Experimental investigations on the state of the friction-welded joint zone in steel hybrid components after process-relevant thermo-mechanical loadings

NASA Astrophysics Data System (ADS)

Behrens, B.-A.; Bouguecha, A.; Vucetic, M.; Peshekhodov, I.; Matthias, T.; Kolbasnikov, N.; Sokolov, S.; Ganin, S.

2016-10-01

As a part of the newly established Collaborative Research Center 1153 (SFB 1153) "Process chain for the manufacturing of hybrid high-performance components by tailored forming" at the Leibniz Universität Hannover, the Institute of Forming Technology and Machines (IFUM) examines the influence of thermo-mechanical stresses on the reduced Young's modulus as well as the hardness of hybrid (steel-steel compound) joined semi-finished products. Currently the expertise in the production of bulk metal formed parts is limited to mono-materials. For manufacturing parts of hybrid materials and also for the methods of the new process routes, practical experience has to be gained. The subproject C1 within the collaborative research center 1153 with the short title "Failure Prediction" deals with the question, if the hybrid semi-finished products fulfill the thermo-mechanical demands or if they fail at the joining zone (JZ) during forging. For this purpose, stresses similar to those in the process were imposed on hybrid semi-finished products by torsion tests by using the thermo-mechanical test system Gleeble 3800. Afterwards, the specimens were examined metallographically and by nanoindentations with the help of a TriboIndenter TI950. Thus, first knowledge on the behaviour of thermo-mechanical stresses on the reduced Young's modulus and the hardness of hybrid joined semi-finished parts was gained.

Hybrid RTM process: Monitoring and processing of composites based on reactive thermoplastic systems

NASA Astrophysics Data System (ADS)

Dkier, Mohamed; Lamnawar, Khalid; Maazouz, Abderrahim

2017-10-01

In this work, hybrid process coupling "Reactive Extrusion" and "Resin Transfer Molding" machine (T-ERTM) equipped with an instrumented mold was designed and developed. Polyamides model matrix according to two kinds of polymerizations were studied as well anionic and chain extension reactions. For the former, different ratios of catalyst and activator were investigated. For the latter, various formulations of prepolymer with chain extender (CA) were studied at different stoichiometry ratios and temperatures. Since that both reaction kinetics are very fast to be monitored at short times by usual technics, the chemo-rheological evolutions were firstly studied ex-situ by coupling rheology with FTIR and dielectric spectroscopy (DRS). Secondly, the T-ERTM process with an "instrumented mold" was developed with specific dielectric sensors in order to in-situ track viscosity and reaction evolution. The in-situ results corroborate the ex-situ ones aforementioned. Overall, a processing window was obtained for each reactive system to ensure a good preform impregnation for the manufacturing of complex and continuous glass fiber-reinforced parts. Herein, the Time-Temperature-Transformation-equivalent diagrams were established to obtain Thermoplastic composites with tailored mechanical and physical properties.

Critical behavior of the contact process in a multiscale network

NASA Astrophysics Data System (ADS)

Ferreira, Silvio C.; Martins, Marcelo L.

2007-09-01

Inspired by dengue and yellow fever epidemics, we investigated the contact process (CP) in a multiscale network constituted by one-dimensional chains connected through a Barabási-Albert scale-free network. In addition to the CP dynamics inside the chains, the exchange of individuals between connected chains (travels) occurs at a constant rate. A finite epidemic threshold and an epidemic mean lifetime diverging exponentially in the subcritical phase, concomitantly with a power law divergence of the outbreak’s duration, were found. A generalized scaling function involving both regular and SF components was proposed for the quasistationary analysis and the associated critical exponents determined, demonstrating that the CP on this hybrid network and nonvanishing travel rates establishes a new universality class.

IT vendor selection model by using structural equation model & analytical hierarchy process

NASA Astrophysics Data System (ADS)

Maitra, Sarit; Dominic, P. D. D.

2012-11-01

Selecting and evaluating the right vendors is imperative for an organization's global marketplace competitiveness. Improper selection and evaluation of potential vendors can dwarf an organization's supply chain performance. Numerous studies have demonstrated that firms consider multiple criteria when selecting key vendors. This research intends to develop a new hybrid model for vendor selection process with better decision making. The new proposed model provides a suitable tool for assisting decision makers and managers to make the right decisions and select the most suitable vendor. This paper proposes a Hybrid model based on Structural Equation Model (SEM) and Analytical Hierarchy Process (AHP) for long-term strategic vendor selection problems. The five steps framework of the model has been designed after the thorough literature study. The proposed hybrid model will be applied using a real life case study to assess its effectiveness. In addition, What-if analysis technique will be used for model validation purpose.

The electrical and thermal transport properties of hybrid zigzag graphene-BN nanoribbons

NASA Astrophysics Data System (ADS)

Gao, Song; Lu, Wei; Zheng, Guo-Hui; Jia, Yalei; Ke, San-Huang

2017-06-01

The electron and phonon transport in hybrid graphene-BN zigzag nanoribbons are investigated by the nonequilibrium Green’s function method combined with density functional theory calculations. A 100% spin-polarized electron transport in a large energy window around the Fermi level is found and this behavior is independent of the ribbon width as long as there contain 3 zigzag carbon chains. The phonon transport calculations show that the ratio of C-chain number to BN-chain number will modify the thermal conductance of the hybrid nanoribbon in a complicated manner.

Estimation of polyclonal IgG4 hybrids in normal human serum.

PubMed

Young, Elizabeth; Lock, Emma; Ward, Douglas G; Cook, Alexander; Harding, Stephen; Wallis, Gregg L F

2014-07-01

The in vivo or in vitro formation of IgG4 hybrid molecules, wherein the immunoglobulins have exchanged half molecules, has previously been reported under experimental conditions. Here we estimate the incidence of polyclonal IgG4 hybrids in normal human serum and comment on the existence of IgG4 molecules with different immunoglobulin light chains. Polyclonal IgG4 was purified from pooled or individual donor human sera and sequentially fractionated using light-chain affinity and size exclusion chromatography. Fractions were analysed by SDS-PAGE, immunoblotting, ELISA, immunodiffusion and matrix-assisted laser-desorption mass spectrometry. Polyclonal IgG4 purified from normal serum contained IgG4κ, IgG4λ and IgG4κ/λ molecules. Size exclusion chromatography showed that IgG4 was principally present in monomeric form (150 000 MW). SDS-PAGE, immunoblotting and ELISA showed the purity of the three IgG4 samples. Immunodiffusion, light-chain sandwich ELISA and mass spectrometry demonstrated that both κ and λ light chains were present on only the IgG4κ/λ molecules. The amounts of IgG4κ/λ hybrid molecules ranged from 21 to 33% from the five sera analysed. Based on the molecular weight these molecules were formed of two IgG4 heavy chains plus one κ and one λ light chain. Polyclonal IgG (IgG4-depleted) was similarly fractionated according to light-chain specificity. No evidence of hybrid IgG κ/λ antibodies was observed. These results indicate that hybrid IgG4κ/λ antibodies compose a substantial portion of IgG4 from normal human serum. © 2014 John Wiley & Sons Ltd.

Analytical pricing formulas for hybrid variance swaps with regime-switching

NASA Astrophysics Data System (ADS)

Roslan, Teh Raihana Nazirah; Cao, Jiling; Zhang, Wenjun

2017-11-01

The problem of pricing discretely-sampled variance swaps under stochastic volatility, stochastic interest rate and regime-switching is being considered in this paper. An extension of the Heston stochastic volatility model structure is done by adding the Cox-Ingersoll-Ross (CIR) stochastic interest rate model. In addition, the parameters of the model are permitted to have transitions following a Markov chain process which is continuous and discoverable. This hybrid model can be used to illustrate certain macroeconomic conditions, for example the changing phases of business stages. The outcome of our regime-switching hybrid model is presented in terms of analytical pricing formulas for variance swaps.

Lean production in improving supply chain performance through hybrid model SCOR 11.0 - system dynamics

NASA Astrophysics Data System (ADS)

Saleh, Chairul; Fatcha Mubiena, Ghaida; Immawan, Taufiq; Hassan, Azmi

2016-02-01

Supply Chain Operation Reference (SCOR) is a method to measure supply chain serving the business process framework, performance indicators and unique technologies to support communication and collaboration among supply chain partners. The objective of this paper is to measure Supply Chain Management performance by using SCOR version 11.0 for production typology of MTS-MTO in Indonesian Batik Industry. This research combines SCOR's model and System Dynamics in order to predict the complex activities on batik industry. The hybrid SCOR-SD could identify the interaction among five attributes with the associated variables simultaneously. The results are obtained after the performance of lean production application is increased and the targets are achieved, even exceeding the target. For reliability attributes that associated with perfect order fulfilment started from 2015 to 2019 respectively are calculated as 80.06%, 103.53%, 105.58%, 93.76%, and 72.17%. Responsiveness attributes associated with the order fulfilment cycle time, respectively 122.45%, 149.10%, 159.26%, 131.53%, and 119.36%. Attributes associated with the total cost of service charge respectively 93.46%, 93.53%, 93.45%, 93.49, and 93.49%. Attributes associated with cash management assets to cash cycle time in a row were 160%, 153%, 146.3%, 150%, and 126.7%. The latter attribute is agility attributes associated with supply chain flexibility upside respectively 100%, 87.2%, 100%, 82%, and 82%.

Ultra-tough and strong, hybrid thin films based on ionically crosslinked polymers and 2D inorganic platelets

NASA Astrophysics Data System (ADS)

Ji, Dong Hwan; Choi, Suji; Kim, Jaeyun; nanobiomaterials lab Team

Integration of high strength and toughness tend to be mutually exclusive and synthesized hybrid films with superior mechanical properties have been difficult to fabricate controllable shapes and various scales. Although diverse synthesized hybrid films consisting of organic matrix and inorganic materials with brick-and-mortar structure, show improved mechanical properties, these films are still limited in toughness and fabrication methods. Herein, we report ultra-tough and strong hybrid thin films with self-assembled uniform microstructures with controllable shapes and various scale based on hydrogel-mediated process. Ca2+-crosslinking in alginate chains and well-aligned alumina platelets in alginate matrix lead to a synergistic enhancement of strength and toughness in the resulting film. Consequentially, Ca2+-crosslinked Alg/Alu films showed outstanding toughness of 29 MJ m-3 and tensile strength of 160 MPa. Furthermore, modifying Alu surface with polyvinylpyrrolidone (PVP), tensile strength was further improved up to 200 MPa. Our results suggest an alternative approach to design and processing of self-assembled hydrogel-mediated hybrid films with outstanding mechanical properties.

A hybrid genetic-simulated annealing algorithm for the location-inventory-routing problem considering returns under e-supply chain environment.

PubMed

Li, Yanhui; Guo, Hao; Wang, Lin; Fu, Jing

2013-01-01

Facility location, inventory control, and vehicle routes scheduling are critical and highly related problems in the design of logistics system for e-business. Meanwhile, the return ratio in Internet sales was significantly higher than in the traditional business. Many of returned merchandise have no quality defects, which can reenter sales channels just after a simple repackaging process. Focusing on the existing problem in e-commerce logistics system, we formulate a location-inventory-routing problem model with no quality defects returns. To solve this NP-hard problem, an effective hybrid genetic simulated annealing algorithm (HGSAA) is proposed. Results of numerical examples show that HGSAA outperforms GA on computing time, optimal solution, and computing stability. The proposed model is very useful to help managers make the right decisions under e-supply chain environment.

Dynamic Properties of DNA-Programmable Nanoparticle Crystallization.

PubMed

Yu, Qiuyan; Zhang, Xuena; Hu, Yi; Zhang, Zhihao; Wang, Rong

2016-08-23

The dynamics of DNA hybridization is very important in DNA-programmable nanoparticle crystallization. Here, coarse-grained molecular dynamics is utilized to explore the structural and dynamic properties of DNA hybridizations for a self-complementary DNA-directed nanoparticle self-assembly system. The hexagonal close-packed (HCP) and close-packed face-centered cubic (FCC) ordered structures are identified for the systems of different grafted DNA chains per nanoparticle, which are in good agreement with the experimental results. Most importantly, the dynamic crystallization processes of DNA hybridizations are elucidated by virtue of the mean square displacement, the percentage of hybridizations, and the lifetime of DNA bonds. The lifetime can be modeled by the DNA dehybridization, which has an exponential form. The lifetime of DNA bonds closely depends on the temperature. A suitable temperature for the DNA-nanoparticle crystallization is obtained in the work. Moreover, a too large volume fraction hinders the self-assembly process due to steric effects. This work provides some essential information for future design of nanomaterials.

Hybridization-based antibody cDNA recovery for the production of recombinant antibodies identified by repertoire sequencing.

PubMed

Valdés-Alemán, Javier; Téllez-Sosa, Juan; Ovilla-Muñoz, Marbella; Godoy-Lozano, Elizabeth; Velázquez-Ramírez, Daniel; Valdovinos-Torres, Humberto; Gómez-Barreto, Rosa E; Martinez-Barnetche, Jesús

2014-01-01

High-throughput sequencing of the antibody repertoire is enabling a thorough analysis of B cell diversity and clonal selection, which may improve the novel antibody discovery process. Theoretically, an adequate bioinformatic analysis could allow identification of candidate antigen-specific antibodies, requiring their recombinant production for experimental validation of their specificity. Gene synthesis is commonly used for the generation of recombinant antibodies identified in silico. Novel strategies that bypass gene synthesis could offer more accessible antibody identification and validation alternatives. We developed a hybridization-based recovery strategy that targets the complementarity-determining region 3 (CDRH3) for the enrichment of cDNA of candidate antigen-specific antibody sequences. Ten clonal groups of interest were identified through bioinformatic analysis of the heavy chain antibody repertoire of mice immunized with hen egg white lysozyme (HEL). cDNA from eight of the targeted clonal groups was recovered efficiently, leading to the generation of recombinant antibodies. One representative heavy chain sequence from each clonal group recovered was paired with previously reported anti-HEL light chains to generate full antibodies, later tested for HEL-binding capacity. The recovery process proposed represents a simple and scalable molecular strategy that could enhance antibody identification and specificity assessment, enabling a more cost-efficient generation of recombinant antibodies.

Side chain engineering of poly-thiophene and its impact on crystalline silicon based hybrid solar cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zellmeier, M.; Rappich, J.; Nickel, N. H.

The influence of ether groups in the side chain of spin coated regioregular polythiophene derivatives on the polymer layer formation and the hybrid solar cell properties was investigated using electrical, optical, and X-ray diffraction experiments. The polymer layers are of high crystallinity but the polymer with 3 ether groups in the side chain (P3TOT) did not show any vibrational fine structure in the UV-Vis spectrum. The presence of ether groups in the side chains leads to better adhesion resulting in thinner and more homogeneous polymer layers. This, in turn, enhances the electronic properties of the planar c-Si/poly-thiophene hybrid solar cell.more » We find that the power conversion efficiency increases with the number of ether groups in the side chains, and a maximum power conversion efficiency of η = 9.6% is achieved even in simple planar structures.« less

Price competition and equilibrium analysis in multiple hybrid channel supply chain

NASA Astrophysics Data System (ADS)

Kuang, Guihua; Wang, Aihu; Sha, Jin

2017-06-01

The amazing boom of Internet and logistics industry prompts more and more enterprises to sell commodity through multiple channels. Such market conditions make the participants of multiple hybrid channel supply chain compete each other in traditional and direct channel at the same time. This paper builds a two-echelon supply chain model with a single manufacturer and a single retailer who both can choose different channel or channel combination for their own sales, then, discusses the price competition and calculates the equilibrium price under different sales channel selection combinations. Our analysis shows that no matter the manufacturer and retailer choose same or different channel price to compete, the equilibrium price does not necessarily exist the equilibrium price in the multiple hybrid channel supply chain and wholesale price change is not always able to coordinate supply chain completely. We also present the sufficient and necessary conditions for the existence of equilibrium price and coordination wholesale price.

Integration of logistic regression, Markov chain and cellular automata models to simulate urban expansion

NASA Astrophysics Data System (ADS)

Jokar Arsanjani, Jamal; Helbich, Marco; Kainz, Wolfgang; Darvishi Boloorani, Ali

2013-04-01

This research analyses the suburban expansion in the metropolitan area of Tehran, Iran. A hybrid model consisting of logistic regression model, Markov chain (MC), and cellular automata (CA) was designed to improve the performance of the standard logistic regression model. Environmental and socio-economic variables dealing with urban sprawl were operationalised to create a probability surface of spatiotemporal states of built-up land use for the years 2006, 2016, and 2026. For validation, the model was evaluated by means of relative operating characteristic values for different sets of variables. The approach was calibrated for 2006 by cross comparing of actual and simulated land use maps. The achieved outcomes represent a match of 89% between simulated and actual maps of 2006, which was satisfactory to approve the calibration process. Thereafter, the calibrated hybrid approach was implemented for forthcoming years. Finally, future land use maps for 2016 and 2026 were predicted by means of this hybrid approach. The simulated maps illustrate a new wave of suburban development in the vicinity of Tehran at the western border of the metropolis during the next decades.

HYDRA: A Middleware-Oriented Integrated Architecture for e-Procurement in Supply Chains

NASA Astrophysics Data System (ADS)

Alor-Hernandez, Giner; Aguilar-Lasserre, Alberto; Juarez-Martinez, Ulises; Posada-Gomez, Ruben; Cortes-Robles, Guillermo; Garcia-Martinez, Mario Alberto; Gomez-Berbis, Juan Miguel; Rodriguez-Gonzalez, Alejandro

The Service-Oriented Architecture (SOA) development paradigm has emerged to improve the critical issues of creating, modifying and extending solutions for business processes integration, incorporating process automation and automated exchange of information between organizations. Web services technology follows the SOA's principles for developing and deploying applications. Besides, Web services are considered as the platform for SOA, for both intra- and inter-enterprise communication. However, an SOA does not incorporate information about occurring events into business processes, which are the main features of supply chain management. These events and information delivery are addressed in an Event-Driven Architecture (EDA). Taking this into account, we propose a middleware-oriented integrated architecture that offers a brokering service for the procurement of products in a Supply Chain Management (SCM) scenario. As salient contributions, our system provides a hybrid architecture combining features of both SOA and EDA and a set of mechanisms for business processes pattern management, monitoring based on UML sequence diagrams, Web services-based management, event publish/subscription and reliable messaging service.

Theoretical modeling of the electronic structure and exchange interactions in a Cu(II)Pc one-dimensional chain

NASA Astrophysics Data System (ADS)

Wu, Wei; Fisher, A. J.; Harrison, N. M.

2011-07-01

We calculate the electronic structure and exchange interactions in a copper(II)phthalocyanine [Cu(II)Pc] crystal as a one-dimensional molecular chain using hybrid exchange density functional theory (DFT). In addition, the intermolecular exchange interactions are also calculated in a molecular dimer using Green’s function perturbation theory (GFPT) to illustrate the underlying physics. We find that the exchange interactions depend strongly on the stacking angle, but weakly on the sliding angle (defined in the text). The hybrid DFT calculations also provide an insight into the electronic structure of the Cu(II)Pc molecular chain and demonstrate that on-site electron correlations have a significant effect on the nature of the ground state, the band gap, and magnetic excitations. The exchange interactions predicted by our DFT calculations and GFPT calculations agree qualitatively with the recent experimental results on newly found η-Cu(II)Pc and the previous results for the α and β phases. This work provides a reliable theoretical basis for the further application of Cu(II)Pc to molecular spintronics and organic-based quantum information processing.

Highly sensitive DNA detection using cascade amplification strategy based on hybridization chain reaction and enzyme-induced metallization

PubMed Central

Yu, Xu; Zhang, Zhi-Ling; Zheng, Si-Yang

2014-01-01

A novel highly sensitive colorimetric assay for DNA detection using cascade amplification strategy based on hybridization chain reaction and enzyme-induced metallization was established. The DNA modified superparamagnetic beads were demonstrated to capture and enrich the target DNA in the hybridization buffer or human plasma. The hybridization chain reaction and enzyme-induced silver metallization on the gold nanoparticles were used as cascade signal amplification for the detection of target DNA. The metalization of silver on the gold nanoparticles induced a significant colour change from red to yellow until black depending on the concentration of the target DNA, which could be recognized by naked eyes. This method showed a good specificity for the target DNA detection, with the capabilty to discriminate single-base-pair mismatched DNA mutation (single nucleotide polymorphism). Meanwhile, this approach exhibited an excellent anti-interference capability with the convenience of the magentic seperation and washing, which enabled its usage in complex biological systems such as human blood plasma. As an added benefit, the utilization of hybridization chain reaction and enzyme-induced metallization improved detection sensitivity down to 10 pM, which is about 100-fold lower than that of traditional unamplified homogeneous assays. PMID:25500528

Therapeutic Approaches for Botulinum Intoxication Targeting Degradation of the Light Chain

DTIC Science & Technology

2013-04-01

SUBJECT TERMS Botulinum toxin , ubiquitin, chimeric toxin light chains, LcA, LcE, Yeast 2 hybrid, intracellular therapy. 16. SECURITY...Synaptic Research will develop dichain hybrids consisting of Clostridium botulinum toxin light chains (LCs) from serotypes A (long-lived) and E...stability to LCs of botulinum toxin can be assessed by mutation of dileucine residues and systematic deletion of residues from LcA-LcE chimeras to provide a

Rapid self-assembly of block copolymers to photonic crystals

DOEpatents

Xia, Yan; Sveinbjornsson, Benjamin R; Grubbs, Robert H; Weitekamp, Raymond; Miyake, Garret M; Atwater, Harry A; Piunova, Victoria; Daeffler, Christopher Scot; Hong, Sung Woo; Gu, Weiyin; Russell, Thomas P.

2016-07-05

The invention provides a class of copolymers having useful properties, including brush block copolymers, wedge-type block copolymers and hybrid wedge and polymer block copolymers. In an embodiment, for example, block copolymers of the invention incorporate chemically different blocks comprising polymer size chain groups and/or wedge groups that significantly inhibit chain entanglement, thereby enhancing molecular self-assembly processes for generating a range of supramolecular structures, such as periodic nanostructures and microstructures. The present invention also provides useful methods of making and using copolymers, including block copolymers.

A Hybrid Genetic-Simulated Annealing Algorithm for the Location-Inventory-Routing Problem Considering Returns under E-Supply Chain Environment

PubMed Central

Guo, Hao; Fu, Jing

2013-01-01

Facility location, inventory control, and vehicle routes scheduling are critical and highly related problems in the design of logistics system for e-business. Meanwhile, the return ratio in Internet sales was significantly higher than in the traditional business. Many of returned merchandise have no quality defects, which can reenter sales channels just after a simple repackaging process. Focusing on the existing problem in e-commerce logistics system, we formulate a location-inventory-routing problem model with no quality defects returns. To solve this NP-hard problem, an effective hybrid genetic simulated annealing algorithm (HGSAA) is proposed. Results of numerical examples show that HGSAA outperforms GA on computing time, optimal solution, and computing stability. The proposed model is very useful to help managers make the right decisions under e-supply chain environment. PMID:24489489

Colorimetric detection of mercury ion based on unmodified gold nanoparticles and target-triggered hybridization chain reaction amplification

NASA Astrophysics Data System (ADS)

Wang, Qing; Yang, Xiaohan; Yang, Xiaohai; Liu, Pei; Wang, Kemin; Huang, Jin; Liu, Jianbo; Song, Chunxia; Wang, Jingjing

2015-02-01

A novel unmodified gold nanoparticles (AuNPs)-based colorimetric strategy for label-free, specific and sensitive mercury ion (Hg2+) detection was demonstrated by using thymine-Hg2+-thymine (T-Hg2+-T) recognition mechanism and hybridization chain reaction (HCR) amplification strategy. In this protocol, a structure-switching probe (H0) was designed to recognize Hg2+ and then propagated a chain reaction of hybridization events between two other hairpin probes (H1 and H2). In the absence of Hg2+, all hairpin probes could stably coexist in solution, the exposed sticky ends of hairpin probes were capable of stabilizing AuNPs. As a result, salt-induced AuNPs aggregation could be effectively prevented. In the presence of Hg2+, thymine bases of H0 could specifically interact with Hg2+ to form stable T-Hg2+-T complex. Consequently, the hairpin structure of H0 probe was changed. As H1/H2 probes were added, the HCR process could be triggered and nicked double-helixes were formed. Since it was difficult for the formed nicked double-helixes to inhibit salt-induced AuNPs aggregation, a red-to-blue color change was observed in the colloid solution as the salt concentration increased. With the elegant amplification effect of HCR, a detection limit of around 30 nM was achieved (S/N = 3), which was about 1-2 orders of magnitudes lower than that of previous unmodified AuNPs-based colorimetric methods. By using the T-Hg2+-T recognition mechanism, high selectivity was also obtained. As an unmodified AuNPs-based colorimetric strategy, the system was simple in design, convenient in operation, and eliminated the requirements of separation processes, chemical modifications, and sophisticated instrumentations.

Bi-parentally inherited species-specific markers identify hybridization between rainbow trout and cutthroat trout subspecies

USGS Publications Warehouse

Ostberg, C.O.; Rodriguez, R.J.

2004-01-01

Eight polymerase chain reaction primer sets amplifying bi-parentally inherited species-specific markers were developed that differentiate between rainbow trout (Oncorhynchus mykiss) and various cutthroat trout (O. clarki) subspecies. The primers were tested within known F1 and first generation hybrid backcrosses and were shown to amplify codominantly within hybrids. Heterozygous individuals also amplified a slower migrating band that was a heteroduplex, caused by the annealing of polymerase chain reaction products from both species. These primer sets have numerous advantages for native cutthroat trout conservation including statistical genetic analyses of known crosses and simple hybrid identification.

The role of hybrid ubiquitin chains in the MyD88 and other innate immune signalling pathways.

PubMed

Cohen, Philip; Strickson, Sam

2017-07-01

The adaptor protein MyD88 is required for signal transmission by toll-like receptors and receptors of the interleukin-1 family of cytokines. MyD88 signalling triggers the formation of Lys63-linked and Met1-linked ubiquitin (K63-Ub, M1-Ub) chains within minutes. The K63-Ub chains, which are formed by the E3 ubiquitin ligases TRAF6, Pellino1 and Pellino2, activate TAK1, the master kinase that switches on mitogen-activated protein (MAP) kinase cascades and initiates activation of the canonical IκB kinase (IKK) complex. The M1-Ub chains, which are formed by the linear ubiquitin chain assembly complex (LUBAC), bind to the NEMO (NF-κB essential modulator) component of the IKK complex and are required for TAK1 to activate IKKs, but not MAP kinases. An essential E3 ligase-independent role of TRAF6 is to recruit LUBAC into the MyD88 signalling complex, where it recognises preformed K63-Ub chains attached to protein components of these complexes, such as IRAK1 (IL-1 receptor-associated kinase), producing ubiquitin chains containing both types of linkage, termed K63/M1-Ub hybrids. The formation of K63/M1-Ub hybrids, which is a feature of several innate immune signalling pathways, permits the co-recruitment of proteins that interact with either K63-Ub or M1-Ub chains. Two likely roles for K63/M1-Ub hybrids are to facilitate the TAK1-dependent activation of the IKK complex and to prevent the hyperactivation of these kinases by recruiting A20 and A20-binding inhibitor of NF-κB1 (ABIN1). These proteins restrict activation of the TAK1 and IKK complexes, probably by competing with them for binding to K63/M1-Ub hybrids. The formation of K63/M1-Ub hybrids may also regulate the rate at which the ubiquitin linkages in these chains are hydrolysed. The IKK-catalysed phosphorylation of some of its substrates permits their recognition by the E3 ligase SCF βTRCP , leading to their Lys48-linked ubiquitylation and proteasomal degradation. Innate immune signalling is therefore controlled by the formation and destruction of three different types of ubiquitin linkage.

The role of hybrid ubiquitin chains in the MyD88 and other innate immune signalling pathways

PubMed Central

Cohen, Philip; Strickson, Sam

2017-01-01

The adaptor protein MyD88 is required for signal transmission by toll-like receptors and receptors of the interleukin-1 family of cytokines. MyD88 signalling triggers the formation of Lys63-linked and Met1-linked ubiquitin (K63-Ub, M1-Ub) chains within minutes. The K63-Ub chains, which are formed by the E3 ubiquitin ligases TRAF6, Pellino1 and Pellino2, activate TAK1, the master kinase that switches on mitogen-activated protein (MAP) kinase cascades and initiates activation of the canonical IκB kinase (IKK) complex. The M1-Ub chains, which are formed by the linear ubiquitin chain assembly complex (LUBAC), bind to the NEMO (NF-κB essential modulator) component of the IKK complex and are required for TAK1 to activate IKKs, but not MAP kinases. An essential E3 ligase-independent role of TRAF6 is to recruit LUBAC into the MyD88 signalling complex, where it recognises preformed K63-Ub chains attached to protein components of these complexes, such as IRAK1 (IL-1 receptor-associated kinase), producing ubiquitin chains containing both types of linkage, termed K63/M1-Ub hybrids. The formation of K63/M1-Ub hybrids, which is a feature of several innate immune signalling pathways, permits the co-recruitment of proteins that interact with either K63-Ub or M1-Ub chains. Two likely roles for K63/M1-Ub hybrids are to facilitate the TAK1-dependent activation of the IKK complex and to prevent the hyperactivation of these kinases by recruiting A20 and A20-binding inhibitor of NF-κB1 (ABIN1). These proteins restrict activation of the TAK1 and IKK complexes, probably by competing with them for binding to K63/M1-Ub hybrids. The formation of K63/M1-Ub hybrids may also regulate the rate at which the ubiquitin linkages in these chains are hydrolysed. The IKK-catalysed phosphorylation of some of its substrates permits their recognition by the E3 ligase SCFβTRCP, leading to their Lys48-linked ubiquitylation and proteasomal degradation. Innate immune signalling is therefore controlled by the formation and destruction of three different types of ubiquitin linkage. PMID:28475177

Optimal design of supply chain network under uncertainty environment using hybrid analytical and simulation modeling approach

NASA Astrophysics Data System (ADS)

Chiadamrong, N.; Piyathanavong, V.

2017-12-01

Models that aim to optimize the design of supply chain networks have gained more interest in the supply chain literature. Mixed-integer linear programming and discrete-event simulation are widely used for such an optimization problem. We present a hybrid approach to support decisions for supply chain network design using a combination of analytical and discrete-event simulation models. The proposed approach is based on iterative procedures until the difference between subsequent solutions satisfies the pre-determined termination criteria. The effectiveness of proposed approach is illustrated by an example, which shows closer to optimal results with much faster solving time than the results obtained from the conventional simulation-based optimization model. The efficacy of this proposed hybrid approach is promising and can be applied as a powerful tool in designing a real supply chain network. It also provides the possibility to model and solve more realistic problems, which incorporate dynamism and uncertainty.

Intersubunit structure within heterodimers of medium-chain prenyl diphosphate synthases. Formation of a hybrid-type heptaprenyl diphosphate synthase.

PubMed

Koike-Takeshita, A; Koyama, T; Ogura, K

1998-10-01

Among prenyltransferases that catalyze the sequential condensation of isopentenyl diphosphate with allylic diphosphate to produce prenyl diphosphates with various chain lengths and stereochemistries, medium-chain prenyl diphosphate synthases are exceptional in that they comprise two dissociable heteromeric protein components. These components exist without binding with each other under physiological conditions, and neither of them has any prenyltransferase activity by itself. In order to elucidate the precise molecular mechanism underlying expression of the catalytic function by such a unique two-component system, we examined the possibility of forming a hybrid between two of the components of three different medium-chain prenyl diphosphate synthases, components I and II of heptaprenyl diphosphate synthase from Bacillus subtilis, components I' and II' of heptaprenyl diphosphate synthase from Bacillus stearothermophilus, and components A and B of hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26. As a result, only the hybrid-type combination of component I and component II' gave distinct prenyltransferase activity. The hybrid-type enzyme catalyzed the synthesis of heptaprenyl diphosphate and showed moderate heat stability, which lay between those of the natural enzymes from B. subtilis and B. stearothermophilus. There is no possibility of forming a hybrid between the heptaprenyl and hexaprenyl diphosphate synthases.

Ultrasensitive detection of nucleic acids and proteins using quartz crystal microbalance and surface plasmon resonance sensors based on target-triggering multiple signal amplification strategy.

PubMed

Sun, Wenbo; Song, Weiling; Guo, Xiaoyan; Wang, Zonghua

2017-07-25

In this study, quartz crystal microbalance (QCM) and surface plasmon resonance (SPR) sensors were combined with template enhanced hybridization processes (TEHP), rolling circle amplification (RCA) and biocatalytic precipitation (BCP) for ultrasensitive detection of DNA and protein. The DNA complementary to the aptamer was released by the specific binding of the aptamer to the target protein and then hybridized with the capture probe and the assistant DNA to form a ternary "Y" junction structure. The initiation chain was generated by the template-enhanced hybridization process which leaded to the rolling circle amplification reaction, and a large number of repeating unit sequences were formed. Hybridized with the enzyme-labeled probes, the biocatalytic precipitation reaction was further carried out, resulting in a large amount of insoluble precipitates and amplifying the detection signal. Under the optimum conditions, detection limits as low as 43 aM for target DNA and 53 aM for lysozyme were achieved. In addition, this method also showed good selectivity and sensitivity in human serum. Copyright © 2017 Elsevier B.V. All rights reserved.

Numerical investigations on the lateral angular co-extrusion of aluminium and steel

NASA Astrophysics Data System (ADS)

Behrens, B.-A.; Klose, C.; Chugreev, A.; Thürer, S. E.; Uhe, J.

2018-05-01

In order to save weight and costs, different materials can be combined within one component. In the novel process chain being developed within the Collaborative Research Centre (CRC) 1153, joined semi-finished workpieces are used to produce hybrid solid components with locally adapted properties. Different materials are joined in an initial step before the forming process takes place. Hereby, the quality of the joining zone is improved by means of the thermo-mechanical treatment during the forming and machining processes. The lateral angular co-extrusion (LACE) approach is used to produce semi-finished workpieces because it allows for the production of coaxial semi-finished products consisting of aluminium and steel. In the further process chain, these semi-finished products are processed into hybrid bearing bushings with locally adapted properties by die forging. In the scope of this work, numerical investigations of the co-extrusion of aluminium-steel compounds were carried out using finite element (FE) simulation in order to examine the influence of the process parameters on the co-extrusion process. For this purpose, the relevant material properties of the aluminium alloy EN AW-6082 were determined experimentally and subsequently implemented in the numerical model. The obtained numerical model was used to study the impact of different ram speeds, press ratios and billet temperatures on the resulting extrusion forces and the material flow. The numerical results have been validated using force-time curves obtained from experimental extrusion tests carried out on a 2.5 MN laboratory extrusion press.

Ultrasensitive electrochemical DNA detection based on dual amplification of circular strand-displacement polymerase reaction and hybridization chain reaction.

PubMed

Wang, Cui; Zhou, Hui; Zhu, Wenping; Li, Hongbo; Jiang, Jianhui; Shen, Guoli; Yu, Ruqin

2013-09-15

We developed a novel electrochemical strategy for ultrasensitive DNA detection using a dual amplification strategy based on the circular strand-displacement polymerase reaction (CSDPR) and the hybridization chain reaction (HCR). In this assay, hybridization of hairpin-shaped capture DNA to target DNA resulted in a conformational change of the capture DNA with a concomitant exposure of its stem. The primer was then hybridized with the exposed stem and triggered a polymerization reaction, allowing a cyclic reaction comprising release of target DNA, hybridization of target with remaining capture DNA, polymerization initiated by the primer. Furthermore, the free part of the primer propagated a chain reaction of hybridization events between two DNA hairpin probes with biotin labels, enabling an electrochemical reading using the streptavidin-alkaline phosphatase. The proposed biosensor showed to have very high sensitivity and selectivity with a dynamic response range through 10fM to 1nM, and the detect limit was as low as 8fM. The proposed strategy could have the potential for molecular diagnostics in complex biological systems. Copyright © 2013 Elsevier B.V. All rights reserved.

Hybrid algorithms for fuzzy reverse supply chain network design.

PubMed

Che, Z H; Chiang, Tzu-An; Kuo, Y C; Cui, Zhihua

2014-01-01

In consideration of capacity constraints, fuzzy defect ratio, and fuzzy transport loss ratio, this paper attempted to establish an optimized decision model for production planning and distribution of a multiphase, multiproduct reverse supply chain, which addresses defects returned to original manufacturers, and in addition, develops hybrid algorithms such as Particle Swarm Optimization-Genetic Algorithm (PSO-GA), Genetic Algorithm-Simulated Annealing (GA-SA), and Particle Swarm Optimization-Simulated Annealing (PSO-SA) for solving the optimized model. During a case study of a multi-phase, multi-product reverse supply chain network, this paper explained the suitability of the optimized decision model and the applicability of the algorithms. Finally, the hybrid algorithms showed excellent solving capability when compared with original GA and PSO methods.

Hybrid Algorithms for Fuzzy Reverse Supply Chain Network Design

PubMed Central

Che, Z. H.; Chiang, Tzu-An; Kuo, Y. C.

2014-01-01

In consideration of capacity constraints, fuzzy defect ratio, and fuzzy transport loss ratio, this paper attempted to establish an optimized decision model for production planning and distribution of a multiphase, multiproduct reverse supply chain, which addresses defects returned to original manufacturers, and in addition, develops hybrid algorithms such as Particle Swarm Optimization-Genetic Algorithm (PSO-GA), Genetic Algorithm-Simulated Annealing (GA-SA), and Particle Swarm Optimization-Simulated Annealing (PSO-SA) for solving the optimized model. During a case study of a multi-phase, multi-product reverse supply chain network, this paper explained the suitability of the optimized decision model and the applicability of the algorithms. Finally, the hybrid algorithms showed excellent solving capability when compared with original GA and PSO methods. PMID:24892057

Side-chain amino-acid-based pH-responsive self-assembled block copolymers for drug delivery and gene transfer.

PubMed

Kumar, Sonu; Acharya, Rituparna; Chatterji, Urmi; De, Priyadarsi

2013-12-10

Developing safe and effective nanocarriers for multitype of delivery system is advantageous for several kinds of successful biomedicinal therapy with the same carrier. In the present study, we have designed amino acid biomolecules derived hybrid block copolymers which can act as a promising vehicle for both drug delivery and gene transfer. Two representative natural chiral amino acid-containing (l-phenylalanine and l-alanine) vinyl monomers were polymerized via reversible addition-fragmentation chain transfer (RAFT) process in the presence of monomethoxy poly(ethylene glycol) based macro-chain transfer agents (mPEGn-CTA) for the synthesis of well-defined side-chain amino-acid-based amphiphilic block copolymers, monomethoxy poly(ethylene glycol)-b-poly(Boc-amino acid methacryloyloxyethyl ester) (mPEGn-b-P(Boc-AA-EMA)). The self-assembled micellar aggregation of these amphiphilic block copolymers were studied by fluorescence spectroscopy, atomic force microscopy (AFM) and scanning electron microscopy (SEM). Potential applications of these hybrid polymers as drug carrier have been demonstrated in vitro by encapsulation of nile red dye or doxorubicin drug into the core of the micellar nanoaggregates. Deprotection of side-chain Boc- groups in the amphiphilic block copolymers subsequently transformed them into double hydrophilic pH-responsive cationic block copolymers having primary amino groups in the side-chain terminal. The DNA binding ability of these cationic block copolymers were further investigated by using agarose gel retardation assay and AFM. The in vitro cytotoxicity assay demonstrated their biocompatible nature and these polymers can serve as "smart" materials for promising bioapplications.

Future Supply Chains Enabled by Continuous Processing-Opportunities Challenges May 20-21 2014 Continuous Manufacturing Symposium.

PubMed

Srai, Jagjit Singh; Badman, Clive; Krumme, Markus; Futran, Mauricio; Johnston, Craig

2015-03-01

This paper examines the opportunities and challenges facing the pharmaceutical industry in moving to a primarily "continuous processing"-based supply chain. The current predominantly "large batch" and centralized manufacturing system designed for the "blockbuster" drug has driven a slow-paced, inventory heavy operating model that is increasingly regarded as inflexible and unsustainable. Indeed, new markets and the rapidly evolving technology landscape will drive more product variety, shorter product life-cycles, and smaller drug volumes, which will exacerbate an already unsustainable economic model. Future supply chains will be required to enhance affordability and availability for patients and healthcare providers alike despite the increased product complexity. In this more challenging supply scenario, we examine the potential for a more pull driven, near real-time demand-based supply chain, utilizing continuous processing where appropriate as a key element of a more "flow-through" operating model. In this discussion paper on future supply chain models underpinned by developments in the continuous manufacture of pharmaceuticals, we have set out; The paper recognizes that although current batch operational performance in pharma is far from optimal and not necessarily an appropriate end-state benchmark for batch technology, the adoption of continuous supply chain operating models underpinned by continuous production processing, as full or hybrid solutions in selected product supply chains, can support industry transformations to deliver right-first-time quality at substantially lower inventory profiles. © 2015 The Authors. Journal of Pharmaceutical Sciences published by Wiley Periodicals, Inc. and the American Pharmacists Association. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Evaluating the green practice of food service supply chain management based on fuzzy DEMATEL-ANP model

NASA Astrophysics Data System (ADS)

Li, Xiaoying; Zhu, Qinghua

2017-01-01

The question on how to evaluate a company's green practice has recently become a key strategic consideration for the food service supply chain management. This paper proposed a novel hybrid model that combines a fuzzy Decision Making Trial And Evaluation Laboratory(DEMATEL) and Analysis Network Process(ANP) methods, which developed the green restaurant criteria and demonstrated the complicated relations among various criteria to help the food service operation to better analyze the real-world situation and determine the different weight value of the criteria .The analysis of the evaluation of green practices will help the food service operation to be clear about the key measures of green practice to improve supply chain management.

Ultrasensitive and selective signal-on electrochemical DNA detection via exonuclease III catalysis and hybridization chain reaction amplification.

PubMed

Ren, Wang; Gao, Zhong Feng; Li, Nian Bing; Luo, Hong Qun

2015-01-15

This work reported a novel, ultrasensitive, and selective platform for electrochemical detection of DNA, employing an integration of exonuclease III (Exo-III) assisted target recycling and hybridization chain reaction (HCR) for the dual signal amplification strategy. The hairpin capture probe DNA (C-DNA) with an Exo-III 3' overhang end was self-assembled on a gold electrode. In the presence of target DNA (T-DNA), C-DNA hybridized with the T-DNA to form a duplex region, exposing its 5' complementary sequence (initiator). Exo-III was applied to selectively digest duplex region from its 3-hydroxyl termini until the duplex was fully consumed, leaving the remnant initiator. The intact T-DNA spontaneously dissociated from the structure and then initiated the next hybridization process as a result of catalysis of the Exo-III. HCR event was triggered by the initiator and two hairpin helper signal probes labeled with methylene blue, facilitating the polymerization of oligonucleotides into a long nicked dsDNA molecule. The numerous exposed remnant initiators can trigger more HCR events. Because of integration of dual signal amplification and the specific HCR process reaction, the resultant sensor showed a high sensitivity for the detection of the target DNA in a linear range from 1.0 fM to 1.0 nM, and a detection limit as low as 0.2 fM. The proposed dual signal amplification strategy provides a powerful tool for detecting different sequences of target DNA by changing the sequence of capture probe and signal probes, holding a great potential for early diagnosis in gene-related diseases. Copyright © 2014 Elsevier B.V. All rights reserved.

Combined subtraction hybridization and polymerase chain reaction amplification procedure for isolation of strain-specific Rhizobium DNA sequences.

PubMed Central

Bjourson, A J; Stone, C E; Cooper, J E

1992-01-01

A novel subtraction hybridization procedure, incorporating a combination of four separation strategies, was developed to isolate unique DNA sequences from a strain of Rhizobium leguminosarum bv. trifolii. Sau3A-digested DNA from this strain, i.e., the probe strain, was ligated to a linker and hybridized in solution with an excess of pooled subtracter DNA from seven other strains of the same biovar which had been restricted, ligated to a different, biotinylated, subtracter-specific linker, and amplified by polymerase chain reaction to incorporate dUTP. Subtracter DNA and subtracter-probe hybrids were removed by phenol-chloroform extraction of a streptavidin-biotin-DNA complex. NENSORB chromatography of the sequences remaining in the aqueous layer captured biotinylated subtracter DNA which may have escaped removal by phenol-chloroform treatment. Any traces of contaminating subtracter DNA were removed by digestion with uracil DNA glycosylase. Finally, remaining sequences were amplified by polymerase chain reaction with a probe strain-specific primer, labelled with 32P, and tested for specificity in dot blot hybridizations against total genomic target DNA from each strain in the subtracter pool. Two rounds of subtraction-amplification were sufficient to remove cross-hybridizing sequences and to give a probe which hybridized only with homologous target DNA. The method is applicable to the isolation of DNA and RNA sequences from both procaryotic and eucaryotic cells. Images PMID:1637166

Photochromic dynamics of organic-inorganic hybrids supported on transparent and flexible recycled PET

NASA Astrophysics Data System (ADS)

Cruz, R. P.; Nalin, M.; Ribeiro, S. J. L.; Molina, C.

2017-04-01

Organic-inorganic hybrids (OIH) synthesized by sol gel process containing phosphotungstic acid (PWA) entrapped have been attracted much attention for ultraviolet sensitive materials. However, the limitations for practical photochromic application of these materials are the poor interaction with flexible polymer substrates such as Poly(ethyleneterephthalate) (PET) and also photo response under ultraviolet radiation. This paper describes the use of the d-ureasil HOI, based on siliceous network grafted through linkages to both ends of polymer chain containing 2.5 poly(oxyethylene) units with PWA entrapped prepared as films on recycled PET. Films were characterized by IR-ATR, XRD, TG/DTG, UV-Vis and Contact angle. XRD patterns showed that both pristine hybrid matrix and those containing PWA are amorphous. IR showed that PWA structure is preserved in the matrix and interactions between them occur by intermolecular forces. Films are thermally stable up to 325 °C and contact angle of 25.1° showed a good wettability between substrate and hybrid matrix. Furthermore, films showed fast photochromic response after 1 min of ultraviolet exposure time. The bleaching process revealed that the relaxation process is dependent of the temperature and the activation energy of 47.2 kJ mol-1 was determined. The properties of these films make them potential candidates for applications in flexible photochromic materials.

Hybrid modeling and empirical analysis of automobile supply chain network

NASA Astrophysics Data System (ADS)

Sun, Jun-yan; Tang, Jian-ming; Fu, Wei-ping; Wu, Bing-ying

2017-05-01

Based on the connection mechanism of nodes which automatically select upstream and downstream agents, a simulation model for dynamic evolutionary process of consumer-driven automobile supply chain is established by integrating ABM and discrete modeling in the GIS-based map. Firstly, the rationality is proved by analyzing the consistency of sales and changes in various agent parameters between the simulation model and a real automobile supply chain. Second, through complex network theory, hierarchical structures of the model and relationships of networks at different levels are analyzed to calculate various characteristic parameters such as mean distance, mean clustering coefficients, and degree distributions. By doing so, it verifies that the model is a typical scale-free network and small-world network. Finally, the motion law of this model is analyzed from the perspective of complex self-adaptive systems. The chaotic state of the simulation system is verified, which suggests that this system has typical nonlinear characteristics. This model not only macroscopically illustrates the dynamic evolution of complex networks of automobile supply chain but also microcosmically reflects the business process of each agent. Moreover, the model construction and simulation of the system by means of combining CAS theory and complex networks supplies a novel method for supply chain analysis, as well as theory bases and experience for supply chain analysis of auto companies.

Enzyme-free and isothermal detection of microRNA based on click-chemical ligation-assisted hybridization coupled with hybridization chain reaction signal amplification.

PubMed

Oishi, Motoi

2015-05-01

An enzyme-free and isothermal microRNA (miRNA) detection method has been developed based on click-chemical ligation-assisted hybridization coupled with hybridization chain reaction (HCR) on magnetic beads (MBs). The click-chemical ligation between an azide-modified probe DNA and a dibenzocyclooctyne-modified probe DNA occurred through the hybridization of target miRNA (miR-141). HCR on MBs was performed by the addition of DNA hairpin monomers (H1 and H2). After magnetic separation and denaturation/rehybridization of HCR products ([H1/H2] n ), the resulting HCR products were analyzed by the fluorescence emitted from an intercalative dye, allowing amplification of the fluorescent signal. The proposed assay had a limit of detection of 0.55 fmol, which was 230-fold more sensitive than that of the HCR on the MBs coupled with a conventional sandwich hybridization assay (without click-chemical ligation) (limit of detection 127 fmol). Additionally, the proposed assay could discriminate between miR-141 and other miR-200 family members. In contrast to quantitative reverse transcription polymerase chain reaction techniques using enzymes and thermal cycling, this is an enzyme-free assay that can be conducted under isothermal conditions and can specifically detect miR-141 in fetal bovine serum.

Preparation and Structural Studies on Hybrid Core-Shell Nanoparticles Consisting of Silica Core and Conjugated Block Copolymer Shell Prepared by Surface-Initiated Polymerization

NASA Astrophysics Data System (ADS)

Chatterjee, Sourav; Karam, Tony; Rosu, Cornelia; Li, Xin; Do, Changwoo; Youm, Sang Gil; Haber, Louis; Russo, Paul; Nesterov, Evgueni

Controlled Kumada catalyst-transfer polymerization occurring by chain-growth mechanism was developed for the synthesis of conjugated polymers and block copolymers from the surface of inorganic substrates such as silica nanoparticles. Although synthesis of conjugated polymers via Kumada polymerization became an established method for solution polymerization, carrying out the same reaction in heterogeneous conditions to form monodisperse polymer chains still remains a challenge. We developed and described a simple and efficient approach to the preparation of surface-immobilized layer of catalytic Ni(II) initiator, and demonstrated using it to prepare polymers and block copolymers on silica nanoparticle. The structure of the resulting hybrid nanostructures was thoroughly studied using small-angle neutron and X-ray scattering, thermal analysis, and optical spectroscopy. The photoexcitation energy transfer processes in the conjugated polymer shell were studied via steady-state and time resolved transient absorption spectroscopy. This study uncovered important details of the energy transfer, which will be discussed in this presentation.

The role of oxygen vacancies in resistive switching behavior of organic-TiO2 hybrid composite

NASA Astrophysics Data System (ADS)

Zhang, Jiahua; Chen, Da; Huang, Shihua

2017-10-01

Effects of polyethylene glycol (PEG) on resistive switching behaviors and mechanisms in organic-TiO2 hybrid composites were investigated. The reversed current-voltage curves in the negative bias during the initial voltage sweeps were first observed in the composites annealed at 150, 200 and 250 °C, which is ascribed to the accumulation of oxygen vacancies and the inhibition effect of polarities of PEG chains. In addition, the volatility of composites with relatively high content of PEG is caused by the inhibition effect of PEG on creating oxygen vacancies. The formation and rupture of oxygen-vacancy filaments was considered as the resistive switching mechanism. Finally, the charging and discharging process in PEG-TiO2 composite annealed at 150 °C results in the instability of the electron-occupied oxygen vacancies and the inhibition of PEG chains. This study demonstrates a new way to investigate the interaction between polymers and TiO2 for understanding the resistive switching mechanism of TiO2-based memories.

Ultrasensitive automated RNA in situ hybridization for kappa and lambda light chain mRNA detects B-cell clonality in tissue biopsies with performance comparable or superior to flow cytometry.

PubMed

Guo, Ling; Wang, Zhen; Anderson, Courtney M; Doolittle, Emerald; Kernag, Siobhan; Cotta, Claudiu V; Ondrejka, Sarah L; Ma, Xiao-Jun; Cook, James R

2018-03-01

The assessment of B-cell clonality is a critical component of the evaluation of suspected lymphoproliferative disorders, but analysis from formalin-fixed, paraffin-embedded tissues can be challenging if fresh tissue is not available for flow cytometry. Immunohistochemical and conventional bright field in situ hybridization stains for kappa and lambda are effective for evaluation of plasma cells but are often insufficiently sensitive to detect the much lower abundance of light chains present in B-cells. We describe an ultrasensitive RNA in situ hybridization assay that has been adapted for use on an automated immunohistochemistry platform and compare results with flow cytometry in 203 consecutive tissues and 104 consecutive bone marrows. Overall, in 203 tissue biopsies, RNA in situ hybridization identified light chain-restricted B-cells in 85 (42%) vs 58 (29%) by flow cytometry. Within 83 B-cell non-Hodgkin lymphomas, RNA in situ hybridization identified restricted B-cells in 74 (89%) vs 56 (67%) by flow cytometry. B-cell clonality could be evaluated in only 23/104 (22%) bone marrow cases owing to poor RNA preservation, but evaluable cases showed 91% concordance with flow cytometry. RNA in situ hybridization allowed for recognition of biclonal/composite lymphomas not identified by flow cytometry and highlighted unexpected findings, such as coexpression of kappa and lambda RNA in 2 cases and the presence of lambda light chain RNA in a T lymphoblastic lymphoma. Automated RNA in situ hybridization showed excellent interobserver reproducibility for manual evaluation (average K=0.92), and an automated image analysis system showed high concordance (97%) with manual evaluation. Automated RNA in situ hybridization staining, which can be adopted on commonly utilized immunohistochemistry instruments, allows for the interpretation of clonality in the context of the morphological features in formalin-fixed, paraffin-embedded tissues with a clinical sensitivity similar or superior to flow cytometry.

Ultrasensitive Automated RNA in situ Hybridization for Kappa and Lambda Light Chain mRNA Detects B-cell Clonality in Tissue Biopsies with Performance Comparable or Superior to Flow Cytometry

PubMed Central

Guo, Ling; Wang, Zhen; Anderson, Courtney M.; Doolittle, Emerald; Kernag, Siobhan; Cotta, Claudiu V.; Ondrejka, Sarah L.; Ma, Xiao-Jun; Cook, James R.

2017-01-01

The assessment of B-cell clonality is a critical component of the evaluation of suspected lymphoproliferative disorders, but analysis from formalin fixed paraffin embedded tissues can be challenging if fresh tissue is not available for flow cytometry. Immunohistochemical and conventional bright field in situ hybridization stains for kappa and lambda are effective for evaluation of plasma cells, but are often insufficiently sensitive to detect the much lower abundance of light chains present in B cells. We describe an ultrasensitive RNA in situ hybridization assay which has been adapted for use on an automated immunohistochemistry platform and compare results with flow cytometry in 203 consecutive tissues and 104 consecutive bone marrows. Overall, in 203 tissue biopsies, RNA in situ hybridization identified light chain restricted B-cells in 85 (42%) vs. 58 (29%) by flow cytometry. Within 83 B-cell non-Hodgkin lymphomas, RNA in situ hybridization identified a restricted B-cells in 74 (89%) vs. 56 (67%) by flow cytometry. B-cell clonality could be evaluated in only 23/104 (22%) bone marrow cases due to poor RNA preservation, but evaluable cases showed 91% concordance with flow cytometry. RNA in situ hybridization allowed for recognition of biclonal/composite lymphomas not identified by flow cytometry, and highlighted unexpected findings, such as coexpression of kappa and lambda RNA in 2 cases and the presence of lambda light chain RNA in a T lymphoblastic lymphoma. Automated RNA in situ hybridization showed excellent interobserver reproducibility for manual evaluation (average K=0.92), and an automated image analysis system showed high concordance (97%) with manual evaluation. Automated RNA in situ hybridization staining, which can be adopted on commonly utilized immunohistochemistry instruments, allows for the interpretation of clonality in the context of the morphologic features in formalin fixed, paraffin embedded tissues with a clinical sensitivity similar or superior to flow cytometry. PMID:29052600

Co-extrusion of semi-finished aluminium-steel compounds

NASA Astrophysics Data System (ADS)

Thürer, S. E.; Uhe, J.; Golovko, O.; Bonk, C.; Bouguecha, A.; Klose, C.; Behrens, B.-A.; Maier, H. J.

2017-10-01

The combination of light metals and steels allows for new lightweight components with wear-resistant functional surfaces. Within the Collaborative Research Centre 1153 novel process chains are developed for the manufacture of such hybrid components. Here, the production process of a hybrid bearing bushing made of the aluminium alloy EN AW-6082 and the case-hardened steel 20MnCr5 is developed. Hybrid semi-finished products are an attractive alternative to conventional ones resulting from massive forming processes where the individual components are joined after the forming process. The actual hybrid semi-finished products were manufactured using a lateral angular co-extrusion (LACE) process. The bearing bushings are subsequently produced by die forging. In the present study, a tool concept for the LACE process is described, which renders the continuous joining of a steel rod with an aluminium tube possible. During the LACE process, the rod is fed into the extrusion die at an angle of approx. 90°. Metallographic analysis of the hybrid profile showed that the mechanical bonding between the different materials begins about 75 mm after the edge of the aluminium sheath. In order to improve the bonding strength, the steel rod is to be preheated during extrusion. Systematic investigations using a dilatometer, considering the maximum possible co-extrusion process parameters, were carried out. The variable parameters for the dilatometer experiments were determined by numerical simulation. In order to form a bond between the materials, the oxide layer needs to be disrupted during the co-extrusion process. In an attempt to better understand this effect, a modified sample geometry with chamfered steel was developed for the dilatometer experiments. The influence of the process parameters on the formation of the intermetallic phase at the interface was analysed by scanning electron microscopy and X-ray diffraction. This article, which was originally published online on 16 October 2017, contained an error in the press ratio, where 9:1 should be 6:1. The corrected ratio appears in the Corrigendum attached to the pdf.

Direct RNA detection without nucleic acid purification and PCR: Combining sandwich hybridization with signal amplification based on branched hybridization chain reaction.

PubMed

Xu, Yao; Zheng, Zhi

2016-05-15

We have developed a convenient, robust and low-cost RNA detection system suitable for high-throughput applications. This system uses a highly specific sandwich hybridization to capture target RNA directly onto solid support, followed by on-site signal amplification via 2-dimensional, branched hybridizing chain polymerization through toehold-mediated strand displacement reaction. The assay uses SYBR Green to detect targets at concentrations as low as 1 pM, without involving nucleic acid purification or any enzymatic reaction, using ordinary oligonucleotides without modification or labeling. The system was demonstrated in the detection of malaria RNA in blood and GAPDH gene expression in cell lysate. Copyright © 2015 Elsevier B.V. All rights reserved.

Tungsten hydride complex as a template in organic inorganic hybrid materials

NASA Astrophysics Data System (ADS)

Montinho, Isilda; Boev, Victor; Fonseca, António M.; Silva, Carlos J. R.; Neves, Isabel C.

2003-03-01

A tungsten hydride complex, [WH 2( η2-OOCCH 3)(Ph 2PCH 2CH 2PPh 2) 2][BPh 4], was dispersed in a hybrid matrix synthesized by a sol-gel process. The host matrix of the so-called ureasil is a network of silica to which oligopolyoxyethylene chains [POE, (OCH 2CH 2) n] are grafted by means of urea cross-links. The free complex and sol-gel materials were characterized by thermal analysis (DSC) and spectroscopic methods (FT-IR and UV/Vis). The data gathered indicate that the tungsten(IV) complex is immobilized in the host matrix, and it exhibits structural properties different from those of the free form. These differences could arise either from distortions caused by steric effects imposed by the structure of hybrid matrix or by interactions with the matrix.

Exploration of the folding dynamics of human telomeric G-quadruplex with a hybrid atomistic structure-based model

NASA Astrophysics Data System (ADS)

Bian, Yunqiang; Ren, Weitong; Song, Feng; Yu, Jiafeng; Wang, Jihua

2018-05-01

Structure-based models or Gō-like models, which are built from one or multiple particular experimental structures, have been successfully applied to the folding of proteins and RNAs. Recently, a variant termed the hybrid atomistic model advances the description of backbone and side chain interactions of traditional structure-based models, by borrowing the description of local interactions from classical force fields. In this study, we assessed the validity of this model in the folding problem of human telomeric DNA G-quadruplex, where local dihedral terms play important roles. A two-state model was developed and a set of molecular dynamics simulations was conducted to study the folding dynamics of sequence Htel24, which was experimentally validated to adopt two different (3 + 1) hybrid G-quadruplex topologies in K+ solution. Consistent with the experimental observations, the hybrid-1 conformation was found to be more stable and the hybrid-2 conformation was kinetically more favored. The simulations revealed that the hybrid-2 conformation folded in a higher cooperative manner, which may be the reason why it was kinetically more accessible. Moreover, by building a Markov state model, a two-quartet G-quadruplex state and a misfolded state were identified as competing states to complicate the folding process of Htel24. Besides, the simulations also showed that the transition between hybrid-1 and hybrid-2 conformations may proceed an ensemble of hairpin structures. The hybrid atomistic structure-based model reproduced the kinetic partitioning folding dynamics of Htel24 between two different folds, and thus can be used to study the complex folding processes of other G-quadruplex structures.

Chromosomal locations of mouse immunoglobulin genes.

PubMed Central

Valbuena, O; Marcu, K B; Croce, C M; Huebner, K; Weigert, M; Perry, R P

1978-01-01

The chromosomal locations of the structural genes coding for the constant portions of mouse heavy (H) and light chain immunoglobulins were studied by molecular hybridization techniques. Complementary DNA probes containing the constant-region sequences of kappa and lambdaI light chain and alpha, gamma2b, and mu heavy chain mRNAs were annealed to a large excess of DNA from a series of eight mouse-human hybrid cell lines that are deficient for various mouse chromosomes. The lines were scored as positive when a high proportion of a probe annealed and negative when an insignificant proportion annealed. Some lines were clearly negative for H and lambda and clearly positive for kappa. Others were positive or intermediate for lambda, positive for kappa and negative for H. Still others, including a line that was selected for the absence of the mouse X chromosome, were positive for all immunoglobulin species. These results demonstrate that the Clambda, Ckappa, and CH genes are located on different autosomes in the mouse. In contrast, the three heavy-chain families exhibited consistently uniform hybridization results, suggesting that the genes for Calpha, Cgamma, and Cmu are located on the same chromosome. A comparison of karyotypic data with hybridization data has limited the possible locations of the Ig genes to only a few chromosomes. PMID:96442

Hybridization chain reaction-based instantaneous derivatization technology for chemiluminescence detection of specific DNA sequences.

PubMed

Wang, Xin; Lau, Choiwan; Kai, Masaaki; Lu, Jianzhong

2013-05-07

We propose here a new amplifying strategy that uses hybridization chain reaction (HCR) to detect specific sequences of DNA, where stable DNA monomers assemble on the magnetic beads only upon exposure to a target DNA. Briefly, in the HCR process, two complementary stable species of hairpins coexist in solution until the introduction of initiator reporter strands triggers a cascade of hybridization events that yield nicked double helices analogous to alternating copolymers. Moreover, a "sandwich-type" detection strategy is employed in our design. Magnetic beads, which are functionalized with capture DNA, are reacted with the target, and sandwiched with the above nicked double helices. Then, chemiluminescence (CL) detection proceeds via an instantaneous derivatization reaction between a specific CL reagent, 3,4,5-trimethoxylphenylglyoxal (TMPG), and the guanine nucleotides within the target DNA, reporter strands and DNA monomers for the generation of light. Our results clearly show that the amplification detection of specific sequences of DNA achieves a better performance (e.g. wide linear response range, low detection limit, and high specificity) as compared to the traditional sandwich type (capture/target/reporter) assays. Upon modification, the approach presented could be extended to detect other types of targets. We believe that this simple technique is promising for improving medical diagnosis and treatment.

Intercalation and structural aspects of macroRAFT agents into MgAl layered double hydroxides.

PubMed

Kostadinova, Dessislava; Cenacchi Pereira, Ana; Lansalot, Muriel; D'Agosto, Franck; Bourgeat-Lami, Elodie; Leroux, Fabrice; Taviot-Guého, Christine; Cadars, Sylvian; Prevot, Vanessa

2016-01-01

Increasing attention has been devoted to the design of layered double hydroxide (LDH)-based hybrid materials. In this work, we demonstrate the intercalation by anion exchange process of poly(acrylic acid) (PAA) and three different hydrophilic random copolymers of acrylic acid (AA) and n -butyl acrylate (BA) with molar masses ranging from 2000 to 4200 g mol -1 synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization, into LDH containing magnesium(II) and aluminium(III) intralayer cations and nitrates as counterions (MgAl-NO 3 LDH). At basic pH, the copolymer chains (macroRAFT agents) carry negative charges which allowed the establishment of electrostatic interactions with the LDH interlayer and their intercalation. The resulting hybrid macroRAFT/LDH materials displayed an expanded interlamellar domain compared to pristine MgAl-NO 3 LDH from 1.36 nm to 2.33 nm. Depending on the nature of the units involved into the macroRAFT copolymer (only AA or AA and BA), the intercalation led to monolayer or bilayer arrangements within the interlayer space. The macroRAFT intercalation and the molecular structure of the hybrid phases were further characterized by Fourier transform infrared (FTIR) and solid-state 13 C, 1 H and 27 Al nuclear magnetic resonance (NMR) spectroscopies to get a better description of the local structure.

Extension of D-H parameter method to hybrid manipulators used in robot-assisted surgery.

PubMed

Singh, Amanpreet; Singla, Ashish; Soni, Sanjeev

2015-10-01

The main focus of this work is to extend the applicability of D-H parameter method to develop a kinematic model of a hybrid manipulator. A hybrid manipulator is a combination of open- and closed-loop chains and contains planar and spatial links. It has been found in the literature that D-H parameter method leads to ambiguities, when dealing with closed-loop chains. In this work, it has been observed that the D-H parameter method, when applied to a hybrid manipulator, results in an orientational inconsistency, because of which the method cannot be used to develop the kinematic model. In this article, the concept of dummy frames is proposed to resolve the orientational inconsistency and to develop the kinematic model of a hybrid manipulator. Moreover, the prototype of 7-degree-of-freedom hybrid manipulator, known as a surgeon-side manipulator to assist the surgeon during a medical surgery, is also developed to validate the kinematic model derived in this work. © IMechE 2015.

All-carbon sp-sp2 hybrid structures: Geometrical properties, current rectification, and current amplification

PubMed Central

Zhang, Zhenhua; Zhang, Junjun; Kwong, Gordon; Li, Ji; Fan, Zhiqiang; Deng, Xiaoqing; Tang, Guiping

2013-01-01

All-carbon sp-sp2 hybrid structures comprised of a zigzag-edged trigonal graphene (ZTG)and carbon chains are proposed and constructed as nanojunctions. It has been found that such simple hybrid structures possess very intriguing propertiesapp:addword:intriguing. The high-performance rectifying behaviors similar to macroscopic p-n junction diodes, such as a nearly linear positive-bias I-V curve (metallic behavior), a very small leakage current under negative bias (insulating behavior), a rather low threshold voltage, and a large bias region contributed to a rectification, can be predicted. And also, a transistor can be built by such a hybrid structure, which can show an extremely high current amplification. This is because a sp-hybrid carbon chain has a special electronic structure which can limit the electronic resonant tunneling of the ZTG to a unique and favorable situation. These results suggest that these hybrid structures might promise importantly potential applications for developing nano-scale integrated circuits. PMID:23999318

A hybrid optimization approach in non-isothermal glass molding

NASA Astrophysics Data System (ADS)

Vu, Anh-Tuan; Kreilkamp, Holger; Krishnamoorthi, Bharathwaj Janaki; Dambon, Olaf; Klocke, Fritz

2016-10-01

Intensively growing demands on complex yet low-cost precision glass optics from the today's photonic market motivate the development of an efficient and economically viable manufacturing technology for complex shaped optics. Against the state-of-the-art replication-based methods, Non-isothermal Glass Molding turns out to be a promising innovative technology for cost-efficient manufacturing because of increased mold lifetime, less energy consumption and high throughput from a fast process chain. However, the selection of parameters for the molding process usually requires a huge effort to satisfy precious requirements of the molded optics and to avoid negative effects on the expensive tool molds. Therefore, to reduce experimental work at the beginning, a coupling CFD/FEM numerical modeling was developed to study the molding process. This research focuses on the development of a hybrid optimization approach in Non-isothermal glass molding. To this end, an optimal configuration with two optimization stages for multiple quality characteristics of the glass optics is addressed. The hybrid Back-Propagation Neural Network (BPNN)-Genetic Algorithm (GA) is first carried out to realize the optimal process parameters and the stability of the process. The second stage continues with the optimization of glass preform using those optimal parameters to guarantee the accuracy of the molded optics. Experiments are performed to evaluate the effectiveness and feasibility of the model for the process development in Non-isothermal glass molding.

HD Diesel Hybrid Truck Powertrain Study

DTIC Science & Technology

2012-09-11

Z39-18 Command Chain ij Army Materiel Command (AMC) - Huntsville, AL :""V-..... Research, Development & Engineering Command (RDECOM) -Aberdeen, MD...WARFIGHTER FOCUSED. Unclassified Li-lon I Ultracap Hybrid Energy Storage Microgrids Radiators Power Controllers for Power Management JP-8 Fuel...hybrid electric vehicle ( Honda Insight) entered this market in 1999 while the first commercial diesel-electric hybrid truck was produced by Navistar in

Solution-processable ambipolar diketopyrrolopyrrole-selenophene polymer with unprecedentedly high hole and electron mobilities.

PubMed

Lee, Junghoon; Han, A-Reum; Kim, Jonggi; Kim, Yiho; Oh, Joon Hak; Yang, Changduk

2012-12-26

There is a fast-growing demand for polymer-based ambipolar thin-film transistors (TFTs), in which both n-type and p-type transistor operations are realized in a single layer, while maintaining simplicity in processing. Research progress toward this end is essentially fueled by molecular engineering of the conjugated backbones of the polymers and the development of process architectures for device fabrication, which has recently led to hole and electron mobilities of more than 1.0 cm(2) V(-1) s(-1). However, ambipolar polymers with even higher performance are still required. By taking into account both the conjugated backbone and side chains of the polymer component, we have developed a dithienyl-diketopyrrolopyrrole (TDPP) and selenophene containing polymer with hybrid siloxane-solubilizing groups (PTDPPSe-Si). A synergistic combination of rational polymer backbone design, side-chain dynamics, and solution processing affords an enormous boost in ambipolar TFT performance, resulting in unprecedentedly high hole and electron mobilities of 3.97 and 2.20 cm(2) V(-1) s(-1), respectively.

Use of Trypanosoma equiperdum infected rabbits as a source of splenic mRNA; construction of cDNA clones and identification of a rabbit mu heavy chain clone.

PubMed

Bernstein, K E; Pavirani, A; Alexander, C; Jacobsen, F; Fitzmaurice, L; Mage, R

1983-01-01

Rabbits were infected by Trypanosoma equiperdum and the splenic mRNA was isolated. In vitro translation of this RNA and immunoprecipitation with anti-light chain, anti-heavy chain, anti-mu and anti-VH antibodies demonstrated that T. equiperdum infection elicits large quantities of splenic mRNA encoding mu and kappa chains. The mu and gamma heavy chains and the kappa light chains synthesized in the cell-free translation system were specifically immunoprecipitated by antisera to heavy chain VHa and light chain kappa b allotypes. In vitro labeling of spleen cells from trypanosome-infected animals demonstrated that the biosynthetically labeled IgM has a mu chain of higher molecular weight than the mu chain synthesized by in vitro translation, a difference that is largely abolished when cellular glycosylation is blocked with the antibiotic tunicamycin. Enrichment for heavy chain or light chain mRNA was achieved by fractionating mRNA from trypanosome-infected animals on a sucrose gradient. cDNA clones carrying mu heavy chain sequences were produced using a 'one tube' protocol and identified by cross species hybridization and hybridization selection. Infection of rabbits with T. equiperdum followed by sucrose gradient enrichment of splenic mRNA has provided sufficient quantities of mRNA encoding mu heavy chain suitable for cDNA cloning.

Hierarchical mesostructured titanium phosphonates with unusual uniform lines of macropores.

PubMed

Ma, Tian-Yi; Lin, Xiu-Zhen; Zhang, Xue-Jun; Yuan, Zhong-Yong

2011-04-01

Organic-inorganic hybrid materials of mesostructured titanium phosphonates with unusual uniform lines of macropores were synthesized by using bis(hexamethylenetriamine) penta(methylenephosphonic acid) (BHMTPMP) as the coupling molecule, through a one-pot hydrothermal process without any surfactant assistance. A wormhole-like mesostructure and many uniform parallel lines of macropores divided by solid ridges in the same direction were confirmed by N(2) sorption, SEM and TEM observations. This novel macropore architecture has never been observed in other metal phosphonate materials, which may be directly related to the structure nature of BHMTPMP with extra long alkyl chains. The structural characterization of FT-IR and MAS NMR revealed the integrity of organic groups inside the hybrid framework. The hybrid materials were also used as adsorbents for heavy metal ions and CO(2), in order to clarify the impacts of the organic contents and organic types on the physicochemical properties of the synthesized hierarchical macro-/mesoporous phosphonate materials.

Molecular genetic analysis of the V kappa Ser group associated with two mouse light chain genetic markers. Complementary DNA cloning and southern hybridization analysis

PubMed Central

1985-01-01

Previous studies (21) have shown that two mouse kappa light (L) chain variable (V) region polymorphisms, the IB-peptide and Efla markers, reflect expression of a characteristic group of V kappa regions, called V kappa Ser, by some inbred strains and not others. Expression of V kappa Ser is controlled by a locus on chromosome 6, the chromosome that contains the kappa locus. To further characterize this V kappa group and begin to analyze the basis for its strain-specific expression, full- length complementary DNA (cDNA) copies were produced of L chain mRNA from the M75 myeloma that had been induced in the C.C58 strain of mice, and which produces a V kappa Ser L chain. The C.C58 strain is congenic with BALB/cAn, differing in the region of chromosome 6 that controls expression of the V kappa polymorphisms and the Lyt-2 and Lyt-3 T cell alloantigens. The complete nucleotide sequence of this cloned cDNA was determined and compared with the nucleotide sequences the most closely related BALB/c myeloma L chains known. Results indicated significant differences throughout the variable region, but particularly toward the 5' portion of the sequence. A probe corresponding to 200 bp of the 5' end of the cloned V kappa Ser cDNA was used in Southern hybridizations of restriction digests of liver DNA from a number of inbred, recombinant, and recombinant inbred strains. Under stringent hybridization conditions, one strongly-hybridizing fragment was observed in Bam HI, Hind III, and Eco RI digests, and based on the size of the fragments, strains could be organized into two groups. The presence of strongly hybridizing Bam HI, Hind III, and Eco RI fragments of 3.2, 2.8, and 2.1 kb, respectively, was found to correlate completely with expression by the strain of the IB-peptide and Efla markers. All nonexpressor strains yielded hybridizing fragments of 7.8, 8.4, and 2.8 kb, respectively. Possible explanations for strain- specific expression of V kappa Ser-associated phenotypic markers are discussed. PMID:3926938

Future supply chains enabled by continuous processing--opportunities and challenges. May 20-21, 2014 Continuous Manufacturing Symposium.

PubMed

Srai, Jagjit Singh; Badman, Clive; Krumme, Markus; Futran, Mauricio; Johnston, Craig

2015-03-01

This paper examines the opportunities and challenges facing the pharmaceutical industry in moving to a primarily "continuous processing"-based supply chain. The current predominantly "large batch" and centralized manufacturing system designed for the "blockbuster" drug has driven a slow-paced, inventory heavy operating model that is increasingly regarded as inflexible and unsustainable. Indeed, new markets and the rapidly evolving technology landscape will drive more product variety, shorter product life-cycles, and smaller drug volumes, which will exacerbate an already unsustainable economic model. Future supply chains will be required to enhance affordability and availability for patients and healthcare providers alike despite the increased product complexity. In this more challenging supply scenario, we examine the potential for a more pull driven, near real-time demand-based supply chain, utilizing continuous processing where appropriate as a key element of a more "flow-through" operating model. In this discussion paper on future supply chain models underpinned by developments in the continuous manufacture of pharmaceuticals, we have set out; The significant opportunities to moving to a supply chain flow-through operating model, with substantial opportunities in inventory reduction, lead-time to patient, and radically different product assurance/stability regimes. Scenarios for decentralized production models producing a greater variety of products with enhanced volume flexibility. Production, supply, and value chain footprints that are radically different from today's monolithic and centralized batch manufacturing operations. Clinical trial and drug product development cost savings that support more rapid scale-up and market entry models with early involvement of SC designers within New Product Development. The major supply chain and industrial transformational challenges that need to be addressed. The paper recognizes that although current batch operational performance in pharma is far from optimal and not necessarily an appropriate end-state benchmark for batch technology, the adoption of continuous supply chain operating models underpinned by continuous production processing, as full or hybrid solutions in selected product supply chains, can support industry transformations to deliver right-first-time quality at substantially lower inventory profiles. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Chlorogenic acid-arabinose hybrid domains in coffee melanoidins: Evidences from a model system.

PubMed

Moreira, Ana S P; Coimbra, Manuel A; Nunes, Fernando M; Passos, Cláudia P; Santos, Sónia A O; Silvestre, Armando J D; Silva, André M N; Rangel, Maria; Domingues, M Rosário M

2015-10-15

Arabinose from arabinogalactan side chains was hypothesized as a possible binding site for chlorogenic acids in coffee melanoidins. To investigate this hypothesis, a mixture of 5-O-caffeoylquinic acid (5-CQA), the most abundant chlorogenic acid in green coffee beans, and (α1 → 5)-L-arabinotriose, structurally related to arabinogalactan side chains, was submitted to dry thermal treatments. The compounds formed during thermal processing were identified by electrospray ionization mass spectrometry (ESI-MS) and characterized by tandem MS (ESI-MS(n)). Compounds composed by one or two CQAs covalently linked with pentose (Pent) residues (1-12) were identified, along with compounds bearing a sugar moiety but composed exclusively by the quinic or caffeic acid moiety of CQAs. The presence of isomers was demonstrated by liquid chromatography online coupled to ESI-MS and ESI-MS(n). Pent1-2CQA were identified in coffee samples. These results give evidence for a diversity of chlorogenic acid-arabinose hybrids formed during roasting, opening new perspectives for their identification in melanoidin structures. Copyright © 2015 Elsevier Ltd. All rights reserved.

Theoretical modeling of the electronic structure and exchange interactions in Cu(II)Pc

NASA Astrophysics Data System (ADS)

Wu, Wei; Fisher, A. J.; Harrison, N. M.; Wang, Hai; Wu, Zhenlin; Gardener, Jules; Heutz, Sandrine; Jones, Tim; Aeppli, Gabriel

2012-12-01

We calculate the electronic structure and exchange interactions in a copper(II)phthalocyanine (Cu(II)Pc) crystal as a one-dimensional molecular chain using hybrid exchange density functional theory (DFT). In addition, the intermolecular exchange interactions are also calculated in a molecular dimer using Green's function perturbation theory (GFPT) to illustrate the underlying physics. We find that the exchange interactions depend strongly on the stacking angle, but weakly on the sliding angle (defined in the text). The hybrid DFT calculations also provide an insight into the electronic structure of the Cu(II)Pc molecular chain and demonstrate that on-site electron correlations have a significant effect on the nature of the ground state, the band gap and magnetic excitations. The exchange interactions predicted by our DFT calculations and GFPT calculations agree qualitatively with the recent experimental results on newly found η-Cu(II)Pc and the previous results for the α- and β-phases. This work provides a reliable theoretical basis for the further application of Cu(II)Pc to molecular spintronics and organic-based quantum information processing.

Llamas: Large-area microphone arrays and sensing systems

NASA Astrophysics Data System (ADS)

Sanz-Robinson, Josue

Large-area electronics (LAE) provides a platform to build sensing systems, based on distributing large numbers of densely spaced sensors over a physically-expansive space. Due to their flexible, "wallpaper-like" form factor, these systems can be seamlessly deployed in everyday spaces. They go beyond just supplying sensor readings, but rather they aim to transform the wealth of data from these sensors into actionable inferences about our physical environment. This requires vertically integrated systems that span the entirety of the signal processing chain, including transducers and devices, circuits, and signal processing algorithms. To this end we develop hybrid LAE / CMOS systems, which exploit the complementary strengths of LAE, enabling spatially distributed sensors, and CMOS ICs, providing computational capacity for signal processing. To explore the development of hybrid sensing systems, based on vertical integration across the signal processing chain, we focus on two main drivers: (1) thin-film diodes, and (2) microphone arrays for blind source separation: 1) Thin-film diodes are a key building block for many applications, such as RFID tags or power transfer over non-contact inductive links, which require rectifiers for AC-to-DC conversion. We developed hybrid amorphous / nanocrystalline silicon diodes, which are fabricated at low temperatures (<200 °C) to be compatible with processing on plastic, and have high current densities (5 A/cm2 at 1 V) and high frequency operation (cutoff frequency of 110 MHz). 2) We designed a system for separating the voices of multiple simultaneous speakers, which can ultimately be fed to a voice-command recognition engine for controlling electronic systems. On a device level, we developed flexible PVDF microphones, which were used to create a large-area microphone array. On a circuit level we developed localized a-Si TFT amplifiers, and a custom CMOS IC, for system control, sensor readout and digitization. On a signal processing level we developed an algorithm for blind source separation in a real, reverberant room, based on beamforming and binary masking. It requires no knowledge about the location of the speakers or microphones. Instead, it uses cluster analysis techniques to determine the time delays for beamforming; thus, adapting to the unique acoustic environment of the room.

Change in IgHV Mutational Status of CLL Suggests Origin From Multiple Clones.

PubMed

Osman, Afaf; Gocke, Christopher D; Gladstone, Douglas E

2017-02-01

Fluorescence in situ hybridization and immunoglobulin (Ig) heavy-chain variable-region (IgHV) mutational status are used to predict outcome in chronic lymphocytic leukemia (CLL). Although DNA aberrations change over time, IgHV sequences and mutational status are considered stable. In a retrospective review, 409 CLL patients, between 2008 and 2015, had IgHV analysis: 56 patients had multiple analyses performed. Seven patients' IgHV results changed: 2 from unmutated to mutated and 5 from mutated to unmutated IgHV sequence. Three concurrently changed their variable heavy-chain sequence. Secondary to allelic exclusion, 2 of the new variable heavy chains produced were biologically nonplausible. The existence of these new nonplausible heavy-chain variable regions suggests either the CLL cancer stem-cell maintains the ability to rearrange a previously silenced IgH allele or more likely that the cancer stem-cell produced at least 2 subclones, suggesting that the CLL cancer stem cell exists before the process of allelic exclusion occurs. Copyright © 2016 Elsevier Inc. All rights reserved.

Influence of miscibility phenomenon on crystalline polymorph transition in poly(vinylidene fluoride)/acrylic rubber/clay nanocomposite hybrid.

PubMed

Abolhasani, Mohammad Mahdi; Naebe, Minoo; Jalali-Arani, Azam; Guo, Qipeng

2014-01-01

In this paper, intercalation of nanoclay in the miscible polymer blend of poly(vinylidene fluoride) (PVDF) and acrylic rubber(ACM) was studied. X-ray diffraction was used to investigate the formation of nanoscale polymer blend/clay hybrid. Infrared spectroscopy and X-ray analysis revealed the coexistence of β and γ crystalline forms in PVDF/Clay nanocomposite while α crystalline form was found to be dominant in PVDF/ACM/Clay miscible hybrids. Flory-Huggins interaction parameter (B) was used to further explain the miscibility phenomenon observed. The B parameter was determined by combining the melting point depression and the binary interaction model. The estimated B values for the ternary PVDF/ACM/Clay and PVDF/ACM pairs were all negative, showing both proper intercalation of the polymer melt into the nanoclay galleries and the good miscibility of PVDF and ACM blend. The B value for the PVDF/ACM blend was almost the same as that measured for the PVDF/ACM/Clay hybrid, suggesting that PVDF chains in nanocomposite hybrids interact with ACM chains and that nanoclay in hybrid systems is wrapped by ACM molecules.

Hybrid supply chain model for material requirement planning under financial constraints: A case study

NASA Astrophysics Data System (ADS)

Curci, Vita; Dassisti, Michele; Josefa, Mula Bru; Manuel, Díaz Madroñero

2014-10-01

Supply chain model (SCM) are potentially capable to integrate different aspects in supporting decision making for enterprise management tasks. The aim of the paper is to propose an hybrid mathematical programming model for optimization of production requirements resources planning. The preliminary model was conceived bottom-up from a real industrial case analysed oriented to maximize cash flow. Despite the intense computational effort required to converge to a solution, optimisation done brought good result in solving the objective function.

Ultrasensitive electrochemical detection of DNA based on Zn²⁺ assistant DNA recycling followed with hybridization chain reaction dual amplification.

PubMed

Qian, Yong; Wang, Chunyan; Gao, Fenglei

2015-01-15

A new strategy to combine Zn(2+) assistant DNA recycling followed with hybridization chain reaction dual amplification was designed for highly sensitive electrochemical detection of target DNA. A gold electrode was used to immobilize molecular beacon (MB) as the recognition probe and perform the amplification procedure. In the presence of the target DNA, the hairpin probe 1 was opened, and the DNAzyme was liberated from the caged structure. The activated DNAzyme hybridized with the MB and catalyzed its cleavage in the presence of Zn(2+) cofactor and resulting in a free DNAzyme strand. Finally, each target-induced activated DNAzyme underwent many cycles triggering the cleavage of MB, thus forming numerous MB fragments. The MB fragments triggered the HCR and formed a long double-helix DNA structure. Because both H1 and H2 were labeled by biotin, a lot of SA-ALP was captured on the electrode surface, thus catalyzing a silver deposition process for electrochemical stripping analysis. This novel cascade signal amplification strategy can detect target DNA down to the attomolar level with a dynamic range spanning 6 orders of magnitude. This highly sensitive and specific assay has a great potential to become a promising DNA quantification method in biomedical research and clinical diagnosis. Copyright © 2014 Elsevier B.V. All rights reserved.

Aspergillus oryzae–Saccharomyces cerevisiae Consortium Allows Bio-Hybrid Fuel Cell to Run on Complex Carbohydrates

PubMed Central

Jahnke, Justin P.; Hoyt, Thomas; LeFors, Hannah M.; Sumner, James J.; Mackie, David M.

2016-01-01

Consortia of Aspergillus oryzae and Saccharomyces cerevisiae are examined for their abilities to turn complex carbohydrates into ethanol. To understand the interactions between microorganisms in consortia, Fourier-transform infrared spectroscopy is used to follow the concentrations of various metabolites such as sugars (e.g., glucose, maltose), longer chain carbohydrates, and ethanol to optimize consortia conditions for the production of ethanol. It is shown that with proper design A. oryzae can digest food waste simulants into soluble sugars that S. cerevisiae can ferment into ethanol. Depending on the substrate and conditions used, concentrations of 13% ethanol were achieved in 10 days. It is further shown that a direct alcohol fuel cell (FC) can be coupled with these A. oryzae-enabled S. cerevisiae fermentations using a reverse osmosis membrane. This “bio-hybrid FC” continually extracted ethanol from an ongoing consortium, enhancing ethanol production and allowing the bio-hybrid FC to run for at least one week. Obtained bio-hybrid FC currents were comparable to those from pure ethanol—water mixtures, using the same FC. The A. oryzae–S. cerevisiae consortium, coupled to a bio-hybrid FC, converted food waste simulants into electricity without any pre- or post-processing. PMID:27681904

Aspergillus oryzae-Saccharomyces cerevisiae Consortium Allows Bio-Hybrid Fuel Cell to Run on Complex Carbohydrates.

PubMed

Jahnke, Justin P; Hoyt, Thomas; LeFors, Hannah M; Sumner, James J; Mackie, David M

2016-02-04

Consortia of Aspergillus oryzae and Saccharomyces cerevisiae are examined for their abilities to turn complex carbohydrates into ethanol. To understand the interactions between microorganisms in consortia, Fourier-transform infrared spectroscopy is used to follow the concentrations of various metabolites such as sugars (e.g., glucose, maltose), longer chain carbohydrates, and ethanol to optimize consortia conditions for the production of ethanol. It is shown that with proper design A. oryzae can digest food waste simulants into soluble sugars that S. cerevisiae can ferment into ethanol. Depending on the substrate and conditions used, concentrations of 13% ethanol were achieved in 10 days. It is further shown that a direct alcohol fuel cell (FC) can be coupled with these A. oryzae-enabled S. cerevisiae fermentations using a reverse osmosis membrane. This "bio-hybrid FC" continually extracted ethanol from an ongoing consortium, enhancing ethanol production and allowing the bio-hybrid FC to run for at least one week. Obtained bio-hybrid FC currents were comparable to those from pure ethanol-water mixtures, using the same FC. The A. oryzae-S. cerevisiae consortium, coupled to a bio-hybrid FC, converted food waste simulants into electricity without any pre- or post-processing.

Partial rescue of glomerular laminin alpha5 mutations by wild-type endothelia produce hybrid glomeruli.

PubMed

Abrahamson, Dale R; St John, Patricia L; Isom, Kathryn; Robert, Barry; Miner, Jeffrey H

2007-08-01

Both endothelial cells and podocytes are sources for laminin alpha1 at the inception of glomerulogenesis and then for laminin alpha5 during glomerular maturation. Why glomerular basement membranes (GBM) undergo laminin transitions is unknown, but this may dictate glomerular morphogenesis. In mice that genetically lack laminin alpha5, laminin alpha5beta2gamma1 is not assembled, vascularized glomeruli fail to form, and animals die at midgestation with neural tube closure and placental deficits. It was previously shown that renal cortices of newborn mice contain endothelial progenitors (angioblasts) and that when embryonic day 12 kidneys are transplanted into newborn kidney, hybrid glomeruli (host-derived endothelium and donor-derived podocytes) result. Reasoning that host endothelium may correct the glomerular phenotype that is seen in laminin alpha5 mutants, alpha5 null embryonic day 12 metanephroi were grafted into wild-type newborn kidney. Hybrid glomeruli were identified in grafts by expression of a host-specific LacZ lineage marker. Labeling of glomerular hybrid GBM with chain-specific antibodies showed a markedly stratified distribution of laminins: alpha5 was found only on the inner endothelial half of GBM, whereas alpha1 located to outer layers beneath mutant podocytes. For measurement of the contribution of host endothelium to hybrid GBM, immunofluorescent signals for laminin alpha5 were quantified: Hybrid GBM contained approximately 50% the normal alpha5 complement as wild-type GBM. Electron microscopy of glomerular hybrids showed vascularization, but podocyte foot processes were absent. It was concluded that (1) endothelial and podocyte-derived laminins remain tethered to their cellular origin, (2) developing endothelial cells contribute large amounts of GBM laminins, and (3) podocyte foot process differentiation may require direct exposure to laminin alpha5.

Complex roles of hybrid lipids in the composition, order, and size of lipid membrane domains.

PubMed

Hassan-Zadeh, Ebrahim; Baykal-Caglar, Eda; Alwarawrah, Mohammad; Huang, Juyang

2014-02-11

Hybrid lipids (HL) are phospholipids with one saturated chain and one unsaturated chain. HL are hypothesized to act as linactants (i.e., 2D surfactants) in cell membranes, reducing line tension and creating nanoscopic lipid domains. Here we compare three hybrid lipids of different chain unsaturation (16:0-18:1PC (POPC), 16:0-18:2PC (PLPC), and 16:0-20:4PC (PAPC)) in their abilities to alter the composition, line tension, order, and compactness of lipid domains. We found that the liquid-ordered (Lo) and liquid-disordered (Ld) lipid domains in PAPC/di18:0PC(DSPC)/cholesterol and PLPC/DSPC/cholesterol mixtures are micrometer-sized, and only the POPC/DSPC/cholesterol system has nanoscopic domains. The results indicate that some HLs with polyunsaturated chains are not linactants, and the monounsaturated POPC displays both properties of weak linactants and "Ld-phase" lipids such as di18:1PC (DOPC). The obtained phase boundaries from giant unilamellar vesicles (GUV) show that both POPC and PLPC partition well in the Lo phases. Our MD simulations reveal that these hybrid lipids decrease the order and compactness of Lo domains. Thus, hybrid lipids distinguish themselves from other lipid groups in this combined "partitioning and loosening" ability, which could explain why the Lo domains of GUVs, which often do not contain HL, are more compact than the raft domains in cell membranes. Our line tension measurement and Monte Carlo simulation both show that even the monounsaturated POPC is a weak linactant with only modest ability to occupy domain boundaries and reduce line tension. A more important property of HLs is that they can reduce physical property differences of Lo and Ld bulk domains, which also reduces line tension at domain boundaries.

Enhanced Proton Conductivity of Sulfonated Hybrid Poly(arylene ether ketone) Membranes by Incorporating an Amino-Sulfo Bifunctionalized Metal-Organic Framework for Direct Methanol Fuel Cells.

PubMed

Ru, Chunyu; Li, Zhenhua; Zhao, Chengji; Duan, Yuting; Zhuang, Zhuang; Bu, Fanzhe; Na, Hui

2018-03-07

Novel side-chain-type sulfonated poly(arylene ether ketone) (SNF-PAEK) containing naphthalene and fluorine moieties on the main chain was prepared in this work, and a new amino-sulfo-bifunctionalized metal-organic framework (MNS, short for MIL-101-NH 2 -SO 3 H) was synthesized via a hydrothermal technology and postmodification. Then, MNS was incorporated into a SNF-PAEK matrix as an inorganic nanofiller to prepare a series of organic-inorganic hybrid membranes (MNS@SNF-PAEK-XX). The mechanical property, methanol resistance, electrochemistry, and other properties of MNS@SNF-PAEK-XX hybrid membranes were characterized in detail. We found that the mechanical strength and methanol resistances of these hybrid membranes were improved by the formation of an ionic cross-linking structure between -NH 2 of MNS and -SO 3 H on the side chain of SNF-PAEK. Particularly, the proton conductivity of these hybrid membranes increased obviously after the addition of MNS. MNS@SNF-PAEK-3% exhibited the proton conductivity of 0.192 S·cm -1 , which was much higher than those of the pristine membrane (0.145 S·cm -1 ) and recast Nafion (0.134 S·cm -1 ) at 80 °C. This result indicated that bifunctionalized MNS rearranged the microstructure of hybrid membranes, which could accelerate the transfer of protons. The hybrid membrane (MNS@SNF-PAEK-3%) showed a better direct methanol fuel cell performance with a higher peak power density of 125.7 mW/cm 2 at 80 °C and a higher open-circuit voltage (0.839 V) than the pristine membrane.

Optimizing non-radiative energy transfer in hybrid colloidal-nanocrystal/silicon structures by controlled nanopillar architectures for future photovoltaic cells

NASA Astrophysics Data System (ADS)

Seitz, O.; Caillard, L.; Nguyen, H. M.; Chiles, C.; Chabal, Y. J.; Malko, A. V.

2012-01-01

To optimize colloidal nanocrystals/Si hybrid structures, nanopillars are prepared and organized via microparticle patterning and Si etching. A monolayer of CdSe nanocrystals is then grafted on the passivated oxide-free nanopillar surfaces, functionalized with carboxy-alkyl chain linkers. This process results to a negligible number of non-radiative surface state defects with a tightly controlled separation between the nanocrystals and Si. Steady-state and time-resolved photoluminescence measurements confirm the close-packing nanocrystal arrangement and the dominance of non-radiative energy transfer from nanocrystals to Si. We suggest that radially doped p-n junction devices based on energy transfer offer a viable approach for thin film photovoltaic devices.

Quantum information processing between different atomic ions

NASA Astrophysics Data System (ADS)

Zhang, Xiang; Zheng, Bo; Zhang, Junhua; Um, Mark; An, Shuoming; Zhao, Tianji; Duan, Luming; Kim, Kihwan

2012-06-01

There is increasing interest in utilizing and combining the advantages of different quantum systems. Here, we discuss the experimental generation of entanglement between the quantum states of different atomic ions through the Coulomb interaction at the same linear radio-frequency trap. This scheme would be extended to implement the teleportation of quantum information from one kind of atom to the other. Moreover, the hybrid system of trapped ions is expected to play an essential role in the realization of a large quantum system, where a quantum state of one species is used for quantum operation and that of the other is for the cooling and stabilization of the whole ion chain. Finally, we will report the experimental progress on building the hybrid trapped ion system.

From molecular chemistry to hybrid nanomaterials. Design and functionalization.

PubMed

Mehdi, Ahmad; Reye, Catherine; Corriu, Robert

2011-02-01

This tutorial review reports upon the organisation and functionalization of two families of hybrid organic-inorganic materials. We attempted to show in both cases the best ways permitting the organisation of materials in terms of properties at the nanometric scale. The first family concerns mesoporous hybrid organic-inorganic materials prepared in the presence of a structure-directing agent. We describe the functionalization of the channel pores of ordered mesoporous silica, that of the silica framework, as well as the functionalization of both of them simultaneously. This family is currently one of the best supports for exploring polyfunctional materials, which can provide a route to interactive materials. The second family concerns lamellar hybrid organic-inorganic materials which is a new class of nanostructured materials. These materials were first obtained by self-assembly, as a result of van der Waals interactions of bridged organosilica precursors containing long alkylene chains during the sol-gel process, without any structure directing agent. This methodology has been extended to functional materials. It is also shown that such materials can be obtained from monosilylated precursors.

Effect of swainsonine on the processing of the asparagine-linked carbohydrate chains of alpha 1-antitrypsin in rat hepatocytes. Evidence for the formation of hybrid oligosaccharides.

PubMed

Gross, V; Tran-Thi, T A; Vosbeck, K; Heinrich, P C

1983-03-25

The biosynthesis of the proteinase inhibitor alpha 1-antitrypsin has been studied in rat hepatocyte primary cultures. Newly synthesized alpha 1-antitrypsin was found in hepatocytes as a glycoprotein of an apparent molecular weight of 49,000 carrying oligosaccharide side chains of the high mannose type. In the hepatocyte medium a secreted alpha 1-antitrypsin of an apparent molecular weight of 54,000 could be identified as a glycoprotein with carbohydrate chains of the complex type. Pulse-chase experiments revealed a precursor-product relationship for the two forms of alpha 1-antitrypsin. When the hepatocytes were treated with swainsonine, an intracellular form of alpha 1-antitrypsin with an apparent molecular weight of 49,000 indistinguishable from that of control cells was found. However, the alpha 1-antitrypsin secreted from swainsonine-treated hepatocytes was different from that present in control media. It was characterized by a lower apparent molecular weight (51,000), a higher amount of [3H]mannose incorporation, half as much incorporation of [3H]galactose, and the same amount of [3H]fucose incorporation compared to alpha 1-antitrypsin of control media. In contrast to the 54,000 complex type alpha 1-antitrypsin from control media the 51,000 alpha 1-antitrypsin from the medium of swainsonine-treated cells was found to be susceptible to the action of endoglucosaminidase H, even when fucose was attached to the proximal GlcNAc residue. alpha 1-Antitrypsin secreted from swainsonine-treated cells combines features usually associated with either high mannose or complex type oligosaccharides and therefore represents a hybrid structure. In spite of its effect on the carbohydrate part of alpha 1-antitrypsin swainsonine did not impair the secretion of the incompletely processed glycoprotein.

Modelling Lean and Green Supply Chain

NASA Astrophysics Data System (ADS)

Duarte, Susana Carla Vieira Lino Medina

The success of an organization depends on the effective control of its supply chain. It is important to recognize new opportunities for organization and its supply chain. In the last few years the approach to lean, agile, resilient and green supply chain paradigms has been addressed in the scientific literature. Research in this field shows that the integration of these concepts revealed some contradictions among so many paradigms. This thesis is mainly focused on the lean and green approaches. Thirteen different management frameworks, embodied in awards, standards and tools were studied to understand if they could contribute for the modelling process of a lean and green approach. The study reveals a number of categories that are common in most management frameworks, providing adequate conditions for a lean and green supply chain transformation. A conceptual framework for the evaluation of a lean and green organization`s supply chain was proposed. The framework considers six key criteria, namely, leadership, people, strategic planning, stakeholders, processes and results. It was proposed an assessment method considering a criteria score for each criterion. The purpose is to understand how lean and green supply chain can be compatible, using principles, practices, techniques or tools (i.e. elements) that support both, a lean and a green approach, in all key criteria. A case study in the automotive upstream supply chain was performed to understand more deeply if the elements proposed for the conceptual framework could be implemented in a real-scenario. Based on the conceptual framework and the case study, a roadmap to achieve a lean-green transformation is presented. The proposed roadmap revealed its contribution to the understanding on how and when an organization`s supply chain should apply the lean and green elements. This study is relevant to practice, as it may assist managers in the adoption of a lean and green supply chain approach, giving insights for the implementation of a hybrid supply chain.

Influence of Miscibility Phenomenon on Crystalline Polymorph Transition in Poly(Vinylidene Fluoride)/Acrylic Rubber/Clay Nanocomposite Hybrid

PubMed Central

Abolhasani, Mohammad Mahdi; Naebe, Minoo; Jalali-Arani, Azam; Guo, Qipeng

2014-01-01

In this paper, intercalation of nanoclay in the miscible polymer blend of poly(vinylidene fluoride) (PVDF) and acrylic rubber(ACM) was studied. X-ray diffraction was used to investigate the formation of nanoscale polymer blend/clay hybrid. Infrared spectroscopy and X-ray analysis revealed the coexistence of β and γ crystalline forms in PVDF/Clay nanocomposite while α crystalline form was found to be dominant in PVDF/ACM/Clay miscible hybrids. Flory-Huggins interaction parameter (B) was used to further explain the miscibility phenomenon observed. The B parameter was determined by combining the melting point depression and the binary interaction model. The estimated B values for the ternary PVDF/ACM/Clay and PVDF/ACM pairs were all negative, showing both proper intercalation of the polymer melt into the nanoclay galleries and the good miscibility of PVDF and ACM blend. The B value for the PVDF/ACM blend was almost the same as that measured for the PVDF/ACM/Clay hybrid, suggesting that PVDF chains in nanocomposite hybrids interact with ACM chains and that nanoclay in hybrid systems is wrapped by ACM molecules. PMID:24551141

Hybrid polyketide synthases

DOEpatents

Fortman, Jeffrey L.; Hagen, Andrew; Katz, Leonard; Keasling, Jay D.; Poust, Sean; Zhang, Jingwei; Zotchev, Sergey

2016-05-10

The present invention provides for a polyketide synthase (PKS) capable of synthesizing an even-chain or odd-chain diacid or lactam or diamine. The present invention also provides for a host cell comprising the PKS and when cultured produces the even-chain diacid, odd-chain diacid, or KAPA. The present invention also provides for a host cell comprising the PKS capable of synthesizing a pimelic acid or KAPA, and when cultured produces biotin.

Structure of pleiotrophin- and hepatocyte growth factor-binding sulfated hexasaccharide determined by biochemical and computational approaches.

PubMed

Li, Fuchuan; Nandini, Chilkunda D; Hattori, Tomohide; Bao, Xingfeng; Murayama, Daisuke; Nakamura, Toshikazu; Fukushima, Nobuhiro; Sugahara, Kazuyuki

2010-09-03

Endogenous pleiotrophin and hepatocyte growth factor (HGF) mediate the neurite outgrowth-promoting activity of chondroitin sulfate (CS)/dermatan sulfate (DS) hybrid chains isolated from embryonic pig brain. CS/DS hybrid chains isolated from shark skin have a different disaccharide composition, but also display these activities. In this study, pleiotrophin- and HGF-binding domains in shark skin CS/DS were investigated. A high affinity CS/DS fraction was isolated using a pleiotrophin-immobilized column. It showed marked neurite outgrowth-promoting activity and strong inhibitory activity against the binding of pleiotrophin to immobilized CS/DS chains from embryonic pig brain. The inhibitory activity was abolished by chondroitinase ABC or B, and partially reduced by chondroitinase AC-I. A pentasulfated hexasaccharide with a novel structure was isolated from the chondroitinase AC-I digest using pleiotrophin affinity and anion exchange chromatographies. It displayed a potent inhibitory effect on the binding of HGF to immobilized shark skin CS/DS chains, suggesting that the pleiotrophin- and HGF-binding domains at least partially overlap in the CS/DS chains involved in the neuritogenic activity. Computational chemistry using molecular modeling and calculations of the electrostatic potential of the hexasaccharide and two pleiotrophin-binding octasaccharides previously isolated from CS/DS hybrid chains of embryonic pig brain identified an electronegative zone potentially involved in the molecular recognition of the oligosaccharides by pleiotrophin. Homology modeling of pleiotrophin based on a related midkine protein structure predicted the binding pocket of pleiotrophin for the oligosaccharides and provided new insights into the molecular mechanism of the interactions between the oligosaccharides and pleiotrophin.

Thermodynamic framework for information in nanoscale systems with memory

NASA Astrophysics Data System (ADS)

Arias-Gonzalez, J. Ricardo

2017-11-01

Information is represented by linear strings of symbols with memory that carry errors as a result of their stochastic nature. Proofreading and edition are assumed to improve certainty although such processes may not be effective. Here, we develop a thermodynamic theory for material chains made up of nanoscopic subunits with symbolic meaning in the presence of memory. This framework is based on the characterization of single sequences of symbols constructed under a protocol and is used to derive the behavior of ensembles of sequences similarly constructed. We then analyze the role of proofreading and edition in the presence of memory finding conditions to make revision an effective process, namely, to decrease the entropy of the chain. Finally, we apply our formalism to DNA replication and RNA transcription finding that Watson and Crick hybridization energies with which nucleotides are branched to the template strand during the copying process are optimal to regulate the fidelity in proofreading. These results are important in applications of information theory to a variety of solid-state physical systems and other biomolecular processes.

Thermodynamic framework for information in nanoscale systems with memory.

PubMed

Arias-Gonzalez, J Ricardo

2017-11-28

Information is represented by linear strings of symbols with memory that carry errors as a result of their stochastic nature. Proofreading and edition are assumed to improve certainty although such processes may not be effective. Here, we develop a thermodynamic theory for material chains made up of nanoscopic subunits with symbolic meaning in the presence of memory. This framework is based on the characterization of single sequences of symbols constructed under a protocol and is used to derive the behavior of ensembles of sequences similarly constructed. We then analyze the role of proofreading and edition in the presence of memory finding conditions to make revision an effective process, namely, to decrease the entropy of the chain. Finally, we apply our formalism to DNA replication and RNA transcription finding that Watson and Crick hybridization energies with which nucleotides are branched to the template strand during the copying process are optimal to regulate the fidelity in proofreading. These results are important in applications of information theory to a variety of solid-state physical systems and other biomolecular processes.

A Model of Risk Analysis in Analytical Methodology for Biopharmaceutical Quality Control.

PubMed

Andrade, Cleyton Lage; Herrera, Miguel Angel De La O; Lemes, Elezer Monte Blanco

2018-01-01

One key quality control parameter for biopharmaceutical products is the analysis of residual cellular DNA. To determine small amounts of DNA (around 100 pg) that may be in a biologically derived drug substance, an analytical method should be sensitive, robust, reliable, and accurate. In principle, three techniques have the ability to measure residual cellular DNA: radioactive dot-blot, a type of hybridization; threshold analysis; and quantitative polymerase chain reaction. Quality risk management is a systematic process for evaluating, controlling, and reporting of risks that may affects method capabilities and supports a scientific and practical approach to decision making. This paper evaluates, by quality risk management, an alternative approach to assessing the performance risks associated with quality control methods used with biopharmaceuticals, using the tool hazard analysis and critical control points. This tool provides the possibility to find the steps in an analytical procedure with higher impact on method performance. By applying these principles to DNA analysis methods, we conclude that the radioactive dot-blot assay has the largest number of critical control points, followed by quantitative polymerase chain reaction, and threshold analysis. From the analysis of hazards (i.e., points of method failure) and the associated method procedure critical control points, we conclude that the analytical methodology with the lowest risk for performance failure for residual cellular DNA testing is quantitative polymerase chain reaction. LAY ABSTRACT: In order to mitigate the risk of adverse events by residual cellular DNA that is not completely cleared from downstream production processes, regulatory agencies have required the industry to guarantee a very low level of DNA in biologically derived pharmaceutical products. The technique historically used was radioactive blot hybridization. However, the technique is a challenging method to implement in a quality control laboratory: It is laborious, time consuming, semi-quantitative, and requires a radioisotope. Along with dot-blot hybridization, two alternatives techniques were evaluated: threshold analysis and quantitative polymerase chain reaction. Quality risk management tools were applied to compare the techniques, taking into account the uncertainties, the possibility of circumstances or future events, and their effects upon method performance. By illustrating the application of these tools with DNA methods, we provide an example of how they can be used to support a scientific and practical approach to decision making and can assess and manage method performance risk using such tools. This paper discusses, considering the principles of quality risk management, an additional approach to the development and selection of analytical quality control methods using the risk analysis tool hazard analysis and critical control points. This tool provides the possibility to find the method procedural steps with higher impact on method reliability (called critical control points). Our model concluded that the radioactive dot-blot assay has the larger number of critical control points, followed by quantitative polymerase chain reaction and threshold analysis. Quantitative polymerase chain reaction is shown to be the better alternative analytical methodology in residual cellular DNA analysis. © PDA, Inc. 2018.

Hybrid and Nonhybrid Lipids Exert Common Effects on Membrane Raft Size and Morphology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heberle, Frederick A; Doktorova, Milka; Goh, Shih Lin

2013-01-01

Nanometer-scale domains in cholesterolrich model membranes emulate lipid rafts in cell plasma membranes (PMs). The physicochemical mechanisms that maintain a finite, small domain size are, however, not well understood. A special role has been postulated for chainasymmetric or hybrid lipids having a saturated sn-1 chain and an unsaturated sn-2 chain. Hybrid lipids generate nanodomains in some model membranes and are also abundant in the PM. It was proposed that they align in a preferred orientation at the boundary of ordered and disordered phases, lowering the interfacial energy and thus reducing domain size. We used small-angle neutron scattering and fluorescence techniquesmore » to detect nanoscopic and modulated liquid phase domains in a mixture composed entirely of nonhybrid lipids and cholesterol. Our results are indistinguishable from those obtained previously for mixtures containing hybrid lipids, conclusively showing that hybrid lipids are not required for the formation of nanoscopic liquid domains and strongly implying a common mechanism for the overall control of raft size and morphology. We discuss implications of these findings for theoretical descriptions of nanodomains.« less

The self-assembly structure and the CO2-philicity of a hybrid surfactant in supercritical CO2: effects of hydrocarbon chain length.

PubMed

Wang, Muhan; Fang, Timing; Wang, Pan; Tang, Xinpeng; Sun, Baojiang; Zhang, Jun; Liu, Bing

2016-10-04

Hybrid surfactants containing both fluorocarbon (FC) and hydrocarbon (HC) chains, as effective CO 2 -philic surfactants, could improve the solubility of polar substances in supercritical CO 2 . Varying the length of the HC of hybrid surfactants is an effective way to improve the CO 2 -philicity. In this paper, we have investigated the effects of the HC length on the self-assembly process and the CO 2 -philicity of hybrid surfactants (F7Hn, n = 1, 4, 7 and 10) in water/CO 2 mixtures using molecular dynamics simulations. It is found that the self-assembly time of F7Hn exhibits a maximum when the length of the HC is equal to that of the FC (F7H7). In this case, the investigation of H-bonds between the water core and CO 2 phase shows that F7H7 has the strongest CO 2 -philicity because it has the best ability to separate water and CO 2 . To explain the origin of the differences in separation ability, the analysis of the structures of the reverse micelles shows that there are two competing mechanisms with a shortening HC. Firstly, the volume of F7Hn is reduced, which thus decreases the separation ability. Moreover, this also leads to the curved conformation of the FC. As a result, the separation ability is enhanced. These two mechanisms are balanced in F7H7, which has the best ability to separate water and CO 2 . Our simulation results demonstrate that the increased volume and the curved conformation of the hybrid surfactant tail could enhance the CO 2 -philicity in F7Hn surfactants. It is expected that this work will provide valuable information for the design of CO 2 -philic surfactants.

Hybrid pathwise sensitivity methods for discrete stochastic models of chemical reaction systems.

PubMed

Wolf, Elizabeth Skubak; Anderson, David F

2015-01-21

Stochastic models are often used to help understand the behavior of intracellular biochemical processes. The most common such models are continuous time Markov chains (CTMCs). Parametric sensitivities, which are derivatives of expectations of model output quantities with respect to model parameters, are useful in this setting for a variety of applications. In this paper, we introduce a class of hybrid pathwise differentiation methods for the numerical estimation of parametric sensitivities. The new hybrid methods combine elements from the three main classes of procedures for sensitivity estimation and have a number of desirable qualities. First, the new methods are unbiased for a broad class of problems. Second, the methods are applicable to nearly any physically relevant biochemical CTMC model. Third, and as we demonstrate on several numerical examples, the new methods are quite efficient, particularly if one wishes to estimate the full gradient of parametric sensitivities. The methods are rather intuitive and utilize the multilevel Monte Carlo philosophy of splitting an expectation into separate parts and handling each in an efficient manner.

Identification of human rotavirus serotype by hybridization to polymerase chain reaction-generated probes derived from a hyperdivergent region of the gene encoding outer capsid protein VP7

DOE Office of Scientific and Technical Information (OSTI.GOV)

Flores, J.; Sears, J.; Schael, I.P.

1990-08-01

We have synthesized {sup 32}P-labeled hybridization probes from a hyperdivergent region (nucleotides 51 to 392) of the rotavirus gene encoding the VP7 glycoprotein by using the polymerase chain reaction method. Both RNA (after an initial reverse transcription step) and cloned cDNA from human rotavirus serotypes 1 through 4 could be used as templates to amplify this region. High-stringency hybridization of each of the four probes to rotavirus RNAs dotted on nylon membranes allowed the specific detection of corresponding sequences and thus permitted identification of the serotype of the strains dotted. The procedure was useful when applied to rotaviruses isolated frommore » field studies.« less

Folding dynamics of linear emulsion polymers into 3D architectures

NASA Astrophysics Data System (ADS)

McMullen, Angus; Bargteil, Dylan; Brujic, Jasna

Colloidal polymers have been limited to inflexible, solid colloids. Here we show that the fluidity of emulsion droplets allows for the self-assembly of flexible droplet chains, which can subsequently be folded into 3D structures via secondary interactions. We achieve this using DNA-guided interactions, to initially form the chain, and then program its folding pathways. When two emulsion droplets labeled with complementary DNA meet, the balance of hybridization energy and droplet deformation yields an equilibrium patch size. Therefore, the concentration of DNA on the surface determines the number of droplet-droplet bonds in the assembly. We find that 96 % of bound droplets successfully self-assemble into chains. Droplet binding is a stochastic process, following a Poisson distribution of lengths. Since the fluid droplets can rearrange, we compare the dynamics of emulsion chains to that of polymers. We also trigger secondary interactions along the chain, causing the formation of specific loops or compact clusters. This approach will allow us to fold our emulsion polymers into a wide array of soft structures, giving us a powerful biomimetic colloidal system to investigate protein folding on the mesoscopic scale. This work was supported by the NSF MRSEC Program (DMR-0820341).

Magnetic properties of hybrid elastomers with magnetically hard fillers: rotation of particles

NASA Astrophysics Data System (ADS)

Stepanov, G. V.; Borin, D. Yu; Bakhtiiarov, A. V.; Storozhenko, P. A.

2017-03-01

Hybrid magnetic elastomers belonging to the family of magnetorheological elastomers contain magnetically hard components and are of the utmost interest for the development of semiactive and active damping devices as well as actuators and sensors. The processes of magnetizing of such elastomers are accompanied by structural rearrangements inside the material. When magnetized, the elastomer gains its own magnetic moment resulting in changes of its magneto-mechanical properties, which remain permanent, even in the absence of external magnetic fields. Influenced by the magnetic field, magnetized particles move inside the matrix forming chain-like structures. In addition, the magnetically hard particles can rotate to align their magnetic moments with the new direction of the external field. Such an elastomer cannot be demagnetized by the application of a reverse field.

Memory effects in annealed hybrid gold nanoparticles/block copolymer bilayers

PubMed Central

2011-01-01

We report on the use of the self-organization process of sputtered gold nanoparticles on a self-assembled block copolymer film deposited by horizontal precipitation Langmuir-Blodgett (HP-LB) method. The morphology and the phase-separation of a film of poly-n-butylacrylate-block-polyacrylic acid (PnBuA-b-PAA) were studied at the nanometric scale by using atomic force microscopy (AFM) and Time of Flight Secondary Ion Mass Spectrometry (TOF-SIMS). The templating capability of the PnBuA-b-PAA phase-separated film was studied by sputtering gold nanoparticles (NPs), forming a film of nanometric thickness. The effect of the polymer chain mobility onto the organization of gold nanoparticle layer was assessed by heating the obtained hybrid PnBuA-b-PAA/Au NPs bilayer at T >Tg. The nanoparticles' distribution onto the different copolymer domains was found strongly affected by the annealing treatment, showing a peculiar memory effect, which modifies the AFM phase response of the Au NPs layer onto the polar domains, without affecting their surfacial composition. The effect is discussed in terms of the peculiar morphological features induced by enhanced mobility of polymer chains on the Au NPs layer. PMID:21711674

Chromosome localization of human genes for clathrin adaptor polypeptides AP2{beta} and AP50 and the clathrin-binding protein, VCP

DOE Office of Scientific and Technical Information (OSTI.GOV)

Druck, T.; Gu, Y.; Prabhala, G.

1995-11-01

Clathrin-coated vesicles, involved in endocytosis and Golgi processing, have a surface lattice containing clathrin triskelia and stoichiometric amounts of additional components termed {open_quotes}assembly proteins,{close_quotes} or APs. The AP form at the plasma membrane, AP2, is composed of two large subunits of 100-115 kDa, denoted AP2{alpha} and AP2{beta}, a medium chain of 50 kDa, designated AP50, and a small chain. We have determined human chromosomal locations of genes for a large AP2{beta} (CLAPB1) and a medium (CLAPM1) AP subunit and of a novel clathrin-binding protein, VCP, that binds clathrin simultaneously with A1`s. Chromosomal in situ hybridization of a human genomic clonemore » demonstrated that the CLAPM1 gene mapped to chromosome region 3q28. The gene for the CLAPB1 large subunit was mapped to 17q11.2-q12 by PCR amplification of an AP2{beta} fragment from a panel of rodent-human hybrid DNAs. To map the human VCP sequence, a human-specific probe was made by RT-PCR of human mRNA using oligonucleotide primers from conserved regions of the porcine sequence. The amplified human fragment served as probe on Southern blots of hybrid DNAs to determine that the human VCP locus maps to chromosome region 9pter-q34. 13 refs., 2 figs.« less

Ultrasensitive electrochemical detection of avian influenza A (H7N9) virus DNA based on isothermal exponential amplification coupled with hybridization chain reaction of DNAzyme nanowires.

PubMed

Yu, Yanyan; Chen, Zuanguang; Jian, Wensi; Sun, Duanping; Zhang, Beibei; Li, Xinchun; Yao, Meicun

2015-02-15

In this work, a simple and label-free electrochemical biosensor with duel amplification strategy was developed for DNA detection based on isothermal exponential amplification (EXPAR) coupled with hybridization chain reaction (HCR) of DNAzymes nanowires. Through rational design, neither the primer nor the DNAzymes containing molecular beacons (MBs) could react with the duplex probe which were fixed on the electrode surface. Once challenged with target, the duplex probe cleaved and triggered the EXPAR mediated target recycle and regeneration circles as well as the HCR process. As a result, a greater amount of targets were generated to cleave the duplex probes. Subsequently, the nanowires consisting of the G-quadruplex units were self-assembled through hybridization with the strand fixed on the electrode surface. In the presence of hemin, the resulting catalytic G-quadruplex-hemin HRP-mimicking DNAzymes were formed. Electrochemical signals can be obtained by measuring the increase in reduction current of oxidized 3.3',5.5'-tetramethylbenzidine sulfate (TMB), which was generated by DNAzyme in the presence of H2O2. This method exhibited ultrahigh sensitivity towards avian influenza A (H7N9) virus DNA sequence with detection limits of 9.4 fM and a detection range of 4 orders of magnitude. The biosensor was also capable of discriminating single-nucleotide difference among concomitant DNA sequences and performed well in spiked cell lysates. Copyright © 2014 Elsevier B.V. All rights reserved.

Ultra-High Speed Analog-to-Digital Converters in 14nm FinFET Process and Usage in Digital and Hybrid Phased Array Systems

DTIC Science & Technology

2017-03-01

enable extremely high dynamic range receivers to be realized in very compact dimensions. This paper provides information on the performance...this is the “Butler Matrix” topology in which N beam angular positions into N matrix ports. With this topology , by selecting a particular...waveguide port to connect a receiver or transmitter chain to a particular beam direction would be enabled. RF phase shifters and amplitude weighting

Inorganic–organic hybrids presenting high basic center content: SBA-15 incorporation, toxic metals sorption and energetic behavior

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oliveira, Fernando J.V.E.; Melo, Maurício A.; Airoldi, Claudio, E-mail: airoldi@iqm.unicamp.br

2013-03-15

Highlights: ► Mesoporous SBA-15 silicas were organofunctionalized with new silylant agents. ► Thiocarbamate was used to enhance the silylating agent chains and basic centers. ► The synthesized pendant chains contain nitrogen and sulfur basic centers. ► The new hybrids sorb toxic cations from aqueous solutions with high efficiency. ► The thermodynamic data demonstrated favorable cation/basic center interactions. - Abstract: Mesoporous SBA-15 samples were organofunctionalized with mono, di- and tri-aminosilanes that previously reacted with thiocarbamide to enhance the organic chains and attach nitrogen and sulfur basic centers to the surface of the solids. These new organosilanes were synthesized through a non-solventmore » approach to reduce both cost and hazardous wastes. The high affinities for both hard and soft Lewis acids due to the combination of nitrogen and sulfur atoms attached to the same pendant chain enabled favorable sorption capacities for Cu{sup 2+}, Cd{sup 2+} and Pb{sup 2+} cations, with maximum capacities of 1.90, 3.48 and 5.30 mmol g{sup −1}, respectively, for the most efficient mesoporous silica. Microcalorimetric investigations allowed the calculation of the thermodynamic data at the solid/liquid interface. All Gibbs energy are negative as expected for spontaneous cation/basic center interactions and the positive entropic values from 49 ± 3 to 108 ± 5 J K{sup −1} mol{sup −1}, also reinforced this favorable interactive process in heterogeneous system. The designed organosilanes covalently bonded to the inorganic siliceous skeleton can be suggested as new materials for toxic metal removal from a wastewater with high efficiency.« less

Use of Hybridization Chain Reaction-Fluorescent In Situ Hybridization To Track Gene Expression by Both Partners during Initiation of Symbiosis.

PubMed

Nikolakakis, K; Lehnert, E; McFall-Ngai, M J; Ruby, E G

2015-07-01

The establishment of a productive symbiosis between Euprymna scolopes, the Hawaiian bobtail squid, and its luminous bacterial symbiont, Vibrio fischeri, is mediated by transcriptional changes in both partners. A key challenge to unraveling the steps required to successfully initiate this and many other symbiotic associations is characterization of the timing and location of these changes. We report on the adaptation of hybridization chain reaction-fluorescent in situ hybridization (HCR-FISH) to simultaneously probe the spatiotemporal regulation of targeted genes in both E. scolopes and V. fischeri. This method revealed localized, transcriptionally coregulated epithelial cells within the light organ that responded directly to the presence of bacterial cells while, at the same time, provided a sensitive means to directly show regulated gene expression within the symbiont population. Thus, HCR-FISH provides a new approach for characterizing habitat transition in bacteria and for discovering host tissue responses to colonization. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Fiber transformation and replacement in low-frequency stimulated rabbit fast-twitch muscles.

PubMed

Schuler, M; Pette, D

1996-08-01

The fast-to-slow conversion of rabbit skeletal muscles by chronic low-frequency (10 Hz, 12 h daily) stimulation involves (1) sequential fast-to-slow fiber-type transitions in the order of type IID-->type IIA-->type I, and (2) the replacement of deteriorating fast-twitch glycolytic fibers by new fibers derived from satellite cells and myotubes. These two processes were analyzed in 30- and 60-day stimulated extensor digitorum longus and tibialis anterior muscles. Fast-to-slow transforming fibers were identified by myofibrillar actomyosin histochemistry as type C fibers and immunohistochemically by their reaction with monoclonal antibodies specific to slow and fast myosin heavy chain isoforms. In situ hybridization of mRNA specific to the myosin heavy chain I isoform identified all fibers expressing slow myosin, i.e., type I and C fibers. The fraction of transforming fibers ranged between 35% and 50% in 30-day stimulated muscles. The percentage of type I fibers (20%) was threefold elevated in extensor digitorum longus muscle, but unaltered (3.5%) in tibialis anterior muscle, suggesting that fast-to-slow fiber conversion was more advanced in the former than in the latter. Fiber replacement was indicated by the finding that the fiber populations of both muscles contained 15% myotubes or small fibers with central nuclei. In situ hybridization revealed that myotubes and small regenerating fibers uniformly expressed myosin heavy chain I mRNA. Similarly, high percentages of slow-myosin-expressing myotubes and small fibers were found in 60-day stimulated muscles.

Using dual-polarization interferometry to study surface-initiated DNA hybridization chain reactions in real time.

PubMed

Huang, Fujian; Xu, Pingping; Liang, Haojun

2014-01-15

In this study we used dual-polarization interferometry to investigate DNA hybridization chain reactions (HCRs) at solid-liquid interfaces. We monitored the effects of variations in mass, thickness, and density of the immobilized initiator on the subsequent HCRs at various salt concentrations. At low salt concentrations, the single-stranded DNA (ssDNA) initiator was attached uniformly to the chip surface. At high salt concentrations, it lay on the surface at the onset of the immobilization process, but the approaching ssDNA forced the pre-immobilized ssDNA strands to extend into solution as a result of increased electrostatic repulsion between the pre-adsorbed and approaching ssDNA chains. Injection of a mixture of H1 and H2 increased the mass and thickness of the films initially, but thereafter the thickness decreased. These changes indicate that the long double-stranded DNA that formed lay on the surface, rather than extended into the solution, thereby suppressing the subsequent initiation activity of the released single-strand parts of H1 and H2. Increasing the salt concentration increased the HCR efficiency and reaction rate. The HCR efficiency of the initiator ssDNA immobilized on its 5' end was higher than that immobilized on its 3' end, suggesting that the released single-strand parts of H1 and H2 close to the chip surface decreased the initiation activity relative to those of the ones extending into solution. © 2013 Elsevier B.V. All rights reserved.

Polymer-based microfluidic chips for isothermal amplification of nucleic acids

NASA Astrophysics Data System (ADS)

Posmitnaya, Y. S.; Rudnitskaya, G. E.; Tupik, A. N.; Lukashenko, T. A.; Bukatin, A. C.; Evstrapov, A. A.

2017-11-01

Creation of low-cost compact devices based on microfluidic platforms for biological and medical research depends on the degree of development and enhancement of prototyping technologies. Two designs of polymer and hybrid microfluidic devices fabricated by soft lithography and intended for isothermal amplification and polymerase chain reaction are presented in this paper. The digital helicase-dependent isothermal amplification was tested in the device containing a droplet generator. Polymerase chain reaction was carried out in the hybrid microfluidic device having ten reaction chambers. A synthesized cDNA fragment of GAPDH housekeeping gene was used as a target.

Functional PMS2 Hybrid Alleles Containing a Pseudogene-Specific Missense Variant Trace Back to a Single Ancient Intrachromosomal Recombination Event

PubMed Central

Ganster, Christina; Wernstedt, Annekatrin; Kehrer-Sawatzki, Hildegard; Messiaen, Ludwine; Schmidt, Konrad; Rahner, Nils; Heinimann, Karl; Fonatsch, Christa; Zschocke, Johannes; Wimmer, Katharina

2012-01-01

Sequence exchange between PMS2 and its pseudogene PMS2CL, embedded in an inverted duplication on chromosome 7p22, has been reported to be an ongoing process that leads to functional PMS2 hybrid alleles containing PMS2- and PMS2CL-specific sequence variants at the 5′-and the 3′-end, respectively. The frequency of PMS2 hybrid alleles, their biological significance, and the mechanisms underlying their formation are largely unknown. Here we show that overall hybrid alleles account for one-third of 384 PMS2 alleles analyzed in individuals of different ethnic backgrounds. Depending on the population, 14–60% of hybrid alleles carry PMS2CL-specific sequences in exons 13–15, the remainder only in exon 15. We show that exons 13–15 hybrid alleles, named H1 hybrid alleles, constitute different haplotypes but trace back to a single ancient intrachromosomal recombination event with crossover. Taking advantage of an ancestral sequence variant specific for all H1 alleles we developed a simple gDNA-based polymerase chain reaction (PCR) assay that can be used to identify H1-allele carriers with high sensitivity and specificity (100 and 99%, respectively). Because H1 hybrid alleles harbor missense variant p.N775S of so far unknown functional significance, we assessed the H1-carrier frequency in 164 colorectal cancer patients. So far, we found no indication that the variant plays a major role with regard to cancer susceptibility. PMID:20186689

Functional PMS2 hybrid alleles containing a pseudogene-specific missense variant trace back to a single ancient intrachromosomal recombination event.

PubMed

Ganster, Christina; Wernstedt, Annekatrin; Kehrer-Sawatzki, Hildegard; Messiaen, Ludwine; Schmidt, Konrad; Rahner, Nils; Heinimann, Karl; Fonatsch, Christa; Zschocke, Johannes; Wimmer, Katharina

2010-05-01

Sequence exchange between PMS2 and its pseudogene PMS2CL, embedded in an inverted duplication on chromosome 7p22, has been reported to be an ongoing process that leads to functional PMS2 hybrid alleles containing PMS2- and PMS2CL-specific sequence variants at the 5'-and the 3'-end, respectively. The frequency of PMS2 hybrid alleles, their biological significance, and the mechanisms underlying their formation are largely unknown. Here we show that overall hybrid alleles account for one-third of 384 PMS2 alleles analyzed in individuals of different ethnic backgrounds. Depending on the population, 14-60% of hybrid alleles carry PMS2CL-specific sequences in exons 13-15, the remainder only in exon 15. We show that exons 13-15 hybrid alleles, named H1 hybrid alleles, constitute different haplotypes but trace back to a single ancient intrachromosomal recombination event with crossover. Taking advantage of an ancestral sequence variant specific for all H1 alleles we developed a simple gDNA-based polymerase chain reaction (PCR) assay that can be used to identify H1-allele carriers with high sensitivity and specificity (100 and 99%, respectively). Because H1 hybrid alleles harbor missense variant p.N775S of so far unknown functional significance, we assessed the H1-carrier frequency in 164 colorectal cancer patients. So far, we found no indication that the variant plays a major role with regard to cancer susceptibility. (c) 2010 Wiley-Liss, Inc.

Added value of lignin as lignin-based hybrid polyurethane for a compatibilizing agent

NASA Astrophysics Data System (ADS)

Ilmiati, S.; Haris Mustafa, J.; Yaumal, A.; Hanum, F.; Chalid, M.

2017-07-01

As biomass-based material, lignin contains abundant hydroxyl groups promising to be used as chain extender in building hybrid polyurethanes. Consisting of polyehtylene glycol (PEG) content as hydrophobic part and lignin as hydrophilic part, the hybrid PU is expected to be as a novel compatibilizing agent in new materials production such as polyblends and composites. The hybrid PU was synthesized via two reaction stages, viz. pre-polyurethanization through reacting 4,4'-Methylenebis (Cyclohexyl Isocyanate) (HMDI) and PEG as polyol, and chain extention through adding lignin in the pre-polyurethanization system. The composition effect of lignin in hybrid PU syntehsis, to chemical structure corelated to hydrophobic to hydrophilic ratio, thermal and morphological properties, was evaluated by measuring NMR, FTIR, DSC, TGA and FE-SEM. The experiments showed that addition of lignin was able to extend the pre-polyurethane into hybrid polyurethane and to increase the lignin/polyol ratio in the hybrid polyurethanes, which were indicated by NMR and FTIR Analysis. And change of the ratio lead to increase the glass transition from 60.9 until 62.1°C and degradation temperature from 413.9 until 416.0°C. Observation of the morphology implied that addition of lignin gave more agglomerations. A Further investigation for this characterization study should be focused on a feasibility for this modified lignin as a novel compatibilizing agent.

Effect of Concentration on the Formation of Molecular Hybrids from T4 DNA

PubMed Central

Kozinski, Andrzej W.; Beer, Michael

1962-01-01

When the thymine of T4 DNA is replaced by 5-BU the melting temperature of T4 DNA is increased from about 83° to about 93°C. Heating and slow cooling of T4 DNA at concentrations of about 30 μg/ml leads to aggregates which consist of several polynucleotide chains which appear in the electron microscope as a branched structure. The aggregates have regions which are true hybrids. When the concentration of T4 DNA is lowered to less than 1 μg/ml the products of hybridization are not aggregates but have the morphology of native DNA molecules and the density labels are distributed as expected from the fusing of two chains of approximately equal length. ImagesFigure 6Figure 7Figure 8 PMID:14459098

Development of an optimized protocol for the detection of classical swine fever virus in formalin-fixed, paraffin-embedded tissues by seminested reverse transcription-polymerase chain reaction and comparison with in situ hybridization.

PubMed

Ha, S-K; Choi, C; Chae, C

2004-10-01

An optimized protocol was developed for the detection of classical swine fever virus (CSFV) in formalin-fixed, paraffin-embedded tissues obtained from experimentally and naturally infected pigs by seminested reverse transcription-polymerase chain reaction (RT-PCR). The results for seminested RT-PCR were compared with those determined by in situ hybridization. The results obtained show that the use of deparaffinization with xylene, digestion with proteinase K, extraction with Trizol LS, followed by seminested RT-PCR is a reliable detection method. An increase in sensitivity was observed as amplicon size decreased. The highest sensitivity for RT-PCR on formalin-fixed, paraffin-embedded tissues RNA was obtained with amplicon sizes less than approximately 200 base pairs. An hybridization signal for CSFV was detected in lymph nodes from 12 experimentally and 12 naturally infected pigs. The sensitivity of seminested RT-PCR compared with in situ hybridization was 100% for CSFV. When only formalin-fixed tissues are available, seminested RT-PCR and in situ hybridization would be useful diagnostic methods for the detection of CSFV nucleic acid.

Hyperbranched Hybridization Chain Reaction for Triggered Signal Amplification and Concatenated Logic Circuits.

PubMed

Bi, Sai; Chen, Min; Jia, Xiaoqiang; Dong, Ying; Wang, Zonghua

2015-07-06

A hyper-branched hybridization chain reaction (HB-HCR) is presented herein, which consists of only six species that can metastably coexist until the introduction of an initiator DNA to trigger a cascade of hybridization events, leading to the self-sustained assembly of hyper-branched and nicked double-stranded DNA structures. The system can readily achieve ultrasensitive detection of target DNA. Moreover, the HB-HCR principle is successfully applied to construct three-input concatenated logic circuits with excellent specificity and extended to design a security-mimicking keypad lock system. Significantly, the HB-HCR-based keypad lock can alarm immediately if the "password" is incorrect. Overall, the proposed HB-HCR with high amplification efficiency is simple, homogeneous, fast, robust, and low-cost, and holds great promise in the development of biosensing, in the programmable assembly of DNA architectures, and in molecular logic operations. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea

PubMed Central

Narihiro, Takashi; Sekiguchi, Yuji

2011-01-01

Summary For the identification and quantification of methanogenic archaea (methanogens) in environmental samples, various oligonucleotide probes/primers targeting phylogenetic markers of methanogens, such as 16S rRNA, 16S rRNA gene and the gene for the α‐subunit of methyl coenzyme M reductase (mcrA), have been extensively developed and characterized experimentally. These oligonucleotides were designed to resolve different groups of methanogens at different taxonomic levels, and have been widely used as hybridization probes or polymerase chain reaction primers for membrane hybridization, fluorescence in situ hybridization, rRNA cleavage method, gene cloning, DNA microarray and quantitative polymerase chain reaction for studies in environmental and determinative microbiology. In this review, we present a comprehensive list of such oligonucleotide probes/primers, which enable us to determine methanogen populations in an environment quantitatively and hierarchically, with examples of the practical applications of the probes and primers. PMID:21375721

Surface supported gold-organic hybrids: on-surface synthesis and surface directed orientation.

PubMed

Zhang, Haiming; Franke, Jörn-Holger; Zhong, Dingyong; Li, Yan; Timmer, Alexander; Arado, Oscar Díaz; Mönig, Harry; Wang, Hong; Chi, Lifeng; Wang, Zhaohui; Müllen, Klaus; Fuchs, Harald

2014-04-09

The surface-assisted synthesis of gold-organic hybrids on Au (111) and Au (100) surfaces is repotred by thermally initiated dehalogenation of chloro-substituted perylene-3,4,9,10-tetracarboxylic acid bisimides (PBIs). Structures and surface-directed alignment of the Au-PBI chains are investigated by scanning tunnelling microscopy in ultra high vacuum conditions. Using dichloro-PBI as a model system, the mechanism for the formation of Au-PBI dimer is revealed with scanning tunnelling microscopy studies and density functional theory calculations. A PBI radical generated from the homolytic C-Cl bond dissociation can covalently bind a surface gold atom and partially pull it out of the surface to form stable PBI-Au hybrid species, which also gives rise to the surface-directed alignment of the Au-PBI chains on reconstructed Au (100) surfaces. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Control of DNA-Functionalized Nanoparticle Assembly

NASA Astrophysics Data System (ADS)

Olvera de La Cruz, Monica

Directed crystallization of a large variety of nanoparticles, including proteins, via DNA hybridization kinetics has led to unique materials with a broad range of crystal symmetries. The nanoparticles are functionalized with DNA chains that link neighboring functionalized units. The shape of the nanoparticle, the DNA length, the sequence of the hybridizing DNA linker and the grafting density determine the crystal symmetries and lattice spacing. By carefully selecting these parameters one can, in principle, achieve all the symmetries found for both atomic and colloidal crystals of asymmetric shapes as well as new symmetries, and drive transitions between them. A scale-accurate coarse-grained model with explicit DNA chains provides the design parameters, including degree of hybridization, to achieve specific crystal structures. The model also provides surface energy values to determine the shape of defect-free single crystals with macroscopic anisotropic properties, as well as the parameters to develop colloidal models that reproduce both the shape of single crystals and their growth kinetics.

Conductivity and properties of polysiloxane-polyether cluster-LiTFSI networks as hybrid polymer electrolytes

NASA Astrophysics Data System (ADS)

Boaretto, Nicola; Joost, Christine; Seyfried, Mona; Vezzù, Keti; Di Noto, Vito

2016-09-01

This report describes the synthesis and the properties of a series of polymer electrolytes, composed of a hybrid inorganic-organic matrix doped with LiTFSI. The matrix is based on ring-like oligo-siloxane clusters, bearing pendant, partially cross-linked, polyether chains. The dependency of the thermo-mechanic and of the transport properties on several structural parameters, such as polyether chains' length, cross-linkers' concentration, and salt concentration is studied. Altogether, the materials show good thermo-mechanical and electrochemical stabilities, with conductivities reaching, at best, 8·10-5 S cm-1 at 30 °C. In conclusion, the cell performances of one representative sample are shown. The scope of this report is to analyze the correlations between structure and properties in networked and hybrid polymer electrolytes. This could help the design of optimized polymer electrolytes for application in lithium metal batteries.

Potential of polyaniline modified clay nanocomposite as a selective decontamination adsorbent for Pb(II) ions from contaminated waters; kinetics and thermodynamic study.

PubMed

Piri, Somayeh; Zanjani, Zahra Alikhani; Piri, Farideh; Zamani, Abbasali; Yaftian, Mohamadreza; Davari, Mehdi

2016-01-01

Nowadays significant attention is to nanocomposite compounds in water cleaning. In this article the synthesis and characterization of conductive polyaniline/clay (PANI/clay) as a hybrid nanocomposite with extended chain conformation and its application for water purification are presented. Clay samples were obtained from the central plain of Abhar region, Abhar, Zanjan Province, Iran. Clay was dried and sieved before used as adsorbent. The conductive polyaniline was inflicted into the layers of clay to fabricate a hybrid material. The structural properties of the fabricated nanocomposite are studied by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR) and scanning electron microscope (SEM). The elimination process of Pb(II) and Cd(II) ions from synthetics aqueous phase on the surface of PANI/clay as adsorbent were evaluated in batch experiments. Flame atomic absorption instrument spectrophotometer was used for determination of the studied ions concentration. Consequence change of the pH and initial metal amount in aqueous solution, the procedure time and the used adsorbent dose as the effective parameters on the removal efficiency was investigated. Surface characterization was exhibited that the clay layers were flaked in the hybrid nanocomposite. The results show that what happen when a nanocomposite polyaniline chain is inserted between the clay layers. The adsorption of ions confirmed a pH dependency procedure and a maximum removal value was seen at pH 5.0. The adsorption isotherm and the kinetics of the adsorption processes were described by Temkin model and pseudo-second-order equation. Time of procedure, pH and initial ion amount have a severe effect on adsorption efficiency of PANI/clay. By using suggested synthesise method, nano-composite as the adsorbent simply will be prepared. The prepared PANI/clay showed excellent adsorption capability for decontamination of Pb ions from contaminated water. Both of suggested synthesise and removal methods are affordable techniques.

Quantitative fluorescent in-situ hybridization: a hypothesized competition mode between two dominant bacteria groups in hydrogen-producing anaerobic sludge processes.

PubMed

Huang, C-L; Chen, C-C; Lin, C-Y; Liu, W-T

2009-01-01

Two hydrogen-producing continuous flow stirred tank reactors (CSTRs) fed respectively with glucose and sucrose were investigated by polymerase chain reaction-denatured gradient gel electrophoresis (PCR-DGGE) and fluorescent in-situ hybridization (FISH). The substrate was fed in a continuous mode decreased from hydraulic retention time (HRT) 10 hours to 6, 5, 4, 3, and 2 hours. Quantitative fluorescent in-situ hybridization (FISH) observations further demonstrated that two morphotypes of bacteria dominated both microbial communities. One was long rod bacteria which can be targeted either by Chis150 probe designed to hybridize the gram positive low G + C bacteria or the specific oligonucleotide probe Lg10-6. The probe Lg10-6, affiliated with Clostridium pasteurianum, was designed and then checked with other reference organisms. The other type, unknown group, which cannot be detected by Chis150 was curved rod bacteria. Notably, the population ratios of the two predominant groups reflected the different operational performance of the two reactors, such as hydrogen producing rates, substrate turnover rates and metabolites compositions. Therefore, a competition mode of the two dominant bacteria groups was hypothesized. In the study, 16S rRNA-based gene library of hydrogen-producing microbial communities was established. The efficiency of hydrogen yields was correlated with substrates (glucose or sucrose), HRT, metabolites compositions (acetate, propionate, butyrate and ethanol), thermal pre-treatment (seed biomass was heated at 100 degrees C for 45 minutes), and microbial communities in the bioreactor, not sludge sources (municipal sewage sludge, alcohol-processing sludge, or bean-processing sludge). The designed specific oligonucleotide probe Lg10-6 also provides us a useful and fast molecular tool to screen hydrogen-producing microbial communities in the future research.

Market surveillance on non-halal additives incorporated in surimi based products using polymerase chain reaction (PCR)-southern hybridization analysis

NASA Astrophysics Data System (ADS)

Aravindran, S.; Sahilah, A. M.; Aminah, A.

2014-09-01

Halal surveillance on halal ingredients incorporated in surimi based products were studied using polymerase chain reaction (PCR)-southern hybridization on chip analysis. The primers used in this technique were targeted on mitochondria DNA (mtDNA) of cytochrome b (cyt b) gene sequence which able to differentiate 7 type (beef, chicken, duck, goat, buffalo, lamb and pork) of species on a single chip. 17 (n = 17*3) different brands of surimi-based product were purchased randomly from Selangor local market in January 2013. Of 17 brands, 3 (n = 3*3) brands were positive for chicken DNA, 1 (n = 1*3) brand was positive for goat DNA, and the remainder 13 brands (n = 13*3) have no DNA species detected. The sensitivity of PCR-southern hybridization primers to detect each meat species was 0.1 ng. In the present study, it is evidence that PCR-Southern Hybridization analysis offered a reliable result due to its highly specific and sensitive properties in detecting non-halal additive such as plasma protein incorporation in surimi-based product.

Physicochemical characterizations of functional hybrid liposomal nanocarriers formed using photo-sensitive lipids

PubMed Central

Kumar Pramanik, Sumit; Losada-Pérez, Patricia; Reekmans, Gunter; Carleer, Robert; D’Olieslaeger, Marc; Vanderzande, Dirk; Adriaensens, Peter; Ethirajan, Anitha

2017-01-01

With recent advances in the field of diagnostics and theranostics, liposomal technology has secured a fortified position as a potential nanocarrier. Specifically, radiation/photo-sensitive liposomes containing photo-polymerizable cross-linking lipids are intriguing as they can impart the vesicles with highly interesting properties such as response to stimulus and improved shell stability. In this work, 1,2-bis(10,12-tricosadiynoyl)-sn-glycero-3-phosphoethanolamine (DTPE) is used as a photo-polymerizable lipid to form functional hybrid-liposomes as it can form intermolecular cross-linking through the diacetylenic groups. Hybrid-liposomes were formulated using mixtures of DTPE and saturated lipids of different chain lengths (dipalmitoylphosphatidylcholine (DPPC) and dimirystoilphosphatidylcholine (DMPC)) at different molar ratios. The physico-chemical characteristics of the liposomes has been studied before and after UV irradiation using a combination of techniques: DSC, QCM-D and solid-state NMR. The results signify the importance of a subtle modification in alkyl chain length on the phase behavior of the hybrid-liposomes and on the degree of crosslinking in the shell. PMID:28406235

Enhanced electrochemical performance of amorphous carbon nanotube-manganese-di-oxide-poly-pyrrole ternary nanohybrid

NASA Astrophysics Data System (ADS)

Pahari, D.; Das, N. S.; Das, B.; Howli, P.; Chattopadhyay, K. K.; Banerjee, D.

2017-12-01

Amorphous carbon nanotubes (a-CNTs) manganese di oxide (MnO2)-poly pyrrole (PPy) ternary nanocomposites have been synthesized by a simple chemical route. The as prepared samples have been characterized with different characterization tools that include field emission scanning and high resolution transmission electron microscopy, Raman, Fourier transformed infrared as well as UV-Vis spectroscopy. The electrochemical performance of all the as prepared pure and hybrid samples have been studied in detail. It has been seen that the ternary hybrid shows efficient electrochemical performance with high value of specific capacitance with good stability even up to 2000 cycles. The superior performance of the hybrid samples can be attributed to the strong synergistic effect between the components resulting electron shuttling along PPy main chains and inter-chain raising built-in continuous conductive network. The ternary composite approach offers an effective solution to enhance the device performance of metal-oxide based supercapacitors for long cycling applications. These studies can well speculate the existence of another supercapacitor hybrid for the use in environment friendly electrode and thus a pollution free nature.

Development and accuracy of quantitative real-time polymerase chain reaction assays for detection and quantification of enterotoxigenic Escherichia coli (ETEC) heat labile and heat stable toxin genes in travelers' diarrhea samples.

PubMed

Youmans, Bonnie P; Ajami, Nadim J; Jiang, Zhi-Dong; Petrosino, Joseph F; DuPont, Herbert L; Highlander, Sarah K

2014-01-01

Enterotoxigenic Escherichia coli (ETEC), the leading bacterial pathogen of travelers' diarrhea, is routinely detected by an established DNA hybridization protocol that is neither sensitive nor quantitative. Quantitative real-time polymerase chain reaction (qPCR) assays that detect the ETEC toxin genes eltA, sta1, and sta2 in clinical stool samples were developed and tested using donor stool inoculated with known quantities of ETEC bacteria. The sensitivity of the qPCR assays is 89%, compared with 22% for the DNA hybridization assay, and the limits of detection are 10,000-fold lower than the DNA hybridization assays performed in parallel. Ninety-three clinical stool samples, previously characterized by DNA hybridization, were tested using the new ETEC qPCR assays. Discordant toxin profiles were observed for 22 samples, notably, four samples originally typed as ETEC negative were ETEC positive. The qPCR assays are unique in their sensitivity and ability to quantify the three toxin genes in clinical stool samples.

Characterization of Mesocarp and Kernel Lipids from Elaeis guineensis Jacq., Elaeis oleifera [Kunth] Cortés, and Their Interspecific Hybrids.

PubMed

Lieb, Veronika M; Kerfers, Margarete R; Kronmüller, Amrei; Esquivel, Patricia; Alvarado, Amancio; Jiménez, Víctor M; Schmarr, Hans-Georg; Carle, Reinhold; Schweiggert, Ralf M; Steingass, Christof B

2017-05-10

Morphological traits, total lipid contents, and fatty acid profiles were assessed in fruits of several accessions of Elaeis oleifera [Kunth] Cortés, Elaeis guineensis Jacq., and their interspecific hybrids. The latter featured the highest mesocarp-to-fruit ratios (77.9-78.2%). The total lipid contents of both E. guineensis mesocarp and kernel were significantly higher than for E. oleifera accessions. Main fatty acids comprised C16:0, C18:1n9, and C18:2n6 in mesocarp and C12:0, C14:0, and C18:1n9 in kernels. E. oleifera samples were characterized by higher proportions of unsaturated long-chain fatty acids. Saturated medium-chain fatty acids supported the clustering of E. guineensis kernels in multivariate statistics. Hybrid mesocarp lipids had an intermediate fatty acid composition, whereas their kernel lipids resembled those of E. oleifera genotypes. Principal component analysis based on lipid contents and proportions of individual fatty acids permitted clear-cut distinction of E. oleifera, E. guineensis, and their hybrids.

Collapse of chain anadiplosis-structured DNA nanowires for highly sensitive colorimetric assay of nucleic acids.

PubMed

Xu, Jianguo; Wu, Zai-Sheng; Chen, Yanru; Zheng, Tingting; Le, Jingqing; Jia, Lee

2017-02-14

In this work, we have proposed a chain anadiplosis-structured DNA nanowire by using two well-defined assembly strands (AS1 and AS2). The presence of a target analyte would drive the single-stranded AS1 dissociate from the pre-formatted nanowire, converting into a fully double-stranded form responsible for extensive accumulation of G-rich cleavage fragment1 (GCF1) because of an autonomously performed polymerization/nicking/displacement process. In turn, the produced GCF1 is able to hybridize with the un-peeled AS2, allowing the replication over AS2 to occur and generate large amounts of G-rich cleavage fragment2 (GCF2) with the ability to hybridize with the un-peeled AS1, thereafter initiating new enzymatic reactions for further collection of GCF1. Because the reactions occur repeatedly, the assembled nanowires gradually dissociated and completely collapsed in the end, achieving the goal of substantial signal amplification for the colorimetric readout of the target analytes. The sensing feasibility is firstly verified by one trigger primer (TP), and then exemplified with the detection of the target, the kras oncogene, with high sensitivity and specificity. As a proof-of-concept strategy, the intelligent signal readout pathway and desired assay ability provide unique insights into the materials research and biological studies.

Unsupervised object segmentation with a hybrid graph model (HGM).

PubMed

Liu, Guangcan; Lin, Zhouchen; Yu, Yong; Tang, Xiaoou

2010-05-01

In this work, we address the problem of performing class-specific unsupervised object segmentation, i.e., automatic segmentation without annotated training images. Object segmentation can be regarded as a special data clustering problem where both class-specific information and local texture/color similarities have to be considered. To this end, we propose a hybrid graph model (HGM) that can make effective use of both symmetric and asymmetric relationship among samples. The vertices of a hybrid graph represent the samples and are connected by directed edges and/or undirected ones, which represent the asymmetric and/or symmetric relationship between them, respectively. When applied to object segmentation, vertices are superpixels, the asymmetric relationship is the conditional dependence of occurrence, and the symmetric relationship is the color/texture similarity. By combining the Markov chain formed by the directed subgraph and the minimal cut of the undirected subgraph, the object boundaries can be determined for each image. Using the HGM, we can conveniently achieve simultaneous segmentation and recognition by integrating both top-down and bottom-up information into a unified process. Experiments on 42 object classes (9,415 images in total) show promising results.

Hybrid pathwise sensitivity methods for discrete stochastic models of chemical reaction systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wolf, Elizabeth Skubak, E-mail: ewolf@saintmarys.edu; Anderson, David F., E-mail: anderson@math.wisc.edu

2015-01-21

Stochastic models are often used to help understand the behavior of intracellular biochemical processes. The most common such models are continuous time Markov chains (CTMCs). Parametric sensitivities, which are derivatives of expectations of model output quantities with respect to model parameters, are useful in this setting for a variety of applications. In this paper, we introduce a class of hybrid pathwise differentiation methods for the numerical estimation of parametric sensitivities. The new hybrid methods combine elements from the three main classes of procedures for sensitivity estimation and have a number of desirable qualities. First, the new methods are unbiased formore » a broad class of problems. Second, the methods are applicable to nearly any physically relevant biochemical CTMC model. Third, and as we demonstrate on several numerical examples, the new methods are quite efficient, particularly if one wishes to estimate the full gradient of parametric sensitivities. The methods are rather intuitive and utilize the multilevel Monte Carlo philosophy of splitting an expectation into separate parts and handling each in an efficient manner.« less

3D hybrid carbon composed of multigraphene bridged by carbon chains

NASA Astrophysics Data System (ADS)

Liu, Lingyu; Hu, Meng; Liu, Chao; Shao, Cancan; Pan, Yilong; Ma, Mengdong; Wu, Yingju; Zhao, Zhisheng; Gao, Guoying; He, Julong

2018-01-01

The element carbon possesses various stable and metastable allotropes; some of them have been applied in diverse fields. The experimental evidences of both carbon chain and graphdiyne have been reported. Here, we reveal the mystery of an enchanting carbon allotrope with sp-, sp2-, and sp3-hybridized carbon atoms using a newly developed ab initio particle-swarm optimization algorithm for crystal structure prediction. This crystalline allotrope, namely m-C12, can be viewed as braided mesh architecture interwoven with multigraphene and carbon chains. The m-C12 meets the criteria for dynamic and mechanical stabilities and is energetically more stable than carbyne and graphdiyne. Analysis of the B/G and Poisson's ratio indicates that this allotrope is ductile. Notably, m-C12 is a superconducting carbon with Tc of 1.13 K, which is rare in the family of carbon allotropes.

New developments in surface technology and prototyping

NASA Astrophysics Data System (ADS)

Himmer, Thomas; Beyer, Eckhard

2003-03-01

Novel lightweight applications in the automotive and aircraft industries require advanced materials and techniques for surface protection as well as direct and rapid manufacturing of the related components and tools. The manufacturing processes presented in this paper are based on multiple additive and subtractive technologies such as laser cutting, laser welding, direct laser metal deposition, laser/plasma hybrid spraying technique or CNC milling. The process chain is similar to layer-based Rapid Prototyping Techniques. In the first step, the 3D CAD geometry is sliced into layers by a specially developed software. These slices are cut by high speed laser cutting and then joined together. In this way laminated tools or parts are built. To improve surface quality and to increase wear resistance a CNC machining center is used. The system consists of a CNC milling machine, in which a 3 kW Nd:YAG laser, a coaxial powder nozzle and a digitizing system are integrated. Using a new laser/plasma hybrid spraying technique, coatings can be deposited onto parts for surface protection. The layers show a low porosity and high adhesion strength, the thickness is up to 0.3 mm, and the lower effort for preliminary surface preparation reduces time and costs of the whole process.

A simple nucleic acid hybridization/latex agglutination assay for the rapid detection of polymerase chain reaction amplicons.

PubMed

Vollenhofer-Schrumpf, Sabine; Buresch, Ronald; Schinkinger, Manfred

2007-03-01

We have developed a new method for the detection of nucleic acid hybridization, based on a simple latex agglutination test that can be evaluated by the unaided eye. Nucleic acid, e.g., a polymerase chain reaction (PCR) product, is denatured and incubated with polystyrene beads carrying covalently bound complementary oligonucleotide sequences. Hybridization of the nucleic acids leads to aggregation of the latex particles, thereby verifying the presence of target sequence. The test is performed at room temperature, and results are available within 10 min. As a proof of principle, the hybridization/latex agglutination assay was applied to the detection of purified PCR fragments either specific for Salmonella spp. or a synthetic sequence, and to the detection of Salmonella enterica in artificially contaminated chicken samples. A few nanograms of purified PCR fragments were detectable. In artificially contaminated chicken samples, 3 colony-forming units (cfu)/25 g were detected in one of three replicates, and 30 cfu/25 g were detected in both of two replicates when samples for PCR were taken directly from primary enrichment, demonstrating the practical applicability of this test system. Even multiplex detection might be achievable. This novel kind of assay could be useful for a range of applications where hybridization of nucleic acids, e.g., PCR fragments, is to be detected.

Novel route of synthesis for cellulose fiber-based hybrid polyurethane

NASA Astrophysics Data System (ADS)

Ikhwan, F. H.; Ilmiati, S.; Kurnia Adi, H.; Arumsari, R.; Chalid, M.

2017-07-01

Polyurethanes, obtained by the reaction of a diisocyanate compound with bifunctional or multifunctional reagent such as diols or polyols, have been studied intensively and well developed. The wide range modifier such as chemical structures and molecular weight to build polyurethanes led to designs of materials that may easily meet the functional product demand and to the extraordinary spreading of these materials in market. Properties of the obtained polymer are related to the chemical structure of polyurethane backbone. A number polyurethanes prepared from biomass-based monomers have been reported. Cellulose fiber, as a biomass material is containing abundant hydroxyl, promising material as chain extender for building hybrid polyurethanes. In previous researches, cellulose fiber was used as filler in synthesis of polyurethane composites. This paper reported a novel route of hybrid polyurethane synthesis, which a cellulose fiber was used as chain extender. The experiment performed by reacting 4,4’-Methylenebis (cyclohexyl isocyanate) (HMDI) and polyethylene glycol with variation of molecular weight to obtained pre-polyurethane, continued by adding micro fiber cellulose (MFC) with variation of type and composition in the mixture. The experiment was evaluated by NMR, FTIR, SEM and STA measurement. NMR and FTIR confirmed the reaction of the hybrid polyurethane. STA showed hybrid polyurethane has good thermal stability. SEM showed good distribution and dispersion of sorghum-based MFC.

Molecular level detection and localization of mechanical damage in collagen enabled by collagen hybridizing peptides.

PubMed

Zitnay, Jared L; Li, Yang; Qin, Zhao; San, Boi Hoa; Depalle, Baptiste; Reese, Shawn P; Buehler, Markus J; Yu, S Michael; Weiss, Jeffrey A

2017-03-22

Mechanical injury to connective tissue causes changes in collagen structure and material behaviour, but the role and mechanisms of molecular damage have not been established. In the case of mechanical subfailure damage, no apparent macroscale damage can be detected, yet this damage initiates and potentiates in pathological processes. Here, we utilize collagen hybridizing peptide (CHP), which binds unfolded collagen by triple helix formation, to detect molecular level subfailure damage to collagen in mechanically stretched rat tail tendon fascicle. Our results directly reveal that collagen triple helix unfolding occurs during tensile loading of collagenous tissues and thus is an important damage mechanism. Steered molecular dynamics simulations suggest that a likely mechanism for triple helix unfolding is intermolecular shearing of collagen α-chains. Our results elucidate a probable molecular failure mechanism associated with subfailure injuries, and demonstrate the potential of CHP targeting for diagnosis, treatment and monitoring of tissue disease and injury.

Novel Polyethylenimine–Acrylamide/SiO 2 Hybrid Hydrogel Sorbent for Rare-Earth-Element Recycling from Aqueous Sources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Qiuming; Wilfong, Walter C.; Kail, Brian W.

Recycling rare earth elements (REEs) becomes increasingly important due to their supply vulnerability and increasing demands in industry, agriculture, and national security. Hybrid hydrogel sorbents were outstanding due to their high stability and selectivity. Organic-inorganic hybrid hydrogels were synthesized by thermo-polymerization of acrylamide onto PEI polymer chain with N,N’-methylene bisacrylamide as a crosslinker. The grafted network was evidenced by DRIFTS and XPS. The porous structure was observed by SEM. Crosslink degree, PEI grafting degree, and SiO 2 concentration were studied to optimize the REEs adsorption. The pH value of the medium greatly affected REE adsorption capacity, where the nearly neutralmore » conditions gave the strongest bonding of REEs to active sites. Moreover, kinetic studies showed that the rate-determining step of the adsorption process was chemical sorption, and that REE diffusion within micropores was the control step for, specifically, intraparticle diffusion. The adsorbents showed excellent selectivity and recyclability for REEs through 5 adsorption-desorption cycles in contact with synthetic acid mine drainage solution. A high separation toward REEs over fouling metals was achieved by using a citrate-based buffer eluent solution. This hybrid hydrogel shows promise for the recycling of REEs from aqueous solutions.« less

Novel Polyethylenimine–Acrylamide/SiO 2 Hybrid Hydrogel Sorbent for Rare-Earth-Element Recycling from Aqueous Sources

DOE PAGES

Wang, Qiuming; Wilfong, Walter C.; Kail, Brian W.; ...

2017-09-14

Recycling rare earth elements (REEs) becomes increasingly important due to their supply vulnerability and increasing demands in industry, agriculture, and national security. Hybrid hydrogel sorbents were outstanding due to their high stability and selectivity. Organic-inorganic hybrid hydrogels were synthesized by thermo-polymerization of acrylamide onto PEI polymer chain with N,N’-methylene bisacrylamide as a crosslinker. The grafted network was evidenced by DRIFTS and XPS. The porous structure was observed by SEM. Crosslink degree, PEI grafting degree, and SiO 2 concentration were studied to optimize the REEs adsorption. The pH value of the medium greatly affected REE adsorption capacity, where the nearly neutralmore » conditions gave the strongest bonding of REEs to active sites. Moreover, kinetic studies showed that the rate-determining step of the adsorption process was chemical sorption, and that REE diffusion within micropores was the control step for, specifically, intraparticle diffusion. The adsorbents showed excellent selectivity and recyclability for REEs through 5 adsorption-desorption cycles in contact with synthetic acid mine drainage solution. A high separation toward REEs over fouling metals was achieved by using a citrate-based buffer eluent solution. This hybrid hydrogel shows promise for the recycling of REEs from aqueous solutions.« less

A Reliable Hybrid Adsorbent for Efficient Radioactive Cesium Accumulation from Contaminated Wastewater

PubMed Central

Awual, Md. Rabiul; Yaita, Tsuyoshi; Miyazaki, Yuji; Matsumura, Daiju; Shiwaku, Hideaki; Taguchi, Tomitsugu

2016-01-01

Cesium (Cs) removal from nuclear liquid wastewater has become an emerging issue for safeguarding public health after the accident at the Fukushima Daiichi Nuclear Power Plant. A novel macrocyclic ligand of o-benzo-p-xylyl-22-crown-6-ether (OBPX22C6) was developed and successfully immobilized onto mesoporous silica for the preparation of hybrid adsorbent. The benzene ring π electron is the part of crown ether of OBPX22C6 for easy orientation of the macrocyclic compound for making the π electron donation with Cs complexation. The potential and feasibility of the hybrid adsorbent as being Cs selective was evaluated in terms of sensitivity, selectivity and reusability. The results clarified that the Cs removal process was rapid and reached saturation within a short time. Considering the effect of competitive ions, sodium (Na) did not markedly affect the Cs adsorption whereas potassium (K) was slightly affected due to the similar ionic radii. However, the oxygen in long ethylene glycol chain in OBPX22C6 was expected to show strong coordination, including Cs-π interaction with Cs even in the presence of the high amount of K and Na. Due to its high selectivity and reusability, significant volume reduction is expected as this promising hybrid adsorbent is used for Cs removal in Fukushima wastewater. PMID:26818070

A Reliable Hybrid Adsorbent for Efficient Radioactive Cesium Accumulation from Contaminated Wastewater.

PubMed

Awual, Md Rabiul; Yaita, Tsuyoshi; Miyazaki, Yuji; Matsumura, Daiju; Shiwaku, Hideaki; Taguchi, Tomitsugu

2016-01-28

Cesium (Cs) removal from nuclear liquid wastewater has become an emerging issue for safeguarding public health after the accident at the Fukushima Daiichi Nuclear Power Plant. A novel macrocyclic ligand of o-benzo-p-xylyl-22-crown-6-ether (OBPX22C6) was developed and successfully immobilized onto mesoporous silica for the preparation of hybrid adsorbent. The benzene ring π electron is the part of crown ether of OBPX22C6 for easy orientation of the macrocyclic compound for making the π electron donation with Cs complexation. The potential and feasibility of the hybrid adsorbent as being Cs selective was evaluated in terms of sensitivity, selectivity and reusability. The results clarified that the Cs removal process was rapid and reached saturation within a short time. Considering the effect of competitive ions, sodium (Na) did not markedly affect the Cs adsorption whereas potassium (K) was slightly affected due to the similar ionic radii. However, the oxygen in long ethylene glycol chain in OBPX22C6 was expected to show strong coordination, including Cs-π interaction with Cs even in the presence of the high amount of K and Na. Due to its high selectivity and reusability, significant volume reduction is expected as this promising hybrid adsorbent is used for Cs removal in Fukushima wastewater.

Larger spontaneous polarization ferroelectric inorganic-organic hybrids: [PbI3](infinity) chains directed organic cations aggregation to Kagomé-shaped tubular architecture.

PubMed

Zhao, Hai-Rong; Li, Dong-Ping; Ren, Xiao-Ming; Song, You; Jin, Wan-Qin

2010-01-13

Four isostructural inorganic-organic hybrid ferroelectric compounds, assembled from achiral 3-R-benzylidene-1-aminopyridiniums (R = NO(2), Br, Cl, or F for 1-4, respectively) and [PbI(3)](-) anions with the chiral Kagomé-shaped tubular aggregating architecture, show larger spontaneous polarizations.

Coordinate changes of myosin light and heavy chain isoforms during forced fiber type transitions in rabbit muscle.

PubMed

Leeuw, T; Pette, D

1996-01-01

Skeletal muscle fibers are versatile entities, capable of changing their phenotype in response to altered functional demands. In the present study, fast-to-slow fiber type transitions were induced in rabbit tibialis anterior (fA) muscles by chronic low-frequency stimulation (CLFS). The time course of changes in relative protein concentrations of fast and slow myosin light chain (MLC) isoforms and changes in their relative synthesis rates by in vivo labeling with [35S]methionine were followed during stimulation periods of up to 60 days. Generally, relative synthesis rates and protein concentrations changed in parallel; i.e., fast isoforms decreased and slow isoforms increased. MLC3f, however, which turns over at a higher rate than the other light chains, exhibited a conspicuous discrepancy between a markedly reduced relative synthesis but only a moderate decrease in protein amount during the initial 2 weeks of CLFS. Apparently, MLC3f is regulated independent of MLC1f, with protein degradation playing an important role in its regulation. The exchange of fast MLC isoforms with their slow counterparts seemed to correspond to the ultimate fast-to-slow (MHCIIa-->MHCI) transition at the MHC level. However, due to an earlier onset of the fast-to-slow transition of the regulatory light chain and the delayed fast-to-slow exchange of the alkali light chains, a spectrum of hybrid isomyosins composed of fast and slow light and heavy chains must have existed transiently in transforming fibers. Such hybrid isomyosins appeared to be restricted to MHCIIa- and MHCI-based combinations. In conclusion, fiber type specific programs that normally coordinate the expression of myofibrillar protein isoforms seem to be maintained during fiber type transitions. Possible differences in post-transcriptional regulation may result in the transient accumulation of atypical combinations of fast and slow MLC and MHC isoforms, giving rise to the appearance of hybrid fibers under the conditions of forced fiber type conversion.

Line active hybrid lipids determine domain size in phase separation of saturated and unsaturated lipids.

PubMed

Brewster, Robert; Safran, Samuel A

2010-03-17

A simple model of the line activity of a hybrid lipid (e.g., POPC) with one fully saturated chain and one partially unsaturated chain demonstrates that these lipids preferentially pack at curved interfaces between phase-separated saturated and unsaturated domains. We predict that the domain sizes typically range from tens to hundreds of nm, depending on molecular interactions and parameters such as molecular volume and area per headgroup in the bulk fluid phase. The role of cholesterol is taken into account by an effective change in the headgroup areas and the domain sizes are predicted to increase with cholesterol concentration. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Hybrid input-output approach to metal production and its application to the introduction of lead-free solders.

PubMed

Nakamura, Shinichiro; Murakami, Shinsuke; Nakajima, Kenichi; Nagasaka, Tetsuya

2008-05-15

The production process of metals such as copper, lead, and zinc is characterized by mutual interconnections and interdependence, as well as by the occurrence of a large number of byproducts, which include precious or rare metals, such as gold, silver, bismuth, and indium. On the basis of the framework of waste input-output (WIO), we present a hybrid 10 model that takes full account of the mutual interdependence among the metal production processes and the interdependence between them and all the other production sectors of the economy as well. The combination of a comprehensive representation of the whole national economy and the introduction of process knowledge of metal production allows for a detailed analysis of different materials-use scenarios under the consideration of full supply chain effects. For illustration, a hypothetical case study of the introduction of lead-free solder involving the production of silver as a byproduct of copper and lead smelting processes was developed and implemented using Japanese data. To meet the increased demand for the recovery and recycling of silver resources from end-of-life products, the final destination of metal silver in terms of products and user categories was estimated, and the target components with the highest silver concentration were identified.

DNA hybridization detection on electrical microarrays using coulostatic pulse technique.

PubMed

Dharuman, V; Nebling, E; Grunwald, T; Albers, J; Blohm, L; Elsholz, B; Wörl, R; Hintsche, R

2006-12-15

We demonstrated a novel application of transient coulostatic pulse technique for the detection of label free DNA hybridization on nm-sized gold interdigitated ultramicroelectrode arrays (Au-IDA) made in silicon technology. The array consists of eight different positions with an Au-IDA pair at each position arranged on the Si-based Biochip. Immobilization of capture probes onto the Au-IDA was accomplished by self-assembling of thiol-modified oligonucleotides. Target hybridization was indicated by a change in the magnitude of the time dependant potential relaxation curve in presence of electroactive Fe(CN)(6)(3-) in the phosphate buffer solution. While complementary DNA hybridization showed 50% increase in the relaxation potential, the non-complementary DNA showed a negligible change. A constant behaviour was noted for all positions. The dsDNA specific intercalating molecule, methylene blue, was found to be enhancing the discrimination effect. The changes in the relaxation potential curves were further corroborated following the ELISA like experiments using ExtraAvidine alkaline phosphatase labelling and redox recycling of para-aminophenol phosphate at IDAs. The coulostatic pulse technique was shown to be useful for identifying DNA sequences from brain tumour gene CK20, human herpes simplex virus, cytomegalovirus, Epstein-Barr virus and M13 phage. Compared to the hybridization of short chain ONTs (27 mers), the hybridization of long chain M13 phage DNA showed three times higher increase in the relaxation curves. The method is fast enough to monitor hybridization interactions in milli or microsecond time scales and is well suitable for miniaturization and integration compared to the common impedance techniques for developing capacitative DNA sensors.

PLGA/liposome hybrid nanoparticles for short-chain ceramide delivery.

PubMed

Zou, Peng; Stern, Stephan T; Sun, Duxin

2014-03-01

Rapid premature release of lipophilic drugs from liposomal lipid bilayer to plasma proteins and biological membranes is a challenge for targeted drug delivery. The purpose of this study is to reduce premature release of lipophilic short-chain ceramides by encapsulating ceramides into liposomal aqueous interior with the aid of poly (lactic-coglycolicacid) (PLGA). BODIPY FL labeled ceramide (FL-ceramide) and BODIPY-TR labeled ceramide (TR-ceramide) were encapsulated into carboxy-terminated PLGA nanoparticles. The negatively charged PLGA nanoparticles were then encapsulated into cationic liposomes to obtain PLGA/liposome hybrids. As a control, FL-ceramide and/or TR ceramide co-loaded liposomes without PLGA were prepared. The release of ceramides from PLGA/liposome hybrids and liposomes in rat plasma, cultured MDA-MB-231 cells, and rat blood circulation was compared using fluorescence resonance energy transfer (FRET) between FL-ceramide (donor) and TR-ceramide (acceptor). FRET analysis showed that FL-ceramide and TR-ceramide in liposomal lipid bilayer were rapidly released during incubation with rat plasma. In contrast, the FL-ceramide and TR-ceramide in PLGA/liposome hybrids showed extended release. FRET images of cells revealed that ceramides in liposomal bilayer were rapidly transferred to cell membranes. In contrast, ceramides in PLGA/liposome hybrids were internalized into cells with nanoparticles simultaneously. Upon intravenous administration to rats, ceramides encapsulated in liposomal bilayer were completely released in 2 min. In contrast, ceramides encapsulated in the PLGA core were retained in PLGA/liposome hybrids for 4 h. The PLGA/liposome hybrid nanoparticles reduced in vitro and in vivo premature release of ceramides and offer a viable platform for targeted delivery of lipophilic drugs.

Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability

PubMed Central

2014-01-01

Hybridization chain reaction (HCR) provides multiplexed, isothermal, enzyme-free, molecular signal amplification in diverse settings. Within intact vertebrate embryos, where signal-to-background is at a premium, HCR in situ amplification enables simultaneous mapping of multiple target mRNAs, addressing a longstanding challenge in the biological sciences. With this approach, RNA probes complementary to mRNA targets trigger chain reactions in which metastable fluorophore-labeled RNA hairpins self-assemble into tethered fluorescent amplification polymers. The properties of HCR lead to straightforward multiplexing, deep sample penetration, high signal-to-background, and sharp subcellular signal localization within fixed whole-mount zebrafish embryos, a standard model system for the study of vertebrate development. However, RNA reagents are expensive and vulnerable to enzymatic degradation. Moreover, the stringent hybridization conditions used to destabilize nonspecific hairpin binding also reduce the energetic driving force for HCR polymerization, creating a trade-off between minimization of background and maximization of signal. Here, we eliminate this trade-off by demonstrating that low background levels can be achieved using permissive in situ amplification conditions (0% formamide, room temperature) and engineer next-generation DNA HCR amplifiers that maximize the free energy benefit per polymerization step while preserving the kinetic trapping property that underlies conditional polymerization, dramatically increasing signal gain, reducing reagent cost, and improving reagent durability. PMID:24712299

Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field.

PubMed

Aguayo, Daniel; González-Nilo, Fernando D; Chipot, Christophe

2012-05-08

Simulation of three models of cardiolipin (CL) containing membranes using a new set of parameters for tetramyristoyl and tetraoleoyl CLs has been developed in the framework of the united-atom CHARMM27-UA and the all-atom CHARMM36 force fields with the aim of performing molecular dynamics (MD) simulations of cardiolipin-containing mixed-lipid membranes. The new parameters use a hybrid representation of all-atom head groups in conjunction with implicit-hydrogen united-atom (UA) to describe the oleoyl and myristoyl chains of the CLs, in lieu of the fully atomistic description, thereby allowing longer simulations to be undertaken. The physicochemical properties of the bilayers were determined and compared with previously reported data. Furthermore, using tetramyristoyl CL mixed with POPG and POPE lipids, a mitochondrial membrane was simulated. The results presented here show the different behavior of the bilayers as a result of the lipid composition, where the length of the acyl chain and the conformation of the headgroup can be associated with the mitochondrial membrane properties. The new hybrid CL parameters prove to be well suited for the simulation of the molecular structure of CL-containing bilayers and can be extended to other lipid bilayers composed of CLs with different acyl chains or alternate head groups.

Mesoscopic modeling for nucleic acid chain dynamics

PubMed Central

Sales-Pardo, M.; Guimerà, R.; Moreira, A. A.; Widom, J.; Amaral, L. A. N.

2007-01-01

To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a mesoscopic-level computational model that provides a new window into nucleic acid dynamics. We model a single-stranded nucleic as a polymer chain whose monomers are the nucleosides. Each monomer comprises a bead representing the sugar molecule and a pin representing the base. The bead-pin complex can rotate about the backbone of the chain. We consider pairwise stacking and hydrogen-bonding interactions. We use a modified Monte Carlo dynamics that splits the dynamics into translational bead motion and rotational pin motion. By performing a number of tests, we first show that our model is physically sound. We then focus on a study of the kinetics of a DNA hairpin—a single-stranded molecule comprising two complementary segments joined by a noncomplementary loop—studied experimentally. We find that results from our simulations agree with experimental observations, demonstrating that our model is a suitable tool for the investigation of the hybridization of single strands. PMID:16089566

From single magnetic adatoms on superconductors to coupled spin chains

NASA Astrophysics Data System (ADS)

Franke, Katharina J.

Magnetic adsorbates on conventional s-wave superconductors lead to exchange interactions that induce Yu-Shiba-Rusinov (YSR) states inside the superconducting energy gap. Here, we employ tunneling spectroscopy at 1.1 K to investigate magnetic atoms and chains on superconducting Pb surfaces. We show that individual Manganese (Mn) atoms give rise to a distinct number of YSR-states. The single-atom junctions are stable over several orders of magnitude in conductance. We identify single-electron tunneling as well as Andreev processes. When the atoms are brought into sufficiently close distance, the Shiba states hybridize, thus giving rise to states with bonding and anti-bonding character. It has been shown that the Pb(110) surface supports the self-assembly of Fe chains, which exhibit fingerprints of Majorana bound states. Using superconducting tips, we resolve a rich subgap structure including peaks at zero energy and low-energy resonances, which overlap with the putative Majorana states. We gratefully acknowledge funding by the Deutsche Forschungsgemeinschaft through collaborative research Grant Sfb 658, and through Grant FR2726/4, as well by the European Research Council through Consolidator Grant NanoSpin.

Electrical Rectification in Betaine Derivatives

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sumpter, Bobby G; Meunier, Vincent; Filho, Antonio G. Souza

2008-01-01

We theoretically investigate the electric rectification in an organic two terminal push-pull molecular device using a combination of ab initio techniques. Our main finding is that the electric rectification is extremely sensitive to the length of the chain, undergoing a complete switching after a specific chain length. This unique process occurs for betainelike donor- bridge-acceptor systems and is directly associated with a conjugated bridge in the presence of an external electric field. The conjugated bridge between the donor and acceptor groups is composed of oligoethylene with sizes ranging from zero to ten C=C units. The appearance of electric rectification occursmore » when the bridge size is equal to 5 units and is complete for those larger than 6 units (i.e. full inversion). This new electronic effect is advantageous for the design of large hybrid organic/inorganic circuits with anincreased majority carrier flow that is necessary for the emerging needs of nanotechnology.« less

A graphical language for reliability model generation

NASA Technical Reports Server (NTRS)

Howell, Sandra V.; Bavuso, Salvatore J.; Haley, Pamela J.

1990-01-01

A graphical interface capability of the hybrid automated reliability predictor (HARP) is described. The graphics-oriented (GO) module provides the user with a graphical language for modeling system failure modes through the selection of various fault tree gates, including sequence dependency gates, or by a Markov chain. With this graphical input language, a fault tree becomes a convenient notation for describing a system. In accounting for any sequence dependencies, HARP converts the fault-tree notation to a complex stochastic process that is reduced to a Markov chain which it can then solve for system reliability. The graphics capability is available for use on an IBM-compatible PC, a Sun, and a VAX workstation. The GO module is written in the C programming language and uses the Graphical Kernel System (GKS) standard for graphics implementation. The PC, VAX, and Sun versions of the HARP GO module are currently in beta-testing.

Micropatterning stretched and aligned DNA using microfluidics and surface patterning for applications in hybridization-mediated templated assembly of nanostructures

NASA Astrophysics Data System (ADS)

Carbeck, Jeffrey; Petit, Cecilia

2004-03-01

Current efforts in nanotechnology use one of two basic approaches: top-down fabrication and bottom-up assembly. Top-down strategies use lithography and contact printing to create patterned surfaces and microfluidic channels that, in turn, can corral and organize nanoscale structures. Bottom-up approaches use templates to direct the assembly of atoms, molecules, and nanoparticles through molecular recognition. The goal of this work is to integrate these strategies by first patterning and orienting DNA molecules through top-down tools so that single DNA chains can then serve as templates for the bottom-up construction of hetero-structures composed of proteins and nanoparticles, both metallic and semi-conducting. The first part of this talk focuses on the top-down strategies used to create microscopic patterns of stretched and aligned molecules of DNA. Specifically, it presents a new method in which molecular combing -- a process by which molecules are deposited and stretched onto a surface by the passage of an air-water interface -- is performed in microchannels. This approach demonstrates that the shape and motion of this interface serve as an effective local field directing the chains dynamically as they are stretched onto the surface. The geometry of the microchannel directs the placement of the DNA molecules, while the geometry of the air-water interface directs the local orientation and curvature of the molecules. This ability to control both the placement and orientation of chains has implication for the use of this technique in genetic analysis and in the bottom up approach to nanofabrication.The second half of this talk presents our bottom-up strategy, which allows placement of nanoparticles along individual DNA chains with a theoretical resolution of less than 1 nm. Specifically, we demonstrate the sequence-specific patterning of nanoparticles via the hybridization of functionalized complementary probes to surface-bound chains of double-stranded DNA. Using this technique, we demonstrate the ability to assemble metals, semiconductors, and a composite of both on a single molecule.

Transcription boundaries of U1 small nuclear RNA.

PubMed Central

Kunkel, G R; Pederson, T

1985-01-01

Transcription-proximal stages of U1 small nuclear RNA biosynthesis were studied by 32P labeling of nascent chains in isolated HeLa cell nuclei. Labeled RNA was hybridized to nitrocellulose-immobilized, single-stranded M13 DNA clones corresponding to regions within or flanking a human U1 RNA gene. Transcription of U1 RNA was inhibited by greater than 95% by alpha-amanitin at 1 microgram/ml, consistent with previous evidence that it is synthesized by RNA polymerase II. No hybridization to DNA immediately adjacent to the 5' end of mature U1 RNA (-6 to -105 nucleotides) was detected, indicating that, like all studied polymerase II initiation, transcription of U1 RNA starts at or very near the cap site. However, in contrast to previously described transcription units for mRNA, in which equimolar transcription occurs for hundreds or thousands of nucleotides beyond the mature 3' end of the mRNA, labeled U1 RNA hybridization dropped off sharply within a very short region (approximately 60 nucleotides) immediately downstream from the 3' end of mature U1 RNA. Also in contrast to pre-mRNA, which is assembled into ribonucleoprotein (RNP) particles while still nascent RNA chains, the U1 RNA transcribed in isolated nuclei did not form RNP complexes by the criterion of reaction with a monoclonal antibody for the small nuclear RNP Sm proteins. This suggests that, unlike pre-mRNA-RNP particle formation, U1 small nuclear RNP assembly does not occur until after the completion of transcription. These results show that, despite their common synthesis by RNA polymerase II, mRNA and U1 small nuclear RNA differ markedly both in their extents of 3' processing and their temporal patterns of RNP assembly. Images PMID:2942763

Estimating raw material equivalents on a macro-level: comparison of multi-regional input-output analysis and hybrid LCI-IO.

PubMed

Schoer, Karl; Wood, Richard; Arto, Iñaki; Weinzettel, Jan

2013-12-17

The mass of material consumed by a population has become a useful proxy for measuring environmental pressure. The "raw material equivalents" (RME) metric of material consumption addresses the issue of including the full supply chain (including imports) when calculating national or product level material impacts. The RME calculation suffers from data availability, however, as quantitative data on production practices along the full supply chain (in different regions) is required. Hence, the RME is currently being estimated by three main approaches: (1) assuming domestic technology in foreign economies, (2) utilizing region-specific life-cycle inventories (in a hybrid framework), and (3) utilizing multi-regional input-output (MRIO) analysis to explicitly cover all regions of the supply chain. While the first approach has been shown to give inaccurate results, this paper focuses on the benefits and costs of the latter two approaches. We analyze results from two key (MRIO and hybrid) projects modeling raw material equivalents, adjusting the models in a stepwise manner in order to quantify the effects of individual conceptual elements. We attempt to isolate the MRIO gap, which denotes the quantitative impact of calculating the RME of imports by an MRIO approach instead of the hybrid model, focusing on the RME of EU external trade imports. While, the models give quantitatively similar results, differences become more pronounced when tracking more detailed material flows. We assess the advantages and disadvantages of the two approaches and look forward to ways to further harmonize data and approaches.

Enhanced DNA Sensing via Catalytic Aggregation of Gold Nanoparticles

PubMed Central

Huttanus, Herbert M.; Graugnard, Elton; Yurke, Bernard; Knowlton, William B.; Kuang, Wan; Hughes, William L.; Lee, Jeunghoon

2014-01-01

A catalytic colorimetric detection scheme that incorporates a DNA-based hybridization chain reaction into gold nanoparticles was designed and tested. While direct aggregation forms an inter-particle linkage from only ones target DNA strand, the catalytic aggregation forms multiple linkages from a single target DNA strand. Gold nanoparticles were functionalized with thiol-modified DNA strands capable of undergoing hybridization chain reactions. The changes in their absorption spectra were measured at different times and target concentrations and compared against direct aggregation. Catalytic aggregation showed a multifold increase in sensitivity at low target concentrations when compared to direct aggregation. Gel electrophoresis was performed to compare DNA hybridization reactions in catalytic and direct aggregation schemes, and the product formation was confirmed in the catalytic aggregation scheme at low levels of target concentrations. The catalytic aggregation scheme also showed high target specificity. This application of a DNA reaction network to gold nanoparticle-based colorimetric detection enables highly-sensitive, field-deployable, colorimetric readout systems capable of detecting a variety of biomolecules. PMID:23891867

DNA typing by microbead arrays and PCR-SSP: apparent false-negative or -positive hybridization or amplification signals disclose new HLA-B and -DRB1 alleles.

PubMed

Rahal, M; Kervaire, B; Villard, J; Tiercy, J-M

2008-03-01

Human leukocyte antigen (HLA) typing by polymerase chain reaction-sequence-specific oligonucleotide (PCR-SSO) hybridization on solid phase (microbead assay) or polymerase chain reaction-sequence-specific primers (PCR-SSP) requires interpretation softwares to detect all possible allele combinations. These programs propose allele calls by taking into account false-positive or false-negative signal(s). The laboratory has the option to validate typing results in the presence of strongly cross-reacting or apparent false-negative signals. Alternatively, these seemingly aberrant signals may disclose novel variants. We report here four new HLA-B (B*5620 and B*5716) and HLA-DRB1 alleles (DRB1*110107 and DRB1*1474) that were detected by apparent false-negative or -positive hybridization or amplification patterns, and ultimately resolved by sequencing. To avoid allele misassignments, a comprehensive evaluation of acquired data as documented in a quality assurance system is therefore required to confirm unambiguous typing interpretation.

In-situ immobilization of quantum dots in polysaccharide-based nanogels for integration of optical pH-sensing, tumor cell imaging, and drug delivery.

PubMed

Wu, Weitai; Aiello, Michael; Zhou, Ting; Berliner, Alexandra; Banerjee, Probal; Zhou, Shuiqin

2010-04-01

We report a class of polysaccharide-based hybrid nanogels that can integrate the functional building blocks for optical pH-sensing, cancer cell imaging, and controlled drug release into a single nanoparticle system, which can offer broad opportunities for combined diagnosis and therapy. The hybrid nanogels were prepared by in-situ immobilization of CdSe quantum dots (QDs) in the interior of the pH and temperature dual responsive hydroxypropylcellulose-poly(acrylic acid) (HPC-PAA) semi-interpenetrating polymer networks. The-OH groups of the HPC chains are designed to sequester the precursor Cd(2+) ions into the nanogels as well as stabilize the in-situ formed CdSe QDs. The pH-sensitive PAA network chains are designed to induce a pH-responsive volume phase transition of the hybrid nanogels. The developed HPC-PAA-CdSe hybrid nanogels combine a strong trap emission at 741nm for sensing physicochemical environment in a pH dependent manner and a visible excitonic emission at 592nm for mouse melanoma B16F10 cell imaging. The hybrid nanogels also provide excellent stability as a drug carrier, which cannot only provide a high drug loading capacity for a model anticancer drug temozolomide, but also offer a pH-triggered sustained-release of the drug molecules in the gel network. Copyright 2010 Elsevier Ltd. All rights reserved.

An enzyme-free flow cytometric bead assay for the sensitive detection of microRNAs based on click nucleic acid ligation-mediated signal amplification.

PubMed

Qi, Yan; Qiu, Liying; Fan, Wenjiao; Liu, Chenghui; Li, Zhengping

2017-08-07

A versatile flow cytometric bead assay (FCBA) coupled with a completely enzyme-free signal amplification mechanism is developed for the sensitive detection of microRNAs (miRNAs). This new strategy integrates click chemistry-mediated ligation chain reaction (CLCR) with hybridization chain reaction (HCR) for enzyme-free signal amplification on magnetic beads (MBs), and a flow cytometer for the robust fluorescence readout of the MBs. Firstly, target miRNA can initiate CLCR on the surface of MBs based on the click chemical ligation between dibenzocyclooctyne (DBCO)- and azide-modified single-stranded DNA (ssDNA) probes, and the amount of ligated ssDNA sequences on the MBs will be proportional to the dosage of target miRNA. Afterward, each of the ligated ssDNA products can trigger a cascade chain reaction of hybridization events between two alternating fluorophore-tagged hairpin probes, resulting in another signal amplification pathway with an amplified accumulation of fluorophores on the MBs. Finally, the fluorophore-anchored MBs are directly and rapidly analyzed by using a flow cytometer without any separation or elution processes. Herein, the click nucleic acid ligation only occurs on the surface of MBs, so the nonspecific ligations are greatly inhibited compared with that of ligation reaction performed in homogeneous solution. Furthermore, the signal amplification by CLCR-HCR is highly efficient but totally enzyme-free, which may overcome the potential drawbacks of conventional enzyme-catalyzed signal amplification protocols and lead to a high sensitivity. The CLCR-HCR-based FCBA has pushed the detection limit of let-7a miRNA down to the femtomolar (fM) level, showing great potential in miRNA-related biological studies and disease diagnosis.

Hybrid organic-inorganic connectivity of NdIII(pyrazine-N,N'-dioxide)[CoIII(CN)6]3- coordination chains for creating near-infrared emissive Nd(iii) showing field-induced slow magnetic relaxation.

PubMed

Chorazy, Szymon; Charytanowicz, Tomasz; Wang, Junhao; Ohkoshi, Shin-Ichi; Sieklucka, Barbara

2018-05-29

A near-infrared emissive and magnetically anisotropic Nd(iii) complex is formed within a hybrid organic-inorganic {[NdIII(pzdo)(H2O)4][CoIII(CN)6]}·0.5(pzdo)·4H2O (1) (pzdo = pyrazine-N,N'-dioxide) ladder chain built of coexisting Nd-pzdo-Nd and Nd-NC-Co molecular bridges. 1 reveals two NdIII-centered properties, a field-induced slow magnetic relaxation of a single-ion origin with a thermal energy barrier of ΔE/kB = 51(2) K at Hdc = 1 kOe, and a near-infrared fluorescence sensitized by organic and inorganic linkers.

Functional lignocellulosic materials prepared by ATRP from a wood scaffold.

PubMed

Cabane, Etienne; Keplinger, Tobias; Künniger, Tina; Merk, Vivian; Burgert, Ingo

2016-08-10

Wood, a natural and abundant source of organic polymers, has been used as a scaffold to develop novel wood-polymer hybrid materials. Through a two-step surface-initiated Atom Transfer Radical Polymerization (ATRP), the porous wood structure can be effectively modified with polymer chains of various nature. In the present study, polystyrene and poly(N-isopropylacrylamide) were used. As shown with various characterization techniques including confocal Raman microscopy, FTIR, and SEM/EDX, the native wood ultrastructure and features are retained and the polymer chains can be introduced deep within the wood, i.e. inside the wood cell walls. The physical properties of the new materials have been studied, and results indicate that the insertion of polymer chains inside the wood cell wall alters the intrinsic properties of wood to yield a hybrid composite material with new functionalities. This approach to the functionalization of wood could lead to the fabrication of a new class of interesting functional materials and promote innovative utilizations of the renewable resource wood.

Switch from hapten-specific immunoglobulin M to immunoglobulin D secretion in a hybrid mouse cell line.

PubMed Central

Neuberger, M S; Rajewsky, K

1981-01-01

From a hybrid mouse cell line (B1-8) that secreted an IgM, lambda 1 anti-(4-hydroxy-3-nitrophenyl)acetyl antibody but that had no detectable surface IgM, selection for a variant with lambda 1 chains on the surface resulted in the isolation of a line that had switched from mu to delta expression. The surface and secreted Igs of this line were typed as IgD with two monoclonal antibodies, and the parental IgM and variant IgD molecules carried the same variable regions as judged by hapten-binding and idiotypic analysis. The surface and secreted delta chains of the IgD variant have apparent molecular weights of 64,000 and 61,000, respectively. However, the unglycosylated secreted delta polypeptide chain has a molecular weight of only 44,000. The secreted IgD exists predominantly in the delta 2 lambda A2 form, does not contain J protein, is relatively stable in serum, and does not fix complement. Images PMID:6940132

Investigation of the interfacial properties of polyurethane/carbon nanotube hybrid composites: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Goclon, Jakub; Panczyk, Tomasz; Winkler, Krzysztof

2018-03-01

Considering the varied applications of hybrid polymer/carbon nanotube composites and the constant progress in the synthesis methods of such materials, we report a theoretical study of interfacial layer formation between pristine single-wall carbon nanotubes (SWCNTs) and polyurethane (PU) using molecular dynamic simulations. We vary the SWCNT diameter and the number of PU chains to examine various PU-SWCNT interaction patterns. Our simulations indicate the important role of intra-chain forces in PU. No regular polymeric structures could be identified on the carbon nanotube surface during the simulations. We find that increasing the SWCNT diameter results in stronger polymer binding. However, higher surface loadings of PU lead to stronger interpenetration by the polymeric segments; this effect is more apparent for SWCNTs with small diameters. Our core finding is that the attached PU binds most strongly to the carbon nanotubes with the largest diameters. Polymer dynamics reveal the loose distribution of PU chains in these systems.

Functional lignocellulosic materials prepared by ATRP from a wood scaffold

PubMed Central

Cabane, Etienne; Keplinger, Tobias; Künniger, Tina; Merk, Vivian; Burgert, Ingo

2016-01-01

Wood, a natural and abundant source of organic polymers, has been used as a scaffold to develop novel wood-polymer hybrid materials. Through a two-step surface-initiated Atom Transfer Radical Polymerization (ATRP), the porous wood structure can be effectively modified with polymer chains of various nature. In the present study, polystyrene and poly(N-isopropylacrylamide) were used. As shown with various characterization techniques including confocal Raman microscopy, FTIR, and SEM/EDX, the native wood ultrastructure and features are retained and the polymer chains can be introduced deep within the wood, i.e. inside the wood cell walls. The physical properties of the new materials have been studied, and results indicate that the insertion of polymer chains inside the wood cell wall alters the intrinsic properties of wood to yield a hybrid composite material with new functionalities. This approach to the functionalization of wood could lead to the fabrication of a new class of interesting functional materials and promote innovative utilizations of the renewable resource wood. PMID:27506369

Bayesian clustering of DNA sequences using Markov chains and a stochastic partition model.

PubMed

Jääskinen, Väinö; Parkkinen, Ville; Cheng, Lu; Corander, Jukka

2014-02-01

In many biological applications it is necessary to cluster DNA sequences into groups that represent underlying organismal units, such as named species or genera. In metagenomics this grouping needs typically to be achieved on the basis of relatively short sequences which contain different types of errors, making the use of a statistical modeling approach desirable. Here we introduce a novel method for this purpose by developing a stochastic partition model that clusters Markov chains of a given order. The model is based on a Dirichlet process prior and we use conjugate priors for the Markov chain parameters which enables an analytical expression for comparing the marginal likelihoods of any two partitions. To find a good candidate for the posterior mode in the partition space, we use a hybrid computational approach which combines the EM-algorithm with a greedy search. This is demonstrated to be faster and yield highly accurate results compared to earlier suggested clustering methods for the metagenomics application. Our model is fairly generic and could also be used for clustering of other types of sequence data for which Markov chains provide a reasonable way to compress information, as illustrated by experiments on shotgun sequence type data from an Escherichia coli strain.

A multiple multicomponent approach to chimeric peptide-peptoid podands.

PubMed

Rivera, Daniel G; León, Fredy; Concepción, Odette; Morales, Fidel E; Wessjohann, Ludger A

2013-05-10

The success of multi-armed, peptide-based receptors in supramolecular chemistry traditionally is not only based on the sequence but equally on an appropriate positioning of various peptidic chains to create a multivalent array of binding elements. As a faster, more versatile and alternative access toward (pseudo)peptidic receptors, a new approach based on multiple Ugi four-component reactions (Ugi-4CR) is proposed as a means of simultaneously incorporating several binding and catalytic elements into organizing scaffolds. By employing α-amino acids either as the amino or acid components of the Ugi-4CRs, this multiple multicomponent process allows for the one-pot assembly of podands bearing chimeric peptide-peptoid chains as appended arms. Tripodal, bowl-shaped, and concave polyfunctional skeletons are employed as topologically varied platforms for positioning the multiple peptidic chains formed by Ugi-4CRs. In a similar approach, steroidal building blocks with several axially-oriented isocyano groups are synthesized and utilized to align the chimeric chains with conformational constrains, thus providing an alternative to the classical peptido-steroidal receptors. The branched and hybrid peptide-peptoid appendages allow new possibilities for both rational design and combinatorial production of synthetic receptors. The concept is also expandable to other multicomponent reactions. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure of rigid polymers confined to nanoparticles: Molecular dynamics simulations insight

DOE PAGES

Maskey, Sabina; Lane, J. Matthew D.; Perahia, Dvora; ...

2016-02-04

Nanoparticles (NPs) grafted with organic layers form hybrids able to retain their unique properties through integration into the mesoscopic scale. The organic layer structure and response often determine the functionality of the hybrids on the mesoscopic length scale. Using molecular dynamics (MD) simulations, we probe the conformation of luminescent rigid polymers, dialkyl poly(p-phenylene ethynylene)s (PPE), end-grafted onto a silica nanoparticle in different solvents as the molecular weights and polymer coverages are varied. We find that, in contrast to NP-grafted flexible polymers, the chains are fully extended independent of the solvent. In toluene and decane, which are good solvents, the graftedmore » PPEs chains assume a similar conformation to that observed in dilute solutions. In water, which is a poor solvent for the PPEs, the polymer chains form one large cluster but remain extended. The radial distribution of the chains around the core of the nanoparticle is homogeneous in good solvents, whereas in poor solvents clusters are formed independent of molecular weights and coverages. As a result, the clustering is distinctively different from the response of grafted flexible and semiflexible polymers.« less

PLGA/liposome hybrid nanoparticles for short-chain ceramide delivery

PubMed Central

Zou, Peng; Stern, Stephan T.; Sun, Duxin

2014-01-01

Purpose Rapid premature release of lipophilic drugs from liposomal lipid bilayer to plasma proteins and biological membranes is a challenge for targeted drug delivery. The purpose of this study is to reduce premature release of lipophilic short-chain ceramides by encapsulating ceramides into liposomal aqueous interior with the aid of poly( lactic-coglycolicacid) (PLGA). Methods BODIPY FL labeled ceramide (FL-ceramide) and BODIPY-TR labeled ceramide (TR-ceramide) were encapsulated into carboxy-terminated PLGA nanoparticles. The negatively charged PLGA nanoparticles were then encapsulated into cationic liposomes to obtain PLGA/liposome hybrids. As a control, FL-ceramide and/or TR ceramide co-loaded liposomes without PLGA were prepared. The release of ceramides from PLGA/liposome hybrids and liposomes in rat plasma, cultured MDA-MB-231 cells, and rat blood circulation was compared using fluorescence resonance energy transfer (FRET) between FL-ceramide (donor) and TR-ceramide (acceptor). Results FRET analysis showed that FL-ceramide and TR-ceramide in liposomal lipid bilayer were rapidly released during incubation with rat plasma. In contrast, the FL-ceramide and TR-ceramide in PLGA/liposome hybrids showed extended release. FRET images of cells revealed that ceramides in liposomal bilayer were rapidly transferred to cell membranes. In contrast, ceramides in PLGA/liposome hybrids were internalized into cells with nanoparticles simultaneously. Upon intravenous administration to rats, ceramides encapsulated in liposomal bilayer were completely released in 2 minutes. In contrast, ceramides encapsulated in the PLGA core were retained in PLGA/liposome hybrids for 4 hours. Conclusions The PLGA/liposome hybrid nanoparticles reduced in vitro and in vivo premature release of ceramides and offer a viable platform for targeted delivery of lipophilic drugs. PMID:24065591

Insertion of Ag atoms into layered MoO{sub 3} via a template route

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shao, Ke, E-mail: shaoke@szu.edu.cn; Wang, Hao

2012-11-15

Graphical abstract: PVP–Ag{sup +} complex self-assembled with inorganic (Mo{sub x}O{sub y}){sub ∞}{sup n−} chains into a layered hybrid, in which the PVP–Ag complex was intercalated between the (Mo{sub x}O{sub y}){sub ∞}{sup n−} layers. Calcinations of this hybrid at 500 °C lead to formation of Ag/MoO{sub 3} nanohybrid. By this method we have successfully inserted Ag atoms into the semiconductor MoO{sub 3} lattice. Display Omitted Highlights: ► We fabricated a PVP–Ag/polyoxomolybdate layered hybrid via in situ self-assembly. ► The PVP–Ag complex has been inserted between the molybdenum oxide layers. ► This layered hybrid transformed into Ag/MoO{sub 3} nanocomposite after calcinations. ►more » HR-TEM images show that Ag atoms of about 1 nm have been inserted in the MoO{sub 3} layers. -- Abstract: We report insertion of Ag atoms into layered MoO{sub 3} via an in situ template route. PVP–Ag{sup +} complex self-assembled with inorganic (Mo{sub x}O{sub y}){sub ∞}{sup n−} chains into a layered hybrid, in which the PVP–Ag complex was intercalated between the (Mo{sub x}O{sub y}){sub ∞}{sup n−} layers. Calcinations of this hybrid at 500 °C lead to formation of Ag/MoO{sub 3} hybrid, in which Ag nanoparticles of about 1 nm have been inserted between the MoO{sub 3} layers. By this method pillared MoO{sub 3} has been obtained very easily. We believe that this research opens new routes to fabricate novel intercalation compounds and metal/semiconductor nanohybrids via an efficient and green route.« less

Interactions between PBEF and oxidative stress proteins-a potential new mechanism underlying PBEF in the pathogenesis of acute lung injury

PubMed Central

Zhang, Li Qin; Adyshev, Djanybek M.; Singleton, Patrick; Li, Hailong; Cepeda, Javier; Huang, Sheng-You; Zou, Xiaoqin; Verin, Alexander D.; Tu, Jiancheng; Garcia, Joe G.N.; Ye, Shui Qing

2008-01-01

Identification of pre-B-cell colony-enhancing factor (PBEF) interacting partners may reveal new molecular mechanisms of PBEF in the pathogenesis of acute lung injury (ALI). The interactions between PBEF and NADH dehydrogenase subunit 1(ND1), ferritin light chain and interferon induced transmembrane 3 (IFITM3) in human pulmonary vascular endothelial cells were identified and validated. ND1, ferritin and IFITM3 are involved in oxidative stress and inflammation. Overexpression of PBEF increased its interactions and intracellular oxidative stress, which can be attenuated by rotenone. The interaction modeling between PBEF and ND1 is consistent with the corresponding experimental finding. These interactions may underlie a novel role of PBEF in the pathogenesis of ALI. Structured summary MINT-6538697: PBEF (uniprotkb:P43490) physically interacts (MI:0218) with NADH1 (uniprotkb:P03886) by two hybrid (MI:0018) MINT-6538811, MINT-6538868: PBEF (uniprotkb:P43490) physically interacts (MI:0218) with interferon-induced transmembra (uniprotkb:Q01628) by anti bait coimmunoprecipitation (MI:0006) MINT-6538787, MINT-6538841: PBEF (uniprotkb:P43490) physically interacts (MI:0218) with NADH1 (uniprotkb:P03886) by anti bait coimmunoprecipitation (MI:0006) MINT-6538755: PBEF (uniprotkb:P43490) physically interacts (MI:0218) with gamma-glutamil-transferase (uniprotkb:P19440) by two hybrid (MI:0018) MINT-6538799, MINT-6538862: PBEF (uniprotkb:P43490) physically interacts (MI:0218) with Ferritin light chain (uniprotkb:P02792) by anti bait coimmunoprecipitation (MI:0006) MINT-6538769: PBEF (uniprotkb:P43490) physically interacts (MI:0218) with E2L6 (uniprotkb:O14933) by two hybrid (MI:0018) MINT-6538741: PBEF (uniprotkb:P43490) physically interacts (MI:0218) with Adenosine A2aR (uniprotkb:P29274) by two hybrid (MI:0018) MINT-6538727: PBEF (uniprotkb:P43490) physically interacts (MI:0218) with interferon-induced transmembra (uniprotkb:Q01628) by two hybrid (MI:0018) MINT-6538712: PBEF (uniprotkb:P43490) physically interacts (MI:0218) with Ferritin light chain (uniprotkb:P02792) by two hybrid (MI:0018) PMID:18486613

Effect of Fluorocarbon and Hydrocarbon Chain Lengths in Hybrid Surfactants for Supercritical CO2.

PubMed

Sagisaka, Masanobu; Ono, Shinji; James, Craig; Yoshizawa, Atsushi; Mohamed, Azmi; Guittard, Frédéric; Rogers, Sarah E; Heenan, Richard K; Yan, Ci; Eastoe, Julian

2015-07-14

Hybrid surfactants containing both fluorocarbon (FC) and hydrocarbon (HC) chains have recently been shown to solubilize water and form elongated reversed micelles in supercritical CO2. To clarify the most effective FC and HC chain lengths, the aggregation behavior and interfacial properties of hybrid surfactants FCm-HCn (FC length m/HC length n = 4/2, 4/4, 6/2, 6/4, 6/5, 6/6, and 6/8) were examined in W/CO2 mixtures as functions of pressure, temperature, and water-to-surfactant molar ratio (W0). The solubilizing power of hybrid surfactants for W/CO2 microemulsions was strongly affected by not only the FC length but also by that of the HC. Although the surfactants having short FC and/or HC tails (namely, m/n = 4/2, 4/4, and 6/2) did not dissolve in supercritical CO2 (even at ∼17 mM, ≤400 bar, temperature ≤ 75 °C, and W0 = 0-40), the other hybrid surfactants were able to yield transparent single-phase W/CO2 mixtures identified as microemulsions. The solubilizing power of FC6-HCm surfactants reached a maximum (W0 ∼ 80 at 45 °C and 350 bar) with a hydrocarbon length, m, of 4. The W0 value of 80 is the highest for a HC-FC hybrid surfactant, matching the highest value reported for a FC surfactant which contained more FC groups. High-pressure small-angle neutron scattering measurements from FCm-HCn/D2O/CO2 microemulsions were consistent with growth of the microemulsion droplets with increasing W0. In addition, not only spherical reversed micelles but also nonspherical assemblies (rodlike or ellipsoidal) were found for the systems with FC6-HCn (n = 4-6). At fixed surfactant concentration and W0 (17 mM and W0 = 20), the longest reversed micelles were obtained for FC6-HC6 where a mean aspect ratio of 6.3 was calculated for the aqueous cores.

Hybrid sparse blind deconvolution: an implementation of SOOT algorithm to real data

NASA Astrophysics Data System (ADS)

Pakmanesh, Parvaneh; Goudarzi, Alireza; Kourki, Meisam

2018-06-01

Getting information of seismic data depends on deconvolution as an important processing step; it provides the reflectivity series by signal compression. This compression can be obtained by removing the wavelet effects on the traces. The recently blind deconvolution has provided reliable performance for sparse signal recovery. In this study, two deconvolution methods have been implemented to the seismic data; the convolution of these methods provides a robust spiking deconvolution approach. This hybrid deconvolution is applied using the sparse deconvolution (MM algorithm) and the Smoothed-One-Over-Two algorithm (SOOT) in a chain. The MM algorithm is based on the minimization of the cost function defined by standards l1 and l2. After applying the two algorithms to the seismic data, the SOOT algorithm provided well-compressed data with a higher resolution than the MM algorithm. The SOOT algorithm requires initial values to be applied for real data, such as the wavelet coefficients and reflectivity series that can be achieved through the MM algorithm. The computational cost of the hybrid method is high, and it is necessary to be implemented on post-stack or pre-stack seismic data of complex structure regions.

A novel SERRS sandwich-hybridization assay to detect specific DNA target.

PubMed

Feuillie, Cécile; Merheb, Maxime Mohamad; Gillet, Benjamin; Montagnac, Gilles; Daniel, Isabelle; Hänni, Catherine

2011-01-01

In this study, we have applied Surface Enhanced Resonance Raman Scattering (SERRS) technology to the specific detection of DNA. We present an innovative SERRS sandwich-hybridization assay that allows specific DNA detection without any enzymatic amplification, such as is the case with Polymerase Chain Reaction (PCR). In some substrates, such as ancient or processed remains, enzymatic amplification fails due to DNA alteration (degradation, chemical modification) or to the presence of inhibitors. Consequently, the development of a non-enzymatic method, allowing specific DNA detection, could avoid long, expensive and inconclusive amplification trials. Here, we report the proof of concept of a SERRS sandwich-hybridization assay that leads to the detection of a specific chamois DNA. This SERRS assay reveals its potential as a non-enzymatic alternative technology to DNA amplification methods (particularly the PCR method) with several applications for species detection. As the amount and type of damage highly depend on the preservation conditions, the present SERRS assay would enlarge the range of samples suitable for DNA analysis and ultimately would provide exciting new opportunities for the investigation of ancient DNA in the fields of evolutionary biology and molecular ecology, and of altered DNA in food frauds detection and forensics.

A Novel SERRS Sandwich-Hybridization Assay to Detect Specific DNA Target

PubMed Central

Gillet, Benjamin; Montagnac, Gilles; Daniel, Isabelle; Hänni, Catherine

2011-01-01

In this study, we have applied Surface Enhanced Resonance Raman Scattering (SERRS) technology to the specific detection of DNA. We present an innovative SERRS sandwich-hybridization assay that allows specific DNA detection without any enzymatic amplification, such as is the case with Polymerase Chain Reaction (PCR). In some substrates, such as ancient or processed remains, enzymatic amplification fails due to DNA alteration (degradation, chemical modification) or to the presence of inhibitors. Consequently, the development of a non-enzymatic method, allowing specific DNA detection, could avoid long, expensive and inconclusive amplification trials. Here, we report the proof of concept of a SERRS sandwich-hybridization assay that leads to the detection of a specific chamois DNA. This SERRS assay reveals its potential as a non-enzymatic alternative technology to DNA amplification methods (particularly the PCR method) with several applications for species detection. As the amount and type of damage highly depend on the preservation conditions, the present SERRS assay would enlarge the range of samples suitable for DNA analysis and ultimately would provide exciting new opportunities for the investigation of ancient DNA in the fields of evolutionary biology and molecular ecology, and of altered DNA in food frauds detection and forensics. PMID:21655320

Anti-cancer activity of new designer hydrogen sulfide-donating hybrids.

PubMed

Kashfi, Khosrow

2014-02-10

Hydrogen sulfide (H2S) is likely to join nitric oxide (NO) and carbon monoxide (CO) as the third gaseous transmitter, influencing an array of intracellular signaling cascades. Thus, H2S is implicated in numerous physiological processes and in the pathology of various diseases. H2S-donating agents that liberate H2S slowly either alone or in combination with NO, the so-called NOSH compounds, are being synthesized, and these have been shown to have great potential against cancer. An accurate determination of H2S levels is challenging. H2S and NO share many similar actions; do these similarities act to potentiate each other? Since many actions of H2S appear to be mediated through inhibition of inflammation and Nuclear factor kappa-light-chain-enhancer of activated B cells is a central player in this scenario, does S-nitrosylation of this transcription factor by NO affect its S-sulfhydration by H2S and vice versa? Deciphering the molecular targets of these novel hybrid agents and having genetically engineered animals should help us move toward targeted therapeutic applications. Human safety data with these new hybrids is essential.

Alternating-current conductivity and dielectric relaxation of bulk iodoargentate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duan, Hai-Bao, E-mail: duanhaibao4660@163.com; Yu, Shan-Shan; Zhou, Hong

Graphical abstract: The electric modulus shows single dielectric relaxation process in the measured frequency range. - Highlights: • The conduction mechanism is described by quantum mechanical tunneling model. • The applications of dielectric modulus give a simple method for evaluating the activation energy of the dielectric relaxation. • The [Ag{sub 2}I{sub 4}]{sup 2−}1-D chain and [Cu(en){sub 2}]{sup 2+} cation column form the layered stacks by hydrogen bond interactions. - Abstract: An inorganic-organic hybrid compound Cu(en){sub 2}Ag{sub 2}I{sub 4} (en = ethylenediamine) (1) was synthesized and single crystal structurally characterized. Along the [001] direction, the inorganic parts form an infinite 1-Dmore » chain and [Cu(en){sub 2}]{sup 2+} cations are separated by inorganic chain. The electrical conductivity and dielectric properties of 1 have been investigated over wide ranges of frequency. The alternating-current conductivities have been fitted to the Almond–West type power law expression with use of a single value of S. It is found that S values for 1 are nearly temperature-independent, which indicates that the conduction mechanism could be quantum mechanical tunneling (QMT) model. The dielectric loss and electric modulus show single dielectric relaxation process. The activation energy obtained from temperature-dependent electric modulus compare with the calculated from the dc conductivity plots.« less

Superhydrophobic hybrid membranes by grafting arc-like macromolecular bridges on graphene sheets: Synthesis, characterization and properties

NASA Astrophysics Data System (ADS)

Mo, Zhao-Hua; Luo, Zheng; Huang, Qiang; Deng, Jian-Ping; Wu, Yi-Xian

2018-05-01

Grafting single end-tethered polymer chains on the surface of graphene is a conventional way to modify the surface properties of graphene oxide. However, grafting arc-like macromolecular bridges on graphene surfaces has been barely reported. Herein, a novel arc-like polydimethylsiloxane (PDMS) macromolecular bridges grafted graphene sheets (GO-g-Arc PDMS) was successfully synthesized via a confined interface reaction at 90 °C. Both the hydrophilic α- and ω-amino groups of linear hydrophobic NH2-PDMS-NH2 macromolecular chains rapidly reacted with epoxy and carboxyl groups on the surfaces of graphene oxide in water suspension to form arc-like PDMS macromolecular bridges on graphene sheets. The grafting density of arc-like PDMS bridges on graphene sheets can reach up to 0.80 mmol g-1 or 1.32 arc-like bridges per nm2 by this confined interface reaction. The water contact angle (WCA) of the hybrid membrane could be increased with increasing both the grafting density and content of covalent arc-like bridges architecture. The superhydrophobic hybrid membrane with a WCA of 153.4° was prepared by grinding of the above arc-like PDMS bridges grafted graphene hybrid, dispersing in ethanol and filtrating by organic filter membrane. This superhydrophobic hybrid membrane shows good self-cleaning and complete oil-water separation properties, which provides potential applications in anticontamination coating and oil-water separation. To the best of our knowledge, this is the first report on the synthesis of functional hybrid membranes by grafting arc-like PDMS macromolecular bridges on graphene sheets via a confined interface reaction.

Amphiphilic graft copolymers from end-functionalized starches: synthesis, characterization, thin film preparation, and small molecule loading.

PubMed

Ryno, Lisa M; Reese, Cassandra; Tolan, McKenzie; O'Brien, Jeffrey; Short, Gabriel; Sorriano, Gerardo; Nettleton, Jason; Fulton, Kayleen; Iovine, Peter M

2014-08-11

End-functionalized macromolecular starch reagents, prepared by reductive amination, were grafted onto a urethane-linked polyester-based backbone using copper-catalyzed azide-alkyne cycloaddition (CuAAC) chemistry to produce novel amphiphilic hybrid graft copolymers. These copolymers represent the first examples of materials where the pendant chains derived from starch biopolymers have been incorporated into a host polymer by a grafting-to approach. The graft copolymers were prepared in good yields (63-90%) with high grafting efficiencies (66-98%). Rigorous quantitative spectroscopic analyses of both the macromolecular building blocks and the final graft copolymers provide a comprehensive analytical toolbox for deciphering the reaction chemistry. Due to the modular nature of both the urethane-linked polyester synthesis and the postpolymerization modification, the starch content of these novel hybrid graft copolymers was easily tuned from 28-53% (w/w). The uptake of two low molecular weight guest molecules into the hybrid polymer thin films was also studied. It was found that binding of 1-naphthol and pterostilbene correlated linearly with amount of starch present in the hybrid polymer. The newly synthesized graft copolymers were highly processable and thermally stable, therefore, opening up significant opportunities in film and coating applications. These results represent a proof-of-concept system for not only the construction of starch-containing copolymers, but also the loading of these novel polymeric materials with active agents.

Graphene Nanoprobes for Real-Time Monitoring of Isothermal Nucleic Acid Amplification.

PubMed

Li, Fan; Liu, Xiaoguo; Zhao, Bin; Yan, Juan; Li, Qian; Aldalbahi, Ali; Shi, Jiye; Song, Shiping; Fan, Chunhai; Wang, Lihua

2017-05-10

Isothermal amplification is an efficient way to amplify DNA with high accuracy; however, the real-time monitoring for quantification analysis mostly relied on expensive and precisely designed probes. In the present study, a graphene oxide (GO)-based nanoprobe was used to real-time monitor the isothermal amplification process. The interaction between GO and different DNA structures was systematically investigated, including single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), DNA 3-helix, and long rolling circle amplification (RCA) and hybridization chain reaction (HCR) products, which existed in one-, two-, and three-dimensional structures. It was found that the high rigid structures exhibited much lower affinity with GO than soft ssDNA, and generally the rigidity was dependent on the length of targets and the hybridization position with probe DNA. On the basis of these results, we successfully monitored HCR amplification process, RCA process, and the enzyme restriction of RCA products with GO nanoprobe; other applications including the detection of the assembly/disassembly of DNA 3-helix structures were also performed. Compared to the widely used end-point detection methods, the GO-based sensing platform is simple, sensitive, cost-effective, and especially in a real-time monitoring mode. We believe such studies can provide comprehensive understandings and evocation on design of GO-based biosensors for broad application in various fields.

Future Supply Chains Enabled by Continuous Processing—Opportunities and Challenges. May 20–21, 2014 Continuous Manufacturing Symposium

PubMed Central

Srai, Jagjit Singh; Badman, Clive; Krumme, Markus; Futran, Mauricio; Johnston, Craig

2015-01-01

This paper examines the opportunities and challenges facing the pharmaceutical industry in moving to a primarily “continuous processing”-based supply chain. The current predominantly “large batch” and centralized manufacturing system designed for the “blockbuster” drug has driven a slow-paced, inventory heavy operating model that is increasingly regarded as inflexible and unsustainable. Indeed, new markets and the rapidly evolving technology landscape will drive more product variety, shorter product life-cycles, and smaller drug volumes, which will exacerbate an already unsustainable economic model. Future supply chains will be required to enhance affordability and availability for patients and healthcare providers alike despite the increased product complexity. In this more challenging supply scenario, we examine the potential for a more pull driven, near real-time demand-based supply chain, utilizing continuous processing where appropriate as a key element of a more “flow-through” operating model. In this discussion paper on future supply chain models underpinned by developments in the continuous manufacture of pharmaceuticals, we have set out; The significant opportunities to moving to a supply chain flow-through operating model, with substantial opportunities in inventory reduction, lead-time to patient, and radically different product assurance/stability regimes. Scenarios for decentralized production models producing a greater variety of products with enhanced volume flexibility. Production, supply, and value chain footprints that are radically different from today's monolithic and centralized batch manufacturing operations. Clinical trial and drug product development cost savings that support more rapid scale-up and market entry models with early involvement of SC designers within New Product Development. The major supply chain and industrial transformational challenges that need to be addressed. The paper recognizes that although current batch operational performance in pharma is far from optimal and not necessarily an appropriate end-state benchmark for batch technology, the adoption of continuous supply chain operating models underpinned by continuous production processing, as full or hybrid solutions in selected product supply chains, can support industry transformations to deliver right-first-time quality at substantially lower inventory profiles. © 2015 The Authors. Journal of Pharmaceutical Sciences published by Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 104:840–849, 2015 PMID:25631279

Exonuclease III-assisted graphene oxide amplified fluorescence anisotropy strategy for ricin detection.

PubMed

Xiao, Xue; Tao, Jing; Zhang, Hong Zhi; Huang, Cheng Zhi; Zhen, Shu Jun

2016-11-15

Graphene oxide (GO) is an excellent fluorescence anisotropy (FA) amplifier. However, in the conventional GO amplified FA strategy, one target can only induce the FA change of one fluorophore on probe, which limits the detection sensitivity. Herein, we developed an exonuclease III (Exo III) aided GO amplified FA strategy by using aptamer as an recognition element and ricin B-chain as a proof-of-concept target. The aptamer was hybridized with a blocker sequence and linked onto the surface of magnetic beads (MBs). Upon the addition of ricin B-chain, blocker was released from the surface of MBs and hybridized with the dye-modified probe DNA on the surface of GO through the toehold-mediated strand exchange reaction. The formed blocker-probe DNA duplex triggered the Exo III-assisted cyclic signal amplification by repeating the hybridization and digestion of probe DNA, liberating the fluorophore with several nucleotides (low FA value). Thus, ricin B-chain could be sensitively detected by the significantly decreased FA. The linear range was from 1.0μg/mL to 13.3μg/mL and the limit of detection (LOD) was 400ng/mL. This method improved the sensitivity of FA assay and it could be generalized to any kind of target detection based on the use of an appropriate aptamer. Copyright © 2016 Elsevier B.V. All rights reserved.

Scanning electrochemical microscopy of graphene/polymer hybrid thin films as supercapacitors: Physical-chemical interfacial processes

NASA Astrophysics Data System (ADS)

Gupta, Sanju; Price, Carson

2015-10-01

Hybrid electrode comprising an electric double-layer capacitor of graphene nanosheets and a pseudocapacitor of the electrically conducting polymers namely, polyaniline; PAni and polypyrrole; PPy are constructed that exhibited synergistic effect with excellent electrochemical performance as thin film supercapacitors for alternative energy. The hybrid supercapacitors were prepared by layer-by-layer (LbL) assembly based on controlled electrochemical polymerization followed by reduction of graphene oxide electrochemically producing ErGO, for establishing intimate electronic contact through nanoscale architecture and chemical stability, producing a single bilayer of (PAni/ErGO)1, (PPy/ErGO)1, (PAni/GO)1 and (PPy/GO)1. The rationale design is to create thin films that possess interconnected graphene nanosheets (GNS) with polymer nanostructures forming well-defined tailored interfaces allowing sufficient surface adsorption and faster ion transport due to short diffusion distances. We investigated their electrochemical properties and performance in terms of gravimetric specific capacitance, Cs, from cyclic voltammograms. The LbL-assembled bilayer films exhibited an excellent Cs of ≥350 F g-1 as compared with constituents (˜70 F g-1) at discharge current density of 0.3 A g-1 that outperformed many other hybrid supercapacitors. To gain deeper insights into the physical-chemical interfacial processes occurring at the electrode/electrolyte interface that govern their operation, we have used scanning electrochemical microscopy (SECM) technique in feedback and probe approach modes. We present our findings from viewpoint of reinforcing the role played by heterogeneous electrode surface composed of nanoscale graphene sheets (conducting) and conducting polymers (semiconducting) backbone with ordered polymer chains via higher/lower probe current distribution maps. Also targeted is SECM imaging that allowed to determine electrochemical (re)activity of surface ion adsorption sites density at solid/liquid interface.

Highly specific detection of genetic modification events using an enzyme-linked probe hybridization chip.

PubMed

Zhang, M Z; Zhang, X F; Chen, X M; Chen, X; Wu, S; Xu, L L

2015-08-10

The enzyme-linked probe hybridization chip utilizes a method based on ligase-hybridizing probe chip technology, with the principle of using thio-primers for protection against enzyme digestion, and using lambda DNA exonuclease to cut multiple PCR products obtained from the sample being tested into single-strand chains for hybridization. The 5'-end amino-labeled probe was fixed onto the aldehyde chip, and hybridized with the single-stranded PCR product, followed by addition of a fluorescent-modified probe that was then enzymatically linked with the adjacent, substrate-bound probe in order to achieve highly specific, parallel, and high-throughput detection. Specificity and sensitivity testing demonstrated that enzyme-linked probe hybridization technology could be applied to the specific detection of eight genetic modification events at the same time, with a sensitivity reaching 0.1% and the achievement of accurate, efficient, and stable results.

Susceptibility of koi x crucian carp and koi x goldfish hybrids to koi herpesvirus (KHV) and the development of KHV disease (KHVD).

PubMed

Bergmann, S M; Sadowski, J; Kiełpiński, M; Bartłomiejczyk, M; Fichtner, D; Riebe, R; Lenk, M; Kempter, J

2010-03-01

Hybrids of koi, Cyprinus carpio x crucian carp, Carassius carassius and koi x goldfish, Carassius auratus, proved to be susceptible to koi herpesvirus (KHV, syn. CyHV-3) and developed KHV disease (KHVD). While hybrids of koi x goldfish were partly resistant to mortality following infection by immersion, most koi x crucian carp hybrids died after bath infection. KHV DNA was detected in dead fish but also in all surviving animals by different polymerase chain reactions (PCRs). According to these results, hybrid crossbreeding does not seem to prevent severe losses associated with KHV in terms of inducing KHVD. The present study showed severe losses after a waterborne KHV infection of between 35% and 100% in koi x goldfish and koi x crucian carp hybrids as well as in SPF carp.

Enzyme- and label-free electrochemical aptasensor for kanamycin detection based on double stir bar-assisted toehold-mediated strand displacement reaction for dual-signal amplification.

PubMed

Hong, Feng; Chen, Xixue; Cao, Yuting; Dong, Youren; Wu, Dazhen; Hu, Futao; Gan, Ning

2018-07-30

It is critically important to detect antibiotic residues for monitoring food safety. In this study, an enzyme- and label-free electrochemical aptasensor for antibiotics, with kanamycin (Kana) as a typical analyte, was developed based on a double stir bar-assisted toehold-mediated strand displacement reaction (dSB-TMSDR) for dual-signal amplification. First, we modified two gold electrodes (E-1 and E-2) with different DNA probes (S1/S2 hybrid probe in E-1 and DNA fuel strand S3 in E-2). In the presence of Kana, an S1/S2 probe can be disassembled from E-1 to form an S2/Kana complex in supernatant. The S2/Kana could react with S3 on E-2 to form S2/S3 hybrid and release Kana through TMSDR. After then, the target recycling was triggered. Subsequently, the formed S2/S3 hybrid can also trigger a hybridization chain reaction (HCR). Consequently, the dual-signal amplification strategy was established, which resulted in many long dsDNA chains on E-2. The chains can associate with methylene blue (MB) as redox probes to produce a current response for the quantification of Kana. The assay exhibited high sensitivity and specificity with a detection limit at 16 fM Kana due to the dual-signal amplification. The double stir bars system can both increase phase separation and prevent leakage of DNA fuel to reduce background interference. Moreover, it allows flexible sequence design of the TMSDR probes. The assay was successfully employed to detect Kana residues in food and showed potential application value in food safety detection. Copyright © 2018 Elsevier B.V. All rights reserved.

An electrochemical impedance biosensor for Hg2+ detection based on DNA hydrogel by coupling with DNAzyme-assisted target recycling and hybridization chain reaction.

PubMed

Cai, Wei; Xie, Shunbi; Zhang, Jin; Tang, Dianyong; Tang, Ying

2017-12-15

In this work, an electrochemical impedance biosensor for high sensitive detection of Hg 2+ was presented by coupling with Hg 2+ -induced activation of Mg 2+ -specific DNAzyme (Mg 2+ -DNAzyme) for target cycling and hybridization chain reaction (HCR) assembled DNA hydrogel for signal amplification. Firstly, we synthesized two different copolymer chains P1 and P2 by modifying hairpin DNA H3 and H4 with acrylamide polymer, respectively. Subsequently, Hg 2+ was served as trigger to activate the Mg 2+ -DNAzyme for selectively cleavage ribonucleobase-modified substrate in the presence of Mg 2+ . The partial substrate strand could dissociate from DNAzyme structure, and hybridize with capture probe H1 to expose its concealed sequence for further hybridization. With the help of the exposed sequence, the HCR between hairpin DNA H3 and H4 in P1 and P2 was initiated, and assembled a layer of DNA cross-linked hydrogel on the electrode surface. The formed non-conductive DNA hydrogel film could greatly hinder the interfacial electronic transfer which provided a possibility for us to construct a high sensitive impedance biosensor for Hg 2+ detection. Under the optimal conditions, the impedance biosensor showed an excellent sensitivity and selectivity toward Hg 2+ in a concentration range of 0.1pM - 10nM with a detection limit of 0.042pM Moreover, the real sample analysis reveal that the proposed biosensor is capable of discriminating Hg 2+ ions in reliable and quantitative manners, indicating this method has a promising potential for preliminary application in routine tests. Copyright © 2017 Elsevier B.V. All rights reserved.

Biosynthesis of small proteoglycan II (decorin) by chondrocytes and evidence for a procore protein.

PubMed

Sawhney, R S; Hering, T M; Sandell, L J

1991-05-15

We have studied the biosynthesis of cartilage dermatan sulfate proteoglycan II (DS-PGII) (decorin) using in vitro translation of mRNA to determine the size of the primary gene product and by radiolabeling the protein in the presence of tunicamycin to inhibit the addition of Asn-linked oligosaccharides. Pulse-chase experiments were performed to examine post-translational processing and secretion. Inhibitors of oligosaccharide processing were used to determine whether DS-PGII molecules containing partially processed oligosaccharides could become proteoglycans and be secreted. Cell-free translation of sucrose gradient-fractionated RNA and subsequent immunoprecipitation of the core protein confirmed that the functional translated mRNA is in the size range of the two mRNA species observed by hybridization of chondrocyte RNA with a bone PGII cloned probe and that the translation product is a single protein with an apparent molecular mass of 42 kDa. Digestion of the intact proteoglycan (average molecular mass = 103 kDa) with chondroitinase ABC or AC results in an approximately 48-49-kDa product. Chondrocytes treated with tunicamycin to inhibit Asn-linked oligosaccharide addition synthesize and secrete a glycosaminoglycan (GAG)-substituted proteoglycan (average molecular mass = 86 kDa), yielding a 42-kDa core protein after chondroitinase ABC digestion, showing that Asn-linked oligosaccharides are not required for the addition of GAG chains or secretion. Following a short pulse (10 min) of [3H]leucine, three glycosylated forms of the DS-PGII core protein were observed, one of which is likely to be the precursor form of PGII predicted by the implied protein sequence of both bovine and human cDNA clones. Following the apparent cleavage of the propeptide, GAG-substituted intracellular core protein is detectable. Susceptibility to endoglycosidase H indicates that approximately one-third of the secreted core protein contains exclusively complex-type Asn-linked oligosaccharides and approximately two-thirds contain high mannose as well as complex-type oligosaccharides. Secreted DS-PGII appears to be fully substituted with three Asn-linked oligosaccharide chains. Inhibitors of oligosaccharide processing, however, permitted secretion of GAG-substituted DS-PGII that was fully (three chains) or incompletely (one or two chains) substituted with partially processed Asn-linked carbohydrate chains. By comparison of chondrocyte DS-PGII with fibroblast DS-PGII, we conclude that the addition and processing of Asn-linked carbohydrate chains are directed by the amino acid sequence of the core protein. The results reported here also suggest that the addition of xylose, the initial step in GAG chain synthesis, occurs early in biosynthesis and is determined by the primary amino acid sequence of the core protein.(ABSTRACT TRUNCATED AT 400 WORDS)

Stabilization of composition fluctuations in mixed membranes by hybrid lipids

NASA Astrophysics Data System (ADS)

Safran, Samuel; Palmieri, Benoit

2013-03-01

A ternary mixture model is proposed to describe composition fluctuations in mixed membranes composed of saturated, unsaturated and hybrid lipids. The asymmetric hybrid lipid has one saturated and one unsaturated hydrocarbon chain and it can reduce the packing incompatibility between saturated and unsaturated lipids. A methodology to recast the free-energy of the lattice in terms of a continuous isotropic field theory is proposed and used to analyze composition fluctuations above the critical temperature. The effect of hybrid lipids on fluctuations domains rich in saturated/unsaturated lipids is predicted. The correlation length of such fluctuations decreases significantly with increasing amounts of hybrids even if the temperature is maintained close to the critical temperature. This provides an upper bound for the domain sizes expected in rafts stabilized by hybrids, above the critical temperature. When the hybrid composition of the membrane is increased further, a crossover value is found above which ``stripe-like'' fluctuations are observed. The wavelength of these fluctuations decreases with increasing hybrid fraction and tends toward a molecular size in a membrane that contains only hybrids.

Image Reconstruction for Hybrid True-Color Micro-CT

PubMed Central

Xu, Qiong; Yu, Hengyong; Bennett, James; He, Peng; Zainon, Rafidah; Doesburg, Robert; Opie, Alex; Walsh, Mike; Shen, Haiou; Butler, Anthony; Butler, Phillip; Mou, Xuanqin; Wang, Ge

2013-01-01

X-ray micro-CT is an important imaging tool for biomedical researchers. Our group has recently proposed a hybrid “true-color” micro-CT system to improve contrast resolution with lower system cost and radiation dose. The system incorporates an energy-resolved photon-counting true-color detector into a conventional micro-CT configuration, and can be used for material decomposition. In this paper, we demonstrate an interior color-CT image reconstruction algorithm developed for this hybrid true-color micro-CT system. A compressive sensing-based statistical interior tomography method is employed to reconstruct each channel in the local spectral imaging chain, where the reconstructed global gray-scale image from the conventional imaging chain served as the initial guess. Principal component analysis was used to map the spectral reconstructions into the color space. The proposed algorithm was evaluated by numerical simulations, physical phantom experiments, and animal studies. The results confirm the merits of the proposed algorithm, and demonstrate the feasibility of the hybrid true-color micro-CT system. Additionally, a “color diffusion” phenomenon was observed whereby high-quality true-color images are produced not only inside the region of interest, but also in neighboring regions. It appears harnessing that this phenomenon could potentially reduce the color detector size for a given ROI, further reducing system cost and radiation dose. PMID:22481806

Polymerase chain reaction-hybridization method using urease gene sequences for high-throughput Ureaplasma urealyticum and Ureaplasma parvum detection and differentiation.

PubMed

Xu, Chen; Zhang, Nan; Huo, Qianyu; Chen, Minghui; Wang, Rengfeng; Liu, Zhili; Li, Xue; Liu, Yunde; Bao, Huijing

2016-04-15

In this article, we discuss the polymerase chain reaction (PCR)-hybridization assay that we developed for high-throughput simultaneous detection and differentiation of Ureaplasma urealyticum and Ureaplasma parvum using one set of primers and two specific DNA probes based on urease gene nucleotide sequence differences. First, U. urealyticum and U. parvum DNA samples were specifically amplified using one set of biotin-labeled primers. Furthermore, amine-modified DNA probes, which can specifically react with U. urealyticum or U. parvum DNA, were covalently immobilized to a DNA-BIND plate surface. The plate was then incubated with the PCR products to facilitate sequence-specific DNA binding. Horseradish peroxidase-streptavidin conjugation and a colorimetric assay were used. Based on the results, the PCR-hybridization assay we developed can specifically differentiate U. urealyticum and U. parvum with high sensitivity (95%) compared with cultivation (72.5%). Hence, this study demonstrates a new method for high-throughput simultaneous differentiation and detection of U. urealyticum and U. parvum with high sensitivity. Based on these observations, the PCR-hybridization assay developed in this study is ideal for detecting and discriminating U. urealyticum and U. parvum in clinical applications. Copyright © 2016 Elsevier Inc. All rights reserved.

Induction of Syndecan-4 by Organic-Inorganic Hybrid Molecules with a 1,10-Phenanthroline Structure in Cultured Vascular Endothelial Cells.

PubMed

Hara, Takato; Kojima, Takayuki; Matsuzaki, Hiroka; Nakamura, Takehiro; Yoshida, Eiko; Fujiwara, Yasuyuki; Yamamoto, Chika; Saito, Shinichi; Kaji, Toshiyuki

2017-02-08

Organic-inorganic hybrid molecules constitute analytical tools used in biological systems. Vascular endothelial cells synthesize and secrete proteoglycans, which are macromolecules consisting of a core protein and glycosaminoglycan side chains. Although the expression of endothelial proteoglycans is regulated by several cytokines/growth factors, there may be alternative pathways for proteoglycan synthesis aside from downstream pathways activated by these cytokines/growth factors. Here, we investigated organic-inorganic hybrid molecules to determine a variant capable of analyzing the expression of syndecan-4, a transmembrane heparan-sulfate proteoglycan, and identified 1,10-phenanthroline ( o -Phen) with or without zinc (Zn-Phen) or rhodium (Rh-Phen). Bovine aortic endothelial cells in culture were treated with these compounds, and the expression of syndecan-4 mRNA and core proteins was determined by real-time reverse transcription polymerase chain reaction and Western blot analysis, respectively. Our findings indicated that o -Phen and Zn-Phen specifically and strongly induced syndecan-4 expression in cultured vascular endothelial cells through activation of the hypoxia-inducible factor-1α/β pathway via inhibition of prolyl hydroxylase-domain-containing protein 2. These results demonstrated an alternative pathway involved in mediating induction of endothelial syndecan-4 expression and revealed organic-inorganic hybrid molecules as effective tools for analyzing biological systems.

New losartan-hydrocaffeic acid hybrids as antihypertensive-antioxidant dual drugs: Ester, amide and amine linkers.

PubMed

García, Gonzalo; Serrano, Isabel; Sánchez-Alonso, Patricia; Rodríguez-Puyol, Manuel; Alajarín, Ramón; Griera, Mercedes; Vaquero, Juan J; Rodríguez-Puyol, Diego; Alvarez-Builla, Julio; Díez-Marqués, María L

2012-04-01

We report new examples of a series of losartan-hydrocaffeic hybrids that bear novel ester, amide and amine linkers. These compounds were made by linking hydrocaffeic acid to the side chain of losartan at the C-5 position of the imidazole ring through different strategies. Experiments performed in cultured cells demonstrate that these new hybrids retain the ability to block the angiotensin II effect and have increased antioxidant ability. Most of them reduced arterial pressure in rats better or as much as losartan. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Spin-polarized electron transport in hybrid graphene-BN nanoribbons

NASA Astrophysics Data System (ADS)

Gao, Song; Lu, Wei; Zheng, Guo-Hui; Jia, Yalei; Ke, San-Huang

2017-05-01

The experimental realization of hybrid graphene and h-BN provides a new way to modify the electronic and transport properties of graphene-based materials. In this work, we investigate the spin-polarized electron transport in hybrid graphene-BN zigzag nanoribbons by performing first-principles nonequilibrium Green’s function method calculations. A 100% spin-polarized electron transport in a large energy window around the Fermi level is found and this behavior is independent of the ribbon width as long as there contain 3 zigzag carbon chains. This behavior may be useful in making perfect spin filters.

Identification and expression analysis of genes involved in early ovary development in diploid gynogenetic hybrids of red crucian carp x common carp.

PubMed

Liu, Dong; Liu, Shaojun; You, Cuiping; Chen, Lin; Liu, Zhen; Liu, Liangguo; Wang, Jing; Liu, Yun

2010-04-01

Diploid eggs of allotetraploid hybrids (red crucian carp female symbol x common carp male symbol), when activated by UV-irradiated sperm of scatter scale carp, can develop into diploid progenies without chromosome duplication treatment. Diploid progenies produce diploid eggs, which develop into diploid population by the same way. To understand the molecular mechanism underlying the production of diploid eggs by the diploid fish, we constructed a forward suppression subtractive hybridization complementary DNA (cDNA) library. The cDNAs from the ovary in proliferation phase were employed as the "tester," and those in growth phase were used as the "driver." Seventy-three cDNA clones that are specifically expressed in proliferation phase were detected by dot-blot hybridization. Sequencing analyses revealed that several of these cDNAs have high homologies to the known sequences in the NCBI database. Their encoded proteins include the protein preventing mitosis catastrophe (PMC), the signal recognition particle 9, the ATP-binding cassette transporter, the glucanase-xylanase fusion protein, and others. These genes were confirmed by reverse transcriptase-polymerase chain reaction. The expression profile of the PMC gene at different time points was analyzed by quantitative real-time polymerase chain reaction. The results indicated that the expression of this suppression subtractive hybridization-identified gene changed during the time course, corresponding with the cellular phenomenon in the ovary development. Our studies provide insights into the molecular mechanism underlying the ovary development of diploid gynogenetic fish.

Discovery of J Chain in African Lungfish (Protopterus dolloi, Sarcopterygii) Using High Throughput Transcriptome Sequencing: Implications in Mucosal Immunity

PubMed Central

Tacchi, Luca; Larragoite, Erin; Salinas, Irene

2013-01-01

J chain is a small polypeptide responsible for immunoglobulin (Ig) polymerization and transport of Igs across mucosal surfaces in higher vertebrates. We identified a J chain in dipnoid fish, the African lungfish (Protopterus dolloi) by high throughput sequencing of the transcriptome. P. dolloi J chain is 161 aa long and contains six of the eight Cys residues present in mammalian J chain. Phylogenetic studies place the lungfish J chain closer to tetrapod J chain than to the coelacanth or nurse shark sequences. J chain expression occurs in all P. dolloi immune tissues examined and it increases in the gut and kidney in response to an experimental bacterial infection. Double fluorescent in-situ hybridization shows that 88.5% of IgM+ cells in the gut co-express J chain, a significantly higher percentage than in the pre-pyloric spleen. Importantly, J chain expression is not restricted to the B-cell compartment since gut epithelial cells also express J chain. These results improve our current view of J chain from a phylogenetic perspective. PMID:23967082

Markov Chain-Like Quantum Biological Modeling of Mutations, Aging, and Evolution.

PubMed

Djordjevic, Ivan B

2015-08-24

Recent evidence suggests that quantum mechanics is relevant in photosynthesis, magnetoreception, enzymatic catalytic reactions, olfactory reception, photoreception, genetics, electron-transfer in proteins, and evolution; to mention few. In our recent paper published in Life, we have derived the operator-sum representation of a biological channel based on codon basekets, and determined the quantum channel model suitable for study of the quantum biological channel capacity. However, this model is essentially memoryless and it is not able to properly model the propagation of mutation errors in time, the process of aging, and evolution of genetic information through generations. To solve for these problems, we propose novel quantum mechanical models to accurately describe the process of creation spontaneous, induced, and adaptive mutations and their propagation in time. Different biological channel models with memory, proposed in this paper, include: (i) Markovian classical model, (ii) Markovian-like quantum model, and (iii) hybrid quantum-classical model. We then apply these models in a study of aging and evolution of quantum biological channel capacity through generations. We also discuss key differences of these models with respect to a multilevel symmetric channel-based Markovian model and a Kimura model-based Markovian process. These models are quite general and applicable to many open problems in biology, not only biological channel capacity, which is the main focus of the paper. We will show that the famous quantum Master equation approach, commonly used to describe different biological processes, is just the first-order approximation of the proposed quantum Markov chain-like model, when the observation interval tends to zero. One of the important implications of this model is that the aging phenotype becomes determined by different underlying transition probabilities in both programmed and random (damage) Markov chain-like models of aging, which are mutually coupled.

Markov Chain-Like Quantum Biological Modeling of Mutations, Aging, and Evolution

PubMed Central

Djordjevic, Ivan B.

2015-01-01

Recent evidence suggests that quantum mechanics is relevant in photosynthesis, magnetoreception, enzymatic catalytic reactions, olfactory reception, photoreception, genetics, electron-transfer in proteins, and evolution; to mention few. In our recent paper published in Life, we have derived the operator-sum representation of a biological channel based on codon basekets, and determined the quantum channel model suitable for study of the quantum biological channel capacity. However, this model is essentially memoryless and it is not able to properly model the propagation of mutation errors in time, the process of aging, and evolution of genetic information through generations. To solve for these problems, we propose novel quantum mechanical models to accurately describe the process of creation spontaneous, induced, and adaptive mutations and their propagation in time. Different biological channel models with memory, proposed in this paper, include: (i) Markovian classical model, (ii) Markovian-like quantum model, and (iii) hybrid quantum-classical model. We then apply these models in a study of aging and evolution of quantum biological channel capacity through generations. We also discuss key differences of these models with respect to a multilevel symmetric channel-based Markovian model and a Kimura model-based Markovian process. These models are quite general and applicable to many open problems in biology, not only biological channel capacity, which is the main focus of the paper. We will show that the famous quantum Master equation approach, commonly used to describe different biological processes, is just the first-order approximation of the proposed quantum Markov chain-like model, when the observation interval tends to zero. One of the important implications of this model is that the aging phenotype becomes determined by different underlying transition probabilities in both programmed and random (damage) Markov chain-like models of aging, which are mutually coupled. PMID:26305258

Hybridized Kibble-Zurek scaling in the driven critical dynamics across an overlapping critical region

NASA Astrophysics Data System (ADS)

Zhai, Liang-Jun; Wang, Huai-Yu; Yin, Shuai

2018-04-01

The conventional Kibble-Zurek scaling describes the scaling behavior in the driven dynamics across a single critical region. In this paper, we study the driven dynamics across an overlapping critical region, in which a critical region (Region A) is overlaid by another critical region (Region B). We develop a hybridized Kibble-Zurek scaling (HKZS) to characterize the scaling behavior in the driven process. According to the HKZS, the driven dynamics in the overlapping region can be described by the critical theories for both Region A and Region B simultaneously. This results in a constraint on the scaling function in the overlapping critical region. We take the quantum Ising chain in an imaginary longitudinal field as an example. In this model, the critical region of the Yang-Lee edge singularity and the critical region of the ferromagnetic-paramagnetic phase transition overlap with each other. We numerically confirm the HKZS by simulating the driven dynamics in this overlapping critical region. The HKZSs in other models are also discussed.

Direct Integration of Red-NIR Emissive Ceramic-like An M6 Xi8 Xa6 Metal Cluster Salts in Organic Copolymers Using Supramolecular Interactions.

PubMed

Robin, Malo; Dumait, Noée; Amela-Cortes, Maria; Roiland, Claire; Harnois, Maxime; Jacques, Emmanuel; Folliot, Hervé; Molard, Yann

2018-04-03

Hybrid nanomaterials made of inorganic nanocomponents dispersed in an organic host raise an increasing interest as low-cost solution-processable functional materials. However, preventing phase segregation while allowing a high inorganic doping content remains a major challenge, and usual methods require a functionalization step prior integration. Herein, we report a new approach to design such nanocomposite in which ceramic-like metallic nanocluster compounds are embedded at 10 wt % in organic copolymers, without any functionalization. Dispersion homogeneity and stability are ensured by weak interactions occurring between the copolymer lateral chains and the nanocluster compound. Hybrids could be ink-jet printed and casted on a blue LED. This proof-of-concept device emits in the red-NIR area and generates singlet oxygen, O 2 ( 1 Δg), of particular interest for lights, display, sensors or photodynamic based therapy applications. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A versatile quantitation platform based on platinum nanoparticles incorporated volumetric bar-chart chip for highly sensitive assays.

PubMed

Wang, Yuzhen; Zhu, Guixian; Qi, Wenjin; Li, Ying; Song, Yujun

2016-11-15

Platinum nanoparticles incorporated volumetric bar-chart chip (PtNPs-V-Chip) is able to be used for point-of-care tests by providing quantitative and visualized readout without any assistance from instruments, data processing, or graphic plotting. To improve the sensitivity of PtNPs-V-Chip, hybridization chain reaction was employed in this quantitation platform for highly sensitive assays that can detect as low as 16 pM Ebola Virus DNA, 0.01ng/mL carcinoembryonic antigen (CEA), and the 10 HER2-expressing cancer cells. Based on this amplified strategy, a 100-fold decrease of detection limit was achieved for DNA by improving the number of platinum nanoparticle catalyst for the captured analyte. This quantitation platform can also distinguish single base mismatch of DNA hybridization and observe the concentration threshold of CEA. The new strategy lays the foundation for this quantitation platform to be applied in forensic analysis, biothreat detection, clinical diagnostics and drug screening. Copyright © 2016 Elsevier B.V. All rights reserved.

Synthesis, Multinuclear NMR Characterization and Dynamic Property of Organic–Inorganic Hybrid Electrolyte Membrane Based on Alkoxysilane and Poly(oxyalkylene) Diamine

PubMed Central

Saikia, Diganta; Pan, Yu-Chi; Kao, Hsien-Ming

2012-01-01

Organic–inorganic hybrid electrolyte membranes based on poly(propylene glycol)-block-poly(ethylene glycol)-block-poly(propylene glycol) bis(2-aminopropyl ether) complexed with LiClO4 via the co-condensation of tetraethoxysilane (TEOS) and 3-(triethoxysilyl)propyl isocyanate have been prepared and characterized. A variety of techniques such as differential scanning calorimetry (DSC), Fourier transform infrared (FTIR) spectroscopy, alternating current (AC) impedance and solid-state nuclear magnetic resonance (NMR) spectroscopy are performed to elucidate the relationship between the structural and dynamic properties of the hybrid electrolyte and the ion mobility. A VTF (Vogel-Tamman-Fulcher)-like temperature dependence of ionic conductivity is observed for all the compositions studied, implying that the diffusion of charge carriers is assisted by the segmental motions of the polymer chains. A maximum ionic conductivity value of 5.3 × 10−5 Scm−1 is obtained at 30 °C. Solid-state NMR results provide a microscopic view of the effects of salt concentrations on the dynamic behavior of the polymer chains. PMID:24958176

Linking 1D Transition-Metal Coordination Polymers and Different Inorganic Boron Oxides To Construct a Series of 3D Inorganic-Organic Hybrid Borates.

PubMed

Zhi, Shao-Chen; Wang, Yue-Lin; Sun, Li; Cheng, Jian-Wen; Yang, Guo-Yu

2018-02-05

Three inorganic-organic hybrid borates, M(1,4-dab)[B 5 O 7 (OH) 3 ] [M = Zn (1), Cd (2), 1,4-dab = 1,4-diaminobutane)] and Co(1,3-dap)[B 4 O 7 ] (3, 1,3-dap = 1,3-diaminopropane), which integrated characteristics of 1D coordination polymers and 1D/3D inorganic boron oxides have been obtained under solvothermal conditions. Compounds 1 and 2 are isostructural and crystallize in a centrosymmetric space group P2 1 /c; the 3D achiral structures of 1 and 2 consist of the nonhelical Zn/Cd-1,4-dap coordination polymers and 1D B-O chains. Compound 3 crystallizes in a chiral space group P4 3 2 1 2; the helical Co-1,3-dap coordination polymer chains are entrained within a 3D B-O network and finally form the chiral framework. Compounds 1-3 represent good examples of using coordination polymers to construct mixed-motif inorganic-organic hybrid borates. Compounds 1 and 2 display blue luminescence when excited with UV light.

Quantum logic between remote quantum registers

NASA Astrophysics Data System (ADS)

Yao, N. Y.; Gong, Z.-X.; Laumann, C. R.; Bennett, S. D.; Duan, L.-M.; Lukin, M. D.; Jiang, L.; Gorshkov, A. V.

2013-02-01

We consider two approaches to dark-spin-mediated quantum computing in hybrid solid-state spin architectures. First, we review the notion of eigenmode-mediated unpolarized spin-chain state transfer and extend the analysis to various experimentally relevant imperfections: quenched disorder, dynamical decoherence, and uncompensated long-range coupling. In finite-length chains, the interplay between disorder-induced localization and decoherence yields a natural optimal channel fidelity, which we calculate. Long-range dipolar couplings induce a finite intrinsic lifetime for the mediating eigenmode; extensive numerical simulations of dipolar chains of lengths up to L=12 show remarkably high fidelity despite these decay processes. We further briefly consider the extension of the protocol to bosonic systems of coupled oscillators. Second, we introduce a quantum mirror based architecture for universal quantum computing that exploits all of the dark spins in the system as potential qubits. While this dramatically increases the number of qubits available, the composite operations required to manipulate dark-spin qubits significantly raise the error threshold for robust operation. Finally, we demonstrate that eigenmode-mediated state transfer can enable robust long-range logic between spatially separated nitrogen-vacancy registers in diamond; disorder-averaged numerics confirm that high-fidelity gates are achievable even in the presence of moderate disorder.

Block and Graft Copolymers of Polyhydroxyalkanoates

NASA Astrophysics Data System (ADS)

Marchessault, Robert H.; Ravenelle, François; Kawada, Jumpei

2004-03-01

Polyhydroxyalkanoates (PHAs) were modified for diblock copolymer and graft polymer by catalyzed transesterification in the melt and by chemical synthesis to extend the side chains of the PHAs, and the polymers were studied by transmission electron microscopy (TEM) X-ray diffraction, thermal analysis and nuclear magnetic resonance (NMR). Catalyzed transesterification in the melt is used to produce diblock copolymers of poly[3-hydroxybutyrate] (PHB) and monomethoxy poly[ethylene glycol] (mPEG) in a one-step process. The resulting diblock copolymers are amphiphilic and self-assemble into sterically stabilized colloidal suspensions of PHB crystalline lamellae. Graft polymer was synthesized in a two-step chemical synthesis from biosynthesized poly[3-hydroxyoctanoate-co-3-hydroxyundecenoate] (PHOU) containing ca. 25 mol chains. 11-mercaptoundecanoic acid reacts with the side chain alkenes of PHOU by the radical addition creating thioether linkage with terminal carboxyl functionalities. The latter groups were subsequently transformed into the amide or ester linkage by tridecylamine or octadecanol, respectively, producing new graft polymers. The polymers have different physical properties than poly[3-hydroxyoctanoate] (PHO) which is the main component of the PHOU, such as non-stickiness and higher thermal stability. The combination of biosynthesis and chemical synthesis produces a hybrid thermoplastic elastomer with partial biodegradability.

Novel molecular host materials based on carbazole/PO hybrids with wide bandgap via unique linkages for solution-processed blue phosphorescent OLEDs

NASA Astrophysics Data System (ADS)

Ye, Hua; Zhou, Kaifeng; Wu, Hongyu; Chen, Kai; Xie, Gaozhan; Hu, Jingang; Yan, Guobing; Ma, Songhua; Su, Shi-Jian; Cao, Yong

2016-10-01

A series of novel molecules with wide bandgap based on electron-withdrawing diphenyl phosphine oxide units and electron-donating carbazolyl moieties through insulated unique linkages of flexible chains terminated by oxygen or sulfur atoms as solution-processable host materials were successfully synthesized for the first time, and their thermal, photophysical, and electrochemical properties were studied thoroughly. These materials possess high triplet energy levels (ET, 2.76-2.77 eV) due to the introduction of alkyl chain to interrupt the conjugation between electron-donor and electron-acceptor. Such high ET could effectively curb the energy from phosphorescent emitter transfer to the host molecules and thus assuring the emission of devices was all from the blue phosphorescent emitter iridium (III) bis [(4,6-difluorophenyl)-pyridinate-N,C2‧]picolinate (FIrpic). Among them, the solution-processed device based on CBCR6OPO without extra vacuum thermal-deposited hole-blocking layer and electron-transporting layer showed the highest maximum current efficiency (CEmax) of 4.16 cd/A. Moreover, the device presented small efficiency roll-off with current efficiency (CE) of 4.05 cd/A at high brightness up to 100 cd/m2. Our work suggests the potential applications of the solution-processable materials with wide bandgap in full-color flat-panel displays and organic lighting.

Nucleic acid in-situ hybridization detection of infectious agents

NASA Astrophysics Data System (ADS)

Thompson, Curtis T.

2000-04-01

Limitations of traditional culture methods and newer polymerase chain reaction (PCR)-based methods for detection and speciation of infectious agents demonstrate the need for more rapid and better diagnostics. Nucleic acid hybridization is a detection technology that has gained wide acceptance in cancer and prenatal cytogenetics. Using a modification of the nucleic acid hybridization technique known as fluorescence in-situ hybridization, infectious agents can be detected in a variety of specimens with high sensitivity and specificity. The specimens derive from all types of human and animal sources including body fluids, tissue aspirates and biopsy material. Nucleic acid hybridization can be performed in less than one hour. The result can be interpreted either using traditional fluorescence microscopy or automated platforms such as micro arrays. This paper demonstrates proof of concept for nucleic acid hybridization detection of different infectious agents. Interpretation within a cytologic and histologic context is possible with fluorescence microscopic analysis, thereby providing confirmatory evidence of hybridization. With careful probe selection, nucleic acid hybridization promises to be a highly sensitive and specific practical diagnostic alternative to culture, traditional staining methods, immunohistochemistry and complicated nucleic acid amplification tests.

Immunohistochemical characterization of slow and fast myosin heavy chain composition of muscle fibres in the styloglossus muscle of the human and macaque (Macaca rhesus).

PubMed

Sokoloff, Alan J; Yang, Betty; Li, Haiyan; Burkholder, Thomas J

2007-06-01

Muscle fibre contractile diversity is thought to be increased by the hybridization of multiple myosin heavy chain (MHC) isoforms in single muscle fibres. Reports of hybrid fibres composed of MHCI and MHCII isoforms in human, but not macaque, tongue muscles, suggest a human adaptation for increased tongue muscle contractile diversity. Here we test whether hybrid fibres composed of MHCI and MHCII are unique to human tongue muscles or are present as well in the macaque. MHC composition of the macaque and human styloglossus was characterized with antibodies that allowed identification of three muscle fibre phenotypes, a slow phenotype composed of MHCI, a fast phenotype composed of MHCII and a hybrid phenotype composed of MHCI and MHCII. The fast phenotype constitutes 68.5% of fibres in the macaque and 43.4% of fibres in the human (P<0.0001). The slow phenotype constitutes 20.2% of fibres in the macaque and 39.3% of fibres in the human (P<0.0001). The hybrid phenotype constitutes 11.2% of fibres in the macaque and 17.3% of fibres in the human (P=0.0002). Macaques and humans do not differ in fiber size (cross-sectional area, diameter). However, measures of fibre size differ by phenotype such that fast>hybrid>slow (P<0.05). These data demonstrate differences in the relative percent of muscle fibre phenotypes in the macaque and human styloglossus but also demonstrate that all three phenotypes are present in both species. These data suggest a similar range of mechanical properties in styloglossus muscle fibres of the macaque and human.

Molecular diagnostics of periodontitis.

PubMed

Korona-Głowniak, Izabela; Siwiec, Radosław; Berger, Marcin; Malm, Anna; Szymańska, Jolanta

2017-01-28

The microorganisms that form dental plaque are the main cause of periodontitis. Their identification and the understanding of the complex relationships and interactions that involve these microorganisms, environmental factors and the host's health status enable improvement in diagnostics and targeted therapy in patients with periodontitis. To this end, molecular diagnostics techniques (both techniques based on the polymerase chain reaction and those involving nucleic acid analysis via hybridization) come increasingly into use. On the basis of a literature review, the following methods are presented: polymerase chain reaction (PCR), real-time polymerase chain reaction (real-time PCR), 16S rRNA-encoding gene sequencing, checkerboard and reverse-capture checkerboard hybridization, microarrays, denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), as well as terminal restriction fragment length polymorphism (TRFLP) and next generation sequencing (NGS). The advantages and drawbacks of each method in the examination of periopathogens are indicated. The techniques listed above allow fast detection of even small quantities of pathogen present in diagnostic material and prove particularly useful to detect microorganisms that are difficult or impossible to grow in a laboratory.

Synthesis and surface properties of polyurethane end-capped with hybrid hydrocarbon/fluorocarbon double-chain phospholipid.

PubMed

Li, Jiehua; Zhang, Yi; Yang, Jian; Tan, Hong; Li, Jianshu; Fu, Qiang

2013-05-01

To improve hemocompatibility of biomedical polyurethanes (PUs), a series of new fluorinated phospholipid end-capped polyurethanes (FPCPUs) as blending PU additives were designed and synthesized using diphenyl methane diisocyanate and 1,4-butanediol as hard segment, poly(tetramethylene glycol), polypropylene glycol, polycarbonate diols, and polyethylene glycol as soft segments, respectively, aminofunctionalized hybrid hydrocarbon/fluorocarbon double-chain phospholipid as end-capper. The bulk structures and surface properties of the obtained FPCPUs were fully characterized by (1)H NMR, Fourier transform infrared, gel permeation chromatography, X-ray photoelectron spectroscopy, differential scanning calorimetry, atomic force microscopy, and water contact angle measurement. It was found that the phosphatidylcholine groups could enrich on the surfaces and subsurfaces with the help of the fluorocarbon chains and self-assemble into mimic biomembrane on these polymer surfaces. These surfaces could effectively suppress fibrinogen adsorption, as evaluated by enzyme-linked immunosorbent assay method. Our work indicates that the FPCPUs should be one of the most potential modified additives for enhancing hemocompatibility of traditional medical PUs. Copyright © 2012 Wiley Periodicals, Inc.

The conformational requirements for the mechanical precipitation of hemoglobin S and other mutants.

PubMed

Roth, E F; Elbaum, D; Bookchin, R M; Nagel, R L

1976-08-01

The mechanical stability of human hemoglobin mutants was studied for the specific effects of single and double amino acid substitutions, the ligand state of each chain, and the effect of hybrids between oxy and cyanmet partners on precipitability. It was found that the beta6Glu leads to Val and the beta73 Asp leads to Asn mutations increased the degree of mechanical precipitation in the liganded but not in the deoxy form. When these mutations occurred on the same chain, the effects were approximately additive. Heat labile mutants such as Hb Gun Hill and Hb Leiden exhibited mechanical instability, but probably through a different mechanism, as very little dependence on ligand state was apparent. Studies with valency hybrids of HbS(alpha2 betas2-and-alpha2 betas2 where = cyanmet) revealed that instability was primarily determined by the state of the betas chain, which must be liganded to confer instability on the tetramer. A good agreement between surface activity and mechanical precipitability of these mutants has been found.

Perhaps More Consideration of Pavlovian–Operant Interaction May Improve the Clinical Efficacy of Behaviorally Based Drug Treatment Programs

PubMed Central

Troisi, Joseph R.

2014-01-01

Drug abuse remains costly. Drug-related cues can evoke cue-reactivity and craving, contributing to relapse. The Pavlovian extinction-based cue-exposure therapy (CET) has not been very successful in treating drug abuse. A functional operant analysis of complex rituals involved in CET is outlined and reinterpreted as an operant heterogeneous chain maintained by observing responses, conditioned reinforcers, and discriminative stimuli. It is further noted that operant functions are not predicated on Pavlovian processes but can be influenced by them in contributing to relapse; several empirical studies from the animal and human literature highlight this view. Cue-reactivity evoked by Pavlovian processes is conceptualized as an operant establishing/motivating operation. CET may be more effective in incorporating an operant-based approach that takes into account the complexity of Pavlovian–operant interaction. Extinction of the operant chain coupled with the shaping of alternative behaviors is proposed as an integrated therapy. It is proposed that operant-based drug abuse treatments (contingency management, voucher programs, and the therapeutic work environment) might consider incorporating cue-reactivity, as establishing/motivating operations, to increase long-term success—a hybrid approach based on Pavlovian–operant interaction. PMID:25346551

Perhaps More Consideration of Pavlovian-Operant Interaction May Improve the Clinical Efficacy of Behaviorally Based Drug Treatment Programs.

PubMed

Troisi, Joseph R

2013-01-01

Drug abuse remains costly. Drug-related cues can evoke cue-reactivity and craving, contributing to relapse. The Pavlovian extinction-based cue-exposure therapy (CET) has not been very successful in treating drug abuse. A functional operant analysis of complex rituals involved in CET is outlined and reinterpreted as an operant heterogeneous chain maintained by observing responses, conditioned reinforcers, and discriminative stimuli. It is further noted that operant functions are not predicated on Pavlovian processes but can be influenced by them in contributing to relapse; several empirical studies from the animal and human literature highlight this view. Cue-reactivity evoked by Pavlovian processes is conceptualized as an operant establishing/motivating operation. CET may be more effective in incorporating an operant-based approach that takes into account the complexity of Pavlovian-operant interaction. Extinction of the operant chain coupled with the shaping of alternative behaviors is proposed as an integrated therapy. It is proposed that operant-based drug abuse treatments (contingency management, voucher programs, and the therapeutic work environment) might consider incorporating cue-reactivity, as establishing/motivating operations, to increase long-term success-a hybrid approach based on Pavlovian-operant interaction.

Mixing of MnPc electronic states at the MnPc/Au(110) interface

NASA Astrophysics Data System (ADS)

Gargiani, Pierluigi; Lisi, Simone; Avvisati, Giulia; Mondelli, Pierluigi; Fatale, Sara; Betti, Maria Grazia

2017-10-01

Manganese-phthalocyanines form assembled chains with a variety of ordered super-structures, flat lying along the Au(110) reconstructed channels. The chains first give rise to a ×5 symmetry reconstruction, while further deposition of MnPc leads to a ×7 periodicity at the completion of the first single layer. A net polarization with the formation of an interface dipole is mainly due to the molecular π-states located on the macrocycles pyrrole rings, while the central metal ion induces a reduction in the polarization, whose amount is related to the Mn-Au interaction. The adsorption-induced interface polarization is compared to other 3d-metal phthalocyanines, to unravel the role of the central metal atom configuration in the interaction process of the d-states. The MnPc adsorption on Au(110) induces the re-hybridization of the electronic states localized on the central metal atom, promoting a charge redistribution of the molecular orbitals of the MnPc molecules. The molecule-substrate interaction is controlled by a symmetry-determined mixing between the electronic states, involving also the molecular empty orbitals with d character hybridized with the nitrogen atoms of the pyrrole ring, as deduced by photoemission and X-ray absorption spectroscopy exploiting light polarization. The symmetry-determined mixing between the electronic states of the Mn metal center and of the Au substrate induces a density of states close to the Fermi level for the ×5 phase.

Investigating the effects of peptoid substitutions in self-assembly of Fmoc-diphenylalanine derivatives.

PubMed

Rajbhandary, Annada; Nilsson, Bradley L

2017-03-01

Low molecular weight agents that undergo self-assembly into fibril networks with hydrogel properties are promising biomaterials. Most low molecular weight hydrogelators are discovered empirically or serendipitously due to imperfect understanding of the mechanisms of self-assembly, the packing structure of self-assembled materials, and how the self-assembly process corresponds to emergent hydrogelation. Herein, the mechanisms of self-assembly and hydrogelation of N-fluorenylmethoxycarbonyl diphenylalanine (Fmoc-PhePhe), a well-studied low molecular weight hydrogelator, is probed by systematic comparison with derivatives in which Phe residues are replaced by corresponding N-benzyl glycine peptoid (Nphe) analogs. Peptoids are peptidomimetics that shift display of side chain functionality from the α-carbon to the terminal nitrogen. This alters the hydrogen bonding capacity, the side chain presentation geometry, amide cis/trans isomerization equilibrium, and β-sheet potential of the peptoid relative to the corresponding amino acid in the context of peptidic polymers. It was found that amino acid/peptoid hybrids Fmoc-Phe-Nphe and Fmoc-Nphe-Phe have altered fibril self-assembly propensity and reduced hydrogelation capacity relative to the parent dipeptide, and that fibril self-assembly of the dipeptoid, Fmoc-Nphe-Nphe, is completely curtailed. These findings provide insight into the potential of low molecular weight peptoids and peptide/peptoid hybrids as hydrogelation agents and illuminate the importance of hydrogen bonding and π-π interaction geometry in facilitating self-assembly of Fmoc-Phe-Phe. © 2016 Wiley Periodicals, Inc.

End product yields from the extraruminal fermentation of various polysaccharide, protein and nucleic acid components of biofuels feedstocks.

PubMed

Weimer, Paul J

2011-02-01

"Extraruminal" fermentations employing in vitro incubation of mixed ruminal bacterial consortia, are capable of converting a complex array of biomass materials to mixtures of volatile fatty acids (VFA), methane, and carbon dioxide. Most of the potential energy in the biomass feedstock is retained in the VFA products, which are potential reactants for electrochemical conversion to hydrocarbon fuels. Quantitative data on VFA yields and proportions from biomass components are necessary for determining industrial feasibility, but such measurements have not been systematically reported. VFA yields and proportions were determined for a variety of carbohydrates, proteins and nucleic acids. Carbohydrates yielded primarily acetic and propionic acids, while proteins also yielded a more favorable product mix (longer average chain length and branched chain VFAs). Addition of certain co-substrates (e.g., glycerol) favorably improved the VFA product mix. The results have implications for hydrocarbon fuel generation from biomass materials by hybrid fermentation/chemical processes. Published by Elsevier Ltd.

Theoretical model to explain the problem-solving process in physics

NASA Astrophysics Data System (ADS)

Lopez, Carlos

2011-03-01

This work reports a theoretical model developed with the aim to explain the mental mechanisms of knowledge building during the problem-solving process in physics using a hybrid approach of assimilation- formation of concepts. The model has been termed conceptual chains and represents graphic diagrams of conceptual dependency, which have yielded information about the background knowledge required during the learning process, as well as about the formation of diverse structures that correspond to distinct forms of networking concepts Additionally, the conceptual constructs of the model have been classified according to five types of knowledge. Evidence was found about the influence of these structures, as well as of the distinct types of knowledge about the degree of difficulty of the problems. I want to be grateful to Laureate International Universities, Baltimore M.D., USA, for the financing granted for the accomplishment of this work.

A Novel Re-keying Function Protocol (NRFP) For Wireless Sensor Network Security

PubMed Central

Abdullah, Maan Younis; Hua, Gui Wei; Alsharabi, Naif

2008-01-01

This paper describes a novel re-keying function protocol (NRFP) for wireless sensor network security. A re-keying process management system for sensor networks is designed to support in-network processing. The design of the protocol is motivated by decentralization key management for wireless sensor networks (WSNs), covering key deployment, key refreshment, and key establishment. NRFP supports the establishment of novel administrative functions for sensor nodes that derive/re-derive a session key for each communication session. The protocol proposes direct connection, in-direct connection and hybrid connection. NRFP also includes an efficient protocol for local broadcast authentication based on the use of one-way key chains. A salient feature of the authentication protocol is that it supports source authentication without precluding innetwork processing. Security and performance analysis shows that it is very efficient in computation, communication and storage and, that NRFP is also effective in defending against many sophisticated attacks. PMID:27873963

A Novel Re-keying Function Protocol (NRFP) For Wireless Sensor Network Security.

PubMed

Abdullah, Maan Younis; Hua, Gui Wei; Alsharabi, Naif

2008-12-04

This paper describes a novel re-keying function protocol (NRFP) for wireless sensor network security. A re-keying process management system for sensor networks is designed to support in-network processing. The design of the protocol is motivated by decentralization key management for wireless sensor networks (WSNs), covering key deployment, key refreshment, and key establishment. NRFP supports the establishment of novel administrative functions for sensor nodes that derive/re-derive a session key for each communication session. The protocol proposes direct connection, in-direct connection and hybrid connection. NRFP also includes an efficient protocol for local broadcast authentication based on the use of one-way key chains. A salient feature of the authentication protocol is that it supports source authentication without precluding in-network processing. Security and performance analysis shows that it is very efficient in computation, communication and storage and, that NRFP is also effective in defending against many sophisticated attacks.

Expression of the long-chain fatty acid receptor GPR120 in the gonadotropes of the mouse anterior pituitary gland.

PubMed

Moriyama, Ryutaro; Deura, Chikaya; Imoto, Shingo; Nose, Kazuhiro; Fukushima, Nobuyuki

2015-01-01

G-protein-coupled receptor 120 (GPR120) has been known to be a receptor of long-chain fatty acids. Here, we investigated GPR120 expression in the mouse pituitary gland via real-time PCR, in situ hybridization, and immunohistochemistry. GPR120 mRNA was abundantly expressed in the pituitary gland of ad-lib fed animals. In situ hybridization and immunohistochemistry revealed GPR120 expression in the gonadotropes of the anterior pituitary gland, but not in thyrotropes, somatotropes, lactotropes, corticotropes, melanotropes, and the posterior pituitary gland. Furthermore, 24 h of fasting induced an increase in GPR120 mRNA expression in the pituitary gland. These results demonstrate that GPR120 in mouse pituitary gonadotropes is upregulated by fasting and that it may play a role in controlling gonadotropin secretion.

Hybridization chain reaction: a versatile molecular tool for biosensing, bioimaging, and biomedicine.

PubMed

Bi, Sai; Yue, Shuzhen; Zhang, Shusheng

2017-07-17

Developing powerful, simple and low-cost DNA amplification techniques is of great significance to bioanalysis and biomedical research. Thus far, many signal amplification strategies have been developed, such as polymerase chain reaction (PCR), rolling circle amplification (RCA), and DNA strand displacement amplification (SDA). In particular, hybridization chain reaction (HCR), a type of toehold-mediated strand displacement (TMSD) reaction, has attracted great interest because of its enzyme-free nature, isothermal conditions, simple protocols, and excellent amplification efficiency. In a typical HCR, an analyte initiates the cross-opening of two DNA hairpins, yielding nicked double helices that are analogous to alternating copolymers. As an efficient amplification platform, HCR has been utilized for the sensitive detection of a wide variety of analytes, including nucleic acids, proteins, small molecules, and cells. In recent years, more complicated sets of monomers have been designed to develop nonlinear HCR, such as branched HCR and even dendritic systems, achieving quadratic and exponential growth mechanisms. In addition, HCR has attracted enormous attention in the fields of bioimaging and biomedicine, including applications in fluorescence in situ hybridization (FISH) imaging, live cell imaging, and targeted drug delivery. In this review, we introduce the fundamentals of HCR and examine the visualization and analysis techniques for HCR products in detail. The most recent HCR developments in biosensing, bioimaging, and biomedicine are subsequently discussed with selected examples. Finally, the review provides insight into the challenges and future perspectives of HCR.

Non-Covalent Fluorescent Labeling of Hairpin DNA Probe Coupled with Hybridization Chain Reaction for Sensitive DNA Detection.

PubMed

Song, Luna; Zhang, Yonghua; Li, Junling; Gao, Qiang; Qi, Honglan; Zhang, Chengxiao

2016-04-01

An enzyme-free signal amplification-based assay for DNA detection was developed using fluorescent hairpin DNA probes coupled with hybridization chain reaction (HCR). The hairpin DNAs were designed to contain abasic sites in the stem moiety. Non-covalent labeling of the hairpin DNAs was achieved when a fluorescent ligand was bound to the abasic sites through hydrogen bonding with the orphan cytosine present on the complementary strand, accompanied by quench of ligand fluorescence. As a result, the resultant probes, the complex formed between the hairpin DNA and ligand, showed almost no fluorescence. Upon hybridization with target DNA, the probe underwent a dehybridization of the stem moiety containing an abasic site. The release of ligand from the abasic site to the solution resulted in an effective fluorescent enhancement, which can be used as a signal. Compared with a sensing system without HCR, a 20-fold increase in the sensitivity was achieved using the sensing system with HCR. The fluorescent intensity of the sensing system increased with the increase in target DNA concentration from 0.5 nM to 100 nM. A single mismatched target ss-DNA could be effectively discriminated from complementary target DNA. Genotyping of a G/C single-nucleotide polymorphism of polymerase chain reaction (PCR) products was successfully demonstrated with the sensing system. Therefore, integrating HCR strategy with non-covalent labeling of fluorescent hairpin DNA probes provides a sensitive and cost-effective DNA assay. © The Author(s) 2016.

Peptides, polypeptides and peptide-polymer hybrids as nucleic acid carriers.

PubMed

Ahmed, Marya

2017-10-24

Cell penetrating peptides (CPPs), and protein transduction domains (PTDs) of viruses and other natural proteins serve as a template for the development of efficient peptide based gene delivery vectors. PTDs are sequences of acidic or basic amphipathic amino acids, with superior membrane trespassing efficacies. Gene delivery vectors derived from these natural, cationic and cationic amphipathic peptides, however, offer little flexibility in tailoring the physicochemical properties of single chain peptide based systems. Owing to significant advances in the field of peptide chemistry, synthetic mimics of natural peptides are often prepared and have been evaluated for their gene expression, as a function of amino acid functionalities, architecture and net cationic content of peptide chains. Moreover, chimeric single polypeptide chains are prepared by a combination of multiple small natural or synthetic peptides, which imparts distinct physiological properties to peptide based gene delivery therapeutics. In order to obtain multivalency and improve the gene delivery efficacies of low molecular weight cationic peptides, bioactive peptides are often incorporated into a polymeric architecture to obtain novel 'polymer-peptide hybrids' with improved gene delivery efficacies. Peptide modified polymers prepared by physical or chemical modifications exhibit enhanced endosomal escape, stimuli responsive degradation and targeting efficacies, as a function of physicochemical and biological activities of peptides attached onto a polymeric scaffold. The focus of this review is to provide comprehensive and step-wise progress in major natural and synthetic peptides, chimeric polypeptides, and peptide-polymer hybrids for nucleic acid delivery applications.

Comparative study of sex pheromone composition and biosynthesis in Helicoverpa armigera, H. assulta and their hybrid.

PubMed

Wang, Hong-Lei; Zhao, Cheng-Hua; Wang, Chen-Zhu

2005-06-01

Two Helicoverpa species, H. armigera and H. assulta use (Z)-11-hexadecenal and (Z)-9-hexadecenal as their sex attractant pheromone components but in opposite ratios. Since both female and male interspecific hybrids produced by female H. assulta and male H. armigera have been obtained in our laboratory, we can make a comparative study of sex pheromone composition and biosynthesis in the two species and their hybrid. With GC and GC-MS analyses using single gland extracts, the ratio of (Z)-9-hexadecenal to (Z)-11-hexadecenal was determined as 2.1:100 in H. armigera, and 1739:100 in H. assulta. The hybrid has a ratio of 4.0: 100, which is closer to that of H. armigera, but significantly different from H. armigera. We investigated pheromone biosynthesis with labeling experiments, using various fatty acid precursors in H. armigera, H. assulta and the hybrid. In H. armigera, (Z)-11-hexadecenal is produced by delta11 desaturation of palmitic acid, followed by reduction and terminal oxidation; (Z)-9-hexadecenal results from delta11 desaturation of stearic acid, followed by one cycle of chain shortening, reduction and terminal oxidation. delta11 desaturase is the unique desaturase for the production of the two pheromone components. In our Chinese strain of H. assulta, palmitic acid is used as the substrate to form both the major pheromone component, (Z)-9-hexadecenal and the minor one, (Z)-11-hexadecenal. Our data suggest that delta9 desaturase is the major desaturase, and delta11 desaturase is responsible for the minor component in H. assulta, which is consistent with previous work. However, the weak chain shortening acting on (Z)-9 and (Z)-11-octadecenoic acid, which is present in the pheromone glands, does occur in this species to produce (Z)-7 and (Z)-9-hexadecenoic acid. In the hybrid, the major pheromone component, (Z)-11-hexadecenal is produced by delta11 desaturation of palmitic acid, followed by reduction and terminal oxidation. The direct fatty acid precursor of the minor component, (Z)-9-hexadecenoic acid is mainly produced by delta9 desaturation of palmitic acid, but also by delta11 desaturation of stearic acid and one cycle of chain shortening. The greater relative amounts of (Z)-9-hexadecenal in the hybrid are due to the fact that both palmitic and stearic acids are used as substrates, whereas only stearic acid is used as substrate in H. armigera. The evolutionary relationships between the desaturases in several Helicoverpa species are also discussed in this paper.

Development of a PCR/LDR/flow-through hybridization assay using a capillary tube, probe DNA-immobilized magnetic beads and chemiluminescence detection.

PubMed

Hommatsu, Manami; Okahashi, Hisamitsu; Ohta, Keisuke; Tamai, Yusuke; Tsukagoshi, Kazuhiko; Hashimoto, Masahiko

2013-01-01

A polymerase chain reaction (PCR)/ligase detection reaction (LDR)/flow-through hybridization assay using chemiluminescence (CL) detection was developed for analyzing point mutations in gene fragments with high diagnostic value for colorectal cancers. A flow-through hybridization format using a capillary tube, in which probe DNA-immobilized magnetic beads were packed, provided accelerated hybridization kinetics of target DNA (i.e. LDR product) to the probe DNA. Simple fluid manipulations enabled both allele-specific hybridization and the removal of non-specifically bound DNA in the wash step. Furthermore, the use of CL detection greatly simplified the detection scheme, since CL does not require a light source for excitation of the fluorescent dye tags on the LDR products. Preliminary results demonstrated that this analytical system could detect both homozygous and heterozygous mutations, without the expensive instrumentation and cumbersome procedures required by conventional DNA microarray-based methods.

Anti-Cancer Activity of New Designer Hydrogen Sulfide-Donating Hybrids

PubMed Central

2014-01-01

Abstract Significance: Hydrogen sulfide (H2S) is likely to join nitric oxide (NO) and carbon monoxide (CO) as the third gaseous transmitter, influencing an array of intracellular signaling cascades. Thus, H2S is implicated in numerous physiological processes and in the pathology of various diseases. Recent Advances: H2S-donating agents that liberate H2S slowly either alone or in combination with NO, the so-called NOSH compounds, are being synthesized, and these have been shown to have great potential against cancer. Critical Issues: An accurate determination of H2S levels is challenging. H2S and NO share many similar actions; do these similarities act to potentiate each other? Since many actions of H2S appear to be mediated through inhibition of inflammation and Nuclear factor kappa-light-chain-enhancer of activated B cells is a central player in this scenario, does S-nitrosylation of this transcription factor by NO affect its S-sulfhydration by H2S and vice versa? Future Directions: Deciphering the molecular targets of these novel hybrid agents and having genetically engineered animals should help us move toward targeted therapeutic applications. Human safety data with these new hybrids is essential. Antioxid. Redox Signal. 20, 831–846. PMID:23581880

DNA-mediated inhibition of peroxidase-like activities on platinum nanoparticles for simple and rapid colorimetric detection of nucleic acids.

PubMed

Chen, Weiwei; Fang, Xueen; Li, Hua; Cao, Hongmei; Kong, Jilie

2017-08-15

In this research, we found that the peroxidase-like activities of noncovalent DNA-Pt hybrid nanoparticles could be obviously blocked, when Pt nanoparticles (PtNPs) were synthesized in situ using DNA as a template. Moreover, this self-assembled synthetic process was very convenient and rapid (within few mintues), and the inhibition mediated by DNA was also very effective. First, by the paper-based analytical device (PAD) we found the catalytic activities of DNA-Pt hybrid nanoparticles exhibited a linear response to the concentration of DNA in the range from 0.0075 to 0.25µM. Then, with the magnetic bead isolated system and target DNA-induced hybridization chain reaction (HCR), we realized the specific target DNA analysis with a low detection of 0.228nM, and demonstrated its effectivity in distinguishing the target DNA from other interferences. To our knowledge, this is the first report that used the nanoassembly between DNA and PtNPs for colorimetric detection of nucleic acids, which was based on DNA-mediated inhibition of catalytic activities of platinum nanoparticles. The results may be useful for understanding the interactions between DNA and metal nanoparticles, and for development of other convenient and effective analytical strategies. Copyright © 2017. Published by Elsevier B.V.

A suite of molecular markers for identifying species, detecting introgression and describing population structure in spadefoot toads (Spea spp.).

PubMed

Pfennig, Karin S; Allenby, Ashley; Martin, Ryan A; Monroy, Anaïs; Jones, Corbin D

2012-09-01

Two congeneric species of spadefoot toad, Spea multiplicata and Spea bombifrons, have been the focus of hybridization studies since the 1970s. Because complex hybrids are not readily distinguished phenotypically, genetic markers are needed to identify introgressed individuals. We therefore developed a set of molecular markers (amplified fragment length polymorphism, polymerase chain reaction-restriction fragment length polymorphism and single nucleotide polymorphism) for identifying pure-species, F1 hybrids and more complex introgressed types. To do so, we tested a series of markers across both species and known hybrids using populations in both allopatry and sympatry. We retained those markers that differentiated the two pure-species and also consistently identified known species hybrids. These markers are well suited for identifying hybrids between these species. Moreover, those markers that show variation within each species can be used in conjunction with existing molecular markers in studies of population structure and gene flow. © 2012 Blackwell Publishing Ltd.

Insight into fast ion migration kinetics of a new hybrid single Li-ion conductor based on aluminate complexes for solid-state Li-ion batteries.

PubMed

Feng, Yancong; Tan, Rui; Zhao, Yan; Gao, Rongtan; Yang, Luyi; Yang, Jinlong; Li, Hao; Zhou, Guofu; Chen, Haibiao; Pan, Feng

2018-03-29

A novel hybrid single Li-ion conductor (SLIC) for a Li-ion solid electrolyte was prepared by mixing aluminate complexes-polyethylene glycol (LiAl-PEG) and polyethylene oxide (PEO) for solid-state Li-ion batteries. The LiAl-PEG/PEO blend possesses high thermal stability and electrochemical stability with an oxidation decomposition voltage up to 4.8 V. Notably, this hybrid SLIC exhibits not only excellent Li-ion migration kinetics, but also good ionic conductivity as high as 4.0 × 10-5 and 2.6 × 10-4 S cm-1 at 30 and 100 °C, respectively, which is much higher than previously reported SLICs. Importantly, by the combination of molecular dynamics simulations and experiment measurements, the mechanisms of Li-ion migration across the SLIC (LiAl-PEG), the salt-in-polymer (LiClO4/PEO) and the optimized SLIC (LiAl-PEG/PEO) were systematically investigated for the first time. The new hopping transport mechanism was verified for the SLIC system at the nanoscale. As for the hybrid SLIC, PEO chains enhance the segmental mobility of the ether-chains bonded with Al atoms, improve the ionicity, and provide extra ionic paths for Li transfer, resulting in the optimized Li-ion migration kinetics of LiAl-PEG/PEO.

(C6H13N)2BiI5: A One-Dimensional Lead-Free Perovskite-Derivative Photoconductive Light Absorber.

PubMed

Zhang, Weichuan; Tao, Kewen; Ji, Chengmin; Sun, Zhihua; Han, Shiguo; Zhang, Jing; Wu, Zhenyue; Luo, Junhua

2018-04-16

Lead-free organic-inorganic hybrid perovskites have recently attracted intense interest as environmentally friendly, low-cost, chemically stable light absorbers. Here, we reported a new one-dimensional (1D) zigzag chainlike light-absorbing hybrid material of (C 6 H 13 N) 2 BiI 5 , in which the corner-sharing octahedral bismuth halide chains are surrounded by organic cations of tetramethylpiperidinium. This unique zigzag 1D hybrid perovskite-derivative material shows a narrow direct band gap of 2.02 eV and long-lived photoluminescence, which is encouraging for optoelectronic applications. Importantly, it behaves as a typical semiconducting material and displays obvious photoresponse in the visible-light range. This work opens a potential pathway for the further application of 1D lead-free hybrids.

Managing challenges of import safety in a global market.

DOT National Transportation Integrated Search

2012-06-01

This collaborative will examine market, regulatory, and hybrid approaches to managing risk from deliberate or unintentional contamination in : imported commodity products from the global supply chain, through research and on-campus activities involvi...

In situ DNA hybridized chain reaction (FISH-HCR) as a better method for quantification of bacteria and archaea within marine sediment

NASA Astrophysics Data System (ADS)

Buongiorno, J.; Lloyd, K. G.; Shumaker, A.; Schippers, A.; Webster, G.; Weightman, A.; Turner, S.

2015-12-01

Nearly 75% of the Earth's surface is covered by marine sediment that is home to an estimated 2.9 x 1029 microbial cells. A substantial impediment to understanding the abundance and distribution of cells within marine sediment is the lack of a consistent and reliable method for their taxon-specific quantification. Catalyzed reporter fluorescent in situ hybridization (CARD-FISH) provides taxon-specific enumeration, but this process requires passing a large enzyme through cell membranes, decreasing its precision relative to general cell counts using a small DNA stain. In 2015, Yamaguchi et al. developed FISH hybridization chain reaction (FISH-HCR) as an in situ whole cell detection method for environmental microorganisms. FISH-HCR amplifies the fluorescent signal, as does CARD-FISH, but it allows for milder cell permeation methods that might prevent yield loss. To compare FISH-HCR to CARD-FISH, we examined bacteria and archaea cell counts within two sediment cores, Lille Belt (~78 meters deep) and Landsort Deep (90 meters deep), which were retrieved from the Baltic Sea Basin during IODP Expedition 347. Preliminary analysis shows that CARD-FISH counts are below the quantification limit for most depths across both cores. By contrast, quantification of cells was possible with FISH-HCR in all examined depths. When quantification with CARD-FISH was above the limit of detection, counts with FISH-HCR were up to 11 fold higher for Bacteria and 3 fold higher for Archaea from the same sediment sample. Further, FISH-HCR counts follow the trends of on board counts nicely, indicating that FISH-HCR may better reflect the cellular abundance within marine sediment than other quantification methods, including qPCR. Using FISH-HCR, we found that archaeal cell counts were on average greater than bacterial cell counts, but within the same order of magnitude.

An oligonucleotide array for the identification and differentiation of bacteria pathogenic on potato.

PubMed

Fessehaie, Anania; De Boer, Solke H; Lévesque, C André

2003-03-01

ABSTRACT Oligonucleotides, 16 to 24 bases long, were selected from the 3' end of the 16S gene and the 16S-23S intergenic spacer regions of bacteria pathogenic on potato, including Clavibacter michiganensis subsp. sepedonicus, Ralstonia solanacearum, and the pectolytic erwinias, including Erwinia carotovora subsp. atroseptica and carotovora and E. chrysanthemi. Oligonucleotides were designed and formatted into an array by pin spotting on nylon membranes. Genomic DNA from bacterial cultures was amplified by polymerase chain reaction using conserved ribosomal primers and labeled simultaneously with digoxigenin-dUTP. Hybridization of amplicons to the array and subsequent serological detection of digoxigenin label revealed different hybridization patterns that were distinct for each species and subspecies tested. Hybridization of amplicons generally was restricted to appropriate homologous oligonucleotides and cross-hybridization with heterologous oligonucleotides was rare. Hybridization patterns were recorded as separate gray values for each hybridized spot and revealed a consistent pattern for multiple strains of each species or subspecies isolated from diverse geographical regions. In preliminary tests, bacteria could be correctly identified and detected by hybridizing to the array amplicons from mixed cultures and inoculated potato tissue.

Toward tailoring Majorana bound states in artificially constructed magnetic atom chains on elemental superconductors

PubMed Central

Thorwart, Michael

2018-01-01

Realizing Majorana bound states (MBS) in condensed matter systems is a key challenge on the way toward topological quantum computing. As a promising platform, one-dimensional magnetic chains on conventional superconductors were theoretically predicted to host MBS at the chain ends. We demonstrate a novel approach to design of model-type atomic-scale systems for studying MBS using single-atom manipulation techniques. Our artificially constructed atomic Fe chains on a Re surface exhibit spin spiral states and a remarkable enhancement of the local density of states at zero energy being strongly localized at the chain ends. Moreover, the zero-energy modes at the chain ends are shown to emerge and become stabilized with increasing chain length. Tight-binding model calculations based on parameters obtained from ab initio calculations corroborate that the system resides in the topological phase. Our work opens new pathways to design MBS in atomic-scale hybrid structures as a basis for fault-tolerant topological quantum computing. PMID:29756034

Toward tailoring Majorana bound states in artificially constructed magnetic atom chains on elemental superconductors.

PubMed

Kim, Howon; Palacio-Morales, Alexandra; Posske, Thore; Rózsa, Levente; Palotás, Krisztián; Szunyogh, László; Thorwart, Michael; Wiesendanger, Roland

2018-05-01

Realizing Majorana bound states (MBS) in condensed matter systems is a key challenge on the way toward topological quantum computing. As a promising platform, one-dimensional magnetic chains on conventional superconductors were theoretically predicted to host MBS at the chain ends. We demonstrate a novel approach to design of model-type atomic-scale systems for studying MBS using single-atom manipulation techniques. Our artificially constructed atomic Fe chains on a Re surface exhibit spin spiral states and a remarkable enhancement of the local density of states at zero energy being strongly localized at the chain ends. Moreover, the zero-energy modes at the chain ends are shown to emerge and become stabilized with increasing chain length. Tight-binding model calculations based on parameters obtained from ab initio calculations corroborate that the system resides in the topological phase. Our work opens new pathways to design MBS in atomic-scale hybrid structures as a basis for fault-tolerant topological quantum computing.

Protective role of the novel hybrid 3,5-dipalmitoyl-nifedipine in a cardiomyoblast culture subjected to simulated ischemia/reperfusion.

PubMed

Santa-Helena, Eduarda; Teixeira, Stefanie; Castro, Micheli Rosa de; Cabrera, Diego da Costa; D'Oca, Caroline Da Ros Montes; D'Oca, Marcelo G Montes; Votto, Ana Paula S; Nery, Luiz Eduardo Maia; Gonçalves, Carla Amorim Neves

2017-08-01

This work investigated the acute effects of the calcium channel blocker nifedipine and its new fatty hybrid derived from palmitic acid, 3,5-dipalmitoyl-nifedipine, compared to endocannabinoid anandamide during the process of inducing ischemia and reperfusion in cardiomyoblast H9c2 heart cells. The cardiomyoblasts were treated in 24 or 96-well plates (according to the test being performed) and maintaining the treatment until the end of hypoxia induction. The molecules were tested at concentrations of 10 and 100μM, cells were treated 24h after assembling the experimental plates and immediately before the I/R. Cell viability, apoptosis and necrosis, and generation of reactive oxygen species were evaluated. Nifedipine and 3,5-dipalmitoyl-nifedipine were used to assess radical scavenging potential and metal chelation. All tested molecules managed to reduce the levels of reactive oxygen species compared to the starvation+vehicle group. In in vitro assays, 3,5-dipalmitoyl-nifedipine showed more antioxidant activity than nifedipine. These results indicate the ability of this molecule to act as a powerful ROS scavenger. Cell viability was highest when cells were induced to I/R by both concentrations of anandamide and the higher concentration of DPN. These treatments also reduced cell death. Therefore, it was demonstrated that the process of hybridization of nifedipine with two palmitic acid chains assigns a greater cardioprotective effect to this molecule, thereby reducing the damage caused by hypoxia and reoxygenation in cardiomyoblast cultures. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Structure of a tethered polymer under flow using molecular dynamics and hybrid molecular-continuum simulations

NASA Astrophysics Data System (ADS)

Delgado-Buscalioni, Rafael; Coveney, Peter V.

2006-03-01

We analyse the structure of a single polymer tethered to a solid surface undergoing a Couette flow. We study the problem using molecular dynamics (MD) and hybrid MD-continuum simulations, wherein the polymer and the surrounding solvent are treated via standard MD, and the solvent flow farther away from the polymer is solved by continuum fluid dynamics (CFD). The polymer represents a freely jointed chain (FJC) and is modelled by Lennard-Jones (LJ) beads interacting through the FENE potential. The solvent (modelled as a LJ fluid) and a weakly attractive wall are treated at the molecular level. At large shear rates the polymer becomes more elongated than predicted by existing theoretical scaling laws. Also, along the normal-to-wall direction the structure observed for the FJC is, surprisingly, very similar to that predicted for a semiflexible chain. Comparison with previous Brownian dynamics simulations (which exclude both solvent and wall potential) indicates that these effects are due to the polymer-solvent and polymer-wall interactions. The hybrid simulations are in perfect agreement with the MD simulations, showing no trace of finite size effects. Importantly, the extra cost required to couple the MD and CFD domains is negligible.

A multiple-scattering polaritonic-operator method for hybrid arrays of metal nanoparticles and quantum emitters

NASA Astrophysics Data System (ADS)

Chatzidakis, Georgios D.; Yannopapas, Vassilios

2018-05-01

We present a new technique for the study of hybrid collections of quantum emitters (atoms, molecules, quantum dots) with nanoparticles. The technique is based on a multiple-scattering polaritonic-operator formalism in conjunction with an electromagnetic coupled dipole method. Apart from collections of quantum emitters and nanoparticles, the method can equally treat the interaction of a collection of quantum emitters with a single nano-object of arbitrary shape in which case the nano-object is treated as a finite three-dimensional lattice of point scatterers. We have applied our method to the case of linear array (chain) of dimers of quantum emitters and metallic nanoparticles wherein the corresponding (geometrical and physical) parameters of the dimers are chosen so as the interaction between the emitter and the nanoparticle lies in the strong-coupling regime in order to enable the formation of plexciton states in the dimer. In particular, for a linear chain of dimers, we show that the corresponding light spectra reveal a multitude of plexciton modes resulting from the hybridization of the plexciton resonances of each individual dimer in a manner similar to the tight-binding description of electrons in solids.

Photoconductivity enhancement and charge transport properties in ruthenium-containing block copolymer/carbon nanotube hybrids.

PubMed

Lo, Kin Cheung; Hau, King In; Chan, Wai Kin

2018-04-05

Functional polymer/carbon nanotube (CNT) hybrid materials can serve as a good model for light harvesting systems based on CNTs. This paper presents the synthesis of block copolymer/CNT hybrids and the characterization of their photocurrent responses by both experimental and computational approaches. A series of functional diblock copolymers was synthesized by reversible addition-fragmentation chain transfer polymerizations for the dispersion and functionalization of CNTs. The block copolymers contain photosensitizing ruthenium complexes and modified pyrene-based anchoring units. The photocurrent responses of the polymer/CNT hybrids were measured by photoconductive atomic force microscopy (PCAFM), from which the experimental data were analyzed by vigorous statistical models. The difference in photocurrent response among different hybrids was correlated to the conformations of the hybrids, which were elucidated by molecular dynamics simulations, and the electronic properties of polymers. The photoresponse of the block copolymer/CNT hybrids can be enhanced by introducing an electron-accepting block between the photosensitizing block and the CNT. We have demonstrated that the application of a rigorous statistical methodology can unravel the charge transport properties of these hybrid materials and provide general guidelines for the design of molecular light harvesting systems.

Integrating DNA strand displacement circuitry to the nonlinear hybridization chain reaction.

PubMed

Zhang, Zhuo; Fan, Tsz Wing; Hsing, I-Ming

2017-02-23

Programmable and modular attributes of DNA molecules allow one to develop versatile sensing platforms that can be operated isothermally and enzyme-free. In this work, we present an approach to integrate upstream DNA strand displacement circuits that can be turned on by a sequence-specific microRNA analyte with a downstream nonlinear hybridization chain reaction for a cascading hyperbranched nucleic acid assembly. This system provides a two-step amplification strategy for highly sensitive detection of the miRNA analyte, conducive for multiplexed detection. Multiple miRNA analytes were tested with our integrated circuitry using the same downstream signal amplification setting, showing the decoupling of nonlinear self-assembly with the analyte sequence. Compared with the reported methods, our signal amplification approach provides an additional control module for higher-order DNA self-assembly and could be developed into a promising platform for the detection of critical nucleic-acid based biomarkers.

A plasmonic colorimetric strategy for visual miRNA detection based on hybridization chain reaction

NASA Astrophysics Data System (ADS)

Miao, Jie; Wang, Jingsheng; Guo, Jinyang; Gao, Huiguang; Han, Kun; Jiang, Chengmin; Miao, Peng

2016-08-01

In this work, a novel colorimetric strategy for miRNA analysis is proposed based on hybridization chain reaction (HCR)-mediated localized surface plasmon resonance (LSPR) variation of silver nanoparticles (AgNPs). miRNA in the sample to be tested is able to release HCR initiator from a solid interface to AgNPs colloid system by toehold exchange-mediated strand displacement, which then triggers the consumption of fuel strands with single-stranded tails for HCR. The final produced long nicked double-stranded DNA loses the ability to protect AgNPs from salt-induced aggregation. The stability variation of the colloid system can then be monitored by recording corresponding UV-vis spectrum and initial miRNA level is thus determined. This sensing system involves only four DNA strands which is quite simple. The practical utility is confirmed to be excellent by employing different biological samples.

Proton-Fueled, Reversible DNA Hybridization Chain Assembly for pH Sensing and Imaging.

PubMed

Liu, Lan; Liu, Jin-Wen; Huang, Zhi-Mei; Wu, Han; Li, Na; Tang, Li-Juan; Jiang, Jian-Hui

2017-07-05

Design of DNA self-assembly with reversible responsiveness to external stimuli is of great interest for diverse applications. We for the first time develop a pH-responsive, fully reversible hybridization chain reaction (HCR) assembly that allows sensitive sensing and imaging of pH in living cells. Our design relies on the triplex forming sequences that form DNA triplex with toehold regions under acidic conditions and then induce a cascade of strand displacement and DNA assembly. The HCR assembly has shown dynamic responses in physiological pH ranges with excellent reversibility and demonstrated the potential for in vitro detection and live-cell imaging of pH. Moreover, this method affords HCR assemblies with highly localized fluorescence responses, offering advantages of improving sensitivity and better selectivity. The proton-fueled, reversible HCR assembly may provide a useful approach for pH-related cell biology study and disease diagnostics.

Majorana Fermion and bound states in the continuum on a cross-shaped quantum dot hybrid structure

NASA Astrophysics Data System (ADS)

Zambrano, David; Ramos, Juan Pablo; Orellana, Pedro

We show how transmission, differential conductance and density of states (DOS) behave when two superconductor/semiconductors topological nanowires are placed next to the ends of a quantum-dot (QD) chain, where the central QD is attached to normal conductors leads. Results in a single QD coupled to two Kitaev chains within the topological phase and a T-shaped QD hybrid structure suggest these kind of system are strong candidates for qubits. We show how bound states in the continuum (BICs) arise as zero energy modes on conductance and DOS for different sets of system parameters showing evidence of Majorana fermions, and we also study how they behave for different numbers (even/odd) of QD in the cross-shaped structure. The authors acknowledge financial support from CONICYT, under Grant PAI-79140064, scholarship 21141034 and from FONDECYT, under Grant 1140571.

Label-Free Fluorescent DNA Dendrimers for microRNA Detection Based On Nonlinear Hybridization Chain Reaction-Mediated Multiple G-Quadruplex with Low Background Signal.

PubMed

Xue, Qingwang; Liu, Chunxue; Li, Xia; Dai, Li; Wang, Huaisheng

2018-04-18

Various fluorescent sensing systems for miRNA detection have been developed, but they mostly contain enzymatic amplification reactions and label procedures. The strict reaction conditions of tool enzymes and the high cost of labeling limit their potential applications, especially in complex biological matrices. Here, we have addressed the difficult problems and report a strategy for label-free fluorescent DNA dendrimers based on enzyme-free nonlinear hybridization chain reaction (HCR)-mediated multiple G-quadruplex for simple, sensitive, and selective detection of miRNAs with low-background signal. In the strategy, a split G-quadruplex (3:1) sequence is ingeniously designed at both ends of two double-stranded DNAs, which is exploited as building blocks for nonlinear HCR assembly, thereby acquiring a low background signal. A hairpin switch probe (HSP) was employed as recognition and transduction element. Upon sensing the target miRNA, the nonlinear HCR assembly of two blocks (blocks-A and blocks-B) was initiated with the help of two single-stranded DNA assistants, resulting in chain-branching growth of DNA dendrimers with multiple G-quadruplex incorporation. With the zinc(II)-protoporphyrin IX (ZnPPIX) selectively intercalated into the multiple G-quadruplexes, fluorescent DNA dendrimers were obtained, leading to an exponential fluorescence intensity increase. Benefiting from excellent performances of nonlinear HCR and low background signal, this strategy possesses the characteristics of a simplified reaction operation process, as well as high sensitivity. Moreover, the proposed fluorescent sensing strategy also shows preferable selectivity, and can be implemented without modified DNA blocks. Importantly, the strategy has also been tested for miRNA quantification with high confidence in breast cancer cells. Thus, this proposed strategy for label-free fluorescent DNA dendrimers based on a nonlinear HCR-mediated multiple G-quadruplex will be turned into an alternative approach for simple, sensitive, and selective miRNA quantification.

Thermoresponsive AuNPs Stabilized by Pillararene-Containing Polymers.

PubMed

Liao, Xiaojuan; Guo, Lei; Chang, Junxia; Liu, Sha; Xie, Meiran; Chen, Guosong

2015-08-01

Pillararene-containing thermoresponsive polymers are synthesized via reversible addition-fragmentation chain transfer polymerization using pillararene derivatives as the effective chain transfer agents for the first time. These polymers can self-assemble into micelles and form vesicles after guest molecules are added. Furthermore, such functional polymers can be further applied to prepare hybrid gold nanoparticles, which integrate the thermoresponsivity of polymers and molecular recognition of pillararenes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analyses of chicken immunoglobulin light chain cDNA clones indicate a few germline V lambda genes and allotypes of the C lambda locus.

PubMed

Parvari, R; Ziv, E; Lentner, F; Tel-Or, S; Burstein, Y; Schechter, I

1987-01-01

cDNA libraries of chicken spleen and Harder gland (a gland enriched with immunocytes) constructed in pBR322 were screened by differential hybridization and by mRNA hybrid-selected translation. Eleven L-chain cDNA clones were identified from which VL probes were prepared and each was annealed with kidney DNA restriction digests. All VL probes revealed the same set of bands, corresponding to about 15 germline VL genes of one subgroup. The nucleotide sequences of six VL clones showed greater than or equal to 85% homology, and the predicted amino acid sequences were identical or nearly identical to the major N-terminal sequence of L-chains in chicken serum. These findings, and the fact that the VL clones were randomly selected from normal lymphoid tissues, strongly indicate that the bulk of chicken L-chains is encoded by a few germline VL genes, probably much less than 15 since many of the VL genes are known to be pseudogenes. Therefore, it is likely that somatic mechanisms operating prior to specific triggering by antigen play a major role in the generation of antibody diversity in chicken. Analysis of the constant region locus (sequencing of CL gene and cDNAs) demonstrate a single CL isotype and suggest the presence of CL allotypes.

Synthesis of novel benzohydrazone-oxadiazole hybrids as β-glucuronidase inhibitors and molecular modeling studies.

PubMed

Taha, Muhammad; Ismail, Nor Hadiani; Imran, Syahrul; Selvaraj, Manikandan; Rahim, Abdul; Ali, Muhammad; Siddiqui, Salman; Rahim, Fazal; Khan, Khalid Mohammed

2015-12-01

A series of compounds consisting of 25 novel oxadiazole-benzohydrazone hybrids (6-30) were synthesized through a five-step reaction sequence and evaluated for their β-glucuronidase inhibitory potential. The IC50 values of compounds 6-30 were found to be in the range of 7.14-44.16μM. Compounds 6, 7, 8, 9, 11, 13, 18, and 25 were found to be more potent than d-saccharic acid 1,4-lactone (48.4±1.25μM). These compounds were further subjected for molecular docking studies to confirm the binding mode towards human β-d-glucuronidase active site. Docking study for compound 13 (IC50=7.14±0.30μM) revealed that it adopts a binding mode that fits within the entire pocket of the binding site of β-d-glucuronidase. Compound 13 has the maximum number of hydrogens bonded to the residues of the active site as compared to the other compounds, that is, the ortho-hydroxyl group forms hydrogen bond with carboxyl side chain of Asp207 (2.1Å) and with hydroxyl group of Tyr508 (2.6Å). The other hydroxyl group forms hydrogen bond with His385 side chain (2.8Å), side chain carboxyl oxygen of Glu540 (2.2Å) and Asn450 side-chain's carboxamide NH (2.1Å). Copyright © 2015 Elsevier Ltd. All rights reserved.

Surface zwitterionicalization of poly(vinylidene fluoride) membranes from the entrapped reactive core-shell silica nanoparticles.

PubMed

Zhu, Li-Jing; Zhu, Li-Ping; Zhang, Pei-Bin; Zhu, Bao-Ku; Xu, You-Yi

2016-04-15

We demonstrate the preparation and properties of poly(vinylidene fluoride) (PVDF) filtration membranes modified via surface zwitterionicalization mediated by reactive core-shell silica nanoparticles (SiO2 NPs). The organic/inorganic hybrid SiO2 NPs grafted with poly(methyl meth acrylate)-block-poly(2-dimethylaminoethyl methacrylate) copolymer (PMMA-b-PDMAEMA) shell were prepared by surface-initiated reversible addition fragmentation chain transfer (SI-RAFT) polymerization and then used as a membrane-making additive of PVDF membranes. The PDMAEMA exposed on membrane surface and pore walls were quaternized into zwitterionic poly(sulfobetaine methacrylate) (PSBMA) using 1,3-propane sultone (1,3-PS) as the quaternization agent. The membrane surface chemistry and morphology were analyzed by attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM), respectively. The hydrophilicity, permeability and antifouling ability of the investigated membranes were evaluated in detail. It was found that the PSBMA chains brought highly-hydrophilic and strong fouling resistant characteristics to PVDF membranes due to the powerful hydration of zwitterionic surface. The SiO2 cores and PMMA chains in the hybrid NPs play a role of anchors for the linking of PSBMA chains to membrane surface. Compared to the traditional strategies for membrane hydrophilic modification, the developed method in this work combined the advantages of both blending and surface reaction. Copyright © 2016 Elsevier Inc. All rights reserved.

Revisiting kinetic boundary conditions at the surface of fuel droplet hydrocarbons: An atomistic computational fluid dynamics simulation

PubMed Central

Nasiri, Rasoul

2016-01-01

The role of boundary conditions at the interface for both Boltzmann equation and the set of Navier-Stokes equations have been suggested to be important for studying of multiphase flows such as evaporation/condensation process which doesn’t always obey the equilibrium conditions. Here we present aspects of transition-state theory (TST) alongside with kinetic gas theory (KGT) relevant to the study of quasi-equilibrium interfacial phenomena and the equilibrium gas phase processes, respectively. A two-state mathematical model for long-chain hydrocarbons which have multi-structural specifications is introduced to clarify how kinetics and thermodynamics affect evaporation/condensation process at the surface of fuel droplet, liquid and gas phases and then show how experimental observations for a number of n-alkane may be reproduced using a hybrid framework TST and KGT with physically reasonable parameters controlling the interface, gas and liquid phases. The importance of internal activation dynamics at the surface of n-alkane droplets is established during the evaporation/condensation process. PMID:27215897

Surface molecular imprinting onto fluorescein-coated magnetic nanoparticlesvia reversible addition fragmentation chain transfer polymerization: A facile three-in-one system for recognition and separation of endocrine disrupting chemicals

NASA Astrophysics Data System (ADS)

Li, Ying; Dong, Cunku; Chu, Jia; Qi, Jingyao; Li, Xin

2011-01-01

In this study, we present a general protocol for the making of surface-imprinted magnetic fluorescence beads viareversible addition-fragmentation chain transfer polymerization. The resulting composites were characterized by X-ray diffraction analysis, transmission electron microscopy, scanning electron microscopy, fluorescence spectroscopy, Fourier transform infrared spectroscopy, and energy dispersive spectroscopy. The as-synthesized beads exhibited homogeneous polymer films (thickness of about 5.7 nm), spherical shape, high fluorescence intensity and magnetic property (Magnetization (Ms) = 3.67 emu g-1). The hybrids bind the original template 17β-estradiol with an appreciable selectivity over structurally related compounds. In addition, the resulting hybrids performed without obvious deterioration after five repeated cycles. This study therefore demonstrates the potential of molecularly imprinted polymers for the recognition and separation of endocrine disrupting chemicals.In this study, we present a general protocol for the making of surface-imprinted magnetic fluorescence beads viareversible addition-fragmentation chain transfer polymerization. The resulting composites were characterized by X-ray diffraction analysis, transmission electron microscopy, scanning electron microscopy, fluorescence spectroscopy, Fourier transform infrared spectroscopy, and energy dispersive spectroscopy. The as-synthesized beads exhibited homogeneous polymer films (thickness of about 5.7 nm), spherical shape, high fluorescence intensity and magnetic property (Magnetization (Ms) = 3.67 emu g-1). The hybrids bind the original template 17β-estradiol with an appreciable selectivity over structurally related compounds. In addition, the resulting hybrids performed without obvious deterioration after five repeated cycles. This study therefore demonstrates the potential of molecularly imprinted polymers for the recognition and separation of endocrine disrupting chemicals. Electronic supplementary information (ESI) available: Supplementary figure S1. The hysteresis loop of Fe3O4 (a), Fe3O4@SiO2 (b), and Fe3O4@SiO2-Dye-SiO2 (c). See DOI: 10.1039/c0nr00614a

[Role of cytology in hematopathological diagnostics].

PubMed

Bode, B; Tinguely, M

2012-07-01

The role of cytology has so far been underrecognized in the diagnostic process of hematopathological questions. This article presents an algorithm which allows a stepwise work-up of cytology specimens obtained by minimally invasive ultrasound-guided fine needle aspiration in patients with unexplained lymph node swelling. Moreover, it is shown how the selective separation of cytology specimens allows the application of immunophenotypic analysis including flow cytometry and immunohistochemistry as well as molecular analyses, such as fluorescence in situ hybridization (FISH) and polymerase chain reaction (PCR) strategies. With the integrative procedure presented, cytology offers an excellent cost-effective tool for the diagnostic approach of patients with suspected hematopathological malignancies allowing a high diagnostic accuracy, ideal for initial diagnosis or follow-up.

Engineered soy oils for new value added applications

NASA Astrophysics Data System (ADS)

Tran, Phuong T.

Soybean oil is an abundant annually renewable resource. It is composed of triglycerides with long chain saturated and unsaturated fatty acids. The presence of unsaturated fatty acids allows for chemical modification to introduce new functionalities to soybean oil. A portfolio of chemically modified soy oil with suitable functional groups has been designed and engineered to serve as the starting material in applications such as polyamides, polyesters, polyurethanes, composites, and lubricants. Anhydride, hydroxyl, and silicone functionalities were introduced to soy oil. Anhydride functionality was introduced using a single-step free radical initiated process, and the chemically modified soy oils were evaluated for potential applications as a composite and lubricant. Hydroxyl functionalities were introduced in a single-step catalytic ozonolysis process recently developed in our labs, which proceeds rapidly and efficiently at room temperature without solvent. The transformed soy oil was used to successfully prepare bio-lubricants with good thermal/oxidative stability and bio-plastics such as polyamides, polyesters, and polyurethanes. A new class of organic-inorganic hybrid materials was prepared by curing vinyltrimethoxysilane functionalized soy oil. This hybrid material could have potential as biobased sealant through a moisture initiated room temperature cure. These new classes of soy-based materials are competitive both in cost and performance to petroleum based materials, but offer the advantage of being biobased.

A two-dimensional organic–inorganic hybrid compound, poly[(ethylenediamine)tri-μ-oxido-oxidocopper(II)molybdenum(VI)

PubMed Central

Gun, Ozgul; VanDerveer, Don; Emirdag-Eanes, Mehtap

2008-01-01

A new organic–inorganic two-dimensional hybrid compound, [CuMoO4(C2H8N2)], has been hydro­thermally synthesized at 443 K. The unit cell contains layers composed of CuN2O4 octa­hedra and MoO4 tetra­hedra. Corner-sharing MoO4 and CuN2O4 polyhedra form CuMoO4 bimetallic sites that are joined together through O atoms, forming an edge-sharing Cu2Mo2O4 chain along the c axis. The one-dimensional chains are further linked through bridging O atoms that join the Cu and Mo atoms into respective chains along the b axis, thus establishing layers in the bc plane. The ethyl­enediamine ligand is coordinated to the Cu atom through its two N atoms and is oriented perpendicularly to the two-dimensional –Cu—O—Mo– layers. The average distance between adjacent layers, as calculated by consideration of the closest and furthest distances between two layers, is 8.7 Å. The oxidation states of the Mo and Cu atoms of VI and II, respectively, were confirmed by bond-valence sum calculations. PMID:21200997

Functionalization of magnetic nanocrystals by oligo (ethylene oxide) chains carrying diazonium and iniferter end groups.

PubMed

Ahmad, Randa; Griffete, Nébéwia; Lamouri, Aazdine; Mangeney, Claire

2013-10-01

The water stability of iron oxide nanoparticles (NPs) is a major issue for biomedical and biological applications. This paper presents a versatile approach for preparing water-soluble iron oxide nanoparticles coated by bifunctional oligo(ethylene oxide) (OEO) chains, carrying on the one side a diazonium end group for covalent grafting at the NP surface and on the other side an iniferter group (diethyl dithiocarbamate) for initiating the growing of poly(methacrylic acid). The nanoparticles were synthesized by coprecipitation in basic media and functionalized in situ by adding the diazonium salt directly in the synthesis medium. Oligo(ethylene oxide) with various chain lengths (from one to three monomer units) was grafted at the NP surface using this approach. The length of the OEO spacer between the NP surface and the iniferter end group was found to be a critical parameter for controlling the colloidal stability of the hybrid NPs. The polymerization time was also shown to strongly influence their colloidal stability, emphasizing the interest to control the interfacial properties of the hybrids for obtaining stable dispersions in water. Copyright © 2013 Elsevier Inc. All rights reserved.

cDNA cloning of rat and human medium chain acyl-CoA dehydrogenase (MCAD)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matsubara, Y.; Kraus, J.P.; Rosenberg, L.E.

MCAD is one of three mitochondrial flavoenzymes which catalyze the first step in the ..beta..-oxidation of straight chain fatty acids. It is a tetramer with a subunit Mr of 45 kDa. MCAD is synthesized in the cytosol as a 49 kDa precursor polypeptide (pMCAD), imported into mitochondria, and cleaved to the mature form. Genetic deficiency of MCAD causes recurrent episodes of hypoglycemic coma accompanied by medium chain dicarboxylic aciduria. Employing a novel approach, the authors now report isolation of partial rat and human cDNA clones encoding pMCAD. mRNA encoding pMCAD was purified to near homogeneity by polysome immunoadsorption using polyclonalmore » monospecific antibody. Single-stranded (/sup 32/P)labeled cDNA probe was synthesized using the enriched mRNA as template, and was used to screen directly 16,000 colonies from a total rat liver cDNA library constructed in pBR322. One clone (600 bp) was detected by in situ hybridization. Hybrid-selected translation with this cDNA yielded a 49 kDa polypeptide indistinguishable in size from rat pMCAD and immunoprecipitable with anti-MCAD antibody. Using the rat cDNA as probe, 43,000 colonies from a human liver cDNA library were screened. Four identical positive clones (400 bp) were isolated and positively identified by hybrid-selected translation and immunoprecipitation. The sizes of rat and human mRNAs encoding pMCAD were 2.2 kb and 2.4 kb, respectively, as determined by Northern blotting.« less

Synthesis of waterborne polyurethane containing alkoxysilane side groups and the properties of the hybrid coating films

NASA Astrophysics Data System (ADS)

Li, Qi; Guo, Longhai; Qiu, Teng; Xiao, Weidong; Du, Dianxing; Li, Xiaoyu

2016-07-01

A series of waterborne polyurethane (WPU) containing alkoxysilane side groups were synthesized by using the dihydroxy functionalized alkoxysilane. The diol with trimethoxysilane groups at the side chains was synthesized via Michael addition between 3-(methacryloxypropyl)trimethoxysilane (MAPTS) and diethanolamine (DEA). The silane diol was applied as the chain extender for the NCO-endcapped prepolymer of isophorone diisocyanate, polycarbonate diol, 2,2-bis(hydroxymethyl) butyric acid and 1,4-butanediol. The products with the silane content varied from 1.2 to 16.5 wt% were dispersed in water after neutralization. The effect of the silane diol on the particle size and morphology of the WPU dispersion was studied by dynamic light scattering (DLS) and transmission electron microscopy (TEM), respectively. X-ray photoelectron spectroscopy (XPS) characterization was carried out on the coating film of the WPU, revealing that the long flexible side chain is favorable for the silane components to emigrate toward the film surface and crosslink during the film formation process. As a result, both the surface contact angle to water and water adsorption of the WPU coating films increased with the silane content. Furthermore, the mechanical properties including the modulus and tensile strength of the films were also improved by the incorporation of silane diol.

Detection of DNA Sequences Refractory to PCR Amplification Using a Biophysical SERRS Assay (Surface Enhanced Resonant Raman Spectroscopy)

PubMed Central

Feuillie, Cécile; Merheb, Maxime M.; Gillet, Benjamin; Montagnac, Gilles; Daniel, Isabelle; Hänni, Catherine

2014-01-01

The analysis of ancient or processed DNA samples is often a great challenge, because traditional Polymerase Chain Reaction – based amplification is impeded by DNA damage. Blocking lesions such as abasic sites are known to block the bypass of DNA polymerases, thus stopping primer elongation. In the present work, we applied the SERRS-hybridization assay, a fully non-enzymatic method, to the detection of DNA refractory to PCR amplification. This method combines specific hybridization with detection by Surface Enhanced Resonant Raman Scattering (SERRS). It allows the detection of a series of double-stranded DNA molecules containing a varying number of abasic sites on both strands, when PCR failed to detect the most degraded sequences. Our SERRS approach can quickly detect DNA molecules without any need for DNA repair. This assay could be applied as a pre-requisite analysis prior to enzymatic reparation or amplification. A whole new set of samples, both forensic and archaeological, could then deliver information that was not yet available due to a high degree of DNA damage. PMID:25502338

Detection of DNA sequences refractory to PCR amplification using a biophysical SERRS assay (Surface Enhanced Resonant Raman Spectroscopy).

PubMed

Feuillie, Cécile; Merheb, Maxime M; Gillet, Benjamin; Montagnac, Gilles; Daniel, Isabelle; Hänni, Catherine

2014-01-01

The analysis of ancient or processed DNA samples is often a great challenge, because traditional Polymerase Chain Reaction - based amplification is impeded by DNA damage. Blocking lesions such as abasic sites are known to block the bypass of DNA polymerases, thus stopping primer elongation. In the present work, we applied the SERRS-hybridization assay, a fully non-enzymatic method, to the detection of DNA refractory to PCR amplification. This method combines specific hybridization with detection by Surface Enhanced Resonant Raman Scattering (SERRS). It allows the detection of a series of double-stranded DNA molecules containing a varying number of abasic sites on both strands, when PCR failed to detect the most degraded sequences. Our SERRS approach can quickly detect DNA molecules without any need for DNA repair. This assay could be applied as a pre-requisite analysis prior to enzymatic reparation or amplification. A whole new set of samples, both forensic and archaeological, could then deliver information that was not yet available due to a high degree of DNA damage.

Meta-analysis of studies using suppression subtractive hybridization and microarrays to investigate the effects of environmental stress on gene transcription in oysters.

PubMed

Anderson, Kelli; Taylor, Daisy A; Thompson, Emma L; Melwani, Aroon R; Nair, Sham V; Raftos, David A

2015-01-01

Many microarray and suppression subtractive hybridization (SSH) studies have analyzed the effects of environmental stress on gene transcription in marine species. However, there have been no unifying analyses of these data to identify common stress response pathways. To address this shortfall, we conducted a meta-analysis of 14 studies that investigated the effects of different environmental stressors on gene expression in oysters. The stressors tested included chemical contamination, hypoxia and infection, as well as extremes of temperature, pH and turbidity. We found that the expression of over 400 genes in a range of oyster species changed significantly after exposure to environmental stress. A repeating pattern was evident in these transcriptional responses, regardless of the type of stress applied. Many of the genes that responded to environmental stress encoded proteins involved in translation and protein processing (including molecular chaperones), the mitochondrial electron transport chain, anti-oxidant activity and the cytoskeleton. In light of these findings, we put forward a consensus model of sub-cellular stress responses in oysters.

Life cycle environmental assessment of lithium-ion and nickel metal hydride batteries for plug-in hybrid and battery electric vehicles.

PubMed

Majeau-Bettez, Guillaume; Hawkins, Troy R; Strømman, Anders Hammer

2011-05-15

This study presents the life cycle assessment (LCA) of three batteries for plug-in hybrid and full performance battery electric vehicles. A transparent life cycle inventory (LCI) was compiled in a component-wise manner for nickel metal hydride (NiMH), nickel cobalt manganese lithium-ion (NCM), and iron phosphate lithium-ion (LFP) batteries. The battery systems were investigated with a functional unit based on energy storage, and environmental impacts were analyzed using midpoint indicators. On a per-storage basis, the NiMH technology was found to have the highest environmental impact, followed by NCM and then LFP, for all categories considered except ozone depletion potential. We found higher life cycle global warming emissions than have been previously reported. Detailed contribution and structural path analyses allowed for the identification of the different processes and value-chains most directly responsible for these emissions. This article contributes a public and detailed inventory, which can be easily be adapted to any powertrain, along with readily usable environmental performance assessments.

Synthesis of HNTs@PEDOT composites via in situ chemical oxidative polymerization and their application in electrode materials

NASA Astrophysics Data System (ADS)

Wang, Fang; Zhang, Xianhong; Ma, Yuhong; Yang, Wantai

2018-01-01

The hybrid composite of poly(3,4-ethylenedioxythiophene) (PEDOT) and halloysite nanotubes (HNTs) was synthesized by a two-step process. First, poly(sodium styrene sulfonate) (PSSNa) was grafted onto HNTs via surface initiated atom transfer radical polymerization. Then with the HNTs-g-PSS as a template and the grafted PSS chains as the counterion dopant, PEDOT was precipitated onto the template via in situ oxidization polymerization of EDOT to form HNTs@PEDOT hybrid composites. The conductivity of HNTs@PEDOT can reach up to 9.35 S/cm with the content of 40% HNTs-g-PSS, which increased almost 78 times than that of pure PEDOT (about 0.12 S/cm) prepared at the similar condition. Further treated with p-toluenesulfonic acid (TsOH) as external dopant, the conductivity of HNTs@PEDOT increased to 24.3 S/cm. The electrochemical properties of the composites were investigated with cyclic voltammetry, galvanostatic charge-discharge and electrochemical impedance spectroscopy with three-electrode cell configuration. The results showed that the capacitance of HNTs@PEDOT composite increased 55% than that of pure PEDOT.

Meta-Analysis of Studies Using Suppression Subtractive Hybridization and Microarrays to Investigate the Effects of Environmental Stress on Gene Transcription in Oysters

PubMed Central

Thompson, Emma L.; Melwani, Aroon R.; Nair, Sham V.; Raftos, David A.

2015-01-01

Many microarray and suppression subtractive hybridization (SSH) studies have analyzed the effects of environmental stress on gene transcription in marine species. However, there have been no unifying analyses of these data to identify common stress response pathways. To address this shortfall, we conducted a meta-analysis of 14 studies that investigated the effects of different environmental stressors on gene expression in oysters. The stressors tested included chemical contamination, hypoxia and infection, as well as extremes of temperature, pH and turbidity. We found that the expression of over 400 genes in a range of oyster species changed significantly after exposure to environmental stress. A repeating pattern was evident in these transcriptional responses, regardless of the type of stress applied. Many of the genes that responded to environmental stress encoded proteins involved in translation and protein processing (including molecular chaperones), the mitochondrial electron transport chain, anti-oxidant activity and the cytoskeleton. In light of these findings, we put forward a consensus model of sub-cellular stress responses in oysters. PMID:25768438

Scanning electrochemical microscopy of graphene/polymer hybrid thin films as supercapacitors: Physical-chemical interfacial processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gupta, Sanju, E-mail: sanju.gupta@wku.edu; Price, Carson

2015-10-15

Hybrid electrode comprising an electric double-layer capacitor of graphene nanosheets and a pseudocapacitor of the electrically conducting polymers namely, polyaniline; PAni and polypyrrole; PPy are constructed that exhibited synergistic effect with excellent electrochemical performance as thin film supercapacitors for alternative energy. The hybrid supercapacitors were prepared by layer-by-layer (LbL) assembly based on controlled electrochemical polymerization followed by reduction of graphene oxide electrochemically producing ErGO, for establishing intimate electronic contact through nanoscale architecture and chemical stability, producing a single bilayer of (PAni/ErGO){sub 1}, (PPy/ErGO){sub 1}, (PAni/GO){sub 1} and (PPy/GO){sub 1}. The rationale design is to create thin films that possess interconnectedmore » graphene nanosheets (GNS) with polymer nanostructures forming well-defined tailored interfaces allowing sufficient surface adsorption and faster ion transport due to short diffusion distances. We investigated their electrochemical properties and performance in terms of gravimetric specific capacitance, C{sub s}, from cyclic voltammograms. The LbL-assembled bilayer films exhibited an excellent C{sub s} of ≥350 F g{sup −1} as compared with constituents (∼70 F g{sup −1}) at discharge current density of 0.3 A g{sup −1} that outperformed many other hybrid supercapacitors. To gain deeper insights into the physical-chemical interfacial processes occurring at the electrode/electrolyte interface that govern their operation, we have used scanning electrochemical microscopy (SECM) technique in feedback and probe approach modes. We present our findings from viewpoint of reinforcing the role played by heterogeneous electrode surface composed of nanoscale graphene sheets (conducting) and conducting polymers (semiconducting) backbone with ordered polymer chains via higher/lower probe current distribution maps. Also targeted is SECM imaging that allowed to determine electrochemical (re)activity of surface ion adsorption sites density at solid/liquid interface.« less

Assessment of hybridization among wild and cultivated Vigna unguiculata subspecies revealed by arbitrarily primed polymerase chain reaction analysis

PubMed Central

Vijaykumar, Archana; Saini, Ajay; Jawali, Narendra

2012-01-01

Background and aims Intra-species hybridization and incompletely homogenized ribosomal RNA repeat units have earlier been reported in 21 accessions of Vigna unguiculata from six subspecies using internal transcribed spacer (ITS) and 5S intergenic spacer (IGS) analyses. However, the relationships among these accessions were not clear from these analyses. We therefore assessed intra-species hybridization in the same set of accessions. Methodology Arbitrarily primed polymerase chain reaction (AP-PCR) analysis was carried out using 12 primers. The PCR products were resolved on agarose gels and the DNA fragments were scored manually. Genetic relationships were inferred by TREECON software using unweighted paired group method with arithmetic averages (UPGMA) cluster analysis evaluated by bootstrapping and compared with previous analyses based on ITS and 5S IGS. Principal results A total of 202 (86 %) fragments were found to be polymorphic and used for generating a genetic distance matrix. Twenty-one V. unguiculata accessions were grouped into three main clusters. The cultivated subspecies (var. unguiculata) and most of its wild progenitors (var. spontanea) were placed in cluster I along with ssp. pubescens and ssp. stenophylla. Whereas var. spontanea were grouped with ssp. alba and ssp. tenuis accessions in cluster II, ssp. alba and ssp. baoulensis were included in cluster III. Close affinities of ssp. unguiculata, ssp. alba and ssp. tenuis suggested inter-subspecies hybridization. Conclusions Multi-locus AP-PCR analysis reveals that intra-species hybridization is prevalent among V. unguiculata subspecies and suggests that grouping of accessions from two different subspecies is not solely due to the similarity in the ITS and 5S IGS regions but also due to other regions of the genome. PMID:22619698

Hybridizing polypyrrole chains with laminated and two-dimensional Ti3C2Tx toward high-performance electromagnetic wave absorption

NASA Astrophysics Data System (ADS)

Tong, Yuan; He, Man; Zhou, Yuming; Zhong, Xi; Fan, Lidan; Huang, Tingyuan; Liao, Qiang; Wang, Yongjuan

2018-03-01

In this study, multilayer sandwich heterostructural Ti3C2Tx MXenes decorated with polypyrrole chains have been synthesized successfully via HF etching treatment and in-situ chemical oxidative polymerization approach. The hybrids were investigated as EM wave absorbers for the first time. It is found that the composites consisting of 25 wt% Ti3C2Tx/PPy hybrids in a paraffin matrix exhibit a minimum reflection loss of -49.2 dB (∼99.99% absorption) at the thickness of 3.2 mm and a maximum effective absorption bandwidth of 4.9 GHz (12.4-17.3 GHz) corresponding to an absorber thickness of 2.0 mm. Additionally, a broad effective absorption bandwidth of 13.7 GHz (4.3-18.0 GHz) can be reached up by adjusting the thickness from 1.5 to 5.0 mm. Furthermore, the highest effective absorption bandwidth of 5.7 GHz can be reached when the mass fraction is 15 wt%. The enhanced comprehensive electromagnetic wave absorption has close correlation with the well-designed heterogeneous multilayered microstructure, generated heterogeneous interfaces, conductive paths, surface functional groups, localized defects and synergistic effect between laminated Ti3C2Tx and conductive polypyrrole network, which significantly improve impedance matching and attenuation abilities. The superior absorbing performance together with strong absorption and broad bandwidth endows the Ti3C2Tx/PPy hybrids with the potential prospect to be advanced EM wave absorbers.

Polymerase chain reaction and DNA probe hybridization to assess the efficacy of diminazene treatment in Trypanosoma brucei-infected cattle.

PubMed

Clausen, P H; Waiswa, C; Katunguka-Rwakishaya, E; Schares, G; Steuber, S; Mehlitz, D

1999-03-01

Four of eight Ankole longhorn cattle experimentally infected with Trypanosoma brucei were treated with 7 mg/kg diminazene aceturate (Berenil, Hoechst AG, Germany) at day 71 postinfection. The trypanocidal activity was monitored using polymerase chain reaction (PCR) and DNA probe hybridization. When extracted parasite DNA (without host DNA) was used, as little as 1 fg per reaction, which is equivalent to about 1-10% of the DNA in a single trypanosome, produced a specific product that was visible as a 177-bp band in an agarose gel. In infected cattle, specific PCR products could be amplified at as early as 1 day postinfection. PCR signals remained positive during infection, except in one sample, although aparasitemic phases occurred. In cases where treatment resulted in a significant clinical improvement, PCR signals disappeared at 3-4 days after the administration of the drug. By contrast, in cattle that showed clinical signs of CNS involvement after treatment, although aparasitemic, and died before the termination of the experiment, specific products could be amplified on several occasions following treatment. The PCR signals generated after treatment could be further enhanced by subsequent slot-blot hybridization with a T. brucei-specific DNA probe. We conclude that PCR coupled with DNA probe hybridization provides a highly sensitive tool for the assessment of therapeutic efficiency and disease progression in trypanosome infections, especially in chronic infections when the level of parasitemia is low or when trypanosomes are sequestered at cryptic sites.

Fabrication of mesoporous metal oxide coated-nanocarbon hybrid materials via a polyol-mediated self-assembly process.

PubMed

Feng, Bingmei; Wang, Huixin; Wang, Dongniu; Yu, Huilong; Chu, Yi; Fang, Hai-Tao

2014-11-06

After clarifying the formation mechanism of a typical metal glycolate precipitate, Ti glycolate, in a polyol-mediated synthesis using acetone as a precipitation medium, we describe a simple template-free approach based on an ethylene glycol-mediated synthesis to fabricate mesoporous metal oxide coated-nanocarbon hybrid materials including TiO₂ coated-carbon nanotube (CNT), SnO₂ coated-CNT, Cu₂O/CuO coated-CNT and TiO₂ coated-graphene sheet (GS). In the approach, metal oxide precursors, metal glycolates, were first deposited on CNTs or GSs, and subsequently transformed to the metal oxide coatings by pyrolysis or hydrolysis. By a comparison between the characterization of two TiO₂-CNT hybrid materials using carboxylated CNTs and pristine CNTs without carboxyl groups, the driving force for initiating the deposition of metal glycolates on the carboxylated CNTs is confirmed to be the hydrogen bonding between the carboxyl groups and the polymer chains in metal glycolate sols. The electrochemical performances of the mesoporous TiO₂ coated-carboxylated CNTs and TiO₂-pristine CNT hybrid materials were investigated. The results show that the mesoporous TiO₂ coated-carboxylated CNT with a uniform core-shell nanostructure exhibits substantial improvement in the rate performance in comparison with its counterpart from 0.5 C to 100 C because of its higher electronic conductivity and shorter diffusion path for the lithium ion. At the extremely high rate of 100 C, the specific capacity of TiO₂ of the former reaches 85 mA h g(-1), twice as high as that of the latter.

Hybrid optimization and Bayesian inference techniques for a non-smooth radiation detection problem

DOE PAGES

Stefanescu, Razvan; Schmidt, Kathleen; Hite, Jason; ...

2016-12-12

In this paper, we propose several algorithms to recover the location and intensity of a radiation source located in a simulated 250 × 180 m block of an urban center based on synthetic measurements. Radioactive decay and detection are Poisson random processes, so we employ likelihood functions based on this distribution. Owing to the domain geometry and the proposed response model, the negative logarithm of the likelihood is only piecewise continuous differentiable, and it has multiple local minima. To address these difficulties, we investigate three hybrid algorithms composed of mixed optimization techniques. For global optimization, we consider simulated annealing, particlemore » swarm, and genetic algorithm, which rely solely on objective function evaluations; that is, they do not evaluate the gradient in the objective function. By employing early stopping criteria for the global optimization methods, a pseudo-optimum point is obtained. This is subsequently utilized as the initial value by the deterministic implicit filtering method, which is able to find local extrema in non-smooth functions, to finish the search in a narrow domain. These new hybrid techniques, combining global optimization and implicit filtering address, difficulties associated with the non-smooth response, and their performances, are shown to significantly decrease the computational time over the global optimization methods. To quantify uncertainties associated with the source location and intensity, we employ the delayed rejection adaptive Metropolis and DiffeRential Evolution Adaptive Metropolis algorithms. Finally, marginal densities of the source properties are obtained, and the means of the chains compare accurately with the estimates produced by the hybrid algorithms.« less

Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units

PubMed Central

Mamonov, Artem B.; Lettieri, Steven; Ding, Ying; Sarver, Jessica L.; Palli, Rohith; Cunningham, Timothy F.; Saxena, Sunil; Zuckerman, Daniel M.

2012-01-01

Building on our recently introduced library-based Monte Carlo (LBMC) approach, we describe a flexible protocol for mixed coarse-grained (CG)/all-atom (AA) simulation of proteins and ligands. In the present implementation of LBMC, protein side chain configurations are pre-calculated and stored in libraries, while bonded interactions along the backbone are treated explicitly. Because the AA side chain coordinates are maintained at minimal run-time cost, arbitrary sites and interaction terms can be turned on to create mixed-resolution models. For example, an AA region of interest such as a binding site can be coupled to a CG model for the rest of the protein. We have additionally developed a hybrid implementation of the generalized Born/surface area (GBSA) implicit solvent model suitable for mixed-resolution models, which in turn was ported to a graphics processing unit (GPU) for faster calculation. The new software was applied to study two systems: (i) the behavior of spin labels on the B1 domain of protein G (GB1) and (ii) docking of randomly initialized estradiol configurations to the ligand binding domain of the estrogen receptor (ERα). The performance of the GPU version of the code was also benchmarked in a number of additional systems. PMID:23162384

Gelator-polysaccharide hybrid hydrogel for selective and controllable dye release.

PubMed

Li, Ping; Dou, Xiao-Qiu; Tang, Yi-Tian; Zhu, Shenmin; Gu, Jiajun; Feng, Chuan-Liang; Zhang, Di

2012-12-01

In this paper, 1,4-bi(phenylalanine-diglycol)-benzene (PDB) based Low-Molecular-Weight-Gelator (LMWG) hydrogels are modified using hydrophilic polysaccharide (sodium alginate). A set of techniques including Fourier transform infrared (FT-IR) spectroscopy, (1)H Nuclear Magnetic Resonance ((1)H NMR), X-ray powder diffraction (XRD), Ultraviolet-Visible (UV-Vis), and circular dichroism (CD) had confirmed a β-turn arrangement of PDB gelators and a semi-interpenetrating network (semi-IPN), which was formed through hydrogen bonds between LMWG fibers and polysaccharide chains. The evaluation of physicochemical properties of hydrogels indicates that gelator-polysaccharide hybrid hydrogels possess better mechanical and water retention properties than LMWG hydrogels. The release study of dyes (model drug) from both LMWG and hybrid hydrogels was carried out. Compared with PDB based hydrogels, hybrid hydrogels show a selective and controllable release property for certain dyes. The results suggest LMWG-polysaccharide hybrid gels may find potential applications as promising drug delivery vehicles for drug molecules. Copyright © 2012 Elsevier Inc. All rights reserved.

Evaluation of Four RNA Extraction Methods for Gene Expression Analyses of Cryptosporidium parvum and Toxoplasma gondii Oocys

EPA Science Inventory

Cryptosporidium spp. and Toxoplasma gondii are important coccidian parasites that have caused waterborne and foodborne disease outbreaks worldwide. Techniques like subtractive hybridization, microarrays, and quantitative reverse transcriptase real-time polymerase chain reaction (...

Hybrid photonic signal processing

NASA Astrophysics Data System (ADS)

Ghauri, Farzan Naseer

This thesis proposes research of novel hybrid photonic signal processing systems in the areas of optical communications, test and measurement, RF signal processing and extreme environment optical sensors. It will be shown that use of innovative hybrid techniques allows design of photonic signal processing systems with superior performance parameters and enhanced capabilities. These applications can be divided into domains of analog-digital hybrid signal processing applications and free-space---fiber-coupled hybrid optical sensors. The analog-digital hybrid signal processing applications include a high-performance analog-digital hybrid MEMS variable optical attenuator that can simultaneously provide high dynamic range as well as high resolution attenuation controls; an analog-digital hybrid MEMS beam profiler that allows high-power watt-level laser beam profiling and also provides both submicron-level high resolution and wide area profiling coverage; and all optical transversal RF filters that operate on the principle of broadband optical spectral control using MEMS and/or Acousto-Optic tunable Filters (AOTF) devices which can provide continuous, digital or hybrid signal time delay and weight selection. The hybrid optical sensors presented in the thesis are extreme environment pressure sensors and dual temperature-pressure sensors. The sensors employ hybrid free-space and fiber-coupled techniques for remotely monitoring a system under simultaneous extremely high temperatures and pressures.

Blood clearance and biodistribution of polymer brush-afforded silica particles prepared by surface-initiated living radical polymerization.

PubMed

Ohno, Kohji; Akashi, Tatsuki; Tsujii, Yoshinobu; Yamamoto, Masaya; Tabata, Yasuhiko

2012-03-12

The physiological properties of polymer brush-afforded silica particles prepared by surface-initiated living radical polymerization were investigated in terms of the circulation lifetime in the blood and distribution in tissues. Hydrophilic polymers consisting mainly of poly(poly(ethylene glycol) methyl ether methacrylate) were grafted onto silica particles by surface-initiated atom transfer radical polymerization that was mediated by a copper complex to produce hairy hybrid particles. A series of hybrid particles was synthesized by varying the diameter of the silica core and the chain length of the polymer brush to examine the relationship between their physicochemical and physiological properties. The hybrid particles were injected intravenously into mice to investigate systematically their blood clearance and body distribution. It was revealed that the structural features of the hybrid particles significantly affected their in vivo pharmacokinetics. Some hybrid particles exhibited an excellently prolonged circulation lifetime in the blood with a half life of ∼20 h. When such hybrid particles were injected intravenously into a tumor-bearing mouse, they preferentially accumulated in tumor tissue. The tumor-targeted delivery was optically visualized using hybrid particles grafted with fluorescence-labeled polymer brushes.

Chemical and Biological Sensing Using Hybridization Chain Reaction.

PubMed

Augspurger, Erik E; Rana, Muhit; Yigit, Mehmet V

2018-05-25

Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. The recent prominence of DNA-based technologies in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions, and solvent types. This programmability and molecular-level control have allowed scientists to create and utilize DNA nanostructures in one, two, and three dimensions (1D, 2D, and 3D). Initially, these 2D and 3D DNA lattices and shapes attracted a broad scientific audience because they are fundamentally captivating and structurally elegant; however, transforming these conceptual architectural blueprints into functional materials is essential for further advancements in the DNA nanotechnology field. Herein, the chemical and biological sensing applications of a 1D DNA self-assembly process known as hybridization chain reaction (HCR) are reviewed. HCR is a one-dimensional (1D) double stranded (ds) DNA assembly process initiated only in the presence of a specific short ssDNA (initiator) and two kinetically trapped DNA hairpin structures. HCR is considered an enzyme-free isothermal amplification process, which shows substantial promise and offers a wide range of applications for in situ chemical and biological sensing. Due to its modular nature, HCR can be programmed to activate only in the presence of highly specific biological and/or chemical stimuli. HCR can also be combined with different types of molecular reporters and detection approaches for various analytical readouts. While the long dsDNA HCR product may not be as structurally attractive as the 2D and 3D DNA networks, HCR is highly instrumental for applied biological, chemical, and environmental sciences, and has therefore been studied to foster a variety of objectives. In this review, we have focused on nucleic acid, protein, metabolite, and heavy metal ion detection using this 1D DNA nanotechnology via fluorescence, electrochemical, and nanoparticle-based methodologies.

De novo transcriptome analysis reveals insights into different mechanisms of growth and immunity in a Chinese soft-shelled turtle hybrid and the parental varieties.

PubMed

Zhang, Haiqi; Xu, Xiaojun; He, Zhongyang; Zheng, Tianlun; Shao, Jianzhong

2017-03-20

The Chinese soft-shelled turtle (Pelodiscus sinensis) is a highly important freshwater aquaculture species in China. The molecular mechanisms underlying changes in immunity and growth in hybrid vigor are not well understood. In the present study, the transcriptomes from significantly different P. sinensis strains (Qingxi black turtle, B and Japanese strain, J) and the resulting hybrid (Zajiao-1, F) were sequenced using an Illumina sequencing platform. Differentially expressed genes (DEGs) between Zajiao-1 and the Qingxi black turtle were enriched mainly in the HTLV-I infection and Hippo signaling pathways, while DEGs between the Zajiao-1 and Japanese strain were enriched mainly in tryptophan metabolism, caner-associated pathways, transcriptional dysregulation in cancer, amebiasis, Fcγ-mediated phagocytosis and the peroxisome pathway. Highly expressed genes involved in the regulation of disorders of the fatty acid biosynthesis, immune and cardiovascular systems in P. sinensis were found among the DEGs. Enrichment categories for gene ontology included cellular processes, metabolic pathways, and the actin cytoskeleton pathway. The reliability of the sequencing data was verified through quantitative real-time polymerase chain reaction analysis of 20 immunity or growth-related genes. These findings offer new insights into heterosis of growth traits and resistance to stresses and potential strategies for selective breeding. Copyright © 2016 Elsevier B.V. All rights reserved.

Pseudoislet of hybrid cellular spheroids from commercial cell lines.

PubMed

Jo, Y H; Nam, B M; Kim, B Y; Nemeno, J G; Lee, S; Yeo, J E; Yang, W; Park, S H; Kim, Y S; Lee, J I

2013-10-01

Investigators conducting diabetes-related research have focused on islet transplantation as a radical therapy for type 1 diabetes mellitus. Pancreatic islet isolation, an essential process, is a very demanding work because of the proteolytic enzymes, species, treatment time, and individual difference. Replacement of primary isolated pancreatic islets must be carried out continuously for various in vitro tests, making primary isolated islets a useful tool for cell transplantation research. Hence, we sought to develop pseudoislets from commercial pancreas-derived cell lines. In this study, we used RIN-5F and RIN-m cells, which secrete insulin, somatostatin, or glucagon. To manufacture hybrid cellular spheroids, the cells were cultured under hanging drop plate and nonadhesive plate methods. We observed that hybrid cellular pseudoislets exhibited an oval shape, with sizes ranging from 590 to 1200 μm. Their morphology was similar to naïve islets. Cell line pseudoislets secreted and expressed insulin, glucagon, and somatostatin, as confirmed by reverse transcriptase polymerase chain reaction, enzyme-linked immunosorbent assay, and immunohistochemistry analyses. Thus, the current artificially manufactured biomimetic pseudoislets resembled pancreatic islets of the endocrine system, appearing as cellular aggregates that secreted insulin, glucagon, and somatostatin. Enhanced immunoisolation techniques may lead to the development of new islet sources for pancreatic transplantation through this pseudoislet strategy. Crown Copyright © 2013. Published by Elsevier Inc. All rights reserved.

Visible-Light Initiated Free-Radical/Cationic Ring-Opening Hybrid Photopolymerization of Methacrylate/Epoxy: Polymerization Kinetics, Crosslinking Structure, and Dynamic Mechanical Properties.

PubMed

Ge, Xueping; Ye, Qiang; Song, Linyong; Misra, Anil; Spencer, Paulette

2015-04-01

The effects of polymerization kinetics and chemical miscibility on the crosslinking structure and mechanical properties of polymers cured by visible-light initiated free-radical/cationic ring-opening hybrid photopolymerization are determined. A three-component initiator system is used and the monomer system contains methacrylates and epoxides. The photopolymerization kinetics is monitored in situ by Fourier transform infrared-attenuated total reflectance. The crosslinking structure is studied by modulated differential scanning calorimetry and dynamic mechanical analysis. X-ray microcomputed tomography is used to evaluate microphase separation. The mechanical properties of polymers formed by hybrid formed by free-radical polymerization. These investigations mark the first time that the benefits of the chain transfer reaction between epoxy and hydroxyl groups of methacrylate, on the crosslinking network and microphase separation during hybrid visible-light initiated photopolymerization, have been determined.

Improved electron transport properties of n-type naphthalenediimide polymers through refined molecular ordering and orientation induced by processing solvents.

PubMed

An, Yujin; Long, Dang Xuan; Kim, Yiho; Noh, Yong-Young; Yang, Changduk

2016-05-14

To determine the role played by the choice of processing solvents in governing the photophysics, microstructure, and charge carrier transport in naphthalenediimide (NDI)-based polymers, we have prepared two new NDI-bithiophene (T2)- and NDI-thienothiophene (TTh)-containing polymers with hybrid siloxane pentyl chains (SiC5) (P(NDI2SiC5-T2) and P(NDI2SiC5-TTh)). Among the various processing solvents studied here, the films prepared using chloroform exhibited far better electron mobilities (0.16 ± 0.1-0.21 ± 0.05 cm(2) V(-1) s(-1)) than the corresponding samples prepared from different solvents, exceeding one order of magnitude higher, indicating the significant influence of the processing solvent on the charge transport. Upon thin-film analysis using atomic force microscopy and grazing incidence X-ray diffraction, we discovered that molecular ordering and orientation are affected by the choice of the processing solvent, which is responsible for the change in the transport characteristics of this class of polymers.

Molecular Effects on Coacervate-Driven Block Copolymer Self Assembly

NASA Astrophysics Data System (ADS)

Lytle, Tyer; Radhakrishna, Mithun; Sing, Charles

Two oppositely charged polymers can undergo associative phase separation in a salt solution in a process known as \\x98complex coacervation. Recent work has used this as a motif to control the self-assembly behavior of a mixture of oppositely-charged block copolymers which form nanoscale structures. The materials formed from these complex coacervate-block copolymers (BCPs) have potential use as drug delivery systems, gels, and sensors. We have developed a hybrid Monte Carlo-Single Chain in a Mean Field (MC-SCMF) simulation method that is able to determine morphological phase diagrams for BCPs. This technique is an efficient way to calculate morphological phase diagrams and provides a clear link between molecular level features and self-assembly behaviors. Morphological phase diagrams showing the effects of polymer concentration, salt concentration, chain length, and charge-block fraction at large charge densities on self-assembly behavior have been determined. An unexpected phase transition from disorder to hexagonal packing at large salt concentrations has been observed for charge-block fractions equal to and larger than 0.5. This is attributed to the salt filling space stabilizing the morphology of the BCP.

Engineering Yarrowia lipolytica as a platform for synthesis of drop-in transportation fuels and oleochemicals

PubMed Central

Xu, Peng; Qiao, Kangjian; Ahn, Woo Suk; Stephanopoulos, Gregory

2016-01-01

Harnessing lipogenic pathways and rewiring acyl-CoA and acyl-ACP (acyl carrier protein) metabolism in Yarrowia lipolytica hold great potential for cost-efficient production of diesel, gasoline-like fuels, and oleochemicals. Here we assessed various pathway engineering strategies in Y. lipolytica toward developing a yeast biorefinery platform for sustainable production of fuel-like molecules and oleochemicals. Specifically, acyl-CoA/acyl-ACP processing enzymes were targeted to the cytoplasm, peroxisome, or endoplasmic reticulum to generate fatty acid ethyl esters and fatty alkanes with tailored chain length. Activation of endogenous free fatty acids and the subsequent reduction of fatty acyl-CoAs enabled the efficient synthesis of fatty alcohols. Engineering a hybrid fatty acid synthase shifted the free fatty acids to a medium chain-length scale. Manipulation of alternative cytosolic acetyl-CoA pathways partially decoupled lipogenesis from nitrogen starvation and unleashed the lipogenic potential of Y. lipolytica. Taken together, the strategies reported here represent promising steps to develop a yeast biorefinery platform that potentially upgrades low-value carbons to high-value fuels and oleochemicals in a sustainable and environmentally friendly manner. PMID:27621436

Use of multiplex polymerase chain reaction-based assay to conduct epidemiological studies on bovine hemoparasites in Mexico.

PubMed

Figueroa, J V; Alvarez, J A; Ramos, J A; Vega, C A; Buening, G M

1993-01-01

A study was conducted to test the applicability of a Polymerase Chain Reaction (PCR)-based approach for the simultaneous detection of the bovine hemoparasites Babesia bigemina, B. bovis and Anaplasma marginale. Bovine blood samples from cattle ranches of a previously determined enzootic zone in the Yucatan Peninsula of Mexico, were collected from peripheral blood and processed for PCR analysis. Blood samples were subjected to DNA amplification by placing an aliquot in a reaction tube containing oligonucleotide primers specific for DNA of each hemoparasite species. The PCR products were detected by Dot-Blot nucleic acid hybridization utilizing nonradioactive, species-specific, digoxigenin PCR-labeled DNA probes. Four hundred twenty one field samples analyzed by the multiplex PCR-DNA probe assay showed 66.7%, 60.1% and 59.6% prevalence rates for B. bigemina, B. bovis and A. marginale, respectively. The multiplex PCR analysis showed that animals with single, double or triple infection could be detected with the parasite specific DNA probes. The procedure is proposed as a valuable tool for the epidemiological analysis in regions where the hemoparasite species are concurrently infecting cattle.

Graphical workstation capability for reliability modeling

NASA Technical Reports Server (NTRS)

Bavuso, Salvatore J.; Koppen, Sandra V.; Haley, Pamela J.

1992-01-01

In addition to computational capabilities, software tools for estimating the reliability of fault-tolerant digital computer systems must also provide a means of interfacing with the user. Described here is the new graphical interface capability of the hybrid automated reliability predictor (HARP), a software package that implements advanced reliability modeling techniques. The graphics oriented (GO) module provides the user with a graphical language for modeling system failure modes through the selection of various fault-tree gates, including sequence-dependency gates, or by a Markov chain. By using this graphical input language, a fault tree becomes a convenient notation for describing a system. In accounting for any sequence dependencies, HARP converts the fault-tree notation to a complex stochastic process that is reduced to a Markov chain, which it can then solve for system reliability. The graphics capability is available for use on an IBM-compatible PC, a Sun, and a VAX workstation. The GO module is written in the C programming language and uses the graphical kernal system (GKS) standard for graphics implementation. The PC, VAX, and Sun versions of the HARP GO module are currently in beta-testing stages.

Protein Detection via Direct Enzymatic Amplification of Short DNA Aptamers

PubMed Central

Fischer, Nicholas O.; Tarasow, Theodore M.; Tok, Jeffrey B.-H.

2008-01-01

Aptamers are single-stranded nucleic acids that fold into defined tertiary structures to bind target molecules with high specificities and affinities. DNA aptamers have garnered much interest as recognition elements for biodetection and diagnostic applications due to their small size, ease of discovery and synthesis, and chemical and thermal stability. Herein, we describe the design and application of a short DNA molecule capable of both protein target binding and amplifiable bioreadout processes. As both recognition and readout capabilities are incorporated into a single DNA molecule, tedious conjugation procedures required for protein-DNA hybrids can be omitted. The DNA aptamer is designed to be amplified directly by either the polymerase chain reaction (PCR) or rolling circle amplification (RCA) processes, taking advantage of real-time amplification monitoring techniques for target detection. A combination of both RCA and PCR provides a wide protein target dynamic range (1 μM to 10 pM). PMID:17980857

DNA based identification of medicinal materials in Chinese patent medicines

NASA Astrophysics Data System (ADS)

Chen, Rong; Dong, Juan; Cui, Xin; Wang, Wei; Yasmeen, Afshan; Deng, Yun; Zeng, Xiaomao; Tang, Zhuo

2012-12-01

Chinese patent medicines (CPM) are highly processed and easy to use Traditional Chinese Medicine (TCM). The market for CPM in China alone is tens of billions US dollars annually and some of the CPM are also used as dietary supplements for health augmentation in the western countries. But concerns continue to be raised about the legality, safety and efficacy of many popular CPM. Here we report a pioneer work of applying molecular biotechnology to the identification of CPM, particularly well refined oral liquids and injections. What's more, this PCR based method can also be developed to an easy to use and cost-effective visual chip by taking advantage of G-quadruplex based Hybridization Chain Reaction. This study demonstrates that DNA identification of specific Medicinal materials is an efficient and cost-effective way to audit highly processed CPM and will assist in monitoring their quality and legality.

Nuclear Proximity of Mtr4 with RNA exosome restricts DNA mutational asymmetry

PubMed Central

Lim, Junghyun; Giri, Pankaj Kumar; Kazadi, David; Laffleur, Brice; Zhang, Wanwei; Grinstein, Veronika; Pefanis, Evangelos; Brown, Lewis M.; Ladewig, Erik; Martin, Ophélie; Chen, Yuling; Rabadan, Raul; Boyer, François; Rothschild, Gerson; Cogné, Michel; Pinaud, Eric; Deng, Haiteng; Basu, Uttiya

2017-01-01

SUMMARY The distribution of sense and antisense strand DNA mutations on transcribed duplex DNA contributes to the development of immune and neural systems along with the progression of cancer. Because developmentally matured B cells undergo biologically programmed strand-specific DNA mutagenesis at focal DNA/RNA hybrid structures, they make a convenient system to investigate strand-specific mutagenesis mechanisms. We demonstrate that the sense and antisense strand DNA mutagenesis at the immunoglobulin heavy chain locus and some other regions of the B cell genome depends upon localized RNA processing protein complex formation in the nucleus. Both the physical proximity and coupled activities of RNA helicase Mtr4 (and Senataxin) with the noncoding RNA processing function of RNA exosome determine the strand specific distribution of DNA mutations. Our study suggests that strand-specific DNA mutagenesis-associated mechanisms will play major roles in other undiscovered aspects of organismic development. PMID:28431250

Tethered Lubricants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Archer, Lynden

We have performed extensive experimental and theoretical studies of interfacial friction, relaxation dynamics, and thermodynamics of polymer chains tethered to points, planes, and particles. A key result from our tribology studies using lateral force microscopy (LFM) measurements of polydisperse brushes of linear and branched chains densely grafted to planar substrates is that there are exceedingly low friction coefficients for these systems. Specific project achievements include: (1) Synthesis of three-tiered lubricant films containing controlled amounts of free and pendent PDMS chains, and investigated the effect of their molecular weight and volume fraction on interfacial friction. (2.) Detailed studies of a familymore » of hairy particles termed nanoscale organic hybrid materials (NOHMs) and demonstration of their use as lubricants.« less

SAChES: Scalable Adaptive Chain-Ensemble Sampling.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swiler, Laura Painton; Ray, Jaideep; Ebeida, Mohamed Salah

We present the development of a parallel Markov Chain Monte Carlo (MCMC) method called SAChES, Scalable Adaptive Chain-Ensemble Sampling. This capability is targed to Bayesian calibration of com- putationally expensive simulation models. SAChES involves a hybrid of two methods: Differential Evo- lution Monte Carlo followed by Adaptive Metropolis. Both methods involve parallel chains. Differential evolution allows one to explore high-dimensional parameter spaces using loosely coupled (i.e., largely asynchronous) chains. Loose coupling allows the use of large chain ensembles, with far more chains than the number of parameters to explore. This reduces per-chain sampling burden, enables high-dimensional inversions and the usemore » of computationally expensive forward models. The large number of chains can also ameliorate the impact of silent-errors, which may affect only a few chains. The chain ensemble can also be sampled to provide an initial condition when an aberrant chain is re-spawned. Adaptive Metropolis takes the best points from the differential evolution and efficiently hones in on the poste- rior density. The multitude of chains in SAChES is leveraged to (1) enable efficient exploration of the parameter space; and (2) ensure robustness to silent errors which may be unavoidable in extreme-scale computational platforms of the future. This report outlines SAChES, describes four papers that are the result of the project, and discusses some additional results.« less

Internal Light Source-Driven Photoelectrochemical 3D-rGO/Cellulose Device Based on Cascade DNA Amplification Strategy Integrating Target Analog Chain and DNA Mimic Enzyme.

PubMed

Lan, Feifei; Liang, Linlin; Zhang, Yan; Li, Li; Ren, Na; Yan, Mei; Ge, Shenguang; Yu, Jinghua

2017-11-01

In this work, a chemiluminescence-driven collapsible greeting card-like photoelectrochemical lab-on-paper device (GPECD) with hollow channel was demonstrated, in which target-triggering cascade DNA amplification strategy was ingeniously introduced. The GPECD had the functions of reagents storage and signal collection, and the change of configuration could control fluidic path, reaction time and alterations in electrical connectivity. In addition, three-dimentional reduced graphene oxide affixed Au flower was in situ grown on paper cellulose fiber for achieving excellent conductivity and biocompatibility. The cascade DNA amplification strategy referred to the cyclic formation of target analog chain and its trigger action to hybridization chain reaction (HCR), leading to the formation of numerous hemin/G-quadruplex DNA mimic enzyme with the presence of hemin. Subjected to the catalysis of hemin/G-quadruplex, the strong chemiluminiscence of luminol-H 2 O 2 system was obtained, which then was used as internal light source to excite photoactive materials realizing the simplification of instrument. In this analyzing process, thrombin served as proof-of-concept, and the concentration of target was converted into the DNA signal output by the specific recognition of aptamer-protein and target analog chain recycling. The target analog chain was produced in quantity with the presence of target, which further triggered abundant HCR and introduced hemin/G-quadruplex into the system. The photocurrent signal was obtained after the nitrogen-doped carbon dots sensitized ZnO was stimulated by chemiluminescence. The proposed GPECD exhibited excellent specificity and sensitivity toward thrombin with a detection limit of 16.7 fM. This judiciously engineered GPECD paved a luciferous way for detecting other protein with trace amounts in bioanalysis and clinical biomedicine.

Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

PubMed

Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

2016-02-01

Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/.

Total synthesis of feglymycin based on a linear/convergent hybrid approach using micro-flow amide bond formation

NASA Astrophysics Data System (ADS)

Fuse, Shinichiro; Mifune, Yuto; Nakamura, Hiroyuki; Tanaka, Hiroshi

2016-11-01

Feglymycin is a naturally occurring, anti-HIV and antimicrobial 13-mer peptide that includes highly racemizable 3,5-dihydroxyphenylglycines (Dpgs). Here we describe the total synthesis of feglymycin based on a linear/convergent hybrid approach. Our originally developed micro-flow amide bond formation enabled highly racemizable peptide chain elongation based on a linear approach that was previously considered impossible. Our developed approach will enable the practical preparation of biologically active oligopeptides that contain highly racemizable amino acids, which are attractive drug candidates.

Cu-containing Keggin-type polyoxometalates-based organic-inorganic hybrids with double electro-catalytic behaviors

NASA Astrophysics Data System (ADS)

Zhou, Wanli; Zheng, Yanping; Peng, Jun

2018-02-01

Four new organic-inorganic hybrids consisting of Keggin-type polyoxometalates: [Cu5(bimpy)5(α-BW12O40)]·4H2O (1), [Cu4(bimpy)4(α-SiW12O40)]·2H2O (2), [Cu4(bimpy)4(α-HPMo12O40)2]·2H2O (3), [Cu2(bimpy)4(H2O)2(α-HPW12O40)2]·8H2O (4) (bimpy = 2,5-bis(1H-imidazol-1-yl)pyridine), have been hydrothermally synthesized. Compounds 1-4 are constructed from Cu/bimpy segments modified different types of Keggin POMs. The 1D double chains of compound 1 are featured by {-Cu/bimpy-POM-Cu/bimpy-}n chains and {-Cu-bimpy-Cu-}n metal-organic chains; compound 2 with 1D "ladder-like" structure stemmed from {-Cu-bimpy-Cu-}n wave-like chains and α-SiW12 clusters; In compound 3, [Cu4(bimpy)4]4+ motifs are linked by α-PMo12 clusters to give rise to a (3,4)-connected two-dimensional architecture with the (83)(86) topology, while compound 4 has a (3,4,5)-connected 3D framework with the (42,6)(42,6,83)(42,65,83) topology. Cyclic voltammetries of compounds 1-4 show discrepant double electro-catalytic properties for reduction of nitrite and oxidation of ascorbic acid owing to variant Keggin-type POMs and Cu/bimpy complexes.

An effective hybrid self-adapting differential evolution algorithm for the joint replenishment and location-inventory problem in a three-level supply chain.

PubMed

Wang, Lin; Qu, Hui; Chen, Tao; Yan, Fang-Ping

2013-01-01

The integration with different decisions in the supply chain is a trend, since it can avoid the suboptimal decisions. In this paper, we provide an effective intelligent algorithm for a modified joint replenishment and location-inventory problem (JR-LIP). The problem of the JR-LIP is to determine the reasonable number and location of distribution centers (DCs), the assignment policy of customers, and the replenishment policy of DCs such that the overall cost is minimized. However, due to the JR-LIP's difficult mathematical properties, simple and effective solutions for this NP-hard problem have eluded researchers. To find an effective approach for the JR-LIP, a hybrid self-adapting differential evolution algorithm (HSDE) is designed. To verify the effectiveness of the HSDE, two intelligent algorithms that have been proven to be effective algorithms for the similar problems named genetic algorithm (GA) and hybrid DE (HDE) are chosen to compare with it. Comparative results of benchmark functions and randomly generated JR-LIPs show that HSDE outperforms GA and HDE. Moreover, a sensitive analysis of cost parameters reveals the useful managerial insight. All comparative results show that HSDE is more stable and robust in handling this complex problem especially for the large-scale problem.

Incorporating Graphene Oxide into Alginate Polymer with a Cationic Intermediate To Strengthen Membrane Dehydration Performance.

PubMed

Guan, Kecheng; Liang, Feng; Zhu, Haipeng; Zhao, Jing; Jin, Wanqin

2018-04-25

Two-dimensional graphene oxide (GO) in hybrid membranes provides fast water transfer across its surface due to the abundant oxygenated functional groups to afford water sorption and the hydrophobic basal plane to create fast transporting pathways. To establish more compatible and efficient interactions for GO and sodium alginate (SA) polymer chains, cations sourced from lignin are employed to decorate GO (labeled as cation-functionalized GO (CG)) nanosheets via cation-π and π-π interactions, providing more interactive sites to confer synergetic benefits with polymer matrix. Cations from CG are also functional to partially interlock SA chains and intensify water diffusion. And with the aid of two-dimensional pathways of CG, fast selective water permeation can be realized through hybrid membranes with CG fillers. In dehydrating aqueous ethanol solution, the hybrid membrane exhibits considerable performance compared with bare SA polymer membrane (long-term stable permeation flux larger than 2500 g m -2 h -1 and water content larger than 99.7 wt %, with feed water content of 10 wt % under 70 °C). The effects of CG content in SA membrane were investigated, and the transport mechanism was correspondingly studied through varying operation conditions and membrane materials. In addition, such a membrane possesses long-term stability and almost unchanged high dehydration capability.

Multi-scale structures and functional properties of starches from Indica hybrid, Japonica and waxy rice.

PubMed

Wang, Shujun; Li, Peiyan; Yu, Jinglin; Guo, Peng; Wang, Shuo

2017-09-01

The structural and functional properties of starches from three rice grains differing in amylose content (19.9, 13.4 and 0.8% for Japonica, Indica hybrid and waxy rice, respectively) were investigated using a range of characterization methods Indica hybrid starch (IHS) had the highest proportion of intermediate (DP 13-24) and long branch chains (DP≥37) and the lowest proportion of short branch chains (DP 6-12), whereas the opposite results were observed for Japonica starch (JS). The results for waxy rice starch (WS) were between those of IHS and JS. Rice starches showed a typical A-type X-ray diffraction pattern with the relative crystallinity ranging from 33.4% for JS to 39.4% for WS. Significant differences were observed in lamellar distance and short-range molecular order characterized by IR ratio of absorbances at 1047/1022cm -1 and full width of half maximum (FWHM) of the band at 480cm -1 . WS showed a higher swelling power and a lower close packing concentration at temperatures from 60 to 90°C. The lower peak viscosity of WS was attributed to the formation of less rigid swollen granules at a concentrated regime. WS showed a higher in vitro digestibility compared with IHS and JS. Copyright © 2017 Elsevier B.V. All rights reserved.

An Effective Hybrid Self-Adapting Differential Evolution Algorithm for the Joint Replenishment and Location-Inventory Problem in a Three-Level Supply Chain

PubMed Central

Chen, Tao; Yan, Fang-Ping

2013-01-01

The integration with different decisions in the supply chain is a trend, since it can avoid the suboptimal decisions. In this paper, we provide an effective intelligent algorithm for a modified joint replenishment and location-inventory problem (JR-LIP). The problem of the JR-LIP is to determine the reasonable number and location of distribution centers (DCs), the assignment policy of customers, and the replenishment policy of DCs such that the overall cost is minimized. However, due to the JR-LIP's difficult mathematical properties, simple and effective solutions for this NP-hard problem have eluded researchers. To find an effective approach for the JR-LIP, a hybrid self-adapting differential evolution algorithm (HSDE) is designed. To verify the effectiveness of the HSDE, two intelligent algorithms that have been proven to be effective algorithms for the similar problems named genetic algorithm (GA) and hybrid DE (HDE) are chosen to compare with it. Comparative results of benchmark functions and randomly generated JR-LIPs show that HSDE outperforms GA and HDE. Moreover, a sensitive analysis of cost parameters reveals the useful managerial insight. All comparative results show that HSDE is more stable and robust in handling this complex problem especially for the large-scale problem. PMID:24453822

Skeletal muscle fiber type conversion during the repair of mouse soleus: potential implications for muscle healing after injury.

PubMed

Matsuura, Tetsuya; Li, Yong; Giacobino, Jean-Paul; Fu, Freddie H; Huard, Johnny

2007-11-01

We used a mouse model of cardiotoxin injury to examine fiber type conversion during muscle repair. We evaluated the soleus muscles of 37 wild-type mice at 2, 4, 8, and 12 weeks after injury. We also used antibodies (fMHC and sMHC) against fast and slow myosin heavy chain to classify the myofibers into three categories: fast-, slow-, and mixed (hybrid)-type myofibers (myofibers expressing both fMHC and sMHC). Our results revealed an increase in the percentage of slow-type myofibers and a decrease in the percentage of fast-type myofibers during the repair process. The percentage of hybrid-type myofibers increased 2 weeks after injury, then gradually decreased over the following 6 weeks. Similarly, our analysis of centronucleated myofibers showed an increase in the percentage of slow-type myofibers and decreases in the percentages of fast- and hybrid-type myofibers. We also investigated the relationship between myofiber type conversion and peroxisome proliferator-activated receptor-gamma coactivator-1alpha (PGC-1alpha). The expression of both PGC-1alpha protein, which is expressed in both the nucleus and the cytoplasm of regenerating myofibers, and sMHC protein increased with time after cardiotoxin injection, but we observed no significant differential expression of fMHC protein in regenerating muscle fibers during muscle repair. PGC-1alpha-positive myofibers underwent fast to slow myofiber type conversion during the repair process. These results suggest that PGC-1alpha contributes to myofiber type conversion after muscle injury and that this phenomenon could influence the recovery of the injured muscle. (c) 2007 Orthopaedic Research Society.

Energetic features of copper and lead sorption by innovative aminoalcohol-functionalized cobalt phyllosilicates.

PubMed

Melo, Maurício Alves; Airoldi, Claudio

2010-11-14

Inorganic-organic cobalt phyllosilicate hybrids were synthesized by the sol-gel procedure under mild non-hydrothermal conditions with a silicon precursor, formed through individual reactions between the silane 3-glycidoxypropyltriethoxysilane and the aminoalcohols ethanol- or diethanolamine. These procedures generated talc-like phyllosilicates containing pendant organic chains with nitrogen and oxygen basic centres located in the interlamellar region. For organofunctionalized phyllosilicates the lamellar structure obtained through the sol-gel method was confirmed by X-ray powder diffraction, while elemental analysis indicated that the densities of the organic groups attached to the new matrices were 3.31 ± 0.05 and 3.08 ± 0.07 mmol g(-1) for hybrids functionalized with ethanol- and diethanolamines, respectively. Infrared spectroscopy and nuclear magnetic resonance in the solid state for (13)C and (29)Si showed that the organic groups are indeed covalently bonded to the inorganic structures and the process of functionalization did not affect the original structures of the silylating agents employed. The thermally stable hybrids presented well-formed particles with a homogeneous distribution of cobalt and nitrogen atoms. Their abilities for copper removal from aqueous solutions gave maximum capacities of sorption of 2.01 ± 0.11 and 2.55 ± 0.15 mmol g(-1) for phyllosilicates containing ethanol- and diethanolamine groups, respectively. For lead sorption the values of 2.59 ± 0.11 and 2.43 ± 0.12 mmol g(-1) were found for this same sequence. These sorption data were adjusted to the non-linear regression of the Langmuir equation. Energetic features related to the interactions between the cations and the pendant basic centres were determined through calorimetric titrations. The acid-basic interactions reflect the spontaneity of the reactions, which are also enthalpically and entropically favourable for these chelating processes at the solid-liquid interface.

In situ amplified electrochemical aptasensing for sensitive detection of adenosine triphosphate by coupling target-induced hybridization chain reaction with the assembly of silver nanotags.

PubMed

Zhou, Qian; Lin, Youxiu; Lin, Yuping; Wei, Qiaohua; Chen, Guonan; Tang, Dianping

2016-01-01

Biomolecular immobilization and construction of the sensing platform are usually crucial for the successful development of a high-efficiency detection system. Herein we report on a novel and label-free signal-amplified aptasensing for sensitive electrochemical detection of small molecules (adenosine triphosphate, ATP, used in this case) by coupling with target-induced hybridization chain reaction (HCR) and the assembly of electroactive silver nanotags. The system mainly consisted of two alternating hairpin probes, a partial-pairing trigger-aptamer duplex DNA and a capture probe immobilized on the electrode. Upon target ATP introduction, the analyte attacked the aptamer and released the trigger DNA, which was captured by capture DNA immobilized on the electrode to form a newly partial-pairing double-stranded DNA. Thereafter, the exposed domain at trigger DNA could be utilized as the initator strand to open the hairpin probes in sequence, and propagated a chain reaction of hybridization events between two alternating hairpins to form a long nicked double-helix. The electrochemical signal derived from the assembled silver nanotags on the nicked double-helix. Under optimal conditions, the electrochemical aptasensor could exhibit a high sensitivity and a low detection limit, and allowed the detection of ATP at a concentration as low as 0.03 pM. Our design showed a high selectivity for target ATP against its analogs because of the high-specificity ATP-aptamer reaction, and its applicable for monitoring ATP in the spiking serum samples. Improtantly, the distinct advantages of the developed aptasensor make it hold a great potential for the development of simple and robust sensing strategies for the detection of other small molecules by controlling the apatmer sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

Electronic shift register memory based on molecular electron-transfer reactions

NASA Technical Reports Server (NTRS)

Hopfield, J. J.; Onuchic, Jose Nelson; Beratan, David N.

1989-01-01

The design of a shift register memory at the molecular level is described in detail. The memory elements are based on a chain of electron-transfer molecules incorporated on a very large scale integrated (VLSI) substrate, and the information is shifted by photoinduced electron-transfer reactions. The design requirements for such a system are discussed, and several realistic strategies for synthesizing these systems are presented. The immediate advantage of such a hybrid molecular/VLSI device would arise from the possible information storage density. The prospect of considerable savings of energy per bit processed also exists. This molecular shift register memory element design solves the conceptual problems associated with integrating molecular size components with larger (micron) size features on a chip.

The potentials and challenges of electron microscopy in the study of atomic chains

NASA Astrophysics Data System (ADS)

Banhart, Florian; Torre, Alessandro La; Romdhane, Ferdaous Ben; Cretu, Ovidiu

2017-04-01

The article is a brief review on the potential of transmission electron microscopy (TEM) in the investigation of atom chains which are the paradigm of a strictly one-dimensional material. After the progress of TEM in the study of new two-dimensional materials, microscopy of free-standing one-dimensional structures is a new challenge with its inherent potentials and difficulties. In-situ experiments in the TEM allowed, for the first time, to generate isolated atomic chains consisting of metals, carbon or boron nitride. Besides having delivered a solid proof for the existence of atomic chains, in-situ TEM studies also enabled us to measure the electrical properties of these fundamental linear structures. While ballistic quantum conductivity is observed in chains of metal atoms, electrical transport in chains of sp1-hybridized carbon is limited by resonant states and reflections at the contacts. Although substantial progress has been made in recent TEM studies of atom chains, fundamental questions have to be answered, concerning the structural stability of the chains, bonding states at the contacts, and the suitability for applications in nanotechnology. Contribution to the topical issue "The 16th European Microscopy Congress (EMC 2016)", edited by Richard Brydson and Pascale Bayle-Guillemaud

Confinement and controlling the effective compressive stiffness of carbyne

NASA Astrophysics Data System (ADS)

Kocsis, Ashley J.; Aditya Reddy Yedama, Neta; Cranford, Steven W.

2014-08-01

Carbyne is a one-dimensional chain of carbon atoms, consisting of repeating sp-hybridized groups, thereby representing a minimalist molecular rod or chain. While exhibiting exemplary mechanical properties in tension (a 1D modulus on the order of 313 nN and a strength on the order of 11 nN), its use as a structural component at the molecular scale is limited due to its relative weakness in compression and the immediate onset of buckling under load. To circumvent this effect, here, we probe the effect of confinement to enhance the mechanical behavior of carbyne chains in compression. Through full atomistic molecular dynamics, we characterize the mechanical properties of a free (unconfined chain) and explore the effect of confinement radius (R), free chain length (L) and temperature (T) on the effective compressive stiffness of carbyne chains and demonstrate that the stiffness can be tuned over an order of magnitude (from approximately 0.54 kcal mol-1 Å2 to 46 kcal mol-1 Å2) by geometric control. Confinement may inherently stabilize the chains, potentially providing a platform for the synthesis of extraordinarily long chains (tens of nanometers) with variable compressive response.

Heavy Traffic Feasible Hybrid Intracycle and Cyclic Sleep for Power Saving in 10G-EPON

PubMed Central

Wang, Liqian; Zhang, Zhiguo; Chen, Xue

2014-01-01

Energy consumption in optical access networks costs carriers substantial operational expense (OPEX) every year and is one of contributing factors for the global warming. To reduce energy consumption in the 10-gigabit Ethernet passive optical network (10G-EPON), a hybrid intracycle and cyclic sleep mechanism is proposed in this paper. Under heavy traffic load, optical network units (ONUs) can utilize short idle slots within each scheduling cycle to enter intracycle sleep without postponing data transmission. In this way, energy conservation is achieved even under heavy traffic load with quality of service (QoS) guarantee. Under light traffic load, ONUs perform long cyclic sleep for several scheduling cycles. The adoption of cyclic sleep instead of intracycle sleep under light traffic load can reduce unnecessary frequent transitions between sleep and full active work caused by using intracycle sleep. Further, the Markov chain of the proposed mechanism is established. The performances of the proposed mechanism and existing approaches are analyzed quantitatively based on the chain. For the proposed mechanism, power saving ability with QoS guarantee even under heavy traffic and better power saving performance than existing approaches are verified by the quantitative analysis. Moreover, simulations validate the above conclusions based on the chain. PMID:25177727

Molecular Machine Powered Surface Programmatic Chain Reaction for Highly Sensitive Electrochemical Detection of Protein.

PubMed

Zhu, Jing; Gan, Haiying; Wu, Jie; Ju, Huangxian

2018-04-17

A bipedal molecular machine powered surface programmatic chain reaction was designed for electrochemical signal amplification and highly sensitive electrochemical detection of protein. The bipedal molecular machine was built through aptamer-target specific recognition for the binding of one target protein with two DNA probes, which hybridized with surface-tethered hairpin DNA 1 (H1) via proximity effect to expose the prelocked toehold domain of H1 for the hybridization of ferrocene-labeled hairpin DNA 2 (H2-Fc). The toehold-mediated strand displacement reaction brought the electrochemical signal molecule Fc close to the electrode and meanwhile released the bipedal molecular machine to traverse the sensing surface by the surface programmatic chain reaction. Eventually, a large number of duplex structures of H1-H2 with ferrocene groups facing to the electrode were formed on the sensor surface to generate an amplified electrochemical signal. Using thrombin as a model target, this method showed a linear detection range from 2 pM to 20 nM with a detection limit of 0.76 pM. The proposed detection strategy was enzyme-free and allowed highly sensitive and selective detection of a variety of protein targets by using corresponding DNA-based affinity probes, showing potential application in bioanalysis.

Simulations of Low-q Disruptions in the Compact Toroidal Hybrid Experiment

NASA Astrophysics Data System (ADS)

Howell, E. C.; Hanson, J. D.; Ennis, D. A.; Hartwell, G. J.; Maurer, D. A.

2017-10-01

Resistive MHD simulations of low-q disruptions in the Compact Toroidal Hybrid Device (CTH) are performed using the NIMROD code. CTH is a current-carrying stellarator used to study the effects of 3D shaping on MHD stability. Experimentally, it is observed that the application of 3D vacuum fields allows CTH to operate with edge safety factor less than 2.0. However, these low-q discharges often disrupt after peak current if the applied 3D fields are too weak. Nonlinear simulations are initialized using model VMEC equilibria representative of low-q discharges with weak vacuum transform. Initially a series of symmetry preserving island chains are excited at the q=6/5, 7/5, 8/5, and 9/5 rational surfaces. These island chains act as transport barriers preventing stochastic magnetic fields in the edge from penetrating into the core. As the simulation progresses, predominately m/n=3/2 and 4/3 instabilities are destabilized. As these instabilities grow to large amplitude they destroy the symmetry preserving islands leading to large regions of stochastic fields. A current spike and loss of core thermal confinement occurs when the innermost island chain (6/5) is destroyed. Work Supported by US-DOE Grant #DE-FG02-03ER54692.

Pathology annual. Part 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fechner, R.E.; Rosen, P.P.

1987-01-01

This book contains 11 selections. Some of the titles are: Applications of in situ DNA hybridization technology to diagnostic surgical pathology; Neoplasms associated with immune deficiencies; Chronic gastritis: The pathologists's role; Necrosis in lymph nodes; Pathologic changes of osteochondrodysplasia in infancy: A review; and Immunoglobulin light chain nephropathies.

Live-Cell MicroRNA Imaging through MnO2 Nanosheet-Mediated DD-A Hybridization Chain Reaction.

PubMed

Ou, Min; Huang, Jin; Yang, Xiaohai; He, Xiaoxiao; Quan, Ke; Yang, Yanjing; Xie, Nuli; Li, Jing; Wang, Kemin

2018-01-18

Innovative techniques to visualize native microRNAs (miRNAs) in live cells can dramatically impact current research on the roles of miRNA in biology and medicine. Here, we report a novel approach for live-cell miRNA imaging using a biodegradable MnO 2 nanosheet-mediated DD-A FRET hybridization chain reaction (HCR). The MnO 2 nanosheets can adsorb DNA hairpin probes and deliver them into live cells. After entering cells, the MnO 2 nanosheets are degraded by cellular GSH. Then, the target miR-21 triggers cascaded assembly of the liberated hairpin probes into long dsDNA polymers, which brings each two FAMs (donor) and one TAMRA (acceptor) into close proximity to generate significantly enhanced DD-A FRET signals, which was discovered and proven by our previous report. We think the developed approach can serve as an excellent intracellular miRNAs detection tool, which promises the potential for biological and disease studies. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Three-dimensional carbon allotropes comprising phenyl rings and acetylenic chains in sp+ sp 2 hybrid networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jian -Tao; Chen, Changfeng; Li, Han -Dong

Here, we here identify by ab initio calculations a new type of three-dimensional (3D) carbon allotropes that consist of phenyl rings connected by linear acetylenic chains in sp+ sp 2 bonding networks. These structures are constructed by inserting acetylenic or diacetylenic bonds into an all sp 2-hybridized rhombohedral polybenzene lattice, and the resulting 3D phenylacetylene and phenyldiacetylene nets comprise a 12-atom and 18-atom rhombohedral primitive unit cells R - 3m symmetry, which are characterized as the 3D chiral crystalline modification of 2D graphyne and graphdiyne, respectively. Simulated phonon spectra reveal that these structures are dynamically stable. Electronic band calculations indicatemore » that phenylacetylene is metallic, while phenyldiacetylene is a semiconductor with an indirect band gap of 0.58 eV. The present results establish a new type of carbon phases and offer insights into their outstanding structural and electronic properties.« less

AFM Imaging of Hybridization Chain Reaction Mediated Signal Transmission between Two DNA Origami Structures.

PubMed

Helmig, Sarah; Gothelf, Kurt Vesterager

2017-10-23

Signal transfer is central to the controlled exchange of information in biology and advanced technologies. Therefore, the development of reliable, long-range signal transfer systems for artificial nanoscale assemblies is of great scientific interest. We have designed such a system for the signal transfer between two connected DNA nanostructures, using the hybridization chain reaction (HCR). Two sets of metastable DNA hairpins, one of which is immobilized at specific points along tracks on DNA origami structures, are polymerized to form a continuous DNA duplex, which is visible using atomic force microscopy (AFM). Upon addition of a designed initiator, the initiation signal is efficiently transferred more than 200 nm from a specific location on one origami structure to an end point on another origami structure. The system shows no significant loss of signal when crossing from one nanostructure to another and, therefore, has the potential to be applied to larger multi-component DNA assemblies. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Three-dimensional carbon allotropes comprising phenyl rings and acetylenic chains in sp+ sp 2 hybrid networks

DOE PAGES

Wang, Jian -Tao; Chen, Changfeng; Li, Han -Dong; ...

2016-04-18

Here, we here identify by ab initio calculations a new type of three-dimensional (3D) carbon allotropes that consist of phenyl rings connected by linear acetylenic chains in sp+ sp 2 bonding networks. These structures are constructed by inserting acetylenic or diacetylenic bonds into an all sp 2-hybridized rhombohedral polybenzene lattice, and the resulting 3D phenylacetylene and phenyldiacetylene nets comprise a 12-atom and 18-atom rhombohedral primitive unit cells R - 3m symmetry, which are characterized as the 3D chiral crystalline modification of 2D graphyne and graphdiyne, respectively. Simulated phonon spectra reveal that these structures are dynamically stable. Electronic band calculations indicatemore » that phenylacetylene is metallic, while phenyldiacetylene is a semiconductor with an indirect band gap of 0.58 eV. The present results establish a new type of carbon phases and offer insights into their outstanding structural and electronic properties.« less

Real-time PCR assay for the diagnosis of pleural tuberculosis

PubMed Central

Cárdenas Bernal, Ana María; Giraldo-Cadavid, Luis Fernando; Prieto Diago, Enrique; Santander, Sandra Paola

2017-01-01

Abstract Introduction: The diagnosis of pleural tuberculosis requires an invasive and time-consuming reference method. Polymerase chain reaction (PCR) is rapid, but validation in pleural tuberculosis is still weak. Objective: To establish the operating characteristics of real-time polymerase chain reaction (RT-PCR) hybridization probes for the diagnosis of pleural tuberculosis. Methods: The validity of the RT-PCR hybridization probes was evaluated compared to a composite reference method by a cross-sectional study at the Hospital Universitario de la Samaritana. 40 adults with lymphocytic pleural effusion were included. Pleural tuberculosis was confirmed (in 9 patients) if the patient had at least one of three tests using the positive reference method: Ziehl-Neelsen or Mycobacterium tuberculosis culture in fluid or pleural tissue, or pleural biopsy with granulomas. Pleural tuberculosis was ruled out (in 31 patients) if all three tests were negative. The operating characteristics of the RT-PCR, using the Mid-P Exact Test, were determined using the OpenEpi 2.3 Software (2009). Results: The RT-PCR hybridization probes showed a sensitivity of 66.7% (95% CI: 33.2%-90.7%) and a specificity of 93.5% (95% CI: 80.3%-98.9%). The PPV was 75.0% (95% CI: 38.8%-95.6%) and a NPV of 90.6% (95% CI: 76.6%-97.6%). Two false positives were found for the test, one with pleural mesothelioma and the other with chronic pleuritis with mesothelial hyperplasia. Conclusions: The RT-PCR hybridization probes had good specificity and acceptable sensitivity, but a negative value cannot rule out pleural tuberculosis. PMID:29021638

Lateral flow nucleic acid biosensor for sensitive detection of microRNAs based on the dual amplification strategy of duplex-specific nuclease and hybridization chain reaction.

PubMed

Ying, Na; Ju, Chuanjing; Sun, Xiuwei; Li, Letian; Chang, Hongbiao; Song, Guangping; Li, Zhongyi; Wan, Jiayu; Dai, Enyong

2017-01-01

MicroRNAs (miRNAs) constitute novel biomarkers for various diseases. Accurate and quantitative analysis of miRNA expression is critical for biomedical research and clinical theranostics. In this study, a method was developed for sensitive and specific detection of miRNAs via dual signal amplification based on duplex specific nuclease (DSN) and hybridization chain reaction (HCR). A reporter probe (RP), comprising recognition sequence (3' end modified with biotin) for a target miRNA of miR-21 and capture sequence (5' end modified with Fam) for HCR product, was designed and synthesized. HCR was initiated by partial sequence of initiator probe (IP), the other part of which can hybridize with capture sequence of RP, and was assembled by hairpin probes modified with biotin (H1-bio and H2-bio). A miR-21 triggered cyclical DSN cleavage of RP, which was immobilized to a streptavidin (SA) coated magnetic bead (MB). The released Fam labeled capture sequence then hybridized with the HCR product to generate a detectable dsDNA. This polymer was then dropped on lateral flow strip and positive result was observed. The proposed method allowed quantitative sequence-specific detection of miR-21 (with a detection limit of 2.1 fM, S/N = 3) in a dynamic range from 100 fM to 100 pM, with an excellent ability to discriminate differences in miRNAs. The method showed acceptable testing recoveries for the determination of miRNAs in serum.

Hybrid nanoporous silicon optical biosensor architectures for biological sample analysis

NASA Astrophysics Data System (ADS)

Bonanno, Lisa M.; Zheng, Hong; DeLouise, Lisa A.

2010-02-01

This work focuses on demonstrating proof-of-concept for a novel nanoparticle optical signal amplification scheme employing hybrid porous silicon (PSi) sensors. We are investigating the development of target responsive hydrogels integrated with PSi optical transducers. These hybrid-PSi sensors can be designed to provide a tunable material response to target concentration ranging from swelling to complete chain dissolution. The corresponding refractive index changes are significant and readily detected by the PSi transducer. However, to increase signal to noise, lower the limit of detection, and provide a visual read out capability, we are investigating the incorporation of high refractive index nanoparticles (NP) into the hydrogel for optical signal amplification. These NPs can be nonspecifically encapsulated, or functionalized with bioactive ligands to bind polymer chains or participate in cross linking. In this work, we demonstrate encapsulation of high refractive index QD nanoparticles into a 5wt% polyacrylamide hydrogel crosslinked with N,N'-methylenebisacrylamide (BIS) and N,N Bis-acryloyl cystamine (BAC). A QD loading (~0.29 wt%) produced a 2X larger optical shift compared to the control. Dissolution of disulphide crosslinks, using Tris[2-carboxyethyl] phosphine (TCEP) reducing agent, induced gel swelling and efficient QD release. We believe this hybrid sensor concept constitutes a versatile technology platform capable of detecting a wide range of bio/chemical targets provided target analogs can be linked to the polymer backbone and crosslinks can be achieved with target responsive multivalent receptors, such a antibodies. The optical signal amplification scheme will enable a lower limit of detection sensitivity not yet demonstrated with PSi technology and colorimetric readout visible to the naked eye.

Nanoscale High Energetic Materials: A Polymeric Nitrogen Chain N8 Confined inside a Carbon Nanotube

NASA Astrophysics Data System (ADS)

Abou-Rachid, Hakima; Hu, Anguang; Timoshevskii, Vladimir; Song, Yanfeng; Lussier, Louis-Simon

2008-05-01

We present a theoretical study of a new hybrid material, nanostructured polymeric nitrogen, where a polymeric nitrogen chain is encapsulated in a carbon nanotube. The electronic and structural properties of the new system are studied by means of ab initio electronic structure and molecular dynamics calculations. Finite temperature simulations demonstrate the stability of this nitrogen phase at ambient pressure and room temperature using carbon nanotube confinement. This nanostructured confinement may open a new path towards stabilizing polynitrogen or polymeric nitrogen at ambient conditions.

Advances in acrylic-alkyd hybrid synthesis and characterization

NASA Astrophysics Data System (ADS)

Dziczkowski, Jamie

2008-10-01

In situ graft acrylic-alkyd hybrid resins were formed by polymerizing acrylic and acrylic-mixed monomers in the presence of alkyds by introduction of a free radical initiator to promote graft formation. Two-dimensional NMR, specifically gradient heteronuclear multiple quantum coherence (gHMQC), was used to clarify specific graft sites of the hybrid materials. Both individual and mixed-monomer systems were produced to determine any individual monomer preferences and to model current acrylic-alkyd systems. Different classes of initiators were used to determine any initiator effects on graft location. The 2D-NMR results confirm grafting at doubly allylic hydrogens located on the fatty acid chains and the polyol segment of the alkyd backbone. The gHMQC spectra show no evidence of grafting across double bonds on either pendant fatty acid groups or THPA unsaturation sites for any of the monomer or mixed monomer systems. It was also determined that choice of initiator has no effect on graft location. In addition, a design of experiments using response surface methodology was utilized to obtain a better understanding of this commercially available class of materials and relate both the chemical and physical properties to one another. A Box-Behnkin design was used, varying the oil length of the alkyd phase, the degree of unsaturation in the polyester backbone, and acrylic to alkyd ratio. Acrylic-alkyd hybrid resins were reduced with an amine/water mixture. Hydrolytic stability was tested and viscoelastic properties were obtained to determine crosslink density. Cured films were prepared and basic coatings properties were evaluated. It was found that the oil length of the alkyd is the most dominant factor for final coatings properties of the resins. Acrylic to alkyd ratio mainly influences the resin properties such as acid number, average molecular weight, and hydrolytic stability. The degree of unsaturation in the alkyd backbone has minimal effects on resin and film performance. Reversible-addition fragmentation polymerization techniques were employed to create a new class of acrylic-alkyd hybrid materials. Medium and long oil alkyds made from the monoglyceride process using soybean oil, glycerol, and phthalic anhydride were modified with a RAFT chain transfer agent. The alkyd macro-RAFT agents were reached by end-capping a medium oil soya-based alkyd with a carboxy-functional trithiocarbonate. The alkyd macro-RAFT agents were then used to create acrylic-alkyd block structures by polymerizing different acrylic monomers, including both acrylates and methacrylates in the presence of the macro-RAFT agent and 2, 2'-azobisisobutyronitrile (AIBN). Co-acrylic segments were reached by complete polymerization of one monomer followed by the addition of a second monomer and additional free radical initiator. The alkyds, macro-RAFT agents and, acrylic-alkyd blocks were characterized by size-exclusion chromatography (SEC), FTIR, and 1H-NMR. Pseudo-first-order kinetics behavior and conversion vs. molecular weight plots show that the RAFT-mediated reaction afforded a more controlled process for the synthesis of acrylated-alkyd materials. Preliminary coatings tests showed that material properties of acrylated-alkyds achieved by RAFT polymerization exhibit good overall coatings properties including adhesion, gloss, hardness, and impact resistance.

Determination of protein folding kinetic types using sequence and predicted secondary structure and solvent accessibility.

PubMed

Zhang, Hua; Zhang, Tuo; Gao, Jianzhao; Ruan, Jishou; Shen, Shiyi; Kurgan, Lukasz

2012-01-01

Proteins fold through a two-state (TS), with no visible intermediates, or a multi-state (MS), via at least one intermediate, process. We analyze sequence-derived factors that determine folding types by introducing a novel sequence-based folding type predictor called FOKIT. This method implements a logistic regression model with six input features which hybridize information concerning amino acid composition and predicted secondary structure and solvent accessibility. FOKIT provides predictions with average Matthews correlation coefficient (MCC) between 0.58 and 0.91 measured using out-of-sample tests on four benchmark datasets. These results are shown to be competitive or better than results of four modern predictors. We also show that FOKIT outperforms these methods when predicting chains that share low similarity with the chains used to build the model, which is an important advantage given the limited number of annotated chains. We demonstrate that inclusion of solvent accessibility helps in discrimination of the folding kinetic types and that three of the features constitute statistically significant markers that differentiate TS and MS folders. We found that the increased content of exposed Trp and buried Leu are indicative of the MS folding, which implies that the exposure/burial of certain hydrophobic residues may play important role in the formation of the folding intermediates. Our conclusions are supported by two case studies.

Site-directed mutagenesis of the regulatory light-chain Ca2+/Mg2+ binding site and its role in hybrid myosins

NASA Astrophysics Data System (ADS)

Reinach, Fernando C.; Nagai, Kiyoshi; Kendrick-Jones, John

1986-07-01

The regulatory light chains, small polypeptides located on the myosin head, regulate the interaction of myosin with actin in response to either Ca2+ or phosphorylation. The demonstration that the regulatory light chains on scallop myosin can be replaced by light chains from other myosins has allowed us to compare the functional capabilities of different light chains1, but has not enabled us to probe the role of features, such as the Ca2+/Mg2+ binding site, that are common to all of them. Here, we describe the use of site-directed mutagenesis to study the function of that site. We synthesized the chicken skeletal myosin light chain in Escherichia coli and constructed mutants with substitutions within the Ca2+/Mg2+ binding site. When the aspartate residues at the first and sixth Ca2+ coordination positions are replaced by uncharged alanines, the light chains have a reduced Ca2+ binding capacity but still bind to scallop myosin with high affinity. Unlike the wild-type skeletal light chain which inhibits myosin interaction with actin, the mutants activate it. Thus, an intact Ca2+/Mg2+ binding site in the N-terminal region of the light chain is essential for regulating the interaction of myosin with actin.

Optimization of Location-Routing Problem for Cold Chain Logistics Considering Carbon Footprint.

PubMed

Wang, Songyi; Tao, Fengming; Shi, Yuhe

2018-01-06

In order to solve the optimization problem of logistics distribution system for fresh food, this paper provides a low-carbon and environmental protection point of view, based on the characteristics of perishable products, and combines with the overall optimization idea of cold chain logistics distribution network, where the green and low-carbon location-routing problem (LRP) model in cold chain logistics is developed with the minimum total costs as the objective function, which includes carbon emission costs. A hybrid genetic algorithm with heuristic rules is designed to solve the model, and an example is used to verify the effectiveness of the algorithm. Furthermore, the simulation results obtained by a practical numerical example show the applicability of the model while provide green and environmentally friendly location-distribution schemes for the cold chain logistics enterprise. Finally, carbon tax policies are introduced to analyze the impact of carbon tax on the total costs and carbon emissions, which proves that carbon tax policy can effectively reduce carbon dioxide emissions in cold chain logistics network.

Biobased lubricants and functional products from Cuphea oil

USDA-ARS?s Scientific Manuscript database

Cuphea (Lythraceae) is an annual plant that produces a small seed rich in saturated medium-chain triacylglycerols (TAGs). With the need for higher seed yields, oil content, and less seed shattering, Oregon State University began developing promising cuphea crosses. Cuphea PSR23 is a hybrid between C...

Hybrid cryptosystem RSA - CRT optimization and VMPC

NASA Astrophysics Data System (ADS)

Rahmadani, R.; Mawengkang, H.; Sutarman

2018-03-01

Hybrid cryptosystem combines symmetric algorithms and asymmetric algorithms. This combination utilizes speeds on encryption/decryption processes of symmetric algorithms and asymmetric algorithms to secure symmetric keys. In this paper we propose hybrid cryptosystem that combine symmetric algorithms VMPC and asymmetric algorithms RSA - CRT optimization. RSA - CRT optimization speeds up the decryption process by obtaining plaintext with dp and p key only, so there is no need to perform CRT processes. The VMPC algorithm is more efficient in software implementation and reduces known weaknesses in RC4 key generation. The results show hybrid cryptosystem RSA - CRT optimization and VMPC is faster than hybrid cryptosystem RSA - VMPC and hybrid cryptosystem RSA - CRT - VMPC. Keyword : Cryptography, RSA, RSA - CRT, VMPC, Hybrid Cryptosystem.

A Multiobjective Optimization Framework for Online Stochastic Optimal Control in Hybrid Electric Vehicles

DOE PAGES

Malikopoulos, Andreas

2015-01-01

The increasing urgency to extract additional efficiency from hybrid propulsion systems has led to the development of advanced power management control algorithms. In this paper we address the problem of online optimization of the supervisory power management control in parallel hybrid electric vehicles (HEVs). We model HEV operation as a controlled Markov chain and we show that the control policy yielding the Pareto optimal solution minimizes online the long-run expected average cost per unit time criterion. The effectiveness of the proposed solution is validated through simulation and compared to the solution derived with dynamic programming using the average cost criterion.more » Both solutions achieved the same cumulative fuel consumption demonstrating that the online Pareto control policy is an optimal control policy.« less

Construction of a restriction map and gene map of the lettuce chloroplast small single-copy region using Southern cross-hybridization.

PubMed

Mitchelson, K R

1996-01-01

The small single-copy region (SSCR) of the chloroplast genome of many higher plants typically contain ndh genes encoding proteins that share homology with subunits of the respiratory-chain reduced nicotinamide adenine dinucleotide (NADH) dehydrogenase complex of mitochondria. A map of the lettuce chloroplast SSCR has been determined by Southern cross-hybridization, taking advantage of the high degree of homology between a tobacco small single-copy fragment and a corresponding lettuce chloroplast fragment. The gene order of the SSCR of lettuce and tobacco chloroplasts is similar. The cross-hybridization method can rapidly create a primary gene map of unknown chloroplast fragments, thus providing detailed information of the localization and arrangement of genes and conserved open reading frame regions.

Finite element model updating using the shadow hybrid Monte Carlo technique

NASA Astrophysics Data System (ADS)

Boulkaibet, I.; Mthembu, L.; Marwala, T.; Friswell, M. I.; Adhikari, S.

2015-02-01

Recent research in the field of finite element model updating (FEM) advocates the adoption of Bayesian analysis techniques to dealing with the uncertainties associated with these models. However, Bayesian formulations require the evaluation of the Posterior Distribution Function which may not be available in analytical form. This is the case in FEM updating. In such cases sampling methods can provide good approximations of the Posterior distribution when implemented in the Bayesian context. Markov Chain Monte Carlo (MCMC) algorithms are the most popular sampling tools used to sample probability distributions. However, the efficiency of these algorithms is affected by the complexity of the systems (the size of the parameter space). The Hybrid Monte Carlo (HMC) offers a very important MCMC approach to dealing with higher-dimensional complex problems. The HMC uses the molecular dynamics (MD) steps as the global Monte Carlo (MC) moves to reach areas of high probability where the gradient of the log-density of the Posterior acts as a guide during the search process. However, the acceptance rate of HMC is sensitive to the system size as well as the time step used to evaluate the MD trajectory. To overcome this limitation we propose the use of the Shadow Hybrid Monte Carlo (SHMC) algorithm. The SHMC algorithm is a modified version of the Hybrid Monte Carlo (HMC) and designed to improve sampling for large-system sizes and time steps. This is done by sampling from a modified Hamiltonian function instead of the normal Hamiltonian function. In this paper, the efficiency and accuracy of the SHMC method is tested on the updating of two real structures; an unsymmetrical H-shaped beam structure and a GARTEUR SM-AG19 structure and is compared to the application of the HMC algorithm on the same structures.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matsuura, Yukihito, E-mail: matsuura@chem.nara-k.ac.jp

The tunneling magnetoresistance (TMR) of a silicon chain sandwiched between nickel electrodes was examined by using first-principles density functional theory. The relative orientation of the magnetization in a parallel-alignment (PA) configuration of two nickel electrodes enhanced the current with a bias less than 0.4 V compared with that in an antiparallel-alignment configuration. Consequently, the silicon chain-nickel electrodes yielded good TMR characteristics. In addition, there was polarized spin current in the PA configuration. The spin polarization of sulfur atoms functioning as a linking bridge between the chain and nickel electrode played an important role in the magnetic effects of the electric current.more » Moreover, the hybridization of the sulfur 3p orbital and σ-conjugated silicon 3p orbital contributed to increasing the total current.« less

Fluorescent hybridization probes for nucleic acid detection.

PubMed

Guo, Jia; Ju, Jingyue; Turro, Nicholas J

2012-04-01

Due to their high sensitivity and selectivity, minimum interference with living biological systems, and ease of design and synthesis, fluorescent hybridization probes have been widely used to detect nucleic acids both in vivo and in vitro. Molecular beacons (MBs) and binary probes (BPs) are two very important hybridization probes that are designed based on well-established photophysical principles. These probes have shown particular applicability in a variety of studies, such as mRNA tracking, single nucleotide polymorphism (SNP) detection, polymerase chain reaction (PCR) monitoring, and microorganism identification. Molecular beacons are hairpin oligonucleotide probes that present distinctive fluorescent signatures in the presence and absence of their target. Binary probes consist of two fluorescently labeled oligonucleotide strands that can hybridize to adjacent regions of their target and generate distinctive fluorescence signals. These probes have been extensively studied and modified for different applications by modulating their structures or using various combinations of fluorophores, excimer-forming molecules, and metal complexes. This review describes the applicability and advantages of various hybridization probes that utilize novel and creative design to enhance their target detection sensitivity and specificity.

A hybrid inventory management system respondingto regular demand and surge demand

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohammad S. Roni; Mingzhou Jin; Sandra D. Eksioglu

2014-06-01

This paper proposes a hybrid policy for a stochastic inventory system facing regular demand and surge demand. The combination of two different demand patterns can be observed in many areas, such as healthcare inventory and humanitarian supply chain management. The surge demand has a lower arrival rate but higher demand volume per arrival. The solution approach proposed in this paper incorporates the level crossing method and mixed integer programming technique to optimize the hybrid inventory policy with both regular orders and emergency orders. The level crossing method is applied to obtain the equilibrium distributions of inventory levels under a givenmore » policy. The model is further transformed into a mixed integer program to identify an optimal hybrid policy. A sensitivity analysis is conducted to investigate the impact of parameters on the optimal inventory policy and minimum cost. Numerical results clearly show the benefit of using the proposed hybrid inventory model. The model and solution approach could help healthcare providers or humanitarian logistics providers in managing their emergency supplies in responding to surge demands.« less

Specific 16S ribosomal RNA targeted oligonucleotide probe against Clavibacter michiganensis subsp. sepedonicus.

PubMed

Mirza, M S; Rademaker, J L; Janse, J D; Akkermans, A D

1993-11-01

In this article we report on the polymerase chain reaction amplification of a partial 16S rRNA gene from the plant pathogenic bacterium Clavibacter michiganensis subsp. sepedonicus. A partial sequence (about 400 base pairs) of the gene was determined that covered two variable regions important for oligonucleotide probe development. A specific 24mer oligonucleotide probe targeted against the V6 region of 16S rRNA was designed. Specificity of the probe was determined using dot blot hybridization. Under stringent conditions (60 degrees C), the probe hybridized with all 16 Cl. michiganensis subsp. sepedonicus strains tested. Hybridization did not occur with 32 plant pathogenic and saprophytic bacteria used as controls under the same conditions. Under less stringent conditions (55 degrees C) the related Clavibacter michiganensis subsp. insidiosus, Clavibacter michiganensis subsp. nebraskensis, and Clavibacter michiganensis subsp. tesselarius also showed hybridization. At even lower stringency (40 degrees C), all Cl. michiganensis subspecies tested including Clavibacter michiganensis subsp. michiganensis showed hybridization signal, suggesting that under these conditions the probe may be used as a species-specific probe for Cl. michiganensis.

Effect of flexibility of grafted polymer on the morphology and property of nanosilica/PVC composites

NASA Astrophysics Data System (ADS)

Zhu, Aiping; Cai, Aiyun; Zhou, Weidong; Shi, Zhehua

2008-04-01

In this study, poly(methyl methacrylate)-grafted-nanosilica (PMMA-g-silica) and a copolymer of styrene (St), n-butyl acrylate (BA) and acrylic acid (AA)-grafted-nanosilica (PSBA-g-silica) hybrid nanoparticles were prepared by using a heterophase polymerization technique in an aqueous system. The grafted polymers made up approximately 50 wt.% of the resulted hybrid nanoparticles which showed a spherical and well-dispersed morphology. The silica hybrid nanoparticles were subsequently used as fillers in a poly(vinyl chloride) (PVC) matrix to fabricate PVC nanocomposite. Morphology study of PVC nanocomposites revealed that both PMMA- and PSBA-grafted-silica had an adhesive interface between the silica and PVC. The tensile strength and elongation to break were found to be improved significantly in comparison with that of untreated nanosilica/PVC composites. Finally our results clearly demonstrated that the properties (e.g. chain flexibility, composition) of the grafted polymer in the hybrid nanoparticles could significantly affect the dispersion behavior of hybrid nanoparticles in PVC matrix, dynamic mechanical thermal properties and mechanical properties of the resulted PVC composites.

Respiratory Chain Complexes in Dynamic Mitochondria Display a Patchy Distribution in Life Cells

PubMed Central

Muster, Britta; Kohl, Wladislaw; Wittig, Ilka; Strecker, Valentina; Joos, Friederike; Haase, Winfried; Bereiter-Hahn, Jürgen; Busch, Karin

2010-01-01

Background Mitochondria, the main suppliers of cellular energy, are dynamic organelles that fuse and divide frequently. Constraining these processes impairs mitochondrial is closely linked to certain neurodegenerative diseases. It is proposed that functional mitochondrial dynamics allows the exchange of compounds thereby providing a rescue mechanism. Methodology/Principal Findings The question discussed in this paper is whether fusion and fission of mitochondria in different cell lines result in re-localization of respiratory chain (RC) complexes and of the ATP synthase. This was addressed by fusing cells containing mitochondria with respiratory complexes labelled with different fluorescent proteins and resolving their time dependent re-localization in living cells. We found a complete reshuffling of RC complexes throughout the entire chondriome in single HeLa cells within 2–3 h by organelle fusion and fission. Polykaryons of fused cells completely re-mixed their RC complexes in 10–24 h in a progressive way. In contrast to the recently described homogeneous mixing of matrix-targeted proteins or outer membrane proteins, the distribution of RC complexes and ATP synthase in fused hybrid mitochondria, however, was not homogeneous but patterned. Thus, complete equilibration of respiratory chain complexes as integral inner mitochondrial membrane complexes is a slow process compared with matrix proteins probably limited by complete fusion. In co-expressing cells, complex II is more homogenously distributed than complex I and V, resp. Indeed, this result argues for higher mobility and less integration in supercomplexes. Conclusion/Significance Our results clearly demonstrate that mitochondrial fusion and fission dynamics favours the re-mixing of all RC complexes within the chondriome. This permanent mixing avoids a static situation with a fixed composition of RC complexes per mitochondrion. PMID:20689601

Assignment of the human PAX4 gene to chromosome band 7q32 by fluorescence in situ hybridization.

PubMed

Tamura, T; Izumikawa, Y; Kishino, T; Soejima, H; Jinno, Y; Niikawa, N

1994-01-01

Of the nine known members of a human paired box-containing gene family (Pax), only PAX4 has not been precisely localized. We screened a cosmid library of human genomic DNA using polymerase chain reaction products for PAX4 as a probe and isolated three positive cosmid clones. Sequence analysis revealed that at least two of them had exon-like sequences and showed extensive homology to Pax-4 in the mouse. These two cosmid clones were mapped to human chromosome band 7q32 by fluorescence in situ hybridization.

Stretchable and semitransparent conductive hybrid hydrogels for flexible supercapacitors.

PubMed

Hao, Guang-Ping; Hippauf, Felix; Oschatz, Martin; Wisser, Florian M; Leifert, Annika; Nickel, Winfried; Mohamed-Noriega, Nasser; Zheng, Zhikun; Kaskel, Stefan

2014-07-22

Conductive polymers showing stretchable and transparent properties have received extensive attention due to their enormous potential in flexible electronic devices. Here, we demonstrate a facile and smart strategy for the preparation of structurally stretchable, electrically conductive, and optically semitransparent polyaniline-containing hybrid hydrogel networks as electrode, which show high-performances in supercapacitor application. Remarkably, the stability can extend up to 35,000 cycles at a high current density of 8 A/g, because of the combined structural advantages in terms of flexible polymer chains, highly interconnected pores, and excellent contact between the host and guest functional polymer phase.

Stabilization process in Saccharomyces intra and interspecific hybrids in fermentative conditions.

PubMed

Pérez-Través, Laura; Lopes, Christian A; Barrio, Eladio; Querol, Amparo

2014-12-01

We evaluated the genetic stabilization of artificial intra- (Saccharomyces cerevisiae) and interspecific (S. cerevisiae × S. kudriavzevii) hybrids under wine fermentative conditions. Large-scale transitions in genome size and genome reorganizations were observed during this process. Interspecific hybrids seem to need fewer generations to reach genetic stability than intraspecific hybrids. The largest number of molecular patterns recovered among the derived clones was observed for intraspecific hybrids, particularly for those obtained by rare-mating. Molecular marker analyses revealed that unstable clones could change during the industrial process to obtain active dry yeast. When no changes in molecular markers and ploidy were observed after this process, no changes in genetic composition were confirmed by comparative genome hybridization, considering the clone as a stable hybrid. According to our results, under these conditions, fermentation steps 3 and 5 (30-50 generations) would suffice to obtain genetically stable interspecific and intraspecific hybrids, respectively. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Checkpointing for a hybrid computing node

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cher, Chen-Yong

2016-03-08

According to an aspect, a method for checkpointing in a hybrid computing node includes executing a task in a processing accelerator of the hybrid computing node. A checkpoint is created in a local memory of the processing accelerator. The checkpoint includes state data to restart execution of the task in the processing accelerator upon a restart operation. Execution of the task is resumed in the processing accelerator after creating the checkpoint. The state data of the checkpoint are transferred from the processing accelerator to a main processor of the hybrid computing node while the processing accelerator is executing the task.

Electrospraying of microfluidic encapsulated cells for the fabrication of cell-laden electrospun hybrid tissue constructs.

PubMed

Weidenbacher, L; Abrishamkar, A; Rottmar, M; Guex, A G; Maniura-Weber, K; deMello, A J; Ferguson, S J; Rossi, R M; Fortunato, G

2017-12-01

The fabrication of functional 3D tissues is a major goal in tissue engineering. While electrospinning is a promising technique to manufacture a structure mimicking the extracellular matrix, cell infiltration into electrospun scaffolds remains challenging. The robust and in situ delivery of cells into such biomimetic scaffolds would potentially enable the design of tissue engineered constructs with spatial control over cellular distribution but often solvents employed in the spinning process are problematic due to their high cytotoxicity. Herein, microfluidic cell encapsulation is used to establish a temporary protection vehicle for the in situ delivery of cells for the development of a fibrous, cell-laden hybrid biograft. Therefore a layer-by-layer process is used by alternating fiber electrospinning and cell spraying procedures. Both encapsulation and subsequent electrospraying of capsules has no negative effect on the viability and myogenic differentiation of murine myoblast cells. Propidium iodide positive stained cells were analyzed to quantify the amount of dead cells and the presence of myosin heavy chain positive cells after the processes was shown. Furthermore, encapsulation successfully protects cells from cytotoxic solvents (such as dimethylformamide) during in situ delivery of the cells into electrospun poly(vinylidene fluoride-co-hexafluoropropylene) scaffolds. The resulting cell-populated biografts demonstrate the clear potential of this approach in the creation of viable tissue engineering constructs. Infiltration of cells and their controlled spatial distribution within fibrous electrospun membranes is a challenging task but allows for the development of functional highly organized 3D hybrid tissues. Combining polymer electrospinning and cell electrospraying in a layer-by-layer approach is expected to overcome current limitations of reduced cell infiltration after traditional static seeding. However, organic solvents, used during the electrospinning process, impede often major issues due to their high cytotoxicity. Utilizing microfluidic encapsulation as a mean to embed cells within a protective polymer casing enables the controlled deposition of viable cells without interfering with the cellular phenotype. The presented techniques allow for novel cell manipulation approaches being significant for enhanced 3D tissue engineering based on its versatility in terms of material and cell selection. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Hybrid zone studies: An interdisciplinary approach for the analysis of evolutionary processes

USGS Publications Warehouse

Scribner, Kim T.

1994-01-01

There has been considerable debate in the ecological and evolutionary literature over the relative importance and rate by which microevolutionary processes operating at the population level result in separation and differentiation of lineages and populations, and ultimately in speciation. Our understanding of evolutionary processes have need greatly enhances through the study of hybridization and hybrid zones. Indeed, hybrid zones have been described as “natural laboratories” (Barton, N. H., and G .M. Hewitt, 189. Adaptation, speciation, and hybrid zones. Nature 341:497-503) or as “windows on the evolutionary processes” (Harrison, R. G. 1990. Hybrid zones: windows on the evolutionary process. Oxford Surveys in Evolutionary Biology 7:69-128). Hybrid zones greatly facilitate analyses of evolutionary dynamics because differences in factors such as mating preference, fertility, and viability are likely to be magnified, making the consequences easier to document over short periods of time.

Electroacoustic miniaturized DNA-biosensor.

PubMed

Gamby, Jean; Lazerges, Mathieu; Pernelle, Christine; Perrot, Hubert; Girault, Hubert H; Tribollet, Bernard

2007-11-01

A micrometer-sized electroacoustic DNA-biosensor was developed. The device included a thin semi-crystalline polyethylene terephthalate (PET) dielectric layer with two Ag microband electrodes on one side and a DNA thiol-labeled monolayer adsorbed on a gold surface on the other. A resonance wave was observed at 29 MHz with a network analyzer, upon AC voltage application between the two Ag electrodes, corresponding to electromechanical coupling induced by molecular dipoles of the PET polymer chain in the dielectric layer. It was found that the device size and geometry were well adapted to detect DNA hybridization, by measuring the capacity of the resonance response evolution: hybridization induced polarization of the dielectric material that affected the electromechanical coupling established in the dielectric layer. The 0.2 mm(2) sensor sensitive area allows detection in small volumes and still has higher detection levels for bioanalytical applications, the non-contact configuration adopted avoids electric faradic reactions that may damage biosensor sensitive layers, and finally, PET is a costless raw material, easy to process and well adapted for large scale production. The well-balanced technological and economic advantages of this kind of device make it a good candidate for biochip integration.

Total Life Cycle-Based Materials Selection for Polymer Metal Hybrid Body-in-White Automotive Components

NASA Astrophysics Data System (ADS)

Grujicic, M.; Sellappan, V.; He, T.; Seyr, Norbert; Obieglo, Andreas; Erdmann, Marc; Holzleitner, Jochen

2009-03-01

Over the last dozen of years, polymer metal hybrid (PMH) technologies have established themselves as viable alternatives for use in light-weight automotive body-in-white bolt-on as well as load-bearing (structural) components. Within the PMH technologies, sheet-metal stamped/formed and thermoplastic injection molding subcomponents are integrated into a singular component/module. Due to attending synergetic effects, the performance of the PMH component typically exceeds that attainable by an alternative single-material technologies. In the present work, a total life cycle (TLC) approach to the selection of metallic and thermoplastic materials (as well as the selection of structural adhesives, where appropriate) is considered. The TLC material selection approach considers the consequences and ramifications of material selection at each major stage of the vehicle manufacturing process chain (press shop, injection molding shop, body shop, paint shop, and assembly), as well as relation to the vehicle performance, durability and the end-of-the-life-of-the-vehicle considerations. The approach is next applied to the case of injection overmolding technology to identify the optimal grade of short glass-fiber reinforced nylon when used in a prototypical PMH load-bearing automotive body-in-white component.

Assessing Telomere Length Using Surface Enhanced Raman Scattering

NASA Astrophysics Data System (ADS)

Zong, Shenfei; Wang, Zhuyuan; Chen, Hui; Cui, Yiping

2014-11-01

Telomere length can provide valuable insight into telomeres and telomerase related diseases, including cancer. Here, we present a brand-new optical telomere length measurement protocol using surface enhanced Raman scattering (SERS). In this protocol, two single strand DNA are used as SERS probes. They are labeled with two different Raman molecules and can specifically hybridize with telomeres and centromere, respectively. First, genome DNA is extracted from cells. Then the telomere and centromere SERS probes are added into the genome DNA. After hybridization with genome DNA, excess SERS probes are removed by magnetic capturing nanoparticles. Finally, the genome DNA with SERS probes attached is dropped onto a SERS substrate and subjected to SERS measurement. Longer telomeres result in more attached telomere probes, thus a stronger SERS signal. Consequently, SERS signal can be used as an indicator of telomere length. Centromere is used as the inner control. By calibrating the SERS intensity of telomere probe with that of the centromere probe, SERS based telomere measurement is realized. This protocol does not require polymerase chain reaction (PCR) or electrophoresis procedures, which greatly simplifies the detection process. We anticipate that this easy-operation and cost-effective protocol is a fine alternative for the assessment of telomere length.

Development and validation of a novel hydrolysis probe real-time polymerase chain reaction for agamid adenovirus 1 in the central bearded dragon (Pogona vitticeps).

PubMed

Fredholm, Daniel V; Coleman, James K; Childress, April L; Wellehan, James F X

2015-03-01

Agamid adenovirus 1 (AgAdv-1) is a significant cause of disease in bearded dragons (Pogona sp.). Clinical manifestations of AgAdv-1 infection are variable and often nonspecific; the manifestations range from lethargy, weight loss, and inappetence, to severe enteritis, hepatitis, and sudden death. Currently, diagnosis of AgAdv-1 infection is achieved through a single published method: standard nested polymerase chain reaction (nPCR) and sequencing. Standard nPCR with sequencing provides reliable sensitivity, specificity, and validation of PCR products. However, this process is comparatively expensive, laborious, and slow. Probe hybridization, as used in a TaqMan assay, represents the best option for validating PCR products aside from the time-consuming process of sequencing. This study developed a real-time PCR (qPCR) assay using a TaqMan probe-based assay, targeting a highly conserved region of the AgAdv-1 genome. Standard curves were generated, detection results were compared with the gold standard conventional PCR and sequencing assay, and limits of detection were determined. Additionally, the qPCR assay was run on samples known to be positive for AgAdv-1 and samples known to be positive for other adenoviruses. Based on the results of these evaluations, this assay allows for a less expensive, rapid, quantitative detection of AgAdv-1 in bearded dragons. © 2015 The Author(s).

Unveiling the hybrid interface in polymer nanocomposites enclosing silsesquioxanes with tunable molecular structure: Spectroscopic, thermal and mechanical properties.

PubMed

D'Arienzo, Massimiliano; Diré, Sandra; Redaelli, Matteo; Borovin, Evgeny; Callone, Emanuela; Di Credico, Barbara; Morazzoni, Franca; Pegoretti, Alessandro; Scotti, Roberto

2018-02-15

Organic-inorganic nanobuilding blocks (NBBs) based on silsesquioxanes (SSQs) have potential applications as nanofillers, thermal stabilizers, and rheological modifiers, which can improve thermomechanical properties of polymer hosts. The possibility to tune both siloxane structure and pendant groups can promote compatibilization and peculiar interactions with a plethora of polymers. However, the control on SSQs molecular architecture and functionalities is usually delicate and requires careful synthetic details. Moreover, investigating the influence of NBBs loading and structure on the hybrid interface and, in turn, on the polymer chains mobility and mechanical properties, may be challenging, especially for low-loaded materials. Herein, we describe the preparation and characterization of polybutadiene (PB) nanocomposites using as innovative fillers thiol-functionalized SSQs nanobuilding blocks (SH-NBBs), with both tailorable functionality and structure. Swelling experiments and, more clearly, solid-state NMR, enlightened a remarkable effect of SH-NBBs on the molecular structure and mobility of the polymeric chains, envisaging the occurrence of chemical interactions at the hybrid interface. Finally, thermal and DMTA analyses revealed that nanocomposites, even containing very low filler loadings (i.e. 1, 3 wt%), exhibited enhanced thermomechanical properties, which seem to be connected not only to the loading, but also to the peculiar cage or ladder-like architecture of SH-NBBs. Copyright © 2017 Elsevier Inc. All rights reserved.

Comprehensive in Vitro Analysis of Acyltransferase Domain Exchanges in Modular Polyketide Synthases and Its Application for Short-Chain Ketone Production

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yuzawa, Satoshi; Deng, Kai; Wang, George

2016-08-22

Type I modular polyketide synthases (PKSs) are polymerases that utilize acyl-CoAs as substrates. Each polyketide elongation reaction is catalyzed by a set of protein domains called a module. Each module usually contains an acyltransferase (AT) domain, which determines the specific acyl-CoA incorporated into each condensation reaction. Although a successful exchange of individual AT domains can lead to the biosynthesis of a large variety of novel compounds, hybrid PKS modules often show significantly decreased activities. Using monomodular PKSs as models, we have systematically analyzed in this paper the segments of AT domains and associated linkers in AT exchanges in vitro andmore » have identified the boundaries within a module that can be used to exchange AT domains while maintaining protein stability and enzyme activity. Importantly, the optimized domain boundary is highly conserved, which facilitates AT domain replacements in most type I PKS modules. To further demonstrate the utility of the optimized AT domain boundary, we have constructed hybrid PKSs to produce industrially important short-chain ketones. Our in vitro and in vivo analysis demonstrated production of predicted ketones without significant loss of activities of the hybrid enzymes. Finally, these results greatly enhance the mechanistic understanding of PKS modules and prove the benefit of using engineered PKSs as a synthetic biology tool for chemical production.« less

Electrochemical detection of C-reactive protein using Copper nanoparticles and hybridization chain reaction amplifying signal.

PubMed

Zhang, Junjun; Zhang, Wenjuan; Guo, Jinjin; Wang, Junchun; Zhang, Yuzhong

2017-12-15

In this study, a sandwich-type electrochemical immunosensor for the detection of C-reactive protein (CRP) is described. In design, Copper nanoparticles (Cu NPs) were used for signal tag and hybridization chain reaction (HCR)amplified output signal. The immunosensor fabrication involved three steps: (i) primary antibodies (Ab 1 ) were immobilized on the surface of gold nanoparticles (Au NPs); (ii) the sandwich-type structure formation contained "primary antibodies-antigen-secondary antibodies conjugated with primer (Ab 2 -S 0 )"; and (iii) long DNA concatemers intercalating amounts of Cu NPs was linked to the sandwich-type structure via hybridization reaction. Differential pulse voltammetry (DPV) was used to record the response signal of the immunosensor in phosphate-buffered saline (PBS). Under optimal conditions, the anodic peak currents of Cu NPs at the peak potential of about 0.08V(VS.SCE) were linear with the logarithm of CRP concentration in the range of 1.0 fg mL -1 to 100 ng mL -1 with a detection limit of 0.33 fg mL -1 (at signal/noise [S/N] = 3). In addition, the practical application of immunosensor was evaluated by analyzing CRP in real human serum samples, the recoveries obtained were within 95.3%-103.8%, indicating the immunosensor possessed potential application ability for practical disease diagnosis. Copyright © 2017 Elsevier Inc. All rights reserved.

A cyclometalated iridium(III) complex used as a conductor for the electrochemical sensing of IFN-γ

NASA Astrophysics Data System (ADS)

Miao, Xiangmin; Ko, Chung-Nga; Vellaisamy, Kasipandi; Li, Zongbing; Yang, Guanjun; Leung, Chung-Hang; Ma, Dik-Lung

2017-02-01

A novel iridium(III) complex was prepared and used as a conductor for sensitive and enzyme-free electrochemical detection of interferon gamma (IFN-γ). This assay is based on a dual signal amplification mechanism involving positively charged gold nanoparticles ((+)AuNPs) and hybridization chain reaction (HCR). To construct the sensor, nafion (Nf) and (+)AuNPs composite membrane was first immobilized onto the electrode surface. Subsequently, a loop-stem structured capture probe (CP) containing a special IFN-γ interact strand was modified onto the (+)AuNP surface via the formation of Au-S bonds. Upon addition of IFN-γ, the loop-stem structure of CP was opened, and the newly exposed “sticky” region of CP then hybridized with DNA hairpin-1 (H1), which in turn opened its hairpin structure for hybridizing with DNA hairpin-2 (H2). Happen of HCR between H1 and H2 thus generated a polymeric duplex DNA (dsDNA) chain. Meanwhile, the iridium(III) complex could interact with the grooves of the dsDNA polymer, producing a strong current signal that was proportional to IFN-γ concentration. Thus, sensitive detection of IFN-γ could be realized with a detection limit down to 16.3 fM. Moreover, satisfied results were achieved by using this method for the detection of IFN-γ in human serum samples.

Ultrasensitive Faraday cage-type electrochemiluminescence assay for femtomolar miRNA-141 via graphene oxide and hybridization chain reaction-assisted cascade amplification.

PubMed

Lu, Jing; Wu, Lin; Hu, Yufang; Wang, Sui; Guo, Zhiyong

2018-06-30

In this study, a novel electrochemiluminescence (ECL) biosensor for sensitive detection of femtomolar miRNA-141 was constructed on the basis of Faraday cage-type strategy via graphene oxide (GO) and hybridization chain reaction (HCR)-assisted cascade amplification. A capture probe (CP) was immobilized on Fe 3 O 4 @SiO 2 @Au nanoparticles as capture unit, which could catch the miRNA-141, and the immobilization of the signal unit (Ru(phen) 3 2+ -HCR/GO) was allowed via nucleic acid hybridization. The prepared biosensor exhibited two advantages for signal amplification: firstly, GO could lap on the electrode surface directly, extending Outer Helmholtz Plane (OHP) of the sensor due to the large surface area and good electronic transport property; secondly, HCR-assisted cascade amplification was designed by anchoring all HCR products on the GO surface, then embedding Ru(phen) 3 2+ as a signal readout pathway. All these signal molecules could take part in electrochemical reactions, thus further enhancing the ECL signal drastically. Therefore, the proposed sensor constructed by integrating HCR with Faraday cage-type strategy displayed an ultrasensitive detection platform for the miRNA-141 with a low detection limit of 0.03 fM. In addition, this proposed biosensor provides a universal platform for analysis of other microRNAs. Copyright © 2018 Elsevier B.V. All rights reserved.

Guidelines in the Choice of Parameters for Hybrid Laser Arc Welding with Fiber Lasers

NASA Astrophysics Data System (ADS)

Eriksson, I.; Powell, J.; Kaplan, A.

Laser arc hybrid welding has been a promising technology for three decades and laser welding in combination with gas metal arc welding (GMAW) has shown that it is an extremely promising technique. On the other hand the process is often considered complicated and difficult to set up correctly. An important factor in setting up the hybrid welding process is an understanding of the GMAW process. It is especially important to understand how the wire feed rate and the arc voltage (the two main parameters) affect the process. In this paper the authors show that laser hybrid welding with a 1 μm laser is similar to ordinary GMAW, and several guidelines are therefore inherited by the laser hybrid process.

Cytogenetics off interpopulation Cuphea lanceolata hybrids.

PubMed

Ali, M S; Knapp, S J

1995-12-01

Cuphea lanceolata Ait. (Lythraceae) is an annual diploid (x = 6) with medium-chain fatty acid rich seed oils. Wild C. lanceolata populations are classified as C. lanceolata f. silenoides or C. lanceolata f. lanceolata on the basis of flower pigment differences. Although these taxa are taxonomically close, their interfertility has not been demonstrated. We describe meiotic phenomena underlying the sterility of hybrids between C. lanceolata f. silenoides (LNS-43) and C. lanceolata f. lanceolata (LNC-78) populations. We assayed metaphase and anaphase I microsporocytes of the parent and hybrid populations. The hybrids were female and male sterile. The mean percentage of stainable pollen was 94.9% for the parents and 1.1% for the hybrids. Chromosomes paired and disjoined normally in the parents (LNS-43 and LNC-78) and abnormally in the hybrids (LNS-43 x LNC-78 and LNC-78 x LNS-43). Univalents, unequal chromosome distributions, and laggards were observed in the hybrids. The mean number of univalents per cell was 0.00 for the parents and 5.95 for the hybrids, the mean number of bivalents per cell was 6.00 for the parents and 1.51 for the hybrids, and the mean number of chiasmata per cell was 9.19 for the parents and 4.04 for the hybrids. The most frequently observed (75%) anaphase I chromosome distribution for the hybrids was 7:5:0 (pole-pole-laggards). The genome affinities of the hybrids were half those of the parents (a mean of 0.5 for the hybrids as opposed to 1.0 for the parents). Although C. lanceolata f. silenoides and C. lanceolata f. lanceolata freely hybridize, their progeny are sterile, and the genetic diversity of LNC-78, and perhaps of C. lanceolata f. lanceolata as a whole, cannot be accessed through hybrids with C. lanceolata f. silenoides or C. viscosissima.

Bayesian inversion of seismic and electromagnetic data for marine gas reservoir characterization using multi-chain Markov chain Monte Carlo sampling

NASA Astrophysics Data System (ADS)

Ren, Huiying; Ray, Jaideep; Hou, Zhangshuan; Huang, Maoyi; Bao, Jie; Swiler, Laura

2017-12-01

In this study we developed an efficient Bayesian inversion framework for interpreting marine seismic Amplitude Versus Angle and Controlled-Source Electromagnetic data for marine reservoir characterization. The framework uses a multi-chain Markov-chain Monte Carlo sampler, which is a hybrid of DiffeRential Evolution Adaptive Metropolis and Adaptive Metropolis samplers. The inversion framework is tested by estimating reservoir-fluid saturations and porosity based on marine seismic and Controlled-Source Electromagnetic data. The multi-chain Markov-chain Monte Carlo is scalable in terms of the number of chains, and is useful for computationally demanding Bayesian model calibration in scientific and engineering problems. As a demonstration, the approach is used to efficiently and accurately estimate the porosity and saturations in a representative layered synthetic reservoir. The results indicate that the seismic Amplitude Versus Angle and Controlled-Source Electromagnetic joint inversion provides better estimation of reservoir saturations than the seismic Amplitude Versus Angle only inversion, especially for the parameters in deep layers. The performance of the inversion approach for various levels of noise in observational data was evaluated - reasonable estimates can be obtained with noise levels up to 25%. Sampling efficiency due to the use of multiple chains was also checked and was found to have almost linear scalability.

Economic and life cycle assessments of biomass utilization for bioenergy products

DOE PAGES

Liu, Weiguo; Wang, Jingxin; Richard, Tom L.; ...

2017-05-04

A modeling process was developed to examine the economic and environmental benefits of utilizing energy crops for biofuels and bioproducts. Three energy crops (hybrid willow, switchgrass and miscanthus) that can potentially grow on marginal agricultural land or abandoned mine land in the northeastern United States were considered in the analytical process for the production of biofuels, biopower and pellet fuel. The supply chain components for both the economic analysis and life cycle modeling processes included feedstock establishment, harvest, transportation, storage, preprocessing, conversion, distribution and final usage. Sensitivity analysis was also conducted to assess the effects of energy crop yield, transportationmore » distance, conversion rate, facility capacity and internal rate of return (IRR) on the production of bioenergy products. The required selling price (RSP) ranged from $ 7.7/GJ to $ 47.9/GJ for different bioproducts. The production of biopower had the highest RSP and pellet fuel had the lowest. The results also indicated that bioenergy production using hybrid willow demonstrated lower RSP than the two perennial grass feedstocks. Pellet production presented the lowest greenhouse gas (GHG) emissions (less than 10 kg CO 2 eq per 1,000 MJ) and fossil energy consumption (less than 150 MJ per 1,000 MJ). The production of biofuel resulted in the highest GHG emissions. Sensitivity analysis indicated that IRR was the most sensitive factor to RSP and followed by conversion rate for biofuel and biopower production. As a result, conversion rate and transportation distance of feedstock presented a significant effect on environmental impacts during the production of the bioproducts.« less

Economic and life cycle assessments of biomass utilization for bioenergy products

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Weiguo; Wang, Jingxin; Richard, Tom L.

A modeling process was developed to examine the economic and environmental benefits of utilizing energy crops for biofuels and bioproducts. Three energy crops (hybrid willow, switchgrass and miscanthus) that can potentially grow on marginal agricultural land or abandoned mine land in the northeastern United States were considered in the analytical process for the production of biofuels, biopower and pellet fuel. The supply chain components for both the economic analysis and life cycle modeling processes included feedstock establishment, harvest, transportation, storage, preprocessing, conversion, distribution and final usage. Sensitivity analysis was also conducted to assess the effects of energy crop yield, transportationmore » distance, conversion rate, facility capacity and internal rate of return (IRR) on the production of bioenergy products. The required selling price (RSP) ranged from $ 7.7/GJ to $ 47.9/GJ for different bioproducts. The production of biopower had the highest RSP and pellet fuel had the lowest. The results also indicated that bioenergy production using hybrid willow demonstrated lower RSP than the two perennial grass feedstocks. Pellet production presented the lowest greenhouse gas (GHG) emissions (less than 10 kg CO 2 eq per 1,000 MJ) and fossil energy consumption (less than 150 MJ per 1,000 MJ). The production of biofuel resulted in the highest GHG emissions. Sensitivity analysis indicated that IRR was the most sensitive factor to RSP and followed by conversion rate for biofuel and biopower production. As a result, conversion rate and transportation distance of feedstock presented a significant effect on environmental impacts during the production of the bioproducts.« less

Experimental realization of a metamaterial detector focal plane array.

PubMed

Shrekenhamer, David; Xu, Wangren; Venkatesh, Suresh; Schurig, David; Sonkusale, Sameer; Padilla, Willie J

2012-10-26

We present a metamaterial absorber detector array that enables room-temperature, narrow-band detection of gigahertz (GHz) radiation in the S band (2-4 GHz). The system is implemented in a commercial printed circuit board process and we characterize the detector sensitivity and angular dependence. A modified metamaterial absorber geometry allows for each unit cell to act as an isolated detector pixel and to collectively form a focal plane array . Each pixel can have a dedicated microwave receiver chain and functions together as a hybrid device tuned to maximize the efficiency of detected power. The demonstrated subwavelength pixel shows detected sensitivity of -77 dBm, corresponding to a radiation power density of 27 nW/m(2), with pixel to pixel coupling interference below -14 dB at 2.5 GHz.

Synthesis and Thermal and Photo Behaviors of New Polyamide/Organocaly Nanocomposites Containing Para Phenylenediacrylic Moiety

NASA Astrophysics Data System (ADS)

Faghihi, Khalil; Soleimani, Masoumeh; Shabanian, Meisam; Abootalebi, Ashraf Sadat

2011-06-01

New type of aromatic polyamide/montmorillonite nanocomposites were produced using solution process in N-methyl-2-pyrolidone. Amide chains were synthesized from 4,4'-diaminodiphenyl sulfone and p-phenylenediacrylic acid in N-methyl-2-pyrolidone. The resulting nanocomposite films containing 5-15 mass % of organoclay were characterized for FT-IR, scanning electronmicroscopy (SEM), X-ray diffraction (XRD), thermogravimetric analysis (TGA), optical transparency and water absorption measurements. The distribution of organoclay and nanostructure of the composites were investigated by (XRD) and SEM analyses. Thermogravimetric analysis indicated an increase in thermal stability of nanocomposites as compared to pristine polyamide. The percentage optical transparency and water absorption of these hybrids was found to be much reduced upon the addition of modified layered silicate indicating decreased permeability.

Label-free technology for the amplified detection of microRNA based on the allosteric hairpin DNA switch and hybridization chain reaction.

PubMed

Cai, Sheng; Cao, Zhijuan; Lau, Choiwan; Lu, Jianzhong

2014-11-21

By using the allosteric hairpin DNA switch, a novel assay for the detection of microRNA (miRNA) let-7a via a hybridization chain reaction (HCR) was introduced. Briefly, the hairpin DNA switch probe is a single-stranded DNA consisting of a streptavidin (SA) aptamer sequence, a target binding sequence and a certain sequence that acts as a trigger of the HCR. In the presence of target let-7a, the hairpin DNA switch would open and expose the stem region sequences, where a part of this sequence acts as initiator sequence strands for the HCR and triggers a cascade of hybridization events that yields nicked double helices analogous to alternating copolymers, another part is the SA aptamer sequence which activates its binding affinity to SA on SA-coated magnetic particles. The hybridization event could be sensitively detected via an instantaneous derivatization reaction between a special chemiluminescence (CL) reagent, 3,4,5-trimethoxylphenylglyoxal (TMPG) and the guanine nucleotides within the target, the hairpin DNA switch probe, and HCR helices to form an unstable CL intermediate for the generation of light. Our results show that the coupling of the hairpin DNA switch probe and the HCR for the amplified detection of let-7a achieves a better performance (e.g. wide linear response range: 0.1-1000 fmol, low detection limit: 0.1 fmol, and high specificity). Furthermore, this approach could be easily applied to the detection of let-7a in human lung cells, and extended to detect other types of miRNA and proteins such as PDGF based on aptamers. We believe such advancements will represent a significant step towards improved diagnostics and more personalized medical treatment.

Flow cytometric detection of human immunodeficiency virus type 1 proviral DNA by the polymerase chain reaction incorporating digoxigenin- or fluorescein-labeled dUTP

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Gang; Olson, J.C.; Pu, R.

1995-10-01

Serological assays are routinely used in the laboratory diagnosis of human immunodeficiency virus type-1 (HrV-1) infection, but the polymerase chain reaction (PCR) is ultimately the most sensitive and direct method for establishing definitive diagnosis. As an alternative to the conventional radioactive PCR procedure we have developed and evaluated a pair of rapid nonradioisotopic flow cytometric detection methods. Using heminested PCR we directly incorporated fluorescein-12-dUTP (fluo-dUTP) or digoxigenin-11-dUTP (dig-dUTP) into the PCR-amplicons. The labeled amplicons were hybridized with biotinylated antisense and sense probes, followed by capture of the hybrid DNA using streptavidin-coated beads which were finally analyzed in a flow cytometermore » by (1) direct detection of the fluorescence intensity of the amplicons incorporating fluo-dUTP and (2) immunodetection of the amplicons incorporating dig-dUTP by anti-digoxigenin IgG labeled with fluorescein isothiocyanate (FITC). Although both assays were functionally comparable with radiolabeled probe in reliably detecting as low as five copies of HIV-1 proviral DNA sequences, the immunodetection of dig-dUTP consistently yielded higher mean channel fluorescence and gave a stable signal over an extended period of 12-14 weeks. In testing a panel of 20 pedigreed PBMC specimens from blood donors with or without HIV-1 infection, the results of both flow cytometric assays were identical with those of the conventional radioactive procedure. Therefore, we conclude that the dig-dUTP incorporation in amplicons, hybridization with a pair of sense-antisense biotinylated probes and immunodetection of hybrids by flow cytometric analyses is the nonisotopic method of choice for PCR-diagnosis of HIV-1 infection. 21 refs., 2 figs., 4 tabs.« less

Comparison of culture, polymerase chain reaction, and fluorescent in situ hybridization for detection of Brachyspira hyodysenteriae and "Brachyspira hampsonii" in pig feces.

PubMed

Wilberts, Bailey L; Warneke, Hallie L; Bower, Leslie P; Kinyon, Joann M; Burrough, Eric R

2015-01-01

Swine dysentery is characterized by mucohemorrhagic diarrhea and can occur following infection by Brachyspira hyodysenteriae or "Brachyspira hampsonii ". A definitive diagnosis is often based on the isolation of strongly beta-hemolytic spirochetes from selective culture or by the application of species-specific polymerase chain reaction (PCR) assays directly to feces. While culture is highly sensitive, it typically requires 6 or more days to complete, and PCR, although rapid, can be limited by fecal inhibition. Fluorescent in situ hybridization (FISH) has been described in formalin-fixed tissues; however, completion requires approximately 2 days. Because of the time constraints of available assays, a same-day FISH assay was developed to detect B. hyodysenteriae and "B. hampsonii " in pig feces using previously described oligonucleotide probes Hyo1210 and Hamp1210 for B. hyodysenteriae and "B. hampsonii", respectively. In situ hybridization was simultaneously compared with culture and PCR on feces spiked with progressive dilutions of spirochetes to determine the threshold of detection for each assay at 0 and 48 hr. The PCR assay on fresh feces and FISH on formalin-fixed feces had similar levels of detection. Culture was the most sensitive method, detecting the target spirochetes at least 2 log-dilutions less when compared to other assays 48 hr after sample preparation. Fluorescent in situ hybridization also effectively detected both target species in formalin-fixed feces from inoculated pigs as part of a previous experiment. Accordingly, FISH on formalin-fixed feces from clinically affected pigs can provide same-day identification and preliminary speciation of spirochetes associated with swine dysentery in North America. © 2014 The Author(s).

Ultrasensitive photoelectrochemical biosensor for the detection of HTLV-I DNA: A cascade signal amplification strategy integrating λ-exonuclease aided target recycling with hybridization chain reaction and enzyme catalysis.

PubMed

Shi, Xiao-Mei; Fan, Gao-Chao; Tang, Xueying; Shen, Qingming; Zhu, Jun-Jie

2018-06-30

Sensitive and specific detection of DNA is of great significance for clinical diagnosis. In this paper, an effective cascade signal amplification strategy was introduced into photoelectrochemical (PEC) biosensor for ultrasensitive detection of human T-cell lymphotropic virus type I (HTLV-I) DNA. This proposed signal amplification strategy integrates λ-exonuclease (λ-Exo) aided target recycling with hybridization chain reaction (HCR) and enzyme catalysis. In the presence of target DNA (tDNA) of HTLV-I, the designed hairpin DNA (h 1 DNA) hybridized with tDNA, subsequently recognized and cleaved by λ-Exo to set free tDNA. With the λ-Exo aided tDNA recycling, an increasing number of DNA fragments (output DNA, oDNA) were released from the digestion of h 1 DNA. Then, triggered by the hybridization of oDNA with capture DNA (cDNA), numerous biotin-labeled hairpin DNAs (h 2 DNA and h 3 DNA) could be loaded onto the photoelectrode via the HCR. Finally, avidin-labeled alkaline phosphatase (avidin-ALP) could be introduced onto the electrode by specific interaction between biotin and avidin. The ALP could catalyze dephosphorylation of phospho-L-ascorbic acid trisodium salt (AAP) to generate an efficient electron donor of ascorbic acid (AA), and thereby greatly increasing the photocurrent signal. By utilizing the proposed cascade signal amplification strategy, the fabricated PEC biosensor exhibited an ultrasensitive and specific detection of HTLV-I DNA down to 11.3 aM, and it also offered an effective strategy to detect other DNAs at ultralow levels. Copyright © 2018 Elsevier B.V. All rights reserved.

Stimuli-Responsive DNA-Based Hydrogels: From Basic Principles to Applications.

PubMed

Kahn, Jason S; Hu, Yuwei; Willner, Itamar

2017-04-18

The base sequence of nucleic acids encodes structural and functional information into the DNA biopolymer. External stimuli such as metal ions, pH, light, or added nucleic acid fuel strands provide triggers to reversibly switch nucleic acid structures such as metal-ion-bridged duplexes, i-motifs, triplex nucleic acids, G-quadruplexes, or programmed double-stranded hybrids of oligonucleotides (DNA). The signal-triggered oligonucleotide structures have been broadly applied to develop switchable DNA nanostructures and DNA machines, and these stimuli-responsive assemblies provide functional scaffolds for the rapidly developing area of DNA nanotechnology. Stimuli-responsive hydrogels undergoing signal-triggered hydrogel-to-solution transitions or signal-controlled stiffness changes attract substantial interest as functional matrices for controlled drug delivery, materials exhibiting switchable mechanical properties, acting as valves or actuators, and "smart" materials for sensing and information processing. The integration of stimuli-responsive oligonucleotides with hydrogel-forming polymers provides versatile means to exploit the functional information encoded in the nucleic acid sequences to yield stimuli-responsive hydrogels exhibiting switchable physical, structural, and chemical properties. Stimuli-responsive DNA-based nucleic acid structures are integrated in acrylamide polymer chains and reversible, switchable hydrogel-to-solution transitions of the systems are demonstrated by applying external triggers, such as metal ions, pH-responsive strands, G-quadruplex, and appropriate counter triggers that bridge and dissociate the polymer chains. By combining stimuli-responsive nucleic acid bridges with thermosensitive poly(N-isopropylacrylamide) (pNIPAM) chains, systems undergoing reversible solution ↔ hydrogel ↔ solid transitions are demonstrated. Specifically, by bridging acrylamide polymer chains by two nucleic acid functionalities, where one type of bridging unit provides a stimuli-responsive element and the second unit acts as internal "bridging memory", shape-memory hydrogels undergoing reversible and switchable transitions between shaped hydrogels and shapeless quasi-liquid states are demonstrated. By using stimuli-responsive hydrogel cross-linking units that can assemble the bridging units by two different input signals, the orthogonally-triggered functions of the shape-memory were shown. Furthermore, a versatile approach to assemble stimuli-responsive DNA-based acrylamide hydrogel films on surfaces is presented. The method involves the activation of the hybridization chain-reaction (HCR) by a surface-confined promoter strand, in the presence of acrylamide chains modified with two DNA hairpin structures and appropriate stimuli-responsive tethers. The resulting hydrogel-modified surfaces revealed switchable stiffness properties and signal-triggered catalytic functions. By applying the method to assemble the hydrogel microparticles, substrate-loaded, stimuli-responsive microcapsules are prepared. The signal-triggered DNA-based hydrogel microcapsules are applied as drug carriers for controlled release. The different potential applications and future perspectives of stimuli responsive hydrogels are discussed. Specifically, the use of these smart materials and assemblies as carriers for controlled drug release and as shape-memory matrices for information storage and inscription and the use of surface-confined stimuli-responsive hydrogels, exhibiting switchable stiffness properties, for catalysis and controlled growth of cells are discussed.

[Identification of human pathogenic variola and monkeypox viruses by real-time polymerase chain reaction].

PubMed

Kostina, E V; Gavrilova, E V; Riabinin, V A; Shchelkunov, S N; Siniakov, A N

2009-01-01

A kit of specific oligonucleotide primers and hybridization probes has been proposed to detect orthopoxviruses (OPV) and to discriminate human pathogenic viruses, such as variola virus and monkey virus by real-time polymerase chain reaction (PCR). For real-time PCR, the following pairs of fluorophore and a fluorescence quencher were used: TAMRA-BHQ2 for genus-specific probes and FAM-BHQ1 for species-specific ones (variola virus, monkeypox virus, ectomelia virus). The specificity of this assay was tested on 38 strains of 6 OPV species and it was 100%.

Charge-transfer dynamics in one-dimensional C 60 chains

NASA Astrophysics Data System (ADS)

Pérez-Dieste, V.; Tamai, A.; Greber, T.; Chiuzbaˇian, S. G.; Patthey, L.

2008-06-01

Charge transfer in highly-ordered C 60 chains grown on a Cu(5 5 3) vicinal surface is studied by means of resonant photoemission. Tuning the light polarization, autoionization of the highest occupied molecular orbital (HOMO) was expected to detect anisotropy in this one-dimensional system. For one monolayer C 60 we found no signature of autoionization. This indicates that for an electron which is excited from the C 1s level of C 60 to the lowest unoccupied molecular orbital (LUMO), hybridization leads to delocalization on the femtosecond time-scale and no influence of the light polarization is observed.

Contamination control in hybrid microelectronic modules. Part 3: Specifications for coating material and process controls

NASA Technical Reports Server (NTRS)

Himmel, R. P.

1975-01-01

Resin systems for coating hybrids prior to hermetic sealing are described. The resin systems are a flexible silicone junction resin system and a flexible cycloaliphatic epoxy resin system. The coatings are intended for application to the hybrid after all the chips have been assembled and wire bonded, but prior to hermetic sealing of the package. The purpose of the coating is to control particulate contamination by immobilizing particles and by passivating the hybrid. Recommended process controls for the purpose of minimizing contamination in hybrid microcircuit packages are given. Emphasis is placed on those critical hybrid processing steps in which contamination is most likely to occur.

ECLAIRs detection plane: current state of development

NASA Astrophysics Data System (ADS)

Lacombe, K.; Pons, R.; Amoros, C.; Atteia, J.-L.; Barret, D.; Billot, M.; Bordon, S.; Cordier, B.; Gevin, O.; Godet, O.; Gonzalez, F.; Houret, B.; Mercier, K.; Mandrou, P.; Marty, W.; Nasser, G.; Rambaud, D.; Ramon, P.; Rouaix, G.; Waegebaert, V.

2014-07-01

ECLAIRs, a 2-D coded-mask imaging camera on-board the Sino-French SVOM space mission, will detect and locate Gamma-ray bursts (GRBs) in near real time in the 4-150 keV energy band. The design of ECLAIRs has been mainly driven by the objective of achieving a low-energy threshold of 4 keV, unprecedented for this type of instrument. The detection plane is an assembly of 6400 Schottky CdTe semiconductor detectors of size 4x4x1 mm3 organized on elementary hybrid matrices of 4x8 detectors. The detectors will be polarized from -300V to -500V and operated at -20°C to reduce both the leakage current and the polarization effect induced by the Schottky contact. The remarkable low-energy threshold homogeneity required for the detection plane has been achieved thanks to: i) an extensive characterization and selection of the detectors, ii) the development of a specific low-noise 32-channel ASIC, iii) the realization of an innovative hybrid module composed of a thick film ceramic (holding 32 CdTe detectors with their high voltage grid), associated to an HTCC ceramic (housing the ASIC chip within an hermetic enclosure). In this paper, we start describing a complete hybrid matrix, and then the manufacturing of a first set of 50 matrices (representing 1600 detectors, i.e. a quarter of ECLAIRs detector's array). We show how this manufacturing allowed to validate the different technologies used for this hybridization, as well as the industrialization processes. During this phase, we systematically measured the leakage current on Detector Ceramics after an outgassing, and the Equivalent Noise Charge (ENC) for each of the 32 channels on ASIC Ceramics, in order to optimize the coupling of the two ceramics. Finally, we performed on each hybrid module, spectral measurements at -20°C in our vacuum chamber, using several calibrated radioactive sources (241Am and 55Fe), to check the performance homogeneity of the 50 modules. The results demonstrated that the 32-detector hybrid matrices presented homogeneous spectral properties and that a lowenergy threshold of 4 keV for each detector could be reached. In conclusion, our hybrid module has obtained the performance required at the SVOM mission level and successfully withstood the space environment tests (TRL 6/7). This development phase has given us the opportunity to build a detector's array prototype (Engineering Model) equipped with 50 hybrid modules. Thanks to this prototype we are in the process of validating a complete detection chain (from the detectors to the backend electronics) and checking the performance. In addition it enables us to consolidate the instrument's mechanical and thermal design, and to write preliminary versions of the quality procedures required for integration, functional tests and calibration steps. At the end of this prototype development and testing, we will be ready to start the detailed design of the detection plane Flight Model.

Sensitive electrochemical assaying of DNA methyltransferase activity based on mimic-hybridization chain reaction amplified strategy.

PubMed

Zhang, Linqun; Liu, Yuanjian; Li, Ying; Zhao, Yuewu; Wei, Wei; Liu, Songqin

2016-08-24

A mimic-hybridization chain reaction (mimic-HCR) amplified strategy was proposed for sensitive electrochemically detection of DNA methylation and methyltransferase (MTase) activity In the presence of methylated DNA, DNA-gold nanoparticles (DNA-AuNPs) were captured on the electrode by sandwich-type assembly. It then triggered mimic-HCR of two hairpin probes to produce many long double-helix chains for numerous hexaammineruthenium (III) chloride ([Ru(NH3)6](3+), RuHex) inserting. As a result, the signal for electrochemically detection of DNA MTase activity could be amplified. If DNA was non-methylated, however, the sandwich-type assembly would not form because the short double-stranded DNAs (dsDNA) on the Au electrode could be cleaved and digested by restriction endonuclease HpaII (HapII) and exonuclease III (Exo III), resulting in the signal decrement. Based on this, an electrochemical approach for detection of M.SssI MTase activity with high sensitivity was developed. The linear range for M.SssI MTase activity was from 0.05 U mL(-1) to 10 U mL(-1), with a detection limit down to 0.03 U mL(-1). Moreover, this detecting strategy held great promise as an easy-to-use and highly sensitive method for other MTase activity and inhibition detection by exchanging the corresponding DNA sequence. Copyright © 2016 Elsevier B.V. All rights reserved.

Polyhydroxyalkanoate-based natural synthetic hybrid copolymer films: A small-angle neutron scattering study

NASA Astrophysics Data System (ADS)

Foster, L. John R.; Knott, Robert; Sanguanchaipaiwong, Vorapat; Holden, Peter J.

2006-11-01

Polyhydroxyalkanoates have attracted attention as biodegradable alternatives to conventional thermoplastics and as biomaterials. Through modification of their biosynthesis using Pseudomonas oleovorans, we have manipulated the material properties of these biopolyesters and produced a natural-synthetic hybrid copolymer of polyhydroxyoctanoate- block-diethylene glycol (PHO- b-DEG). A mixture of PHO and PHO-DEG were solvent cast from analytical grade chloroform and analysed using small-angle neutron scattering. A scattering pattern, easily distinguished above the background, was displayed by the films with a diffraction ring at q∼0.12 Å -1. This narrow ring of intensity is suggestive of a highly ordered system. Analysis of the diffraction pattern supported this concept and showed a d-spacing of approximately 50 Å. In addition, conformation of the hybrid polymer chains can be manipulated to support their self-assembly into ordered microporous films.

Organic/inorganic hybrid filters based on dendritic and cyclodextrin "nanosponges" for the removal of organic pollutants from water.

PubMed

Arkas, Michael; Allabashi, Roza; Tsiourvas, Dimitris; Mattausch, Eva-Maria; Perfler, Reinhard

2006-04-15

Long-alkyl chain functionalized poly(propylene imine) dendrimer, poly(ethylene imine) hyperbranched polymer, and beta-cyclodextrin derivatives, which are completely insoluble in water, have the property of encapsulating organic pollutants from water. Ceramic porous filters can be impregnated with these compounds resulting in hybrid organic/ inorganic filter modules. These hybrid filter modules were tested for the effective purification of water, by continuous filtration experiments, employing a variety of water pollutants. It has been established that polycyclic aromatic hydrocarbons (PAHs) can be removed very efficiently (more than 95%), and final concentrations of several ppb (microg/ L) are easily obtained. Representatives of the pollutant group of trihalogen methanes (THMs), monoaromatic hydrocarbons (BTX), and pesticides (simazine) can also be removed (>80%), although the filters are saturated considerably faster in these cases.

In situ hybridization of hepatitis C virus RNA in liver cells of an experimentally infected rhesus macaque.

PubMed

Majerowicz, Selma; Grief, Christopher; Ferguson, Debora; Airano, Renata C; Baptista, Marcia L; Pinto, Marcelo A; Barth, Ortrud Monika

2004-10-01

The liver tissue of a rhesus macaque inoculated with hepatitis C virus (HCV) has been analyzed for the presence of HCV RNA using the technique of in situ hybridization, both at light and electron microscopy levels. The animal was inoculated by the intrasplenic route using a HCV infected autogenic hepatocyte transplant. The serum sample used to infect the hepatocyte cells was characterized by polymerase chain reaction technique and shown to be positive for HCV RNA, genotype 3 with 10(7) RNA copies/ml. In situ hybridization was performed using a complementary negative strand probe made with the specific primer. We were able to detect and localize viral RNA in altered membranes of the rough endoplasmic reticulum of infected liver cells, showing evidence of virus replication in vivo.

Phase transition in organic-inorganic perovskite (C9H19NH3)2 PbI2Br2 of long-chain alkylammonium

NASA Astrophysics Data System (ADS)

Abid, H.; Trigui, A.; Mlayah, A.; Hlil, E. K.; Abid, Y.

2012-01-01

Single perovskite slab alkylammonium lead iodides bromides (C9H19NH3)2PbI2Br2 is a new member of the family of hybrid organic-inorganic perovskite compounds. It exhibits a single structural phase transition with changes in the conformation of alkylammonium chains below room temperature. Differential scanning calorimetry (DSC), powder X-ray diffraction and FT-Raman spectroscopy were used to investigate this phase transition. These changes were characterized by a decreased conformational disorder of the methylene units of the alkyl chains. Phase transition was examined in light of the interesting optical properties of this material, as well as the relevance of this system as models for phase transitions in lipid bilayers.

Direct visualization of quasi-ordered oxygen chain structures on Au(110)-(1 × 2)

NASA Astrophysics Data System (ADS)

Hiebel, F.; Montemore, M. M.; Kaxiras, E.; Friend, C. M.

2016-08-01

The Au(110) surface offers unique advantages for atomically-resolved model studies of catalytic oxidation processes on gold. We investigate the adsorption of oxygen on Au(110) using a combination of scanning tunneling microscopy (STM) and density functional theory (DFT) methods. We identify the typical (empty-states) STM contrast resulting from adsorbed oxygen as atomic-sized dark features of electronic origin. DFT-based image simulations confirm that chemisorbed oxygen is generally detected indirectly, from the binding-induced electronic structure modification of gold. STM images show that adsorption occurs without affecting the general structure of the pristine Au(110) missing-row reconstruction. The tendency to form one-dimensional structures is observed already at low coverage (< 0.05 ML), with oxygen adsorbing on alternate sides of the reconstruction ridges. Consistently, calculations yield preferred adsorption on the (111) facets of the reconstruction, on a 3-fold coordination site, with increased stability when adsorbed in chains. Gold atoms with two oxygen neighbors exhibit enhanced electronic hybridization with the O states. Finally, the species observed are reactive to CO oxidation at 200 K and desorption of CO2 leaves a clean and ordered gold surface.

Somatic diversification in the heavy chain variable region genes expressed by human autoantibodies bearing a lupus-associated nephritogenic anti-DNA idiotype

DOE Office of Scientific and Technical Information (OSTI.GOV)

Demaison, C.; Chastagner, P.; Theze, J.

1994-01-18

Monoclonal anti-DNA antibodies bearing a lupus nephritis-associated idiotype were derived from five patients with systemic lupus erythematosus (SLE). Genes encoding their heavy (H)-chain variable (V[sub H]) regions were cloned and sequenced. When compared with their closest V[sub h] germ-line gene relatives, these sequences exhibit a number of silent (S) and replacement (R) substitutions. The ratios of R/S mutations were much higher in the complementarity-determining regions (CDRs) of the antibodies than in the framework regions. Molecular amplification of genomic V[sub H] genes and Southern hybridization with somatic CDR2-specific oligonucleotide probes showed that the configuration of the V[sub H] genes corresponding tomore » V[sub H] sequences in the nephritogenic antibodies is not present in the patient's own germ-line DNA, implying that the B-cell clones underwent somatic mutation in vivo. These findings, together with the characteristics of the diversity and junctional gene elements utilized to form the antibody, indicate that these autoantibodies have been driven through somatic selection processes reminiscent of those that govern antibody responses triggered by exogenous stimuli.« less

Protein phosphorylation differs significantly among ontogenetic phases in Malus seedlings

PubMed Central

2014-01-01

Background Although protein phosphorylation is an important post-translational modification affecting protein function and metabolism, dynamic changes in this process during ontogenesis remain unexplored in woody angiosperms. Methods Phosphorylated proteins from leaves of three apple seedlings at juvenile, adult vegetative and reproductive stages were extracted and subjected to alkaline phosphatase pre-treatment. After separating the proteins by two-dimensional gel electrophoresis and phosphoprotein-specific Pro-Q Diamond staining, differentially expressed phosphoproteins were identified by MALDI-TOF-TOF mass spectrometry. Results A total of 107 phosphorylated protein spots on nine gels (three ontogenetic phases × three seedlings) were identified by MALDI-TOF-TOF mass spectrometry. The 55 spots of ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco) large-chain fragments varied significantly in protein abundance and degree of phosphorylation among ontogenetic phases. Abundances of the 27 spots corresponding to Rubisco activase declined between juvenile and reproductive phases. More extensively, phosphorylated β-tubulin chain spots with lower isoelectric points were most abundant during juvenile and adult vegetative phases. Conclusions Protein phosphorylation varied significantly during vegetative phase change and floral transition in apple seedlings. Most of the observed changes were consistent among seedlings and between hybrid populations. PMID:24904238

Organic-inorganic hybrid mesoporous silicas: functionalization, pore size, and morphology control.

PubMed

Park, Sung Soo; Ha, Chang-Sik

2006-01-01

Topological design of mesoporous silica materials, pore architecture, pore size, and morphology are currently major issues in areas such as catalytic conversion of bulky molecules, adsorption, host-guest chemistry, etc. In this sense, we discuss the pore size-controlled mesostructure, framework functionalization, and morphology control of organic-inorganic hybrid mesoporous silicas by which we can improve the applicability of mesoporous materials. First, we explain that the sizes of hexagonal- and cubic-type pores in organic-inorganic hybrid mesoporous silicas are well controlled from 24.3 to 98.0 A by the direct micelle-control method using an organosilica precursor and surfactants with different alkyl chain lengths or triblock copolymers as templates and swelling agents incorporated in the formed micelles. Second, we describe that organic-inorganic hybrid mesoporous materials with various functional groups form various external morphologies such as rod, cauliflower, film, rope, spheroid, monolith, and fiber shapes. Third, we discuss that transition metals (Ti and Ru) and rare-earth ions (Eu(3+) and Tb(3+)) are used to modify organic-inorganic hybrid mesoporous silica materials. Such hybrid mesoporous silica materials are expected to be applied as excellent catalysts for organic reactions, photocatalysis, optical devices, etc. c) 2006 The Japan Chemical Journal Forum and Wiley Periodicals, Inc.

3D- Printed Poly(ε-caprolactone) Scaffold Integrated with Cell-laden Chitosan Hydrogels for Bone Tissue Engineering.

PubMed

Dong, Liang; Wang, Shao-Jie; Zhao, Xin-Rong; Zhu, Yu-Fang; Yu, Jia-Kuo

2017-10-17

Synthetic polymeric scaffolds are commonly used in bone tissue engineering (BTE) due to their biocompatibility and adequate mechanical properties. However, their hydrophobicity and the lack of specific cell recognition sites confined their practical application. In this study, to improve the cell seeding efficiency and osteoinductivity, an injectable thermo-sensitive chitosan hydrogel (CSG) was incorporated into a 3D-printed poly(ε-caprolactone) (PCL) scaffold to form a hybrid scaffold. To demonstrate the feasibility of this hybrid system for BTE application, rabbit bone marrow mesenchymal stem cells (BMMSCs) and bone morphogenetic protein-2 (BMP-2) were encapsulated in CSG. Pure PCL scaffolds were used as controls. Cell proliferation and viability were investigated. Osteogenic gene expressions of BMMSCs in various scaffolds were determined with reverse transcription polymerase chain reaction (RT-PCR). Growth factor releasing profile and mechanical tests were performed. CCK-8 assay confirmed greater cell retention and proliferation in chitosan and hybrid groups. Confocal microscopy showed even distribution of cells in the hybrid system. After 2-week osteogenic culture in vitro, BMMSCs in hybrid and chitosan scaffolds showed stronger osteogenesis and bone-matrix formation. To conclude, chitosan/PCL hybrid scaffolds are a favorable platform for BTE due to its capacity to carry cells and drugs, and excellent mechanical strength.

Effects of plant size, temperature, and light intensity on flowering of Phalaenopsis hybrids in Mediterranean greenhouses.

PubMed

Paradiso, Roberta; De Pascale, Stefania

2014-01-01

Mediterranean greenhouses for cultivation of Phalaenopsis orchids reproduce the warm, humid, and shaded environment of tropical underbrush. Heating represents the highest production cost, due to the high thermal requirements and the long unproductive phase of juvenility, in which plants attain the critical size for flowering. Our researches aimed to investigate the effect of plant size, temperature, and light intensity, during the phase of flower induction, on flowering of modern genotypes selected for Mediterranean greenhouses. Three experiments were carried out to compare (i) plant size: reduced size versus size considered optimal for flowering (hybrids "Sogo Yukidian," "Chain Xen Diamond," and "Pinlong"); (ii) temperature: moderate reduction of temperature versus standard thermal regime (hybrid "Premium"); (iii) light intensity: supplemental lighting versus reference light intensity (hybrid "Premium"). The premature exposure of plants to the inductive treatment delayed the beginning of flowering and reduced the flower stem quality, in all the tested hybrids. In "Premium," the lower temperature did not affect flowering earliness and commercial quality of flower stems compared to the standard regime, whereas it promoted stem branching. In the same hybrid, supplemental lighting anticipated flowering and promoted the emission of the second stem and the stem branching, compared to the reference light regime.

A study on the electrical, optical, and physicochemical properties of poly(MMA-co-MAA)/ poly(3,4-ethylenedioxythiophene) hybrid thin films.

PubMed

Han, Yong-Hyeon; Kim, Hyeong Eun; Hwangbo, Kyung-Hee; Yim, Jin-Heong; Cho, Kuk Young

2013-08-01

Poly(3,4-ethylenedioxythiophene) (PEDOT) has good properties as a conductive polymer such as high conductivity, optical transmittance, and chemical stability, while offering relatively weak physicochemical properties. The main purpose of this paper is to improve physicochemical properties such as solvent resistance and pencil hardness of PEDOT. Carboxyl groups in the poly(MMA-co-MAA) polymer chains can effectively crosslink each other in the presence of aziridine, resulting in physicochemically robust PEDOT/poly(MMA-co-MAA) hybrid conductive films. The electrical conductivity, optical properties, and physicochemical properties of the hybrid conductive film were compared by varying the solid content and poly(MMA-co-MAA) portion in the coating precursor solution. From the results, the transparency and surface resistance of the hybrid film show a tendency to decrease with increasing solid content in the coating precursor. Moreover, solvent resistance and hardness were dramatically enhanced by hybridization of PEDOT and crosslinked poly(MMA-co-MAA) due to curing reactions between carboxyl groups. The chemical composition of 30 wt-% of poly(MMA-co-MAA) (MMA:MAA mole ratio 9:1) and 3 wt-% - 5 wt-% of aziridine yields the best physicochemical properties of poly(MMA-co-MAA)/PEDOT hybrid thin films.

Effectiveness evaluation of double-layered satellite network with laser and microwave hybrid links based on fuzzy analytic hierarchy process

NASA Astrophysics Data System (ADS)

Zhang, Wei; Rao, Qiaomeng

2018-01-01

In order to solve the problem of high speed, large capacity and limited spectrum resources of satellite communication network, a double-layered satellite network with global seamless coverage based on laser and microwave hybrid links is proposed in this paper. By analyzing the characteristics of the double-layered satellite network with laser and microwave hybrid links, an effectiveness evaluation index system for the network is established. And then, the fuzzy analytic hierarchy process, which combines the analytic hierarchy process and the fuzzy comprehensive evaluation theory, is used to evaluate the effectiveness of the double-layered satellite network with laser and microwave hybrid links. Furthermore, the evaluation result of the proposed hybrid link network is obtained by simulation. The effectiveness evaluation process of the proposed double-layered satellite network with laser and microwave hybrid links can help to optimize the design of hybrid link double-layered satellite network and improve the operating efficiency of the satellite system.

Bacterial biodiversity from an anaerobic up flow bioreactor with ANAMMOX activity inoculated with swine sludge

USDA-ARS?s Scientific Manuscript database

The present study aimed to identify organisms with ANAMMOX activity in a reactor maintained in a laboratory. Molecular methods as fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR) and cloning of 16S-rDNA genes probing for Planctomycetes were performed. Seventeen clones were ...

INTEGRATE: Driving Transformational Change - JISEA 2018 Annual Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

This report demonstrates 2017 highlights of the Joint Institute for Strategic Energy Analysis' (JISEA's) work. The Annual Report overviews JISEA's research and analysis accomplishments in natural gas and methane emissions; nuclear-renewable hybrid energy systems; the Clean Energy Manufacturing Analysis Center's work in global supply chains; the 21st Century Power Partnership; and more.

Qualitative variation in proanthocyanidin composition of Populus species and hybrids: genetics is the key.

PubMed

Scioneaux, Ashley N; Schmidt, Michael A; Moore, Melissa A; Lindroth, Richard L; Wooley, Stuart C; Hagerman, Ann E

2011-01-01

The literature on proanthocyanidins (tannins) in ecological systems is dominated by quantitative studies. Despite evidence that the qualitative characteristics (subunit type, polymer chain length) of these complex polyphenolics are important determinants of biological activity, little is known about genetic and environmental controls on the type of proanthocyanidins produced by plants. We tested the hypothesis that genetics, season, developmental stage, and environment determine proanthocyanidin qualitative characteristics by using four Populus "cross types" (narrowleaf [P. angustifolia], Fremont [P. fremontii], F1 hybrids, and backcrosses to narrowleaf). We used thiolysis and HPLC analysis to characterize the proanthocyanidins, and found that genetics strongly control composition. The narrowleaf plants accumulate mixed procyanidin/prodelphinidins with average composition epicatechin(11)-epigallocatechin(8)-catechin(2)-catechin((terminal)). Backcross genotypes produce mixed procyanidin/prodelphinidins similar to narrowleaf, while Fremont makes procyanidin dimers, and the F1 plants contain procyanidin heptamers. Less striking effects were noted for genotype × environment, while season and developmental zone had little effect on proanthocyanidin composition or chain length. We discuss the metabolic and ecological consequences of differences in condensed tannin qualitative traits.

Dielectrophoresis of gold nanoparticles conjugated to DNA origami structures

PubMed Central

Wiens, Matthew; Lakatos, Mathias; Heerwig, Andreas; Ostermaier, Frieder; Haufe, Nora

2016-01-01

Summary DNA nanostructures are promising construction materials to bridge the gap between self-assembly of functional molecules and conventional top-down fabrication methods in nanotechnology. Their positioning onto specific locations of a microstructured substrate is an important task towards this aim. Here we study manipulation and positioning of pristine and of gold nanoparticle-conjugated tubular DNA origami structures using ac dielectrophoresis. The dielectrophoretic behavior was investigated employing fluorescence microscopy. For the pristine origami, a significant dielectrophoretic response was found to take place in the megahertz range, whereas, due to the higher polarizability of the metallic nanoparticles, the nanoparticle/DNA hybrid structures required a lower electrical field strength and frequency for a comparable trapping at the edges of the electrode structure. The nanoparticle conjugation additionally resulted in a remarkable alteration of the DNA structure arrangement. The growth of linear, chain-like structures in between electrodes at applied frequencies in the megahertz range was observed. The long-range chain formation is caused by a local, gold nanoparticle-induced field concentration along the DNA nanostructures, which in turn, creates dielectrophoretic forces that enable the observed self-alignment of the hybrid structures. PMID:27547612

Detection of tet(M) and tet(O) using the polymerase chain reaction in bacteria isolated from patients with periodontal disease.

PubMed

Olsvik, B; Olsen, I; Tenover, F C

1995-04-01

The polymerase chain reaction was used to examine 114 tetracycline-resistant anaerobic and facultative anaerobic bacterial isolates from patients with periodontal disease for the tet(M) and tet(O) genes. A 740-base-pair fragment of the tet(M) gene was amplified from 84 of 114 isolates, and a 519-base-pair fragment of the tet(O) gene was amplified from 13 streptococcal isolates. Six of 7 tetracycline-resistant isolates of Veillonella spp. and tetracycline-resistant isolates of Eubacterium spp. (n = 3), Eubacterium saburreum (n = 1), Streptococcus intermedius (n = 5) and Gemella morbillorum (n = 2) all harbored the tet(M) gene. The tet(M) and tet(O) negative as well as selected positive isolates were tested for the tet(K) and tet(L) genes using DNA probes. All isolates of Staphylococcus spp. (n = 11) hybridized with the tet(K) probe. None of the isolates tested hybridized with the probe for tet(L). This is the first report of the tet(M) gene in the facultative bacterium G. morbillorum and in E. saburreum.

Highly sensitive antibody-aptamer sensor for vascular endothelial growth factor based on hybridization chain reaction and pH meter/indicator.

PubMed

Xu, Huifeng; Kou, Fangxia; Ye, Hongzhi; Wang, Zongwen; Huang, Suixin; Liu, Xianxiang; Zhu, Xi; Lin, Zhenyu; Chen, Guonan

2017-12-01

Vascular endothelial growth factor (VEGF) is a crucial signaling protein for the tumor growth and metastasis, which is also acted as the biomarkers for various diseases. In this research, we fabricate an aptamer-antibody sensor for point-of-care test of VEGF. Firstly, target VEGF is captured by antibody immobilized on the microplate, and then binds with aptamer to form the sandwich structure. Next, with the assist of glucose oxidase (GOx)-functionalized ssDNAs, hybridization chain reaction occurs using the aptamer as the primer. Thus, GOx are greatly gathered on the microplate, which catalyzes the oxidization of glucose, leading to the pH change. As a result, the detect limit at a signal-to-noise was estimated to be 0.5pg/mL of target by pH meter, and 1.6pg/mL of VEGF was able to be distinguished by naked eyes. Meanwhile, this method has been used assay VEGF in the serum with the satisfactory results. Copyright © 2017. Published by Elsevier B.V.

Drastic stabilization of parallel DNA hybridizations by a polylysine comb-type copolymer with hydrophilic graft chain.

PubMed

Miyoshi, Daisuke; Ueda, Yu-Mi; Shimada, Naohiko; Nakano, Shu-Ichi; Sugimoto, Naoki; Maruyama, Atsushi

2014-09-01

Electrostatic interactions play a major role in protein-DNA interactions. As a model system of a cationic protein, herein we focused on a comb-type copolymer of a polycation backbone and dextran side chains, poly(L-lysine)-graft-dextran (PLL-g-Dex), which has been reported to form soluble interpolyelectrolyte complexes with DNA strands. We investigated the effects of PLL-g-Dex on the conformation and thermodynamics of DNA oligonucleotides forming various secondary structures. Thermodynamic analysis of the DNA structures showed that the parallel conformations involved in both DNA duplexes and triplexes were significantly and specifically stabilized by PLL-g-Dex. On the basis of thermodynamic parameters, it was further possible to design DNA switches that undergo structural transition responding to PLL-g-Dex from an antiparallel duplex to a parallel triplex even with mismatches in the third strand hybridization. These results suggest that polycationic molecules are able to induce structural polymorphism of DNA oligonucleotides, because of the conformation-selective stabilization effects. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ubiquitin-specific Protease 11 (USP11) Deubiquitinates Hybrid Small Ubiquitin-like Modifier (SUMO)-Ubiquitin Chains to Counteract RING Finger Protein 4 (RNF4)*

PubMed Central

Hendriks, Ivo A.; Schimmel, Joost; Eifler, Karolin; Olsen, Jesper V.; Vertegaal, Alfred C. O.

2015-01-01

Ring finger protein 4 (RNF4) is a SUMO-targeted ubiquitin E3 ligase with a pivotal function in the DNA damage response (DDR). SUMO interaction motifs (SIMs) in the N-terminal part of RNF4 tightly bind to SUMO polymers, and RNF4 can ubiquitinate these polymers in vitro. Using a proteomic approach, we identified the deubiquitinating enzyme ubiquitin-specific protease 11 (USP11), a known DDR-component, as a functional interactor of RNF4. USP11 can deubiquitinate hybrid SUMO-ubiquitin chains to counteract RNF4. SUMO-enriched nuclear bodies are stabilized by USP11, which functions downstream of RNF4 as a counterbalancing factor. In response to DNA damage induced by methyl methanesulfonate, USP11 could counteract RNF4 to inhibit the dissolution of nuclear bodies. Thus, we provide novel insight into cross-talk between ubiquitin and SUMO and uncover USP11 and RNF4 as a balanced SUMO-targeted ubiquitin ligase/protease pair with a role in the DDR. PMID:25969536

Towards development of new ornamental plants: status and progress in wide hybridization.

PubMed

Kuligowska, Katarzyna; Lütken, Henrik; Müller, Renate

2016-07-01

The present review provides insights into the key findings of the hybridization process, crucial factors affecting the adaptation of new technologies within wide hybridization of ornamental plants and presents perspectives of further development of this strategy. Wide hybridization is one of the oldest breeding techniques that contributed enormously to the development of modern plant cultivars. Within ornamental breeding, it represents the main source of genetic variation. During the long history of wide hybridization, a number of methods were implemented allowing the evolution from a conventional breeding tool into a modern methodology. Nowadays, the research on model plants and crop species increases our understanding of reproductive isolation among distant species and partly explains the background of the traditional approaches previously used for overcoming hybridization barriers. Characterization of parental plants and hybrids is performed using molecular and cytological techniques that strongly facilitate breeding processes. Molecular markers and sequencing technologies are used for the assessment of genetic relationships among plants, as the genetic distance is typically depicted as one of the most important factors influencing cross-compatibility in hybridization processes. Furthermore, molecular marker systems are frequently applied for verification of hybrid state of the progeny. The flow cytometry and genomic in situ hybridization are used in the assessment of hybridization partners and characterization of hybrid progeny in relation to genome stabilization as well as genome recombination and introgression. In the future, new research and technologies are likely to provide more detailed information about genes and pathways responsible for interspecific reproductive isolation. Ultimately, this knowledge will enable development of strategies for obtaining compatible lines for hybrid production. Recent development in sequencing technologies and availability of sequence data will also facilitate creation of new molecular markers that will advance marker-assisted selection in hybridization process.

Exchange coupling transformations in Cu (II) heterospin complexes of “breathing crystals” under structural phase transitions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morozov, Vitaly A.; Petrova, Marina V.; Lukzen, Nikita N., E-mail: luk@tomo.nsc.ru

2015-08-15

Family of “breathing crystals” is the polymer-chain complexes of Cu(hfac){sub 2} with nitroxides. The polymer chains consist of one-, two- or three-spin clusters. The “breathing crystals” experience simultaneous magnetic and Jahn-Teller type structural phase transitions with change of total cluster spin and drastic change of bond lengths (ca. 10-12%). For the first time the intra-cluster magnetic couplings in ”breathing crystals” have been calculated both by band structure methods GGA + U and hybrid DFT (B3LYP and PBE0) for the isolated exchange clusters. The temperature dependence of the magnetic coupling constant was calculated for two polymer-chain compounds of the “breathing crystal”more » family - C{sub 21}H{sub 19}CuF{sub 12}N{sub 4}O{sub 6} with the chains containing two-spin clusters and C{sub 22}H{sub 21}CuF{sub 12}N{sub 4}O{sub 6} with the chains of alternating three-spin clusters and one-spin sites. It was found that adding a Hubbard-like parameter not only to the copper 3d electrons but also to the oxygen 2p electrons (GGA + U{sub d} + U{sub p} approach) results in an improved description of exchange coupling in the “breathing crystal” compounds. At the same time treatment of the isolated clusters by a large basis hybrid DFT with high computational cost provides a similar quality fit of the experimental magneto-chemical data as that for the GGA + U{sub d} + U{sub p} band structure calculation scheme. Our calculations also showed that in spite of the abrupt transformation of the magnetic coupling constant under the phase transition, the band gap in the “breathing crystals” remains about the same value with temperature decrease.« less

Techno-economic assessment of hybrid extraction and distillation processes for furfural production from lignocellulosic biomass.

PubMed

Nhien, Le Cao; Long, Nguyen Van Duc; Kim, Sangyong; Lee, Moonyong

2017-01-01

Lignocellulosic biomass is one of the most promising alternatives for replacing mineral resources to overcome global warming, which has become the most important environmental issue in recent years. Furfural was listed by the National Renewable Energy Laboratory as one of the top 30 potential chemicals arising from biomass. However, the current production of furfural is energy intensive and uses inefficient technology. Thus, a hybrid purification process that combines extraction and distillation to produce furfural from lignocellulosic biomass was considered and investigated in detail to improve the process efficiency. This effective hybrid process depends on the extracting solvent, which was selected based on a comprehensive procedure that ranged from solvent screening to complete process design. Various solvents were first evaluated in terms of their extraction ability. Then, the most promising solvents were selected to study the separation feasibility. Eventually, processes that used the three best solvents (toluene, benzene, and butyl chloride) were designed and optimized in detail using Aspen Plus. Sustainability analysis was performed to evaluate these processes in terms of their energy requirements, total annual costs (TAC), and carbon dioxide (CO 2 ) emissions. The results showed that butyl chloride was the most suitable solvent for the hybrid furfural process because it could save 44.7% of the TAC while reducing the CO 2 emissions by 45.5% compared to the toluene process. In comparison with the traditional purification process using distillation, this suggested hybrid extraction/distillation process can save up to 19.2% of the TAC and reduce 58.3% total annual CO 2 emissions. Furthermore, a sensitivity analysis of the feed composition and its effect on the performance of the proposed hybrid system was conducted. Butyl chloride was found to be the most suitable solvent for the hybrid extraction/distillation process of furfural production. The proposed hybrid sequence was more favorable than the traditional distillation process when the methanol fraction of the feed stream was <3% and more benefit could be obtained when that fraction decreased.

Length-scale and strain rate-dependent mechanism of defect formation and fracture in carbon nanotubes under tensile loading

NASA Astrophysics Data System (ADS)

Javvaji, Brahmanandam; Raha, S.; Mahapatra, D. Roy

2017-02-01

Electromagnetic and thermo-mechanical forces play a major role in nanotube-based materials and devices. Under high-energy electron transport or high current densities, carbon nanotubes fail via sequential fracture. The failure sequence is governed by certain length scale and flow of current. We report a unified phenomenological model derived from molecular dynamic simulation data, which successfully captures the important physics of the complex failure process. Length-scale and strain rate-dependent defect nucleation, growth, and fracture in single-walled carbon nanotubes with diameters in the range of 0.47 to 2.03 nm and length which is about 6.17 to 26.45 nm are simulated. Nanotubes with long length and small diameter show brittle fracture, while those with short length and large diameter show transition from ductile to brittle fracture. In short nanotubes with small diameters, we observe several structural transitions like Stone-Wales defect initiation, its propagation to larger void nucleation, formation of multiple chains of atoms, conversion to monatomic chain of atoms, and finally complete fracture of the carbon nanotube. Hybridization state of carbon-carbon bonds near the end cap evolves, leading to the formation of monatomic chain in short nanotubes with small diameter. Transition from ductile to brittle fracture is also observed when strain rate exceeds a critical value. A generalized analytical model of failure is established, which correlates the defect energy during the formation of atomic chain with aspect ratio of the nanotube and strain rate. Variation in the mechanical properties such as elastic modulus, tensile strength, and fracture strain with the size and strain rate shows important implications in mitigating force fields and ways to enhance the life of electronic devices and nanomaterial conversion via fracture in manufacturing.

Selective amplification of T-cell receptor variable region species is demonstrable but not essential in early lesions of psoriasis vulgaris: analysis by anchored polymerase chain reaction and hypervariable region size spectratyping.

PubMed

Vekony, M A; Holder, J E; Lee, A J; Horrocks, C; Eperon, I C; Camp, R D

1997-07-01

Several groups have investigated the role of T cells in the pathogenesis of psoriasis by determination of T-cell receptor (TCR) B-chain variable (V) region usage, both in chronic plaque (psoriasis vulgaris) and guttate forms, with various results. Because there are no data on TCR expression in early psoriasis vulgaris, when specific cellular immune events may be expected to be most pronounced, we have analyzed early lesions (less than 3 wk old) of ten patients, with highly reproducible results. We have developed a highly controlled anchored polymerase chain reaction (PCR) method in which TCR beta chain species are all amplified with the same primer pair and products are quantified by dot blot hybridization with BV family-specific oligonucleotide probes. Overexpression of certain TCR BV genes was observed in the majority of lesional biopsies, but in samples in which the expanded BV family formed more than 10% of total lesional BV (half of the samples analyzed), BV2 and BV6 predominated. The consistency of overexpression of these BV species between patients was much less than in previous studies of TCRBV usage in established chronic plaque psoriasis lesions. Complementarity-determining region 3 (CDR3) size spectratyping demonstrated evidence for selective clonal T cell accumulation in less than half of the lesional samples showing BV expansion. These results indicate that selective amplification of TCRBV species occurs in early psoriasis vulgaris but is not essential to the pathogenic process and may be more important in the maintenance or expansion of chronic lesions.

Fabrication of mesoporous metal oxide coated-nanocarbon hybrid materials via a polyol-mediated self-assembly process

NASA Astrophysics Data System (ADS)

Feng, Bingmei; Wang, Huixin; Wang, Dongniu; Yu, Huilong; Chu, Yi; Fang, Hai-Tao

2014-11-01

After clarifying the formation mechanism of a typical metal glycolate precipitate, Ti glycolate, in a polyol-mediated synthesis using acetone as a precipitation medium, we describe a simple template-free approach based on an ethylene glycol-mediated synthesis to fabricate mesoporous metal oxide coated-nanocarbon hybrid materials including TiO2 coated-carbon nanotube (CNT), SnO2 coated-CNT, Cu2O/CuO coated-CNT and TiO2 coated-graphene sheet (GS). In the approach, metal oxide precursors, metal glycolates, were first deposited on CNTs or GSs, and subsequently transformed to the metal oxide coatings by pyrolysis or hydrolysis. By a comparison between the characterization of two TiO2-CNT hybrid materials using carboxylated CNTs and pristine CNTs without carboxyl groups, the driving force for initiating the deposition of metal glycolates on the carboxylated CNTs is confirmed to be the hydrogen bonding between the carboxyl groups and the polymer chains in metal glycolate sols. The electrochemical performances of the mesoporous TiO2 coated-carboxylated CNTs and TiO2-pristine CNT hybrid materials were investigated. The results show that the mesoporous TiO2 coated-carboxylated CNT with a uniform core-shell nanostructure exhibits substantial improvement in the rate performance in comparison with its counterpart from 0.5 C to 100 C because of its higher electronic conductivity and shorter diffusion path for the lithium ion. At the extremely high rate of 100 C, the specific capacity of TiO2 of the former reaches 85 mA h g-1, twice as high as that of the latter.After clarifying the formation mechanism of a typical metal glycolate precipitate, Ti glycolate, in a polyol-mediated synthesis using acetone as a precipitation medium, we describe a simple template-free approach based on an ethylene glycol-mediated synthesis to fabricate mesoporous metal oxide coated-nanocarbon hybrid materials including TiO2 coated-carbon nanotube (CNT), SnO2 coated-CNT, Cu2O/CuO coated-CNT and TiO2 coated-graphene sheet (GS). In the approach, metal oxide precursors, metal glycolates, were first deposited on CNTs or GSs, and subsequently transformed to the metal oxide coatings by pyrolysis or hydrolysis. By a comparison between the characterization of two TiO2-CNT hybrid materials using carboxylated CNTs and pristine CNTs without carboxyl groups, the driving force for initiating the deposition of metal glycolates on the carboxylated CNTs is confirmed to be the hydrogen bonding between the carboxyl groups and the polymer chains in metal glycolate sols. The electrochemical performances of the mesoporous TiO2 coated-carboxylated CNTs and TiO2-pristine CNT hybrid materials were investigated. The results show that the mesoporous TiO2 coated-carboxylated CNT with a uniform core-shell nanostructure exhibits substantial improvement in the rate performance in comparison with its counterpart from 0.5 C to 100 C because of its higher electronic conductivity and shorter diffusion path for the lithium ion. At the extremely high rate of 100 C, the specific capacity of TiO2 of the former reaches 85 mA h g-1, twice as high as that of the latter. Electronic supplementary information (ESI) available. See DOI: 10.1039/C4NR04254A

High-resolution studies of the Majorana atomic chain platform

NASA Astrophysics Data System (ADS)

Feldman, Benjamin E.; Randeria, Mallika T.; Li, Jian; Jeon, Sangjun; Xie, Yonglong; Wang, Zhijun; Drozdov, Ilya K.; Andrei Bernevig, B.; Yazdani, Ali

2017-03-01

Ordered assemblies of magnetic atoms on the surface of conventional superconductors can be used to engineer topological superconducting phases and realize Majorana fermion quasiparticles (MQPs) in a condensed matter setting. Recent experiments have shown that chains of Fe atoms on Pb generically have the required electronic characteristics to form a one-dimensional topological superconductor and have revealed spatially resolved signatures of localized MQPs at the ends of such chains. Here we report higher-resolution measurements of the same atomic chain system performed using a dilution refrigerator scanning tunnelling microscope (STM). With significantly better energy resolution than previous studies, we show that the zero-bias peak (ZBP) in Fe chains has no detectable splitting from hybridization with other states. The measurements also reveal that the ZBP exhibits a distinctive `double eye’ spatial pattern on nanometre length scales. Theoretically we show that this is a general consequence of STM measurements of MQPs with substantial spectral weight in the superconducting substrate, a conclusion further supported by measurements of Pb overlayers deposited on top of the Fe chains. Finally, we report experiments performed with superconducting tips in search of the particle-hole symmetric MQP signature expected in such measurements.

Phase transitions and dielectric properties of a hexagonal ABX3 perovskite-type organic-inorganic hybrid compound: [C3H4NS][CdBr3].

PubMed

Liao, Wei-Qiang; Ye, Heng-Yun; Zhang, Yi; Xiong, Ren-Gen

2015-06-21

A new organic-inorganic hexagonal perovskite-type compound with the formula ABX3, thiazolium tribromocadmate(ii) (1), in which thiazolium cations are situated in the space between the one-dimensional chains of face-sharing CdBr(6) octahedra, has been successfully synthesized. Systematic characterizations including differential scanning calorimetry measurements, variable-temperature structural analyses, and dielectric measurements reveal that it undergoes two structural phase transitions, at 180 and 146 K. These phase transitions are accompanied by remarkable dielectric relaxation and anisotropy. The thiazolium cations remain orientationally disordered during the two phase transition processes. The origins of the phase transitions at 180 and 146 K are ascribed to the slowing down and reorientation of the molecular motions of the cations, respectively. Moreover, the dielectric relaxation process well described by the Cole-Cole equation and the prominent dielectric anisotropy are also connected with the dynamics of the dipolar thiazolium cations.

Detection of hepatitis C virus RNA using ligation-dependent polymerase chain reaction in formalin-fixed, paraffin-embedded liver tissues.

PubMed Central

Park, Y. N.; Abe, K.; Li, H.; Hsuih, T.; Thung, S. N.; Zhang, D. Y.

1996-01-01

Reverse transcription polymerase chain reaction (RT-PCR) has been used to detect hepatitis C virus (HCV) sequences in liver tissue. However, RT-PCR has a variable detection sensitivity, especially on routinely processed formalin-fixed, paraffin-embedded (FFPE) specimens. RNA-RNA and RNA-protein cross-links formed during formalin fixation is the major limiting factor preventing reverse trans criptase from extending the primers. To overcome this problem, we applied the ligation-dependent PCR (LD-PCR) for the detection of HCV RNA in FFPE liver tissue. This method uses two capture probes for RNA isolation and two hemiprobes for the subsequent PCR. Despite cross-links, the capture probes and the hemiprobes are able to form hybrids with HCV RNAs released from the FFPE tissue. The hybrids are isolated through binding of the capture probes to paramagnetic beads. The hemiprobes are then ligated by a T4 DNA ligase to form a full probe that serves as a template for the Taq DNA polymerase. A total of 22 FFPE liver specimens, 21 with hepatocellular carcinoma (HCC) and 1 with biliary cirrhosis secondary to bile duct atresia were selected for this study, of which 13 patients were HCV seropositive and 9 seronegative. HCV RNA was detectable by ID-PCR from all 13 HCV-seropositive HCCs and from 5 of 8 HCV-seronegative HCCs but not from the HCV-seronegative liver with biliary atresia. By contrast, RT-PCR detected HCV sequences in only 5 of the HCV-sero-positive and in 1 of the HCV-seronegative HCCs. To resolve the discordance between the LD-PCR and RT-PCR results, RT-PCR was performed on frozen liver tissue of the discrepant specimens, which confirmed the LD-PCR positive results. In conclusion, LD-PCR is a more sensitive method than RT-PCR for the detection of HCV sequences in routinely processed liver tissues. A high rate of HCV infection (86%) is found in HCC specimens, indicating a previously underestimated role of HCV in HCC pathogenesis. Images Figure 2 PMID:8909238

Hybrid laser arc welding: State-of-art review

NASA Astrophysics Data System (ADS)

Acherjee, Bappa

2018-02-01

Hybrid laser arc welding simultaneously utilizes the arc welding and the laser welding, in a common interaction zone. The synergic effects of laser beam and eclectic arc in the same weld pool results in an increase of welding speed and penetration depth along with the enhancement of gap bridging capability and process stability. This paper presents the current status of this hybrid technique in terms of research, developments and applications. Effort is made to present a comprehensive technical know-how about this process through a systematic review of research articles, industrial catalogues, technical notes, etc. In the introductory part of the review, an overview of the hybrid laser arc welding is presented, including operation principle, process requirements, historical developments, benefits and drawbacks of the process. This is followed by a detailed discussion on control parameters those govern the performance of hybrid laser arc welding process. Thereafter, a report of improvements of performance and weld qualities achieved by using hybrid welding process is presented based on review of several research papers. The succeeding sections furnish the examples of industrial applications and the concluding remarks.

Interaction of both plasmas in CO2 laser-MAG hybrid welding of carbon steel

NASA Astrophysics Data System (ADS)

Kutsuna, Muneharu; Chen, Liang

2003-03-01

Researches and developments of laser and arc hybrid welding has been curried out since in 1978. Especially, CO2 laser and TIG hybrid welding has been studied for increasing the penetration depth and welding speed. Recently laser and MIG/MAG/Plasma hybrid welding processes have been developed and applied to industries. It was recognized as a new welding process that promote the flexibility of the process for increasing the penetration depth, welding speed and allowable joint gap and improving the quality of the welds. In the present work, CO2 Laser-MAG hybrid welding of carbon steel (SM490) was investigated to make clear the phenomenon and characteristics of hybrid welding process comparing with laser welding and MAG process. The effects of many process parameters such as welding current, arc voltage, welding speed, defocusing distance, laser-to-arc distance on penetration depth, bead shape, spatter, arc stability and plasma formation were investigated in the present work. Especially, the interaction of laser plasma and MAG arc plasma was considered by changing the laser to arc distance (=DLA).

Multicolor Luminescence from Conjugates of Genetically Encoded Elastin-like Polymers and Terpyridine-Lanthanides

DOE PAGES

Ghosh, Koushik; Balog, Eva Rose M.; Kahn, Jennifer L.; ...

2015-08-20

Functional hybrid materials with optically active metal-ligand moieties embedded within a polymer matrix have a great potential in (bio)materials science, including applications in light-emitting diode devices. Here, we report a simple strategy to incorporate terpyridine derivatives into the side chains of elastin-like polymers (ELPs). The further binding of trivalent lanthanide ions with the terpyridine ligands generated an array of photoluminescence ranging from the visible to the near-infrared regions. Lastly, as thin films, these ELP-based optical materials also exhibited distinct morphologies that depend upon the temperature of the aqueous solutions from which the hybrid polymers were spin coated or drop cast.

Functionalization of reduced graphene oxide by electroactive polymer for biosensing applications

NASA Astrophysics Data System (ADS)

Nguyen, Le Huy; Dzung Nguyen, Tuan; Hoang Tran, Vinh; Thu Huyen Dang, Thi; Tran, Dai Lam

2014-09-01

A novel biosensing platform was designed by the functionalizing reduced graphene oxide sheets (rGO) with electroactive copolymer juglone. The composite film showed well-defined, stable electroactivity in a biocompatible buffer medium. Square wave voltammetry is used to record the redox signal for DNA hybridization. Current increase upon hybridization (signal-on) evidenced that short DNA target as well as polymerase chain reaction (PCR), so called ‘real sample’ products, related to different lineages of Mycobacterium tuberculosis strain. The signal-on reached ∼40% with 1 nM of short DNA (25 mer) target, while PCR product (Africanum, EAI and Beijing strains) produced a current change of ∼20%.

Polyoxometalate-Based Organic-Inorganic Hybrids as Antitumor Drugs.

PubMed

Fu, Lei; Gao, Hanqin; Yan, Mei; Li, Shouzhu; Li, Xinyu; Dai, Zhifei; Liu, Shaoqin

2015-06-24

Polyoxometalates (POMs) have shown encouraging antitumor activity. However, their cytotoxicity in normal cells and unspecific interactions with biomolecules are two major obstacles that impede the practical applications of POMs in clinical cancer treatment. Derivatization of POMs with more biocompatible organic ligands is expected to cause a synergetic effect and achieve improved bioactivity and biospecificity. Herein, the synthesis of an amphiphilic organic-inorganic hybrid is reported by grafting a long-chain organoalkoxysilane lipid onto a POM. The amphiphilic POM hybrid could spontaneously assemble into the vesicles and exhibits enhanced antitumor activity for human colorectal cancer cell lines (HT29) compared to that of parent POMs. This detailed study reveals that the amphiphilic nature of POM hybrids enables the as-formed vesicles to easily bind to the cell membranes and then be uptaken by the cells, thus leading to a substantial increase in antitumor activity. Such prominent antitumor action is mostly accomplished via cell apoptosis, which ultimately results in cell death. Our finding demonstrates that novel POM hybrids-based drugs with increased bioactivity could be obtained by decorating POMs with selective organic ligands. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The efficacy of chimeric vaccines constructed with PEP-1 and Ii-Key linking to a hybrid epitope from heterologous viruses.

PubMed

Liu, Xue-lan; Shan, Wen-jie; Xu, Shan-shan; Zhang, Jin-jing; Xu, Fa-zhi; Xia, Sheng-lin; Dai, Yin

2015-09-01

The heterologous epitope-peptide from different viruses may represent an attractive candidate vaccine. In order to evaluate the role of cell-permeable peptide (PEP-1) and Ii-Key moiety from the invariant chain (Ii) of MHC on the heterologous peptide chimeras, we linked the two vehicles to hybrid epitopes on the VP2 protein (aa197-209) of the infectious bursal disease virus and HN protein (aa345-353) of the Newcastle disease virus. The chimeric vaccines were prepared and injected into mice. The immune effects were measured by indirect ELISA. The results showed that the vehicle(s) could significantly boost immune effects against the heterologous epitope peptide. The Ii-Key-only carrier induced more effective immunological responses, compared with the PEP-1 and Ii-Key hybrid vehicle. The carrier-peptide hybrids all showed strong colocalization with major histocompatibility complex (MHC) class II molecules compared with the epitope-peptide (weakly-binding) after co-transfection into 293T cells. Together, our results lay the groundwork for designing new hybrid vaccines based on Ii-Key and/or PEP-1 peptides. Copyright © 2015 The International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

Optimization of Location–Routing Problem for Cold Chain Logistics Considering Carbon Footprint

PubMed Central

Wang, Songyi; Tao, Fengming; Shi, Yuhe

2018-01-01

In order to solve the optimization problem of logistics distribution system for fresh food, this paper provides a low-carbon and environmental protection point of view, based on the characteristics of perishable products, and combines with the overall optimization idea of cold chain logistics distribution network, where the green and low-carbon location–routing problem (LRP) model in cold chain logistics is developed with the minimum total costs as the objective function, which includes carbon emission costs. A hybrid genetic algorithm with heuristic rules is designed to solve the model, and an example is used to verify the effectiveness of the algorithm. Furthermore, the simulation results obtained by a practical numerical example show the applicability of the model while provide green and environmentally friendly location-distribution schemes for the cold chain logistics enterprise. Finally, carbon tax policies are introduced to analyze the impact of carbon tax on the total costs and carbon emissions, which proves that carbon tax policy can effectively reduce carbon dioxide emissions in cold chain logistics network. PMID:29316639

Surface functionalization of quantum dots with fine-structured pH-sensitive phospholipid polymer chains.

PubMed

Liu, Yihua; Inoue, Yuuki; Ishihara, Kazuhiko

2015-11-01

To add novel functionality to quantum dots (QDs), we synthesized water-soluble and pH-responsive block-type polymers by reversible addition-fragmentation chain transfer (RAFT) polymerization. The polymers were composed of cytocompatible 2-methacryloyloxyethyl phosphorylcholine (MPC) polymer segments, which contain a small fraction of active ester groups and can be used to conjugate biologically active compounds to the polymer, and pH-responsive poly(2-(N,N-diethylamino) ethyl methacrylate (DEAEMA)) segments. One terminal of the polymer chain had a hydrophobic alkyl group that originated from the RAFT initiator. This hydrophobic group can bind to the hydrophobic layer on the QD surface. A fluorescent dye was conjugated to the polymer chains via the active ester group. The block-type polymers have an amphiphilic nature in aqueous medium. The polymers were thus easily bound to the QD surface upon evaporation of the solvent from a solution containing the block-type polymer and QDs, yielding QD/fluorescence dye-conjugated polymer hybrid nanoparticles. Fluorescence resonance energy transfer (FRET) between the QDs (donors) and the fluorescent dye molecules (acceptors) was used to obtain information on the conformational dynamics of the immobilized polymers. Higher FRET efficiency of the QD/fluorescent dye-conjugated polymer hybrid nanoparticles was observed at pH 7.4 as compared to pH 5.0 due to a stretching-shrinking conformational motion of the poly(DEAEMA) segments in response to changes in pH. We concluded that the block-type MPC polymer-modified nanoparticles could be used to evaluate the pH of cells via FRET fluorescence based on the cytocompatibility of the MPC polymer. Copyright © 2015 Elsevier B.V. All rights reserved.

Genes encoding Xenopus laevis Ig L chains: Implications for the evolution of [kappa] and [lambda] chains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zezza, D.J.; Stewart, S.E.; Steiner, L.A.

1992-12-15

Xenopus laevis Ig contain two distinct types of L chains, designated [rho] or L1 and [sigma] or L2. The authors have analyzed Xenopus genomic DNA by Southern blotting with cDNA probes specific for L1 V and C regions. Many fragments hybridized to the V probe, but only one or two fragments hybridized to the C probe. Corresponding C, J, and V gene segments were identified on clones isolated from a genomic library prepared from the same DNA. One clone contains a C gene segment separated from a J gene segment by an intron of 3.4 kb. The J and Cmore » gene segments are nearly identical in sequence to cDNA clones analyzed previously. The C segment is somewhat more similar and the J segment considerably more similar in sequence to the corresponding segments of mammalian [kappa] chains than to those of mammalian [lambda] chains. Upstream of the J segment is a typical recombination signal sequence with a spacer of 23 bp, as in J[kappa]. A second clone from the library contains four V gene segments, separated by 2.1 to 3.6 kb. Two of these, V1 and V3, have the expected structural and regulatory features of V genes, and are very similar in sequence to each other and to mammalian V[kappa]. A third gene segment, V2, resembles V1 and V3 in its coding region and nearby 5[prime]-flanking region, but diverges in sequence 5[prime] to position [minus]95 with loss of the octamer promoter element. The fourth V-like segment is similar to the others at the 3[prime]-end, but upstream of codon 64 bears no resemblance in sequence to any Ig V region. All four V segments have typical recombination signal sequences with 12-bp spacers at their 3[prime]-ends, as in V[kappa]. Taken together, the data suggest that Xenopus L1 L chain genes are members of the [kappa] gene family. 80 refs., 9 figs.« less

Hybrid lattice gas simulations of flow through porous media

NASA Astrophysics Data System (ADS)

Becklehimer, Jeffrey Lynn

1997-10-01

This study introduces a suite of models designed to investigate transport phenomena in simulated porous media such as rigid or quenched sediment and clay-like deformable environments. This is achieved by using a variety of techniques that are borrowed from the field of statistical physics. These techniques include percolation, lattice gas, and cellular automata. A percolation-based model is used to study a porous medium by using rods and chains of various shapes and sizes to model the porous media formed by sediments. This is further extended to model clay-like deformable media by interacting heavy sediment particles. An interacting lattice gas computer simulation model based on the Metropolis algorithm is used to study the transport properties of fluid particles and permeability of a porous sediment. Finally, a hybrid lattice gas model is introduced by combining the Metropolis Monte Carlo method with a direct simulation which involves the collision rules as in cellular automata. This model is then used to study shock propagation in a fluid filled porous medium. This study is then extended to study shock propagation through in a fluid filled elastic porous medium. Several interesting and new results were obtained. These results show that for rigid chain percolation the percolation threshold shows a dependence on the chain length of pc~ Lc-1/2 and the jamming coverage decreases with the chain length as Lc- 1/3. For the random SAW-like chains the percolation threshold decays with the chain length as Lc- 0.01 and the jamming coverage as Lc-1/3. The fluid flow model shows that permeability depends nonmonotonically on the concentration of the fluid. For some fluids at a fixed porosity, the permeability increases on increasing the bias until a certain value Bc above which it decreases. Also, it was found that a shock propagates in a drift-like fashion when in a rigid porous medium when the porosity is high; low porosity damps out the shock front very quickly. For a shock propagating in a clay-like porous medium an unusually super-fast power-law behavior is observed for the RMS displacements of the fluid and clay particles.

Fabricating a hybrid imaging device

NASA Technical Reports Server (NTRS)

Wadsworth, Mark (Inventor); Atlas, Gene (Inventor)

2003-01-01

A hybrid detector or imager includes two substrates fabricated under incompatible processes. An array of detectors, such as charged-coupled devices, are formed on the first substrate using a CCD fabrication process, such as a buried channel or peristaltic process. One or more charge-converting amplifiers are formed on a second substrate using a CMOS fabrication process. The two substrates are then bonded together to form a hybrid detector.

Bayesian inversion of seismic and electromagnetic data for marine gas reservoir characterization using multi-chain Markov chain Monte Carlo sampling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ren, Huiying; Ray, Jaideep; Hou, Zhangshuan

In this study we developed an efficient Bayesian inversion framework for interpreting marine seismic amplitude versus angle (AVA) and controlled source electromagnetic (CSEM) data for marine reservoir characterization. The framework uses a multi-chain Markov-chain Monte Carlo (MCMC) sampler, which is a hybrid of DiffeRential Evolution Adaptive Metropolis (DREAM) and Adaptive Metropolis (AM) samplers. The inversion framework is tested by estimating reservoir-fluid saturations and porosity based on marine seismic and CSEM data. The multi-chain MCMC is scalable in terms of the number of chains, and is useful for computationally demanding Bayesian model calibration in scientific and engineering problems. As a demonstration,more » the approach is used to efficiently and accurately estimate the porosity and saturations in a representative layered synthetic reservoir. The results indicate that the seismic AVA and CSEM joint inversion provides better estimation of reservoir saturations than the seismic AVA-only inversion, especially for the parameters in deep layers. The performance of the inversion approach for various levels of noise in observational data was evaluated – reasonable estimates can be obtained with noise levels up to 25%. Sampling efficiency due to the use of multiple chains was also checked and was found to have almost linear scalability.« less

Influence of shielding gas pressure on welding characteristics in CO2 laser-MIG hybrid welding process

NASA Astrophysics Data System (ADS)

Chen, Yanbin; Lei, Zhenglong; Li, Liqun; Wu, Lin

2006-01-01

The droplet transfer behavior and weld characteristics have been investigated under different pressures of shielding gas in CO2 laser and metal inert/active gas (laser-MIG) hybrid welding process. The experimental results indicate that the inherent droplet transfer frequency and stable welding range of conventional MIG arc are changed due to the interaction between CO2 laser beam and MIG arc in laser-MIG hybrid welding process, and the shielding gas pressure has a crucial effect on welding characteristics. When the pressure of shielding gas is low in comparison with MIG welding, the frequency of droplet transfer decreases, and the droplet transfer becomes unstable in laser-MIG hybrid welding. So the penetration depth decreases, which shows the characteristic of unstable hybrid welding. However, when the pressure of shielding gas increases to a critical value, the hybrid welding characteristic is changed from unstable hybrid welding to stable hybrid welding, and the frequency of droplet transfer and the penetration depth increase significantly.

Influence of electrical and hybrid heating on bread quality during baking.

PubMed

Chhanwal, N; Ezhilarasi, P N; Indrani, D; Anandharamakrishnan, C

2015-07-01

Energy efficiency and product quality are the key factors for any food processing industry. The aim of the study was to develop energy and time efficient baking process. The hybrid heating (Infrared + Electrical) oven was designed and fabricated using two infrared lamps and electric heating coils. The developed oven can be operated in serial or combined heating modes. The standardized baking conditions were 18 min at 220°C to produce the bread from hybrid heating oven. Effect of baking with hybrid heating mode (H-1 and H-2, hybrid oven) on the quality characteristics of bread as against conventional heating mode (C-1, pilot scale oven; C-2, hybrid oven) was studied. The results showed that breads baked in hybrid heating mode (H-2) had higher moisture content (28.87%), higher volume (670 cm(3)), lower crumb firmness value (374.6 g), and overall quality score (67.0) comparable to conventional baking process (68.5). Moreover, bread baked in hybrid heating mode showed 28% reduction in baking time.

Exploring the mechanisms of DNA hybridization on a surface

NASA Astrophysics Data System (ADS)

Schmitt, Terry J.; Rogers, J. Brandon; Knotts, Thomas A.

2013-01-01

DNA microarrays are a potentially disruptive technology in the medical field, but their use in such settings is limited by poor reliability. Microarrays work on the principle of hybridization and can only be as reliable as this process is robust, yet little is known at the molecular level about how the surface affects the hybridization process. This work uses advanced molecular simulation techniques and an experimentally parameterized coarse-grain model to determine the mechanism by which hybridization occurs on surfaces. The results show that hybridization proceeds through a mechanism where the untethered (target) strand often flips orientation. For evenly lengthed strands, the surface stabilizes hybridization (compared to the bulk system) by reducing the barriers involved in the flipping event. For unevenly lengthed strands, the surface destabilizes hybridization compared to the bulk, but the degree of destabilization is dependent on the location of the matching sequence. Taken as a whole, the results offer an unprecedented view into the hybridization process on surfaces and provide some insights as to the poor reproducibility exhibited by microarrays.

Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees.

PubMed

Zhu, Sha; Degnan, James H; Goldstien, Sharyn J; Eldon, Bjarki

2015-09-15

There has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously. Hybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingman's coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the F ST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes. Hybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.

Synthesis of hybrid cellulose nanocomposite bonded with dopamine SiO2/TiO2 and its antimicrobial activity

NASA Astrophysics Data System (ADS)

Ramesh, Sivalingam; Kim, Gwang-Hoon; Kim, Jaehwan; Kim, Joo-Hyung

2015-04-01

Organic-inorganic hybrid material based cellulose was synthesized by the sol-gel approach. The explosion of activity in this area in the past decade has made tremendous progress in industry or academic both fundamental understanding of sol-gel process and applications of new functionalized hybrid materials. In this present research work, we focused on cellulose-dopamine functionalized SiO2/TiO2 hybrid nanocomposite by sol-gel process. The cellulose-dopamine hybrid nanocomposite was synthesized via γ-aminopropyltriethoxysilane (γ-APTES) coupling agent by in-situ sol-gel process. The chemical structure of cellulose-amine functionalized dopamine bonding to cellulose structure with covalent cross linking hybrids was confirmed by FTIR spectral analysis. The morphological analysis of cellulose-dopamine nanoSiO2/TiO2 hybrid nanocomposite materials was characterized by XRD, SEM and TEM. From this different analysis results indicate that the optical transparency, thermal stability, control morphology of cellulose-dopamine-SiO2/TiO2 hybrid nanocomposite. Furthermore cellulose-dopamine-SiO2/TiO2 hybrid nanocomposite was tested against pathogenic bacteria for antimicrobial activity.

Bayesian inversion of seismic and electromagnetic data for marine gas reservoir characterization using multi-chain Markov chain Monte Carlo sampling

DOE PAGES

Ren, Huiying; Ray, Jaideep; Hou, Zhangshuan; ...

2017-10-17

In this paper we developed an efficient Bayesian inversion framework for interpreting marine seismic Amplitude Versus Angle and Controlled-Source Electromagnetic data for marine reservoir characterization. The framework uses a multi-chain Markov-chain Monte Carlo sampler, which is a hybrid of DiffeRential Evolution Adaptive Metropolis and Adaptive Metropolis samplers. The inversion framework is tested by estimating reservoir-fluid saturations and porosity based on marine seismic and Controlled-Source Electromagnetic data. The multi-chain Markov-chain Monte Carlo is scalable in terms of the number of chains, and is useful for computationally demanding Bayesian model calibration in scientific and engineering problems. As a demonstration, the approach ismore » used to efficiently and accurately estimate the porosity and saturations in a representative layered synthetic reservoir. The results indicate that the seismic Amplitude Versus Angle and Controlled-Source Electromagnetic joint inversion provides better estimation of reservoir saturations than the seismic Amplitude Versus Angle only inversion, especially for the parameters in deep layers. The performance of the inversion approach for various levels of noise in observational data was evaluated — reasonable estimates can be obtained with noise levels up to 25%. Sampling efficiency due to the use of multiple chains was also checked and was found to have almost linear scalability.« less

Bayesian inversion of seismic and electromagnetic data for marine gas reservoir characterization using multi-chain Markov chain Monte Carlo sampling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ren, Huiying; Ray, Jaideep; Hou, Zhangshuan

In this paper we developed an efficient Bayesian inversion framework for interpreting marine seismic Amplitude Versus Angle and Controlled-Source Electromagnetic data for marine reservoir characterization. The framework uses a multi-chain Markov-chain Monte Carlo sampler, which is a hybrid of DiffeRential Evolution Adaptive Metropolis and Adaptive Metropolis samplers. The inversion framework is tested by estimating reservoir-fluid saturations and porosity based on marine seismic and Controlled-Source Electromagnetic data. The multi-chain Markov-chain Monte Carlo is scalable in terms of the number of chains, and is useful for computationally demanding Bayesian model calibration in scientific and engineering problems. As a demonstration, the approach ismore » used to efficiently and accurately estimate the porosity and saturations in a representative layered synthetic reservoir. The results indicate that the seismic Amplitude Versus Angle and Controlled-Source Electromagnetic joint inversion provides better estimation of reservoir saturations than the seismic Amplitude Versus Angle only inversion, especially for the parameters in deep layers. The performance of the inversion approach for various levels of noise in observational data was evaluated — reasonable estimates can be obtained with noise levels up to 25%. Sampling efficiency due to the use of multiple chains was also checked and was found to have almost linear scalability.« less

Effect of hybrid, maturity, and mechanical processing of corn silage on intake and digestibility by beef cattle.

PubMed

Andrae, J G; Hunt, C W; Pritchard, G T; Kennington, L R; Harrison, J H; Kezar, W; Mahanna, W

2001-09-01

A study involving a 2 x 2 x 2 factorial arrangement of treatments was conducted to evaluate effects of hybrid (Pioneer 3335 and 3489), maturity (half milkline and blacklayer), and mechanical processing (field chopper with and without on-board rollers engaged) on intake and digestibility of corn silage. Forty Angus steers (322 +/- 5.2 kg BW) were assigned to the eight silage treatments (five steers per treatment) and individually fed using electronic gates. Diets consisted of 60% corn silage and 40% chopped alfalfa hay (DM basis). Following a 5-d adaptation period, intake was measured for 7 d and subsequently fecal samples were collected for 5 d. Chromic oxide (5 g/d) was fed beginning 7 d before fecal sample collection and digestibility was determined by the ratio of Cr in the feed and feces. Steers were reallocated to treatments and these procedures were repeated, providing 10 observations per treatment. In addition, all silages were ruminally incubated in six mature cows for 0, 8, 16, 24, 48, and 96 h to determine extent and rate of DM, starch, NDF, and ADF disappearance. Processing increased DMI of hybrid 3489 but did not affect DMI of hybrid 3335 (hybrid x processing; P < 0.06). Total tract digestibility of DM, starch, NDF, and ADF decreased (P < 0.01) as plant maturity increased. Maturity tended to decrease starch digestibility more for hybrid 3489 than for hybrid 3335 (hybrid x maturity; P < 0.10). Processing increased (P < 0.01) starch digestibility but decreased (P < 0.01) NDF and ADF digestibility, resulting in no processing effect on DM digestibility. There was a numerical trend for processing to increase starch digestibility more for latethan for early-maturity corn silage (maturity x processing; P = 0.11). Processing increased in situ rates of DM and starch disappearance and maturity decreased in situ disappearance rates of starch and fiber. These data indicate that hybrid, maturity, and processing all affect corn silage digestibility. Mechanical processing of corn silage increased starch digestibility, which may have been associated with the observed decreased fiber digestibility.

Economic Evaluation of a Hybrid Desalination System Combining Forward and Reverse Osmosis

PubMed Central

Choi, Yongjun; Cho, Hyeongrak; Shin, Yonghyun; Jang, Yongsun; Lee, Sangho

2015-01-01

This study seeks to evaluate the performance and economic feasibility of the forward osmosis (FO)–reverse osmosis (RO) hybrid process; to propose a guideline by which this hybrid process might be more price-competitive in the field. A solution-diffusion model modified with film theory was applied to analyze the effects of concentration polarization, water, and salt transport coefficient on flux, recovery, seawater concentration, and treated wastewater of the FO process of an FO-RO hybrid system. A simple cost model was applied to analyze the effects of flux; recovery of the FO process; energy; and membrane cost on the FO-RO hybrid process. The simulation results showed that the water transport coefficient and internal concentration polarization resistance are very important factors that affect performance in the FO process; however; the effect of the salt transport coefficient does not seem to be large. It was also found that the flux and recovery of the FO process, the FO membrane, and the electricity cost are very important factors that influence the water cost of an FO-RO hybrid system. This hybrid system can be price-competitive with RO systems when its recovery rate is very high, the flux and the membrane cost of the FO are similar to those of the RO, and the electricity cost is expensive. The most important thing in commercializing the FO process is enhancing performance (e.g.; flux and the recovery of FO membranes). PMID:26729176

Structure and optical properties of several organic-inorganic hybrids containing corner-sharing chains of bismuth iodide octahedra.

PubMed

Mitzi, D B; Brock, P

2001-04-23

Two organic-inorganic bismuth iodides of the form (H3N-R-NH3)BiI5 are reported, each containing long and relatively flexible organic groups, R. The norganic framework in each case consists of distorted BiI6 octahedra sharing cis vertexes to form zigzag chains. Crystals of (H3NC18H24S2NH3)BiI5 were grown from a slowly cooled ethylene glycol/2-butanol solution containing bismuth(III) iodide and AETH.2HI, where AETH = 1,6-bis[5'-(2' '-aminoethyl)-2'-thienyl]hexane. The new compound, (H2AETH)BiI5, adopts an orthorhombic (Aba2) cell with the lattice parameters a = 20.427(3) A, b = 35.078(5) A, c = 8.559(1) A, and Z = 8. The structure consists of corrugated layers of BiI5(2-) chains, with Bi-I bond lengths ranging from 2.942(3) to 3.233(3) A, separated by layers of the organic (H2AETH)(2+) cations. Crystals of the analogous (H3NC12H24NH3)BiI5 compound were also prepared from a concentrated aqueous hydriodic acid solution containing bismuth(III) iodide and the 1,12-dodecanediamine (DDDA) salt, DDDA.2HI. (H2DDDA)BiI5 crystallizes in an orthorhombic (Ibam) cell with a = 17.226(2) A, b = 34.277(4) A, c = 8.654(1) A, and Z = 8. The Bi-I bonds range in length from 2.929(1) to 3.271(1) A. While the inorganic chain structure is nearly identical for the two title compounds, as well as for the previously reported (H3NC6H12NH3)BiI5 [i.e., (H2DAH)BiI5] structure, the packing of the chains is strongly influenced by the choice of organic cation. Optical absorption spectra for thermally ablated thin films of the three organic-inorganic hybrids containing BiI5(2-) chains are reported as a function of temperature (25-290 K). The dominant long-wavelength feature in each case is attributed to an exciton band, which is apparent at room temperature and, despite the similar inorganic chain structure, varies in position from 491 to 541 nm (at 25 K).

Fabricating a hybrid imaging device having non-destructive sense nodes

NASA Technical Reports Server (NTRS)

Wadsworth, Mark (Inventor); Atlas, Gene (Inventor)

2001-01-01

A hybrid detector or imager includes two substrates fabricated under incompatible processes. An array of detectors, such as charged-coupled devices, are formed on the first substrate using a CCD fabrication process, such as a buried channel or peristaltic process. One or more charge-converting amplifiers are formed on a second substrate using a CMOS fabrication process. The two substrates are then bonded together to form a hybrid detector.

Tuning conductivity in boron nanowire by edge geometry

NASA Astrophysics Data System (ADS)

Bhuyan, Prabal Dev; Gupta, Sanjeev K.; Sonvane, Yogesh; Gajjar, P. N.

2018-04-01

In present study, we have investigated electronic and temperature dependent transport properties of carbyne like linear chain and ribbon like zigzag structures of Boron (B) nanowire. The linear chain structure showed higher electric and thermal conductivity, as it is sp-hybridized, than its counterpart ribbon (R) structure. However the conductivity of ribbon structure increases with increases in width due to edge geometry effect. The ribbon (3R) structure showed high electric and thermal conductivity of 8.0×1019 1/Ω m s and 0.59×1015 W/ m K respectively. Interestingly we have observed that B linear chain showed higher thermal conductivity of 0.23×1015 W/ m K than its ribbon R and 2R structure above 600K. Because of high Seebeck co-efficient of boron chain and ribbon (R) structures at low temperature, they could find applications in thermoelectric sensors. Our results show that tuning conductivity property of boron nanowire could be of great interest in research for future electric connector in nanodevices.

On-chip synthesis of fine-tuned bone-seeking hybrid nanoparticles.

PubMed

Hasani-Sadrabadi, Mohammad Mahdi; Dashtimoghadam, Erfan; Bahlakeh, Ghasem; Majedi, Fatemeh S; Keshvari, Hamid; Van Dersarl, Jules J; Bertsch, Arnaud; Panahifar, Arash; Renaud, Philippe; Tayebi, Lobat; Mahmoudi, Morteza; Jacob, Karl I

2015-01-01

Here we report a one-step approach for reproducible synthesis of finely tuned targeting multifunctional hybrid nanoparticles (HNPs). A microfluidic-assisted method was employed for controlled nanoprecipitation of bisphosphonate-conjugated poly(D,L-lactide-co-glycolide) chains, while coencapsulating superparamagnetic iron oxide nanoparticles and the anticancer drug Paclitaxel. Smaller and more compact HNPs with narrower size distribution and higher drug loading were obtained at microfluidic rapid mixing regimen compared with the conventional bulk method. The HNPs were shown to have a strong affinity for hydroxyapatite, as demonstrated in vitro bone-binding assay, which was further supported by molecular dynamics simulation results. In vivo proof of concept study verified the prolonged circulation of targeted microfluidic HNPs. Biodistribution as well as noninvasive bioimaging experiments showed high tumor localization and suppression of targeted HNPs to the bone metastatic tumor. The hybrid bone-targeting nanoparticles with adjustable characteristics can be considered as promising nanoplatforms for various theragnostic applications.

Product demand forecasts using wavelet kernel support vector machine and particle swarm optimization in manufacture system

NASA Astrophysics Data System (ADS)

Wu, Qi

2010-03-01

Demand forecasts play a crucial role in supply chain management. The future demand for a certain product is the basis for the respective replenishment systems. Aiming at demand series with small samples, seasonal character, nonlinearity, randomicity and fuzziness, the existing support vector kernel does not approach the random curve of the sales time series in the space (quadratic continuous integral space). In this paper, we present a hybrid intelligent system combining the wavelet kernel support vector machine and particle swarm optimization for demand forecasting. The results of application in car sale series forecasting show that the forecasting approach based on the hybrid PSOWv-SVM model is effective and feasible, the comparison between the method proposed in this paper and other ones is also given, which proves that this method is, for the discussed example, better than hybrid PSOv-SVM and other traditional methods.

A new microcolumn-type microchip for examining the expression of chimeric fusion genes using a nucleic acid sandwich hybridization technique.

PubMed

Ohnishi, Michihiro; Sasaki, Naoyuki; Kishimoto, Takuya; Watanabe, Hidetoshi; Takagi, Masatoshi; Mizutani, Shuki; Kishii, Noriyuki; Yasuda, Akio

2014-11-01

We report a new type of microcolumn installed in a microchip. The architecture allows use of a nucleic acid sandwich hybridization technique to detect a messenger RNA (mRNA) chain as a target. Data are presented that demonstrate that the expression of a chimeric fusion gene can be detected. The microcolumn was filled with semi-transparent microbeads made of agarose gel that acted as carriers, allowing increased efficiency of the optical detection of fluorescence from the microcolumn. The hybrid between the target trapped on the microbeads and a probe DNA labeled with a fluorescent dye was detected by measuring the intensity of the fluorescence from the microcolumn directly. These results demonstrate an easy and simple method for determining the expression of chimeric fusion genes with no preamplification. Copyright © 2014 Elsevier B.V. All rights reserved.

Highly fluorescent and morphology-controllable graphene quantum dots-chitosan hybrid xerogels for in vivo imaging and pH-sensitive drug carrier.

PubMed

Lv, Ouyang; Tao, Yongxin; Qin, Yong; Chen, Chuanxiang; Pan, Yan; Deng, Linhong; Liu, Li; Kong, Yong

2016-10-01

Highly fluorescent graphene quantum dots (GQDs)-chitosan (CS) hybrid xerogels (GQDs-CS) were facilely synthesized, and the morphology of GQDs-CS was controllable by varying the content of GQDs in the xerogel. The GQDs-CS exhibited a porous and three-dimensional (3D) network structure when the content of GQDs reached 43% (wt%) in the xerogel, which was beneficial for drug loading and sustained release. The as-prepared GQDs-CS could also be applied for in vivo imaging since it showed strong blue, green and red luminescence under excitation of varying wavelengths. Moreover, the pH-induced protonation/deprotonation of the -NH2 groups on CS chains can result in a pH-dependent drug delivery behavior of the GQDs-CS hybrid xerogel. Copyright © 2016 Elsevier B.V. All rights reserved.

Mixed-Timescale Per-Group Hybrid Precoding for Multiuser Massive MIMO Systems

NASA Astrophysics Data System (ADS)

Teng, Yinglei; Wei, Min; Liu, An; Lau, Vincent; Zhang, Yong

2018-05-01

Considering the expensive radio frequency (RF) chain, huge training overhead and feedback burden issues in massive MIMO, in this letter, we propose a mixed-timescale per-group hybrid precoding (MPHP) scheme under an adaptive partially-connected RF precoding structure (PRPS), where the RF precoder is implemented using an adaptive connection network (ACN) and M analog phase shifters (APSs), where M is the number of antennas at the base station (BS). Exploiting the mixed-time stage channel state information (CSI) structure, the joint-design of ACN and APSs is formulated as a statistical signal-to-leakage-and-noise ratio (SSLNR) maximization problem, and a heuristic group RF precoding (GRFP) algorithm is proposed to provide a near-optimal solution. Simulation results show that the proposed design advances at better energy efficiency (EE) and lower hardware cost, CSI signaling overhead and computational complexity than the conventional hybrid precoding (HP) schemes.

Enzymatic Reaction with Unnatural Substrates: DNA Photolyase (Escherichia coli) Recognizes and Reverses Thymine [2+2] Dimers in the DNA Strand of a DNA/PNA Hybrid Duplex

NASA Astrophysics Data System (ADS)

Ramaiah, Danaboyina; Kan, Yongzhi; Koch, Troels; Orum, Henrik; Schuster, Gary B.

1998-10-01

Peptide nucleic acids (PNA) are mimics with normal bases connected to a pseudopeptide chain that obey Watson--Crick rules to form stable duplexes with itself and natural nucleic acids. This has focused attention on PNA as therapeutic or diagnostic reagents. Duplexes formed with PNA mirror some but not all properties of DNA. One fascinating aspect of PNA biochemistry is their reaction with enzymes. Here we show an enzyme reaction that operates effectively on a PNA/DNA hybrid duplex. A DNA oligonucleotide containing a cis, syn-thymine [2+2] dimer forms a stable duplex with PNA. The hybrid duplex is recognized by photolyase, and irradiation of the complex leads to the repair of the thymine dimer. This finding provides insight into the enzyme mechanism and provides a means for the selective repair of thymine photodimers.

Formation of diploid and triploid hybrid groupers (hybridization of Epinephelus coioides ♀ × Epinephelus lanceolatus ♂) and their 5S gene analysis.

PubMed

Huang, Wen; Qin, Qinbo; Yang, Huirong; Li, Shuisheng; Hu, Chaoqun; Wang, Yude; Zhang, Yong; Liu, Shaojun; Lin, Haoran

2016-10-07

Interspecies hybridization is widely used to achieve heterosis or hybrid vigor, which has been observed and harnessed by breeders for centuries. Natural allopolyploid hybrids generally exhibit more superior heterosis than both the diploid progenies and their parental species. However, polyploid formation processes have been long ignored, the genetic basis of heterosis in polyploids remains elusive. In the present study, triploid hybrids had been demonstrated to contain two sets of chromosomes from mother species and one set from father species. Cellular polyploidization process in the embryos had been traced. The triploid hybrids might be formed by failure formation of the second polarized genome during the second meiosis stage. Four spindle centers were observed in anaphase stage of the first cell division. Three spindle centers were observed in side of cell plate after the first cell division. The 5S rDNA genes of four types of groupers were cloned and analyzed. The diploid and triploid hybrids had been proved to contain the tandem chimera structures which were recombined by maternal and paternal monomer units. The results indicated that genome re-fusion had occurred in the hybrid progenies. To further elucidate the genetic patterns of diploid and triploid hybrids, fluorescence chromosome location had been carried out, maternal 5S gene (M-386) were used as the probe. The triploid hybrids contained fewer fluorescence loci numbers than the maternal species. The results indicated that participation of paternal 5S gene in the triploid hybrid genome had degraded the match rates of M-386 probe. Our study is the first to investigate the cellular formation processes of natural allopolyploids in hybrid fish, the cellular polyploidization process may be caused by failure formation of the second polarized genome during the meiosis, and our results will provide the molecular basis of hybrid vigor in interspecies hybridization.

Programmed self-assembly of DNA/RNA for biomedical applications

NASA Astrophysics Data System (ADS)

Wang, Pengfei

Three self-assembly strategies were utilized for assembly of novel functional DNA/RNA nanostructures. RNA-DNA hybrid origami method was developed to fabricate nano-objects (ribbon, rectangle, and triangle) with precisely controlled geometry. Unlike conventional DNA origami which use long DNA single strand as scaffold, a long RNA single strand was used instead, which was folded by short DNA single strands (staples) into prescribed objects through sequence specific hybridization between RNA and DNA. Single stranded tiles (SST) and RNA-DNA hybrid origami were utilized to fabricate a variety of barcode-like nanostructures with unique patterns by expanding a plain rectangle via introducing spacers (10-bp dsDNA segment) between parallel duplexes. Finally, complex 2D array and 3D polyhedrons with multiple patterns within one structure were assembled from simple DNA motifs. Two demonstrations of biomedical applications of DNA nanotechnology were presented. Firstly, lambda-DNA was used as template to direct the fabrication of multi-component magnetic nanoparticle chains. Nuclear magnetic relaxation (NMR) characterization showed superb magnetic relaxativity of the nanoparticle chains which have large potential to be utilized as MRI contrast agents. Secondly, DNA nanotechnology was introduced into the conformational study of a routinely used catalytic DNAzyme, the RNA-cleaving 10-23 DNAzyme. The relative angle between two flanking duplexes of the catalytic core was determined (94.8°), which shall be able to provide a clue to further understanding of the cleaving mechanism of this DNAzyme from a conformational perspective.

Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing.

PubMed

Shah, Sheel; Lubeck, Eric; Schwarzkopf, Maayan; He, Ting-Fang; Greenbaum, Alon; Sohn, Chang Ho; Lignell, Antti; Choi, Harry M T; Gradinaru, Viviana; Pierce, Niles A; Cai, Long

2016-08-01

Accurate and robust detection of mRNA molecules in thick tissue samples can reveal gene expression patterns in single cells within their native environment. Preserving spatial relationships while accessing the transcriptome of selected cells is a crucial feature for advancing many biological areas - from developmental biology to neuroscience. However, because of the high autofluorescence background of many tissue samples, it is difficult to detect single-molecule fluorescence in situ hybridization (smFISH) signals robustly in opaque thick samples. Here, we draw on principles from the emerging discipline of dynamic nucleic acid nanotechnology to develop a robust method for multi-color, multi-RNA imaging in deep tissues using single-molecule hybridization chain reaction (smHCR). Using this approach, single transcripts can be imaged using epifluorescence, confocal or selective plane illumination microscopy (SPIM) depending on the imaging depth required. We show that smHCR has high sensitivity in detecting mRNAs in cell culture and whole-mount zebrafish embryos, and that combined with SPIM and PACT (passive CLARITY technique) tissue hydrogel embedding and clearing, smHCR can detect single mRNAs deep within thick (0.5 mm) brain slices. By simultaneously achieving ∼20-fold signal amplification and diffraction-limited spatial resolution, smHCR offers a robust and versatile approach for detecting single mRNAs in situ, including in thick tissues where high background undermines the performance of unamplified smFISH. © 2016. Published by The Company of Biologists Ltd.

Quantitative real-time polymerase chain reaction for the verification of genomic imbalances detected by microarray-based comparative genomic hybridization.

PubMed

Yu, Shihui; Kielt, Matthew; Stegner, Andrew L; Kibiryeva, Nataliya; Bittel, Douglas C; Cooley, Linda D

2009-12-01

The American College of Medical Genetics guidelines for microarray analysis for constitutional cytogenetic abnormalities require abnormal or ambiguous results from microarray-based comparative genomic hybridization (aCGH) analysis be confirmed by an alternative method. We employed quantitative real-time polymerase chain reaction (qPCR) technology using SYBR Green I reagents for confirmation of 93 abnormal aCGH results (50 deletions and 43 duplications) and 54 parental samples. A novel qPCR protocol using DNA sequences coding for X-linked lethal diseases in males for designing reference primers was established. Of the 81 sets of test primers used for confirmation of 93 abnormal copy number variants (CNVs) in 80 patients, 71 sets worked after the initial primer design (88%), 9 sets were redesigned once, and 1 set twice because of poor amplification. Fifty-four parental samples were tested using 33 sets of test primers to follow up 34 CNVs in 30 patients. Nineteen CNVs were confirmed as inherited, 13 were negative in both parents, and 2 were inconclusive due to a negative result in a single parent. The qPCR assessment clarified aCGH results in two cases and corrected a fluorescence in situ hybridization result in one case. Our data illustrate that qPCR methodology using SYBR Green I reagents is accurate, highly sensitive, specific, rapid, and cost-effective for verification of chromosomal imbalances detected by aCGH in the clinical setting.

Strategic Co-Location in a Hybrid Process Involving Desalination and Pressure Retarded Osmosis (PRO).

PubMed

Sim, Victor S T; She, Qianhong; Chong, Tzyy Haur; Tang, Chuyang Y; Fane, Anthony G; Krantz, William B

2013-07-04

This paper focuses on a Hybrid Process that uses feed salinity dilution and osmotic power recovery from Pressure Retarded Osmosis (PRO) to achieve higher overall water recovery. This reduces the energy consumption and capital costs of conventional seawater desalination and water reuse processes. The Hybrid Process increases the amount of water recovered from the current 66.7% for conventional seawater desalination and water reuse processes to a potential 80% through the use of reclaimed water brine as an impaired water source. A reduction of up to 23% in energy consumption is projected via the Hybrid Process. The attractiveness is amplified by potential capital cost savings ranging from 8.7%-20% compared to conventional designs of seawater desalination plants. A decision matrix in the form of a customizable scorecard is introduced for evaluating a Hybrid Process based on the importance of land space, capital costs, energy consumption and membrane fouling. This study provides a new perspective, looking at processes not as individual systems but as a whole utilizing strategic co-location to unlock the synergies available in the water-energy nexus for more sustainable desalination.

Proteomic analysis reveals strong mitochondrial involvement in cytoplasmic male sterility of pepper (Capsicum annuum L.).

PubMed

Guo, Jinju; Wang, Peng; Cheng, Qing; Sun, Limin; Wang, Hongyu; Wang, Yutong; Kao, Lina; Li, Yanan; Qiu, Tuoyu; Yang, Wencai; Shen, Huolin

2017-09-25

Although cytoplasmic male sterility (CMS) is widely used for developing pepper hybrids, its molecular mechanism remains unclear. In this study, we used a high-throughput proteomics method called label-free to compare protein abundance across a pepper CMS line (A-line) and its isogenic maintainer line (B-line). Data are available via ProteomeXchange with identifier PXD006104. Approximately 324 differentially abundant protein species were identified and quantified; among which, 47 were up-accumulated and 140 were down-accumulated in the A-line; additionally, 75 and 62 protein species were specifically accumulated in the A-line and B-line, respectively. Protein species involved in pollen exine formation, pyruvate metabolic processes, the tricarboxylic acid cycle, the mitochondrial electron transport chain, and oxidative stress response were observed to be differentially accumulated between A-line and B-line, suggesting their potential roles in the regulation of pepper pollen abortion. Based on our data, we proposed a potential regulatory network for pepper CMS that unifies these processes. Artificial emasculation is a major obstacle in pepper hybrid breeding for its high labor cost and poor seed purity. While the use of cytoplasmic male sterility (CMS) in hybrid system is seriously frustrated because a long time is needed to cultivate male sterility line and its isogenic restore line. Transgenic technology is an effective and rapid method to obtain male sterility lines and its widely application has very important significance in speeding up breeding process in pepper. Although numerous studies have been conducted to select the genes related to male sterility, the molecular mechanism of cytoplasmic male sterility in pepper remains unknown. In this study, we used the high-throughput proteomic method called "label-free", coupled with liquid chromatography-quadrupole mass spectrometry (LC-MS/MS), to perform a novel comparison of expression profiles in a CMS pepper line and its maintainer line. Based on our results, we proposed a potential regulated protein network involved in pollen development as a novel mechanism of pepper CMS. Copyright © 2017. Published by Elsevier B.V.

DNA Hydrogel with Tunable pH-Responsive Properties Produced by Rolling Circle Amplification.

PubMed

Xu, Wanlin; Huang, Yishun; Zhao, Haoran; Li, Pan; Liu, Guoyuan; Li, Jing; Zhu, Chengshen; Tian, Leilei

2017-12-22

Recently, smart DNA hydrogels, which are generally formed by the self-assembly of oligonucleotides or through the cross-linking of oligonucleotide-polymer hybrids, have attracted tremendous attention. However, the difficulties of fabricating DNA hydrogels limit their practical applications. We report herein a novel method for producing pH-responsive hydrogels by rolling circle amplification (RCA). In this method, pH-sensitive cross-linking sites were introduced into the polymeric DNA chains during DNA synthesis. As the DNA sequence can be precisely defined by its template, the properties of such hydrogels can be finely tuned in a very facile way through template design. We have investigated the process of hydrogel formation and pH-responsiveness to provide rationales for functional hydrogel design based on the RCA reaction. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The fate of Helicobacter pylori phagocytized by Acanthamoeba polyphaga demonstrated by fluorescent in situ hybridization and quantitative polymerization chain reaction tests

EPA Science Inventory

Helicobacter pylori able to express green fluorescent protein, as well as an ATCC strain, and a clinical isolate of this pathogen were evaluated for their ability to survive predation by Acanthamoeba polyphaga. Ingestion was evaluated by microscopic observation of the GFP-H. pyl...

Triggered and catalyzed self-assembly of hyperbranched DNA structures for logic operations and homogeneous CRET biosensing of microRNA.

PubMed

Bi, Sai; Yue, Shuzhen; Wu, Qiang; Ye, Jiayan

2016-04-07

Toehold-mediated strand displacement-based nanocircuits are developed by integrating catalytic hairpin assembly (CHA) with hybridization chain reaction (HCR), which achieves self-assembly of hyperbranched DNA structures and is readily utilized as an enzyme-free amplifier for homogeneous CRET detection of microRNA with high sensitivity and selectivity.

USE OF AN IMMOBILIZED/SOLUBLE HYBRID ATRP CATALYST SYSTEM FOR THE PREPARATION OF BLOCK COPOLYMERS, RANDOM COPOLYMERS AND POLYMERS WITH HIGH CHAIN END FUNCTIONALITY. (R829580)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Atomistic simulation of graphene-based polymer nanocomposites

NASA Astrophysics Data System (ADS)

Rissanou, Anastassia N.; Bačová, Petra; Harmandaris, Vagelis

2016-05-01

Polymer/graphene nanostructured systems are hybrid materials which have attracted great attention the last years both for scientific and technological reasons. In the present work atomistic Molecular Dynamics simulations are performed for the study of graphene-based polymer nanocomposites composed of pristine, hydrogenated and carboxylated graphene sheets dispersed in polar (PEO) and nonpolar (PE) short polymer matrices (i.e., matrices containing chains of low molecular weight). Our focus is twofold; the one is the study of the structural and dynamical properties of short polymer chains and the way that they are affected by functionalized graphene sheets while the other is the effect of the polymer matrices on the behavior of graphene sheets.

Synthesis of silica-polymer core-shell nanoparticles by reversible addition-fragmentation chain transfer polymerization.

PubMed

Moraes, John; Ohno, Kohji; Maschmeyer, Thomas; Perrier, Sébastien

2013-10-14

Hybrid nanoparticles hold great promise for a range of applications such as drug-delivery vectors or colloidal crystal self-assemblies. The challenge of preparing highly monodisperse particles for these applications has recently been overcome by using living radical polymerization techniques. In particular, the use of reversible addition-fragmentation chain transfer (RAFT), initiated from silica surfaces, yields well-defined particles from a range of precursor monomers resulting in nanoparticles of tailored sizes that are accessible via the rational selection of polymerization conditions. Furthermore, using RAFT allows post-polymerization modification to afford multifunctional, monodisperse, nanostructures under mild and non-stringent reaction conditions.

Merging high doxorubicin loading with pronounced magnetic response and bio-repellent properties in hybrid drug nanocarriers.

PubMed

Bakandritsos, Aristides; Papagiannopoulos, Aristeidis; Anagnostou, Eleni N; Avgoustakis, Konstantinos; Zboril, Radek; Pispas, Stergios; Tucek, Jiri; Ryukhtin, Vasyl; Bouropoulos, Nikolaos; Kolokithas-Ntoukas, Argiris; Steriotis, Theodore A; Keiderling, Uwe; Winnefeld, Frank

2012-08-06

Hybrid magnetic drug nanocarriers are prepared via a self-assembly process of poly(methacrylic acid)-graft-poly(ethyleneglycol methacrylate) (p(MAA-g-EGMA)) on growing iron oxide nanocrystallites. The nanocarriers successfully merge together bio-repellent properties, pronounced magnetic response, and high loading capacity for the potent anticancer drug doxorubicin (adriamicin), in a manner not observed before in such hybrid colloids. High magnetic responses are accomplished by engineering the size of the magnetic nanocrystallites (∼13.5 nm) following an aqueous single-ferrous precursor route, and through adjustment of the number of cores in each colloidal assembly. Complementing conventional magnetometry, the magnetic response of the nanocarriers is evaluated by magnetophoretic experiments providing insight into their internal organization and on their response to magnetic manipulation. The structural organization of the graft-copolymer, locked on the surface of the nanocrystallites, is further probed by small-angle neutron scattering on single-core colloids. Analysis showed that the MAA segments selectively populate the area around the magnetic nanocrystallites, while the poly(ethylene glycol)-grafted chains are arranged as protrusions, pointing towards the aqueous environment. These nanocarriers are screened at various pHs and in highly salted media by light scattering and electrokinetic measurements. According to the results, their stability is dramatically enhanced, as compared to uncoated nanocrystallites, owing to the presence of the external protective PEG canopy. The nanocarriers are also endowed with bio-repellent properties, as evidenced by stability assays using human blood plasma as the medium. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A thermochemical-biochemical hybrid processing of lignocellulosic biomass for producing fuels and chemicals.

PubMed

Shen, Yanwen; Jarboe, Laura; Brown, Robert; Wen, Zhiyou

2015-12-01

Thermochemical-biological hybrid processing uses thermochemical decomposition of lignocellulosic biomass to produce a variety of intermediate compounds that can be converted into fuels and chemicals through microbial fermentation. It represents a unique opportunity for biomass conversion as it mitigates some of the deficiencies of conventional biochemical (pretreatment-hydrolysis-fermentation) and thermochemical (pyrolysis or gasification) processing. Thermochemical-biological hybrid processing includes two pathways: (i) pyrolysis/pyrolytic substrate fermentation, and (ii) gasification/syngas fermentation. This paper provides a comprehensive review of these two hybrid processing pathways, including the characteristics of fermentative substrates produced in the thermochemical stage and microbial utilization of these compounds in the fermentation stage. The current challenges of these two biomass conversion pathways include toxicity of the crude pyrolytic substrates, the inhibition of raw syngas contaminants, and the mass-transfer limitations in syngas fermentation. Possible approaches for mitigating substrate toxicities are discussed. The review also provides a summary of the current efforts to commercialize hybrid processing. Copyright © 2015 Elsevier Inc. All rights reserved.

A Three-State System Based on Branched DNA Hybrids.

PubMed

He, Shiliang; Richert, Clemens

2018-03-26

There is a need for materials that respond to chemical or physical stimuli through a change in their structure. While a transition between water-soluble form and solid is not uncommon for DNA-based structures, systems that transition between three different states at room temperature and ambient pressure are rare. Here we report the preparation of branched DNA hybrids with eight oligodeoxycytidylate arms via solution-phase, H-phosphonate-based synthesis. Some hybrids assemble into hydrogels upon lowering the pH, acting as efficient gelators at pH 4-6, but can also transition into a more condensed solid state form upon exposure to divalent cations. Together with the homogeneous solutions that the i-motif-forming compounds give at neutral pH, three-state systems result. Each state has its own color, if chromophores are included in the system. The assembly and gelation properties can be tuned by choosing the chain length of the arms. Their responsive properties make the dC-rich DNA hybrids candidates for smart material applications. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Short Communication Quick method for identifying horse (Equus caballus) and donkey (Equus asinus) hybrids.

PubMed

Franco, M M; Santos, J B F; Mendonça, A S; Silva, T C F; Antunes, R C; Melo, E O

2016-09-23

The domestication of the Equus genus 5000-6000 years ago has influenced the history of human civilization. As soon as horse and donkey species had been domesticated, they were crossbred, producing humanity's first documented attempt at animal genome manipulation. Since then, the mule (male donkey x female horse) and the reciprocal cross (the hinny, male horse x female donkey) have been the most common equine hybrids in the world. Due to their hybrid vigor, mules and hinnies have been intensively used for carrying loads and people and for tilling the land. Despite their importance, visual distinction of mules and hinnies is difficult due to high phenotypic resemblance. However, the distinction between these two hybrids is of pivotal importance for equid breeders and ranchers. In this study, an easy, low-cost, effective, and fast multiplex-polymerase chain reaction method was developed to distinguish the maternal origin of mules and hinnies, targeting the hyper-variable mitochondrial DNA D-loop region. This methodology can help breeders, ranchers, animal science professionals, and researchers manage their equine herds with more confidence and precision.

System-wide hybrid MPC-PID control of a continuous pharmaceutical tablet manufacturing process via direct compaction.

PubMed

Singh, Ravendra; Ierapetritou, Marianthi; Ramachandran, Rohit

2013-11-01

The next generation of QbD based pharmaceutical products will be manufactured through continuous processing. This will allow the integration of online/inline monitoring tools, coupled with an efficient advanced model-based feedback control systems, to achieve precise control of process variables, so that the predefined product quality can be achieved consistently. The direct compaction process considered in this study is highly interactive and involves time delays for a number of process variables due to sensor placements, process equipment dimensions, and the flow characteristics of the solid material. A simple feedback regulatory control system (e.g., PI(D)) by itself may not be sufficient to achieve the tight process control that is mandated by regulatory authorities. The process presented herein comprises of coupled dynamics involving slow and fast responses, indicating the requirement of a hybrid control scheme such as a combined MPC-PID control scheme. In this manuscript, an efficient system-wide hybrid control strategy for an integrated continuous pharmaceutical tablet manufacturing process via direct compaction has been designed. The designed control system is a hybrid scheme of MPC-PID control. An effective controller parameter tuning strategy involving an ITAE method coupled with an optimization strategy has been used for tuning of both MPC and PID parameters. The designed hybrid control system has been implemented in a first-principles model-based flowsheet that was simulated in gPROMS (Process System Enterprise). Results demonstrate enhanced performance of critical quality attributes (CQAs) under the hybrid control scheme compared to only PID or MPC control schemes, illustrating the potential of a hybrid control scheme in improving pharmaceutical manufacturing operations. Copyright © 2013 Elsevier B.V. All rights reserved.

In situ hybridization reveals that type I and III collagens are produced by pericytes in the anterior pituitary gland of rats.

PubMed

Fujiwara, Ken; Jindatip, Depicha; Kikuchi, Motoshi; Yashiro, Takashi

2010-12-01

Type I and III collagens widely occur in the rat anterior pituitary gland and are the main components of the extracellular matrix (ECM). Although ECM components possibly play an important role in the function of the anterior pituitary gland, little is known about collagen-producing cells. Type I collagen is a heterotrimer of two α1(I) chains (the product of the col1a1 gene) and one α2(I) chain (the product of the col1a2 gene). Type III collagen is a homotrimer of α1(III) chains (the product of the col3a1 gene). We used in situ hybridization with digoxigenin-labeled cRNA probes to examine the expression of col1a1, col1a2, and col3a1 mRNAs in the pituitary gland of adult rats. mRNA expression for these collagen genes was clearly observed, and cells expressing col1a1, col1a2, and col3a1 mRNA were located around capillaries in the gland. We also investigated the possible double-staining of collagen mRNA and pituitary hormones, S-100 protein (a marker of folliculo-stellate cells), or desmin (a marker of pericytes). Col1a1 and col3a1 mRNA were identified in desmin-immunopositive cells. Thus, only pericytes produce type I and III collagens in the rat anterior pituitary gland.

Conceptual design of distillation-based hybrid separation processes.

PubMed

Skiborowski, Mirko; Harwardt, Andreas; Marquardt, Wolfgang

2013-01-01

Hybrid separation processes combine different separation principles and constitute a promising design option for the separation of complex mixtures. Particularly, the integration of distillation with other unit operations can significantly improve the separation of close-boiling or azeotropic mixtures. Although the design of single-unit operations is well understood and supported by computational methods, the optimal design of flowsheets of hybrid separation processes is still a challenging task. The large number of operational and design degrees of freedom requires a systematic and optimization-based design approach. To this end, a structured approach, the so-called process synthesis framework, is proposed. This article reviews available computational methods for the conceptual design of distillation-based hybrid processes for the separation of liquid mixtures. Open problems are identified that must be addressed to finally establish a structured process synthesis framework for such processes.

Synthesis, characterization and antibacterial activity of hybrid chitosan-cerium oxide nanoparticles: As a bionanomaterials.

PubMed

Senthilkumar, R P; Bhuvaneshwari, V; Ranjithkumar, R; Sathiyavimal, S; Malayaman, V; Chandarshekar, B

2017-11-01

The hybrid chitosan cerium oxide nanoparticles were prepared for the first time by green chemistry approach using plant leaf extract. The intense peak observed around 292nm in the UV-vis spectrum indicate the formation of cerium oxide nanoparticles. The XRD pattern revealed that the hybrid chitosan-cerium oxide nanoparticles have a polycrystalline structure with cubic fluorite phase. The FTIR spectrum of prepared samples showed the formation of Ce-O bonds and chitosan main chains COC and CO. The FESEM image of hybrid chitosan cerium oxide nanoparticles revealed that the particles are spherical in shape with grains size varying from 23.12nm to 89.91nm. EDAX analysis confirmed the presence of Ce, O, C and N elements in the prepared sample. TEM images showed that the prepared hybrid chitosan-cerium oxide nanoparticles are predominantly uniform in size and most of the particles are spherical in shape with less agglomeration and the particles size varies from 3.61nm to 24.40nm. The prepared chitosan cerium oxide nanoparticles of 50μL concentration showed good antibacterial properties against test pathogens, which was confirmed by the FESEM analysis. The prepared small particle size facilitate that these hybrid ChiCO 2 NPs could effectively be used in biomedical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

[Super sweet corn hybrid sh2 adaptability for industrial canning process].

PubMed

Ortiz de Bertorelli, Ligia; De Venanzi, Frank; Alfonzo, Braunnier; Camacho, Candelario

2002-12-01

The super sweet corns Krispy king, Victor and 324 (sh2 hybrids) were evaluated to determine their adaptabilities to the industrial canning process as whole kernels. All these hybrids and Bonanza (control) were sown in San Joaquín (Carabobo, Venezuela), harvested and canned. After 110 days storage at room temperature they were analyzed to be compared physically, chemically and sensorially with Bonanza hybrid. Results did not show significant differences among most of the physical characteristics, except for percentage of broken kernels which was higher in 324 hybrid. Chemical parameters showed significant differences (P < 0.05) comparing each super sweet hybrid with Bonanza. The super sweet hybrids presented a higher sugar content and soluble solid of the brine than Bonanza, also a lower pH. The super sweet whole kernel presented a lower soluble solids content than Bonanza but they were not significant (Krispy king and 324). Appearance, odor and overall quality were the same for super sweet hybrids and Bonanza (su). Color, flavor and sweetness were better for 324 than all the other hybrids. Super sweet hybrids presented a very good adaptation to the canning process, having as an advantage that doesn't require sugar addition in the brine and a very good texture (firm and crispy).

Simultaneous direct detection of Shiga-toxin producing Escherichia coli (STEC) strains by optical biosensing with oligonucleotide-functionalized gold nanoparticles

NASA Astrophysics Data System (ADS)

Quintela, Irwin A.; de Los Reyes, Benildo G.; Lin, Chih-Sheng; Wu, Vivian C. H.

2015-01-01

A simultaneous direct detection of Shiga-toxin producing strains of E. coli (STEC; ``Big Six'' - O26, O45, O103, O111, O121, and O145) as well as O157 strains by optical biosensing with oligonucleotide-functionalized gold nanoparticles (AuNPs) was developed. Initially, conserved regions of stx genes were amplified by asymmetric polymerase chain reaction (asPCR). Pairs of single stranded thiol-modified oligonucleotides (30-mer) were immobilized onto AuNPs and used as probes to capture regions of stx1 (119-bp) and/or stx2 (104-bp) genes from STEC strains. DNA samples from pure cultures and food samples were sandwich hybridized with AuNP-oligo probes at optimal conditions (50 °C, 30 min). A complex was formed from the hybridization of AuNP-probes and target DNA fragments that retained the initial red color of the reaction solutions. For non-target DNA, a color change from red to purplish-blue was observed following an increase in salt concentration, thus providing the basis of simultaneous direct colorimetric detection of target DNA in the samples. Enrichment and pooling systems were incorporated to efficiently process a large number of food samples (ground beef and blueberries) and detection of live targets. The detection limit was <1 log CFU g-1, requiring less than 1 h to complete after DNA sample preparation with 100% specificity. Gel electrophoresis verified AuNP-DNA hybridization while spectrophotometric data and transmission electron microscope (TEM) images supported color discrimination based on the occurrence of molecular aggregation. In conclusion, the significant features of this approach took advantage of the unique colorimetric properties of AuNPs as a low-cost and simple approach yet with high specificity for simultaneous detection of STEC strains.A simultaneous direct detection of Shiga-toxin producing strains of E. coli (STEC; ``Big Six'' - O26, O45, O103, O111, O121, and O145) as well as O157 strains by optical biosensing with oligonucleotide-functionalized gold nanoparticles (AuNPs) was developed. Initially, conserved regions of stx genes were amplified by asymmetric polymerase chain reaction (asPCR). Pairs of single stranded thiol-modified oligonucleotides (30-mer) were immobilized onto AuNPs and used as probes to capture regions of stx1 (119-bp) and/or stx2 (104-bp) genes from STEC strains. DNA samples from pure cultures and food samples were sandwich hybridized with AuNP-oligo probes at optimal conditions (50 °C, 30 min). A complex was formed from the hybridization of AuNP-probes and target DNA fragments that retained the initial red color of the reaction solutions. For non-target DNA, a color change from red to purplish-blue was observed following an increase in salt concentration, thus providing the basis of simultaneous direct colorimetric detection of target DNA in the samples. Enrichment and pooling systems were incorporated to efficiently process a large number of food samples (ground beef and blueberries) and detection of live targets. The detection limit was <1 log CFU g-1, requiring less than 1 h to complete after DNA sample preparation with 100% specificity. Gel electrophoresis verified AuNP-DNA hybridization while spectrophotometric data and transmission electron microscope (TEM) images supported color discrimination based on the occurrence of molecular aggregation. In conclusion, the significant features of this approach took advantage of the unique colorimetric properties of AuNPs as a low-cost and simple approach yet with high specificity for simultaneous detection of STEC strains. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr05869k

Hybrid respiration in the denitrifying mitochondria of Fusarium oxysporum.

PubMed

Takaya, Naoki; Kuwazaki, Seigo; Adachi, Yoshiaki; Suzuki, Sawako; Kikuchi, Tomoko; Nakamura, Hiro; Shiro, Yoshitsugu; Shoun, Hirofumi

2003-04-01

Induction of the mitochondrial nitrate-respiration (denitrification) system of the fungus Fusarium oxysporum requires the supply of low levels of oxygen (O(2)). Here we show that O(2) and nitrate (NO(3)(-)) respiration function simultaneously in the mitochondria of fungal cells incubated under hypoxic, denitrifying conditions in which both O(2) and NO(3)(-) act as the terminal electron acceptors. The NO(3)(-) and nitrite (NO(2)(-)) reductases involved in fungal denitrification share the mitochondrial respiratory chain with cytochrome oxidase. F. oxysporum cytochrome c(549) can serve as an electron donor for both NO(2)(-) reductase and cytochrome oxidase. We are the first to demonstrate hybrid respiration in respiring eukaryotic mitochondria.

Gene encoding the collagen type I and thrombospondin receptor CD36 is located on chromosome 7q11. 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fernandez-Ruiz, E.; Armesilla, A.L.; Sanchez-Madrid, F.

The human CD36 is a member of a gene family of structurally related glycoproteins and functions as a receptor for collagen type I and thrombospondin. CD36 also binds to red blood cells infected with the human malaria parasite Plasmodium falciparum. In the present study, the CD36 gene was assigned to chromosome 7 by using the polymerase chain reaction with DNA from human-hamster somatic cell hybrids. Furthermore, the use of a CD36 genomic probe has allowed the localization of the CD36 locus to the 7q11.2 band by fluorescence in situ hybridization coupled with GTG-banding. 14 refs., 2 figs.

Molecular assessment of collagen denaturation in decellularized tissues using a collagen hybridizing peptide.

PubMed

Hwang, Jeongmin; San, Boi Hoa; Turner, Neill J; White, Lisa J; Faulk, Denver M; Badylak, Stephen F; Li, Yang; Yu, S Michael

2017-04-15

Decellularized extracellular matrix (ECM) derived from tissues and organs are emerging as important scaffold materials for regenerative medicine. Many believe that preservation of the native ECM structure during decellularization is highly desirable. However, because effective techniques to assess the structural damage in ECM are lacking, the disruptive effects of a decellularization method and the impact of the associated structural damage upon the scaffold's regenerative capacity are often debated. Using a novel collagen hybridizing peptide (CHP) that specifically binds to unfolded collagen chains, we investigated the molecular denaturation of collagen in the ECM decellularized by four commonly used cell-removing detergents: sodium dodecyl sulfate (SDS), 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS), sodium deoxycholate (SD), and Triton X-100. Staining of the detergent-treated porcine ligament and urinary bladder matrix with carboxyfluorescein-labeled CHP demonstrated that SDS and Triton X-100 denature the triple helical collagen molecule while CHAPS and SD do not, although second harmonic generation imaging and transmission electron microscopy (TEM) revealed that all four detergents disrupt collagen fibrils. Our findings from the CHP staining were further confirmed by the circular dichroism spectra of intact triple helical collagen molecules in CHAPS and SD solutions, and the TEM images of CHP-conjugated gold nanoparticles binding only to the SDS and Triton X-100 treated collagen fibrils. CHP is a powerful new tool for direct and reliable measurement of denatured collagen molecules in decellularized tissues. It is expected to have wide applications in the development and standardization of the tissue/organ decellularization technology. Preservation of the native ECM structure in decellularized tissues is highly desirable, since denaturation of ECM molecules (e.g., collagen) during decellularization can strongly influence the cellular response. Unfortunately, conventional techniques (SEM, SHG) are not conducive to identifying denatured collagen molecules in tissues. We demonstrate the first investigation into the molecular denaturation of collagen in decellularized ECM enabled by a novel Collagen Hybridizing Peptide (CHP) that specifically binds to unfolded collagen chains. We show that SDS and Triton X-100 denature collagen molecules while CHAPS and SD cannot. Such detection has been nearly impossible with other existing techniques. The CHP technique will advance our understanding about the effect of the cell-removing process on ECM, and lead to development of the decellularization technology. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Molecular assessment of collagen denaturation in decellularized tissues using a collagen hybridizing peptide

PubMed Central

Hwang, Jeongmin; San, Boi Hoa; Turner, Neill J.; White, Lisa J.; Faulk, Denver M.; Badylak, Stephen F.; Li, Yang; Yu, S. Michael

2017-01-01

Decellularized extracellular matrix (ECM) derived from tissues and organs are emerging as important scaffold materials for regenerative medicine. Many believe that preservation of the native ECM structure during decellularization is highly desirable. However, because effective techniques to assess the structural damage in ECM are lacking, the disruptive effects of a decellularization method and the impact of the associated structural damage upon the scaffold’s regenerative capacity are often debated. Using a novel collagen hybridizing peptide (CHP) that specifically binds to unfolded collagen chains, we investigated the molecular denaturation of collagen in the ECM decellularized by four commonly used cellremoving detergents: sodium dodecyl sulfate (SDS), 3-[(3-cholamidopropyl)dimethylammonio]-1-propa nesulfonate (CHAPS), sodium deoxycholate (SD), and Triton X-100. Staining of the detergent-treated porcine ligament and urinary bladder matrix with carboxyfluorescein-labeled CHP demonstrated that SDS and Triton X-100 denature the triple helical collagen molecule while CHAPS and SD do not, although second harmonic generation imaging and transmission electron microscopy (TEM) revealed that all four detergents disrupt collagen fibrils. Our findings from the CHP staining were further confirmed by the circular dichroism spectra of intact triple helical collagen molecules in CHAPS and SD solutions, and the TEM images of CHP-conjugated gold nanoparticles binding only to the SDS and Triton X-100 treated collagen fibrils. CHP is a powerful new tool for direct and reliable measurement of denatured collagen molecules in decellularized tissues. It is expected to have wide applications in the development and standardization of the tissue/organ decellularization technology. Statement of Significance Preservation of the native ECM structure in decellularized tissues is highly desirable, since denaturation of ECM molecules (e.g., collagen) during decellularization can strongly influence the cellular response. Unfortunately, conventional techniques (SEM, SHG) are not conducive to identifying denatured collagen molecules in tissues. We demonstrate the first investigation into the molecular denaturation of collagen in decellularized ECM enabled by a novel Collagen Hybridizing Peptide (CHP) that specifically binds to unfolded collagen chains. We show that SDS and Triton X-100 denature collagen molecules while CHAPS and SD cannot. Such detection has been nearly impossible with other existing techniques. The CHP technique will advance our understanding about the effect of the cell-removing process on ECM, and lead to development of the decellularization technology. PMID:28161576

Comparison of global brain gene expression profiles between inbred long-sleep and inbred short-sleep mice by high-density gene array hybridization.

PubMed

Xu, Y; Ehringer, M; Yang, F; Sikela, J M

2001-06-01

Inbred long-sleep (ILS) and short-sleep (ISS) mice show significant central nervous system-mediated differences in sleep time for sedative dose of ethanol and are frequently used as a rodent model for ethanol sensitivity. In this study, we have used complementary DNA (cDNA) array hybridization methodology to identify genes that are differentially expressed between the brains of ILS and ISS mice. To carry out this analysis, we used both the gene discovery array (GDA) and the Mouse GEM 1 Microarray. GDA consists of 18,378 nonredundant mouse cDNA clones on a single nylon filter. Complex probes were prepared from total brain mRNA of ILS or ISS mice by using reverse transcription and 33P labeling. The labeled probes were hybridized in parallel to the gene array filters. Data from GDA experiments were analyzed with SQL-Plus and Oracle 8. The GEM microarray includes 8,730 sequence-verified clones on a glass chip. Two fluorescently labeled probes were used to hybridize a microarray simultaneously. Data from GEM experiments were analyzed by using the GEMTools software package (Incyte). Differentially expressed genes identified from each method were confirmed by relative quantitative reverse transcription-polymerase chain reaction (RT-PCR). A total of 41 genes or expressed sequence tags (ESTs) display significant expression level differences between brains of ILS and ISS mice after GDA, GEM1 hybridization, and quantitative RT-PCR confirmation. Among them, 18 clones were expressed higher in ILS mice, and 23 clones were expressed higher in ISS mice. The individual gene or EST's function and mapping information have been analyzed. This study identified 41 genes that are differentially expressed between brains of ILS and ISS mice. Some of them may have biological relevance in mediation of phenotypic variation between ILS and ISS mice for ethanol sensitivity. This study also demonstrates that parallel gene expression comparison with high-density cDNA arrays is a rapid and efficient way to discover potential genes and pathways involved in alcoholism and alcohol-related physiologic processes.

Interaction of CO with an Au monatomic chain at different strains: Electronic structure and ballistic transport

NASA Astrophysics Data System (ADS)

Sclauzero, Gabriele; Dal Corso, Andrea; Smogunov, Alexander

2012-04-01

We study the energetics, the electronic structure, and the ballistic transport of an infinite Au monatomic chain with an adsorbed CO molecule. We find that the bridge adsorption site is energetically favored with respect to the atop site, both at the equilibrium Au-Au spacing of the chain and at larger spacings. Instead, a substitutional configuration requires a very elongated Au-Au bond, well above the rupture distance of the pristine Au chain. The electronic structure properties can be described by the Blyholder model, which involves the formation of bonding/antibonding pairs of 5σ and 2π states through the hybridization between molecular levels of CO and metallic states of the chain. In the atop geometry, we find an almost vanishing conductance due to the 5σ antibonding states giving rise to a Fano-like destructive interference close to the Fermi energy. In the bridge geometry, instead, the same states are shifted to higher energies and the conductance reduction with respect to pristine Au chain is much smaller. We also examine the effects of strain on the ballistic transport, finding opposite behaviors for the atop and bridge conductances. Only the bridge geometry shows a strain dependence compatible with the experimental conductance traces.

How did the platypus get its sex chromosome chain? A comparison of meiotic multiples and sex chromosomes in plants and animals.

PubMed

Gruetzner, Frank; Ashley, Terry; Rowell, David M; Marshall Graves, Jennifer A

2006-04-01

The duck-billed platypus is an extraordinary mammal. Its chromosome complement is no less extraordinary, for it includes a system in which ten sex chromosomes form an extensive meiotic chain in males. Such meiotic multiples are unprecedented in vertebrates but occur sporadically in plant and invertebrate species. In this paper, we review the evolution and formation of meiotic multiples in plants and invertebrates to try to gain insights into the origin of the platypus meiotic multiple. We describe the meiotic hurdles that translocated mammalian chromosomes face, which make longer chains disadvantageous in mammals, and we discuss how sex chromosomes and dosage compensation might have affected the evolution of sex-linked meiotic multiples. We conclude that the evolutionary conservation of the chain in monotremes, the structural properties of the translocated chromosomes and the highly accurate segregation at meiosis make the platypus system remarkably different from meiotic multiples in other species. We discuss alternative evolutionary models, which fall broadly into two categories: either the chain is the result of a sequence of translocation events from an ancestral pair of sex chromosomes (Model I) or the entire chain came into being at once by hybridization of two populations with different chromosomal rearrangements sharing monobrachial homology (Model II).

Strategic Co-Location in a Hybrid Process Involving Desalination and Pressure Retarded Osmosis (PRO)

PubMed Central

Sim, Victor S.T.; She, Qianhong; Chong, Tzyy Haur; Tang, Chuyang Y.; Fane, Anthony G.; Krantz, William B.

2013-01-01

This paper focuses on a Hybrid Process that uses feed salinity dilution and osmotic power recovery from Pressure Retarded Osmosis (PRO) to achieve higher overall water recovery. This reduces the energy consumption and capital costs of conventional seawater desalination and water reuse processes. The Hybrid Process increases the amount of water recovered from the current 66.7% for conventional seawater desalination and water reuse processes to a potential 80% through the use of reclaimed water brine as an impaired water source. A reduction of up to 23% in energy consumption is projected via the Hybrid Process. The attractiveness is amplified by potential capital cost savings ranging from 8.7%–20% compared to conventional designs of seawater desalination plants. A decision matrix in the form of a customizable scorecard is introduced for evaluating a Hybrid Process based on the importance of land space, capital costs, energy consumption and membrane fouling. This study provides a new perspective, looking at processes not as individual systems but as a whole utilizing strategic co-location to unlock the synergies available in the water-energy nexus for more sustainable desalination. PMID:24956940

Hybrid micromachining using a nanosecond pulsed laser and micro EDM

NASA Astrophysics Data System (ADS)

Kim, Sanha; Kim, Bo Hyun; Chung, Do Kwan; Shin, Hong Shik; Chu, Chong Nam

2010-01-01

Micro electrical discharge machining (micro EDM) is a well-known precise machining process that achieves micro structures of excellent quality for any conductive material. However, the slow machining speed and high tool wear are main drawbacks of this process. Though the use of deionized water instead of kerosene as a dielectric fluid can reduce the tool wear and increase the machine speed, the material removal rate (MRR) is still low. In contrast, laser ablation using a nanosecond pulsed laser is a fast and non-wear machining process but achieves micro figures of rather low quality. Therefore, the integration of these two processes can overcome the respective disadvantages. This paper reports a hybrid process of a nanosecond pulsed laser and micro EDM for micromachining. A novel hybrid micromachining system that combines the two discrete machining processes is introduced. Then, the feasibility and characteristics of the hybrid machining process are investigated compared to conventional EDM and laser ablation. It is verified experimentally that the machining time can be effectively reduced in both EDM drilling and milling by rapid laser pre-machining prior to micro EDM. Finally, some examples of complicated 3D micro structures fabricated by the hybrid process are shown.

Study of microstructural characterization and ionic conductivity of a chemical-covalent polyether-siloxane hybrid doped with LiClO4.

PubMed

Liang, Wuu-Jyh; Chen, Ying-Pin; Wu, Chien-Pang; Kuo, Ping-Lin

2005-12-29

The chemical-covalent polyether-siloxane hybrids (EDS) doped with various amounts of LiClO4 salt were characterized by FT-IR, DSC, TGA, and solid-state NMR spectra as well as impedance measurements. These observations indicate that different types of complexes by the interactions of Li+ and ClO4- ions are formed within the hybrid host, and the formation of transient cross-links between Li+ ions and ether oxygens results in the increase in T(g) of polyether segments and the decrease in thermal stability of hybrid electrolyte. Initially a cation complexation dominated by the oxirane-cleaved cross-link site and PEO block is present, and after the salt-doped level of O/Li+ = 20, the complexation through the PPO block becomes more prominent. Moreover, a significant degree of ionic association is examined in the polymer-salt complexes at higher salt uptakes. A VTF-like temperature dependence of ionic conductivity is observed in all of the investigated salt concentrations, implying that the diffusion of charge carrier is assisted by the segmental motions of the polymer chains. The behavior of ion transport in these hybrid electrolytes is further correlated with the interactions between ions and polymer host.

Host Adaptation and Speciation through Hybridization and Polyploidy in Phytophthora

PubMed Central

Bertier, Lien; Leus, Leen; D’hondt, Liesbet; de Cock, Arthur W. A. M.; Höfte, Monica

2013-01-01

It is becoming increasingly evident that interspecific hybridization is a common event in phytophthora evolution. Yet, the fundamental processes underlying interspecific hybridization and the consequences for its ecological fitness and distribution are not well understood. We studied hybridization events in phytophthora clade 8b. This is a cold-tolerant group of plant pathogenic oomycetes in which six host-specific species have been described that mostly attack winter-grown vegetables. Hybrid characterization was done by sequencing and cloning of two nuclear (ITS and Ypt1) and two mitochondrial loci (Cox1 and Nadh1) combined with DNA content estimation using flow cytometry. Three different mtDNA haplotypes were recovered among the presumed hybrid isolates, dividing the hybrids into three types, with different parental species involved. In the nuclear genes, additivity, i.e. the presence of two alleles coming from different parents, was detected. Hybrid isolates showed large variations in DNA content, which was positively correlated with the additivity in nuclear loci, indicating allopolyploid hybridization followed by a process of diploidization. Moreover, indications of homeologous recombination were found in the hybrids by cloning ITS products. The hybrid isolates have been isolated from a range of hosts that have not been reported previously for clade 8b species, indicating that they have novel pathogenic potential. Next to this, DNA content measurements of the non-hybrid clade 8b species suggest that polyploidy is a common feature of this clade. We hypothesize that interspecific hybridization and polyploidy are two linked phenomena in phytophthora, and that these processes might play an important and ongoing role in the evolution of this genus. PMID:24386473

Efficient hybrid evolutionary algorithm for optimization of a strip coiling process

NASA Astrophysics Data System (ADS)

Pholdee, Nantiwat; Park, Won-Woong; Kim, Dong-Kyu; Im, Yong-Taek; Bureerat, Sujin; Kwon, Hyuck-Cheol; Chun, Myung-Sik

2015-04-01

This article proposes an efficient metaheuristic based on hybridization of teaching-learning-based optimization and differential evolution for optimization to improve the flatness of a strip during a strip coiling process. Differential evolution operators were integrated into the teaching-learning-based optimization with a Latin hypercube sampling technique for generation of an initial population. The objective function was introduced to reduce axial inhomogeneity of the stress distribution and the maximum compressive stress calculated by Love's elastic solution within the thin strip, which may cause an irregular surface profile of the strip during the strip coiling process. The hybrid optimizer and several well-established evolutionary algorithms (EAs) were used to solve the optimization problem. The comparative studies show that the proposed hybrid algorithm outperformed other EAs in terms of convergence rate and consistency. It was found that the proposed hybrid approach was powerful for process optimization, especially with a large-scale design problem.

Polymerase Chain Reaction Assays For Diagnosis of Pneumocystis Carinii Infections

DTIC Science & Technology

1993-03-25

completing ano rCtew-e- the cOlleCtoIn Of Informationt Send comments regarding this bu •rden es•lratf or An- other A•iep Of this collection ot information...Hybridization was carril out at 45 C in 5 ml Hybrisol III containing 4 pmole of P labeled probe. After hybridiLation, the blot was washed three times at room

Automotive Lithium-ion Battery Supply Chain and U.S. Competitiveness Considerations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chung, Donald; Elgqvist, Emma; Santhanagopalan, Shriram

2015-06-01

This study highlights the U.S. foothold in automotive lithium-ion battery (LIB) production, globally. U.S.-based manufacturers comprise 17% of global production capacity. With increasing demand for electric and hybrid electric vehicles and U.S. vehicle manufacturers' proximity to customers, there is a growing opportunity for the United States to compete globally in the automotive LIB market.

Archaeal ribonuclease P proteins have potential for biotechnological applications where precise hybridization of nucleic acids is needed.

PubMed

Miyanoshita, Mitsuru; Nakashima, Takashi; Kakuta, Yoshimitsu; Kimura, Makoto

2015-01-01

Fluorescence resonance energy transfer-based assay showed that archaeal ribonuclease P (RNase P) proteins significantly promoted DNA annealing and strand displacement. Moreover, we found that archaeal RNase P proteins could discriminate nucleotide exchanges in DNA chains via their activity accelerating DNA strand displacement, suggesting that they have potential for biotechnological application to genetic diagnosis.

Disseminated Mycobacterium avium--intracellulare complex infection in a miniature schnauzer.

PubMed

Miller, M A; Greene, C E; Brix, A E

1995-01-01

A two-year-old, spayed female, miniature schnauzer was evaluated for respiratory distress associated with a compressive cervical mass. Generalized mycobacterial infection was diagnosed from aspirates of several enlarged lymph nodes. Tissue specimens further identified Mycobacterium avium--intracellulare using polymerase chain reaction followed by nucleic acid hybridization. Treatment with enrofloxacin, clofazamine, rifampin, and interferon did not result in long-term success.

Bovine leukemia virus infection in a juvenile alpaca with multicentric lymphoma

PubMed Central

Lee, Laura C.; Scarratt, William K.; Buehring, Gertrude C.; Saunders, Geoffrey K.

2012-01-01

A 13-month-old alpaca (Vicugna pacos) was presented for mandibular masses and weight loss. Histopathology of biopsy tissue was consistent with lymphoma. The alpaca was euthanized and necropsy revealed lymphoma masses in multiple organs. Immunohistochemistry for T- and B-cell typing was inconclusive. Serology and in-situ polymerase chain reaction hybridization were positive for bovine leukemia virus. PMID:22942445

Influence of acid chain length on the properties of TiO2 prepared by sol-gel method and LC-MS studies of methylene blue photodegradation.

PubMed

Bakre, Pratibha V; Volvoikar, Prajesh S; Vernekar, Amit A; Tilve, S G

2016-07-15

Nano-sized titanium dioxide photocatalysts were synthesized by hybrid hydrolytic nonhydrolytic sol-gel method using aliphatic organic acid templates to study the effect of chain length on their properties. X-ray diffraction pattern indicated crystalline anatase phase. The Barrett-Joyner-Halenda surface area measurement gave surface area ranging from 98.4 to 205.5m(2)/g and was found to be dependent on the chain length of the aliphatic acid. The longer chain acids rendered the material with high surface area. The organic acids acted as bidentate ligand and a surfactant in controlling the size and the mesoporosity. The size of the TiO2 nanoparticulate was found to be in the range of 10-18nm. The catalyst prepared by employing long chain acids octanoic acid and palmitic acid had smaller size, narrow pore radius, higher surface area and showed better photocatalytic activity than the commercially available Degussa P25 catalyst for the degradation of methylene blue dye. A new intermediate was identified by tandem liquid chromatography mass spectrometry studies during the degradation of methylene blue solution. Copyright © 2016 Elsevier Inc. All rights reserved.

Conformation and dynamics of polymer chains on dirty surfaces: A discrete-to-continuum approach

NASA Astrophysics Data System (ADS)

Foo, Grace M.; Pandey, R. B.

1998-07-01

A discrete-to-continuum (DC) simulation approach is introduced to study the statics and dynamics of polymer chains in two dimensions with quenched barriers, a dirty surface. In our DC hybrid approach, the large-scale relaxation of polymer chains on a discrete disordered lattice is followed by off-lattice simulation using a bead-spring chain model with a finitely extensible nonlinear elastic (FENE) potential for covalent bonds and Lennard-Jones (LJ) potential for nonbonded interactions. Segregation/folding of chains, which occurs at low temperatures (T=0.2, 1.0) with LJ interaction, becomes more difficult as the concentration of barriers increases, due to a screening effect of the barriers. In contrast to the chains' contraction at high temperature (i.e., T=5) and their collapse in athermal systems, chains are elongated on increasing the barrier concentration—a barrier-induced stretching. Variations of the root-mean-square (rms) displacements of the center of mass (Rcm) of the chains and their center node (Rcn) with time (t) show power-law behaviors (Rcm˜tν1, Rcn˜tν2) with nonuniversal exponents in the range ν1≃0.40-0.05 and ν2≃0.30-0.05, respectively, depending on temperature and barrier concentration. The radius of gyration (Rg) and the average bond length () expand on increasing the barrier concentration at low temperature and contract at high temperature, which is consistent with the variation of the width of the radial distribution function.

Local recurrence as immunoglobulin G4 (IgG4)-related disease 10 years after radiotherapy to ocular adnexal extranodal marginal zone B-cell lymphoma of mucosa-associated lymphoid tissue.

PubMed

Matsuo, Toshihiko; Ichimura, Kouichi; Yoshino, Tadashi

2011-01-01

In 2000, a 48-year-old woman developed a left orbital mass with lacrimal gland involvement and then, in 2003, a right orbital mass with lacrimal gland involvement, both of which were diagnosed as extranodal marginal zone B-cell lymphoma of mucosa-associated lymphoid tissue (MALT lymphoma). She underwent 30 Gy external beam radiation to bilateral orbital lesions. The lymphoma cells in both lesions did not share the same clonality, as shown by amplification by polymerase chain reaction of the immunoglobulin heavy chain gene. Immunoglobulin light chain analysis by immunohistochemistry and messenger RNA in situ hybridization showed λ chain monotype in the left orbital lesion but κ chain monotype in the right orbital lesion. She developed recurrent left orbital mass with high uptake on fluorodeoxyglucose positron emission tomography fused with computed tomography in 2010, and excisional biopsy disclosed the formation of follicles and infiltration with immunoglobulin G4 (IgG4)-positive plasma cells mainly in interfollicular areas. The immunoglobulin light chain analysis showed the λ chain and κ chain bitype. With the immunohistopathological diagnosis of IgG4-related disease, the serum IgG4 level was found to show elevation at 376 mg/dL, and the patient chose observation. This is the first reported case of development of IgG4-related disease after bilataral orbital MALT lymphoma with external beam radiotherapy.

T-cell receptor V sub. alpha. and C sub. alpha. alleles associated with multiple sclerosis and myasthenia gravis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oksenberg, J.R.; Cavalli-Sforza, L.L.; Steinman, L.

1989-02-01

Polymorphic markers in genes encoding the {alpha} chain of the human T-cell receptor (TcR) have been detected by Southern blot analysis in Pss I digests. Polymorphic bands were observed at 6.3 and 2.0 kilobases (kb) with frequencies of 0.30 and 0.44, respectively, in the general population. Using the polymerase chain reaction (PCR) method, the authors amplified selected sequences derived from the full-length TcR {alpha} cDNA probe. These PcR products were used as specific probes to demonstrate that the 6.3-kb polymorphic fragment hybridizes to the variable (V)-region probe and the 2.0-kb fragment hybridizes to the constant (C)-region probe. Segregation of themore » polymorphic bands was analyzed in family studies. To look for associations between these markers and autoimmune diseases, the authors have studied the restriction fragment length polymorphism distribution of the Pss I markers in patients with multiple sclerosis, myasthenia gravis, and Graves disease. Significant differences in the frequency of the polymorphic V{sub {alpha}} and C{sub {alpha}} markers were identified between patients and healthy individuals.« less

Preparation and Characterization of C60/Graphene Hybrid Nanostructures.

PubMed

Chen, Chuanhui; Mills, Adam; Zheng, Husong; Li, Yanlong; Tao, Chenggang

2018-05-15

Physical thermal deposition in a high vacuum environment is a clean and controllable method for fabricating novel molecular nanostructures on graphene. We present methods for depositing and passively manipulating C60 molecules on rippled graphene that advance the pursuit of realizing applications involving 1D C60/graphene hybrid structures. The techniques applied in this exposition are geared towards high vacuum systems with preparation areas capable of supporting molecular deposition as well as thermal annealing of the samples. We focus on C60 deposition at low pressure using a homemade Knudsen cell connected to a scanning tunneling microscopy (STM) system. The number of molecules deposited is regulated by controlling the temperature of the Knudsen cell and the deposition time. One-dimensional (1D) C60 chain structures with widths of two to three molecules can be prepared via tuning of the experimental conditions. The surface mobility of the C60 molecules increases with annealing temperature allowing them to move within the periodic potential of the rippled graphene. Using this mechanism, it is possible to control the transition of 1D C60 chain structures to a hexagonal close packed quasi-1D stripe structure.

A Hybrid Secure Scheme for Wireless Sensor Networks against Timing Attacks Using Continuous-Time Markov Chain and Queueing Model.

PubMed

Meng, Tianhui; Li, Xiaofan; Zhang, Sha; Zhao, Yubin

2016-09-28

Wireless sensor networks (WSNs) have recently gained popularity for a wide spectrum of applications. Monitoring tasks can be performed in various environments. This may be beneficial in many scenarios, but it certainly exhibits new challenges in terms of security due to increased data transmission over the wireless channel with potentially unknown threats. Among possible security issues are timing attacks, which are not prevented by traditional cryptographic security. Moreover, the limited energy and memory resources prohibit the use of complex security mechanisms in such systems. Therefore, balancing between security and the associated energy consumption becomes a crucial challenge. This paper proposes a secure scheme for WSNs while maintaining the requirement of the security-performance tradeoff. In order to proceed to a quantitative treatment of this problem, a hybrid continuous-time Markov chain (CTMC) and queueing model are put forward, and the tradeoff analysis of the security and performance attributes is carried out. By extending and transforming this model, the mean time to security attributes failure is evaluated. Through tradeoff analysis, we show that our scheme can enhance the security of WSNs, and the optimal rekeying rate of the performance and security tradeoff can be obtained.

New hybrid lead iodides: From one-dimensional chain to two-dimensional layered perovskite structure

NASA Astrophysics Data System (ADS)

Xiong, Kecai; Liu, Wei; Teat, Simon J.; An, Litao; Wang, Hao; Emge, Thomas J.; Li, Jing

2015-10-01

Two new hybrid lead halides (H2BDA)[PbI4] (1) (H2BDA=1,4-butanediammonium dication) and (HNPEIM)[PbI3] (2) (HNPEIM=N-​phenyl-ethanimidamidine cation) have been synthesized and structurally characterized. X-ray diffraction analyses reveal that compound 1 features a two-dimensional corner-sharing perovskite layer whereas compound 2 contains one-dimensional edge-sharing double chains. The N-​phenyl-ethanimidamidine cation within compound 2 was generated in-situ under solvothermal conditions. The optical absorption spectra collected at room temperature suggest that both compounds are semiconductors having direct band gaps, with estimated values of 2.64 and 2.73 eV for 1 and 2, respectively. Results from the density functional theory (DFT) calculations are consistent with the experimental data. Density of states (DOS) analysis reveals that in both compounds 1 and 2, the energy states in the valence band maximum region are iodine 5p atomic orbitals with a small contribution from lead 6s, while in the region of conduction band minimum, the major contributions are from the inorganic (Pb 6p atomic orbitals) and organic components (C and N 2p atomic orbitals) in compound 1 and 2, respectively.

A Hybrid Secure Scheme for Wireless Sensor Networks against Timing Attacks Using Continuous-Time Markov Chain and Queueing Model

PubMed Central

Meng, Tianhui; Li, Xiaofan; Zhang, Sha; Zhao, Yubin

2016-01-01

Wireless sensor networks (WSNs) have recently gained popularity for a wide spectrum of applications. Monitoring tasks can be performed in various environments. This may be beneficial in many scenarios, but it certainly exhibits new challenges in terms of security due to increased data transmission over the wireless channel with potentially unknown threats. Among possible security issues are timing attacks, which are not prevented by traditional cryptographic security. Moreover, the limited energy and memory resources prohibit the use of complex security mechanisms in such systems. Therefore, balancing between security and the associated energy consumption becomes a crucial challenge. This paper proposes a secure scheme for WSNs while maintaining the requirement of the security-performance tradeoff. In order to proceed to a quantitative treatment of this problem, a hybrid continuous-time Markov chain (CTMC) and queueing model are put forward, and the tradeoff analysis of the security and performance attributes is carried out. By extending and transforming this model, the mean time to security attributes failure is evaluated. Through tradeoff analysis, we show that our scheme can enhance the security of WSNs, and the optimal rekeying rate of the performance and security tradeoff can be obtained. PMID:27690042

Non-Fermi-Liquid Behavior in Transport Through Co-Doped Au Chains

NASA Astrophysics Data System (ADS)

Di Napoli, S.; Weichselbaum, A.; Roura-Bas, P.; Aligia, A. A.; Mokrousov, Y.; Blügel, S.

2013-05-01

We calculate the conductance as a function of temperature G(T) through Au monatomic chains containing one Co atom as a magnetic impurity, and connected to two conducting leads with a fourfold symmetry axis. Using the information derived from ab initio calculations, we construct an effective model H^eff that hybridizes a 3d7 quadruplet at the Co site with two 3d8 triplets through the hopping of 5dxz and 5dyz electrons of Au. The quadruplet is split by spin anisotropy due to spin-orbit coupling. Solving H^eff with the numerical renormalization group we find that at low temperatures G(T)=a-bT and the ground state impurity entropy is ln⁡(2)/2, a behavior similar to the two-channel Kondo model. Stretching the chain leads to a non-Kondo phase, with the physics of the underscreened Kondo model at the quantum critical point.

Correlation between protein secondary structure, backbone bond angles, and side-chain orientations.

PubMed

Lundgren, Martin; Niemi, Antti J

2012-08-01

We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C(α) carbon of a protein backbone, and for this we develop new visualization techniques to analyze high-resolution x-ray structures in the Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse-grained energy function to describe the ensuing side-chain geometry in terms of the C(β) carbon orientations. The energy function can model the side-chain geometry with a subatomic precision. As an example we construct the C(α)-C(β) structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 Å in root-mean-square distance from the experimental x-ray structure.

Effect of tethering on the surface dynamics of a thin polymer melt layer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uğur, Gökçe; Akgun, Bulent; Jiang, Zhang

The surface height fluctuations of a layer of low molecular weight (2.2k) untethered perdeuterated polystyrene (dPS) chains adjacent to a densely grafted polystyrene brush are slowed dramatically. Due to the interpenetration of the brush with the layer of “untethered chains” a hydrodynamic continuum theory can only describe the fluctuations when the effective thickness of the film is taken to be that which remains above the swollen brush. Furthermore, the portion of the film of initially untethered chains that interpenetrates with the brush becomes so viscous as to effectively play the role of a rigid substrate. They provide a route formore » tailoring polymer layer surface properties such as wetting, adhesion and friction, since these hybrid samples contain a covalently tethered layer at the bottom, does not readily dewet, and are more robust than thin layers of untethered short chains on rigid substrates.« less

Markov chain Monte Carlo techniques applied to parton distribution functions determination: Proof of concept

NASA Astrophysics Data System (ADS)

Gbedo, Yémalin Gabin; Mangin-Brinet, Mariane

2017-07-01

We present a new procedure to determine parton distribution functions (PDFs), based on Markov chain Monte Carlo (MCMC) methods. The aim of this paper is to show that we can replace the standard χ2 minimization by procedures grounded on statistical methods, and on Bayesian inference in particular, thus offering additional insight into the rich field of PDFs determination. After a basic introduction to these techniques, we introduce the algorithm we have chosen to implement—namely Hybrid (or Hamiltonian) Monte Carlo. This algorithm, initially developed for Lattice QCD, turns out to be very interesting when applied to PDFs determination by global analyses; we show that it allows us to circumvent the difficulties due to the high dimensionality of the problem, in particular concerning the acceptance. A first feasibility study is performed and presented, which indicates that Markov chain Monte Carlo can successfully be applied to the extraction of PDFs and of their uncertainties.

Synthesis of Photocrosslinkable and Amine Containing Multifunctional Nanoparticles via Polymerization-Induced Self-Assembly.

PubMed

Huang, Jianbing; Li, Decai; Liang, Hui; Lu, Jiang

2017-08-01

Photo-crosslinkable and amine-containing block copolymer nanoparticles are synthesized via reversible addition-fragmentation chain transfer (RAFT) polymerization-induced self-assembly of a multifunctional core-forming monomer, 2-((3-(4-(diethylamino)phenyl)acryloyl)oxy)ethyl methacrylate (DEMA), using poly(2-hydroxypropyl methacrylate) macromolecular chain transfer agent as a steric stabilizer in methanol at 65 °C. By tuning the chain length of PDEMA, a range of nanoparticle morphologies (sphere, worm, and vesicle) can be obtained. Since cinnamate groups can easily undergo a [2 + 2] cycloaddition of the carbon-carbon double bonds upon UV irradiation, the as-prepared block copolymer nanoparticles are readily stabilized by photo-crosslinking to produce anisotropic nanoparticles. The crosslinked block copolymer nanoparticles can be used as templates for in situ formation polymer/gold hybrid nanoparticles. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of tethering on the surface dynamics of a thin polymer melt layer

DOE PAGES

Uğur, Gökçe; Akgun, Bulent; Jiang, Zhang; ...

2016-05-13

The surface height fluctuations of a layer of low molecular weight (2.2k) untethered perdeuterated polystyrene (dPS) chains adjacent to a densely grafted polystyrene brush are slowed dramatically. Due to the interpenetration of the brush with the layer of “untethered chains” a hydrodynamic continuum theory can only describe the fluctuations when the effective thickness of the film is taken to be that which remains above the swollen brush. Furthermore, the portion of the film of initially untethered chains that interpenetrates with the brush becomes so viscous as to effectively play the role of a rigid substrate. They provide a route formore » tailoring polymer layer surface properties such as wetting, adhesion and friction, since these hybrid samples contain a covalently tethered layer at the bottom, does not readily dewet, and are more robust than thin layers of untethered short chains on rigid substrates.« less

Fabrication of three-dimensional hybrid nanostructure-embedded ITO and its application as a transparent electrode for high-efficiency solution processable organic photovoltaic devices.

PubMed

Kim, Jeong Won; Jeon, Hwan-Jin; Lee, Chang-Lyoul; Ahn, Chi Won

2017-03-02

Well-aligned, high-resolution (10 nm), three-dimensional (3D) hybrid nanostructures consisting of patterned cylinders and Au islands were fabricated on ITO substrates using an ion bombardment process and a tilted deposition process. The fabricated 3D hybrid nanostructure-embedded ITO maintained its excellent electrical and optical properties after applying a surface-structuring process. The solution processable organic photovoltaic device (SP-OPV) employing a 3D hybrid nanostructure-embedded ITO as the anode displayed a 10% enhancement in the photovoltaic performance compared to the photovoltaic device prepared using a flat ITO electrode, due to the improved charge collection (extraction and transport) efficiency as well as light absorbance by the photo-active layer.

Synthesis and Self-Assembly of Cellulose Microfibrils from Reconstituted Cellulose Synthase.

PubMed

Cho, Sung Hyun; Purushotham, Pallinti; Fang, Chao; Maranas, Cassandra; Díaz-Moreno, Sara M; Bulone, Vincent; Zimmer, Jochen; Kumar, Manish; Nixon, B Tracy

2017-09-01

Cellulose, the major component of plant cell walls, can be converted to bioethanol and is thus highly studied. In plants, cellulose is produced by cellulose synthase, a processive family-2 glycosyltransferase. In plant cell walls, individual β-1,4-glucan chains polymerized by CesA are assembled into microfibrils that are frequently bundled into macrofibrils. An in vitro system in which cellulose is synthesized and assembled into fibrils would facilitate detailed study of this process. Here, we report the heterologous expression and partial purification of His-tagged CesA5 from Physcomitrella patens Immunoblot analysis and mass spectrometry confirmed enrichment of PpCesA5. The recombinant protein was functional when reconstituted into liposomes made from yeast total lipid extract. The functional studies included incorporation of radiolabeled Glc, linkage analysis, and imaging of cellulose microfibril formation using transmission electron microscopy. Several microfibrils were observed either inside or on the outer surface of proteoliposomes, and strikingly, several thinner fibrils formed ordered bundles that either covered the surfaces of proteoliposomes or were spawned from liposome surfaces. We also report this arrangement of fibrils made by proteoliposomes bearing CesA8 from hybrid aspen. These observations describe minimal systems of membrane-reconstituted CesAs that polymerize β-1,4-glucan chains that coalesce to form microfibrils and higher-ordered macrofibrils. How these micro- and macrofibrils relate to those found in primary and secondary plant cell walls is uncertain, but their presence enables further study of the mechanisms that govern the formation and assembly of fibrillar cellulosic structures and cell wall composites during or after the polymerization process controlled by CesA proteins. © 2017 American Society of Plant Biologists. All Rights Reserved.

Synthesis and Self-Assembly of Cellulose Microfibrils from Reconstituted Cellulose Synthase1[OPEN

PubMed Central

Purushotham, Pallinti; Fang, Chao; Maranas, Cassandra; Bulone, Vincent

2017-01-01

Cellulose, the major component of plant cell walls, can be converted to bioethanol and is thus highly studied. In plants, cellulose is produced by cellulose synthase, a processive family-2 glycosyltransferase. In plant cell walls, individual β-1,4-glucan chains polymerized by CesA are assembled into microfibrils that are frequently bundled into macrofibrils. An in vitro system in which cellulose is synthesized and assembled into fibrils would facilitate detailed study of this process. Here, we report the heterologous expression and partial purification of His-tagged CesA5 from Physcomitrella patens. Immunoblot analysis and mass spectrometry confirmed enrichment of PpCesA5. The recombinant protein was functional when reconstituted into liposomes made from yeast total lipid extract. The functional studies included incorporation of radiolabeled Glc, linkage analysis, and imaging of cellulose microfibril formation using transmission electron microscopy. Several microfibrils were observed either inside or on the outer surface of proteoliposomes, and strikingly, several thinner fibrils formed ordered bundles that either covered the surfaces of proteoliposomes or were spawned from liposome surfaces. We also report this arrangement of fibrils made by proteoliposomes bearing CesA8 from hybrid aspen. These observations describe minimal systems of membrane-reconstituted CesAs that polymerize β-1,4-glucan chains that coalesce to form microfibrils and higher-ordered macrofibrils. How these micro- and macrofibrils relate to those found in primary and secondary plant cell walls is uncertain, but their presence enables further study of the mechanisms that govern the formation and assembly of fibrillar cellulosic structures and cell wall composites during or after the polymerization process controlled by CesA proteins. PMID:28768815

Simulation study of the initial crystallization processes of poly(3-hexylthiophene) in solution: ordering dynamics of main chains and side chains.

PubMed

Takizawa, Yuumi; Shimomura, Takeshi; Miura, Toshiaki

2013-05-23

We study the initial nucleation dynamics of poly(3-hexylthiophene) (P3HT) in solution, focusing on the relationship between the ordering process of main chains and that of side chains. We carried out Langevin dynamics simulation and found that the initial nucleation processes consist of three steps: the ordering of ring orientation, the ordering of main-chain vectors, and the ordering of side chains. At the start, the normal vectors of thiophene rings aligned in a very short time, followed by alignment of main-chain end-to-end vectors. The flexible side-chain ordering took almost 5 times longer than the rigid-main-chain ordering. The simulation results indicated that the ordering of side chains was induced after the formation of the regular stack structure of main chains. This slow ordering dynamics of flexible side chains is one of the factors that cause anisotropic nuclei growth, which would be closely related to the formation of nanofiber structures without external flow field. Our simulation results revealed how the combined structure of the planar and rigid-main-chain backbones and the sparse flexible side chains lead to specific ordering behaviors that are not observed in ordinary linear polymer crystallization processes.

How to polymerize ethylene in a highly controlled fashion?

PubMed

Kempe, Rhett

2007-01-01

Very fast, reversible, polyethylene (PE) chain transfer or complex-catalysed "Aufbaureaktion" describes a "living" chain-growing process on a main-group metal or zinc atom; this process is catalysed by an organo-transition-metal or lanthanide complex. PE chains are transferred very fast between the two metal sites and chain growth takes place through ethylene insertion into the transition-metal- or lanthanide-carbon bond-coordinative chain-transfer polymerisation (CCTP). The transferred chains "rest" at the main-group or zinc centre, at which chain-termination processes like beta-H transfer/elimination are of low significance. Such protocols can be used to synthesise very narrowly distributed PE materials (M(w)/M(n)<1.1 up to a molecular weight of about 4000 g mol(-1)) with differently functionalised end groups. Higher molecular-weight polymers can be obtained with a slightly increased M(w)/M(n), since diffusion control and precipitation of the polymers influences the chain-transfer process. Recently, a few transition-metal- or lanthanide-based catalyst systems that catalyse such a highly reversible chain-growing process have been described. They are summarised and compared within this contribution.

Mechanical reinforcement and environmental effects on a nylon-6/clay nanocomposite

NASA Astrophysics Data System (ADS)

Shelley, J. Stebbins

2000-10-01

Hybridization, or modifying the organic polymers with inorganic constituents, is one method of achieving mechanical property improvements in polymeric materials while preserving processing characteristics. Toyota Central Research developed, and Ube Industries commercialized, one such hybrid nanocomposite: nylon-6/montmorillonite clay. This dissertation explores mechanisms of reinforcement in these nylon-6/clay nanocomposites and studies their degradation by atmospheric pollutants. A 100% improvement in modulus, 77% improvement in yield stress, and 54°C improvement in heat distortion temperature over nylon-6 were observed in extruded 5 wt% clay nanocomposite sheets. Infrared absorption spectrography and dynamic mechanical analysis were used to investigate the mechanisms of reinforcement in these nanocomposites. The improved mechanical properties, increased heat distortion temperature, reduced diffusion rate, and lower susceptibility to degradation in NO x observed where attributed to constraint of polymer chain motion by interaction with clay lamellae. Changes in the loss tangent peak in the glass transition region of the dynamic mechanical data provide an estimate of the volume of chains constrained by complexation of their mid-chain amide oxygen groups with the charged clay lamellae. X-ray analysis, optical microscopy, and light scattering were used to study changes in crystallization due to this complexation. Photomicrographs indicate that the morphology of the crystallites change from spherulitic to planar with the addition of clay. Decreases in diffusion rates of water and total water absorption were demonstrated in immersion experiments. Complexation of nylon-6 with 5 wt% clay reduces the total absorption of water by over 16%. The plane stress fracture toughness of extruded 5 wt% clay nanocomposite was 46% greater than that of nylon-6. The degradation of the nanocomposites in calcium chloride solution and NOx was examined through post exposure residual tensile and stress cracking experiments. CaCl 2 solution degraded the mechanical responses of the nanocomposite materials in proportion to the amount of water absorbed. NOx exposure degraded the mechanical performance regardless of the constraining effect of clay lamellae and the reduced diffusion rate in the nanocomposites. The stress cracking response of the nanocomposite in NOx (apparently not diffusion driven) resulted in a 650% increase in the time to failure of 5 wt% clay nanocomposites over unmodified nylon-6 for the same normalized stress intensity factor.

Accumulation of worn-out GBM material substantially contributes to mesangial matrix expansion in diabetic nephropathy.

PubMed

Kriz, Wilhelm; Löwen, Jana; Federico, Giuseppina; van den Born, Jacob; Gröne, Elisabeth; Gröne, Hermann Josef

2017-06-01

Thickening of the glomerular basement membrane (GBM) and expansion of the mesangial matrix are hallmarks of diabetic nephropathy (DN), generally considered to emerge from different sites of overproduction: GBM components from podocytes and mesangial matrix from mesangial cells. Reevaluation of 918 biopsies with DN revealed strong evidence that these mechanisms are connected to each other, wherein excess GBM components fail to undergo degradation and are deposited in the mesangium. These data do not exclude that mesangial cells also synthesize components that contribute to the accumulation of matrix in the mesangium. Light, electron microscopic, immunofluorescence, and in situ hybridization studies clearly show that the thickening of the GBM is due not only to overproduction of components of the mature GBM (α3 and α5 chains of collagen IV and agrin) by podocytes but also to resumed increased synthesis of the α1 chain of collagen IV and of perlecan by endothelial cells usually seen during embryonic development. We hypothesize that these abnormal production mechanisms are caused by different processes: overproduction of mature GBM-components by the diabetic milieu and regression of endothelial cells to an embryonic production mode by decreased availability of mediators from podocytes. Copyright © 2017 the American Physiological Society.

Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases

PubMed Central

Lambert, Abigail R.; Kuhar, Ryan; Jarjour, Jordan; Kulshina, Nadia; Parmeggiani, Fabio; Danaher, Patrick; Gano, Jacob; Baker, David; Stoddard, Barry L.; Scharenberg, Andrew M.

2012-01-01

Although engineered LAGLIDADG homing endonucleases (LHEs) are finding increasing applications in biotechnology, their generation remains a challenging, industrial-scale process. As new single-chain LAGLIDADG nuclease scaffolds are identified, however, an alternative paradigm is emerging: identification of an LHE scaffold whose native cleavage site is a close match to a desired target sequence, followed by small-scale engineering to modestly refine recognition specificity. The application of this paradigm could be accelerated if methods were available for fusing N- and C-terminal domains from newly identified LHEs into chimeric enzymes with hybrid cleavage sites. Here we have analyzed the structural requirements for fusion of domains extracted from six single-chain I-OnuI family LHEs, spanning 40–70% amino acid identity. Our analyses demonstrate that both the LAGLIDADG helical interface residues and the linker peptide composition have important effects on the stability and activity of chimeric enzymes. Using a simple domain fusion method in which linker peptide residues predicted to contact their respective domains are retained, and in which limited variation is introduced into the LAGLIDADG helix and nearby interface residues, catalytically active enzymes were recoverable for ∼70% of domain chimeras. This method will be useful for creating large numbers of chimeric LHEs for genome engineering applications. PMID:22684507

Genetic structure of soil population of fungus Fusarium oxysporum Schlechtend.: Fr.: Molecular reidentification of the species and genetic differentiation of isolates using polymerase chain reaction technique with universal primers (UP-PCR)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bulat, S.A.; Mironenko, N.V.; Zholkevich, Yu.G.

1995-07-01

The genetic structure of three soil populations of fungus Fusarium oxysporum was analyzed using polymerase chain reaction with universal primers (UP-PCR). Distinct UP-PCR variants revealed by means of cross-dot hybridization of amplified DNA and restriction analysis of nuclear ribosomal DNA represent subspecies or sibling species of F. oxysporum. The remaining isolates of F. oxysporum showed moderate UP-PCR polymorphism characterized by numerous types, whose relatedness was analyzed by computer treatment of the UP-PCR patterns. The genetic distance trees based on the UP-PCR patterns, which were obtained with different universal primers, demonstrated similar topology. This suggests that evolutionarily important genome rearrangements correlativelymore » occur within the entire genome. Isolates representing different UP-PCR polymorphisms were encountered in all populations, being distributed asymmetrically in two of these. In general, soil populations of F. oxysporum were represented by numerous genetically isolated groups with a similar genome structure. The genetic heterogeneity of the isolates within these groups is likely to be caused by the parasexual process. The usefulness of the UP-PCR technique for population studies of F. oxysporum was demonstrated. 39 refs., 7 figs., 2 tabs.« less

Hybrid polypeptides having cellobiohydrolase activity and polynucleotides encoding same

DOEpatents

Liu, Ye; Shaghasi, Tarana

2016-11-01

The present invention provides hybrid polypeptides having cellobiohydrolase activity. The present invention also provides polynucleotides encoding the hybrid polypeptides; nucleic acid constructs, vectors and host cells comprising the polynucleotides; and processes of using the hybrid polypeptides.

Structural and Morphological Investigation for Water-Processed Graphene Oxide/Single-Walled Carbon Nanotubes Hybrids

NASA Astrophysics Data System (ADS)

Muda, M. R.; Ramli, M. M.; Mat Isa, S. S.; Halin, D. S. C.; Talip, L. F. A.; Mazelan, N. S.; Anhar, N. A. M.; Danial, N. A.

2017-06-01

New group of materials derived from hybridization of single walled carbon nanotubes (SWCNTs) and graphene oxide (GO) which resulting novel three dimensional (3D) materials generates an outstanding properties compared to corresponding SWCNTs and GO/Graphene. In this paper, we describe a simple approach using water processing method to develop integrated rGO/GO-SWCNT hybrids with different hybrid ratios. The hybrid ratios were varied into three divided ratio and the results were compared between pristine SWCNTs and GO in order to investigate the structural density and morphology of these carbonaceous materials. With an optimized ratio of rGO/GO-SWCNT, the hybrid shows a well-organized hybrid film structures with less defects density sites. The optimized mixture ratio emphasized the important of both rGO and SWCNTs in the hybrid structures. Morphological structural and defects density degrees were examined by Field Emission Scanning Electron Microscopy (FESEM) and Raman spectroscopy.

Feasibility of using continuous chromatography in downstream processing: Comparison of costs and product quality for a hybrid process vs. a conventional batch process.

PubMed

Ötes, Ozan; Flato, Hendrik; Winderl, Johannes; Hubbuch, Jürgen; Capito, Florian

2017-10-10

The protein A capture step is the main cost-driver in downstream processing, with high attrition costs especially when using protein A resin not until end of resin lifetime. Here we describe a feasibility study, transferring a batch downstream process to a hybrid process, aimed at replacing batch protein A capture chromatography with a continuous capture step, while leaving the polishing steps unchanged to minimize required process adaptations compared to a batch process. 35g of antibody were purified using the hybrid approach, resulting in comparable product quality and step yield compared to the batch process. Productivity for the protein A step could be increased up to 420%, reducing buffer amounts by 30-40% and showing robustness for at least 48h continuous run time. Additionally, to enable its potential application in a clinical trial manufacturing environment cost of goods were compared for the protein A step between hybrid process and batch process, showing a 300% cost reduction, depending on processed volumes and batch cycles. Copyright © 2017 Elsevier B.V. All rights reserved.

Improvement of flavor profiles in Chinese rice wine by creating fermenting yeast with superior ethanol tolerance and fermentation activity.

PubMed

Yang, Yijin; Xia, Yongjun; Lin, Xiangna; Wang, Guangqiang; Zhang, Hui; Xiong, Zhiqiang; Yu, Haiyan; Yu, Jianshen; Ai, Lianzhong

2018-06-01

Producing alcoholic beverages with novel flavor are desirable for winemakers. We created fermenting yeast with superior ethanol tolerance and fermentation activity to improve the flavor profiles of Chinese rice wine. Strategies of ethanol domestication, ultraviolet mutagenesis (UV) and protoplast fusion were conducted to create yeast hybrids with excellent oenological characteristic. The obtained diploid hybrid F23 showed a cell viability of 6.2% under 25% ethanol, whereas its diploid parental strains could not survive under 20% ethanol. During Chinese rice wine-making, compared to diploid parents, F23 produced 7.07%-12.44% higher yield of ethanol. Flavor analysis indicated that the total content of flavor compounds in F23 wine was 19.99-26.55% higher than that of parent wines. Specifically, F23 exhibited higher capacity in producing 2-phenylethanol, short-chain and long-chain fatty-acid ethyl-ester than diploid parents. Compared to diploid parents, F23 introduced more flavor contributors with odor activity values (OAVs) above one to Chinese rice wine, and those contributors were found with higher OAVs. Based on principal component analysis (PCA), the flavor characteristic of F23 wine was similar to each of parent wine. Additionally, sensory evaluation showed that F23 wine was highly assessed for its intensive levels in fruit-aroma, alcohol-aroma and mouthfeel. Hybrid F23 not only displayed superior flavor production and oenological performance in making Chinese rice wine, but also could act as potential "mixed-like" starter to enrich wine style and differentiation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Pressure-induced superconductivity in CaC2

PubMed Central

Li, Yan-Ling; Luo, Wei; Zeng, Zhi; Lin, Hai-Qing; Mao, Ho-kwang; Ahuja, Rajeev

2013-01-01

Carbon can exist as isolated dumbbell, 1D chain, 2D plane, and 3D network in carbon solids or carbon-based compounds, which attributes to its rich chemical binding way, including sp-, sp2-, and sp3-hybridized bonds. sp2-hybridizing carbon always captures special attention due to its unique physical and chemical property. Here, using an evolutionary algorithm in conjunction with ab initio method, we found that, under compression, dumbbell carbon in CaC2 can be polymerized first into 1D chain and then into ribbon and further into 2D graphite sheet at higher pressure. The C2/m structure transforms into an orthorhombic Cmcm phase at 0.5 GPa, followed by another orthorhombic Immm phase, which is stabilized in a wide pressure range of 15.2–105.8 GPa and then forced into MgB2-type phase with wide range stability up to at least 1 TPa. Strong electron–phonon coupling λ in compressed CaC2 is found, in particular for Immm phase, which has the highest λ value (0.562–0.564) among them, leading to its high superconducting critical temperature Tc (7.9∼9.8 K), which is comparable with the 11.5 K value of CaC6. Our results show that calcium not only can stabilize carbon sp2 hybridization at a larger range of pressure but also can contribute in superconducting behavior, which would further ignite experimental and theoretical interest in alkaline–earth metal carbides to uncover their peculiar physical properties under extreme conditions. PMID:23690580

Sequestration of dyes from artificially prepared textile effluent using RSM-CCD optimized hybrid backbone based adsorbent-kinetic and equilibrium studies.

PubMed

Sukriti; Sharma, Jitender; Chadha, Amritpal Singh; Pruthi, Vaishali; Anand, Prerna; Bhatia, Jaspreet; Kaith, B S

2017-04-01

Present work reports the synthesis of semi-Interpenetrating Network Polymer (semi-IPN) using Gelatin-Gum xanthan hybrid backbone and polyvinyl alcohol in presence of l-tartaric acid and ammonium persulphate as the crosslinker-initiator system. Reaction parameters were optimized with Response Surface Methodology (RSM) in order to maximize the percent gel fraction of the synthesized sample. Polyvinyl alcohol, l-Tartaric acid, ammonium persulphate, reaction temperature, time and pH of the reaction medium were found to make an impact on the percentage gel fraction obtained. Incorporation of polyvinyl alcohol chains onto hybrid backbone and crosslinking between the different polymer chains were confirmed through techniques like FTIR, SEM-EDX and XRD. Semi-IPN was found to be very efficient in the removal of cationic dyes rhodamine-B (70%) and auramine-O (63%) from a mixture with an adsorbent dose of 700 mg, initial concentration of rhodamine-B 6 mgL -1 and auramine-O 26 mgL -1 , at an time interval of 22-25 h and 30 °C temp. Further to determine the nature of adsorption Langmuir and Freundlich adsorption isotherm models were studied and it was found that Langmuir adsorption isotherm was the best fit model for the removal of mixture of dyes. Kinetic studies for the sorption of dyes favored the reaction mechanism to occur via a pseudo second order pathway with R 2 value about 0.99. Copyright © 2017 Elsevier Ltd. All rights reserved.

Electrochemical sensor for glutathione detection based on mercury ion triggered hybridization chain reaction signal amplification.

PubMed

Wang, Yonghong; Jiang, Lun; Leng, Qinggang; Wu, Yaohui; He, Xiaoxiao; Wang, Kemin

2016-03-15

In this work, we design a new simple and highly sensitive strategy for electrochemical detection of glutathione (GSH) via mercury ion (Hg(2+)) triggered hybridization chain reaction (HCR) signal amplification. It is observed that in the absence of GSH, a specific thymine-Hg(2+)-thymine (T-Hg(2+)-T) coordination can fold into hairpin structures. While in the presence of GSH, it thus can be chelated with Hg(2+), resulting in Hg(2+) released from the T-Hg(2+)-T hairpin complex which then forms into ssDNA structure to further hybridize with the surface-immobilized capture DNA probe on the gold electrode with a sticky tail left. The presence of two hairpin helper probes through HCR leads to the formation of extended dsDNA superstructure on the electrode surface, which therefore causes the intercalation of numerous electroactive species ([Ru(NH3)6](3+)) into the dsDNA grooves, followed by a significantly amplified signal output whose intensity is related to the concentration of the GSH. Taking advantage of merits of enzyme-free amplification power of the HCR, the inherent high sensitivity of the electrochemical technique, and label-free detection which utilizes an electroactive species as a signaling molecule that binds to the anionic phosphate backbone of DNA strands via electrostatic force, not only does the proposed strategy enable sensitive detection of GSH, but show high selectivity against other amino acid, making our method a simple and sensitive addition to the amplified GSH detection. Copyright © 2015 Elsevier B.V. All rights reserved.

Designing of an artificial light energy converter in the form of short-chain dyad when combined with core-shell gold/silver nanocomposites.

PubMed

Dutta Pal, Gopa; Paul, Somnath; Bardhan, Munmun; De, Asish; Ganguly, Tapan

2017-06-05

UV-vis absorption, steady state and time resolved fluorescence and absorption spectroscopic investigations demonstrate that the short chain dyad MNTMA when combined with gold-silver core-shell (Au@Ag) nanocomposite , forms elongated conformers in the excited state whereas for the dyad - Ag (spherical) system the majority of dyads remains in a folded conformation. In the dyad-core-shell nanocomposite system, energy wasting charge recombination rate slows down primarily due to elongated conformation and thus it may be anticipated that this hybrid nanocomposite system may serve as a better light energy conversion device. Copyright © 2017 Elsevier B.V. All rights reserved.

A temperature-dependent coarse-grained model for the thermoresponsive polymer poly(N-isopropylacrylamide).

PubMed

Abbott, Lauren J; Stevens, Mark J

2015-12-28

A coarse-grained (CG) model is developed for the thermoresponsive polymer poly(N-isopropylacrylamide) (PNIPAM), using a hybrid top-down and bottom-up approach. Nonbonded parameters are fit to experimental thermodynamic data following the procedures of the SDK (Shinoda, DeVane, and Klein) CG force field, with minor adjustments to provide better agreement with radial distribution functions from atomistic simulations. Bonded parameters are fit to probability distributions from atomistic simulations using multi-centered Gaussian-based potentials. The temperature-dependent potentials derived for the PNIPAM CG model in this work properly capture the coil-globule transition of PNIPAM single chains and yield a chain-length dependence consistent with atomistic simulations.

Detection of trypanosomatid Phytomonas parasitic in plants by polymerase chain reaction amplification of small subunit ribosomal DNA.

PubMed

Teixeira, M M; Campaner, M; Camargo, E P

1994-01-01

To improve the diagnosis of Phytomonas infections in plants, we developed a polymerase chain reaction (PCR) assay using synthetic oligonucleotides complementary to conserved sequences of the 18S small subunit ribosomal (SSU) gene. From 10 ng upward of DNA of cultures of Phytomonas isolated from plants, fruits, and insects, PCR amplified an 800-bp DNA band that, after restriction analysis and probe hybridization, proved to be of 18S rDNA Phytomonas origin. PCR was also done with sap samples of tomatoes experimentally infected with Phytomonas, yielding amplified 800-bp ribosomal DNA bands before any flagellate could be detected by microscopic examination of the fruit sap.

Effect of membrane properties on the performance of a hybrid GAC and ultrafiltration process for water treatment.

PubMed

Qiao, Tiejun; Wu, Guangxue; Zhang, Xihui; Au, Doris W T; Zhang, Jinsong

2012-06-01

The performance of a hybrid granular activated carbon (GAC) and ultrafiltration (UF) process for water treatment was investigated using five types of UF membranes. The removal percentages for chemical oxygen demand (COD(Mn)), particles (> or = 2 microm) and total bacteria by the hybrid process were 30-40%, 98-99% and 76-92%, respectively. No invertebrates were detected in the hybrid process effluent. Transmembrane pressure and specific permeate flux (SPF) of the five types of membranes varied. With decreasing membrane pore sizes, removal of COD(Mn) and particles increased, whereas SPF firstly decreased and then increased. Hydrophilic membranes had a relatively high COD(Mn) removal potential, but did not obviously affect particle removal or SPF.

Airborne-pollen pool and mating pattern in a hybrid zone between Pinus pumila and P. parviflora var. pentaphylla.

PubMed

Ito, Megumi; Suyama, Yoshihisa; Ohsawa, Takeshi A; Watano, Yasuyuki

2008-12-01

The reproductive isolation barriers and the mating patterns among Pinus pumila, P. parviflora var. pentaphylla and their hybrids were examined by flowering phenology and genetic assays of three life stages: airborne-pollen grains, adults and seeds, in a hybrid zone on Mount Apoi, Hokkaido, Japan. Chloroplast DNA composition of the airborne-pollen was determined by single-pollen polymerase chain reaction. Mating patterns were analysed by estimating the molecular hybrid index of the seed parent, their seed embryos and pollen parents. The observation of flowering phenology showed that the flowering of P. pumila precedes that of P. parviflora var. pentaphylla by about 6 to 10 days within the same altitudinal ranges. Although this prezygotic isolation barrier is effective, the genetic assay of airborne-pollen showed that the two pine species, particularly P. pumila, still have chances to form F(1) hybrid seeds. Both parental species showed a strong assortative mating pattern; F(1) seeds were found in only 1.4% of seeds from P. pumila mother trees and not at all in P. parviflora var. pentaphylla. The assortative mating was concluded as the combined result of flowering time differentiation and cross-incompatibility. In contrast to the parental species, hybrids were fertilized evenly by the two parental species and themselves. The breakdown of prezygotic barriers (intermediate flowering phenology) and cross-incompatibility may account for the unselective mating. It is suggested that introgression is ongoing on Mount Apoi through backcrossing between hybrids and parental species, despite strong isolation barriers between the parental species.

Developmental trajectories and breakdown in F1 interpopulation hybrids of Tribolium castaneum

PubMed Central

Drury, Douglas W; Ehmke, Ross C; Jideonwo, Victoria N; Wade, Michael J

2013-01-01

When hybrid inviability is an indirect by-product of local adaptation, we expect its degree of severity between pairs of populations to vary and to be sensitive to the environment. While complete reciprocal hybrid inviability is the outcome of the gradual process of local adaptation, it is not representative of the process of accumulation of incompatibility. In the flour beetle, Tribolium castaneum, some pairs of populations exhibit complete, reciprocal F1 hybrid incompatibility while other pairs are fully or partially compatible. We characterize this naturally occurring variation in the degree and timing of expression of the hybrid incompatible phenotype to better understand the number of genes or developmental processes contributing to speciation. We assessed the morphological and developmental variation in four Tribolium castaneum populations and their 12 possible F1 hybrids at each life-history stage from egg to adult. We find that the rate of hybrid larval development is affected in all interpopulation crosses, including those eventually producing viable, fertile adults. Hybrid incompatibility manifests early in development as changes in the duration of instars and diminished success in the transition between instars are relative to the parent populations. Parent populations with similar developmental profiles may produce hybrids with disrupted development. The degree and timing of expression of hybrid inviability depends upon populations crossed, direction of the cross, and environment in which hybrids are raised. Our findings suggest that the coordinated expression of genes involved in transitional periods of development is the underlying cause of hybrid incompatibility in this species. PMID:23919145