001-10-09

    This invention provides compositions for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, these composition scan be used to palliate certain inflammatory and immunological conditions.

  1. Inhibition of selectin binding

    Energy Technology Data Exchange (ETDEWEB)

    Nagy, J.O.; Spevak, W.R.; Dasgupta, F.; Bertozzi, C.

    1999-10-05

    This invention provides a system for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10{sup 6} fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, this system can be used to palliate certain inflammatory and immunological conditions.

  2. Inhibition of selectin binding

    Energy Technology Data Exchange (ETDEWEB)

    Nagy, Jon O. (Rodeo, CA); Spevak, Wayne R. (Albany, CA); Dasgupta, Falguni (New Delhi, IN); Bertozzi, Caroline (Albany, CA)

    1999-01-01

    This invention provides compositions for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, these composition scan be used to palliate certain inflammatory and immunological conditions.

  3. Inhibition of selectin binding

    Energy Technology Data Exchange (ETDEWEB)

    Nagy, J.O.; Spevak, W.R.; Dasgupta, F.; Bertozzi, C.

    1999-11-16

    This invention provides compositions for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10{sup 6} fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, these composition scan be used to palliate certain inflammatory and immunological conditions.

  4. Inhibition of selectin binding

    Energy Technology Data Exchange (ETDEWEB)

    Nagy, Jon O. (Rodeo, CA); Spevak, Wayne R. (Albany, CA); Dasgupta, Falguni (New Delhi, IN); Bertozzi, Carolyn (Albany, CA)

    1999-10-05

    This invention provides a system for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, this system can be used to palliate certain inflammatory and immunological conditions.

  5. 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.

  6. 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...

  7. 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.

  8. 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."...

  9. 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.

  10. 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…

  11. 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.

  12. 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

  13. 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...

  14. 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

  15. Targeted Chemical Wedges Reveal the Role of Allosteric DNA Modulation in Protein — DNA Assembly

    OpenAIRE

    Moretti, Rocco; Donato, Leslie J.; Brezinski, Mary L.; Stafford, Ryan L.; Hoff, Helena; Thorson, Jon S.; Dervan, Peter B.; Ansari, Aseem Z.

    2008-01-01

    The cooperative assembly of multiprotein complexes results from allosteric modulations of DNA structure as well as direct intermolecular contacts between proteins. Such cooperative binding plays a critical role in imparting exquisite sequence specificity on the homeobox transcription factor (Hox) family of developmental transcription factors. A well-characterized example includes the interaction of Hox proteins with extradenticle (Exd), a highly conserved DNA binding transcription factor. Alt...

  16. 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.

  17. Types for DSP Assembler Programs

    DEFF Research Database (Denmark)

    Larsen, Ken

    2006-01-01

    of a block of memory, thus enabling type checking of programs that directly manage and reuse memory. I show that both the baseline type system and the extended type system can be used to give type annotations to handwritten DSP assembler code, and that these annotations precisely and succinctly......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...... assembler language. However, programming in assembler causes numerous problems, such as memory corruption, for instance. To test the thesis I define a model assembler language called Featherweight DSP which captures some of the essential features of a real custom DSP used in the industrial partner's digital...

  18. 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.

  19. 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.

  20. In silico docking of forchlorfenuron (FCF to septins suggests that FCF interferes with GTP binding.

    Directory of Open Access Journals (Sweden)

    Dimitrios Angelis

    Full Text Available Septins are GTP-binding proteins that form cytoskeleton-like filaments, which are essential for many functions in eukaryotic organisms. Small molecule compounds that disrupt septin filament assembly are valuable tools for dissecting septin functions with high temporal control. To date, forchlorfenuron (FCF is the only compound known to affect septin assembly and functions. FCF dampens the dynamics of septin assembly inducing the formation of enlarged stable polymers, but the underlying mechanism of action is unknown. To investigate how FCF binds and affects septins, we performed in silico simulations of FCF docking to all available crystal structures of septins. Docking of FCF with SEPT2 and SEPT3 indicated that FCF interacts preferentially with the nucleotide-binding pockets of septins. Strikingly, FCF is predicted to form hydrogen bonds with residues involved in GDP-binding, mimicking nucleotide binding. FCF docking with the structure of SEPT2-GppNHp, a nonhydrolyzable GTP analog, and SEPT7 showed that FCF may assume two alternative non-overlapping conformations deeply into and on the outer side of the nucleotide-binding pocket. Surprisingly, FCF was predicted to interact with the P-loop Walker A motif GxxxxGKS/T, which binds the phosphates of GTP, and the GTP specificity motif AKAD, which interacts with the guanine base of GTP, and highly conserved amino acids including a threonine, which is critical for GTP hydrolysis. Thus, in silico FCF exhibits a conserved mechanism of binding, interacting with septin signature motifs and residues involved in GTP binding and hydrolysis. Taken together, our results suggest that FCF stabilizes septins by locking them into a conformation that mimics a nucleotide-bound state, preventing further GTP binding and hydrolysis. Overall, this study provides the first insight into how FCF may bind and stabilize septins, and offers a blueprint for the rational design of FCF derivatives that could target septins with

  1. 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

  2. Programmable DNA scaffolds for spatially-ordered protein assembly

    Science.gov (United States)

    Chandrasekaran, Arun Richard

    2016-02-01

    Ever since the notion of using DNA as a material was realized, it has been employed in the construction of complex structures that facilitate the assembly of nanoparticles or macromolecules with nanometer-scale precision. Specifically, tiles fashioned from DNA strands and DNA origami sheets have been shown to be suitable as scaffolds for immobilizing proteins with excellent control over their spatial positioning. Supramolecular assembly of proteins into periodic arrays in one or more dimensions is one of the most challenging aspects in the design of scaffolds for biomolecular investigations and macromolecular crystallization. This review provides a brief overview of how various biomolecular interactions with high degree of specificity such as streptavidin-biotin, antigen-antibody, and aptamer-protein interactions have been used to fabricate linear and multidimensional assemblies of structurally intact and functional proteins. The use of DNA-binding proteins as adaptors, polyamide recognition on DNA scaffolds and oligonucleotide linkers for protein assembly are also discussed.Ever since the notion of using DNA as a material was realized, it has been employed in the construction of complex structures that facilitate the assembly of nanoparticles or macromolecules with nanometer-scale precision. Specifically, tiles fashioned from DNA strands and DNA origami sheets have been shown to be suitable as scaffolds for immobilizing proteins with excellent control over their spatial positioning. Supramolecular assembly of proteins into periodic arrays in one or more dimensions is one of the most challenging aspects in the design of scaffolds for biomolecular investigations and macromolecular crystallization. This review provides a brief overview of how various biomolecular interactions with high degree of specificity such as streptavidin-biotin, antigen-antibody, and aptamer-protein interactions have been used to fabricate linear and multidimensional assemblies of structurally

  3. 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

  4. 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

  5. ASSEMBLY TRANSFER SYSTEM DESCRIPTION DOCUMENT

    International Nuclear Information System (INIS)

    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

  6. 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...

  7. 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

  8. 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)

  9. MOX fuel assembly

    International Nuclear Information System (INIS)

    The fuel assembly of the present invention comprises at least one water rod, first fuel rods filled with uranium/plutonium mixed oxide fuels, second fuel rods having axial length shorter than that of the first fuel rods and third fuel rods containing burnable poisons. If the third fuel rods are arranged on the same row and adjacent columns or on the same column and adjacent row relative to the positions where the second fuel rods are arranged or the position of the water rod replacing fuel rods, in other words, at a position extremely close to them, neutron spectrum is made softer and the neutron flux distribution is made higher. As a result, negative reactivity worth of the burnable poisons contained in the third fuel rods is enhanced, accordingly, a reactivity suppression effect comparable with that in conventional cases can be obtained by so much even if the number of the third fuel rods is reduced. The number of the MOX fuel rods is increased than a conventional case by so much as replacing the third fuel rods with the MOX fuel rods by the reduced amount thereby enabling to improve the efficiency using plutonium. (N.H.)

  10. Control rod assembly

    International Nuclear Information System (INIS)

    In a control rod assembly comprising an extension rod extended upwardly from the upper end of a control rod main body disposed in a reactor core and an extension tube engaging a grip portion disposed to an upper portion of the extension rod for suspending the control rod main body, a shrinkable portion is disposed to a part of the extension tube or extension rod, or a grip portion shrinkable in the axial direction is disposed to the extension rod. Further, a spring is interposed to a portion of the extension tube and bellows are disposed to the inner side or the outer side of the spring. A double-cylindrical temperature sensing member is disposed surrounding the outer side of the bellows or the spring. Liquid metals are sealed in the temperature sensing member or the bellows. This can improve the response of the coolants to the temperature elevation and can suppress the change of the reactor core insertion amount relative to temperature change during usual operation. (T.M.)

  11. Nuclear fuel assembly

    International Nuclear Information System (INIS)

    In a nuclear fuel assembly comprising a nuclear fuel bundle in which a plurality of nuclear rods are bond by an upper tie plate, spacers and lower tie plate and a channel box containing them, the inner surface of the channel box and the surface of the lower tie plate opposing thereto are fabricated into step-like configuration respectively and the two fabricated surfaces are opposed to each other to constitute a step-like labyrinth flow channel. With such a configuration, when a fluid flows from higher pressure to lower pressure side, pressure loss is caused due to fluid friction in proportion with the length of the flow channel, due to the change of the flowing direction and, further, in accordance with deceleration or acceleration at each of the stepped portions. The total for each of the pressure loses constitutes the total pressure loss in the labyrinth. That is, if the pressure difference between the inside and the outside of the channel box is identical, the amount of leakage is reduced by so much as the increase of the total pressure loss, to thereby improve the stability of the reactor core and fuel economy. (T.M.)

  12. 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.

  13. 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...

  14. The conformational state of the nucleosome entry–exit site modulates TATA box-specific TBP binding

    OpenAIRE

    Aaron R Hieb; Gansen, Alexander; Böhm, Vera; Langowski, Jörg

    2014-01-01

    The TATA binding protein (TBP) is a critical transcription factor used for nucleating assembly of the RNA polymerase II machinery. TBP binds TATA box elements with high affinity and kinetic stability and in vivo is correlated with high levels of transcription activation. However, since most promoters use less stable TATA-less or TATA-like elements, while also competing with nucleosome occupancy, further mechanistic insight into TBP's DNA binding properties and ability to access chromatin is n...

  15. Influence of self-assembly on intercalative DNA binding interaction of double-chain surfactant Co(III) complexes containing imidazo[4,5-f][1,10]phenanthroline and dipyrido[3,2-d:2'-3'-f]quinoxaline ligands: experimental and theoretical study.

    Science.gov (United States)

    Nagaraj, Karuppiah; Velmurugan, Gunasekaran; Sakthinathan, Subramanian; Venuvanalingam, Ponnambalam; Arunachalam, Sankaralingam

    2014-12-28

    A new class of surfactant Co(III) complexes, cis-[Co(ip)2(C12H25NH2)2](ClO4)3 (1) and cis-[Co(dpq)2(C12H25NH2)2](ClO4)3 (2) (ip = imidazo[4,5-f][1,10]phenanthroline, dpq = dipyrido[3,2-d:2'-3'-f]quinoxaline), have been synthesized and characterized by various spectroscopic and physico-chemical techniques. The critical micelle concentration (CMC) values of these complexes in aqueous solution were obtained from conductance measurements. The specific conductivity data (at 303, 308, 313, 318 and 323 K) served for the evaluation of the temperature-dependent CMC and the thermodynamics of micellization (ΔG(0)(m), ΔH(0)(m) and ΔS(0)(m)). The trend in DNA-binding affinities and the spectral properties of a series of complexes, cis-[Co(ip)2(C12H25NH2)2](ClO4)3 (1) and cis-[Co(dpq)2(C12H25NH2)2](ClO4)3 (2), have been experimentally and theoretically investigated. The experimental results indicate that the size and shape of the intercalated ligand and hydrophobicity of the complexes have a marked effect on the binding affinity of the complexes to CT DNA in intercalation mode, and the order of their intrinsic DNA-binding constants Kb is Kb(1) extended aromatic ring and optical properties of the complexes can be reasonably explained by applying the DFT calculations. The energy gap between HOMO and LUMO indicates that these complexes are prone to interact with CT DNA. Further, molecular docking calculations have also been performed to understand the nature of binding of the complexes and the result confirms that the complexes interact with CT DNA through the alkyl chain. The cytotoxic activity of these complexes on human liver carcinoma cancer cells were determined adopting MTT assay and specific staining techniques, which revealed that the viability of the cells thus treated was significantly decreased and the cells succumbed to apoptosis as seen in the changes in the nuclear morphology and cytoplasmic features. PMID:25354359

  16. 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.

  17. Bearing assemblies, apparatuses, and motor assemblies using the same

    Energy Technology Data Exchange (ETDEWEB)

    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.

  18. 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.

  19. 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.

  20. Directed Assembly of Gold Nanoparticles

    DEFF Research Database (Denmark)

    Westerlund, Axel Rune Fredrik; Bjørnholm, Thomas

    2009-01-01

    As a complement to common "top-down" lithography techniques, "bottom-up" assembly techniques are emerging as promising tools to build nanoscale structures in a predictable way. Gold nanoparticles that are stable and relatively easy to synthesize are important building blocks in many such structures...... due to their useful optical and electronic properties. Programmed assembly of gold nanoparticles in one, two, and three dimensions is therefore of large interest. This review focuses on the progress from the last three years in the field of directed gold nanoparticle and nanorod assembly using...

  1. Lil3 Assembles with Proteins Regulating Chlorophyll Synthesis in Barley.

    Directory of Open Access Journals (Sweden)

    Astrid Mork-Jansson

    Full Text Available The light-harvesting-like (LIL proteins are a family of membrane proteins that share a chlorophyll a/b-binding motif with the major light-harvesting antenna proteins of oxygenic photoautotrophs. LIL proteins have been associated with the regulation of tetrapyrrol biosynthesis, and plant responses to light-stress. Here, it was found in a native PAGE approach that chlorophyllide, and chlorophyllide plus geranylgeraniolpyrophosphate trigger assembly of Lil3 in three chlorine binding fluorescent protein bands, termed F1, F2, and F3. It is shown that light and chlorophyllide trigger accumulation of protochlorophyllide-oxidoreductase, and chlorophyll synthase in band F3. Chlorophyllide and chlorophyll esterified to geranylgeraniol were identified as basis of fluorescence recorded from band F3. A direct interaction between Lil3, CHS and POR was confirmed in a split ubiquitin assay. In the presence of light or chlorophyllide, geranylgeraniolpyrophosphate was shown to trigger a loss of the F3 band and accumulation of Lil3 and geranylgeranyl reductase in F1 and F2. No direct interaction between Lil3 and geranylgeraniolreductase was identified in a split ubiquitin assay; however, accumulation of chlorophyll esterified to phytol in F1 and F2 corroborated the enzymes assembly. Chlorophyll esterified to phytol and the reaction center protein psbD of photosystem II were identified to accumulate together with psb29, and APX in the fluorescent band F2. Data show that Lil3 assembles with proteins regulating chlorophyll synthesis in etioplasts from barley (Hordeum vulgare L..

  2. 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

    2016-01-01

    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. PMID:27113637

  3. Cyclophilin 40 facilitates HSP90-mediated RISC assembly in plants.

    Science.gov (United States)

    Iki, Taichiro; Yoshikawa, Manabu; Meshi, Tetsuo; Ishikawa, Masayuki

    2012-01-18

    Posttranscriptional gene silencing is mediated by RNA-induced silencing complexes (RISCs) that contain AGO proteins and single-stranded small RNAs. The assembly of plant AGO1-containing RISCs depends on the molecular chaperone HSP90. Here, we demonstrate that cyclophilin 40 (CYP40), protein phosphatase 5 (PP5), and several other proteins with the tetratricopeptide repeat (TPR) domain associates with AGO1 in an HSP90-dependent manner in extracts of evacuolated tobacco protoplasts (BYL). Intriguingly, CYP40, but not the other TPR proteins, could form a complex with small RNA duplex-bound AGO1. Moreover, CYP40 that was synthesized by in-vitro translation using BYL uniquely facilitated binding of small RNA duplexes to AGO1, and as a result, increased the amount of mature RISCs that could cleave target RNAs. CYP40 was not contained in mature RISCs, indicating that the association is transient. Addition of PP5 or cyclophilin-binding drug cyclosporine A prevented the association of endogenous CYP40 with HSP90-AGO1 complex and inhibited RISC assembly. These results suggest that a complex of AGO1, HSP90, CYP40, and a small RNA duplex is a key intermediate of RISC assembly in plants. PMID:22045333

  4. 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.

  5. Analysis of Illumina Microbial Assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Clum, Alicia; Foster, Brian; Froula, Jeff; LaButti, Kurt; Sczyrba, Alex; Lapidus, Alla; Woyke, Tanja

    2010-05-28

    Since the emerging of second generation sequencing technologies, the evaluation of different sequencing approaches and their assembly strategies for different types of genomes has become an important undertaken. Next generation sequencing technologies dramatically increase sequence throughput while decreasing cost, making them an attractive tool for whole genome shotgun sequencing. To compare different approaches for de-novo whole genome assembly, appropriate tools and a solid understanding of both quantity and quality of the underlying sequence data are crucial. Here, we performed an in-depth analysis of short-read Illumina sequence assembly strategies for bacterial and archaeal genomes. Different types of Illumina libraries as well as different trim parameters and assemblers were evaluated. Results of the comparative analysis and sequencing platforms will be presented. The goal of this analysis is to develop a cost-effective approach for the increased throughput of the generation of high quality microbial genomes.

  6. Shingle assembly with support bracket

    Science.gov (United States)

    Almy, Charles

    2007-01-02

    A shingle system, mountable to a support surface, includes overlapping shingle assemblies. Each shingle assembly comprises a support bracket, having upper and lower ends, secured to a shingle body. The upper end has an upper support portion, extending away from the shingle body, and an upper support-surface-engaging part, engageable with a support surface so that the upper edge of the shingle body is positionable at a first distance from the support surface to create a first gap therebetween. The lower end has a lower support portion extending away from the lower surface. The support brackets create: (1) a second gap between shingle bodies of the first and second shingle assemblies, and (2) an open region beneath the first shingle assembly fluidly coupling the first and second gaps.

  7. 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.

  8. 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.

  9. Structural and dynamic properties of linker histone H1 binding to DNA

    OpenAIRE

    Dootz, Rolf; Toma, Adriana C.; 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. ...

  10. Proteomic Screening Method for Phosphopeptide Motif Binding Proteins Using Peptide Libraries

    OpenAIRE

    Christofk, Heather R.; Wu, Ning; Cantley, Lewis C.; John M. Asara

    2011-01-01

    Phosphopeptide binding domains mediate the directed and localized assembly of protein complexes essential to intracellular kinase signaling. To identify phosphopeptide binding proteins, we developed a proteomic screening method using immobilized partially-degenerate phosphopeptide mixtures combined with SILAC and microcapillary LC/MS/MS. The method was used to identify proteins that specifically bound to phosphorylated peptide library affinity matrices, including pTyr, and the motifs pSer/pTh...

  11. 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 ...

  12. 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...

  13. Monomeric Yeast Frataxin is an Iron Binding Protein†

    Energy Technology Data Exchange (ETDEWEB)

    Cook, J.; Bencze, K; Jankovic, A; Crater, A; Busch, C; Bradley, P; Stemmler, A; Spaller, M; Stemmler, T

    2009-01-01

    Friedreich's ataxia, an autosomal cardio- and neurodegenerative disorder that affects 1 in 50000 humans, is caused by decreased levels of the protein frataxin. Although frataxin is nuclear-encoded, it is targeted to the mitochondrial matrix and necessary for proper regulation of cellular iron homeostasis. Frataxin is required for the cellular production of both heme and iron-sulfur (Fe-S) clusters. Monomeric frataxin binds with high affinity to ferrochelatase, the enzyme involved in iron insertion into porphyrin during heme production. Monomeric frataxin also binds to Isu, the scaffold protein required for assembly of Fe-S cluster intermediates. These processes (heme and Fe-S cluster assembly) share requirements for iron, suggesting that monomeric frataxin might function as the common iron donor. To provide a molecular basis to better understand frataxin's function, we have characterized the binding properties and metal-site structure of ferrous iron bound to monomeric yeast frataxin. Yeast frataxin is stable as an iron-loaded monomer, and the protein can bind two ferrous iron atoms with micromolar binding affinity. Frataxin amino acids affected by the presence of iron are localized within conserved acidic patches located on the surfaces of both helix-1 and strand-1. Under anaerobic conditions, bound metal is stable in the high-spin ferrous state. The metal-ligand coordination geometry of both metal-binding sites is consistent with a six-coordinate iron-(oxygen/nitrogen) based ligand geometry, surely constructed in part from carboxylate and possibly imidazole side chains coming from residues within these conserved acidic patches on the protein. On the basis of our results, we have developed a model for how we believe yeast frataxin interacts with iron.

  14. Monomeric Yeast Frataxin is an Iron-Binding Protein

    Energy Technology Data Exchange (ETDEWEB)

    Cook,J.; Bencze, K.; Jankovic, A.; Crater, A.; Busch, C.; Bradley, P.; Stemmler, A.; Spaller, M.; Stemmler, T.

    2006-01-01

    Friedreich's ataxia, an autosomal cardio- and neurodegenerative disorder that affects 1 in 50 000 humans, is caused by decreased levels of the protein frataxin. Although frataxin is nuclear-encoded, it is targeted to the mitochondrial matrix and necessary for proper regulation of cellular iron homeostasis. Frataxin is required for the cellular production of both heme and iron-sulfur (Fe-S) clusters. Monomeric frataxin binds with high affinity to ferrochelatase, the enzyme involved in iron insertion into porphyrin during heme production. Monomeric frataxin also binds to Isu, the scaffold protein required for assembly of Fe-S cluster intermediates. These processes (heme and Fe-S cluster assembly) share requirements for iron, suggesting that monomeric frataxin might function as the common iron donor. To provide a molecular basis to better understand frataxin's function, we have characterized the binding properties and metal-site structure of ferrous iron bound to monomeric yeast frataxin. Yeast frataxin is stable as an iron-loaded monomer, and the protein can bind two ferrous iron atoms with micromolar binding affinity. Frataxin amino acids affected by the presence of iron are localized within conserved acidic patches located on the surfaces of both helix-1 and strand-1. Under anaerobic conditions, bound metal is stable in the high-spin ferrous state. The metal-ligand coordination geometry of both metal-binding sites is consistent with a six-coordinate iron-(oxygen/nitrogen) based ligand geometry, surely constructed in part from carboxylate and possibly imidazole side chains coming from residues within these conserved acidic patches on the protein. On the basis of our results, we have developed a model for how we believe yeast frataxin interacts with iron.

  15. Monomeric Yeast Frataxin is an Iron-Binding Protein

    International Nuclear Information System (INIS)

    Friedreich's ataxia, an autosomal cardio- and neurodegenerative disorder that affects 1 in 50 000 humans, is caused by decreased levels of the protein frataxin. Although frataxin is nuclear-encoded, it is targeted to the mitochondrial matrix and necessary for proper regulation of cellular iron homeostasis. Frataxin is required for the cellular production of both heme and iron-sulfur (Fe-S) clusters. Monomeric frataxin binds with high affinity to ferrochelatase, the enzyme involved in iron insertion into porphyrin during heme production. Monomeric frataxin also binds to Isu, the scaffold protein required for assembly of Fe-S cluster intermediates. These processes (heme and Fe-S cluster assembly) share requirements for iron, suggesting that monomeric frataxin might function as the common iron donor. To provide a molecular basis to better understand frataxin's function, we have characterized the binding properties and metal-site structure of ferrous iron bound to monomeric yeast frataxin. Yeast frataxin is stable as an iron-loaded monomer, and the protein can bind two ferrous iron atoms with micromolar binding affinity. Frataxin amino acids affected by the presence of iron are localized within conserved acidic patches located on the surfaces of both helix-1 and strand-1. Under anaerobic conditions, bound metal is stable in the high-spin ferrous state. The metal-ligand coordination geometry of both metal-binding sites is consistent with a six-coordinate iron-(oxygen/nitrogen) based ligand geometry, surely constructed in part from carboxylate and possibly imidazole side chains coming from residues within these conserved acidic patches on the protein. On the basis of our results, we have developed a model for how we believe yeast frataxin interacts with iron

  16. TIGER: tiled iterative genome assembler

    OpenAIRE

    Wu Xiao-Long; Heo Yun; El Hajj Izzat; Hwu Wen-Mei; Chen Deming; Ma Jian

    2012-01-01

    Abstract Background With the cost reduction of the next-generation sequencing (NGS) technologies, genomics has provided us with an unprecedented opportunity to understand fundamental questions in biology and elucidate human diseases. De novo genome assembly is one of the most important steps to reconstruct the sequenced genome. However, most de novo assemblers require enormous amount of computational resource, which is not accessible for most research groups and medical personnel. Results We ...

  17. 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....

  18. 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.

  19. 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!

  20. 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

  1. General Assembly debate on IAEA

    International Nuclear Information System (INIS)

    On 3 November 1959, the General Assembly of the United Nations considered the annual report of the International Atomic Energy Agency, the first report to cover a full operational year of the Agency - 1 July 1959 to 30 June 1959, more recent developments having been summarized in a preface. At the end of the debate the Assembly adopted a resolution, submitted jointly by Czechoslovakia, the Union of South Africa and the United Arab Republic, taking note of the report

  2. Combinatorial Synthesis, Screening, and Binding Studies of Highly Functionalized Polyamino-amido Oligomers for Binding to Folded RNA

    Directory of Open Access Journals (Sweden)

    Jonathan K. Pokorski

    2012-01-01

    Full Text Available Folded RNA molecules have recently emerged as critical regulatory elements in biological pathways, serving not just as carriers of genetic information but also as key components in enzymatic assemblies. In particular, the transactivation response element (TAR of the HIV genome regulates transcriptional elongation by interacting specifically with the Tat protein, initiating the recruitment of the elongation complex. Preventing this interaction from occurring in vivo halts HIV replication, thus making RNA-binding molecules an intriguing pharmaceutical target. Using α-amino acids as starting materials, we have designed and synthesized a new class of polyamino-amido oligomers, called PAAs, specifically for binding to folded RNA structures. The PAA monomers were readily incorporated into a 125-member combinatorial library of PAA trimers. In order to rapidly assess RNA binding, a quantum dot-based fluorescent screen was developed to visualize RNA binding on-resin. The binding affinities of hits were quantified using a terbium footprinting assay, allowing us to identify a ligand (SFF with low micromolar affinity (kd=14 μM for TAR RNA. The work presented herein represents the development of a flexible scaffold that can be easily synthesized, screened, and subsequently modified to provide ligands specific for binding to folded RNAs.

  3. 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

  4. Self-assembly of three-legged patchy particles into polyhedral cages

    International Nuclear Information System (INIS)

    The self-assembly of rigid three-legged building blocks into polyhedral cages is investigated by patchy particle simulations. A four-site anisotropic interaction potential is introduced to make pairs of overlapping legs bind in an anti-parallel fashion, thereby forming the edges of a polyhedron of pentagons and hexagons. A torsional potential, reflecting an asymmetry or polarity in the legs' binding potential, proves crucial for the successful formation of closed fullerene-like cages. Self-assembly proceeds by a nucleation-and-growth mechanism, with a high success rate of cage closure. The size distribution of the self-assembled buckyballs is largely determined by the pucker angle of the particle. Nature explores a similar building block, the clathrin triskelion, to regulate vesicle formation at the cell membrane during endocytosis.

  5. 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

  6. DNA-binding residues and binding mode prediction with binding-mechanism concerned models

    OpenAIRE

    Oyang Yen-Jen; Liu Yu-Cheng; Huang Chun-Chin; Huang Yu-Feng; Huang Chien-Kang

    2009-01-01

    Abstract Background Protein-DNA interactions are essential for fundamental biological activities including DNA transcription, replication, packaging, repair and rearrangement. Proteins interacting with DNA can be classified into two categories of binding mechanisms - sequence-specific and non-specific binding. Protein-DNA specific binding provides a mechanism to recognize correct nucleotide base pairs for sequence-specific identification. Protein-DNA non-specific binding shows sequence indepe...

  7. Carboplatin binding to histidine

    International Nuclear Information System (INIS)

    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

  8. 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.

  9. 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

  10. 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.

  11. Heteromeric assembly of P2X subunits

    Directory of Open Access Journals (Sweden)

    Ralf Hausmann

    2013-12-01

    Full Text Available Transcripts and/or proteins of P2X receptor (P2XR subunits have been found in virtually all mammalian tissues. Generally more than one of the seven known P2X subunits have been identified in a given cell type. Six of the seven cloned P2X subunits can efficiently form functional homotrimeric ion channels in recombinant expression systems. This is in contrast to other ligand-gated ion channel families, such as the Cys-loop or glutamate receptors, where homomeric assemblies seem to represent the exception rather than the rule. P2XR mediated responses recorded from native tissues rarely match exactly the biophysical and pharmacological properties of heterologously expressed homomeric P2XRs. Heterotrimerization of P2X subunits is likely to account for this observed diversity. While the existence of heterotrimeric P2X2/3Rs and their role in physiological processes is well established, the composition of most other P2XR heteromers and/or the interplay between distinct trimeric receptor complexes in native tissues is not clear. After a description of P2XR assembly and the structure of the intersubunit ATP-binding site, this review summarizes the distribution of P2XR subunits in selected mammalian cell types and the biochemically and/or functionally characterized heteromeric P2XRs that have been observed upon heterologous co-expression of P2XR subunits. We further provide examples where the postulated heteromeric P2XRs have been suggested to occur in native tissues and an overview of the currently available pharmacological tools that have been used to discriminate between homo- and heteromeric P2XRs

  12. 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 §...

  13. 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...

  14. 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....

  15. 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...

  16. 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

  17. 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

  18. Controlled short-linkage assembly of functional nano-objects

    International Nuclear Information System (INIS)

    Graphical abstract: - Highlights: • Fast photoconjugation of nanoparticles on surface. • Non-destructive feature guarantees intact function of nanoparticles. • Direct contact between nano-objects allows efficient photon and electron transfer. • Possibility of generating patterned nanoparticle assemblies on surface. • Open new opportunities for assembling chemical sensors. - Abstract: In this work, we report a method that allows the deterministic, photo-controlled covalent assembly of nanoparticles directly on surface. As a model system, we study the conjugation of molecularly imprinted polymer (MIP) nanoparticles on a glass surface and confirm that the immobilized nanoparticles maintain their molecular recognition functionality. The glass slide was first modified with perfluorophenylazide and then used to bind MIP nanoparticles under UV irradiation. After each step the surface was analyzed by water contact angle measurement, fluorescence microscopy, scanning electron microscopy, and/or synchrotron-based X-ray photoelectron spectroscopy. The MIP nanoparticles immobilized on the glass surface remained stable and maintained specific binding for the template molecule, propranolol. The method developed in this work allows MIP nanoparticles to be directly coupled to a flat surface, offering a straightforward means to construct robust chemical sensors. Using the reported photo conjugation method, it is possible to generate patterned assembly of nanoparticles using a photomask. Since perfluorophenylazide-based photochemistry works with all kinds of organic material, the method developed in this work is expected to enable immobilization of not only MIPs but also other kinds of organic and inorganic–organic core–shell particles for various applications involving photon or electron transfer

  19. Collagen binding to Staphylococcus aureus

    International Nuclear Information System (INIS)

    Staphylococcus aureus can bind soluble collagen in a specific, saturable manner. We have previously shown that some variability exists in the degree of collagen binding between different strains of heat-killed, formaldehyde-fixed S. aureus which are commercially available as immunologic reagents. The present study demonstrates that live S. aureus of the Cowan 1 strain binds amounts of collagen per organism equivalent to those demonstrated previously in heat-killed, formaldehyde-fixed bacteria but has an affinity over 100 times greater, with Kd values of 9.7 X 10(-11) M and 4.3 X 10(-8) M for live and heat-killed organisms, respectively. Studies were also carried out with S. aureus killed by ionizing radiation, since this method of killing the organism seemed less likely to alter the binding moieties on the surface than did heat killing. Bacteria killed by exposure to gamma radiation bound collagen in a manner essentially indistinguishable from that of live organisms. Binding of collagen to irradiated cells of the Cowan 1 strain was rapid, with equilibrium reached by 30 min at 22 degrees C, and was fully reversible. The binding was not inhibited by fibronectin, fibrinogen, C1q, or immunoglobulin G, suggesting a binding site for collagen distinct from those for these proteins. Collagen binding was virtually eliminated in trypsin-treated organisms, indicating that the binding site has a protein component. Of four strains examined, Cowan 1 and S. aureus ATCC 25923 showed saturable, specific binding, while strains Woods and S4 showed a complete lack of binding. These results suggest that some strains of S. aureus contain high-affinity binding sites for collagen. While the number of binding sites per bacterium varied sixfold in the two collagen-binding strains, the apparent affinity was similar

  20. Assembly of the Ebola Virus Nucleoprotein from a Chaperoned VP35 Complex.

    Science.gov (United States)

    Kirchdoerfer, Robert N; Abelson, Dafna M; Li, Sheng; Wood, Malcolm R; Saphire, Erica Ollmann

    2015-07-01

    Ebolavirus NP oligomerizes into helical filaments found at the core of the virion, encapsidates the viral RNA genome, and serves as a scaffold for additional viral proteins within the viral nucleocapsid. We identified a portion of the phosphoprotein homolog VP35 that binds with high affinity to nascent NP and regulates NP assembly and viral genome binding. Removal of the VP35 peptide leads to NP self-assembly via its N-terminal oligomerization arm. NP oligomerization likely causes a conformational change between the NP N- and C-terminal domains, facilitating RNA binding. These functional data are complemented by crystal structures of the NP°-VP35 complex at 2.4 Å resolution. The interactions between NP and VP35 illuminated by these structures are conserved among filoviruses and provide key targets for therapeutic intervention. PMID:26119732

  1. Assembly of the Ebola Virus Nucleoprotein from a Chaperoned VP35 Complex

    Directory of Open Access Journals (Sweden)

    Robert N. Kirchdoerfer

    2015-07-01

    Full Text Available Ebolavirus NP oligomerizes into helical filaments found at the core of the virion, encapsidates the viral RNA genome, and serves as a scaffold for additional viral proteins within the viral nucleocapsid. We identified a portion of the phosphoprotein homolog VP35 that binds with high affinity to nascent NP and regulates NP assembly and viral genome binding. Removal of the VP35 peptide leads to NP self-assembly via its N-terminal oligomerization arm. NP oligomerization likely causes a conformational change between the NP N- and C-terminal domains, facilitating RNA binding. These functional data are complemented by crystal structures of the NP°-VP35 complex at 2.4 Å resolution. The interactions between NP and VP35 illuminated by these structures are conserved among filoviruses and provide key targets for therapeutic intervention.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Melanin binding radiopharmaceuticals

    International Nuclear Information System (INIS)

    We have determined the biodistribution an uptake by the Greene melanoma in the Syrian golden hamster with 21 radiopharmaceuticals. Maximum % uptake and the time at which this occurred are listed. It is essential to know maximum tumor to background ration and the time after injection that this occurs to determine suitability for tumor scanning. The importance of species variation deserves mention. Detection of eye melanoma in humans was quite variable whereas in hamsters it was quite easy to obtain a positive scan with a single pinhole. We then looked at brain uptake in man and found it (the brain scan) to be significant. In addition, we found a high uptake by the lung, something not found in hamsters but not entirely unsuspected of a amine, such as 123I-4,3DMQ. Finally, our clinical experience has shown us some of the vagaries of melanoma-seeking radiopharmaceuticals. This reflects the complexity of melanin and melanin-binding and points out the necessity for a more detailed analysis of the mechanisms involved in melanin binding radionuclides

  7. Swivel base for fuel assembly storage

    International Nuclear Information System (INIS)

    An invention is described the principal object of which is to provide a nuclear fuel assembly storage rack capable of supporting spent fuel assemblies without generating stresses in the fuel assemblies. The storage rack consists of a lower and upper support for supporting and retaining the spent fuel assemblies in their vertical positions. Relief from any stresses in the fuel assembly during storage is obtained by the provision of a swivel base in the lower support. (U.K.)

  8. QUAST: quality assessment tool for genome assemblies

    OpenAIRE

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

    2013-01-01

    Summary: Limitations of genome sequencing techniques have led to dozens of assembly algorithms, none of which is perfect. A number of methods for comparing assemblers have been developed, but none is yet a recognized benchmark. Further, most existing methods for comparing assemblies are only applicable to new assemblies of finished genomes; the problem of evaluating assemblies of previously unsequenced species has not been adequately considered. Here, we present QUAST—a quality assessment too...

  9. Next Generation Sequence Assembly with AMOS

    OpenAIRE

    Treangen, Todd J; Sommer, Dan D; Angly, Florent E; Koren, Sergey; Pop, Mihai

    2011-01-01

    A Modular Open-Source Assembler (AMOS) was designed to offer a modular approach to genome assembly. AMOS includes a wide range of tools for assembly, including lightweight de novo assemblers Minimus and Minimo, and Bambus 2, a robust scaffolder able to handle metagenomic and polymorphic data. This protocol describes how to configure and use AMOS for the assembly of Next Generation sequence data. Additionally, we provide three tutorial examples that include bacterial, viral, and metagenomic da...

  10. Benchmark assemblies of the Los Alamos Critical Assemblies Facility

    International Nuclear Information System (INIS)

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

  11. 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.

  12. Self-Assembly of Plasmonic Nanoclusters for Optical Metauids

    Science.gov (United States)

    Schade, Nicholas Benjamin

    I discuss experimental progress towards developing a material with an isotropic, negative index of refraction at optical frequencies. The simplest way to make such a material is to create a metafluid, or a disordered collection of subwavelength, isotropic electromagnetic resonators. Small clusters of metal particles, such as tetrahedra, serve as these constituents. What is needed are methods for manufacturing these structures with high precision and in sufficient yield that their resonances are identical. Jonathan Fan et al. [Science, 328 (5982), 1135-1138, 2010] demonstrated that colloidal self-assembly is a means of preparing electromagnetic resonators from metal nanoparticles. However, the resonances are sensitive to the separation gaps between particles. Standard synthesis routes for metal nanoparticles yield crystals or nanoshells that are inadequate for metafluids due to polydispersity, faceting, and thermal instabilities. To ensure that the separation gaps and resonances are uniform, more monodisperse spherical particles are needed. An additional challenge is the self-assembly of tetrahedral clusters in high yield from these particles. In self-assembly approaches that others have examined previously, the yield of any particular type of cluster is low. In this dissertation I present solutions to several of these problems, developed in collaboration with my research group and others. We demonstrate that slow chemical etching can transform octahedral gold crystals into ultrasmooth, monodisperse nanospheres. The particles can serve as seeds for the growth of larger octahedra which can in turn be etched. The size of the gold nanospheres can therefore be adjusted as desired. We further show that in colloidal mixtures of two sphere species that strongly bind to one another, the sphere size ratio determines the size distribution of self-assembled clusters. At a critical size ratio, tetrahedral clusters assemble in high yield. We explain the experimentally observed

  13. 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.

  14. 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

  15. Nuclear fuel assembly debris filter

    International Nuclear Information System (INIS)

    This patent describes a nuclear fuel assembly having fuel rods held in a spaced array by grid assemblies, guide tubes extending through the grid assemblies and attached at their upper and lower ends to an upper end fitting and a lower end fitting, the end fittings having openings therethrough for coolant flow, and a debris filter. The debris filter comprises: a plate attached to the bottom periphery of and spanning the lower end fitting; and the plate having substantially triangular-shaped flow holes therethrough that each measure approximately 0.181 inch from the base to the apex with the majority of the triangular- shaped flow holes arranged in groups of four to define square clusters that each measure approximately 0.405 inch on each side whereby the portions of the plate between the flow holes in each cluster are diagonally oriented relative to the sides of the plate

  16. Control rod guide tube assembly

    International Nuclear Information System (INIS)

    An improved fuel assembly is described as consisting of a sleeve that engages one end of a control rod guide tube essentially fixing the guide tube to one of the fuel assembly end structures. The end of the sleeve protrudes above the surface of the end fitting. The outer surface of the sleeve has a peripheral groove that engages the resilient sides of a cellular grid or lattice shaped lock. This lock fixes the sleeve in position between the various elements that comprise the end fitting, thereby eliminating a profusion of costly and potentially troublesome nuts, threaded studs and the like that are frequently employed in the fuel assemblies that are presently in use

  17. 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...

  18. 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

  19. 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.

  20. 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

  1. 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...

  2. 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...

  3. 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)

  4. 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.

  5. 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

  6. 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 that...... increases upon formation of inclusion complexes with lipophilic drugs. However, the stability of such aggregates is not sufficient for parenteral administration. In this review CD polymers and CD containing nanoparticles are categorized, with focus on self-assembled CD nanoparticles. It is described how the...

  7. Apollo Telescope Mount Spar Assembly

    Science.gov (United States)

    1969-01-01

    The Apollo Telescope Mount (ATM), designed and developed by the Marshall Space Flight Center, served as the primary scientific instrument unit aboard the Skylab. The ATM contained eight complex astronomical instruments designed to observe the Sun over a wide spectrum from visible light to x-rays. This image shows the ATM spar assembly. All solar telescopes, the fine Sun sensors, and some auxiliary systems are mounted on the spar, a cruciform lightweight perforated metal mounting panel that divides the 10-foot long canister lengthwise into four equal compartments. The spar assembly was nested inside a cylindrical canister that fit into the rack, a complex frame, and was protected by the solar shield.

  8. 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.

  9. iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences

    Directory of Open Access Journals (Sweden)

    Zheng Yi

    2011-11-01

    Full Text Available Abstract Background Expressed Sequence Tags (ESTs have played significant roles in gene discovery and gene functional analysis, especially for non-model organisms. For organisms with no full genome sequences available, ESTs are normally assembled into longer consensus sequences for further downstream analysis. However current de novo EST assembly programs often generate large number of assembly errors that will negatively affect the downstream analysis. In order to generate more accurate consensus sequences from ESTs, tools are needed to reduce or eliminate errors from de novo assemblies. Results We present iAssembler, a pipeline that can assemble large-scale ESTs into consensus sequences with significantly higher accuracy than current existing assemblers. iAssembler employs MIRA and CAP3 assemblers to generate initial assemblies, followed by identifying and correcting two common types of transcriptome assembly errors: 1 ESTs from different transcripts (mainly alternatively spliced transcripts or paralogs are incorrectly assembled into same contigs; and 2 ESTs from same transcripts fail to be assembled together. iAssembler can be used to assemble ESTs generated using the traditional Sanger method and/or the Roche-454 massive parallel pyrosequencing technology. Conclusion We compared performances of iAssembler and several other de novo EST assembly programs using both Roche-454 and Sanger EST datasets. It demonstrated that iAssembler generated significantly more accurate consensus sequences than other assembly programs.

  10. Novel inhibitor binding site discovery on HIV-1 capsid N-terminal domain by NMR and X-ray crystallography.

    Science.gov (United States)

    Goudreau, Nathalie; Lemke, Christopher T; Faucher, Anne-Marie; Grand-Maître, Chantal; Goulet, Sylvie; Lacoste, Jean-Eric; Rancourt, Jean; Malenfant, Eric; Mercier, Jean-François; Titolo, Steve; Mason, Stephen W

    2013-05-17

    The HIV-1 capsid (CA) protein, a domain of Gag, which participates in formation of both the mature and immature capsid, represents a potential target for anti-viral drug development. Characterization of hits obtained via high-throughput screening of an in vitro capsid assembly assay led to multiple compounds having this potential. We previously presented the characterization of two inhibitor series that bind the N-terminal domain of the capsid (CA(NTD)), at a site located at the bottom of its helical bundle, often referred to as the CAP-1 binding site. In this work we characterize a novel series of benzimidazole hits. Initial optimization of this series led to compounds with improved in vitro assembly and anti-viral activity. Using NMR spectroscopy we found that this series binds to a unique site on CA(NTD), located at the apex of the helical bundle, well removed from previously characterized binding sites for CA inhibitors. 2D (1)H-(15)N HSQC and (19)F NMR showed that binding of the benzimidazoles to this distinct site does not affect the binding of either cyclophilin A (CypA) to the CypA-binding loop or a benzodiazepine-based CA assembly inhibitor to the CAP-1 site. Unfortunately, while compounds of this series achieved promising in vitro assembly and anti-viral effects, they also were found to be quite sensitive to a number of naturally occurring CA(NTD) polymorphisms observed among clinical isolates. Despite the negative impact of this finding for drug development, the discovery of multiple inhibitor binding sites on CA(NTD) shows that capsid assembly is much more complex than previously realized. PMID:23496828

  11. Analysis of stress granule assembly in Schizosaccharomyces pombe.

    Science.gov (United States)

    Wang, Chun-Yu; Wen, Wei-Ling; Nilsson, Daniel; Sunnerhagen, Per; Chang, Tien-Hsien; Wang, Shao-Win

    2012-04-01

    Stress granules (SGs) are cytoplasmic aggregates of RNA and proteins in eukaryotic cells that are rapidly induced in response to environmental stress, but are not seen in cells growing under favorable conditions. SGs have been primarily studied in mammalian cells. The existence of SGs in the fission yeast and the distantly related budding yeast was demonstrated only recently. In both species, they contain many orthologs of the proteins seen in mammalian SGs. In this study, we have characterized these proteins and determined their involvement in the assembly of fission yeast SGs, in particular, the homolog of human G3BP proteins. G3BP interacts with the deubiquitinating protease USP10 and plays an important role in the assembly of SGs. We have also identified Ubp3, an ortholog of USP10, as an interaction partner of the fission yeast G3BP-like protein Nxt3 and required for its stability. Under thermal stress, like their human orthologs, both Nxt3 and Ubp3 rapidly relocalize to cytoplasmic foci that contain the SG marker poly(A)-binding protein Pabp. However, in contrast to G3BP1 and USP10, neither deletion nor overexpression of nxt3(+) or ubp3(+) affected the assembly of fission yeast SGs as judged by the relocalization of Pabp. Similar results were observed in mutants defective in orthologs of SG components that are known to affect SG assembly in human and in budding yeast, such as ataxia-2 and TIA-like proteins. Together, our data indicate that despite similar protein compositions, the underlying molecular mechanisms for the assembly of SGs could be distinct between species. PMID:22328580

  12. 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...

  13. 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.

  14. Kinetics of self-assembly via facilitated diffusion: Formation of the transcription complex

    Science.gov (United States)

    Kalay, Ziya

    2015-10-01

    We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in three dimensions and one dimension. Our study is motivated by single-molecule-level observations revealing the dynamics of transcription factors that bind to the deoxyribonucleic acid at early stages of transcription. We calculate the probability that a complex made up of a given number of molecules is completely formed, as well as the distribution of completion times, upon the binding of a seed molecule at a target site on the filament (without explicitly modeling the three-dimensional diffusion that precedes binding). We compare two different mechanisms of assembly where molecules bind in sequential and random order. Our results indicate that while the probability of completion is greater for random binding, the completion time scales exponentially with the size of the complex; in contrast, it scales as a power law or slower for sequential binding, asymptotically. Furthermore, we provide model predictions for the dissociation and residence times of the seed molecule, which are observables accessible in single-molecule tracking experiments.

  15. 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.

  16. Hybrid Nanomaterials: One Dimensional Nanoparticle Assemblies

    Science.gov (United States)

    Sharma, Nikhil; Pochan, Darrin

    2007-03-01

    One-dimensional nanoparticle assemblies have potential applications in sensing, as plasmon and energy waveguides and in the conduction of novel signals such as phonons and spin states. Herein we present two strategies for the fabrication of such assemblies. Micro and meso-scale particle assemblies have been produced via a coaxial electrospinning process that results in assemblies of particles (silica and silver) encapsulated within a polymer nanofiber (polyethylene oxide). The method has been demonstrated successfully in the creation of 1D assemblies of differently sized silica particles. The effect of change in solution concentrations and relative flow rates in internal and external channels of the coaxial electrospinning apparatus on the structure of these assemblies has been investigated. Nano-scale assemblies of gold particles have been prepared by templating gold nanoparticles on a 20 amino acid peptide that displays laminated morphology. These assemblies are formed as laterally spaced one-dimensional nanoparticle assemblies.

  17. 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.

  18. 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’.

  19. 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.

  20. Cholesterol-binding viral proteins in virus entry and morphogenesis.

    Science.gov (United States)

    Schroeder, Cornelia

    2010-01-01

    Up to now less than a handful of viral cholesterol-binding proteins have been characterized, in HIV, influenza virus and Semliki Forest virus. These are proteins with roles in virus entry or morphogenesis. In the case of the HIV fusion protein gp41 cholesterol binding is attributed to a cholesterol recognition consensus (CRAC) motif in a flexible domain of the ectodomain preceding the trans-membrane segment. This specific CRAC sequence mediates gp41 binding to a cholesterol affinity column. Mutations in this motif arrest virus fusion at the hemifusion stage and modify the ability of the isolated CRAC peptide to induce segregation of cholesterol in artificial membranes.Influenza A virus M2 protein co-purifies with cholesterol. Its proton translocation activity, responsible for virus uncoating, is not cholesterol-dependent, and the transmembrane channel appears too short for integral raft insertion. Cholesterol binding may be mediated by CRAC motifs in the flexible post-TM domain, which harbours three determinants of binding to membrane rafts. Mutation of the CRAC motif of the WSN strain attenuates virulence for mice. Its affinity to the raft-non-raft interface is predicted to target M2 protein to the periphery of lipid raft microdomains, the sites of virus assembly. Its influence on the morphology of budding virus implicates M2 as factor in virus fission at the raft boundary. Moreover, M2 is an essential factor in sorting the segmented genome into virus particles, indicating that M2 also has a role in priming the outgrowth of virus buds.SFV E1 protein is the first viral type-II fusion protein demonstrated to directly bind cholesterol when the fusion peptide loop locks into the target membrane. Cholesterol binding is modulated by another, proximal loop, which is also important during virus budding and as a host range determinant, as shown by mutational studies. PMID:20213541

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

    OpenAIRE

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

    2014-01-01

    Background Nicotiana benthamiana is an allo-tetraploid plant, which can be challenging for de novo transcriptome assemblies due to homeologous and duplicated gene copies. Transcripts generated from such genes can be distinct yet highly similar in sequence, with markedly differing expression levels. This can lead to unassembled, partially assembled or mis-assembled contigs. Due to the different properties of de novo assemblers, no one assembler with any one given parameter space can re-assembl...

  2. 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.

  3. 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

  4. Small Parts Assembler Work Sample.

    Science.gov (United States)

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

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

  5. 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

  6. 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.

  7. Flow resistance in rod assemblies

    International Nuclear Information System (INIS)

    The general form of relation between the resistance force and the velocity vector, resistance tensor structure and possible types of anisotropy in the flow thorough such structures as rod or tube assemblies are under discussion. Some questions of experimental determination of volumetric resistance force tensor are also under consideration. (author)

  8. 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...

  9. 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.

  10. 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.

  11. 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.

  12. CISA: Contig Integrator for Sequence Assembly of Bacterial Genomes

    OpenAIRE

    Lin, Shin-Hung; Liao, Yu-Chieh

    2013-01-01

    A plethora of algorithmic assemblers have been proposed for the de novo assembly of genomes, however, no individual assembler guarantees the optimal assembly for diverse species. Optimizing various parameters in an assembler is often performed in order to generate the most optimal assembly. However, few efforts have been pursued to take advantage of multiple assemblies to yield an assembly of high accuracy. In this study, we employ various state-of-the-art assemblers to generate different set...

  13. 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

  14. 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.

  15. 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...

  16. 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

  17. Compact MCP assemblies for mass spectrometers

    International Nuclear Information System (INIS)

    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.)

  18. 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.

  19. Varactor diode assembly with low parasitic reactances

    Science.gov (United States)

    Dickens, L. E.

    1975-01-01

    Development of varactor diode assembly overcomes parasitic reactances of conventional varactor packages. In specially constructed assembly very high idler-frequency to signal-frequency ratios are used to obtain low-noise operation over maximum bandwidth.

  20. Binding affinity and specificity of neuromyelitis optica autoantibodies to aquaporin-4 M1/M23 isoforms and orthogonal arrays.

    Science.gov (United States)

    Crane, Jonathan M; Lam, Chiwah; Rossi, Andrea; Gupta, Tripta; Bennett, Jeffrey L; Verkman, A S

    2011-05-01

    Autoantibodies against astrocyte water channel aquaporin-4 (AQP4) are highly specific for the neuroinflammatory disease neuromyelitis optica (NMO). We measured the binding of NMO autoantibodies to AQP4 in human astrocyte-derived U87MG cells expressing M1 and/or M23 AQP4, or M23 mutants that do not form orthogonal array of particles (OAPs). Binding affinity was quantified by two-color fluorescence ratio imaging of cells stained with NMO serum or a recombinant monoclonal NMO autoantibody (NMO-rAb), together with a C terminus anti-AQP4 antibody. NMO-rAb titrations showed binding with dissociation constants down to 44 ± 7 nm. Different NMO-rAbs and NMO patient sera showed a wide variation in NMO-IgG binding to M1 versus M23 AQP4. Differences in binding affinity rather than stoichiometry accounted for M1 versus M23 binding specificity, with consistently greater affinity of NMO-IgG binding to M23 than M1 AQP4. Binding and OAP measurements in cells expressing different M1:M23 ratios or AQP4 mutants indicated that the differential binding of NMO-IgG to M1 versus M23 was due to OAP assembly rather than to differences in the M1 versus M23 N termini. Purified Fab fragments of NMO-IgG showed similar patterns of AQP4 isoform binding, indicating that structural changes in the AQP4 epitope upon array assembly, and not bivalent cross-linking of whole IgG, result in the greater binding affinity to OAPs. Our study establishes a quantitative assay of NMO-IgG binding to AQP4 and indicates remarkable, OAP-dependent heterogeneity in NMO autoantibody binding specificity. PMID:21454592

  1. Electrostatic assembly of protein lysozyme on DNA visualized by atomic force microscopy

    International Nuclear Information System (INIS)

    In the present work, atomic force microscopy (AFM) has been used to study the assembly of protein lysozyme on DNA molecule. Based on the electrostatic interaction, the positively charged lysozyme can easily bind onto the negatively charged DNA molecule surface. The protein molecules appear as globular objects on the DNA scaffold, which are distinguishable in the AFM images. At the same time, lysozyme molecules can be assembled onto DNA as dense or sporadic pattern by varying the protein concentration. This work may provide fundamental aspects for building protein nanostructures and studying of DNA-protein interaction

  2. 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...

  3. 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.

  4. 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.

  5. 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...

  6. 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

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. System for assembling nuclear fuel elements

    International Nuclear Information System (INIS)

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

  12. LHC Magnet Assembly Facility in building 181

    CERN Multimedia

    CERN IT-UDS audio video service

    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

  13. 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

  14. Elastocapillary-mediated interfacial assembly

    Science.gov (United States)

    Evans, Arthur

    2015-11-01

    Particles confined to an interface are present in a large number of industrial applications and ubiquitous in cellular biophysics. Interactions mediated by the interface, such as capillary effects in the presence of surface tension, give rise to rafts and aggregates whose structure is ultimately determined by geometric characteristics of these adsorbed particles. A common strategy for assembling interfacial structures relies on exploiting these interactions by tuning particle anisotropy, either by constructing rigid particles with heterogeneous wetting properties or fabricating particles that have a naturally anisotropic shape. Less explored, however, is the scenario where the interface causes the particles to deform. In this talk I will discuss the implications for interfacial assembly using elastocapillary-mediated interactions. The competition between surface energy and elasticity can wrinkle and buckle adsorbed soft particles, leading to complicated (but programmable) aggregates.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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)

  20. Visualization Software for Molecular Assemblies

    OpenAIRE

    Goddard, Thomas D; Ferrin, Thomas E.

    2007-01-01

    Software for viewing three-dimensional models and maps of viruses, ribosomes, filaments and other molecular assemblies is advancing on many fronts. New developments include molecular representations that offer better control over level of detail, lighting that improves the perception of depth, and two-dimensional projections that simplify data interpretation. Programmable graphics processors offer quality, speed and visual effects not previously possible, while 3D printers, haptic interaction...

  1. [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

  2. 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.

  3. Structural domains of vault proteins: a role for the coiled coil domain in vault assembly.

    Science.gov (United States)

    van Zon, Arend; Mossink, Marieke H; Schoester, Martijn; Scheffer, George L; Scheper, Rik J; Sonneveld, Pieter; Wiemer, Erik A C

    2002-03-01

    Vaults consist of multiple copies of three proteins (MVP, VPARP, and TEP1) and several untranslated RNAs. The function of vaults is unknown but the typical and evolutionary conserved structure indicates a role in intracellular transport. Although all vault components have been identified and characterized, not much is known about vault protein assembly. In this study we identified and analyzed structural domains involved in vault assembly with emphasis on protein-protein interactions. Using a yeast two-hybrid system, we demonstrate within MVP an intramolecular binding site and show that MVP molecules interact with each other via their coiled coil domain. We show that purified MVP is able to bind calcium, most likely at calcium-binding EF-hands. No interactions could be detected between TEP1 and other vault proteins. However, the N-terminal half of MVP binds to a specific domain in the C-terminus of VPARP. Furthermore, VPARP contains amino acid stretches mediating intramolecular binding. PMID:11855821

  4. 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...

  5. Mapping regions of the matrix protein of vesicular stomatitis virus which bind to ribonucleocapsids, liposomes, and monoclonal antibodies.

    OpenAIRE

    Ogden, J R; Pal, R; Wagner, R R

    1986-01-01

    The matrix (M) protein of vesicular stomatitis virus (VSV) appears to function as a bridge between the ribonucleocapsid (RNP) core and the envelope in assembly of the virion. Two such properties would necessitate at least one site for interaction with the nucleocapsid and one with the envelope. In this study M protein was found to mediate the in vitro binding to RNP cores of phospholipid vesicles, representing membrane structures. The M protein could bind initially to either the vesicles or t...

  6. Discovery of dual inhibitors targeting both HIV-1 capsid and human cyclophilin A to inhibit the assembly and uncoating of the viral capsid.

    Science.gov (United States)

    Li, Jiebo; Tan, Zhiwu; Tang, Shixing; Hewlett, Indira; Pang, Ruifang; He, Meizi; He, Shanshan; Tian, Baohe; Chen, Kan; Yang, Ming

    2009-04-15

    HIV-1 assembly and disassembly (uncoating) processes are critical for the HIV-1 replication. HIV-1 capsid (CA) and human cyclophilin A (CypA) play essential roles in these processes. We designed and synthesized a series of thiourea compounds as HIV-1 assembly and disassembly dual inhibitors targeting both HIV-1 CA protein and human CypA. The SIV-induced syncytium antiviral evaluation indicated that all of the inhibitors displayed antiviral activities in SIV-infected CEM cells at the concentration of 0.6-15.8 microM for 50% of maximum effective rate. Their abilities to bind CA and CypA were determined by ultraviolet spectroscopic analysis, fluorescence binding affinity and PPIase inhibition assay. Assembly studies in vitro demonstrated that the compounds could potently disrupt CA assembly with a dose-dependent manner. All of these molecules could bind CypA with binding affinities (Kd values) of 51.0-512.8 microM. Fifteen of the CypA binding compounds showed potent PPIase inhibitory activities (IC(50) valuesHIV-1 Protease or to HIV-1 Integrase in the enzyme assays. These results suggested that 15 compounds could block HIV-1 replication by inhibiting the PPIase activity of CypA to interfere with capsid disassembly and disrupting CA assembly. PMID:19328002

  7. 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...

  8. 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

  9. 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

  10. Adsorption Dynamics and Self-Assembled L-cysteine on Au(100)

    DEFF Research Database (Denmark)

    Engelbrekt, Christian; Nazmutdinov, Renat R.; Yan, Jiawei;

    As the only amino acid with a functional thiol group, L - cysteine offers a strong perspective both for binding to gold and other metals, and for gentle immobilization of biomolecules. Binding to single - crystal, atomically planar surfaces offers the additional perspective that bound L - cysteine...... can be structurally mapped at the single - molecule level . In this work, we have followed the adsorption of L - cysteine on single - crystal Au(100) by measuring the electrode potential dynamics during the adsorption process. In situ STM revealed the structure of the self - assembled ordered layers...

  11. 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.

  12. 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...

  13. 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.

  14. 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

  15. 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 Omura

    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.

  16. 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...

  17. 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.

  18. Mitochondrial heat-shock protein hsp60 is essential for assembly of proteins imported into yeast mitochondria

    OpenAIRE

    Cheng, Ming Yuan; Hartl, Franz-Ulrich; Martin, Jörg; Pollock, Robert A.; Kalousek, Frantisek; Neupert, Walter; Hallberg, Elisabeth M.; Hallberg, Richard L.; Horwich, Arthur

    1989-01-01

    A nuclear encoded mitochondrial heat-shock protein hsp60 is required for the assembly into oligomeric complexes of proteins imported into the mitochondrial matrix. hsp60 is a member of the 'chaperonin' class of protein factors, which include the Escherichia coli groEL protein and the Rubisco subunit-binding protein of chloroplasts

  19. 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

  20. 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

  1. 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.

  2. 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.

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

    Science.gov (United States)

    Li, Lixin; Atef, Ahmed; Piatek, Agnieszka; Ali, Zahir; Piatek, Marek; Aouida, Mustapha; Sharakuu, Altanbadralt; Mahjoub, Ali; Wang, Guangchao; Khan, Suhail; Fedoroff, Nina V; Zhu, Jian-Kang; Mahfouz, Magdy M

    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. PMID:23300258

  4. Windows Presentation Foundation & Data Binding

    OpenAIRE

    JANDA, Vilém

    2010-01-01

    The aim of this work is a course in the form of e-learning study materials for the interpretation of technology Data Binding in Windows Presentation Foundation (WPF). In the first, mostly theoretical part will be done a description and interpretation of the elements of technology, focusing on WPF Data Binding. In the second part, is available methodology and training course with their own interpretive audio-visual files for self-study. The lectures are supplemented by solved examples, and exa...

  5. 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

  6. 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

  7. 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.

  8. 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...

  9. 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.

  10. 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...

  11. Cooperation of multiple chaperones required for the assembly of mammalian 20S proteasomes

    DEFF Research Database (Denmark)

    Hirano, Y.; Hayashi, H.; Iemura, S.; Hendil, K. B.; Niwa, S.; Kishimoto, T.; Natsume, T.; Tanaka, K.; Murata, S.

    2006-01-01

    proteasomes is assisted by proteasome-specific chaperones, named PAC1, PAC2, and hUmp1, but the details are still unknown. Here, we report the identification of a chaperone, designated PAC3, as a component of a rings. Although it can intrinsically bind directly to both a and ß subunits, PAC3 dissociates...... describe a cooperative system of multiple chaperones involved in the correct assembly of mammalian 20S proteasomes....

  12. 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...

  13. Identification of CP12 as a Novel Calcium-Binding Protein in Chloroplasts

    Directory of Open Access Journals (Sweden)

    Agostinho Gomes Rocha

    2013-08-01

    Full Text Available Calcium plays an important role in the regulation of several chloroplast processes. However, very little is still understood about the calcium fluxes or calcium-binding proteins present in plastids. Indeed, classical EF-hand containing calcium-binding proteins appears to be mostly absent from plastids. In the present study we analyzed the stroma fraction of Arabidopsis chloroplasts for the presence of novel calcium-binding proteins using 2D-PAGE separation followed by calcium overlay assay. A small acidic protein was identified by mass spectrometry analyses as the chloroplast protein CP12 and the ability of CP12 to bind calcium was confirmed with recombinant proteins. CP12 plays an important role in the regulation of the Calvin-Benson-Bassham Cycle participating in the assembly of a supramolecular complex between phosphoribulokinase and glyceraldehyde 3-phosphate dehydrogenase, indicating that calcium signaling could play a role in regulating carbon fixation.

  14. 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

  15. Integrated Self-Assembly of the Mms6 Magnetosome Protein to Form an Iron-Responsive Structure

    Directory of Open Access Journals (Sweden)

    Marit Nilsen-Hamilton

    2013-07-01

    Full Text Available A common feature of biomineralization proteins is their self-assembly to produce a surface consistent in size with the inorganic crystals that they produce. Mms6, a small protein of 60 amino acids from Magnetospirillum magneticum strain AMB-1 that promotes the in vitro growth of superparamagnetic magnetite nanocrystals, assembles in aqueous solution to form spherical micelles that could be visualized by TEM and AFM. The results reported here are consistent with the view that the N and C-terminal domains interact with each other within one polypeptide chain and across protein units in the assembly. From studies to determine the amino acid residues important for self-assembly, we identified the unique GL repeat in the N-terminal domain with additional contributions from amino acids in other positions, throughout the molecule. Analysis by CD spectroscopy identified a structural change in the iron-binding C-terminal domain in the presence of Fe3+. A change in the intrinsic fluorescence of tryptophan in the N-terminal domain showed that this structural change is transmitted through the protein. Thus, self-assembly of Mms6 involves an interlaced structure of intra- and inter-molecular interactions that results in a coordinated structural change in the protein assembly with iron binding.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-12-15

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

  17. Fuel assembly self-excited vibration and test methodology

    International Nuclear Information System (INIS)

    PWR fuel assemblies normally experience low amplitude, random vibration under normal reactor flow conditions. This normal fuel assembly vibration has almost no impact on grid-rod fretting wear. However, some fuel assembly designs experience a high resonant fuel assembly vibration under normal axial flow conditions. This anomalous fuel assembly vibration is defined as fuel assembly self-excitation vibration (FASE), because the assembly vibrates resonantly without any external periodic excitation force. Fuel assembly self-excitation vibration can cause severe grid-rod fretting if the assembly operates at the flow rate, which causes high fuel assembly vibration. This paper will describe the characteristics of fuel assembly self-excitation vibration and the test methodology to identify the fuel assembly vibration. Several fuel assembly designs are compared under standard test conditions. The causes for the fuel assembly self-excitation vibration are analyzed and discussed. The test acceptance criteria are defined for newly developed PWR fuel assemblies. (authors)

  18. Semiconductor nanocrystals covalently bound to solid inorganic surfaces using self-assembled monolayers

    Science.gov (United States)

    Alivisatos, A. Paul; Colvin, Vicki L.

    1998-01-01

    Methods are described for attaching semiconductor nanocrystals to solid inorganic surfaces, using self-assembled bifunctional organic monolayers as bridge compounds. Two different techniques are presented. One relies on the formation of self-assembled monolayers on these surfaces. When exposed to solutions of nanocrystals, these bridge compounds bind the crystals and anchor them to the surface. The second technique attaches nanocrystals already coated with bridge compounds to the surfaces. Analyses indicate the presence of quantum confined clusters on the surfaces at the nanolayer level. These materials allow electron spectroscopies to be completed on condensed phase clusters, and represent a first step towards synthesis of an organized assembly of clusters. These new products are also disclosed.

  19. Self-assembled mesoporous carbon films for platinum metal catalyst loading

    International Nuclear Information System (INIS)

    This work demonstrates the use of self-assembled carbon films in designing fuel cell electrode. Well-dispersed mesoporous carbon particles were prepared based on the spontaneous and strong chemisorption of polyoxometalate (POM) solution on carbon surface. Electrostatically self-assembled films of the POM stabilized carbon interlaced with cationic polyelectrolyte binding layer were useful for confining electrodeposition of platinum (Pt) catalyst. The structure and morphology of the resulting films were characterized by X-ray diffraction and scanning electron microscopy respectively. The electrocatalytic activities of Pt deposited on the self-assembled carbon films toward the degradation of small organic molecules are largely dependent on the quantity of Pt and carbon. This work represents a simply controlled test-bed for fundamental studies on loading metal catalysts on ordered mesoporous carbon films for catalysis.

  20. 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

  1. 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.

  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. 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.

  4. Self-assembled molecular rafts at liquid|liquid interfaces for four-electron oxygen reduction.

    Science.gov (United States)

    Olaya, Astrid J; Schaming, Delphine; Brevet, Pierre-Francois; Nagatani, Hirohisa; Zimmermann, Tomas; Vanicek, Jiri; Xu, Hai-Jun; Gros, Claude P; Barbe, Jean-Michel; Girault, Hubert H

    2012-01-11

    The self-assembly of the oppositely charged water-soluble porphyrins, cobalt tetramethylpyridinium porphyrin (CoTMPyP(4+)) and cobalt tetrasulphonatophenyl porphyrin (CoTPPS(4-)), at the interface with an organic solvent to form molecular "rafts", provides an excellent catalyst to perform the interfacial four-electron reduction of oxygen by lipophilic electron donors such as tetrathiafulvalene (TTF). The catalytic activity and selectivity of the self-assembled catalyst toward the four-electron pathway was found to be as good as that of the Pacman type cofacial cobalt porphyrins. The assembly has been characterized by UV-visible spectroscopy, Surface Second Harmonic Generation, and Scanning Electron Microscopy. Density functional theory calculations confirm the possibility of formation of the catalytic CoTMPyP(4+)/ CoTPPS(4-) complex and its capability to bind oxygen. PMID:22107335

  5. 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.

  6. 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.

  7. 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

  8. j5 DNA assembly design automation software.

    Science.gov (United States)

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

    2012-01-20

    Recent advances in Synthetic Biology have yielded standardized and automatable DNA assembly protocols that enable a broad range of biotechnological research and development. Unfortunately, the experimental design required for modern scar-less multipart DNA assembly methods is frequently laborious, time-consuming, and error-prone. Here, we report the development and deployment of a web-based software tool, j5, which automates the design of scar-less multipart DNA assembly protocols including SLIC, Gibson, CPEC, and Golden Gate. The key innovations of the j5 design process include cost optimization, leveraging DNA synthesis when cost-effective to do so, the enforcement of design specification rules, hierarchical assembly strategies to mitigate likely assembly errors, and the instruction of manual or automated construction of scar-less combinatorial DNA libraries. Using a GFP expression testbed, we demonstrate that j5 designs can be executed with the SLIC, Gibson, or CPEC assembly methods, used to build combinatorial libraries with the Golden Gate assembly method, and applied to the preparation of linear gene deletion cassettes for E. coli. The DNA assembly design algorithms reported here are generally applicable to broad classes of DNA construction methodologies and could be implemented to supplement other DNA assembly design tools. Taken together, these innovations save researchers time and effort, reduce the frequency of user design errors and off-target assembly products, decrease research costs, and enable scar-less multipart and combinatorial DNA construction at scales unfeasible without computer-aided design. PMID:23651006

  9. 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

  10. A non-canonical mechanism for Crm1-export cargo complex assembly.

    Science.gov (United States)

    Fischer, Ute; Schäuble, Nico; Schütz, Sabina; Altvater, Martin; Chang, Yiming; Faza, Marius Boulos; Panse, Vikram Govind

    2015-01-01

    The transport receptor Crm1 mediates the export of diverse cargos containing leucine-rich nuclear export signals (NESs) through complex formation with RanGTP. To ensure efficient cargo release in the cytoplasm, NESs have evolved to display low affinity for Crm1. However, mechanisms that overcome low affinity to assemble Crm1-export complexes in the nucleus remain poorly understood. In this study, we reveal a new type of RanGTP-binding protein, Slx9, which facilitates Crm1 recruitment to the 40S pre-ribosome-associated NES-containing adaptor Rio2. In vitro, Slx9 binds Rio2 and RanGTP, forming a complex. This complex directly loads Crm1, unveiling a non-canonical stepwise mechanism to assemble a Crm1-export complex. A mutation in Slx9 that impairs Crm1-export complex assembly inhibits 40S pre-ribosome export. Thus, Slx9 functions as a scaffold to optimally present RanGTP and the NES to Crm1, therefore, triggering 40S pre-ribosome export. This mechanism could represent one solution to the paradox of weak binding events underlying rapid Crm1-mediated export. PMID:25895666

  11. 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

  12. 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).

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    Kiran Gopinath Bankar

    2015-09-01

    In this study, we aimed at obtaining an ameliorated de novo transcriptome assembly with sequence reads obtained from Illumina platform and assembled using Trinity Assembler. We found that, primary transcriptome assembly obtained as a result of Trinity can be ameliorated on the basis of transcript length, coverage, and depth and protein homology. Our approach to ameliorate is reproducible and could enhance the sensitivity and specificity of the assembled transcriptome which could be critical for validation of the assembled transcripts and for planning various downstream biological assays.

  15. 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.

  16. 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.

  17. Self-assembled controllable microswimmers

    Science.gov (United States)

    Grosjean, Galien; Lagubeau, Guillaume; Darras, Alexis; Lumay, Geoffroy; Hubert, Maxime; Vandewalle, Nicolas

    2015-11-01

    Because they cause a deformation of the interface, floating particles interact. In particular, identical particles attract each other. To counter this attraction, particles possessing a large magnetic moment m-> are used. When m-> is perpendicular to the surface, dipole-dipole interaction is repulsive. This competition of forces can lead to the spontaneous formation of organized structures. By using submillimetric steel spheres for which m-> ~ B-> , interdistances in the system can be precisely tuned. Here, we deform these self-assemblies by adding a horizontal contribution m-> to the magnetic moment. Time reversal symmetry is broken in the system, leading to locomotion at low Reynolds number. Moreover, swimming direction depends on the orientation of field, meaning that swimming trajectories can be finely controlled. A model allows to understand the breaking of symmetry, while a study of the vibration modes gives further informations on the dynamics of this sytem. Because this system forms by self-assembly, it allows miniaturization with applications such as cargo transport or solvent flows. It is highly versatile, being composed of simple passive particles and controlled by magnetic fields.

  18. The VEGA Assembly Spectrum Code

    International Nuclear Information System (INIS)

    The VEGA is assembly spectrum code, developed as a design tool for producing a few-group averaged cross section data for a wide range of reactor types including both thermal and fast reactors. It belongs to a class of codes, which may be characterized by the separate stages for micro group, spectrum and macro group assembly calculations. The theoretical foundation for the development of the VEGA code was integral transport theory in the first-flight collision probability formulation. Two versions of VEGA are now in use, VEGA-1 established on standard equivalence theory and VEGA-2 based on new subgroup method applicable for any geometry for which a flux solution is possible. This paper describes a features which are unique to the VEGA codes with concentration on the basic principles and algorithms used in the proposed subgroup method. Presented validation of this method, comprise the results for a homogenous uranium-plutonium mixture and a PWR cell containing a recycled uranium-plutonium oxide. Example application for a realistic fuel dissolver benchmark problem , which was extensive analyzed in the international calculations, is also included. (author)

  19. 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.

  20. 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.

  1. The $K$-theory of assemblers

    OpenAIRE

    Zakharevich, Inna

    2014-01-01

    In this paper we introduce the notion of an assembler, which formally encodes "cutting and pasting" data. An assembler has an associated $K$-theory spectrum, in which $\\pi_0$ is the free abelian group of objects of the assembler modulo the cutting and pasting relations, and in which the higher homotopy groups encode further geometric invariants. The goal of this paper is to prove structural theorems about this $K$-theory spectrum, including analogs of Quillen's localization and d\\'evissage th...

  2. 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.

  3. 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.

  4. 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. ...

  5. Optics assembly for high power laser tools

    Energy Technology Data Exchange (ETDEWEB)

    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.

  6. 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...

  7. Thermodynamic characterization of the peptide assembly inhibitor binding to HIV-1 capsid protein

    Czech Academy of Sciences Publication Activity Database

    Kožíšek, Milan; Durčák, Jindřich; Konvalinka, Jan

    2013-01-01

    Roč. 10, Suppl. 1 (2013), S37-S37. ISSN 1742-4690. [Frontiers of Retrovirology: Complex retorviruses, retroelements and their hosts. 16.09.2013-18.09.2013, Cambridge] R&D Projects: GA ČR GA13-19561S Institutional support: RVO:61388963 Keywords : HIV -1 capsid protein * CAI Subject RIV: EE - Microbiology, Virology http://www.retrovirology.com/content/10/S1/P108

  8. A spectroscopic method to estimate the binding potency of amphiphile assemblies

    Czech Academy of Sciences Publication Activity Database

    Pohle, W.; Gauger, D. R.; Andrushchenko, Valery; Bouř, Petr; Billes, F.

    Florence : -, 2010 - (Becucci, M.; Gellini, C.; Schettino, V.). s. 160-160 [EUCMOS 2010. European Congress on Molecular Spectroscopy /30./. 29.08.2010-03.09.2010, Florence] Institutional research plan: CEZ:AV0Z40550506 Keywords : spectroscopic method * Karl-Fischer titration * IR spectroscopy Subject RIV: CF - Physical ; Theoretical Chemistry

  9. 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

  10. 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...

  11. 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.

  12. Fuel assembly for a boiling water reactor

    International Nuclear Information System (INIS)

    A boiling water reactor fuel assembly is described which has vertical fuel rods and guide tubes positioned below the fuel rods and receiving control rod fingers and acting as water pipes, the guide tubes each being formed of a plurality of parts including a part secured to a grid plate positioned in the fuel assembly container, and low parts which fit into holes formed in the bottom of the fuel assembly. There is a flexible connection between the upper and lower parts of the guide tubes to allow for a certain tolerance in the procedure of manufacturing the various parts to allow insertion of the fuel rod bundle into the fuel assembly container

  13. Snubber assembly for a control rod drive

    International Nuclear Information System (INIS)

    A snubber cartridge assembly is mounted to the nozzle of a control rod drive mechanism to insure that the snubber assembly will be located within the liquid filled section of a nuclear reactor vessel whenever the control rod drive is assembled thereto. The snubber assembly includes a piston mounted proximate to the control rod connecting end of the control rod drive leadscrew to allow the piston to travel within the liquid filled snubber cartridge and controllably exhaust liquid therefrom during a ''scram'' condition. The snubber cartridge provides three separate areas of increasing resistance to piston travel to insure a speedy but safe ''scram'' of the control rod into the reactor

  14. Self-assembled nanomaterials for photoacoustic imaging.

    Science.gov (United States)

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

    2016-02-01

    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. PMID:26757620

  15. Design of the ITER tokamak assembly tools

    International Nuclear Information System (INIS)

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

  16. 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.

  17. 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

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

    DEFF Research Database (Denmark)

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

    2005-01-01

    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...

  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.