Dielectric properties of polyhedral oligomeric silsesquioxane (POSS)-based nanocomposites at 77k

International Nuclear Information System (INIS)

Pan, Ming-Jen; Gorzkowski, Edward; McAllister, Kelly

2011-01-01

The goal of this study is to develop dielectric nanocomposites for high energy density applications at liquid nitrogen temperature by utilizing a unique nano-material polyhedral oligomeric silsesquioxanes (POSS). A POSS molecule is consisted of a silica cage core with 8 silicon and 12 oxygen atoms and organic functional groups attached to the corners of the cage. In this study, we utilize POSS for the fabrication of nanocomposites both as a silica nanoparticle filler to enhance the breakdown strength and as a surfactant for effective dispersion of high permittivity ceramic nanoparticles in a polymer matrix. The matrix materials selected for the study are polyvinylidene fluoride (PVDF) and poly(methyl methacrylate) (PMMA). The ceramic nanoparticles are barium strontium titanate (BST 50/50) and strontium titanate. The dielectric properties of the solution-cast nanocomposites films were correlated to the composition and processing conditions. We determined that the addition of POSS did not provide enhanced dielectric performance in PVDF- and PMMA-based materials at either room temperature or 77K. In addition, we found that the dielectric breakdown strength of PMMA is lower at 77K than at room temperature, contradicting literature data.

Polyhedral oligomeric silsesquioxane (POSS)–poly(ethylene glycol) (PEG) hybrids as injectable biomaterials

International Nuclear Information System (INIS)

Engstrand, Johanna; López, Alejandro; Engqvist, Håkan; Persson, Cecilia

2012-01-01

One of the major issues with the currently available injectable biomaterials for hard tissue replacement is the mismatch between their mechanical properties and those of the surrounding bone. Hybrid bone cements that combine the benefits of tough polymeric and bioactive ceramic materials could become a good alternative. In this work, polyhedral oligomeric silsesquioxane (POSS) was copolymerized with poly(ethylene glycol) (PEG) to form injectable in situ cross-linkable hybrid cements. The hybrids were characterized in terms of their mechanical, rheological, handling and in vitro bioactive properties. The results indicated that hybridization improves the mechanical and bioactive properties of POSS and PEG. The Young moduli of the hybrids were lower than those of commercial cements and more similar to those of cancellous bone. Furthermore, the strength of the hybrids was similar to that of commercial cements. Calcium deficient hydroxyapatite grew on the surface of the hybrids after 28 days in PBS, indicating bioactivity. The study showed that PEG–POSS-based hybrid materials are a promising alternative to commercial bone cements. (paper)

Flow cytometry evidence of human granulocytes interaction with polyhedral oligomeric silsesquioxanes: effect of nanoparticle charge

International Nuclear Information System (INIS)

Renò, Filippo; Rizzi, Manuela; Pittarella, Pamela; Carniato, Fabio; Olivero, Francesco; Marchese, Leonardo

2013-01-01

Nanoparticles (NPs) entering the human body are immediately confronted with the innate part of human immune system. In particular, monocyte and neutrophil granulocytes readily clear particles by phagocytosis, even if in the case of NPs the uptake mechanism may be classified as macropinocytosis. Among engineered nanoparticles, in the last years, siliceous materials have emerged as promising materials for several applications ranging from catalysis to biomedical. The polyhedral oligomeric silsesquioxanes (POSS) are nanodimensional, easily synthesizable molecular compounds and POSS-based systems are promising carriers for biological molecules. In this work, the ability of human granulocytes to uptake positively and negatively charged POSS was measured using a simple flow cytometry analysis based on cell size modifications. The data obtained showed that after a 30 min exposure only positive NPs were uptaken by human granulocyte using both macropinocytosis and clathrin-mediated mechanisms as demonstrated by uptake inhibition mediated by amiloride and chlorpromazine. (paper)

Ultrafast preparation of a polyhedral oligomeric silsesquioxane-based ionic liquid hybrid monolith via photoinitiated polymerization, and its application to capillary electrochromatography of aromatic compounds.

Science.gov (United States)

Zhang, Bingyu; Lei, Xiaoyun; Deng, Lijun; Li, Minsheng; Yao, Sicong; Wu, Xiaoping

2018-06-06

An ionic liquid hybrid monolithic capillary column was prepared within 7 min via photoinitiated free-radical polymerization of an ionic liquid monomer (1-butyl-3-vinylimidazolium-bis[(trifluoromethyl)sulfonyl]imide); VBIMNTF 2 ) and a methacryl substituted polyhedral oligomeric silsesquioxane (POSS-MA) acting as a cross-linker. The effects of composition of prepolymerization solution and initiation time on the porous structure and electroosmotic flow (EOF) of monolithic column were investigated. The hybrid monolith was characterized by scanning electron microscopy and FTIR. Owing to the introduction of a rigid nanosized POSS silica core and ionic liquids with multiple interaction sites, the monolithic column has a well-defined 3D skeleton morphology, good mechanical stability, and a stable anodic electroosmotic flow. The hybrid monolithic stationary phase was applied to the capillary electrochromatographic separation of various alkylbenzenes, phenols, anilines and polycyclic aromatic hydrocarbons (PAHs). The column efficiency is highest (98,000 plates/m) in case of alkylbenzenes. Mixed-mode retention mechanisms including hydrophobic interactions, π-π stacking, electrostatic interaction and electrophoretic mobility can be observed. This indicates the potential of this material in terms of efficient separation of analytes of different structural type. Graphical Abstract Preparation of a mixed-mode ionic liquid hybrid monolithic column via photoinitiated polymerization of methacryl substituted polyhedral oligomeric silsesquioxane (POSS-MA) and 1-butyl-3-vinylimidazolium-bis[(trifluoromethyl)sulfonyl]imide (VBIMNTF 2 ) ionic liquid for use in capillary electrochromatography.

Multiwalled carbon nanotubes@octavinyl polyhedral oligomeric silsesquioxanes nanocomposite preparation via cross-linking reaction in acidic media

Energy Technology Data Exchange (ETDEWEB)

Somasekharan, Lakshmipriya; Thomas, Sabu [Mahatma Gandhi University, International and Interuniversity Centre for Nanoscience and Nanotechnology (India); Comoy, Corinne [Université de Lorraine, SRSMC, UMR 7565 (France); Sivasankarapillai, Anilkumar [NSS Hindu College (India); Kalarikkal, Nandakumar [Mahatma Gandhi University, International and Interuniversity Centre for Nanoscience and Nanotechnology (India); Lamouroux, Emmanuel, E-mail: Emmanuel.Lamouroux@univ-lorraine.fr [Université de Lorraine, SRSMC, UMR 7565 (France)

2016-11-15

Multiwalled carbon nanotubes have unique properties allowing their use in a wide range of applications—from microelectronics to biomedical and polymer fields. Nevertheless, a crucial aspect for their use resides in the ease of handling them during the process. Here, we report a facile route to prepare multiwalled carbon nanotubes@octavinyl polyhedral oligomeric silsesquioxanes (MWCNT@POSS) nanocomposite. The method involves the formation of a covalent bond between carboxylated MWCNTs and OV-POSS using acid-catalyzed electrophilic addition reaction. The resulting nanocomposite have been characterized by Fourier transform infrared spectroscopy (FTIR), powder X-Ray diffraction (PXRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and thermogravimetric analysis (TGA). The results confirmed that the formation of MWCNT@POSS nanocomposite did not deteriorate MWCNT structure or morphology. Here, we used a 1:1 ratio of carboxylated MWCNTs and OV-POSS and the POSS content in the nanocomposite was 39.5 wt%.

Structure-properties relationships of polyhedral oligomeric silsesquioxane (POSS filled PS nanocomposites

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J. J. Schwab

2012-07-01

Full Text Available The polyhedral oligomeric silsesquioxane (POSS additivated polystyrene (PS based nanocomposites were prepared by melt processing and the structure-properties relationships of the POSS-PS systems were compared to those of the neat PS. In order to investigate the effect of these structural parameters on the final properties of the polymer nanocomposites, five different kinds of POSS samples were used, in particular, POSS with different inorganic cage and with different organic pendent groups. The rheological investigation suggests clearly that the POSS acts as a plasticizer and that the processability of the PS was positively modified. The affinity between the POSS samples and the PS matrix was estimated by the calculated theoretical solubility parameters, considering the Hoy’s method and by morphology analysis. Minor difference between the solubility parameter of POSS and the matrix means better compatibility and no aggregation tendency. Furthermore, the POSS loading leads to a decrease of the rigidity, of the glass transition temperature and of the damping factor of the nanocomposite systems. The loading of different POSS molecules with open cage leads to a more pronounced effect on all the investigated properties that the loading of the POSS molecules with closed cage. Moreover, the melt properties are significantly influenced by the type of inorganic framework, by the type of the pendent organic groups and by the interaction between the POSS organic groups and the host matrix, while, the solid state properties appears to be influenced more by the kind of cage.

Structural Analysis of Polyhedral Oligomeric Silsesquioxane Coated SiC Nanoparticles and Their Applications in Thermoset Polymers

International Nuclear Information System (INIS)

Reza-E-Rabby, M.; Jeelani, Sh.; Rangari, V. K.

2015-01-01

The SiC nanoparticles (NPs) were sonochemically coated with Octa Isobutyl (OI) polyhedral oligomeric silsesquioxane (POSS) to create a compatible interface between particle and thermoset polymer. X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR), and X-ray diffraction (XRD) techniques were used to analyze the structure of OI-POSS coated SiC nanoparticles. These results revealed the formation of a covalent bonding between SiC and OI-POSS. The transmission electron microscopy (TEM) analysis of OI-POSS coated SiC nanoparticles has also shown the indication of attachment between these two nanoparticles. The OI-POSS coated SiC nanoparticles were further reinforced into a thermoset resin system in order to evaluate mechanical and thermal properties of nano composites. The flexural strength, modulus, and glass transition temperature were found to be enhanced while SiC and OI-POSS coated SiC were infused into epoxy system compared to those properties of neat epoxy resin

Structural Analysis of Polyhedral Oligomeric Silsesquioxane Coated SiC Nanoparticles and Their Applications in Thermoset Polymers

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Md. Reza-E-Rabby

2015-01-01

Full Text Available The SiC nanoparticles (NPs were sonochemically coated with OctaIsobutyl (OI polyhedral oligomeric silsesquioxane (POSS to create a compatible interface between particle and thermoset polymer. X-ray photoelectron spectroscopy (XPS, Fourier transform infrared spectroscopy (FTIR, and X-ray diffraction (XRD techniques were used to analyze the structure of OI-POSS coated SiC nanoparticles. These results revealed the formation of a covalent bonding between SiC and OI-POSS. The transmission electron microscopy (TEM analysis of OI-POSS coated SiC nanoparticles has also shown the indication of attachment between these two nanoparticles. The OI-POSS coated SiC nanoparticles were further reinforced into a thermoset resin system in order to evaluate mechanical and thermal properties of nanocomposites. The flexural strength, modulus, and glass transition temperature were found to be enhanced while SiC and OI-POSS coated SiC were infused into epoxy system compared to those properties of neat epoxy resin.

Preparation of polyhedral oligomeric silsesquioxane based hybrid monoliths by ring-opening polymerization for capillary LC and CEC.

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Lin, Hui; Zhang, Zhenbin; Dong, Jing; Liu, Zhongshan; Ou, Junjie; Zou, Hanfa

2013-09-01

A new organic-inorganic hybrid monolith was prepared by the ring-opening polymerization of octaglycidyldimethylsilyl polyhedral oligomeric silsesquioxane (POSS) with 1,4-butanediamine (BDA) using 1-propanol, 1,4-butanediol, and PEG 10,000 as a porogenic system. Benefiting from the moderate phase separation process, the resulting poly(POSS-co-BDA) hybrid monolith possessed a uniform microstructure and exhibited excellent performance in chromatographic applications. Neutral, acidic, and basic compounds were successfully separated on the hybrid monolith in capillary LC (cLC), and high column efficiencies were achieved in all of the separations. In addition, as the amino groups could generate a strong EOF, the hybrid monolith was also applied in CEC for the separation of neutral and polar compounds, and a satisfactory performance was obtained. These results demonstrate that the poly(POSS-co-BDA) hybrid monolith is a good separation media in chromatographic separations of various types of compounds by both cLC and CEC. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Coatings of molecularly imprinted polymers based on polyhedral oligomeric silsesquioxane for open tubular capillary electrochromatography.

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Zhao, Qing-Li; Zhou, Jin; Zhang, Li-Shun; Huang, Yan-Ping; Liu, Zhao-Sheng

2016-05-15

Polyhedral oligomeric silsesquioxane (POSS) was successfully applied, for the first time, to prepare imprinted monolithic coating for capillary electrochromatography. The imprinted monolithic coating was synthesized with a mixture of PSS-(1-Propylmethacrylate)-heptaisobutyl substituted (MA 0702), S-amlodipine (template), methacrylic acid (functional monomer), and 2-methacrylamidopropyl methacrylate (crosslinker), in a porogenic mixture of toluene-isooctane. The influence of synthesis parameters on the imprinting effect and separation performance, including the amount of MA 0702, the ratio of template to monomer, and the ratio of monomer to crosslinker, was investigated. The greatest resolution for enantiomers separation on the imprinted monolithic column prepared with MA 0702 was up to 22.3, about 2 times higher than that prepared in absence of the POSS. Column efficiency on the POSS-based MIP coatings was beyond 30,000 plate m(-1). The comparisons between MIP coating synthesized with the POSS and without the POSS were made in terms of selectivity, column efficiency, and resolution. POSS-based MIP capillaries with naproxen or zopiclone was also prepared and separation of enantiomers can be achieved. Copyright © 2016 Elsevier B.V. All rights reserved.

Construction of porous cationic frameworks by crosslinking polyhedral oligomeric silsesquioxane units with N-heterocyclic linkers

Science.gov (United States)

Chen, Guojian; Zhou, Yu; Wang, Xiaochen; Li, Jing; Xue, Shuang; Liu, Yangqing; Wang, Qian; Wang, Jun

2015-06-01

In fields of materials science and chemistry, ionic-type porous materials attract increasing attention due to significant ion-exchanging capacity for accessing diversified applications. Facing the fact that porous cationic materials with robust and stable frameworks are very rare, novel tactics that can create new type members are highly desired. Here we report the first family of polyhedral oligomeric silsesquioxane (POSS) based porous cationic frameworks (PCIF-n) with enriched poly(ionic liquid)-like cationic structures, tunable mesoporosities, high surface areas (up to 1,025 m2 g-1) and large pore volumes (up to 0.90 cm3 g-1). Our strategy is designing the new rigid POSS unit of octakis(chloromethyl)silsesquioxane and reacting it with the rigid N-heterocyclic cross-linkers (typically 4,4‧-bipyridine) for preparing the desired porous cationic frameworks. The PCIF-n materials possess large surface area, hydrophobic and special anion-exchanging property, and thus are used as the supports for loading guest species PMo10V2O405- the resultant hybrid behaves as an efficient heterogeneous catalyst for aerobic oxidation of benzene and H2O2-mediated oxidation of cyclohexane.

Morphological evolution in dewetting polystyrene/polyhedral oligomeric silsesquioxane thin film bilayers.

Science.gov (United States)

Paul, Rituparna; Karabiyik, Ufuk; Swift, Michael C; Hottle, John R; Esker, Alan R

2008-05-06

Morphological evolution in dewetting thin film bilayers of polystyrene (PS) and a polyhedral oligomeric silsesquioxane (POSS), trisilanolphenyl-POSS (TPP), was studied as a function of annealing temperature and annealing time. The results demonstrate unique dewetting morphologies in PS/TPP bilayers at elevated temperatures that are significantly different from those typically observed in dewetting polymer/polymer bilayers. During temperature ramp studies by optical microscopy (OM) in the reflection mode, PS/TPP bilayers form cracks with a weak optical contrast at approximately 130 degrees C. The crack formation is attributed to tensile stresses within the upper TPP layer. The weak optical contrast of the cracks observed in the bilayers for annealing temperatures below approximately 160 degrees C is consistent with the cracking and dewetting of only the upper TPP layer from the underlying PS layer. The optical contrast of the morphological features is significantly enhanced at annealing temperatures of >160 degrees C. This observation suggests dewetting of both the upper TPP and the lower PS layers that results in the exposure of the silicon substrate. Upon annealing the PS/TPP bilayers at 200 degrees C in a temperature jump experiment, the upper TPP layer undergoes instantaneous cracking as observed by OM. These cracks in the upper TPP layer serve as nucleation sites for rapid dewetting and aggregation of the TPP layer, as revealed by OM and atomic force microscopy (AFM). X-ray photoelectron spectroscopy (XPS) results indicated that dewetting of the lower PS layer ensued for annealing times >5 min and progressed up to 90 min. For annealing times >90 min, OM, AFM, and XPS results revealed complete dewetting of both the layers with the formation of TPP encapsulated PS droplets.

Endohedral complexes of Polyhedral Oligomeric Silsesquioxane (POSS) cages with transition metal dihydrides

Energy Technology Data Exchange (ETDEWEB)

Wang, Xiqiao; Corn, John; Hagelberg, Frank, E-mail: hagelber@etsu.edu

2013-11-29

Highlights: • Comparative studies of POSS cages with endohedral metal dihydrides. • Exothermic inclusion was found for the T{sub 10} cage with MH{sub 2}, M = Ti, Ru, Os, Pt. • Within this group of metal atoms, the only exothermic MH{sub 4}@T{sub m} unit is that with M = Os. • Enhanced hydrogen atom density, as compared to free MH{sub 4}, was found in the cage. • No exothermic solutions were identified for MH{sub 6}@T{sub 10}. - Abstract: Polyhedral Oligomeric Silsesquioxane (POSS) cages are investigated in terms of their potential to enclose small metal hydrides, with the objective of defining conditions that maximize the number of encapsulated hydrogen atoms. Systems of the form MH{sub 2n}@T{sub m}, where n = 1–3, m = 8, 10, and M comprises metal atom species of the groups IV, VI, VIII, X, and XII, are studied by methods of ab initio and density functional theory (DFT). The resulting composites are categorized with respect to their structural and energetic features. For MH{sub 2}@T{sub 8}, it is found in all cases considered that including MH{sub 2} into the POSS cage is an endothermic process. For MH{sub 2}@T{sub 10} and M = Ti, Ru, Os, Pt, inclusion of the MH{sub 2} guest into the cage turns out to be exothermic, and also leaves the cage intact. For MH{sub 4}@T{sub m}, this behavior is only observed for one system, OsH{sub 4}@T{sub 10}.

Unusual Emission of Polystyrene-Based Alternating Copolymers Incorporating Aminobutyl Maleimide Fluorophore-Containing Polyhedral Oligomeric Silsesquioxane Nanoparticles

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Mohamed Gamal Mohamed

2017-03-01

Full Text Available In this study, we synthesized an unusual 2-aminobutyl maleimide isobutyl polyhedral oligomeric silsesquioxane (MIPOSS-NHBu monomer lacking conventional fluorescent groups. We then prepared poly(styrene-alt-2-aminobutyl maleimide isobutyl POSS [poly(S-alt-MIPOSS-NHBu] and poly(4-acetoxystyrene-alt-2-aminobutyl maleimide isobutyl POSS [poly(AS-alt-MIPOSS-NHBu] copolymers through facile free radical copolymerizations using azobisisobutyronitrile as the initiator and tetrahydrofuran as the solvent. A poly(4-hydroxystyrene-alt-2-aminobutyl maleimide isobutyl POSS [poly(HS-alt-MIPOSS-NHBu] copolymer was prepared through acetoxyl hydrazinolysis of poly(AS-alt-MIPOSS-NHBu. We employed 1H, 13C, and 29Si nuclear magnetic resonance spectroscopy; Fourier transform infrared spectroscopy; differential scanning calorimetry; and photoluminescence spectroscopy to investigate the structures and the thermal and optical properties of the monomers and novel POSS-containing alternating copolymers. Intramolecular hydrogen bonding between the amino and dihydrofuran-2,5-dione group and clustering of the locked C=O groups from the POSS nanoparticles in the MIPOSS-NHBu units restricted the intramolecular motion of the polymer chain, causing it to exhibit strong light emission. As a result, the MIPOSS-NHBu monomer and the poly(AS-alt-MIPOSS-NHBu copolymer both have potential applicability in the detection of metal ions with good selectivity.

Development of Biodegradable Poly(citrate)-Polyhedral Oligomeric Silsesquioxanes Hybrid Elastomers with High Mechanical Properties and Osteogenic Differentiation Activity.

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Du, Yuzhang; Yu, Meng; Chen, Xiaofeng; Ma, Peter X; Lei, Bo

2016-02-10

Biodegradable elastomeric biomaterials have attracted much attention in tissue engineering due to their biomimetic viscoelastic behavior and biocompatibility. However, the low mechanical stability at hydrated state, fast biodegradation in vivo, and poor osteogenic activity greatly limited bioelastomers applications in bone tissue regeneration. Herein, we develop a series of poly(octanediol citrate)-polyhedral oligomeric silsesquioxanes (POC-POSS) hybrids with highly tunable elastomeric behavior (hydrated state) and biodegradation and osteoblasts biocompatibility through a facile one-pot thermal polymerization strategy. POC-POSS hybrids show significantly improved stiffness and ductility in either dry or hydrated conditions, as well as good antibiodegradation ability (20-50% weight loss in 3 months). POC-POSS hybrids exhibit significantly enhanced osteogenic differentiation through upregulating alkaline phosphatase (ALP) activity, calcium deposition, and expression of osteogenic markers (ALPL, BGLAP, and Runx2). The high mechanical stability at hydrated state and enhanced osteogenic activity make POC-POSS hybrid elastomers promising as scaffolds and nanoscale vehicles for bone tissue regeneration and drug delivery. This study may also provide a new strategy (controlling the stiffness under hydrated condition) to design advanced hybrid biomaterials with high mechanical properties under physiological condition for tissue regeneration applications.

Fouling behaviors of polybenzimidazole (PBI)-polyhedral oligomeric silsesquioxane (POSS)/polyacrylonitrile (PAN) hollow fiber membranes for engineering osmosis processes

KAUST Repository

Chen, Sicong; Fu, Xiuzhu; Chung, Neal Tai-Shung

2014-01-01

This paper investigated the individual effects of reverse salt flux and permeate flux on fouling behaviors of as-spun and annealed polybenzimidazole (PBI)-polyhedral oligomeric silsesquioxane (POSS)/polyacrylonitrile (PAN) hollow fiber membranes under forward osmosis (FO) and pressure retarded osmosis (PRO) processes. Two types of membrane fouling had been studied; namely, inorganic fouling (CaSO4·2H2O gypsum scaling) during FO operations and organic fouling (sodium alginate fouling) during PRO operations. It is found that gypsum scaling on the membrane surface may be inhibited and even eliminated with an increase in reverse MgCl2 flux due to competitive formations of MgSO4° and CaSO4·2H2O. In contrast, the increase of reverse NaCl flux exhibits a slight enhancement on alginate fouling in both FO and PRO processes. Comparing to the reverse salt flux, the permeate flux always plays a dominant role in fouling. Therefore, lesser fouling has been observed on the membrane surface under the pressurized PRO process than FO process because the reduced initial flux mitigates the fouling phenomena more significantly than the enhancement caused by an increase in reverse NaCl flux. © 2013 Elsevier B.V.

Fouling behaviors of polybenzimidazole (PBI)-polyhedral oligomeric silsesquioxane (POSS)/polyacrylonitrile (PAN) hollow fiber membranes for engineering osmosis processes

KAUST Repository

Chen, Sicong

2014-02-01

This paper investigated the individual effects of reverse salt flux and permeate flux on fouling behaviors of as-spun and annealed polybenzimidazole (PBI)-polyhedral oligomeric silsesquioxane (POSS)/polyacrylonitrile (PAN) hollow fiber membranes under forward osmosis (FO) and pressure retarded osmosis (PRO) processes. Two types of membrane fouling had been studied; namely, inorganic fouling (CaSO4·2H2O gypsum scaling) during FO operations and organic fouling (sodium alginate fouling) during PRO operations. It is found that gypsum scaling on the membrane surface may be inhibited and even eliminated with an increase in reverse MgCl2 flux due to competitive formations of MgSO4° and CaSO4·2H2O. In contrast, the increase of reverse NaCl flux exhibits a slight enhancement on alginate fouling in both FO and PRO processes. Comparing to the reverse salt flux, the permeate flux always plays a dominant role in fouling. Therefore, lesser fouling has been observed on the membrane surface under the pressurized PRO process than FO process because the reduced initial flux mitigates the fouling phenomena more significantly than the enhancement caused by an increase in reverse NaCl flux. © 2013 Elsevier B.V.

Composite polymer electrolyte containing ionic liquid and functionalized polyhedral oligomeric silsesquioxanes for anhydrous PEM applications.

Science.gov (United States)

Subianto, Surya; Mistry, Mayur K; Choudhury, Namita Roy; Dutta, Naba K; Knott, Robert

2009-06-01

A new type of supported liquid membrane was made by combining an ionic liquid (IL) with a Nafion membrane reinforced with multifunctional polyhedral oligomeric silsesquioxanes (POSSs) using a layer-by-layer strategy for anhydrous proton-exchange membrane (PEM) application. The POSS was functionalized by direct sulfonation, and the sulfonated POSS (S-POSS) was incorporated into Nafion 117 membranes by the infiltration method. The resultant hybrid membrane shows strong ionic interaction between the Nafion matrix and the multifunctional POSS, resulting in increased glass transition temperature and thermal stability at very low loadings of S-POSS (1%). The presence of S-POSS has also improved the proton conductivity especially at low humidities, where it shows a marked increase due to its confinement in the ionic domains and promotes water uptake by capillary condensation. In order to achieve anhydrous conductivity, the IL 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BMI-BTSI) was incorporated into these membranes to provide proton conduction in the absence of water. Although the incorporation of an IL shows a plasticizing effect on the Nafion membrane, the S-POSS composite membrane with an IL shows a higher modulus at high temperatures compared to Nafion 117 and a Nafion-IL membrane, with significantly higher proton conductivity (5 mS/cm at 150 degrees C with 20% IL). This shows the ability of the multifunctional POSS and IL to work symbiotically to achieve the desirable proton conductivity and mechanical properties of such membranes by enhancing the ionic interaction within the material.

Development of the optical sensor for discriminating isomers of fatty acids based on emissive network polymers composed of polyhedral oligomeric silsesquioxane.

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Narikiyo, Hayato; Kakuta, Takahiro; Matsuyama, Hiroki; Gon, Masayuki; Tanaka, Kazuo; Chujo, Yoshiki

2017-07-01

It was shown that water-soluble network polymers composed of polyhedral oligomeric silsesquioxane (POSS) had hydrophobic spaces inside the network because of strong hydrophobicity of the cubic silica cage. In this study, the water-soluble POSS network polymers connected with triphenylamine derivatives (TPA-POSS) were synthesized, and their functions as a sensor for discriminating the geometric isomers of fatty acids were investigated. Accordingly, in the photoluminescence spectra, different time-courses of intensity and peak wavelengths of the emission bands were detected from the TPA-POSS-containing solution in the presence of cis- or trans-fatty acids during incubation. Furthermore, variable time-dependent changes were obtained by changing coexisting ratios between two geometric isomers. From the mechanistic investigation, it was implied that these changes could be originated from the difference in the degree of interaction between the POSS networks and each fatty acid. Our data could be applicable for constructing a sensing material for generation and proportion of trans-fatty acids in the oil. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structure–property relationships in hybrid dental nanocomposite resins containing monofunctional and multifunctional polyhedral oligomeric silsesquioxanes

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Wang WG

2014-02-01

Full Text Available Weiguo Wang,1,* Xiang Sun,1,* Li Huang,2,* Yu Gao,1 Jinghao Ban,1 Lijuan Shen,1 Jihua Chen1 1Department of Prosthodontics, 2Department of General Dentistry and Emergency, School of Stomatology, Fourth Military Medical University, Xi'an, People's Republic of China*These authors contributed equally to this workAbstract: Organic-inorganic hybrid materials, such as polyhedral oligomeric silsesquioxanes (POSS, have the potential to improve the mechanical properties of the methacrylate-based composites and resins used in dentistry. In this article, nanocomposites of methacryl isobutyl POSS (MI-POSS [bears only one methacrylate functional group] and methacryl POSS (MA-POSS [bears eight methacrylate functional groups] were investigated to determine the effect of structures on the properties of dental resin. The structures of the POSS-containing networks were determined by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, and Fourier transform infrared spectroscopy. Monofunctional POSS showed a strong tendency toward aggregation and crystallization, while multifunctional POSS showed higher miscibility with the dimethacrylate monomer. The mechanical properties and wear resistance decreased with increasing amounts of MI-POSS, indicating that the MI-POSS agglomerates act as the mechanical weak point in the dental resins. The addition of small amounts of MA-POSS improved the mechanical and shrinkage properties. However, samples with a higher MA-POSS concentration showed lower flexural strength and flexural modulus, indicating that there is a limited range in which the reinforcement properties of MA-POSS can operate. This concentration dependence is attributed to phase separation at higher concentrations of POSS, which affects the structural integrity, and thus, the mechanical and shrinkage properties of the dental resin. Our results show that resin with 3% MA-POSS is a potential candidate for resin-based dental materials

Development of a polymeric ionic liquid coating for direct-immersion solid-phase microextraction using polyhedral oligomeric silsesquioxane as cross-linker.

Science.gov (United States)

Chen, Chunyan; Liang, Xiaotong; Wang, Jianping; Zou, Ying; Hu, Huiping; Cai, Qingyun; Yao, Shouzhuo

2014-06-27

A novel solid-phase microextraction (SPME) fiber was developed by chemical binding of a crosslinked polymeric ionic liquid (PIL) on the surface of an anodized Ti wire, and was applied in direct-immersion mode for the extraction of perfluorinated compounds (PFCs) from water samples coupled with high performance liquid chromatography-tandem mass spectrometry analysis. The PIL coatings were synthesized by using 1-vinyl-3-hexylimidazolium hexafluorophosphate as monomer and methylacryloyl-substituted polyhedral oligomeric silsesquioxane (POSS) as cross-linker via free radical reaction. The proposed fiber coating exhibited high mechanical stability due to the chemical bonding between the coating and the Ti wire surface. The integration of POSS reagent enhanced the organic solvent resistance of the coating. The parameters affecting the extraction performance of the fiber coating including extraction time, pH of solution, ionic strength and desorption conditions were optimized. The developed PIL-POSS fiber showed good linearity (R<0.998) between 0.1 and 50ngmL(-1) with method detection limits ranging from 0.005 to 0.08ngmL(-1) depending on the analyte, and with relative standard deviation for single-fiber repeatability and fiber-to-fiber reproducibility less than 8.6% and 9.5%, respectively. Copyright © 2014 Elsevier B.V. All rights reserved.

Bioactivity and properties of a dental adhesive functionalized with polyhedral oligomeric silsesquioxanes (POSS) and bioactive glass.

Science.gov (United States)

Rizk, Marta; Hohlfeld, Lisa; Thanh, Loan Tao; Biehl, Ralf; Lühmann, Nicole; Mohn, Dirk; Wiegand, Annette

2017-09-01

This study aimed to analyze the effect of infiltrating a commercial adhesive with nanosized bioactive glass (BG-Bi) particles or methacryl-functionalized polyhedral oligomeric silsesquioxanes (POSS) on material properties and bioactivity. An acetone-based dental adhesive (Solobond Plus adhesive, VOCO GmbH, Cuxhaven, Germany) was infiltrated with nanosized bioactive glass particles (0.1 or 1wt%), or with monofunctional or multifunctional POSS particles (10 or 20wt%). Unfilled adhesive served as control. Dispersion and hydrodynamic radius of the nanoparticles were studied by dynamic light scattering. Set specimens were immersed for 28days in artificial saliva at 37°C, and surfaces were mapped for the formation of calcium phospate (Ca/P) precipitates (scanning electron microscopy/energy-dispersive X-ray spectroscopy). Viscosity (rheometry) and the structural characteristic of the networks were studied, such as degree of conversion (FTIR spectroscopy), sol fraction and water sorption. POSS particles showed a good dispersion of the particles for both types of particles being smaller than 3nm, while the bioactive glass particles had a strong tendency to agglomerate. All nanoparticles induced the formation of Ca/P precipitates. The viscosity of the adhesive was not or only slightly increased by POSS particle addition but strongly increased by the bioactive glass particles. The degree of conversion, water sorption and sol fraction showed a maintained or improved network structure and properties when filled with BG-Bi and multifunctional POSS, however, less polymerization was found when loading a monofunctional POSS. Multifunctional POSS may be incorporated into dental adhesives to provide a bioactive potential without changing material properties adversely. Copyright © 2017 The Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Smooth polyhedral surfaces

KAUST Repository

Gü nther, Felix; Jiang, Caigui; Pottmann, Helmut

2017-01-01

Polyhedral surfaces are fundamental objects in architectural geometry and industrial design. Whereas closeness of a given mesh to a smooth reference surface and its suitability for numerical simulations were already studied extensively, the aim of our work is to find and to discuss suitable assessments of smoothness of polyhedral surfaces that only take the geometry of the polyhedral surface itself into account. Motivated by analogies to classical differential geometry, we propose a theory of smoothness of polyhedral surfaces including suitable notions of normal vectors, tangent planes, asymptotic directions, and parabolic curves that are invariant under projective transformations. It is remarkable that seemingly mild conditions significantly limit the shapes of faces of a smooth polyhedral surface. Besides being of theoretical interest, we believe that smoothness of polyhedral surfaces is of interest in the architectural context, where vertices and edges of polyhedral surfaces are highly visible.

Smooth polyhedral surfaces

KAUST Repository

Günther, Felix

2017-03-15

Polyhedral surfaces are fundamental objects in architectural geometry and industrial design. Whereas closeness of a given mesh to a smooth reference surface and its suitability for numerical simulations were already studied extensively, the aim of our work is to find and to discuss suitable assessments of smoothness of polyhedral surfaces that only take the geometry of the polyhedral surface itself into account. Motivated by analogies to classical differential geometry, we propose a theory of smoothness of polyhedral surfaces including suitable notions of normal vectors, tangent planes, asymptotic directions, and parabolic curves that are invariant under projective transformations. It is remarkable that seemingly mild conditions significantly limit the shapes of faces of a smooth polyhedral surface. Besides being of theoretical interest, we believe that smoothness of polyhedral surfaces is of interest in the architectural context, where vertices and edges of polyhedral surfaces are highly visible.

Fabrication of boronate-decorated polyhedral oligomeric silsesquioxanes grafted cotton fiber for the selective enrichment of nucleosides in urine.

Science.gov (United States)

Gao, Li; Wei, Yinmao

2016-06-01

Various cotton fiber based boronate-affinity adsorbents are recently developed for the sample pretreatment of cis-diol-containing biomolecules, but most do not have efficient capacity due to limited binding sites on the surface of cotton fibers. To increase the density of boronate groups on the surface of cotton fiber, polyhedral oligomeric silsesquioxanes were used to modify cotton fiber to provide plentiful reactive sites for subsequent functionalization with 4-formylphenylboronic acid. The new adsorbent showed special recognition ability towards cis-diols and high adsorption capacity (175 μg/g for catechol, 250 μg/g for dopamine, 400 μg/g for adenosine). The in-pipette-tip solid-phase extraction was investigated under different conditions, including pH and ionic strength of solution, adsorbent amount, pipette times, washing solvent, and elution solvent. The in-pipette-tip solid-phase extraction coupled with high-performance liquid chromatography was used to analyze four nucleosides in urine samples. Under the optimal extraction conditions, the detection limits were determined to be between 5.1 and 6.1 ng/mL (S/N  =  3), and the linearity ranged from 20 to 500 ng/mL for these analytes. The accuracy of the analytical method was examined by studying the relative recoveries of analytes in real urine samples with recoveries varying from 83 to 104% (RSD = 3.9-10.2%, n = 3). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interaction of polyhedral oligomeric silsesquioxanes and dipalmitoylphosphatidylcholine at the air/water interface: Thermodynamic and rheological study.

Science.gov (United States)

Skrzypiec, M; Georgiev, G As; Rojewska, M; Prochaska, K

2017-10-01

Polyhedral oligomeric silsesquioxanes (POSS) derivatives containing open silsesquioxane cage bear great potential for biomedical applications and therefore their lateral interactions with phospholipids, major biomembranes and drug vehicles constituent, should be studied in detail. That is why the properties of surface films by two POSS-derivatives, POSS-polyethylene glycol (POSS-PEG) and POSS-perfluoroalkyl (POSS-OFP), pure and in presence of 1,2-dipalmitoyl-sn-glycerol-3-phosphocholine (DPPC) were studied using Langmuir surface balance. Side chains of opposite nature (PEG is hydrophilic; OFP is hydrophobic) were selected, so that to evaluate their impact on polymers' surface properties. Two types of measurements were performed: (i) the miscibility of POSS-derivatives with DPPC was evaluated via thermodynamic analysis of the surface pressure (π)-area (A) isotherms and (ii) the dilatational rheology of selected POSS-polymer containing films was studied by the stress relaxation method. Fourier transformation analysis of the relaxation transients allows to access films' dynamic interfacial properties in broad frequency range (10 -5 -1Hz). Film morphology was monitored with Brewster Angle Microscopy. PEG moiety enabled POSS-PEG to stably incorporate in DPPC films, modifying their equilibrium and dynamic properties. In contrast OFP chains excluded from interactions with other molecules and diminished PEG-OFP amphiphilicity. Therefore at high packing densities (π≥25mN/m) PEG-OFP was expelled from the air/water interface in DPPC/PEG-OFP mixtures, and the binary films equilibrium and dynamic surface properties were determined primarily by DPPC. Thus the choice of POSS side chains can play key role in biomedical applications depending on whether strong or weak incorporation of POSS-polymers in lipid environment is aimed for. Copyright © 2017 Elsevier B.V. All rights reserved.

Polyhedral patterns

KAUST Repository

Jiang, Caigui; Tang, Chengcheng; Vaxman, Amir; Wonka, Peter; Pottmann, Helmut

2015-01-01

We study the design and optimization of polyhedral patterns, which are patterns of planar polygonal faces on freeform surfaces. Working with polyhedral patterns is desirable in architectural geometry and industrial design. However, the classical

Polyhedral patterns

KAUST Repository

Jiang, Caigui

2015-10-27

We study the design and optimization of polyhedral patterns, which are patterns of planar polygonal faces on freeform surfaces. Working with polyhedral patterns is desirable in architectural geometry and industrial design. However, the classical tiling patterns on the plane must take on various shapes in order to faithfully and feasibly approximate curved surfaces. We define and analyze the deformations these tiles must undertake to account for curvature, and discover the symmetries that remain invariant under such deformations. We propose a novel method to regularize polyhedral patterns while maintaining these symmetries into a plethora of aesthetic and feasible patterns.

Surface modification of a polyhedral oligomeric silsesquioxane poly(carbonate-urea) urethane (POSS-PCU) nanocomposite polymer as a stent coating for enhanced capture of endothelial progenitor cells.

Science.gov (United States)

Tan, Aaron; Farhatnia, Yasmin; Goh, Debbie; G, Natasha; de Mel, Achala; Lim, Jing; Teoh, Swee-Hin; Malkovskiy, Andrey V; Chawla, Reema; Rajadas, Jayakumar; Cousins, Brian G; Hamblin, Michael R; Alavijeh, Mohammad S; Seifalian, Alexander M

2013-12-01

An unmet need exists for the development of next-generation multifunctional nanocomposite materials for biomedical applications, particularly in the field of cardiovascular regenerative biology. Herein, we describe the preparation and characterization of a novel polyhedral oligomeric silsesquioxane poly(carbonate-urea) urethane (POSS-PCU) nanocomposite polymer with covalently attached anti-CD34 antibodies to enhance capture of circulating endothelial progenitor cells (EPC). This material may be used as a new coating for bare metal stents used after balloon angioplasty to improve re-endothelialization. Biophysical characterization techniques were used to assess POSS-PCU and its subsequent functionalization with anti-CD34 antibodies. Results indicated successful covalent attachment of anti-CD34 antibodies on the surface of POSS-PCU leading to an increased propensity for EPC capture, whilst maintaining in vitro biocompatibility and hemocompatibility. POSS-PCU has already been used in 3 first-in-man studies, as a bypass graft, lacrimal duct and a bioartificial trachea. We therefore postulate that its superior biocompatibility and unique biophysical properties would render it an ideal candidate for coating medical devices, with stents as a prime example. Taken together, anti-CD34 functionalized POSS-PCU could form the basis of a nano-inspired polymer platform for the next generation stent coatings.

n-th Roots in finite polyhedral and centro-polyhedral groups

Indian Academy of Sciences (India)

Probability in finite groups; roots of elements; polyhedral groups; centro- polyhedral groups. 2010 Mathematics ... An element g of a finite group G is said to have an n-th root if there exists an element h ∈ G such that g = hn (n is a ..... For the proof of the fourth part, we must consider two cases: (i) m is odd and 4|d,. (ii) m, d are ...

Coating of Carbon Fiber with Polyhedral Oligomeric Silsesquioxane (POSS to Enhance Mechanical Properties and Durability of Carbon/Vinyl Ester Composites

Directory of Open Access Journals (Sweden)

Mujib Khan

2011-09-01

Full Text Available Our continuing quest to improve the performance of polymer composites under moist and saltwater environments has gained momentum in recent years with the reinforcement of inorganic nanoparticles into the polymer. The key to mitigate degradation of composites under such environments is to maintain the integrity of the fiber/matrix (F/M interface. In this study, the F/M interface of carbon/vinyl ester composites has been modified by coating the carbon fiber with polyhedral oligomeric silsesquioxane (POSS. POSS is a nanostructured inorganic-organic hybrid particle with a cubic structure having silicon atoms at the core and linked to oxygen atoms. The advantage of using POSS is that the silicon atoms can be linked to a substituent that can be almost any chemical group known in organic chemistry. Cubic silica cores are ‘hard particles’ and are about 0.53 nm in diameter. The peripheral organic unit is a sphere of about 1–3 nm in diameter. Further, cubic structure of POSS remains intact during the polymerization process and therefore with appropriate functional groups, if installed on the fiber surface, would provide a stable and strong F/M interface. Two POSS systems with two different functional groups; namely, octaisobutyl and trisilanolphenyl have been investigated. A set of chemical and mechanical procedures has been developed to coat carbon fibers with POSS, and to fabricate layered composites with vinyl ester resin. Interlaminar shear and low velocity impact tests have indicated around 17–38% improvement in mechanical properties with respect to control samples made without the POSS coating. Saltwater and hygrothermal tests at various environmental conditions have revealed that coating with POSS reduces water absorption by 20–30% and retains the composite properties.

Phenyl hepta cyclopentyl – polyhedral oligomeric silsesquioxane (ph,hcp-POSS/Polystyrene (PS nanocomposites: the influence of substituents in the phenyl group on the thermal stability

Directory of Open Access Journals (Sweden)

I. Blanco

2012-12-01

Full Text Available Some new Polystyrene (PS nanocomposites were prepared by using two Polyhedral Oligomeric Silsesquioxanes (POSSs, namely RR’7(SiO1.58 (where R = 4-methoxyphenyl or 2,4-difluorophenyl and R’ = cyclopentyl, as fillers, and their degradation was studied to investigate the effect of the electron-donor or electron-withdrawing character of the phenyl group substituents on thermal stability. Nanocomposites were synthesized by in situ polymerization of styrene in the presence of various concentrations of POSS. Proton nuclear magnetic resonance (1H NMR spectra indicated that the POSS content in the obtained nanocomposites was higher than that in reactant mixtures. Inherent viscosity (ηinh and glass transition temperature (Tg determinations indicated that the average molar mass of polymer in 4-methoxynanocomposites was the same than neat PS, while it was much lower in 2,4-difluoro derivatives. Degradations were carried out in both flowing nitrogen and static air atmospheres, in the scanning mode, at various heating rates, and temperature at 5% mass loss (T5% and the activation energy (Ea of degradation of various nanocomposites were determined. The values obtained for 4-methoxyderivatives were higher than unfilled PS thus indicating higher thermal stability. Conversely, the values found for 2,4-difluoro derivatives were lower, in some cases even than those of neat PS. The results were discussed and interpreted.

Electrospun poly(vinylidene fluoride) copolymer/octahydroxy-polyhedral oligomeric silsesquioxane nanofibrous mats as ionic liquid host: enhanced salt dissociation and its function in electrochromic device

International Nuclear Information System (INIS)

Zhou, Rui; Pramoda, Kumari Pallathadka; Liu, Wanshuang; Zhou, Dan; Ding, Guoqiang; He, Chaobin; Leong, Yew Wei; Lu, Xuehong

2014-01-01

Highlights: • The well dispersed POSS-OH promotes the dissociation of both LiClO 4 and BMIM + BF 4 − . • POSS-OH significantly increases the ionic conductivity and lithium transference number. • POSS-OH containing electrolyte improves the optical contrast of electrochromic device. - Abstract: Electrospun polymer nanofibrous mats loaded with ionic liquids (ILs) and lithium salts are promising non-volatile electrolytes owing to their high ionic conductivities. However, the large cations of ILs are difficult to diffuse into solid electrodes, whereas the lithium ions in ILs tend to form anionic complexes with the IL anions, reducing the number of free lithium ions. To address these issues, octa(3-hydroxy-3-methylbutyldimethylsiloxy) polyhedral oligomeric silsesquioxane (POSS-OH), which has large specific surface area and functionality number, is incorporated into electrospun poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-co-HFP) nanofibrous mats, and the mats are used to host LiClO 4 /1-butyl-3-methylimidazolium tetrafluoroborate (BMIM + BF 4 − ). It is found that POSS-OH can significantly increase both ionic conductivity and lithium transference number of the electrolytes owing to the Lewis acid-base interactions of POSS-OH with ClO 4 − and BF 4 − . The electrochromic device using the hybrid mat (with 5 wt% POSS-OH) loaded with LiClO 4 /BMIM + BF 4 − as the electrolyte shows significantly improved transmittance contrast and switching time, as a result of increased number of free lithium ions

Molecular Modeling of Interfacial Behaviors of Nanomaterials

Science.gov (United States)

2007-05-01

potential was originally designed for the modeling of mixed covalent- ionic bonding and was successfully used to describe oxides in crystalline, glassy, and...is separates from the bulk liquid polymer, i.e., the structure of this layer, as influenced by that of the meatal surface, is significantly more...Striolo, J. Kieffer, and P. Cummings, ’Evaluation of Force- fields for molecular simulation of polyhedral oligomeric silsesquioxanes,’ J. Phys. Chem

Nanomodified Carbon/Carbon Composites for Intermediate Temperature

Science.gov (United States)

2007-08-31

7] Properties Values Appearance Light yellow liquid (material is waxy at room temperature) Specific Gravity 1.245 Ionic Cl (ppm) ᝺ Ionic Na and K...and several types of nanoparticles: chemically modified montmorillonite (MMT) organoclays, polyhedral oligomeric silsesquioxanes (POSS®), carbon...montmorillonite (MMT) organoclays, carbon nanofibers, polyhedral oligomeric silsesquioxanes (POSS®), nanosilica, nano- silicon carbide (n-SiC), and

Synthesis and characterization of polyhedral and quasi-sphere non-polyhedral Pt nanoparticles: effects of their various surface morphologies and sizes on electrocatalytic activity for fuel cell applications

International Nuclear Information System (INIS)

Long, Nguyen Viet; Ohtaki, Michitaka; Hien, Tong Duy; Jalem, Randy; Nogami, Masayuki

2011-01-01

In this article, polyhedral and non-polyhedral Pt nanoparticles were prepared by modified polyol method using AgNO 3 as a good structure-modifying agent. Their TEM and HRTEM images showed the particle size in the range of 8–16 nm for both the above cases. The structures and properties of the surfaces of Pt nanoparticles were investigated through cyclic voltammetry in dilute perchloric acid (HClO 4 ) electrolyte solution. A comparison of the electrocatalytic property in methanol electrooxidation was made. Here, the effects of polyhedral and non-polyhedral morphologies on their catalytic properties were studied. The results revealed that the special catalytic activity of quasi-sphere non-polyhedral Pt nanoparticles is higher than that of polyhedral Pt nanoparticles. In addition, Pt nanoparticles of un-sharp and quasi-sphere morphologies exhibit the tolerance to poisoning species better than that of Pt nanoparticles of sharp and polyhedral morphologies due to the various morphologies of the catalyst surfaces in the chronoamperometric plots. Therefore, these experimental evidences showed the morphology-dependent catalytic property according to the various morphologies and complexity of their catalyst surfaces.

Modeling IrisCode and its variants as convex polyhedral cones and its security implications.

Science.gov (United States)

Kong, Adams Wai-Kin

2013-03-01

IrisCode, developed by Daugman, in 1993, is the most influential iris recognition algorithm. A thorough understanding of IrisCode is essential, because over 100 million persons have been enrolled by this algorithm and many biometric personal identification and template protection methods have been developed based on IrisCode. This paper indicates that a template produced by IrisCode or its variants is a convex polyhedral cone in a hyperspace. Its central ray, being a rough representation of the original biometric signal, can be computed by a simple algorithm, which can often be implemented in one Matlab command line. The central ray is an expected ray and also an optimal ray of an objective function on a group of distributions. This algorithm is derived from geometric properties of a convex polyhedral cone but does not rely on any prior knowledge (e.g., iris images). The experimental results show that biometric templates, including iris and palmprint templates, produced by different recognition methods can be matched through the central rays in their convex polyhedral cones and that templates protected by a method extended from IrisCode can be broken into. These experimental results indicate that, without a thorough security analysis, convex polyhedral cone templates cannot be assumed secure. Additionally, the simplicity of the algorithm implies that even junior hackers without knowledge of advanced image processing and biometric databases can still break into protected templates and reveal relationships among templates produced by different recognition methods.

Sub-polyhedral scheduling using (unit-)two-variable-per-inequality polyhedra

OpenAIRE

Upadrasta , Ramakrishna; Cohen , Albert

2013-01-01

International audience; Polyhedral compilation has been successful in the design and implementation of complex loop nest optimizers and parallelizing compilers. The algorithmic complexity and scalability limitations remain one important weakness. We address it using sub-polyhedral under-aproximations of the systems of constraints resulting from affine scheduling problems. We propose a sub-polyhedral scheduling technique using (Unit-)Two-Variable-Per-Inequality or (U)TVPI Polyhedra. This techn...

Preparation and characterization of polyhedral oligomer silsesquioxane nanocomposites incorporated in epoxy resin

International Nuclear Information System (INIS)

Longhi, Marielen; Zini, Lucas Pandolphi; Birriel, Eliena Jonko; Kunst, Sandra Raquel; Zattera, Ademir Jose

2015-01-01

The incorporation of nanofiller in thermosetting like epoxy resin as has been studied in order to modify its properties. In this research, nanocomposites were obtained by incorporating 5% by weight of three polyhedral oligomeric silsesquioxane (POSS) with different number of functionalization: Glicidilisobutil-POSS, Triglicidilisobutil- POSS and Glicicil POSS in an epoxy matrix by sonification process. The nanocomposites were characterized by analysis of X-ray diffraction (DRX), transmission electron microscopy (TEM) and thermogravimetric analysis (TGA). The DRX analysis showed the characteristic peak of POSS and TEM images showed that there is a difference in the dispersion of nanocages for the difference in the number of epoxy groups on the POSS. The incorporation of Glicidilisobutil-POSS showed a significant increase in the glass transition temperature (Tg) value, and also that the most effective from the viewpoint of the dispersion, on the other hand, the Glycidyl-POSS had a greater influence on the thermal stability demonstrating that the dispersion medium is an important characteristic to define the most desirable properties. (author)

Modelling the interdependence between the stoichiometry of receptor oligomerization and ligand binding for a coexisting dimer/tetramer receptor system.

Science.gov (United States)

Rovira, X; Vivó, M; Serra, J; Roche, D; Strange, P G; Giraldo, J

2009-01-01

Many G protein-coupled receptors have been shown to exist as oligomers, but the oligomerization state and the effects of this on receptor function are unclear. For some G protein-coupled receptors, in ligand binding assays, different radioligands provide different maximal binding capacities. Here we have developed mathematical models for co-expressed dimeric and tetrameric species of receptors. We have considered models where the dimers and tetramers are in equilibrium and where they do not interconvert and we have also considered the potential influence of the ligands on the degree of oligomerization. By analogy with agonist efficacy, we have considered ligands that promote, inhibit or have no effect on oligomerization. Cell surface receptor expression and the intrinsic capacity of receptors to oligomerize are quantitative parameters of the equations. The models can account for differences in the maximal binding capacities of radioligands in different preparations of receptors and provide a conceptual framework for simulation and data fitting in complex oligomeric receptor situations.

Facile synthesis of a boronate affinity sorbent from mesoporous nanomagnetic polyhedral oligomeric silsesquioxanes composite and its application for enrichment of catecholamines in human urine

Energy Technology Data Exchange (ETDEWEB)

He, Haibo, E-mail: hbhe2006@shu.edu.cn [Department of Chemistry, Shanghai University, Shanghai 200444 (China); Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072 (China); Zhou, Ziqing; Dong, Chen; Wang, Xin [Department of Chemistry, Shanghai University, Shanghai 200444 (China); Yu, Qiong-wei [Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072 (China); Lei, Yunyi; Luo, Liqiang [Department of Chemistry, Shanghai University, Shanghai 200444 (China); Feng, Yuqi [Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072 (China)

2016-11-09

A boronate-decorated nanomagnetic organic-inorganic hybrid material was facilely synthesized by utilizing the nanomagnetic polyhedral oligomeric silsesquioxanes (POSS) composite (Fe{sub 3}O{sub 4}@POSS) as the base platform. A simple copolymerization occurred between 3-acrylamidophenylboronic acid (AAPBA) and the residual end vinyl groups supplied by the substrate. Here the special emphasis was placed on the octavinyl POSS, which not only acted as the building blocks for a hybrid architecture but also facilitated the process of grafting boronate groups onto the surface of POSS based nanomagnetic composite (Fe{sub 3}O{sub 4}@POSS). The successful immobilization of affinity ligand-AAPBA on the Fe{sub 3}O{sub 4}@POSS was confirmed by Fourier transform infrared (FT-IR), elemental analysis, inductively coupled plasma atomic emission spectrometer (ICP-AES), field emission scanning electron microscope. A magnetic solid-phase extraction (MSPE) for cis-diols enrichment was developed using the as-prepared Fe{sub 3}O{sub 4}@POSS-AAPBA material as an affinity sorbent and three catecholamines (CAs), namely noradrenaline, epinephrine and isoprenaline, as model analytes. Under the optimal extraction conditions, sensitive and simultaneous analysis of three CAs from the urine sample was achieved by high-performance liquid chromatography with UV detection (HPLC-UV). The limits of detection (LOD, S/N = 3) and the limits of quantitation (LOQ, S/N = 10) for the target analytes were 0.81–1.32 ng mL{sup −1} and 2.70–4.40 ng mL{sup −1}, respectively. Also good recoveries (85.5–101.7%) and repeatability (RSD≤10.1%) were obtained by this method. This work not only showed a facility for the utilization of Fe{sub 3}O{sub 4}@POSS as a substrate for constructing a boronate functionalized nanomagnetic sorbent, but also demonstrated the capability of the derived material for recognition of trace amount of cis-diols biomolecules presented in complicated biological matrices

Clustered deep shadow maps for integrated polyhedral and volume rendering

KAUST Repository

Bornik, Alexander; Knecht, Wolfgang; Hadwiger, Markus; Schmalstieg, Dieter

2012-01-01

This paper presents a hardware-accelerated approach for shadow computation in scenes containing both complex volumetric objects and polyhedral models. Our system is the first hardware accelerated complete implementation of deep shadow maps, which

n-th Roots in finite polyhedral and centro-polyhedral groups

Indian Academy of Sciences (India)

The probability that a randomly chosen element in a non-abelian finite group has a square root, has been investigated by certain authors in recent years. In this paper, this probability will be generalized for the -th roots when ≥ 2 and it will be computed for every finite polyhedral group and all of the finite ...

Form-finding with polyhedral meshes made simple

KAUST Repository

Tang, Chengcheng

2014-07-27

We solve the form-finding problem for polyhedral meshes in a way which combines form, function and fabrication; taking care of user-specified constraints like boundary interpolation, planarity of faces, statics, panel size and shape, enclosed volume, and last, but not least, cost. Our main application is the interactive modeling of meshes for architectural and industrial design. Our approach can be described as guided exploration of the constraint space whose algebraic structure is simplified by introducing auxiliary variables and ensuring that constraints are at most quadratic. Computationally, we perform a projection onto the constraint space which is biased towards low values of an energy which expresses desirable "soft" properties like fairness. We have created a tool which elegantly handles difficult tasks, such as taking boundary-alignment of polyhedral meshes into account, planarization, fairing under planarity side conditions, handling hybrid meshes, and extending the treatment of static equilibrium to shapes which possess overhanging parts.

Form-finding with polyhedral meshes made simple

KAUST Repository

Tang, Chengcheng; Sun, Xiang; Gomes, Maria Alexandra; Wallner, Johannes; Pottmann, Helmut

2014-01-01

We solve the form-finding problem for polyhedral meshes in a way which combines form, function and fabrication; taking care of user-specified constraints like boundary interpolation, planarity of faces, statics, panel size and shape, enclosed volume, and last, but not least, cost. Our main application is the interactive modeling of meshes for architectural and industrial design. Our approach can be described as guided exploration of the constraint space whose algebraic structure is simplified by introducing auxiliary variables and ensuring that constraints are at most quadratic. Computationally, we perform a projection onto the constraint space which is biased towards low values of an energy which expresses desirable "soft" properties like fairness. We have created a tool which elegantly handles difficult tasks, such as taking boundary-alignment of polyhedral meshes into account, planarization, fairing under planarity side conditions, handling hybrid meshes, and extending the treatment of static equilibrium to shapes which possess overhanging parts.

[Formian 2 and a Formian Function for Processing Polyhedric Configurations

Science.gov (United States)

Nooshin, H.; Disney, P. L.; Champion, O. C.

1996-01-01

The work began in October 1994 with the following objectives: (1) to produce an improved version of the programming language Formian; and (2) to create a means for computer aided handling of polyhedric configurations including the geodesic forms of all kinds. A new version of Formian, referred to as Formian 2, is being implemented to operate in the Windows 95 environment. It is an ideal tool for configuration management in a convenient and user-friendly manner. The second objective was achieved by creating a standard Formian function that allows convenient handling of all types of polyhedric configurations. In particular, the focus of attention is on polyhedric configurations that are of importance in architectural and structural engineering fields. The natural medium for processing of polyhedric configurations is a programming language that incorporates the concepts of 'formex algebra'. Formian is such a programming language in which the processing of polyhedric configurations can be carried out using the standard elements of the language. A description of this function is included in a chapter for a book entitled 'Beyond the Cube: the Architecture of space Frames and Polyhedra'. A copy of this chapter is appended.

Orally administrated cinnamon extract reduces β-amyloid oligomerization and corrects cognitive impairment in Alzheimer's disease animal models.

Directory of Open Access Journals (Sweden)

Anat Frydman-Marom

Full Text Available An increasing body of evidence indicates that accumulation of soluble oligomeric assemblies of β-amyloid polypeptide (Aβ play a key role in Alzheimer's disease (AD pathology. Specifically, 56 kDa oligomeric species were shown to be correlated with impaired cognitive function in AD model mice. Several reports have documented the inhibition of Aβ plaque formation by compounds from natural sources. Yet, evidence for the ability of common edible elements to modulate Aβ oligomerization remains an unmet challenge. Here we identify a natural substance, based on cinnamon extract (CEppt, which markedly inhibits the formation of toxic Aβ oligomers and prevents the toxicity of Aβ on neuronal PC12 cells. When administered to an AD fly model, CEppt rectified their reduced longevity, fully recovered their locomotion defects and totally abolished tetrameric species of Aβ in their brain. Furthermore, oral administration of CEppt to an aggressive AD transgenic mice model led to marked decrease in 56 kDa Aβ oligomers, reduction of plaques and improvement in cognitive behavior. Our results present a novel prophylactic approach for inhibition of toxic oligomeric Aβ species formation in AD through the utilization of a compound that is currently in use in human diet.

Space-filling polyhedral sorbents

Energy Technology Data Exchange (ETDEWEB)

Haaland, Peter

2016-06-21

Solid sorbents, systems, and methods for pumping, storage, and purification of gases are disclosed. They derive from the dynamics of porous and free convection for specific gas/sorbent combinations and use space filling polyhedral microliths with facial aplanarities to produce sorbent arrays with interpenetrating interstitial manifolds of voids.

The effect of polyhedral oligomeric silsesquioxane dispersant and low surface energy additives on spectrally selective paint coatings with self-cleaning properties

Energy Technology Data Exchange (ETDEWEB)

Jerman, Ivan; Kozelj, Matjaz; Orel, Boris [National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana (Slovenia)

2010-02-15

Thickness-Insensitive Spectrally Selective (TISS) paint coatings were made of fluoropolymer resin binder (Lumiflon (LF), Asahi Glass Co., Ltd., Japan) and their water- and oil-repellent properties were obtained (contact angle: {theta}{sub water}{proportional_to}150 , {theta}{sub n-hexadecane}{proportional_to}55 ) by the addition of Polyhedral Oligomeric Silsesquioxane (POSS) characterized by amino (AP), isooctyl (IO) and perfluoro (PF) groups (i.e. AP{sub 2}IO{sub 4}PF{sub 2}) attached on the silsesquioxane cube (-SiO{sub 3/2}){sub 8}. Paint dispersions were made by modifying of black spinel pigment with trisilanol isobutyl (IB{sub 7}T{sub 7}(OH){sub 3}) POSS dispersant and with a single-capped silane isobutyltrimethoxysilane (IBTMS). Infrared and {sup 29}Si NMR spectra measurements were used for the identification of the structural characteristic of the corresponding POSS compounds. Surface free energy values of the pure cross-linked (no pigment added) LF binder which was determined from the measured contact angles for water, diiodomethane and formamide revealed the {gamma}{sup tot} value of the LF unpigmented resin with added AP{sub 2}IO{sub 4}PF{sub 2} T{sub 8} POSS was about 16.4 mN/m, which led to the {theta}{sub water}{proportional_to}110 , indicating enhancement of the hydrophobicity of the pure LF resin binder ({theta}{sub water}{proportional_to}89 ). SEM micrographs, which were used for the assessment of the TISS paint coating surface morphology confirmed the beneficial dispersive effect of IB{sub 7} T{sub 7}(OH){sub 3} dispersant as compared to the IBTMS silane. The presence of large Aluminium flake pigment and finely ground black pigment led to the formation of TISS paint coating surface, which exhibited bi-hierarchical roughness, resulting in water sliding angles of less than 10 , indicating the possible self-cleaning effect ({theta}{sub water}>150 and {theta}{sub n-hexadecane}{proportional_to}55 ). The use of POSS dispersant and POSS low surface energy

Form-finding with polyhedral meshes made simple

KAUST Repository

Tang, Chengcheng

2015-08-09

We solve the form-finding problem for polyhedral meshes in a way which combines form, function and fabrication; taking care of user-specified constraints like boundary interpolation, planarity of faces, statics, panel size and shape, enclosed volume, and cost. Our main application is the interactive modeling of meshes for architectural and industrial design. Our approach can be described as guided exploration of the constraint space whose algebraic structure is simplified by introducing auxiliary variables and ensuring that constraints are at most quadratic.

Form-finding with polyhedral meshes made simple

KAUST Repository

Tang, Chengcheng; Sun, Xiang; Gomes, Alexandra; Wallner, Johannes; Pottmann, Helmut

2015-01-01

We solve the form-finding problem for polyhedral meshes in a way which combines form, function and fabrication; taking care of user-specified constraints like boundary interpolation, planarity of faces, statics, panel size and shape, enclosed volume, and cost. Our main application is the interactive modeling of meshes for architectural and industrial design. Our approach can be described as guided exploration of the constraint space whose algebraic structure is simplified by introducing auxiliary variables and ensuring that constraints are at most quadratic.

Polyhedral meshing in numerical analysis of conjugate heat transfer

Science.gov (United States)

Sosnowski, Marcin; Krzywanski, Jaroslaw; Grabowska, Karolina; Gnatowska, Renata

2018-06-01

Computational methods have been widely applied in conjugate heat transfer analysis. The very first and crucial step in such research is the meshing process which consists in dividing the analysed geometry into numerous small control volumes (cells). In Computational Fluid Dynamics (CFD) applications it is desirable to use the hexahedral cells as the resulting mesh is characterized by low numerical diffusion. Unfortunately generating such mesh can be a very time-consuming task and in case of complicated geometry - it may not be possible to generate cells of good quality. Therefore tetrahedral cells have been implemented into commercial pre-processors. Their advantage is the ease of its generation even in case of very complex geometry. On the other hand tetrahedrons cannot be stretched excessively without decreasing the mesh quality factor, so significantly larger number of cells has to be used in comparison to hexahedral mesh in order to achieve a reasonable accuracy. Moreover the numerical diffusion of tetrahedral elements is significantly higher. Therefore the polyhedral cells are proposed within the paper in order to combine the advantages of hexahedrons (low numerical diffusion resulting in accurate solution) and tetrahedrons (rapid semi-automatic generation) as well as to overcome the disadvantages of both the above mentioned mesh types. The major benefit of polyhedral mesh is that each individual cell has many neighbours, so gradients can be well approximated. Polyhedrons are also less sensitive to stretching than tetrahedrons which results in better mesh quality leading to improved numerical stability of the model. In addition, numerical diffusion is reduced due to mass exchange over numerous faces. This leads to a more accurate solution achieved with a lower cell count. Therefore detailed comparison of numerical modelling results concerning conjugate heat transfer using tetrahedral and polyhedral meshes is presented in the paper.

Molecular basis of coiled-coil oligomerization-state specificity.

Science.gov (United States)

Ciani, Barbara; Bjelic, Saša; Honnappa, Srinivas; Jawhari, Hatim; Jaussi, Rolf; Payapilly, Aishwarya; Jowitt, Thomas; Steinmetz, Michel O; Kammerer, Richard A

2010-11-16

Coiled coils are extensively and successfully used nowadays to rationally design multistranded structures for applications, including basic research, biotechnology, nanotechnology, materials science, and medicine. The wide range of applications as well as the important functions these structures play in almost all biological processes highlight the need for a detailed understanding of the factors that control coiled-coil folding and oligomerization. Here, we address the important and unresolved question why the presence of particular oligomerization-state determinants within a coiled coil does frequently not correlate with its topology. We found an unexpected, general link between coiled-coil oligomerization-state specificity and trigger sequences, elements that are indispensable for coiled-coil formation. By using the archetype coiled-coil domain of the yeast transcriptional activator GCN4 as a model system, we show that well-established trimer-specific oligomerization-state determinants switch the peptide's topology from a dimer to a trimer only when inserted into the trigger sequence. We successfully confirmed our results in two other, unrelated coiled-coil dimers, ATF1 and cortexillin-1. We furthermore show that multiple topology determinants can coexist in the same trigger sequence, revealing a delicate balance of the resulting oligomerization state by position-dependent forces. Our experimental results should significantly improve the prediction of the oligomerization state of coiled coils. They therefore should have major implications for the rational design of coiled coils and consequently many applications using these popular oligomerization domains.

Clustered deep shadow maps for integrated polyhedral and volume rendering

KAUST Repository

Bornik, Alexander

2012-01-01

This paper presents a hardware-accelerated approach for shadow computation in scenes containing both complex volumetric objects and polyhedral models. Our system is the first hardware accelerated complete implementation of deep shadow maps, which unifies the computation of volumetric and geometric shadows. Up to now such unified computation was limited to software-only rendering . Previous hardware accelerated techniques can handle only geometric or only volumetric scenes - both resulting in the loss of important properties of the original concept. Our approach supports interactive rendering of polyhedrally bounded volumetric objects on the GPU based on ray casting. The ray casting can be conveniently used for both the shadow map computation and the rendering. We show how anti-aliased high-quality shadows are feasible in scenes composed of multiple overlapping translucent objects, and how sparse scenes can be handled efficiently using clustered deep shadow maps. © 2012 Springer-Verlag.

Hamiltonian cycles in polyhedral maps

Indian Academy of Sciences (India)

We present a necessary and sufficient condition for existence of a contractible, non-separating and non-contractible separating Hamiltonian cycle in the edge graph of polyhedral maps on surfaces.We also present algorithms to construct such cycles whenever it exists where one of them is linear time and another is ...

A simple gel electrophoresis method for separating polyhedral gold nanoparticles

Science.gov (United States)

Kim, Suhee; Lee, Hye Jin

2015-07-01

In this paper, a simple approach to separate differently shaped and sized polyhedral gold nanoparticles (NPs) within colloidal solutions via gel electrophoresis is described. Gel running parameters for separating efficiently gold NPs including gel composition, added surfactant types and applied voltage were investigated. The plasmonic properties and physical structure of the separated NPs extracted from the gel matrix were then investigated using transmission electron microscopy (TEM) and UV-vis spectrophotometry respectively. Data analysis revealed that gel electrophoresis conditions of a 1.5 % agarose gel with 0.1 % sodium dodecyl sulfate (SDS) surfactant under an applied voltage of 100 V resulted in the selective isolation of ~ 50 nm polyhedral shaped gold nanoparticles. Further efforts are underway to apply the method to purify biomolecule-conjugated polyhedral Au NPs that can be readily used for NP-enhanced biosensing platforms.

A Novel Type of Polyhedral Viruses Infecting Hyperthermophilic Archaea.

Science.gov (United States)

Liu, Ying; Ishino, Sonoko; Ishino, Yoshizumi; Pehau-Arnaudet, Gérard; Krupovic, Mart; Prangishvili, David

2017-07-01

Encapsidation of genetic material into polyhedral particles is one of the most common structural solutions employed by viruses infecting hosts in all three domains of life. Here, we describe a new virus of hyperthermophilic archaea, Sulfolobus polyhedral virus 1 (SPV1), which condenses its circular double-stranded DNA genome in a manner not previously observed for other known viruses. The genome complexed with virion proteins is wound up sinusoidally into a spherical coil which is surrounded by an envelope and further encased by an outer polyhedral capsid apparently composed of the 20-kDa virion protein. Lipids selectively acquired from the pool of host lipids are integral constituents of the virion. None of the major virion proteins of SPV1 show similarity to structural proteins of known viruses. However, minor structural proteins, which are predicted to mediate host recognition, are shared with other hyperthermophilic archaeal viruses infecting members of the order Sulfolobales The SPV1 genome consists of 20,222 bp and contains 45 open reading frames, only one-fifth of which could be functionally annotated. IMPORTANCE Viruses infecting hyperthermophilic archaea display a remarkable morphological diversity, often presenting architectural solutions not employed by known viruses of bacteria and eukaryotes. Here we present the isolation and characterization of Sulfolobus polyhedral virus 1, which condenses its genome into a unique spherical coil. Due to the original genomic and architectural features of SPV1, the virus should be considered a representative of a new viral family, "Portogloboviridae." Copyright © 2017 American Society for Microbiology.

Interactive volume visualization of general polyhedral grids

KAUST Repository

Muigg, Philipp; Hadwiger, Markus; Doleisch, Helmut; Grö ller, Eduard M.

2011-01-01

This paper presents a novel framework for visualizing volumetric data specified on complex polyhedral grids, without the need to perform any kind of a priori tetrahedralization. These grids are composed of polyhedra that often are non

Large-scale, rapid synthesis and application in surface-enhanced Raman spectroscopy of sub-micrometer polyhedral gold nanocrystals

International Nuclear Information System (INIS)

Guo Shaojun; Wang Yuling; Wang Erkang

2007-01-01

Macromolecule-protected sub-micrometer polyhedral gold nanocrystals have been facilely prepared by heating an aqueous solution containing poly (N-vinyl-2-pyrrolidone) (PVP) and HAuCl 4 without adding other reducing agents. Scanning electron microscopy (SEM), energy-dispersive x-ray spectroscopy (EDX), ultraviolet-visible-near-infrared spectroscopy (UV-vis-NIR), and x-ray diffraction (XRD) were employed to characterize the obtained polyhedral gold nanocrystals. It is found that the 10:1 molar ratio of PVP to gold is a key factor for obtaining quasi-monodisperse polyhedral gold nanocrystals. Furthermore, the application of polyhedral gold nanocrystals in surface-enhanced Raman scattering (SERS) was investigated by using 4-aminothiophenol (4-ATP) as a probe molecule. The results indicated that the sub-micrometer polyhedral gold nanocrystals modified on the ITO substrate exhibited higher SERS activity compared to the traditional gold nanoparticle modified film. The enhancement factor (EF) on polyhedral gold nanocrystals was about six times larger than that obtained on aggregated gold nanoparticles (∼25 nm)

Towards reproducible experimental studies for non-convex polyhedral shaped particles

Directory of Open Access Journals (Sweden)

Wilke Daniel N.

2017-01-01

Full Text Available The packing density and flat bottomed hopper discharge of non-convex polyhedral particles are investigated in a systematic experimental study. The motivation for this study is two-fold. Firstly, to establish an approach to deliver quality experimental particle packing data for non-convex polyhedral particles that can be used for characterization and validation purposes of discrete element codes. Secondly, to make the reproducibility of experimental setups as convenient and readily available as possible using affordable and accessible technology. The primary technology for this study is fused deposition modeling used to 3D print polylactic acid (PLA particles using readily available 3D printer technology. A total of 8000 biodegradable particles were printed, 1000 white particles and 1000 black particles for each of the four particle types considered in this study. Reproducibility is one benefit of using fused deposition modeling to print particles, but an extremely important additional benefit is that specific particle properties can be explicitly controlled. As an example in this study the volume fraction of each particle can be controlled i.e. the effective particle density can be adjusted. In this study the particle volumes reduces drastically as the non-convexity is increased, however all printed white particles in this study have the same mass within 2% of each other.

Towards reproducible experimental studies for non-convex polyhedral shaped particles

Science.gov (United States)

Wilke, Daniel N.; Pizette, Patrick; Govender, Nicolin; Abriak, Nor-Edine

2017-06-01

The packing density and flat bottomed hopper discharge of non-convex polyhedral particles are investigated in a systematic experimental study. The motivation for this study is two-fold. Firstly, to establish an approach to deliver quality experimental particle packing data for non-convex polyhedral particles that can be used for characterization and validation purposes of discrete element codes. Secondly, to make the reproducibility of experimental setups as convenient and readily available as possible using affordable and accessible technology. The primary technology for this study is fused deposition modeling used to 3D print polylactic acid (PLA) particles using readily available 3D printer technology. A total of 8000 biodegradable particles were printed, 1000 white particles and 1000 black particles for each of the four particle types considered in this study. Reproducibility is one benefit of using fused deposition modeling to print particles, but an extremely important additional benefit is that specific particle properties can be explicitly controlled. As an example in this study the volume fraction of each particle can be controlled i.e. the effective particle density can be adjusted. In this study the particle volumes reduces drastically as the non-convexity is increased, however all printed white particles in this study have the same mass within 2% of each other.

Polyhedral Boranes: A Versatile Building Block for Nanoporous Materials

Science.gov (United States)

Clingerman, Daniel Jon

The studies described in this dissertation examine several new concepts related to polyhedral boranes and their applications towards the synthesis of novel nanoporous materials. The unique thermal and chemical robustness, rigidity, quasi-spherical geometry, and high boron content of polyhedral boranes are explored to generate materials not possible with typical organic synthons. Aside from the fundamental synthetic work, this work was also aimed at solving larger global issues such as energy storage and new routes to therapeutics. Chapter 2 highlights the discovery of the first highly porous carborane-based metal-organic framework, where the spherical nature of the carborane increases volumetric surface area without reducing pore volume. Chapter 3 examines the first tritopic carborane-based ligand and the stabilizing effect the rigid, sterically bulky carboranyl groups have on highly porous topologies not stable with typical organic ligands. Chapters 4 and 5 describe the use of polyhedral borane-based ligands as a means to influence and generate unexpected topologies. Lastly, chapter 6 explores using a simple carborane-based ligand that harnesses the power of coordination-driven assembly to rapidly generate a high boron-containing supramolecular cuboctahedron.

osFP: a web server for predicting the oligomeric states of fluorescent proteins.

Science.gov (United States)

Simeon, Saw; Shoombuatong, Watshara; Anuwongcharoen, Nuttapat; Preeyanon, Likit; Prachayasittikul, Virapong; Wikberg, Jarl E S; Nantasenamat, Chanin

2016-01-01

Currently, monomeric fluorescent proteins (FP) are ideal markers for protein tagging. The prediction of oligomeric states is helpful for enhancing live biomedical imaging. Computational prediction of FP oligomeric states can accelerate the effort of protein engineering efforts of creating monomeric FPs. To the best of our knowledge, this study represents the first computational model for predicting and analyzing FP oligomerization directly from the amino acid sequence. After data curation, an exhaustive data set consisting of 397 non-redundant FP oligomeric states was compiled from the literature. Results from benchmarking of the protein descriptors revealed that the model built with amino acid composition descriptors was the top performing model with accuracy, sensitivity and specificity in excess of 80% and MCC greater than 0.6 for all three data subsets (e.g. training, tenfold cross-validation and external sets). The model provided insights on the important residues governing the oligomerization of FP. To maximize the benefit of the generated predictive model, it was implemented as a web server under the R programming environment. osFP affords a user-friendly interface that can be used to predict the oligomeric state of FP using the protein sequence. The advantage of osFP is that it is platform-independent meaning that it can be accessed via a web browser on any operating system and device. osFP is freely accessible at http://codes.bio/osfp/ while the source code and data set is provided on GitHub at https://github.com/chaninn/osFP/.Graphical Abstract.

Constitutive equations for discrete electromagnetic problems over polyhedral grids

International Nuclear Information System (INIS)

Codecasa, Lorenzo; Trevisan, Francesco

2007-01-01

In this paper a novel approach is proposed for constructing discrete counterparts of constitutive equations over polyhedral grids which ensure both consistency and stability of the algebraic equations discretizing an electromagnetic field problem. The idea is to construct discrete constitutive equations preserving the thermodynamic relations for constitutive equations. In this way, consistency and stability of the discrete equations are ensured. At the base, a purely geometric condition between the primal and the dual grids has to be satisfied for a given primal polyhedral grid, by properly choosing the dual grid. Numerical experiments demonstrate that the proposed discrete constitutive equations lead to accurate approximations of the electromagnetic field

Oligomerization interface of RAGE receptor revealed by MS-monitored hydrogen deuterium exchange.

Directory of Open Access Journals (Sweden)

Ewa Sitkiewicz

Full Text Available Activation of the receptor for advanced glycation end products (RAGE leads to a chronic proinflammatory signal, affecting patients with a variety of diseases. Potentially beneficial modification of RAGE activity requires understanding the signal transduction mechanism at the molecular level. The ligand binding domain is structurally uncoupled from the cytoplasmic domain, suggesting receptor oligomerization is a requirement for receptor activation. In this study, we used hydrogen-deuterium exchange and mass spectrometry to map structural differences between the monomeric and oligomeric forms of RAGE. Our results indicated the presence of a region shielded from exchange in the oligomeric form of RAGE and led to the identification of a new oligomerization interface localized at the linker region between domains C1 and C2. Based on this finding, a model of a RAGE dimer and higher oligomeric state was constructed.

OLIGOMERIZATION AND LIQUEFACTION OF ETHYLENE

African Journals Online (AJOL)

oligomerize ethylene gas in a packed bed reactor operated at 100-300°C under apressure of 500psi and ... The gas flow was then switched back to N, gas and temperature controller was simultaneously set to the desired reaction temperature. Once the desired .... be considered non-ideal for ethylene oligomerization.

Polyhedral combinatorics of UPGMA cones

OpenAIRE

Davidson, Ruth; Sullivant, Seth

2013-01-01

Distance-based methods such as UPGMA (Unweighted Pair Group Method with Arithmetic Mean) continue to play a significant role in phylogenetic research. We use polyhedral combinatorics to analyze the natural subdivision of the positive orthant induced by classifying the input vectors according to tree topologies returned by the algorithm. The partition lattice informs the study of UPGMA trees. We give a closed form for the extreme rays of UPGMA cones on n taxa, and compute the normalized volume...

Chemical Hydrogen Storage Using Polyhedral Borane Anions and Aluminum-Ammonia-Borane Complexes

Energy Technology Data Exchange (ETDEWEB)

Hawthorne, M. Frederick; Jalisatgi, Satish S.; Safronov, Alexander V.; Lee, Han Beak; Wu, Jianguo

2010-10-01

Phase 1. Hydrolysis of borohydride compounds offer the potential for significant hydrogen storage capacity, but most work to date has focused on one particular anion, BH4-, which requires high pH for stability. Other borohydride compounds, in particular polyhedral borane anions offer comparable hydrogen storage capacity without requiring high pH media and their long term thermal and hydrolytic stability coupled with non-toxic nature make them a very attractive alternative to NaBH4. The University of Missouri project provided the overall program focal point for the investigation of catalytic hydrolysis of polyhedral borane anions for hydrogen release. Due to their inherent stability, a transition metal catalyst was necessary for the hydrolysis of polyhedral borane anions. Transition metal ions such as cobalt, nickel, palladium and rhodium were investigated for their catalytic activity in the hydrolysis of nido-KB11H14, closo-K2B10H10, and closo-K2B12H12. The rate of hydrolysis follows first-order kinetics with respect to the concentration of the polyhedral borane anion and surface area of the rhodium catalyst. The rate of hydrolysis depends upon a) choice of polyhedral borane anion, c) concentration of polyhedral borane anion, d) surface area of the rhodium catalyst and e) temperature of the reaction. In all cases the yield of hydrogen was 100% which corresponds to ~7 wt% of hydrogen (based on material wt%). Phase 2. The phase 2 of program at the University of Missouri was focused upon developing aluminum ammonia-boranes (Al-AB) as chemical hydrogen storage materials, specifically their synthesis and studies of their dehydrogenation. The ammonia borane molecule (AB) is a demonstrated source of chemically stored hydrogen (19.6 wt%) which meets DOE performance parameters except for its regeneration from spent AB and elemental hydrogen. The presence of an aluminum center bonded to multiple AB residues might combine the efficiency of AB dehydrogenation with an aluminum

MURI Center for Materials Chemistry in the Space Environment

Science.gov (United States)

2006-11-30

ionic species in relevant reaction environments, surface photochemistry expertise, synchrotron-based measurement and irradiation, synthesis of structural...and Ne+ ions with dodecanethiolate and semifluorinated dodecanethiolate self-assembled monolayers (SAM), polyhedral oligomeric silsesquioxane (POSS...POSS/Kapton models as gas phase species, and with alkane thiol self assembled monolayers on gold surfaces, and with liquid squalane. We have also

Polyhedral Oligomeric Silsesquioxane (POSS) Styrene Macromers

National Research Council Canada - National Science Library

Haddad, Timothy

2001-01-01

.... Cyclohexyl, cyclopentyl and isobutyl substituted POSS-stryenes (at 30 weight % loadings) undergo free radical bulk polymerizations with styrene to produce polymers with an enhanced modulus above the glass transition temperature...

An Improved Computing Method for 3D Mechanical Connectivity Rates Based on a Polyhedral Simulation Model of Discrete Fracture Network in Rock Masses

Science.gov (United States)

Li, Mingchao; Han, Shuai; Zhou, Sibao; Zhang, Ye

2018-06-01

Based on a 3D model of a discrete fracture network (DFN) in a rock mass, an improved projective method for computing the 3D mechanical connectivity rate was proposed. The Monte Carlo simulation method, 2D Poisson process and 3D geological modeling technique were integrated into a polyhedral DFN modeling approach, and the simulation results were verified by numerical tests and graphical inspection. Next, the traditional projective approach for calculating the rock mass connectivity rate was improved using the 3D DFN models by (1) using the polyhedral model to replace the Baecher disk model; (2) taking the real cross section of the rock mass, rather than a part of the cross section, as the test plane; and (3) dynamically searching the joint connectivity rates using different dip directions and dip angles at different elevations to calculate the maximum, minimum and average values of the joint connectivity at each elevation. In a case study, the improved method and traditional method were used to compute the mechanical connectivity rate of the slope of a dam abutment. The results of the two methods were further used to compute the cohesive force of the rock masses. Finally, a comparison showed that the cohesive force derived from the traditional method had a higher error, whereas the cohesive force derived from the improved method was consistent with the suggested values. According to the comparison, the effectivity and validity of the improved method were verified indirectly.

Image of the World on polyhedral maps and globes

Directory of Open Access Journals (Sweden)

Pędzich Paweł

2016-12-01

Full Text Available Application of polyhedrons as image surface in cartographic projections has a tradition of more than 200 years. The first maps relying on polyhedrons appeared in the 19th century. One of the first maps which based on an original polyhedral projection using a regular octahedron was constructed by the Californian architect Bernard Cahill in 1909. Other well known polyhedral projections and maps included Buckminster Fuller’s projection and map into icosahedron from 1954 and S. Waterman’s projection into truncated octahedron from 1996, which resulted in the “butterfly” map. Polyhedrons as image surface have the advantage of allowing a continuous image of continents of the Earth with low projection distortion. Such maps can be used for many purposes, such as presentation of tectonic plates or geographic discoveries.

Logical and Geometrical Distance in Polyhedral Aristotelian Diagrams in Knowledge Representation

Directory of Open Access Journals (Sweden)

Lorenz Demey

2017-09-01

Full Text Available Aristotelian diagrams visualize the logical relations among a finite set of objects. These diagrams originated in philosophy, but recently, they have also been used extensively in artificial intelligence, in order to study (connections between various knowledge representation formalisms. In this paper, we develop the idea that Aristotelian diagrams can be fruitfully studied as geometrical entities. In particular, we focus on four polyhedral Aristotelian diagrams for the Boolean algebra B 4 , viz. the rhombic dodecahedron, the tetrakis hexahedron, the tetraicosahedron and the nested tetrahedron. After an in-depth investigation of the geometrical properties and interrelationships of these polyhedral diagrams, we analyze the correlation (or lack thereof between logical (Hamming and geometrical (Euclidean distance in each of these diagrams. The outcome of this analysis is that the Aristotelian rhombic dodecahedron and tetrakis hexahedron exhibit the strongest degree of correlation between logical and geometrical distance; the tetraicosahedron performs worse; and the nested tetrahedron has the lowest degree of correlation. Finally, these results are used to shed new light on the relative strengths and weaknesses of these polyhedral Aristotelian diagrams, by appealing to the congruence principle from cognitive research on diagram design.

Cartilage oligomeric matrix protein enhances the vascularization of acellular nerves

Directory of Open Access Journals (Sweden)

Wei-ling Cui

2016-01-01

Full Text Available Vascularization of acellular nerves has been shown to contribute to nerve bridging. In this study, we used a 10-mm sciatic nerve defect model in rats to determine whether cartilage oligomeric matrix protein enhances the vascularization of injured acellular nerves. The rat nerve defects were treated with acellular nerve grafting (control group alone or acellular nerve grafting combined with intraperitoneal injection of cartilage oligomeric matrix protein (experimental group. As shown through two-dimensional imaging, the vessels began to invade into the acellular nerve graft from both anastomotic ends at day 7 post-operation, and gradually covered the entire graft at day 21. The vascular density, vascular area, and the velocity of revascularization in the experimental group were all higher than those in the control group. These results indicate that cartilage oligomeric matrix protein enhances the vascularization of acellular nerves.

A new equi-dimensional fracture model using polyhedral cells for microseismic data sets

KAUST Repository

Al-Hinai, Omar

2017-04-09

We present a method for modeling flow in porous media in the presence of complex fracture networks. The approach utilizes the Mimetic Finite Difference (MFD) method. We employ a novel equi-dimensional approach for meshing fractures. By using polyhedral cells we avoid the common challenge in equi-dimensional fracture modeling of creating small cells at the intersection point. We also demonstrate how polyhedra can mesh complex fractures without introducing a large number of cells. We use polyhedra and the MFD method a second time for embedding fracture boundaries in the matrix domain using a “cut-cell” paradigm. The embedding approach has the advantage of being simple and localizes irregular cells to the area around the fractures. It also circumvents the need for conventional mesh generation, which can be challenging when applied to complex fracture geometries. We present numerical results confirming the validity of our approach for complex fracture networks and for different flow models. In our first example, we compare our method to the popular dual-porosity technique. Our second example compares our method with directly meshed fractures (single-porosity) for two-phase flow. The third example demonstrates two-phase flow for the case of intersecting ellipsoid fractures in three-dimensions, which are typical in microseismic analysis of fractures. Finally, we demonstrate our method on a two-dimensional fracture network produced from microseismic field data.

A new equi-dimensional fracture model using polyhedral cells for microseismic data sets

KAUST Repository

Al-Hinai, Omar; Dong, Rencheng; Srinivasan, Sanjay; Wheeler, Mary F.

2017-01-01

We present a method for modeling flow in porous media in the presence of complex fracture networks. The approach utilizes the Mimetic Finite Difference (MFD) method. We employ a novel equi-dimensional approach for meshing fractures. By using polyhedral cells we avoid the common challenge in equi-dimensional fracture modeling of creating small cells at the intersection point. We also demonstrate how polyhedra can mesh complex fractures without introducing a large number of cells. We use polyhedra and the MFD method a second time for embedding fracture boundaries in the matrix domain using a “cut-cell” paradigm. The embedding approach has the advantage of being simple and localizes irregular cells to the area around the fractures. It also circumvents the need for conventional mesh generation, which can be challenging when applied to complex fracture geometries. We present numerical results confirming the validity of our approach for complex fracture networks and for different flow models. In our first example, we compare our method to the popular dual-porosity technique. Our second example compares our method with directly meshed fractures (single-porosity) for two-phase flow. The third example demonstrates two-phase flow for the case of intersecting ellipsoid fractures in three-dimensions, which are typical in microseismic analysis of fractures. Finally, we demonstrate our method on a two-dimensional fracture network produced from microseismic field data.

Dimerization and oligomerization of the chaperone calreticulin

DEFF Research Database (Denmark)

Jørgensen, Charlotte S; Ryder, L Rebekka; Steinø, Anne

2003-01-01

protein. Using PAGE, urea gradient gel electrophoresis, capillary electrophoresis and MS, we show that dimerization through the SH group can be induced by lowering the pH to 5-6, heating, or under conditions that favour partial unfolding such as urea concentrations above 2.6 m or SDS concentrations above...... that favour partial unfolding or an intramolecular local conformational change that allows oligomerization, resulting in a heterogeneous mixture of oligomers consisting of up to 10 calreticulin monomers. The oligomeric calreticulin was very stable, but oligomerization was partially reversed by addition of 8 m...

Rheological Behavior of Entangled Polystyrene-Polyhedral Oligosilsesquioxane (POSS) Copolymer

National Research Council Canada - National Science Library

Wu, Jian; Mather, Patrick T; Haddad, Timothy S; Kim, Gyeong-Man

2006-01-01

...: random copolymers of polystyrene (PS) and styryl-based polyhedral oligosilsesquioxane (POSS), R7(Si8O12)(C6H4CH=CH2), with R = isobutyl (iBu). A series of styrene-styryl POSS random copolymers with 0, 6, 15, 30, 50 wt...

Reversible peptide oligomerization over nanoscale gold surfaces

Directory of Open Access Journals (Sweden)

Kazushige Yokoyama

2015-11-01

Full Text Available A selective oligomeric formation of amyloid beta 1-40 (Ab1-40 monomers over a nanogold colloidal surface was investigated. An unfolded Ab1-40 monomer is considered to construct a dimer or trimer based oligomeric form with its hydrophobic segment placing outward under an acidic condition. Under a basic condition, a conformation of Ab is expected to take a folded monomeric form with its hydrophilic segment folded inward, avoiding the networking with residual colloidal particles. The most probable oligomeric form constructed over a 20 nm gold colloidal surface within a 25 ℃ to 65 ℃ temperature range is a dimer based unit and that over 30 or 40 nm gold colloidal surface below 15 ℃ is concluded to be a trimer based unit. However, selective oligomerization was not successfully reproduced under the rest of the conditions. A dipole-induced dipole interaction must cause a flexible structural change between folded and unfolded forms.

Interactive volume visualization of general polyhedral grids

KAUST Repository

Muigg, Philipp

2011-12-01

This paper presents a novel framework for visualizing volumetric data specified on complex polyhedral grids, without the need to perform any kind of a priori tetrahedralization. These grids are composed of polyhedra that often are non-convex and have an arbitrary number of faces, where the faces can be non-planar with an arbitrary number of vertices. The importance of such grids in state-of-the-art simulation packages is increasing rapidly. We propose a very compact, face-based data structure for representing such meshes for visualization, called two-sided face sequence lists (TSFSL), as well as an algorithm for direct GPU-based ray-casting using this representation. The TSFSL data structure is able to represent the entire mesh topology in a 1D TSFSL data array of face records, which facilitates the use of efficient 1D texture accesses for visualization. In order to scale to large data sizes, we employ a mesh decomposition into bricks that can be handled independently, where each brick is then composed of its own TSFSL array. This bricking enables memory savings and performance improvements for large meshes. We illustrate the feasibility of our approach with real-world application results, by visualizing highly complex polyhedral data from commercial state-of-the-art simulation packages. © 2011 IEEE.

Naming polyhedra by general face-spirals - theory and applications to fullerenes and other polyhedral molecules

DEFF Research Database (Denmark)

Wirz, Lukas; Schwerdtfeger, Peter; Avery, James Emil

2018-01-01

We present a general face-spiral algorithm for cubic polyhedral graphs (including fullerenes and fulleroids), and extend it to the full class of all polyhedral graphs by way of the leapfrog transform. This yields compact canonical representations of polyhedra with a simple and intuitive geometrical...... polyhedral molecules, and an especially compact form for the special class of fullerenes. A unique numbering of vertices is obtained as a byproduct of the spiral algorithm. This is required to denote modifications of the parent cage in IUPAC naming schemes. Similarly, the symmetry group of the molecule can...... be found together with the canonical general spiral at negligible cost. The algorithm is fully compatible with the classical spiral algorithm developed by Manolopoulos for fullerenes, i. e., classical spirals are accepted as input, and spiralable graphs lead to identical output. We prove that the algorithm...

Transient oligomerization of the SARS-CoV N protein--implication for virus ribonucleoprotein packaging.

Science.gov (United States)

Chang, Chung-ke; Chen, Chia-Min Michael; Chiang, Ming-hui; Hsu, Yen-lan; Huang, Tai-huang

2013-01-01

The nucleocapsid (N) phosphoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV) packages the viral genome into a helical ribonucleocapsid and plays a fundamental role during viral self-assembly. The N protein consists of two structural domains interspersed between intrinsically disordered regions and dimerizes through the C-terminal structural domain (CTD). A key activity of the protein is the ability to oligomerize during capsid formation by utilizing the dimer as a building block, but the structural and mechanistic bases of this activity are not well understood. By disulfide trapping technique we measured the amount of transient oligomers of N protein mutants with strategically located cysteine residues and showed that CTD acts as a primary transient oligomerization domain in solution. The data is consistent with the helical oligomer packing model of N protein observed in crystal. A systematic study of the oligomerization behavior revealed that altering the intermolecular electrostatic repulsion through changes in solution salt concentration or phosphorylation-mimicking mutations affects oligomerization propensity. We propose a biophysical mechanism where electrostatic repulsion acts as a switch to regulate N protein oligomerization.

Polymorphism and mesomorphism of oligomeric surfactants: effect of the degree of oligomerization.

Science.gov (United States)

Jurašin, D; Pustak, A; Habuš, I; Šmit, I; Filipović-Vinceković, N

2011-12-06

A series of cationic oligomeric surfactants (quaternary dodecyldimethylammonium ions with two, three, or four chains connected by an ethylene spacer at the headgroup level, abbreviated as dimer, trimer, and tetramer) were synthesized and characterized. The influence of the degree of oligomerization on their polymorphic and mesomorphic properties was investigated by means of X-ray diffraction, polarizing optical microscopy, thermogravimetry, and differential scanning calorimetry. All compounds display layered arrangements with interdigitated dodecyl chains. The increase in the degree of oligomerization increases the interlayer distance and decreases the ordering in the solid phase; whereas the dimer sample is fully crystalline with well-developed 3D ordering and the trimer and tetramer crystallize as highly ordered crystal smectic phases. The number of thermal phase transitions and sequence of phases are markedly affected by the number of dodecyl chains. Anhydrous samples exhibit polymorphism and thermotropic mesomorphism of the smectic type, with the exception of the tetramer that displays only transitions at higher temperature associated with decomposition and melting. All hydrated compounds form lyotropic mesophases showing reversible phase transitions upon heating and cooling. The sequence of liquid-crystalline phases for the dimer, typical of concentrated ionic surfactant systems, comprises a hexagonal phase at lower temperatures and a smectic phase at higher temperatures. In contrast, the trimer and tetramer reveal textures of the hexagonal phase. © 2011 American Chemical Society

hp-version discontinuous Galerkin methods on polygonal and polyhedral meshes

CERN Document Server

Cangiani, Andrea; Georgoulis, Emmanuil H; Houston, Paul

2017-01-01

Over the last few decades discontinuous Galerkin finite element methods (DGFEMs) have been witnessed tremendous interest as a computational framework for the numerical solution of partial differential equations. Their success is due to their extreme versatility in the design of the underlying meshes and local basis functions, while retaining key features of both (classical) finite element and finite volume methods. Somewhat surprisingly, DGFEMs on general tessellations consisting of polygonal (in 2D) or polyhedral (in 3D) element shapes have received little attention within the literature, despite the potential computational advantages. This volume introduces the basic principles of hp-version (i.e., locally varying mesh-size and polynomial order) DGFEMs over meshes consisting of polygonal or polyhedral element shapes, presents their error analysis, and includes an extensive collection of numerical experiments. The extreme flexibility provided by the locally variable elemen t-shapes, element-sizes, and elemen...

Rheological Behavior of Entangled Polystyrene-Polyhedral Oligosilsesquioxane (POSS) Copolymer (Postprint)

National Research Council Canada - National Science Library

Wu, Jian; Mather, Patrick T; Haddad, Timothy S; Kim, Gyeong-Man

2006-01-01

...: random copolymers of polystyrene (PS) and styryl-based polyhedral oligosilsesquioxane (POSS), R7(Si8O12)(C6H4CH=CH2), with R = isobutyl (iBu). A series of styrene-styryl POSS random copolymers with 0, 6, 15, 30, 50 wt...

Topology and Oligomerization of Mono- and Oligomeric Proteins Regulate Their Half-Lives in the Cell.

Science.gov (United States)

Mallik, Saurav; Kundu, Sudip

2018-06-05

To find additional structural constraints (besides disordered segments) that regulate protein half-life in the cell, we herein assess the influence of native topology of monomeric and sequestration of oligomeric proteins into multimeric complexes in yeast, human, and mouse. Native topology acts as a molecular marker of globular protein's mechanical resistance and consequently captures their half-life variations on genome scale. Sequestration into multimeric complexes elongates oligomeric protein half-life in the cell, presumably by burying ubiquitinoylation sites and disordered segments required for proteasomal recognition. The latter effect is stronger for proteins associated with multiple complexes and for those binding early during complex self-assembly, including proteins that oligomerize with large proportions of surface buried. After gene duplication, diversification of topology and sequestration into non-identical sets of complexes alter half-lives of paralogous proteins during the course of evolution. Thus, native topology and sequestration into multimeric complexes reflect designing principles of proteins to regulate their half-lives. Copyright © 2018 Elsevier Ltd. All rights reserved.

Preparation and characterization of polyhedral oligomer silsesquioxane nanocomposites incorporated in epoxy resin; Elaboracao e caracterizacao de nanocompositos de oligomero poliedrico de silsesquioxano incorporados na resina epoxidica

Energy Technology Data Exchange (ETDEWEB)

Longhi, Marielen; Zini, Lucas Pandolphi; Birriel, Eliena Jonko; Kunst, Sandra Raquel; Zattera, Ademir Jose, E-mail: marielen_longhi@hotmail.com [Universidade de Caxias do Sul (LPOL/UCS), RS (Brazil). Laboratorio de Polimeros; Pistor, Vinicius [Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS (Brazil)

2015-07-01

The incorporation of nanofiller in thermosetting like epoxy resin as has been studied in order to modify its properties. In this research, nanocomposites were obtained by incorporating 5% by weight of three polyhedral oligomeric silsesquioxane (POSS) with different number of functionalization: Glicidilisobutil-POSS, Triglicidilisobutil- POSS and Glicicil POSS in an epoxy matrix by sonification process. The nanocomposites were characterized by analysis of X-ray diffraction (DRX), transmission electron microscopy (TEM) and thermogravimetric analysis (TGA). The DRX analysis showed the characteristic peak of POSS and TEM images showed that there is a difference in the dispersion of nanocages for the difference in the number of epoxy groups on the POSS. The incorporation of Glicidilisobutil-POSS showed a significant increase in the glass transition temperature (Tg) value, and also that the most effective from the viewpoint of the dispersion, on the other hand, the Glycidyl-POSS had a greater influence on the thermal stability demonstrating that the dispersion medium is an important characteristic to define the most desirable properties. (author)

Transient oligomerization of the SARS-CoV N protein--implication for virus ribonucleoprotein packaging.

Directory of Open Access Journals (Sweden)

Chung-ke Chang

Full Text Available The nucleocapsid (N phosphoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV packages the viral genome into a helical ribonucleocapsid and plays a fundamental role during viral self-assembly. The N protein consists of two structural domains interspersed between intrinsically disordered regions and dimerizes through the C-terminal structural domain (CTD. A key activity of the protein is the ability to oligomerize during capsid formation by utilizing the dimer as a building block, but the structural and mechanistic bases of this activity are not well understood. By disulfide trapping technique we measured the amount of transient oligomers of N protein mutants with strategically located cysteine residues and showed that CTD acts as a primary transient oligomerization domain in solution. The data is consistent with the helical oligomer packing model of N protein observed in crystal. A systematic study of the oligomerization behavior revealed that altering the intermolecular electrostatic repulsion through changes in solution salt concentration or phosphorylation-mimicking mutations affects oligomerization propensity. We propose a biophysical mechanism where electrostatic repulsion acts as a switch to regulate N protein oligomerization.

Polygonal Prism Mesh in the Viscous Layers for the Polyhedral Mesh Generator, PolyGen

International Nuclear Information System (INIS)

Lee, Sang Yong; Park, Chan Eok; Kim, Shin Whan

2015-01-01

Polyhedral mesh has been known to have some benefits over the tetrahedral mesh. Efforts have been made to set up a polyhedral mesh generation system with open source programs SALOME and TetGen. The evaluation has shown that the polyhedral mesh generation system is promising. But it is necessary to extend the capability of the system to handle the viscous layers to be a generalized mesh generator. A brief review to the previous works on the mesh generation for the viscous layers will be made in section 2. Several challenging issues for the polygonal prism mesh generation will be discussed as well. The procedure to generate a polygonal prism mesh will be discussed in detail in section 3. Conclusion will be followed in section 4. A procedure to generate meshes in the viscous layers with PolyGen has been successfully designed. But more efforts have to be exercised to find the best way for the generating meshes for viscous layers. Using the extrusion direction of the STL data will the first of the trials in the near future

Status of the Polyhedral Mesh Generator using SALOME PLATFORM and TetGen

International Nuclear Information System (INIS)

Lee, Sang Yong; Park, Chan Eok; Kim, Shin Whan

2014-01-01

Recently developed porous body approach codes such as SPACE and CUPID require a CAD system to estimate the porosity. Since they use the unstructured mesh and they also require reliable mesh generation system. The combination of CAD system and mesh generation system is necessary to cope with a large number of cells and the complex fluid system with structural materials inside. In the past, a CAD system Pro/Engineer and mesh generator Pointwise were evaluated for this application. But, the cost of those commercial CAD and mesh generator is sometimes a great burden. Therefore, efforts have been made to set up a mesh generation system with open source programs. The evaluation of the TetGen has been made in focusing the application for the polyhedral mesh generation. In this paper, SALOME will be described for the efforts to combine TetGen with it. In section 2, brief introduction will be made on the CAD and mesh generation capability of SALOME and Tetgen. SALOME and TetGen codes are being integrated to construct robust polyhedral mesh generator. Procedures to merge boundary faces and to cut concave cells are developed to remove concave cells to get final convex polyhedral mesh. Treating the internal boundary face, i.e. non-manifold face will be the next task in the future investigation

Protic Cationic Oligomeric Ionic Liquids of the Urethane Type

DEFF Research Database (Denmark)

Shevchenko, V. V.; Stryutsky, A. V.; Klymenko, N. S.

2014-01-01

Protic oligomeric cationic ionic liquids of the oligo(ether urethane) type are synthesized via the reaction of an isocyanate prepolymer based on oligo(oxy ethylene)glycol with M = 1000 with hexamethylene-diisocyanate followed by blocking of the terminal isocyanate groups with the use of amine...... derivatives of imidazole, pyridine, and 3-methylpyridine and neutralization of heterocycles with ethanesulfonic acid and p-toluenesulfonic acid. The structures and properties of the synthesized oligomeric ionic liquids substantially depend on the structures of the ionic groups. They are amorphous at room...... temperature, but ethanesulfonate imidazolium and pyridinium oligomeric ionic liquids form a low melting crystalline phase. The proton conductivities of the oligomeric ionic liquids are determined by the type of cation in the temperature range 80-120 degrees C under anhydrous conditions and vary within five...

Oligoaniline-containing electrochromic polymers with tunable properties

Directory of Open Access Journals (Sweden)

Y. Li

2018-07-01

Full Text Available Electrochromic polymers have attracted much attention due to their potential applications in displays, smart windows, intelligent mirrors, and wearable devices. Here, a novel polyamic acid containing aniline pentamer with improved electrochromic properties and new functionalities was synthesized via oxidative coupling polymerization, followed by postpolymerization of tetraaniline, polyhedral oligomeric silsesquioxane, and fluorene, respectively. With the introduction of tetraaniline pendants, the resultant polymer exhibits improved electrochromic performance with high optical contrast value and rapid switching rate, because of the high content of electrochromic units in the polymeric structure. The polyamic acid functionalized with polyhedral oligomeric silsesquioxane, demonstrates a great enhancement of switching rate in the electrochromism, due to the rapid electrolyte migration through polymer film under electrochemical potentials. In addition, a new electrofluorochromic feature is easily achieved through the introduction of fluorescent fluorene groups into the polymeric architecture.

Different domains are critical for oligomerization compatibility of different connexins

Science.gov (United States)

MARTÍNEZ, Agustín D.; MARIPILLÁN, Jaime; ACUÑA, Rodrigo; MINOGUE, Peter J.; BERTHOUD, Viviana M.; BEYER, Eric C.

2011-01-01

Oligomerization of connexins is a critical step in gap junction channel formation. Some members of the connexin family can oligomerize with other members and form functional heteromeric hemichannels [e.g. Cx43 (connexin 43) and Cx45], but others are incompatible (e.g. Cx43 and Cx26). To find connexin domains important for oligomerization, we constructed chimaeras between Cx43 and Cx26 and studied their ability to oligomerize with wild-type Cx43, Cx45 or Cx26. HeLa cells co-expressing Cx43, Cx45 or Cx26 and individual chimaeric constructs were analysed for interactions between the chimaeras and the wild-type connexins using cell biological (subcellular localization by immunofluorescence), functional (intercellular diffusion of microinjected Lucifer yellow) and biochemical (sedimentation velocity through sucrose gradients) assays. All of the chimaeras containing the third transmembrane domain of Cx43 interacted with wild-type Cx43 on the basis of co-localization, dominant-negative inhibition of intercellular communication, and altered sedimentation velocity. The same chimaeras also interacted with co-expressed Cx45. In contrast, immunofluorescence and intracellular diffusion of tracer suggested that other domains influenced oligomerization compatibility when chimaeras were co-expressed with Cx26. Taken together, these results suggest that amino acids in the third transmembrane domain are critical for oligomerization with Cx43 and Cx45. However, motifs in different domains may determine oligomerization compatibility in members of different connexin subfamilies. PMID:21348854

Topology, isomorphic smoothness and polyhedrality in Banach spaces

OpenAIRE

Smith, Richard J.

2018-01-01

In recent decades, topology has come to play an increasing role in some geometric aspects of Banach space theory. The class of so-called $w^*$-locally relatively compact sets was introduced recently by Fonf, Pallares, Troyanski and the author, and were found to be a useful topological tool in the theory of isomorphic smoothness and polyhedrality in Banach spaces. We develop the topological theory of these sets and present some Banach space applications.

Polyhedral meshing as an innovative approach to computational domain discretization of a cyclone in a fluidized bed CLC unit

Directory of Open Access Journals (Sweden)

Sosnowski Marcin

2017-01-01

Full Text Available Chemical Looping Combustion (CLC is a technology that allows the separation of CO2, which is generated by the combustion of fossil fuels. The majority of process designs currently under investigation are systems of coupled fluidized beds. Advances in the development of power generation system using CLC cannot be introduced without using numerical modelling as a research tool. The primary and critical activity in numerical modelling is the computational domain discretization. It influences the numerical diffusion as well as convergence of the model and therefore the overall accuracy of the obtained results. Hence an innovative approach of computational domain discretization using polyhedral (POLY mesh is proposed in the paper. This method reduces both the numerical diffusion of the mesh as well as the time cost of preparing the model for subsequent calculation. The major advantage of POLY mesh is that each individual cell has many neighbours, so gradients can be much better approximated in comparison to commonly-used tetrahedral (TET mesh. POLYs are also less sensitive to stretching than TETs which results in better numerical stability of the model. Therefore detailed comparison of numerical modelling results concerning subsection of CLC system using tetrahedral and polyhedral mesh is covered in the paper.

SALOME PLATFORM and TetGen for Polyhedral Mesh Generation

Energy Technology Data Exchange (ETDEWEB)

Lee, Sang Yong; Park, Chan Eok; Kim, Shin Whan [KEPCO E and C Company, Inc., Daejeon (Korea, Republic of)

2014-05-15

SPACE and CUPID use the unstructured mesh and they also require reliable mesh generation system. The combination of CAD system and mesh generation system is necessary to cope with a large number of cells and the complex fluid system with structural materials inside. In the past, a CAD system Pro/Engineer and mesh generator Pointwise were evaluated for this application. But, the cost of those commercial CAD and mesh generator is sometimes a great burden. Therefore, efforts have been made to set up a mesh generation system with open source programs. The evaluation of the TetGen has been made in focusing the application for the polyhedral mesh generation. In this paper, SALOME will be evaluated for the efforts in conjunction with TetGen. In section 2, review will be made on the CAD and mesh generation capability of SALOME. SALOME and TetGen codes are being integrated to construct robust polyhedral mesh generator. Edge removal on the flat surface and vertex reattachment to the solid are two challenging tasks. It is worthwhile to point out that the Python script capability of the SALOME should be fully utilized for the future investigation.

High Content Analysis of Compositional Heterogeneities to Study GPCR Oligomerization

DEFF Research Database (Denmark)

Walsh, Samuel McEwen

In this thesis I demonstrate how the natural compositional heterogeneities of synthetic and living cell model systems can be used to quantitate the mechanics of G-protein coupled receptor (GPCR) oligomerization with Förster resonance energy transfer (FRET). The thesis is structured around three a...

How to collect and process large polyhedral viruses of insects

Science.gov (United States)

W. D. Rollinson; F. B. Lewis

1962-01-01

Polyhedral viruses have proved highly effective and very practical for control of certain pine sawflies; and a method of collecting and processing the small polyhedra (5 microns or less) characteristic of sawflies has been described. There is experimental evidence that the virus diseases of many Lepidopterous insects can be used similarly for direct control. The...

An engineered allosteric switch in leucine-zipper oligomerization.

Science.gov (United States)

Gonzalez, L; Plecs, J J; Alber, T

1996-06-01

Controversy remains about the role of core side-chain packing in specifying protein structure. To investigate the influence of core packing on the oligomeric structure of a coiled coil, we engineered a GCN4 leucine zipper mutant that switches from two to three strands upon binding the hydrophobic ligands cyclohexane and benzene. In solution these ligands increased the apparent thermal stability and the oligomerization order of the mutant leucine zipper. The crystal structure of the peptide-benzene complex shows a single benzene molecule bound at the engineered site in the core of the trimer. These results indicate that coiled coils are well-suited to function as molecular switches and emphasize that core packing is an important determinant of oligomerization specificity.

Fernando Cassinello Pérez, polyhedral architect

Directory of Open Access Journals (Sweden)

M. Centellas Soler

2017-03-01

Full Text Available The work of architect Fernando Cassinello Pérez (Almería, 1928-Madrid, 1975 rests on three pillars: architectural production focused on the design and construction of housing and hotel establishments, academic activity as Professor of Construction at the Escuela de Arquitectura de Madrid, and research concern developed in the IETcc of which he became director, and exercised as an author of books and research papers, as disseminator lecturer, speaker at major conferences or as an active member of international associations linked to construction with concrete. This article will review his prolific activity as polyhedral architect and will find interesting works that designed and built by relying on extensive contemporary and international architectural culture.

Convex polyhedral abstractions, specialisation and property-based predicate splitting in Horn clause verification

DEFF Research Database (Denmark)

Kafle, Bishoksan; Gallagher, John Patrick

2014-01-01

We present an approach to constrained Horn clause (CHC) verification combining three techniques: abstract interpretation over a domain of convex polyhedra, specialisation of the constraints in CHCs using abstract interpretation of query-answer transformed clauses, and refinement by splitting...... in conjunction with specialisation for propagating constraints it can frequently solve challenging verification problems. This is a contribution in itself, but refinement is needed when it fails, and the question of how to refine convex polyhedral analyses has not been studied much. We present a refinement...... technique based on interpolants derived from a counterexample trace; these are used to drive a property-based specialisation that splits predicates, leading in turn to more precise convex polyhedral analyses. The process of specialisation, analysis and splitting can be repeated, in a manner similar...

Oligomerization in health and disease

CERN Document Server

Giraldo, Jesus

2013-01-01

This special volume of Progress in Molecular Biology and Translational Science focuses on oligomerization in health and disease. Contributions from leading authorities Informs and updates on all the latest developments in the field.

Polyhedral and semidefinite programming methods in combinatorial optimization

CERN Document Server

Tunçel, Levent

2010-01-01

Since the early 1960s, polyhedral methods have played a central role in both the theory and practice of combinatorial optimization. Since the early 1990s, a new technique, semidefinite programming, has been increasingly applied to some combinatorial optimization problems. The semidefinite programming problem is the problem of optimizing a linear function of matrix variables, subject to finitely many linear inequalities and the positive semidefiniteness condition on some of the matrix variables. On certain problems, such as maximum cut, maximum satisfiability, maximum stable set and geometric r

Theoretical Studies of Group IVA and Group IVB Chemistry

Science.gov (United States)

2012-01-13

novel ionic liquids . We have performed very high level CCSD(T) calculations on one such species, Al13- to predict its ionization potential in nearly...Precursors. Polyhedral oligomeric silsesquioxanes (POSS) are three- dimensional Si-O cage compounds that have many uses, because of their resistance

Preparation and Characterization of Polyhedral Oligosilsesquioxanes

Science.gov (United States)

Cordes, David B.; Lickiss, Paul D.

Polyhedral OligoSilSesquioxanes are often abbreviated by the acronym POS or POSS® and are compounds of the general formula Sin O3n/2Rn (often denoted as TnRn). The commonest of these compounds are the cubic T8R8 POS species since many hydrolysis/condensation reactions of simple RSiX3 compounds (X = Cl, OMe or OEt) give the T8R8 cage as a major product, usually along with small amounts of other TnRn cages and polymeric by-products. Few T4R4 POS have been prepared as they seem to require very bulky R-groups to stabilize the strained POS system and to prevent formation of larger, more stable POS cages.

Flexible Polyhedral Surfaces with Two Flat Poses

Directory of Open Access Journals (Sweden)

Hellmuth Stachel

2015-05-01

Full Text Available We present three types of polyhedral surfaces, which are continuously flexible and have not only an initial pose, where all faces are coplanar, but pass during their self-motion through another pose with coplanar faces (“flat pose”. These surfaces are examples of so-called rigid origami, since we only admit exact flexions, i.e., each face remains rigid during the motion; only the dihedral angles vary. We analyze the geometry behind Miura-ori and address Kokotsakis’ example of a flexible tessellation with the particular case of a cyclic quadrangle. Finally, we recall Bricard’s octahedra of Type 3 and their relation to strophoids.

Computer-Aided Panoramic Images Enriched by Shadow Construction on a Prism and Pyramid Polyhedral Surface

Directory of Open Access Journals (Sweden)

Jolanta Dzwierzynska

2017-10-01

Full Text Available The aim of this study is to develop an efficient and practical method of a direct mapping of a panoramic projection on an unfolded prism and pyramid polyhedral projection surface with the aid of a computer. Due to the fact that straight lines very often appear in any architectural form we formulate algorithms which utilize data about lines and draw panoramas as plots of functions in Mathcad software. The ability to draw panoramic images of lines enables drawing a wireframe image of an architectural object. The application of the multicenter projection, as well as the idea of shadow construction in the panoramic representation, aims at achieving a panoramic image close to human perception. The algorithms are universal as the application of changeable base elements of panoramic projection—horizon height, station point location, number of polyhedral walls—enables drawing panoramic images from various viewing positions. However, for more efficient and easier drawing, the algorithms should be implemented in some graphical package. The representation presented in the paper and the method of its direct mapping on a flat unfolded projection surface can find application in the presentation of architectural spaces in advertising and art when drawings are displayed on polyhedral surfaces and can be observed from multiple viewing positions.

Biophysical characterization of GPCR oligomerization

DEFF Research Database (Denmark)

Mathiasen, Signe

level, and revealed the existence of several dimerization interfaces, each with specific kinetics. Finally we investigated how a property of the membrane solubilizing GPCRs affected oligomerization. We observed a dramatic decrease in oligomer stability with increasing geometrical membrane curvature. We...

Protein dimerization and oligomerization in biology

National Research Council Canada - National Science Library

Matthews, Jacqueline M

2012-01-01

.... However, protein function is so often linked to both homo- and hetero-oligomerization and many heterologous interactions likely evolved from homologous interaction, so this volume also covers many...

Polyhedral shape model for terrain correction of gravity and gravity gradient data based on an adaptive mesh

Science.gov (United States)

Guo, Zhikui; Chen, Chao; Tao, Chunhui

2016-04-01

Since 2007, there are four China Da yang cruises (CDCs), which have been carried out to investigate polymetallic sulfides in the southwest Indian ridge (SWIR) and have acquired both gravity data and bathymetry data on the corresponding survey lines(Tao et al., 2014). Sandwell et al. (2014) published a new global marine gravity model including the free air gravity data and its first order vertical gradient (Vzz). Gravity data and its gradient can be used to extract unknown density structure information(e.g. crust thickness) under surface of the earth, but they contain all the mass effect under the observation point. Therefore, how to get accurate gravity and its gradient effect of the existing density structure (e.g. terrain) has been a key issue. Using the bathymetry data or ETOPO1 (http://www.ngdc.noaa.gov/mgg/global/global.html) model at a full resolution to calculate the terrain effect could spend too much computation time. We expect to develop an effective method that takes less time but can still yield the desired accuracy. In this study, a constant-density polyhedral model is used to calculate the gravity field and its vertical gradient, which is based on the work of Tsoulis (2012). According to gravity field attenuation with distance and variance of bathymetry, we present an adaptive mesh refinement and coarsening strategies to merge both global topography data and multi-beam bathymetry data. The local coarsening or size of mesh depends on user-defined accuracy and terrain variation (Davis et al., 2011). To depict terrain better, triangular surface element and rectangular surface element are used in fine and coarse mesh respectively. This strategy can also be applied to spherical coordinate in large region and global scale. Finally, we applied this method to calculate Bouguer gravity anomaly (BGA), mantle Bouguer anomaly(MBA) and their vertical gradient in SWIR. Further, we compared the result with previous results in the literature. Both synthetic model

Effects of Glycine, Water, Ammonia, and Ammonium Bicarbonate on the Oligomerization of Methionine

Science.gov (United States)

Huang, Rui; Furukawa, Yoshihiro; Otake, Tsubasa; Kakegawa, Takeshi

2017-06-01

The abiotic oligomerization of amino acids may have created primordial, protein-like biological catalysts on the early Earth. Previous studies have proposed and evaluated the potential of diagenesis for the amino acid oligomerization, simulating the formation of peptides that include glycine, alanine, and valine, separately. However, whether such conditions can promote the formation of peptides composed of multiple amino acids remains unclear. Furthermore, the chemistry of pore water in sediments should affect the oligomerization and degradation of amino acids and oligomers, but these effects have not been studied extensively. In this study, we investigated the effects of water, ammonia, ammonium bicarbonate, pH, and glycine on the oligomerization and degradation of methionine under high pressure (150 MPa) and high temperature conditions (175 °C) for 96 h. Methionine is more difficult to oligomerize than glycine and methionine dimer was formed in the incubation of dry powder of methionine. Methionine oligomers as long as trimers, as well as methionylglycine and glycylmethionine, were formed under every condition with these additional compounds. Among the compounds tested, the oligomerization reaction rate was accelerated by the presence of water and by an increase in pH. Ammonia also increased the oligomerization rate but consumed methionine by side reactions and resulted in the rapid degradation of methionine and its peptides. Similarly, glycine accelerated the oligomerization rate of methionine and the degradation of methionine, producing water, ammonia, and bicarbonate through its decomposition. With Gly, heterogeneous dimers (methionylglycine and glycylmethionine) were formed in greater amounts than with other additional compounds although smaller amount of these heterogeneous dimers were formed with other additional compounds. These results suggest that accelerated reaction rates induced by water and co-existing reactive compounds promote the oligomerization

Decompositions of the polyhedral product functor with applications to moment-angle complexes and related spaces.

Science.gov (United States)

Bahri, A; Bendersky, M; Cohen, F R; Gitler, S

2009-07-28

This article gives a natural decomposition of the suspension of a generalized moment-angle complex or partial product space which arises as the polyhedral product functor described below. The introduction and application of the smash product moment-angle complex provides a precise identification of the stable homotopy type of the values of the polyhedral product functor. One direct consequence is an analysis of the associated cohomology. For the special case of the complements of certain subspace arrangements, the geometrical decomposition implies the homological decomposition in earlier work of others as described below. Because the splitting is geometric, an analogous homological decomposition for a generalized moment-angle complex applies for any homology theory. Implied, therefore, is a decomposition for the Stanley-Reisner ring of a finite simplicial complex, and natural generalizations.

Asymmetrical Polyhedral Configuration of Giant Vesicles Induced by Orderly Array of Encapsulated Colloidal Particles.

Science.gov (United States)

Natsume, Yuno; Toyota, Taro

2016-01-01

Giant vesicles (GVs) encapsulating colloidal particles by a specific volume fraction show a characteristic configuration under a hypertonic condition. Several flat faces were formed in GV membrane with orderly array of inner particles. GV shape changed from the spherical to the asymmetrical polyhedral configuration. This shape deformation was derived by entropic interaction between inner particles and GV membrane. Because a part of inner particles became to form an ordered phase in the region neighboring the GV membrane, free volume for the other part of particles increased. Giant vesicles encapsulating colloidal particles were useful for the model of "crowding effect" which is the entropic interaction in the cell.

Bending-active reciprocal structures based on equilateral polyhedral geometries

DEFF Research Database (Denmark)

Popovic Larsen, Olga; BRANCART, Stijn; DE TEMMERMAN, Niels

2017-01-01

As mutually supported beam structures, reciprocal frames limit the number of components that are joined at each connection to two. However, this system of intermediate connections introduces undesirable bending moments in the beam elements. By utilising elastic deformation to create curved...... of parts of reciprocal bending-active components based on a selection of polyhedral dome types. To simplify the assembly of the structures and avoid the manual bending of the components on site, we introduce the concept of a double-layered, pre-bent component. Finally, this paper presents the development...

Screening of drugs inhibiting in vitro oligomerization of Cu/Zn-superoxide dismutase with a mutation causing amyotrophic lateral sclerosis

Directory of Open Access Journals (Sweden)

Itsuki Anzai

2016-08-01

Full Text Available Dominant mutations in Cu/Zn-superoxide dismutase (SOD1 gene have been shown to cause a familial form of amyotrophic lateral sclerosis (SOD1-ALS. A major pathological hallmark of this disease is abnormal accumulation of mutant SOD1 oligomers in the affected spinal motor neurons. While no effective therapeutics for SOD1-ALS is currently available, SOD1 oligomerization will be a good target for developing cures of this disease. Recently, we have reproduced the formation of SOD1 oligomers abnormally cross-linked via disulfide bonds in a test tube. Using our in vitro model of SOD1 oligomerization, therefore, we screened 640 FDA-approved drugs for inhibiting the oligomerization of SOD1 proteins, and three effective classes of chemical compounds were identified. Those hit compounds will provide valuable information on the chemical structures for developing a novel drug candidate suppressing the abnormal oligomerization of mutant SOD1 and possibly curing the disease.

Approximation of scalar and vector transport problems on polyhedral meshes

International Nuclear Information System (INIS)

Cantin, Pierre

2016-01-01

This thesis analyzes, at the continuous and at the discrete level on polyhedral meshes, the scalar and the vector transport problems in three-dimensional domains. These problems are composed of a diffusive term, an advective term, and a reactive term. In the context of Friedrichs systems, the continuous problems are analyzed in Lebesgue graph spaces. The classical positivity assumption on the Friedrichs tensor is generalized so as to consider the case of practical interest where this tensor takes null or slightly negative values. A new scheme converging at the order 3/2 is devised for the scalar advection-reaction problem using scalar degrees of freedom attached to mesh vertices. Two new schemes considering as well scalar degrees of freedom attached to mesh vertices are devised for the scalar transport problem and are robust with respect to the dominant regime. The first scheme converges at the order 1/2 when advection effects are dominant and at the order 1 when diffusion effects are dominant. The second scheme improves the accuracy by converging at the order 3/2 when advection effects are dominant. Finally, a new scheme converging at the order 1/2 is devised for the vector advection-reaction problem considering only one scalar degree of freedom per mesh edge. The accuracy and the efficiency of all these schemes are assessed on various test cases using three-dimensional polyhedral meshes. (author)

Zn(2+) site engineering at the oligomeric interface of the dopamine transporter

DEFF Research Database (Denmark)

Norgaard-Nielsen, Kristine; Norregaard, Lene; Hastrup, Hanne

2002-01-01

Increasing evidence suggests that Na(+)/Cl(-)-dependent neurotransmitter transporters exist as homo-oligomeric proteins. However, the functional implication of this oligomerization remains unclear. Here we demonstrate the engineering of a Zn(2+) binding site at the predicted dimeric interface...

Crystal Structure of the Marburg Virus VP35 Oligomerization Domain

Energy Technology Data Exchange (ETDEWEB)

Bruhn, Jessica F.; Kirchdoerfer, Robert N.; Urata, Sarah M.; Li, Sheng; Tickle, Ian J.; Bricogne, Gérard; Saphire, Erica Ollmann (Scripps); (Globel Phasing); (UCSD)

2016-11-09

Marburg virus (MARV) is a highly pathogenic filovirus that is classified in a genus distinct from that of Ebola virus (EBOV) (generaMarburgvirusandEbolavirus, respectively). Both viruses produce a multifunctional protein termed VP35, which acts as a polymerase cofactor, a viral protein chaperone, and an antagonist of the innate immune response. VP35 contains a central oligomerization domain with a predicted coiled-coil motif. This domain has been shown to be essential for RNA polymerase function. Here we present crystal structures of the MARV VP35 oligomerization domain. These structures and accompanying biophysical characterization suggest that MARV VP35 is a trimer. In contrast, EBOV VP35 is likely a tetramer in solution. Differences in the oligomeric state of this protein may explain mechanistic differences in replication and immune evasion observed for MARV and EBOV.

IMPORTANCEMarburg virus can cause severe disease, with up to 90% human lethality. Its genome is concise, only producing seven proteins. One of the proteins, VP35, is essential for replication of the viral genome and for evasion of host immune responses. VP35 oligomerizes (self-assembles) in order to function, yet the structure by which it assembles has not been visualized. Here we present two crystal structures of this oligomerization domain. In both structures, three copies of VP35 twist about each other to form a coiled coil. This trimeric assembly is in contrast to tetrameric predictions for VP35 of Ebola virus and to known structures of homologous proteins in the measles, mumps, and Nipah viruses. Distinct oligomeric states of the Marburg and Ebola virus VP35 proteins may explain differences between them in polymerase function and immune evasion. These findings may provide a more accurate understanding of the

Robust Hinf control of uncertain switched systems defined on polyhedral sets with Filippov solutions

DEFF Research Database (Denmark)

Ahmadi, Mohamadreza; Mojallali, Hamed; Wisniewski, Rafal

2012-01-01

This paper considers the control problem of a class of uncertain switched systems defined on polyhedral sets known as piecewise linear systems where, instead of the conventional Carathe ́odory solutions, Filippov solutions are studied. In other words, in contrast to the previous studies, solutions...

Cartilage oligomeric matrix protein specific antibodies are pathogenic

DEFF Research Database (Denmark)

Geng, Hui; Nandakumar, Kutty Selva; Pramhed, Anna

2012-01-01

-specific monoclonal antibodies (mAbs). METHODS: B cell immunodominant regions on the COMP molecule were measured with a novel enzyme-linked immunosorbent assay using mammalian expressed full-length mouse COMP as well as a panel of recombinant mouse COMP fragments. 18 mAbs specific to COMP were generated......ABSTRACT: INTRODUCTION: Cartilage oligomeric matrix protein (COMP) is a major non-collagenous component of cartilage. Earlier, we developed a new mouse model for rheumatoid arthritis using COMP. This study was undertaken to investigate the epitope specificity and immunopathogenicity of COMP...

Mesophase behaviour of polyhedral particles

KAUST Repository

Agarwal, Umang; Escobedo, Fernando A.

2011-01-01

Translational and orientational excluded-volume fields encoded in particles with anisotropic shapes can lead to purely entropy-driven assembly of morphologies with specific order and symmetry. To elucidate this complex correlation, we carried out detailed Monte Carlo simulations of six convex space-filling polyhedrons, namely, truncated octahedrons, rhombic dodecahedrons, hexagonal prisms, cubes, gyrobifastigiums and triangular prisms. Simulations predict the formation of various new liquid-crystalline and plastic-crystalline phases at intermediate volume fractions. By correlating these findings with particle anisotropy and rotational symmetry, simple guidelines for predicting phase behaviour of polyhedral particles are proposed: high rotational symmetry is in general conducive to mesophase formation, with low anisotropy favouring plastic-solid behaviour and intermediate anisotropy (or high uniaxial anisotropy) favouring liquid-crystalline behaviour. It is also found that dynamical disorder is crucial in defining mesophase behaviour, and that the apparent kinetic barrier for the liquid-mesophase transition is much lower for liquid crystals (orientational order) than for plastic solids (translational order). © 2011 Macmillan Publishers Limited. All rights reserved.

Mesophase behaviour of polyhedral particles

KAUST Repository

Agarwal, Umang

2011-02-13

Translational and orientational excluded-volume fields encoded in particles with anisotropic shapes can lead to purely entropy-driven assembly of morphologies with specific order and symmetry. To elucidate this complex correlation, we carried out detailed Monte Carlo simulations of six convex space-filling polyhedrons, namely, truncated octahedrons, rhombic dodecahedrons, hexagonal prisms, cubes, gyrobifastigiums and triangular prisms. Simulations predict the formation of various new liquid-crystalline and plastic-crystalline phases at intermediate volume fractions. By correlating these findings with particle anisotropy and rotational symmetry, simple guidelines for predicting phase behaviour of polyhedral particles are proposed: high rotational symmetry is in general conducive to mesophase formation, with low anisotropy favouring plastic-solid behaviour and intermediate anisotropy (or high uniaxial anisotropy) favouring liquid-crystalline behaviour. It is also found that dynamical disorder is crucial in defining mesophase behaviour, and that the apparent kinetic barrier for the liquid-mesophase transition is much lower for liquid crystals (orientational order) than for plastic solids (translational order). © 2011 Macmillan Publishers Limited. All rights reserved.

Elucidation of amyloid beta-protein oligomerization mechanisms: discrete molecular dynamics study.

Science.gov (United States)

Urbanc, B; Betnel, M; Cruz, L; Bitan, G; Teplow, D B

2010-03-31

Oligomers of amyloid beta-protein (Abeta) play a central role in the pathology of Alzheimer's disease. Of the two predominant Abeta alloforms, Abeta(1-40) and Abeta(1-42), Abeta(1-42) is more strongly implicated in the disease. We elucidated the structural characteristics of oligomers of Abeta(1-40) and Abeta(1-42) and their Arctic mutants, [E22G]Abeta(1-40) and [E22G]Abeta(1-42). We simulated oligomer formation using discrete molecular dynamics (DMD) with a four-bead protein model, backbone hydrogen bonding, and residue-specific interactions due to effective hydropathy and charge. For all four peptides under study, we derived the characteristic oligomer size distributions that were in agreement with prior experimental findings. Unlike Abeta(1-40), Abeta(1-42) had a high propensity to form paranuclei (pentameric or hexameric) structures that could self-associate into higher-order oligomers. Neither of the Arctic mutants formed higher-order oligomers, but [E22G]Abeta(1-40) formed paranuclei with a similar propensity to that of Abeta(1-42). Whereas the best agreement with the experimental data was obtained when the charged residues were modeled as solely hydrophilic, further assembly from spherical oligomers into elongated protofibrils was induced by nonzero electrostatic interactions among the charged residues. Structural analysis revealed that the C-terminal region played a dominant role in Abeta(1-42) oligomer formation whereas Abeta(1-40) oligomerization was primarily driven by intermolecular interactions among the central hydrophobic regions. The N-terminal region A2-F4 played a prominent role in Abeta(1-40) oligomerization but did not contribute to the oligomerization of Abeta(1-42) or the Arctic mutants. The oligomer structure of both Arctic peptides resembled Abeta(1-42) more than Abeta(1-40), consistent with their potentially more toxic nature.

A fluorimetric readout reporting the kinetics of nucleotide-induced human ribonucleotide reductase oligomerization.

Science.gov (United States)

Fu, Yuan; Lin, Hongyu; Wisitpitthaya, Somsinee; Blessing, William A; Aye, Yimon

2014-11-24

Human ribonucleotide reductase (hRNR) is a target of nucleotide chemotherapeutics in clinical use. The nucleotide-induced oligomeric regulation of hRNR subunit α is increasingly being recognized as an innate and drug-relevant mechanism for enzyme activity modulation. In the presence of negative feedback inhibitor dATP and leukemia drug clofarabine nucleotides, hRNR-α assembles into catalytically inert hexameric complexes, whereas nucleotide effectors that govern substrate specificity typically trigger α-dimerization. Currently, both knowledge of and tools to interrogate the oligomeric assembly pathway of RNR in any species in real time are lacking. We therefore developed a fluorimetric assay that reliably reports on oligomeric state changes of α with high sensitivity. The oligomerization-directed fluorescence quenching of hRNR-α, covalently labeled with two fluorophores, allows for direct readout of hRNR dimeric and hexameric states. We applied the newly developed platform to reveal the timescales of α self-assembly, driven by the feedback regulator dATP. This information is currently unavailable, despite the pharmaceutical relevance of hRNR oligomeric regulation. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Membrane-mediated oligomerization of G protein coupled receptors and its implications for GPCR function

Directory of Open Access Journals (Sweden)

Stefan Gahbauer

2016-10-01

Full Text Available The dimerization or even oligomerization of G protein coupled receptors (GPCRs causes ongoing, controversial debates about its functional role and the coupled biophysical, biochemical or biomedical implications. A continously growing number of studies hints to a relation between oligomerization and function of GPCRs and strengthens the assumption that receptor assembly plays a key role in the regulation of protein function. Additionally, progress in the structural analysis of GPCR-G protein and GPCR-ligand interactions allows to distinguish between actively functional and non-signalling complexes. Recent findings further suggest that the surrounding membrane, i.e. its lipid composition may modulate the preferred dimerization interface and as a result the abundance of distinct dimeric conformations. In this review, the association of GPCRs and the role of the membrane in oligomerization will be discussed. An overview of the different reported oligomeric interfaces is provided and their capability for signaling discussed. The currently available data is summarized with regard to the formation of GPCR oligomers, their structures and dependency on the membrane microenvironment as well as the coupling of oligomerization to receptor function.

Zero point energy of polyhedral water clusters.

Science.gov (United States)

Anick, David J

2005-06-30

Polyhedral water clusters (PWCs) are cage-like (H2O)n clusters where every O participates in exactly three H bonds. For a database of 83 PWCs, 8 zero point energy (ZPE) was calculated at the B3LYP/6-311++G** level. ZPE correlates negatively with electronic energy (E0): each increase of 1 kcal/mol in E0 corresponds to a decrease of about 0.11 kcal/mol in ZPE. For each n, a set of four connectivity parameters accounts for 98% or more of the variance in ZPE. Linear regression of ZPE against n and this set gives an RMS error of 0.13 kcal/mol. The contributions to ZPE from stretch modes only (ZPE(S)) and from torsional modes only (ZPE(T)) also correlate strongly with E0 and with each other.

Genetic noise control via protein oligomerization

Energy Technology Data Exchange (ETDEWEB)

Ghim, C; Almaas, E

2008-06-12

Gene expression in a cell entails random reaction events occurring over disparate time scales. Thus, molecular noise that often results in phenotypic and population-dynamic consequences sets a fundamental limit to biochemical signaling. While there have been numerous studies correlating the architecture of cellular reaction networks with noise tolerance, only a limited effort has been made to understand the dynamical role of protein-protein associations. We have developed a fully stochastic model for the positive feedback control of a single gene, as well as a pair of genes (toggle switch), integrating quantitative results from previous in vivo and in vitro studies. In particular, we explicitly account for the fast protein binding-unbinding kinetics, RNA polymerases, and the promoter/operator sequences of DNA. We find that the overall noise-level is reduced and the frequency content of the noise is dramatically shifted to the physiologically irrelevant high-frequency regime in the presence of protein dimerization. This is independent of the choice of monomer or dimer as transcription factor and persists throughout the multiple model topologies considered. For the toggle switch, we additionally find that the presence of a protein dimer, either homodimer or heterodimer, may significantly reduce its intrinsic switching rate. Hence, the dimer promotes the robust function of bistable switches by preventing the uninduced (induced) state from randomly being induced (uninduced). The specific binding between regulatory proteins provides a buffer that may prevent the propagation of fluctuations in genetic activity. The capacity of the buffer is a non-monotonic function of association-dissociation rates. Since the protein oligomerization per se does not require extra protein components to be expressed, it provides a basis for the rapid control of intrinsic or extrinsic noise. The stabilization of phenotypically important toggle switches, and nested positive feedback loops in

Zn(2+) site engineering at the oligomeric interface of the dopamine transporter.

Science.gov (United States)

Norgaard-Nielsen, Kristine; Norregaard, Lene; Hastrup, Hanne; Javitch, Jonathan A; Gether, Ulrik

2002-07-31

Increasing evidence suggests that Na(+)/Cl(-)-dependent neurotransmitter transporters exist as homo-oligomeric proteins. However, the functional implication of this oligomerization remains unclear. Here we demonstrate the engineering of a Zn(2+) binding site at the predicted dimeric interface of the dopamine transporter (DAT) corresponding to the external end of transmembrane segment 6. Upon binding to this site, which involves a histidine inserted in position 310 (V310H) and the endogenous Cys306 within the same DAT molecule, Zn(2+) potently inhibits [(3)H]dopamine uptake. These data provide indirect evidence that conformational changes critical for the translocation process may occur at the interface between two transporter molecules in the oligomeric structure.

Polybenzimidazole and sulfonated polyhedral oligosilsesquioxane composite membranes for high temperature polymer electrolyte membrane fuel cells

DEFF Research Database (Denmark)

Aili, David; Allward, Todd; Alfaro, Silvia Martinez

2014-01-01

Composite membranes based on poly(2,2′(m-phenylene)-5,5́bibenzimidazole) (PBI) and sulfonated polyhedral oligosilsesquioxane (S-POSS) with S-POSS contents of 5 and 10wt.% were prepared by solution casting as base materials for high temperature polymer electrolyte membrane fuel cells. With membranes...

Induced oligomerization targets Golgi proteins for degradation in lysosomes.

Science.gov (United States)

Tewari, Ritika; Bachert, Collin; Linstedt, Adam D

2015-12-01

Manganese protects cells against forms of Shiga toxin by down-regulating the cycling Golgi protein GPP130. Down-regulation occurs when Mn binding causes GPP130 to oligomerize and traffic to lysosomes. To determine how GPP130 is redirected to lysosomes, we tested the role of GGA1 and clathrin, which mediate sorting in the canonical Golgi-to-lysosome pathway. GPP130 oligomerization was induced using either Mn or a self-interacting version of the FKBP domain. Inhibition of GGA1 or clathrin specifically blocked GPP130 redistribution, suggesting recognition of the aggregated GPP130 by the GGA1/clathrin-sorting complex. Unexpectedly, however, GPP130's cytoplasmic domain was not required, and redistribution also occurred after removal of GPP130 sequences needed for its normal cycling. Therefore, to test whether aggregate recognition might be a general phenomenon rather than one involving a specific GPP130 determinant, we induced homo-oligomerization of two unrelated Golgi-targeted constructs using the FKBP strategy. These were targeted to the cis- and trans-Golgi, respectively, using domains from mannosidase-1 and galactosyltransferase. Significantly, upon oligomerization, each redistributed to peripheral punctae and was degraded. This occurred in the absence of detectable UPR activation. These findings suggest the unexpected presence of quality control in the Golgi that recognizes aggregated Golgi proteins and targets them for degradation in lysosomes. © 2015 Tewari et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Thermal Degradation Mechanism of a Thermostable Polyester Stabilized with an Open-Cage Oligomeric Silsesquioxane

Directory of Open Access Journals (Sweden)

Yolanda Bautista

2017-12-01

Full Text Available A polyester composite was prepared through the polymerization of an unsaturated ester resin with styrene and an open-cage oligomeric silsesquioxane with methacrylate groups. The effect of the open-cage oligomeric silsesquioxane on the thermal stability of the thermostable polyester was studied using both thermogravimetric analysis and differential thermal analysis. The results showed that the methacryl oligomeric silsesquioxane improved the thermal stability of the polyester. The decomposition mechanism of the polyester/oligomer silsesquioxane composite was proposed by Fourier transform infrared spectroscopy (FTIR analysis of the volatiles.

Characterization of oligomerization of a peptide from the ebola virus glycoprotein by small-angle neutron scattering

International Nuclear Information System (INIS)

Egorov, V. V.; Gorshkov, A. N.; Murugova, T. N.; Vasin, A. V.; Lebedev, D. V.; Isaev-Ivanov, V. V.; Kiselev, O. I.

2016-01-01

Transmission electron microscopy (TEM) and small-angle neutron scattering (SANS) studies showed that model peptides QNALVCGLRQ (G33) and QNALVCGLRG (G31) corresponding to region 551–560 of the GP protein of the Sudan Ebola virus are prone to oligomerization in solution. Both peptides can form amyloid-like fibrills. The G33 peptide forms fibrils within one day of incubation, whereas the fibrillogenesis of the G31 peptide is observed only after incubation for several months. The possible role of the observed processes in the pathogenesis and the possibility of applying a combination of the TEM and SANS techniques to search for new compounds that are able to influence the protein oligomerization are discussed

Characterization of oligomerization of a peptide from the ebola virus glycoprotein by small-angle neutron scattering

Energy Technology Data Exchange (ETDEWEB)

Egorov, V. V., E-mail: vlaegur@omrb.pnpi.spb.ru [National Research Center “Kurchatov Institute”, Konstantinov Petersburg Nuclear Physics Institute (Russian Federation); Gorshkov, A. N. [Ministry of Health of the Russian Federation, Research Institute of Influenza (Russian Federation); Murugova, T. N. [Joint Institute for Nuclear Research (Russian Federation); Vasin, A. V. [Ministry of Health of the Russian Federation, Research Institute of Influenza (Russian Federation); Lebedev, D. V.; Isaev-Ivanov, V. V. [National Research Center “Kurchatov Institute”, Konstantinov Petersburg Nuclear Physics Institute (Russian Federation); Kiselev, O. I. [Ministry of Health of the Russian Federation, Research Institute of Influenza (Russian Federation)

2016-01-15

Transmission electron microscopy (TEM) and small-angle neutron scattering (SANS) studies showed that model peptides QNALVCGLRQ (G33) and QNALVCGLRG (G31) corresponding to region 551–560 of the GP protein of the Sudan Ebola virus are prone to oligomerization in solution. Both peptides can form amyloid-like fibrills. The G33 peptide forms fibrils within one day of incubation, whereas the fibrillogenesis of the G31 peptide is observed only after incubation for several months. The possible role of the observed processes in the pathogenesis and the possibility of applying a combination of the TEM and SANS techniques to search for new compounds that are able to influence the protein oligomerization are discussed.

Characterization of oligomerization of a peptide from the ebola virus glycoprotein by small-angle neutron scattering

Science.gov (United States)

Egorov, V. V.; Gorshkov, A. N.; Murugova, T. N.; Vasin, A. V.; Lebedev, D. V.; Isaev-Ivanov, V. V.; Kiselev, O. I.

2016-01-01

Transmission electron microscopy (TEM) and small-angle neutron scattering (SANS) studies showed that model peptides QNALVCGLRQ (G33) and QNALVCGLRG (G31) corresponding to region 551-560 of the GP protein of the Sudan Ebola virus are prone to oligomerization in solution. Both peptides can form amyloid-like fibrills. The G33 peptide forms fibrils within one day of incubation, whereas the fibrillogenesis of the G31 peptide is observed only after incubation for several months. The possible role of the observed processes in the pathogenesis and the possibility of applying a combination of the TEM and SANS techniques to search for new compounds that are able to influence the protein oligomerization are discussed.

Oligomerization process

Science.gov (United States)

Smith, L.A. Jr.; Hearn, D.; Jones, E.M. Jr.

1991-03-26

A liquid phase process is described for oligomerization of C[sub 4] and C[sub 5] isoolefins or the etherification thereof with C[sub 1] to C[sub 6] alcohols wherein the reactants are contacted in a reactor with a fixed bed acid cation exchange resin catalyst at an LHSV of 5 to 20, pressure of 0 to 400 psig and temperature of 120 to 300 F wherein the improvement is the operation of the reactor at a pressure to maintain the reaction mixture at its boiling point whereby at least a portion but less than all of the reaction mixture is vaporized. By operating at the boiling point and allowing a portion of the reaction mixture to vaporize, the exothermic heat of reaction is dissipated by the formation of more boil up and the temperature in the reactor is controlled. 2 figures.

Biocatalytically Oligomerized Epicatechin with Potent and Specific Anti-proliferative Activity for Human Breast Cancer Cells

Directory of Open Access Journals (Sweden)

Ramaswamy Nagarajan

2008-11-01

Full Text Available Catechins, naturally occurring flavonoids derived from wine and green tea, are known to exhibit multiple health benefits. Epigallocatechin gallate (EGCG is one of the most widely investigated catechins, but its efficacy in cancer therapy is still inconsistent and limited. The poor stability of EGCG has contributed to the disparity in the reported anti-cancer activity and other beneficial properties. Here we report an innovative enzymatic strategy for the oligomerization of catechins (specifically epicatechin that yields stable, water-soluble oligomerized epicatechins with enhanced and highly specific anti-proliferative activity for human breast cancer cells. This one-pot oxidative oligomerization is carried out in ambient conditions using Horseradish Peroxidase (HRP as a catalyst yielding water-soluble oligo(epicatechins. The oligomerized epicatechins obtained exhibit excellent growth inhibitory effects against human breast cancer cells with greater specificity towards growth-inhibiting cancer cells as opposed to normal cells, achieving a high therapeutic differential. Our studies indicate that water-soluble oligomeric epicatechins surpass EGCG in stability, selectivity and efficacy at lower doses.

Polyhedral Lyapunov functions structurally ensure global asymptotic stability of dynamical networks iff the Jacobian is non-singular

NARCIS (Netherlands)

Blanchini, Franco; Giordano, G.

2017-01-01

For a vast class of dynamical networks, including chemical reaction networks (CRNs) with monotonic reaction rates, the existence of a polyhedral Lyapunov function (PLF) implies structural (i.e., parameter-free) local stability. Global structural stability is ensured under the additional

Methyl methacrylate oligomerically-modified clay and its poly(methyl methacrylate) nanocomposites

International Nuclear Information System (INIS)

Zheng Xiaoxia; Jiang, David D.; Wilkie, Charles A.

2005-01-01

A methyl methacrylate oligomerically-modified clay was used to prepare poly(methyl methacrylate) clay nanocomposites by melt blending and the effect of the clay loading level on the modified clay and corresponding nanocomposite was studied. These nanocomposites were characterized by X-ray diffraction, transmission electron microscopy, thermogravimetric analysis and cone calorimetry. The results show a mixed intercalated/delaminated morphology with good nanodispersion. The compatibility between the methylacrylate-subsituted clay and poly(methyl methacrylate) (PMMA) are greatly improved compared to other oligomerically-modified clays

Catalyst-controlled oligomerization for the collective synthesis of polypyrroloindoline natural products.

Science.gov (United States)

Jamison, Christopher R; Badillo, Joseph J; Lipshultz, Jeffrey M; Comito, Robert J; MacMillan, David W C

2017-12-01

In nature, many organisms generate large families of natural product metabolites that have related molecular structures as a means to increase functional diversity and gain an evolutionary advantage against competing systems within the same environment. One pathway commonly employed by living systems to generate these large classes of structurally related families is oligomerization, wherein a series of enzymatically catalysed reactions is employed to generate secondary metabolites by iteratively appending monomers to a growing serial oligomer chain. The polypyrroloindolines are an interesting class of oligomeric natural products that consist of multiple cyclotryptamine subunits. Herein we describe an iterative application of asymmetric copper catalysis towards the synthesis of six distinct oligomeric polypyrroloindoline natural products: hodgkinsine, hodgkinsine B, idiospermuline, quadrigemine H and isopsychotridine B and C. Given the customizable nature of the small-molecule catalysts employed, we demonstrate that this strategy is further amenable to the construction of quadrigemine H-type alkaloids not isolated previously from natural sources.

Oligomerization of G protein-coupled receptors: computational methods.

Science.gov (United States)

Selent, J; Kaczor, A A

2011-01-01

Recent research has unveiled the complexity of mechanisms involved in G protein-coupled receptor (GPCR) functioning in which receptor dimerization/oligomerization may play an important role. Although the first high-resolution X-ray structure for a likely functional chemokine receptor dimer has been deposited in the Protein Data Bank, the interactions and mechanisms of dimer formation are not yet fully understood. In this respect, computational methods play a key role for predicting accurate GPCR complexes. This review outlines computational approaches focusing on sequence- and structure-based methodologies as well as discusses their advantages and limitations. Sequence-based approaches that search for possible protein-protein interfaces in GPCR complexes have been applied with success in several studies, but did not yield always consistent results. Structure-based methodologies are a potent complement to sequence-based approaches. For instance, protein-protein docking is a valuable method especially when guided by experimental constraints. Some disadvantages like limited receptor flexibility and non-consideration of the membrane environment have to be taken into account. Molecular dynamics simulation can overcome these drawbacks giving a detailed description of conformational changes in a native-like membrane. Successful prediction of GPCR complexes using computational approaches combined with experimental efforts may help to understand the role of dimeric/oligomeric GPCR complexes for fine-tuning receptor signaling. Moreover, since such GPCR complexes have attracted interest as potential drug target for diverse diseases, unveiling molecular determinants of dimerization/oligomerization can provide important implications for drug discovery.

The role of oligomerization and cooperative regulation in protein function: the case of tryptophan synthase.

Directory of Open Access Journals (Sweden)

M Qaiser Fatmi

Full Text Available The oligomerization/co-localization of protein complexes and their cooperative regulation in protein function is a key feature in many biological systems. The synergistic regulation in different subunits often enhances the functional properties of the multi-enzyme complex. The present study used molecular dynamics and Brownian dynamics simulations to study the effects of allostery, oligomerization and intermediate channeling on enhancing the protein function of tryptophan synthase (TRPS. TRPS uses a set of α/β-dimeric units to catalyze the last two steps of L-tryptophan biosynthesis, and the rate is remarkably slower in the isolated monomers. Our work shows that without their binding partner, the isolated monomers are stable and more rigid. The substrates can form fairly stable interactions with the protein in both forms when the protein reaches the final ligand-bound conformations. Our simulations also revealed that the α/β-dimeric unit stabilizes the substrate-protein conformation in the ligand binding process, which lowers the conformation transition barrier and helps the protein conformations shift from an open/inactive form to a closed/active form. Brownian dynamics simulations with a coarse-grained model illustrate how protein conformations affect substrate channeling. The results highlight the complex roles of protein oligomerization and the fine balance between rigidity and dynamics in protein function.

Potential Energy Surfaces and Dynamics of High Energy Species

Science.gov (United States)

2009-04-13

explored include ionic liquids and a range of high-nitrogen content and nitrogen-oxygen content species. Polyhedral oligomeric silisesquioxanes are...Approved for Public Release 13. SUPPLEMENTARY NOTES 14. ABSTRACT Several papers on ionic liquids have been published or submitted as a result of this...in energetic ionic liquids . These are variously substituted triazolium, tertazolium, and pentazolium cations. The heats of formation of all species

Symmetry and Algorithmic Complexity of Polyominoes and Polyhedral Graphs

KAUST Repository

Zenil, Hector

2018-02-24

We introduce a definition of algorithmic symmetry able to capture essential aspects of geometric symmetry. We review, study and apply a method for approximating the algorithmic complexity (also known as Kolmogorov-Chaitin complexity) of graphs and networks based on the concept of Algorithmic Probability (AP). AP is a concept (and method) capable of recursively enumeration all properties of computable (causal) nature beyond statistical regularities. We explore the connections of algorithmic complexity---both theoretical and numerical---with geometric properties mainly symmetry and topology from an (algorithmic) information-theoretic perspective. We show that approximations to algorithmic complexity by lossless compression and an Algorithmic Probability-based method can characterize properties of polyominoes, polytopes, regular and quasi-regular polyhedra as well as polyhedral networks, thereby demonstrating its profiling capabilities.

Symmetry and Algorithmic Complexity of Polyominoes and Polyhedral Graphs

KAUST Repository

Zenil, Hector; Kiani, Narsis A.; Tegner, Jesper

2018-01-01

We introduce a definition of algorithmic symmetry able to capture essential aspects of geometric symmetry. We review, study and apply a method for approximating the algorithmic complexity (also known as Kolmogorov-Chaitin complexity) of graphs and networks based on the concept of Algorithmic Probability (AP). AP is a concept (and method) capable of recursively enumeration all properties of computable (causal) nature beyond statistical regularities. We explore the connections of algorithmic complexity---both theoretical and numerical---with geometric properties mainly symmetry and topology from an (algorithmic) information-theoretic perspective. We show that approximations to algorithmic complexity by lossless compression and an Algorithmic Probability-based method can characterize properties of polyominoes, polytopes, regular and quasi-regular polyhedra as well as polyhedral networks, thereby demonstrating its profiling capabilities.

N-Glycosylation instead of cholesterol mediates oligomerization and apical sorting of GPI-APs in FRT cells.

Science.gov (United States)

Imjeti, Naga Salaija; Lebreton, Stéphanie; Paladino, Simona; de la Fuente, Erwin; Gonzalez, Alfonso; Zurzolo, Chiara

2011-12-01

Sorting of glycosylphosphatidyl-inositol--anchored proteins (GPI-APs) in polarized epithelial cells is not fully understood. Oligomerization in the Golgi complex has emerged as the crucial event driving apical segregation of GPI-APs in two different kind of epithelial cells, Madin-Darby canine kidney (MDCK) and Fisher rat thyroid (FRT) cells, but whether the mechanism is conserved is unknown. In MDCK cells cholesterol promotes GPI-AP oligomerization, as well as apical sorting of GPI-APs. Here we show that FRT cells lack this cholesterol-driven oligomerization as apical sorting mechanism. In these cells both apical and basolateral GPI-APs display restricted diffusion in the Golgi likely due to a cholesterol-enriched membrane environment. It is striking that N-glycosylation is the critical event for oligomerization and apical sorting of GPI-APs in FRT cells but not in MDCK cells. Our data indicate that at least two mechanisms exist to determine oligomerization in the Golgi leading to apical sorting of GPI-APs. One depends on cholesterol, and the other depends on N-glycosylation and is insensitive to cholesterol addition or depletion.

Gravity Gradient Tensor of Arbitrary 3D Polyhedral Bodies with up to Third-Order Polynomial Horizontal and Vertical Mass Contrasts

Science.gov (United States)

Ren, Zhengyong; Zhong, Yiyuan; Chen, Chaojian; Tang, Jingtian; Kalscheuer, Thomas; Maurer, Hansruedi; Li, Yang

2018-03-01

During the last 20 years, geophysicists have developed great interest in using gravity gradient tensor signals to study bodies of anomalous density in the Earth. Deriving exact solutions of the gravity gradient tensor signals has become a dominating task in exploration geophysics or geodetic fields. In this study, we developed a compact and simple framework to derive exact solutions of gravity gradient tensor measurements for polyhedral bodies, in which the density contrast is represented by a general polynomial function. The polynomial mass contrast can continuously vary in both horizontal and vertical directions. In our framework, the original three-dimensional volume integral of gravity gradient tensor signals is transformed into a set of one-dimensional line integrals along edges of the polyhedral body by sequentially invoking the volume and surface gradient (divergence) theorems. In terms of an orthogonal local coordinate system defined on these edges, exact solutions are derived for these line integrals. We successfully derived a set of unified exact solutions of gravity gradient tensors for constant, linear, quadratic and cubic polynomial orders. The exact solutions for constant and linear cases cover all previously published vertex-type exact solutions of the gravity gradient tensor for a polygonal body, though the associated algorithms may differ in numerical stability. In addition, to our best knowledge, it is the first time that exact solutions of gravity gradient tensor signals are derived for a polyhedral body with a polynomial mass contrast of order higher than one (that is quadratic and cubic orders). Three synthetic models (a prismatic body with depth-dependent density contrasts, an irregular polyhedron with linear density contrast and a tetrahedral body with horizontally and vertically varying density contrasts) are used to verify the correctness and the efficiency of our newly developed closed-form solutions. Excellent agreements are obtained

Controlling amyloid-beta peptide(1-42) oligomerization and toxicity by fluorinated nanoparticles.

Science.gov (United States)

Saraiva, Ana M; Cardoso, Isabel; Pereira, M Carmo; Coelho, Manuel A N; Saraiva, Maria João; Möhwald, Helmuth; Brezesinski, Gerald

2010-09-03

The amyloid-beta peptide (Abeta) is a major fibrillar component of neuritic plaques in Alzheimer's disease brains and is related to the pathogenesis of the disease. Soluble oligomers that precede fibril formation have been proposed as the main neurotoxic species that contributes to neurodegeneration and dementia. We hypothesize that oligomerization and cytotoxicity can be repressed by nanoparticles (NPs) that induce conformational changes in Abeta42. We show here that fluorinated and hydrogenated NPs with different abilities to change Abeta42 conformation influence oligomerization as assessed by atomic force microscopy, immunoblot and SDS-PAGE. Fluorinated NPs, which promote an increase in alpha-helical content, exert an antioligomeric effect, whereas hydrogenated analogues do not and lead to aggregation. Cytotoxicity assays confirmed our hypothesis by indicating that the conformational conversion of Abeta42 into an alpha-helical-enriched secondary structure also has antiapoptotic activity, thereby increasing the viability of cells treated with oligomeric species.

DNA structure modulates the oligomerization properties of the AAV initiator protein Rep68.

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Jorge Mansilla-Soto

2009-07-01

Full Text Available Rep68 is a multifunctional protein of the adeno-associated virus (AAV, a parvovirus that is mostly known for its promise as a gene therapy vector. In addition to its role as initiator in viral DNA replication, Rep68 is essential for site-specific integration of the AAV genome into human chromosome 19. Rep68 is a member of the superfamily 3 (SF3 helicases, along with the well-studied initiator proteins simian virus 40 large T antigen (SV40-LTag and bovine papillomavirus (BPV E1. Structurally, SF3 helicases share two domains, a DNA origin interaction domain (OID and an AAA(+ motor domain. The AAA(+ motor domain is also a structural feature of cellular initiators and it functions as a platform for initiator oligomerization. Here, we studied Rep68 oligomerization in vitro in the presence of different DNA substrates using a variety of biophysical techniques and cryo-EM. We found that a dsDNA region of the AAV origin promotes the formation of a complex containing five Rep68 subunits. Interestingly, non-specific ssDNA promotes the formation of a double-ring Rep68, a known structure formed by the LTag and E1 initiator proteins. The Rep68 ring symmetry is 8-fold, thus differing from the hexameric rings formed by the other SF3 helicases. However, similiar to LTag and E1, Rep68 rings are oriented head-to-head, suggesting that DNA unwinding by the complex proceeds bidirectionally. This novel Rep68 quaternary structure requires both the DNA binding and AAA(+ domains, indicating cooperativity between these regions during oligomerization in vitro. Our study clearly demonstrates that Rep68 can oligomerize through two distinct oligomerization pathways, which depend on both the DNA structure and cooperativity of Rep68 domains. These findings provide insight into the dynamics and oligomeric adaptability of Rep68 and serve as a step towards understanding the role of this multifunctional protein during AAV DNA replication and site-specific integration.

Transient structural distortion of metal-free Cu/Zn superoxide dismutase triggers aberrant oligomerization

DEFF Research Database (Denmark)

Teilum, Kaare; Smith, Melanie H; Schulz, Eike

2009-01-01

remained enigmatic, however, as is the case in other protein-misfolding diseases. Here, we target the critical conformational change that defines the earliest step toward aggregation. Using nuclear spin relaxation dispersion experiments, we identified a short-lived (0.4 ms) and weakly populated (0.......7%) conformation of metal-depleted SOD1 that triggers aberrant oligomerization. This excited state emanates from the folded ground state and is suppressed by metal binding, but is present in both the disulfide-oxidized and disulfide-reduced forms of the protein. Our results pinpoint a perturbed region......Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease linked to the misfolding of Cu/Zn superoxide dismutase (SOD1). ALS-related defects in SOD1 result in a gain of toxic function that coincides with aberrant oligomerization. The structural events triggering oligomerization have...

Effect Of Oligomeric Enteral Nutrition On Symptoms Of Acute Radiation Enteritis

International Nuclear Information System (INIS)

Dubinsky, P.

2008-01-01

Radiotherapy of abdominal and pelvic tumours is frequently associated with acute radiation enteritis. Predominant symptoms include diarrhea, watery stools, abdominal pain, nausea and vomiting. There are very few effective interventions available for this condition. Enteral oligomeric nutrition has been used in bowel diseases with functional failure similar to radiation enteritis. The aim of presented work was to observe occurrence of symptoms of radiation enteritis in patients undergoing abdominal or pelvic radiotherapy. Apart from diet and pharmacological therapy, oral oligomeric enteral nutrition (Peptisorb Powder Nutricia) at the dose of 1000 - 2000 ml per day was administered for minimum of 4 days. Planned period of administration was 14 days and longer. Symptoms of radiation enteritis were evaluated at the beginning and in the end of administration. Prevalence of all evaluated symptoms of radiation enteritis was decreased and difference was statistically significant for diarrhea, watery stools, abdominal pain, nausea and vomiting. The use of evaluated oligomeric nutritional support might, in conjunction with pharmacotherapy and diet, alleviate symptoms of acute radiation enteritis and maintain nutritional status of patients. (author)

Stability of human interferon-beta 1: oligomeric human interferon-beta 1 is inactive but is reactivated by monomerization.

Science.gov (United States)

Utsumi, J; Yamazaki, S; Kawaguchi, K; Kimura, S; Shimizu, H

1989-10-05

Human interferon-beta 1 is extremely stable is a low ionic strength solution of pH 2 such as 10 mM HCl at 37 degrees C. However, the presence of 0.15 M NaCl led to a remarkable loss of antiviral activity. The molecular-sieve high-performance liquid chromatography revealed that, whereas completely active human interferon-beta 1 eluted as a 25 kDa species (monomeric form), the inactivated preparation eluted primarily as a 90 kDa species (oligomeric form). The specific activity (units per mg protein) of the oligomeric form was approx. 10% of that of the monomeric form. This observation shows that oligomeric human interferon-beta 1 is apparently in an inactive form. When the oligomeric eluate was resolved by polyacrylamide gel containing sodium dodecyl sulphate (SDS), it appeared to be monomeric under non-reducing conditions. Monomerization of the oligomeric human interferon-beta 1 by treatment with 1% SDS, fully regenerated its antiviral activity. These results suggest that the inactivation of the human interferon-beta 1 preparation was caused by its oligomerization via hydrophobic interactions without the formation of intermolecular disulphide bonds. These oligomers can be dissociated by SDS to restore biological activity.

Polymer dynamics in rubbery epoxy networks/polyhedral oligomeric silsesquioxanes nanocomposites

Czech Academy of Sciences Publication Activity Database

Kourkoutsaki, T.; Logakis, E.; Kroutilová, Irena; Matějka, Libor; Nedbal, J.; Pissis, P.

2009-01-01

Roč. 113, č. 4 (2009), s. 2569-2582 ISSN 0021-8995 R&D Projects: GA AV ČR IAA400500701 Institutional research plan: CEZ:AV0Z40500505 Keywords : nanocomposites * dielectric properties * rubbery epoxy networks Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.203, year: 2009

Polymer Nanocomposites Designed with Polyhedral Oligomeric Silsesquioxanes (POSS) and Plastics

National Research Council Canada - National Science Library

Haddad, Timothy; Mabry, Joseph

2005-01-01

.... These applications include space-survivable coatings and fire-resistant materials. Due to their physical size, POSS incorporation in polymers generally serves to reduce chain mobility, thus affecting both thermal and mechanical properties...

Functionalization of Fluoroalkyl Polyhedral Oligomeric Silsesquioxanes (F-POSS) (Post Print)

Science.gov (United States)

2012-08-01

7Si7O9(ONa)3, has been derivatized with long-chain fluorinated trichlorosilanes to produce low surface energy materials (8). However, these shorter propyl ...such as tetrahydrofuran and chloroform . Currently a more in-depth analysis of these polymerizations is being undertaken. Figure 16. Static contact

Concentration-dependent oligomerization of cross-linked complexes between ferredoxin and ferredoxin–NADP+ reductase

International Nuclear Information System (INIS)

Kimata-Ariga, Yoko; Kubota-Kawai, Hisako; Lee, Young-Ho; Muraki, Norifumi; Ikegami, Takahisa; Kurisu, Genji; Hase, Toshiharu

2013-01-01

Highlights: •Cross-linked complexes of ferredoxin (Fd) and Fd–NADP + reductase form oligomers. •In the crystal structures, Fd- and FNR moieties swap across the molecules. •The complexes exhibit concentration-dependent oligomerization at sub-milimolar order. -- Abstract: Ferredoxin–NADP + reductase (FNR) forms a 1:1 complex with ferredoxin (Fd), and catalyzes the electron transfer between Fd and NADP + . In our previous study, we prepared a series of site-specifically cross-linked complexes of Fd and FNR, which showed diverse electron transfer properties. Here, we show that X-ray crystal structures of the two different Fd–FNR cross-linked complexes form oligomers by swapping Fd and FNR moieties across the molecules; one complex is a dimer from, and the other is a successive multimeric form. In order to verify whether these oligomeric structures are formed only in crystal, we investigated the possibility of the oligomerization of these complexes in solution. The mean values of the particle size of these cross-linked complexes were shown to increase with the rise of protein concentration at sub-milimolar order, whereas the size of dissociable wild-type Fd:FNR complex was unchanged as analyzed by dynamic light scattering measurement. The oligomerization products were detected by SDS–PAGE after chemical cross-linking of these complexes at the sub-milimolar concentrations. The extent and concentration-dependent profile of the oligomerizaion were differentiated between the two cross-linked complexes. These results show that these Fd–FNR cross-linked complexes exhibit concentration-dependent oligomerization, possibly through swapping of Fd and FNR moieties also in solution. These findings lead to the possibility that some native multi-domain proteins may present similar phenomenon in vivo

POSS Ionic Liquid.

Science.gov (United States)

Tanaka, Kazuo; Ishiguro, Fumiyasu; Chujo, Yoshiki

2010-12-22

We report the synthesis of a stable room-temperature ionic liquid consisting of an octacarboxy polyhedral oligomeric silsesquioxane (POSS) anion and an imidazolium cation. The introduction of the POSS moiety enhances the thermal stability and reduces the melting temperature. From an evaluation of the thermodynamic parameters during the melting, it was found that the rigidity and cubic structure of POSS can contribute to the enhancement of these thermal properties.

Cobalt Oxide on N-Doped Carbon for 1-Butene Oligomerization to Produce Linear Octenes

Energy Technology Data Exchange (ETDEWEB)

Zhao, Dongting [Department; Xu, Zhuoran [Department; Chada, Joseph P. [Department; Carrero, Carlos A. [Department; Rosenfeld, Devon C. [The Dow Chemical Company, 2301 N. Brazosport Boulevard, Freeport, Texas 77541-3257, United States; Rogers, Jessica L. [The Dow Chemical Company, 2301 N. Brazosport Boulevard, Freeport, Texas 77541-3257, United States; Hermans, Ive [Department; Huber, George W. [Department

2017-10-02

Cobalt oxide supported on N-doped carbon catalysts were investigated for 1-butene oligomerization. The materials were synthesized by treating activated carbon with nitric acid and subsequently with NH3 at 200, 400, 600, and 800 °C, followed by impregnation with cobalt. The 1-butene oligomerization selectivity increased with ammonia treatment temperature of the carbon support. The oligomerization selectivity of cobalt oxide on N-doped carbon synthesized at 800 °C (800A-CoOx/N-C) is 2.6 times higher than previously reported cobalt oxide on N-doped carbon synthesized with NH4OH (2A-CoOx/N-C). Over 70% of the butene dimers were linear C8 olefins for all catalysts. The oligomerization selectivity increased with 1-butene conversion. The catalysts were characterized by elemental analysis, N2 adsorption, X-ray diffraction (XRD), X-ray absorption spectroscopy (XAS), and X-ray photoelectron spectroscopy (XPS). The nitrogen content of the catalysts increases with ammonia treatment temperature as confirmed by elemental analysis. The surface content of pyridinic nitrogen with a binding energy of 398.4 ± 0.1 eV increased with ammonia treatment temperature as evidenced by deconvolution of N 1s XPS spectra.

An investigation of the use of cerium and polyhedral oligomeric silsesquioxanes for the protection of polymeric epoxy compounds in the low Earth orbit environment

Science.gov (United States)

Piness, Jessica Miriam

Low Earth orbit presents many hazards for composites including atomic oxygen, UV radiation, thermal cycling, micrometeoroids, and high energy protons. Atomic oxygen and vacuum ultraviolet radiation are of concern for space-bound polymeric materials as they degrade the polymers used as matrices for carbon fiber composites, which are used in satellites and space vehicles due to their high strength to weight ratios. Epoxy-amine thermosets comprise a common class of matrix due to processability and good thermal attributes. Polyhedral oligomeric silsesquioxanes (POSS) have shown the ability to reduce erosion in polyimides, polyurethanes, and other polymers when exposed to atomic oxygen. The POSS particle is composed of a SiO1.5 cage from which up to eight organic pendant groups are attached at the silicon corners of the cage. POSS reduced atomic oxygen impact on polymers by a process known as glassification wherein the organic pendants are removed from the cage upon atomic oxygen exposure and then the cage rearranges to a passive silica network. In addition, POSS shows good UV absorbance in the UVb and UVc ranges and POSS can aid dispersion of titanium dioxide in a nanocomposite. In this work, Chapter I focuses on hazards in low Earth orbit, strategies for protecting organic material in orbit, and the capabilities of POSS. Chapter II details the experimental practices used in this work. Chapter III focuses on work to induce POSS phase separation and layering at the surface of an epoxy-amine thermoset. Generally, POSS is dispersed throughout a nanocomposite, and in the process of erosion by atomic oxygen, some polymer mass loss is lost before enough POSS is exposed to begin glassification. Locating POSS at a surface of composite could possibly reduce this mass loss and the objective of this research was to investigate the formation of POSS-rich surfaces. Three POSS derivatives with different pendant groups were chosen. The POSS derivatives had a range of miscibilities

Endocytic pathways mediating oligomeric Aβ42 neurotoxicity

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Laxton Kevin

2010-05-01

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

Metal-Organic Frameworks Triggered High-Efficiency Li storage in Fe-Based Polyhedral Nanorods for Lithium-ion Batteries

International Nuclear Information System (INIS)

Shen, Lisha; Song, Huawei; Wang, Chengxin

2017-01-01

Recently, metal organic framework (MOF) nanostructures have been frequently reported in the field of energy storage, specifically for Li-ion or Na-ion storage. By inter-separating the active sites of metal cluster and organic ligands, MOF nanostructures are exceptionally promising for realizing fast ion exchange and high-efficiency transportation and addressing the intricate issues that the energy-intensive Li-ion batteries have faced over many years. The related ion-storage mechanism remains to be explored. Is the traditional redox reaction mechanism operative for these nanostructure, as it is for transitional metal oxide? Herein, taking [Fe_3O(BDC)_3(H_2O)_2(NO_3)]n (Fe-MIL-88B) as an example, an Fe-based metal organic polyhedral nanorods of MIL–88 B structure was designed as an anode for Li-ion storage. When tested at 60 mA g"−"1, the nanoporous Fe-MIL–88 B polyhedral nanorods retained a reversible capacity of 744.5 mAh g"−"1 for more than 400 cycles. Ex situ characterizations of the post-cycled electrodes revealed that both the transition metal ions and the organic ligands contributed to the high reversible specific capacity. The polyhedral nanorods electrodes held the metal-organic skeleton together throughout the battery operation, although in a somewhat different manner than the pristine ones. This further substantiated that some MOF nanostructures are more appropriate than others for stable lithiation/delithiation processes. State-of-the-art CR2032 full cells showed that a high capacity of 86.8 mAh g"−"1 that was retained after 100 cycles (herein, the capacity for the full cell was calculated based on both the weight of the anode and the cathode, and the charge-discharge rate was 0.25C), when commercial LiFePO_4 powders were used as the cathode.

A Small-Molecule Inhibitor of Bax and Bak Oligomerization Prevents Genotoxic Cell Death and Promotes Neuroprotection.

Science.gov (United States)

Niu, Xin; Brahmbhatt, Hetal; Mergenthaler, Philipp; Zhang, Zhi; Sang, Jing; Daude, Michael; Ehlert, Fabian G R; Diederich, Wibke E; Wong, Eve; Zhu, Weijia; Pogmore, Justin; Nandy, Jyoti P; Satyanarayana, Maragani; Jimmidi, Ravi K; Arya, Prabhat; Leber, Brian; Lin, Jialing; Culmsee, Carsten; Yi, Jing; Andrews, David W

2017-04-20

Aberrant apoptosis can lead to acute or chronic degenerative diseases. Mitochondrial outer membrane permeabilization (MOMP) triggered by the oligomerization of the Bcl-2 family proteins Bax/Bak is an irreversible step leading to execution of apoptosis. Here, we describe the discovery of small-molecule inhibitors of Bax/Bak oligomerization that prevent MOMP. We demonstrate that these molecules disrupt multiple, but not all, interactions between Bax dimer interfaces thereby interfering with the formation of higher-order oligomers in the MOM, but not recruitment of Bax to the MOM. Small-molecule inhibition of Bax/Bak oligomerization allowed cells to evade apoptotic stimuli and rescued neurons from death after excitotoxicity, demonstrating that oligomerization of Bax is essential for MOMP. Our discovery of small-molecule Bax/Bak inhibitors provides novel tools for the investigation of the mechanisms leading to MOMP and will ultimately facilitate development of compounds inhibiting Bax/Bak in acute and chronic degenerative diseases. Copyright © 2017 Elsevier Ltd. All rights reserved.

RIG-I self-oligomerization is either dispensable or very transient for signal transduction.

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Jade Louber

Full Text Available Effective host defence against viruses depends on the rapid triggering of innate immunity through the induction of a type I interferon (IFN response. To this end, microbe-associated molecular patterns are detected by dedicated receptors. Among them, the RIG-I-like receptors RIG-I and MDA5 activate IFN gene expression upon sensing viral RNA in the cytoplasm. While MDA5 forms long filaments in vitro upon activation, RIG-I is believed to oligomerize after RNA binding in order to transduce a signal. Here, we show that in vitro binding of synthetic RNA mimicking that of Mononegavirales (Ebola, rabies and measles viruses leader sequences to purified RIG-I does not induce RIG-I oligomerization. Furthermore, in cells devoid of endogenous functional RIG-I-like receptors, after activation of exogenous Flag-RIG-I by a 62-mer-5'ppp-dsRNA or by polyinosinic:polycytidylic acid, a dsRNA analogue, or by measles virus infection, anti-Flag immunoprecipitation and specific elution with Flag peptide indicated a monomeric form of RIG-I. Accordingly, when using the Gaussia Luciferase-Based Protein Complementation Assay (PCA, a more sensitive in cellula assay, no RIG-I oligomerization could be detected upon RNA stimulation. Altogether our data indicate that the need for self-oligomerization of RIG-I for signal transduction is either dispensable or very transient.

Human α4β2 nicotinic acetylcholine receptor as a novel target of oligomeric α-synuclein.

Directory of Open Access Journals (Sweden)

Qiang Liu

Full Text Available Cigarette smoking is associated with a decreased incidence of Parkinson disease (PD through unknown mechanisms. Interestingly, a decrease in the numbers of α4β2 nicotinic acetylcholine receptors (α4β2-nAChRs in PD patients suggests an α4β2-nAChR-mediated cholinergic deficit in PD. Although oligomeric forms of α-synuclein have been recognized to be toxic and involved in the pathogenesis of PD, their direct effects on nAChR-mediated cholinergic signaling remains undefined. Here, we report for the first time that oligomeric α-synuclein selectively inhibits human α4β2-nAChR-mediated currents in a dose-dependent, non-competitive and use-independent manner. We show that pre-loading cells with guanyl-5'-yl thiophosphate fails to prevent this inhibition, suggesting that the α-synuclein-induced inhibition of α4β2-nAChR function is not mediated by nAChR internalization. By using a pharmacological approach and cultures expressing transfected human nAChRs, we have shown a clear effect of oligomeric α-synuclein on α4β2-nAChRs, but not on α4β4- or α7-nAChRs, suggesting nAChR subunit selectivity of oligomeric α-synuclein-induced inhibition. In addition, by combining the size exclusion chromatography and atomic force microscopy (AFM analyses, we find that only large (>4 nm oligomeric α-synuclein aggregates (but not monomeric, small oligomeric or fibrillar α-synuclein aggregates exhibit the inhibitory effect on human α4β2-nAChRs. Collectively, we have provided direct evidence that α4β2-nAChR is a sensitive target to mediate oligomeric α-synuclein-induced modulation of cholinergic signaling, and our data imply that therapeutic strategies targeted toward α4β2-nAChRs may have potential for developing new treatments for PD.

Catalytic oligomerization of terminal alkynes promoted by organo-f-complexes

International Nuclear Information System (INIS)

Straub, T.; Haskel, A.; Eisen, M.S.

1995-01-01

Organoactinides of the type Cp* 2 AcMe 2 (Cp*=C 5 Me 5 ; Ac=Th, U) are active catalyst precursors for the oligomerization of terminal alkynes HC triple-bond CR (R=alkyl, aryl, SiMe 3 ). The regioselectivity and the extent of oligomerization strongly depend on the alkyne substituent R, whereas the catalytic reactivity is similar for 1 and 2. In the presence of one of these organoactinides, for example, HCCSiMe 3 regioselectively oligomerizes to the head-to-tail dimer 3 (5%) and the trimer 4 (95%). 1 and 2 react with the terminal alkynes, releasing methane, to the corresponding bisacetylide complexes which are active species and in the catalytic reactions. The bisacetylide complex (η 5 -C 5 Me 5 ) 2 U(CCPh) 2 was identified by proton NMR spectroscopy. Subsequent insertion of alkyne molecules in the actinide-carbon σ-bonds leads to the formation of actinide-alkenyl complexes. The turnover limiting step is the release of the organic oligomer from the actinide-organyl complex. A species of the latter has been spectroscopically characterized in the trimerization reaction of HCCSiMe 3 . In this poster, the catalytic reactivity of the actinide alkyls 1 and 2 with various mono-substituted alkynes as well as the spectroscopic characterization of the key organometallic intermediate complexes in the catalytic cycle and a detailed mechanistic discussion are given

Anesthetic propofol attenuates the isoflurane-induced caspase-3 activation and Aβ oligomerization.

Directory of Open Access Journals (Sweden)

Yiying Zhang

Full Text Available Accumulation and deposition of β-amyloid protein (Aβ are the hallmark features of Alzheimer's disease. The inhalation anesthetic isoflurane has been shown to induce caspase activation and increase Aβ accumulation. In addition, recent studies suggest that isoflurane may directly promote the formation of cytotoxic soluble Aβ oligomers, which are thought to be the key pathological species in AD. In contrast, propofol, the most commonly used intravenous anesthetic, has been reported to have neuroprotective effects. We therefore set out to compare the effects of isoflurane and propofol alone and in combination on caspase-3 activation and Aβ oligomerization in vitro and in vivo. Naïve and stably-transfected H4 human neuroglioma cells that express human amyloid precursor protein, the precursor for Aβ; neonatal mice; and conditioned cell culture media containing secreted human Aβ40 or Aβ42 were treated with isoflurane and/or propofol. Here we show for the first time that propofol can attenuate isoflurane-induced caspase-3 activation in cultured cells and in the brain tissues of neonatal mice. Furthermore, propofol-mediated caspase inhibition occurred when there were elevated levels of Aβ. Finally, isoflurane alone induces Aβ42, but not Aβ40, oligomerization, and propofol can inhibit the isoflurane-mediated oligomerization of Aβ42. These data suggest that propofol may mitigate the caspase-3 activation by attenuating the isoflurane-induced Aβ42 oligomerization. Our findings provide novel insights into the possible mechanisms of isoflurane-induced neurotoxicity that may aid in the development of strategies to minimize potential adverse effects associated with the administration of anesthetics to patients.

N-(1-Pyrenyl Maleimide Induces Bak Oligomerization and Mitochondrial Dysfunction in Jurkat Cells

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Pei-Rong Huang

2015-01-01

Full Text Available N-(1-pyrenyl maleimide (NPM is a fluorescent reagent that is frequently used as a derivatization agent for the detection of thio-containing compounds. NPM has been shown to display a great differential cytotoxicity against hematopoietic cancer cells. In this study, the molecular mechanism by which NPM induces apoptosis was examined. Here, we show that treatment of Jurkat cells with NPM leads to Bak oligomerization, loss of mitochondrial membrane potential (Δψm, and release of cytochrome C from mitochondria to cytosol. Induction of Bak oligomerization appears to play a critical role in NPM-induced apoptosis, as downregulation of Bak by shRNA significantly prevented NPM-induced apoptosis. Inhibition of caspase 8 by Z-IETD-FMK and/or depletion of Bid did not affect NPM-induced oligomerization of Bak. Taken together, these results suggest that NPM-induced apoptosis is mediated through a pathway that is independent of caspase-8 activation.

Oligomerization of optically active N-(4-hydroxyphenylmandelamide in the presence of β-cyclodextrin and the minor role of chirality

Directory of Open Access Journals (Sweden)

Helmut Ritter

2014-10-01

Full Text Available The oxidative oligomerization of a chiral mandelamide derivative (N-(4-hydroxyphenylmandelamide, 1 was performed in the presence of horseradish peroxidase, laccase and N,N'-bis(salicylideneethylenediamine-iron(II to obtain chiral oligophenols 2. The low enantioselectivity of the enzymatic catalyzed asymmetric enantiomer-differentiating oligomerizations was investigated. In addition, the poor influence of cyclodextrin on the enantioselectivity of enzymatic catalyzed asymmetric enantiomer-differentiating oligomerizations was studied.

40 CFR 721.3100 - Oligomeric silicic acid ester compound with a hy-droxyl-al-kyla-mine.

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Oligomeric silicic acid ester compound with a hy-droxyl-al-kyla-mine. 721.3100 Section 721.3100 Protection of Environment ENVIRONMENTAL... Significant New Uses for Specific Chemical Substances § 721.3100 Oligomeric silicic acid ester compound with a...

Bacterial flagellar capping proteins adopt diverse oligomeric states

Energy Technology Data Exchange (ETDEWEB)

Postel, Sandra; Deredge, Daniel; Bonsor, Daniel A.; Yu, Xiong; Diederichs, Kay; Helmsing, Saskia; Vromen, Aviv; Friedler, Assaf; Hust, Michael; Egelman, Edward H.; Beckett, Dorothy; Wintrode, Patrick L.; Sundberg, Eric J. (UV); (Braunschweig); (Maryland-MED); (Konstanz); (Maryland); (Hebrew)

2016-09-24

Flagella are crucial for bacterial motility and pathogenesis. The flagellar capping protein (FliD) regulates filament assembly by chaperoning and sorting flagellin (FliC) proteins after they traverse the hollow filament and exit the growing flagellum tip. In the absence of FliD, flagella are not formed, resulting in impaired motility and infectivity. Here, we report the 2.2 Å resolution X-ray crystal structure of FliD fromPseudomonas aeruginosa, the first high-resolution structure of any FliD protein from any bacterium. Using this evidence in combination with a multitude of biophysical and functional analyses, we find thatPseudomonasFliD exhibits unexpected structural similarity to other flagellar proteins at the domain level, adopts a unique hexameric oligomeric state, and depends on flexible determinants for oligomerization. Considering that the flagellin filaments on which FliD oligomers are affixed vary in protofilament number between bacteria, our results suggest that FliD oligomer stoichiometries vary across bacteria to complement their filament assemblies.

Chemical activation of bituminous coal for hampering oligomerization of organic contaminants.

Science.gov (United States)

Yan, Liang; Sorial, George A

2011-12-15

Activated carbons prepared by KOH activation of bituminous coal were studied for hampering oligomerization of phenolic compounds on its surface. A total of 24 activated carbons with different microporosity and BET surface area were created. The effect of the different variables of the activation process (KOH/bituminous coal ratio, heating temperature, activation time, and flow rate of nitrogen gas) on critical carbon parameters was analyzed. The impact of activated carbon on oligomerization was examined by conducting isotherm experiments at a neutral pH on Carbon(exp) produced with optimal characteristics and granular activated carbon (GAC) F400 for phenol, 2-methylphenol and 2-ethylphenol. These isotherms were collected under anoxic (absence of molecular oxygen) and oxic (presence of molecular oxygen) conditions. The single solute adsorption of phenol, 2-methylphenol and 2-ethylphenol on Carbon(exp) showed no obvious differences between oxic and anoxic environment, which indicated that the Carbon(exp) sample is very effective in hampering the oligomerization of phenolic compounds under oxic conditions. On the other hand, F400, which have lower micropore percentage and BET surface area, significant increases in the adsorptive capacity had been observed when molecular oxygen was present. Copyright © 2011 Elsevier B.V. All rights reserved.

Kinetics in Signal Transduction Pathways Involving Promiscuous Oligomerizing Receptors Can Be Determined by Receptor Specificity : Apoptosis Induction by TRAIL

NARCIS (Netherlands)

Szegezdi, Eva; van der Sloot, Almer M.; Mahalingam, Devalingam; O'Leary, Lynda; Cool, Robbert H.; Munoz, Ines G.; Montoya, Guillermo; Quax, Wim J.; de Jong, Steven; Samali, Afshin; Serrano, Luis

Here we show by computer modeling that kinetics and outcome of signal transduction in case of hetero-oligomerizing receptors of a promiscuous ligand largely depend on the relative amounts of its receptors. Promiscuous ligands can trigger the formation of nonproductive receptor complexes, which slows

Compatible discrete operator schemes on polyhedral meshes for elliptic and Stokes equations

International Nuclear Information System (INIS)

Bonelle, Jerome

2014-01-01

This thesis presents a new class of spatial discretization schemes on polyhedral meshes, called Compatible Discrete Operator (CDO) schemes and their application to elliptic and Stokes equations In CDO schemes, preserving the structural properties of the continuous equations is the leading principle to design the discrete operators. De Rham maps define the degrees of freedom according to the physical nature of fields to discretize. CDO schemes operate a clear separation between topological relations (balance equations) and constitutive relations (closure laws). Topological relations are related to discrete differential operators, and constitutive relations to discrete Hodge operators. A feature of CDO schemes is the explicit use of a second mesh, called dual mesh, to build the discrete Hodge operator. Two families of CDO schemes are considered: vertex-based schemes where the potential is located at (primal) mesh vertices, and cell-based schemes where the potential is located at dual mesh vertices (dual vertices being in one-to-one correspondence with primal cells). The CDO schemes related to these two families are presented and their convergence is analyzed. A first analysis hinges on an algebraic definition of the discrete Hodge operator and allows one to identify three key properties: symmetry, stability, and P0-consistency. A second analysis hinges on a definition of the discrete Hodge operator using reconstruction operators, and the requirements on these reconstruction operators are identified. In addition, CDO schemes provide a unified vision on a broad class of schemes proposed in the literature (finite element, finite element, mimetic schemes... ). Finally, the reliability and the efficiency of CDO schemes are assessed on various test cases and several polyhedral meshes. (author)

Conformational detection of p53's oligomeric state by FlAsH Fluorescence

OpenAIRE

Webber, Tawnya M.; Allen, Andrew C.; Ma, Wai Kit; Molloy, Rhett G.; Kettelkamp, Charisse N.; Dow, Caitlin A.; Gage, Matthew J.

2009-01-01

The p53 tumor suppressor protein is a critical checkpoint in prevention of tumor formation, and the function of p53 is dependent on proper formation of the active tetramer. In vitro studies have shown that p53 binds DNA most efficiently as a tetramer, though inactive p53 is predicted to be monomeric in vivo. We demonstrate that FlAsH binding can be used to distinguish between oligomeric states of p53, providing a potential tool to explore p53 oligomerization in vivo. The FlAsH tetra-cysteine ...

Crystal Structure of the Oligomeric Form of Lassa Virus Matrix Protein Z.

Science.gov (United States)

Hastie, Kathryn M; Zandonatti, Michelle; Liu, Tong; Li, Sheng; Woods, Virgil L; Saphire, Erica Ollmann

2016-05-01

The arenavirus matrix protein Z is highly multifunctional and occurs in both monomeric and oligomeric forms. The crystal structure of a dodecamer of Z from Lassa virus, presented here, illustrates a ring-like structure with a highly basic center. Mutagenesis demonstrates that the dimeric interface within the dodecamer and a Lys-Trp-Lys triad at the center of the ring are important for oligomerization. This structure provides an additional template to explore the many functions of Z. The arenavirus Lassa virus causes hundreds of thousands of infections each year, many of which develop into fatal hemorrhagic fever. The arenavirus matrix protein Z is multifunctional, with at least four distinct roles. Z exists in both monomeric and oligomeric forms, each of which likely serves a specific function in the viral life cycle. Here we present the dodecameric form of Lassa virus Z and demonstrate that Z forms a "wreath" with a highly basic center. This structure and that of monomeric Z now provide a pair of critical templates by which the multiple roles of Z in the viral life cycle may be interpreted. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Homologous ELISA for detection of oligomeric human TNF: properties of the assay.

Science.gov (United States)

Petyovka, N; Lyach, L; Voitenok, N N

1995-10-26

In order to quantify oligomeric human tumor necrosis factor-alpha (TNF), we have developed a sensitive homologous enzyme-linked immunosorbent assay (Hm-ELISA) using the same monoclonal antibody (MoAb) for both solid and liquid phase. Different anti-TNF MoAb have been compared in terms of their efficacy in the Hm-ELISA, affinity, neutralization capacity and epitope specificity. The data suggest, that effectiveness in the Hm-ELISA may represent a novel characteristic of MoAb. Of the MoAbs tested, 5 N was capable of recognizing oligomeric TNF in the Hm-ELISA with a detection limit of 15 pg/ml. Furthermore, using Hm-ELISA against human TNF, interleukin-8 (IL-8) and lymphotoxin, we have demonstrated that these cytokines are oligomeric in physiological solutions, but are converted into monomeric forms in the presence of the non-ionic detergent Tween 20. High salt buffer was employed to abrogate a nonspecific false positive reaction in the Hm-ELISA found in nearly half of the plasma samples obtained from healthy subjects. Finally, a good correlation between the Hm-ELISA and the L929 bioassay was observed for natural and recombinant TNF measured in human plasma.

Cartilage oligomeric matrix protein in patients with juvenile idiopathic arthritis

DEFF Research Database (Denmark)

Bjørnhart, Birgitte; Juul, Anders; Nielsen, Susan

2009-01-01

Cartilage oligomeric matrix protein (COMP) has been identified as a prognostic marker of progressive joint destruction in rheumatoid arthritis. In this population based study we evaluated associations between plasma concentrations of COMP, disease activity, and growth velocity in patients...

Fourth class of convex equilateral polyhedron with polyhedral symmetry related to fullerenes and viruses.

Science.gov (United States)

Schein, Stan; Gayed, James Maurice

2014-02-25

The three known classes of convex polyhedron with equal edge lengths and polyhedral symmetry--tetrahedral, octahedral, and icosahedral--are the 5 Platonic polyhedra, the 13 Archimedean polyhedra--including the truncated icosahedron or soccer ball--and the 2 rhombic polyhedra reported by Johannes Kepler in 1611. (Some carbon fullerenes, inorganic cages, icosahedral viruses, geodesic structures, and protein complexes resemble these fundamental shapes.) Here we add a fourth class, "Goldberg polyhedra," which are also convex and equilateral. We begin by decorating each of the triangular facets of a tetrahedron, an octahedron, or an icosahedron with the T vertices and connecting edges of a "Goldberg triangle." We obtain the unique set of internal angles in each planar face of each polyhedron by solving a system of n equations and n variables, where the equations set the dihedral angle discrepancy about different types of edge to zero, and the variables are a subset of the internal angles in 6gons. Like the faces in Kepler's rhombic polyhedra, the 6gon faces in Goldberg polyhedra are equilateral and planar but not equiangular. We show that there is just a single tetrahedral Goldberg polyhedron, a single octahedral one, and a systematic, countable infinity of icosahedral ones, one for each Goldberg triangle. Unlike carbon fullerenes and faceted viruses, the icosahedral Goldberg polyhedra are nearly spherical. The reasoning and techniques presented here will enable discovery of still more classes of convex equilateral polyhedra with polyhedral symmetry.

Self-assembled amphiphilic polyhedral oligosilsesquioxane (POSS) grafted poly(vinyl alcohol) (PVA) nanoparticles

International Nuclear Information System (INIS)

Sheikh, Faheem A.; Barakat, Nasser A.M.; Kim, Byoung-Suhk; Aryal, Santosh; Khil, Myung-Seob; Kim, Hak-Yong

2009-01-01

In the present study, spherical nanoparticles (NPs) containing polyhedral oligosilsesquioxane (POSS) as an inner hydrophobic core and poly(vinyl alcohol) PVA as a hydrophilic outer shell were prepared by dialysis approach. Preparation of amphiphilic POSS-grafted-PVA co-polymer was characterized by 1 H NMR and FT-IR. The results indicated urethane linkage between monoisocyanate group of POSS macromer and the hydroxyl groups of PVA. The dynamic light scattering (DLS) and electrophoretic light scattering (ELS) of the NPs revealed that they have an average hydrodynamic diameter and negative zeta (ζ)-potential of 215 nm and - 161 mV, respectively. Atomic force microscopy (AFM) and bio-transmission electron microscope (BIO-TEM) have shown unagglomerated NPs within a diameter range of 60-90 nm. The prepared NPs were investigated to improve the control release of anticancer drug; paclitaxel as a model drug. Due to drug loading, the hydrodynamic diameter and negative zeta (ζ)-potential have changed to 325 nm and - 14 mV, respectively. In addition, in-vitro drug release experiments were conducted; the obtained results explicated continuous release for over 40 days. However, in case of using pure drug only, the drug completely released within 1 h.

Descriptive and Computer Aided Drawing Perspective on an Unfolded Polyhedral Projection Surface

Science.gov (United States)

Dzwierzynska, Jolanta

2017-10-01

The aim of the herby study is to develop a method of direct and practical mapping of perspective on an unfolded prism polyhedral projection surface. The considered perspective representation is a rectilinear central projection onto a surface composed of several flat elements. In the paper two descriptive methods of drawing perspective are presented: direct and indirect. The graphical mapping of the effects of the representation is realized directly on the unfolded flat projection surface. That is due to the projective and graphical connection between points displayed on the polyhedral background and their counterparts received on the unfolded flat surface. For a significant improvement of the construction of line, analytical algorithms are formulated. They draw a perspective image of a segment of line passing through two different points determined by their coordinates in a spatial coordinate system of axis x, y, z. Compared to other perspective construction methods that use information about points, for computer vision and the computer aided design, our algorithms utilize data about lines, which are applied very often in architectural forms. Possibility of drawing lines in the considered perspective enables drawing an edge perspective image of an architectural object. The application of the changeable base elements of perspective as a horizon height and a station point location enable drawing perspective image from different viewing positions. The analytical algorithms for drawing perspective images are formulated in Mathcad software, however, they can be implemented in the majority of computer graphical packages, which can make drawing perspective more efficient and easier. The representation presented in the paper and the way of its direct mapping on the flat unfolded projection surface can find application in presentation of architectural space in advertisement and art.

Oligomeric models for estimation of polydimethylsiloxane-water partition ratios with COSMO-RS theory: impact of the combinatorial term on absolute error.

Science.gov (United States)

Parnis, J Mark; Mackay, Donald

2017-03-22

A series of 12 oligomeric models for polydimethylsiloxane (PDMS) were evaluated for their effectiveness in estimating the PDMS-water partition ratio, K PDMS-w . Models ranging in size and complexity from the -Si(CH 3 ) 2 -O- model previously published by Goss in 2011 to octadeca-methyloctasiloxane (CH 3 -(Si(CH 3 ) 2 -O-) 8 CH 3 ) were assessed based on their RMS error with 253 experimental measurements of log K PDMS-w from six published works. The lowest RMS error for log K PDMS-w (0.40 in log K) was obtained with the cyclic oligomer, decamethyl-cyclo-penta-siloxane (D5), (-Si(CH 3 ) 2 -O-) 5 , with the mixing-entropy associated combinatorial term included in the chemical potential calculation. The presence or absence of terminal methyl groups on linear oligomer models is shown to have significant impact only for oligomers containing 1 or 2 -Si(CH 3 ) 2 -O- units. Removal of the combinatorial term resulted in a significant increase in the RMS error for most models, with the smallest increase associated with the largest oligomer studied. The importance of inclusion of the combinatorial term in the chemical potential for liquid oligomer models is discussed.

Receptor oligomerization in family B1 of G-protein-coupled receptors

DEFF Research Database (Denmark)

Roed, Sarah Norklit; Ørgaard, Anne; Jørgensen, Rasmus

2012-01-01

, the glucagon receptor, and the receptors for parathyroid hormone (PTHR1 and PTHR2). The dysregulation of several family B1 receptors is involved in diseases, such as diabetes, chronic inflammation, and osteoporosis which underlines the pathophysiological importance of this GPCR subfamily. In spite of this......, investigation of family B1 receptor oligomerization and especially its pharmacological importance is still at an early stage. Even though GPCR oligomerization is a well-established phenomenon, there is a need for more investigations providing a direct link between these interactions and receptor functionality......The superfamily of the seven transmembrane G-protein-coupled receptors (7TM/GPCRs) is the largest family of membrane-associated receptors. GPCRs are involved in the pathophysiology of numerous human diseases, and they constitute an estimated 30-40% of all drug targets. During the last two decades...

Investigation of prototypal MOFs consisting of polyhedral cages with accessible Lewis-acid sites for quinoline synthesis.

Science.gov (United States)

Gao, Wen-Yang; Leng, Kunyue; Cash, Lindsay; Chrzanowski, Matthew; Stackhouse, Chavis A; Sun, Yinyong; Ma, Shengqian

2015-03-21

A series of prototypal metal-organic frameworks (MOFs) consisting of polyhedral cages with accessible Lewis-acid sites, have been systematically investigated for Friedländer annulation reaction, a straightforward approach to synthesizing quinoline and its derivatives. Amongst them MMCF-2 demonstrates significantly enhanced catalytic activity compared with the benchmark MOFs, HKUST-1 and MOF-505, as a result of a high-density of accessible Cu(II) Lewis acid sites and large window size in the cuboctahedral cage-based nanoreactor of MMCF-2.

Physiological relevance of plant 2-Cys peroxiredoxin overoxidation level and oligomerization status.

Science.gov (United States)

Cerveau, Delphine; Ouahrani, Djelloul; Marok, Mohamed Amine; Blanchard, Laurence; Rey, Pascal

2016-01-01

Peroxiredoxins are ubiquitous thioredoxin-dependent peroxidases presumed to display, upon environmental constraints, a chaperone function resulting from a redox-dependent conformational switch. In this work, using biochemical and genetic approaches, we aimed to unravel the factors regulating the redox status and the conformation of the plastidial 2-Cys peroxiredoxin (2-Cys PRX) in plants. In Arabidopsis, we show that in optimal growth conditions, the overoxidation level mainly depends on the availability of thioredoxin-related electron donors, but not on sulfiredoxin, the enzyme reducing the 2-Cys PRX overoxidized form. We also observed that upon various physiological temperature, osmotic and light stress conditions, the overoxidation level and oligomerization status of 2-Cys PRX can moderately vary depending on the constraint type. Further, no major change was noticed regarding protein conformation in water-stressed Arabidopsis, barley and potato plants, whereas species-dependent up- and down-variations in overoxidation were observed. In contrast, both 2-Cys PRX overoxidation and oligomerization were strongly induced during a severe oxidative stress generated by methyl viologen. From these data, revealing that the oligomerization status of plant 2-Cys PRX does not exhibit important variation and is not tightly linked to the protein redox status upon physiologically relevant environmental constraints, the possible in planta functions of 2-Cys PRX are discussed. © 2015 John Wiley & Sons Ltd.

An Investigation of Chemical Landscapes in Aqueous Electrosprays by Tracking Oligomerization of Isoprene

KAUST Repository

Junior, Adair Gallo

2017-12-01

Electrospray ionization mass spectrometry (ESIMS) is widely used to characterize neutral and ionic species in solvents. Typically, electrical, thermal, and pneumatic potentials are applied to create electrosprays from which charged ionic species are ejected for downstream analysis by mass spectrometry. Most recently, ESIMS has been exploited to investigate ambient proton transfer reactions at air-water interfaces in real time. We assessed the validity of these experiments via complementary laboratory experiments. Specifically, we characterized the products of two reaction scenarios via ESIMS and proton nuclear magnetic resonance (1H-NMR): (i) emulsions of pH-adjusted water and isoprene (C5H8) that were mechanically agitated, and (ii) electrosprays of pH-adjusted water that were collided with gas-phase isoprene. Our experiments unambiguously demonstrate that, while isoprene does not oligomerize in emulsions, it does undergo protonation and oligomerization in electrosprays, both with and without pH-adjusted water, confirming that C-C bonds form along myriad high-energy pathways during electrospray ionization. We also compared our experimental results with some quantum mechanics simulations of isoprene molecules interacting with hydronium at different hydration levels (gas versus liquid phase). In agreement with our experiments, the kinetic barriers to protonation and oligomerization of isoprene were inaccessible under ambient conditions. Rather, the gas-phase chemistries during electrospray ionization drove the oligomerization of isoprene. Therefore, we consider that ESIMS could induce artifacts in interfacial reactions. These findings warrant a reassessment of previous reports on tracking chemistries under ambient conditions at liquid-vapor interfaces via ESIMS. Further, we took some high-speed images of electrosprays where it was possible to observe the main characteristics of the phenomena, i.e. Taylor cone, charge separation, and Coulomb fission. Finally, we took

Catalysis of the Oligomerization of O-Phospho-Serine, Aspartic Acid, or Glutamic Acid by Cationic Micelles

Science.gov (United States)

Bohler, Christof; Hill, Aubrey R., Jr.; Orgel, Leslie E.

1996-01-01

Treatment of relatively concentrated aqueous solutions of 0-phospho-serine (50 mM), aspartic acid (100 mM) or glutamic acid (100 mM) with carbonyldiimidazole leads to the formation of an activated intermediate that oligomerizes efficiently. When the concentration of amino acid is reduced tenfold, few long oligomers can be detected. Positively-charged cetyltrimethyl ammonium bromide micelles concentrate the negatively-charged activated intermediates of the amino acids at their surfaces and catalyze efficient oligomerization even from dilute solutions.

Multi-PAS domain-mediated protein oligomerization of PpsR from Rhodobacter sphaeroides

International Nuclear Information System (INIS)

Heintz, Udo; Meinhart, Anton; Winkler, Andreas

2014-01-01

Crystal structures of two truncated variants of the transcription factor PpsR from R. sphaeroides are presented that enabled the phasing of a triple PAS domain construct. Together, these structures reveal the importance of α-helical PAS extensions for multi-PAS domain-mediated protein oligomerization and function. Per–ARNT–Sim (PAS) domains are essential modules of many multi-domain signalling proteins that mediate protein interaction and/or sense environmental stimuli. Frequently, multiple PAS domains are present within single polypeptide chains, where their interplay is required for protein function. Although many isolated PAS domain structures have been reported over the last decades, only a few structures of multi-PAS proteins are known. Therefore, the molecular mechanism of multi-PAS domain-mediated protein oligomerization and function is poorly understood. The transcription factor PpsR from Rhodobacter sphaeroides is such a multi-PAS domain protein that, in addition to its three PAS domains, contains a glutamine-rich linker and a C-terminal helix–turn–helix DNA-binding motif. Here, crystal structures of two N-terminally and C-terminally truncated PpsR variants that comprise a single (PpsR Q-PAS1 ) and two (PpsR N-Q-PAS1 ) PAS domains, respectively, are presented and the multi-step strategy required for the phasing of a triple PAS domain construct (PpsR ΔHTH ) is illustrated. While parts of the biologically relevant dimerization interface can already be observed in the two shorter constructs, the PpsR ΔHTH structure reveals how three PAS domains enable the formation of multiple oligomeric states (dimer, tetramer and octamer), highlighting that not only the PAS cores but also their α-helical extensions are essential for protein oligomerization. The results demonstrate that the long helical glutamine-rich linker of PpsR results from a direct fusion of the N-cap of the PAS1 domain with the C-terminal extension of the N-domain that plays an important

An exact line integral representation of the physical optics scattered field: the case of a perfectly conducting polyhedral structure illuminated by electric Hertzian dipoles

DEFF Research Database (Denmark)

Johansen, Peter M.; Breinbjerg, Olav

1995-01-01

An exact line integral representation of the electric physical optics scattered field is presented. This representation applies to scattering configurations with perfectly electrically conducting polyhedral structures illuminated by a finite number of electric Hertzian dipoles. The positions...

Interference with RUNX1/ETO Leukemogenic Function by Cell-Penetrating Peptides Targeting the NHR2 Oligomerization Domain

Directory of Open Access Journals (Sweden)

Yvonne Bartel

2013-01-01

Full Text Available The leukemia-associated fusion protein RUNX1/ETO is generated by the chromosomal translocation t(8;21 which appears in about 12% of all de novo acute myeloid leukemias (AMLs. Essential for the oncogenic potential of RUNX1/ETO is the oligomerization of the chimeric fusion protein through the nervy homology region 2 (NHR2 within ETO. In previous studies, we have shown that the intracellular expression of peptides containing the NHR2 domain inhibits RUNX1/ETO oligomerization, thereby preventing cell proliferation and inducing differentiation of RUNX1/ETO transformed cells. Here, we show that introduction of a recombinant TAT-NHR2 fusion polypeptide into the RUNX1/ETO growth-dependent myeloid cell line Kasumi-1 results in decreased cell proliferation and increased numbers of apoptotic cells. This effect was highly specific and mediated by binding the TAT-NHR2 peptide to ETO sequences, as TAT-polypeptides containing the oligomerization domain of BCR did not affect cell proliferation or apoptosis in Kasumi-1 cells. Thus, the selective interference with NHR2-mediated oligomerization by peptides represents a challenging but promising strategy for the inhibition of the leukemogenic potential of RUNX1/ETO in t(8;21-positive leukemia.

Forward calculation of gravity and its gradient using polyhedral representation of density interfaces: an application of spherical or ellipsoidal topographic gravity effect

Science.gov (United States)

Zhang, Yi; Chen, Chao

2018-02-01

A density interface modeling method using polyhedral representation is proposed to construct 3-D models of spherical or ellipsoidal interfaces such as the terrain surface of the Earth and applied to forward calculating gravity effect of topography and bathymetry for regional or global applications. The method utilizes triangular facets to fit undulation of the target interface. The model maintains almost equal accuracy and resolution at different locations of the globe. Meanwhile, the exterior gravitational field of the model, including its gravity and gravity gradients, is obtained simultaneously using analytic solutions. Additionally, considering the effect of distant relief, an adaptive computation process is introduced to reduce the computational burden. Then features and errors of the method are analyzed. Subsequently, the method is applied to an area for the ellipsoidal Bouguer shell correction as an example and the result is compared to existing methods, which shows our method provides high accuracy and great computational efficiency. Suggestions for further developments and conclusions are drawn at last.

Protic ionic liquids based on the dimeric and oligomeric anions: [(AcO)xH(x-1)]-.

Science.gov (United States)

Johansson, K M; Izgorodina, E I; Forsyth, M; MacFarlane, D R; Seddon, K R

2008-05-28

We describe a fluidity and conductivity study as a function of composition in N-methylpyrrolidine-acetic acid mixtures. The simple 1 : 1 acid-base mixture appears to form an ionic liquid, but its degree of ionicity is quite low and such liquids are better thought of as poorly dissociated mixtures of acid and base. The composition consisting of 3 moles acetic acid and 1 mole N-methylpyrrolidine is shown to form the highest ionicity mixture in this binary due to the presence of oligomeric anionic species [(AcO)(x)H(x-1)](-) stabilised by hydrogen bonds. These oligomeric species, being weaker bases than the acetate anion, shift the proton transfer equilibrium towards formation of ionic species, thus generating a higher degree of ionicity than is present at the 1 : 1 composition. A Walden plot analysis, thermogravimetric behaviour and proton NMR data, as well as ab initio calculations of the oligomeric species, all support this conclusion.

A piecewise linear finite element discretization of the diffusion equation for arbitrary polyhedral grids

Energy Technology Data Exchange (ETDEWEB)

Bailey, T S; Adams, M L [Texas A M Univ., Dept. of Nuclear Engineering, College Station, TX (United States); Yang, B; Zika, M R [Lawrence Livermore National Lab., Livermore, CA (United States)

2005-07-01

We develop a piecewise linear (PWL) Galerkin finite element spatial discretization for the multi-dimensional radiation diffusion equation. It uses piecewise linear weight and basis functions in the finite element approximation, and it can be applied on arbitrary polygonal (2-dimensional) or polyhedral (3-dimensional) grids. We show that this new PWL method gives solutions comparable to those from Palmer's finite-volume method. However, since the PWL method produces a symmetric positive definite coefficient matrix, it should be substantially more computationally efficient than Palmer's method, which produces an asymmetric matrix. We conclude that the Galerkin PWL method is an attractive option for solving diffusion equations on unstructured grids. (authors)

Spontaneous growth of the polyhedral fullerene crystals in the supersaturated Ni-C(60) composite

Czech Academy of Sciences Publication Activity Database

Vacík, Jiří; Lavrentiev, Vasyl; Michalcová, A.; Abe, H.; Horák, Pavel

2011-01-01

Roč. 509, č. 1 (2011), S380-S383 ISSN 0925-8388. [17th International Symposium on Metastable, Amorphous and Nanostructured Materials (ISMANAM 2010). Zurich, 04.09.2010-09.06.2010] R&D Projects: GA ČR GAP107/11/1856; GA AV ČR(CZ) KAN400480701; GA AV ČR(CZ) IAA400320901; GA AV ČR IAA200480702; GA ČR GA106/09/1264; GA MŠk(CZ) LC06041 Institutional research plan: CEZ:AV0Z10480505; CEZ:AV0Z40320502 Keywords : Nickel * Fullerene s * Phase separation * Polyhedral particles Subject RIV: JJ - Other Materials Impact factor: 2.289, year: 2011

A Free Energy Barrier Caused by the Refolding of an Oligomeric Intermediate Controls the Lag Time of Amyloid Formation by hIAPP.

Science.gov (United States)

Serrano, Arnaldo L; Lomont, Justin P; Tu, Ling-Hsien; Raleigh, Daniel P; Zanni, Martin T

2017-11-22

Transiently populated oligomers formed en route to amyloid fibrils may constitute the most toxic aggregates associated with many amyloid-associated diseases. Most nucleation theories used to describe amyloid aggregation predict low oligomer concentrations and do not take into account free energy costs that may be associated with structural rearrangements between the oligomer and fiber states. We have used isotope labeling and two-dimensional infrared spectroscopy to spectrally resolve an oligomeric intermediate during the aggregation of the human islet amyloid protein (hIAPP or amylin), the protein associated with type II diabetes. A structural rearrangement includes the F 23 G 24 A 25 I 26 L 27 region of hIAPP, which starts from a random coil structure, evolves into ordered β-sheet oligomers containing at least 5 strands, and then partially disorders in the fibril structure. The supercritical concentration is measured to be between 150 and 250 μM, which is the thermodynamic parameter that sets the free energy of the oligomers. A 3-state kinetic model fits the experimental data, but only if it includes a concentration independent free energy barrier >3 kcal/mol that represents the free energy cost of refolding the oligomeric intermediate into the structure of the amyloid fibril; i.e., "oligomer activation" is required. The barrier creates a transition state in the free energy landscape that slows fibril formation and creates a stable population of oligomers during the lag phase, even at concentrations below the supercritical concentration. Largely missing in current kinetic models is a link between structure and kinetics. Our experiments and modeling provide evidence that protein structural rearrangements during aggregation impact the populations and kinetics of toxic oligomeric species.

Arc is a flexible modular protein capable of reversible self-oligomerization

Science.gov (United States)

Myrum, Craig; Baumann, Anne; Bustad, Helene J.; Flydal, Marte Innselset; Mariaule, Vincent; Alvira, Sara; Cuéllar, Jorge; Haavik, Jan; Soulé, Jonathan; Valpuesta, José Maria; Márquez, José Antonio; Martinez, Aurora; Bramham, Clive R.

2015-01-01

The immediate early gene product Arc (activity-regulated cytoskeleton-associated protein) is posited as a master regulator of long-term synaptic plasticity and memory. However, the physicochemical and structural properties of Arc have not been elucidated. In the present study, we expressed and purified recombinant human Arc (hArc) and performed the first biochemical and biophysical analysis of hArc's structure and stability. Limited proteolysis assays and MS analysis indicate that hArc has two major domains on either side of a central more disordered linker region, consistent with in silico structure predictions. hArc's secondary structure was estimated using CD, and stability was analysed by CD-monitored thermal denaturation and differential scanning fluorimetry (DSF). Oligomerization states under different conditions were studied by dynamic light scattering (DLS) and visualized by AFM and EM. Biophysical analyses show that hArc is a modular protein with defined secondary structure and loose tertiary structure. hArc appears to be pyramid-shaped as a monomer and is capable of reversible self-association, forming large soluble oligomers. The N-terminal domain of hArc is highly basic, which may promote interaction with cytoskeletal structures or other polyanionic surfaces, whereas the C-terminal domain is acidic and stabilized by ionic conditions that promote oligomerization. Upon binding of presenilin-1 (PS1) peptide, hArc undergoes a large structural change. A non-synonymous genetic variant of hArc (V231G) showed properties similar to the wild-type (WT) protein. We conclude that hArc is a flexible multi-domain protein that exists in monomeric and oligomeric forms, compatible with a diverse, hub-like role in plasticity-related processes. PMID:25748042

Chondrogenic potential of bone marrow–derived mesenchymal stem cells on a novel, auricular-shaped, nanocomposite scaffold

Directory of Open Access Journals (Sweden)

Kavi H Patel

2013-12-01

Full Text Available Reconstruction of the human auricle remains a challenge to plastic surgeons, and current approaches are not ideal. Tissue engineering provides a promising alternative. This study aims to evaluate the chondrogenic potential of bone marrow–derived mesenchymal stem cells on a novel, auricular-shaped polymer. The proposed polyhedral oligomeric silsesquioxane-modified poly(hexanolactone/carbonateurethane/urea nanocomposite polymer has already been transplanted in patients as the world’s first synthetic trachea, tear duct and vascular bypass graft. The nanocomposite scaffold was fabricated via a coagulation/salt-leaching method and shaped into an auricle. Adult bone marrow–derived mesenchymal stem cells were isolated, cultured and seeded onto the scaffold. On day 21, samples were sent for scanning electron microscopy, histology and immunofluorescence to assess for neocartilage formation. Cell viability assay confirmed cytocompatability and normal patterns of cellular growth at 7, 14 and 21 days after culture. This study demonstrates the potential of a novel polyhedral oligomeric silsesquioxane-modified poly(hexanolactone/carbonateurethane/urea scaffold for culturing bone marrow–derived mesenchymal stem cells in chondrogenic medium to produce an auricular-shaped construct. This is supported by scanning electron microscopy, histological and immunofluorescence analysis revealing markers of chondrogenesis including collagen type II, SOX-9, glycosaminoglycan and elastin. To the best of our knowledge, this is the first report of stem cell application on an auricular-shaped scaffold for tissue engineering purposes. Although many obstacles remain in producing a functional auricle, this is a promising step forward.

A Minimum Path Algorithm Among 3D-Polyhedral Objects

Science.gov (United States)

Yeltekin, Aysin

1989-03-01

In this work we introduce a minimum path theorem for 3D case. We also develop an algorithm based on the theorem we prove. The algorithm will be implemented on the software package we develop using C language. The theorem we introduce states that; "Given the initial point I, final point F and S be the set of finite number of static obstacles then an optimal path P from I to F, such that PA S = 0 is composed of straight line segments which are perpendicular to the edge segments of the objects." We prove the theorem as well as we develop the following algorithm depending on the theorem to find the minimum path among 3D-polyhedral objects. The algorithm generates the point Qi on edge ei such that at Qi one can find the line which is perpendicular to the edge and the IF line. The algorithm iteratively provides a new set of initial points from Qi and exploits all possible paths. Then the algorithm chooses the minimum path among the possible ones. The flowchart of the program as well as the examination of its numerical properties are included.

DC-SIGN neck domain is a pH-sensor controlling oligomerization: SAXS and hydrodynamic studies of extracellular domain.

Science.gov (United States)

Tabarani, Georges; Thépaut, Michel; Stroebel, David; Ebel, Christine; Vivès, Corinne; Vachette, Patrice; Durand, Dominique; Fieschi, Franck

2009-08-07

DC-SIGN is a C-type lectin receptor of dendritic cells and is involved in the early stages of numerous infectious diseases. DC-SIGN is organized into a tetramer enabling multivalent interaction with pathogens. Once formed, the DC-SIGN-pathogen complex can be internalized into compartments of increasing acidity. We have studied the pH dependence of the oligomerization state and conformation of the entire extracellular domain and neck region. We present evidence for equilibrium between the monomeric and tetrameric states of the extracellular domain, which exhibits a marked dependence with respect to both pH and ionic strength. Using solution x-ray scattering we have obtained a molecular envelope of the extracellular domain in which a model has been built. Our results highlight the central role of the neck domain in the pH-sensitive control of the oligomerization state, in the extended conformation of the protein, and in carbohydrate recognition domain organization and presentation. This work opens new insight into the molecular mechanism of ligand release and points to new avenues to block the first step of this important infection pathway.

A piecewise linear finite element discretization of the diffusion equation for arbitrary polyhedral grids

Energy Technology Data Exchange (ETDEWEB)

Bailey, T.S.; Adams, M.L. [Texas A M Univ., Dept. of Nuclear Engineering, College Station, TX (United States); Yang, B.; Zika, M.R. [Lawrence Livermore National Lab., Livermore, CA (United States)

2005-07-01

We develop a piecewise linear (PWL) Galerkin finite element spatial discretization for the multi-dimensional radiation diffusion equation. It uses piecewise linear weight and basis functions in the finite element approximation, and it can be applied on arbitrary polygonal (2-dimensional) or polyhedral (3-dimensional) grids. We show that this new PWL method gives solutions comparable to those from Palmer's finite-volume method. However, since the PWL method produces a symmetric positive definite coefficient matrix, it should be substantially more computationally efficient than Palmer's method, which produces an asymmetric matrix. We conclude that the Galerkin PWL method is an attractive option for solving diffusion equations on unstructured grids. (authors)

Oligomerization and polymerization of the filovirus matrix protein VP40

International Nuclear Information System (INIS)

Timmins, Joanna; Schoehn, Guy; Kohlhaas, Christine; Klenk, Hans-Dieter; Ruigrok, Rob W.H.; Weissenhorn, Winfried

2003-01-01

The matrix protein VP40 from Ebola virus plays an important role in the assembly process of virus particles by interacting with cellular factors, cellular membranes, and the ribonuclearprotein particle complex. Here we show that the N-terminal domain of VP40 folds into a mixture of two different oligomeric states in vitro, namely hexameric and octameric ringlike structures, as detected by gel filtration chromatography, chemical cross-linking, and electron microscopy. Octamer formation depends largely on the interaction with nucleic acids, which in turn confers in vitro SDS resistance. Refolding experiments with a nucleic acid free N-terminal domain preparation reveal a mostly dimeric form of VP40, which is transformed into an SDS resistant octamer upon incubation with E. coli nucleic acids. In addition, we demonstrate that the N-terminal domain of Marburg virus VP40 also folds into ringlike structures, similar to Ebola virus VP40. Interestingly, Marburg virus VP40 rings reveal a high tendency to polymerize into rods composed of stacked rings. These results may suggest distinct roles for different oligomeric forms of VP40 in the filovirus life cycle

Epoxy networks reinforced with polyhedral oligomeric silsesquioxanes (POSS). 1. Structure and morphology

Czech Academy of Sciences Publication Activity Database

Matějka, Libor; Strachota, Adam; Pleštil, Josef; Whelan, P.; Steinhart, Miloš; Šlouf, Miroslav

2004-01-01

Roč. 37, č. 25 (2004), s. 9449-9456 ISSN 0024-9297 R&D Projects: GA AV ČR IAA4050008 Grant - others:European Community's Human Potential Programme(XE) HPRN/CT-2002-00306 Institutional research plan: CEZ:AV0Z4050913 Keywords : POSS * epoxy network * structure of nanocomposites Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.898, year: 2004

Receptor Oligomerization as a Process Modulating Cellular Semiotics

DEFF Research Database (Denmark)

Giorgi, Franco; Bruni, Luis Emilio; Maggio, Roberto

2010-01-01

be another level of quality control that may help maintaining GPCRs rather stable throughout evolution. We propose here receptor oligomerization to be a basic molecular mechanism controlling GPCRs redundancy in many different cell types, and the plasma membrane as the first hierarchical cell structure...... at which selective categorical sensing may occur. Categorical sensing can be seen as the cellular capacity for identifying and ordering complex patterns of mixed signals out of a contextual matrix, i.e., the recognition of meaningful patterns out of ubiquitous signals. In this context, redundancy...

Effects of Bentonite on p-Methoxybenzyl Acetate: A Theoretical Model for Oligomerization via an Electrophilic-Substitution Mechanism

Directory of Open Access Journals (Sweden)

Manuel Salmón

2011-02-01

Full Text Available Tonsil Actisil FF, a commercial bentonitic clay, promotes the formation of a series of electrophilic-aromatic-substitution products from para-methoxybenzyl acetate in carbon disulfide. The molecules obtained correspond to linear isomeric dimers, trimers, tetramers and a pentamer, according to their spectroscopic data. A clear indication of the title mechanistic pathway for the oligomerization growth was obtained from the analysis of a set of computational-chemistry calculations using the density-functional-theory level B3LYP/6-311++G(d,p. The corresponding conclusions were based on the computed dipole moments, the HOMO/LUMO distributions, and a natural-populations analysis of the studied molecules.

An Intramolecular Salt Bridge in Bacillus thuringiensis Cry4Ba Toxin Is Involved in the Stability of Helix α-3, Which Is Needed for Oligomerization and Insecticidal Activity.

Science.gov (United States)

Pacheco, Sabino; Gómez, Isabel; Sánchez, Jorge; García-Gómez, Blanca-Ines; Soberón, Mario; Bravo, Alejandra

2017-10-15

Bacillus thuringiensis three-domain Cry toxins kill insects by forming pores in the apical membrane of larval midgut cells. Oligomerization of the toxin is an important step for pore formation. Domain I helix α-3 participates in toxin oligomerization. Here we identify an intramolecular salt bridge within helix α-3 of Cry4Ba (D111-K115) that is conserved in many members of the family of three-domain Cry toxins. Single point mutations such as D111K or K115D resulted in proteins severely affected in toxicity. These mutants were also altered in oligomerization, and the mutant K115D was more sensitive to protease digestion. The double point mutant with reversed charges, D111K-K115D, recovered both oligomerization and toxicity, suggesting that this salt bridge is highly important for conservation of the structure of helix α-3 and necessary to promote the correct oligomerization of the toxin. IMPORTANCE Domain I has been shown to be involved in oligomerization through helix α-3 in different Cry toxins, and mutations affecting oligomerization also elicit changes in toxicity. The three-dimensional structure of the Cry4Ba toxin reveals an intramolecular salt bridge in helix α-3 of domain I. Mutations that disrupt this salt bridge resulted in changes in Cry4Ba oligomerization and toxicity, while a double point reciprocal mutation that restored the salt bridge resulted in recovery of toxin oligomerization and toxicity. These data highlight the role of oligomer formation as a key step in Cry4Ba toxicity. Copyright © 2017 American Society for Microbiology.

Oligomerization of a Glucagon-like Peptide 1 Analog: Bridging Experiment and Simulations

DEFF Research Database (Denmark)

Frederiksen, Tine Maja; Sønderby, Pernille; Ryberg, Line A.

2015-01-01

The glucagon-like peptide 1 (GLP-1) analog, liraglutide, is a GLP-1 agonist and is used in the treatment of type-2 diabetes mellitus and obesity. From a pharmaceutical perspective, it is important to know the oligomerization state of liraglutide with respect to stability. Compared to GLP-1...

Development of highly open polyhedral networks from vitreous carbon for orthopaedic applications

Science.gov (United States)

Güiza-Argüello, V.; Bayona-Becerra, M.; Cruz-Orellana, S.; Córdoba-Tuta, E.

2017-01-01

Highly open polyhedral networks were fabricated using an economical and environmentally friendly template route. Recycled cellulose foams were impregnated with a sucrose resin and then pyrolyzed in order to produce reticulated vitreous carbon foams with morphological features that closely resemble trabecular bone. Also, cell sizes ~1mm were achieved, a trait that will allow the mechanical reinforcement of such scaffolds using a biomaterial coating without compromising the pore size that favors osteoblast cell infiltration and growth (200-500µm). Moreover, initial studies showed that carbonization conditions have an effect on the mechanical properties of the synthesized foams and, therefore, such process parameters could be further evaluated towards the enhancement of the mechanical resistance of the scaffolds. The materials developed here are visualized as the porous component of a synthetic bone graft with features that could help overcome the current limitations associated with the medical treatments used for bone defect repair.

Influence of oligomeric resins on traction and rolling resistance of silica tire treads

NARCIS (Netherlands)

Vleugels, N.; Pille-Wolf, W.; Dierkes, Wilma K.; Noordermeer, Jacobus W.M.

2016-01-01

This study concerns the silica-reinforcement of synthetic rubber compounds for passenger tire treads with the objective to gain insight into the beneficial effects of oligomeric resins, derived from natural and synthetic monomers, on the major tire performance factors: rolling resistance and (wet)

Influence of oligomeric resins on traction and rolling resistance of silica tire treads

NARCIS (Netherlands)

Vleugels, N.; Pille-Wolf, W.; Dierkes, Wilma K.; Noordermeer, Jacobus W.M.

2013-01-01

This study concerns the silica-reinforcement of synthetic rubber compounds for passenger tire treads with the objective to gain insight into the beneficial effects of oligomeric resins, derived from natural and synthetic monomers, on the major tire performance factors: Rolling Resistance and (Wet)

Hydration effect on the electronic transport properties of oligomeric phenylene ethynylene molecular junctions

International Nuclear Information System (INIS)

Zong-Liang, Li; Huai-Zhi, Li; Yong, Ma; Guang-Ping, Zhang; Chuan-Kui, Wang

2010-01-01

A first-principles computational method based on the hybrid density functional theory is developed to simulate the electronic transport properties of oligomeric phenylene ethynylene molecular junctions with H 2 O molecules accumulated in the vicinity as recently reported by Na et al. [Nanotechnology 18 424001 (2007)]. The numerical results show that the hydrogen bonds between the oxygen atoms of the oligomeric phenylene ethynylene molecule and H 2 O molecules result in the localisation of the molecular orbitals and lead to the lower transition peaks. The H 2 O molecular chains accumulated in the vicinity of the molecular junction can not only change the electronic structure of the molecular junctions, but also open additional electronic transport pathways. The obvious influence of H 2 O molecules on the electronic structure of the molecular junction and its electronic transport properties is thus demonstrated. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

The modification of nanocomposite hybrid polymer surfaces by exposure to oxygen containing plasmas

Science.gov (United States)

Figueiredo, Ashley; Zimmermann, Katherine; Augustine, Brian; Hughes, Chris; Chusuei, Charles

2006-11-01

The wetting properties of the surfaces of the nanocomposite hybrid polymer poly[(propylmethacryl-heptaisobutyl- polyhedral oligomeric silsequioxane)-co-(methylmethacrylate)] (POSS-PMMA)has been studied before and after exposure to plasmas containing oxygen. The contact angle of water droplets on the surface showed a substantial decrease after plasma exposure indicating an increase in the hydrophilicity of the surface. A model was developed in which the plasma preferentially removed organic material including both the PMMA backbone and isobutyl groups from the corners of the POSS cages leaving behind a surface characterized by the silicon oxide-like POSS material. Measurements of surface concentrations of oxygen, silicon, and carbon by x-ray photoelectron spectroscopy (XPS) showed an increase in the amount of oxygen and silicon compared to carbon and the appropriate chemical shifts were observed in the XPS data to support the model of Si-O enrichment on the surface. Variable angle spectroscopic ellipsometry (VASE) and atomic force microscopy (AFM) measurements also supported the model and these results will be presented.

Free-energy landscape of protein oligomerization from atomistic simulations

Science.gov (United States)

Barducci, Alessandro; Bonomi, Massimiliano; Prakash, Meher K.; Parrinello, Michele

2013-01-01

In the realm of protein–protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of the driving molecular interactions and the transient intermediate species. The latter are often short-lived and thus remain elusive to most experimental investigations. Molecular simulations provide a unique tool to shed light onto these complex processes complementing experimental data. Here we combine advanced sampling techniques, such as metadynamics and parallel tempering, to characterize the oligomerization landscape of fibritin foldon domain. This system is an evolutionarily optimized trimerization motif that represents an ideal model for experimental and computational mechanistic studies. Our results are fully consistent with previous experimental nuclear magnetic resonance and kinetic data, but they provide a unique insight into fibritin foldon assembly. In particular, our simulations unveil the role of nonspecific interactions and suggest that an interplay between thermodynamic bias toward native structure and residual conformational disorder may provide a kinetic advantage. PMID:24248370

Mechanics of the mannitol transporter from Escherichia coli : substrate-probing and oligomeric structure

NARCIS (Netherlands)

Veldhuis, Gertjan

2006-01-01

Gertjan Veldhuis bestudeerde de mannitoltransporter van Escherichia coli, EnzymeIImtl (EIImtl), om meer inzicht te krijgen in het bindingsmechanisme en de oligomere toestand van dit membraaneiwit. Hij concludeerde onder andere dat dimeer EIImtl één mannitol bindt, de dimeer zeer stabiel is en dat

The Agrobacterium tumefaciens Transcription Factor BlcR Is Regulated via Oligomerization

Energy Technology Data Exchange (ETDEWEB)

Pan, Yi; Fiscus, Valena; Meng, Wuyi; Zheng, Zhida; Zhang, Lian-Hui; Fuqua, Clay; Chen, Lingling (IMCB-Singapore); (Indiana)

2012-02-08

The Agrobacterium tumefaciens BlcR is a member of the emerging isocitrate lyase transcription regulators that negatively regulates metabolism of {gamma}-butyrolactone, and its repressing function is relieved by succinate semialdehyde (SSA). Our crystal structure showed that BlcR folded into the DNA- and SSA-binding domains and dimerized via the DNA-binding domains. Mutational analysis identified residues, including Phe{sup 147}, that are important for SSA association; BlcR{sup F147A} existed as tetramer. Two BlcR dimers bound to target DNA and in a cooperative manner, and the distance between the two BlcR-binding sequences in DNA was critical for BlcR-DNA association. Tetrameric BlcR{sup F147A} retained DNA binding activity, and importantly, this activity was not affected by the distance separating the BlcR-binding sequences in DNA. SSA did not dissociate tetrameric BlcR{sup F147A} or BlcR{sup F147A}-DNA. As well as in the SSA-binding site, Phe{sup 147} is located in a structurally flexible loop that may be involved in BlcR oligomerization. We propose that SSA regulates BlcR DNA-binding function via oligomerization.

Single-molecule diffusometry reveals the nucleotide-dependent oligomerization pathways of Nicotiana tabacum Rubisco activase

Science.gov (United States)

Wang, Quan; Serban, Andrew J.; Wachter, Rebekka M.; Moerner, W. E.

2018-03-01

Oligomerization plays an important role in the function of many proteins, but a quantitative picture of the oligomer distribution has been difficult to obtain using existing techniques. Here we describe a method that combines sub-stoichiometric labeling and recently developed single-molecule diffusometry to measure the size distribution of oligomers under equilibrium conditions in solution, one molecule at a time. We use this technique to characterize the oligomerization behavior of Nicotiana tabacum (Nt) Rubisco activase (Nt-Rca), a chaperone-like AAA-plus ATPase essential in regulating carbon fixation during photosynthesis. We directly observed monomers, dimers, and a tetramer/hexamer mixture and extracted their fractional abundance as a function of protein concentration. We show that the oligomerization pathway of Nt-Rca is nucleotide dependent: ATPγS binding strongly promotes tetramer/hexamer formation from dimers and results in a preferred tetramer/hexamer population for concentrations in the 1-10 μM range. Furthermore, we directly observed dynamic assembly and disassembly processes of single complexes in real time and from there estimated the rate of subunit exchange to be ˜0.1 s-1 with ATPγS. On the other hand, ADP binding destabilizes Rca complexes by enhancing the rate of subunit exchange by >2 fold. These observations provide a quantitative starting point to elucidate the structure-function relations of Nt-Rca complexes. We envision the method to fill a critical gap in defining and quantifying protein assembly pathways in the small-oligomer regime.

The effects of oligomerization on Saccharomyces cerevisiae Mcm4/6/7 function

Directory of Open Access Journals (Sweden)

Davey Megan J

2010-09-01

Full Text Available Abstract Background Minichromosome maintenance proteins (Mcm 2, 3, 4, 5, 6 and 7 are related by sequence and form a variety of complexes that unwind DNA, including Mcm4/6/7. A Mcm4/6/7 trimer forms one half of the Mcm2-7 hexameric ring and can be thought of as the catalytic core of Mcm2-7, the replicative helicase in eukaryotic cells. Oligomeric analysis of Mcm4/6/7 suggests that it forms a hexamer containing two Mcm4/6/7 trimers, however, under certain conditions trimeric Mcm4/6/7 has also been observed. The functional significance of the different Mcm4/6/7 oligomeric states has not been assessed. The results of such an assessment would have implications for studies of both Mcm4/6/7 and Mcm2-7. Results Here, we show that Saccharomyces cerevisiae Mcm4/6/7 reconstituted from individual subunits exists in an equilibrium of oligomeric forms in which smaller oligomers predominate in the absence of ATP. In addition, we found that ATP, which is required for Mcm4/6/7 activity, shifts the equilibrium towards larger oligomers, likely hexamers of Mcm4/6/7. ATPγS and to a lesser extent ADP also shift the equilibrium towards hexamers. Study of Mcm4/6/7 complexes containing mutations that interfere with the formation of inter-subunit ATP sites (arginine finger mutants indicates that full activity of Mcm4/6/7 requires all of its ATP sites, which are formed in a hexamer and not a trimer. In keeping with this observation, Mcm4/6/7 binds DNA as a hexamer. Conclusions The minimal functional unit of Mcm4/6/7 is a hexamer. One of the roles of ATP binding by Mcm4/6/7 may be to stabilize formation of hexamers.

Direct Evidence of Intrinsic Blue Fluorescence from Oligomeric Interfaces of Human Serum Albumin.

Science.gov (United States)

Bhattacharya, Arpan; Bhowmik, Soumitra; Singh, Amit K; Kodgire, Prashant; Das, Apurba K; Mukherjee, Tushar Kanti

2017-10-10

The molecular origin behind the concentration-dependent intrinsic blue fluorescence of human serum albumin (HSA) is not known yet. This unusual blue fluorescence is believed to be a characteristic feature of amyloid-like fibrils of protein/peptide and originates due to the delocalization of peptide bond electrons through the extended hydrogen bond networks of cross-β-sheet structure. Herein, by combining the results of spectroscopy, size exclusion chromatography, native gel electrophoresis, and confocal microscopy, we have shown that the intrinsic blue fluorescence of HSA exclusively originates from oligomeric interfaces devoid of any amyloid-like fibrillar structure. Our study suggests that this low energy fluorescence band is not due to any particular residue/sequence, but rather it is a common feature of self-assembled peptide bonds. The present findings of intrinsic blue fluorescence from oligomeric interfaces pave the way for future applications of this unique visual phenomenon for early stage detection of various protein aggregation related human diseases.

Pro-inflammatory delipidizing cytokines reduce adiponectin secretion from human adipocytes without affecting adiponectin oligomerization

NARCIS (Netherlands)

Simons, Peter J.; van den Pangaart, Petra S.; Aerts, Johannes M. F. G.; Boon, Louis

2007-01-01

Adiponectin and, especially, its oligomeric complex composition have been suggested to be critical in determining insulin sensitivity. Pro-inflammatory cytokines play an important role in the development of insulin resistance in obesity and associated diseases. Therefore, we investigated the effect

Detection of Amyloid Beta (Aβ) Oligomeric Composition Using Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI MS)

Science.gov (United States)

Wang, Jasmine S.-H.; Whitehead, Shawn N.; Yeung, Ken K.-C.

2018-02-01

The use of MALDI MS as a fast and direct method to detect the Aβ oligomers of different masses is examined in this paper. Experimental results suggest that Aβ oligomers are ionized and detected as singly charged ions, and thus, the resulting mass spectrum directly reports the oligomer size distribution. Validation experiments were performed to verify the MS data against artifacts. Mass spectra collected from modified Aβ peptides with different propensities for aggregation were compared. Generally, the relative intensities of multimers were higher from samples where oligomerization was expected to be more favorable, and vice versa. MALDI MS was also able to detect the differences in oligomeric composition before and after the incubation/oligomerization step. Such differences in sample composition were also independently confirmed with an in vitro Aβ toxicity study on primary rat cortical neurons. An additional validation was accomplished through removal of oligomers from the sample using molecular weight cutoff filters; the resulting MS data correctly reflected the removal at the expected cutoff points. The results collectively validated the ability of MALDI MS to assess the monomeric/multimeric composition of Aβ samples. [Figure not available: see fulltext.

Purification, crystallization and preliminary crystallographic analysis of Est-Y29: a novel oligomeric β-lactamase

International Nuclear Information System (INIS)

Kim, SeungBum; Joo, Sangbum; Yoon, Sangyoung; Kim, Sungsoo; Moon, Jongkook; Ryu, Yeonwoo; Kim, Kyeong Kyu; Kim, T. Doohun

2009-01-01

Est-Y29, a novel oligomeric class C β-lactamase from a metagenomic library, was crystallized in space group I4 1 and diffraction data were collected to 1.49 Å resolution. β-Lactam antibiotics such as penicillins and cephalosporins have a four-atom ring as a common element in their structure. The β-lactamases, which catalyze the inactivation of these antibiotics, are of great interest because of their high incidence in pathogenic bacteria. A novel oligomeric class C β-lactamase (Est-Y29) from a metagenomic library was expressed, purified and crystallized. The recombinant protein was expressed in Escherichia coli with an N-terminal 6×His tag and purified to homogeneity. EstY-29 was crystallized and X-ray intensity data were collected to 1.49 Å resolution using synchrotron radiation

Inhibiting α-synuclein oligomerization by stable cell-penetrating β-synuclein fragments recovers phenotype of Parkinson's disease model flies.

Directory of Open Access Journals (Sweden)

Ronit Shaltiel-Karyo

Full Text Available The intracellular oligomerization of α-synuclein is associated with Parkinson's disease and appears to be an important target for disease-modifying treatment. Yet, to date, there is no specific inhibitor for this aggregation process. Using unbiased systematic peptide array analysis, we identified molecular interaction domains within the β-synuclein polypeptide that specifically binds α-synuclein. Adding such peptide fragments to α-synuclein significantly reduced both amyloid fibrils and soluble oligomer formation in vitro. A retro-inverso analogue of the best peptide inhibitor was designed to develop the identified molecular recognition module into a drug candidate. While this peptide shows indistinguishable activity as compared to the native peptide, it is stable in mouse serum and penetrates α-synuclein over-expressing cells. The interaction interface between the D-amino acid peptide and α-synuclein was mapped by Nuclear Magnetic Resonance spectroscopy. Finally, administering the retro-inverso peptide to a Drosophila model expressing mutant A53T α-synuclein in the nervous system, resulted in a significant recovery of the behavioral abnormalities of the treated flies and in a significant reduction in α-synuclein accumulation in the brains of the flies. The engineered retro-inverso peptide can serve as a lead for developing a novel class of therapeutic agents to treat Parkinson's disease.

Multicoil2: predicting coiled coils and their oligomerization states from sequence in the twilight zone.

Directory of Open Access Journals (Sweden)

Jason Trigg

Full Text Available The alpha-helical coiled coil can adopt a variety of topologies, among the most common of which are parallel and antiparallel dimers and trimers. We present Multicoil2, an algorithm that predicts both the location and oligomerization state (two versus three helices of coiled coils in protein sequences. Multicoil2 combines the pairwise correlations of the previous Multicoil method with the flexibility of Hidden Markov Models (HMMs in a Markov Random Field (MRF. The resulting algorithm integrates sequence features, including pairwise interactions, through multinomial logistic regression to devise an optimized scoring function for distinguishing dimer, trimer and non-coiled-coil oligomerization states; this scoring function is used to produce Markov Random Field potentials that incorporate pairwise correlations localized in sequence. Multicoil2 significantly improves both coiled-coil detection and dimer versus trimer state prediction over the original Multicoil algorithm retrained on a newly-constructed database of coiled-coil sequences. The new database, comprised of 2,105 sequences containing 124,088 residues, includes reliable structural annotations based on experimental data in the literature. Notably, the enhanced performance of Multicoil2 is evident when tested in stringent leave-family-out cross-validation on the new database, reflecting expected performance on challenging new prediction targets that have minimal sequence similarity to known coiled-coil families. The Multicoil2 program and training database are available for download from http://multicoil2.csail.mit.edu.

Both Ca2+ and Zn2+ are essential for S100A12 protein oligomerization and function

Directory of Open Access Journals (Sweden)

Shekhtman Alexander

2009-04-01

Full Text Available Abstract Background Human S100A12 is a member of the S100 family of EF-hand calcium-modulated proteins that are associated with many diseases including cancer, chronic inflammation and neurological disorders. S100A12 is an important factor in host/parasite defenses and in the inflammatory response. Like several other S100 proteins, it binds zinc and copper in addition to calcium. Mechanisms of zinc regulation have been proposed for a number of S100 proteins e.g. S100B, S100A2, S100A7, S100A8/9. The interaction of S100 proteins with their targets is strongly dependent on cellular microenvironment. Results The aim of the study was to explore the factors that influence S100A12 oligomerization and target interaction. A comprehensive series of biochemical and biophysical experiments indicated that changes in the concentration of calcium and zinc led to changes in the oligomeric state of S100A12. Surface plasmon resonance confirmed that the presence of both calcium and zinc is essential for the interaction of S100A12 with one of its extracellular targets, RAGE – the Receptor for Advanced Glycation End products. By using a single-molecule approach we have shown that the presence of zinc in tissue culture medium favors both the oligomerization of exogenous S100A12 protein and its interaction with targets on the cell surface. Conclusion We have shown that oligomerization and target recognition by S100A12 is regulated by both zinc and calcium. Our present work highlighted the potential role of calcium-binding S100 proteins in zinc metabolism and, in particular, the role of S100A12 in the cross talk between zinc and calcium in cell signaling.

Design of a minimal protein oligomerization domain by a structural approach.

Science.gov (United States)

Burkhard, P; Meier, M; Lustig, A

2000-12-01

Because of the simplicity and regularity of the alpha-helical coiled coil relative to other structural motifs, it can be conveniently used to clarify the molecular interactions responsible for protein folding and stability. Here we describe the de novo design and characterization of a two heptad-repeat peptide stabilized by a complex network of inter- and intrahelical salt bridges. Circular dichroism spectroscopy and analytical ultracentrifugation show that this peptide is highly alpha-helical and 100% dimeric tinder physiological buffer conditions. Interestingly, the peptide was shown to switch its oligomerization state from a dimer to a trimer upon increasing ionic strength. The correctness of the rational design principles used here is supported by details of the atomic structure of the peptide deduced from X-ray crystallography. The structure of the peptide shows that it is not a molten globule but assumes a unique, native-like conformation. This de novo peptide thus represents an attractive model system for the design of a molecular recognition system.

Determination of Mechanical and Surface Properties of Semicrystalline Polyhedral Oligomeric Silsequioxane (POSS) Nanocomposites

National Research Council Canada - National Science Library

Moody, Laura E; Marchant, Darrell; Grabow, Wade W; Lee, Andre Y; Mabry, Joseph M

2005-01-01

.... This study examines the ability of POSS to improve the mechanical and surface properties of three semicrystalline polymers, fluorinated ethylene-propylene (FEP), poly(vinylidene fluoride) (PVDF...

Determination of Mechanical and Surface Properties of Semicrystalline Polyhedral Oligomeric Silsesquioxane (POSS) Nanocomposites

National Research Council Canada - National Science Library

Moody, Laura E; Marchant, Darrell; Grabow, Wade W; Lee, Andre Y; Mabry, Joseph M

2005-01-01

INTRODUCTION: (1) Nanomodification of semicrystalline polymers -- unequalled thermal, mechanical and surface properties at low volume fractions that cannot be obtained using conventional fillers; (2...

Morphology and Viscoelastic Properties of Polystyrene Blended with Fully Condensed Polyhedral Oligomeric Silsesquioxanes

National Research Council Canada - National Science Library

Namani, Madhu; Geng, Hai-Ping; Lee, Andre; Blanski, Rusty L

2004-01-01

.... Experiments were performed using a nearly-monodisperse molecular weight polystyrene (PS) blended with varying amounts of two fully condensed POSS molecules surrounded with phenethyl and styrenyl groups...

Morphology and Viscoelastic Properties of Polystyrene Blended with Fully Condensed Polyhedral Oligomeric Silsesquioxanes

Science.gov (United States)

2004-10-18

NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR( S ) Madhu Namani ; Hai-Ping Geng; Andre Lee; Rusty Blanski 5d. PROJECT NUMBER 4847 5e...TASK NUMBER 0249 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME( S ) AND ADDRESS(ES) Air Force Research Laboratory (AFMC),AFRL/PRSM,10 E...Saturn Blvd.,Edwards AFB,CA,93524-7680 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING AGENCY NAME( S ) AND ADDRESS(ES) 10. SPONSOR

Crystal structures from the Plasmodium peroxiredoxins: new insights into oligomerization and product binding.

Science.gov (United States)

Qiu, Wei; Dong, Aiping; Pizarro, Juan C; Botchkarsev, Alexei; Min, Jinrong; Wernimont, Amy K; Hills, Tanya; Hui, Raymond; Artz, Jennifer D

2012-03-19

Plasmodium falciparum is the protozoan parasite primarily responsible for more than one million malarial deaths, annually, and is developing resistance to current therapies. Throughout its lifespan, the parasite is subjected to oxidative attack, so Plasmodium antioxidant defences are essential for its survival and are targets for disease control. To further understand the molecular aspects of the Plasmodium redox system, we solved 4 structures of Plasmodium peroxiredoxins (Prx). Our study has confirmed PvTrx-Px1 to be a hydrogen peroxide (H2O2)-sensitive peroxiredoxin. We have identified and characterized the novel toroid octameric oligomer of PyTrx-Px1, which may be attributed to the interplay of several factors including: (1) the orientation of the conserved surface/buried arginine of the NNLA(I/L)GRS-loop; and (2) the C-terminal tail positioning (also associated with the aforementioned conserved loop) which facilitates the intermolecular hydrogen bond between dimers (in an A-C fashion). In addition, a notable feature of the disulfide bonds in some of the Prx crystal structures is discussed. Finally, insight into the latter stages of the peroxiredoxin reaction coordinate is gained. Our structure of PyPrx6 is not only in the sulfinic acid (RSO2H) form, but it is also with glycerol bound in a way (not previously observed) indicative of product binding. The structural characterization of Plasmodium peroxiredoxins provided herein provides insight into their oligomerization and product binding which may facilitate the targeting of these antioxidant defences. Although the structural basis for the octameric oligomerization is further understood, the results yield more questions about the biological implications of the peroxiredoxin oligomerization, as multiple toroid configurations are now known. The crystal structure depicting the product bound active site gives insight into the overoxidation of the active site and allows further characterization of the leaving group

Fluorescence reporters for Hfq oligomerization and RNA annealing

Science.gov (United States)

Panja, Subrata; Woodson, Sarah A.

2015-01-01

Fluorescence spectroscopy is a sensitive technique for detecting protein-protein, protein-RNA and RNA-RNA interactions, requiring only nanomolar concentrations of labeled components. Fluorescence anisotropy provides information about the assembly of multi-subunit proteins, while molecular beacons provide a sensitive and quantitative reporter for base pairing between complementary RNAs. Here we present a detailed protocol for labeling Hfq protein with cyanine 3-maleimide and dansyl chloride to study the protein oligomerization and RNA binding by semi-native polyacrylamide gel electrophoresis (PAGE) and fluorescence anisotropy. We also present a detailed protocol for measuring the rate of annealing between a molecular beacon and a target RNA in the presence of Hfq using a stopped-flow spectrometer. PMID:25579597

Electron Microscopy Structural Insights into CPAP Oligomeric Behavior

DEFF Research Database (Denmark)

Alvarez-Cabrera, Ana L; Delgado, Sandra; Gil-Carton, David

2017-01-01

Centrosomal P4.1-associated protein (CPAP) is a cell cycle regulated protein fundamental for centrosome assembly and centriole elongation. In humans, the region between residues 897-1338 of CPAP mediates interactions with other proteins and includes a homodimerization domain. CPAP mutations cause...... into clearly different regular 3D maps (putatively corresponding to dimers and tetramers) and direct observation of individual images representing other complexes of HsCPAP(897-1338) (i.e., putative flexible monomers and higher-order multimers), we report a dynamic oligomeric behavior of this protein, where...... of different oligomers of CPAP, suggesting further insights to understand how this protein works, contributing to the elucidation of control mechanisms for centriole biogenesis....

Domain architecture and oligomerization properties of the paramyxovirus PIV 5 hemagglutinin-neuraminidase (HN) protein.

Science.gov (United States)

Yuan, Ping; Leser, George P; Demeler, Borries; Lamb, Robert A; Jardetzky, Theodore S

2008-09-01

The mechanism by which the paramyxovirus hemagglutinin-neuraminidase (HN) protein couples receptor binding to activation of virus entry remains to be fully understood, but the HN stalk is thought to play an important role in the process. We have characterized ectodomain constructs of the parainfluenza virus 5 HN to understand better the underlying architecture and oligomerization properties that may influence HN functions. The PIV 5 neuraminidase (NA) domain is monomeric whereas the ectodomain forms a well-defined tetramer. The HN stalk also forms tetramers and higher order oligomers with high alpha-helical content. Together, the data indicate that the globular NA domains form weak intersubunit interactions at the end of the HN stalk tetramer, while stabilizing the stalk and overall oligomeric state of the ectodomain. Electron microscopy of the HN ectodomain reveals flexible arrangements of the NA and stalk domains, which may be important for understanding how these two HN domains impact virus entry.

Conformational detection of p53's oligomeric state by FlAsH Fluorescence.

Science.gov (United States)

Webber, Tawnya M; Allen, Andrew C; Ma, Wai Kit; Molloy, Rhett G; Kettelkamp, Charisse N; Dow, Caitlin A; Gage, Matthew J

2009-06-19

The p53 tumor suppressor protein is a critical checkpoint in prevention of tumor formation, and the function of p53 is dependent on proper formation of the active tetramer. In vitro studies have shown that p53 binds DNA most efficiently as a tetramer, though inactive p53 is predicted to be monomeric in vivo. We demonstrate that FlAsH binding can be used to distinguish between oligomeric states of p53, providing a potential tool to explore p53 oligomerization in vivo. The FlAsH tetra-cysteine binding motif has been incorporated along the dimer and tetramer interfaces in the p53 tetramerization domain to create reporters for the dimeric and tetrameric states of p53, though the geometry of the four cysteines is critical for efficient FlAsH binding. Furthermore, we demonstrate that FlAsH binding can be used to monitor tetramer formation in real-time. These results demonstrate the potential for using FlAsH fluorescence to monitor protein-protein interactions in vivo.

Procedimiento de corte en cuerpos sólidos poliédricos // Section procedure in solid polyhedral bodies.

Directory of Open Access Journals (Sweden)

A. Miguel Iznaga Benítez

2000-10-01

Full Text Available El conocimiento de la estructura de datos de los modelos geométricos ha posibilitado el desarrollo de algoritmos parasolucionar problemas complejos. Estos algoritmos han facilitado a su vez, la automatización en las oficinas de diseño através de los medios computacionales.Por tal motivo, se presenta el desarrollo de un algoritmo para la obtención de cortes y secciones en cuerpos geométricospoliédricos, se plantean las etapas fundamentales del algoritmo y a través de un ejercicio se ejemplifica el mismo.Este algoritmo puede ser utilizado en la creación de software que ayuden al proceso docente.Palabras claves: enseñanza, gráfica, separación de sólidos, geometría, dibujo, algoritmo, CAD._________________________________________________________________________Abstract:The knowledge of data structure in geometric models has facilitated the development of algorithms to solve complexproblems. These algorithms have facilitated in turn, the automation in the design by computational means. For such reason,is presented the development of an algorithm for the obtaining of sections in polyhedral geometric bodies, the fundamentalstages of the algorithm are stated and illustrated using an example.This algorithm can be use in the software creation that will help to the educational processKey words: section, separation of solids, algorithm, geometric modeling, graphic, CAD. teaching.

Quantifying the thermodynamic interactions of polyhedral boranes in solution to guide nanocomposite fabrication

Energy Technology Data Exchange (ETDEWEB)

Mutz, M. [University of Tennessee, Department of Chemistry (United States); Eastwood, Eric [Honeywell Kansas City Plant (United States); Lee, Mark E. [University of Missouri (United States); Bowen, Daniel E. [Honeywell Kansas City Plant (United States); Dadmun, M. D., E-mail: dad@utk.edu [University of Tennessee, Department of Chemistry (United States)

2012-11-15

The solubility of boron containing nanoparticles in a variety of solvents is quantified using static light scattering in conjunction with refractometry. Four polyhedral boranes were tested in this work, using refractometry to obtain dn/dc, while static light scattering quantifies A{sub 2}. A{sub 2} obtained from these measurements was then used to calculate {chi}, the solute-solvent interaction parameter, and the Hildebrand solubility parameter, {delta}, which provides a quantifiable method to identify good solvents. Of the nanoparticles studied, 1,3-di-o-carboranylpropane is thermodynamically stable in toluene, with a {chi} less than 0.5, a solubility limit of 2.47 mg/mL, and all solutions remaining clear with no visible particle settling. For all of the particles tested, there was good correlation between the physical observations of the solutions, {chi}, and {delta}. For instance, lower values of {chi} correspond to a smaller radius of gyration (R{sub g}). A list of suitable solvents based on {delta} is also presented.

Quantifying the thermodynamic interactions of polyhedral boranes in solution to guide nanocomposite fabrication

International Nuclear Information System (INIS)

Mutz, M.; Eastwood, Eric; Lee, Mark E.; Bowen, Daniel E.; Dadmun, M. D.

2012-01-01

The solubility of boron containing nanoparticles in a variety of solvents is quantified using static light scattering in conjunction with refractometry. Four polyhedral boranes were tested in this work, using refractometry to obtain dn/dc, while static light scattering quantifies A 2 . A 2 obtained from these measurements was then used to calculate χ, the solute–solvent interaction parameter, and the Hildebrand solubility parameter, δ, which provides a quantifiable method to identify good solvents. Of the nanoparticles studied, 1,3-di-o-carboranylpropane is thermodynamically stable in toluene, with a χ less than 0.5, a solubility limit of 2.47 mg/mL, and all solutions remaining clear with no visible particle settling. For all of the particles tested, there was good correlation between the physical observations of the solutions, χ, and δ. For instance, lower values of χ correspond to a smaller radius of gyration (R g ). A list of suitable solvents based on δ is also presented.

The cysteines of the extracellular loop are crucial for trafficking of human organic cation transporter 2 to the plasma membrane and are involved in oligomerization.

Science.gov (United States)

Brast, Sabine; Grabner, Alexander; Sucic, Sonja; Sitte, Harald H; Hermann, Edwin; Pavenstädt, Hermann; Schlatter, Eberhard; Ciarimboli, Giuliano

2012-03-01

Human organic cation transporter 2 (hOCT2) is involved in transport of many endogenous and exogenous organic cations, mainly in kidney and brain cells. Because the quaternary structure of transmembrane proteins plays an essential role for their cellular trafficking and function, we investigated whether hOCT2 forms oligomeric complexes, and if so, which part of the transporter is involved in the oligomerization. A yeast 2-hybrid mating-based split-ubiquitin system (mbSUS), fluorescence resonance energy transfer, Western blot analysis, cross-linking experiments, immunofluorescence, and uptake measurements of the fluorescent organic cation 4-(4-(dimethylamino)styryl)-N-methylpyridinium were applied to human embryonic kidney 293 (HEK293) cells transfected with hOCT2 and partly also to freshly isolated human proximal tubules. The role of cysteines for oligomerization and trafficking of the transporter to the plasma membranes was investigated in cysteine mutants of hOCT2. hOCT2 formed oligomers both in the HEK293 expression system and in native human kidneys. The cysteines of the large extracellular loop are important to enable correct folding, oligomeric assembly, and plasma membrane insertion of hOCT2. Mutation of the first and the last cysteines of the loop at positions 51 and 143 abolished oligomer formation. Thus, the cysteines of the extracellular loop are important for correct trafficking of the transporter to the plasma membrane and for its oligomerization.

Chaperonin of Group I: Oligomeric Spectrum and Biochemical and Biological Implications

Directory of Open Access Journals (Sweden)

Silvia Vilasi

2018-01-01

Full Text Available Chaperonins play various physiological roles and can also be pathogenic. Elucidation of their structure, e.g., oligomeric status and post-translational modifications (PTM, is necessary to understand their functions and mechanisms of action in health and disease. Group I chaperonins form tetradecamers with two stacked heptameric rings. The tetradecamer is considered the typical functional complex for folding of client polypeptides. However, other forms such as the monomer and oligomers with smaller number of subunits than the classical tetradecamer, also occur in cells. The properties and functions of the monomer and oligomers, and their roles in chaperonin-associated diseases are still incompletely understood. Chaperonin I in eukaryotes occurs in various locations, not just the mitochondrion, which is its canonical place of residence and function. Eukaryotic Chaperonin I, namely Hsp60 (designated HSP60 or HSPD1 in humans has, indeed, been found in the cytosol; the plasma-cell membrane; on the outer surface of cells; in the intercellular space; in biological liquids such as lymph, blood, and cerebrospinal fluid; and in secretions, for instance saliva and urine. Hsp60 has also been found in cell-derived vesicles such as exosomes. The functions of Hsp60 in all these non-canonical locales are still poorly characterized and one of the questions not yet answered is in what form, i.e., monomer or oligomer, is the chaperonin present in these non-canonical locations. In view of the steady increase in interest on chaperonopathies over the last several years, we have studied human HSP60 to determine its role in various diseases, its locations in cells and tissues and migrations in the body, and its post-translational modifications that might have an impact on its location and function. We also carried out experiments to characterize the oligomeric status of extramitochondrial of HSP60 in solution. Here, we provide an overview of our results, focusing on

Understanding the Influence of oligomeric resins on traction and rolling resistance of silica tire treads

NARCIS (Netherlands)

Vleugels, N.; Pille-Wolf, W.; Dierkes, Wilma K.; Noordermeer, Jacobus W.M.

2015-01-01

This study concerns the silica reinforcement of styrene–butadiene rubber compounds for passenger car tire treads, with the objective of gaining greater insight into the beneficial effects of oligomeric resins. The major tire performance factors predicted are rolling resistance and (wet) skid

Genetic noise control via protein oligomerization

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Almaas Eivind

2008-11-01

Full Text Available Abstract Background Gene expression in a cell entails random reaction events occurring over disparate time scales. Thus, molecular noise that often results in phenotypic and population-dynamic consequences sets a fundamental limit to biochemical signaling. While there have been numerous studies correlating the architecture of cellular reaction networks with noise tolerance, only a limited effort has been made to understand the dynamic role of protein-protein interactions. Results We have developed a fully stochastic model for the positive feedback control of a single gene, as well as a pair of genes (toggle switch, integrating quantitative results from previous in vivo and in vitro studies. In particular, we explicitly account for the fast binding-unbinding kinetics among proteins, RNA polymerases, and the promoter/operator sequences of DNA. We find that the overall noise-level is reduced and the frequency content of the noise is dramatically shifted to the physiologically irrelevant high-frequency regime in the presence of protein dimerization. This is independent of the choice of monomer or dimer as transcription factor and persists throughout the multiple model topologies considered. For the toggle switch, we additionally find that the presence of a protein dimer, either homodimer or heterodimer, may significantly reduce its random switching rate. Hence, the dimer promotes the robust function of bistable switches by preventing the uninduced (induced state from randomly being induced (uninduced. Conclusion The specific binding between regulatory proteins provides a buffer that may prevent the propagation of fluctuations in genetic activity. The capacity of the buffer is a non-monotonic function of association-dissociation rates. Since the protein oligomerization per se does not require extra protein components to be expressed, it provides a basis for the rapid control of intrinsic or extrinsic noise. The stabilization of regulatory circuits

A piecewise linear finite element discretization of the diffusion equation for arbitrary polyhedral grids

Energy Technology Data Exchange (ETDEWEB)

Bailey, Teresa S. [Texas A and M University, Department of Nuclear Engineering, College Station, TX 77843-3133 (United States)], E-mail: baileyte@tamu.edu; Adams, Marvin L. [Texas A and M University, Department of Nuclear Engineering, College Station, TX 77843-3133 (United States)], E-mail: mladams@tamu.edu; Yang, Brian [Lawrence Livermore National Laboratory, Livermore, CA 94551 (United States); Zika, Michael R. [Lawrence Livermore National Laboratory, Livermore, CA 94551 (United States)], E-mail: zika@llnl.gov

2008-04-01

We develop a piecewise linear (PWL) Galerkin finite element spatial discretization for the multi-dimensional radiation diffusion equation. It uses recently introduced piecewise linear weight and basis functions in the finite element approximation and it can be applied on arbitrary polygonal (2D) or polyhedral (3D) grids. We first demonstrate some analytical properties of the PWL method and perform a simple mode analysis to compare the PWL method with Palmer's vertex-centered finite-volume method and with a bilinear continuous finite element method. We then show that this new PWL method gives solutions comparable to those from Palmer's. However, since the PWL method produces a symmetric positive-definite coefficient matrix, it should be substantially more computationally efficient than Palmer's method, which produces an asymmetric matrix. We conclude that the Galerkin PWL method is an attractive option for solving diffusion equations on unstructured grids.

A piecewise linear finite element discretization of the diffusion equation for arbitrary polyhedral grids

International Nuclear Information System (INIS)

Bailey, Teresa S.; Adams, Marvin L.; Yang, Brian; Zika, Michael R.

2008-01-01

We develop a piecewise linear (PWL) Galerkin finite element spatial discretization for the multi-dimensional radiation diffusion equation. It uses recently introduced piecewise linear weight and basis functions in the finite element approximation and it can be applied on arbitrary polygonal (2D) or polyhedral (3D) grids. We first demonstrate some analytical properties of the PWL method and perform a simple mode analysis to compare the PWL method with Palmer's vertex-centered finite-volume method and with a bilinear continuous finite element method. We then show that this new PWL method gives solutions comparable to those from Palmer's. However, since the PWL method produces a symmetric positive-definite coefficient matrix, it should be substantially more computationally efficient than Palmer's method, which produces an asymmetric matrix. We conclude that the Galerkin PWL method is an attractive option for solving diffusion equations on unstructured grids

The Pseudo signal peptide of the corticotropin-releasing factor receptor type 2A prevents receptor oligomerization.

Science.gov (United States)

Teichmann, Anke; Rutz, Claudia; Kreuchwig, Annika; Krause, Gerd; Wiesner, Burkhard; Schülein, Ralf

2012-08-03

N-terminal signal peptides mediate the interaction of native proteins with the translocon complex of the endoplasmic reticulum membrane and are cleaved off during early protein biogenesis. The corticotropin-releasing factor receptor type 2a (CRF(2(a))R) possesses an N-terminal pseudo signal peptide, which represents a so far unique domain within the large protein family of G protein-coupled receptors (GPCRs). In contrast to a conventional signal peptide, the pseudo signal peptide remains uncleaved and consequently forms a hydrophobic extension at the N terminus of the receptor. The functional consequence of the presence of the pseudo signal peptide is not understood. Here, we have analyzed the significance of this domain for receptor dimerization/oligomerization in detail. To this end, we took the CRF(2(a))R and the homologous corticotropin-releasing factor receptor type 1 (CRF(1)R) possessing a conventional cleaved signal peptide and conducted signal peptide exchange experiments. Using single cell and single molecule imaging methods (fluorescence resonance energy transfer and fluorescence cross-correlation spectroscopy, respectively) as well as biochemical experiments, we obtained two novel findings; we could show that (i) the CRF(2(a))R is expressed exclusively as a monomer, and (ii) the presence of the pseudo signal peptide prevents its oligomerization. Thus, we have identified a novel functional domain within the GPCR protein family, which plays a role in receptor oligomerization and which may be useful to study the functional significance of this process in general.

Catalytic Oligomerization of Terminal Alkynes by Lanthanide Carbyls (η5-C5Me5)2LnCH(SiMe3)2 (Ln = Y, La, Ce)

NARCIS (Netherlands)

Heeres, H.J.; Teuben, J.H.

1991-01-01

Lanthanide and group 3 carbyls Cp*2LnCH(SiMe3)2 (1, Ln = Y; 2, Ln = La; 3, Ln = Ce) are active catalyst precursors for the oligomerization of terminal alkynes HC≡CR (R = alkyl, aryl, SiMe3). The regioselectivity and the extent of oligomerization depend strongly on the lanthanide applied as well as

Bimolecular Fluorescence Complementation of Alpha-synuclein Demonstrates its Oligomerization with Dopaminergic Phenotype in Mice

Directory of Open Access Journals (Sweden)

Waijiao Cai

2018-03-01

Full Text Available Alpha-synuclein (αSyn is encoded by the first causal gene identified in Parkinson's disease (PD and is the main component of Lewy bodies, a pathological hallmark of PD. aSyn-based animal models have contributed to our understanding of PD pathophysiology and to the development of therapeutics. Overexpression of human wildtype αSyn by viral vectors in rodents recapitulates the loss of dopaminergic neurons from the substantia nigra, another defining pathological feature of the disease. The development of a rat model exhibiting bimolecular fluorescence complementation (BiFC of αSyn by recombinant adeno-associated virus facilitates detection of the toxic αSyn oligomers species. We report here neurochemical, neuropathological and behavioral characterization of BiFC of αSyn in mice. Overexpression and oligomerization of αSyn through BiFC is detected by conjugated fluorescence. Reduced striatal dopamine and loss of nigral dopaminergic neurons are accompanied neuroinflammation and abnormal motor activities. Our mouse model may provide a valuable tool to study the role of αSyn in PD and to explore therapeutic approaches. Keywords: Parkinson's disease, Alpha-synuclein, Mouse model, Oligomers, Neuroinflammation

Estimating Small-Body Gravity Field from Shape Model and Navigation Data

Science.gov (United States)

Park, Ryan S.; Werner, Robert A.; Bhaskaran, Shyam

2008-01-01

This paper presents a method to model the external gravity field and to estimate the internal density variation of a small-body. We first discuss the modeling problem, where we assume the polyhedral shape and internal density distribution are given, and model the body interior using finite elements definitions, such as cubes and spheres. The gravitational attractions computed from these approaches are compared with the true uniform-density polyhedral attraction and the level of accuracies are presented. We then discuss the inverse problem where we assume the body shape, radiometric measurements, and a priori density constraints are given, and estimate the internal density variation by estimating the density of each finite element. The result shows that the accuracy of the estimated density variation can be significantly improved depending on the orbit altitude, finite-element resolution, and measurement accuracy.

PREPARATION AND PROPERTIES OF MMA/1-PROPYLMETHACRYLATE-POSS COPOLYMER WITH ATOM TRANSFER RADICAL POLYMERIZATION

Institute of Scientific and Technical Information of China (English)

He-xin Zhang; Ho-young Lee; Young-jun Shin; Dong-ho Lee; Seok Kyun Noh

2008-01-01

The methyl methacrylate(MMA)/1-propylmethacrylate-polyhedral oligomeric silsesquioxane(PM-POSS) copolymers were synthesized via atom transfer radical polymerization with CuBr as catalyst.The unreacted PM-POSS monomer could be removed completely by washing the copolymerization product with n-hexane.The copolymers were characterized with 1H-NMR,X-ray diffraction,difierential scanning calorimetry,thermogravimetric analysis and gel permeatlon chromatography.With increasing PM-POSS feed ratio.the total conversion increased while the glass transition temperatures of copolymer decreased.The thermogravimetric analysis demonstrated that the thermal stability of copolymer improved slightly with PM-POSS addition.The molecular weight of copolymers increased with incorporation of PM-POSS.

The N-terminus of TDP-43 promotes its oligomerization and enhances DNA binding affinity

Energy Technology Data Exchange (ETDEWEB)

Chang, Chung-ke [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Wu, Tzong-Huah [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China); Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biochemistry, Academia Sinica, Taipei 115, Taiwan (China); Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan (China); Wu, Chu-Ya [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China); Graduate Institute of Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan (China); Chiang, Ming-hui; Toh, Elsie Khai-Woon [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Hsu, Yin-Chih; Lin, Ku-Feng [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China); Liao, Yu-heng [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Huang, Tai-huang, E-mail: bmthh@gate.sinica.edu.tw [Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan (China); Department of Physics, National Taiwan Normal University, Taipei 106, Taiwan (China); Huang, Joseph Jen-Tse, E-mail: jthuang@chem.sinica.edu.tw [Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan (China)

2012-08-24

Highlights: Black-Right-Pointing-Pointer The N-terminus of TDP-43 contains an independently folded structural domain (NTD). Black-Right-Pointing-Pointer The structural domains of TDP-43 are arranged in a beads-on-a-string fashion. Black-Right-Pointing-Pointer The NTD promotes TDP-43 oligomerization in a concentration-dependent manner. Black-Right-Pointing-Pointer The NTD may assist nucleic acid-binding activity of TDP-43. -- Abstract: TDP-43 is a DNA/RNA-binding protein associated with different neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD-U). Here, the structural and physical properties of the N-terminus on TDP-43 have been carefully characterized through a combination of nuclear magnetic resonance (NMR), circular dichroism (CD) and fluorescence anisotropy studies. We demonstrate for the first time the importance of the N-terminus in promoting TDP-43 oligomerization and enhancing its DNA-binding affinity. An unidentified structural domain in the N-terminus is also disclosed. Our findings provide insights into the N-terminal domain function of TDP-43.

Oligomerization of optineurin and its oxidative stress- or E50K mutation-driven covalent cross-linking: possible relationship with glaucoma pathology.

Directory of Open Access Journals (Sweden)

Jie Gao

Full Text Available The optineurin gene, OPTN, is one of the causative genes of primary open-angle glaucoma. Although oligomerization of optineurin in cultured cells was previously observed by gel filtration analysis and blue native gel electrophoresis (BNE, little is known about the characteristics of optineurin oligomers. Here, we aimed to analyze the oligomeric state of optineurin and factors affecting oligomerization, such as environmental stimuli or mutations in OPTN. Using BNE or immunoprecipitation followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE, we demonstrated that both endogenous and transfected optineurin exist as oligomers, rather than monomers, in NIH3T3 cells. We also applied an in situ proximity ligation assay to visualize the self-interaction of optineurin in fixed HeLaS3 cells and found that the optineurin oligomers were localized diffusely in the cytoplasm. Optineurin oligomers were usually detected as a single band of a size equal to that of the optineurin monomer upon SDS-PAGE, while an additional protein band of a larger size was observed when cells were treated with H2O2. We showed that larger protein complex is optineurin oligomers by immunoprecipitation and termed it covalent optineurin oligomers. In cells expressing OPTN bearing the most common glaucoma-associated mutation, E50K, covalent oligomers were formed even without H2O2 stimulation. Antioxidants inhibited the formation of E50K-induced covalent oligomers to various degrees. A series of truncated constructs of OPTN was used to reveal that covalent oligomers may be optineurin trimers and that the ubiquitin-binding domain is essential for formation of these trimers. Our results indicated that optineurin trimers may be the basic unit of these oligomers. The oligomeric state can be affected by many factors that induce covalent bonds, such as H2O2 or E50K, as demonstrated here; this provides novel insights into the pathogenicity of E50K. Furthermore

Mechanism of the electrochemical oligomerization of thionaphteneindole: a spectroscopic study

Science.gov (United States)

Poggi, Gabriella; Casalbore Miceli, Giuseppe; Beggiato, Giancarlo; Emmi, Salvatore S.

1997-10-01

The UV, visible and NIR spectra recorded during electrolysis of TNI in CH 2Cl 2 have been studied as a function of electrolysis time and of the quantity of charge exchanged. Among the oligomeric species that might be responsible for the behaviour observed, particular attention has been devoted to dimers of TNI characterized by different charges, presence of unpaired electrons, and deprotonation of the amino hydrogens. A sample of these species has been described theoretically by means of the PM3 semiempirical hamiltonian and their spectra have been computed giving results in reasonable agreement with the observed transitions.

Involvement of C-Terminal Histidines in Soybean PM1 Protein Oligomerization and Cu2+ Binding.

Science.gov (United States)

Liu, Guobao; Liu, Ke; Gao, Yang; Zheng, Yizhi

2017-06-01

Late embryogenesis abundant (LEA) proteins are widely distributed among plant species, where they contribute to abiotic stress tolerance. LEA proteins can be classified into seven groups according to conserved sequence motifs. The PM1 protein from soybean, which belongs to the Pfam LEA_1 group, has been shown previously to be at least partially natively unfolded, to bind metal ions and potentially to stabilize proteins and membranes. Here, we investigated the role of the PM1 C-terminal domain and in particular the multiple histidine residues in this half of the protein. We constructed recombinant plasmids expressing full-length PM1 and two truncated forms, PM1-N and PM1-C, which represent the N- and C-terminal halves of the protein, respectively. Immunoblotting and cross-linking experiments showed that full-length PM1 forms oligomers and high molecular weight (HMW) complexes in vitro and in vivo, while PM1-C, but not PM1-N, also formed oligomers and HMW complexes in vitro. When the histidine residues in PM1 and PM1-C were chemically modified, oligomerization was abolished, suggesting that histidines play a key role in this process. Furthermore, we demonstrated that high Cu2+ concentrations promote oligomerization and induce PM1 and PM1-C to form HMW complexes. Therefore, we speculate that PM1 proteins not only maintain ion homeostasis in the cytoplasm, but also potentially stabilize and protect other proteins during abiotic stress by forming a large, oligomeric molecular shield around biological targets. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Skeleton polyhedral rearrangements of 8-alkyl-7,9-dicarba-nido-undecaborate(-1) anion to 11-alkyl-2,7-dicarba-nido-undecaborane(13) and to 9-alkyl-7,8-dicarba-nido-undecaborate(-1) anion. Molecular structure of 2,7-Me2-11-PhCH2-2,7-C2B9H10

International Nuclear Information System (INIS)

Zakharkin, K.I.; Zhigareva, G.G.; Antonovich, V.A.; Yanovskij, A.I.; Struchkov, Yu.T.

1986-01-01

Using the methods of 1 H and 11 B NMR-spectroscopy and X-ray diffraction analysis skeleton polyhedral rearrangements of carboranes are studied. During protonation of anion 8-R-7, 9-R' 2 -7, 9-C 2 B 9 H 9 - the skeleton polyhedral rearrangement in the series of nido-carboranes, resulting in 2,7-R' 2 -11-R-2, 7-C 2 B 9 H 10 (R=Me, PhCH 2 , R'=H, Me) is observed. The rearrangement is reversible. On the detachment of two protons from 2,7-Me 2 -11-PhCH 2 -2,7-C 2 B 9 H 10 and during subsequent protonation the skeleton polyhedral rearrangement with the formation of anion 9-PhCH 2 -7,8-Me 2 -7,8-C 2 B 9 H 9 - takes place

78 FR 65561 - D-Glucopyranose, oligomeric, decyl octyl glycosides; Exemption from the Requirement of a Tolerance

Science.gov (United States)

2013-11-01

... metabolize D-glucopyranose, oligomeric, C 10 -C 16 -alkyl glycosides to water-soluble substances... polyoxyethylene polymers and fatty acids; carriers such as clay and diatomaceous earth; thickeners such as... exposure through drinking water and in residential settings, but does not include occupational exposure...

Development, validation and evaluation of an analytical method for the determination of monomeric and oligomeric procyanidins in apple extracts.

Science.gov (United States)

Hollands, Wendy J; Voorspoels, Stefan; Jacobs, Griet; Aaby, Kjersti; Meisland, Ane; Garcia-Villalba, Rocio; Tomas-Barberan, Francisco; Piskula, Mariusz K; Mawson, Deborah; Vovk, Irena; Needs, Paul W; Kroon, Paul A

2017-04-28

There is a lack of data for individual oligomeric procyanidins in apples and apple extracts. Our aim was to develop, validate and evaluate an analytical method for the separation, identification and quantification of monomeric and oligomeric flavanols in apple extracts. To achieve this, we prepared two types of flavanol extracts from freeze-dried apples; one was an epicatechin-rich extract containing ∼30% (w/w) monomeric (-)-epicatechin which also contained oligomeric procyanidins (Extract A), the second was an oligomeric procyanidin-rich extract depleted of epicatechin (Extract B). The parameters considered for method optimisation were HPLC columns and conditions, sample heating, mass of extract and dilution volumes. The performance characteristics considered for method validation included standard linearity, method sensitivity, precision and trueness. Eight laboratories participated in the method evaluation. Chromatographic separation of the analytes was best achieved utilizing a Hilic column with a binary mobile phase consisting of acidic acetonitrile and acidic aqueous methanol. The final method showed linearity for epicatechin in the range 5-100μg/mL with a correlation co-efficient >0.999. Intra-day and inter-day precision of the analytes ranged from 2 to 6% and 2 to 13% respectively. Up to dp3, trueness of the method was >95% but decreased with increasing dp. Within laboratory precision showed RSD values <5 and 10% for monomers and oligomers, respectively. Between laboratory precision was 4 and 15% (Extract A) and 7 and 30% (Extract B) for monomers and oligomers, respectively. An analytical method for the separation, identification and quantification of procyanidins in an apple extract was developed, validated and assessed. The results of the inter-laboratory evaluation indicate that the method is reliable and reproducible. Copyright © 2017. Published by Elsevier B.V.

Structural basis for TatA oligomerization: an NMR study of Escherichia coli TatA dimeric structure.

Directory of Open Access Journals (Sweden)

Yi Zhang

Full Text Available Many proteins are transported across lipid membranes by protein translocation systems in living cells. The twin-arginine transport (Tat system identified in bacteria and plant chloroplasts is a unique system that transports proteins across membranes in their fully-folded states. Up to date, the detailed molecular mechanism of this process remains largely unclear. The Escherichia coli Tat system consists of three essential transmembrane proteins: TatA, TatB and TatC. Among them, TatB and TatC form a tight complex and function in substrate recognition. The major component TatA contains a single transmembrane helix followed by an amphipathic helix, and is suggested to form the translocation pore via self-oligomerization. Since the TatA oligomer has to accommodate substrate proteins of various sizes and shapes, the process of its assembly stands essential for understanding the translocation mechanism. A structure model of TatA oligomer was recently proposed based on NMR and EPR observations, revealing contacts between the transmembrane helices from adjacent subunits. Herein we report the construction and stabilization of a dimeric TatA, as well as the structure determination by solution NMR spectroscopy. In addition to more extensive inter-subunit contacts between the transmembrane helices, we were also able to observe interactions between neighbouring amphipathic helices. The side-by-side packing of the amphipathic helices extends the solvent-exposed hydrophilic surface of the protein, which might be favourable for interactions with substrate proteins. The dimeric TatA structure offers more detailed information of TatA oligomeric interface and provides new insights on Tat translocation mechanism.

Zinc and the iron donor frataxin regulate oligomerization of the scaffold protein to form new Fe-S cluster assembly centers.

Science.gov (United States)

Galeano, B K; Ranatunga, W; Gakh, O; Smith, D Y; Thompson, J R; Isaya, G

2017-06-21

Early studies of the bacterial Fe-S cluster assembly system provided structural details for how the scaffold protein and the cysteine desulfurase interact. This work and additional work on the yeast and human systems elucidated a conserved mechanism for sulfur donation but did not provide any conclusive insights into the mechanism for iron delivery from the iron donor, frataxin, to the scaffold. We previously showed that oligomerization is a mechanism by which yeast frataxin (Yfh1) can promote assembly of the core machinery for Fe-S cluster synthesis both in vitro and in cells, in such a manner that the scaffold protein, Isu1, can bind to Yfh1 independent of the presence of the cysteine desulfurase, Nfs1. Here, in the absence of Yfh1, Isu1 was found to exist in two forms, one mostly monomeric with limited tendency to dimerize, and one with a strong propensity to oligomerize. Whereas the monomeric form is stabilized by zinc, the loss of zinc promotes formation of dimer and higher order oligomers. However, upon binding to oligomeric Yfh1, both forms take on a similar symmetrical trimeric configuration that places the Fe-S cluster coordinating residues of Isu1 in close proximity of iron-binding residues of Yfh1. This configuration is suitable for docking of Nfs1 in a manner that provides a structural context for coordinate iron and sulfur donation to the scaffold. Moreover, distinct structural features suggest that in physiological conditions the zinc-regulated abundance of monomeric vs. oligomeric Isu1 yields [Yfh1]·[Isu1] complexes with different Isu1 configurations that afford unique functional properties for Fe-S cluster assembly and delivery.

Oligomeric adiponectin forms and their complexes in the blood of healthy donors and patients with type 2 diabetes mellitus.

Science.gov (United States)

Kogan, Alexander E; Filatov, Vladimir L; Kolosova, Olga V; Katrukha, Ivan A; Mironova, Ekaterina V; Zhuravleva, Natalya S; Nagibin, Oleg A; Kara, Andrei N; Bereznikova, Anastasiya V; Katrukha, Alexey G

2013-01-01

Adiponectin (Adn) is a protein that circulates in the blood in several oligomeric forms, namely low-, medium-, and high-molecular-weight forms. Adn may serve as a risk factor for type 2 diabetes mellitus (T2DM). The aims of this work were (1) to produce monoclonal antibodies (MAbs) specific to different Adn oligomeric forms, (2) to design immunoassays suitable for measuring the Adn forms present in human blood, and (3) to investigate the changes in Adn forms that occur in patients with T2DM. Gel filtration, fluoroimmunoassays, and Western blotting were utilized as major techniques in this study. MAbs recognizing various oligomeric forms of Adn were obtained. Complexes between Adn and complement component C1q and between the low molecular weight form of Adn and albumin were described in human blood. A decrease in the total Adn and Adn-albumin complex levels in the blood of patients with T2DM and no difference in the levels of the Adn-C1q complex in comparison with healthy volunteers were demonstrated. An Adn94-Adn63 fluoroimmunoassay was selected as the technique that most accurately measured the mass ratio of Adn oligomers in blood samples, and an Adn214-Adn27 assay that measured the low-molecular-weight form of Adn only.

DFT study on the impact of the methylaluminoxane cocatalyst in ethylene oligomerization using a titanium-based catalyst

KAUST Repository

Pasha, Farhan Ahmad; Basset, Jean-Marie; Toulhoat, Hervé ; De Bruin, Theodorus J M

2015-01-01

A computational study within the framework of density functional theory is presented on the oligomerization of ethylene to yield 1-hexene using [(η5-C5H4CMe2C6H5)]TiCl3/MAO] catalyst. This study explicitly takes into account a methylaluminoxane (MAO) cocatalyst model, where the MAO cluster has become an anionic species after having abstracted one chloride anion, yielding a cationic activated catalyst. Hence, the reaction profile was calculated using the zwitterionic system, and the potential energy surface has been compared to the cationic catalytic system. Modest differences were found between the two free energy profiles. However, we show for the first time that the use of a realistic zwitterionic model is required to obtain a Brønsted-Evans-Polanyi relationship between the energy barriers and reaction energies.

DFT study on the impact of the methylaluminoxane cocatalyst in ethylene oligomerization using a titanium-based catalyst

KAUST Repository

Pasha, Farhan Ahmad

2015-01-26

A computational study within the framework of density functional theory is presented on the oligomerization of ethylene to yield 1-hexene using [(η5-C5H4CMe2C6H5)]TiCl3/MAO] catalyst. This study explicitly takes into account a methylaluminoxane (MAO) cocatalyst model, where the MAO cluster has become an anionic species after having abstracted one chloride anion, yielding a cationic activated catalyst. Hence, the reaction profile was calculated using the zwitterionic system, and the potential energy surface has been compared to the cationic catalytic system. Modest differences were found between the two free energy profiles. However, we show for the first time that the use of a realistic zwitterionic model is required to obtain a Brønsted-Evans-Polanyi relationship between the energy barriers and reaction energies.

In situ oligomerization of 2-(thiophen-3-yl)acetate intercalated into Zn{sub 2}Al layered double hydroxide

Energy Technology Data Exchange (ETDEWEB)

Tronto, Jairo, E-mail: jairotronto@ufv.br [Universidade Federal de Viçosa, Instituto de Ciências Exatas e Tecnológicas, Campus de Rio Parsanaíba, Rodovia BR 354 km 310, Cx. Postal 22, CEP, 38.810-000 Rio Paranaíba, MG (Brazil); Pinto, Frederico G.; Costa, Liovando M. da [Universidade Federal de Viçosa, Instituto de Ciências Exatas e Tecnológicas, Campus de Rio Parsanaíba, Rodovia BR 354 km 310, Cx. Postal 22, CEP, 38.810-000 Rio Paranaíba, MG (Brazil); Leroux, Fabrice; Dubois, Marc [Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand (France); CNRS, UMR 6296, ICCF, BP 80026, F-6317 Clermont-Ferrand (France); Valim, João B. [Universidade de São Paulo, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Departamento de Química, Av. dos Bandeirantes 3900, CEP 14.040-901, Ribeirão Preto, SP (Brazil)

2015-01-15

A layered double hydroxide (LDH) with cation composition Zn{sub 2}Al was intercalated with 2-(thiophen-3-yl)acetate (3-TA) monomers. To achieve in situ polymerization and/or oligomerization of the intercalated monomers, soft thermal treatments were carried out, and subsequent hybrid LDH materials were analyzed by means of several characterization techniques using powder X-ray diffraction (PXRD), Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), {sup 13}C CP–MAS nuclear magnetic resonance (NMR), electron spin resonance (EPR), scanning electron microscopy (SEM), and transmission electron microscopy (TEM), inductively coupled plasma optical emission spectroscopy (ICP–OES), and elemental analysis. PXRD analysis suggested that the intercalated monomers formed a bilayer. Thermal treatment of the hybrid LDH assembly above 120 °C provokes partially the breakdown of the layered structure, generating the phase zincite. EPR results indicated that vicinal monomers (oligomerization) were bound to each other after hydrothermal or thermal treatment, leading to a polaron response characteristic of electron conductivity localized on a restricted number of thiophene-based monomer segments. Localized unpaired electrons exist in the material and interact with the {sup 27}Al nuclei of the LDH layers by superhyperfine coupling. These unpaired electrons also interact with the surface of ZnO (O{sup 2−} vacancies), formed during the thermal treatments. - Graphical abstract: We synthesized a layered double hydroxide (LDH) with cation composition Zn{sub 2}Al, intercalated with 2-(thiophen-3-yl)acetate (3-TA) monomers, by coprecipitation at constant pH. We thermally treated the material, to achieve in situ polymerization and/or oligomerization of the intercalated monomers. - Highlights: • A Zn{sub 2}Al–LDH was intercalated with 2-(thiophen-3-yl)acetate monomers. • To achieve in situ oligomerization of the monomers, thermal treatments were made. �

Age- and brain region-dependent α-synuclein oligomerization is attributed to alterations in intrinsic enzymes regulating α-synuclein phosphorylation in aging monkey brains.

Science.gov (United States)

Chen, Min; Yang, Weiwei; Li, Xin; Li, Xuran; Wang, Peng; Yue, Feng; Yang, Hui; Chan, Piu; Yu, Shun

2016-02-23

We previously reported that the levels of α-syn oligomers, which play pivotal pathogenic roles in age-related Parkinson's disease (PD) and dementia with Lewy bodies, increase heterogeneously in the aging brain. Here, we show that exogenous α-syn incubated with brain extracts from older cynomolgus monkeys and in Lewy body pathology (LBP)-susceptible brain regions (striatum and hippocampus) forms higher amounts of phosphorylated and oligomeric α-syn than that in extracts from younger monkeys and LBP-insusceptible brain regions (cerebellum and occipital cortex). The increased α-syn phosphorylation and oligomerization in the brain extracts from older monkeys and in LBP-susceptible brain regions were associated with higher levels of polo-like kinase 2 (PLK2), an enzyme promoting α-syn phosphorylation, and lower activity of protein phosphatase 2A (PP2A), an enzyme inhibiting α-syn phosphorylation, in these brain extracts. Further, the extent of the age- and brain-dependent increase in α-syn phosphorylation and oligomerization was reduced by inhibition of PLK2 and activation of PP2A. Inversely, phosphorylated α-syn oligomers reduced the activity of PP2A and showed potent cytotoxicity. In addition, the activity of GCase and the levels of ceramide, a product of GCase shown to activate PP2A, were lower in brain extracts from older monkeys and in LBP-susceptible brain regions. Our results suggest a role for altered intrinsic metabolic enzymes in age- and brain region-dependent α-syn oligomerization in aging brains.

Contribution to the reconstruction of scenes made of cylindrical and polyhedral objects from sequences of images obtained by a moving camera

International Nuclear Information System (INIS)

Viala, Marc

1992-01-01

Environment perception is an important process which enables a robot to perform actions in an unknown scene. Although many sensors exist to 'give sight', the camera seems to play a leading part. This thesis deals with the reconstruction of scenes made of cylindrical and polyhedral objects from sequences of images provided by a moving camera. Two methods are presented. Both are based on the evolution of apparent contours of objects in a sequence. The first approach has been developed considering that camera motion is known. Despite the good results obtained by this method, the specific conditions it requires makes its use limited. In order to avoid an accurate evaluation of camera motion, we introduce another method allowing, at the same time, to estimate the object parameters and camera positions. In this approach, only is needed a 'poor' knowledge of camera displacements supplied by the control system of the robotic platform, in which the camera is embedded. An optimal integration of a priori information, as well as the dynamic feature of the state model to estimate, lead us to use the Kalman filter. Experiments conducted with synthetic and real images proved the reliability of these methods. Camera calibration set-up is also suggested to achieve the most accurate scene models resulting from reconstruction processes. (author) [fr

Implication of the oligomeric state of the N-terminal PTX3 domain in cumulus matrix assembly.

Science.gov (United States)

Ievoli, Elena; Lindstedt, Ragnar; Inforzato, Antonio; Camaioni, Antonella; Palone, Francesca; Day, Anthony J; Mantovani, Alberto; Salvatori, Giovanni; Salustri, Antonietta

2011-06-01

Pentraxin 3 (PTX3) plays a key role in the formation of the hyaluronan-rich matrix of the cumulus oophorus surrounding ovulated eggs that is required for successful fertilization and female fertility. PTX3 is a multimeric protein consisting of eight identical protomers held together by a combination of non-covalent interactions and disulfide bonds. Recent findings suggest that the oligomeric status of PTX3 is important for stabilizing the cumulus matrix. Because the role of PTX3 in the cumulus resides in the unique N-terminal sequence of the protomer, we investigated further this issue by testing the ability of distinct Cys/Ser mutants of recombinant N-terminal region of PTX3 (N(_)PTX3) with different oligomeric arrangement to promote in vitro normal expansion in cumuli from Ptx3-null mice. Here we report that the dimer of the N(_)PTX3 is unable to rescue cumulus matrix organization, and that the tetrameric assembly of the protein is the minimal oligomeric state required for accomplishing this function. We have previously demonstrated that PTX3 binds to HCs of IαI and TSG-6, which are essential for cumulus matrix formation and able to interact with hyaluronan. Interestingly, here we show by solid-phase binding experiments that the dimer of the N(_)PTX3 retains the ability to bind to both IαI and TSG-6, suggesting that the octameric structure of PTX3 provides multiple binding sites for each of these ligands. These findings support the hypothesis that PTX3 contributes to cumulus matrix organization by cross-linking HA polymers through interactions with multiple HCs of IαI and/or TSG-6. The N-terminal PTX3 tetrameric oligomerization was recently reported to be also required for recognition and inhibition of FGF2. Given that this growth factor has been detected in the mammalian preovulatory follicle, we wondered whether FGF2 negatively influences cumulus expansion and PTX3 may also serve in vivo to antagonize its activity. We found that a molar excess of FGF2, above

Spa47 is an oligomerization-activated type three secretion system (T3SS) ATPase from Shigella flexneri.

Science.gov (United States)

Burgess, Jamie L; Jones, Heather B; Kumar, Prashant; Toth, Ronald T; Middaugh, C Russell; Antony, Edwin; Dickenson, Nicholas E

2016-05-01

Gram-negative pathogens often use conserved type three secretion systems (T3SS) for virulence. The Shigella type three secretion apparatus (T3SA) penetrates the host cell membrane and provides a unidirectional conduit for injection of effectors into host cells. The protein Spa47 localizes to the base of the apparatus and is speculated to be an ATPase that provides the energy for T3SA formation and secretion. Here, we developed an expression and purification protocol, producing active Spa47 and providing the first direct evidence that Spa47 is a bona fide ATPase. Additionally, size exclusion chromatography and analytical ultracentrifugation identified multiple oligomeric species of Spa47 with the largest greater than 8 fold more active for ATP hydrolysis than the monomer. An ATPase inactive Spa47 point mutant was then engineered by targeting a conserved Lysine within the predicted Walker A motif of Spa47. Interestingly, the mutant maintained a similar oligomerization pattern as active Spa47, but was unable to restore invasion phenotype when used to complement a spa47 null S. flexneri strain. Together, these results identify Spa47 as a Shigella T3SS ATPase and suggest that its activity is linked to oligomerization, perhaps as a regulatory mechanism as seen in some related pathogens. Additionally, Spa47 catalyzed ATP hydrolysis appears to be essential for host cell invasion, providing a strong platform for additional studies dissecting its role in virulence and providing an attractive target for anti-infective agents. © 2016 The Protein Society.

Changes in the oligomerization potential of the division inhibitor UgtP co-ordinate Bacillus subtilis cell size with nutrient availability.

Science.gov (United States)

Chien, An-Chun; Zareh, Shannon Kian Gharabiklou; Wang, Yan Mei; Levin, Petra Anne

2012-11-01

How cells co-ordinate size with growth and development is a major, unresolved question in cell biology. In previous work we identified the glucosyltransferase UgtP as a division inhibitor responsible for increasing the size of Bacillus subtilis cells under nutrient-rich conditions. In nutrient-rich medium, UgtP is distributed more or less uniformly throughout the cytoplasm and concentrated at the cell poles and/or the cytokinetic ring. Under these conditions, UgtP interacts directly with FtsZ to inhibit division and increase cell size. Conversely, under nutrient-poor conditions, UgtP is sequestered away from FtsZ in punctate foci, and division proceeds unimpeded resulting in a reduction in average cell size. Here we report that nutrient-dependent changes in UgtP's oligomerization potential serve as a molecular rheostat to precisely co-ordinate B. subtilis cell size with nutrient availability. Our data indicate UgtP interacts with itself and the essential cell division protein FtsZ in a high-affinity manner influenced in part by UDP glucose, an intracellular proxy for nutrient availability. These findings support a model in which UDP-glc-dependent changes in UgtP's oligomerization potential shift the equilibrium between UgtP•UgtP and UgtP•FtsZ, fine-tuning the amount of FtsZ available for assembly into the cytokinetic ring and with it cell size. © 2012 Blackwell Publishing Ltd.

Regulation of complement by cartilage oligomeric matrix protein allows for a novel molecular diagnostic principle in rheumatoid arthritis

DEFF Research Database (Denmark)

Happonen, Kaisa E; Saxne, Tore; Aspberg, Anders

2010-01-01

Cartilage oligomeric matrix protein (COMP) is a structural component of cartilage, where it catalyzes collagen fibrillogenesis. Elevated amounts of COMP are found in serum during increased turnover of cartilage associated with active joint disease, such as rheumatoid arthritis (RA) and osteoarthr...

Oligomerization of glycine and alanine catalyzed by iron oxides: implications for prebiotic chemistry.

Science.gov (United States)

Shanker, Uma; Bhushan, Brij; Bhattacharjee, G; Kamaluddin

2012-02-01

Iron oxide minerals are probable constituents of the sediments present in geothermal regions of the primitive earth. They might have adsorbed different organic monomers (amino acids, nucleotides etc.) and catalyzed polymerization processes leading to the formation of the first living cell. In the present work we tested the catalytic activity of three forms of iron oxides (Goethite, Akaganeite and Hematite) in the intermolecular condensation of each of the amino acids glycine and L-alanine. The effect of zinc oxide and titanium dioxide on the oligomerization has also been studied. Oligomerization studies were performed for 35 days at three different temperatures 50, 90 and 120°C without applying drying/wetting cycling. The products formed were characterized by HPLC and ESI-MS techniques. All three forms of iron oxides catalyzed peptide bond formation (23.2% of gly2 and 10.65% of ala2). The reaction was monitored every 7 days. Formation of peptides was observed to start after 7 days at 50°C. Maximum yield of peptides was found after 35 days at 90°C. Reaction at 120°C favors formation of diketopiperazine derivatives. It is also important to note that after 35 days of reaction, goethite produced dimer and trimer with the highest yield among the oxides tested. We suggest that the activity of goethite could probably be due to its high surface area and surface acidity.

Eicosanoyl-5-hydroxytryptamide (EHT prevents Alzheimer's disease-related cognitive and electrophysiological impairments in mice exposed to elevated concentrations of oligomeric beta-amyloid.

Directory of Open Access Journals (Sweden)

Kesava Asam

Full Text Available Soluble forms of oligomeric beta-amyloid (Aβ are thought to play a central role in Alzheimer's disease (AD. Transgenic manipulation of methylation of the serine/threonine protein phosphatase, PP2A, was recently shown to alter the sensitivity of mice to AD-related impairments resulting from acute exposure to elevated levels of Aβ. In addition, eicosanoyl-5-hydroxytryptamide (EHT, a naturally occurring component from coffee beans that modulates PP2A methylation, was shown to confer therapeutic benefits in rodent models of AD and Parkinson's disease. Here, we tested the hypothesis that EHT protects animals from the pathological effects of exposure to elevated levels of soluble oligomeric Aβ. We treated mice with EHT-containing food at two different doses and assessed the sensitivity of these animals to Aβ-induced behavioral and electrophysiological impairments. We found that EHT administration protected animals from Aβ-induced cognitive impairments in both a radial-arm water maze and contextual fear conditioning task. We also found that both chronic and acute EHT administration prevented Aβ-induced impairments in long-term potentiation. These data add to the accumulating evidence suggesting that interventions with pharmacological agents, such as EHT, that target PP2A activity may be therapeutically beneficial for AD and other neurological conditions.

On the evaluation of the gravity effects of polyhedral bodies and a consistent treatment of related singularities

Science.gov (United States)

D'Urso, M. G.

2013-03-01

We show that the singularities which can affect the computation of the gravity effects (potential, gravity and tensor gradient fields) can be systematically addressed by invoking distribution theory and suitable formulas of differential calculus. Thus, differently from previous contributions on the subject, the use of a-posteriori corrections of the formulas derived in absence of singularities can be ruled out. The general approach presented in the paper is further specialized to the case of polyhedral bodies and detailed for a rectangular prism having a constant mass density. With reference to this last case, we derive novel expressions for the related gravitational field, as well as for its first and second derivative, at an observation point coincident with a prism vertex and show that they turn out to be more compact than the ones reported in the specialized literature.

Styrene oligomerization as a molecular probe reaction for zeolite acidity: a UV-Vis spectroscopy and DFT study

NARCIS (Netherlands)

Buurmans, I.L.C.; Pidko, E.A.; Groot, de J.M.; Stavitski, E.; Santen, van R.A.; Weckhuysen, B.M.

2010-01-01

A series of H-ZSM-5 crystallites with different framework Si/Al ratios was studied by analyzing the kinetics and reaction mechanism of the oligomerization of 4-fluorostyrene as molecular probe reaction for Brønsted acidity. The formation of carbocationic species was followed by UV-Vis spectroscopy.

Moyamoya disease-associated protein mysterin/RNF213 is a novel AAA+ ATPase, which dynamically changes its oligomeric state

Science.gov (United States)

Morito, Daisuke; Nishikawa, Kouki; Hoseki, Jun; Kitamura, Akira; Kotani, Yuri; Kiso, Kazumi; Kinjo, Masataka; Fujiyoshi, Yoshinori; Nagata, Kazuhiro

2014-03-01

Moyamoya disease is an idiopathic human cerebrovascular disorder that is characterized by progressive stenosis and abnormal collateral vessels. We recently identified mysterin/RNF213 as its first susceptibility gene, which encodes a 591-kDa protein containing enzymatically active P-loop ATPase and ubiquitin ligase domains and is involved in proper vascular development in zebrafish. Here we demonstrate that mysterin further contains two tandem AAA+ ATPase modules and forms huge ring-shaped oligomeric complex. AAA+ ATPases are known to generally mediate various biophysical and mechanical processes with the characteristic ring-shaped structure. Fluorescence correlation spectroscopy and biochemical evaluation suggested that mysterin dynamically changes its oligomeric forms through ATP/ADP binding and hydrolysis cycles. Thus, the moyamoya disease-associated gene product is a unique protein that functions as ubiquitin ligase and AAA+ ATPase, which possibly contributes to vascular development through mechanical processes in the cell.

Moyamoya disease-associated protein mysterin/RNF213 is a novel AAA+ ATPase, which dynamically changes its oligomeric state

Science.gov (United States)

Morito, Daisuke; Nishikawa, Kouki; Hoseki, Jun; Kitamura, Akira; Kotani, Yuri; Kiso, Kazumi; Kinjo, Masataka; Fujiyoshi, Yoshinori; Nagata, Kazuhiro

2014-01-01

Moyamoya disease is an idiopathic human cerebrovascular disorder that is characterized by progressive stenosis and abnormal collateral vessels. We recently identified mysterin/RNF213 as its first susceptibility gene, which encodes a 591-kDa protein containing enzymatically active P-loop ATPase and ubiquitin ligase domains and is involved in proper vascular development in zebrafish. Here we demonstrate that mysterin further contains two tandem AAA+ ATPase modules and forms huge ring-shaped oligomeric complex. AAA+ ATPases are known to generally mediate various biophysical and mechanical processes with the characteristic ring-shaped structure. Fluorescence correlation spectroscopy and biochemical evaluation suggested that mysterin dynamically changes its oligomeric forms through ATP/ADP binding and hydrolysis cycles. Thus, the moyamoya disease-associated gene product is a unique protein that functions as ubiquitin ligase and AAA+ ATPase, which possibly contributes to vascular development through mechanical processes in the cell. PMID:24658080

Synaptic transmission block by presynaptic injection of oligomeric amyloid beta

Science.gov (United States)

Moreno, Herman; Yu, Eunah; Pigino, Gustavo; Hernandez, Alejandro I.; Kim, Natalia; Moreira, Jorge E.; Sugimori, Mutsuyuki; Llinás, Rodolfo R.

2009-01-01

Early Alzheimer's disease (AD) pathophysiology is characterized by synaptic changes induced by degradation products of amyloid precursor protein (APP). The exact mechanisms of such modulation are unknown. Here, we report that nanomolar concentrations of intraaxonal oligomeric (o)Aβ42, but not oAβ40 or extracellular oAβ42, acutely inhibited synaptic transmission at the squid giant synapse. Further characterization of this phenotype demonstrated that presynaptic calcium currents were unaffected. However, electron microscopy experiments revealed diminished docked synaptic vesicles in oAβ42-microinjected terminals, without affecting clathrin-coated vesicles. The molecular events of this modulation involved casein kinase 2 and the synaptic vesicle rapid endocytosis pathway. These findings open the possibility of a new therapeutic target aimed at ameliorating synaptic dysfunction in AD. PMID:19304802

Cartilage oligomeric matrix protein deficiency promotes early onset and the chronic development of collagen-induced arthritis

DEFF Research Database (Denmark)

Geng, Hui; Carlsen, Stefan; Nandakumar, Kutty

2008-01-01

ABSTRACT: INTRODUCTION: Cartilage oligomeric matrix protein (COMP) is a homopentameric protein in cartilage. The development of arthritis, like collagen-induced arthritis (CIA), involves cartilage as a target tissue. We have investigated the development of CIA in COMP-deficient mice. METHODS: COMP......-deficient mice in the 129/Sv background were backcrossed for 10 generations against B10.Q mice, which are susceptible to chronic CIA. COMP-deficient and wild-type mice were tested for onset, incidence, and severity of arthritis in both the collagen and collagen antibody-induced arthritis models. Serum anti......-collagen II and anti-COMP antibodies as well as serum COMP levels in arthritic and wild-type mice were measured by enzyme-linked immunosorbent assay. RESULTS: COMP-deficient mice showed a significant early onset and increase in the severity of CIA in the chronic phase, whereas collagen II-antibody titers were...

Recurring polyhedral motifs in the amorphous indium gallium zinc oxide network

Energy Technology Data Exchange (ETDEWEB)

Divya; Deepak [Department of Materials Science and Engineering, Indian Institute of Technology, Kanpur (India); National Center for Flexible Electronics, Indian Institute of Technology, Kanpur (India); Prasad, Rajendra [Department of Physics, Indian Institute of Technology, Kanpur (India)

2017-02-15

The coordination polyhedra around the cations are the building blocks of ionic solids. For amorphous InGaZn oxide (a-IGZO), these coordination polyhedra are identified to investigate properties that depend on short range interactions. Therefore, in this first principles based study, a large number (10) of samples of a-IGZO were prepared by ab initio melt-and-quench molecular dynamics, so that several distinct samples of the amorphous landscape are obtained corresponding to local minima in energy. Based on a method of comparing bond angles between metal and oxygen atoms, the identified polyhedra were matched to the polyhedral motifs present in the related crystalline systems, such as, InGaZnO{sub 4}, In{sub 2}O{sub 3}, Ga{sub 2}O{sub 3}, and ZnO. Consequently, we find, the a-IGZO primarily consists of the following polyhedra: a tetrahedron from space group 199 and an octahedron from space group 206 of In{sub 2}O{sub 3}; a tetrahedron from space group 12 and an octahedron from space group 167 of Ga{sub 2}O{sub 3}; a tetrahedron from space group 186 of ZnO; zinc and gallium trigonal bipyramids from c-IGZO; and one zinc fourfold, one zinc fivefold, and one indium fivefold coordination polyhedra that occur only in the amorphous phase. Thus, we were able to reduce the description of structure from 360 to 10 groups of polyhedra. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Recurring polyhedral motifs in the amorphous indium gallium zinc oxide network

International Nuclear Information System (INIS)

Divya; Deepak; Prasad, Rajendra

2017-01-01

The coordination polyhedra around the cations are the building blocks of ionic solids. For amorphous InGaZn oxide (a-IGZO), these coordination polyhedra are identified to investigate properties that depend on short range interactions. Therefore, in this first principles based study, a large number (10) of samples of a-IGZO were prepared by ab initio melt-and-quench molecular dynamics, so that several distinct samples of the amorphous landscape are obtained corresponding to local minima in energy. Based on a method of comparing bond angles between metal and oxygen atoms, the identified polyhedra were matched to the polyhedral motifs present in the related crystalline systems, such as, InGaZnO_4, In_2O_3, Ga_2O_3, and ZnO. Consequently, we find, the a-IGZO primarily consists of the following polyhedra: a tetrahedron from space group 199 and an octahedron from space group 206 of In_2O_3; a tetrahedron from space group 12 and an octahedron from space group 167 of Ga_2O_3; a tetrahedron from space group 186 of ZnO; zinc and gallium trigonal bipyramids from c-IGZO; and one zinc fourfold, one zinc fivefold, and one indium fivefold coordination polyhedra that occur only in the amorphous phase. Thus, we were able to reduce the description of structure from 360 to 10 groups of polyhedra. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

N-terminal aliphatic residues dictate the structure, stability, assembly, and small molecule binding of the coiled-coil region of cartilage oligomeric matrix protein.

Science.gov (United States)

Gunasekar, Susheel K; Asnani, Mukta; Limbad, Chandani; Haghpanah, Jennifer S; Hom, Wendy; Barra, Hanna; Nanda, Soumya; Lu, Min; Montclare, Jin Kim

2009-09-15

The coiled-coil domain of cartilage oligomeric matrix protein (COMPcc) assembles into a homopentamer that naturally recognizes the small molecule 1,25-dihydroxyvitamin D(3) (vit D). To identify the residues critical for the structure, stability, oligomerization, and binding to vit D as well as two other small molecules, all-trans-retinol (ATR) and curcumin (CCM), here we perform an alanine scanning mutagenesis study. Ten residues lining the hydrophobic pocket of COMPcc were mutated into alanine; of the mutated residues, the N-terminal aliphatic residues L37, L44, V47, and L51 are responsible for maintaining the structure and function. Furthermore, two polar residues, T40 and Q54, within the N-terminal region when converted into alanine improve the alpha-helical structure, stability, and self-assembly behavior. Helical stability, oligomerization, and binding appear to be linked in a manner in which mutations that abolish helical structure and assembly bind poorly to vit D, ATR, and CCM. These results provide not only insight into COMPcc and its functional role but also useful guidelines for the design of stable, pentameric coiled-coils capable of selectively storing and delivering various small molecules.

Characterization and ageing study of poly(lactic acid) films plasticized with oligomeric lactic acid

OpenAIRE

Burgos, Nuria; Martino, Verónica P.; Jiménez, Alfonso

2013-01-01

Poly(lactic acid) (PLA) was melt-blended with a bio-based oligomeric lactic acid (OLA) plasticizer at different concentrations between 15 wt% and 25 wt% in order to enhance PLA ductility and to get a fully biodegradable material with potential application in films manufacturing. OLA was an efficient plasticizer for PLA, as it caused a significant decrease on glass transition temperature (Tg) while improving considerably ductile properties. Only one Tg value was observed in all cases and no ap...

Fingolimod phosphate attenuates oligomeric amyloid β-induced neurotoxicity via increased brain-derived neurotrophic factor expression in neurons.

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Yukiko Doi

Full Text Available The neurodegenerative processes that underlie Alzheimer's disease are mediated, in part, by soluble oligomeric amyloid β, a neurotoxic protein that inhibits hippocampal long-term potentiation, disrupts synaptic plasticity, and induces the production of reactive oxygen species. Here we show that the sphingosine-1-phosphate (S1P receptor (S1PR agonist fingolimod phosphate (FTY720-P-a new oral drug for multiple sclerosis-protects neurons against oligomeric amyloid β-induced neurotoxicity. We confirmed that primary mouse cortical neurons express all of the S1P receptor subtypes and FTY720-P directly affects the neurons. Treatment with FTY720-P enhanced the expression of brain-derived neurotrophic factor (BDNF in neurons. Moreover, blocking BDNF-TrkB signaling with a BDNF scavenger, TrkB inhibitor, or ERK1/2 inhibitor almost completely ablated these neuroprotective effects. These results suggested that the neuroprotective effects of FTY720-P are mediated by upregulated neuronal BDNF levels. Therefore, FTY720-P may be a promising therapeutic agent for neurodegenerative diseases, such as Alzheimer's disease.

MxiN Differentially Regulates Monomeric and Oligomeric Species of the Shigella Type Three Secretion System ATPase Spa47.

Science.gov (United States)

Case, Heather B; Dickenson, Nicholas E

2018-04-17

Shigella rely entirely on the action of a single type three secretion system (T3SS) to support cellular invasion of colonic epithelial cells and to circumvent host immune responses. The ATPase Spa47 resides at the base of the Shigella needle-like type three secretion apparatus (T3SA), supporting protein secretion through the apparatus and providing a likely means for native virulence regulation by Shigella and a much needed target for non-antibiotic therapeutics to treat Shigella infections. Here, we show that MxiN is a differential regulator of Spa47 and that its regulatory impact is determined by the oligomeric state of the Spa47 ATPase, with which it interacts. In vitro and in vivo characterization shows that interaction of MxiN with Spa47 requires the six N-terminal residues of Spa47 that are also necessary for stable Spa47 oligomer formation and activation. This interaction with MxiN negatively influences the activity of Spa47 oligomers while upregulating the ATPase activity of monomeric Spa47. Detailed kinetic analyses of monomeric and oligomeric Spa47 in the presence and absence of MxiN uncover additional mechanistic insights into the regulation of Spa47 by MxiN, suggesting that the MxiN/Spa47 species resulting from interaction with monomeric and oligomeric Spa47 are functionally distinct and that both could be involved in Shigella T3SS regulation. Uncovering regulation of Spa47 by MxiN addresses an important gap in the current understanding of how Shigella controls T3SA activity and provides the first description of differential T3SS ATPase regulation by a native T3SS protein.

Toughening of Epoxy Adhesives by Combined Interaction of Carbon Nanotubes and Silsesquioxanes

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Giuseppina Barra

2017-09-01

Full Text Available The extensive use of adhesives in many structural applications in the transport industry and particularly in the aeronautic field is due to numerous advantages of bonded joints. However, still many researchers are working to enhance the mechanical properties and rheological performance of adhesives by using nanoadditives. In this study the effect of the addition of Multi-Wall Carbon Nanotubes (MWCNTs with Polyhedral Oligomeric Silsesquioxane (POSS compounds, either Glycidyl Oligomeric Silsesquioxanes (GPOSS or DodecaPhenyl Oligomeric Silsesquioxanes (DPHPOSS to Tetraglycidyl Methylene Dianiline (TGMDA epoxy formulation, was investigated. The formulations contain neither a tougher matrix such as elastomers nor other additives typically used to provide a closer match in the coefficient of thermal expansion in order to discriminate only the effect of the addition of the above-mentioned components. Bonded aluminium single lap joints were made using both untreated and Chromic Acid Anodisation (CAA-treated aluminium alloy T2024 adherends. The effects of the different chemical functionalities of POSS compounds, as well as the synergistic effect between the MWCNT and POSS combination on adhesion strength, were evaluated by viscosity measurement, tensile tests, Dynamic Mechanical Analysis (DMA, single lap joint shear strength tests, and morphological investigation. The best performance in the Lap Shear Strength (LSS of the manufactured joints has been found for treated adherends bonded with epoxy adhesive containing MWCNTs and GPOSS. Carbon nanotubes have been found to play a very effective bridging function across the fracture surface of the bonded joints.

Computational Study of the Effect of Confinement within Microporous Structures on the Activity and Selectivity of Metallocene Catalysts for Ethylene Oligomerization

KAUST Repository

Toulhoat, Hervé; Lontsi Fomena, Mireille; de Bruin, Theodorus

2011-01-01

The effect of confinement within some zeolitic structures on the activity and selectivity of metallocene catalysts for the ethylene oligomerization has been investigated using grand canonical Monte Carlo simulations (GCMC). The following zeolite

Crystal engineering of giant molecules based on perylene diimide conjugated polyhedral oligomeric silsesquioxane nano-atom

Science.gov (United States)

Ren, He

Molecular architectures and topologies are found contributing to the formation of supramolecular structures of giant molecules. Dr. Cheng's research group developed a diverse of giant molecules via precisely controlled chemistry synthetic routes. These giant molecules can be categorized into several different families, namely giant surfactants, giant shape amphiphiles and giant polyhedron. By analyzing the hierarchical structures of these carefully designed and precisely synthesized giant molecules, the structural factors which affect, or even dominates, in some cases, the formation of supramolecular structures are revealed in these intensive researches. The results will further contribute to the understanding of dependence of supramolecular structures on molecular designs as well as molecular topology, and providing a practical solution to the scaling up of microscopic molecular functionalities to macroscopic material properties. Molecular Nano Particles (MNPs), including fullerene (C60), POSS, Polyoxometalate (POM) and proteins etc., is defined and applied as a specific type of building blocks in the design and synthesis of giant molecules. The persistence in shape and symmetry is considered as one of the major properties of MNPs. This persistence will support the construction of giant molecules for further supramolecular structures' study by introducing specific shapes, or precisely located side groups which will facilitate self-assembling behaviors with pre-programmed secondary interactions. Dictating material physical properties by its chemical composition is an attractive yet currently failed approach in the study of materials. However, the pursuit of determining material properties by microscopic molecular level properties is never seized, and found its solution when the idea of crystal engineering is raised: should each atom in the material is located exactly where it is designed to be and is properly bonded, the property of the material is hence determined. In such "bottom-up" approach, the precise fabrication of 2 nm 100 nm nanostructures, is of great research interest. In this thesis, crystal engineering of giant molecules based on PDI conjugated POSS Nano-Atom (PDI-BPOSS) nano-atoms via self-assembly is performed and studied. Herein, three different giant molecules were synthesized: shape amphiphile, m-phenyl-(PDI-BPOSS)2 (S1) and tetrahedron, R-(PDI-BPOSS)4 (S2) and S-(PDI-BPOSS)4 (S3). Single crystals were grown for S1 and S2, X-ray diffraction (XRD), Scanning Electron Microscopy (SEM) and transmission electron microscopy (TEM) were performed, and crystal structures of these samples were determined, while hexagonal superlattice without crystal order can be observed for S3 to exhibit crystal-like morphology.

Self-Assembly Behavior and pH-Stimuli-Responsive Property of POSS-Based Amphiphilic Block Copolymers in Solution

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Yiting Xu

2018-05-01

Full Text Available Stimuli-responsive polymeric systems containing special responsive moieties can undergo alteration of chemical structures and physical properties in response to external stimulus. We synthesized a hybrid amphiphilic block copolymer containing methoxy polyethylene glycol (MePEG, methacrylate isobutyl polyhedral oligomeric silsesquioxane (MAPOSS and 2-(diisopropylaminoethyl methacrylate (DPA named MePEG-b-P(MAPOSS-co-DPA via atom transfer radical polymerization (ATRP. Spherical micelles with a core-shell structure were obtained by a self-assembly process based on MePEG-b-P(MAPOSS-co-DPA, which showed a pH-responsive property. The influence of hydrophobic chain length on the self-assembly behavior was also studied. The pyrene release properties of micelles and their ability of antifouling were further studied.

Facile hydrothermal synthesis of polyhedral Fe3O4 nanocrystals, influencing factors and application in the electrochemical detection of H2O2

International Nuclear Information System (INIS)

Yuan Kefeng; Ni Yonghong; Zhang Li

2012-01-01

Highlights: ► Fe 3 O 4 polyhedra had been successfully synthesized by a facile hydrothermal technology. ► The as-obtained product exhibited the room-temperature ferrimagnetic property. ► The final product could be prepared into an electrochemical sensor for the detection of H 2 O 2 . - Abstract: Polyhedral Fe 3 O 4 nanocrystals have been successfully synthesized by a facile hydrothermal technique, employing FeSO 4 ·7H 2 O, N 2 H 4 and NH 3 ·H 2 O as the reactants without the assistance of any surfactant. The phase of the as-obtained Fe 3 O 4 was characterized by X-ray powder diffraction (XRD) and further proved by Rietveld refinement of XRD data. Energy dispersive spectrometry (EDS) and scanning electron microscopy (SEM) were used for the composition and morphology analyses of the final product. Some factors influencing the formation of polyhedral Fe 3 O 4 nanocrystals were systematically investigated, including the reaction temperature and time, and the original volume ratio of NH 3 ·H 2 O/N 2 H 4 ·H 2 O. It was found that the as-prepared Fe 3 O 4 polyhedra exhibited a good electrochemical property in 0.1 M phosphate buffer solution (PBS) with pH 7.0 and could be prepared into an electrochemical sensor for the detection of H 2 O 2 . The linear response range of the sensor was 10.0 × 10 −6 to 140.0 × 10 −6 M and a sensitivity was 11.05 μA/mM. Furthermore, the room-temperature magnetic property of the product was also investigated.

Synthesis and Characterization of Polyfunctional Polyhedral Silsesquioxane Cages

Science.gov (United States)

Sulaiman, Santy

Recent studies on octameric polyhedral silsesquioxanes, (RSiO1.5 )8, indicate that the silsesquioxane cage is not just a passive component but appears to be involved in electron delocalization with conjugated organic tethers in the excited state. This dissertation presents the synthesis and characterization of (RSiO1.5)8 molecules with unique photophysical properties that provide support for the existence of conjugation that involves the (RSiO1.5)8 cage. The dissertation first discusses the elaboration of octavinylsilsesquioxane via cross-metathesis to form styrenyl-functionalized octasilsesquioxane molecules. Subsequent Heck coupling reactions of p-bromostyrenyl derivative provides vinylstilbene-functionalized octasilsesquioxane. The amino derivative, NH2VinylStilbeneOS, show highly red-shifted emission spectrum (100 nm from the simple organic analog p-vinylstilbene) and high two-photon absorption (TPA) cross-section value (100 GM/moiety), indicating charge-transfer processes involving the silsesquioxane cage as the electron acceptor. The unique photophysical properties of polyfunctional luminescent cubic silsesquioxanes synthesized from ortho-8-, (2,5)-16-, and 24-brominated octaphenylsilsesquioxane (OPS) via Heck coupling show how the steric interactions of the organic tethers at the silsesquioxane cage corner affect conjugation with the silsesquioxane cage. Furthermore, the high TPA cross-section (10 GM/moiety) and photoluminescence quantum yield (20%) of OPS functionalized with 24 acetoxystyrenyl groups suggest that the existence excited states in these molecules with similar energies and decay rates: normal radiative pi- pi* transition and charge transfer involving the silsesquioxane cage. The fluoride ion-catalyzed rearrangement reactions of cage and polymeric silsesquioxanes provide a convenient route to a mixture of deca- and dodecameric silsesquioxane molecules in high yields, giving us the opportunity to investigate the effect of silsesquioxane cage

An Asymmetric Deuterium Labeling Strategy to Identify Interprotomer and Intraprotomer NOEs in Oligomeric Proteins

International Nuclear Information System (INIS)

Jasanoff, Alan

1998-01-01

A major difficulty in determining the structure of an oligomeric protein by NMR is the problem of distinguishing inter- from intraprotomer NOEs. In order to address this issue in studies of the 27 kD compact trimeric domain of the MHC class II-associated invariant chain, we compared the 13C NOESY-HSQC spectrum of a uniformly 13C-labeled trimer with the spectrum of the same trimer labeled with 13C in only one protomer, and with deuterium in the other two protomers. The spectrum of the unmixed trimer included both inter- and intraprotomer NOEs while the spectrum of the mixed trimer included only intraprotomer peaks. NOEs clearly absent from the spectrum of the mixed trimer could be confidently assigned to interprotomer interactions. Asymmetrically labeled trimers were isolated by refolding a 13C-labeled shorter form of the protein with a 2H-labeled longer form, chromatographically purifying trimers with only one short chain, and then processing with trypsin to yield only protomers with the desired N- and C-termini. In contrast to earlier studies, in which statistical mixtures of differently labeled protomers were analyzed, our procedure generated only a well-defined 1:2 oligomer, and no other mixed oligomers were present. This increased the maximum possible concentration of NMR-active protomers and thus the sensitivity of the experiments. Related methods should be applicable to many oligomeric proteins, particularly those with slow protomer exchange rates

Nanomolar oligomerization and selective co-aggregation of α-synuclein pathogenic mutants revealed by single-molecule fluorescence

Science.gov (United States)

Sierecki, Emma; Giles, Nichole; Bowden, Quill; Polinkovsky, Mark E.; Steinbeck, Janina; Arrioti, Nicholas; Rahman, Diya; Bhumkar, Akshay; Nicovich, Philip R.; Ross, Ian; Parton, Robert G.; Böcking, Till; Gambin, Yann

2016-01-01

Protein aggregation is a hallmark of many neurodegenerative diseases, notably Alzheimer’s and Parkinson’s disease. Parkinson’s disease is characterized by the presence of Lewy bodies, abnormal aggregates mainly composed of α-synuclein. Moreover, cases of familial Parkinson’s disease have been linked to mutations in α-synuclein. In this study, we compared the behavior of wild-type (WT) α-synuclein and five of its pathological mutants (A30P, E46K, H50Q, G51D and A53T). To this end, single-molecule fluorescence detection was coupled to cell-free protein expression to measure precisely the oligomerization of proteins without purification, denaturation or labelling steps. In these conditions, we could detect the formation of oligomeric and pre-fibrillar species at very short time scale and low micromolar concentrations. The pathogenic mutants surprisingly segregated into two classes: one group forming large aggregates and fibrils while the other tending to form mostly oligomers. Strikingly, co-expression experiments reveal that members from the different groups do not generally interact with each other, both at the fibril and monomer levels. Together, this data paints a completely different picture of α-synuclein aggregation, with two possible pathways leading to the development of fibrils. PMID:27892477

Experimental Validation of a Coupled Fluid-Multibody Dynamics Model for Tanker Trucks

Science.gov (United States)

2007-11-08

PFEM ) [17] in which the particles are used to generate a polyhedral finite element mesh every time step using an extended Delaunay tesselation. The...interpolation of the solution field onto the new mesh. • Particle methods require a large number of particles to accurately model the free surface. The PFEM

Structural adaptation of the subunit interface of oligomeric thermophilic and hyperthermophilic enzymes.

Science.gov (United States)

Maugini, Elisa; Tronelli, Daniele; Bossa, Francesco; Pascarella, Stefano

2009-04-01

Enzymes from thermophilic and, particularly, from hyperthermophilic organisms are surprisingly stable. Understanding of the molecular origin of protein thermostability and thermoactivity attracted the interest of many scientist both for the perspective comprehension of the principles of protein structure and for the possible biotechnological applications through application of protein engineering. Comparative studies at sequence and structure levels were aimed at detecting significant differences of structural parameters related to protein stability between thermophilic and hyperhermophilic structures and their mesophilic homologs. Comparative studies were useful in the identification of a few recurrent themes which the evolution utilized in different combinations in different protein families. These studies were mostly carried out at the monomer level. However, maintenance of a proper quaternary structure is an essential prerequisite for a functional macromolecule. At the environmental temperatures experienced typically by hyper- and thermophiles, the subunit interactions mediated by the interface must be sufficiently stable. Our analysis was therefore aimed at the identification of the molecular strategies adopted by evolution to enhance interface thermostability of oligomeric enzymes. The variation of several structural properties related to protein stability were tested at the subunit interfaces of thermophilic and hyperthermophilic oligomers. The differences of the interface structural features observed between the hyperthermophilic and thermophilic enzymes were compared with the differences of the same properties calculated from pairwise comparisons of oligomeric mesophilic proteins contained in a reference dataset. The significance of the observed differences of structural properties was measured by a t-test. Ion pairs and hydrogen bonds do not vary significantly while hydrophobic contact area increases specially in hyperthermophilic interfaces. Interface

Synthesis of Zirconium-Containing Polyhedral Oligometallasilsesquioxane as an Efficient Thermal Stabilizer for Silicone Rubber

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Jiedong Qiu

2018-05-01

Full Text Available Free radicals play a negative role during the thermal degradation of silicone rubber (SR. Quenching free radicals is proposed to be an efficient way to improve the thermal-oxidative stability of SR. In this work, a novel zirconium-containing polyhedral oligometallasilsesquioxane (Zr-POSS with free-radical quenching capability was synthesized and characterized. The incorporation of Zr-POSS effectively improved the thermal-oxidative stability of SR. The T5 (temperature at 5% weight loss of SR/Zr-POSS significantly increased by 31.7 °C when compared to the unmodified SR. Notably, after aging 12 h at 280 °C, SR/Zr-POSS was still retaining about 65%, 60%, 75%, and 100% of the tensile strength, tear strength, elongation at break, and hardness before aging, respectively, while the mechanical properties of the unmodified SR were significantly decreased. The possible mechanism of Zr-POSS for improving the thermal-oxidative stability of SR was intensively studied and it was revealed that the POSS structure could act as a limiting point to suppress the random scission reaction of backbone. Furthermore, Zr could quench the free radicals by its empty orbital and transformation of valence states. Therefore, it effectively suppressed the thermal-oxidative degradation and crosslinking reaction of the side chains.

Oligomeric protein structure networks: insights into protein-protein interactions

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Brinda KV

2005-12-01

Full Text Available Abstract Background Protein-protein association is essential for a variety of cellular processes and hence a large number of investigations are being carried out to understand the principles of protein-protein interactions. In this study, oligomeric protein structures are viewed from a network perspective to obtain new insights into protein association. Structure graphs of proteins have been constructed from a non-redundant set of protein oligomer crystal structures by considering amino acid residues as nodes and the edges are based on the strength of the non-covalent interactions between the residues. The analysis of such networks has been carried out in terms of amino acid clusters and hubs (highly connected residues with special emphasis to protein interfaces. Results A variety of interactions such as hydrogen bond, salt bridges, aromatic and hydrophobic interactions, which occur at the interfaces are identified in a consolidated manner as amino acid clusters at the interface, from this study. Moreover, the characterization of the highly connected hub-forming residues at the interfaces and their comparison with the hubs from the non-interface regions and the non-hubs in the interface regions show that there is a predominance of charged interactions at the interfaces. Further, strong and weak interfaces are identified on the basis of the interaction strength between amino acid residues and the sizes of the interface clusters, which also show that many protein interfaces are stronger than their monomeric protein cores. The interface strengths evaluated based on the interface clusters and hubs also correlate well with experimentally determined dissociation constants for known complexes. Finally, the interface hubs identified using the present method correlate very well with experimentally determined hotspots in the interfaces of protein complexes obtained from the Alanine Scanning Energetics database (ASEdb. A few predictions of interface hot

Mutations increasing exposure of a receptor binding site epitope in the soluble and oligomeric forms of the caprine arthritis-encephalitis lentivirus envelope glycoprotein

International Nuclear Information System (INIS)

Hoetzel, Isidro; Cheevers, William P.

2005-01-01

The caprine arthritis-encephalitis (CAEV) and ovine maedi-visna (MVV) viruses are resistant to antibody neutralization, a feature shared with all other lentiviruses. Whether the CAEV gp135 receptor binding site(s) (RBS) in the functional surface envelope glycoprotein (Env) is protected from antibody binding, allowing the virus to resist neutralization, is not known. Two CAEV gp135 regions were identified by extrapolating a gp135 structural model that could affect binding of antibodies to the RBS: the V1 region and a short sequence analogous in position to the human immunodeficiency virus type 1 gp120 loop B postulated to be located between two major domains of CAEV gp135. Mutation of isoleucine-166 to alanine in the putative loop B of gp135 increased the affinity of soluble gp135 for the CAEV receptor(s) and goat monoclonal antibody (Mab) F7-299 which recognizes an epitope overlapping the gp135 RBS. The I166A mutation also stabilized or exposed the F7-299 epitope in anionic detergent buffers, indicating that the I166A mutation induces conformational changes and stabilizes the RBS of soluble gp135 and enhances Mab F7-299 binding. In contrast, the affinity of a V1 deletion mutant of gp135 for the receptor and Mab F7-299 and its structural stability did not differ from that of the wild-type gp135. However, both the I166A mutation and the V1 deletion of gp135 increased cell-to-cell fusion activity and binding of Mab F7-299 to the oligomeric Env. Therefore, the CAEV gp135 RBS is protected from antibody binding by mechanisms both dependent and independent of Env oligomerization which are disrupted by the V1 deletion and the I166A mutation, respectively. In addition, we found a correlation between side-chain β-branching at amino acid position 166 and binding of Mab F7-299 to oligomeric Env and cell-to-cell fusion, suggesting local secondary structure constraints in the region around isoleucine-166 as one determinant of gp135 RBS exposure and antibody binding

Oxygen Plasma Modification of Poss-Coated Kapton(Registered TradeMark) HN Films

Science.gov (United States)

Wohl, C. J.; Belcher, M. A.; Ghose, S.; Connell, J. W.

2008-01-01

The surface energy of a material depends on both surface composition and topographic features. In an effort to modify the surface topography of Kapton(Registered TradeMark) HN film, organic solutions of a polyhedral oligomeric silsesquioxane, octakis(dimethylsilyloxy)silsesquioxane (POSS), were spray-coated onto the Kapton(Registered TradeMark) HN surface. Prior to POSS application, the Kapton(Registered TradeMark) HN film was activated by exposure to radio frequency (RF)-generated oxygen plasma. After POSS deposition and solvent evaporation, the films were exposed to various durations of RF-generated oxygen plasma to create a topographically rich surface. The modified films were characterized using optical microscopy, attenuated total reflection infrared (ATR-IR) spectroscopy, and high-resolution scanning electron microscopy (HRSEM). The physical properties of the modified films will be presented.

Phosphate and HEPES buffers potently affect the fibrillation and oligomerization mechanism of Alzheimer's Aβ peptide

International Nuclear Information System (INIS)

Garvey, Megan; Tepper, Katharina; Haupt, Caroline; Knuepfer, Uwe; Klement, Karolin; Meinhardt, Jessica; Horn, Uwe; Balbach, Jochen; Faendrich, Marcus

2011-01-01

Highlights: → Sodium phosphate buffer accelerated Aβ(1-40) nucleation relative to HEPES. → Aβ(1-40) fibrils formed in the two buffers show only minor structural differences. → NMR revealed that Aβ(1-40) histidine residues mediate buffer dependent changes. -- Abstract: The oligomerization of Aβ peptide into amyloid fibrils is a hallmark of Alzheimer's disease. Due to its biological relevance, phosphate is the most commonly used buffer system for studying the formation of Aβ and other amyloid fibrils. Investigation into the characteristics and formation of amyloid fibrils frequently relies upon material formed in vitro, predominantly in phosphate buffers. Herein, we examine the effects on the fibrillation and oligomerization mechanism of Aβ peptide that occur due solely to the influence of phosphate buffer. We reveal that significant differences in amyloid fibrillation are observed due to fibrillation being initiated in phosphate or HEPES buffer (at physiological pH and temperature). Except for the differing buffer ions, all experimental parameters were kept constant. Fibril formation was assessed using fluorescently monitored kinetic studies, microscopy, X-ray fiber diffraction and infrared and nuclear magnetic resonance spectroscopies. Based on this set up, we herein reveal profound effects on the mechanism and speed of Aβ fibrillation. The three histidine residues at positions 6, 13 and 14 of Aβ(1-40) are instrumental in these mechanistic changes. We conclude that buffer plays a more significant role in fibril formation than has been generally acknowledged.

Constitutive homo- and hetero-oligomerization of TbetaRII-B, an alternatively spliced variant of the mouse TGF-beta type II receptor

DEFF Research Database (Denmark)

Krishnaveni, Manda S; Hansen, Jakob Lerche; Seeger, Werner

2006-01-01

, but the oligomerization pattern and dynamics of TbetaRII splice variants in live cells has not been demonstrated thus far. Using co-immunoprecipitation and bioluminescence resonance energy transfer (BRET), we demonstrate that the mouse TbetaRII receptor splice variant TbetaRII-B is capable of forming ligand...

Reversible unfolding of infectious prion assemblies reveals the existence of an oligomeric elementary brick.

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Angélique Igel-Egalon

2017-09-01

Full Text Available Mammalian prions, the pathogens that cause transmissible spongiform encephalopathies, propagate by self-perpetuating the structural information stored in the abnormally folded, aggregated conformer (PrPSc of the host-encoded prion protein (PrPC. To date, no structural model related to prion assembly organization satisfactorily describes how strain-specified structural information is encoded and by which mechanism this information is transferred to PrPC. To achieve progress on this issue, we correlated the PrPSc quaternary structural transition from three distinct prion strains during unfolding and refolding with their templating activity. We reveal the existence of a mesoscopic organization in PrPSc through the packing of a highly stable oligomeric elementary subunit (suPrP, in which the strain structural determinant (SSD is encoded. Once kinetically trapped, this elementary subunit reversibly loses all replicative information. We demonstrate that acquisition of the templating interface and infectivity requires structural rearrangement of suPrP, in concert with its condensation. The existence of such an elementary brick scales down the SSD support to a small oligomer and provide a basis of reflexion for prion templating process and propagation.

Exceptionally High Electric Double Layer Capacitances of Oligomeric Ionic Liquids.

Science.gov (United States)

Matsumoto, Michio; Shimizu, Sunao; Sotoike, Rina; Watanabe, Masayoshi; Iwasa, Yoshihiro; Itoh, Yoshimitsu; Aida, Takuzo

2017-11-15

Electric double layer (EDL) capacitors are promising as next-generation energy accumulators if their capacitances and operation voltages are both high. However, only few electrolytes can simultaneously fulfill these two requisites. Here we report that an oligomeric ionic liquid such as IL4 TFSI with four imidazolium ion units in its structure provides a wide electrochemical window of ∼5.0 V, similar to monomeric ionic liquids. Furthermore, electrochemical impedance measurements using Au working electrodes demonstrated that IL4 TFSI exhibits an exceptionally high EDL capacitance of ∼66 μF/cm 2 , which is ∼6 times as high as those of monomeric ionic liquids so far reported. We also found that an EDL-based field effect transistor (FET) using IL4 TFSI as a gate dielectric material and SrTiO 3 as a channel material displays a very sharp transfer curve with an enhanced carrier accumulation capability of ∼64 μF/cm 2 , as determined by Hall-effect measurements.

Polyhedral microcrystals encapsulating bone morphogenetic protein 2 improve healing in the alveolar ridge.

Science.gov (United States)

Matsumoto, Goichi; Ueda, Takayo; Sugita, Yoshihiko; Kubo, Katsutoshi; Mizoguchi, Megumi; Kotani, Eiji; Oda, Naoki; Kawamata, Shin; Segami, Natsuki; Mori, Hajime

2015-08-01

Atelocollagen sponges incorporating polyhedra encapsulating bone morphogenetic protein 2 (BMP-2) were implanted into lateral bone defects in the mandible. Half of the bone defects on the left side were treated with atelocollagen sponges containing 1.8 × 10(7) BMP-2 polyhedra, and half were treated with sponges containing 3.6 × 10(6) BMP-2 polyhedra. As controls, we treated the right-side bone defects in each animal with an atelocollagen sponge containing 5 µg of recombinant human BMP-2 (rhBMP-2) or 1.8 × 10(7) empty polyhedral. After a healing period of six months, whole mandibles were removed for micro-computed tomography (CT) and histological analyses. Micro-CT images showed that more bone had formed at all experimental sites than at control sites. However, the density of the new bone was not significantly higher at sites with an atelocollagen sponge containing BMP-2 polyhedra than at sites with an atelocollagen sponge containing rhBMP-2 or empty polyhedra. Histological examination confirmed that the BMP-2 polyhedra almost entirely replaced the atelocollagen sponges and connected the original bone with the regenerated bone. These results show that the BMP-2 delivery system facilitates the regeneration of new bone in the mandibular alveolar bone ridge and has an advance in the technology of bone regeneration for implant site development. © The Author(s) 2015.

Effect of Polyhedral Oligomeric Silsesquioxane (POSS) Substituents on the Rheological Behavior in Butyl Methacrylate/POSS Copolymers

Science.gov (United States)

2008-10-27

was repeated twice, dissolving the product in chloroform and diethyl ether, respectively. The polymer was dried at 60 °C under vacuum overnight...the Tg of the i Bu remains the same. Table 1. Tg for Butyl Methacrylate-co- Propyl Methacryl POSS Polymers with Various POSS Substituents

Model-based recognition of 3-D objects by geometric hashing technique

International Nuclear Information System (INIS)

Severcan, M.; Uzunalioglu, H.

1992-09-01

A model-based object recognition system is developed for recognition of polyhedral objects. The system consists of feature extraction, modelling and matching stages. Linear features are used for object descriptions. Lines are obtained from edges using rotation transform. For modelling and recognition process, geometric hashing method is utilized. Each object is modelled using 2-D views taken from the viewpoints on the viewing sphere. A hidden line elimination algorithm is used to find these views from the wire frame model of the objects. The recognition experiments yielded satisfactory results. (author). 8 refs, 5 figs

Oligomeric rare-earth metal cluster complexes with endohedral transition metal atoms

Energy Technology Data Exchange (ETDEWEB)

Steinberg, Simon; Zimmermann, Sina; Brühmann, Matthias; Meyer, Eva; Rustige, Christian; Wolberg, Marike; Daub, Kathrin; Bell, Thomas; Meyer, Gerd, E-mail: gerd.meyer@uni-koeln.de

2014-11-15

Comproportionation reactions of rare-earth metal trihalides (RX{sub 3}) with the respective rare-earth metals (R) and transition metals (T) led to the formation of 22 oligomeric R cluster halides encapsulating T, in 19 cases for the first time. The structures of these compounds were determined by single-crystal X-ray diffraction and are composed of trimers ((T{sub 3}R{sub 11})X{sub 15}-type, P6{sub 3}/m), tetramers ((T{sub 4}R{sub 16})X{sub 28}(R{sub 4}) (P-43m), (T{sub 4}R{sub 16})X{sub 20} (P4{sub 2}/nnm), (T{sub 4}R{sub 16})X{sub 24}(RX{sub 3}){sub 4} (I4{sub 1}/a) and (T{sub 4}R{sub 16})X{sub 23} (C2/m) types of structure) and pentamers ((Ru{sub 5}La{sub 14}){sub 2}Br{sub 39}, Cc) of (TR{sub r}){sub n} (n=2–5) clusters. These oligomers are further enveloped by inner (X{sup i}) as well as outer (X{sup a}) halido ligands, which possess diverse functionalities and interconnect like oligomers through i–i, i–a and/or a–i bridges. The general features of the crystal structures for these new compounds are discussed and compared to literature entries as well as different structure types with oligomeric T centered R clusters. Dimers and tetramers originating from the aggregation of (TR{sub 6}) octahedra via common edges are more frequent than trimers and pentamers, in which the (TR{sub r}) clusters share common faces. - Graphical abstract: Rare earth-metal cluster complexes with endohedral transition metal atoms (TR{sub 6}) may connect via common edges or faces to form dimers, trimers, tetramers and pentamers of which the tetramers are the most prolific. Packing effects and electron counts play an important role. - Highlights: • Rare-earth metal cluster complexes encapsulate transition metal atoms. • Oligomers are built via connection of octahedral clusters via common edges or faces. • Dimers through pentamers with closed structures are known. • Tetramers including a tetrahedron of endohedral atoms are the most prolific.

Iron-induced oligomerization of human FXN^81-210 and bacterial CyaY frataxin and the effect of iron chelators

DEFF Research Database (Denmark)

Ahlgren, Eva Christina; Fekry, Mostafa; Wiemann, Mathias

2017-01-01

long forms, FXN42-210 and FXN56-210, have been shown to spontaneously form oligomeric particles stabilized by the extended N-terminal sequence. The short variant FXN81-210, on other hand, has only been observed in the monomeric state. However, a highly homologous E. coli frataxin CyaY, which also lacks...

Assessing heterogeneity in oligomeric AAA+ machines.

Science.gov (United States)

Sysoeva, Tatyana A

2017-03-01

ATPases Associated with various cellular Activities (AAA+ ATPases) are molecular motors that use the energy of ATP binding and hydrolysis to remodel their target macromolecules. The majority of these ATPases form ring-shaped hexamers in which the active sites are located at the interfaces between neighboring subunits. Structural changes initiate in an active site and propagate to distant motor parts that interface and reshape the target macromolecules, thereby performing mechanical work. During the functioning cycle, the AAA+ motor transits through multiple distinct states. Ring architecture and placement of the catalytic sites at the intersubunit interfaces allow for a unique level of coordination among subunits of the motor. This in turn results in conformational differences among subunits and overall asymmetry of the motor ring as it functions. To date, a large amount of structural information has been gathered for different AAA+ motors, but even for the most characterized of them only a few structural states are known and the full mechanistic cycle cannot be yet reconstructed. Therefore, the first part of this work will provide a broad overview of what arrangements of AAA+ subunits have been structurally observed focusing on diversity of ATPase oligomeric ensembles and heterogeneity within the ensembles. The second part of this review will concentrate on methods that assess structural and functional heterogeneity among subunits of AAA+ motors, thus bringing us closer to understanding the mechanism of these fascinating molecular motors.

Antibodies against alpha-synuclein reduce oligomerization in living cells.

Directory of Open Access Journals (Sweden)

Thomas Näsström

Full Text Available Recent research implicates soluble aggregated forms of α-synuclein as neurotoxic species with a central role in the pathogenesis of Parkinson's disease and related disorders. The pathway by which α-synuclein aggregates is believed to follow a step-wise pattern, in which dimers and smaller oligomers are initially formed. Here, we used H4 neuroglioma cells expressing α-synuclein fused to hemi:GFP constructs to study the effects of α-synuclein monoclonal antibodies on the early stages of aggregation, as quantified by Bimolecular Fluorescence Complementation assay. Widefield and confocal microscopy revealed that cells treated for 48 h with monoclonal antibodies internalized antibodies to various degrees. C-terminal and oligomer-selective α-synuclein antibodies reduced the extent of α-synuclein dimerization/oligomerization, as indicated by decreased GFP fluorescence signal. Furthermore, ELISA measurements on lysates and conditioned media from antibody treated cells displayed lower α-synuclein levels compared to untreated cells, suggesting increased protein turnover. Taken together, our results propose that extracellular administration of monoclonal antibodies can modify or inhibit early steps in the aggregation process of α-synuclein, thus providing further support for passive immunization against diseases with α-synuclein pathology.

Oligomeric forms of the metastasis-related Mts1 (S100A4) protein stimulate neuronal differentiation in cultures of rat hippocampal neurons

DEFF Research Database (Denmark)

Novitskaya, V; Grigorian, M; Kriajevska, M

2000-01-01

protein family. The oligomeric but not the dimeric form of Mts1 strongly induces differentiation of cultured hippocampal neurons. A mutant with a single Y75F amino acid substitution, which stabilizes the dimeric form of Mts1, is unable to promote neurite extension. Disulfide bonds do not play an essential...

Synthesis of POSS-based ionic conductors with low glass transition temperatures for efficient solid-state dye-sensitized solar cells.

Science.gov (United States)

Zhang, Wei; Wang, Zhong-Sheng

2014-07-09

Replacing liquid-state electrolytes with solid-state electrolytes has been proven to be an effective way to improve the durability of dye-sensitized solar cells (DSSCs). We report herein the synthesis of amorphous ionic conductors based on polyhedral oligomeric silsesquioxane (POSS) with low glass transition temperatures for solid-state DSSCs. As the ionic conductor is amorphous and in the elastomeric state at the operating temperature of DSSCs, good pore filling in the TiO2 film and good interfacial contact between the solid-state electrolyte and the TiO2 film can be guaranteed. When the POSS-based ionic conductor containing an allyl group is doped with only iodine as the solid-state electrolyte without any other additives, power conversion efficiency of 6.29% has been achieved with good long-term stability under one-sun soaking for 1000 h.

Liquid Crystal Microlens Using Nanoparticle-Induced Vertical Alignment

Directory of Open Access Journals (Sweden)

Shug-June Hwang

2015-01-01

Full Text Available The nanoparticle-induced vertical alignment (NIVA of the nematic liquid crystals (LC is applied to achieve an adaptive flat LC microlens with hybrid-aligned nematic (HAN mode by dropping polyhedral oligomeric silsesquioxane (POSS nanoparticle solution on a homogeneous alignment layer. The vertical alignment induced by the POSS nanoparticles resulted in the formation of a hybrid-aligned LC layer with concentric nonuniform distribution of the refractive index in the planar LC cell, which subsequently played the role of the lens, even in the absence of any applied voltages. The dimensions of the concentric HAN structure significantly depend on the volume of the microdroplet and the POSS concentration. The focus effect of this flat microlens was observed while electrically controlling its focal length using the applied voltages from −50 mm to −90 mm.

Polyhedral-Like NiMn-Layered Double Hydroxide/Porous Carbon as Electrode for Enhanced Electrochemical Performance Supercapacitors.

Science.gov (United States)

Yu, Mei; Liu, Ruili; Liu, Jianhua; Li, Songmei; Ma, Yuxiao

2017-11-01

Polyhedral-like NiMn-layered double hydroxide/porous carbon (NiMn-LDH/PC-x) composites are successfully synthesized by hydrothermal method (x = 1, 2 means different mass percent of porous carbon (PC) in composites). The NiMn-LDH/PC-1 composites possess specific capacitance 1634 F g -1 at a current density of 1 A g -1 , and it is much better than that of pure LDH (1095 F g -1 at 1 A g -1 ). Besides, the sample can retain 84.58% of original capacitance after 3000 cycles at 15 A g -1 . An asymmetric supercapacitor with NiMn-LDH/PC-1 as anode and activated carbon as cathode is fabricated, and the supercapacitor can achieve an energy density of 18.60 Wh kg -1 at a power density of 225.03 W kg -1 . The enhanced electrochemical performance attributes to the high faradaic pseudocapacitance of NiMn-LDH, the introduction of PC, and the 3D porous structure of LDH/PC-1 composites. The introduction of PC hinders serious agglomeration of LDH and further accelerates ions transport. The encouraging results indicate that these materials are one of the most potential candidates for energy storage devices. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Shape-controlled synthesis of Pt-Pd core-shell nanoparticles exhibiting polyhedral morphologies by modified polyol method

International Nuclear Information System (INIS)

Long, Nguyen Viet; Asaka, Toru; Matsubara, Takashi; Nogami, Masayuki

2011-01-01

Pt-Pd core-shell nanoparticles were synthesized by a simple synthetic method. First, Pt nanoparticles were synthesized in a controlled manner via the reduction of chloroplantinic acid hexahydrate in ethylene glycol (EG) at 160 deg. C in the presence of silver nitrate and the stabilization of polyvinylpyrrolidon. AgNO 3 used acts as a structure-modifying agent to the morphology of the Pt nanoparticles. These Pt nanoparticles function as the seeds for the successive reduction of sodium tetrachloropalladate (II) hydrate in EG under stirring for 15 min at 160 deg. C in order to synthesize Pt-Pd core-shell nanoparticles. To characterize the as-prepared Pt-Pd nanoparticles, transmission electron microscopy (TEM) and high-resolution TEM are used. The high-resolution elemental mappings were carried out using the combination of scanning TEM and X-ray energy-dispersive spectroscopy. The results also demonstrate the homogeneous nucleation and growth of the Pd metal shell on the definite Pt core. The synthesized Pt-Pd core-shell nanoparticles exhibit a sharp and polyhedral morphology. The epitaxial growth of the controlled Pd shells on the Pt cores via a polyol method was observed. It is suggested that Frank-van der Merwe and Stranski-Krastanov growth modes coexisted in the nucleation and growth of Pt-Pd core-shell nanoparticles.

Insight into the template effect of vesicles on the laccase-catalyzed oligomerization of N-phenyl-1,4-phenylenediamine from Raman spectroscopy and cyclic voltammetry measurements

Science.gov (United States)

Ležaić, Aleksandra Janoševic; Luginbühl, Sandra; Bajuk-Bogdanović, Danica; Pašti, Igor; Kissner, Reinhard; Rakvin, Boris; Walde, Peter; Ćirić-Marjanović, Gordana

2016-08-01

We report about the first Raman spectroscopy study of a vesicle-assisted enzyme-catalyzed oligomerization reaction. The aniline dimer N-phenyl-1,4-phenylenediamine (= p-aminodiphenylamine, PADPA) was oxidized and oligomerized with Trametes versicolor laccase and dissolved O2 in the presence of sodium bis(2-ethylhexyl)sulfosuccinate (AOT) vesicles (80-100 nm diameter) as templates. The conversion of PADPA into oligomeric products, poly(PADPA), was monitored during the reaction by in situ Raman spectroscopy. The results obtained are compared with UV/vis/NIR and EPR measurements. All three complementary methods indicate that at least some of the poly(PADPA) products, formed in the presence of AOT vesicles, resemble the conductive emeraldine salt form of polyaniline (PANI-ES). The Raman measurements also show that structural units different from those of “ordinary” PANI-ES are present too. Without vesicles PANI-ES-like products are not obtained. For the first time, the as-prepared stable poly(PADPA)-AOT vesicle suspension was used directly to coat electrodes (without product isolation) for investigating redox activities of poly(PADPA) by cyclic voltammetry (CV). CV showed that poly(PADPA) produced with vesicles is redox active not only at pH 1.1-as expected for PANI-ES-but also at pH 6.0, unlike PANI-ES and poly(PADPA) synthesized without vesicles. This extended pH range of the redox activity of poly(PADPA) is important for applications.

Oligomerization of adenosin-5´-O-ylmethylphosphonate, an isopolar AMP analogue: Evaluation of the route to short oligoadenylates

Czech Academy of Sciences Publication Activity Database

Pressová, Martina; Buděšínský, Miloš; Kóšiová, Ivana; Kopecký, V. Jr.; Cvačka, Josef; Kašička, Václav; Šimák, Ondřej; Točík, Zdeněk; Rosenberg, Ivan

2010-01-01

Roč. 93, č. 3 (2010), s. 277-289 ISSN 0006-3525 R&D Projects: GA MŠk(CZ) LC06077; GA MŠk(CZ) LC06061; GA AV ČR KAN200520801; GA ČR GA203/09/0820; GA ČR GA202/09/0193 Grant - others:EMIL-FW6(XE) 503569 Institutional research plan: CEZ:AV0Z40550506 Keywords : spontaneous oligomerization * oligoadenylates * phosphonate linkage Subject RIV: CC - Organic Chemistry Impact factor: 2.572, year: 2010

Selective binding and oligomerization of the murine granulocyte colony-stimulating factor receptor by a low molecular weight, nonpeptidyl ligand.

Science.gov (United States)

Doyle, Michael L; Tian, Shin-Shay; Miller, Stephen G; Kessler, Linda; Baker, Audrey E; Brigham-Burke, Michael R; Dillon, Susan B; Duffy, Kevin J; Keenan, Richard M; Lehr, Ruth; Rosen, Jon; Schneeweis, Lumelle A; Trill, John; Young, Peter R; Luengo, Juan I; Lamb, Peter

2003-03-14

Granulocyte colony-stimulating factor regulates neutrophil production by binding to a specific receptor, the granulocyte colony-stimulating factor receptor, expressed on cells of the granulocytic lineage. Recombinant forms of granulocyte colony-stimulating factor are used clinically to treat neutropenias. As part of an effort to develop granulocyte colony-stimulating factor mimics with the potential for oral bioavailability, we previously identified a nonpeptidyl small molecule (SB-247464) that selectively activates murine granulocyte colony-stimulating factor signal transduction pathways and promotes neutrophil formation in vivo. To elucidate the mechanism of action of SB-247464, a series of cell-based and biochemical assays were performed. The activity of SB-247464 is strictly dependent on the presence of zinc ions. Titration microcalorimetry experiments using a soluble murine granulocyte colony-stimulating factor receptor construct show that SB-247464 binds to the extracellular domain of the receptor in a zinc ion-dependent manner. Analytical ultracentrifugation studies demonstrate that SB-247464 induces self-association of the N-terminal three-domain fragment in a manner that is consistent with dimerization. SB-247464 induces internalization of granulocyte colony-stimulating factor receptor on intact cells, consistent with a mechanism involving receptor oligomerization. These data show that small nonpeptidyl compounds are capable of selectively binding and inducing productive oligomerization of cytokine receptors.

Core-6 fucose and the oligomerization of the 1918 pandemic influenza viral neuraminidase

International Nuclear Information System (INIS)

Wu, Zhengliang L.; Zhou, Hui; Ethen, Cheryl M.; Reinhold, Vernon N.

2016-01-01

The 1918 H1N1 influenza virus was responsible for one of the most deadly pandemics in human history. Yet to date, the structure component responsible for its virulence is still a mystery. In order to search for such a component, the neuraminidase (NA) antigen of the virus was expressed, which led to the discovery of an active form (tetramer) and an inactive form (dimer and monomer) of the protein due to different glycosylation. In this report, the N-glycans from both forms were released and characterized by mass spectrometry. It was found that the glycans from the active form had 26% core-6 fucosylated, while the glycans from the inactive form had 82% core-6 fucosylated. Even more surprisingly, the stalk region of the active form was almost completely devoid of core-6-linked fucose. These findings were further supported by the results obtained from in vitro incorporation of azido fucose and "3H-labeled fucose using core-6 fucosyltransferase, FUT8. In addition, the incorporation of fucose did not change the enzymatic activity of the active form, implying that core-6 fucose is not directly involved in the enzymatic activity. It is postulated that core-6 fucose prohibits the oligomerization and subsequent activation of the enzyme. - Graphical abstract: Proposed mechanism for how core-fucose prohibits the tetramerization of the 1918 pandemic viral neuraminidase. Only the cross section of the stalk region with two N-linked glycans are depicted for clarity. (A) Carbohydrate–carbohydrate interaction on non-fucosylated monomer allows tetramerization. (B) Core-fucosylation disrupts the interaction and prevents the tetramerization. - Highlights: • Expressed 1918 pandemic influenza viral neuraminidase has inactive and active forms. • The inactive form contains high level of core-6 fucose, while the active form lacks such modification. • Core fucose could interfere the oligomerization of the neuraminidase and thus its activation. • This discovery may explain why

Core-6 fucose and the oligomerization of the 1918 pandemic influenza viral neuraminidase

Energy Technology Data Exchange (ETDEWEB)

Wu, Zhengliang L., E-mail: Leon.wu@bio-techne.com [Bio-Techne Inc., 614 McKinley Place NE, Minneapolis, MN 55413 (United States); Zhou, Hui [Gregg Hall, UNH Glycomics Center, University of New Hampshire (United States); Ethen, Cheryl M. [Bio-Techne Inc., 614 McKinley Place NE, Minneapolis, MN 55413 (United States); Reinhold, Vernon N., E-mail: Vernon.Reinhold@unh.edu [Gregg Hall, UNH Glycomics Center, University of New Hampshire (United States)

2016-04-29

The 1918 H1N1 influenza virus was responsible for one of the most deadly pandemics in human history. Yet to date, the structure component responsible for its virulence is still a mystery. In order to search for such a component, the neuraminidase (NA) antigen of the virus was expressed, which led to the discovery of an active form (tetramer) and an inactive form (dimer and monomer) of the protein due to different glycosylation. In this report, the N-glycans from both forms were released and characterized by mass spectrometry. It was found that the glycans from the active form had 26% core-6 fucosylated, while the glycans from the inactive form had 82% core-6 fucosylated. Even more surprisingly, the stalk region of the active form was almost completely devoid of core-6-linked fucose. These findings were further supported by the results obtained from in vitro incorporation of azido fucose and {sup 3}H-labeled fucose using core-6 fucosyltransferase, FUT8. In addition, the incorporation of fucose did not change the enzymatic activity of the active form, implying that core-6 fucose is not directly involved in the enzymatic activity. It is postulated that core-6 fucose prohibits the oligomerization and subsequent activation of the enzyme. - Graphical abstract: Proposed mechanism for how core-fucose prohibits the tetramerization of the 1918 pandemic viral neuraminidase. Only the cross section of the stalk region with two N-linked glycans are depicted for clarity. (A) Carbohydrate–carbohydrate interaction on non-fucosylated monomer allows tetramerization. (B) Core-fucosylation disrupts the interaction and prevents the tetramerization. - Highlights: • Expressed 1918 pandemic influenza viral neuraminidase has inactive and active forms. • The inactive form contains high level of core-6 fucose, while the active form lacks such modification. • Core fucose could interfere the oligomerization of the neuraminidase and thus its activation. • This discovery may explain

A S52P mutation in the 'α-crystallin domain' of Mycobacterium leprae HSP18 reduces its oligomeric size and chaperone function.

Science.gov (United States)

Nandi, Sandip K; Rehna, Elengikal A A; Panda, Alok K; Shiburaj, Sugathan; Dharmalingam, Kuppamuthu; Biswas, Ashis

2013-12-01

Mycobacterium leprae HSP18 is a small heat shock protein (sHSP). It is a major immunodominant antigen of M. leprae pathogen. Previously, we have reported the existence of two M. leprae HSP18 variants in various leprotic patients. One of the variants has serine at position 52, whereas the other one has proline at the same position. We have also reported that HSP18 having proline at position 52 (HSP18P(52)) is a nonameric protein and exhibits chaperone function. However, the structural and functional characterization of wild-type HSP18 having serine at position 52 (HSP18S(52)) is yet to be explored. Furthermore, the implications of the S52P mutation on the structure and chaperone function of HSP18 are not well understood. Therefore, we cloned and purified these two HSP18 variants. We found that HSP18S(52) is also a molecular chaperone and an oligomeric protein. Intrinsic tryptophan fluorescence and far-UV CD measurements revealed that the S52P mutation altered the tertiary and secondary structure of HSP18. This point mutation also reduced the oligomeric assembly and decreased the surface hydrophobicity of HSP18, as revealed by HPLC and 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid binding studies, respectively. Mutant protein was less stable against thermal and chemical denaturation and was more susceptible towards tryptic cleavage than wild-type HSP18. HSP18P(52) had lower chaperone function and was less effective in protecting thermal killing of Escherichia coli than HSP18S(52). Taken together, our data suggest that serine 52 is important for the larger oligomerization and chaperone function of HSP18. Because both variants differ in stability and function, they may have different roles in the survival of M. leprae in infected hosts. © 2013 FEBS.

Correlation between crystallization behaviour and interfacial interactions in plasticized PLA/POSS nanocomposites

Energy Technology Data Exchange (ETDEWEB)

Kodal, Mehmet, E-mail: mehmet.kodal@kocaeli.edu.tr; Şirin, Hümeyra; Özkoç, Güralp, E-mail: guralp.ozkoc@kocaeli.edu.tr [Department of Chemical Engineering, Kocaeli University, 41380, Kocaeli Turkey (Turkey)

2016-03-09

In this study, the correlation between crystallization behavior and surface chemistry of polyhedral oligomeric silsesquioxanes (POSS) for plasticized poly(lactic acid) (PLA)/POSS nanocomposites was investigated. Four different kinds of POSS particles having different chemical structures were used. Poly(ethylene glycol) (PEG, 8000 g/mol) was utilized as the plasticiser. The nanocomposites were melt-compounded in an Xplore Instruments 15 cc twin screw microcompounder at 180°C barrel temperature and 100 rpm screw speed. Non-isothermal crystallization behaviour of PLA/PEG/POSS nanocomposites were evaluated from common kinetic models such as Avrami and Avrami-Ozawa and Kissinger by using the thermal data obtained from differantial scanning calorimetry (DSC). A polarized optical microscope (POM) equipped with a hot-stage was used to examine the morphology during the crystal growth. In order to investigate the interfacial interactions between POSS particles and plasticized PLA, thermodynamic work of adhesion approach was adopted using the experimentally determined surface energies. A strong correlation was obtained between interfacial chemistry and the nucleation rate in plasticized PLA/POSS nanocomposites. It was found that the polar interactions were the dominating factor which determines the nucleation activity of the POSS particles.

Correlation between crystallization behaviour and interfacial interactions in plasticized PLA/POSS nanocomposites

International Nuclear Information System (INIS)

Kodal, Mehmet; Şirin, Hümeyra; Özkoç, Güralp

2016-01-01

In this study, the correlation between crystallization behavior and surface chemistry of polyhedral oligomeric silsesquioxanes (POSS) for plasticized poly(lactic acid) (PLA)/POSS nanocomposites was investigated. Four different kinds of POSS particles having different chemical structures were used. Poly(ethylene glycol) (PEG, 8000 g/mol) was utilized as the plasticiser. The nanocomposites were melt-compounded in an Xplore Instruments 15 cc twin screw microcompounder at 180°C barrel temperature and 100 rpm screw speed. Non-isothermal crystallization behaviour of PLA/PEG/POSS nanocomposites were evaluated from common kinetic models such as Avrami and Avrami-Ozawa and Kissinger by using the thermal data obtained from differantial scanning calorimetry (DSC). A polarized optical microscope (POM) equipped with a hot-stage was used to examine the morphology during the crystal growth. In order to investigate the interfacial interactions between POSS particles and plasticized PLA, thermodynamic work of adhesion approach was adopted using the experimentally determined surface energies. A strong correlation was obtained between interfacial chemistry and the nucleation rate in plasticized PLA/POSS nanocomposites. It was found that the polar interactions were the dominating factor which determines the nucleation activity of the POSS particles.

Facile hydrothermal synthesis of polyhedral Fe{sub 3}O{sub 4} nanocrystals, influencing factors and application in the electrochemical detection of H{sub 2}O{sub 2}

Energy Technology Data Exchange (ETDEWEB)

Yuan Kefeng [College of Chemistry and Materials Science, Anhui Key Laboratory of Functional Molecular Solids, Anhui Normal University, Wuhu 241000 (China); Ni Yonghong, E-mail: niyh@mail.ahnu.edu.cn [College of Chemistry and Materials Science, Anhui Key Laboratory of Functional Molecular Solids, Anhui Normal University, Wuhu 241000 (China); Zhang Li [College of Chemistry and Materials Science, Anhui Key Laboratory of Functional Molecular Solids, Anhui Normal University, Wuhu 241000 (China)

2012-08-15

Highlights: Black-Right-Pointing-Pointer Fe{sub 3}O{sub 4} polyhedra had been successfully synthesized by a facile hydrothermal technology. Black-Right-Pointing-Pointer The as-obtained product exhibited the room-temperature ferrimagnetic property. Black-Right-Pointing-Pointer The final product could be prepared into an electrochemical sensor for the detection of H{sub 2}O{sub 2}. - Abstract: Polyhedral Fe{sub 3}O{sub 4} nanocrystals have been successfully synthesized by a facile hydrothermal technique, employing FeSO{sub 4}{center_dot}7H{sub 2}O, N{sub 2}H{sub 4} and NH{sub 3}{center_dot}H{sub 2}O as the reactants without the assistance of any surfactant. The phase of the as-obtained Fe{sub 3}O{sub 4} was characterized by X-ray powder diffraction (XRD) and further proved by Rietveld refinement of XRD data. Energy dispersive spectrometry (EDS) and scanning electron microscopy (SEM) were used for the composition and morphology analyses of the final product. Some factors influencing the formation of polyhedral Fe{sub 3}O{sub 4} nanocrystals were systematically investigated, including the reaction temperature and time, and the original volume ratio of NH{sub 3}{center_dot}H{sub 2}O/N{sub 2}H{sub 4}{center_dot}H{sub 2}O. It was found that the as-prepared Fe{sub 3}O{sub 4} polyhedra exhibited a good electrochemical property in 0.1 M phosphate buffer solution (PBS) with pH 7.0 and could be prepared into an electrochemical sensor for the detection of H{sub 2}O{sub 2}. The linear response range of the sensor was 10.0 Multiplication-Sign 10{sup -6} to 140.0 Multiplication-Sign 10{sup -6} M and a sensitivity was 11.05 {mu}A/mM. Furthermore, the room-temperature magnetic property of the product was also investigated.

Polyhedral Oligomeric Silsesquioxane (POSS) Dianiline as a Replacement for Toxic Methylenedianiline in PMR-15: Chemistry and Properties

Science.gov (United States)

2016-08-22

integrals in the 5.9-6.3ppm region, which correspond to the pair of protons on the double bond of the nadic anhydride endcap, were calibrated to 4. This was...Chapter 4. A piston was inserted into the mold cavity and the mold assembly was placed into a 1-ton heated press to cure. With minimal pressure applied...5824. Web. Wu, S. “Synthesis and Characterization of Semiaromatic Polyimides Containing POSS in Main Chain Derived from Double -Decker-Shaped

Epoxy networks reinforced with polyhedral oligomeric silsesquioxanes: structure and segmental dynamics as studied by solid-state NMR

Czech Academy of Sciences Publication Activity Database

Brus, Jiří; Urbanová, Martina; Strachota, Adam

2008-01-01

Roč. 41, č. 2 (2008), s. 372-386 ISSN 0024-9297 R&D Projects: GA AV ČR IAA400500602 Institutional research plan: CEZ:AV0Z40500505 Keywords : solid-state NMR * polymer networks * polysilsequioxanes Subject RIV: CD - Macromolecular Chemistry Impact factor: 4.407, year: 2008

Hydrolyzable Tannins of Tamaricaceous Plants. 7.1 Structures and Cytotoxic Properties of Oligomeric Ellagitannins from Leaves of Tamarix nilotica and Cultured Tissues of Tamarix tetrandra.

Science.gov (United States)

Orabi, Mohamed A A; Taniguchi, Shoko; Sakagami, Hiroshi; Yoshimura, Morio; Amakura, Yoshiaki; Hatano, Tsutomu

2016-04-22

Partially unacylated new oligomeric hydrolyzable tannins, nilotinin T2 (1, trimer) and nilotinin Q1 (2, tetramer), together with four known trimers, nilotinin T1 (3) and hirtellins T1-T3 (4-6), and a dimer, tamarixinin B (7), were isolated from the aqueous acetone extracts of leaves of Tamarix nilotica. Among them, the new trimer 1 and the known trimers 4 and 6, in addition to the partially unacylated new trimer nilotinin T3 (8), the known dimers nilotinin D3 (9) and tamarixinin C (10), and the monomer tellimagrandin I (11), were isolated from the cultured shoots of Tamarix tetrandra. The structures of the new hydrolyzable tannins were established by chromatographic analyses and extensive 1D and 2D NMR, HRESI-TOFMS, and ECD spectroscopic experiments. Among the new oligomeric tannins, the particular unacylated position of a glucose core is attributed to a possible biosynthetic route. Isolation of the same oligomeric tannins from cultured shoots of T. tetrandra emphasizes the unique biogenetic ability of the obtained cultures on production of the structurally and biologically characteristic tamaricaceous tannins commonly produced by the intact Tamarix plants. Additionally, tannins obtained in the present study together with gemin D (12) and 1,3-di-O-galloyl-4,6-O-(aS)-hexahydroxydiphenoyl-β-d-glucose (13), from our previous investigation of the leaves of T. nilotica, exhibited variable tumor-specific cytotoxic effects. The ellagitannin trimers 4, 6, and 8 and the dimer 9 exerted predominant tumor-selective cytotoxic effects with high specificity toward human promyelocytic leukemia cells.

Oligomeric recombinant H5 HA1 vaccine produced in bacteria protects ferrets from homologous and heterologous wild-type H5N1 influenza challenge and controls viral loads better than subunit H5N1 vaccine by eliciting high-affinity antibodies.

Science.gov (United States)

Verma, Swati; Dimitrova, Milena; Munjal, Ashok; Fontana, Juan; Crevar, Corey J; Carter, Donald M; Ross, Ted M; Khurana, Surender; Golding, Hana

2012-11-01

Recombinant hemagglutinin from influenza viruses with pandemic potential can be produced rapidly in various cell substrates. In this study, we compared the functionality and immunogenicity of bacterially produced oligomeric or monomeric HA1 proteins from H5N1 (A/Vietnam/1203/04) with those of the egg-based licensed subunit H5N1 (SU-H5N1) vaccine in ferrets challenged with homologous or heterologous H5N1 highly pathogenic influenza strains. Ferrets were vaccinated twice with the oligomeric or monomeric rHA1 or with SU-H5N1 (Sanofi Pasteur) emulsified with Titermax adjuvant and were challenged with wild-type homologous (A/Vietnam/1203/04; clade 1) or heterologous (A/Whooperswan/Mongolia/244/2005; clade 2.2) virus. Only the oligomeric rHA1 (not the monomeric rHA1) immunogen and the SU-H5N1 vaccine provided protection against the lethality and morbidity of homologous and heterologous highly pathogenic H5N1. Oligomeric rHA1 generated more cross-neutralizing antibodies and higher levels of serum antibody binding to HA1, with stronger avidity and a better IgG/IgM ratio, than monomeric HA1 and SU-H5N1 vaccines, as determined by surface plasmon resonance (SPR). Importantly, viral loads after heterologous H5N1 challenge were more efficiently controlled in ferrets vaccinated with the oligomeric rHA1 immunogen than in SU-H5N1-vaccinated ferrets. The reduction of viral loads in the nasal washes correlated strongly with higher-avidity antibodies to oligomeric rHA1 derived from H5N1 clade 1 and clade 2.2 viruses, as measured by SPR. This is the first study to show the role of antibody avidity for the HA1 globular head domain in reduction of viral loads in the upper respiratory tract, which could significantly reduce viral transmission.

Diverse oligomeric states of CEACAM IgV domains.

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Bonsor, Daniel A; Günther, Sebastian; Beadenkopf, Robert; Beckett, Dorothy; Sundberg, Eric J

2015-11-03

Carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) comprise a large family of cell surface adhesion molecules that bind to themselves and other family members to carry out numerous cellular functions, including proliferation, signaling, differentiation, tumor suppression, and survival. They also play diverse and significant roles in immunity and infection. The formation of CEACAM oligomers is caused predominantly by interactions between their N-terminal IgV domains. Although X-ray crystal structures of CEACAM IgV domain homodimers have been described, how CEACAMs form heterodimers or remain monomers is poorly understood. To address this key aspect of CEACAM function, we determined the crystal structures of IgV domains that form a homodimeric CEACAM6 complex, monomeric CEACAM8, and a heterodimeric CEACAM6-CEACAM8 complex. To confirm and quantify these interactions in solution, we used analytical ultracentrifugation to measure the dimerization constants of CEACAM homodimers and isothermal titration calorimetry to determine the thermodynamic parameters and binding affinities of CEACAM heterodimers. We found the CEACAM6-CEACAM8 heterodimeric state to be substantially favored energetically relative to the CEACAM6 homodimer. Our data provide a molecular basis for the adoption of the diverse oligomeric states known to exist for CEACAMs and suggest ways in which CEACAM6 and CEACAM8 regulate the biological functions of one another, as well as of additional CEACAMs with which they interact, both in cis and in trans.

A novel POSS-coated quantum dot for biological application

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Rizvi SB

2012-08-01

Full Text Available Sarwat B Rizvi,1 Lara Yildirimer,1 Shirin Ghaderi,1 Bala Ramesh,1 Alexander M Seifalian,1,2 Mo Keshtgar1,21UCL Centre for Nanotechnology and Regenerative Medicine, Division of Surgery and Interventional Science, University College London, United Kingdom; 2Royal Free Hampstead NHS Trust Hospital, London, United KingdomAbstract: Quantum dots (QDs are fluorescent semiconductor nanocrystals that have the potential for major advancements in the field of nanomedicine through their unique photophysical properties. They can potentially be used as fluorescent probes for various biomedical imaging applications, including cancer localization, detection of micrometastasis, image guided surgery, and targeted drug delivery. Their main limitation is toxicity, which requires a biologically compatible surface coating to shield the toxic core from the surrounding environment. However, this leads to an increase in QD size that may lead to problems of excretion and systemic sequestration. We describe a one pot synthesis, characterization, and in vitro cytotoxicity of a novel polyhedral oligomeric silsesquioxane (POSS-coated CdTe-cored QD using mercaptosuccinic acid (MSA and D-cysteine as stabilizing agents. Characterization was performed using transmission electron microscopy Fourier transform infrared spectroscopy, and photoluminescence studies. POSS-coated QDs demonstrated high colloidal stability and enhanced photostability on high degrees of ultraviolet (UV excitation compared to QDs coated with MSA and D-cysteine alone (P value < 0.05. In vitro toxicity studies showed that both POSS and MSA-QDs were significantly less toxic than ionized salts of Cd+2 and Te-2. Confocal microscopy confirmed high brightness of POSS-QDs in cells at both 1 and 24 hours, indicating that these QDs are rapidly taken up by cells and remain photostable in a biological environment. We therefore conclude that a POSS coating confers biological compatibility, photostability, and colloidal

The slice balance approach (SBA): a characteristic-based, multiple balance SN approach on unstructured polyhedral meshes

International Nuclear Information System (INIS)

Grove, R.E.

2005-01-01

The Slice Balance Approach (SBA) is an approach for solving geometrically-complex, neutral-particle transport problems within a multi-group discrete ordinates (S N ) framework. The salient feature is an angle-dependent spatial decomposition. We approximate general surfaces with arbitrary polygonal faces and mesh the geometry with arbitrarily-shaped polyhedral cells. A cell-local spatial decomposition divides cells into angle-dependent slices for each S N direction. This subdivision follows from a characteristic-based view of the transport problem. Most balance-based characteristic methods use it implicitly; we use it explicitly and exploit its properties. Our mathematical approach is a multiple balance approach using exact spatial moments balance equations on cells and slices along with auxiliary relations on slices. We call this the slice balance approach; it is a characteristic-based multiple balance approach. The SBA is intentionally general and can extend differencing schemes to arbitrary 2-D and 3-D meshes. This work contributes to development of general-geometry deterministic transport capability to complement Monte Carlo capability for large, geometrically-complex transport problems. The purpose of this paper is to describe the SBA. We describe the spatial decomposition and mathematical framework and highlight a few interesting properties. We sketch the derivation of two solution schemes, a step characteristic scheme and a diamond-difference-like scheme, to illustrate the approach and we present interesting results for a 2-D problem. (author)

Carbon Domains on MoS2/TiO2 System via Catalytic Acetylene Oligomerization: Synthesis, Structure, and Surface Properties

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Sara Cravanzola

2017-11-01

Full Text Available Carbon domains have been obtained at the surface of a MoS2/TiO2 (Evonik, P25 system via oligomerization and cyclotrimerization reactions involved in the interaction of the photoactive material with acetylene. Firstly, MoS2 nanosheets have been synthesized at the surface of TiO2, via sulfidation of a molybdenum oxide precursor with H2S (bottom-up method. Secondly, the morphology and the structure, the optical and the vibrational properties of the obtained materials, for each step of the synthesis procedure, have been investigated by microscopy and spectroscopy methods. In particular, transmission electron microscopy images provide a simple tool to highlight the effectiveness of the sulfidation process, thus showing 1L, 2L, and stacked MoS2 nanosheets anchored to the surface of TiO2 nanoparticles. Lastly, in-situ FTIR spectroscopy investigation gives insights into the nature of the oligomerized species, showing that the formation of both polyenic and aromatic systems can be taken into account, being their formation promoted by both Ti and Mo catalytic sites. This finding gives an opportunity for the assembly of extended polyenic, polyaromatic, or mixed domains firmly attached at the surface of photoactive materials. The presented approach, somehow different from the carbon adding or doping processes of TiO2, is of potential interest for the advanced green chemistry and energy conversion/transport applications.

Protective Effects of Testosterone on Presynaptic Terminals against Oligomeric β-Amyloid Peptide in Primary Culture of Hippocampal Neurons

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Chi-Fai Lau

2014-01-01

Full Text Available Increasing lines of evidence support that testosterone may have neuroprotective effects. While observational studies reported an association between higher bioavailable testosterone or brain testosterone levels and reduced risk of Alzheimer’s disease (AD, there is limited understanding of the underlying neuroprotective mechanisms. Previous studies demonstrated that testosterone could alleviate neurotoxicity induced by β-amyloid (Aβ, but these findings mainly focused on neuronal apoptosis. Since synaptic dysfunction and degeneration are early events during the pathogenesis of AD, we aim to investigate the effects of testosterone on oligomeric Aβ-induced synaptic changes. Our data suggested that exposure of primary cultured hippocampal neurons to oligomeric Aβ could reduce the length of neurites and decrease the expression of presynaptic proteins including synaptophysin, synaptotagmin, and synapsin-1. Aβ also disrupted synaptic vesicle recycling and protein folding machinery. Testosterone preserved the integrity of neurites and the expression of presynaptic proteins. It also attenuated Aβ-induced impairment of synaptic exocytosis. By using letrozole as an aromatase antagonist, we further demonstrated that the effects of testosterone on exocytosis were unlikely to be mediated through the estrogen receptor pathway. Furthermore, we showed that testosterone could attenuate Aβ-induced reduction of HSP70, which suggests a novel mechanism that links testosterone and its protective function on Aβ-induced synaptic damage. Taken together, our data provide further evidence on the beneficial effects of testosterone, which may be useful for future drug development for AD.

Formation of semisolid, oligomerized aqueous SOA: lab simulations of cloud processing.

Science.gov (United States)

Hawkins, Lelia N; Baril, Molly J; Sedehi, Nahzaneen; Galloway, Melissa M; De Haan, David O; Schill, Gregory P; Tolbert, Margaret A

2014-02-18

Glyoxal, methylglyoxal, glycolaldehyde, and hydroxyacetone form N-containing and oligomeric compounds during simulated cloud processing with small amines. Using a novel hygroscopicity tandem differential mobility analysis (HTDMA) system that allows varied humidification times, the hygroscopic growth (HG) of each of the resulting products of simulated cloud processing was measured. Continuous water uptake (gradual deliquescence) was observed beginning at ∼ 40% RH for all aldehyde-methylamine products. Particles containing ionic reaction products of either glyoxal or glycine were most hygroscopic, with HG between 1.16 and 1.20 at 80% RH. Longer humidification times (up to 20 min) produced an increase in growth factors for glyoxal-methylamine (19% by vol) and methylglyoxal-methylamine (8% by vol) aerosol, indicating that unusually long equilibration times can be required for HTDMA measurements of such particles. Glyoxal- and methylglyoxal-methylamine aerosol particles shattered in Raman microscopy impact-flow experiments, revealing that the particles were semisolid. Similar experiments on glycolaldehyde- and hydroxyacetone-methylamine aerosol found that the aerosol particles were liquid when dried for glyoxal > glycolaldehyde = hydroxyacetone, likely caused by the speed of oligomer formation in each system.

Assembly of the intrinsic factor domains and oligomerization of the protein in the presence of cobalamin

DEFF Research Database (Denmark)

Fedosov, Sergey N; Fedosova, Natalya U; Berglund, Lars

2004-01-01

oligomerized. A mixture of two fragments IF(30) + IF(20) and Cbl produced a firm complex, IF(30+20).Cbl, which could not associate to dimers. In contrast to IF(30+20).Cbl, the saturated full-length monomers IF(50).Cbl dimerized with K(d) approximately 1 microM. We suggest a two-domain organization of the full......-length protein, where two distant units, IF(30) and IF(20), can be assembled only by Cbl. They are connected by a protease-sensitive link, whose native structure is likely to be important for dimerization. However, linkage between two domains is not compulsory for Cbl binding. Advantages of the two...

Novel elastomer dye-functionalised POSS nanocomposites: Enhanced colourimetric, thermomechanical and thermal properties

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R. A. Shanks

2012-05-01

Full Text Available Nanocomposites consisting of poly(styrene-b-butadiene-b-styrene (SBS and polyhedral oligomeric silsesquioxanes (POSS were prepared using a solvent dispersion method. POSS molecules were functionalised with two dichlorotriazine reactive dyes (CI Reactive Blue 4, CI Reactive Red 2 prior to compounding. Infrared spectroscopy confirmed functionalisation.Scanning electron microscopy revealed an increase in filler aggregation with concentration, with preferential phase selectivity. Ultraviolet spectroscopy and colourimetry confirmed colour uniformity and suggested that colour intensity could be controlled. Functionalised POSS improved thermal stability by imparting restrictions on SBS chain motions. Tensile stress-strain analysis revealed an increase in modulus with filler concentration, while creep deformation decreased and permanent strain increased with POSS content. Storage modulus, loss modulus and glass transition temperature increased with filler content due to effective SBS-POSS interaction. Nanocomposite properties were influenced by the phase the filler was dispersed throughout and the structure of the dye chromophore.

Structure of the large terminase from a hyperthermophilic virus reveals a unique mechanism for oligomerization and ATP hydrolysis.

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Xu, Rui-Gang; Jenkins, Huw T; Antson, Alfred A; Greive, Sandra J

2017-12-15

The crystal structure of the large terminase from the Geobacillus stearothermophilus bacteriophage D6E shows a unique relative orientation of the N-terminal adenosine triphosphatase (ATPase) and C-terminal nuclease domains. This monomeric 'initiation' state with the two domains 'locked' together is stabilized via a conserved C-terminal arm, which may interact with the portal protein during motor assembly, as predicted for several bacteriophages. Further work supports the formation of an active oligomeric state: (i) AUC data demonstrate the presence of oligomers; (ii) mutational analysis reveals a trans-arginine finger, R158, indispensable for ATP hydrolysis; (iii) the location of this arginine is conserved with the HerA/FtsK ATPase superfamily; (iv) a molecular docking model of the pentamer is compatible with the location of the identified arginine finger. However, this pentameric model is structurally incompatible with the monomeric 'initiation' state and is supported by the observed increase in kcat of ATP hydrolysis, from 7.8 ± 0.1 min-1 to 457.7 ± 9.2 min-1 upon removal of the C-terminal nuclease domain. Taken together, these structural, biophysical and biochemical data suggest a model where transition from the 'initiation' state into a catalytically competent pentameric state, is accompanied by substantial domain rearrangements, triggered by the removal of the C-terminal arm from the ATPase active site. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Structure-based design of a disulfide-linked oligomeric form of the simian virus 40 (SV40) large T antigen DNA-binding domain

International Nuclear Information System (INIS)

Meinke, Gretchen; Phelan, Paul; Fradet-Turcotte, Amélie; Archambault, Jacques; Bullock, Peter A.

2011-01-01

With the aim of forming the ‘lock-washer’ conformation of the origin-binding domain of SV40 large T antigen in solution, using structure-based analysis an intermolecular disulfide bridge was engineered into the origin-binding domain to generate higher order oligomers in solution. The 1.7 Å resolution structure shows that the mutant forms a spiral in the crystal and has the de novo disulfide bond at the protein interface, although structural rearrangements at the interface are observed relative to the wild type. The modular multifunctional protein large T antigen (T-ag) from simian virus 40 orchestrates many of the events needed for replication of the viral double-stranded DNA genome. This protein assembles into single and double hexamers on specific DNA sequences located at the origin of replication. This complicated process begins when the origin-binding domain of large T antigen (T-ag ODB) binds the GAGGC sequences in the central region (site II) of the viral origin of replication. While many of the functions of purified T-ag OBD can be studied in isolation, it is primarily monomeric in solution and cannot assemble into hexamers. To overcome this limitation, the possibility of engineering intermolecular disulfide bonds in the origin-binding domain which could oligomerize in solution was investigated. A recent crystal structure of the wild-type T-ag OBD showed that this domain forms a left-handed spiral in the crystal with six subunits per turn. Therefore, we analyzed the protein interface of this structure and identified two residues that could potentially support an intermolecular disulfide bond if changed to cysteines. SDS–PAGE analysis established that the mutant T-ag OBD formed higher oligomeric products in a redox-dependent manner. In addition, the 1.7 Å resolution crystal structure of the engineered disulfide-linked T-ag OBD is reported, which establishes that oligomerization took place in the expected manner

Convenient Model for Systems with Hystereses-Control

DEFF Research Database (Denmark)

Wisniewski, Rafal; Leth, John-Josef

2011-01-01

We establish a model of a system with hystereses, which allows for standard stability analysis of fixed points and closed orbits. To this end, we represent a system with hystereses as a piecewise-affine switched system that consists of a family of dynamical systems defined on disjoint polyhedral ....... Thereby, the analysis of a system with hystereses can be seen as the analysis of a dynamical system on a manifold, locally in chars. This dynamical system corresponds to a differential equation with discontinuous right hand side which solution is shown to exist and to be unique....

Combining 3d Volume and Mesh Models for Representing Complicated Heritage Buildings

Science.gov (United States)

Tsai, F.; Chang, H.; Lin, Y.-W.

2017-08-01

This study developed a simple but effective strategy to combine 3D volume and mesh models for representing complicated heritage buildings and structures. The idea is to seamlessly integrate 3D parametric or polyhedral models and mesh-based digital surfaces to generate a hybrid 3D model that can take advantages of both modeling methods. The proposed hybrid model generation framework is separated into three phases. Firstly, after acquiring or generating 3D point clouds of the target, these 3D points are partitioned into different groups. Secondly, a parametric or polyhedral model of each group is generated based on plane and surface fitting algorithms to represent the basic structure of that region. A "bare-bones" model of the target can subsequently be constructed by connecting all 3D volume element models. In the third phase, the constructed bare-bones model is used as a mask to remove points enclosed by the bare-bones model from the original point clouds. The remaining points are then connected to form 3D surface mesh patches. The boundary points of each surface patch are identified and these boundary points are projected onto the surfaces of the bare-bones model. Finally, new meshes are created to connect the projected points and original mesh boundaries to integrate the mesh surfaces with the 3D volume model. The proposed method was applied to an open-source point cloud data set and point clouds of a local historical structure. Preliminary results indicated that the reconstructed hybrid models using the proposed method can retain both fundamental 3D volume characteristics and accurate geometric appearance with fine details. The reconstructed hybrid models can also be used to represent targets in different levels of detail according to user and system requirements in different applications.

Computational Study of the Effect of Confinement within Microporous Structures on the Activity and Selectivity of Metallocene Catalysts for Ethylene Oligomerization

KAUST Repository

Toulhoat, Hervé

2011-03-02

The effect of confinement within some zeolitic structures on the activity and selectivity of metallocene catalysts for the ethylene oligomerization has been investigated using grand canonical Monte Carlo simulations (GCMC). The following zeolite (host) frameworks displaying different pore sizes, have been studied as solid hosts: mazzite (MAZ), AIPO-8 (AET), UTD-1F (DON), faujasite (FAU), and VPI-5 (VFI). Intermediates and transition states involved in the ethylene trimerization reaction catalyzed by a Ti-based catalyst [(η5-C5H4CMe2C6H 5)TiCl3/MAO] have been used as sorbates (guests). We have demonstrated linear correlations with slope aH,j between the adsorption enthalpy and the molecular volume Vm of the sorbates, each holding for a given microporous host below a host-specific threshold V mmax,j. Beyond this maximal molecular volume, the adsorption vanishes due to steric exclusion. aH,j increases, and Vmmax,j decreases with decreasing host pore size, in line with the confinement concept. We moreover showed that, in the limit of vanishing loading (Henry regime), the enthalpies and entropies of adsorption in a given host are linearly correlated. We have defined a host-specific confinement compensation temperature a j, which refers to a temperature where the stabilizing adsorption enthalpic interactions are canceled out against the loss in entropy. However, calculated aj are much larger than the operating temperatures. With a setup microkinetic model, we predict that the activity and selectivity of the confined Ti-catalyst in ethylene oligomerization can be significantly altered with respect to homogeneous phase conditions, since the adsorption free energies of transition states and intermediates also become functions of aH,j and Vm. We have applied this theory to predict the optimum host pore size to get maximum α-octene production, instead of α-hexene, which is primarily produced in the homogeneous phase. We also predict a significantly increased activity for

Grain breakage under uniaxial compression, through 3D DEM modelling

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Nader François

2017-01-01

Full Text Available A breakable grain model is presented, using the concept of particles assembly. Grains of polyhedral shapes are generated, formed by joining together tetrahedral subgrains using cohesive bonds. Single grain crushing simulations are performed for multiple values of the intra-granular cohesion to study the effect on the grain’s strength. The same effect of intra-granular cohesion is studied under oedometric compression on samples of around 800 grains, which allows the evaluation of grain breakage model on the macroscopic behaviour. Grain size distribution curves and grain breakage ratios are monitored throughout the simulations.

Assessment of Escherichia coli selenophosphate synthetase oligomeric states by analytical ultracentrifugation and small angle X-ray scattering

Energy Technology Data Exchange (ETDEWEB)

Silva, I.R.; Faim, F.M.; Oliveira Neto, M.; Thiemann, O.H. [Universidade de Sao Paulo (USP-SC), Sao Carlos, SP (Brazil); Borges, J.C. [Universidade de Sao Paulo (IQSC/USP), Sao Carlos, SP (Brazil). Inst. de Quimica

2012-07-01

Full text: Selenium is an essential micronutrient for many organisms and is present in selenium-containing proteins as selenocysteine (Sec) and RNAs as selenouridine. Specific selenium incorporation into selenoproteins and RNAs requires the generation of a biologically active selenium donor compound, selenophosphate, which is produced from the activation of selenide with adenosine 5-triphosphate (ATP) in a reaction catalyzed by Selenophosphate Synthetase (SELD). Therefore, SELD is a key enzyme of the selenium pathway in the cell. The Escherichia coli SELD open reading frame was cloned into pET28a (Novagen) expression vector and the recombinant protein was over expressed in Escherichia coli BL21(DE3) strain. In order to purify the protein, we used metal-chelate affinity chromatography followed by a gel filtration step. Analytical Ultracentrifugation (AUC) and Small Angle X-ray Scattering (SAXS) were employed to study the oligomeric states of the soluble protein. The results of AUC revealed dimer-tetramer and tetramer-octamer equilibrium at low concentrations of protein, with dissociation constants of 70 2 and 560 40 M, respectively. Moreover, the SAXS results pointed the oligomeric state of the protein at higher concentrations as predominantly dimeric and the p(r) and the SAXS envelope revealed the SELD as elongated. We also performed initial crystallization trials with protein samples at 7 mg/ml in 96-well sitting-drop crystallization plates at room temperature using a crystallization robot. Needle crystals appeared after some days. X-ray diffraction for these crystals were tested in the MX2 beamline at the Brazilian Synchrotron Laboratory (LNLS Campinas). We are now working to improve these crystals in order to obtain suitable crystals for structure determination. (author)

IntraGolgi distribution of the Conserved Oligomeric Golgi (COG) complex

International Nuclear Information System (INIS)

Vasile, Eliza; Oka, Toshihiko; Ericsson, Maria; Nakamura, Nobuhiro; Krieger, Monty

2006-01-01

The Conserved Oligomeric Golgi (COG) complex is an eight-subunit (Cog1-8) peripheral Golgi protein involved in membrane trafficking and glycoconjugate synthesis. COG appears to participate in retrograde vesicular transport and is required to maintain normal Golgi structure and function. COG mutations interfere with normal transport, distribution, and/or stability of Golgi proteins associated with glycoconjugate synthesis and trafficking, and lead to failure of spermatogenesis in Drosophila melanogaster, misdirected migration of gonadal distal tip cells in Caenorhabditis elegans, and type II congenital disorders of glycosylation in humans. The mechanism by which COG influences Golgi structure and function is unclear. Immunogold electron microscopy was used to visualize the intraGolgi distribution of a functional, hemagglutinin epitope-labeled COG subunit, Cog1-HA, that complements the Cog1-deficiency in Cog1-null Chinese hamster ovary cells. COG was found to be localized primarily on or in close proximity to the tips and rims of the Golgi's cisternae and their associated vesicles and on vesicles and vesiculo-tubular structures seen on both the cis and trans-Golgi Network faces of the cisternal stacks, in some cases on COPI containing vesicles. These findings support the proposal that COG is directly involved in controlling vesicular retrograde transport of Golgi resident proteins throughout the Golgi apparatus

One motif to bind them: A small-XXX-small motif affects transmembrane domain 1 oligomerization, function, localization, and cross-talk between two yeast GPCRs.

Science.gov (United States)

Lock, Antonia; Forfar, Rachel; Weston, Cathryn; Bowsher, Leo; Upton, Graham J G; Reynolds, Christopher A; Ladds, Graham; Dixon, Ann M

2014-12-01

G protein-coupled receptors (GPCRs) are the largest family of cell-surface receptors in mammals and facilitate a range of physiological responses triggered by a variety of ligands. GPCRs were thought to function as monomers, however it is now accepted that GPCR homo- and hetero-oligomers also exist and influence receptor properties. The Schizosaccharomyces pombe GPCR Mam2 is a pheromone-sensing receptor involved in mating and has previously been shown to form oligomers in vivo. The first transmembrane domain (TMD) of Mam2 contains a small-XXX-small motif, overrepresented in membrane proteins and well-known for promoting helix-helix interactions. An ortholog of Mam2 in Saccharomyces cerevisiae, Ste2, contains an analogous small-XXX-small motif which has been shown to contribute to receptor homo-oligomerization, localization and function. Here we have used experimental and computational techniques to characterize the role of the small-XXX-small motif in function and assembly of Mam2 for the first time. We find that disruption of the motif via mutagenesis leads to reduction of Mam2 TMD1 homo-oligomerization and pheromone-responsive cellular signaling of the full-length protein. It also impairs correct targeting to the plasma membrane. Mutation of the analogous motif in Ste2 yielded similar results, suggesting a conserved mechanism for assembly. Using co-expression of the two fungal receptors in conjunction with computational models, we demonstrate a functional change in G protein specificity and propose that this is brought about through hetero-dimeric interactions of Mam2 with Ste2 via the complementary small-XXX-small motifs. This highlights the potential of these motifs to affect a range of properties that can be investigated in other GPCRs. Copyright © 2014. Published by Elsevier B.V.

Ion Channel Conformation and Oligomerization Assessment by Site-Directed Spin Labeling and Pulsed-EPR.

Science.gov (United States)

Pliotas, Christos

2017-01-01

Mechanosensitive (MS) ion channels are multimeric integral membrane proteins that respond to increased lipid bilayer tension by opening their nonselective pores to release solutes and relieve increased cytoplasmic pressure. These systems undergo major conformational changes during gating and the elucidation of their mechanism requires a deep understanding of the interplay between lipids and proteins. Lipids are responsible for transmitting lateral tension to MS channels and therefore play a key role in obtaining a molecular-detail model for mechanosensation. Site-directed spin labeling combined with electron paramagnetic resonance (EPR) spectroscopy is a powerful spectroscopic tool in the study of proteins. The main bottleneck for its use relates to challenges associated with successful isolation of the protein of interest, introduction of paramagnetic labels on desired sites, and access to specialized instrumentation and expertise. The design of sophisticated experiments, which combine a variety of existing EPR methodologies to address a diversity of specific questions, require knowledge of the limitations and strengths, characteristic of each particular EPR method. This chapter is using the MS ion channels as paradigms and focuses on the application of different EPR techniques to ion channels, in order to investigate oligomerization, conformation, and the effect of lipids on their regulation. The methodology we followed, from the initial strategic selection of mutants and sample preparation, including protein purification, spin labeling, reconstitution into lipid mimics to the complete set-up of the pulsed-EPR experiments, is described in detail. © 2017 Elsevier Inc. All rights reserved.

Porous polyhedral and fusiform Co3O4 anode materials for high-performance lithium-ion batteries

International Nuclear Information System (INIS)

Huang, Guoyong; Xu, Shengming; Lu, Shasha; Li, Linyan; Sun, Hongyu

2014-01-01

Graphical abstract: - Abstract: Co 3 O 4 is commonly used as a potential anode material for Li-ion batteries (LIBs). In this study, novel porous polyhedral and fusiform Co 3 O 4 powders have been synthesized successfully through the hydrothermal method with different solvents followed by thermal treatment. It is shown that both of the polyhedrons (1.0-3.0 μm in side length) and the spindles (2.0-5.0 μm in length, 0.5-2.0 μm in width) are composed of similar irregular nanoparticles (20-200 nm in diameter, 20-40 nm in thickness) bonded to each other. Evaluated by electrochemical measurements, both of them have high initial discharge capacities (1374.4 mAhg −1 and 1326.3 mAhg −1 ) and enhanced cycling stabilities at the low rate (the capacity retention ratios at 0.1 C after 70 cycles are 91.6% and 92.2%, respectively). However, the rate capability of the spindles (93.8%, 90.1% and 98.9% of the second discharge capacities after 70 cycles at 0.5 C, 1 C and 2 C, respectively) is better than the polyhedrons’ (only 76.2%, 42.1% and 59.3% under the same conditions). Remarkable, the unique morphologies and special structures may be extended to synthesize other similar transition metal oxides (NiO, Fe 3 O 4 , et al.) as high performance anodes for LIBs

The long N-terminus of the human monocarboxylate transporter 8 is a target of ubiquitin-dependent proteasomal degradation which regulates protein expression and oligomerization capacity.

Science.gov (United States)

Zwanziger, Denise; Schmidt, Mathias; Fischer, Jana; Kleinau, Gunnar; Braun, Doreen; Schweizer, Ulrich; Moeller, Lars Christian; Biebermann, Heike; Fuehrer, Dagmar

2016-10-15

Monocarboxylate transporter 8 (MCT8) equilibrates thyroid hormones between the extra- and the intracellular sides. MCT8 exists either with a short or a long N-terminus, but potential functional differences between both variants are yet not known. We, therefore, generated MCT8 constructs which are different in N-terminal length: MCT8(1-613), MCT8(25-613), MCT8(49-613) and MCT8(75-613). The M75G substitution prevents translation of MCT8(75-613) and ensures expression of full-length MCT8 protein. The K56G substitution was made to prevent ubiquitinylation. Cell-surface expression, localization and proteasomal degradation were investigated using C-terminally GFP-tagged MCT8 constructs (HEK293 and MDCK1 cells) and oligomerization capacity was determined using N-terminally HA- and C-terminally FLAG-tagged MCT8 constructs (COS7 cells). MCT8(1-613)-GFP showed a lower protein expression than the shorter MCT8(75-613)-GFP protein. The proteasome inhibitor lactacystin increased MCT8(1-613)-GFP protein amount, suggesting proteasomal degradation of MCT8 with the long N-terminus. Ubiquitin conjugation of MCT8(1-613)-GFP was found by immuno-precipitation. A diminished ubiquitin conjugation caused by K56G substitution resulted in increased MCT8(1-613)-GFP protein expression. Sandwich ELISA was performed to investigate if the bands at higher molecular weight observed in Western blot analysis are due to MCT8 oligomerization, which was indeed shown. Our data imply a role of the long N-terminus of MCT8 as target of ubiquitin-dependent proteasomal degradation affecting MCT8 amount and subsequently oligomerization capacity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Cyclic GMP-AMP synthase is activated by double-stranded DNA-induced oligomerization.

Science.gov (United States)

Li, Xin; Shu, Chang; Yi, Guanghui; Chaton, Catherine T; Shelton, Catherine L; Diao, Jiasheng; Zuo, Xiaobing; Kao, C Cheng; Herr, Andrew B; Li, Pingwei

2013-12-12

Cyclic GMP-AMP synthase (cGAS) is a cytosolic DNA sensor mediating innate antimicrobial immunity. It catalyzes the synthesis of a noncanonical cyclic dinucleotide, 2',5' cGAMP, that binds to STING and mediates the activation of TBK1 and IRF-3. Activated IRF-3 translocates to the nucleus and initiates the transcription of the IFN-β gene. The structure of mouse cGAS bound to an 18 bp dsDNA revealed that cGAS interacts with dsDNA through two binding sites, forming a 2:2 complex. Enzyme assays and IFN-β reporter assays of cGAS mutants demonstrated that interactions at both DNA binding sites are essential for cGAS activation. Mutagenesis and DNA binding studies showed that the two sites bind dsDNA cooperatively and that site B plays a critical role in DNA binding. The structure of mouse cGAS bound to dsDNA and 2',5' cGAMP provided insight into the catalytic mechanism of cGAS. These results demonstrated that cGAS is activated by dsDNA-induced oligomerization. Copyright © 2013 Elsevier Inc. All rights reserved.

Role of redox environment on the oligomerization of higher molecular weight adiponectin

Directory of Open Access Journals (Sweden)

Nuñez Martha

2011-05-01

Full Text Available Abstract Background Adiponectin is an adipocyte-secreted hormone with insulin-sensitizing and anti-inflammatory actions. The assembly of trimeric, hexameric, and higher molecular weight (HMW species of adiponectin is a topic of significant interest because physiological actions of adiponectin are oligomer-specific. In addition, adiponectin assembly is an example of oxidative oligomerization of multi-subunit protein complexes in endoplasmic reticulum (ER. Results We previously reported that trimers assemble into HMW adiponectin via intermediates stabilized by disulfide bonds, and complete oxidation of available cysteines locks adiponectin in hexameric conformation. In this study, we examined the effects of redox environment on the rate of oligomer formation and the distribution of oligomers. Reassembly of adiponectin under oxidizing conditions accelerated disulfide bonding but favored formation of hexamers over the HMW species. Increased ratios of HMW to hexameric adiponectin could be achieved rapidly under oxidizing conditions by promoting disulfide rearrangement. Conclusions Based upon these observations, we propose oxidative assembly of multi-subunit adiponectin complexes in a defined and stable redox environment is favored under oxidizing conditions coupled with high rates of disulfide rearrangement.

Discovery of Nanomolar Desmuramylpeptide Agonists of the Innate Immune Receptor Nucleotide-Binding Oligomerization Domain-Containing Protein 2 (NOD2) Possessing Immunostimulatory Properties.

Science.gov (United States)

Gobec, Martina; Tomašič, Tihomir; Štimac, Adela; Frkanec, Ruža; Trontelj, Jurij; Anderluh, Marko; Mlinarič-Raščan, Irena; Jakopin, Žiga

2018-04-12

Muramyl dipeptide (MDP), a fragment of bacterial peptidoglycan, has long been known as the smallest fragment possessing adjuvant activity, on the basis of its agonistic action on the nucleotide-binding oligomerization domain-containing protein 2 (NOD2). There is a pressing need for novel adjuvants, and NOD2 agonists provide an untapped source of potential candidates. Here, we report the design, synthesis, and characterization of a series of novel acyl tripeptides. A pivotal structural element for molecular recognition by NOD2 has been identified, culminating in the discovery of compound 9, the most potent desmuramylpeptide NOD2 agonist to date. Compound 9 augmented pro-inflammatory cytokine release from human peripheral blood mononuclear cells in synergy with lipopolysaccharide. Furthermore, it was able to induce ovalbumin-specific IgG titers in a mouse model of adjuvancy. These findings provide deeper insights into the structural requirements of desmuramylpeptides for NOD2-activation and highlight the potential use of NOD2 agonists as adjuvants for vaccines.

Polyhedral charge-packing model for blood pH changes in disease ...

African Journals Online (AJOL)

Administrator

2007-05-02

May 2, 2007 ... The six negatively charged hydroxyl ions occupy the six vertices of the octahedron, while the lone proton,. H+, occupies the octahedral hole at the centroid. ... ge packing can account for the common pH of 7.4 of mammals, in spite of other differences that are well known (Jackson, 1997). In the original model ...

Hierarchical Self-Organization of AB _n Dendron-like Molecules into a Supramolecular Lattice Sequence

Energy Technology Data Exchange (ETDEWEB)

Feng, Xueyan [Department; Zhang, Ruimeng [Department; Li, Yiwen [College; Hong, You-lee [RIKEN CLST-JEOL; JEOL RESONANCE; Guo, Dong [Department; Lang, Kening [Department; Wu, Kuan-Yi [Department; Huang, Mingjun [Department; Mao, Jialin [Department; Wesdemiotis, Chrys [Department; Nishiyama, Yusuke [RIKEN CLST-JEOL; JEOL RESONANCE; Zhang, Wei [Department; Zhang, Wei [South; Miyoshi, Toshikazu [Department; Li, Tao [X-ray; Cheng, Stephen Z. D. [Department

2017-08-07

To understand the hierarchical self-organization behaviors of soft materials as well as their dependence on molecular geometry, a series of ABn dendron-type giant molecules based on polyhedral oligomeric silsesquioxane (POSS) nanoparticles were designed and synthesized. The apex of these molecules is a hydrophilic POSS cage with fourteen hydroxyl groups (denoted DPOSS). At its periphery, there are different numbers (n = 1–8) of hydrophobic POSS cages with seven isobutyl groups (denoted BPOSS), connected to the apical DPOSS via flexible dendron type linker(s). With varying the BPOSS number from one to seven, a supramolecular lattice formation sequence ranging from lamella (DPOSS-BPOSS), double gyroid (space group of Ia3d, DPOSS-BPOSS2), hexagonal cylinder (space group of P6mm, DPOSS-BPOSS3), Frank-Kasper A15 (space group of Pm3n, DPOSS-BPOSS4, DPOSS-BPOSS5, and DPOSS-BPOSS6), to Frank-Kasper sigma (space group of P42/mnm, DPOSS-BPOSS7) phases can be observed. The nanostructure formations in this series of ABn dendron-type giant molecules are mainly directed by the macromolecular geometric shapes. Furthermore, within each spherical motif, the soft spherical core is consisted of hydrophilic DPOSS cages with flexible linkages, while the hydrophobic BPOSS cages form the relative rigid shell and contact with neighbors to provide decreased interfaces among the spherical motifs for constructing final polyhedral motifs in these Frank-Kasper lattices. This study provides the design principle of macromolecules with specific geometric shapes and functional groups to achieve anticipated structures and macroscopic properties.

Aquaporin-Based Biomimetic Polymeric Membranes: Approaches and Challenges

DEFF Research Database (Denmark)

Habel, Joachim Erich Otto; Hansen, Michael; Kynde, Søren

2015-01-01

In recent years, aquaporin biomimetic membranes (ABMs) for water separation have gained considerable interest. Although the first ABMs are commercially available, there are still many challenges associated with further ABM development. Here, we discuss the interplay of the main components of ABMs...... thin film interfacial polymerization techniques. Finally, we describe some new developments in interfacial polymerization using polyhedral oligomeric silsesquioxane cages for increasing the physical and chemical durability of thin film composite membranes.......In recent years, aquaporin biomimetic membranes (ABMs) for water separation have gained considerable interest. Although the first ABMs are commercially available, there are still many challenges associated with further ABM development. Here, we discuss the interplay of the main components of ABMs...... for investigating AQP incorporation including freeze-fracture transmission electron microscopy, fluorescence correlation spectroscopy, stopped-flow light scattering, and small-angle X-ray scattering. Third, we focus on recent efforts in embedding reconstituted AQPs in membrane designs that are based on conventional...

Anhydrous proton conducting composite membranes containing Nafion and triazole modified POSS

International Nuclear Information System (INIS)

Lei, M.; Wang, Y.G.; Zhang, F.F.; Huang, C.; Xu, X.; Zhang, R.; Fan, D.Y.

2014-01-01

Development of membrane electrolytes having reasonable proton conductivity and mechanical strength under anhydrous conditions is of great importance for proton exchange membrane fuel cells operated at elevated temperature. With the introduction of triazole modified polyhedral oligomeric silsesquioxanes (Tz-POSS) into Nafion membrane, the formed composite electrolytes exhibit improved mechanical properties compared to pristine Nafion membrane due to the well distribution of Tz-POSS inside the membrane. The anhydrous proton conductivity of the formed composite membranes increases initially with the increase in temperature, reaching about 0.02 Scm −1 at 140 °C. With further increase in temperature to about 150 °C, the composite membrane reaches its glass transition point above which the proton conductivity decreases dramatically. The performance of assembled single cell from composite membrane is slightly dependent on humidification conditions at 95 °C, reaching 0.45 V at 600 mAcm −2 using hydrogen and oxygen as reaction gases

Space Environmental Effects on Coated Tether Materials

Science.gov (United States)

Gittemeier, Keith A.; Hawk, Clark W.; Finckenor, Miria M.; Watts, Ed

2005-01-01

The University of Alabama in Huntsville s Propulsion Research Center has teamed with NASA's Marshall Space Flight Center (MSFC) to research the effects of atomic oxygen (AO) bombardment on coated tether materials. Tethers Unlimited Inc. has provided several candidate tether materials with various coatings for AO exposure in MSFC s Atomic Oxygen Beam Facility. Additional samples were exposed to ultraviolet (UV) radiation at MSFC. AO erodes most organic materials, and ultraviolet radiation embrittles polymers. This test series was performed to determine the effect of AO and UV on the mechanical integrity of tether materials that were treated with AO-protective coatings, such as polyhedral oligomeric silsesquioxane (POSS) or metallization. Both TUI's Multi-Application Survivable Tether (MAST) Experiment and Marshall Space Flight Center s Momentum Exchange Electrodynamic Reboost (MXER) programs will benefit from this research by helping to determine tether materials and coatings that give the longest life with the lowest mass penalty.

Thickness-Dependent Order-to-Order Transitions of Bolaform-like Giant Surfactant in Thin Films

Energy Technology Data Exchange (ETDEWEB)

Hsu, Chih-Hao; Yue, Kan; Wang, Jing; Dong, Xue-Hui; Xia, Yanfeng; Jiang, Zhang [X-ray; Thomas, Edwin L. [Department; Cheng, Stephen Z. D.

2017-09-07

Controlling self-assembled nanostructures in thin films allows the bottom-up fabrication of ordered nanoscale patterns. Here we report the unique thickness-dependent phase behavior in thin films of a bolaform-like giant surfactant, which consists of butyl- and hydroxyl-functionalized polyhedral oligomeric silsesquioxane (BPOSS and DPOSS) cages telechelically located at the chain ends of a polystyrene (PS) chain with 28 repeating monomers on average. In the bulk, BPOSS-PS28-DPOSS forms a double gyroid (DG) phase. Both grazing incidence small angle X-ray scattering and transmission electron microscopy techniques are combined to elucidate the thin film structures. Interestingly, films with thicknesses thinner than 200 nm exhibit an irreversible phase transition from hexagonal perforated layer (HPL) to compressed hexagonally packed cylinders (c-HEX) at 130 °C, while films with thickness larger than 200 nm show an irreversible transition from HPL to DG at 200 °C. The thickness-controlled transition pathway suggests possibilities to obtain diverse patterns via thin film self-assembly.

Aquaporin-Based Biomimetic Polymeric Membranes: Approaches and Challenges

Science.gov (United States)

Habel, Joachim; Hansen, Michael; Kynde, Søren; Larsen, Nanna; Midtgaard, Søren Roi; Jensen, Grethe Vestergaard; Bomholt, Julie; Ogbonna, Anayo; Almdal, Kristoffer; Schulz, Alexander; Hélix-Nielsen, Claus

2015-01-01

In recent years, aquaporin biomimetic membranes (ABMs) for water separation have gained considerable interest. Although the first ABMs are commercially available, there are still many challenges associated with further ABM development. Here, we discuss the interplay of the main components of ABMs: aquaporin proteins (AQPs), block copolymers for AQP reconstitution, and polymer-based supporting structures. First, we briefly cover challenges and review recent developments in understanding the interplay between AQP and block copolymers. Second, we review some experimental characterization methods for investigating AQP incorporation including freeze-fracture transmission electron microscopy, fluorescence correlation spectroscopy, stopped-flow light scattering, and small-angle X-ray scattering. Third, we focus on recent efforts in embedding reconstituted AQPs in membrane designs that are based on conventional thin film interfacial polymerization techniques. Finally, we describe some new developments in interfacial polymerization using polyhedral oligomeric silsesquioxane cages for increasing the physical and chemical durability of thin film composite membranes. PMID:26264033

Organic-inorganic hybrid carbon dots for cell imaging

Science.gov (United States)

Liu, Huan; Zhang, Hongwen; Li, Jiayu; Tang, Yuying; Cao, Yu; Jiang, Yan

2018-04-01

In this paper, nitrogen-doped carbon dots (CDs) had been synthesized directly by one-step ultrasonic treatment under mild conditions. During the functionalization process, Octa-aminopropyl polyhedral oligomeric silsesquioxane hydrochloride salt (OA-POSS) was used as stabilizing and passivation agent, which lead to self-assembling of CDs in aqueous medium solution. OA-POSS was obtained via hydrolytic condensation of γ-aminopropyl triethoxy silane (APTES). The average size of CDs prepared was approximately 3.3 nm with distribution between 2.5 nm and 4.5 nm. The prepared organic-inorganic hybrid carbon dots have several characteristics such as photoluminescence emission wavelength, efficient cellular uptake, and good biocompatibility. The results indicate that OA-POSS can maintain the fluorescence properties of the carbon dots effectively, and reduced cytotoxicity provides the possibility for biomedical applications. More than 89% of the Hela cells were viable when incubated with 2 mg ml‑1 or lesser organic-inorganic hybrid carbon dots. Thus, it provides a potential for multicolor imaging with HeLa cells.

Preparation and Physicochemical Properties of Functionalized Silica/Octamethacryl-Silsesquioxane Hybrid Systems

Directory of Open Access Journals (Sweden)

Karolina Szwarc-Rzepka

2013-01-01

Full Text Available Alkoxysilane-grafted silica/polyhedral oligomeric silsesquioxane with methacryl substituents (SiO2/silane/POSS hybrid material was synthesized according to hydrolyzation and condensation reactions in the so-called “bifunctionalization process.” It is a new attractive system because of its physicochemical, especially thermal and structural, properties. This innovative method of preparation as well as specific physicochemical and useful properties determine the potential applications of such products in many industries. The structure and physicochemical parameters of obtained hybrid systems were characterized using infrared spectroscopy (FTIR, 13C and 29Si solid-state nuclear magnetic resonance (CP MAS NMR, and thermal analysis. The mechanism of bifunctionalization reaction was proposed. The chemical immobilization of silane coupling agent and Methacryl POSS onto silica support surface was noted during the study. Those changes caused a significant increase in the hydrophobic character of fillers obtained. Moreover, changes in thermal stability of SiO2/silane/POSS hybrid systems in comparison to pure POSS modifier were also observed.

Tangible nanocomposites with diverse properties for heart valve application

Science.gov (United States)

Vignesh Vellayappan, Muthu; Balaji, Arunpandian; Priyadarshini Subramanian, Aruna; Aruna John, Agnes; Jaganathan, Saravana Kumar; Murugesan, Selvakumar; Mohandas, Hemanth; Supriyanto, Eko; Yusof, Mustafa

2015-06-01

Cardiovascular disease claims millions of lives every year throughout the world. Biomaterials are used widely for the treatment of this fatal disease. With the advent of nanotechnology, the use of nanocomposites has become almost inevitable in the field of biomaterials. The versatile properties of nanocomposites, such as improved durability and biocompatibility, make them an ideal choice for various biomedical applications. Among the various nanocomposites, polyhedral oligomeric silsesquioxane-poly(carbonate-urea)urethane, bacterial cellulose with polyvinyl alcohol, carbon nanotubes, graphene oxide and nano-hydroxyapatite nanocomposites have gained popularity as putative choices for biomaterials in cardiovascular applications owing to their superior properties. In this review, various studies performed utilizing these nanocomposites for improving the mechanical strength, anti-calcification potential and hemocompatibility of heart valves are reviewed and summarized. The primary motive of this work is to shed light on the emerging nanocomposites for heart valve applications. Furthermore, we aim to promote the prospects of these nanocomposites in the campaign against cardiovascular diseases.

Tangible nanocomposites with diverse properties for heart valve application

International Nuclear Information System (INIS)

Vellayappan, Muthu Vignesh; Balaji, Arunpandian; Subramanian, Aruna Priyadarshini; John, Agnes Aruna; Jaganathan, Saravana Kumar; Supriyanto, Eko; Yusof, Mustafa; Murugesan, Selvakumar; Mohandas, Hemanth

2015-01-01

Cardiovascular disease claims millions of lives every year throughout the world. Biomaterials are used widely for the treatment of this fatal disease. With the advent of nanotechnology, the use of nanocomposites has become almost inevitable in the field of biomaterials. The versatile properties of nanocomposites, such as improved durability and biocompatibility, make them an ideal choice for various biomedical applications. Among the various nanocomposites, polyhedral oligomeric silsesquioxane-poly(carbonate-urea)urethane, bacterial cellulose with polyvinyl alcohol, carbon nanotubes, graphene oxide and nano-hydroxyapatite nanocomposites have gained popularity as putative choices for biomaterials in cardiovascular applications owing to their superior properties. In this review, various studies performed utilizing these nanocomposites for improving the mechanical strength, anti-calcification potential and hemocompatibility of heart valves are reviewed and summarized. The primary motive of this work is to shed light on the emerging nanocomposites for heart valve applications. Furthermore, we aim to promote the prospects of these nanocomposites in the campaign against cardiovascular diseases. (review)

Self-assembly of dodecaphenyl POSS thin films

Science.gov (United States)

Handke, Bartosz; Klita, Łukasz; Niemiec, Wiktor

2017-12-01

The self-assembly abilities of Dodecaphenyl Polyhedral Oligomeric Silsesquioxane thin films on Si(1 0 0) surfaces were studied. Due to their thermal properties - relatively low sublimation temperature and preservation of molecular structure - cage type silsesquioxanes are ideal material for the preparation of a thin films by Physical Vapor Deposition. The Ultra-High Vacuum environment and the deposition precision of the PVD method enable the study of early stages of thin film growth and its molecular organization. X-ray Reflectivity and Atomic Force Microscopy measurements allow to pursuit size-effects in the structure of thin films with thickness ranges from less than a single molecular layer up to several tens of layers. Thermal treatment of the thin films triggered phase change: from a poorly ordered polycrystalline film into a well-ordered multilayer structure. Self-assembly of the layers is the effect of the π-stacking of phenyl rings, which force molecules to arrange in a superlattice, forming stacks of alternating organic-inorganic layers.

Simultaneous separation and identification of oligomeric procyanidins and anthocyanin-derived pigments in raw red wine by HPLC-UV-ESI-MSn.

Science.gov (United States)

Pati, S; Losito, I; Gambacorta, G; La Notte, E; Palmisano, F; Zambonin, P G

2006-07-01

Samples of raw red wine (Primitivo di Manduria, Apulia, Southern Italy) were analysed without any pre-treatment (except 1:2 dilution with water) using HPLC with detection based on UV absorbance and Electrospray Ionisation Sequential Mass Spectrometry (ESI-MSn, with n = 1-3) in a series configuration. In particular, absorbance at 520 nm was monitored for UV detection in order to identify pigments responsible for wine colour. On the other hand, two subsequent stages of MS detection based on positive ions were adopted. The first consisted of an explorative MS acquisition, aimed at the individuation of the m/z ratios for positively charged compounds; the second was based on fragmentation of the detected ions within an ion trap analyser, followed by MS/MS and, if required, MS3 acquisitions. The synergy between UV detection and MSn analysis led to the identification of 41 pigments, which can be classified into five groups: grape anthocyanins, pyranoanthocyanins, vinyl-linked anthocyanin-flavanol pigments, ethyl-bridged anthocyanin-flavanol pigments and flavanol-anthocyanin compounds. Many isomeric and oligomeric structures were found within each group. A further class of compounds, not absorbing in the visible spectrum, could be also characterised by ESI-MSn and corresponded to B-type procyanidins, i.e. proanthocyanidins arising from C4-->C8/C4-->C6 couplings between catechin or epicatechin units. In particular, oligomeric structures (from dimers to pentamers), often present with several isomers, were identified and their fragmentation patterns clarified.

Sn-doped polyhedral In2O3 particles: Synthesis, characterization, and origins of luminous emission in wide visible range

International Nuclear Information System (INIS)

Zhu Yunqing; Chen Yiqing

2012-01-01

Sn-doped octahedronal and tetrakaidecahedronal In 2 O 3 particles were successfully synthesized by simple thermal evaporation of indium grains using SnO as dopant. Structural characterization results demonstrated that the Sn-doped tetrakaidecahedronal In 2 O 3 particle had additional six {001} crystal surfaces compared with the octahedronal one. The luminous properties of both samples were characterized by photoluminescence (PL) and cathodoluminescence (CL) spectroscopy. A broad visible luminous emission around 570 nm was observed. Studies revealed that the emission consisted of three peaks of 511 nm, 564 nm, and 622 nm, which were attributed to radioactive recombination centers such as single ionized oxygen vacancy, indium interstitial, and antisite oxygen, respectively. We believe that the Sn donor level plays an important role in the visible luminous emission. - Graphical abstract: With more oxygen vacancies and tin doping. ITO particles can exhibit a better CL performance. Sn donor level near the conduction band edge plays an important role in luminous emission in wide visible range. Highlights: ► Polyhedral ITO particles synthesized by thermal evaporation using SnO as dopant. ► Broad visible luminous emission around 570 nm. ► Sn donor level plays an important role in the visible emission. ► ITO particles with more oxygen vacancies have better CL performance in visible range.

Sedimentation Velocity Analysis of Large Oligomeric Chromatin Complexes Using Interference Detection.

Science.gov (United States)

Rogge, Ryan A; Hansen, Jeffrey C

2015-01-01

Sedimentation velocity experiments measure the transport of molecules in solution under centrifugal force. Here, we describe a method for monitoring the sedimentation of very large biological molecular assemblies using the interference optical systems of the analytical ultracentrifuge. The mass, partial-specific volume, and shape of macromolecules in solution affect their sedimentation rates as reflected in the sedimentation coefficient. The sedimentation coefficient is obtained by measuring the solute concentration as a function of radial distance during centrifugation. Monitoring the concentration can be accomplished using interference optics, absorbance optics, or the fluorescence detection system, each with inherent advantages. The interference optical system captures data much faster than these other optical systems, allowing for sedimentation velocity analysis of extremely large macromolecular complexes that sediment rapidly at very low rotor speeds. Supramolecular oligomeric complexes produced by self-association of 12-mer chromatin fibers are used to illustrate the advantages of the interference optics. Using interference optics, we show that chromatin fibers self-associate at physiological divalent salt concentrations to form structures that sediment between 10,000 and 350,000S. The method for characterizing chromatin oligomers described in this chapter will be generally useful for characterization of any biological structures that are too large to be studied by the absorbance optical system. © 2015 Elsevier Inc. All rights reserved.

Cartilage oligomeric matrix protein in patients with juvenile idiopathic arthritis: relation to growth and disease activity

DEFF Research Database (Denmark)

Bjørnhart, Birgitte; Juul, Anders; Nielsen, Susan

2009-01-01

OBJECTIVE: Cartilage oligomeric matrix protein (COMP) has been identified as a prognostic marker of progressive joint destruction in rheumatoid arthritis. In this population based study we evaluated associations between plasma concentrations of COMP, disease activity, and growth velocity...... in patients with recent-onset juvenile idiopathic arthritis (JIA). COMP levels in JIA and healthy children were compared with those in healthy adults. Plasma levels of insulin-like growth factor I (IGF-1), which has been associated with COMP expression and growth velocity, were studied in parallel. METHODS......: 87 patients with JIA entered the study, including oligoarticular JIA (n = 34), enthesitis-related arthritis (n = 8), polyarticular rheumatoid factor (RF)-positive JIA (n = 2), polyarticular RF-negative JIA (n = 27), systemic JIA (n = 6), and undifferentiated JIA (n = 10). Plasma levels of COMP were...

MAK33 antibody light chain amyloid fibrils are similar to oligomeric precursors.

Directory of Open Access Journals (Sweden)

Manuel Hora

Full Text Available Little structural information is available so far on amyloid fibrils consisting of immunoglobulin light chains. It is not understood which features of the primary sequence of the protein result in fibril formation. We report here MAS solid-state NMR studies to identify the structured core of κ-type variable domain light chain fibrils. The core contains residues of the CDR2 and the β-strands D, E, F and G of the native immunoglobulin fold. The assigned core region of the fibril is distinct in comparison to the core identified in a previous solid-state NMR study on AL-09 by Piehl at. al, suggesting that VL fibrils can adopt different topologies. In addition, we investigated a soluble oligomeric intermediate state, previously termed the alternatively folded state (AFS, using NMR and FTIR spectroscopy. The NMR oligomer spectra display a high degree of similarity when compared to the fibril spectra, indicating a high structural similarity of the two aggregation states. Based on comparison to the native state NMR chemical shifts, we suggest that fibril formation via domain-swapping seems unlikely. Moreover, we used our results to test the quality of different amyloid prediction algorithms.

Model for the architecture of caveolae based on a flexible, net-like assembly of Cavin1 and Caveolin discs.

Science.gov (United States)

Stoeber, Miriam; Schellenberger, Pascale; Siebert, C Alistair; Leyrat, Cedric; Helenius, Ari; Grünewald, Kay

2016-12-13

Caveolae are invaginated plasma membrane domains involved in mechanosensing, signaling, endocytosis, and membrane homeostasis. Oligomers of membrane-embedded caveolins and peripherally attached cavins form the caveolar coat whose structure has remained elusive. Here, purified Cavin1 60S complexes were analyzed structurally in solution and after liposome reconstitution by electron cryotomography. Cavin1 adopted a flexible, net-like protein mesh able to form polyhedral lattices on phosphatidylserine-containing vesicles. Mutating the two coiled-coil domains in Cavin1 revealed that they mediate distinct assembly steps during 60S complex formation. The organization of the cavin coat corresponded to a polyhedral nano-net held together by coiled-coil segments. Positive residues around the C-terminal coiled-coil domain were required for membrane binding. Purified caveolin 8S oligomers assumed disc-shaped arrangements of sizes that are consistent with the discs occupying the faces in the caveolar polyhedra. Polygonal caveolar membrane profiles were revealed in tomograms of native caveolae inside cells. We propose a model with a regular dodecahedron as structural basis for the caveolae architecture.

Data in support of the identification of neuronal and astrocyte proteins interacting with extracellularly applied oligomeric and fibrillar α-synuclein assemblies by mass spectrometry.

Science.gov (United States)

Shrivastava, Amulya Nidhi; Redeker, Virginie; Fritz, Nicolas; Pieri, Laura; Almeida, Leandro G; Spolidoro, Maria; Liebmann, Thomas; Bousset, Luc; Renner, Marianne; Léna, Clément; Aperia, Anita; Melki, Ronald; Triller, Antoine

2016-06-01

α-Synuclein (α-syn) is the principal component of Lewy bodies, the pathophysiological hallmark of individuals affected by Parkinson disease (PD). This neuropathologic form of α-syn contributes to PD progression and propagation of α-syn assemblies between neurons. The data we present here support the proteomic analysis used to identify neuronal proteins that specifically interact with extracellularly applied oligomeric or fibrillar α-syn assemblies (conditions 1 and 2, respectively) (doi: 10.15252/embj.201591397[1]). α-syn assemblies and their cellular partner proteins were pulled down from neuronal cell lysed shortly after exposure to exogenous α-syn assemblies and the associated proteins were identified by mass spectrometry using a shotgun proteomic-based approach. We also performed experiments on pure cultures of astrocytes to identify astrocyte-specific proteins interacting with oligomeric or fibrillar α-syn (conditions 3 and 4, respectively). For each condition, proteins interacting selectively with α-syn assemblies were identified by comparison to proteins pulled-down from untreated cells used as controls. The mass spectrometry data, the database search and the peak lists have been deposited to the ProteomeXchange Consortium database via the PRIDE partner repository with the dataset identifiers PRIDE: PXD002256 to PRIDE: PXD002263 and doi: 10.6019/PXD002256 to 10.6019/PXD002263.

Fusion of the Mycobacterium tuberculosis antigen 85A to an oligomerization domain enhances its immunogenicity in both mice and non-human primates.

Directory of Open Access Journals (Sweden)

Alexandra J Spencer

Full Text Available To prevent important infectious diseases such as tuberculosis, malaria and HIV, vaccines inducing greater T cell responses are required. In this study, we investigated whether fusion of the M. tuberculosis antigen 85A to recently described adjuvant IMX313, a hybrid avian C4bp oligomerization domain, could increase T cell responses in pre-clinical vaccine model species. In mice, the fused antigen 85A showed consistent increases in CD4(+ and CD8(+ T cell responses after DNA and MVA vaccination. In rhesus macaques, higher IFN-γ responses were observed in animals vaccinated with MVA-Ag85A IMX313 after both primary and secondary immunizations. In both animal models, fusion to IMX313 induced a quantitative enhancement in the response without altering its quality: multifunctional cytokines were uniformly increased and differentiation into effector and memory T cell subsets was augmented rather than skewed. An extensive in vivo characterization suggests that IMX313 improves the initiation of immune responses as an increase in antigen 85A specific cells was observed as early as day 3 after vaccination. This report demonstrates that antigen multimerization using IMX313 is a simple and effective cross-species method to improve vaccine immunogenicity with potentially broad applicability.

A Comparative Theoretical and Computational Study on Robust Counterpart Optimization: I. Robust Linear Optimization and Robust Mixed Integer Linear Optimization

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Li, Zukui; Ding, Ran; Floudas, Christodoulos A.

2011-01-01

Robust counterpart optimization techniques for linear optimization and mixed integer linear optimization problems are studied in this paper. Different uncertainty sets, including those studied in literature (i.e., interval set; combined interval and ellipsoidal set; combined interval and polyhedral set) and new ones (i.e., adjustable box; pure ellipsoidal; pure polyhedral; combined interval, ellipsoidal, and polyhedral set) are studied in this work and their geometric relationship is discussed. For uncertainty in the left hand side, right hand side, and objective function of the optimization problems, robust counterpart optimization formulations induced by those different uncertainty sets are derived. Numerical studies are performed to compare the solutions of the robust counterpart optimization models and applications in refinery production planning and batch process scheduling problem are presented. PMID:21935263

Cartilage oligomeric matrix protein enhances matrix assembly during chondrogenesis of human mesenchymal stem cells.

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Haleem-Smith, Hana; Calderon, Raul; Song, Yingjie; Tuan, Rocky S; Chen, Faye H

2012-04-01

Cartilage oligomeric matrix protein/thrombospondin-5 (COMP/TSP5) is an abundant cartilage extracellular matrix (ECM) protein that interacts with major cartilage ECM components, including aggrecan and collagens. To test our hypothesis that COMP/TSP5 functions in the assembly of the ECM during cartilage morphogenesis, we have employed mesenchymal stem cell (MSC) chondrogenesis in vitro as a model to examine the effects of COMP over-expression on neo-cartilage formation. Human bone marrow-derived MSCs were transfected with either full-length COMP cDNA or control plasmid, followed by chondrogenic induction in three-dimensional pellet or alginate hydrogel culture. MSC chondrogenesis and ECM production was estimated based on quantitation of sulfated glycosaminoglycan (sGAG) accumulation, immunohistochemistry of the presence and distribution of cartilage ECM proteins, and real-time RT-PCR analyis of mRNA expression of cartilage markers. Our results showed that COMP over-expression resulted in increased total sGAG content during the early phase of MSC chondrogenesis, and increased immuno-detectable levels of aggrecan and collagen type II in the ECM of COMP-transfected pellet and alginate cultures, indicating more abundant cartilaginous matrix. COMP transfection did not significantly increase the transcript levels of the early chondrogenic marker, Sox9, or aggrecan, suggesting that enhancement of MSC cartilage ECM was effected at post-transcriptional levels. These findings strongly suggest that COMP functions in mesenchymal chondrogenesis by enhancing cartilage ECM organization and assembly. The action of COMP is most likely mediated not via direct changes in cartilage matrix gene expression but via interactions of COMP with other cartilage ECM proteins, such as aggrecan and collagens, that result in enhanced assembly and retention.

CARTILAGE OLIGOMERIC MATRIX PROTEIN ENHANCES MATRIX ASSEMBLY DURING CHONDROGENESIS OF HUMAN MESENCHYMAL STEM CELLS

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Haleem-Smith, Hana; Calderon, Raul; Song, Yingjie; Tuan, Rocky S.; Chen, Faye H.

2011-01-01

Cartilage oligomeric matrix protein/thrombospondin-5 (COMP/TSP5) is an abundant cartilage extracellular matrix (ECM) protein that interacts with major cartilage ECM components, including aggrecan and collagens. To test our hypothesis that COMP/TSP5 functions in the assembly of the ECM during cartilage morphogenesis, we have employed mesenchymal stem cell (MSC) chondrogenesis in vitro as a model to examine the effects of COMP over-expression on neo-cartilage formation. Human bone marrow-derived MSCs were transfected with either full-length COMP cDNA or control plasmid, followed by chondrogenic induction in three-dimensional pellet or alginate-hydrogel culture. MSC chondrogenesis and ECM production was estimated based on quantitation of sulfated glycosaminoglycan (sGAG) accumulation, immunohistochemistry of the presence and distribution of cartilage ECM proteins, and real-time RT-PCR analyis of mRNA expression of cartilage markers. Our results showed that COMP over-expression resulted in increased total sGAG content during the early phase of MSC chondrogenesis, and increased immuno-detectable levels of aggrecan and collagen type II in the ECM of COMP-transfected pellet and alginate cultures, indicating more abundant cartilaginous matrix. COMP transfection did not significantly increase the transcript levels of the early chondrogenic marker, Sox9, or aggrecan, suggesting that enhancement of MSC cartilage ECM was effected at post-transcriptional levels. These findings strongly suggest that COMP functions in mesenchymal chondrogenesis by enhancing cartilage ECM organization and assembly. The action of COMP is most likely mediated not via direct changes in cartilage matrix gene expression but via interactions of COMP with other cartilage ECM proteins, such as aggrecan and collagens, that result in enhanced assembly and retention. PMID:22095699

Binding and Oligomerization of Modified and Native Bt Toxins in Resistant and Susceptible Pink Bollworm.

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Josue Ocelotl

Full Text Available Insecticidal proteins from Bacillus thuringiensis (Bt are used extensively in sprays and transgenic crops for pest control, but their efficacy is reduced when pests evolve resistance. Better understanding of the mode of action of Bt toxins and the mechanisms of insect resistance is needed to enhance the durability of these important alternatives to conventional insecticides. Mode of action models agree that binding of Bt toxins to midgut proteins such as cadherin is essential for toxicity, but some details remain unresolved, such as the role of toxin oligomers. In this study, we evaluated how Bt toxin Cry1Ac and its genetically engineered counterpart Cry1AcMod interact with brush border membrane vesicles (BBMV from resistant and susceptible larvae of Pectinophora gossypiella (pink bollworm, a global pest of cotton. Compared with Cry1Ac, Cry1AcMod lacks 56 amino acids at the amino-terminus including helix α-1; previous work showed that Cry1AcMod formed oligomers in vitro without cadherin and killed P. gossypiella larvae harboring cadherin mutations linked with >1000-fold resistance to Cry1Ac. Here we found that resistance to Cry1Ac was associated with reduced oligomer formation and insertion. In contrast, Cry1AcMod formed oligomers in BBMV from resistant larvae. These results confirm the role of cadherin in oligomerization of Cry1Ac in susceptible larvae and imply that forming oligomers without cadherin promotes toxicity of Cry1AcMod against resistant P. gossypiella larvae that have cadherin mutations.

Structural Models of Water and Ice Regarding the Energy of Hydrogen Bonding

OpenAIRE

Ignat Ignatov; Oleg Mosin

2015-01-01

In this review it is reported about the research on the structure of water and ice and intermolecular water cyclic associates (clusters) with general formula (Н2О)n and their charged ionic clusters [(Н2О)n]+ and [(Н2О)n]- by means of computer modelling and spectroscopy methods as 1Н-NMR, IR-spectroscopy, DNES, EXAFS-spectroscopy, X-Ray and neurons diffraction. The computer calculation of polyhedral nanoclusters (Н2О)n, where n = 3–20 are carried out. Based on this data the main structural mat...

Inside-out signaling promotes dynamic changes in the carcinoembryonic antigen-related cellular adhesion molecule 1 (CEACAM1) oligomeric state to control its cell adhesion properties.

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Patel, Prerna C; Lee, Hannah S W; Ming, Aaron Y K; Rath, Arianna; Deber, Charles M; Yip, Christopher M; Rocheleau, Jonathan V; Gray-Owen, Scott D

2013-10-11

Cell-cell contacts are fundamental to multicellular organisms and are subject to exquisite levels of control. The carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) can engage in both cis-homophilic (parallel) oligomerization and trans-homophilic (anti-parallel) binding. In this study, we establish that the CEACAM1 transmembrane domain has a propensity to form cis-dimers via the transmembrane-embedded (432)GXXXG(436) motif and that this basal state is overcome when activated calmodulin binds to the CEACAM1 cytoplasmic domain. Although mutation of the (432)GXXXG(436) motif reduced CEACAM1 oligomerization, it did not affect surface localization of the receptor or influence CEACAM1-dependent cellular invasion by the pathogenic Neisseria. The mutation did, however, have a striking effect on CEACAM1-dependent cellular aggregation, increasing both the kinetics of cell-cell association and the size of cellular aggregates formed. CEACAM1 association with tyrosine kinase c-Src and tyrosine phosphatases SHP-1 and SHP-2 was not affected by the (432)GXXXG(436) mutation, consistent with their association with the monomeric form of wild type CEACAM1. Collectively, our results establish that a dynamic oligomer-to-monomer shift in surface-expressed CEACAM1 facilitates trans-homophilic binding and downstream effector signaling.

Substitution of proline32 by α-methylproline preorganizes β2-microglobulin for oligomerization but not for aggregation into amyloids.

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Torbeev, Vladimir; Ebert, Marc-Olivier; Dolenc, Jozica; Hilvert, Donald

2015-02-25

Conversion of soluble folded proteins into insoluble amyloids generally proceeds in three distinct mechanistic stages: (1) initial protein misfolding into aggregation-competent conformers, (2) subsequent formation of oligomeric species and, finally, (3) self-assembly into extended amyloid fibrils. In the work reported herein, we interrogated the amyloidogenesis mechanism of human β2-microglobulin (β2m), which is thought to be triggered by a pivotal cis-trans isomerization of a proline residue at position 32 in the polypeptide, with nonstandard amino acids. Using chemical protein synthesis we prepared a β2m analogue in which Pro32 was replaced by the conformationally constrained amino acid α-methylproline (MePro). The strong propensity of MePro to adopt a trans prolyl bond led to enhanced population of a non-native [trans-MePro32]β2m protein conformer, which readily formed oligomers at neutral pH. In the presence of the antibiotic rifamycin SV, which inhibits amyloid growth of wild-type β2m, [MePro32]β2m was nearly quantitatively converted into different spherical oligomeric species. Self-assembly into amyloid fibrils was not observed in the absence of seeding, however, even at low pH (<3), where wild-type β2m spontaneously forms amyloids. Nevertheless, we found that aggregation-preorganized [MePro32]β2m can act in a prion-like fashion, templating misfolded conformations in a natively folded protein. Overall, these results provide detailed insight into the role of cis-trans isomerization of Pro32 and ensuing structural rearrangements that lead to initial β2m misfolding and aggregation. They corroborate the view that conformational protein dynamics enabled by reversible Pro32 cis-trans interconversion rather than simple population of the trans conformer is critical for both nucleation and subsequent growth of β2m amyloid structures.

Active site CP-loop dynamics modulate substrate binding, catalysis, oligomerization, stability, over-oxidation and recycling of 2-Cys Peroxiredoxins.

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Kamariah, Neelagandan; Eisenhaber, Birgit; Eisenhaber, Frank; Grüber, Gerhard

2018-04-01

Peroxiredoxins (Prxs) catalyse the rapid reduction of hydrogen peroxide, organic hydroperoxide and peroxynitrite, using a fully conserved peroxidatic cysteine (C P ) located in a conserved sequence Pxxx(T/S)xxC P motif known as C P -loop. In addition, Prxs are involved in cellular signaling pathways and regulate several redox-dependent process related disease. The effective catalysis of Prxs is associated with alterations in the C P -loop between reduced, Fully Folded (FF), and oxidized, Locally Unfolded (LU) conformations, which are linked to dramatic changes in the oligomeric structure. Despite many studies, little is known about the precise structural and dynamic roles of the C P -loop on Prxs functions. Herein, the comprehensive biochemical and biophysical studies on Escherichia coli alkyl hydroperoxide reductase subunit C (EcAhpC) and the C P -loop mutants, EcAhpC-F45A and EcAhpC-F45P reveal that the reduced form of the C P -loop adopts conformational dynamics, which is essential for effective peroxide reduction. Furthermore, the point mutants alter the structure and dynamics of the reduced form of the C P -loop and, thereby, affect substrate binding, catalysis, oligomerization, stability and overoxidiation. In the oxidized form, due to restricted C P -loop dynamics, the EcAhpC-F45P mutant favours a decamer formation, which enhances the effective recycling by physiological reductases compared to wild-type EcAhpC. In addition, the study reveals that residue F45 increases the specificity of Prxs-reductase interactions. Based on these studies, we propose an evolution of the C P -loop with confined sequence conservation within Prxs subfamilies that might optimize the functional adaptation of Prxs into various physiological roles. Copyright © 2018 Elsevier Inc. All rights reserved.

Hydroxychloroquine induces inhibition of collagen type II and oligomeric matrix protein COMP expression in chondrocytes

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Tao Li

2016-06-01

Full Text Available The aim of this study was to investigate the effect of hydroxychloroquine on the level of collagen type II and oligomeric matrix protein COMP expression in chondrocytes of knee osteoarthritis. The rate of growth in cartilage cells was analyzed using MTT assay whereas the Col-2 and COMP expression levels were detected by RT-PCR and Western blotting analyses. For the determination of MMP-13 expression, ELISA test was used. The results revealed no significant change in the rate of cartilage cell proliferation in hydroxychloroquine-treated compared to untreated cells. Hydroxychloro-quine treatment exhibited concentration- and time-dependent effect on the inhibition of collagen type II and COMP expression in chondrocytes. However, its treatment caused a significant enhancement in the expression levels of MMP-13 compared to the untreated cells. Therefore, hydroxychloro-quine promotes expression of MMP-13 and reduces collagen type II and COMP expression levels in chondrocytes without any significant change in the growth of cells.

RNAi reduces expression and intracellular retention of mutant cartilage oligomeric matrix protein.

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Karen L Posey

2010-04-01

Full Text Available Mutations in cartilage oligomeric matrix protein (COMP, a large extracellular glycoprotein expressed in musculoskeletal tissues, cause two skeletal dysplasias, pseudoachondroplasia and multiple epiphyseal dysplasia. These mutations lead to massive intracellular retention of COMP, chondrocyte death and loss of growth plate chondrocytes that are necessary for linear growth. In contrast, COMP null mice have only minor growth plate abnormalities, normal growth and longevity. This suggests that reducing mutant and wild-type COMP expression in chondrocytes may prevent the toxic cellular phenotype causing the skeletal dysplasias. We tested this hypothesis using RNA interference to reduce steady state levels of COMP mRNA. A panel of shRNAs directed against COMP was tested. One shRNA (3B reduced endogenous and recombinant COMP mRNA dramatically, regardless of expression levels. The activity of the shRNA against COMP mRNA was maintained for up to 10 weeks. We also demonstrate that this treatment reduced ER stress. Moreover, we show that reducing steady state levels of COMP mRNA alleviates intracellular retention of other extracellular matrix proteins associated with the pseudoachondroplasia cellular pathology. These findings are a proof of principle and the foundation for the development of a therapeutic intervention based on reduction of COMP expression.

Complex structure of the fission yeast SREBP-SCAP binding domains reveals an oligomeric organization.

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Gong, Xin; Qian, Hongwu; Shao, Wei; Li, Jingxian; Wu, Jianping; Liu, Jun-Jie; Li, Wenqi; Wang, Hong-Wei; Espenshade, Peter; Yan, Nieng

2016-11-01

Sterol regulatory element-binding protein (SREBP) transcription factors are master regulators of cellular lipid homeostasis in mammals and oxygen-responsive regulators of hypoxic adaptation in fungi. SREBP C-terminus binds to the WD40 domain of SREBP cleavage-activating protein (SCAP), which confers sterol regulation by controlling the ER-to-Golgi transport of the SREBP-SCAP complex and access to the activating proteases in the Golgi. Here, we biochemically and structurally show that the carboxyl terminal domains (CTD) of Sre1 and Scp1, the fission yeast SREBP and SCAP, form a functional 4:4 oligomer and Sre1-CTD forms a dimer of dimers. The crystal structure of Sre1-CTD at 3.5 Å and cryo-EM structure of the complex at 5.4 Å together with in vitro biochemical evidence elucidate three distinct regions in Sre1-CTD required for Scp1 binding, Sre1-CTD dimerization and tetrameric formation. Finally, these structurally identified domains are validated in a cellular context, demonstrating that the proper 4:4 oligomeric complex formation is required for Sre1 activation.

Design and Characterization of Liquidlike POSS-Based Hybrid Nanomaterials Synthesized via Ionic Bonding and Their Interactions with CO 2

KAUST Repository

Petit, Camille

2013-10-01

Liquidlike nanoparticle organic hybrid materials (NOHMs) were designed and synthesized by ionic grafting of polymer chains onto nanoscale silica units called polyhedral oligomeric silsesquioxane (POSS). The properties of these POSS-based NOHMs relevant to CO2 capture, in particular thermal stability, swelling, viscosity, as well as their interactions with CO 2, were investigated using thermogravimetric analyses, differential scanning calorimetry, and NMR and ATR FT-IR spectroscopies. The results indicate that POSS units significantly enhance the thermal stability of the hybrid materials, and their porous nature also contributes to the overall CO 2 capture capacity of NOHMs. The viscosity of the synthesized NOHMs was comparable to those reported for ionic liquids, and rapidly decreased as the temperature increased. The sorption of CO2 in POSS-based NOHMs also reduced their viscosities. The swelling behavior of POSS-based NOHMs was similar to that of previously studied nanoparticle-based NOHMs, and this generally resulted in less volume increase in NOHMs compared to their corresponding polymers for the same amount of CO2 loading. © 2013 American Chemical Society.

Determination of grafting conversion degree in PS/PS-graft-POSS/POSS hybrid nanocomposites obtained through reactive processing

International Nuclear Information System (INIS)

Bianchi, Otavio; Repenning, Gustavo B.; Mauler, Raquel S.; Oliveira, Ricardo V.B.; Canto, Leonardo B.

2011-01-01

Hybrid nanocomposites of polystyrene (PS) and polyhedral oligomeric silsesquioxanes (POSS) - PS/PS-graft-POSS/POSS - with different grafting degrees were prepared by reactive melt processing using dicumyl peroxide (DCP) as initiator in the presence or absence of styrene monomer as radical transfer agent. Gel permeation chromatography (GPC) using triple-detector and proton nuclear magnetic resonance (NMR 1 H) analyses were used together to determine the conversion degree of PS-graft-POSS as a function of the reactive processing conditions adopted. GPC was employed to evaluate the effects of grafting (PS-graft-POSS) and PS chains degradation (β scission) that occur simultaneously during processing on the variation of average molecular masses and distributions for each PS/POSS sample. PS/POSS systems processed with styrene showed higher weight average molecular weights (M w ) and lower polydispersity indexes (M w /M n ), as a result of higher grafting (PS-graft-POSS) conversion (28-40%) and lower PS chain degradation level, as compared to PS/POSS systems processed without styrene in which the degree of grafting conversion was around 25-28%. (author)

On the decoupling of relaxation modes in a molecular liquid caused by isothermal introduction of 2 nm structural inhomogeneities.

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Ueno, Kazuhide; Angell, C Austen

2011-12-08

To support a new interpretation of the origin of the dynamic heterogeneity observed pervasively in fragile liquids as they approach their glass transition temperatures T(g), we demonstrate that the introduction of ~2 nm structural inhomogeneities into a homogeneous glass former leads to a decoupling of diffusion from viscosity similar to that observed during the cooling of orthoterphenyl (OTP) below T(A,) where Arrhenius behavior is lost. Further, the decoupling effect grows stronger as temperature decreases (and viscosity increases). The liquid is cresol, and the ~2 nm inhomogeneities are cresol-soluble asymmetric derivatized tetrasiloxy-based (polyhedral oligomeric silsesquioxane (POSS)) molecules. The decoupling is the phenomenon predicted by Onsager in discussing the approach to a liquid-liquid phase separation with decreasing temperature. In the present case the observations support the notion of a polyamorphic transition in fragile liquids that is hidden below the glass transition. A similar decoupling can be expected as a globular protein is dissolved in dilute aqueous solutions or in protic ionic liquids. © 2011 American Chemical Society

Nanopatterning via Self-Assembly of a Lamellar-Forming Polystyrene-block-Poly(dimethylsiloxane Diblock Copolymer on Topographical Substrates Fabricated by Nanoimprint Lithography

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Dipu Borah

2018-01-01

Full Text Available The self-assembly of a lamellar-forming polystyrene-block-poly(dimethylsiloxane (PS-b-PDMS diblock copolymer (DBCP was studied herein for surface nanopatterning. The DBCP was synthesized by sequential living anionic polymerization of styrene and hexamethylcyclotrisiloxane (D3. The number average molecular weight (Mn, polydispersity index (Mw/Mn and PS volume fraction (φps of the DBCP were MnPS = 23.0 kg mol−1, MnPDMS = 15.0 kg mol−1, Mw/Mn = 1.06 and φps = 0.6. Thin films of the DBCP were cast and solvent annealed on topographically patterned polyhedral oligomeric silsesquioxane (POSS substrates. The lamellae repeat distance or pitch (λL and the width of the PDMS features (dL are ~35 nm and ~17 nm, respectively, as determined by SEM. The chemistry of the POSS substrates was tuned, and the effects on the self-assembly of the DBCP noted. The PDMS nanopatterns were used as etching mask in order to transfer the DBCP pattern to underlying silicon substrate by a complex plasma etch process yielding sub-15 nm silicon features.

Structural elements regulating amyloidogenesis: a cholinesterase model system.

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Létitia Jean

2008-03-01

Full Text Available Polymerization into amyloid fibrils is a crucial step in the pathogenesis of neurodegenerative syndromes. Amyloid assembly is governed by properties of the sequence backbone and specific side-chain interactions, since fibrils from unrelated sequences possess similar structures and morphologies. Therefore, characterization of the structural determinants driving amyloid aggregation is of fundamental importance. We investigated the forces involved in the amyloid assembly of a model peptide derived from the oligomerization domain of acetylcholinesterase (AChE, AChE(586-599, through the effect of single point mutations on beta-sheet propensity, conformation, fibrilization, surfactant activity, oligomerization and fibril morphology. AChE(586-599 was chosen due to its fibrilization tractability and AChE involvement in Alzheimer's disease. The results revealed how specific regions and residues can control AChE(586-599 assembly. Hydrophobic and/or aromatic residues were crucial for maintaining a high beta-strand propensity, for the conformational transition to beta-sheet, and for the first stage of aggregation. We also demonstrated that positively charged side-chains might be involved in electrostatic interactions, which could control the transition to beta-sheet, the oligomerization and assembly stability. Further interactions were also found to participate in the assembly. We showed that some residues were important for AChE(586-599 surfactant activity and that amyloid assembly might preferentially occur at an air-water interface. Consistently with the experimental observations and assembly models for other amyloid systems, we propose a model for AChE(586-599 assembly in which a steric-zipper formed through specific interactions (hydrophobic, electrostatic, cation-pi, SH-aromatic, metal chelation and polar-polar would maintain the beta-sheets together. We also propose that the stacking between the strands in the beta-sheets along the fiber axis could

Interplay of histidine residues of the Alzheimer’s disease Aβ peptide governs its Zn-induced oligomerization

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Istrate, Andrey N.; Kozin, Sergey A.; Zhokhov, Sergey S.; Mantsyzov, Alexey B.; Kechko, Olga I.; Pastore, Annalisa; Makarov, Alexander A.; Polshakov, Vladimir I.

2016-02-01

Conformational changes of Aβ peptide result in its transformation from native monomeric state to the toxic soluble dimers, oligomers and insoluble aggregates that are hallmarks of Alzheimer’s disease (AD). Interactions of zinc ions with Aβ are mediated by the N-terminal Aβ1-16 domain and appear to play a key role in AD progression. There is a range of results indicating that these interactions trigger the Aβ plaque formation. We have determined structure and functional characteristics of the metal binding domains derived from several Aβ variants and found that their zinc-induced oligomerization is governed by conformational changes in the minimal zinc binding site 6HDSGYEVHH14. The residue H6 and segment 11EVHH14, which are part of this site are crucial for formation of the two zinc-mediated interaction interfaces in Aβ. These structural determinants can be considered as promising targets for rational design of the AD-modifying drugs aimed at blocking pathological Aβ aggregation.

Experimental Characterization and Modeling of the Fracturing Behavior of Marcellus Shale

Science.gov (United States)

Jin, C.; Li, W.; Sageman, B. B.; Cusatis, G.

2014-12-01

Adequate knowledge and prediction of mechanical properties of shale are pivotal to the design of hydraulic fractures. The urgent technical challenge of such an endeavor is how to translate the highly heterogeneous nature of shale into a predictive model of the mechanical properties. Our group addressed this challenge by adopting a combined experimental and numerical approach to investigate fracture processes and failure mechanisms of shale.Lattice Discrete Particle Model (LDPM), having shown superior capabilities in predicting qualitative and quantitative behavior of concrete and concrete-like materials, as shown in Fig. 1, has been adopted to simulate mesoscale behavior of shale. The polyhedral cell system defining the geometric attributes of the rock microstructure is built via a 3D tessellation procedure based on X-ray microtomography results of microstructure and grain size distribution of shale specimens. The adopted tessellation procedure makes use of well-established packing algorithms for no-contact spherical particle placement and non-overlapping volume tessellation. The polyhedral particles interact through triangular facets where appropriate measure of stresses and strains are defined. Especially, LDPM is extended to simulate transversely isotropic materials by using orientation-dependent and strain-dependent strength limits coupled with orientation-dependent normal and shear stiffnesses on each facet. Appropriate interface constitutive equations are formulated to simulate all phenomena occurring at a scale that is smaller than the resolution of LDPM system, including microscopic fracture, frictional contact, particle breakage, pore collapse, and distributed damage. Bedding planes and natural joints are characterized by greatly decreased strength limits for facets within that region. To calibrate/validate the LDPM model, microscopic and mesoscopic experiments, including Brazilian tests, uniaxial compression tests, and three point-bending tests, are

Data in support of the identification of neuronal and astrocyte proteins interacting with extracellularly applied oligomeric and fibrillar α-synuclein assemblies by mass spectrometry

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Amulya Nidhi Shrivastava

2016-06-01

Full Text Available α-Synuclein (α-syn is the principal component of Lewy bodies, the pathophysiological hallmark of individuals affected by Parkinson disease (PD. This neuropathologic form of α-syn contributes to PD progression and propagation of α-syn assemblies between neurons. The data we present here support the proteomic analysis used to identify neuronal proteins that specifically interact with extracellularly applied oligomeric or fibrillar α-syn assemblies (conditions 1 and 2, respectively (doi: 10.15252/embj.201591397 [1]. α-syn assemblies and their cellular partner proteins were pulled down from neuronal cell lysed shortly after exposure to exogenous α-syn assemblies and the associated proteins were identified by mass spectrometry using a shotgun proteomic-based approach. We also performed experiments on pure cultures of astrocytes to identify astrocyte-specific proteins interacting with oligomeric or fibrillar α-syn (conditions 3 and 4, respectively. For each condition, proteins interacting selectively with α-syn assemblies were identified by comparison to proteins pulled-down from untreated cells used as controls. The mass spectrometry data, the database search and the peak lists have been deposited to the ProteomeXchange Consortium database via the PRIDE partner repository with the dataset identifiers PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002256 to PRIDE: http://www.ebi.ac.uk/pride/archive/projects/PXD002263 and doi: 10.6019/http://www.ebi.ac.uk/pride/archive/projects/PXD002256 to 10.6019/http://www.ebi.ac.uk/pride/archive/projects/PXD002263.

Therapeutic advantage of pro-electrophilic drugs to activate the Nrf2/ARE pathway in Alzheimer's disease models.

Science.gov (United States)

Lipton, Stuart A; Rezaie, Tayebeh; Nutter, Anthony; Lopez, Kevin M; Parker, James; Kosaka, Kunio; Satoh, Takumi; McKercher, Scott R; Masliah, Eliezer; Nakanishi, Nobuki

2016-12-01

Alzheimer's disease (AD) is characterized by synaptic and neuronal loss, which occurs at least partially through oxidative stress induced by oligomeric amyloid-β (Aβ)-peptide. Carnosic acid (CA), a chemical found in rosemary and sage, is a pro-electrophilic compound that is converted to its active form by oxidative stress. The active form stimulates the Keap1/Nrf2 transcriptional pathway and thus production of phase 2 antioxidant enzymes. We used both in vitro and in vivo models. For in vitro studies, we evaluated protective effects of CA on primary neurons exposed to oligomeric Aβ. For in vivo studies, we used two transgenic mouse models of AD, human amyloid precursor protein (hAPP)-J20 mice and triple transgenic (3xTg AD) mice. We treated these mice trans-nasally with CA twice weekly for 3 months. Subsequently, we performed neurobehavioral tests and quantitative immunohistochemistry to assess effects on AD-related phenotypes, including learning and memory, and synaptic damage. In vitro, CA reduced dendritic spine loss in rat neurons exposed to oligomeric Aβ. In vivo, CA treatment of hAPP-J20 mice improved learning and memory in the Morris water maze test. Histologically, CA increased dendritic and synaptic markers, and decreased astrogliosis, Aβ plaque number, and phospho-tau staining in the hippocampus. We conclude that CA exhibits therapeutic benefits in rodent AD models and since the FDA has placed CA on the 'generally regarded as safe' (GRAS) list, thus obviating the need for safety studies, human clinical trials will be greatly expedited.

The Leishmania donovani UMP Synthase Is Essential for Promastigote Viability and Has an Unusual Tetrameric Structure That Exhibits Substrate-controlled Oligomerization

Energy Technology Data Exchange (ETDEWEB)

French, Jarrod B.; Yates, Phillip A.; Soysa, D.Radika; Boitz, Jan M.; Carter, Nicola S.; Chang, Bailey; Ullman, Buddy; Ealick, Steven E. (Oregon HSU); (Cornell)

2011-08-09

The final two steps of de novo uridine 5'-monophosphate (UMP) biosynthesis are catalyzed by orotate phosphoribosyltransferase (OPRT) and orotidine 5'-monophosphate decarboxylase (OMPDC). In most prokaryotes and simple eukaryotes these two enzymes are encoded by separate genes, whereas in mammals they are expressed as a bifunctional gene product called UMP synthase (UMPS), with OPRT at the N terminus and OMPDC at the C terminus. Leishmania and some closely related organisms also express a bifunctional enzyme for these two steps, but the domain order is reversed relative to mammalian UMPS. In this work we demonstrate that L. donovani UMPS (LdUMPS) is an essential enzyme in promastigotes and that it is sequestered in the parasite glycosome. We also present the crystal structure of the LdUMPS in complex with its product, UMP. This structure reveals an unusual tetramer with two head to head and two tail to tail interactions, resulting in two dimeric OMPDC and two dimeric OPRT functional domains. In addition, we provide structural and biochemical evidence that oligomerization of LdUMPS is controlled by product binding at the OPRT active site. We propose a model for the assembly of the catalytically relevant LdUMPS tetramer and discuss the implications for the structure of mammalian UMPS.

Protein phosphatase 2a (PP2A binds within the oligomerization domain of striatin and regulates the phosphorylation and activation of the mammalian Ste20-Like kinase Mst3

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Jones Candace A

2011-10-01

Full Text Available Abstract Background Striatin, a putative protein phosphatase 2A (PP2A B-type regulatory subunit, is a multi-domain scaffolding protein that has recently been linked to several diseases including cerebral cavernous malformation (CCM, which causes symptoms ranging from headaches to stroke. Striatin association with the PP2A A/C (structural subunit/catalytic subunit heterodimer alters PP2A substrate specificity, but targets and roles of striatin-associated PP2A are not known. In addition to binding the PP2A A/C heterodimer to form a PP2A holoenzyme, striatin associates with cerebral cavernous malformation 3 (CCM3 protein, the mammalian Mps one binder (MOB homolog, Mob3/phocein, the mammalian sterile 20-like (Mst kinases, Mst3, Mst4 and STK25, and several other proteins to form a large signaling complex. Little is known about the molecular architecture of the striatin complex and the regulation of these sterile 20-like kinases. Results To help define the molecular organization of striatin complexes and to determine whether Mst3 might be negatively regulated by striatin-associated PP2A, a structure-function analysis of striatin was performed. Two distinct regions of striatin are capable of stably binding directly or indirectly to Mob3--one N-terminal, including the coiled-coil domain, and another more C-terminal, including the WD-repeat domain. In addition, striatin residues 191-344 contain determinants necessary for efficient association of Mst3, Mst4, and CCM3. PP2A associates with the coiled-coil domain of striatin, but unlike Mob3 and Mst3, its binding appears to require striatin oligomerization. Deletion of the caveolin-binding domain on striatin abolishes striatin family oligomerization and PP2A binding. Point mutations in striatin that disrupt PP2A association cause hyperphosphorylation and activation of striatin-associated Mst3. Conclusions Striatin orchestrates the regulation of Mst3 by PP2A. It binds Mst3 likely as a dimer with CCM3 via

Single Site Silica Supported Tetramethyl Niobium by the SOMC Strategy: Synthesis, Characterization and Structure-Activity Relationship in Ethylene Oligomerization Reaction

KAUST Repository

Hamieh, Ali Imad Ali

2017-06-06

Silica supported Tetramethyl niobium complex [(≡SiO)NbMe4] 2 has been isolated by surface alkylation of [(≡SiO-)NbCl3Me] 1 with dimethyl zinc in pentane. 1 can be easily synthesized by grafting of NbCl3Me2 on to the surface of partially dehydroxylated silica by the SOMC strategy. Precise structural analysis was carried out by the FTIR, advance solid state NMR, elemental analysis and mass balance techniques (gas quantification after treating 2 with degassed water) . Complex 1 was found to be active in the ethylene oligomerization to produce up to C30, whereas to our surprise complex 2 selectively dimerizes ethylene into 1-butene in the absence of a co-catalyst at the same conversion levels.

Two intestinal specific nuclear factors binding to the lactase-phlorizin hydrolase and sucrase-isomaltase promoters are functionally related oligomeric molecules

DEFF Research Database (Denmark)

Troelsen, J T; Mitchelmore, C; Sjöström, H

1994-01-01

Lactase-phlorizin hydrolase (LPH) and sucrase-isomaltase (SI) are enterocyte-specific gene products. The identification of regulatory cis-elements in the promoter of these two genes has enabled us to carry out comparative studies of the corresponding intestinal-specific nuclear factors (NF-LPH1...... and SIF1-BP). Electrophoretic mobility shift assays demonstrated that the two nuclear factors compete for binding on the same cis-elements. The molecular size of the DNA binding polypeptide is estimated to be approximately 50 kDa for both factors. In the native form the factors are found as 250 k......Da oligomeric complexes. Based on these results NF-LPH1 and SIF1-BP are suggested to be either identical or closely related molecules....

Single Site Silica Supported Tetramethyl Niobium by the SOMC Strategy: Synthesis, Characterization and Structure-Activity Relationship in Ethylene Oligomerization Reaction

KAUST Repository

Hamieh, Ali Imad Ali; Dey, Raju; Nekoueishahraki, Bijan; Samantaray, Manoja; Chen, Yin; Abou-Hamad, Edy; Basset, Jean-Marie

2017-01-01

Silica supported Tetramethyl niobium complex [(≡SiO)NbMe4] 2 has been isolated by surface alkylation of [(≡SiO-)NbCl3Me] 1 with dimethyl zinc in pentane. 1 can be easily synthesized by grafting of NbCl3Me2 on to the surface of partially dehydroxylated silica by the SOMC strategy. Precise structural analysis was carried out by the FTIR, advance solid state NMR, elemental analysis and mass balance techniques (gas quantification after treating 2 with degassed water) . Complex 1 was found to be active in the ethylene oligomerization to produce up to C30, whereas to our surprise complex 2 selectively dimerizes ethylene into 1-butene in the absence of a co-catalyst at the same conversion levels.

Nucleotide-Binding Oligomerization Domain-1 and -2 Play No Role in Controlling Brucella abortus Infection in Mice

Directory of Open Access Journals (Sweden)

Fernanda S. Oliveira

2012-01-01

Full Text Available Nucleotide-binding oligomerization domain proteins (NODs are modular cytoplasmic proteins implicated in the recognition of peptidoglycan-derived molecules. Further, several in vivo studies have demonstrated a role for Nod1 and Nod2 in host defense against bacterial pathogens. Here, we demonstrated that macrophages from NOD1-, NOD2-, and Rip2-deficient mice produced lower levels of TNF-α following infection with live Brucella abortus compared to wild-type mice. Similar reduction on cytokine synthesis was not observed for IL-12 and IL-6. However, NOD1, NOD2, and Rip2 knockout mice were no more susceptible to infection with virulent B. abortus than wild-type mice. Additionally, spleen cells from NOD1-, NOD2-, and Rip2-deficient mice showed unaltered production of IFN-γ compared to C57BL/6 mice. Taken together, this study demonstrates that NOD1, NOD2 and Rip2 are dispensable for the control of B. abortus during in vivo infection.

Functional significance of the oligomeric structure of the Na,K-pump from radiation inactivation and ligand binding

International Nuclear Information System (INIS)

Norby, J.G.; Jensen, J.

1991-01-01

The present article is concerned with the oligomeric structure and function of the Na,K-pump (Na,K-ATPase). The questions we have addressed, using radiation inactivation and target size analysis as well as ligand binding, are whether the minimal structural unit and the functional unit have more than one molecule of the catalytic subunit, alpha. The authors first discuss the fundamentals of the radiation inactivation method and emphasize the necessity for rigorous internal standardization with enzymes of known molecular mass. They then demonstrate that the radiation inactivation of Na,K-ATPase is a stepwise process which leads to intermediary fragments of the alpha-subunit with partial catalytic activity. From the target size analysis it is most likely that the membrane-bound Na,K-ATPase is structurally organized as a diprotomer containing two alpha-subunits. Determination of ADP- and ouabain-binding site stoichiometry favors a theory with one substrate site per (alpha beta) 2. 47 references

Interactive Modeling of Architectural Freeform Structures - Combining Geometry with Fabrication and Statics

KAUST Repository

Jiang, Caigui

2014-09-01

This paper builds on recent progress in computing with geometric constraints, which is particularly relevant to architectural geometry. Not only do various kinds of meshes with additional properties (like planar faces, or with equilibrium forces in their edges) become available for interactive geometric modeling, but so do other arrangements of geometric primitives, like honeycomb structures. The latter constitute an important class of geometric objects, with relations to “Lobel” meshes, and to freeform polyhedral patterns. Such patterns are particularly interesting and pose research problems which go beyond what is known for meshes, e.g. with regard to their computing, their flexibility, and the assessment of their fairness.

The role of Vif oligomerization and RNA chaperone activity in HIV-1 replication.

Science.gov (United States)

Batisse, Julien; Guerrero, Santiago; Bernacchi, Serena; Sleiman, Dona; Gabus, Caroline; Darlix, Jean-Luc; Marquet, Roland; Tisné, Carine; Paillart, Jean-Christophe

2012-11-01

The viral infectivity factor (Vif) is essential for the productive infection and dissemination of HIV-1 in non-permissive cells that involve most natural HIV-1 target cells. Vif counteracts the packaging of two cellular cytidine deaminases named APOBEC3G (A3G) and A3F by diverse mechanisms including the recruitment of an E3 ubiquitin ligase complex and the proteasomal degradation of A3G/A3F, the inhibition of A3G mRNA translation or by a direct competition mechanism. In addition, Vif appears to be an active partner of the late steps of viral replication by participating in virus assembly and Gag processing, thus regulating the final stage of virion formation notably genomic RNA dimerization and by inhibiting the initiation of reverse transcription. Vif is a small pleiotropic protein with multiple domains, and recent studies highlighted the importance of Vif conformation and flexibility in counteracting A3G and in binding RNA. In this review, we will focus on the oligomerization and RNA chaperone properties of Vif and show that the intrinsic disordered nature of some Vif domains could play an important role in virus assembly and replication. Experimental evidence demonstrating the RNA chaperone activity of Vif will be presented. Copyright © 2012 Elsevier B.V. All rights reserved.

Influence of oligomeric herbicidal ionic liquids with MCPA and Dicamba anions on the community structure of autochthonic bacteria present in agricultural soil

Energy Technology Data Exchange (ETDEWEB)

Ławniczak, Ł., E-mail: lukasz.k.lawniczak@wp.pl [Department of Chemical Technology, Poznan University of Technology, 60-965 Poznan (Poland); Syguda, A., E-mail: Anna.Syguda@put.poznan.pl [Department of Chemical Technology, Poznan University of Technology, 60-965 Poznan (Poland); Borkowski, A., E-mail: a.borkowski@uw.edu.pl [Faculty of Geology, University of Warsaw, 02-089 Warsaw (Poland); Cyplik, P., E-mail: pcyplik@wp.pl [Department of Biotechnology and Food Microbiology, University of Life Sciences in Poznan, 60-627 Poznan (Poland); Marcinkowska, K., E-mail: k.marcinkowska@iorpib.poznan.pl [Institute of Plant Protection - National Research Institute, Poznan 60-318 (Poland); Wolko, Ł., E-mail: wolko@o2.pl [Department of Biochemistry and Biotechnology, Poznań University of Life Sciences in Poznan, 60-632 Poznan (Poland); Praczyk, T., E-mail: t.praczyk@iorpib.poznan.pl [Institute of Plant Protection - National Research Institute, Poznan 60-318 (Poland); Chrzanowski, Ł., E-mail: Lukasz.Chrzanowski@put.poznan.pl [Department of Chemical Technology, Poznan University of Technology, 60-965 Poznan (Poland); Pernak, J., E-mail: Juliusz.Pernak@put.poznan.pl [Department of Chemical Technology, Poznan University of Technology, 60-965 Poznan (Poland)

2016-09-01

The aim of this study was to evaluate the impact of selected herbicidal ionic liquids (HILs), which exhibit high efficacy in terms of weed control and low toxicity, but may be persistent due to limited biodegradability, on the community structure of autochthonic bacteria present in agricultural soil. Four different oligomeric HILs (with two types of cations and different ratio of herbicidal anions) were synthesized and characterized by employing {sup 1}H and {sup 13}C NMR. The results of biodegradation assay indicated that none of the tested HILs could be classified as readily biodegradable (biodegradation rate ranged from 0 to 7%). The conducted field studies confirmed that the herbicidal efficacy of the HILs was higher compared to the reference herbicide mixture by 10 to 30%, depending on the dose and weed species. After termination of field studies, the soil treated with the tested HILs was subjected to next generation sequencing in order to investigate the potential changes in the bacterial community structure. Proteobacteria was the dominant phylum in all studied samples. Treatment with the studied HILs resulted in an increase of Actinobacteria compared to the reference herbicidal mixture. Differenced among the studied HILs were generally associated with a significantly higher abundance of Bacteroidetes in case of 1-HIL-Dicamba 1/3 and Firmicutes in case of 2-HIL-Dicamba 1/3. - Highlights: • Impact of herbicidal ionic liquids on bacterial community structure was studied. • Oligomeric herbicidal ionic liquids were effective but not readily biodegradable. • Next generation sequencing was used to evaluate shifts in bacterial abundance. • Treatment during field trials resulted in changes at class and species level. • Use of herbicidal ionic liquids affects the structure of autochthonic soil bacteria.

Influence of oligomeric herbicidal ionic liquids with MCPA and Dicamba anions on the community structure of autochthonic bacteria present in agricultural soil

International Nuclear Information System (INIS)

Ławniczak, Ł.; Syguda, A.; Borkowski, A.; Cyplik, P.; Marcinkowska, K.; Wolko, Ł.; Praczyk, T.; Chrzanowski, Ł.; Pernak, J.

2016-01-01

The aim of this study was to evaluate the impact of selected herbicidal ionic liquids (HILs), which exhibit high efficacy in terms of weed control and low toxicity, but may be persistent due to limited biodegradability, on the community structure of autochthonic bacteria present in agricultural soil. Four different oligomeric HILs (with two types of cations and different ratio of herbicidal anions) were synthesized and characterized by employing "1H and "1"3C NMR. The results of biodegradation assay indicated that none of the tested HILs could be classified as readily biodegradable (biodegradation rate ranged from 0 to 7%). The conducted field studies confirmed that the herbicidal efficacy of the HILs was higher compared to the reference herbicide mixture by 10 to 30%, depending on the dose and weed species. After termination of field studies, the soil treated with the tested HILs was subjected to next generation sequencing in order to investigate the potential changes in the bacterial community structure. Proteobacteria was the dominant phylum in all studied samples. Treatment with the studied HILs resulted in an increase of Actinobacteria compared to the reference herbicidal mixture. Differenced among the studied HILs were generally associated with a significantly higher abundance of Bacteroidetes in case of 1-HIL-Dicamba 1/3 and Firmicutes in case of 2-HIL-Dicamba 1/3. - Highlights: • Impact of herbicidal ionic liquids on bacterial community structure was studied. • Oligomeric herbicidal ionic liquids were effective but not readily biodegradable. • Next generation sequencing was used to evaluate shifts in bacterial abundance. • Treatment during field trials resulted in changes at class and species level. • Use of herbicidal ionic liquids affects the structure of autochthonic soil bacteria.

Molecular cloning and functional characterization of duck nucleotide-binding oligomerization domain 1 (NOD1).

Science.gov (United States)

Li, Huilin; Jin, Hui; Li, Yaqian; Liu, Dejian; Foda, Mohamed Frahat; Jiang, Yunbo; Luo, Rui

2017-09-01

Nucleotide-binding oligomerization domain 1 (NOD1) is an imperative cytoplasmic pattern recognition receptor (PRR) and considered as a key member of the NOD-like receptor (NLR) family which plays a critical role in innate immunity through sensing microbial components derived from bacterial peptidoglycan. In the current study, the full-length of duck NOD1 (duNOD1) cDNA from duck embryo fibroblasts (DEFs) was cloned. Multiple sequence alignment and phylogenetic analysis demonstrated that duNOD1 exhibited a strong evolutionary relationship with chicken and rock pigeon NOD1. Tissue-specific expression analysis showed that duNOD1 was widely distributed in various organs, with the highest expression observed in the liver. Furthermore, duNOD1 overexpression induced NF-κB activation in DEFs and the CARD domain is crucial for duNOD1-mediated NF-κB activation. In addition, silencing the duNOD1 decreased the activity of NF-κB in DEFs stimulated by iE-DAP. Overexpression of duNOD1 significantly increased the expression of TNF-α, IL-6, and RANTES in DEFs. These findings highlight the crucial role of duNOD1 as an intracellular sensor in duck innate immune system. Copyright © 2017 Elsevier Ltd. All rights reserved.

Generalization techniques to reduce the number of volume elements for terrain effect calculations in fully analytical gravitational modelling

Science.gov (United States)

Benedek, Judit; Papp, Gábor; Kalmár, János

2018-04-01

Beyond rectangular prism polyhedron, as a discrete volume element, can also be used to model the density distribution inside 3D geological structures. The calculation of the closed formulae given for the gravitational potential and its higher-order derivatives, however, needs twice more runtime than that of the rectangular prism computations. Although the more detailed the better principle is generally accepted it is basically true only for errorless data. As soon as errors are present any forward gravitational calculation from the model is only a possible realization of the true force field on the significance level determined by the errors. So if one really considers the reliability of input data used in the calculations then sometimes the "less" can be equivalent to the "more" in statistical sense. As a consequence the processing time of the related complex formulae can be significantly reduced by the optimization of the number of volume elements based on the accuracy estimates of the input data. New algorithms are proposed to minimize the number of model elements defined both in local and in global coordinate systems. Common gravity field modelling programs generate optimized models for every computation points ( dynamic approach), whereas the static approach provides only one optimized model for all. Based on the static approach two different algorithms were developed. The grid-based algorithm starts with the maximum resolution polyhedral model defined by 3-3 points of each grid cell and generates a new polyhedral surface defined by points selected from the grid. The other algorithm is more general; it works also for irregularly distributed data (scattered points) connected by triangulation. Beyond the description of the optimization schemes some applications of these algorithms in regional and local gravity field modelling are presented too. The efficiency of the static approaches may provide even more than 90% reduction in computation time in favourable

Quantitative modelling of amyloidogenic processing and its influence by SORLA in Alzheimer's disease.

Science.gov (United States)

Schmidt, Vanessa; Baum, Katharina; Lao, Angelyn; Rateitschak, Katja; Schmitz, Yvonne; Teichmann, Anke; Wiesner, Burkhard; Petersen, Claus Munck; Nykjaer, Anders; Wolf, Jana; Wolkenhauer, Olaf; Willnow, Thomas E

2012-01-04

The extent of proteolytic processing of the amyloid precursor protein (APP) into neurotoxic amyloid-β (Aβ) peptides is central to the pathology of Alzheimer's disease (AD). Accordingly, modifiers that increase Aβ production rates are risk factors in the sporadic form of AD. In a novel systems biology approach, we combined quantitative biochemical studies with mathematical modelling to establish a kinetic model of amyloidogenic processing, and to evaluate the influence by SORLA/SORL1, an inhibitor of APP processing and important genetic risk factor. Contrary to previous hypotheses, our studies demonstrate that secretases represent allosteric enzymes that require cooperativity by APP oligomerization for efficient processing. Cooperativity enables swift adaptive changes in secretase activity with even small alterations in APP concentration. We also show that SORLA prevents APP oligomerization both in cultured cells and in the brain in vivo, eliminating the preferred form of the substrate and causing secretases to switch to a less efficient non-allosteric mode of action. These data represent the first mathematical description of the contribution of genetic risk factors to AD substantiating the relevance of subtle changes in SORLA levels for amyloidogenic processing as proposed for patients carrying SORL1 risk alleles.

Giant surfactants of poly(ethylene oxide)- b-polystyrene-(molecular nanoparticle): nanoparticle-driven self-assembly with sub-10-nm nanostructures in thin films

Science.gov (United States)

Hsu, Chih-Hao; Lin, Zhiwei; Dong, Xue-Hui; Hsieh, I.-Fan; Cheng, Stephen Z. D.

2014-03-01

Giant surfactants are built upon precisely attaching shape- and volume-persistent molecular nanoparticles (MNP) to polymeric flexible tails. The unique class of self-assembling materials, giant surfactants, has been demonstrated to form self-assembled ordered nanostructures, and their self-assembly behaviors are remarkably sensitive to primary chemical structures. In this work, two sets of giant surfactants with functionalized MNP attached to diblock copolymer tails were studied in thin films. Carboxylic acid-functionalized [60]fullerene (AC60) tethered with PEO- b-PS (PEO-PS-AC60) represents an ABA' (hydrophilic-hydrophobic-hydrophilic) giant surfactant, and fluoro-functionalized polyhedral oligomeric silsesquioxane (FPOSS) tethered with PEO- b-PS (PEO-PS-FPOSS) represents an ABC (hydrophilic-hydrophobic-omniphobic) one. The dissimilar chemical natures of the MNPs result in different arrangement of MNPs in self-assembled structures, the dispersion of AC60 in PEO domain and the single domain of FPOSS. Moreover, the chemically bonded MNPs could induce the originally disordered small molecular PEO- b-PS to form ordered cylindrical and lamellar structure, as evidenced by TEM and GISAXS, leading to sub-10-nm nanostructures of copolymer in the thin film state.

A targeted nanoglobular contrast agent from host-guest self-assembly for MR cancer molecular imaging.

Science.gov (United States)

Zhou, Zhuxian; Han, Zhen; Lu, Zheng-Rong

2016-04-01

The clinical application of nanoparticular Gd(III) based contrast agents for tumor molecular MRI has been hindered by safety concerns associated with prolonged tissue retention, although they can produce strong tumor enhancement. In this study, a targeted well-defined cyclodextrin-based nanoglobular contrast agent was developed through self-assembly driven by host-guest interactions for safe and effective cancer molecular MRI. Multiple β-cyclodextrins attached POSS (polyhedral oligomeric silsesquioxane) nanoglobule was used as host molecule. Adamantane-modified macrocyclic Gd(III) contrast agent, cRGD (cyclic RGDfK peptide) targeting ligand and fluorescent probe was used as guest molecules. The targeted host-guest nanoglobular contrast agent cRGD-POSS-βCD-(DOTA-Gd) specifically bond to αvβ3 integrin in malignant 4T1 breast tumor and provided greater contrast enhancement than the corresponding non-targeted agent. The agent also provided significant fluorescence signal in tumor tissue. The histological analysis of the tumor tissue confirmed its specific and effective targeting to αvβ3 integrin. The targeted imaging agent has a potential for specific cancer molecular MR and fluorescent imaging. Copyright © 2016 Elsevier Ltd. All rights reserved.

Chemical modification of hybrid nanostructures (POSS for application as lubricant

Directory of Open Access Journals (Sweden)

Caroline Luvison

2014-08-01

Full Text Available Polyhedral oligomeric silsesquioxanes (POSS are hybrid structures type RSiO15n, with n organic groups R. These molecules can be easily functionalized by simply changing the chemical constitution of the organic groups. In this work, chemical modification of POSS-NH2 was performed by amidation reaction with butyric acid at elevated temperature, 160°C. The formation of the amide group is evinced by the appearance of NH angular deformation band at 1540 cm-1 in the FTIR spectra. Approximately 40% of the amino groups reacted, according to titration results. The formation of the amide groups resulted in a shift of the glass transition temperature (Tg from -36.9°C to -25.6°C for the modified-POSS sample. Both POSS-NH2 and modified-POSS samples exhibited similar thermal degradation pattern. Analysis of the pairs distribution function (PDF has determined that the hybrid nanoparticles are separated by a periodic distance of approximately 1.32 nm. POSS-NH2 and modified-POSS exhibit newtonian behavior, which will range from 10-1 s-1 and 1000 s-1. The viscosity decreased with increasing temperature, a typical behavior of liquid lubricants.

Pleiotropic benefit of monomeric and oligomeric flavanols on vascular health--a randomized controlled clinical pilot study.

Science.gov (United States)

Weseler, Antje R; Ruijters, Erik J B; Drittij-Reijnders, Marie-José; Reesink, Koen D; Haenen, Guido R M M; Bast, Aalt

2011-01-01

Cardiovascular diseases are expanding to a major social-economic burden in the Western World and undermine man's deep desire for healthy ageing. Epidemiological studies suggest that flavanol-rich foods (e.g. grapes, wine, chocolate) sustain cardiovascular health. For an evidenced-based application, however, sound clinical data on their efficacy are strongly demanded. In a double-blind, randomized, placebo-controlled intervention study we supplemented 28 male smokers with 200 mg per day of monomeric and oligomeric flavanols (MOF) from grape seeds. At baseline, after 4 and 8 weeks we measured macro- and microvascular function and a cluster of systemic biomarkers for major pathological processes occurring in the vasculature: disturbances in lipid metabolism and cellular redox balance, and activation of inflammatory cells and platelets. In the MOF group serum total cholesterol and LDL decreased significantly (P ≤ 0.05) by 5% (n = 11) and 7% (n = 9), respectively in volunteers with elevated baseline levels. Additionally, after 8 weeks the ratio of glutathione to glutathione disulphide in erythrocytes rose from baseline by 22% (n = 15, Pbenefit of an 8 weeks supplementation with 200 mg/d MOF in humans. ClinicalTrials.gov NCT00742287.

Crystal structure of the Haemophilus influenzae Hap adhesin reveals an intercellular oligomerization mechanism for bacterial aggregation

Science.gov (United States)

Meng, Guoyu; Spahich, Nicole; Kenjale, Roma; Waksman, Gabriel; St Geme, Joseph W

2011-01-01

Bacterial biofilms are complex microbial communities that are common in nature and are being recognized increasingly as an important determinant of bacterial virulence. However, the structural determinants of bacterial aggregation and eventual biofilm formation have been poorly defined. In Gram-negative bacteria, a major subgroup of extracellular proteins called self-associating autotransporters (SAATs) can mediate cell–cell adhesion and facilitate biofilm formation. In this study, we used the Haemophilus influenzae Hap autotransporter as a prototype SAAT to understand how bacteria associate with each other. The crystal structure of the H. influenzae HapS passenger domain (harbouring the SAAT domain) was determined to 2.2 Å by X-ray crystallography, revealing an unprecedented intercellular oligomerization mechanism for cell–cell interaction. The C-terminal SAAT domain folds into a triangular-prism-like structure that can mediate Hap–Hap dimerization and higher degrees of multimerization through its F1–F2 edge and F2 face. The intercellular multimerization can give rise to massive buried surfaces that are required for overcoming the repulsive force between cells, leading to bacterial cell–cell interaction and formation of complex microcolonies. PMID:21841773

Single Site Mutations in the Hetero-oligomeric Mrp Antiporter from Alkaliphilic Bacillus pseudofirmus OF4 That Affect Na+/H+ Antiport Activity, Sodium Exclusion, Individual Mrp Protein Levels, or Mrp Complex Formation*

OpenAIRE

Morino, Masato; Natsui, Shinsuke; Ono, Tomohiro; Swartz, Talia H.; Krulwich, Terry A.; Ito, Masahiro

2010-01-01

Mrp systems are widely distributed and structurally complex cation/proton antiporters. Antiport activity requires hetero-oligomeric complexes of all six or seven hydrophobic Mrp proteins (MrpA–MrpG). Here, a panel of site-directed mutants in conserved or proposed motif residues was made in the Mrp Na+(Li+)/H+ antiporter from an alkaliphilic Bacillus. The mutant operons were expressed in antiporter-deficient Escherichia coli KNabc and assessed for antiport properties, support of sodium resista...

Model systems in photosynthesis research

International Nuclear Information System (INIS)

Katz, J.J.; Hindman, J.C.

1981-01-01

After a general discussion of model studies in photosynthesis research, three recently developed model systems are described. The current status of covalently linked chlorophyll pairs as models for P700 and P865 is first briefly reviewed. Mg-tris(pyrochlorophyllide)1,1,1-tris(hydroxymethyl) ethane triester in its folded configuration is then discussed as a rudimentary antenna-photoreaction center model. Finally, self-assembled chlorophyll systems that contain a mixture of monomeric, oligomeric and special pair chlorophyll are shown to have fluorescence emission characteristics that resemble thoe of intact Tribonema aequale at room temperature in that both show fluorescence emission at 675 and 695 nm. In the self-assembled systems the wavelength of the emitted fluorescence depends on the wavelength of excitation, arguing that energy transfer between different chlorophyll species in these systems may be more complex than previously suspected

Insights into Basal Signaling Regulation, Oligomerization, and Structural Organization of the Human G-Protein Coupled Receptor 83.

Directory of Open Access Journals (Sweden)

Anne Müller

Full Text Available The murine G-protein coupled receptor 83 (mGPR83 is expressed in the hypothalamus and was previously suggested to be involved in the regulation of metabolism. The neuropeptide PEN has been recently identified as a potent GPR83 ligand. Moreover, GPR83 constitutes functionally relevant hetero-oligomers with other G-protein coupled receptors (GPCR such as the ghrelin receptor (GHSR or GPR171. Previous deletion studies also revealed that the long N-terminal extracellular receptor domain (eNDo of mGPR83 may act as an intra-molecular ligand, which participates in the regulation of basal signaling activity, which is a key feature of GPCR function. Here, we investigated particular amino acids at the eNDo of human GPR83 (hGPR83 by side-directed mutagenesis to identify determinants of the internal ligand. These studies were accompanied by structure homology modeling to combine functional insights with structural information. The capacity for hetero-oligomer formation of hGPR83 with diverse family A GPCRs such as the melanocortin-4 receptor (MC4R was also investigated, with a specific emphasis on the impact of the eNDo on oligomerization and basal signaling properties. Finally, we demonstrate that hGPR83 exhibits an unusual basal signaling for different effectors, which also supports signaling promiscuity. hGPR83 interacts with a variety of hypothalamic GPCRs such as the MC4R or GHSR. These interactions are not dependent on the ectodomain and most likely occur at interfaces constituted in the transmembrane regions. Moreover, several amino acids at the transition between the eNDo and transmembrane helix 1 were identified, where mutations lead also to biased basal signaling modulation.

EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA); Scientific Opinion on the substantiation of health claims related to oligomeric procyanidins (OPCs) from grape (Vitis vinifera L.) seeds and improvement of visual adaptation to the dark (ID 680) pursuant to Article 13(1) of Regulation

DEFF Research Database (Denmark)

Tetens, Inge

claims in relation to oligomeric procyanidins (OPCs) from grape (Vitis vinifera L.) seeds and improvement of visual adaptation to the dark. The scientific substantiation is based on the information provided by the Member States in the consolidated list of Article 13 health claims and references that EFSA...... has received from Member States or directly from stakeholders. The food constituent that is the subject of the health claim is oligomeric procyanidins (OPCs) from grape (Vitis vinifera L.) seeds. The Panel considers that OPCs from grape (Vitis vinifera L.) seeds are sufficiently characterised....... The claimed effect is “ocular system: OPCs play an important role in the structure and physiological functions of cornea, OPCs protect the cornea and improve visual adaptation to low luminances”. The target population is assumed to be the general population. In the context of the proposed wordings...

Research on the attitude detection technology of the tetrahedron robot

Science.gov (United States)

Gong, Hao; Chen, Keshan; Ren, Wenqiang; Cai, Xin

2017-10-01

The traditional attitude detection technology can't tackle the problem of attitude detection of the polyhedral robot. Thus we propose a novel algorithm of multi-sensor data fusion which is based on Kalman filter. In the algorithm a tetrahedron robot is investigated. We devise an attitude detection system for the polyhedral robot and conduct the verification of data fusion algorithm. It turns out that the minimal attitude detection system we devise could capture attitudes of the tetrahedral robot in different working conditions. Thus the Kinematics model we establish for the tetrahedron robot is correct and the feasibility of the attitude detection system is proven.

Prolonged Exposure of Cortical Neurons to Oligomeric Amyloid-β Impairs NMDA Receptor Function Via NADPH Oxidase-Mediated ROS Production: Protective Effect of Green Tea (--Epigallocatechin-3-Gallate

Directory of Open Access Journals (Sweden)

Yan He

2011-01-01

Full Text Available Excessive production of Aβ (amyloid β-peptide has been shown to play an important role in the pathogenesis of AD (Alzheimer's disease. Although not yet well understood, aggregation of Aβ is known to cause toxicity to neurons. Our recent study demonstrated the ability for oligomeric Aβ to stimulate the production of ROS (reactive oxygen species in neurons through an NMDA (N-methyl-D-aspartate-dependent pathway. However, whether prolonged exposure of neurons to aggregated Aβ is associated with impairment of NMDA receptor function has not been extensively investigated. In the present study, we show that prolonged exposure of primary cortical neurons to Aβ oligomers caused mitochondrial dysfunction, an attenuation of NMDA receptor-mediated Ca2+ influx and inhibition of NMDA-induced AA (arachidonic acid release. Mitochondrial dysfunction and the decrease in NMDA receptor activity due to oligomeric Aβ are associated with an increase in ROS production. Gp91ds-tat, a specific peptide inhibitor of NADPH oxidase, and Mn(III-tetrakis(4-benzoic acid-porphyrin chloride, an ROS scavenger, effectively abrogated Aβ-induced ROS production. Furthermore, Aβ-induced mitochondrial dysfunction, impairment of NMDA Ca2+ influx and ROS production were prevented by pretreatment of neurons with EGCG [(–-epigallocatechin-3-gallate], a major polyphenolic component of green tea. Taken together, these results support a role for NADPH oxidase-mediated ROS production in the cytotoxic effects of Aβ, and demonstrate the therapeutic potential of EGCG and other dietary polyphenols in delaying onset or retarding the progression of AD.

Intrinsic flexibility of porous materials; theory, modelling and the flexibility window of the EMT zeolite framework

International Nuclear Information System (INIS)

Fletcher, Rachel E.; Wells, Stephen A.; Leung, Ka Ming; Edwards, Peter P.; Sartbaeva, Asel

2015-01-01

Framework materials possess intrinsic flexibility which can be investigated using geometric simulation. We review framework flexibility properties in energy materials and present novel results on the flexibility window of the EMT zeolite framework containing 18-crown-6 ether as a structure directing agent (SDA). Framework materials have structures containing strongly bonded polyhedral groups of atoms connected through their vertices. Typically the energy cost for variations of the inter-polyhedral geometry is much less than the cost of distortions of the polyhedra themselves – as in the case of silicates, where the geometry of the SiO 4 tetrahedral group is much more strongly constrained than the Si—O—Si bridging angle. As a result, framework materials frequently display intrinsic flexibility, and their dynamic and static properties are strongly influenced by low-energy collective motions of the polyhedra. Insight into these motions can be obtained in reciprocal space through the ‘rigid unit mode’ (RUM) model, and in real-space through template-based geometric simulations. We briefly review the framework flexibility phenomena in energy-relevant materials, including ionic conductors, perovskites and zeolites. In particular we examine the ‘flexibility window’ phenomenon in zeolites and present novel results on the flexibility window of the EMT framework, which shed light on the role of structure-directing agents. Our key finding is that the crown ether, despite its steric bulk, does not limit the geometric flexibility of the framework

Discrete Curvature Theories and Applications

KAUST Repository

Sun, Xiang

2016-08-25

Discrete Di erential Geometry (DDG) concerns discrete counterparts of notions and methods in di erential geometry. This thesis deals with a core subject in DDG, discrete curvature theories on various types of polyhedral surfaces that are practically important for free-form architecture, sunlight-redirecting shading systems, and face recognition. Modeled as polyhedral surfaces, the shapes of free-form structures may have to satisfy di erent geometric or physical constraints. We study a combination of geometry and physics { the discrete surfaces that can stand on their own, as well as having proper shapes for the manufacture. These proper shapes, known as circular and conical meshes, are closely related to discrete principal curvatures. We study curvature theories that make such surfaces possible. Shading systems of freeform building skins are new types of energy-saving structures that can re-direct the sunlight. From these systems, discrete line congruences across polyhedral surfaces can be abstracted. We develop a new curvature theory for polyhedral surfaces equipped with normal congruences { a particular type of congruences de ned by linear interpolation of vertex normals. The main results are a discussion of various de nitions of normality, a detailed study of the geometry of such congruences, and a concept of curvatures and shape operators associated with the faces of a triangle mesh. These curvatures are compatible with both normal congruences and the Steiner formula. In addition to architecture, we consider the role of discrete curvatures in face recognition. We use geometric measure theory to introduce the notion of asymptotic cones associated with a singular subspace of a Riemannian manifold, which is an extension of the classical notion of asymptotic directions. We get a simple expression of these cones for polyhedral surfaces, as well as convergence and approximation theorems. We use the asymptotic cones as facial descriptors and demonstrate the

An Origami Approximation to the Cosmic Web

Science.gov (United States)

Neyrinck, Mark C.

2016-10-01

The powerful Lagrangian view of structure formation was essentially introduced to cosmology by Zel'dovich. In the current cosmological paradigm, a dark-matter-sheet 3D manifold, inhabiting 6D position-velocity phase space, was flat (with vanishing velocity) at the big bang. Afterward, gravity stretched and bunched the sheet together in different places, forming a cosmic web when projected to the position coordinates. Here, I explain some properties of an origami approximation, in which the sheet does not stretch or contract (an assumption that is false in general), but is allowed to fold. Even without stretching, the sheet can form an idealized cosmic web, with convex polyhedral voids separated by straight walls and filaments, joined by convex polyhedral nodes. The nodes form in `polygonal' or `polyhedral' collapse, somewhat like spherical/ellipsoidal collapse, except incorporating simultaneous filament and wall formation. The origami approximation allows phase-space geometries of nodes, filaments, and walls to be more easily understood, and may aid in understanding spin correlations between nearby galaxies. This contribution explores kinematic origami-approximation models giving velocity fields for the first time.

High-Performance Oligomeric Catholytes for Effective Macromolecular Separation in Nonaqueous Redox Flow Batteries.

Science.gov (United States)

Hendriks, Koen H; Robinson, Sophia G; Braten, Miles N; Sevov, Christo S; Helms, Brett A; Sigman, Matthew S; Minteer, Shelley D; Sanford, Melanie S

2018-02-28

Nonaqueous redox flow batteries (NRFBs) represent an attractive technology for energy storage from intermittent renewable sources. In these batteries, electrical energy is stored in and extracted from electrolyte solutions of redox-active molecules (termed catholytes and anolytes) that are passed through an electrochemical flow cell. To avoid battery self-discharge, the anolyte and catholyte solutions must be separated by a membrane in the flow cell. This membrane prevents crossover of the redox active molecules, while simultaneously allowing facile transport of charge-balancing ions. A key unmet challenge for the field is the design of redox-active molecule/membrane pairs that enable effective electrolyte separation while maintaining optimal battery properties. Herein, we demonstrate the development of oligomeric catholytes based on tris(dialkylamino)cyclopropenium (CP) salts that are specifically tailored for pairing with size-exclusion membranes composed of polymers of intrinsic microporosity (PIMs). Systematic studies were conducted to evaluate the impact of oligomer size/structure on properties that are crucial for flow battery performance, including cycling stability, charge capacity, solubility, electron transfer kinetics, and crossover rates. These studies have led to the identification of a CP-derived tetramer in which these properties are all comparable, or significantly improved, relative to the monomeric counterpart. Finally, a proof-of-concept flow battery is demonstrated by pairing this tetrameric catholyte with a PIM membrane. After 6 days of cycling, no crossover is detected, demonstrating the promise of this approach. These studies provide a template for the future design of other redox-active oligomers for this application.

Analysis of monomeric and oligomeric organophosphorus flame retardants in fish muscle tissues using liquid chromatography–electrospray ionization tandem mass spectrometry: Application to Nile tilapia (Oreochromis niloticus) from an e-waste processing area in northern Vietnam

OpenAIRE

Matsukami, Hidenori; Suzuki, Go; Tue, Nguyen Minh; Tuyen, Le Huu; Viet, Pham Hung; Takahashi, Shin; Tanabe, Shinsuke; Takigami, Hidetaka

2016-01-01

Using electrospray ionization tandem mass spectrometry combined with liquid chromatography (LC), a novel analytical method was developed to quantify eight monomeric organophosphorus flame retardants (m-PFRs) and three oligomeric organophosphorus flame retardants (o-PFRs) in fish muscle samples. The optimization and validation experiments indicate that the developed method can determine accurately the concentrations of analytes in fish muscle samples. The recoveries of analytes in fish muscle ...

The Building Game: From Enumerative Combinatorics to Conformational Diffusion

Science.gov (United States)

Johnson-Chyzhykov, Daniel; Menon, Govind

2016-08-01

We study a discrete attachment model for the self-assembly of polyhedra called the building game. We investigate two distinct aspects of the model: (i) enumerative combinatorics of the intermediate states and (ii) a notion of Brownian motion for the polyhedral linkage defined by each intermediate that we term conformational diffusion. The combinatorial configuration space of the model is computed for the Platonic, Archimedean, and Catalan solids of up to 30 faces, and several novel enumerative results are generated. These represent the most exhaustive computations of this nature to date. We further extend the building game to include geometric information. The combinatorial structure of each intermediate yields a systems of constraints specifying a polyhedral linkage and its moduli space. We use a random walk to simulate a reflected Brownian motion in each moduli space. Empirical statistics of the random walk may be used to define the rates of transition for a Markov process modeling the process of self-assembly.

Optimization of oligomeric enzyme activity in ionic liquids using Rhodotorula glutinis yeast phenylalanine ammonia lyase.

Science.gov (United States)

Barron, Christiaan C; Sponagle, Brandon J D; Arivalagan, Pugazhendhi; D'Cunha, Godwin B

2017-01-01

Phenylalanine ammonia lyase (E.C.4.3.1.24, PAL) activity of Rhodotorula glutinis yeast has been demonstrated in four commonly used ionic liquids. PAL forward reaction was carried out in 1-butyl-3-methylimidazolium methyl sulfate ([BMIM][MeSO 4 ]), 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF 4 ]), 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF 6 ]) and 1-butyl-3-methylimidazolium lactate ([BMIM][lactate]). Our experiments have revealed that PAL is catalytically active in ionic liquids and the enzyme activity in ([BMIM][PF 6 ]) is comparable to that obtained in aqueous buffer medium. Different conditions were optimized for maximal PAL forward activity including time of incubation (30.0min) L -phenylalanine substrate concentration (30.0mM), nature of buffer (50.0mM Tris-HCl), pH (9.0), temperature (37°C), and speed of agitation (100 rev min -1 ). Under these optimized conditions, about 83% conversion of substrate to product was obtained for the PAL forward reaction that was determined using UV spectroscopy at 290nm. PAL reverse reaction in ([BMIM][PF 6 ]) was determined spectrophotometrically at 520nm; and about 59% substrate conversion was obtained. This data provides further knowledge in enzyme biocatalysis in non-aqueous media, and may be of importance when studying the function of other oligomeric/multimeric proteins and enzymes in ionic liquids. Copyright © 2016 Elsevier Inc. All rights reserved.

Hexokinase 2 from Saccharomyces cerevisiae: regulation of oligomeric structure by in vivo phosphorylation at serine-14.

Science.gov (United States)

Behlke, J; Heidrich, K; Naumann, M; Müller, E C; Otto, A; Reuter, R; Kriegel, T

1998-08-25

Homodimeric hexokinase 2 from Saccharomyces cerevisiae is known to have two sites of phosphorylation: for serine-14 the modification in vivo increases with glucose exhaustion [Kriegel et al. (1994) Biochemistry 33, 148-152], while for serine-157 it occurs in vitro with ATP in the presence of nonphosphorylateable five-carbon analogues of glucose [Heidrich et al. (1997) Biochemistry 36, 1960-1964]. We show now by site-directed mutagenesis and sedimentation analysis that serine-14 phosphorylation affects the oligomeric state of hexokinase, its substitution by glutamate causing complete dissociation; glutamate exchange for serine-157 does not. Phosphorylation of wild-type hexokinase at serine-14 likewise causes dissociation in vitro. In view of the higher glucose affinity of monomeric hexokinase and the high hexokinase concentration in yeast [Womack, F., and Colowick, S. P. (1978) Arch. Biochem. Biophys. 191, 742-747; Mayes, E. L., Hoggett, J. G., and Kellett, G. L. (1983) Eur. J. Biochem. 133, 127-134], we speculate that the in vivo phosphorylation at serine-14 as transiently occurring in glucose derepression might provide a mechanism to improve glucose utilization from low level and/or that nuclear localization of the monomer might be involved in the signal transduction whereby glucose causes catabolite repression.

Glycerol-Induced Aggregation of the Oligomeric L-Asparaginase II from E. coli Monitored with ATR-FTIR

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Koba Adeishvili

2001-06-01

Full Text Available Abstract: In this paper attenuated total reflectance Fourier transform infrared spectroscopy has been employed for the study of the structural composition of aggregates of the oligomeric L-asparaginase II from E.coli formed in the presence of glycerol after the induction of refolding of the protein. Apart from the perfect coincidence of the secondary structure composition of EcA2 as determined by FTIR and crystallography [1], it has also been shown that secondary structure of protein in asparaginase deposits is similar to that of the native conformation: 20.7% extended, 22.3% disordered, 31.4% helix and 25.6% turn/bend/β sheet. Certain structural similarities in the range of experimental error was observed for all three protein deposits presented in this paper, indicating a common structural basis for the composition of this types of aggregates. It is concluded that in the constitution of such precipitates, a partially folded (molten globule like state(s is involved, and its stabilisation is a key factor leading to the aggregation. The results presented in this paper might serve to be a good explanation and an excellent basis for the fundamental theory of protein (oligomers precipitation by osmotic substances.

Controlling the shape of membrane protein polyhedra

Science.gov (United States)

Li, Di; Kahraman, Osman; Haselwandter, Christoph A.

2017-03-01

Membrane proteins and lipids can self-assemble into membrane protein polyhedral nanoparticles (MPPNs). MPPNs have a closed spherical surface and a polyhedral protein arrangement, and may offer a new route for structure determination of membrane proteins and targeted drug delivery. We develop here a general analytic model of how MPPN self-assembly depends on bilayer-protein interactions and lipid bilayer mechanical properties. We find that the bilayer-protein hydrophobic thickness mismatch is a key molecular control parameter for MPPN shape that can be used to bias MPPN self-assembly towards highly symmetric and uniform MPPN shapes. Our results suggest strategies for optimizing MPPN shape for structural studies of membrane proteins and targeted drug delivery.

Biophysical investigation of type A PutAs reveals a conserved core oligomeric structure

Energy Technology Data Exchange (ETDEWEB)

Korasick, David A. [Department of Biochemistry, University of Missouri, Columbia MO USA; Singh, Harkewal [Department of Chemistry, University of Missouri, Columbia MO USA; Pemberton, Travis A. [Department of Chemistry, University of Missouri, Columbia MO USA; Luo, Min [Department of Chemistry, University of Missouri, Columbia MO USA; Dhatwalia, Richa [Department of Chemistry, University of Missouri, Columbia MO USA; Tanner, John J. [Department of Biochemistry, University of Missouri, Columbia MO USA; Department of Chemistry, University of Missouri, Columbia MO USA

2017-08-01

Many enzymes form homooligomers, yet the functional significance of self-association is seldom obvious. Herein, we examine the connection between oligomerization and catalytic function for proline utilization A (PutA) enzymes. PutAs are bifunctional enzymes that catalyze both reactions of proline catabolism. Type A PutAs are the smallest members of the family, possessing a minimal domain architecture consisting of N-terminal proline dehydrogenase and C-terminal l-glutamate-γ-semialdehyde dehydrogenase modules. Type A PutAs form domain-swapped dimers, and in one case (Bradyrhizobium japonicum PutA), two of the dimers assemble into a ring-shaped tetramer. Whereas the dimer has a clear role in substrate channeling, the functional significance of the tetramer is unknown. To address this question, we performed structural studies of four-type A PutAs from two clades of the PutA tree. The crystal structure of Bdellovibrio bacteriovorus PutA covalently inactivated by N-propargylglycine revealed a fold and substrate-channeling tunnel similar to other PutAs. Small-angle X-ray scattering (SAXS) and analytical ultracentrifugation indicated that Bdellovibrio PutA is dimeric in solution, in contrast to the prediction from crystal packing of a stable tetrameric assembly. SAXS studies of two other type A PutAs from separate clades also suggested that the dimer predominates in solution. To assess whether the tetramer of B. japonicum PutA is necessary for catalytic function, a hot spot disruption mutant that cleanly produces dimeric protein was generated. The dimeric variant exhibited kinetic parameters similar to the wild-type enzyme. These results implicate the domain-swapped dimer as the core structural and functional unit of type A PutAs.

Non-transferrin-bound iron (NTBI uptake by T lymphocytes: evidence for the selective acquisition of oligomeric ferric citrate species.

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Joao Arezes

Full Text Available Iron is an essential nutrient in several biological processes such as oxygen transport, DNA replication and erythropoiesis. Plasma iron normally circulates bound to transferrin. In iron overload disorders, however, iron concentrations exceed transferrin binding capacity and iron appears complexed with low molecular weight molecules, known as non-transferrin-bound iron (NTBI. NTBI is responsible for the toxicity associated with iron-overload pathologies but the mechanisms leading to NTBI uptake are not fully understood. Here we show for the first time that T lymphocytes are able to take up and accumulate NTBI in a manner that resembles that of hepatocytes. Moreover, we show that both hepatocytes and T lymphocytes take up the oligomeric Fe3Cit3 preferentially to other iron-citrate species, suggesting the existence of a selective NTBI carrier. These results provide a tool for the identification of the still elusive ferric-citrate cellular carrier and may also open a new pathway towards the design of more efficient iron chelators for the treatment of iron overload disorders.

Reversibility and two state behaviour in the thermal unfolding of oligomeric TIM barrel proteins.

Science.gov (United States)

Romero-Romero, Sergio; Costas, Miguel; Rodríguez-Romero, Adela; Alejandro Fernández-Velasco, D

2015-08-28

Temperature is one of the main variables that modulate protein function and stability. Thermodynamic studies of oligomeric proteins, the dominant protein natural form, have been often hampered because irreversible aggregation and/or slow reactions are common. There are no reports on the reversible equilibrium thermal unfolding of proteins composed of (β/α)8 barrel subunits, albeit this "TIM barrel" topology is one of the most abundant and versatile in nature. We studied the eponymous TIM barrel, triosephosphate isomerase (TIM), belonging to five species of different bacterial taxa. All of them were found to be catalytically efficient dimers. The three-dimensional structure of four enzymes was solved at high/medium resolution. Irreversibility and kinetic control were observed in the thermal unfolding of two TIMs, while for the other three the thermal unfolding was found to follow a two-state equilibrium reversible process. Shifts in the global stability curves of these three proteins are related to the organismal temperature range of optimal growth and modulated by variations in maximum stability temperature and in the enthalpy change at that temperature. Reversibility appears to correlate with the low isoelectric point, the absence of a residual structure in the unfolded state, small cavity volume in the native state, low conformational stability and a low melting temperature. Furthermore, the strong coupling between dimer dissociation and monomer unfolding may reduce aggregation and favour reversibility. It is therefore very thought-provoking to find that a common topological ensemble, such as the TIM barrel, can unfold/refold in the Anfinsen way, i.e. without the help of the cellular machinery.

Lack of Both Nucleotide-Binding Oligomerization Domain-Containing Proteins 1 and 2 Primes T Cells for Activation-Induced Cell Death.

Science.gov (United States)

Kasimsetty, Sashi G; Shigeoka, Alana A; Scheinok, Andrew A; Gavin, Amanda L; Ulevitch, Richard J; McKay, Dianne B

2017-08-01

Nucleotide-binding oligomerization domain (Nod)-containing proteins Nod1 and Nod2 play important roles in the innate immune response to pathogenic microbes, but mounting data suggest these pattern recognition receptors might also play key roles in adaptive immune responses. Targeting Nod1 and Nod2 signaling pathways in T cells is likely to provide a new strategy to modify inflammation in a variety of disease states, particularly those that depend on Ag-induced T cell activation. To better understand how Nod1 and Nod2 proteins contribute to adaptive immunity, this study investigated their role in alloantigen-induced T cell activation and asked whether their absence might impact in vivo alloresponses using a severe acute graft versus host disease model. The study provided several important observations. We found that the simultaneous absence of Nod1 and Nod2 primed T cells for activation-induced cell death. T cells from Nod1 × 2 -/- mice rapidly underwent cell death upon exposure to alloantigen. The Nod1 × 2 -/- T cells had sustained p53 expression that was associated with downregulation of its negative regulator MDM2. In vivo, mice transplanted with an inoculum containing Nod1 × 2 -/- T cells were protected from severe graft versus host disease. The results show that the simultaneous absence of Nod1 and Nod2 is associated with accelerated T cell death upon alloantigen encounter, suggesting these proteins might provide new targets to ameliorate T cell responses in a variety of inflammatory states, including those associated with bone marrow or solid organ transplantation. Copyright © 2017 by The American Association of Immunologists, Inc.

3D analytical field calculation using triangular magnet segments applied to a skewed linear permanent magnet actuator

NARCIS (Netherlands)

Janssen, J.L.G.; Paulides, J.J.H.; Lomonova, E.

2010-01-01

This paper presents novel analytical expressions which describe the 3D magnetic field of arbitrarily magnetized triangular-shaped charged surfaces. These versatile expressions are suitable to model triangularshaped permanent magnets and can be expanded to any polyhedral shape. Many applications are

3D Analytical field calculation using triangular magnet segments applied to a skewed linear permanent magnet actuator

NARCIS (Netherlands)

Janssen, J.L.G.; Paulides, J.J.H.; Lomonova, E.

2009-01-01

This paper presents novel analytical expressions which describe the 3D magnetic field of arbitrarily magnetized triangular-shaped charged surfaces. These versatile expressions are suitable to model triangularshaped permanent magnets and can be expanded to any polyhedral shape. Many applications are

Activation of nucleotide oligomerization domain 2 (NOD2 by human cytomegalovirus initiates innate immune responses and restricts virus replication.

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Arun Kapoor

Full Text Available Nucleotide-binding oligomerization domain 2 (NOD2 is an important innate immune sensor of bacterial pathogens. Its induction results in activation of the classic NF-κB pathway and alternative pathways including type I IFN and autophagy. Although the importance of NOD2 in recognizing RNA viruses has recently been identified, its role in sensing DNA viruses has not been studied. We report that infection with human cytomegalovirus (HCMV results in significant induction of NOD2 expression, beginning as early as 2 hours post infection and increasing steadily 24 hours post infection and afterwards. Infection with human herpesvirus 1 and 2 does not induce NOD2 expression. While the HCMV-encoded glycoprotein B is not required for NOD2 induction, a replication competent virion is necessary. Lentivirus-based NOD2 knockdown in human foreskin fibroblasts (HFFs and U373 glioma cells leads to enhanced HCMV replication along with decreased levels of interferon beta (IFN-β and the pro-inflammatory cytokine, IL8. NOD2 induction in HCMV-infected cells activates downstream NF-κB and interferon pathways supported by reduced nuclear localization of NF-κB and pIRF3 in NOD2 knockdown HFFs. Stable overexpression of NOD2 in HFFs restricts HCMV replication in association with increased levels of IFN-β and IL8. Similarly, transient overexpression of NOD2 in U373 cells or its downstream kinase, RIPK2, results in decreased HCMV replication and enhanced cytokine responses. However, overexpression of a mutant NOD2, 3020insC, associated with severe Crohn's disease, results in enhanced HCMV replication and decreased levels of IFN-β in U373 cells. These results show for the first time that NOD2 plays a significant role in HCMV replication and may provide a model for studies of HCMV recognition by the host cell and HCMV colitis in Crohn's disease.

Parallel numerical modeling of hybrid-dimensional compositional non-isothermal Darcy flows in fractured porous media

Science.gov (United States)

Xing, F.; Masson, R.; Lopez, S.

2017-09-01

This paper introduces a new discrete fracture model accounting for non-isothermal compositional multiphase Darcy flows and complex networks of fractures with intersecting, immersed and non-immersed fractures. The so called hybrid-dimensional model using a 2D model in the fractures coupled with a 3D model in the matrix is first derived rigorously starting from the equi-dimensional matrix fracture model. Then, it is discretized using a fully implicit time integration combined with the Vertex Approximate Gradient (VAG) finite volume scheme which is adapted to polyhedral meshes and anisotropic heterogeneous media. The fully coupled systems are assembled and solved in parallel using the Single Program Multiple Data (SPMD) paradigm with one layer of ghost cells. This strategy allows for a local assembly of the discrete systems. An efficient preconditioner is implemented to solve the linear systems at each time step and each Newton type iteration of the simulation. The numerical efficiency of our approach is assessed on different meshes, fracture networks, and physical settings in terms of parallel scalability, nonlinear convergence and linear convergence.

Surface morphology and dewettability of self-organized thermosets involving epoxy and POSS-capped poly(ethylene oxide) telechelics

International Nuclear Information System (INIS)

Wang, Lei; Zheng, Sixun

2012-01-01

A heptaphenyl polyhedral oligomeric silsesquioxane-capped poly(ethylene oxide) (POSS-capped PEO) telechelics was synthesized via the Huisgen 1,3-dipolar cycloaddition between 3-azidopropylheptaphenyl POSS and α,ω-dialkynyl-terminated poly(ethylene oxide). The organic–inorganic amphiphile was incorporated into epoxy to obtain the organic–inorganic nanocomposites. The morphology of the nanocomposites was investigated by means of atomic force microscopy (AFM) and dynamic mechanical thermal analysis (DMTA). It was found that the epoxy thermosets containing POSS-capped PEO telechelics were microphase-separated. The formation of the nanophases in the thermosets followed a self-assembly mechanism. The static contact angle measurements show that the nanocomposites displayed a significant enhancement in surface hydrophobicity as well as reduction in surface free energy. The improvement in surface dewettability was ascribed to the enrichment of POSS cages at the surface of the nanocomposites and the formation of the specific surface morphology as evidenced by X-ray photoelectron spectroscopy (XPS) and surface atomic force microscopy (AFM). -- Highlights: ► POSS-capped PEO telechelics was synthesized via click chemistry approach. ► The organic–inorganic amphiphile can be self-assembled into the nanophases in epoxy. ► The hybrid nanocomposites were successfully prepared via a self-assembly approach. ► The nanocomposites displayed a significant enhancement in surface hydrophobicity.

Real-time two-dimensional imaging of potassium ion distribution using an ion semiconductor sensor with charged coupled device technology.

Science.gov (United States)

Hattori, Toshiaki; Masaki, Yoshitomo; Atsumi, Kazuya; Kato, Ryo; Sawada, Kazuaki

2010-01-01

Two-dimensional real-time observation of potassium ion distributions was achieved using an ion imaging device based on charge-coupled device (CCD) and metal-oxide semiconductor technologies, and an ion selective membrane. The CCD potassium ion image sensor was equipped with an array of 32 × 32 pixels (1024 pixels). It could record five frames per second with an area of 4.16 × 4.16 mm(2). Potassium ion images were produced instantly. The leaching of potassium ion from a 3.3 M KCl Ag/AgCl reference electrode was dynamically monitored in aqueous solution. The potassium ion selective membrane on the semiconductor consisted of plasticized poly(vinyl chloride) (PVC) with bis(benzo-15-crown-5). The addition of a polyhedral oligomeric silsesquioxane to the plasticized PVC membrane greatly improved adhesion of the membrane onto Si(3)N(4) of the semiconductor surface, and the potential response was stabilized. The potential response was linear from 10(-2) to 10(-5) M logarithmic concentration of potassium ion. The selectivity coefficients were K(K(+),Li(+))(pot) = 10(-2.85), K(K(+),Na(+))(pot) = 10(-2.30), K(K(+),Rb(+))(pot) =10(-1.16), and K(K(+),Cs(+))(pot) = 10(-2.05).

Characteristic of Hybrid Cellulose-Amino Functionalized POSS-Silica Nanocomposite and Antimicrobial Activity

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Sivalingam Ramesh

2015-01-01

Full Text Available Recently, cellulose has much attention as an emerging renewable nanomaterial which holds promising properties having unique piezoelectricity, insulating, and biodegradable nature for various applications. Also, the modified properties of cellulose by appropriate chemical modifications in various functional groups with outstanding properties or significantly improved physical, chemical, biological, and electronic properties will widen the way for it to be utilized in different usages. Therefore, in this paper, cellulose-functionalized polyhedral oligomeric silsesquioxanes (POSS based materials were considered an important class of high-performance hybrid nanocomposite materials. To functionalize the regenerated cellulose, amino functionalized POSS material was synthesized via sol-gel covalent crosslinking process in presence of amino coupling agent. In this reaction, tetraethoxsilane (TEOS and γ-aminopropyltriethoxy silane (γ-APTES as coupling agent for metal precursors were selected. The chemical structure of cellulose-amine functionalized bonding and covalent crosslinking hybrids was confirmed by FTIR and 1H NMR spectral analysis. From the TEM results, well-dispersed hybrid cellulose-functionalized POSS-silica composites are observed. The resulting cellulose-POSS-silica hybrid nanocomposites materials provided significantly improved the optical transparency, and thermal and morphological properties to compare the cellulose-silica hybrid materials. Further, antimicrobial test against pathogenic bacteria was carried out.

A Biodesigned Nanocomposite Biomaterial for Auricular Cartilage Reconstruction.

Science.gov (United States)

Nayyer, Leila; Jell, Gavin; Esmaeili, Ali; Birchall, Martin; Seifalian, Alexander M

2016-05-01

Current biomaterials for auricular replacement are associated with high rates of infection and extrusion. The development of new auricular biomaterials that mimic the mechanical properties of native tissue and promote desirable cellular interactions may prevent implant failure. A porous 3D nanocomposite scaffold (NS) based on POSS-PCU (polyhedral oligomeric silsesquioxane nanocage into polycarbonate based urea-urethane) is developed with an elastic modulus similar to native ear. In vitro biological interactions on this NS reveal greater protein adsorption, increased fibroblast adhesion, proliferation, and collagen production compared with Medpor (the current synthetic auricular implant). In vivo, the POSS-PCU with larger pores (NS2; 150-250 μm) have greater tissue ingrowth (≈5.8× and ≈1.4 × increase) than the POSS-PCU with smaller pores (NS1; 100-50 μm) and when compared to Medpor (>100 μm). The NS2 with the larger pores demonstrates a reduced fibrotic encapsulation compared with NS1 and Medpor (≈4.1× and ≈1.6×, respectively; P response for all materials may indicate that the elastic modulus and pore size of the implant scaffold could be important design considerations for influencing fibrotic responses to auricular and other soft tissue implants. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Preparation and evaluation of a novel hybrid monolithic column based on pentafluorobenzyl imidazolium bromide ionic liquid.

Science.gov (United States)

Shan, Yuanhong; Qiao, Lizhen; Shi, Xianzhe; Xu, Guowang

2015-01-02

To develop a novel hybrid monolithic column based on pentafluorobenzyl imidazolium bromide ionic liquid, a new ionic liquid monomer was synthesized from 1-vinylimidazole and pentafluorobenzyl bromide. By employing a facile one-step copolymerization of polyhedral-oligomeric-silsesquioxane-type (POSS) cross-linking agent and the home-made ionic liquid monomer, the hybrid monolithic columns were in situ fabricated in fused-silica capillary. The morphology of monolithic column was characterized by scanning electron microscope (SEM) and the chemical composition was confirmed by Fourier-transform infrared spectroscopy (FT-IR) and elemental analysis. Excellent mechanical stability and slight swelling propensity were exhibited which was ascribed to the rigid hybrid monolithic skeleton. Reproducibility results of run-to-run, column-to-column, batch-to-batch and day-to-day were investigated and the RSDs were less than 0.46%, 1.84%, 3.96% and 3.17%, respectively. The mixed-mode retention mechanism with hydrophobic interaction, π-π stacking, ion-exchange, electrostatic interaction and dipole-dipole interaction was explored systematically using analytes with different structure types. Satisfied separation capability and column efficiency were achieved for the analysis of small molecular compounds such as alkylbenzenes, polycyclic aromatic hydrocarbons, nucleosides and halogenated compounds. Copyright © 2014 Elsevier B.V. All rights reserved.

PES/POSS Soluble Veils as Advanced Modifiers for Multifunctional Fiber Reinforced Composites

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Gianluca Cicala

2017-07-01

Full Text Available Novel polyhedral oligomeric silsesquioxanes (POSS-filled thermoplastic electrospun veils were used to tailor the properties of the interlaminar region of epoxy-based composites. The veils were designed to be soluble upon curing in the epoxy matrix, so that POSS could be released within the interlaminar region. Three different POSS contents, varying from 1 to 10 wt %, were tested while the percentage of coPolyethersulphone (coPES dissolved in the epoxy resin was kept to a fixed value of 10 wt %. Good quality veils could be obtained at up to 10 wt % of POSS addition, with the nanofibers’ diameters varying from 861 nm for the coPES to 428 nm upon POSS addition. The feasibility of the soluble veils to disperse POSS in the interlaminar region was proved, and the effect of POSS on phase morphology and viscoelastic properties studied. POSS was demonstrated to significantly affect the morphology and viscoelastic properties of epoxy composites, especially for the percentages 1% and 5%, which enabled the composites to avoid POSS segregates occurring. A dynamic mechanical analysis showed a significant improvement to the storage modulus, and a shift of more than 30 °C due to the POSS cages hindering the motion of the molecular chains and network junctions.

Surface-initiated ring-opening metathesis polymerization (SI-ROMP) to attach a tethered organic corona onto CdSe/ZnS core/shell quantum dots

Energy Technology Data Exchange (ETDEWEB)

Vatansever, Fatma, E-mail: vatansever.fatma@mgh.harvard.edu; Hamblin, Michael R., E-mail: hamblin@helix.mgh.harvard.edu [Massachusetts General Hospital, Wellman Center for Photomedicine (United States)

2016-10-15

Core–shell CdSe/ZnS quantum dots (QDs) are useful as tunable photostable fluorophores for multiple applications in industry, biology, and medicine. However, to achieve the optimum optical properties, the surface of the QDs must be passivated to remove charged sites that might bind extraneous substances and allow aggregation. Here we describe a method of growing an organic polymer corona onto the QD surface using the bottom-up approach of surface-initiated ring-opening metathesis polymerization (SI-ROMP) with Grubbs catalyst. CdSe/ZnS QDs were first coated with mercaptopropionic acid by displacing the original tri-octylphosphine oxide layer, and then reacted with 7-octenyl dimethyl chlorosilane. The resulting octenyl double bonds allowed the attachment of ruthenium alkylidene groups as a catalyst. A subsequent metathesis reaction with strained bicyclic monomers (norbornene-dicarbonyl chloride (NDC), and a mixture of NDC and norbornenylethylisobutyl-polyhedral oligomeric silsesquioxane (norbornoPOSS)) allowed the construction of tethered organic homo-polymer or co-polymer layers onto the QD. Compounds were characterized by FT-IR, 1H-NMR, X-ray photoelectron spectroscopy, differential scanning calorimetry, and transmission electron microscopy. Atomic force microscopy showed that the coated QDs were separate and non-aggregated with a range of diameter of 48–53 nm.

Hydrogen bonding strength of diblock copolymers affects the self-assembled structures with octa-functionalized phenol POSS nanoparticles.

Science.gov (United States)

Lu, Yi-Syuan; Yu, Chia-Yu; Lin, Yung-Chih; Kuo, Shiao-Wei

2016-02-28

In this study, the influence of the functional groups by the diblock copolymers of poly(styrene-b-4-vinylpyridine) (PS-b-P4VP), poly(styrene-b-2-vinylpyridine) (PS-b-P2VP), and poly(styrene-b-methyl methacrylate) (PS-b-PMMA) on their blends with octa-functionalized phenol polyhedral oligomeric silsesquioxane (OP-POSS) nanoparticles (NPs) was investigated. The relative hydrogen bonding strengths in these blends follow the order PS-b-P4VP/OP-POSS > PS-b-P2VP/OP-POSS > PS-b-PMMA/OP-POSS based on the Kwei equation from differential scanning calorimetry (DSC) and Fourier transform infrared spectroscopic analyses. Small-angle X-ray scattering and transmission electron microscopic analyses show that the morphologies of the self-assembly structures are strongly dependent on the hydrogen bonding strength at relatively higher OP-POSS content. The PS-b-P4VP/OP-POSS hybrid complex system with the strongest hydrogen bonds shows the order-order transition from lamellae to cylinders and finally to body-centered cubic spheres upon increasing OP-POSS content. However, PS-b-P2VP/OP-POSS and PS-b-PMMA/OP-POSS hybrid complex systems, having relatively weaker hydrogen bonds, transformed from lamellae to cylinder structures at lower OP-POSS content (50 wt%).

Structural fingerprints and their evolution during oligomeric vs. oligomer-free amyloid fibril growth.

Science.gov (United States)

Foley, Joseph; Hill, Shannon E; Miti, Tatiana; Mulaj, Mentor; Ciesla, Marissa; Robeel, Rhonda; Persichilli, Christopher; Raynes, Rachel; Westerheide, Sandy; Muschol, Martin

2013-09-28

Deposits of fibrils formed by disease-specific proteins are the molecular hallmark of such diverse human disorders as Alzheimer's disease, type II diabetes, or rheumatoid arthritis. Amyloid fibril formation by structurally and functionally unrelated proteins exhibits many generic characteristics, most prominently the cross β-sheet structure of their mature fibrils. At the same time, amyloid formation tends to proceed along one of two separate assembly pathways yielding either stiff monomeric filaments or globular oligomers and curvilinear protofibrils. Given the focus on oligomers as major toxic species, the very existence of an oligomer-free assembly pathway is significant. Little is known, though, about the structure of the various intermediates emerging along different pathways and whether the pathways converge towards a common or distinct fibril structures. Using infrared spectroscopy we probed the structural evolution of intermediates and late-stage fibrils formed during in vitro lysozyme amyloid assembly along an oligomeric and oligomer-free pathway. Infrared spectroscopy confirmed that both pathways produced amyloid-specific β-sheet peaks, but at pathway-specific wavenumbers. We further found that the amyloid-specific dye thioflavin T responded to all intermediates along either pathway. The relative amplitudes of thioflavin T fluorescence responses displayed pathway-specific differences and could be utilized for monitoring the structural evolution of intermediates. Pathway-specific structural features obtained from infrared spectroscopy and Thioflavin T responses were identical for fibrils grown at highly acidic or at physiological pH values and showed no discernible effects of protein hydrolysis. Our results suggest that late-stage fibrils formed along either pathway are amyloidogenic in nature, but have distinguishable structural fingerprints. These pathway-specific fingerprints emerge during the earliest aggregation events and persist throughout the

Structural fingerprints and their evolution during oligomeric vs. oligomer-free amyloid fibril growth

Science.gov (United States)

Foley, Joseph; Hill, Shannon E.; Miti, Tatiana; Mulaj, Mentor; Ciesla, Marissa; Robeel, Rhonda; Persichilli, Christopher; Raynes, Rachel; Westerheide, Sandy; Muschol, Martin

2013-09-01

Deposits of fibrils formed by disease-specific proteins are the molecular hallmark of such diverse human disorders as Alzheimer's disease, type II diabetes, or rheumatoid arthritis. Amyloid fibril formation by structurally and functionally unrelated proteins exhibits many generic characteristics, most prominently the cross β-sheet structure of their mature fibrils. At the same time, amyloid formation tends to proceed along one of two separate assembly pathways yielding either stiff monomeric filaments or globular oligomers and curvilinear protofibrils. Given the focus on oligomers as major toxic species, the very existence of an oligomer-free assembly pathway is significant. Little is known, though, about the structure of the various intermediates emerging along different pathways and whether the pathways converge towards a common or distinct fibril structures. Using infrared spectroscopy we probed the structural evolution of intermediates and late-stage fibrils formed during in vitro lysozyme amyloid assembly along an oligomeric and oligomer-free pathway. Infrared spectroscopy confirmed that both pathways produced amyloid-specific β-sheet peaks, but at pathway-specific wavenumbers. We further found that the amyloid-specific dye thioflavin T responded to all intermediates along either pathway. The relative amplitudes of thioflavin T fluorescence responses displayed pathway-specific differences and could be utilized for monitoring the structural evolution of intermediates. Pathway-specific structural features obtained from infrared spectroscopy and Thioflavin T responses were identical for fibrils grown at highly acidic or at physiological pH values and showed no discernible effects of protein hydrolysis. Our results suggest that late-stage fibrils formed along either pathway are amyloidogenic in nature, but have distinguishable structural fingerprints. These pathway-specific fingerprints emerge during the earliest aggregation events and persist throughout the

Association of Nucleotide-binding Oligomerization Domain Receptors with Peptic Ulcer and Gastric Cancer.

Science.gov (United States)

Mohammadian Amiri, Rajeeh; Tehrani, Mohsen; Taghizadeh, Shirin; Shokri-Shirvani, Javad; Fakheri, Hafez; Ajami, Abolghasem

2016-10-01

Host innate immunity can affect the clinical outcomes of Helicobacter pylori infection, including gastritis, gastric ulcer, gastric adenocarcinoma, and MALT lymphoma. Nucleotide binding oligomerization domain (NOD)-1 and -2 are two molecules of innate immunity which are involved in the host defense against H. pylori. This study aimed to evaluate the effect of the expression level of NOD1 and NOD2 on the susceptibility to gastric cancer as well as peptic ulcer in individuals with H. pylori infection. The gene expression levels of these molecules were compared in three groups of non-ulcer dyspepsia (NUD) as a control group (n=52); peptic ulcer disease (PUD), (n=53); and gastric cancer (GC), (n=39). Relative expression levels of NOD1 in patients with GC were higher than those of NUD and PUD (p<0.001 and P<0.001, respectively). Similarly in case of NOD1, PUD group showed higher level of expression than NUD group (p<0.01). However, there was no significant difference between H. pylori -positive and -negative patients in NUD, PUD, or GC groups. Moreover, the expression levels of NOD2 showed no significant difference among NUD, PUD, or GC groups, while among H. pylori-positive patients, it was higher in GC group than NUD  and PUD groups (p<0.05 and p<0.01, respectively). In addition, positive correlation coefficients were attained between NOD1 and NOD2 expressions in patients with NUD (R2 Linear=0.349, p<0.001), PUD (R2 Linear=0.695, p<0.001), and GC (R2 Linear=0.385, p<0.001). Collectively, the results suggest that the chronic activation of NOD1 and NOD2 receptors might play a role in the development of gastric cancer.

Analysis of oligomeric transition of silkworm small heat shock protein sHSP20.8 using high hydrostatic pressure native PAGE

Science.gov (United States)

Fujisawa, Tetsuro; Ueda, Toshifumi; Kameyama, Keiichi; Aso, Yoichi; Ishiguro, Ryo

2013-06-01

The small heat shock proteins (sHSPs) solubilize thermo-denatured proteins without adenosine triphosphate energy consumption to facilitate protein refolding. sHSP20.8 is one of the silkworm (Bombyx mori) sHSPs having only one cystein in the N-terminal domain: Cys43. We report a simple measurement of oligomeric transition of sHSP20.8 using high hydrostatic pressure native polyacrylamide gel electrophoresis (high hydrostatic pressure (HP) native polyacrylamide gel electrophoresis (PAGE)). At ambient pressure under oxydative condition, the native PAGE of thermal transition of sHSP20.8 oligomer displayed a cooperative association. In contrast, HP native PAGE clearly demonstrated that sHSP20.8 dissociated at 80 MPa and 25°C, and the resultant molecular species gradually reassociated with time under that condition. In addition, the reassociation process was suppressed in the presence of the reductant. These results are consistent with the idea that sHSP20.8 oligomer temporally dissociates at the first thermo-sensing step and reassociates with the oxidation of Cys43.

Oligomeric protein complexes of apolipoproteins stabilize the internal fluid environment of organism in redfins of the Tribolodon genus [Pisces; Cypriniformes, Cyprinidae].

Science.gov (United States)

Andreeva, Alla M; Serebryakova, Marina V; Lamash, Nina E

2017-06-01

One of the most important functions of plasma proteins in vertebrates is their participation in osmotic homeostasis in the organism. Modern concepts about plasma proteins and their capillary filtration are based on a model of large monomeric proteins that are able to penetrate the interstitial space. At the same time, it was revealed that a considerable amount of oligomeric complexes are present in the low-molecular-weight (LM) protein fraction in the extracellular fluids of fishes. The functions of these complexes are unknown. In the present study, we investigated the LM-fraction proteins in the plasma and interstitial fluid (IF) of redfins of the genus Tribolodon. This fish alternatively spends parts of its life cycle in saline and fresh waters. We identified the protein Wap65, serpins and apolipoproteins in this fraction. By combining the methods of 2D-E under native and denaturing conditions with MALDI, we demonstrated that only apolipoproteins formed complexes. We showed that serum apolipoproteins (АроА-I, Аро-14) were present in the form of homooligomeric complexes that were dissociated with the release of monomeric forms of proteins in the course of capillary filtration to IF. Dissociation of homooligomers is not directly correlated with the change in salinity but is correlated with seasonal dynamics. We found that there was a significant decrease in the total protein concentration in IF relative to plasma. Therefore, we suggested that dissociation of homooligomeric complexes from various apolipoproteins supports the isoosmoticity of extracellular fluids relative to capillary wall stabilization through a fluid medium in fish. Copyright © 2017 Elsevier Inc. All rights reserved.

Functional and structural studies of the disulfide isomerase DsbC from the plant pathogen Xylella fastidiosa reveals a redox-dependent oligomeric modulation in vitro.

Science.gov (United States)

Santos, Clelton A; Toledo, Marcelo A S; Trivella, Daniela B B; Beloti, Lilian L; Schneider, Dilaine R S; Saraiva, Antonio M; Crucello, Aline; Azzoni, Adriano R; Souza, Alessandra A; Aparicio, Ricardo; Souza, Anete P

2012-10-01

Xylella fastidiosa is a Gram-negative bacterium that grows as a biofilm inside the xylem vessels of susceptible plants and causes several economically relevant crop diseases. In the present study, we report the functional and low-resolution structural characterization of the X. fastidiosa disulfide isomerase DsbC (XfDsbC). DsbC is part of the disulfide bond reduction/isomerization pathway in the bacterial periplasm and plays an important role in oxidative protein folding. In the present study, we demonstrate the presence of XfDsbC during different stages of X. fastidiosa biofilm development. XfDsbC was not detected during X. fastidiosa planktonic growth; however, after administering a sublethal copper shock, we observed an overexpression of XfDsbC that also occurred during planktonic growth. These results suggest that X. fastidiosa can use XfDsbC in vivo under oxidative stress conditions similar to those induced by copper. In addition, using dynamic light scattering and small-angle X-ray scattering, we observed that the oligomeric state of XfDsbC in vitro may be dependent on the redox environment. Under reducing conditions, XfDsbC is present as a dimer, whereas a putative tetrameric form was observed under nonreducing conditions. Taken together, our findings demonstrate the overexpression of XfDsbC during biofilm formation and provide the first structural model of a bacterial disulfide isomerase in solution. © 2012 The Authors Journal compilation © 2012 FEBS.

Supplementary Material for: A new mode of SAM domain mediated oligomerization observed in the CASKIN2 neuronal scaffolding protein

KAUST Repository

Smirnova, Ekaterina; Kwan, Jamie; Siu, Ryan; Gao, Xin; Zoidl, Georg; Demeler, Borries; Saridakis, Vivian; Donaldson, Logan

2016-01-01

Abstract Background CASKIN2 is a homolog of CASKIN1, a scaffolding protein that participates in a signaling network with CASK (calcium/calmodulin-dependent serine kinase). Despite a high level of homology between CASKIN2 and CASKIN1, CASKIN2 cannot bind CASK due to the absence of a CASK Interaction Domain and consequently, may have evolved undiscovered structural and functional distinctions. Results We demonstrate that the crystal structure of the Sterile Alpha Motif (SAM) domain tandem (SAM1-SAM2) oligomer from CASKIN2 is different than CASKIN1, with the minimal repeating unit being a dimer, rather than a monomer. Analytical ultracentrifugation sedimentation velocity methods revealed differences in monomer/dimer equilibria across a range of concentrations and ionic strengths for the wild type CASKIN2 SAM tandem and a structure-directed double mutant that could not oligomerize. Further distinguishing CASKIN2 from CASKIN1, EGFP-tagged SAM tandem proteins expressed in Neuro2a cells produced punctae that were distinct both in shape and size. Conclusions This study illustrates a new way in which neuronal SAM domains can assemble into large macromolecular assemblies that might concentrate and amplify synaptic responses.

Cartilage oligomeric matrix protein associates differentially with erosions and synovitis and has a different temporal course in cyclic citrullinated peptide antibody (anti-CCP)-positive versus anti-CCP-negative early rheumatoid arthritis

DEFF Research Database (Denmark)

Christensen, Anne F; Lindegaard, Hanne; Hørslev-Petersen, Kim

2011-01-01

-suppressive effect. We aimed to compare circulating cartilage oligomeric matrix protein (COMP), a marker of cartilage turnover, in untreated anti-CCP-positive and anti-CCP-negative RA, and to study the temporal pattern of COMP through 4 years of treatment, including the relationship to imaging and clinical findings.......048). In anti-CCP-positive patients, COMP exhibited a parabolic course over 4 years, while COMP in anti-CCP-negative patients had an almost linear course. In anti-CCP-positive patients, COMP was associated with MRI edema and erosion score, while COMP was correlated with synovitis score in anti...

Role of Nucleotide-Binding Oligomerization Domain-Containing (NOD 2 in Host Defense during Pneumococcal Pneumonia.

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Tijmen J Hommes

Full Text Available Streptococcus (S. pneumoniae is the most common causative pathogen in community-acquired pneumonia. Nucleotide-binding oligomerization domain-containing (NOD 2 is a pattern recognition receptor located in the cytosol of myeloid cells that is able to detect peptidoglycan fragments of S. pneumoniae. We here aimed to investigate the role of NOD2 in the host response during pneumococcal pneumonia. Phagocytosis of S. pneumoniae was studied in NOD2 deficient (Nod2-/- and wild-type (Wt alveolar macrophages and neutrophils in vitro. In subsequent in vivo experiments Nod2-/- and Wt mice were inoculated with serotype 2 S. pneumoniae (D39, an isogenic capsule locus deletion mutant (D39Δcps or serotype 3 S. pneumoniae (6303 via the airways, and bacterial growth and dissemination and the lung inflammatory response were evaluated. Nod2-/- alveolar macrophages and blood neutrophils displayed a reduced capacity to internalize pneumococci in vitro. During pneumonia caused by S. pneumoniae D39 Nod2-/- mice were indistinguishable from Wt mice with regard to bacterial loads in lungs and distant organs, lung pathology and neutrophil recruitment. While Nod2-/- and Wt mice also had similar bacterial loads after infection with the more virulent S. pneumoniae 6303 strain, Nod2-/- mice displayed a reduced bacterial clearance of the normally avirulent unencapsulated D39Δcps strain. These results suggest that NOD2 does not contribute to host defense during pneumococcal pneumonia and that the pneumococcal capsule impairs recognition of S. pneumoniae by NOD2.

Oligomerization of Bacillus subtilis DesR is required for fine tuning regulation of membrane fluidity.

Science.gov (United States)

Najle, Sebastián R; Inda, María E; de Mendoza, Diego; Cybulski, Larisa E

2009-10-01

The DesK-DesR two-component system regulates the order of membrane lipids in the bacterium Bacillus subtilis by controlling the expression of the des gene coding for the delta 5-acyl-lipid desaturase. To activate des transcription, the membrane-bound histidine kinase DesK phosphorylates the response regulator DesR. This covalent modification of the regulatory domain of dimeric DesR promotes, in a cooperative fashion, the hierarchical occupation of two adjacent, non-identical, DesR-P binding sites, so that there is a shift in the equilibrium toward the tetrameric active form of the response regulator. However, the mechanism of regulation of DesR activity by phosphorylation and oligomerization is not well understood. We employed deletion analysis and reporter fusions to study the role of the N-terminal domain on DesR activity. In addition, electromobility shift assays were used to analyze the binding capacity of the transcription factor to deletion mutants of the des promoter. We show that DesR lacking the N-terminal domain is still able to bind to the des promoter. We also demonstrate that if the RA site is moved closer to the -35 region of Pdes, the adjacent site RB is dispensable for activation. Our results indicate that the unphosphorylated regulatory domain of DesR obstructs the access of the recognition helix of DesR to its DNA target. In addition, we present evidence showing that RB is physiologically relevant to control the activation of the des gene when the levels of DesR-P reach a critical threshold.

Structurally designed attenuated subunit vaccines for S. aureus LukS-PV and LukF-PV confer protection in a mouse bacteremia model.

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Hatice Karauzum

Full Text Available Previous efforts towards S. aureus vaccine development have largely focused on cell surface antigens to induce opsonophagocytic killing aimed at providing sterile immunity, a concept successfully applied to other Gram-positive pathogens such as Streptococcus pneumoniae. However, these approaches have largely failed, possibly in part due to the remarkable diversity of the staphylococcal virulence factors such as secreted immunosuppressive and tissue destructive toxins. S. aureus produces several pore-forming toxins including the single subunit alpha hemolysin as well as bicomponent leukotoxins such as Panton-Valentine leukocidin (PVL, gamma hemolysins (Hlg, and LukED. Here we report the generation of highly attenuated mutants of PVL subunits LukS-PV and LukF-PV that were rationally designed, based on an octameric structural model of the toxin, to be deficient in oligomerization. The attenuated subunit vaccines were highly immunogenic and showed significant protection in a mouse model of S. aureus USA300 sepsis. Protection against sepsis was also demonstrated by passive transfer of rabbit immunoglobulin raised against LukS-PV. Antibodies to LukS-PV inhibited the homologous oligomerization of LukS-PV with LukF-PV as well heterologous oligomerization with HlgB. Importantly, immune sera from mice vaccinated with the LukS mutant not only inhibited the PMN lytic activity produced by the PVL-positive USA300 but also blocked PMN lysis induced by supernatants of PVL-negative strains suggesting a broad protective activity towards other bicomponent toxins. These findings strongly support the novel concept of an anti-virulence, toxin-based vaccine intended for prevention of clinical S. aureus invasive disease, rather than achieving sterile immunity. Such a multivalent vaccine may include attenuated leukotoxins, alpha hemolysin, and superantigens.

Enzymatic Transformation and Bonding of Sulfonamide Antibiotics to Model Humic Substances

Directory of Open Access Journals (Sweden)

J. Schwarz

2015-01-01

Full Text Available Sulfonamides are consumed as pharmaceutical antibiotics and reach agricultural soils with excreta used as fertilizer. Subsequently, nonextractable residues rapidly form in soil, which has been researched in a couple of studies. To further elucidate conditions, strength, and mechanisms of the fixation to soil humic substances, three selected sulfonamides were investigated using the biochemical oligomerization of substituted phenols as a model for the humification process. Catechol, guaiacol, and vanillin were enzymatically reacted using laccase from Trametes versicolor. In the presence of the substituted phenols alone, the concentration of sulfonamides decreased. This decrease was even more pronounced when additional laccase was present. Upon the enzymatic oligomerization of the substituted phenols to a humic-like structure the sulfonamides were sorbed, transformed, sequestered, and nonextractable bound. Sulfonamides were transformed depending on their molecular properties. Fractions of different bonding strength were determined using a sequential extraction procedure. Isolated nonextractable products were analyzed by chromatographic, spectroscopic, and calorimetric methods to identify coupling and bonding mechanisms of the sulfonamides. Differential scanning calorimetry measurements suggested cross-linking of such incorporated sulfonamides in humic oligomers. Nuclear magnetic resonance spectroscopy measurements showed clear differences between the vanillin-sulfapyridine oligomer and the parent sulfapyridine indicating bound residue formation through covalent binding.

Continued biological investigations of boron-rich oligomeric phosphate diesters (OPDs). Tumor-selective boron agents for BNCT

International Nuclear Information System (INIS)

Lee, Mark W.; Shelly, Kenneth; Kane, Robert R.; Hawthorne, M. Frederick

2006-01-01

Clinical success of Boron Neutron Capture Therapy will rely on the selective intracellular delivery of high concentrations of boron-10 to tumor tissue. In order for a boron agent to facilitate clinical success, the simultaneous needs of obtaining a high tumor dose, high tumor selectivity, and low systemic toxicity must be realized. Boron-rich oligomeric phosphate diesters (OPDs) are a class of highly water-soluble compounds containing up to 40% boron by weight. Previous work in our groups demonstrated that once placed in the cytoplasm of tumor cells, OPDs quickly accumulate within the cell nucleus. The objective of the current study was to determine the biodistribution of seven different free OPDs in BALB/c mice bearing EMT6 tumors. Fructose solutions containing between 1.4 and 6.4 micrograms of boron per gram of tissue were interveinously injected in mice seven to ten days after tumor implantation. At intervals during the study, animals were euthanized and samples of tumor, blood, liver, kidney, brain and skin were collected and analyzed for boron content using ICP-AES. Tumor boron concentrations of between 5 and 29 ppm were achieved and maintained over the 72-hour time course of each experiment. Several OPDs demonstrated high tumor selectivity with one oligomer exhibiting a tumor to blood ratio of 35:1. The apparent toxicity of each oligomer was assessed through animal behavior during the experiment and necropsy of each animal upon sacrifice. (author)

Collagen XII and XIV, New Partners of Cartilage Oligomeric Matrix Protein in the Skin Extracellular Matrix Suprastructure*

Science.gov (United States)

Agarwal, Pallavi; Zwolanek, Daniela; Keene, Douglas R.; Schulz, Jan-Niklas; Blumbach, Katrin; Heinegård, Dick; Zaucke, Frank; Paulsson, Mats; Krieg, Thomas; Koch, Manuel; Eckes, Beate

2012-01-01

The tensile and scaffolding properties of skin rely on the complex extracellular matrix (ECM) that surrounds cells, vasculature, nerves, and adnexus structures and supports the epidermis. In the skin, collagen I fibrils are the major structural component of the dermal ECM, decorated by proteoglycans and by fibril-associated collagens with interrupted triple helices such as collagens XII and XIV. Here we show that the cartilage oligomeric matrix protein (COMP), an abundant component of cartilage ECM, is expressed in healthy human skin. COMP expression is detected in the dermal compartment of skin and in cultured fibroblasts, whereas epidermis and HaCaT cells are negative. In addition to binding collagen I, COMP binds to collagens XII and XIV via their C-terminal collagenous domains. All three proteins codistribute in a characteristic narrow zone in the superficial papillary dermis of healthy human skin. Ultrastructural analysis by immunogold labeling confirmed colocalization and further revealed the presence of COMP along with collagens XII and XIV in anchoring plaques. On the basis of these observations, we postulate that COMP functions as an adapter protein in human skin, similar to its function in cartilage ECM, by organizing collagen I fibrils into a suprastructure, mainly in the vicinity of anchoring plaques that stabilize the cohesion between the upper dermis and the basement membrane zone. PMID:22573329

Collagen XII and XIV, new partners of cartilage oligomeric matrix protein in the skin extracellular matrix suprastructure.

Science.gov (United States)

Agarwal, Pallavi; Zwolanek, Daniela; Keene, Douglas R; Schulz, Jan-Niklas; Blumbach, Katrin; Heinegård, Dick; Zaucke, Frank; Paulsson, Mats; Krieg, Thomas; Koch, Manuel; Eckes, Beate

2012-06-29

The tensile and scaffolding properties of skin rely on the complex extracellular matrix (ECM) that surrounds cells, vasculature, nerves, and adnexus structures and supports the epidermis. In the skin, collagen I fibrils are the major structural component of the dermal ECM, decorated by proteoglycans and by fibril-associated collagens with interrupted triple helices such as collagens XII and XIV. Here we show that the cartilage oligomeric matrix protein (COMP), an abundant component of cartilage ECM, is expressed in healthy human skin. COMP expression is detected in the dermal compartment of skin and in cultured fibroblasts, whereas epidermis and HaCaT cells are negative. In addition to binding collagen I, COMP binds to collagens XII and XIV via their C-terminal collagenous domains. All three proteins codistribute in a characteristic narrow zone in the superficial papillary dermis of healthy human skin. Ultrastructural analysis by immunogold labeling confirmed colocalization and further revealed the presence of COMP along with collagens XII and XIV in anchoring plaques. On the basis of these observations, we postulate that COMP functions as an adapter protein in human skin, similar to its function in cartilage ECM, by organizing collagen I fibrils into a suprastructure, mainly in the vicinity of anchoring plaques that stabilize the cohesion between the upper dermis and the basement membrane zone.

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

KAUST Repository

Lensink, Marc F.; Velankar, Sameer; Kryshtafovych, Andriy; Huang, Shen-You; Schneidman-Duhovny, Dina; Sali, Andrej; Segura, Joan; Fernandez-Fuentes, Narcis; Viswanath, Shruthi; Elber, Ron; Grudinin, Sergei; Popov, Petr; Neveu, Emilie; Lee, Hasup; Baek, Minkyung; Park, Sangwoo; Heo, Lim; Rie Lee, Gyu; Seok, Chaok; Qin, Sanbo; Zhou, Huan-Xiang; Ritchie, David W.; Maigret, Bernard; Devignes, Marie-Dominique; Ghoorah, Anisah; Torchala, Mieczyslaw; Chaleil, Raphaë l A.G.; Bates, Paul A.; Ben-Zeev, Efrat; Eisenstein, Miriam; Negi, Surendra S.; Weng, Zhiping; Vreven, Thom; Pierce, Brian G.; Borrman, Tyler M.; Yu, Jinchao; Ochsenbein, Franç oise; Guerois, Raphaë l; Vangone, Anna; Rodrigues, Joã o P.G.L.M.; van Zundert, Gydo; Nellen, Mehdi; Xue, Li; Karaca, Ezgi; Melquiond, Adrien S.J.; Visscher, Koen; Kastritis, Panagiotis L.; Bonvin, Alexandre M.J.J.; Xu, Xianjin; Qiu, Liming; Yan, Chengfei; Li, Jilong; Ma, Zhiwei; Cheng, Jianlin; Zou, Xiaoqin; Shen, Yang; Peterson, Lenna X.; Kim, Hyung-Rae; Roy, Amit; Han, Xusi; Esquivel-Rodriguez, Juan; Kihara, Daisuke; Yu, Xiaofeng; Bruce, Neil J.; Fuller, Jonathan C.; Wade, Rebecca C.; Anishchenko, Ivan; Kundrotas, Petras J.; Vakser, Ilya A.; Imai, Kenichiro; Yamada, Kazunori; Oda, Toshiyuki; Nakamura, Tsukasa; Tomii, Kentaro; Pallara, Chiara; Romero-Durana, Miguel; Jimé nez-Garcí a, Brian; Moal, Iain H.; Fé rnandez-Recio, Juan; Joung, Jong Young; Kim, Jong Yun; Joo, Keehyoung; Lee, Jooyoung; Kozakov, Dima; Vajda, Sandor; Mottarella, Scott; Hall, David R.; Beglov, Dmitri; Mamonov, Artem; Xia, Bing; Bohnuud, Tanggis; Del Carpio, Carlos A.; Ichiishi, Eichiro; Marze, Nicholas; Kuroda, Daisuke; Roy Burman, Shourya S.; Gray, Jeffrey J.; Chermak, Edrisse; Cavallo, Luigi; Oliva, Romina; Tovchigrechko, Andrey; Wodak, Shoshana J.

2016-01-01

We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. © 2016 Wiley Periodicals, Inc.

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

KAUST Repository

Lensink, Marc F.

2016-04-28

We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. © 2016 Wiley Periodicals, Inc.

Analysis of the Surface of Deposited Copper After Electroerosion Treatment

Science.gov (United States)

Ablyaz, T. R.; Simonov, M. Yu.; Shlykov, E. S.

2018-03-01

An electron microscope analysis of the surface of deposited copper is performed after a profiling-piercing electroerosion treatment. The deposited copper is treated with steel, duralumin, and copper electrode tools at different pulse energies. The treatment with the duralumin electrode produces on the treated surface a web-like structure and cubic-morphology polyhedral dimples about 10 μm in size. The main components of the surface treated with the steel electrode are developed polyhedral dimples with a size of 10 - 50 μm. After the treatment with the copper electrode the main components of the treated surface are large polyhedral dimples about 30 - 80 μm in size.

First C/sub 4/-functionalisation of condensed tannins. Phlobatannins as prototype of a new class of C-ring isomerised oligomers. Die eerste C/sub 4/-funksionalisering van gekondenseerde tanniene. Flobatanniene as prototipe van 'n nuwe klas van C-ring geisomeriseerde oligomere

Energy Technology Data Exchange (ETDEWEB)

Steenkamp, J A

1986-06-01

This thesis comprises besides the characterisation of new oligomeric flavenoids from the core wood of the indigeneous Colophosphermum mopane, an investigation into the C/sub 4/-functionalisation of flavan-3-ol analogues. The first peltogynoid biflavenoid and prototypes of a new series C-ring isomerised condensed tannins, namely the phlobatannins, were isolated. Besides /sup 1/H- nmr-parameters for structure analysis, the natural phlobatannins were characterised and the unique ring isomerisation was investigated.

Metastable Amyloid Phases and their Conversion to Mature Fibrils

Science.gov (United States)

Muschol, Martin; Miti, Tatiana; Mulaj, Mentor; Schmit, Jeremy

Self-assembly of proteins into amyloid fibrils plays a key role in both functional biological responses and pathogenic disorders which include Alzheimer's disease and type II diabetes. Amyloid fibril assembly frequently generates compact oligomeric and curvilinear polymeric intermediates which are implicated to be toxic to cells. Yet, the relation between these early-stage oligomeric aggregates and late-stage rigid fibrils, which are the hallmark structure of amyloid plaques, has remained unclear. Our measurements indicate that lysozyme amyloid oligomers and their curvilinear fibrils only form after crossing a salt and protein concentration dependent threshold. These oligomeric aggregates are structurally distinct from rigid fibrils and are metastable against nucleation and growth of rigid fibrils. Our experimental transition boundaries match well with colloidal model predictions accounting for salt-modulated charge repulsion. We also report our preliminary findings on the mechanism by which these metastable oligomeric phases are converted into stable amyloid fibrils.

Nucleotide-binding oligomerization domain 2 (NOD2) activation induces apoptosis of human oral squamous cell carcinoma cells.

Science.gov (United States)

Yoon, Hyo-Eun; Ahn, Mee-Young; Kwon, Seong-Min; Kim, Dong-Jae; Lee, Jun; Yoon, Jung-Hoon

2016-04-01

Microbial Pattern-recognition receptors (PRRs), such as nucleotide-binding oligomerization domains (NODs), are essential for mammalian innate immune response. This study was designed to determine the effect of NOD1 and NOD2 agonist on innate immune responses and antitumor activity in oral squamous cell carcinoma (OSCC) cells. NODs expression was examined by RT-PCR, and IL-8 production by NODs agonist was examined by ELISA. Western blot analysis was performed to determine the MAPK activation in response to their agonist. Cell proliferation was determined by MTT assay. Flow cytometry and Western blot analysis were performed to determine the MDP-induced cell death. The levels of NODs were apparently expressed in OSCC cells. NODs agonist, Tri-DAP and MDP, led to the production of IL-8 and MAPK activation. NOD2 agonist, MDP, inhibited the proliferation of YD-10B cells in a dose-dependent manner. Also, the ratio of Annexin V-positive cells and cleaved PARP was increased by MDP treatment in YD-10B cells, suggesting that MDP-induced cell death in YD-10B cells may be owing to apoptosis. Our results indicate that NODs are functionally expressed in OSCC cells and can trigger innate immune responses. In addition, NOD2 agonist inhibited cell proliferation and induced apoptosis. These findings provide the potential value of MDP as novel candidates for antitumor agents of OSCC. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Autosomal dominant precocious osteoarthropathy due to a mutation of the cartilage oligomeric matrix protein (COMP) gene: further expansion of the phenotypic variations of COMP defects

Energy Technology Data Exchange (ETDEWEB)

Kawaji, Hiroyuki [Department of Orthopaedic Surgery, Sanyudo Hospital, 6-1-219 Chuou, Yonezawa, Yamagata 992-0045 (Japan); Nishimura, Gen [Department of Radiology, Nasu Chuou Hospital, Tochigi (Japan); Watanabe, Sobei; Sasaki, Akira; Sano, Tokuhisa [Department of Orthopaedic Surgery, Tohoku Kohsei-Nenkin Hospital, Miyagi (Japan); Mabuchi, Akihiko; Ikeda, Toshiyuki; Ikegawa, Shiro [Laboratory for Bone and Joint Diseases, SNP Research Center, Tokyo (Japan); Ohashi, Hirofumi [Division of Medical Genetics, Saitama Children' s Medical Center, Saitama (Japan)

2002-12-01

We report on a Japanese family of four generations with an autosomal dominant precocious osteoarthropathy. The cardinal clinical manifestations of affected individuals were painful weight-bearing large joints, which started in late childhood or adolescence. The radiological hallmarks included coxa plana, mild epiphyseal dysplasia of the knee, and round talar domes with tibiotalar slant in childhood, which evolved into degenerative joint diseases in adulthood. The disease phenotype was cosegregated with a mutation of the cartilage oligomeric matrix protein (COMP) gene in the family members, who underwent molecular evaluation. COMP mutations have been reported in a mild form of multiple epiphyseal dysplasia (MED), Ribbing type, as well as allied disorders with more severe manifestations, such as MED Fairbank type and pseudoachondroplasia. Unlike previously reported cases with the Ribbing type, the present patients did not have short stature or brachydactyly. This report expands further the phenotypic variations of COMP defects. (orig.)

Single site mutations in the hetero-oligomeric Mrp antiporter from alkaliphilic Bacillus pseudofirmus OF4 that affect Na+/H+ antiport activity, sodium exclusion, individual Mrp protein levels, or Mrp complex formation.

Science.gov (United States)

Morino, Masato; Natsui, Shinsuke; Ono, Tomohiro; Swartz, Talia H; Krulwich, Terry A; Ito, Masahiro

2010-10-01

Mrp systems are widely distributed and structurally complex cation/proton antiporters. Antiport activity requires hetero-oligomeric complexes of all six or seven hydrophobic Mrp proteins (MrpA-MrpG). Here, a panel of site-directed mutants in conserved or proposed motif residues was made in the Mrp Na(+)(Li(+))/H(+) antiporter from an alkaliphilic Bacillus. The mutant operons were expressed in antiporter-deficient Escherichia coli KNabc and assessed for antiport properties, support of sodium resistance, membrane levels of each Mrp protein, and presence of monomeric and dimeric Mrp complexes. Antiport did not depend on a VFF motif or a conserved tyrosine pair, but a role for a conserved histidine in a potential quinone binding site of MrpA was supported. The importance of several acidic residues for antiport was confirmed, and the importance of additional residues was demonstrated (e.g. three lysine residues conserved across MrpA, MrpD, and membrane-bound respiratory Complex I subunits (NuoL/M/N)). The results extended indications that MrpE is required for normal membrane levels of other Mrp proteins and for complex formation. Moreover, mutations in several other Mrp proteins lead to greatly reduced membrane levels of MrpE. Thus, changes in either of the two Mrp modules, MrpA-MrpD and MrpE-MrpG, influence the other. Two mutants, MrpB-P37G and MrpC-Q70A, showed a normal phenotype but lacked the MrpA-MrpG monomeric complex while retaining the dimeric hetero-oligomeric complex. Finally, MrpG-P81A and MrpG-P81G mutants exhibited no antiport activity but supported sodium resistance and a low [Na(+)](in). Such mutants could be used to screen hypothesized but uncharacterized sodium efflux functions of Mrp apart from Na(+) (Li(+))/H(+) antiport.

On a novel method to synthesize POSS-based hybrids: An example of the preparation of TPU based system

Directory of Open Access Journals (Sweden)

O. Monticelli

2013-12-01

Full Text Available A novel method to prepare polymer/polyhedral oligomeric silsesquioxanes (POSS hybrids by melt reactive blending is proposed in this paper, by the controlled polymer chain scission and reaction of chain ends with functional silsesquioxanes. Application to thermoplastic polyurethanes (TPU is addressed, taking advantage of the polyurethane chain scission equilibrium reaction, leading to the formation of highly reactive isocyanate and hydroxyl chain ends. Despite the isocyanate chemistry has been widely studied for the preparation of polymer/POSS hybrids by in situ copolymerisation, the exploitation of similar chemical processes in an industrially viable and environmental friendly melt blending process is currently an open research field. In this work, the reaction in the molten state of dihydroxyl-functionalised POSS with the polyurethane chain is demonstrated to produce a TPU/POSS hybrids. The effect of POSS concentration on nanomorphology, thermal properties and surface properties is studied, showing significant changes compared to pristine TPU. In particular, an increase of glass transition temperature is observed in the presence of reactive POSS (ΔT up to about 10°C in the presence of 10 wt% loading. Furthermore, an increase of surface water wettability, evidenced by the decrease of water contact angle from 95° for pristine TPU to 70° in TPU containing 10"wt% of reactive POSS, is found.

Formation of nanophases in epoxy thermosets containing amphiphilic block copolymers with linear and star-like topologies.

Science.gov (United States)

Wang, Lei; Zhang, Chongyin; Cong, Houluo; Li, Lei; Zheng, Sixun; Li, Xiuhong; Wang, Jie

2013-07-11

In this work, we investigated the effect of topological structures of block copolymers on the formation of the nanophase in epoxy thermosets containing amphiphilic block copolymers. Two block copolymers composed of poly(ε-caprolactone) (PCL) and poly(2,2,2-trifluoroethyl acrylate) (PTFEA) blocks were synthesized to possess linear and star-shaped topologies. The star-shaped block copolymer composed a polyhedral oligomeric silsesquioxane (POSS) core and eight poly(ε-caprolactone)-block-poly(2,2,2-trifluoroethyl acrylate) (PCL-b-PTFEA) diblock copolymer arms. Both block copolymers were synthesized via the combination of ring-opening polymerization and reversible addition-fragmentation chain transfer/macromolecular design via the interchange of xanthate (RAFT/MADIX) process; they were controlled to have identical compositions of copolymerization and lengths of blocks. Upon incorporating both block copolymers into epoxy thermosets, the spherical PTFEA nanophases were formed in all the cases. However, the sizes of PTFEA nanophases from the star-like block copolymer were significantly lower than those from the linear diblock copolymer. The difference in the nanostructures gave rise to the different glass transition behavior of the nanostructured thermosets. The dependence of PTFEA nanophases on the topologies of block copolymers is interpreted in terms of the conformation of the miscible subchain (viz. PCL) at the surface of PTFEA microdomains and the restriction of POSS cages on the demixing of the thermoset-philic block (viz. PCL).

Periodic imidazolium-bridged hybrid monolith for high-efficiency capillary liquid chromatography with enhanced selectivity.

Science.gov (United States)

Qiao, Xiaoqiang; Zhang, Niu; Han, Manman; Li, Xueyun; Qin, Xinying; Shen, Shigang

2017-03-01

A novel periodic imidazolium-bridged hybrid monolithic column was developed. With diene imidazolium ionic liquid 1-allyl-3-vinylimidazolium bromide as both cross-linker and organic functionalized reagent, a new periodic imidazolium-bridged hybrid monolithic column was facilely prepared in capillary with homogeneously distributed cationic imidazolium by a one-step free-radical polymerization with polyhedral oligomeric silsesquioxane methacryl substituted. The successful preparation of the new column was verified by Fourier transform infrared spectroscopy, scanning electron microscopy, elemental analysis, and surface area analysis. Most interestingly, the bonded amount of 1-allyl-3-vinylimidazolium bromide of the new column is three times higher than that of the conventional imidazolium-embedded hybrid monolithic column and the specific surface area of the column reached 478 m 2 /g. The new column exhibited high stability, excellent separation efficiency, and enhanced separation selectivity. The column efficiency reached 151 000 plates/m for alkylbenzenes. Furthermore, the new column was successfully used for separation of highly polar nucleosides and nucleic acid bases with pure water as mobile phase and even bovine serum albumin tryptic digest. All these results demonstrate the periodic imidazolium-bridged hybrid monolithic column is a good separation media and can be used for chromatographic separation of small molecules and complex biological samples with high efficiency. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Gypsum (CaSO4·2H2O) Scaling on Polybenzimidazole and Cellulose Acetate Hollow Fiber Membranes under Forward Osmosis

Science.gov (United States)

Chen, Si Cong; Su, Jincai; Fu, Feng-Jiang; Mi, Baoxia; Chung, Tai-Shung

2013-01-01

We have examined the gypsum (CaSO4·2H2O) scaling phenomena on membranes with different physicochemical properties in forward osmosis (FO) processes. Three hollow fiber membranes made of (1) cellulose acetate (CA), (2) polybenzimidazole (PBI)/polyethersulfone (PES) and (3) PBI-polyhedral oligomeric silsesquioxane (POSS)/polyacrylonitrile (PAN) were studied. For the first time in FO processes, we have found that surface ionic interactions dominate gypsum scaling on the membrane surface. A 70% flux reduction was observed on negatively charged CA and PBI membrane surfaces, due to strong attractive forces. The PBI membrane surface also showed a slightly positive charge at a low pH value of 3 and exhibited a 30% flux reduction. The atomic force microscopy (AFM) force measurements confirmed a strong repulsive force between gypsum and PBI at a pH value of 3. The newly developed PBI-POSS/PAN membrane had ridge morphology and a contact angle of 51.42° ± 14.85° after the addition of hydrophilic POSS nanoparticles and 3 min thermal treatment at 95 °C. Minimal scaling and an only 1.3% flux reduction were observed at a pH value of 3. Such a ridge structure may reduce scaling by not providing a locally flat surface to the crystallite at a pH value of 3; thus, gypsum would be easily washed away from the surface. PMID:24957062

Low Loss Nanostructured Polymers for Chip-scale Waveguide Amplifiers.

Science.gov (United States)

Chen, George F R; Zhao, Xinyu; Sun, Yang; He, Chaobin; Tan, Mei Chee; Tan, Dawn T H

2017-06-13

On-chip waveguide amplifiers offer higher gain in small device sizes and better integration with photonic devices than the commonly available fiber amplifiers. However, on-chip amplifiers have yet to make its way into the mainstream due to the limited availability of materials with ideal light guiding and amplification properties. A low-loss nanostructured on-chip channel polymeric waveguide amplifier was designed, characterized, fabricated and its gain experimentally measured at telecommunication wavelength. The active polymeric waveguide core comprises of NaYF 4 :Yb,Er,Ce core-shell nanocrystals dispersed within a SU8 polymer, where the nanoparticle interfacial characteristics were tailored using hydrolyzed polyhedral oligomeric silsesquioxane-graft-poly(methyl methacrylate) to improve particle dispersion. Both the enhanced IR emission intensity from our nanocrystals using a tri-dopant scheme and the reduced scattering losses from our excellent particle dispersion at a high solid loading of 6.0 vol% contributed to the outstanding optical performance of our polymeric waveguide. We achieved one of the highest reported gain of 6.6 dB/cm using a relatively low coupled pump power of 80 mW. These polymeric waveguide amplifiers offer greater promise for integrated optical circuits due to their processability and integration advantages which will play a key role in the emerging areas of flexible communication and optoelectronic devices.

vQRS Based on Hybrids of CNT with PMMA-POSS and PS-POSS Copolymers to Reach the Sub-PPM Detection of Ammonia and Formaldehyde at Room Temperature Despite Moisture

Directory of Open Access Journals (Sweden)

Abhishek Sachan

2017-07-01

Full Text Available Nanocomposite-based quantum resistive vapour sensors (vQRS have been developed from the assembly of hybrid copolymers of polyhedral oligomeric silsesquioxane (POSS and poly(methyl methacrylate (PMMA or poly(styrene (PS with carbon nanotubes (CNT. The originality of the resulting conducting architecture is expected to be responsible for the ability of the transducer to detect sub-ppm concentrations of ammonia and formaldehyde at room temperature despite the presence of humidity. In particular, the boosting effect of POSS is evidenced in CNT-based nanocomposite vQRS. The additive fabrication by spraying layer-by-layer provides (sLbL is an effective method to control the reproducibility of the transducers’ chemo-resistive responses. In dry atmosphere, the two types of sensors showed a high sensitivity towards both hazardous gases, as they were able to detect 300 ppb of formaldehyde and 500 ppb of ammonia with a sufficiently good signal to noise ratio (SNR > 10. They also exhibited a quick response times less than 5 s for both vapours and, even in the presence of 100 ppm of water, they were able to detect small amounts of gases (1.5 ppm of NH3 and 9 ppm of CH2O. The results suggest promising applications of POSS-based vQRS for air quality or volatolome monitoring.

Gypsum (CaSO42H2O) scaling on polybenzimidazole and cellulose acetate hollow fiber membranes under forward osmosis

KAUST Repository

Chen, Si Cong

2013-11-08

We have examined the gypsum (CaSO42H2O) scaling phenomena on membranes with different physicochemical properties in forward osmosis (FO) processes. Three hollow fiber membranes made of (1) cellulose acetate (CA), (2) polybenzimidazole (PBI)/polyethersulfone (PES) and (3) PBI-polyhedral oligomeric silsesquioxane (POSS)/polyacrylonitrile (PAN) were studied. For the first time in FO processes, we have found that surface ionic interactions dominate gypsum scaling on the membrane surface. A 70% flux reduction was observed on negatively charged CA and PBI membrane surfaces, due to strong attractive forces. The PBI membrane surface also showed a slightly positive charge at a low pH value of 3 and exhibited a 30% flux reduction. The atomic force microscopy (AFM) force measurements confirmed a strong repulsive force between gypsum and PBI at a pH value of 3. The newly developed PBI-POSS/PAN membrane had ridge morphology and a contact angle of 51.42 14.85 after the addition of hydrophilic POSS nanoparticles and 3 min thermal treatment at 95 C. Minimal scaling and an only 1.3% flux reduction were observed at a pH value of 3. Such a ridge structure may reduce scaling by not providing a locally flat surface to the crystallite at a pH value of 3; thus, gypsum would be easily washed away from the surface. 2013 by the authors; licensee MDPI, Basel, Switzerland.

Kinetic Analysis for Macrocyclizations Involving Anionic Template at the Transition State

Directory of Open Access Journals (Sweden)

Vicente Martí-Centelles

2012-01-01

competitive oligomerization/polymerization processes yielding undesired oligomeric/polymeric byproducts. The effect of anions has also been included in the kinetic models, as they can act as catalytic templates in the transition state reducing and stabilizing the transition state. The corresponding differential equation systems for each kinetic model can be solved numerically. Through a comprehensive analysis of these results, it is possible to obtain a better understanding of the different parameters that are involved in the macrocyclization reaction mechanism and to develop strategies for the optimization of the desired processes.

Classical density functional theory & simulations on a coarse-grained model of aromatic ionic liquids.

Science.gov (United States)

Turesson, Martin; Szparaga, Ryan; Ma, Ke; Woodward, Clifford E; Forsman, Jan

2014-05-14

A new classical density functional approach is developed to accurately treat a coarse-grained model of room temperature aromatic ionic liquids. Our major innovation is the introduction of charge-charge correlations, which are treated in a simple phenomenological way. We test this theory on a generic coarse-grained model for aromatic RTILs with oligomeric forms for both cations and anions, approximating 1-alkyl-3-methyl imidazoliums and BF₄⁻, respectively. We find that predictions by the new density functional theory for fluid structures at charged surfaces are very accurate, as compared with molecular dynamics simulations, across a range of surface charge densities and lengths of the alkyl chain. Predictions of interactions between charged surfaces are also presented.

(Pressure + volume + temperature) properties for binary oligomeric solutions of poly(ethylene glycol mono-4-octylphenyl ether) with 1-octanol or acetophenone at pressures up to 50 MPa

International Nuclear Information System (INIS)

Lee, M.-J.; Ku, T.-J.; Lin Homu

2009-01-01

Densities were measured with a high-pressure densitometer for two binary oligomeric systems of poly(ethylene glycol mono-4-octylphenyl ether) (PEGOPE) with 1-octanol or acetophenone at temperatures from 298.15 K to 348.15 K and pressures up to 50 MPa. While the excess volumes are negative in (acetophenone + PEGOPE) over the entire composition range, those are found to change from positive to negative with increasing mole fraction of the solvent in (1-octanol + PEGOPE). The pressure-effect on the liquid densities can be represented accurately by the Tait equation. Moreover, an empirical equation with two characteristic parameters correlates well the PVT data over the entire experimental conditions for each binary system. The experimental specific volumes were also correlated with the Flory-Orwoll-Vrij (FOV) and the Schotte equations of state to within the experimental uncertainty.

Effect of valine 106 on structure-function relation of cytosolic human thymidine kinase - Kinetic properties and oligomerization pattern of nine substitution mutants of V106

DEFF Research Database (Denmark)

Frederiksen, Hanne; Berenstein, Dvora; Munch-Petersen, Birgitte

2004-01-01

Information on the regulation and structure-function relation of enzymes involved in DNA precursor synthesis is pivotal, as defects in several of these enzymes have been found to cause depletion or deletion of mitochondrial DNA resulting in severe diseases. Here, the effect of amino acid 106...... and characterized nine mutants of amino acid 106 differing in size, conformation and polarity. According to their oligomerization pattern and thymidine kinetics, the TK1 mutants can be divided into two groups. Group I (V106A, V106I and V106T) behaves like V106WT, in that pre-assay exposure to ATP induces reversible...... transition from a dimer with low catalytic activity to a tetramer with high catalytic activity. Group II (V106G, V106H, V106K, V106L and V106Q) behaves like V106M in that they are permanently high activity tetramers, irrespective of ATP exposure. We conclude that size and conformation of amino acid 106...

Report on UQ Assessmentsto support SESAME wire-wrappedbundle experiment

Energy Technology Data Exchange (ETDEWEB)

Popov, Emilian L. [ORNL; Pointer, William David [ORNL

2017-10-01

This work assesses the influence of assumptions made when generating a mesh of a wire-wrappedgeometry. The contact region between a wire and its adjacent pin is commonly modeled by eitherembedding the wire to the adjacent pin or trimming the wire so that a gap separates the wire from itsadjacent pin. These models are referred to as close-gap and open-gap approaches herein and are applied totwo geometries. The first geometry consists of a single pin wire-wrapped subchannel. A polyhedral meshand a hexahedral mesh are generated. The second and third geometry are a 7-pin and a 19-pinwire-wrapped bundles meshed with polyhedral elements only. Pressure drops are obtained with theSTAR-CCM+computational fluid dynamic package. Sensitivity analyses of the mesh density, the meshtype, and the turbulent models are performed. Numerical results show that the best match to theexperimental data and to the Cheng-Todreas correlation is obtained with the combination of a hexahedralmesh, the shear stress transport (SST) turbulent model, and the open-gap approach. In the case of the 7-pingeometry, the best results are obtained with the open-gap approach and the SST turbulent model. The19-pin geometry yields contradictory results to the 7-pin geometry results, and thus will require furtherinvestigations.

Increased serum cartilage oligomeric matrix protein levels and decreased patellar bone mineral density in patients with chondromalacia patellae.

Science.gov (United States)

Murphy, E; FitzGerald, O; Saxne, T; Bresnihan, B

2002-11-01

Chondromalacia patellae is a potentially disabling disorder characterised by features of patellar cartilage degradation. To evaluate markers of cartilage and bone turnover in patients with chondromalacia patellae. 18 patients with chondromalacia patellae were studied. Serum cartilage oligomeric matrix protein (s-COMP) and bone sialoprotein (s-BSP) levels were measured by enzyme linked immunosorbent assay (ELISA) and compared with those of age and sex matched healthy control subjects. Periarticular bone mineral density (BMD) of both knee joints was assessed by dual energy x ray absorptiometry (DXA). s-COMP levels were significantly raised in all patients with chondromalacia patellae compared with healthy control subjects (p=0.0001). s-BSP levels did not differ significantly between the groups (p=0.41). BMD of the patella was significantly reduced in patients with chondromalacia patellae compared with the control subjects (p=0.016). In patients with bilateral chondromalacia patellae, BMD of the patella was lower in the more symptomatic knee joint (p=0.005). Changes in periarticular BMD were localised to the patella and were not present in femoral regions. Neither s-COMP (p=0.18) nor s-BSP (p=0.40) levels correlated with patellar BMD. Increased s-COMP levels, reflecting cartilage degradation, and reduced BMD localised to the patella may represent clinically useful markers in the diagnosis and monitoring of patients with chondromalacia patellae. Measures of cartilage degradation did not correlate with loss of patellar bone density, suggesting dissociated pathophysiological mechanisms.

Predicting success of oligomerized pool engineering (OPEN for zinc finger target site sequences

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Goodwin Mathew J

2010-11-01

Full Text Available Abstract Background Precise and efficient methods for gene targeting are critical for detailed functional analysis of genomes and regulatory networks and for potentially improving the efficacy and safety of gene therapies. Oligomerized Pool ENgineering (OPEN is a recently developed method for engineering C2H2 zinc finger proteins (ZFPs designed to bind specific DNA sequences with high affinity and specificity in vivo. Because generation of ZFPs using OPEN requires considerable effort, a computational method for identifying the sites in any given gene that are most likely to be successfully targeted by this method is desirable. Results Analysis of the base composition of experimentally validated ZFP target sites identified important constraints on the DNA sequence space that can be effectively targeted using OPEN. Using alternate encodings to represent ZFP target sites, we implemented Naïve Bayes and Support Vector Machine classifiers capable of distinguishing "active" targets, i.e., ZFP binding sites that can be targeted with a high rate of success, from those that are "inactive" or poor targets for ZFPs generated using current OPEN technologies. When evaluated using leave-one-out cross-validation on a dataset of 135 experimentally validated ZFP target sites, the best Naïve Bayes classifier, designated ZiFOpT, achieved overall accuracy of 87% and specificity+ of 90%, with an ROC AUC of 0.89. When challenged with a completely independent test set of 140 newly validated ZFP target sites, ZiFOpT performance was comparable in terms of overall accuracy (88% and specificity+ (92%, but with reduced ROC AUC (0.77. Users can rank potentially active ZFP target sites using a confidence score derived from the posterior probability returned by ZiFOpT. Conclusion ZiFOpT, a machine learning classifier trained to identify DNA sequences amenable for targeting by OPEN-generated zinc finger arrays, can guide users to target sites that are most likely to function

Polyhedral charge-packing model for blood pH changes in disease ...

African Journals Online (AJOL)

packing pH zone' (From pH = 7.30, for tetrahedral, to pH = 7.65 for dodecahedral packing), which lies in the neighborhood of the well known physiological pH range. Literature is cited in support of pH 7.65 as the extreme upper limit of tolerable ...

The N terminus of cGAS de-oligomerizes the cGAS:DNA complex and lifts the DNA size restriction of core-cGAS activity.

Science.gov (United States)

Lee, Arum; Park, Eun-Byeol; Lee, Janghyun; Choi, Byong-Seok; Kang, Suk-Jo

2017-03-01

Cyclic GMP-AMP synthase (cGAS) is a DNA-sensing enzyme in the innate immune system. Recent studies using core-cGAS lacking the N terminus investigated the mechanism for binding of double-stranded (ds) DNA and synthesis of 2',3'-cyclic GMP-AMP (cGAMP), a secondary messenger that ultimately induces type I interferons. However, the function of the N terminus of cGAS remains largely unknown. Here, we found that the N terminus enhanced the activity of core-cGAS in vivo. Importantly, the catalytic activity of core-cGAS decreased as the length of double-stranded DNA (dsDNA) increased, but the diminished activity was restored by addition of the N terminus. Furthermore, the N terminus de-oligomerized the 2 : 2 complex of core-cGAS and dsDNA into a 1 : 1 complex, suggesting that the N terminus enhanced the activity of core-cGAS by facilitating formation of a monomeric complex of cGAS and DNA. © 2017 Federation of European Biochemical Societies.

The CoxD protein, a novel AAA+ ATPase involved in metal cluster assembly: hydrolysis of nucleotide-triphosphates and oligomerization.

Directory of Open Access Journals (Sweden)

Tobias Maisel

Full Text Available CoxD of the α-proteobacterium Oligotropha carboxidovorans is a membrane protein which is involved in the posttranslational biosynthesis of the [CuSMoO₂] cluster in the active site of the enzyme CO dehydrogenase. The bacteria synthesize CoxD only in the presence of CO. Recombinant CoxD produced in E. coli K38 pGP1-2/pETMW2 appeared in inclusion bodies from where it was solubilized by urea and refolded by stepwise dilution. Circular dichroism spectroscopy revealed the presence of secondary structural elements in refolded CoxD. CoxD is a P-loop ATPase of the AAA-protein family. Refolded CoxD catalyzed the hydrolysis of MgATP yielding MgADP and inorganic phosphate at a 1∶1∶1 molar ratio. The reaction was inhibited by the slow hydrolysable MgATP-γ-S. GTPase activity of CoxD did not exceed 2% of the ATPase activity. Employing different methods (non linear regression, Hanes and Woolf, Lineweaver-Burk, preparations of CoxD revealed a mean K(M value of 0.69±0.14 mM ATP and an apparent V(max value of 19.3±2.3 nmol ATP hydrolyzed min⁻¹ mg⁻¹. Sucrose density gradient centrifugation and gel filtration showed that refolded CoxD can exist in various multimeric states (2-mer, 4-mer or 6-mer, preferentially as hexamer or dimer. Within weeks the hexamer dissociates into the dimer, a process which can be reversed by MgATP or MgATP-γ-S within hours. Only the hexamers and the dimers exhibited MgATPase activity. Transmission electron microscopy of negatively stained CoxD preparations revealed distinct particles within a size range of 10-16 nm, which further corroborates the oligomeric organization. The 3D structure of CoxD was modeled with the 3D structure of BchI from Rhodobacter capsulatus as template. It has the key elements of an AAA+ domain in the same arrangement and at same positions as in BchI and displays the characteristic inserts of the PS-II-insert clade. Possible functions of CoxD in [CuSMoO₂] cluster assembly are discussed.

Effect of (OPC) oligomeric pronthocyanidine extracted of grape seed on chromosomal aberrations for Tc 99m sulfur colloid in laboratory animal

International Nuclear Information System (INIS)

Alwan, I. F.; Ahmed, A.M.; Mohamad, H. A.

2012-12-01

The aims study to assess the protective material (OPC) oligomeric pronthocyanidine grape seed extract, to decrease the effect of Technetium 99 m radiation used in on the (Chromosomal Aberration) in the genes for bone marrow in laboratory animals. Been diagnosed by a composite (OPC) optical spectrometer (UV.vis) to determine the wavelength of the compound, for the purpose of examination and analysis by a high-purity HPLC to determine the components of grape seed extract. Has been handing laboratory animals, grape seed extract material (OPC) at a dose (150 mg/kg) for two weeks and then were injected to the solution of sulfur colloidal label with Tc 99 m doses of radiation to the following quantity (400 u ci, 250 u ci, 150 u ci / 0.1 m1). The treated animals by extract (OPC) showed decrease in the proportion of chromosomal changes resulting from the impact of injection differences dose compared to animals injected to the same radiation dose and non treated animal with (OPC). The result indicated there are significant differences (p>0.05) at the level of changes in chromosomal in genes of animals untreated compared with the group of animals treated with (OPC) and injected with the same radiation dose compared a control animal group. (Author)

S. aureus MscL is a pentamer in vivo but of variable stoichiometries in vitro: implications for detergent-solubilized membrane proteins.

Directory of Open Access Journals (Sweden)

Michael R Dorwart

Full Text Available While the bacterial mechanosensitive channel of large conductance (MscL is the best studied biological mechanosensor and serves as a paradigm for how a protein can sense and respond to membrane tension, the simple matter of its oligomeric state has led to debate, with models ranging from tetramers to hexamers. Indeed, two different oligomeric states of the bacterial mechanosensitive channel MscL have been resolved by X-ray crystallography: The M. tuberculosis channel (MtMscL is a pentamer, while the S. aureus protein (SaMscL forms a tetramer. Because several studies suggest that, like MtMscL, the E. coli MscL (EcoMscL is a pentamer, we re-investigated the oligomeric state of SaMscL. To determine the structural organization of MscL in the cell membrane we developed a disulfide-trapping approach. Surprisingly, we found that virtually all SaMscL channels in vivo are pentameric, indicating this as the physiologically relevant and functional oligomeric state. Complementing our in vivo results, we purified SaMscL and assessed its oligomeric state using three independent approaches (sedimentation equilibrium centrifugation, crosslinking, and light scattering and established that SaMscL is a pentamer when solubilized in Triton X-100 and C(8E(5 detergents. However, performing similar experiments on SaMscL solubilized in LDAO, the detergent used in the crystallographic study, confirmed the tetrameric oligomerization resolved by X-ray crystallography. We further demonstrate that this stoichiometric shift is reversible by conventional detergent exchange experiments. Our results firmly establish the pentameric organization of SaMscL in vivo. Furthermore they demonstrate that detergents can alter the subunit stoichiometry of membrane protein complexes in vitro; thus, in vivo assays are necessary to firmly establish a membrane protein's true functionally relevant oligomeric state.

S. aureus MscL is a pentamer in vivo but of variable stoichiometries in vitro: implications for detergent-solubilized membrane proteins.

Science.gov (United States)

Dorwart, Michael R; Wray, Robin; Brautigam, Chad A; Jiang, Youxing; Blount, Paul

2010-12-07

While the bacterial mechanosensitive channel of large conductance (MscL) is the best studied biological mechanosensor and serves as a paradigm for how a protein can sense and respond to membrane tension, the simple matter of its oligomeric state has led to debate, with models ranging from tetramers to hexamers. Indeed, two different oligomeric states of the bacterial mechanosensitive channel MscL have been resolved by X-ray crystallography: The M. tuberculosis channel (MtMscL) is a pentamer, while the S. aureus protein (SaMscL) forms a tetramer. Because several studies suggest that, like MtMscL, the E. coli MscL (EcoMscL) is a pentamer, we re-investigated the oligomeric state of SaMscL. To determine the structural organization of MscL in the cell membrane we developed a disulfide-trapping approach. Surprisingly, we found that virtually all SaMscL channels in vivo are pentameric, indicating this as the physiologically relevant and functional oligomeric state. Complementing our in vivo results, we purified SaMscL and assessed its oligomeric state using three independent approaches (sedimentation equilibrium centrifugation, crosslinking, and light scattering) and established that SaMscL is a pentamer when solubilized in Triton X-100 and C(8)E(5) detergents. However, performing similar experiments on SaMscL solubilized in LDAO, the detergent used in the crystallographic study, confirmed the tetrameric oligomerization resolved by X-ray crystallography. We further demonstrate that this stoichiometric shift is reversible by conventional detergent exchange experiments. Our results firmly establish the pentameric organization of SaMscL in vivo. Furthermore they demonstrate that detergents can alter the subunit stoichiometry of membrane protein complexes in vitro; thus, in vivo assays are necessary to firmly establish a membrane protein's true functionally relevant oligomeric state.

Linking microscopic spatial patterns of tissue destruction in emphysema to macroscopic decline in stiffness using a 3D computational model.

Directory of Open Access Journals (Sweden)

Harikrishnan Parameswaran

2011-04-01

Full Text Available Pulmonary emphysema is a connective tissue disease characterized by the progressive destruction of alveolar walls leading to airspace enlargement and decreased elastic recoil of the lung. However, the relationship between microscopic tissue structure and decline in stiffness of the lung is not well understood. In this study, we developed a 3D computational model of lung tissue in which a pre-strained cuboidal block of tissue was represented by a tessellation of space filling polyhedra, with each polyhedral unit-cell representing an alveolus. Destruction of alveolar walls was mimicked by eliminating faces that separate two polyhedral either randomly or in a spatially correlated manner, in which the highest force bearing walls were removed at each step. Simulations were carried out to establish a link between the geometries that emerged and the rate of decline in bulk modulus of the tissue block. The spatially correlated process set up by the force-based destruction lead to a significantly faster rate of decline in bulk modulus accompanied by highly heterogeneous structures than the random destruction pattern. Using the Karhunen-Loève transformation, an estimator of the change in bulk modulus from the first four moments of airspace cell volumes was setup. Simulations were then obtained for tissue destruction with different idealized alveolar geometry, levels of pre-strain, linear and nonlinear elasticity assumptions for alveolar walls and also mixed destruction patterns where both random and force-based destruction occurs simultaneously. In all these cases, the change in bulk modulus from cell volumes was accurately estimated. We conclude that microscopic structural changes in emphysema and the associated decline in tissue stiffness are linked by the spatial pattern of the destruction process.

Phosphatidylinositol 4,5-Bisphosphate (PI(4,5)P2)-dependent Oligomerization of Fibroblast Growth Factor 2 (FGF2) Triggers the Formation of a Lipidic Membrane Pore Implicated in Unconventional Secretion*

Science.gov (United States)

Steringer, Julia P.; Bleicken, Stephanie; Andreas, Helena; Zacherl, Sonja; Laussmann, Mareike; Temmerman, Koen; Contreras, F. Xabier; Bharat, Tanmay A. M.; Lechner, Johannes; Müller, Hans-Michael; Briggs, John A. G.; García-Sáez, Ana J.; Nickel, Walter

2012-01-01

Fibroblast growth factor 2 (FGF2) is a critical mitogen with a central role in specific steps of tumor-induced angiogenesis. It is known to be secreted by unconventional means bypassing the endoplasmic reticulum/Golgi-dependent secretory pathway. However, the mechanism of FGF2 membrane translocation into the extracellular space has remained elusive. Here, we show that phosphatidylinositol 4,5-bisphosphate-dependent membrane recruitment causes FGF2 to oligomerize, which in turn triggers the formation of a lipidic membrane pore with a putative toroidal structure. This process is strongly up-regulated by tyrosine phosphorylation of FGF2. Our findings explain key requirements of FGF2 secretion from living cells and suggest a novel self-sustained mechanism of protein translocation across membranes with a lipidic membrane pore being a transient translocation intermediate. PMID:22730382