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Sample records for invariant chain fragment

  1. Criticality in translation-invariant parafermion chains

    NASA Astrophysics Data System (ADS)

    Li, Wei; Yang, Shuo; Tu, Hong-Hao; Cheng, Meng

    2015-03-01

    In this work, we numerically study critical phases in translation-invariant ZN parafermion chains with both nearest- and next-nearest-neighbor hopping terms. The model can be mapped to a ZN spin model with nearest-neighbor couplings via a generalized Jordan-Wigner transformation and translational invariance ensures that the spin model is always self-dual. We first study the low-energy spectrum of chains with only nearest-neighbor coupling, which are mapped onto standard self-dual ZN clock models. For 3 ≤N ≤6 , we match the numerical results to the known conformal field theory(CFT) identification. We then analyze in detail the phase diagram of a N =3 chain with both nearest and next-nearest-neighbor hopping and six critical phases with central charges being 4 /5 , 1, or 2 are found. We find continuous phase transitions between c =1 and 2 phases, while the phase transition between c =4 /5 and 1 is conjectured to be of Kosterlitz-Thouless type.

  2. Criticality in Translation-Invariant Parafermion Chains

    NASA Astrophysics Data System (ADS)

    Li, Wei; Yang, Shuo; Tu, Hong-Hao; Cheng, Meng

    2014-03-01

    Parafermionic zero modes have been recently proposed to emerge at certain topological defects in Abelian fractional quantum Hall systems. In this work, we investigate the phase diagram of a translationally invariant Z3 parafermion chain, with nearest- and next-nearest-neighbor hopping terms. The model can be mapped to a Z3 Potts model with nearest-neighbor couplings via a generalized Jordan-Wigner transformation. The phase diagram is obtained numerically via accurate density matrix renormalization group method, and six gapless phases with central charges being 4/5, 1 or 2 are found. By checking the energy derivatives, we observe continuous phase transitions between c = 1 and c = 2 phases, while the phase transition between c = 4 / 5 and c = 1 is conjectured to be of Kosterlitz-Thouless type.

  3. Faunal Communities Are Invariant to Fragmentation in Experimental Seagrass Landscapes.

    PubMed

    Lefcheck, Jonathan S; Marion, Scott R; Lombana, Alfonso V; Orth, Robert J

    2016-01-01

    Human-driven habitat fragmentation is cited as one of the most pressing threats facing many coastal ecosystems today. Many experiments have explored the consequences of fragmentation on fauna in one foundational habitat, seagrass beds, but have either surveyed along a gradient of existing patchiness, used artificial materials to mimic a natural bed, or sampled over short timescales. Here, we describe faunal responses to constructed fragmented landscapes varying from 4-400 m2 in two transplant garden experiments incorporating live eelgrass (Zostera marina L.). In experiments replicated within two subestuaries of the Chesapeake Bay, USA across multiple seasons and non-consecutive years, we comprehensively censused mesopredators and epifaunal communities using complementary quantitative methods. We found that community properties, including abundance, species richness, Simpson and functional diversity, and composition were generally unaffected by the number of patches and the size of the landscape, or the intensity of sampling. Additionally, an index of competition based on species co-occurrences revealed no trends with increasing patch size, contrary to theoretical predictions. We extend conclusions concerning the invariance of animal communities to habitat fragmentation from small-scale observational surveys and artificial experiments to experiments conducted with actual living plants and at more realistic scales. Our findings are likely a consequence of the rapid life histories and high mobility of the organisms common to eelgrass beds, and have implications for both conservation and restoration, suggesting that even small patches can rapidly promote abundant and diverse faunal communities.

  4. Faunal Communities Are Invariant to Fragmentation in Experimental Seagrass Landscapes.

    PubMed

    Lefcheck, Jonathan S; Marion, Scott R; Lombana, Alfonso V; Orth, Robert J

    2016-01-01

    Human-driven habitat fragmentation is cited as one of the most pressing threats facing many coastal ecosystems today. Many experiments have explored the consequences of fragmentation on fauna in one foundational habitat, seagrass beds, but have either surveyed along a gradient of existing patchiness, used artificial materials to mimic a natural bed, or sampled over short timescales. Here, we describe faunal responses to constructed fragmented landscapes varying from 4-400 m2 in two transplant garden experiments incorporating live eelgrass (Zostera marina L.). In experiments replicated within two subestuaries of the Chesapeake Bay, USA across multiple seasons and non-consecutive years, we comprehensively censused mesopredators and epifaunal communities using complementary quantitative methods. We found that community properties, including abundance, species richness, Simpson and functional diversity, and composition were generally unaffected by the number of patches and the size of the landscape, or the intensity of sampling. Additionally, an index of competition based on species co-occurrences revealed no trends with increasing patch size, contrary to theoretical predictions. We extend conclusions concerning the invariance of animal communities to habitat fragmentation from small-scale observational surveys and artificial experiments to experiments conducted with actual living plants and at more realistic scales. Our findings are likely a consequence of the rapid life histories and high mobility of the organisms common to eelgrass beds, and have implications for both conservation and restoration, suggesting that even small patches can rapidly promote abundant and diverse faunal communities. PMID:27244652

  5. Faunal Communities Are Invariant to Fragmentation in Experimental Seagrass Landscapes

    PubMed Central

    Marion, Scott R.; Lombana, Alfonso V.; Orth, Robert J.

    2016-01-01

    Human-driven habitat fragmentation is cited as one of the most pressing threats facing many coastal ecosystems today. Many experiments have explored the consequences of fragmentation on fauna in one foundational habitat, seagrass beds, but have either surveyed along a gradient of existing patchiness, used artificial materials to mimic a natural bed, or sampled over short timescales. Here, we describe faunal responses to constructed fragmented landscapes varying from 4–400 m2 in two transplant garden experiments incorporating live eelgrass (Zostera marina L.). In experiments replicated within two subestuaries of the Chesapeake Bay, USA across multiple seasons and non-consecutive years, we comprehensively censused mesopredators and epifaunal communities using complementary quantitative methods. We found that community properties, including abundance, species richness, Simpson and functional diversity, and composition were generally unaffected by the number of patches and the size of the landscape, or the intensity of sampling. Additionally, an index of competition based on species co-occurrences revealed no trends with increasing patch size, contrary to theoretical predictions. We extend conclusions concerning the invariance of animal communities to habitat fragmentation from small-scale observational surveys and artificial experiments to experiments conducted with actual living plants and at more realistic scales. Our findings are likely a consequence of the rapid life histories and high mobility of the organisms common to eelgrass beds, and have implications for both conservation and restoration, suggesting that even small patches can rapidly promote abundant and diverse faunal communities. PMID:27244652

  6. Matrix product states for su(2) invariant quantum spin chains

    NASA Astrophysics Data System (ADS)

    Zadourian, Rubina; Fledderjohann, Andreas; Klümper, Andreas

    2016-08-01

    A systematic and compact treatment of arbitrary su(2) invariant spin-s quantum chains with nearest-neighbour interactions is presented. The ground-state is derived in terms of matrix product states (MPS). The fundamental MPS calculations consist of taking products of basic tensors of rank 3 and contractions thereof. The algebraic su(2) calculations are carried out completely by making use of Wigner calculus. As an example of application, the spin-1 bilinear-biquadratic quantum chain is investigated. Various physical quantities are calculated with high numerical accuracy of up to 8 digits. We obtain explicit results for the ground-state energy, entanglement entropy, singlet operator correlations and the string order parameter. We find an interesting crossover phenomenon in the correlation lengths.

  7. On the fragmentation of biomolecules: Fragmentation of alanine dipeptide along the polypeptide chain

    SciTech Connect

    Solov'yov, I. A. Yakubovich, A. V.; Solov'yov, A. V.; Greiner, W.

    2006-09-15

    The interaction potential between amino acids in alanine dipeptide has been studied for the first time taking into account exact molecular geometry. Ab initio calculation has been performed in the framework of density functional theory taking into account all electrons in the system. The fragmentation of dipeptide along the polypeptide chain, as well as the interaction between alanines, has been considered. The energy of the system has been analyzed as a function of the distance between fragments for all possible dipeptide fragmentation channels. Analysis of the energy barriers makes it possible to estimate the characteristic fragmentation times and to determine the degree of applicability of classical electrodynamics for describing the system energy.

  8. All exactly solvable U(1)-invariant quantum spin 1 chains from Hecke algebra

    SciTech Connect

    Alcarez, F.C. ); Koberle, R. ); Lima-Santos, A. )

    1992-12-10

    In this paper, the authors obtain all exactly integrable spin 1 quantum chains, which are U(1) invariant and satisfy the Hecke algebra. The authors present various generalizations for arbitrary spin S and discuss their solution via Bethe ansatz methods.

  9. Development trends for generation of single-chain antibody fragments.

    PubMed

    Farajnia, Safar; Ahmadzadeh, Vahideh; Tanomand, Asghar; Veisi, Kamal; Khosroshahi, Shiva Ahdi; Rahbarnia, Leila

    2014-10-01

    Recombinant antibodies are increasingly being employed as therapeutic agents especially in combination with anti-cancer drugs. The single-chain antibody fragments are small antigen-binding proteins which provide the most commonly used antibody formats for diagnostic and therapeutic purposes. These antibody fragments have more rapid tumor penetration and clearance from the serum relative to full-length monoclonal antibodies. There are in vitro antibody-display technologies such as phage display, cell surface display, ribosome display and mRNA display that can be used to isolate high specificity and affinity single-chain antibodies against a wide variety of targets. We review these strategies for generation of stable and active antibody fragments in the present article.

  10. 'Green' reversible addition-fragmentation chain-transfer (RAFT) polymerization

    NASA Astrophysics Data System (ADS)

    Semsarilar, Mona; Perrier, Sébastien

    2010-10-01

    Reversible addition-fragmentation chain-transfer (RAFT) polymerization has revolutionized the field of polymer synthesis as a versatile tool for the production of complex polymeric architectures. As for all chemical processes, research and development in RAFT have to focus on the design and application of chemical products and processes that have a minimum environmental impact, and follow the principles of 'green' chemistry. In this Review, we summarize some of the green features of the RAFT process, and review the recent advances in the production of degradable polymers obtained from RAFT polymerization. Its use to modify biodegradable and renewable inorganic and organic materials to yield more functional products with enhanced applications is also covered. RAFT is a promising candidate for answering both the increasing need of modern society to employ highly functional polymeric materials and the global requirements for developing sustainable chemicals and processes.

  11. Experimental research of methods for clustering and selecting image fragments using spatial invariant equivalent models

    NASA Astrophysics Data System (ADS)

    Krasilenko, Vladimir G.; Lazarev, Alexander A.; Nikitovich, Diana V.

    2014-08-01

    In the paper, we show that the nonlinear spatial non-linear equivalency functions on the basis of continuous logic equivalence (nonequivalence) operations have better discriminatory properties for comparing images. Further, using the equivalent model of multiport neural networks and associative memory, (including matrix-matrix and matrix-tensor with adaptive-weighted correlation, multi-port neural-net auto-associative and hetero-associative memory (MP NN AAM and HAM ) and the proposed architecture based on them, we show how we can modify these models and architectures for space-invariant associative recognition and clustering (high performance parallel clustering processing) images. We consider possible implementations of 2D image classifiers, devices for partitioning image fragments into clusters and their architectures. The main base unit of such architectures is a matrix-matrix or matrix-tensor equivalentor, which can be implemented on the basis of two traditional correlators. We show that the classifiers based on the equivalency paradigm and optoelectronic architectures with space-time integration and parallel-serial 2D images processing have advantages such as increased memory capacity (more than ten times of the number of neurons!), High performance in different modes . We present the results of associative significant dimension (128x128, 610x340) image recognition - renewal modeling. It will be shown that these models are capable to recognize images with a significant percentage (20- 30%) damaged pixels. The experimental results show that such models can be successfully used for auto-and heteroassociative pattern recognition. We show simulation results of using these modifications for clustering and learning models and algorithms for cluster analysis of specific images and divide them into categories of the array. Show example of a cluster division of image fragments, letters and graphics for clusters with simultaneous formation of the outputweighted spatial

  12. Gladiolus plants transformed with single-chain variable fragment antibodies to Cucumber mosaic virus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Transgenic plants of Gladiolus ‘Peter Pears’ or ‘Jenny Lee’ were developed that contain single-chain variable fragments (scFv) to Cucumber mosaic virus (CMV) subgroup I or II. The CMV subgroup I heavy and light chain scFv fragments were placed under control of either the duplicated CaMV 35S or suga...

  13. Algebraic Bethe ansatz for the quantum group invariant open XXZ chain at roots of unity

    NASA Astrophysics Data System (ADS)

    Gainutdinov, Azat M.; Nepomechie, Rafael I.

    2016-08-01

    For generic values of q, all the eigenvectors of the transfer matrix of the Uq sl (2)-invariant open spin-1/2 XXZ chain with finite length N can be constructed using the algebraic Bethe ansatz (ABA) formalism of Sklyanin. However, when q is a root of unity (q =e iπ / p with integer p ≥ 2), the Bethe equations acquire continuous solutions, and the transfer matrix develops Jordan cells. Hence, there appear eigenvectors of two new types: eigenvectors corresponding to continuous solutions (exact complete p-strings), and generalized eigenvectors. We propose general ABA constructions for these two new types of eigenvectors. We present many explicit examples, and we construct complete sets of (generalized) eigenvectors for various values of p and N.

  14. The influence of invariant chain on the positive selection of single T cell receptor specificities.

    PubMed

    Tourne, S; Nakano, N; Viville, S; Benoist, C; Mathis, D

    1995-07-01

    The appearance of peptide-loaded major histocompatibility complex (MHC) class II molecules at the cell surface depends critically on the invariant chain (Ii). We have studied the influence of Ii on the positive selection of CD4+ T cells, mediated by class II molecules expressed on thymic stromal cells. Invariant chain-deficient mice (Iio) were crossed with different T cell receptor (TcR) transgenic strains and the emergence of mature CD4 single-positive thymocytes measured in Iio/TcR transgenic offspring. Positive selection was nearly absent in Iio/2B4 mice, which display receptors specific for a moth cytochrome c (MCC) peptide in the context of Ek. In addition, no T cell response was elicited when nontransgenic Iio animals were injected with this peptide, even though antigen-presenting cells (APC) from such mice were perfectly capable of presenting it, suggesting that selection of the entire anti-MCC 88-103 repertoire depends on Ii. Positive selection also appeared strongly reduced in another line of Iio/TcR transgenic mice (Iio/BDC2.5). However, in sharp contrast, a third line (Iio/3A9) exhibited almost normal positive selection of thymocytes displaying the transgene-encoded receptor. These thymocytes were exported to the periphery: peripheral T cells could respond normally to the appropriate peptide in vitro. The most likely interpretation of these findings is that selection of most CD4+ T cells depends on MHC class II complexes loaded with peptide in an Ii-dependent pathway, but some can be selected on class II complexes that are either loaded along an alternative, Ii-independent, route or are empty. This is consistent with the involvement of peptide in positive selection of CD4+ T cells, for which there exists little prior evidence. PMID:7621862

  15. Reversible addition-fragmentation chain transfer polymerization in microemulsion.

    PubMed

    O'Donnell, Jennifer M

    2012-04-21

    This tutorial review first details the uncontrolled microemulsion polymerization mechanism, and the RAFT polymerization mechanism to provide the necessary background for examining the RAFT microemulsion polymerization mechanism. The effect of the chain transfer agent per micelle ratio and the chain transfer agent aqueous solubility on the RAFT microemulsion polymerization kinetics, polymer molecular weight and polydispersity, and polymer nanoparticle size are discussed with a focus on oil-in-water microemulsions. Modeling of RAFT microemulsion polymerization kinetics and the resulting final polymer molecular weight are presented to assist with the analysis of observed experimental trends. Lastly, the current significance of RAFT microemulsion polymerization and the future directions are discussed. PMID:22246214

  16. Side chain chemistry mediates backbone fragmentation in hydrogen deficient peptide radicals.

    PubMed

    Sun, Qingyu; Nelson, Hosea; Ly, Tony; Stoltz, Brian M; Julian, Ryan R

    2009-02-01

    A crown ether based, photolabile radical precursor which forms noncovalent complexes with peptides has been prepared. The peptide/precursor complexes can be electrosprayed, isolated in an ion trap, and then subjected to laser photolysis and collision induced dissociation to generate hydrogen deficient peptide radicals. It is demonstrated that these peptide radicals behave very differently from the hydrogen rich peptide radicals generated by electron capture methods. In fact, it is shown that side chain chemistry dictates both the occurrence and relative abundance of backbone fragments that are observed. Fragmentation at aromatic residues occurs preferentially over most other amino acids. The origin of this selectivity relates to the mechanism by which backbone dissociation is initiated. The first step is abstraction of a beta-hydrogen from the side chain, followed by beta-elimination to yield primarily a-type fragment ions. Calculations reveal that those side chains which can easily lose a beta-hydrogen correlate well with experimentally favored sites for backbone fragmentation. In addition, radical mediated side chain losses from the parent peptide are frequently observed. Eleven amino acids exhibit unique mass losses from side chains which positively identify that particular amino acid as part of the parent peptide. Therefore, side chain losses allow one to unambiguously narrow the possible sequences for a parent peptide, which when combined with predictable backbone fragmentation should lead to greatly increased confidence in peptide identification.

  17. Exogenous Thyropin from p41 Invariant Chain Diminishes Cysteine Protease Activity and Affects IL-12 Secretion during Maturation of Human Dendritic Cells

    PubMed Central

    Zavašnik-Bergant, Tina; Bergant Marušič, Martina

    2016-01-01

    Dendritic cells (DC) play a pivotal role as antigen presenting cells (APC) and their maturation is crucial for effectively eliciting an antigen-specific immune response. The p41 splice variant of MHC class II-associated chaperone, called invariant chain p41 Ii, contains an amino acid sequence, the p41 fragment, which is a thyropin-type inhibitor of proteolytic enzymes. The effects of exogenous p41 fragment and related thyropin inhibitors acting on human immune cells have not been reported yet. In this study we demonstrate that exogenous p41 fragment can enter the endocytic pathway of targeted human immature DC. Internalized p41 fragment has contributed to the total amount of the immunogold labelled p41 Ii-specific epitope, as quantified by transmission electron microscopy, in particular in late endocytic compartments with multivesicular morphology where antigen processing and binding to MHC II take place. In cell lysates of treated immature DC, diminished enzymatic activity of cysteine proteases has been confirmed. Internalized exogenous p41 fragment did not affect the perinuclear clustering of acidic cathepsin S-positive vesicles typical of mature DC. p41 fragment is shown to interfere with the nuclear translocation of NF-κB p65 subunit in LPS-stimulated DC. p41 fragment is also shown to reduce the secretion of interleukin-12 (IL-12/p70) during the subsequent maturation of treated DC. The inhibition of proteolytic activity of lysosomal cysteine proteases in immature DC and the diminished capability of DC to produce IL-12 upon their subsequent maturation support the immunomodulatory potential of the examined thyropin from p41 Ii. PMID:26960148

  18. Invariant chain is a new chaperone for TLR7 in B cells.

    PubMed

    Tohmé, Mira; Manoury, Bénédicte

    2015-12-01

    The innate immune system provides the first barrier against pathogens. Intracellular Toll-like receptors (TLR3, 7 and 9) localise in endosomes and sense nucleotides from viruses and bacteria. This recognition induces their conformational changes resulting in the production of proinflammatory cytokines and MHC class II (MHCII) antigenic presentation. In the absence of stimulation, TLRs are retained in the endoplasmic reticulum. Upon stimulation, they relocate to the endo-lysosomal compartment, allowing the recruitment of the adaptor molecules, MyD88 or TRIF. Increasing evidences describe a cross talk between proteins that regulate both innate and adaptive immune responses. For example, proteolytic enzymes which are required for breaking down exogenous antigen to generate suitable peptides for MHCII molecules are also essential to activate endosomal TLRs and MHCII molecules were recently described to regulate TLR signalling. But other proteins are possibly involved and regulated differentially between cell types. We have observed that intracellular TLR trafficking and signalling in B cells are different from dendritic cells and macrophages and involved the MHCII chaperone molecule, the invariant chain (Ii). PMID:26198699

  19. The human-specific invariant chain isoform Iip35 modulates Iip33 trafficking and function.

    PubMed

    Sand, Kine Marita Knudsen; Landsverk, Ole J B; Berg-Larsen, Axel; Bakke, Oddmund; Gregers, Tone F

    2014-10-01

    The invariant chain (Ii) is a multifunctional protein, which has an essential role in the assembly and transport of major histocompatibility complex class II (MHC II) molecules. From a single gene, Ii is synthesized as four different isoforms: Iip33, Iip35, Iip41 and Iip43. Iip35 and Iip43 are specific to humans, and are formed due to an upstream alternative translation site, resulting in an N-terminal extension of 16 amino acids. This extension harbors a strong endoplasmic reticulum (ER) retention motif. Consequently, Iip35 or Iip43 expressed alone are retained in the ER, whereas Iip33 and Iip41 rapidly traffic to the endosomal pathway. Endogenously expressed, the four isoforms form mixed heterotrimers in the ER; however, mainly due to the absence of the Iip35/p43 isoforms in mice, little is known about how they influence general Ii function. In this study, we have co-expressed Iip33 and Iip35 in human cells with and without MHC II to gain a better understanding of how Iip35 isoform influences the cellular properties of Iip33. We find that Iip35 significantly affects the properties of Iip33. In the presence of Iip35, the transport of Iip33 out of the ER is delayed, its half-life is dramatically prolonged and its ability to induce enlarged endosomes and delayed endosomal maturation is abrogated.

  20. Steroids with a side chain containing a heterocyclic fragment: synthesis and transformations

    NASA Astrophysics Data System (ADS)

    Baranovskii, Aleksander V.; Litvinovskaya, Raisa P.; Khripach, Vladimir A.

    1993-07-01

    The latest data on the methods for the formation of the side chains of steroids containing a heterocyclic fragment are surveyed and described systematically. Attention is concentrated on the methods for the transformation of heterocycles in order to achieve the stereoselective formation of chiral centres in the side chain characteristic of a series of natural polyhydroxysteroids - ecdysones, brassinosteroids, vitamin D metabolites, etc. The bibliography includes 133 references.

  1. Adenovirus-based vaccine against Listeria monocytogenes: extending the concept of invariant chain linkage.

    PubMed

    Jensen, Søren; Steffensen, Maria Abildgaard; Jensen, Benjamin Anderschou Holbech; Schlüter, Dirk; Christensen, Jan Pravsgaard; Thomsen, Allan Randrup

    2013-10-15

    The use of replication-deficient adenoviruses as vehicles for transfer of foreign genes offers many advantages in a vaccine setting, eliciting strong cellular immune responses involving both CD8(+) and CD4(+) T cells. Further improving the immunogenicity, tethering of the inserted target Ag to MHC class II-associated invariant chain (Ii) greatly enhances both the presentation of most target Ags, as well as overall protection against viral infection, such as lymphocytic choriomeningitis virus (LCMV). The present study extends this vaccination concept to include protection against intracellular bacteria, using Listeria monocytogenes as a model organism. Protection in C57BL/6 mice against recombinant L. monocytogenes expressing an immunodominant epitope of the LCMV glycoprotein (GP33) was greatly accelerated, augmented, and prolonged following vaccination with an adenoviral vaccine encoding GP linked to Ii compared with vaccination with the unlinked vaccine. Studies using knockout mice demonstrated that CD8(+) T cells were largely responsible for this protection, which is mediated through perforin-dependent lysis of infected cells and IFN-γ production. Taking the concept a step further, vaccination of C57BL/6 (L. monocytogenes-resistant) and BALB/c (L. monocytogenes-susceptible) mice with adenoviral vectors encoding natural L. monocytogenes-derived soluble Ags (listeriolysin O and p60) revealed that tethering of these Ags to Ii markedly improved the vaccine-induced CD8(+) T cell response to two of three epitopes studied. More importantly, Ii linkage accelerated and augmented vaccine-induced protection in both mouse strains and prolonged protection, in particular that induced by the weak Ag, p60, in L. monocytogenes-susceptible BALB/c mice.

  2. Estimates of Comet Fragment Masses from Impact Crater Chains on Callisto and Ganymede

    NASA Technical Reports Server (NTRS)

    McKinnon, William B.; Schenk, Paul M.

    1995-01-01

    Chains of impact craters, or catenae, have been identified in Voyager images of Callisto and Ganymede. Although these resemble in some respects secondary crater chains, the source craters and basins for the catenae cannot be identified. The best explanation is a phenomenon similar to that displayed by former comet Shoemaker-Levy 9; tidal (or other) breakup close to Jupiter followed by gradual orbital separation of the fragments and collision with a Galilean satellite on the outbound leg of the trajectory. Because the trajectories must pass close to Jupiter, this constrains the impact geometry (velocity and impact angle) of the individual fragments. For the dominant classes of impactors, short period Jupiter-family comets and asteroids, velocities at Callisto and Ganymede are dominated by Jovian gravity and a satellite's orbital motion, and are insensitive to the pre-fragmentation heliocentric velocity; velocities are insensitive to satellite gravity for all impactor classes. Complex crater shapes on Callisto and Ganymede are determined from Voyager images and Schmidt-Holsapple scaling is used to back out individual fragment masses. We find that comet fragment radii are generally less than about 500 m (for ice densities) but can be larger. These estimates can be compared with those for the Shoemaker-Levy 9 impactors.

  3. An extended patch-dynamic framework for food chains in fragmented landscapes.

    PubMed

    Liao, Jinbao; Chen, Jiehong; Ying, Zhixia; Hiebeler, David E; Nijs, Ivan

    2016-09-09

    Habitat destruction, a key determinant of species loss, can be characterized by two components, patch loss and patch fragmentation, where the former refers to the reduction in patch availability, and the latter to the division of the remaining patches. Classical metacommunity models have recently explored how food web dynamics respond to patch loss, but the effects of patch fragmentation have largely been overlooked. Here we develop an extended patch-dynamic model that tracks the patch occupancy of the various trophic links subject to colonization-extinction-predation dynamics by incorporating species dispersal with patch connectivity. We found that, in a simple food chain, species at higher trophic level become extinct sooner with increasing patch loss and fragmentation due to the constraint in resource availability, confirming the trophic rank hypothesis. Yet, effects of fragmentation on species occupancy are largely determined by patch loss, with maximal fragmentation effects occurring at intermediate patch loss. Compared to the spatially explicit simulations that we also performed, the current model with pair approximation generates similar community patterns especially in spatially clustered landscapes. Overall, our extended framework can be applied to model more complex food webs in fragmented landscapes, broadening the scope of existing metacommunity theory.

  4. An extended patch-dynamic framework for food chains in fragmented landscapes

    PubMed Central

    Liao, Jinbao; Chen, Jiehong; Ying, Zhixia; Hiebeler, David E.; Nijs, Ivan

    2016-01-01

    Habitat destruction, a key determinant of species loss, can be characterized by two components, patch loss and patch fragmentation, where the former refers to the reduction in patch availability, and the latter to the division of the remaining patches. Classical metacommunity models have recently explored how food web dynamics respond to patch loss, but the effects of patch fragmentation have largely been overlooked. Here we develop an extended patch-dynamic model that tracks the patch occupancy of the various trophic links subject to colonization-extinction-predation dynamics by incorporating species dispersal with patch connectivity. We found that, in a simple food chain, species at higher trophic level become extinct sooner with increasing patch loss and fragmentation due to the constraint in resource availability, confirming the trophic rank hypothesis. Yet, effects of fragmentation on species occupancy are largely determined by patch loss, with maximal fragmentation effects occurring at intermediate patch loss. Compared to the spatially explicit simulations that we also performed, the current model with pair approximation generates similar community patterns especially in spatially clustered landscapes. Overall, our extended framework can be applied to model more complex food webs in fragmented landscapes, broadening the scope of existing metacommunity theory. PMID:27608823

  5. An extended patch-dynamic framework for food chains in fragmented landscapes.

    PubMed

    Liao, Jinbao; Chen, Jiehong; Ying, Zhixia; Hiebeler, David E; Nijs, Ivan

    2016-01-01

    Habitat destruction, a key determinant of species loss, can be characterized by two components, patch loss and patch fragmentation, where the former refers to the reduction in patch availability, and the latter to the division of the remaining patches. Classical metacommunity models have recently explored how food web dynamics respond to patch loss, but the effects of patch fragmentation have largely been overlooked. Here we develop an extended patch-dynamic model that tracks the patch occupancy of the various trophic links subject to colonization-extinction-predation dynamics by incorporating species dispersal with patch connectivity. We found that, in a simple food chain, species at higher trophic level become extinct sooner with increasing patch loss and fragmentation due to the constraint in resource availability, confirming the trophic rank hypothesis. Yet, effects of fragmentation on species occupancy are largely determined by patch loss, with maximal fragmentation effects occurring at intermediate patch loss. Compared to the spatially explicit simulations that we also performed, the current model with pair approximation generates similar community patterns especially in spatially clustered landscapes. Overall, our extended framework can be applied to model more complex food webs in fragmented landscapes, broadening the scope of existing metacommunity theory. PMID:27608823

  6. Invariant exchange perturbation theory for multicenter systems and its application to the calculation of magnetic chains in manganites

    SciTech Connect

    Orlenko, E. V. Ershova, E. V.; Orlenko, F. E.

    2013-10-15

    The formalism of exchange perturbation theory is presented with regard to the general principles of constructing an antisymmetric vector with the use of the Young diagrams and tableaux in which the coordinate and spin parts are not separated. The form of the energy and wave function corrections coincides with earlier obtained expressions, which are reduced in the present paper to a simpler form of a symmetry-adapted perturbation operator, which preserves all intercenter exchange contributions. The exchange perturbation theory (EPT) formalism itself is presented in the standard form of invariant perturbation theory that takes into account intercenter electron permutations between overlapping nonorthogonal states. As an example of application of the formalism of invariant perturbation theory, we consider the magnetic properties of perovskite manganites La{sub 1/3}Ca{sub 2/3}MnO{sub 3} that are associated with the charge and spin ordering in magnetic chains of manganese. We try to interpret the experimental results obtained from the study of the effect of doping the above alloys by the model of superexchange interaction in manganite chains that is constructed on the basis of the exchange perturbation theory (EPT) formalism. The model proposed makes it possible to carry out a quantitative analysis of the effect of substitution of manganese atoms by doping elements with different electron configurations on the electronic structure and short-range order in a magnetic chain of manganites.

  7. A Novel Single-Chain Antibody Fragment for Detection of Mannose 6-Phosphate-Containing Proteins

    PubMed Central

    Müller-Loennies, Sven; Galliciotti, Giovanna; Kollmann, Katrin; Glatzel, Markus; Braulke, Thomas

    2010-01-01

    Newly synthesized soluble lysosomal hydrolases require mannose 6-phosphate (Man6P) residues on their oligosaccharides for their transport to lysosomes. The formation of Man6P residues is catalyzed by the GlcNAc-1-phosphotransferase, which is defective in the lysosomal storage disorders mucolipidosis type II (ML II) and ML III. Both hypersecretion and reduced intracellular level of lysosomal enzymes as well as direct sequencing of GlcNAc-1-phosphotransferase genes are important diagnostic markers for ML II and ML III. A high-affinity Man6P-specific single-chain antibody fragment was generated, allowing the rapid indirect demonstration of defective GlcNAc-1-phosphotransferase. In media and extracts of cultured fibroblasts of healthy controls but not of ML II and ML III patients, several Man6P-containing proteins could be detected by anti-Man6P Western blotting. Immunoprecipitation of Man6P-containing proteins from conditioned media or mouse brain extracts followed by arylsulfatase A and cathepsin D Western blotting confirmed the specificity of the antibody fragment for lysosomal proteins. Application of the antibody fragment in immunohistochemistry of human brain slices from nonaffected patients showed strong neuronal immunoreactivity, which was not observed in cortical sections of an ML II patient. Finally, in brain extracts of a novel GlcNAc-1-phosphotransferase knock-in mouse no Man6P-containing proteins were detectable. Thus, the single-chain antibody fragment against Man6P was demonstrated to allow the specific, rapid, and convenient detection of Man6P-containing proteins and facilitates the diagnosis of ML II and ML III. PMID:20472886

  8. Transport and intracellular distribution of MHC class II molecules and associated invariant chain in normal and antigen-processing mutant cell lines.

    PubMed

    Riberdy, J M; Avva, R R; Geuze, H J; Cresswell, P

    1994-06-01

    We have compared the intracellular transport and subcellular distribution of MHC class II-invariant chain complexes in a wild-type HLA-DR3 homozygous cell line and a mutant cell line, T2.DR3. The latter has a defect in antigen processing and accumulates HLA-DR3 molecules associated with an invariant chain-derived peptide (CLIP) rather than the normal complement of peptides derived from endocytosed proteins. We find that in the wild-type cells, CLIP is transiently associated with HLA-DR3 molecules, suggesting that the peptide is a normal class II-associated intermediate generated during proteolysis of the invariant chain. In the mutant cell line proteolysis of the invariant chain is less efficient, and HLA-DR3/CLIP complexes are generated much more slowly. Examination of the mutant cell line by immunoelectronmicroscopy shows that class II-invariant chain complexes accumulate intracellularly in large acidic vesicles which contain lysosomal markers, including beta-hexosaminidase, cathepsin D, and the lysosomal membrane protein CD63. The markers in these vesicles are identical to those seen in the class II-containing vesicles (MIICs) seen in the wild-type cells but the morphology is drastically different. The vesicles in the mutant cells are endocytic, as measured by the internalization of BSA-gold conjugates. The implication of these findings for antigen processing in general and the nature of the mutation in particular are discussed.

  9. Bond breaking in a Morse chain under tension: Fragmentation patterns, higher index saddles, and bond healing

    NASA Astrophysics Data System (ADS)

    Mauguière, F. A. L.; Collins, P.; Ezra, G. S.; Wiggins, S.

    2013-04-01

    We investigate the fragmentation dynamics of an atomic chain under tensile stress. We have classified the location, stability type (indices), and energy of all equilibria for the general n-particle chain, and have highlighted the importance of saddle points with index >1. We show that for an n = 2-particle chain under tensile stress the index 2 saddle plays a central role in organizing the dynamics. We apply normal form theory to analyze phase space structure and dynamics in a neighborhood of the index 2 saddle. We define a phase dividing surface (DS) that enables us to classify trajectories passing through a neighborhood of the saddle point using the values of the integrals associated with the normal form. We also generalize our definition of the dividing surface and define an extended dividing surface (EDS), which is used to sample and classify all trajectories that pass through a phase space neighborhood of the index 2 saddle at total energies less than that of the saddle. Classical trajectory simulations are used to study fragmentation patterns for the n = 2 chain under tension. That is, we investigate the relative probability for breaking one bond versus concerted fission of several (two, in this case) bonds. Initial conditions for trajectories are obtained by sampling the EDS at constant energy. We sample trajectories at fixed energies both above and below the energy of the saddle. The fate of trajectories (single versus multiple bond breakage) is explored as a function of the location of the initial condition on the EDS, and a connection made to the work of Chesnavich on collision-induced dissociation. A significant finding is that we can readily identify trajectories that exhibit bond healing. Such trajectories pass outside the nominal (index 1) transition state for single bond dissociation, but return to the potential well region, possibly several times, before ultimately dissociating.

  10. [Characterization of aldehyde dehydrogenase gene fragment from mung bean Vigna radiata using the polymerase chain reaction].

    PubMed

    Ponomarev, A G; Bubiakina, V V; Tatarinova, T D; Zelenin, S M

    1998-01-01

    Two degenerate oligonucleotide sequence primers and polymerase chain reactions on total DNA have been utilized to clone on 651--bp gene fragment coding the central part of amino acid sequence of an earlier unknown aldehyde dehydrogenase (ALDH) from mung bean. The deduced partial amino acid sequence for this aldehyde dehydrogenase shows about 65% sequence identity to ALDHs of Vibrio cholerae Rhodococcus sp., Alcaligenes eutrophus and about 45% sequence identity to mammalian ALDHs 1 and 2, ALDHs of Aspergillus niger and A, nidulans, the betain aldehyde dehydrogenase from spinach. Alignment of the mung bean aldehyde dehydrogenase partial amino acid sequence with the sequence of 16 NAD(P)(+)-dependent aldehyde dehydrogenases has demonstrated that all strictly conserved amino acid residues and all three conservative regions are identical. PMID:9778740

  11. A chondroitin sulfate chain attached to the bone dentin matrix protein 1 NH2-terminal fragment.

    PubMed

    Qin, Chunlin; Huang, Bingzhen; Wygant, James N; McIntyre, Bradley W; McDonald, Charles H; Cook, Richard G; Butler, William T

    2006-03-24

    Dentin matrix protein 1 (DMP1) is an acidic noncollagenous protein shown by gene ablations to be critical for the proper mineralization of bone and dentin. In the extracellular matrix of these tissues DMP1 is present as fragments representing the NH2-terminal (37 kDa) and COOH-terminal (57 kDa) portions of the cDNA-deduced amino acid sequence. During our separation of bone noncollagenous proteins, we observed a high molecular weight, DMP1-related component (designated DMP1-PG). We purified DMP1-PG with a monoclonal anti-DMP1 antibody affinity column. Amino acid analysis and Edman degradation of tryptic peptides proved that the core protein for DMP1-PG is the 37-kDa fragment of DMP1. Chondroitinase treatments demonstrated that the slower migration rate of DMP1-PG is due to the presence of glycosaminoglycan. Quantitative disaccharide analysis indicated that the glycosaminoglycan is made predominantly of chondroitin 4-sulfate. Further analysis on tryptic peptides led us to conclude that a single glycosaminoglycan chain is linked to the core protein via Ser74, located in the Ser74-Gly75 dipeptide, an amino acid sequence specific for the attachment of glycosaminoglycans. Our findings show that in addition to its existence as a phosphoprotein, the NH2-terminal fragment from DMP1 occurs as a proteoglycan. Amino acid sequence alignment analysis showed that the Ser74-Gly75 dipeptide and its flanking regions are highly conserved among a wide range of species from caiman to the Homo sapiens, indicating that this glycosaminoglycan attachment domain has survived an extremely long period of evolution pressure, suggesting that the glycosaminoglycan may be critical for the basic biological functions of DMP1.

  12. A collagen-binding EGFR single-chain Fv antibody fragment for the targeted cancer therapy.

    PubMed

    Liang, Hui; Li, Xiaoran; Chen, Bing; Wang, Bin; Zhao, Yannan; Zhuang, Yan; Shen, He; Zhang, Zhijun; Dai, Jianwu

    2015-07-10

    Collagen, a primary component of the extracellular matrix (ECM), is highly expressed in a variety of cancers and influences the tumor microenvironment by increasing the recruitment of macrophages and endothelial cells. Therefore, collagen is a highly promising target for cancer therapy. The collagen-binding domain (CBD) can dynamically bind to collagen and achieve the sustained release of CBD-fused protein in the collagen network. Here, we developed a collagen-binding epidermal growth factor receptor (EGFR) antibody fragment for targeting the collagen-rich ECM in tumors. The single chain fragment variable (scFv) of cetuximab was fused to CBD (CBD-scFv) and expressed in Pichia pastoris. CBD-scFv preserved the antigen binding domain and anti-tumor activity of cetuximab in vitro. Moreover, CBD-scFv displayed a collagen binding ability due to the function of CBD. In vivo experiments revealed that CBD-scFv bound to collagen and achieved sustained release in tumors. Furthermore, CBD-scFv significantly suppressed the growth of tumors in A431 xenografts. Therefore, CBD-scFv had a potential therapeutic value for the collagen-rich carcinomas. The specific target and sustained release of CBD-scFv in tumors could be a new approach for targeted drug delivery in cancer therapy.

  13. From cysteine to longer chain thiols: thermodynamic analysis of cadmium binding by phytochelatins and their fragments.

    PubMed

    Chekmeneva, Elena; Gusmão, Rui; Díaz-Cruz, José Manuel; Ariño, Cristina; Esteban, Miquel

    2011-08-01

    Isothermal Titration Calorimetry (ITC) was used to study the binding of Cd(2+) by phytochelatins ((γGlu-Cys)(n)-Gly, PC(n); n = 1-5) and their selected fragments (Cys, Cys-Gly and γGlu-Cys) in order to understand the influence of the chain length on the complex stabilities and the origin of the enhanced affinities in Tris buffer at pH 7.5 and 8.5 and at 25 °C. Different complexes are formed with glutathione (GSH) and its fragments, Cys, Cys-Gly and γGlu-Cys, and their stabilities depend on the corresponding pK(a) value of the thiol group in the ligands. The stability of Cd-PC(n) complexes increases moving towards higher PC(2-5), as well as the complexing capacity expressed as the number of metal ions that can be bound by one ligand molecule. The affinity of Cd(2+) for the PC(n) can be described by the following GSH < PC(2) < PC(3)≤ PC(4)≤ PC(5) sequence. On the basis of these thermodynamic data it is possible to explain the abundance of certain Cd-PC(n) complexes found in nature. The comprehension of the thermodynamic rules that govern the interactions of Cd(2+) with PC(n) and their constituents is of great service in the research with real plant samples subjected to metal stress and in the development of new strategies of bio/phytoremediation.

  14. Mutagenicity Assessment of Organophosphates using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Assay

    PubMed Central

    Bhinder, Preety; Chaudhry, Asha

    2013-01-01

    Objectives: In this study we have evaluated the mutagenicity of organophosphate pesticides acephate, chlorpyrifos, and profenofos using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay with the mosquito Culex quinquefasciatus taken as an experimental model. Materials and Methods: Second instar larvae were treated with LC20 of each pesticide for 24 h and mutations induced in the sequence of mitochondrial COII gene (690bp) were studied from restriction patterns generated with AluI, PacI, and PsiI restriction endonucleases. Results: Variations in the number and size of digested fragments were recorded from treated individuals compared with controls showing that the restriction enzymes created a cut at different locations. In addition, sequences of COII gene from control and treated individuals were also used to confirm the RFLP patterns. From the sequence alignment data, it was found that mutations caused the destruction and generation of restriction sites in the gene sequence of treated individuals. Conclusion: This study indicates that all the three pesticides had potential to induce mutations in the normal sequence of COII gene and also advocates the use of PCR-RFLP assay as an efficient, rapid, and sensitive technique to detect mutagenicity of pesticides. PMID:24403735

  15. Poly(vinyl ester) Block Copolymers Synthesized by Reversible Addition−Fragmentation Chain Transfer Polymerizations

    SciTech Connect

    Lipscomb, Corinne E.; Mahanthappa, Mahesh K.

    2009-07-31

    Homopolymerizations and block copolymerizations of vinyl acetate (VAc), vinyl pivalate (VPv), and vinyl benzoate (VBz) by reversible addition-fragmentation chain transfer (RAFT) polymerization have been studied. Polymerizations of VAc initiated with 2,2{prime}-azobis(isobutyronitrile) (AIBN) at 60 C using two different xanthate RAFT agents C{sub 2}H{sub 5}OC(=S)SR (R = -CH(CH{sub 3})CO{sub 2}C{sub 2}H{sub 5} (1) and -CH(CH{sub 3})O{sub 2}CC(CH{sub 3}){sub 3} (2)) were examined to elucidate the dependence of the polydispersities of the resulting polymers on the RAFT agent leaving group R. RAFT agent 2, in which the leaving R-group mimics a growing vinyl ester polymer chain, consistently yields poly(vinyl acetates) having broader polydispersities than those synthesized using 1 (M{sub n} = 3.6-14 kg/mol and M{sub w}/M{sub n} = 1.15-1.33). While VPv exhibits similar controlled polymerization behavior to VAc, RAFT homopolymerizations of VBz mediated by 1 indicate this electron-deficient vinyl ester requires higher temperatures to effect controlled polymerizations to yield polymers having M{sub n} = 4-14 kg/mol and M{sub w}/M{sub n} = 1.29-1.53. Chain extension reactions from xanthate-terminated vinyl ester homopolymers with VAc, VPv, and VBz proceed with variable efficiencies to furnish block copolymers that microphase separate in the melt state as determined by small-angle X-ray scattering.

  16. Amino and Acetamide Functional Group Effects on the Ionization and Fragmentation of Sugar Chains in Positive-Ion Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Yamagaki, Tohru; Sugahara, Kohtaro; Watanabe, Takehiro

    2014-01-01

    To elucidate the influence of amino (-NH2) and acetamide (-NHCOCH3, -NAc) groups in sugar chains on their ionization and fragmentation, cycloamyloses (cyclodextrins, CyDs) and lacto-oligosaccharide are analyzed by MALDI TOF/TOF and ESI Q-TOF mass spectrometry. CyD derivatives substituted by amino or acetamide groups are ideal analytes to extract the function group effects, which are amino-CyD with one hexosamine (HexNH2) and acetamide-CyD with one N-acetyl hexosamine (HexNAc). Interestingly, the relative ion intensities and isotope-like patterns in their product ion spectra depend on the functional groups and ion forms of sugar chains. Consequently, the results indicate that a proton (H+) localizes on the amino group of the amino sugar, and that the proton (H+) induces their fragmentation. Sodium cation (Na+) attachment is independent from amino group and exerts no influence on their fragmentation patterns in amino group except for mono- and disaccharide fragment ions because there is the possibility of the reducing end effect. In contrast, a sodium cation localizes much more frequently on the acetamide group in acetamide-CyDs because the chemical species with HexNAc are stable. Thus, their ions with HexNAc are abundant. These results are consistent with the fragmentation of lacto-neo- N-tetraose and maltotetraose, suggesting that a sodium cation generally localizes much more frequently on the acetamide group in sugar chains.

  17. Invariant chain as a vehicle to load antigenic peptides on human MHC class I for cytotoxic T-cell activation.

    PubMed

    Wälchli, Sébastien; Kumari, Shraddha; Fallang, Lars-Egil; Sand, Kine M K; Yang, Weiwen; Landsverk, Ole J B; Bakke, Oddmund; Olweus, Johanna; Gregers, Tone F

    2014-03-01

    Protective T-cell responses depend on efficient presentation of antigen (Ag) in the context of major histocompatibility complex class I (MHCI) and class II (MHCII) molecules. Invariant chain (Ii) serves as a chaperone for MHCII molecules and mediates trafficking to the endosomal pathway. The genetic exchange of the class II-associated Ii peptide (CLIP) with antigenic peptides has proven efficient for loading of MHCII and activation of specific CD4(+) T cells. Here, we investigated if Ii could similarly activate human CD8(+) T cells when used as a vehicle for cytotoxic T-cell (CTL) epitopes. The results show that wild type Ii, and Ii in which CLIP was replaced by known CTL epitopes from the cancer targets MART-1 or CD20, coprecipitated with HLA-A*02:01 and mediated colocalization in the endosomal pathway. Furthermore, HLA-A*02:01-positive cells expressing CLIP-replaced Ii efficiently activated Ag-specific CD8(+) T cells in a TAP- and proteasome-independent manner. Finally, dendritic cells transfected with mRNA encoding IiMART-1 or IiCD20 primed naïve CD8(+) T cells. The results show that Ii carrying antigenic peptides in the CLIP region can promote efficient presentation of the epitopes to CTLs independently of the classical MHCI peptide loading machinery, facilitating novel vaccination strategies against cancer.

  18. [Isolation of a gamma heavy chain fragment from normal human serum].

    PubMed

    Irurzun, P L; Miranda, M P

    1976-01-01

    Several components of catodic electrophoretic migration in serum and urine are present in normal individuals and in rabbit serum. There also exists in man and in some animals, serum fractions of low molecular weight. These types of serum components may be or may not be related with the IgG. In a previous study we have isolated two components in the slow catodic electrophoretic area of the normal human serum (NHS). One of them was identified as an IgG subclass and the other component presented a clear line of precipitation to gamma heavy chain specific immuno-serum. This latter component was found in the post gamma-globulin area crossing the IgG arc in the I.E. analysis. Its molecular weight was variable from 3700 to 9500. In this paper a differential analysis of the gamma fragment isolated for us, is made and its relationship with Fc subfragments of pepsin-digested IgG is studied. In order to obtain this comparative study, the electrophoresis, gel diffusion immunoelectrophoresis gel chromatography and analytic ultracentrifugation techniques are employed. The post-gammaglobulin fraction has been isolated from total normal human serum without previous manipulation, or with the gammaglobulin fraction precipitated with saturated ammonium sulphate, in Sephadex G-200 chromatography. These two fractions present similar immunelectrophoretical characteristics. The constant sedimentation is 0.90 S and the approximated molecular weight is 7000. Since the pepsin digestion of IgG produced Fc subfragments of low molecular weight, we have isolated and submitted this immunoglobulin to peptic digestion. The G-75 Sephadex filtration shows an isolated post-gamma-globulin of I.E. sedimentation constant and molecular weight whose characteristics are similar to the isolated serum post-gammaglobulin fraction. The antigenical analysis in I.D. shows a total identity between the pepsin digested post-gammaglobulin and the fragment obtained for us from the human serum to an anti-heavy gamma

  19. Peptide docking of HIV-1 p24 with single chain fragment variable (scFv) by CDOCKER algorithm

    NASA Astrophysics Data System (ADS)

    Karim, Hana Atiqah Abdul; Tayapiwatana, Chatchai; Nimmanpipug, Piyarat; Zain, Sharifuddin M.; Rahman, Noorsaadah Abdul; Lee, Vannajan Sanghiran

    2014-10-01

    In search for the important residues that might have involve in the binding interaction between the p24 caspid protein of HIV-1 fragment (MET68 - PRO90) with the single chain fragment variable (scFv) of FAB23.5, modern computational chemistry approach has been conducted and applied. The p24 fragment was initially taken out from the 1AFV protein molecule consisting of both light (VL) and heavy (VH) chains of FAB23.5 as well as the HIV-1 caspid protein. From there, the p24 (antigen) fragment was made to dock back into the protein pocket receptor (antibody) by using the CDOCKER algorithm to conduct the molecular docking process. The score calculated from the CDOCKER gave 15 possible docked poses with various docked ligand's positions, the interaction energy as well as the binding energy. The best docked pose that imitates the original antigen's position was determined and further processed to the In Situ minimization to obtain the residues interaction energy as well as to observe the hydrogen bonds interaction in the protein-peptide complex. Based on the results demonstrated, the specific residues in the complex that have shown immense lower interaction energies in the 5Å vicinity region from the peptide are from the heavy chain (VH:TYR105) and light chain (VL: ASN31, TYR32, and GLU97). Those residues play vital roles in the binding mechanism of Antibody-Antigen (Ab-Ag) complex of p24 with FAB23.5.

  20. Development of single chain variable fragment (scFv) antibodies against surface proteins of ‘Ca. Liberibacter asiaticus’

    Technology Transfer Automated Retrieval System (TEKTRAN)

    ‘Ca. Liberibacter asiaticus’ is the causal agent of citrus huanglongbing, the most serious disease of citrus worldwide. We have developed and applied immunization and affinity screening methods to develop a primary library of recombinant single chain variable fragment (scFv) antibodies in an M13 vec...

  1. The Fragments of the Photosynthetic Electron Transfer Chain in Model Systems

    PubMed Central

    Krasnovsky, A. A.

    1972-01-01

    In this paper the recent research from our laboratory is reviewed. Short fragments of the photochemical electron transfer chain of photosynthesis were reproduced in aqueous detergent solutions or in organic solvents. The function of photosystem I is reproduced in a ternary system of chlorophylls, electron donors (dienols, sulfhydryl compounds, hydrazine, etc.), and electron acceptors (viologens, nicotinamide-adenine dinucleotide [NAD], flavines, etc.). Chlorophyll-photosensitized reduction of viologens in some cases is activated by oxygen at the expense of active reductants formed during the photosensitized oxidation of an initial electron donor (thiourea). Chlorophyll-photosensitized oxidoreduction of cytochromes is activated by flavines, viologens, vitamin K derivatives, and some other redox systems (cofactors of cyclic photophosphorylation). The primary mechanism of the reactions studied depends on the reversible chlorophyll photooxidoreduction. In binary systems, chlorophyll (monomeric or aggregated) and electron donor or electron acceptor, reversible photoreduction or photooxidation is observed. Irreversible bacteriochlorophyll oxidation leads to the formation of chlorophyll and protochlorophyll analogues; irreversible protochlorophyll photoreduction results in chlorophyll-like pigment appearance. The photodisaggregation of chlorophyll was observed. The models of photosystem II studied were the photochemical oxygen evolution in aqueous solutions of electron acceptors (ferric compounds, quinone), photosensitized in the near UV part of the spectrum by inorganic semiconductors (tungsten, titanium, and zinc oxides). All reactions described are based on electron (hydrogen) transfer photosensitized by pigment system. PMID:4338745

  2. Anti-Staphylococcus aureus single-chain variable region fragments provide protection against mastitis in mice.

    PubMed

    Wang, Man; Zhang, Yan; Zhu, Jianguo

    2016-03-01

    Staphylococcus aureus is a leading causative agent of bovine mastitis, which can result in significant economic losses to the dairy industry. However, available vaccines against bovine mastitis do not confer adequate protection, although passive immunization with antibodies may be useful to prevent disease. Hence, we constructed a bovine single-chain variable region fragment (scFv) phage display library using cDNAs from peripheral blood lymphocytes of cows with S. aureus-induced mastitis. After four rounds of selection, eight scFvs that bound S. aureus antigens with high affinity were obtained. The framework regions of the variable domains (VH and VL) of the eight scFvs were highly conserved, and the complementarity-determining regions (CDRs) displayed significant diversity, especially CDR3 of the VH domain. All eight scFvs inhibited S. aureus growth in culture medium. Lactating mice were challenged by injecting S. aureus into the fourth mammary gland. Histopathological analysis showed that treatment with these scFvs prior to bacterial challenge maintained the structure of the mammary acini, decreased infiltration of polymorphonuclear neutrophils, increased levels of interferon-gamma and interleukin-4, and reduced tumor necrosis factor-alpha levels in mammary tissues, as compared with mice treatment with physiological saline (P < 0.05). These novel bovine scFvs may be suitable candidates for therapeutic agents for the prevention of S. aureus-induced bovine mastitis.

  3. Construction of an antimyoglobin single-chain variable fragment with rapid reaction kinetics.

    PubMed

    Jang, Jun-Hyuck; Kim, Dong-Hyung; Paek, Se-Hwan; Woo, Eui-Jeon; Kim, Young-Wan

    2016-01-01

    Antibodies with rapid reaction kinetics (high association and dissociation rates), named reversible antibodies, are used to perform continuous monitoring of sensitive disease biomarkers. In cases of acute myocardial infarction (AMI), continuous monitoring and early diagnosis are important. Human myoglobin (Myo) is a useful biomarker for AMI during the early stage after the onset of symptoms. In this study, a single-chain variable fragment (scFv) specific to Myo was derived from an IgG antibody that has rapid reaction kinetics. Enzyme-linked immunosorbent assay revealed that recombinant scFv exhibited 3.8-fold reduced affinity compared with the parent IgG antibody based on the antibody concentration necessary for 50% of the maximum signal. The scFv retained the rapid reaction kinetic mode with average kon and koff of 2.63 × 10(5) M(-1) Sec(-1) and 3.25 × 10(-3) Sec(-1) , respectively, which were reduced to 10- and 2.3-fold compared with those of the parent antibody. The equilibrium constant for the association of the scFv (KA = 8.09 × 10(7) M(-1) ) was 4.6-fold lower than that of its parent IgG antibody. This scFv may be a starting point for further mutagenesis/kinetic and structural analyses providing valuable insight into the mechanism of reversible antibodies.

  4. Multi-channeled single chain variable fragment (scFv) based microfluidic device for explosives detection.

    PubMed

    Charles, Paul T; Davis, Jasmine; Adams, André A; Anderson, George P; Liu, Jinny L; Deschamps, Jeffrey R; Kusterbeck, Anne W

    2015-11-01

    The development of explosives detection technologies has increased significantly over the years as environmental and national security agencies implement tighter pollution control measures and methods for improving homeland security. 2, 4, 6-Trinitrotoluene (TNT), known primarily as a component in munitions, has been targeted for both its toxicity and carcinogenic properties that if present at high concentrations can be a detriment to both humans, marine and plant ecosystems. Enabling end users with environmental detection and monitoring systems capable of providing real-time, qualitative and quantitative chemical analysis of these toxic compounds would be extremely beneficial. Reported herein is the development of a multi-channeled microfluidic device immobilized with single chain fragment variable (scFv) recombinant proteins specific for the explosive, TNT. Fluorescence displacement immunoassays performed under constant flow demonstrated trace level sensitivity and specificity for TNT. The utility of three multi-channeled devices immobilized with either (1) scFv recombinant protein, (2) biotinylated-scFv (bt-scFv) and (3) monoclonal anti-TNT (whole IgG molecule) were investigated and compared. Fluorescence dose response curves, crossreactivity measurements and limits of detection (LOD) for TNT were determined. Fluorescence displacement immunoassays for TNT in natural seawater demonstrated detection limits at sub-parts-per-billion levels (0.5 ppb) utilizing the microfluidic device with immobilized bt-scFv. PMID:26452845

  5. The fragments of the photosynthetic electron transfer chain in model systems.

    PubMed

    Krasnovsky, A A

    1972-07-01

    In this paper the recent research from our laboratory is reviewed. Short fragments of the photochemical electron transfer chain of photosynthesis were reproduced in aqueous detergent solutions or in organic solvents. The function of photosystem I is reproduced in a ternary system of chlorophylls, electron donors (dienols, sulfhydryl compounds, hydrazine, etc.), and electron acceptors (viologens, nicotinamide-adenine dinucleotide [NAD], flavines, etc.). Chlorophyll-photosensitized reduction of viologens in some cases is activated by oxygen at the expense of active reductants formed during the photosensitized oxidation of an initial electron donor (thiourea). Chlorophyll-photosensitized oxidoreduction of cytochromes is activated by flavines, viologens, vitamin K derivatives, and some other redox systems (cofactors of cyclic photophosphorylation). The primary mechanism of the reactions studied depends on the reversible chlorophyll photooxidoreduction. In binary systems, chlorophyll (monomeric or aggregated) and electron donor or electron acceptor, reversible photoreduction or photooxidation is observed. Irreversible bacteriochlorophyll oxidation leads to the formation of chlorophyll and protochlorophyll analogues; irreversible protochlorophyll photoreduction results in chlorophyll-like pigment appearance. The photodisaggregation of chlorophyll was observed. The models of photosystem II studied were the photochemical oxygen evolution in aqueous solutions of electron acceptors (ferric compounds, quinone), photosensitized in the near UV part of the spectrum by inorganic semiconductors (tungsten, titanium, and zinc oxides). All reactions described are based on electron (hydrogen) transfer photosensitized by pigment system.

  6. Multi-channeled single chain variable fragment (scFv) based microfluidic device for explosives detection.

    PubMed

    Charles, Paul T; Davis, Jasmine; Adams, André A; Anderson, George P; Liu, Jinny L; Deschamps, Jeffrey R; Kusterbeck, Anne W

    2015-11-01

    The development of explosives detection technologies has increased significantly over the years as environmental and national security agencies implement tighter pollution control measures and methods for improving homeland security. 2, 4, 6-Trinitrotoluene (TNT), known primarily as a component in munitions, has been targeted for both its toxicity and carcinogenic properties that if present at high concentrations can be a detriment to both humans, marine and plant ecosystems. Enabling end users with environmental detection and monitoring systems capable of providing real-time, qualitative and quantitative chemical analysis of these toxic compounds would be extremely beneficial. Reported herein is the development of a multi-channeled microfluidic device immobilized with single chain fragment variable (scFv) recombinant proteins specific for the explosive, TNT. Fluorescence displacement immunoassays performed under constant flow demonstrated trace level sensitivity and specificity for TNT. The utility of three multi-channeled devices immobilized with either (1) scFv recombinant protein, (2) biotinylated-scFv (bt-scFv) and (3) monoclonal anti-TNT (whole IgG molecule) were investigated and compared. Fluorescence dose response curves, crossreactivity measurements and limits of detection (LOD) for TNT were determined. Fluorescence displacement immunoassays for TNT in natural seawater demonstrated detection limits at sub-parts-per-billion levels (0.5 ppb) utilizing the microfluidic device with immobilized bt-scFv.

  7. Single Chain Variable Fragment against Nicastrin Inhibits the γ-Secretase Activity*

    PubMed Central

    Hayashi, Ikuo; Takatori, Sho; Urano, Yasuomi; Iwanari, Hiroko; Isoo, Noriko; Osawa, Satoko; Fukuda, Maiko A.; Kodama, Tatsuhiko; Hamakubo, Takao; Li, Tong; Wong, Philip C.; Tomita, Taisuke; Iwatsubo, Takeshi

    2009-01-01

    γ-Secretase is a membrane protein complex that catalyzes intramembrane proteolysis of a variety of substrates including the amyloid β precursor protein of Alzheimer disease. Nicastrin (NCT), a single-pass membrane glycoprotein that harbors a large extracellular domain, is an essential component of the γ-secretase complex. Here we report that overexpression of a single chain variable fragment (scFv) against NCT as an intrabody suppressed the γ-secretase activity. Biochemical analyses revealed that the scFv disrupted the proper folding and the appropriate glycosyl maturation of the endogenous NCT, which are required for the stability of the γ-secretase complex and the intrinsic proteolytic activity, respectively, implicating the dual role of NCT in the γ-secretase complex. Our results also highlight the importance of the calnexin cycle in the functional maturation of the γ-secretase complex. The engineered intrabodies may serve as rationally designed, molecular targeting tools for the discovery of novel actions of the membrane proteins. PMID:19684016

  8. Effects of protein engineering and rational mutagenesis on crystal lattice of single chain antibody fragments

    PubMed Central

    Kalyoncu, Sibel; Hyun, Jeongmin; Pai, Jennifer C.; Johnson, Jennifer L.; Entzminger, Kevin; Jain, Avni; Heaner, David P.; Morales, Ivan A.; Truskett, Thomas M.; Maynard, Jennifer A.; Lieberman, Raquel L.

    2014-01-01

    Protein crystallization is dependent upon, and sensitive to, the intermolecular contacts that assist in ordering proteins into a three dimensional lattice. Here we used protein engineering and mutagenesis to affect the crystallization of single chain antibody fragments (scFvs) that recognize the EE epitope (EYMPME) with high affinity. These hypercrystallizable scFvs are under development to assist difficult proteins, such as membrane proteins, in forming crystals, by acting as crystallization chaperones. Guided by analyses of intermolecular crystal lattice contacts, two second-generation anti-EE scFvs were produced, which bind to proteins with installed EE tags. Surprisingly, although non-complementarity determining region (CDR) lattice residues from the parent scFv framework remained unchanged through the processes of protein engineering and rational design, crystal lattices of the derivative scFvs differ. Comparison of energy calculations and the experimentally-determined lattice interactions for this basis set provides insight into the complexity of the forces driving crystal lattice choice and demonstrates the availability of multiple well-ordered surface features in our scFvs capable of forming versatile crystal contacts. PMID:24615866

  9. Effects of ionization mode on charge-site-remote and related fragmentation reactions of long-chain quaternary ammonium ions.

    PubMed

    Seto, C; Grossert, J S; Waddell, D S; Curtis, J M; Boyd, R K

    2001-05-01

    Comparison of collisionally activated fragment spectra of long-chain quaternary ammonium ions, formed by liquid-assisted secondary ion mass spectrometry (LSIMS) and electrospray ionization (ESI), shows the latter are dominated by radical cations while the former yield mainly even-electron charge-site-remote (CSR) fragments, similar to the report for different precursors by Cheng et al., J. Am. Soc. Mass Spectrom. 1998, 9, 840. Here, mixed-site fragmentation products (formal loss of a radical directly bonded to the nitrogen plus a radical derived from the long chain) are of comparable importance for both ionization techniques. These observations are difficult to understand if the CSR ions are formed by a concerted rearrangement-elimination reaction, since precollision internal energies of the ESI ions are much lower than those of the ions from LSIMS. Alternatively, if one discards the concerted mechanism for high-energy CA, and assumes that the even-electron fragments are predominantly formed via homolytic bond cleavage, the colder radical cations from ESI survive to the detector while the more energized counterparts from LSIMS preferentially lose a hydrogen atom to yield the CSR ions, as proposed by Wysocki and Ross (Int. J. Mass Spectrom. Ion Processes 1991, 104, 179). The present work also attempts to reconcile discrepancies involving critical energies and known structures for neutral fragments. PMID:11349955

  10. Production of an anti-idiotypic antibody single chain variable fragment vaccine against Edwardsiella tarda.

    PubMed

    Qin, Hong; Jin, Xiaohang; Huang, Weiquan; Liu, Yulin

    2010-02-01

    Edwardsiella tarda is the pathogen responsible for edwardsiellosis, a serious infectious disease of freshwater and marine fish species, and currently recognized to be the species pathogenic for human. An anti-idiotypic monoclonal antibody (mAb), 1E11, has been developed. It mimics the protective epitope of E. tarda and can prevent fish from infection of E. tarda. In this study, the correct variable heavy (VH) and variable light (VL) genes were obtained from 1E11 by using bioinformatics methods, and a 15 amino acid (Gly4Ser)3 linker was used to hold the two V domains together for the construction of VL-linker-VH form of single chain variable fragment (scFv) gene. Then, the scFv was subcloned into the vector pET-28a, expressed in the Escherichia coli BL21 cells, and identified by SDS-PAGE and western blotting. Red drum (Sciaenops ocellatus L.) weighing about 50 g was subjected to challenge with different E. tarda strains after 4 weeks followed by vaccination, the mortality rates and relative percentage survival were recorded and calculated, and the survival rate of fish in the scFv subgroups was obviously higher than that of control subgroups (P<0.01). Enzyme-linked immunosorbent assay results show that after 4 weeks of post-vaccination, the level of specific antibody in fish sera of scFv groups was significantly higher than control groups. This study indicates that the recombinant antibody scFv was successfully developed, and it may serve as an effective vaccine candidate against E. tarda. PMID:20119624

  11. Identification of fungemia agents using the polymerase chain reaction and restriction fragment length polymorphism analysis.

    PubMed

    Santos, M S; Souza, E S; S Junior, R M; Talhari, S; Souza, J V B

    2010-08-01

    Prompt and specific identification of fungemia agents is important in order to define clinical treatment. However, in most cases conventional culture identification can be considered to be time-consuming and not without errors. The aim of the present study was to identify the following fungemia agents: Candida albicans, Candida parapsilosis, Candida tropicalis, Candida glabrata, Cryptococcus neoformans, Cryptococcus gattii, and Histoplasma capsulatum using the polymerase chain reaction and restriction fragment length polymorphism analysis (PCR/RFLP). More specifically: a) to evaluate 3 different amplification regions, b) to investigate 3 different restriction enzymes, and c) to use the best PCR/RFLP procedure to indentify 60 fungemia agents from a culture collection. All 3 pairs of primers (ITS1/ITS4, NL4/ITS5 and Primer1/Primer2) were able to amplify DNA from the reference strains. However, the size of these PCR products did not permit the identification of all the species studied. Three restriction enzymes were used to digest the PCR products: HaeIII, Ddel and Bfal. Among the combinations of pairs of primers and restriction enzymes, only one (primer pair NL4/ITS5 and restriction enzyme Ddel) produced a specific RFLP pattern for each microorganism studied. Sixty cultures of fungemia agents (selected from the culture collection of Fundação de Medicina Tropical do Amazonas--FMTAM) were correctly identified by PCR/RFLP using the prime pair NL4/ITS5 and Ddel. We conclude that the method proved to be both simple and reproducible, and may offer potential advantages over phenotyping methods.

  12. Exploiting Cross-reactivity to Neutralize Two Different Scorpion Venoms with One Single Chain Antibody Fragment*

    PubMed Central

    Riaño-Umbarila, Lidia; Contreras-Ferrat, Gabriel; Olamendi-Portugal, Timoteo; Morelos-Juárez, Citlalli; Corzo, Gerardo; Possani, Lourival D.; Becerril, Baltazar

    2011-01-01

    We report the optimization of a family of human single chain antibody fragments (scFv) for neutralizing two scorpion venoms. The parental scFv 3F recognizes the main toxins of Centruroides noxius Hoffmann (Cn2) and Centruroides suffusus suffusus (Css2), albeit with low affinity. This scFv was subjected to independent processes of directed evolution to improve its recognition toward Cn2 (Riaño-Umbarila, L., Juárez-González, V. R., Olamendi-Portugal, T., Ortíz-León, M., Possani, L. D., and Becerril, B. (2005) FEBS J. 272, 2591–2601) and Css2 (this work). Each evolved variant showed strong cross-reactivity against several toxins, and was capable of neutralizing Cn2 and Css2. Furthermore, each variant neutralized the whole venoms of the above species. As far as we know, this is the first report of antibodies with such characteristics. Maturation processes revealed key residue changes to attain expression, stability, and affinity improvements as compared with the parental scFv. Combination of these changes resulted in the scFv LR, which is capable of rescuing mice from severe envenomation by 3 LD50 of freshly prepared whole venom of C. noxius (7.5 μg/20 g of mouse) and C. suffusus (26.25 μg/20 g of mouse), with surviving rates between 90 and 100%. Our research is leading to the formulation of an antivenom consisting of a discrete number of human scFvs endowed with strong cross-reactivity and low immunogenicity. PMID:21156801

  13. Identification of fungemia agents using the polymerase chain reaction and restriction fragment length polymorphism analysis.

    PubMed

    Santos, M S; Souza, E S; S Junior, R M; Talhari, S; Souza, J V B

    2010-08-01

    Prompt and specific identification of fungemia agents is important in order to define clinical treatment. However, in most cases conventional culture identification can be considered to be time-consuming and not without errors. The aim of the present study was to identify the following fungemia agents: Candida albicans, Candida parapsilosis, Candida tropicalis, Candida glabrata, Cryptococcus neoformans, Cryptococcus gattii, and Histoplasma capsulatum using the polymerase chain reaction and restriction fragment length polymorphism analysis (PCR/RFLP). More specifically: a) to evaluate 3 different amplification regions, b) to investigate 3 different restriction enzymes, and c) to use the best PCR/RFLP procedure to indentify 60 fungemia agents from a culture collection. All 3 pairs of primers (ITS1/ITS4, NL4/ITS5 and Primer1/Primer2) were able to amplify DNA from the reference strains. However, the size of these PCR products did not permit the identification of all the species studied. Three restriction enzymes were used to digest the PCR products: HaeIII, Ddel and Bfal. Among the combinations of pairs of primers and restriction enzymes, only one (primer pair NL4/ITS5 and restriction enzyme Ddel) produced a specific RFLP pattern for each microorganism studied. Sixty cultures of fungemia agents (selected from the culture collection of Fundação de Medicina Tropical do Amazonas--FMTAM) were correctly identified by PCR/RFLP using the prime pair NL4/ITS5 and Ddel. We conclude that the method proved to be both simple and reproducible, and may offer potential advantages over phenotyping methods. PMID:20640387

  14. Urine of patients with early prostate cancer contains lower levels of light chain fragments of inter-alpha-trypsin inhibitor and saposin B but increased expression of an inter-alpha-trypsin inhibitor heavy chain 4 fragment.

    PubMed

    Jayapalan, Jaime J; Ng, Keng L; Shuib, Adawiyah S; Razack, Azad H A; Hashim, Onn H

    2013-06-01

    The present study was aimed at the identification of proteins that are differentially expressed in the urine of patients with prostate cancer (PCa), those with benign prostatic hyperplasia (BPH) and age-matched healthy male control subjects. Using a combination of 2DE and MS/MS, significantly lower expression of urinary saposin B and two different fragments of inter-alpha-trypsin inhibitor light chain (ITIL) was demonstrated in the PCa patients compared to the controls. However, only one of the ITIL fragments was significantly different between the PCa and BPH patients. When image analysis was performed on urinary proteins that were transferred onto NC membranes and detected using a lectin that binds to O-glycans, a truncated fragment of inter-alpha-trypsin inhibitor heavy chain 4 was the sole protein found to be significantly enhanced in the PCa patients compared to the controls. Together, these urinary peptide fragments might be useful complementary biomarkers to indicate PCa as well as to distinguish it from BPH, although further epidemiological evidence on the specificity and sensitivity of the protein candidates is required. PMID:23417432

  15. Urine of patients with early prostate cancer contains lower levels of light chain fragments of inter-alpha-trypsin inhibitor and saposin B but increased expression of an inter-alpha-trypsin inhibitor heavy chain 4 fragment.

    PubMed

    Jayapalan, Jaime J; Ng, Keng L; Shuib, Adawiyah S; Razack, Azad H A; Hashim, Onn H

    2013-06-01

    The present study was aimed at the identification of proteins that are differentially expressed in the urine of patients with prostate cancer (PCa), those with benign prostatic hyperplasia (BPH) and age-matched healthy male control subjects. Using a combination of 2DE and MS/MS, significantly lower expression of urinary saposin B and two different fragments of inter-alpha-trypsin inhibitor light chain (ITIL) was demonstrated in the PCa patients compared to the controls. However, only one of the ITIL fragments was significantly different between the PCa and BPH patients. When image analysis was performed on urinary proteins that were transferred onto NC membranes and detected using a lectin that binds to O-glycans, a truncated fragment of inter-alpha-trypsin inhibitor heavy chain 4 was the sole protein found to be significantly enhanced in the PCa patients compared to the controls. Together, these urinary peptide fragments might be useful complementary biomarkers to indicate PCa as well as to distinguish it from BPH, although further epidemiological evidence on the specificity and sensitivity of the protein candidates is required.

  16. Highly Amyloidogenic Two-chain Peptide Fragments Are Released upon Partial Digestion of Insulin with Pepsin*♦

    PubMed Central

    Piejko, Marcin; Dec, Robert; Babenko, Viktoria; Hoang, Agnieszka; Szewczyk, Monika; Mak, Paweł; Dzwolak, Wojciech

    2015-01-01

    Proteases play a well recognized role in the emergence of highly aggregation-prone protein fragments in vivo, whereas in vitro limited proteolysis is often employed to probe different phases of amyloidogenic pathways. Here, we show that addition of moderate amounts of pepsin to acidified bovine insulin at close to physiological temperature results in an abrupt self-assembly of amyloid-like fibrils from partially digested insulin fragments. Biochemical analysis of the pepsin-induced fibrils implicates peptide fragments (named H) consisting of the 13 or 15 N-terminal residues of the A-chain and 11 or 13 N-terminal residues of the B-chain linked by the disulfide bond between Cys-7A–Cys-7B as the main constituents. There are up to eight pepsin-cleavage sites remaining within the double chain peptide, which become protected upon fast fibrillation unless concentration of the enzyme is increased resulting in complete digestion of insulin. Controlled re-association of H-peptides leads to “explosive” fibrillation only under nonreducing conditions implying the key role of the disulfide bond in their amyloidogenicity. Such re-assembled amyloid is similar in terms of morphology and infrared features to typical bovine insulin fibrils, although it lacks the ability to seed the intact protein. PMID:25586185

  17. Design and construction of a new human naïve single-chain fragment variable antibody library, IORISS1.

    PubMed

    Pasello, Michela; Zamboni, Silvia; Mallano, Alessandra; Flego, Michela; Picci, Piero; Cianfriglia, Maurizio; Scotlandi, Katia

    2016-04-20

    Human monoclonal antibodies are a powerful tool with increasingly successful exploitations and the single chain fragment variable format can be considered the building block for the implementation of more complex and effective antibody-based constructs. Phage display is one of the best and most efficient methods to isolate human antibodies selected from an efficient and variable phage display library. We report a method for the construction of a human naïve single-chain variable fragment library, termed IORISS1. Many different sets of oligonucleotide primers as well as optimized electroporation and ligation reactions were used to generate this library of 1.2×10(9) individual clones. The key difference is the diversity of variable gene templates, which was derived from only 15 non-immunized human donors. The method described here, was used to make a new human naïve single-chain fragment variable phage display library that represents a valuable source of diverse antibodies that can be used as research reagents or as a starting point for the development of therapeutics. Using biopanning, we determined the ability of IORISS1 to yield antibodies. The results we obtained suggest that, by using an optimized protocol, an efficient phage antibody library can be generated. PMID:26945728

  18. Decreased HLA-DR antigen-associated invariant chain (CD74) mRNA expression predicts mortality after septic shock

    PubMed Central

    2013-01-01

    Introduction Septic syndromes remain the leading cause of mortality in intensive care units (ICU). Septic patients rapidly develop immune dysfunctions, the intensity and duration of which have been linked with deleterious outcomes. Decreased mRNA expressions of major histocompatibility complex (MHC) class II-related genes have been reported after sepsis. We investigated whether their mRNA levels in whole blood could predict mortality in septic shock patients. Methods A total of 93 septic shock patients were included. On the third day after shock, the mRNA expressions of five MHC class II-related genes (CD74, HLA-DRA, HLA-DMB, HLA-DMA, CIITA) were measured by qRT-PCR and monocyte human leukocyte antigen-DR (mHLA-DR) by flow cytometry. Results A significant correlation was found among MHC class II related gene expressions. Among mRNA markers, the best prognostic value was obtained for CD74 (HLA-DR antigen-associated invariant chain). For this parameter, the area under the receiver operating characteristic curve (AUC) was calculated (AUC = 0.67, 95% confidence interval (CI) = 0.55 to 0.79; P = 0.01) as well as the optimal cut-off value. After stratification based on this threshold, survival curves showed that a decreased CD74 mRNA level was associated with increased mortality after septic shock (Log rank test, P = 0.0043, Hazard Ratio = 3.0, 95% CI: 1.4 to 6.5). Importantly, this association remained significant after multivariate logistic regression analysis including usual clinical confounders (that is, severity scores, P = 0.026, Odds Ratio = 3.4, 95% CI: 1.2 to 9.8). Conclusion Decreased CD74 mRNA expression significantly predicts 28-day mortality after septic shock. After validation in a larger multicentric study, this biomarker could become a robust predictor of death in septic patients. PMID:24321376

  19. Polymer-grafted lignin surfactants prepared via reversible addition-fragmentation chain-transfer polymerization.

    PubMed

    Gupta, Chetali; Washburn, Newell R

    2014-08-12

    Kraft lignin grafted with hydrophilic polymers has been prepared using reversible addition-fragmentation chain-transfer (RAFT) polymerization and investigated for use as a surfactant. In this preliminary study, polyacrylamide and poly(acrylic acid) were grafted from a lignin RAFT macroinitiator at average initiator site densities estimated to be 2 per particle and 17 per particle. The target degrees of polymerization were 50 and 100, but analysis of cleaved polyacrylamide was consistent with a higher average molecular weight, suggesting not all sites were able to participate in the polymerization. All materials were readily soluble in water, and dynamic light scattering data indicate polymer-grafted lignin coexisted in isolated and aggregated forms in aqueous media. The characteristic size was 15-20 nm at low concentrations, and aggregation appeared to be a stronger function of degree of polymerization than graft density. These species were surface active, reducing the surface tension to as low as 60 dyn/cm at 1 mg/mL, and a greater decrease was observed than for polymer-grafted silica nanoparticles, suggesting that the lignin core was also surface active. While these lignin surfactants were soluble in water, they were not soluble in hexanes. Thus, it was unexpected that water-in-oil emulsions formed in all surfactant compositions and solvent ratios tested, with average droplet sizes of 10-20 μm. However, although polymer-grafted lignin has structural features similar to nanoparticles used in Pickering emulsions, its interfacial behavior was qualitatively different. While at air-water interfaces, the hydrophilic grafts promote effective reductions in surface tension, we hypothesize that the low grafting density in these lignin surfactants favors partitioning into the hexanes side of the oil-water interface because collapsed conformations of the polymer grafts improve interfacial coverage and reduce water-hexanes interactions. We propose that polymer-grafted lignin

  20. Regulation of chain length in two diatoms as a growth-fragmentation process

    NASA Astrophysics Data System (ADS)

    Gherardi, Marco; Amato, Alberto; Bouly, Jean-Pierre; Cheminant, Soizic; Ferrante, Maria Immacolata; d'Alcalá, Maurizio Ribera; Iudicone, Daniele; Falciatore, Angela; Cosentino Lagomarsino, Marco

    2016-08-01

    Chain formation in diatoms is relevant because of several aspects of their adaptation to the ecosystem. However, the tools to quantify the regulation of their assemblage and infer specific mechanisms in a laboratory setting are scarce. To address this problem, we define an approach based on a statistical physics model of chain growth and separation in combination with experimental evaluation of chain-length distributions. Applying this combined analysis to data from Chaetoceros decipiens and Phaeodactylum tricornutum, we find that cells of the first species control chain separation, likely through a cell-to-cell communication process, while the second species only modulates the separation rate. These results promote quantitative methods for characterizing chain formation in several chain-forming species and in diatoms in particular.

  1. Regulation of chain length in two diatoms as a growth-fragmentation process.

    PubMed

    Gherardi, Marco; Amato, Alberto; Bouly, Jean-Pierre; Cheminant, Soizic; Ferrante, Maria Immacolata; d'Alcalá, Maurizio Ribera; Iudicone, Daniele; Falciatore, Angela; Cosentino Lagomarsino, Marco

    2016-08-01

    Chain formation in diatoms is relevant because of several aspects of their adaptation to the ecosystem. However, the tools to quantify the regulation of their assemblage and infer specific mechanisms in a laboratory setting are scarce. To address this problem, we define an approach based on a statistical physics model of chain growth and separation in combination with experimental evaluation of chain-length distributions. Applying this combined analysis to data from Chaetoceros decipiens and Phaeodactylum tricornutum, we find that cells of the first species control chain separation, likely through a cell-to-cell communication process, while the second species only modulates the separation rate. These results promote quantitative methods for characterizing chain formation in several chain-forming species and in diatoms in particular. PMID:27627344

  2. A novel variable antibody fragment dimerized by leucine zippers with enhanced neutralizing potency against rabies virus G protein compared to its corresponding single-chain variable antibody fragment.

    PubMed

    Li, Zhuang; Cheng, Yue; Xi, Hualong; Gu, Tiejun; Yuan, Ruosen; Chen, Xiaoxu; Jiang, Chunlai; Kong, Wei; Wu, Yongge

    2015-12-01

    Fatal rabies can be prevented effectively by post-exposure prophylactic (PEP) with rabies immunoglobulin (RIG). Single-chain variable fragments (scFv), which are composed of a variable heavy chain (VH) and a variable light chain (VL) connected by a peptide linker, can potentially be used to replace RIG. However, in our previous study, a scFv (scFV57S) specific for the rabies virus (RV) G protein showed a lower neutralizing potency than that of its parent IgG due to lower stability and altered peptide assembly pattern. In monoclonal antibodies, the VH and VL interact non-covalently, while in scFvs the VH is connected covalently with the VL by the artificial linker. In this study, we constructed and expressed two peptides 57VL-JUN-HIS and 57VH-FOS-HA in Escherichia coli. The well-known Fos and Jun leucine zippers were utilized to dimerize VH and VL similarly to the IgG counterpart. The two peptides assembled to form zipFv57S in vitro. Due to the greater similarity in structure with IgG, the zipFv57S protein showed a higher binding ability and affinity resulting in notable improvement of in vitro neutralizing activity over its corresponding scFv. The zipFv57S protein was also found to be more stable and showed similar protective rate as RIG in mice challenged with a lethal dose of RV. Our results not only indicated zipFv57S as an ideal alternative for RIG in PEP but also offered a novel and efficient hetero-dimerization pattern of VH and VL leading to enhanced neutralizing potency.

  3. Intracellular interference of tick-borne flavivirus infection by using a single-chain antibody fragment delivered by recombinant Sindbis virus.

    PubMed Central

    Jiang, W; Venugopal, K; Gould, E A

    1995-01-01

    A single-chain antibody fragment that identifies a neutralizing epitope on the envelope protein of louping ill and some other tick-borne flaviviruses was previously expressed in soluble form from bacteria and shown to be functionally active in vitro. To see whether or not the single-chain antibody could bind and inactivate infectious virus in vivo, we have used recombinant Sindbis virus as a delivery vehicle for intracellular expression of the antibody fragment. The variable genes and interchain linker encoding the single-chain antibody were cloned into a double subgenomic Sindbis virus expression vector to generate recombinant Sindbis virus. Infection with this recombinant Sindbis virus provided high-level cytoplasmic expression of the antibody fragment in mammalian cells. We demonstrate (i) that the antibody fragment was antigen binding and (ii) that louping ill virus infectivity was significantly reduced in the presence of intracellular antibody expressed by the superinfecting recombinant Sindbis virus. PMID:7815482

  4. Calmodulin Polymerase Chain Reaction-Restriction Fragment Length Polymorphism for Leishmania Identification and Typing.

    PubMed

    Miranda, Aracelis; Samudio, Franklyn; González, Kadir; Saldaña, Azael; Brandão, Adeilton; Calzada, Jose E

    2016-08-01

    A precise identification of Leishmania species involved in human infections has epidemiological and clinical importance. Herein, we describe a preliminary validation of a restriction fragment length polymorphism assay, based on the calmodulin intergenic spacer region, as a tool for detecting and typing Leishmania species. After calmodulin amplification, the enzyme HaeIII yielded a clear distinction between reference strains of Leishmania mexicana, Leishmania amazonensis, Leishmania infantum, Leishmania lainsoni, and the rest of the Viannia reference species analyzed. The closely related Viannia species: Leishmania braziliensis, Leishmania panamensis, and Leishmania guyanensis, are separated in a subsequent digestion step with different restriction enzymes. We have developed a more accessible molecular protocol for Leishmania identification/typing based on the exploitation of part of the calmodulin gene. This methodology has the potential to become an additional tool for Leishmania species characterization and taxonomy.

  5. Cathepsin S, but not cathepsin L, participates in the MHC class II-associated invariant chain processing in large yellow croaker (Larimichthys crocea).

    PubMed

    Li, Qiuhua; Ao, Jingqun; Mu, Yinnan; Yang, Zhijun; Li, Ting; Zhang, Xin; Chen, Xinhua

    2015-12-01

    Two cysteine proteases, cathepsin S (CatS) and cathepsin L (CatL), have been identified as the key enzymes involved in the processing of invariant chain (Ii chain) in mammals. However, little is known about the roles of fish cathepsins in the Ii chain processing. In this study, large yellow croaker cathepsin S (LycCatS) and L (LycCatL) were identified and characterized. Based on the sequence comparison and phylogenetic analysis, both LycCatS and LycCatL are highly conserved to their counterparts in teleost. These two cathepsins were constitutively expressed in all tissues and immune-related cells tested, although at different levels. Both recombinant LycCatS (rLycCatS) and LycCatL (rLycCatL) possess the typical cysteine protease activity. Like other mammalian endopeptidase cathepsins, rLycCatS and rLycCatL could be autocatalytically activated to remove propeptides and release active mature peptides. On the other hand, the autocatalytic activation of rLycCatL could be inhibited by recombinant large yellow croaker Ii chain (rLyc-TR-Ii), but the autocatalytic activation of rLycCatS was not affected by rLyc-TR-Ii. Furthermore, the activated rLycCatS can efficiently process rLyc-TR-Ii in a stepwise manner in vitro, while the activated rLycCatL can not. These data indicate that cathepsin S may be the main cathepsin involved in the Ii chain processing in bony fish.

  6. Cathepsin S, but not cathepsin L, participates in the MHC class II-associated invariant chain processing in large yellow croaker (Larimichthys crocea).

    PubMed

    Li, Qiuhua; Ao, Jingqun; Mu, Yinnan; Yang, Zhijun; Li, Ting; Zhang, Xin; Chen, Xinhua

    2015-12-01

    Two cysteine proteases, cathepsin S (CatS) and cathepsin L (CatL), have been identified as the key enzymes involved in the processing of invariant chain (Ii chain) in mammals. However, little is known about the roles of fish cathepsins in the Ii chain processing. In this study, large yellow croaker cathepsin S (LycCatS) and L (LycCatL) were identified and characterized. Based on the sequence comparison and phylogenetic analysis, both LycCatS and LycCatL are highly conserved to their counterparts in teleost. These two cathepsins were constitutively expressed in all tissues and immune-related cells tested, although at different levels. Both recombinant LycCatS (rLycCatS) and LycCatL (rLycCatL) possess the typical cysteine protease activity. Like other mammalian endopeptidase cathepsins, rLycCatS and rLycCatL could be autocatalytically activated to remove propeptides and release active mature peptides. On the other hand, the autocatalytic activation of rLycCatL could be inhibited by recombinant large yellow croaker Ii chain (rLyc-TR-Ii), but the autocatalytic activation of rLycCatS was not affected by rLyc-TR-Ii. Furthermore, the activated rLycCatS can efficiently process rLyc-TR-Ii in a stepwise manner in vitro, while the activated rLycCatL can not. These data indicate that cathepsin S may be the main cathepsin involved in the Ii chain processing in bony fish. PMID:26475363

  7. CONSTRAINTS ON THE LORENTZ INVARIANCE VIOLATION WITH GAMMA-RAY BURSTS VIA A MARKOV CHAIN MONTE CARLO APPROACH

    SciTech Connect

    Pan, Yu; Gong, Yungui; Cao, Shuo; Zhu, Zong-Hong; Gao, He

    2015-07-20

    In the quantum theory of gravity, for photons we expect the Lorentz Invariance Violation (LIV) and the modification of the dispersion relation between energy and momentum. The effect of the energy-dependent velocity due to the modified dispersion relation for photons was studied in the standard cosmological context by using a sample of gamma-ray bursts (GRBs). In this paper we mainly discuss the possible LIV effect of using different cosmological models for the accelerating universe. Due to the degeneracies among model parameters, the GRBs’ time delay data are combined with the cosmic microwave background data from the Planck first-year release, the baryon acoustic oscillation data at six different redshifts, and Union2 Type Ia supernovae data to constrain both the model parameters and the LIV effect. We find no evidence of the LIV.

  8. Expression and Functional Properties of an Anti-Triazophos High-Affinity Single-Chain Variable Fragment Antibody with Specific Lambda Light Chain.

    PubMed

    Liu, Rui; Liang, Xiao; Xiang, Dandan; Guo, Yirong; Liu, Yihua; Zhu, Guonian

    2016-01-01

    Triazophos is a widely used organophosphorous insecticide that has potentially adverse effects to organisms. In the present study, a high-affinity single-chain variable fragment (scFv) antibody with specific lambda light chain was developed for residue monitoring. First, the specific variable regions were correctly amplified from a hybridoma cell line 8C10 that secreted monoclonal antibody (mAb) against triazophos. The regions were then assembled as scFv via splicing by overlap extension polymerase chain reaction. Subsequently, the recombinant anti-triazophos scFv-8C10 was successfully expressed in Escherichia coli strain HB2151 in soluble form, purified through immobilized metal ion affinity chromatography, and verified via Western blot and peptide mass fingerprinting analyses. Afterward, an indirect competitive enzyme-linked immunosorbent assay was established based on the purified anti-triazophos scFv-8C10 antibody. The assay exhibited properties similar to those based on the parent mAb, with a high sensitivity (IC50 of 1.73 ng/mL) to triazophos and no cross reaction for other organophosphorus pesticides; it was reliable in detecting triazophos residues in spiked water samples. Moreover, kinetic measurement using a surface plasmon resonance biosensor indicated that the purified scFv-8C10 antibody had a high affinity of 1.8 × 10(-10) M and exhibited good binding stability. Results indicated that the recombinant high-affinity scFv-8C10 antibody was an effective detection material that would be promising for monitoring triazophos residues in environment samples. PMID:27338340

  9. Expression and Functional Properties of an Anti-Triazophos High-Affinity Single-Chain Variable Fragment Antibody with Specific Lambda Light Chain

    PubMed Central

    Liu, Rui; Liang, Xiao; Xiang, Dandan; Guo, Yirong; Liu, Yihua; Zhu, Guonian

    2016-01-01

    Triazophos is a widely used organophosphorous insecticide that has potentially adverse effects to organisms. In the present study, a high-affinity single-chain variable fragment (scFv) antibody with specific lambda light chain was developed for residue monitoring. First, the specific variable regions were correctly amplified from a hybridoma cell line 8C10 that secreted monoclonal antibody (mAb) against triazophos. The regions were then assembled as scFv via splicing by overlap extension polymerase chain reaction. Subsequently, the recombinant anti-triazophos scFv-8C10 was successfully expressed in Escherichia coli strain HB2151 in soluble form, purified through immobilized metal ion affinity chromatography, and verified via Western blot and peptide mass fingerprinting analyses. Afterward, an indirect competitive enzyme-linked immunosorbent assay was established based on the purified anti-triazophos scFv-8C10 antibody. The assay exhibited properties similar to those based on the parent mAb, with a high sensitivity (IC50 of 1.73 ng/mL) to triazophos and no cross reaction for other organophosphorus pesticides; it was reliable in detecting triazophos residues in spiked water samples. Moreover, kinetic measurement using a surface plasmon resonance biosensor indicated that the purified scFv-8C10 antibody had a high affinity of 1.8 × 10−10 M and exhibited good binding stability. Results indicated that the recombinant high-affinity scFv-8C10 antibody was an effective detection material that would be promising for monitoring triazophos residues in environment samples. PMID:27338340

  10. Study on the performance of polycarboxylate-based superplasticizers synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization

    NASA Astrophysics Data System (ADS)

    Yu, Binbin; Zeng, Zhong; Ren, Qinyu; Chen, Yang; Liang, Mei; Zou, Huawei

    2016-09-01

    A series of block type polycarboxylate-based superplasticizers (PCs) with different molecular architectures were synthesized with macromonomer butenyl alkylene polyoxyethylene-polyoxypropylene ether (BAPP) and acrylic acid (AA) by reversible addition-fragmentation chain transfer (RAFT) polymerization. Fourier-Transformed Infrared (FTIR) Spectroscopy and dynamic light scattering (DLS) were applied to investigate the PCs' molecular structure. The dispersion capacity of the PCs in cement were also measured, and the results showed that the polycarboxylic dispersing agents prepared by this method were suitable for portlant cement. It was found that the PCs could affect the hydration process, which was performed through retarding the generation of ettringite in the hydrated product. Our studies with X-ray diffraction (XRD), scanning electron microscopy (SEM) and compressive strength measurement of hydrated production were all supporting this conclusion.

  11. Expression of functional single-chain variable domain fragment antibody (scFv) against mycotoxin zearalenone in Pichia pastoris.

    PubMed

    Chang, Hyun-Joo; Choi, Sung-Wook; Chun, Hyang Sook

    2008-10-01

    A synthetic gene coding for single-chain variable domain fragment antibody against mycotoxin zearalenone (scFv-ZEN) has been designed, constructed and expressed in Pichia pastoris. The native scFv-ZEN sequence was optimized to Pichia preference codon usage. The expression level of codon-optimized scFv-ZEN was slightly higher than that of native scFv-ZEN, and its maximum yield reached 328 mg total protein/l in flask culture. The binding activities of two selected clones to ZEN using surface plasmon resonance analysis were comparable or better than that of monoclonal antibody. Our results demonstrate the potential of soluble scFv-ZEN for developing a rapid and affordable immunoassay for detection of ZEN in food and feedstuff. PMID:18575809

  12. Surface-imprinted magnetic particles for highly selective sulfonamides recognition prepared by reversible addition fragmentation chain transfer polymerization.

    PubMed

    Xie, Xiaoyu; Liu, Xia; Pan, Xiaoyan; Chen, Liang; Wang, Sicen

    2016-01-01

    In this work, novel magnetic molecularly imprinted polymers (MMIPs) were prepared by reversible addition fragmentation chain transfer (RAFT) polymerization using sulfamerazine as the template. With the controlled/living property of RAFT polymerization, the resulting MMIPs showed high selectivity for sulfonamides recognition. The MMIPs were characterized by transmission electron microscopy, Fourier transform infrared, vibrating sample magnetometer, X-ray diffraction, X-ray photoelectron spectroscopy, and thermogravimetric analysis. The static and selectivity binding experiments demonstrated the desirable adsorption capacity and high selectivity of the MMIPs. The developed MMIPs were used as the solid-phase extraction sorbents to selectively extract four sulfonamides from aqueous solution. The recoveries of the spiked pond water ranged from 61.2 to 94.1% with RSD lower than 6.5%. This work demonstrated a versatile approach for the preparation of well-constructed MMIPs for application in the field of solid-phase extraction. PMID:26637219

  13. A functional recombinant single-chain T cell receptor fragment capable of selectively targeting antigen-presenting cells.

    PubMed

    Epel, Malka; Ellenhorn, Joshua D; Diamond, Don J; Reiter, Yoram

    2002-11-01

    Specificity in the immune system is dictated and regulated by specific recognition of peptide/major histocompatibility complexes (MHC) by the T cell receptor (TCR). Such peptide/MHC complexes are a desirable target for novel approaches in immunotherapy because of their highly restricted fine specificity. Recently a potent anti-human p53 CD8(+) cytotoxic T lymphocyte (CTL) response has been developed in HLA-A2 transgenic mice after immunization with peptides corresponding to HLA-A2 motifs from human p53. An alpha/beta T-cell receptor was cloned from such CTL which exhibited a moderately high affinity to the human p53(149-157) peptide. In this report, we investigated the possibility of using a recombinant tumor-specific TCR for antigen-specific elimination of cells that express the specific MHC-peptide complex. To this end, we constructed a functional single-chain Fv fragment from the cloned TCR and fused it to a very potent cytotoxic molecule, a truncated form of Pseudomonas exotoxin A (PE38). The p53 TCR scFv-P38 fusion protein was generated by in vitro refolding from bacterially-expressed inclusion bodies, and was found to be functional by its ability to bind antigen-presenting cells (APC) which express the specific p53-derived peptide. Moreover, we have shown that the p53-specific TCR scFv-PE38 molecule specifically kills APC in a peptide-dependent manner. These results represent the first time that a TCR-derived recombinant single-chain Fv fragment has been used as a targeting moiety to deliver a cytotoxic effector molecule to cells and has been able to mediate the efficient killing of the particular cell population that expresses the specific MHC/peptide complex. Similarly to antibody-based targeting approaches, TCR with tumor cell specificity represent attractive candidates for generating new, very specific targeting moieties for various modes of cancer immunotherapy. PMID:12384808

  14. Development of single-chain variable fragments (scFv) against influenza virus targeting hemagglutinin subunit 2 (HA2).

    PubMed

    Li, Tai-Wei; Cheng, Shu-Fang; Tseng, Yen-Tzu; Yang, Yu-Chih; Liu, Wen-Chun; Wang, Sheng-Cyuan; Chou, Mei-Ju; Lin, Yu-Jen; Wang, Yueh; Hsiao, Pei-Wen; Wu, Suh-Chin; Chang, Ding-Kwo

    2016-01-01

    Influenza A viruses (IAV) are widespread in birds and domestic poultry, occasionally causing severe epidemics in humans and posing health threats. Hence, the need to develop a strategy for prophylaxis or therapy, such as a broadly neutralizing antibody against IAV, is urgent. In this study, single-chain variable fragment (scFv) phage display technology was used to select scFv fragments recognizing influenza envelope proteins. The Tomlinson I and J scFv phage display libraries were screened against the recombinant HA2 protein (rHA2) for three rounds. Only the third-round elution sample of the Tomlinson J library showed high binding affinity to rHA2, from which three clones (3JA18, 3JA62, and 3JA78) were chosen for preparative-scale production as soluble antibody by E. coli. The clone 3JA18 was selected for further tests due to its broad affinity for influenza H1N1, H3N2 and H5N1. Simulations of the scFv 3JA18-HA trimer complex revealed that the complementarity-determining region of the variable heavy chain (VH-CDR2) bound the stem region of HA. Neutralization assays using a peptide derived from VH-CDR2 also supported the simulation model. Both the selected antibody and its derived peptide were shown to suppress infection with H5N1 and H1N1 viruses, but not H3N2 viruses. The results also suggested that the scFvs selected from rHA2 could have neutralizing activity by interfering with the function of the HA stem region during virus entry into target cells.

  15. A Strategy for Generating a Broad-Spectrum Monoclonal Antibody and Soluble Single-Chain Variable Fragments against Plant Potyviruses.

    PubMed

    Liu, Han-Lin; Lin, Wei-Fang; Hu, Wen-Chi; Lee, Yung-An; Chang, Ya-Chun

    2015-10-01

    Potyviruses are major pathogens that often cause mixed infection in calla lilies. To reduce the time and cost of virus indexing, a detection method for the simultaneous targeting of multiple potyviruses was developed by generating a broad-spectrum monoclonal antibody (MAb) for detecting the greatest possible number of potyviruses. The conserved 121-amino-acid core regions of the capsid proteins of Dasheen mosaic potyvirus (DsMV), Konjak mosaic potyvirus (KoMV), and Zantedeschia mild mosaic potyvirus (ZaMMV) were sequentially concatenated and expressed as a recombinant protein for immunization. After hybridoma cell fusion and selection, one stable cell line that secreted a group-specific antibody, named C4 MAb, was selected. In the reaction spectrum test, the C4 MAb detected at least 14 potyviruses by indirect enzyme-linked immunosorbent assay (I-ELISA) and Western blot analysis. Furthermore, the variable regions of the heavy (VH) and light (VL) chains of the C4 MAb were separately cloned and constructed as single-chain variable fragments (scFvs) for expression in Escherichia coli. Moreover, the pectate lyase E (PelE) signal peptide of Erwinia chrysanthemi S3-1 was added to promote the secretion of C4 scFvs into the medium. According to Western blot analysis and I-ELISA, the soluble C4 scFv (VL-VH) fragment showed a binding specificity similar to that of the C4 MAb. Our results demonstrate that a recombinant protein derived from fusion of the conserved regions of viral proteins has the potential to produce a broad-spectrum MAb against a large group of viruses and that the PelE signal peptide can improve the secretion of scFvs in E. coli.

  16. A single-chain variable fragment intrabody prevents intracellular polymerization of Z α1-antitrypsin while allowing its antiproteinase activity

    PubMed Central

    Ordóñez, Adriana; Pérez, Juan; Tan, Lu; Dickens, Jennifer A.; Motamedi-Shad, Neda; Irving, James A.; Haq, Imran; Ekeowa, Ugo; Marciniak, Stefan J.; Miranda, Elena; Lomas, David A.

    2015-01-01

    Mutant Z α1-antitrypsin (E342K) accumulates as polymers within the endoplasmic reticulum (ER) of hepatocytes predisposing to liver disease, whereas low levels of circulating Z α1-antitrypsin lead to emphysema by loss of inhibition of neutrophil elastase. The ideal therapy should prevent polymer formation while preserving inhibitory activity. Here we used mAb technology to identify interactors with Z α1-antitrypsin that comply with both requirements. We report the generation of an mAb (4B12) that blocked α1-antitrypsin polymerization in vitro at a 1:1 molar ratio, causing a small increase of the stoichiometry of inhibition for neutrophil elastase. A single-chain variable fragment (scFv) intrabody was generated based on the sequence of mAb4B12. The expression of scFv4B12 within the ER (scFv4B12KDEL) and along the secretory pathway (scFv4B12) reduced the intracellular polymerization of Z α1-antitrypsin by 60%. The scFv4B12 intrabody also increased the secretion of Z α1-antitrypsin that retained inhibitory activity against neutrophil elastase. MAb4B12 recognized a discontinuous epitope probably located in the region of helices A/C/G/H/I and seems to act by altering protein dynamics rather than binding preferentially to the native state. This novel approach could reveal new target sites for small-molecule intervention that may block the transition to aberrant polymers without compromising the inhibitory activity of Z α1-antitrypsin.—Ordóñez, A., Pérez, J., Tan, L., Dickens, J. A., Motamedi-Shad, N., Irving, J. A., Haq, I., Ekeowa, U., Marciniak, S. J., Miranda, E., Lomas, D. A. A single-chain variable fragment intrabody prevents intracellular polymerization of Z α1-antitrypsin while allowing its antiproteinase activity. PMID:25757566

  17. A Strategy for Generating a Broad-Spectrum Monoclonal Antibody and Soluble Single-Chain Variable Fragments against Plant Potyviruses

    PubMed Central

    Liu, Han-Lin; Lin, Wei-Fang; Hu, Wen-Chi; Lee, Yung-An

    2015-01-01

    Potyviruses are major pathogens that often cause mixed infection in calla lilies. To reduce the time and cost of virus indexing, a detection method for the simultaneous targeting of multiple potyviruses was developed by generating a broad-spectrum monoclonal antibody (MAb) for detecting the greatest possible number of potyviruses. The conserved 121-amino-acid core regions of the capsid proteins of Dasheen mosaic potyvirus (DsMV), Konjak mosaic potyvirus (KoMV), and Zantedeschia mild mosaic potyvirus (ZaMMV) were sequentially concatenated and expressed as a recombinant protein for immunization. After hybridoma cell fusion and selection, one stable cell line that secreted a group-specific antibody, named C4 MAb, was selected. In the reaction spectrum test, the C4 MAb detected at least 14 potyviruses by indirect enzyme-linked immunosorbent assay (I-ELISA) and Western blot analysis. Furthermore, the variable regions of the heavy (VH) and light (VL) chains of the C4 MAb were separately cloned and constructed as single-chain variable fragments (scFvs) for expression in Escherichia coli. Moreover, the pectate lyase E (PelE) signal peptide of Erwinia chrysanthemi S3-1 was added to promote the secretion of C4 scFvs into the medium. According to Western blot analysis and I-ELISA, the soluble C4 scFv (VL-VH) fragment showed a binding specificity similar to that of the C4 MAb. Our results demonstrate that a recombinant protein derived from fusion of the conserved regions of viral proteins has the potential to produce a broad-spectrum MAb against a large group of viruses and that the PelE signal peptide can improve the secretion of scFvs in E. coli. PMID:26209665

  18. Genetic divergence between Mexican Opuntia accessions inferred by polymerase chain reaction-restriction fragment length polymorphism analysis.

    PubMed

    Samah, S; Valadez-Moctezuma, E; Peláez-Luna, K S; Morales-Manzano, S; Meza-Carrera, P; Cid-Contreras, R C

    2016-01-01

    Molecular methods are powerful tools in characterizing and determining relationships between plants. The aim of this study was to study genetic divergence between 103 accessions of Mexican Opuntia. To accomplish this, polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis of three chloroplast intergenic spacers (atpB-rbcL, trnL-trnF, and psbA-trnH), one chloroplast gene (ycf1), two nuclear genes (ppc and PhyC), and one mitochondrial gene (cox3) was conducted. The amplified products from all the samples had very similar molecular sizes, and there were only very small differences between the undigested PCR amplicons for all regions, with the exception of ppc. We obtained 5850 bp from the seven regions, and 136 fragments were detected with eight enzymes, 37 of which (27.2%) were polymorphic. We found that 40% of the fragments from the chloroplast regions were polymorphic, 9.8% of the bands detected in the nuclear genes were polymorphic, and 20% of the bands in the mitochondrial locus were polymorphic. trnL-trnF and psbA-trnH were the most variable regions. The Nei and Li/Dice distance was very short, and ranged from 0 to 0.12; indeed, 77 of the 103 genotypes had the same genetic profile. All the xoconostle accessions (acidic fruits) were grouped together without being separated from three genotypes of prickly pear (sweet fruits). We assume that the genetic divergence between prickly pears and xoconostles is very low, and question the number of Opuntia species currently considered in Mexico. PMID:27323120

  19. Genetic divergence between Mexican Opuntia accessions inferred by polymerase chain reaction-restriction fragment length polymorphism analysis.

    PubMed

    Samah, S; Valadez-Moctezuma, E; Peláez-Luna, K S; Morales-Manzano, S; Meza-Carrera, P; Cid-Contreras, R C

    2016-06-03

    Molecular methods are powerful tools in characterizing and determining relationships between plants. The aim of this study was to study genetic divergence between 103 accessions of Mexican Opuntia. To accomplish this, polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis of three chloroplast intergenic spacers (atpB-rbcL, trnL-trnF, and psbA-trnH), one chloroplast gene (ycf1), two nuclear genes (ppc and PhyC), and one mitochondrial gene (cox3) was conducted. The amplified products from all the samples had very similar molecular sizes, and there were only very small differences between the undigested PCR amplicons for all regions, with the exception of ppc. We obtained 5850 bp from the seven regions, and 136 fragments were detected with eight enzymes, 37 of which (27.2%) were polymorphic. We found that 40% of the fragments from the chloroplast regions were polymorphic, 9.8% of the bands detected in the nuclear genes were polymorphic, and 20% of the bands in the mitochondrial locus were polymorphic. trnL-trnF and psbA-trnH were the most variable regions. The Nei and Li/Dice distance was very short, and ranged from 0 to 0.12; indeed, 77 of the 103 genotypes had the same genetic profile. All the xoconostle accessions (acidic fruits) were grouped together without being separated from three genotypes of prickly pear (sweet fruits). We assume that the genetic divergence between prickly pears and xoconostles is very low, and question the number of Opuntia species currently considered in Mexico.

  20. Taxonomic and ecological discrimination of Fagaceae species based on internal transcribed spacer polymerase chain reaction-restriction fragment length polymorphism.

    PubMed

    Coutinho, João Paulo; Carvalho, Ana; Lima-Brito, José

    2014-11-26

    The internal transcribed spacer (ITS) of ribosomal DNA has been used to confirm taxonomic classifications and define phylogenies in several plant species following sequencing or polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) techniques. In this study, co-dominant ITS PCR-RFLP molecular markers were produced in 30 Fagaceae individuals belonging to the Castanea, Fagus and Quercus genera in order to assess the potential of this technique for taxonomic discrimination and determination of phylogenies. The complete ITS region (ITS1-5.8S rRNA-ITS2) was amplified in most of the Fagaceae individuals as a single fragment of ∼700 bp. The ITS amplified products were digested with nine restriction enzymes, but only four (HaeIII, HpaII, TaqI and Sau96I) produced polymorphic/discriminative patterns. The total expected heterozygosity (HE) was 20.31 % and the gene diversity (I), 32.97 %. The ITS polymorphism was higher within the Quercus genus (85.3 %). The ITS PCR-RFLP markers clustered the Fagaceae species according to genus or infrageneric group (in the case of Quercus sp. individuals). Five oaks did not cluster in line with the adopted infrageneric classification, but three of these were grouped according to their actual ecological distributions. The ITS PCR-RFLP markers indicated their potential for phylogenetic studies since all Fagaceae individuals were discriminated according to genus, and most of the oaks were clustered according to infrageneric group or ecological area.

  1. Identification of roots of woody species using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis

    PubMed

    Bobowski; Hole; Wolf; Bryant

    1999-03-01

    Within the last two decades, substantial progress has been made in understanding seed-bank dynamics and the contribution of the soil seed bank to a postdisturbance plant community. There has been relatively little progress, however, in understanding perennial bud-bank dynamics and the contribution of the soil bud bank to secondary succession. This lack of information is due primarily to the inability to reliably identify roots, rhizomes and lignotubers that lie dormant beneath the soil surface. This investigation addressed the issue of identification of below-ground woody structures. The first objective was to develop a method that used molecular tools to identify woody plant species from subsoil tissue samples. The second objective was to develop a key in which molecular markers served as criteria for the identification and differentiation of selected tree and shrub species common to the mountains of northeast Oregon and southeast Washington. Application of restriction fragment length polymorphism (RFLP) analysis of polymerase chain reaction (PCR)-amplified rbcL appears to be a reliable method to identify and differentiate 15 plants to the genus level. Two restriction enzymes, DpnII and HhaI, provided restriction site polymorphisms in the PCR product. The fragment number and length were used to develop an identification key. However, plants not analysed in this 'exploratory key' might share the same banding patterns, resulting in a false identification of unknowns. PMID:10199009

  2. Leishmania spp. identification by polymerase chain reaction-restriction fragment length polymorphism analysis and its applications in French Guiana.

    PubMed

    Simon, Stéphane; Veron, Vincent; Carme, Bernard

    2010-02-01

    Leishmania (Viannia) guyanensis was for many years the only species commonly identified in French Guiana, but precise species identifications were quite rare. We describe a new restriction fragment length polymorphism-polymerase chain reaction technique using a 615-bp fragment of the RNA polymerase II gene and 2 restriction enzymes, TspRI and HgaI. Seven reference strains (Leishmania (Leishmania) amazonensis, Leishmania (Viannia) lainsoni, Leishmania (Viannia) braziliensis, L. (V.) guyanensis, Leishmania (Viannia) naiffi, Leishmania (Leishmania) major, Leishmania (Leishmania) infantum) and 112 clinical samples from positive lesions were used for the development of the technique. The rates of positive species identification were 85.7% for punch skin biopsy specimens, 93.1% for positive Giemsa-stained smears, and 100% for positive culture supernatants. In the framework of cutaneous leishmaniasis species surveillance for the 2006 to 2008 period, parasite identification was carried out for 199 samples from different patients. The prevalence of the various Leishmania spp. was 84.4% for L. (V.) guyanensis, 8.0% for L. (V.) braziliensis, 5.0% for L. (L.) amazonensis, and 2.6% for L. (V.) lainsoni. L. (V.) braziliensis seems to be locally an emerging pathogen.

  3. DNA fragment length polymorphism analysis of Mycobacterium tuberculosis isolates by arbitrarily primed polymerase chain reaction.

    PubMed

    Palittapongarnpim, P; Chomyc, S; Fanning, A; Kunimoto, D

    1993-04-01

    Strain identification of Mycobacterium tuberculosis would prove whether transmission had occurred between individuals. A method to characterize strains of M. tuberculosis has been developed utilizing polymerase chain reaction (PCR). Purified chromosomal DNA of cultured clinical samples of M. tuberculosis were subjected to PCR using short (10-12 nucleotide) oligonucleotide primers. PCR products visualized after agarose gel electrophoresis and ethidium bromide staining demonstrated that different strains of M. tuberculosis give different banding patterns. This technique was used to confirm the relationship between cases of tuberculosis in several clusters, prove the lack of relationship between 2 isolates with the same antibiotic-resistance pattern, confirm a suspected mislabeling event, and suggest the source of infection in a case of tuberculous meningitis. This method is rapid and simple and does not require radioactive probes.

  4. Serrumab: a novel human single chain-fragment antibody with multiple scorpion toxin-neutralizing capacities.

    PubMed

    Pucca, Manuela Berto; Cerni, Felipe Augusto; Peigneur, Steve; Arantes, Eliane Candiani; Tytgat, Jan; Barbosa, José Elpidio

    2014-01-01

    In Brazil, scorpion envenomation is an important public health problem. The yellow scorpion, Tityus serrulatus (Ts), is considered the most dangerous species in the country, being responsible for the most severe clinical cases of envenomation. Currently, the administration of serum produced in horses is recognized and used as a treatment for accidents with scorpions. However, horse herds' maintenance is costly and the antibodies are heterologous, which can cause anaphylaxis and Serum Sickness. In the present work, a human monoclonal fragment antibody, Serrumab, has been analysed. Toxin neutralizing effects of Serrumab were evaluated using a two-electrode voltage-clamp technique. The results show that Serrumab presented a high neutralizing effect against Ts β-toxins (Ts1, 43.2% and Ts2, 68.8%) and none or low neutralizing effect against α-toxins (Ts3, 0% and Ts5, 10%). Additional experiments demonstrated that Serrumab was also able to neutralize the action of toxins from other scorpion genus (Css II, 45.96% and Lqh III, 100%/β- and α-toxins, respectively). This work indicated that Serrumab is able to neutralize many toxins in Ts venom, and could being considered as a neutralizing antibody for formulating a human anti-scorpion serum in Brazil. Additionally, this work demonstrated that Serrumab could neutralize different toxins from distinct scorpion genus. All these results reinforce the idea that Serrumab is a scFv antibody with multiple neutralizing capacities and a promising candidate for inclusion in scorpion anti-venoms against different genera. PMID:24001307

  5. [Application of polymerase chain reaction-restriction fragment length polymorphism and lab-on-a-chip technology to the identification of fish species from Bohai Bay].

    PubMed

    Li, Xiao; Qu, Yanyan; Zhang, Piqiao; Zhang, Jin; Zhang, Lihua; Huang, Daliang; Zhang, Yukui

    2011-07-01

    Nine representative fish species from Bohai Bay were identified by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and lab-on-a-chip technology. The nine fish species were Pseudosciaena polyactis, Lateolabrax japonicus, Scomberomorus niphonius, Pneumatophorus japonicus, Pseudopleuronectes yokohamae, Collichthys lucidus, Sebastes schlegeli, Cleisthenes herzensteini and Saurida elongata. The 464 bp fragment of mitochondrial cytochrome b gene was amplified and further digested by Dde I , Hae III and Nla III. The digested DNA fragments were analyzed by microfluidic capillary electrophoresis. The nine fish species were fully discriminated. The results demonstrated that the proposed method is efficient, precise and fast in fish species identification.

  6. Early career: Templating of liquid crystal microstructures by reversible addition-fragmentation chain transfer polymerization

    SciTech Connect

    Heinen, Jennifer M.

    2014-12-31

    This research has shown that the microstructure of self-assembled copolymers can be decoupled from the polymer chemistry. The simplest polymer architecture, linear block copolymers, is valuable for a broad range of applications, including adhesives and coatings, medical devices, electronics and energy storage, because these block copolymers reproducibly self-assemble into microphase separated nanoscale domains. Unfortunately, the self-assembled microstructure is tuned by polymer composition, thus limiting the potential to simultaneously optimize chemical, mechanical, and transport properties for desired applications. To this end, much work was been put into manipulating block copolymer self-assembly independently of polymer composition. These efforts have included the use of additives or solvents to alter polymer chain conformation, the addition of a third monomer to produce ABC triblock terpolymers, architectures with mixed blocks, such as tapered/gradient polymers, and the synthesis of other nonlinear molecular architectures. This work has shown that the microstructures formed by linear ABC terpolymers can be altered by controlling the architecture of the polymer molecules at a constant monomer composition, so that the microstructure is tuned independently from the chemical properties.

  7. Amplification refractory mutation system polymerase chain reaction versus optimized polymerase chain reaction restriction-fragment length polymorphism for apolipoprotein E genotyping of majorly depressed patients.

    PubMed

    You, Hongmin; Chen, Jin; Zhou, Jingjing; Huang, Hua; Pan, Junxi; Wang, Ziye; Lv, Lin; Zhang, Lujun; Li, Juan; Qin, Bin; Yang, Yongtao; Xie, Peng

    2015-11-01

    Major depressive disorder (MDD) is a prevalent, debilitating mood disorder that has been associated with several genetic polymorphisms. One such polymorphism, namely that of apolipoprotein E (APOE), has three allelic forms (ε2, ε3 and ε4) that encode for six unique isoforms of the APOE protein. A growing number of techniques have been developed for APOE genotyping; however, not all polymerase chain reaction (PCR)‑based genotyping techniques are equally accurate or cost‑effective. In order to find a more accurate and cost‑effective APOE genotyping method for MDD screening in large populations, the present study comparatively evaluated two genotyping methods, amplification refractory mutation system PCR (ARMS‑PCR) and optimized PCR restriction‑fragment length polymorphism (PCR‑RFLP), in blood samples taken from a population of 708 MDD patients. Although either of the two methods were able to detect all six unique APOE genotypes, comparisons of the two methods with Sanger sequencing demonstrated that ARMS‑PCR (94%) was significantly more accurate than optimized PCR‑RFLP (82%). ARMS‑PCR should prove useful in quickly verifying ambiguous results obtained by other APOE genotyping methods and can be cost-effectively performed in the setting of a small laboratory or a population-based screening program.

  8. Recombinant single-chain Fv antibody fragment-alkaline phosphatase conjugate for one-step immunodetection in molecular hybridization.

    PubMed

    Muller, B H; Chevrier, D; Boulain, J C; Guesdon, J L

    1999-07-30

    Using phage-display technology, a recombinant single-chain Fv antibody fragment (scFv) was rapidly generated from the K16-16 hybridoma secreting mouse monoclonal antibody (MAb) that binds to acetylaminofluorene-labeled DNA (AAF-DNA). The selected A4 phage-scFv specifically bound to AAF-DNA. The anti-AAF scFv gene was then recloned into a fusion vector for the production of a hybrid protein comprising the antibody fragment fused to a potent bacterial alkaline phosphatase variant (PhoAv). The anti-AAF scFv-PhoAv hybrid protein was bifunctional and possessed both antigen binding capacity and PhoA activity. The recombinant conjugate was directly used, without further purification, for one-step immunodetection in dot-blot hybridization. The detection limit was identical and the test was quicker than the conventional two-step procedure with the purified anti-AAF MAb revealed with a secondary enzyme-labeled antibody. To assess the value of this new reagent for the immunodetection of genomic nucleic acids, genomic DNAs of Campylobacter jejuni and Campylobacter coli were then one-step immunodetected with non-purified recombinant scFv-PhoAv conjugate in a Southern-blot hybridization experiment. The present study shows that the genetic fusion with PhoAv provides a new tool for immunodetection which presents easier and quicker production and use with the same sensitivity and specificity as classical reagents. The recombinant anti-AAF scFv-PhoAv conjugate is a promising alternative reagent for applications involving the immunodetection of specific DNA or RNA sequences, such as the detection and characterization of microorganisms.

  9. Generation and characterization of a human single-chain fragment variable (scFv) antibody against cytosine deaminase from Yeast

    PubMed Central

    Mallano, Alessandra; Zamboni, Silvia; Carpinelli, Giulia; Santoro, Filippo; Flego, Michela; Ascione, Alessandro; Gellini, Mara; Tombesi, Marina; Podo, Franca; Cianfriglia, Maurizio

    2008-01-01

    Background The ability of cytosine deaminase (CD) to convert the antifungal agent 5-fluorocytosine (5-FC) into one of the most potent and largely used anticancer compound such as 5-fluorouracil (5-FU) raised considerable interest in this enzyme to model gene or antibody – directed enzyme-prodrug therapy (GDEPT/ADEPT) aiming to improve the therapeutic ratio (benefit versus toxic side-effects) of cancer chemotherapy. The selection and characterization of a human monoclonal antibody in single chain fragment (scFv) format represents a powerful reagent to allow in in vitro and in vivo detection of CD expression in GDEPT/ADEPT studies. Results An enzymatic active recombinant CD from yeast (yCD) was expressed in E. coli system and used as antigen for biopanning approach of the large semi-synthetic ETH-2 antibody phage library. Several scFvs were isolated and specificity towards yCD was confirmed by Western blot and ELISA. Further, biochemical and functional investigations demonstrated that the binding of specific scFv with yCD did not interfere with the activity of the enzyme in converting 5-FC into 5-FU. Conclusion The construction of libraries of recombinant antibody fragments that are displayed on the surface of filamentous phage, and the selection of phage antibodies against target antigens, have become an important biotechnological tool in generating new monoclonal antibodies for research and clinical applications. The scFvH5 generated by this method is the first human antibody which is able to detect yCD in routinary laboratory techniques without interfering with its enzymatic function. PMID:18783590

  10. Development of single chain variable fragment (scFv) antibodies against Xylella fastidiosa subsp. pauca by phage display.

    PubMed

    Yuan, Qing; Jordan, Ramon; Brlansky, Ronald H; Istomina, Olga; Hartung, John

    2015-10-01

    Xylella fastidiosa is a member of the gamma proteobacteria. It is fastidious, insect-vectored and xylem-limited and causes a variety of diseases, some severe, on a wide range of economically important perennial crops, including grape and citrus. Antibody based detection assays are commercially available for X. fastidiosa, and are effective at the species, but not at the subspecies level. We have made a library of scFv antibody fragments directed against X. fastidiosa subsp. pauca strain 9a5c (citrus) by using phage display technology. Antibody gene repertoires were PCR-amplified using 23 primers for the heavy chain variable region (V(H)) and 21 primers for the light chain variable region (V(L)). The V(H) and V(L) were joined by overlap extension PCR, and then the genes of the scFv library were ligated into the phage vector pKM19. The library contained 1.2×10(7) independent clones with full-length scFv inserts. In each of 3cycles of affinity-selection with 9a5c, about 1.0×10(12) phage were used for panning with 4.1×10(6), 7.1×10(6), 2.1×10(7) phage recovered after the first, second and third cycles, respectively. Sixty-six percent of clones from the final library bound X. fastidiosa 9a5c in an ELISA. Some of these scFv antibodies recognized strain 9a5c and did not recognize X. fastidiosa strains that cause Pierce's disease of grapevine.

  11. Development of single chain variable fragment (scFv) antibodies against Xylella fastidiosa subsp. pauca by phage display.

    PubMed

    Yuan, Qing; Jordan, Ramon; Brlansky, Ronald H; Istomina, Olga; Hartung, John

    2015-10-01

    Xylella fastidiosa is a member of the gamma proteobacteria. It is fastidious, insect-vectored and xylem-limited and causes a variety of diseases, some severe, on a wide range of economically important perennial crops, including grape and citrus. Antibody based detection assays are commercially available for X. fastidiosa, and are effective at the species, but not at the subspecies level. We have made a library of scFv antibody fragments directed against X. fastidiosa subsp. pauca strain 9a5c (citrus) by using phage display technology. Antibody gene repertoires were PCR-amplified using 23 primers for the heavy chain variable region (V(H)) and 21 primers for the light chain variable region (V(L)). The V(H) and V(L) were joined by overlap extension PCR, and then the genes of the scFv library were ligated into the phage vector pKM19. The library contained 1.2×10(7) independent clones with full-length scFv inserts. In each of 3cycles of affinity-selection with 9a5c, about 1.0×10(12) phage were used for panning with 4.1×10(6), 7.1×10(6), 2.1×10(7) phage recovered after the first, second and third cycles, respectively. Sixty-six percent of clones from the final library bound X. fastidiosa 9a5c in an ELISA. Some of these scFv antibodies recognized strain 9a5c and did not recognize X. fastidiosa strains that cause Pierce's disease of grapevine. PMID:26232710

  12. Expression and characterization of single-chain variable fragment antibody against staphylococcal enterotoxin A in Escherichia coli.

    PubMed

    Chen, Weifeng; Hu, Li; Liu, Aiping; Li, Jinquan; Chen, Fusheng; Wang, Xiaohong

    2014-11-01

    The staphylococcal enterotoxins (SEs) are potent gastrointestinal exotoxins synthesized by Staphylococcus aureus, which is responsible for various diseases including septicemia, food poisoning, and toxic shock syndrome, as well as bovine mastitis. Among them, staphylococcal enterotoxin A (SEA) is one of the most commonly present serotypes in staphylococcal food poisoning cases. In this study, the stable hybridoma 3C12 producing anti-SEA monoclonal antibody was established with an equilibrium dissociation constant (KD) of 1.48 × 10(-8) mol·L(-1), its ScFv-coding genes were obtained and then the anti-SEA single chain variable fragment (ScFv) protein was expressed in Escherichia coli. Characterization of the expressed target ScFv protein was analyzed by sodium dodecyl sulfate - polyacrylamide gel electrophoresis, Western blot, and enzyme-linked immunosorbent assay. The results demonstrated that the recombinant anti-SEA ScFv protein retained a specific binding activity for SEA, and the KD value of the soluble ScFv was about 3.75 × 10(-7) mol·L(-1). The overall yield of bioactive anti-SEA ScFv in E. coli flask culture was more than 10 mg·L(-1).

  13. Limits of a rapid identification of common Mediterranean sandflies using polymerase chain reaction-restriction fragment length polymorphism

    PubMed Central

    Bounamous, Azzedine; Lehrter, Véronique; Hadj-Henni, Leila; Delecolle, Jean-Claude; Depaquit, Jérôme

    2014-01-01

    A total of 131 phlebotomine Algerian sandflies have been processed in the present study. They belong to the species Phlebotomus bergeroti, Phlebotomus alexandri, Phlebotomus sergenti, Phlebotomus chabaudi, Phlebotomus riouxi, Phlebotomus perniciosus, Phlebotomus longicuspis, Phlebotomus perfiliewi, Phlebotomus ariasi, Phlebotomus chadlii, Sergentomyia fallax, Sergentomyia minuta, Sergentomyia antennata, Sergentomyia schwetzi, Sergentomyia clydei, Sergentomyia christophersi and Grassomyia dreyfussi. They have been characterised by sequencing of a part of the cytochrome b (cyt b), t RNA serine and NADH1 on the one hand and of the cytochrome C oxidase I of the mitochondrial DNA (mtDNA) on the other hand. Our study highlights two sympatric populations within P. sergenti in the area of its type-locality and new haplotypes of P. perniciosus and P. longicuspis without recording the specimens called lcx previously found in North Africa. We tried to use a polymerase chain reaction-restriction fragment length polymorphism method based on a combined double digestion of each marker. These method is not interesting to identify sandflies all over the Mediterranean Basin. PMID:24936911

  14. Characterization of a single-chain variable fragment specific to Cronobacter spp. from hybridoma based on outer membrane protein A.

    PubMed

    Chen, Qiming; Tao, Tingting; Bie, Xiaomei; Lu, Fengxia; Li, Yuanhong; Lu, Zhaoxin

    2016-10-01

    Monoclonal antibody and polyclonal antibody specific to Cronobacter spp. had been reported in previous studies. However, the preparation of single-chain variable fragment (scFv) was faster and convenient. Hence, the aim of this study was to construct a scFv using outer membrane protein A (OmpA) of C. sakazakii as antigen. The protein sequences of OmpA of Cronobacter spp. were analyzed first. The results showed protein OmpA with length of 347 amino acids was conserved in Cronobacter genus (94.83%-100% of protein identity) and was greater than that observed for the other genera tested (8.28-91.64% of protein identity). Then, purified protein OmpA expressed in E. coli was used to prepare hybridoma and to construct scFv further. The scFv was named scFvH81 and analyzed by bioinformatics. The model of scFvH81 built by homologous modeling had a good quality (residues in disallowed regions: 3%) and showed that scFvH81 had a standard pocket-like site. Purified scFvH81 was prepared by denaturation and renaturation of inclusion body and it showed a good specificity and its affinity of Ka=2.39×10(6)M(-1). Therefore, it could be used in the detection and the pathogenesis study of Cronobacter spp. PMID:27498230

  15. Single chain variable fragment antibodies block aggregation and toxicity induced by familial ALS-linked mutant forms of SOD1

    PubMed Central

    Ghadge, Ghanashyam D.; Pavlovic, John; Koduvayur, Sujatha P.; Kay, Brian K.; Roos, Raymond P.

    2013-01-01

    Approximately 10% of amyotrophic lateral sclerosis (ALS) cases are familial (known as FALS) with an autosomal dominant inheritance pattern, and ~25% of FALS cases are caused by mutations in Cu/Zn superoxide dismutase (SOD1). There is convincing evidence that mutant SOD1 (mtSOD1) kills motor neurons (MNs) because of a gain-of-function toxicity, most likely related to aggregation of mtSOD1. A number of recent reports have suggested that antibodies can be used to treat mtSOD1-induced FALS. To follow up on the use of antibodies as potential therapeutics, we generated single chain fragments of variable region antibodies (scFvs) against SOD1, and then expressed them as ‘intrabodies’ within a motor neuron cell line. In the present study, we describe isolation of human scFvs that interfere with mtSOD1 in vitro aggregation and toxicity. These scFvs may have therapeutic potential in sporadic ALS, as well as FALS, given that sporadic ALS may also involve abnormalities in the SOD1 protein or activity. PMID:23607939

  16. Affinity maturation of single-chain variable fragment specific for aflatoxin B(1) using yeast surface display.

    PubMed

    Min, Won-Ki; Kim, Sung-Gun; Seo, Jin-Ho

    2015-12-01

    As aflatoxin B1 is one of the most toxic mycotoxins, it is important to detect and to quantify aflatoxin B1 accurately by immunological methods. To enhance aflatoxin B1-binding affinity of the single-chain variable fragment, yeast surface display technique combined with fluorescence-activated cell sorting was applied. A randomly mutated scFv library was subjected to 4 rounds of fluorescence-activated cell sorting, resulting in isolation of 5 scFv variants showing an affinity improvement compared to the parental wild type scFv. The best scFv with a 9-fold improvement in affinity for aflatoxin B1 exhibited similar specificity to the monoclonal antibody. Most of the mutations in scFv-M37 were located outside of the canonical antigen-contact loops, suggesting that its affinity improvement might be driven by an allosteric effect inducing scFv-M37 to form a more favorable binding pocket for aflatoxin B1 than the wild type scFv. PMID:26041237

  17. Improved Polymerase Chain Reaction-restriction Fragment Length Polymorphism Genotyping of Toxic Pufferfish by Liquid Chromatography/Mass Spectrometry.

    PubMed

    Miyaguchi, Hajime

    2016-09-20

    An improved version of a polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) method for genotyping toxic pufferfish species by liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) is described. DNA extraction is carried out using a silica membrane-based DNA extraction kit. After the PCR amplification using a detergent-free PCR buffer, restriction enzymes are added to the solution without purifying the reaction solution. A reverse-phase silica monolith column and a Fourier transform high resolution mass spectrometer having a modified Kingdon trap analyzer are employed for separation and detection, respectively. The mobile phase, consisting of 400 mM 1,1,1,3,3,3-hexafluoro-2-propanol, 15 mM triethylamine (pH 7.9) and methanol, is delivered at a flow rate of 0.4 ml/min. The cycle time for LC/ESI-MS analysis is 8 min including equilibration of the column. Deconvolution software having an isotope distribution model of the oligonucleotide is used to calculate the corresponding monoisotopic mass from the mass spectrum. For analysis of oligonucleotides (range 26-79 nucleotides), mass accuracy was 0.62 ± 0.74 ppm (n = 280) and excellent accuracy and precision were sustained for 180 hr without use of a lock mass standard.

  18. Polymerase chain reaction-restriction fragment length polymorphism method for differentiation of uropathogenic specific protein gene types.

    PubMed

    Lai, Yun Mei; Zaw, Myo Thura; Shamsudin, Shamsul Bahari; Lin, Zaw

    2016-08-01

    The putative pathogenicity island (PAI) containing the uropathogenic specific protein (usp) gene and three small open reading frames (orfU1, orfU2, and orfU3) encoding 98, 97, and 96 amino acid proteins is widely distributed among uropathogenic Escherichia coli (UPEC) strains. This PAI was designated as PAIusp. Sequencing analysis of PAIusp has revealed that the usp gene can be divided into two types - uspI and uspII - based on sequence variation at the 3' terminal region and the number and position of orfUs differ from strain to strain. Based on usp gene types and orfU sequential patterns, PAIusp can be divided into four subtypes. Subtyping of PAIusp is a useful method to characterize UPEC strains. In this study, we developed a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method to differentiate usp gene types. This method could correctly identify the usp gene type in usp-positive UPEC strains in our laboratory.

  19. Limits of a rapid identification of common Mediterranean sandflies using polymerase chain reaction-restriction fragment length polymorphism.

    PubMed

    Bounamous, Azzedine; Lehrter, Véronique; Hadj-Henni, Leila; Delecolle, Jean-Claude; Depaquit, Jérôme

    2014-07-01

    A total of 131 phlebotomine Algerian sandflies have been processed in the present study. They belong to the species Phlebotomus bergeroti, Phlebotomus alexandri, Phlebotomus sergenti, Phlebotomus chabaudi, Phlebotomus riouxi, Phlebotomus perniciosus, Phlebotomus longicuspis, Phlebotomus perfiliewi, Phlebotomus ariasi, Phlebotomus chadlii, Sergentomyia fallax, Sergentomyia minuta, Sergentomyia antennata, Sergentomyia schwetzi, Sergentomyia clydei, Sergentomyia christophersi and Grassomyia dreyfussi. They have been characterised by sequencing of a part of the cytochrome b (cyt b), t RNA serine and NADH1 on the one hand and of the cytochrome C oxidase I of the mitochondrial DNA (mtDNA) on the other hand. Our study highlights two sympatric populations within P. sergenti in the area of its type-locality and new haplotypes of P. perniciosus and P. longicuspis without recording the specimens called lcx previously found in North Africa. We tried to use a polymerase chain reaction-restriction fragment length polymorphism method based on a combined double digestion of each marker. These method is not interesting to identify sandflies all over the Mediterranean Basin.

  20. Haplotyping the human T-cell receptor. beta. -chain gene complex by use of restriction fragment length polymorphisms

    SciTech Connect

    Charmley, P.; Chao, A.; Gatti, R.A. ); Concannon, P. ); Hood, L. )

    1990-06-01

    The authors have studied the genetic segregation of human T-cell receptor {beta}-chain (TCR{beta}) genes on chromosome 7q in 40 CEPH (Centre d'Etude du Polymorphisme Humain) families by using restriction fragment length polymorphisms (RFLPs). They constructed haplotypes from eight RFLPs by using variable- and constant-region cDNA probes, which detect polymorphisms that span more than 600 kilobases of the TCR{beta} gene complex. Analysis of allele distributions between TCR{beta} genes revealed significant linkage disequilibrium between only 6 of the 28 different pairs of RFLPs. This linkage disequilibrium strongly influences the most efficient order to proceed for typing of these RFLPs in order to achieve maximum genetic informativeness, which in this study revealed a 97.3% level of heterozygosity within the TCR{beta} gene complex. The results should provide new insight into recent reports of disease associations with the TCR{beta} gene complex and should assist in designing future experiments to detect or confirm the existence of disease-susceptibility loci in this region of the human genome.

  1. Improved Polymerase Chain Reaction-restriction Fragment Length Polymorphism Genotyping of Toxic Pufferfish by Liquid Chromatography/Mass Spectrometry.

    PubMed

    Miyaguchi, Hajime

    2016-01-01

    An improved version of a polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) method for genotyping toxic pufferfish species by liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) is described. DNA extraction is carried out using a silica membrane-based DNA extraction kit. After the PCR amplification using a detergent-free PCR buffer, restriction enzymes are added to the solution without purifying the reaction solution. A reverse-phase silica monolith column and a Fourier transform high resolution mass spectrometer having a modified Kingdon trap analyzer are employed for separation and detection, respectively. The mobile phase, consisting of 400 mM 1,1,1,3,3,3-hexafluoro-2-propanol, 15 mM triethylamine (pH 7.9) and methanol, is delivered at a flow rate of 0.4 ml/min. The cycle time for LC/ESI-MS analysis is 8 min including equilibration of the column. Deconvolution software having an isotope distribution model of the oligonucleotide is used to calculate the corresponding monoisotopic mass from the mass spectrum. For analysis of oligonucleotides (range 26-79 nucleotides), mass accuracy was 0.62 ± 0.74 ppm (n = 280) and excellent accuracy and precision were sustained for 180 hr without use of a lock mass standard. PMID:27684516

  2. Optimized extraction of a single-chain variable fragment of antibody by using aqueous micellar two-phase systems.

    PubMed

    Malpiedi, Luciana P; Nerli, Bibiana B; Taqueda, Maria E S; Abdalla, Dulcineia S P; Pessoa, Adalberto

    2015-07-01

    In this work, the purification of a single-chain variable fragment (scFv) of an antibody by using liquid-liquid extraction in aqueous micellar two-phase systems was optimized by means of central composite design. Protein partitioning assays were performed by using the selected system composition in previous works: Triton X-114 at 4% wt/wt, yeast fermentation supernatant at 60% wt/wt, McIlvaine buffer pH 7.00. The other system component concentrations, Cibacron Blue F3GA (CB), Fabsorbent™ F1P HF (HF) and NaCl, were selected as independent variables. ScFv recovery percentage (%R) and purification factor (PF) were selected as the responses. According to the optimization process both, scFv recovery percentage and purification factor were favored with the addition of HF and NaCl in a range of concentrations around the central point of the second central composite design (HF 0.0120% w/w, CB 0.0200% w/w, NaCl 0.200% w/w). These experimental conditions allowed the concentration and pre-purification of scFv in the micelle-rich bottom phase of the systems with a recovery percentage superior to 88% and a purification factor of approximately 3.5. These results improved the previously presented works and demonstrated the convenience of using aqueous micellar two-phase systems as a first step in the purification of scFv molecules.

  3. Scale invariance vs conformal invariance

    NASA Astrophysics Data System (ADS)

    Nakayama, Yu

    2015-03-01

    In this review article, we discuss the distinction and possible equivalence between scale invariance and conformal invariance in relativistic quantum field theories. Under some technical assumptions, we can prove that scale invariant quantum field theories in d = 2 space-time dimensions necessarily possess the enhanced conformal symmetry. The use of the conformal symmetry is well appreciated in the literature, but the fact that all the scale invariant phenomena in d = 2 space-time dimensions enjoy the conformal property relies on the deep structure of the renormalization group. The outstanding question is whether this feature is specific to d = 2 space-time dimensions or it holds in higher dimensions, too. As of January 2014, our consensus is that there is no known example of scale invariant but non-conformal field theories in d = 4 space-time dimensions under the assumptions of (1) unitarity, (2) Poincaré invariance (causality), (3) discrete spectrum in scaling dimensions, (4) existence of scale current and (5) unbroken scale invariance in the vacuum. We have a perturbative proof of the enhancement of conformal invariance from scale invariance based on the higher dimensional analogue of Zamolodchikov's c-theorem, but the non-perturbative proof is yet to come. As a reference we have tried to collect as many interesting examples of scale invariance in relativistic quantum field theories as possible in this article. We give a complementary holographic argument based on the energy-condition of the gravitational system and the space-time diffeomorphism in order to support the claim of the symmetry enhancement. We believe that the possible enhancement of conformal invariance from scale invariance reveals the sublime nature of the renormalization group and space-time with holography. This review is based on a lecture note on scale invariance vs conformal invariance, on which the author gave lectures at Taiwan Central University for the 5th Taiwan School on Strings and

  4. Vitamin D3 Suppresses Class II Invariant Chain Peptide Expression on Activated B-Lymphocytes: A Plausible Mechanism for Downregulation of Acute Inflammatory Conditions.

    PubMed

    Danner, Omar K; Matthews, Leslie R; Francis, Sharon; Rao, Veena N; Harvey, Cassie P; Tobin, Richard P; Wilson, Ken L; Alema-Mensah, Ernest; Newell Rogers, M Karen; Childs, Ed W

    2016-01-01

    Class II invariant chain peptide (CLIP) expression has been demonstrated to play a pivotal role in the regulation of B cell function after nonspecific polyclonal expansion. Several studies have shown vitamin D3 helps regulate the immune response. We hypothesized that activated vitamin D3 suppresses CLIP expression on activated B-cells after nonspecific activation or priming of C57BL/6 mice with CpG. This study showed activated vitamin D3 actively reduced CLIP expression and decreased the number of CLIP(+) B-lymphocytes in a dose and formulation dependent fashion. Flow cytometry was used to analyze changes in mean fluorescent intensity (MFI) based on changes in concentration of CLIP on activated B-lymphocytes after treatment with the various formulations of vitamin D3. The human formulation of activated vitamin D (calcitriol) had the most dramatic reduction in CLIP density at an MFI of 257.3 [baseline of 701.1 (P value = 0.01)]. Cholecalciferol and alfacalcidiol had no significant reduction in MFI at 667.7 and 743.0, respectively. Calcitriol seemed to best reduce CLIP overexpression in this ex vivo model. Bioactive vitamin D3 may be an effective compliment to other B cell suppression therapeutics to augment downregulation of nonspecific inflammation associated with many autoimmune disorders. Further study is necessary to confirm these findings.

  5. Vitamin D3 Suppresses Class II Invariant Chain Peptide Expression on Activated B-Lymphocytes: A Plausible Mechanism for Downregulation of Acute Inflammatory Conditions.

    PubMed

    Danner, Omar K; Matthews, Leslie R; Francis, Sharon; Rao, Veena N; Harvey, Cassie P; Tobin, Richard P; Wilson, Ken L; Alema-Mensah, Ernest; Newell Rogers, M Karen; Childs, Ed W

    2016-01-01

    Class II invariant chain peptide (CLIP) expression has been demonstrated to play a pivotal role in the regulation of B cell function after nonspecific polyclonal expansion. Several studies have shown vitamin D3 helps regulate the immune response. We hypothesized that activated vitamin D3 suppresses CLIP expression on activated B-cells after nonspecific activation or priming of C57BL/6 mice with CpG. This study showed activated vitamin D3 actively reduced CLIP expression and decreased the number of CLIP(+) B-lymphocytes in a dose and formulation dependent fashion. Flow cytometry was used to analyze changes in mean fluorescent intensity (MFI) based on changes in concentration of CLIP on activated B-lymphocytes after treatment with the various formulations of vitamin D3. The human formulation of activated vitamin D (calcitriol) had the most dramatic reduction in CLIP density at an MFI of 257.3 [baseline of 701.1 (P value = 0.01)]. Cholecalciferol and alfacalcidiol had no significant reduction in MFI at 667.7 and 743.0, respectively. Calcitriol seemed to best reduce CLIP overexpression in this ex vivo model. Bioactive vitamin D3 may be an effective compliment to other B cell suppression therapeutics to augment downregulation of nonspecific inflammation associated with many autoimmune disorders. Further study is necessary to confirm these findings. PMID:27313879

  6. Fusion of HCV Nonstructural Antigen to MHC Class II–associated Invariant Chain Enhances T-cell Responses Induced by Vectored Vaccines in Nonhuman Primates

    PubMed Central

    Capone, Stefania; Naddeo, Mariarosaria; D'Alise, Anna Morena; Abbate, Adele; Grazioli, Fabiana; Del Gaudio, Annunziata; Del Sorbo, Mariarosaria; Esposito, Maria Luisa; Ammendola, Virginia; Perretta, Gemma; Taglioni, Alessandra; Colloca, Stefano; Nicosia, Alfredo; Cortese, Riccardo; Folgori, Antonella

    2014-01-01

    Despite viral vectors being potent inducers of antigen-specific T cells, strategies to further improve their immunogenicity are actively pursued. Of the numerous approaches investigated, fusion of the encoded antigen to major histocompatibility complex class II–associated invariant chain (Ii) has been reported to enhance CD8+ T-cell responses. We have previously shown that adenovirus vaccine encoding nonstructural (NS) hepatitis C virus (HCV) proteins induces potent T-cell responses in humans. However, even higher T-cell responses might be required to achieve efficacy against different HCV genotypes or therapeutic effect in chronically infected HCV patients. In this study, we assessed fusion of the HCV NS antigen to murine and human Ii expressed by the chimpanzee adenovirus vector ChAd3 or recombinant modified vaccinia Ankara in mice and nonhuman primates (NHPs). A dramatic increase was observed in outbred mice in which vaccination with ChAd3 expressing the fusion antigen resulted in a 10-fold increase in interferon-γ+ CD8+ T cells. In NHPs, CD8+ T-cell responses were enhanced and accelerated with vectors encoding the Ii-fused antigen. These data show for the first time that the enhancement induced by vector vaccines encoding li-fused antigen was not species specific and can be translated from mice to NHPs, opening the way for testing in humans. PMID:24476798

  7. Vitamin D3 Suppresses Class II Invariant Chain Peptide Expression on Activated B-Lymphocytes: A Plausible Mechanism for Downregulation of Acute Inflammatory Conditions

    PubMed Central

    Danner, Omar K.; Matthews, Leslie R.; Francis, Sharon; Rao, Veena N.; Harvey, Cassie P.; Tobin, Richard P.; Wilson, Ken L.; Alema-Mensah, Ernest; Newell Rogers, M. Karen; Childs, Ed W.

    2016-01-01

    Class II invariant chain peptide (CLIP) expression has been demonstrated to play a pivotal role in the regulation of B cell function after nonspecific polyclonal expansion. Several studies have shown vitamin D3 helps regulate the immune response. We hypothesized that activated vitamin D3 suppresses CLIP expression on activated B-cells after nonspecific activation or priming of C57BL/6 mice with CpG. This study showed activated vitamin D3 actively reduced CLIP expression and decreased the number of CLIP+ B-lymphocytes in a dose and formulation dependent fashion. Flow cytometry was used to analyze changes in mean fluorescent intensity (MFI) based on changes in concentration of CLIP on activated B-lymphocytes after treatment with the various formulations of vitamin D3. The human formulation of activated vitamin D (calcitriol) had the most dramatic reduction in CLIP density at an MFI of 257.3 [baseline of 701.1 (P value = 0.01)]. Cholecalciferol and alfacalcidiol had no significant reduction in MFI at 667.7 and 743.0, respectively. Calcitriol seemed to best reduce CLIP overexpression in this ex vivo model. Bioactive vitamin D3 may be an effective compliment to other B cell suppression therapeutics to augment downregulation of nonspecific inflammation associated with many autoimmune disorders. Further study is necessary to confirm these findings. PMID:27313879

  8. Fractals and fragmentation

    NASA Technical Reports Server (NTRS)

    Turcotte, D. L.

    1986-01-01

    The use of renormalization group techniques on fragmentation problems is examined. The equations which represent fractals and the size-frequency distributions of fragments are presented. Method for calculating the size distributions of asteriods and meteorites are described; the frequency-mass distribution for these interplanetary objects are due to fragmentation. The application of two renormalization group models to fragmentation is analyzed. It is observed that the models yield a fractal behavior for fragmentation; however, different values for the fractal dimension are produced . It is concluded that fragmentation is a scale invariant process and that the fractal dimension is a measure of the fragility of the fragmented material.

  9. Single-chain Fv antibody fragments retain binding properties of the monoclonal antibody raised against peptide P1 of the human prion protein.

    PubMed

    Skrlj, Nives; Serbec, Vladka Curin; Dolinar, Marko

    2010-03-01

    Prion diseases are incurable neurodegenerative diseases that affect both humans and animals. The infectious agent is a pathogenic form of the prion protein that accumulates in brain as amyloids. Currently, there is neither cure nor reliable preclinical diagnostics on the market available. The growing number of reports shows that passive immunisation is one of the most promising strategies for prion disease therapy, where antibodies against prions may prevent and even cure the infection. Since antibodies are large molecules and, thus, might not be suitable for the therapy, different antibody fragments are a good alternative. Therefore, we have designed and prepared single-chain antibody fragments (scFvs) derived from the PrP(Sc)-specific murine monoclonal antibody V5B2. Using a new expression vector pMD204, we produced scFvs in two opposing chain orientations in the periplasm of Escherichia coli. Both recombinant antibody fragments retained the specificity of the parent antibody and one of these exhibited binding properties comparable to the corresponding murine Fab fragments with the affinity in nM range. Our monovalent antibody fragments are of special interest in view of possible therapeutic reagents for prion diseases as well as for development of a new generation of diagnostics. PMID:19597999

  10. Expression and purification of a novel therapeutic single-chain variable fragment antibody against BNP from inclusion bodies of Escherichia coli.

    PubMed

    Bu, Dawei; Zhou, Yuwei; Tang, Jian; Jing, Fang; Zhang, Wei

    2013-12-01

    Abnormal brain natriuretic peptide (BNP) secretion is regarded as the dominating mechanism of cerebral salt wasting syndrome (CSW), which results from a renal loss of sodium and water during intracranial disease leading to hyponatremia. Scale preparation of therapeutic single-chain variable fragment (scFv) that can neutralize elevated circulating BNP may have potential value for clinical use. In this report, we used a recently isolated humanized anti-BNP scFv fragment (3C1) as model antibody (Ab) to evaluate the potential of scale production of this therapeutic protein. The truncated gene encoding for scFv fragment cloned in pET22b (+) was mainly overexpressed as inclusion bodies in Escherichia coli (E. coli) Rosetta (DE3) pLysS cells. The insoluble fragment was solubilized and purified by Ni-NTA agarose resin under denaturation conditions, and recovered via an effective refolding buffer containing 50 mM Tris-HCl, pH 8.0, 0.15 M NaCl, 1 mM EDTA, 0.5 M arginine, 2 mM GSH, 1 mM GSSG, and 5% glycerol. The refolded scFv fragment was concentrated by PEG20000, and dialyzed in PBS (containing 5% glycerol, pH 7.4). The final yield was approximately 10.2 mg active scFv fragment per liter of culture (3.4 g wet weight cells). The scFv fragment was more than 95% pure assessed by SDS-PAGE assay. Recombinant scFv fragment with His tag displayed its immunoreactivity with anti-His tag Ab by western blotting. ELISA showed the scFv fragment specifically bound to BNP, and it displayed similar activity as the traditional anti-BNP monoclonal Ab (mAb). Thus, the current strategy allows convenient small-scale production of this therapeutic protein.

  11. The protective effects and underlying mechanism of an anti-oligomeric Aβ42 single-chain variable fragment antibody.

    PubMed

    Zhang, Yuan; Chen, Xu; Liu, Jinyu; Zhang, Yingjiu

    2015-12-01

    Oligomeric Aβ42 aggregates have been identified as one of the major neurotoxic components of Alzheimer's disease (AD). Immunotherapy targeted against these Aβ42 aggregates has been proposed as an appropriate therapeutic approach for the treatment of AD. Here, we report an anti-oligomeric Aβ42 single-chain variable fragment (scFv) antibody, named MO6, obtained from the human antibody library of a healthy donor. ScFv MO6 specifically recognized and bound to the oligomeric Aβ42 (Aβ42 oligomers and immature protofibrils; 18-37 kDa), and reduced their levels mainly by blocking their formation, although scFv MO6 also induced disaggregation of Aβ42 aggregates. More importantly, scFv MO6 ameliorated or attenuated Aβ42-induced cytotoxicity and increased cell viability by up to 33%. Furthermore, scFv MO6 efficiently passed through an in vitro blood-brain barrier (BBB) model with a delivery efficiency of 66% after 60 min post-administration. ScFv MO6 is a monovalent antibody with an affinity constant (KD) of 5.2×10(-6) M for Aβ42 oligomers. Molecular docking simulations of Aβ42 to scFv MO6 revealed that the approach and specific binding of scFv MO6 to oligomeric Aβ42 aggregates was achieved by conformational recognition and directed induction, which resulted in a more dynamic adaptation of Aβ42 to scFv MO6, occurring mainly in the N-terminal (3-4), middle (12-19) and C-terminal (34-42) regions of Aβ42. This binding mode of scFv MO6 to Aβ42 explains its protective effects against oligomeric Aβ42. Our findings may be applied for the design of a smaller antibody specific for Aβ42 oligermers. PMID:26256421

  12. A single-chain variable fragment intrabody prevents intracellular polymerization of Z α1-antitrypsin while allowing its antiproteinase activity.

    PubMed

    Ordóñez, Adriana; Pérez, Juan; Tan, Lu; Dickens, Jennifer A; Motamedi-Shad, Neda; Irving, James A; Haq, Imran; Ekeowa, Ugo; Marciniak, Stefan J; Miranda, Elena; Lomas, David A

    2015-06-01

    Mutant Z α1-antitrypsin (E342K) accumulates as polymers within the endoplasmic reticulum (ER) of hepatocytes predisposing to liver disease, whereas low levels of circulating Z α1-antitrypsin lead to emphysema by loss of inhibition of neutrophil elastase. The ideal therapy should prevent polymer formation while preserving inhibitory activity. Here we used mAb technology to identify interactors with Z α1-antitrypsin that comply with both requirements. We report the generation of an mAb (4B12) that blocked α1-antitrypsin polymerization in vitro at a 1:1 molar ratio, causing a small increase of the stoichiometry of inhibition for neutrophil elastase. A single-chain variable fragment (scFv) intrabody was generated based on the sequence of mAb4B12. The expression of scFv4B12 within the ER (scFv4B12KDEL) and along the secretory pathway (scFv4B12) reduced the intracellular polymerization of Z α1-antitrypsin by 60%. The scFv4B12 intrabody also increased the secretion of Z α1-antitrypsin that retained inhibitory activity against neutrophil elastase. MAb4B12 recognized a discontinuous epitope probably located in the region of helices A/C/G/H/I and seems to act by altering protein dynamics rather than binding preferentially to the native state. This novel approach could reveal new target sites for small-molecule intervention that may block the transition to aberrant polymers without compromising the inhibitory activity of Z α1-antitrypsin. PMID:25757566

  13. A single-chain variable fragment intrabody prevents intracellular polymerization of Z α1-antitrypsin while allowing its antiproteinase activity.

    PubMed

    Ordóñez, Adriana; Pérez, Juan; Tan, Lu; Dickens, Jennifer A; Motamedi-Shad, Neda; Irving, James A; Haq, Imran; Ekeowa, Ugo; Marciniak, Stefan J; Miranda, Elena; Lomas, David A

    2015-06-01

    Mutant Z α1-antitrypsin (E342K) accumulates as polymers within the endoplasmic reticulum (ER) of hepatocytes predisposing to liver disease, whereas low levels of circulating Z α1-antitrypsin lead to emphysema by loss of inhibition of neutrophil elastase. The ideal therapy should prevent polymer formation while preserving inhibitory activity. Here we used mAb technology to identify interactors with Z α1-antitrypsin that comply with both requirements. We report the generation of an mAb (4B12) that blocked α1-antitrypsin polymerization in vitro at a 1:1 molar ratio, causing a small increase of the stoichiometry of inhibition for neutrophil elastase. A single-chain variable fragment (scFv) intrabody was generated based on the sequence of mAb4B12. The expression of scFv4B12 within the ER (scFv4B12KDEL) and along the secretory pathway (scFv4B12) reduced the intracellular polymerization of Z α1-antitrypsin by 60%. The scFv4B12 intrabody also increased the secretion of Z α1-antitrypsin that retained inhibitory activity against neutrophil elastase. MAb4B12 recognized a discontinuous epitope probably located in the region of helices A/C/G/H/I and seems to act by altering protein dynamics rather than binding preferentially to the native state. This novel approach could reveal new target sites for small-molecule intervention that may block the transition to aberrant polymers without compromising the inhibitory activity of Z α1-antitrypsin.

  14. Rapid detection of clarithromycin resistant Helicobacter pylori strains in Spanish patients by polymerase chain reaction-restriction fragment length polymorphism

    PubMed Central

    Agudo, Sonia; Pérez-Pérez, Guillermo; Alarcón, Teresa; López-Brea, Manuel

    2014-01-01

    Introduction The aim of this study was to characterize the mutations types present in the 23S rRNA gene related to H. pylori clarithromycin-resistance strains in Spain and evaluate a novel PCR-RFLP method for detection of the most frequent point mutation in our population. Methods Gastric biopsies were obtained by endoscopy from patients with gastric symptoms. H. pylori was cultured according to standard microbiological procedures and clarithromycin resistance was determined by E-test. DNA extraction was performed by NucliSens platform with the NucliSens magnetic extraction reagents (bioMérieux) according to the manufacturer instructions. Analyses for point mutations in 23S rRNA gene strains were performed by sequence analysis of amplified polymerase chain reaction products. Restriction fragment length polymorphism was performed using BsaI enzyme to detect restriction sites that correspond to the mutation (A2143G). Result We found 42 out of 118 (35.6%) strains resistant to clarithromycin by E-test. E-test results were confirmed for the presence of point mutation in 34 (88.1%) of these strains. Mutation A2143G was found in 85.3% of the strains. Analyses with the restriction enzyme BsaI was able to confirm the presence of A2143G mutation. There were 8 H. pylori strains resistant to clarithromycin by E-test but without any point mutation in the 23 rRNA gene. Conclusion We conclude that PCR-RFLP is a reliable method to detect clarithromycin-resistance H. pylori strains in countries with a high prevalence of clarithromycin-resistance as Spain It may be useful before choosing regimens of H. pylori eradication. PMID:21412667

  15. Development of single chain variable fragment (scFv) antibodies against surface proteins of 'Ca. Liberibacter asiaticus'.

    PubMed

    Yuan, Qing; Jordan, Ramon; Brlansky, Ronald H; Minenkova, Olga; Hartung, John

    2016-03-01

    'Candidatus Liberibacter asiaticus' is the causal agent of citrus huanglongbing, the most serious disease of citrus worldwide. We have developed and applied immunization and affinity screening methods to develop a primary library of recombinant single chain variable fragment (scFv) antibodies in an M13 vector, pKM19. The antibody population is enriched for antibodies that bind antigens of 'Ca. Liberibacter asiaticus'. The primary library has more than 10(7) unique antibodies and the genes that encode them. We have screened this library for antibodies that bind to specifically-chosen proteins that are present on the surface of 'Ca. Liberibacter asiaticus'. These proteins were used as targets for affinity-based selection of scFvs that bind to the major outer membrane protein, OmpA; the polysaccharide capsule protein KpsF; a protein component of the type IV pilus (CapF); and, two flagellar proteins FlhA and FlgI. These scFvs have been used in ELISA and dot blot assays against purified protein antigens and 'Ca. Liberibacter asiaticus' infected plant extracts. We have also recloned many of these scFvs into a plasmid expression vector designed for the production of scFvs. Screening of these scFvs was more efficient when phage-bound, rather than soluble scFvs, were used. We have demonstrated a technology to produce antibodies at will and against any protein target encoded by 'Ca. Liberibacter asiaticus'. Applications could include advanced diagnostic methods for huanglongbing and the development of immune labeling reagents for in planta applications. PMID:26744234

  16. [Species identification of grouper and snapper in Taiwan Strait using polymerase chain reaction-restriction fragment length polymorphism analysis and lab-on-a-chip system].

    PubMed

    Chen, Shuangya; Zhang, Jin; Chen, Weiling; Xu, Dunming; Zhou, Yu

    2011-07-01

    Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis and lab-on-a-chip system were used to identify grouper and snapper species in Taiwan Strait. A fragment of 464 bp length of mitochondrial cytochrome b gene was amplified by PCR and the products were digested with restriction enzymes Dde I , Hae III and NLa III, individually. The fragments generated after digestion were further resolved on the DNA Chip. Eight grouper species and five snapper species were successfully identified. The results demonstrated that PCR-RFLP analysis and lab-on-a-chip system provide a fast, easy, automated, and reliable analysis approach. This approach is potential for the purpose of fish adulteration control.

  17. Antigen processing by epidermal Langerhans cells correlates with the level of biosynthesis of major histocompatibility complex class II molecules and expression of invariant chain

    PubMed Central

    1990-01-01

    Two prior studies with a small number of T cell lines have shown that the presentation of native protein antigens by epidermal Langerhans cells (LC) is regulated. When freshly isolated, LC are efficient antigen-presenting cells (APC), but after a period of culture LC are inefficient or even inactive. The deficit in culture seems to be a selective loss in antigen processing, since cultured LC are otherwise rich in major histocompatibility complex (MHC) class II products and are active APC for alloantigens and mitogens, which do not require processing. We have extended the analysis by studying presentation to bulk populations of primed lymph node and a T-T hybrid. Only freshly isolated LC can be pulsed with the protein antigens myoglobin and conalbumin, but once pulsed, antigen is retained in an immunogenic form for at least 2 d. The acquisition of antigen, presumably as MHC-peptide complexes, is inhibited if the fresh LC are exposed to foreign protein in the presence of chloroquine or cycloheximide. The latter, in contrast, improves the efficacy of antigen pulsing in anti-Ig- stimulated B blasts. In additional studies of mechanism, we noted that both fresh and cultured LC endocytose similar amounts of an antigen, rhodamineovalbumin, into perinuclear granules. However, freshly isolated LC synthesize high levels class II MHC molecules and express higher amounts of the class II-associated invariant chain. Fresh LC are at least 5-10 times more active than many other cells types in the level of biosynthesis of MHC class II products. These findings provide a physiologic model in which newly synthesized MHC class II molecules appear to be the principal vehicle for effective antigen processing by APC of the dendritic cell lineage. Another APC, the B lymphoblast, does not appear to require newly synthesized MHC class II molecules for presentation. PMID:2121888

  18. Parasite Manipulation of the Invariant Chain and the Peptide Editor H2-DM Affects Major Histocompatibility Complex Class II Antigen Presentation during Toxoplasma gondii Infection.

    PubMed

    Leroux, Louis-Philippe; Nishi, Manami; El-Hage, Sandy; Fox, Barbara A; Bzik, David J; Dzierszinski, Florence S

    2015-10-01

    Toxoplasma gondii is an obligate intracellular protozoan parasite. This apicomplexan is the causative agent of toxoplasmosis, a leading cause of central nervous system disease in AIDS. It has long been known that T. gondii interferes with major histocompatibility complex class II (MHC-II) antigen presentation to attenuate CD4(+) T cell responses and establish persisting infections. Transcriptional downregulation of MHC-II genes by T. gondii was previously established, but the precise mechanisms inhibiting MHC-II function are currently unknown. Here, we show that, in addition to transcriptional regulation of MHC-II, the parasite modulates the expression of key components of the MHC-II antigen presentation pathway, namely, the MHC-II-associated invariant chain (Ii or CD74) and the peptide editor H2-DM, in professional antigen-presenting cells (pAPCs). Genetic deletion of CD74 restored the ability of infected dendritic cells to present a parasite antigen in the context of MHC-II in vitro. CD74 mRNA and protein levels were, surprisingly, elevated in infected cells, whereas MHC-II and H2-DM expression was inhibited. CD74 accumulated mainly in the endoplasmic reticulum (ER), and this phenotype required live parasites, but not active replication. Finally, we compared the impacts of genetic deletion of CD74 and H2-DM genes on parasite dissemination toward lymphoid organs in mice, as well as activation of CD4(+) T cells and interferon gamma (IFN-γ) levels during acute infection. Cyst burdens and survival during the chronic phase of infection were also evaluated in wild-type and knockout mice. These results highlight the fact that the infection is influenced by multiple levels of parasite manipulation of the MHC-II antigen presentation pathway. PMID:26195549

  19. Functional humanization of an anti-CD16 Fab fragment: obstacles of switching from murine {lambda} to human {lambda} or {kappa} light chains.

    PubMed

    Schlapschy, Martin; Fogarasi, Marton; Gruber, Helga; Gresch, Oliver; Schäfer, Claudia; Aguib, Yasmine; Skerra, Arne

    2009-03-01

    An alphaCD30xalphaCD16 bispecific monoclonal antibody (MAb) was previously shown to induce remission of Hodgkin's disease refractory to chemo- and radiotherapy through specific activation of natural killer (NK) cells, but the appearance of a human anti-mouse antibody (HAMA) response prevented its use for prolonged therapy. Here, we describe an effort to humanize the Fab arm directed against FcgammaRIII (CD16), which-in context with the previously humanized CD30 Fab fragment-provides the necessary component for the design of a clinically useful bispecific antibody. Thus, the CDRs of the anti-CD16 mouse IgG1/lambda MAb A9 were grafted onto human Ig sequences. In a first attempt, the murine V(lambda) domain was converted to a humanized lambda chain, which led, however, to complete loss of antigen-binding activity and extremely poor folding efficiency upon periplasmic expression in Escherichia coli. Hence, its CDRs were transplanted onto a human kappa light chain in a second attempt, which resulted in a functional recombinant Fab fragment, yet with 100-fold decreased antigen affinity. In the next step, an in vitro affinity maturation was performed, wherein random mutations were introduced into the humanized V(H) and V(kappa) domains through error-prone PCR, followed by a filter sandwich colony screening assay for increased binding activity towards the bacterially produced extracellular CD16 fragment. Finally, an optimized Fab fragment was obtained, which carries nine additional amino acid exchanges and exhibits an affinity that is within a factor of 2 identical to that of the original murine A9 Fab fragment. The resulting humanized Fab fragment was fully functional with respect to binding of the recombinant CD16 antigen in enzyme-linked immunosorbent assay and in cytofluorimetry with CD16-positive granulocytes, thus providing a promising starting point for the preparation of a fully human bispecific antibody that permits the therapeutic recruitment of NK cells.

  20. Characterization of environmental quality of forest fragments changes in Jundiaí-Mirim river basin-Brazil using the Markov Chain model

    NASA Astrophysics Data System (ADS)

    Hasimoto Fengler, Felipe; Leite de Moraes, Jener Fernando; Irio Ribeiro, Admilson; Peche Filho, Afonso; Araujo de Medeiros, Gerson; Baldin Damame, Desirée; Márcia Longo, Regina

    2015-04-01

    In Brazil is common practice the concurrency of large urban centers water catchment in distant sites. There's no policy to preserve strategic springs in the urban territory. Thus, rural areas, located in the surrounds of municipals, usually provide water and others environment services to the population that reside on cities. The Jundiaí-Mirim river basin, located in the most urbanized state in Brazil, São Paulo, composes an interesting example of this situation. It is located in a rural area near large urban centers, with large industrial parks, near the capital of state. As result of expansion of the cities on its surrounds their lands have had a historic of monetary valorization, making its territories attractive to the housing market. Consequently, the region has an intense process of urbanization that resulted in an increasing environmental disturbance in the areas of natural vegetation. In the other hand, the watershed is the principal water supplier of Jundiaí city, and houses forest remaining of an important Biome in Brazil, the Atlantic Rain Forest. Given the need to preserve its water production capacity and the forest remnants there, this study modeled the environmental quality of forest fragments through indicators of disturbance and evaluated the changes that occur between 1972 and 2013 using the Markov Chain model. The environment quality was determined by nine indicators of environmental disturbance (distance of urban areas, roads, edge land use, size, distance of others forest fragments, land capacity of use, watershed forest cover, number of forest fragments in the watersheds, shape of the forest fragment), obtained by techniques of Geoprocessing, and integrated by Multicriteria Analysis. The Markov Chain model showed a constant tendency of deteriorating in natural vegetation environmental quality, attributed to the intense process of occupation of the river basin. The results showed a historical trend of transformation in forest fragments with

  1. Functional Production and Characterization of a Fibrin-Specific Single-Chain Antibody Fragment from Bacillus subtilis: Effects of Molecular Chaperones and a Wall-Bound Protease on Antibody Fragment Production

    PubMed Central

    Wu, Sau-Ching; Yeung, Jonathan C.; Duan, Yanjun; Ye, Ruiqiong; Szarka, Steven J.; Habibi, Hamid R.; Wong, Sui-Lam

    2002-01-01

    To develop an ideal blood clot imaging and targeting agent, a single-chain antibody (SCA) fragment based on a fibrin-specific monoclonal antibody, MH-1, was constructed and produced via secretion from Bacillus subtilis. Through a systematic study involving a series of B. subtilis strains, insufficient intracellular and extracytoplasmic molecular chaperones and high sensitivity to wall-bound protease (WprA) were believed to be the major factors that lead to poor production of MH-1 SCA. Intracellular and extracytoplasmic molecular chaperones apparently act in a sequential manner. The combination of enhanced coproduction of both molecular chaperones and wprA inactivation leads to the development of an engineered B. subtilis strain, WB800HM[pEPP]. This strain allows secretory production of MH-1 SCA at a level of 10 to 15 mg/liter. In contrast, with WB700N (a seven-extracellular-protease-deficient strain) as the host, no MH-1 SCA could be detected in both secreted and cellular fractions. Secreted MH-1 SCA from WB800HM[pMH1, pEPP] could be affinity purified using a protein L matrix. It retains comparable affinity and specificity as the parental MH-1 monoclonal antibody. This expression system can potentially be applied to produce other single-chain antibody fragments, especially those with folding and protease sensitivity problems. PMID:12089002

  2. Invariant death

    PubMed Central

    Frank, Steven A.

    2016-01-01

    In nematodes, environmental or physiological perturbations alter death’s scaling of time. In human cancer, genetic perturbations alter death’s curvature of time. Those changes in scale and curvature follow the constraining contours of death’s invariant geometry. I show that the constraints arise from a fundamental extension to the theories of randomness, invariance and scale. A generalized Gompertz law follows. The constraints imposed by the invariant Gompertz geometry explain the tendency of perturbations to stretch or bend death’s scaling of time. Variability in death rate arises from a combination of constraining universal laws and particular biological processes. PMID:27785361

  3. Identification of blood meal sources of Lutzomyia longipalpis using polymerase chain reaction-restriction fragment length polymorphism analysis of the cytochrome B gene.

    PubMed

    Soares, Vítor Yamashiro Rocha; Silva, Jailthon Carlos da; Silva, Kleverton Ribeiro da; Pires e Cruz, Maria do Socorro; Santos, Marcos Pérsio Dantas; Ribolla, Paulo Eduardo Martins; Alonso, Diego Peres; Coelho, Luiz Felipe Leomil; Costa, Dorcas Lamounier; Costa, Carlos Henrique Nery

    2014-06-01

    An analysis of the dietary content of haematophagous insects can provide important information about the transmission networks of certain zoonoses. The present study evaluated the potential of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the mitochondrial cytochrome B (cytb) gene to differentiate between vertebrate species that were identified as possible sources of sandfly meals. The complete cytb gene sequences of 11 vertebrate species available in the National Center for Biotechnology Information database were digested with Aci I, Alu I, Hae III and Rsa I restriction enzymes in silico using Restriction Mapper software. The cytb gene fragment (358 bp) was amplified from tissue samples of vertebrate species and the dietary contents of sandflies and digested with restriction enzymes. Vertebrate species presented a restriction fragment profile that differed from that of other species, with the exception of Canis familiaris and Cerdocyon thous. The 358 bp fragment was identified in 76 sandflies. Of these, 10 were evaluated using the restriction enzymes and the food sources were predicted for four: Homo sapiens (1), Bos taurus (1) and Equus caballus (2). Thus, the PCR-RFLP technique could be a potential method for identifying the food sources of arthropods. However, some points must be clarified regarding the applicability of the method, such as the extent of DNA degradation through intestinal digestion, the potential for multiple sources of blood meals and the need for greater knowledge regarding intraspecific variations in mtDNA.

  4. SCEDS: protein fragments for molecular replacement in Phaser

    SciTech Connect

    McCoy, Airlie J.; Nicholls, Robert A.; Schneider, Thomas R.

    2013-11-01

    Protein fragments suitable for use in molecular replacement can be generated by normal-mode perturbation, analysis of the difference distance matrix of the original versus normal-mode perturbed structures, and SCEDS, a score that measures the sphericity, continuity, equality and density of the resulting fragments. A method is described for generating protein fragments suitable for use as molecular-replacement (MR) template models. The template model for a protein suspected to undergo a conformational change is perturbed along combinations of low-frequency normal modes of the elastic network model. The unperturbed structure is then compared with each perturbed structure in turn and the structurally invariant regions are identified by analysing the difference distance matrix. These fragments are scored with SCEDS, which is a combined measure of the sphericity of the fragments, the continuity of the fragments with respect to the polypeptide chain, the equality in number of atoms in the fragments and the density of C{sup α} atoms in the triaxial ellipsoid of the fragment extents. The fragment divisions with the highest SCEDS are then used as separate template models for MR. Test cases show that where the protein contains fragments that undergo a change in juxtaposition between template model and target, SCEDS can identify fragments that lead to a lower R factor after ten cycles of all-atom refinement with REFMAC5 than the original template structure. The method has been implemented in the software Phaser.

  5. Construction and bacterial expression of a recombinant single-chain antibody fragment against Wuchereria bancrofti SXP-1 antigen for the diagnosis of lymphatic filariasis.

    PubMed

    Kamatchi, R; Charumathi, J; Ravishankaran, R; Kaliraj, P; Meenakshisundaram, S

    2016-01-01

    Global programmes to eliminate lymphatic filariasis (GPELF) require mapping, monitoring and evaluation using filarial antigen diagnostic kits. To meet this objective, a functional single-chain fragment variable (ScFv) specific for filarial Wuchereria bancrofti SXP-1 (Wb-SXP-1) antigen was constructed for the diagnosis of active filarial infection, an alternative to the production of complete antibodies using hybridomas. The variable heavy chain (VH) and the variable light chain (kappa) (Vκ) genes were amplified from the mouse hybridoma cell line and were linked together with a flexible linker by overlap extension polymerase chain reaction (PCR). The ScFv construct (Vκ-Linker-VH) was expressed as a fusion protein with N-terminal His tag in Escherichia coli and purified using immobilized metal affinity chromatography (IMAC) without the addition of reducing agents. Immunoblotting and sandwich enzyme-linked immunosorbent assay (ELISA) were used to analyse the antigen binding affinity of purified ScFv. The purified ScFv was found to recognize recombinant and native Wb-SXP-1 antigen in microfilariae (Mf)-positive patient sera. The affinity of ScFv was comparable with that of the monoclonal antibody. The development of recombinant ScFv to replace monoclonal antibody for detection of filarial antigen was achieved. The recombinant ScFv was purified, on-column refolded and its detection ability validated using field samples.

  6. Construction and bacterial expression of a recombinant single-chain antibody fragment against Wuchereria bancrofti SXP-1 antigen for the diagnosis of lymphatic filariasis.

    PubMed

    Kamatchi, R; Charumathi, J; Ravishankaran, R; Kaliraj, P; Meenakshisundaram, S

    2016-01-01

    Global programmes to eliminate lymphatic filariasis (GPELF) require mapping, monitoring and evaluation using filarial antigen diagnostic kits. To meet this objective, a functional single-chain fragment variable (ScFv) specific for filarial Wuchereria bancrofti SXP-1 (Wb-SXP-1) antigen was constructed for the diagnosis of active filarial infection, an alternative to the production of complete antibodies using hybridomas. The variable heavy chain (VH) and the variable light chain (kappa) (Vκ) genes were amplified from the mouse hybridoma cell line and were linked together with a flexible linker by overlap extension polymerase chain reaction (PCR). The ScFv construct (Vκ-Linker-VH) was expressed as a fusion protein with N-terminal His tag in Escherichia coli and purified using immobilized metal affinity chromatography (IMAC) without the addition of reducing agents. Immunoblotting and sandwich enzyme-linked immunosorbent assay (ELISA) were used to analyse the antigen binding affinity of purified ScFv. The purified ScFv was found to recognize recombinant and native Wb-SXP-1 antigen in microfilariae (Mf)-positive patient sera. The affinity of ScFv was comparable with that of the monoclonal antibody. The development of recombinant ScFv to replace monoclonal antibody for detection of filarial antigen was achieved. The recombinant ScFv was purified, on-column refolded and its detection ability validated using field samples. PMID:26693887

  7. Static and Dynamic Magnetic Response of Fragmented Haldane-like Spin Chains in Layered Li3Cu2SbO6

    NASA Astrophysics Data System (ADS)

    Koo, Changhyun; Zvereva, Elena A.; Shukaev, Igor L.; Richter, Michael; Stratan, Mikhail I.; Vasiliev, Alexander N.; Nalbandyan, Vladimir B.; Klingeler, Rüdiger

    2016-08-01

    The structure and the magnetic properties of layered Li3Cu2SbO6 are investigated by powder X-ray diffraction, static susceptibility, and electron spin resonance studies up to 330 GHz. The XRD data experimentally verify the space group C2/m with halved unit cell volume in contrast to previously reported C2/c. In addition, the data show significant Li/Cu-intersite exchange. Static magnetic susceptibility and ESR measurements show two magnetic contributions, i.e., quasi-free spins at low-temperature and a spin-gapped magnetic subsystem, with about half of the spins being associated to each subsystem. The data suggest ferromagnetic-antiferromagnetic alternating chains with JFM = -285 K and JAFM = 160 K with a significant amount of Li-defects in the chains. The results are discussed in the scenario of fragmented 1D S = 1 AFM chains with a rather high defect concentration of about 17% and associated S = 1/2 edge states of the resulting finite Haldane chains.

  8. Molecular variation analysis of Aspergillus flavus using polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer rDNA region

    PubMed Central

    Zarrin, Majid; Erfaninejad, Maryam

    2016-01-01

    Aspergillus flavus is the second most common disease-causing species of Aspergillus in humans. The fungus is frequently associated with life-threatening infections in immunocompromised hosts. The primary aim of the present study was to analyze the genetic variability among different isolates of A. flavus using polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP). A total of 62 A. flavus isolates were tested in the study. Molecular variability was searched for by analysis of the PCR amplification of the internal transcribed spacer (ITS) regions of ribosomal DNA using restriction enzymes. PCR using primers for ITS1 and ITS4 resulted in a product of ~600 bp. Amplicons were subjected to digestion with restriction endonucleases EcoRI, HaeIII and TaqI. Digestion of the PCR products using these restriction enzymes produced different patterns of fragments among the isolates, with different sizes and numbers of fragments, revealing genetic variability. In conclusion, ITS-RFLP is a useful molecular tool in screening for nucleotide polymorphisms among A. flavus isolates. PMID:27588085

  9. Identification of Pork Contamination in Meatballs of Indonesia Local Market Using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) Analysis.

    PubMed

    Erwanto, Yuny; Abidin, Mohammad Zainal; Sugiyono, Eko Yasin Prasetyo Muslim; Rohman, Abdul

    2014-10-01

    This research applied and evaluated a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using cytochrome b gene to detect pork contamination in meatballs from local markets in Surabaya and Yogyakarta regions, Indonesia. To confirm the effectiveness and specificity of this fragment, thirty nine DNA samples from different meatball shops were isolated and amplified, and then the PCR amplicon was digested by BseDI restriction enzyme to detect the presence of pork in meatballs. BseDI restriction enzyme was able to cleave porcine cytochrome b gene into two fragments (131 bp and 228 bp). Testing the meatballs from the local market showed that nine of twenty meatball shops in Yogyakarta region were detected to have pork contamination, but there was no pork contamination in meatball shops in Surabaya region. In conclusion, specific PCR amplification of cytochrome b gen and cleaved by BseDI restriction enzymes seems to be a powerful technique for the identification of pork presence in meatball because of its simplicity, specificity and sensitivity. Furthermore, pork contamination intended for commercial products of sausage, nugget, steak and meat burger can be checked. The procedure is also much cheaper than other methods based on PCR, immunodiffusion and other techniques that need expensive equipment.

  10. The Potential of Poly[N-(2-hydroxypropyl)methacrylamide] via Reversible Addition-Fragmentation Chain Transfer Polymerization as Safe Nanocarrier.

    PubMed

    Zhang, Yanhong; Guo, Chunhua; Li, Shuo; Luo, Kui; Hu, Jiani; Gu, Zhongwei

    2016-06-01

    N-(2-hydroxypropyl)methacrylamide (HPMA) copolymers have been presented as nanoscale drug/gene delivery systems and imaging probes, and the well-defined HPMA copolymers prepared via reversible addition-fragmentation chain transfer (RAFT) polymerization promote their to clinical trials, as the significant enhanced anticancer efficacy. The biosafety is another issue associated with the carriers. In this study, we prepared the linear and branched HPMA copolymers labeled with Cy5.5 via RAFT polymerization and click chemistry, and their potential biosafety was studied. The linear copolymer was prepared via RAFT polymerization mediated by the ends-functionalized peptide chain transfer agent (peptide2CTA), resulting in well-defined and block linear HPMA copolymer with molecular weight (MW) of 98 kDa. Additionally, the branched HPMA copolymer was also prepared via RAFT polymerization. Followed by Cy5.5 labeling, the two copolymers showed negative zeta potential and their accumulation into tumor was studied by in vivo optical fluorescence imaging in the nude mice with breast tumors. The biosafety studies on in vitro cytotoxicity and hemocompatibility studies, including hemolysis tests, plasma coagulation and thromboelastography assay were carried out well, demonstrating that the linear HPMA copolymer-Cy5.5 with MW around 100 kDa and biodegradable moiety in the main chain might be utilized as safe nanoscale carrier. PMID:27427626

  11. Double Gene Targeting Multiplex Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Assay Discriminates Beef, Buffalo, and Pork Substitution in Frankfurter Products.

    PubMed

    Hossain, M A Motalib; Ali, Md Eaqub; Abd Hamid, Sharifah Bee; Asing; Mustafa, Shuhaimi; Mohd Desa, Mohd Nasir; Zaidul, I S M

    2016-08-17

    Beef, buffalo, and pork adulteration in the food chain is an emerging and sensitive issue. Current molecular techniques to authenticate these species depend on polymerase chain reaction (PCR) assays involving long and single targets which break down under natural decomposition and/or processing treatments. This novel multiplex polymerase chain reaction-restriction fragment length polymorphism assay targeted two different gene sites for each of the bovine, buffalo, and porcine materials. This authentication ensured better security, first through a complementation approach because it is highly unlikely that both sites will be missing under compromised states, and second through molecular fingerprints. Mitochondrial cytochrome b and ND5 genes were targeted, and all targets (73, 90, 106, 120, 138, and 146 bp) were stable under extreme boiling and autoclaving treatments. Target specificity and authenticity were ensured through cross-amplification reaction and restriction digestion of PCR products with AluI, EciI, FatI, and CviKI-1 enzymes. A survey of Malaysian frankfurter products revealed rampant substitution of beef with buffalo but purity in porcine materials.

  12. Double Gene Targeting Multiplex Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Assay Discriminates Beef, Buffalo, and Pork Substitution in Frankfurter Products.

    PubMed

    Hossain, M A Motalib; Ali, Md Eaqub; Abd Hamid, Sharifah Bee; Asing; Mustafa, Shuhaimi; Mohd Desa, Mohd Nasir; Zaidul, I S M

    2016-08-17

    Beef, buffalo, and pork adulteration in the food chain is an emerging and sensitive issue. Current molecular techniques to authenticate these species depend on polymerase chain reaction (PCR) assays involving long and single targets which break down under natural decomposition and/or processing treatments. This novel multiplex polymerase chain reaction-restriction fragment length polymorphism assay targeted two different gene sites for each of the bovine, buffalo, and porcine materials. This authentication ensured better security, first through a complementation approach because it is highly unlikely that both sites will be missing under compromised states, and second through molecular fingerprints. Mitochondrial cytochrome b and ND5 genes were targeted, and all targets (73, 90, 106, 120, 138, and 146 bp) were stable under extreme boiling and autoclaving treatments. Target specificity and authenticity were ensured through cross-amplification reaction and restriction digestion of PCR products with AluI, EciI, FatI, and CviKI-1 enzymes. A survey of Malaysian frankfurter products revealed rampant substitution of beef with buffalo but purity in porcine materials. PMID:27501408

  13. A VL-linker-VH Orientation Dependent Single Chain Variable Antibody Fragment Against Rabies Virus G Protein with Enhanced Neutralizing Potency in vivo.

    PubMed

    Cheng, Yue; Li, Zhuang; Xi, Hualong; Gu, Tiejun; Yuan, Ruosen; Chen, Xiaoxu; Jiang, Chunlai; Kong, Wei; Wu, Yongge

    2016-01-01

    Lethal rabies can be prevented effectively by post-exposure prophylactic (PEP) with rabies immunoglobulin (RIG). Single-chain variable fragment (scFv), which is composed of a variable heavy chain (VH) and variable light chain (VL) connected by a peptide linker, may be developed as alternative to RIG for neutralizing rabies virus (RV). However, our previously constructed scFv (FV57S) with the (NH2) VH-linker-VL (COOH) orientation showed a lower neutralizing potency than its parent RIG. This orientation may inhibit FV57S from refolding into an intact and correct conformation. Therefore, the RFV57S protein with a VL-linker-VH orientation was constructed based on FV57S. A HIS tag was incorporated to aid in purification and detection of RFV57S and FV57S. However, abilities of RFV57S and FV57S to bind with the anti-HIS tag mAb were different. Therefore, a novel direct ELISA was established by utilizing a biotin-labeled truncated glycoprotein of RV. Although with similar stability and in vitro neutralizing potency as FV57S, RFV57S showed enhanced binding ability, affinity and in vivo protective efficacy against lethal dose of RV. Our studies support the feasibility of developing a scFv with reversed orientation and provide a novel method for evaluating the binding ability, stability and affinity of engineered antibodies recognizing linear epitope.

  14. Amino acid sequence of the amino-terminal 24 kDa fragment of the heavy chain of chicken gizzard myosin.

    PubMed

    Maita, T; Onishi, H; Yajima, E; Matsuda, G

    1987-07-01

    Chicken gizzard myosin was modified with N-iodoacetyl-N'-(5-sulfo-1-naphthyl)-ethylenediamine (IAEDANS) in the presence of ATP and in 0.15 M KCl, where the myosin assumed 10S conformation. From the tryptic digest of the modified myosin, a fluorescent fragment (24 kilodaltons) was isolated by gel filtration on a Sephadex G-100 column followed by chromatography on a CM 52 column. The amino acid sequence of the fragment was analyzed by conventional methods, and was: (S,Z)K-P-L-S-D-D-E-K-F-L-F-V-D-K-N-F-V-N-N-P-L-A-Q-A-D-W-S-A-K-K- L-V-W-V-P-S-E-K-H-G-F-E-A-A-S-I-K-E-E-K-G-D-E-V-T-V-E-L-Q-E-N-G-K-K- V-T-L-S-K-D-D-I-Q-K-M-N-P-P-K-F-S-K-V-E-D-M-A-E-L-T-C-L-N-E-A-S-V-L- H-N-L-R-E-R-Y-F-S-G-L-I-Y-T-Y-S-G-L-F-C-V-V-I-N-P-Y-K-Q-L-P-I-Y-S-E-K-I- I-D-M-Y-K-G-K-K-R-H-E-M-P-P-H-I-Y-A-I-A-D-T-A-Y-R-S-M-L-Q-D-R-E-D-Q- S-I-L-C-T-G-E-S-G-A-G-K-T-E-N-T-K-K-V-I-Q-Y-L-A-V-V-A-S-S-H-K-G-K. The amino-terminus was blocked, and the fragment was assigned as an amino-terminal part of the heavy chain of gizzard myosin. Position 127 was occupied by epsilon-N-trimethyllysine. Trp-130 of rabbit skeletal myosin heavy chain, which was reported to cross-link to an azide derivative of ATP by Okamoto and Yount (Proc. Natl. Acad. Sci. U.S. 82, 1575-1579 (1985], was replaced by glutamine in gizzard myosin. Cys-93 of the fragment is the amino acid residue whose reaction with IAEDANS alters the ATPase activity of gizzard myosin (Onishi, H. (1985) J. Biochem. 98, 81-86).

  15. Amplification of ribulose biphosphate carboxylase/oxygenase large subunit (RuBisCO LSU) gene fragments from Thiobacillus ferrooxidans and a moderate thermophile using polymerase chain reaction.

    PubMed

    Holden, P J; Brown, R W

    1993-07-01

    Southern blot analysis of DNA from an iron-oxidising moderate thermophile NMW-6 and from Thiobacillus ferrooxidans strain TFI-35 demonstrated sequences homologous to the RuBisCO LSU gene of Synechococcus. DNA fragments (457 bp) encoding part of the RuBisCO LSU gene (amino acids 73-200) were amplified from the genomic DNA of Thiobacillus ferrooxidans and the moderate thermophile NMW-6 using the polymerase chain reaction (PCR) technique (Saiki et al. (1985) Science 233, 1350-1354). A comparison with the LSU sequences from T. ferrooxidans, Alcaligenes eutrophus, Chromatium vinosum, Synechococcus and Spinacea oleracea, which all have RuBisCOs with a hexadecameric structure, showed that the RuBisCO LSU gene sequence from NMW-6 appeared to be most closely related to that of the hydrogen bacterium A. eutrophus which showed 71.9% homology at the amino acid level. Despite its physiological similarity, T. ferrooxidans showed only 64.1% homology to the amino acid sequence from NMW-6 and had the lowest DNA homology (60.9%) of the hexadecameric type RuBisCOs. In the region sequenced, T. ferrooxidans and the RuBisCOs of the phototrophs C. vinosum, Synechococcus and S. oleracea, had 17 residues that were completely conserved which were substituted in both NMW-6 and A. eutrophus, 11 of these being identical substitutions. Comparison of the nucleotide and derived amino acid sequences of the RuBisCO LSU fragment from T. ferrooxidans with other RuBisCO sequences indicated a closer relationship to the hexadecameric type LSU genes of photosynthetic origin than to that of A. eutrophus. The T. ferrooxidans amino acid sequence showed 93.8%, 78.9% and 77.3% homology, respectively, to the C. vinosum, Synechococcus and S. oleracea (spinach) sequences but only 56.2% to A. eutrophus. The DNA sequence from Rhodospirillum rubrum, which has the atypical large subunit dimer RuBisCO structure with no small subunit, showed 39.2% and 42.7% homology, respectively, with the sequences of NMW-6 and T

  16. Amino acid sequence of the 203-residue fragment of the heavy chain of chicken gizzard myosin containing the SH1-type cysteine residue.

    PubMed

    Onishi, H; Maita, T; Miyanishi, T; Watanabe, S; Matsuda, G

    1986-12-01

    A fluorescent fragment of Mr = 23,800 was obtained by the papain digestion of N-iodoacetyl-N'-(5-sulfo-1-naphthyl)ethylene diamine (abbreviated as IAEDANS)-modified chicken gizzard myosin. The fragment was isolated by gel filtration on a Sephadex G-100 column in the presence of 5 M guanidine-HCl followed by anion exchange chromatography on a QAE Sephadex A-50 column. This fragment contained 203 amino acid residues which could be assigned as a COOH-terminal part of the S-1 heavy chain based on the homology with the known sequence of rabbit skeletal myosin fragment. The amino acid sequence was K-G-M-F-R-T-V- G-Q-L-Y-K-E-Q-L-T-K-L-M-T-T-L-R-N-T-N-P-N-F-V-R-C-I-I-P-N-H-E-K-R-A- G-K-L-D-A-H-L-V-L-E-Q-L-R-C-N-G-V-L-E-G-I-R-I-C-R-Q-G-F-P-N-R-I-V-F-Q- E-F-R-Q-R-Y-E-I-L-A-A-N-A-I-P-K-G-F-M-D-G-K-Q-A-C-I-L-M -I-K-A-L-E-L- D-P-N-L-Y-R-I-G-Q-S-K-I-F-F-R-T-G-V-L-A-H-L-E-E-E-R-D-L-K- I-T-D-V-I-I-A- F-Q-A-Q-C-R-G-Y-L-A-R-K-A-F-A-K-R-Q-Q-Q-L-T-A-M-K-V-I-Q-R-N-C-A -A-Y-L-K-L-R-N-W-Q-W-W-R-L-F-T-K-V-K-P-L-L-Q-V-T-R. The cysteine residue which was modified with IAEDANS was of the SH1 type (Cys-65). Pro-197 was suggested to be the NH2-terminal boundary of the alpha-helical coiled-coil rod sequence of gizzard myosin, based on the homology with the nematode sequence reported by MacLachlan and Karn (Proc. Natl. Acad. Sci. U.S. 80, 4253-4257 (1983)). Three different COOH-terminal peptides (Val-Lys-Pro-Leu-Leu-Gln-Val-Thr-Arg, Val-Lys-Pro-Leu-Leu-Gln, and Val-Lys-Pro-Leu-Leu) were isolated from the tryptic digest of this fragment.(ABSTRACT TRUNCATED AT 400 WORDS)

  17. Purification and on-column refolding of a single-chain antibody fragment against rabies virus glycoprotein expressed in Escherichia coli.

    PubMed

    Xi, Hualong; Yuan, Ruosen; Chen, Xiaoxu; Gu, Tiejun; Cheng, Yue; Li, Zhuang; Jiang, Chunlai; Kong, Wei; Wu, Yongge

    2016-10-01

    An anti-rabies virus single-chain antibody fragment of an anti-glycoprotein with the VL-linker-VH orientation, designated scFv57RN, was successfully and conveniently prepared in this study. The scFv57RN protein was mainly expressed in inclusion bodies in Escherichia coli. After washing and purification, the inclusion bodies were finally obtained with an on-column refolding procedure. Further purification by gel exclusion chromatography was performed to remove inactive multimers. About 360 mg of final product was recovered from 1 L of bacterial culture. The final product showed a high neutralizing titer of 950 IU/mg to the CVS-11 strain as measured using the rapid fluorescent focus inhibition test. Our study demonstrated a highly efficient method to mass produce scFV57RN with activity from inclusion bodies, which may be applied in the purification of other insoluble proteins.

  18. Examination of meat components in commercial dog and cat feed by using polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLPs) technique.

    PubMed

    Wang, Hsien-Chi; Lee, Shu-Hwae; Chang, Tien-Jye; Wong, Min-Liang

    2004-07-01

    It has been shown that certain slow neurological diseases such as bovine spongiform encephalopathy (also known as "mad cow" disease) could be transmitted through contaminated food intake by animals; therefore, the examination of meat components in commercial feeds is important for the control of the disease in public health. The combination of polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLPs) technique was applied to examine the meat components in dog and cat commercial feeds. The partial nucleotide sequence (359 bp) of animal mitochondrial cytochrome b (cytb, CYT) gene was amplified by PCR and then digested with restriction enzyme Alu I or Mbo I. In this work, eight brands of commercial dog and cat feeds available in Taiwan were examined. All brands of dog feeds that were tested contained meat from four different animals (cattle, pig, goat and chicken). In cat feeds, the chicken meat was found in five out of eight brands. PMID:15297759

  19. Polymerase chain reaction-restriction fragment length polymorphism method to distinguish three mealybug groups within the Planococcus citri-P. minor species complex (Hemiptera: Coccoidea: Pseudococcidae).

    PubMed

    Rung, A; Miller, D R; Scheffer, S J

    2009-02-01

    The mealybug species Planococcus citri (Risso) and Planococcus minor (Maskell) (Hemiptera: Coccoidea: Pseudococcidae) have special significance to U.S. quarantine and U.S. agriculture. Commonly intercepted at U.S. ports-of-entry, they are difficult to identify based on morphological characters. This study presents a molecular method for distinguishing P. citri, P. minor, and a genetically distinct group that is morphologically identical to P. citri, from Hawaii. This method uses polymerase chain reaction (PCR) followed by restriction fragment polymorphism analysis (RFLP) using the restriction enzymes BspH1, BsmH1, and HpH1. The resulting band patterns can be visualized in a 2% agarose gel and are sufficient to differentiate between the three entities mentioned above. PCR-RFLP diagnostics can be used for all life stages and is cheaper and faster than DNA sequencing.

  20. Examination of meat components in commercial dog and cat feed by using polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLPs) technique.

    PubMed

    Wang, Hsien-Chi; Lee, Shu-Hwae; Chang, Tien-Jye; Wong, Min-Liang

    2004-07-01

    It has been shown that certain slow neurological diseases such as bovine spongiform encephalopathy (also known as "mad cow" disease) could be transmitted through contaminated food intake by animals; therefore, the examination of meat components in commercial feeds is important for the control of the disease in public health. The combination of polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLPs) technique was applied to examine the meat components in dog and cat commercial feeds. The partial nucleotide sequence (359 bp) of animal mitochondrial cytochrome b (cytb, CYT) gene was amplified by PCR and then digested with restriction enzyme Alu I or Mbo I. In this work, eight brands of commercial dog and cat feeds available in Taiwan were examined. All brands of dog feeds that were tested contained meat from four different animals (cattle, pig, goat and chicken). In cat feeds, the chicken meat was found in five out of eight brands.

  1. Development of a biotinylated broad-specificity single-chain variable fragment antibody and a sensitive immunoassay for detection of organophosphorus pesticides.

    PubMed

    Zhao, Fengchun; Tian, Yuan; Wang, Huimin; Liu, Jiye; Han, Xiao; Yang, Zhengyou

    2016-09-01

    Organophosphorus pesticides (OPs) are the most widely used pesticides in agriculture, and OP residues have been broadly reported in food and environmental samples. The aim of this study is to develop a recombinant antibody-based broad-specificity immunoassay for OPs. A phage display library was prepared from a mouse pre-immunized with a generic immunogen of OPs, and a single-chain variable fragment (scFv) antibody was selected. The selected scFv antibody was fused with biotin acceptor domain (BAD) and overexpressed as an inclusion body in Escherichia coli BL21 (DE3). Then, the protein was refolded by stepwise urea gradient dialysis and biotinylated in vitro by E. coli biotin ligase (BirA). Subsequently, the scFv-BAD protein was purified from the biotinylated system with high yield (66.7 mg L(-1)) and confirmed by SDS-PAGE and Western blot. Based on the biotinylated scFv-BAD, a sensitive and broad-specificity competitive indirect enzyme-linked immunosorbent assay (ciELISA) for detection of OPs was developed. The cross-reactivity (CR) studies demonstrated that the ciELISA described here exhibited the broadest detection spectrum for OPs up to now, and 30 OPs could be determined with 50 % inhibition value (IC50) values ranging from 19.4 to 515.2 ng mL(-1). Moreover, the developed ciELISA was used for the recovery study of the spiked samples and showed satisfactory recoveries. Graphical Abstract Schematic diagram of the development of biotinylated broad-specificity single-chain variable fragment antibody-based immunoassay for organophosphorus pesticides. PMID:27411546

  2. Molecular typing of Iranian mycobacteria isolates by polymerase chain reaction-restriction fragment length polymorphism analysis of 360-bp rpoB gene

    PubMed Central

    Hadifar, Shima; Moghim, Sharareh; Fazeli, Hossein; GhasemianSafaei, Hajieh; Havaei, Seyed Asghar; Farid, Fariba; Esfahani, Bahram Nasr

    2015-01-01

    Background: Diagnosis and typing of Mycobacterium genus provides basic tools for investigating the epidemiology and pathogenesis of this group of bacteria. Polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis (PRA) is an accurate method providing diagnosis and typing of species of mycobacteria. The present study is conducted by the purpose of determining restriction fragment profiles of common types of mycobacteria by PRA method of rpoB gene in this geographical region. Materials and Methods: Totally 60 clinical and environmental isolates from February to October, 2013 were collected and subcultured and identified by phenotypic methods. A 360 bp fragment of the rpoB gene amplified by PCR and products were digested by MspI and HaeIII enzymes. Results: In the present study, of all mycobacteria isolates identified by PRA method, 13 isolates (21.66%) were Mycobacterium tuberculosis, 34 isolates (56.66%) were rapidly growing Nontuberculosis Mycobacteria (NTM) that including 26 clinical isolates (43.33%) and 8 environmental isolates (13.33%), 11 isolates (18.33%) were clinical slowly growing NTM. among the clinical NTM isolates, Mycobacterium fortuitum Type I with the frequency of 57.77% was the most prevalent type isolates. Furthermore, an unrecorded of the PRA pattern of Mycobacterium conceptionense (HeaIII: 120/90/80, MspI: 120/105/80) was found. This study demonstrated that the PRA method was high discriminatory power for identification and typing of mycobacteria species and was able to identify 96.6% of all isolates. Conclusion: Based on the result of this study, rpoB gene could be a potentially useful tool for identification and investigation of molecular epidemiology of mycobacterial species. PMID:26380237

  3. Synthesis and pre-clinical evaluation of an (18)F-labeled single-chain antibody fragment for PET imaging of epithelial ovarian cancer.

    PubMed

    Sharma, Sai Kiran; Wuest, Melinda; Way, Jenilee D; Bouvet, Vincent R; Wang, Monica; Wuest, Frank R

    2016-01-01

    Anti-CA125 antibodies have been used in immunoassays to quantify levels of shed antigen in the serum of patients who are under surveillance for epithelial ovarian cancer (EOC). However, there is currently no molecular imaging probe in the clinic for the assessment of CA125 expression in vivo. The present study describes the development of an (18)F-labeled single-chain variable fragment (scFv) for PET imaging of CA125 in preclinical EOC models. Anti-CA125 scFv was derived from MAb-B43.13 by recombinant expression of the fragment in E.coli. Fragment scFv-B43.13 was purified via immobilized metal affinity chromatography and characterized for antigen binding via immuno-staining and flow cytometry. Prosthetic group N-succinimidyl 4-[(18)F]fluorobenzoate ([(18)F]SFB) was used for radiolabeling of scFv-B43.13. Preclinical ovarian cancer models were developed based on ovarian cancer cell lines OVCAR3 (CA125-positive) and SKOV3 (CA125-negative) in NIH-III mice. The radiopharmacological profile of (18)F-labeled scFv-B43.13 ([(18)F]FBz-scFv-B43.13) was studied with PET. [(18)F]FBz-scFv-B43.13 was prepared in radiochemical yields of 3.7 ± 1.8% (n = 5) at an effective specific activity of 3.88 ± 0.76 GBq/µmol (n = 5). The radiotracer demonstrated selective uptake in CA125-positive OVCAR3 cells and virtually no uptake in CA125-negative SKOV3 cells. Standardized uptake values (SUV) of radioactivity uptake in OVCAR3 tumors was 0.5 (n = 3) and 0.3 (n = 2) in SKOV3 tumors after 60 min post injection (p.i.). PMID:27508105

  4. Synthesis and pre-clinical evaluation of an 18F-labeled single-chain antibody fragment for PET imaging of epithelial ovarian cancer

    PubMed Central

    Sharma, Sai Kiran; Wuest, Melinda; Way, Jenilee D; Bouvet, Vincent R; Wang, Monica; Wuest, Frank R

    2016-01-01

    Anti-CA125 antibodies have been used in immunoassays to quantify levels of shed antigen in the serum of patients who are under surveillance for epithelial ovarian cancer (EOC). However, there is currently no molecular imaging probe in the clinic for the assessment of CA125 expression in vivo. The present study describes the development of an 18F-labeled single-chain variable fragment (scFv) for PET imaging of CA125 in preclinical EOC models. Anti-CA125 scFv was derived from MAb-B43.13 by recombinant expression of the fragment in E.coli. Fragment scFv-B43.13 was purified via immobilized metal affinity chromatography and characterized for antigen binding via immuno-staining and flow cytometry. Prosthetic group N-succinimidyl 4-[18F]fluorobenzoate ([18F]SFB) was used for radiolabeling of scFv-B43.13. Preclinical ovarian cancer models were developed based on ovarian cancer cell lines OVCAR3 (CA125-positive) and SKOV3 (CA125-negative) in NIH-III mice. The radiopharmacological profile of 18F-labeled scFv-B43.13 ([18F]FBz-scFv-B43.13) was studied with PET. [18F]FBz-scFv-B43.13 was prepared in radiochemical yields of 3.7 ± 1.8% (n = 5) at an effective specific activity of 3.88 ± 0.76 GBq/µmol (n = 5). The radiotracer demonstrated selective uptake in CA125-positive OVCAR3 cells and virtually no uptake in CA125-negative SKOV3 cells. Standardized uptake values (SUV) of radioactivity uptake in OVCAR3 tumors was 0.5 (n = 3) and 0.3 (n = 2) in SKOV3 tumors after 60 min post injection (p.i.). PMID:27508105

  5. Improved biological activity of a single chain antibody fragment against human epidermal growth factor receptor 2 (HER2) expressed in the periplasm of Escherichia coli.

    PubMed

    Akbari, Vajihe; Sadeghi, Hamid Mir Mohammad; Jafarian-Dehkordi, Abbas; Abedi, Daryoush; Chou, C Perry

    2015-12-01

    A novel monoclonal antibody against human epidermal growth factor receptor 2 (HER2), i.e., pertuzumab (Perjeta®) developed by Genentech, has been verified to be effective in treating metastatic HER2-overexpressing breast cancer. The fact that the presence of the Fc region of the anti-HER2 is uncritical for growth inhibition of tumor cells suggests the potential biological activity of the associated antibody fragments. In the present study, we report functional expression of anti-HER2his-scFv, a single-chain variable fragment (scFv) derived from pertuzumab, in the periplasm of Escherichia coli and its purification. Biological activity of the soluble scFv produced in this manner was characterized using immunofluorescent staining, immunocytochemistry, flow cytometry and cytotoxicity assay. The effect of anti-HER2his-scFv on HER2 dimerization was also assessed by tyrosine kinase assay. It was observed that the purified scFv had a high specificity and affinity to HER2 receptors expressed on the surface of tumor cells with a selective cytotoxic effect on HER2-overexpressing SK-OV-3 cells. In addition, anti-HER2his-scFv was able to suppress phosphorylation of HER2 in the presence of heregulin. The results suggest that anti-HER2his-scFv can be a potential candidate for various therapeutic and diagnosis applications.

  6. Selection of a human butyrylcholinesterase-like antibody single-chain variable fragment resistant to AChE inhibitors from a phage library expressed in E. coli

    PubMed Central

    Podestà, Adriano; Rossi, Serena; Massarelli, Ilaria; Carpi, Sara; Adinolfi, Barbara; Fogli, Stefano; Bianucci, Anna Maria; Nieri, Paola

    2014-01-01

    Organophosphates are potent poisoning agents that cause severe cholinergic toxicity. Current treatment has been reported to be unsatisfactory and novel antidotes are needed. In this study, we used a single-chain variable fragment (scFv) library to select a recombinant antibody fragment (WZ1–14.2.1) with butyrylcholinesterase-like catalytic activity by using an innovative method integrating genetic selection and the bait-and-switch strategy. Ellman assay demonstrated that WZ1–14.2.1 has Michaelis-Menten kinetics in the hydrolysis of all the three substrates used, acetylthiocholine, propionylthiocholine and butyrylthiocholine. Notably, the catalytic activity was resistant to the following acetylcholinesterase inhibitors: neostigmine, iso-OMPA, chlorpyrifos oxon, dichlorvos, and paraoxon ethyl. Otherwise, the enzymatic activity of WZ1–14.2.1 was inhibited by the selective butyrylcholinesterase inhibitor, ethopropazine, and by the Ser-blocking agent phenylmethanesuphonyl fluoride. A hypothetical 3D structure of the WZ1–14.2.1 catalytic site, compatible with functional results, is proposed on the basis of a molecular modeling analysis. PMID:24675419

  7. Selection of a human butyrylcholinesterase-like antibody single-chain variable fragment resistant to AChE inhibitors from a phage library expressed in E. coli.

    PubMed

    Podestà, Adriano; Rossi, Serena; Massarelli, Ilaria; Carpi, Sara; Adinolfi, Barbara; Fogli, Stefano; Bianucci, Anna Maria; Nieri, Paola

    2014-01-01

    Organophosphates are potent poisoning agents that cause severe cholinergic toxicity. Current treatment has been reported to be unsatisfactory and novel antidotes are needed. In this study, we used a single-chain variable fragment (scFv) library to select a recombinant antibody fragment (WZ1-14.2.1) with butyrylcholinesterase-like catalytic activity by using an innovative method integrating genetic selection and the bait-and-switch strategy. Ellman assay demonstrated that WZ1-14.2.1 has Michaelis-Menten kinetics in the hydrolysis of all the three substrates used, acetylthiocholine, propionylthiocholine and butyrylthiocholine. Notably, the catalytic activity was resistant to the following acetylcholinesterase inhibitors: neostigmine, iso-OMPA, chlorpyrifos oxon, dichlorvos, and paraoxon ethyl. Otherwise, the enzymatic activity of WZ1-14.2.1 was inhibited by the selective butyrylcholinesterase inhibitor, ethopropazine, and by the Ser-blocking agent phenylmethanesuphonyl fluoride. A hypothetical 3D structure of the WZ1-14.2.1 catalytic site, compatible with functional results, is proposed on the basis of a molecular modeling analysis.

  8. Single Chain Variable Fragments Produced in Escherichia coli against Heat-Labile and Heat-Stable Toxins from Enterotoxigenic E. coli

    PubMed Central

    Andrade, Fernanda B.; Nepomuceno, Roberto; Silva, Anderson; Munhoz, Danielle D.; Yamamoto, Bruno B.; Luz, Daniela; Abreu, Patrícia A. E.; Horton, Denise S. P. Q.; Elias, Waldir P.; Ramos, Oscar H. P.; Piazza, Roxane M. F.

    2015-01-01

    Background Diarrhea is a prevalent pathological condition frequently associated to the colonization of the small intestine by enterotoxigenic Escherichia coli (ETEC) strains, known to be endemic in developing countries. These strains can produce two enterotoxins associated with the manifestation of clinical symptoms that can be used to detect these pathogens. Although several detection tests have been developed, minimally equipped laboratories are still in need of simple and cost-effective methods. With the aim to contribute to the development of such diagnostic approaches, we describe here two mouse hybridoma-derived single chain fragment variable (scFv) that were produced in E. coli against enterotoxins of ETEC strains. Methods and Findings Recombinant scFv were developed against ETEC heat-labile toxin (LT) and heat-stable toxin (ST), from previously isolated hybridoma clones. This work reports their design, construction, molecular and functional characterization against LT and ST toxins. Both antibody fragments were able to recognize the cell-interacting toxins by immunofluorescence, the purified toxins by ELISA and also LT-, ST- and LT/ST-producing ETEC strains. Conclusion The developed recombinant scFvs against LT and ST constitute promising starting point for simple and cost-effective ETEC diagnosis. PMID:26154103

  9. Polymerase chain reaction-restriction fragment length polymorphism assays to distinguish Liriomyza huidobrensis (Diptera: Agromyzidae) from associated species on lettuce cropping systems in Italy.

    PubMed

    Masetti, Antonio; Luchetti, Andrea; Mantovani, Barbara; Burgio, Giovanni

    2006-08-01

    The pea leafminer, Liriomyza huidobrensis (Blanchard) (Diptera: Agromyzidae), is a serious insect pest infesting open field lettuce plantings in northern Italy. In these cropping systems, it coexists with several other agromyzid species that have negligible economic importance on open field vegetables. The rapid detection of L. huidobrensis is crucial for effective management strategies, but the identification of agromyzids to species can be very difficult at adult as well at immature stages. In this study, a polymerase chain reaction (PCR)-restriction fragment length polymorphism assay is proposed to separate L. huidobrensis from Liriomyza bryoniae (Kaltenbach), Liriomyza trifolii (Burgess), and Chromatomyia horticola (Goureau), which usually occur in the same lettuce plantings. An approximately 1,031-bp region of the mitochondrial genome encompassing the 3' region of cytochrome oxidase I, the whole leucine tRNA, and all of the cytochrome oxidase II was amplified by PCR and digested using the enzymes PvuII and SnaBI separately. Both endonucleases cut the amplicons of L. huidobrensis in two fragments, whereas the original band was not cleaved in the other analyzed species. The presence of Dacnusa spp. DNA does not bias the assay, because the PCR conditions and the primer set here described do not amplify any tract of this endoparasitic wasp genome. PMID:16937681

  10. Single-chain Variable Fragment Albumin Fusions Bind the Neonatal Fc Receptor (FcRn) in a Species-dependent Manner

    PubMed Central

    Andersen, Jan Terje; Cameron, Jason; Plumridge, Andrew; Evans, Leslie; Sleep, Darrell; Sandlie, Inger

    2013-01-01

    Albumin has a serum half-life of 3 weeks in humans. This has been utilized to extend the serum persistence of biopharmaceuticals that are fused to albumin. In light of the fact that the neonatal Fc receptor (FcRn) is a key regulator of albumin homeostasis, it is crucial to address how fusion of therapeutics to albumin impacts binding to FcRn. Here, we report on a detailed molecular investigation on how genetic fusion of a short peptide or an single-chain variable fragment (scFv) fragment to human serum albumin (HSA) influences pH-dependent binding to FcRn from mouse, rat, monkey, and human. We have found that fusion to the N- or C-terminal end of HSA only slightly reduces receptor binding, where the most noticeable effect is seen after fusion to the C-terminal end. Furthermore, in contrast to the observed strong binding to human and monkey FcRn, HSA and all HSA fusions bound very poorly to mouse and rat versions of the receptor. Thus, we demonstrate that conventional rodents are limited as preclinical models for analysis of serum half-life of HSA-based biopharmaceuticals. This finding is explained by cross-species differences mainly found within domain III (DIII) of albumin. Our data demonstrate that although fusion, particularly to the C-terminal end, may slightly reduce the affinity for FcRn, HSA is versatile as a carrier of biopharmaceuticals. PMID:23818524

  11. Cloning and expression in Escherichia coli of a human gelatinase B-inhibitory single-chain immunoglobulin variable fragment (scFv).

    PubMed

    Zhou, N; Paemen, L; Opdenakker, G; Froyen, G

    1997-09-15

    The murine monoclonal antibody REGA-3G12 selectively and specifically inhibits the activity of human gelatinase B. The cDNA fragments which encode the variable regions of the light and heavy chains were isolated by PCR-mediated cloning and sequenced. Single-chain Fv expression constructs for Escherichia coli were generated in which c-myc tag sequences were encoded. Inducible expression of the scFv and secretion to the periplasm were obtained with higher yields when the c-myc tag sequence was positioned at the amino-terminal side. The inhibitory activity of purified scFv on neutrophil gelatinase B was tested in a gelatin degradation assay and it was found to possess a similar specific activity as that of the intact monoclonal antibody and of the pepsin-clipped F(ab')2 derivative. This shows for the first time that inhibition of soluble enzymes with scFv is possible and opens new perspectives for the treatment of diseases with excessive and detrimental enzyme production in the host.

  12. Construction, expression, and characterization of a single-chain variable fragment antibody against 2,4-dichlorophenoxyacetic acid in the hemolymph of silkworm larvae.

    PubMed

    Sakamoto, Seiichi; Pongkitwitoon, Benyakan; Nakamura, Seiko; Sasaki-Tabata, Kaori; Tanizaki, Yusuke; Maenaka, Katsumi; Tanaka, Hiroyuki; Morimoto, Satoshi

    2011-07-01

    A single-chain variable fragment antibody against herbicide, 2,4-dichlorophenoxyacetic acid (2,4-D-scFv) has been successfully expressed in the hemolymph of silkworm larvae using a rapid Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid DNA system. Variable heavy- and light-chain domains were cloned directly from the cDNA of the hybridoma cell line 2C4 and assembled together with flexible peptide linker (Gly(4)Ser)(3) between two domains. The yield of functional 2,4-D-scFv after purification was 640 μg per 30 ml of hemolymph, which is equivalent to 21.3 mg per liter of hemolymph. The characterization of 2,4-D-scFv using an indirect competitive enzyme-linked immunosorbent assay (icELISA) revealed that it has wide cross-reactivities against 2,4,5-trichlorophenoxyacetic acid (65.5%), 2,4-dichlorophenol (47.9%), and 2,4-dichlorobenzoic acid (26.0%), making it possible to apply 2,4-D-scFv to icELISA for detecting/determining 2,4-D and its metabolites. Judging from its cost and time requirements and its ease of handling, this BmNPV bacmid DNA expression system is more useful for expressing functional scFv than bacterial systems, which frequently require costly and time-consuming refolding.

  13. Screening and identification of human ZnT8-specific single-chain variable fragment (scFv) from type 1 diabetes phage display library.

    PubMed

    Wu, Qian; Wang, Xiaodong; Gu, Yong; Zhang, Xiao; Qin, Yao; Chen, Heng; Xu, Xinyu; Yang, Tao; Zhang, Mei

    2016-07-01

    Zinc transporter 8 (ZnT8) is a major autoantigen and a predictive marker in type 1 diabetes (T1D). To investigate ZnT8-specific antibodies, a phage display library from T1D was constructed and single-chain antibodies against ZnT8 were screened and identified. Human T1D single-chain variable fragment (scFv) phage display library consists of approximately 1×10(8) clones. After four rounds of bio-panning, seven unique clones were positive by phage ELISA. Among them, C27 and C22, which demonstrated the highest affinity to ZnT8, were expressed in Escherichia coli Top10F' and then purified by affinity chromatography. C27 and C22 specifically bound ZnT8 N/C fusion protein and ZnT8 C terminal dimer with one Arg325Trp mutation. The specificity to human islet cells of these scFvs were further confirmed by immunohistochemistry. In conclusion, we have successfully constructed a T1D phage display antibody library and identified two ZnT8-specific scFv clones, C27 and C22. These ZnT8-specific scFvs are potential agents in immunodiagnostic and immunotherapy of T1D. PMID:27270580

  14. Grafting of molecularly imprinted polymers from the surface of silica gel particles via reversible addition-fragmentation chain transfer polymerization: a selective sorbent for theophylline.

    PubMed

    Li, Yong; Zhou, Wen-Hui; Yang, Huang-Hao; Wang, Xiao-Ru

    2009-07-15

    Molecularly imprinted polymers (MIPs) were grafted successfully from the surface of silica gel particles via surface initiated reversible addition-fragmentation chain transfer (RAFT) polymerization using RAFT agent functionalized silica gel as the chain transfer agent. The intrinsic characteristics of the controlled/living polymerization mechanism of RAFT allowed for the effective control of the grafting process. Thus the grafting copolymerization of methacrylic acid and divinyl benzene in the presence of template theophylline led to thin MIP film coating silica gel (MIP-Silica). The thickness of MIP film prepared in this study is about 1.98 nm, which was calculated from the nitrogen sorption analysis results. Measured binding kinetics for theophylline to the MIP-Silica and MIPs prepared by conventional bulk polymerization demonstrated that MIP-Silica had improved mass-transfer properties. In addition, the theophylline-imprinted MIP-Silica was used as the sorbent in solid-phase extraction to determine theophylline in blood serum with satisfactory recovery higher than 90%. Nonspecific adsorption of interfering compounds can be eliminated by a simple elution with acetonitrile, without sacrificing the selective binding of theophylline.

  15. Determination of locust bean gum and guar gum by polymerase chain reaction and restriction fragment length polymorphism analysis.

    PubMed

    Meyer, K; Rosa, C; Hischenhuber, C; Meyer, R

    2001-01-01

    A polymerase chain reaction (PCR) was developed to differentiate the thickening agents locust bean gum (LBG) and the cheaper guar gum in finished food products. Universal primers for amplification of the intergenic spacer region between trnL 3' (UAA) exon and trnF (GAA) gene in the chloroplast (cp) genome and subsequent restriction analysis were applied to differentiate guar gum and LBG. The presence of <5% (w/w) guar gum powder added to LBG powder was detectable. Based on data obtained from sequencing this intergenic spacer region, a second PCR method for the specific detection of guar gum DNA was also developed. This assay detected guar gum powder in LBG in amounts as low as 1% (w/w). Both methods successfully detected guar gum and/or LBG in ice cream stabilizers and in foodstuffs, such as dairy products, ice cream, dry seasoning mixes, a finished roasting sauce, and a fruit jelly product, but not in products with highly degraded DNA, such as tomato ketchup and sterilized chocolate cream. Both methods detected guar gum and LBG in ice cream and fresh cheese at levels <0.1%. PMID:11234856

  16. Genetic polymorphism of toll-like receptors 4 gene by polymerase chain reaction-restriction fragment length polymorphisms, polymerase chain reaction-single-strand conformational polymorphism to correlate with mastitic cows

    PubMed Central

    Gupta, Pooja H.; Patel, Nirmal A.; Rank, D. N.; Joshi, C. G.

    2015-01-01

    Aim: An attempt has been made to study the toll-like receptors 4 (TLR4) gene polymorphism from cattle DNA to correlate with mastitis cows. Materials and Methods: In present investigation, two fragments of TLR4 gene named T4CRBR1 and T4CRBR2 of a 316 bp and 382 bp were amplified by polymerase chain reaction (PCR), respectively from Kankrej (22) and Triple cross (24) cattle. The genetic polymorphisms in the two populations were detected by a single-strand conformational polymorphism in the first locus and by digesting the fragments with restriction endonuclease Alu I in the second one. Results: Results showed that both alleles (A and B) of two loci were found in all the two populations and the value of polymorphism information content indicated that these were highly polymorphic. Statistical results of χ2 test indicated that two polymorphism sites in the two populations fit with Hardy–Weinberg equilibrium (p<0.05). Meanwhile, the effect of polymorphism of TLR4 gene on the somatic cell score (SCS) indicated the cattle with allele a in T4CRBR1 showed lower SCS than that of allele B (p<0.05). Thus, the allele A might play an important role in mastitis resistance in cows. Conclusion: The relationship between the bovine mastitis trait and the polymorphism of TLR4 gene indicated that the bovine TLR4 gene may play an important role in mastitis resistance. PMID:27047144

  17. Single chain fragment variable antibodies developed by using as target the 3rd fibronectin type III homologous repeat fragment of human neural cell adhesion molecule L1 promote cell migration and neuritogenesis.

    PubMed

    Tang, Dan-Yang; Yu, Yang; Zhao, Xuan-Jun; Schachner, Melitta; Zhao, Wei-Jiang

    2015-01-15

    L1CAM plays important roles during ontogeny, including promotion of neuronal cell migration and neuritogenesis, and stimulation of axonal outgrowth, fasciculation and myelination. These functions are at least partially exerted through a 16-mer amino acid sequence in the third fibronectin type III-like repeat of L1, which associates with several interaction partners, including integrins, other adhesion molecules and growth factor receptors. Here, using the Tomlinson I library for phage display, we obtained two single-chain variable fragment antibodies (scFvs) against this peptide sequence of human L1, hereafter called H3 peptide. Both scFvs recognize the H3 peptide and the extracellular domain of L1, as tested by enzyme-linked immunosorbent assay (ELISA), Western blot analysis and immunofluorescence staining of L1 expresssing cells. Furthermore, both scFvs reduce U-87 MG cell adhesion to fibronectin, while stimulating cell migration. Application of scFvs to human neuroblastoma SK-N-SH cells promote process outgrowth. Similar to triggering of endogenous L1 functions at the cell surface, both scFvs activate the signal transducers Erk and Src in these cells. Our results indicate that scFvs against a functionally pivotal domain in L1 trigger its regeneration-beneficial functions in vitro, encouraging thoughts on therapy of neurodegenerative diseases in the hope to ameliorate human nervous system diseases. PMID:25447207

  18. Effect of decreasing the affinity of the class II-associated invariant chain peptide on the MHC class II peptide repertoire in the presence or absence of H-2M.

    PubMed

    Honey, Karen; Forbush, Katherine; Jensen, Peter E; Rudensky, Alexander Y

    2004-04-01

    The class II-associated invariant chain peptide (CLIP) region of the invariant chain (Ii) directly influences MHC class II presentation by occupying the MHC class II peptide-binding groove, thereby preventing premature loading of peptides. Different MHC class II alleles exhibit distinct affinities for CLIP, and a low affinity interaction has been associated with decreased dependence upon H-2M and increased susceptibility to rheumatoid arthritis, suggesting that decreased CLIP affinity alters the MHC class II-bound peptide repertoire, thereby promoting autoimmunity. To examine the role of CLIP affinity in determining the MHC class II peptide repertoire, we generated transgenic mice expressing either wild-type human Ii or human Ii containing a CLIP region of low affinity for MHC class II. Our data indicate that although degradation intermediates of Ii containing a CLIP region with decreased affinity for MHC class II do not remain associated with I-A(b), this does not substantially alter the peptide repertoire bound by MHC class II or increase autoimmune susceptibility in the mice. This implies that the affinity of the CLIP:MHC class II interaction is not a strong contributory factor in determining the probability of developing autoimmunity. In contrast, in the absence of H-2M, MHC class II peptide repertoire diversity is enhanced by decreasing the affinity of CLIP for MHC class II, although MHC class II cell surface expression is reduced. Thus, we show clearly, in vivo, the critical chaperone function of H-2M, which preserves MHC class II molecules for high affinity peptide binding upon dissociation of Ii degradation intermediates. PMID:15034026

  19. Dark coupling and gauge invariance

    SciTech Connect

    Gavela, M.B.; Honorez, L. Lopez; Rigolin, S. E-mail: llopezho@ulb.ac.be E-mail: stefano.rigolin@pd.infn.it

    2010-11-01

    We study a coupled dark energy-dark matter model in which the energy-momentum exchange is proportional to the Hubble expansion rate. The inclusion of its perturbation is required by gauge invariance. We derive the linear perturbation equations for the gauge invariant energy density contrast and velocity of the coupled fluids, and we determine the initial conditions. The latter turn out to be adiabatic for dark energy, when assuming adiabatic initial conditions for all the standard fluids. We perform a full Monte Carlo Markov Chain likelihood analysis of the model, using WMAP 7-year data.

  20. An anti-Aβ (amyloid β) single-chain variable fragment prevents amyloid fibril formation and cytotoxicity by withdrawing Aβ oligomers from the amyloid pathway.

    PubMed

    Marín-Argany, Marta; Rivera-Hernández, Geovanny; Martí, Joaquim; Villegas, Sandra

    2011-07-01

    Aβ (amyloid β) immunotherapy has been revealed as a possible tool in Alzheimer's disease treatment. In contrast with complete antibodies, the administration of scFvs (single-chain variable fragments) produces neither meningoencephalitis nor cerebral haemorrhage. In the present study, the recombinant expression of scFv-h3D6, a derivative of an antibody specific for Aβ oligomers, is presented, as well as the subsequent proof of its capability to recover the toxicity induced by the Aβ1-42 peptide in the SH-SY5Y neuroblastoma cell line. To gain insight into the conformational changes underlying the prevention of Aβ toxicity by this antibody fragment, the conformational landscape of scFv-h3D6 upon temperature perturbation is also described. Heating the native state does not lead to any extent of unfolding, but rather directly to a β-rich intermediate state which initiates an aggregation pathway. This aggregation pathway is not an amyloid fibril pathway, as is that followed by the Aβ peptide, but rather a worm-like fibril pathway which, noticeably, turns out to be non-toxic. On the other hand, this pathway is thermodynamically and kinetically favoured when the scFv-h3D6 and Aβ1-42 oligomers form a complex in native conditions, explaining how the scFv-h3D6 withdraws Aβ1-42 oligomers from the amyloid pathway. To our knowledge, this is the first description of a conformational mechanism by which a scFv prevents Aβ-oligomer cytotoxicity.

  1. Generation of human single-chain variable fragment antibodies specific to dengue virus non-structural protein 1 that interfere with the virus infectious cycle.

    PubMed

    Poungpair, Ornnuthchar; Bangphoomi, Kunan; Chaowalit, Prapaipit; Sawasdee, Nunghathai; Saokaew, Nichapatr; Choowongkomon, Kiattawee; Chaicumpa, Wanpen; Yenchitsomanus, Pa-thai

    2014-01-01

    Severe forms of dengue virus (DENV) infection frequently cause high case fatality rate. Currently, there is no effective vaccine against the infection. Clinical cases are given only palliative treatment as specific anti-DENV immunotherapy is not available and it is urgently required. In this study, human single-chain variable fragment (HuScFv) antibodies that bound specifically to the conserved non-structural protein-1 (NS1) of DENV and interfered with the virus replication cycle were produced by using phage display technology. Recombinant NS1 (rNS1) of DENV serotype 2 (DENV2) was used as antigen in phage bio-panning to select phage clones that displayed HuScFv from antibody phage display library. HuScFv from two phagemid transformed E. coli clones, i.e., clones 11 and 13, bound to the rNS1 as well as native NS1 in both secreted and intracellular forms. Culture fluids of the HuScFv11/HuScFv13 exposed DENV2 infected cells had significant reduction of the infectious viral particles, implying that the antibody fragments affected the virus morphogenesis or release. HuScFv epitope mapping by phage mimotope searching revealed that HuScFv11 bound to amino acids 1-14 of NS1, while the HuScFv13 bound to conformational epitope at the C-terminal portion of the NS1. Although the functions of the epitopes and the molecular mechanism of the HuScFv11 and HuScFv13 require further investigations, these small antibodies have high potential for development as anti-DENV biomolecules. PMID:24492300

  2. High efficient expression of a functional humanized single-chain variable fragment (scFv) antibody against CD22 in Pichia pastoris.

    PubMed

    Zarei, Najmeh; Vaziri, Behrouz; Shokrgozar, Mohammad Ali; Mahdian, Reza; Fazel, Ramin; Khalaj, Vahid

    2014-12-01

    Single-chain variable fragments (scFvs) have recently emerged as attractive candidates in targeted immunotherapy of various malignancies. The anti-CD22 scFv is able to target CD22, on B cell surface and is being considered as a promising molecule in targeted immunotherapy of B cell malignancies. The recombinant anti-CD22 scFv has been successfully expressed in Escherichia coli; however, the insufficient production yield has been a major bottleneck for its therapeutic application. The methylotrophic yeast Pichia pastoris has become a highly popular expression host for the production of a wide variety of recombinant proteins such as antibody fragments. In this study, we used the Pichia expression system to express a humanized scFv antibody against CD22. The full-length humanized scFv gene was codon optimized, cloned into the pPICZαA and expressed in GS115 strain. The maximum production level of the scFv (25 mg/L) were achieved at methanol concentration, 1 %; pH 6.0; inoculum density, OD600 = 3 and the induction time of 72 h. The correlation between scFv gene dosage and expression level was also investigated by real-time PCR, and the results confirmed the presence of such correlation up to five gene copies. Immunofluorescence and flow cytometry studies and Biacore analysis demonstrated binding to CD22 on the surface of human lymphoid cell line Raji and recombinant soluble CD22, respectively. Taken together, the presented data suggest that the Pichia pastoris can be considered as an efficient host for the large-scale production of anti-CD22 scFv as a promising carrier for targeted drug delivery in treatment of CD22(+) B cell malignancies. PMID:25239038

  3. The fragmentations of [M-H]- anions derived from underivatised peptides. The side-chain loss of H2S from Cys. A joint experimental and theoretical study.

    PubMed

    Bilusich, Daniel; Brinkworth, Craig S; McAnoy, Andrew M; Bowie, John H

    2003-01-01

    Loss of H2S is the characteristic Cys side-chain fragmentation of the [M-H]- anions of Cys-containing peptides. A combination of experiment and theory suggests that this reaction is initiated from the Cys enolate anion as follows: RNH-(-)C(CH2SH)CONHR' Ø [RNHC(=CH2)CONHR' (HS-)] Ø [RNHC(=CH2)CO-HNR'-H]-+H2S. This process is facile. Calculations at the HF/6-31G(d)//AM1 level of theory indicate that the initial anion needs only > or =20.1 kcal mol(-1) of excess energy to effect loss of H2S. Loss of CH2S is a minor process, RNHCH(CH2SH)CON(-)-R' Ø RNHCH(CH2S-)CONHR' Ø RNH -CHCONHR+CH2S, requiring an excess energy of > or =50.2 kcal mol(-1). When Cys occupies the C-terminal end of a peptide, the major fragmentation from the [M-H]- species involves loss of (H2S+CO2). A deuterium-labelling study suggests that this could either be a charge-remote reaction (a process which occurs remote from and uninfluenced by the charged centre in the molecule), or an anionic reaction initiated from the C-terminal CO2- group. These processes have barriers requiring the starting material to have an excess energy of > or =79.6 (charge-remote) or > or =67.1 (anion-directed) kcal mol(-1), respectively, at the HF/6-31G(d)//AM1 level of theory. The corresponding losses of CH2O and H2O from the [M-H]- anions of Ser-containing peptides require > or =35.6 and > or =44.4 kcal mol(-1) of excess energy (calculated at the AM1 level of theory), explaining why loss of CH2O is the characteristic side-chain loss of Ser in the negative ion mode. PMID:14608618

  4. Production and characterization of a single-chain variable fragment linked alkaline phosphatase fusion protein for detection of O,O-diethyl organophosphorus pesticides in a one-step enzyme-linked immunosorbent assay

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A single-chain variable fragment (scFv) and alkaline phosphatase (AP) fusion protein for detection of O, O-diethyl organophosphorus pesticides (OPs) was produced and characterized. The scFv gene was prepared by cloning VL and VH genes from a hybridoma cell secreting monoclonal antibody with broad-s...

  5. Analysis of the rDNA internal transcribed spacer region of the Fusarium species by polymerase chain reaction-restriction fragment length polymorphism

    PubMed Central

    ZARRIN, MAJID; GANJ, FARZANEH; FARAMARZI, SAMA

    2016-01-01

    The Fusarium species are a widely spread phytopathogen identified in an extensive variety of hosts. The Fusarium genus is one of the most heterogeneous fungi and is difficult to classify. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis is a useful method in detection of DNA polymorphism in objective sequences. The aim of the present study was to identify the phylogenetic associations and usefulness of the internal transcribed spacer (ITS) region as a genetic marker within the most clinically important strain of the Fusarium species. A total of 50 strains of Fusarium spp. were used in the study, including environmental, clinical and reference isolates. The primers ITS1 and ITS4 were used in the study. Two restriction enzymes, HaeIII and SmaI, were assessed for the digestion of PCR products. A PCR product of ~550-base pairs was generated for each Fusarium species. The digested products with HaeIII and SmaI demonstrated that the bands generated for the medically significant Fusarium species, including F. solani, F. oxysporum, F. verticillidea, F. proliferatum and F. fujikuri, have different restriction enzyme patterns. In conclusion, it appears that the PCR-RFLP method used in the present study produces a sufficient restriction profile for differentiation of the most medically significant Fusarium species. PMID:27073635

  6. Synthesis of magnetic molecularly imprinted polymers by reversible addition fragmentation chain transfer strategy and its application in the Sudan dyes residue analysis.

    PubMed

    Xie, Xiaoyu; Chen, Liang; Pan, Xiaoyan; Wang, Sicen

    2015-07-31

    Magnetic molecularly imprinted polymers (MMIPs) have become a hotspot owing to the dual functions of target recognition and magnetic separation. In this study, the MMIPs were obtained by the surface-initiated reversible addition fragmentation chain transfer (RAFT) polymerization using Sudan I as the template. The resultant MMIPs were characterized by transmission electron microscope, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, vibrating sample magnetometer, and X-ray diffraction. Benefiting from the controlled/living property of the RAFT strategy, the uniform MIP layer was successfully grafted on the surface of RAFT agent-modified Fe3O4@SiO2 nanoparticles, favoring the fast mass transfer and rapid binding kinetics. The developed MMIPs were used as the solid-phase extraction sorbents to selectively extract four Sudan dyes (Sudan I, II, III, and IV) from chili powder samples. The recoveries of the spiked samples in chili powder samples ranged from 74.1 to 93.3% with RSD lower than 6.4% and the relative standard uncertainty lower than 0.029. This work provided a good platform for the extraction and removal of Sudan dyes in complicated matrixes and demonstrated a bright future for the application of the well-constructed MMIPs in the field of solid-phase extraction. PMID:26077971

  7. Mapping of antigenic determinants on a SAT2 foot-and-mouth disease virus using chicken single-chain antibody fragments.

    PubMed

    Opperman, Pamela A; Maree, Francois F; Van Wyngaardt, Wouter; Vosloo, Wilna; Theron, Jacques

    2012-08-01

    Recombinant single-chain variable fragments (scFvs) of antibodies make it possible to localize antigenic and immunogenic determinants, identify protective epitopes and can be exploited for the design of improved diagnostic tests and vaccines. A neutralizing epitope, as well as other potential antigenic sites of a SAT2 foot-and-mouth disease virus (FMDV) were identified using phage-displayed scFvs. Three unique ZIM/7/83-specific scFvs, designated scFv1, scFv2 and scFv3, were isolated. Further characterization of these scFvs revealed that only scFv2 was capable of neutralizing the ZIM/7/83 virus and was used to generate neutralization-resistant virus variants. Sequence analysis of the P1 region of virus escaping neutralization revealed a residue change from His to Arg at position 159 of the VP1 protein. Residue 159 is not only surface exposed but is also located at the C-terminal base of the G-H loop, a known immunogenic region of FMDV. A synthetic peptide, of which the sequence corresponded to the predicted antigenic site of the VP1 G-H loop of ZIM/7/83, inhibited binding of scFv2 to ZIM/7/83 in a concentration-dependent manner. This region can therefore be considered in the design of SAT2 vaccine seed viruses for the regional control of FMD in Africa.

  8. Receptor specificity of influenza viruses from birds and mammals: new data on involvement of the inner fragments of the carbohydrate chain.

    PubMed

    Gambaryan, Alexandra; Yamnikova, Svetlana; Lvov, Dmitryi; Tuzikov, Alexander; Chinarev, Alexander; Pazynina, Galina; Webster, Robert; Matrosovich, Mikhail; Bovin, Nicolai

    2005-04-10

    We studied receptor-binding properties of influenza virus isolates from birds and mammals using polymeric conjugates of sialooligosaccharides terminated with common Neu5Ac alpha2-3Gal beta fragment but differing by the structure of the inner part of carbohydrate chain. Viruses isolated from distinct avian species differed by their recognition of the inner part of oligosaccharide receptor. Duck viruses displayed high affinity for receptors having beta1-3 rather than beta1-4 linkage between Neu5Ac alpha2-3Gal-disaccharide and penultimate N-acetylhexosamine residue. Fucose and sulfate substituents at this residue had negative and low effect, respectively, on saccharide binding to duck viruses. By contrast, gull viruses preferentially bound to receptors bearing fucose at N-acetylglucosamine residue, whereas chicken and mammalian viruses demonstrated increased affinity for oligosaccharides that harbored sulfo group at position 6 of (beta1-4)-linked GlcNAc. These data suggest that although all avian influenza viruses preferentially bind to Neu5Ac alpha2-3Gal-terminated receptors, the fine receptor specificity of the viruses varies depending on the avian species. Further studies are required to determine whether observed host-dependent differences in the receptor specificity of avian viruses can affect their ability to infect humans.

  9. Structural Basis of Neutralization of the Major Toxic Component from the Scorpion Centruroides noxius Hoffmann by a Human-derived Single-chain Antibody Fragment

    SciTech Connect

    Canul-Tec, Juan Carlos; Riaño-Umbarila, Lidia; Rudiño-Piñera, Enrique; Becerril, Baltazar; Possani, Lourival D.; Torres-Larios, Alfredo

    2011-08-09

    It has previously been reported that several single-chain antibody fragments of human origin (scFv) neutralize the effects of two different scorpion venoms through interactions with the primary toxins of Centruroides noxius Hoffmann (Cn2) and Centruroides suffusus suffusus (Css2). Here we present the crystal structure of the complex formed between one scFv (9004G) and the Cn2 toxin, determined in two crystal forms at 2.5 and 1.9 {angstrom} resolution. A 15-residue span of the toxin is recognized by the antibody through a cleft formed by residues from five of the complementarity-determining regions of the scFv. Analysis of the interface of the complex reveals three features. First, the epitope of toxin Cn2 overlaps with essential residues for the binding of {beta}-toxins to its Na+ channel receptor site. Second, the putative recognition of Css2 involves mainly residues that are present in both Cn2 and Css2 toxins. Finally, the effect on the increase of affinity of previously reported key residues during the maturation process of different scFvs can be inferred from the structure. Taken together, these results provide the structural basis that explain the mechanism of the 9004G neutralizing activity and give insight into the process of directed evolution that gave rise to this family of neutralizing scFvs.

  10. Authentication of anglerfish species (Lophius spp) by means of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and forensically informative nucleotide sequencing (FINS) methodologies.

    PubMed

    Espiñeira, Montserrat; González-Lavín, Nerea; Vieites, Juan M; Santaclara, Francisco J

    2008-11-26

    Lophius represents the most important genus of the family Lophiidae from a commercial point of view. The main marketing formats of the species included in this genus are tails and cheeks, making impossible the species identification on the basis of their morphological characters. In the present study, two methods based on the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and phylogenetic analysis of DNA sequences [forensically informative nucleotide sequencing (FINS)] were developed to differentiate the seven species contained in the genus Lophius. In both cases, the molecular marker studied was the cytochrome oxidase subunit I gene (COI). The RFLP analysis of the PCR products digested with the endonuclease Mbo I generated species-specific restriction profiles, and the phylogenetic analysis showing a neighbor-joining tree with independent nodes was strongly supported for all of the studied species. These methods were applied to 40 commercial samples, allowing us to detect the samples incorrectly labeled. The fraudulent labeling ratio was higher in processed products (68.75%) than whole fish (31.25%). The species subjected to mislabeling were L. budegassa (68.75%), L. vomerinus (18.75%), and L. piscatorius (12.5%). Therefore, both methodologies can be independently used to authenticate the species belonging to the genus Lophius, being useful to check the fulfillment of labeling regulations of seafood products and to verify the correct traceability of commercial trade and the control of fisheries. PMID:18975961

  11. Screening for JH1 genetic defect carriers in Jersey cattle by a polymerase chain reaction and restriction fragment length polymorphism assay.

    PubMed

    Zhang, Yi; Guo, Gang; Huang, Hetian; Lu, Lu; Wang, Lijie; Fang, Lingzhao; Liu, Lin; Wang, Yachun; Zhang, Shengli

    2015-09-01

    An autosomal recessive genetic defect termed JH1 has been associated with early embryonic loss in the Jersey cattle breed. The genetic basis has been identified as a cytosine to thymine mutation in the CWC15 gene that changes an amino acid from arginine to a stop code. To screen for JH1 carriers in an imported Jersey population in China, a method based on a polymerase chain reaction amplification followed by a restriction fragment length polymorphism assay (PCR-RFLP) was developed for the accurate diagnosis of the JH1 allele. A total of 449 randomly chosen cows were examined with the PCR-RFLP assay, and 31 were identified as JH1 carriers, corresponding to a carrier frequency of 6.9%. The PCR-RFLP method was validated by DNA sequencing of 8 positive and 13 negative samples, with all 21 samples giving the expected DNA sequence. In addition, 3 negative and 3 positive samples were confirmed by a commercial microarray-based single nucleotide polymorphism assay. Finally, samples from 9 bulls in the United States of known status were correctly identified as carriers (5 bulls) or noncarriers (4 bulls). As the JH1 defect has most likely spread worldwide, implementing routine screening is necessary to avoid the risk of carrier-to-carrier matings and to gradually eradicate the deleterious gene.

  12. Giardia duodenalis in Damascus, Syria: Identification of Giardia genotypes in a sample of human fecal isolates using polymerase chain reaction and restriction fragment length polymorphism analyzing method.

    PubMed

    Skhal, Dania; Aboualchamat, Ghalia; Al Nahhas, Samar

    2016-02-01

    Giardia duodenalis is a common gastrointestinal parasite that infects humans and many other mammals. It is most prevalent in many developing and industrialized countries. G. duodenalis is considered to be a complex species. While no morphological distinction among different assemblages exist, it can be genetically differentiated into eight major assemblages: A to H. The aim of this study was to determine the genetic heterogeneity of G. duodenalis in human isolates (a study conducted for the first time in Syria). 40 fecal samples were collected from three different hospitals during the hot summer season of 2014. Extraction of genomic DNA from all Giardia positive samples (based on a microscopic examination) was performed using QIAamp DNA Stool Mini Kit. β-giardin gene was used to differentiate between different Giardia assemblages. The 514 bp fragment was amplified using the Polymerase Chain Reaction method, followed by digestion in HaeIII restriction enzyme. Our result showed that genotype A was more frequent than genotype B, 27/40 (67.5%); 4/40 (10%) respectively. A mixed genotype of A+B was only detected in 9 isolates (22.5%). This is the first molecular study performed on G. duodenalis isolates in Syria in order to discriminate among the different genotypes. Further expanded studies using more genes are needed to detect and identify the Giardia parasite at the level of assemblage and sub-assemblage.

  13. Authentication of anglerfish species (Lophius spp) by means of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and forensically informative nucleotide sequencing (FINS) methodologies.

    PubMed

    Espiñeira, Montserrat; González-Lavín, Nerea; Vieites, Juan M; Santaclara, Francisco J

    2008-11-26

    Lophius represents the most important genus of the family Lophiidae from a commercial point of view. The main marketing formats of the species included in this genus are tails and cheeks, making impossible the species identification on the basis of their morphological characters. In the present study, two methods based on the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and phylogenetic analysis of DNA sequences [forensically informative nucleotide sequencing (FINS)] were developed to differentiate the seven species contained in the genus Lophius. In both cases, the molecular marker studied was the cytochrome oxidase subunit I gene (COI). The RFLP analysis of the PCR products digested with the endonuclease Mbo I generated species-specific restriction profiles, and the phylogenetic analysis showing a neighbor-joining tree with independent nodes was strongly supported for all of the studied species. These methods were applied to 40 commercial samples, allowing us to detect the samples incorrectly labeled. The fraudulent labeling ratio was higher in processed products (68.75%) than whole fish (31.25%). The species subjected to mislabeling were L. budegassa (68.75%), L. vomerinus (18.75%), and L. piscatorius (12.5%). Therefore, both methodologies can be independently used to authenticate the species belonging to the genus Lophius, being useful to check the fulfillment of labeling regulations of seafood products and to verify the correct traceability of commercial trade and the control of fisheries.

  14. Hybrid metabolic flux analysis and recombinant protein prediction in Pichia pastoris X-33 cultures expressing a single-chain antibody fragment.

    PubMed

    Isidro, Inês A; Portela, Rui M; Clemente, João J; Cunha, António E; Oliveira, Rui

    2016-09-01

    Despite the growing importance of the Pichia pastoris expression system as industrial workhorse, the literature is almost absent in systematic studies on how culture medium composition affects central carbon fluxes and heterologous protein expression. In this study we investigate how 26 variations of the BSM+PTM1 medium impact central carbon fluxes and protein expression in a P. pastoris X-33 strain expressing a single-chain antibody fragment. To achieve this goal, we adopted a hybrid metabolic flux analysis (MFA) methodology, which is a modification of standard MFA to predict the rate of synthesis of recombinant proteins. Hybrid MFA combines the traditional parametric estimation of central carbon fluxes with non-parametric statistical modeling of product-related quantitative or qualitative measurements as a function of central carbon fluxes. It was observed that protein yield variability was 53.6 % (relative standard deviation) among the different experiments. Protein yield is much more sensitive to medium composition than biomass growth, which is mainly determined by the carbon source availability and main salts. Hybrid MFA was able to describe accurately the protein yield with normalized RMSE of 6.3 % over 5 independent experiments. The metabolic state that promotes high protein yields is characterized by high overall metabolic rates through main central carbon pathways concomitantly with a relative shift of carbon flux from biosynthetic towards energy generating pathways. PMID:27129458

  15. Identification of Echinococcus granulosus strains using polymerase chain reaction-restriction fragment length polymorphism amongst livestock in Moroto district, Uganda.

    PubMed

    Chamai, Martin; Omadang, Leonard; Erume, Joseph; Ocaido, Michael; Oba, Peter; Othieno, Emmanuel; Bonaventure, Straton; Kitibwa, Annah

    2016-01-01

    A descriptive study was conducted to identify the different strains of Echinococcus granulosus occurring in livestock in Moroto district, Uganda. Echinococcus cysts from 104 domestic animals, including cattle, sheep, goats and camels, were taken and examined by microscopy, polymerase chain reaction with restriction fragment length polymorphism and Sanger DNA sequencing. Echinococcus granulosus genotypes or strains were identified through use of Bioinformatics tools: BioEdit, BLAST and MEGA6. The major finding of this study was the existence of a limited number of E. granulosus genotypes from cattle, goats, sheep and camels. The most predominant genotype was G1 (96.05%), corresponding to the common sheep strain. To a limited extent (3.95%), the study revealed the existence of Echinococcus canadensis G6/7 in three (n = 3) of the E. granulosus-positive samples. No other strains of E. granulosus were identified. It was concluded that the common sheep strain of Echinococcus sensu stricto and G6/7 of E. canadensis were responsible for echinococcal disease in Moroto district, Uganda. PMID:27543147

  16. Novel polymerase chain reaction-restriction fragment length polymorphism assay to determine internal transcribed spacer-2 group in the Chagas disease vector, Triatoma dimidiata (Latreille, 1811).

    PubMed

    Richards, Bethany; Rúa, Nicholas M de la; Monroy, Carlota; Stevens, Lori; Dorn, Patricia L

    2013-06-01

    Triatoma dimidiata is the most important Chagas disease insect vector in Central America as this species is primarily responsible for Trypanosoma cruzi transmission to humans, the protozoan parasite that causes Chagas disease. T. dimidiata sensu lato is a genetically diverse assemblage of taxa and effective vector control requires a clear understanding of the geographic distribution and epidemiological importance of its taxa. The nuclear ribosomal internal transcribed spacer 2 (ITS-2) is frequently used to infer the systematics of triatomines. However, oftentimes amplification and sequencing of ITS-2 fails, likely due to both the large polymerase chain reaction (PCR) product and polymerase slippage near the 5' end. To overcome these challenges we have designed new primers that amplify only the 3'-most 200 base pairs of ITS-2. This region distinguishes the ITS-2 group for 100% of known T. dimidiata haplotypes. Furthermore, we have developed a PCR-restriction fragment length polymorphism (RFLP) approach to determine the ITS-2 group, greatly reducing, but not eliminating, the number of amplified products that need to be sequenced. Although there are limitations with this new PCR-RFLP approach, its use will help with understanding the geographic distribution of T. dimidiata taxa and can facilitate other studies characterising the taxa, e.g. their ecology, evolution and epidemiological importance, thus improving vector control.

  17. Molecular engineering of high affinity single-chain antibody fragment for endothelial targeting of proteins and nanocarriers in rodents and humans.

    PubMed

    Greineder, Colin F; Hood, Elizabeth D; Yao, Anning; Khoshnejad, Makan; Brenner, Jake S; Johnston, Ian H; Poncz, Mortimer; Gottstein, Claudia; Muzykantov, Vladimir R

    2016-03-28

    Endothelial cells (EC) represent an important target for pharmacologic intervention, given their central role in a wide variety of human pathophysiologic processes. Studies in lab animal species have established that conjugation of drugs and carriers with antibodies directed to surface targets like the Platelet Endothelial Cell Adhesion Molecule-1 (PECAM-1, a highly expressed endothelial transmembrane protein) help to achieve specific therapeutic interventions in ECs. To translate such "vascular immunotargeting" to clinical practice, it is necessary to replace antibodies by advanced ligands that are more amenable to use in humans. We report the molecular design of a single chain variable antibody fragment (scFv) that binds with high affinity to human PECAM-1 and cross-reacts with its counterpart in rats and other animal species, allowing parallel testing in vivo and in human endothelial cells in microfluidic model. Site-specific modification of the scFv allows conjugation of protein cargo and liposomes, enabling their endothelial targeting in these models. This study provides a template for molecular engineering of ligands, enabling studies of drug targeting in animal species and subsequent use in humans. PMID:26855052

  18. Magnetic molecularly imprinted polymers synthesized by surface-initiated reversible addition-fragmentation chain transfer polymerization for the enrichment and determination of synthetic estrogens in aqueous solution.

    PubMed

    Chen, Fangfang; Zhang, Jingjing; Wang, Minjun; Kong, Jie

    2015-08-01

    Magnetic molecularly imprinted polymers have attracted significant interest because of their multifunctionality of selective recognition of target molecules and rapid magnetic response. In this contribution, magnetic molecularly imprinted polymers were synthesized via surface-initiated reversible addition addition-fragmentation chain transfer polymerization using diethylstilbestrol as the template for the enrichment of synthetic estrogens. The uniform imprinted surface layer and the magnetic property of the magnetic molecularly imprinted polymers favored a fast binding kinetics and rapid analysis of target molecules. The static and selective binding experiments demonstrated a desirable adsorption capacity and good selectivity of the magnetic molecularly imprinted polymers in comparison to magnetic non-molecularly imprinted polymers. Accordingly, a corresponding analytical method was developed in which magnetic molecularly imprinted polymers were employed as magnetic solid-phase extraction materials for the concentration and determination of four synthetic estrogens (diethylstilbestrol, hexestrol, dienestrol, and bisphenol A) in fish pond water. The recoveries of these synthetic estrogens in spiked fish pond water samples ranged from 61.2 to 99.1% with a relative standard deviation of lower than 6.3%. This study provides a versatile approach to prepare well-defined magnetic molecularly imprinted polymers sorbents for the analysis of synthetic estrogens in water solution. PMID:25989155

  19. Identification of Echinococcus granulosus strains using polymerase chain reaction-restriction fragment length polymorphism amongst livestock in Moroto district, Uganda.

    PubMed

    Chamai, Martin; Omadang, Leonard; Erume, Joseph; Ocaido, Michael; Oba, Peter; Othieno, Emmanuel; Bonaventure, Straton; Kitibwa, Annah

    2016-07-29

    A descriptive study was conducted to identify the different strains of Echinococcus granulosus occurring in livestock in Moroto district, Uganda. Echinococcus cysts from 104 domestic animals, including cattle, sheep, goats and camels, were taken and examined by microscopy, polymerase chain reaction with restriction fragment length polymorphism and Sanger DNA sequencing. Echinococcus granulosus genotypes or strains were identified through use of Bioinformatics tools: BioEdit, BLAST and MEGA6. The major finding of this study was the existence of a limited number of E. granulosus genotypes from cattle, goats, sheep and camels. The most predominant genotype was G1 (96.05%), corresponding to the common sheep strain. To a limited extent (3.95%), the study revealed the existence of Echinococcus canadensis G6/7 in three (n = 3) of the E. granulosus-positive samples. No other strains of E. granulosus were identified. It was concluded that the common sheep strain of Echinococcus sensu stricto and G6/7 of E. canadensis were responsible for echinococcal disease in Moroto district, Uganda.

  20. The sub-nanomolar binding of DNA-RNA hybrids by the single-chain Fv fragment of antibody S9.6.

    PubMed

    Phillips, Damilola D; Garboczi, David N; Singh, Kavita; Hu, Zonglin; Leppla, Stephen H; Leysath, Clinton E

    2013-08-01

    The monoclonal antibody S9.6 binds DNA-RNA hybrids with high affinity, making it useful in research and diagnostic applications, such as in microarrays and in the detection of R-loops. A single-chain variable fragment (scFv) of S9.6 was produced, and its affinities for various synthetic nucleic acid hybrids were measured by surface plasmon resonance (SPR). S9.6 exhibits dissociation constants of approximately 0.6 nM for DNA-RNA and, surprisingly, 2.7 nM for RNA-RNA hybrids that are AU-rich. The affinity of the S9.6 scFv did not appear to be strongly influenced by various buffer conditions or by ionic strength below 500 mM NaCl. The smallest epitope that was strongly bound by the S9.6 scFv contained six base pairs of DNA-RNA hybrid. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.

  1. Mapping the carriage of flaA-restriction fragment length polymorphism Campylobacter genotypes on poultry carcasses through the processing chain and comparison to clinical isolates.

    PubMed

    Duffy, Lesley L; Blackall, Patrick J; Cobbold, Rowland N; Fegan, Narelle

    2015-06-01

    Poultry are considered a major source for campylobacteriosis in humans. A total of 1866 Campylobacter spp. isolates collected through the poultry processing chain were typed using flaA-restriction fragment length polymorphism to measure the impact of processing on the genotypes present. Temporally related human clinical isolates (n = 497) were also typed. Isolates were obtained from whole chicken carcass rinses of chickens collected before scalding, after scalding, before immersion chilling, after immersion chilling and after packaging as well as from individual caecal samples. A total of 32 genotypes comprising at least four isolates each were recognised. Simpson's Index of Diversity (D) was calculated for each sampling site within each flock, for each flock as a whole and for the clinical isolates. From caecal collection to after packaging samples the D value did not change in two flocks, decreased in one flock and increased in the fourth flock. Dominant genotypes occurred in each flock but their constitutive percentages changed through processing. There were 23 overlapping genotypes between clinical and chicken isolates. The diversity of Campylobacter is flock dependant and may alter through processing. This study confirms that poultry are a source of campylobacteriosis in the Australian population although other sources may contribute.

  2. Synthesis of magnetic molecularly imprinted polymers by reversible addition fragmentation chain transfer strategy and its application in the Sudan dyes residue analysis.

    PubMed

    Xie, Xiaoyu; Chen, Liang; Pan, Xiaoyan; Wang, Sicen

    2015-07-31

    Magnetic molecularly imprinted polymers (MMIPs) have become a hotspot owing to the dual functions of target recognition and magnetic separation. In this study, the MMIPs were obtained by the surface-initiated reversible addition fragmentation chain transfer (RAFT) polymerization using Sudan I as the template. The resultant MMIPs were characterized by transmission electron microscope, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, vibrating sample magnetometer, and X-ray diffraction. Benefiting from the controlled/living property of the RAFT strategy, the uniform MIP layer was successfully grafted on the surface of RAFT agent-modified Fe3O4@SiO2 nanoparticles, favoring the fast mass transfer and rapid binding kinetics. The developed MMIPs were used as the solid-phase extraction sorbents to selectively extract four Sudan dyes (Sudan I, II, III, and IV) from chili powder samples. The recoveries of the spiked samples in chili powder samples ranged from 74.1 to 93.3% with RSD lower than 6.4% and the relative standard uncertainty lower than 0.029. This work provided a good platform for the extraction and removal of Sudan dyes in complicated matrixes and demonstrated a bright future for the application of the well-constructed MMIPs in the field of solid-phase extraction.

  3. Production and characterization of monoclonal antibody and its recombinant single chain variable fragment specific for a food-born mycotoxin, fumonisin B1.

    PubMed

    Min, Won-Ki; Cho, Young-Jin; Park, Jun-Bock; Bae, Yi-Hyun; Kim, Eun-Jeong; Park, Kyungmoon; Park, Yong-Cheol; Seo, Jin-Ho

    2010-01-01

    Fumonisin B(1) (FMB(1)) is a food-born mycotoxin produced by Fusarium moniliforme. Monoclonal antibody against FMB(1) (anti-FMB(1) mAb) was produced in the hybridoma DV9, which was established from a BALB/c mouse immunized with bovine serum albumin conjugated FMB(1) (FMB(1)-BSA). A competitive direct enzyme-linked immunosorbent assay (ELISA) showed that anti-FMB(1) mAb has about 10 ppb of minimum FMB(1) detection concentration and 220 ppb of 50% inhibition concentration (IC(50)). Much lower cross-reactivity of anti-FMB(1) mAb on ochratoxin A, aflatoxin B(1) and deoxynivalenol provided that anti-FMB(1) mAb was specific for FMB(1). The gene coding single chain variable fragment against FMB(1) (anti-FMB(1) scFv) was cloned from the hybridoma DV9 and was expressed in recombinant Escherichia coli. Insoluble anti-FMB(1) scFv required optimization of its refolding condition, and hence functional scFv was obtained. By using indirect ELISA, about 12-fold lower binding activity of anti-FMB(1) scFv on FMB(1)-BSA was obtained in comparison with that of the parental mAb. PMID:19597742

  4. High-level production in Pichia pastoris of an anti-p185HER-2 single-chain antibody fragment using an alternative secretion expression vector.

    PubMed

    Gurkan, Cemal; Symeonides, Stefan N; Ellar, David J

    2004-02-01

    The methylotrophic yeast Pichia pastoris has become a highly popular expression host for the recombinant production of a wide variety of proteins. Initial success with this system was greatly facilitated by the development of versatile expression vectors that were almost exclusively based on the strong, tightly regulated promoter of the P. pastoris major alcohol oxidase gene ( AOX1 ). For example, pIB4 is an Escherichia coli - P. pastoris shuttle vector that also uses the AOX1 promoter to allow intracellular expression of endogenous and foreign genes in the latter organism. Since the eukaryotic advantages of P. pastoris would be best harnessed through the secretory targeting of the recombinant proteins, we modified the pIB4 vector by adding the Saccharomyces cerevisiae alpha-factor secretion signal immediately upstream of its multiple cloning site. Here we describe the construction of this modified vector, pIB4alpha, and its successful use for the high-level expression and secretion of a functional single-chain antibody fragment (scFv), C6.5, which targets p185(HER-2), a cell-surface glycoprotein overexpressed in about 30% of human breast and ovarian cancers. The PCR strategy used for the subcloning of the C6.5 construct into pIB4alpha also introduced a short DNA sequence coding for a C-terminal hexahistidine tag, which allowed subsequent purification of the secreted scFv, by immobilized-metal-affinity chromatography, to a yield of 70 mg x l(-1) of shake-flask culture. In conclusion, our results suggest that the secretion expression vector pIB4alpha not only complements the original pIB4 vector for intracellular expression in P. pastoris, but might also constitute an attractive alternative to the commercially available secretion expression vectors. PMID:12962542

  5. Successful engineering of a highly potent single-chain variable-fragment (scFv) bispecific antibody to target disialoganglioside (GD2) positive tumors.

    PubMed

    Cheng, Ming; Santich, Brian H; Xu, Hong; Ahmed, Mahiuddin; Huse, Morgan; Cheung, Nai-Kong V

    2016-06-01

    Engineering potent bispecific antibodies from single-chain variable fragments (scFv) remains difficult due to the inherent instability and insufficient binding of scFv's compared to their parental immunoglobulin format. Previously, we described a scFv-based bispecific antibody (scBA) against disialoganglioside (GD2) based on the anti-GD2 murine 5F11-scFv and the anti-CD3 huOKT3-scFv (5F11-scBA). In this study, we substituted the 5F11-scFv with the higher affinity (13-fold) hu3F8-scFv to form hu3F8-scBA. With this modification, hu3F8-scBA redirected T cells to kill GD2(+) cancer cell lines with up to 5,000-fold higher potency (femtomolar EC50) compared with 5F11-scBA (picomolar EC50) in cytotoxicity assays, even against target cells with low GD2 densities. Furthermore, hu3F8-scBA induced stronger T-cell activation than 5F11-scBA, as measured by Ca(2+) flux and cytokine release. Additionally, in vivo, hu3F8-scBA suppressed tumor growth and prolonged mice survival much more effectively than 5F11-scBA, in both neuroblastoma and melanoma xenograft models. We conclude that the functional properties of scBA's can be increased substantially by relatively modest increases in antigen affinity.

  6. HC fragment (C-terminal portion of the heavy chain) of tetanus toxin activates protein kinase C isoforms and phosphoproteins involved in signal transduction.

    PubMed Central

    Gil, C; Chaib-Oukadour, I; Blasi, J; Aguilera, J

    2001-01-01

    A recent report [Gil, Chaib-Oukadour, Pelliccioni and Aguilera (2000) FEBS Lett. 481, 177-182] describes activation of signal transduction pathways by tetanus toxin (TeTx), a Zn(2+)-dependent endopeptidase synthesized by the Clostridium tetani bacillus, which is responsible for tetanus disease. In the present work, specific activation of protein kinase C (PKC) isoforms and of intracellular signal-transduction pathways, which include nerve-growth-factor (NGF) receptor trkA, phospholipase C(PLC)gamma-1 and extracellular regulated kinases (ERKs) 1 and 2, by the recombinant C-terminal portion of the TeTx heavy chain (H(C)-TeTx) is reported. The activation of PKC isoforms was assessed through their translocation from the soluble (cytosolic) compartment to the membranous compartment, showing that clear translocation of PKC-alpha, -beta, -gamma and -delta isoforms exists, whereas PKC-epsilon showed a slight decrease in its soluble fraction immunoreactivity. The PKC-zeta isoform showed no consistent response. Using immunoprecipitation assays against phosphotyrosine residues, time- and dose-dependent increases in tyrosine phosphorylation were observed in the trkA receptor, PLCgamma-1 and ERK-1/2. The effects shown by the H(C)-TeTx fragment on tyrosine phosphorylation were compared with the effects produced by NGF. The trkA and ERK-1/2 activation were corroborated using phospho-specific antibodies against trkA phosphorylated on Tyr(490), and antibodies against Thr/Tyr phosphorylated ERK-1/2. Moreover, PLCgamma-1 phosphorylation was supported by its H(C)-TeTx-induced translocation to the membranous compartment, an event related to PLCgamma-1 activation. Since H(C)-TeTx is the domain responsible for membrane binding and lacks catalytic activity, the activations described here must be exclusively triggered by the interaction of TeTx with a membrane component. PMID:11336640

  7. Matrilineage differentiation of the genus Tetragonisca using mitochondrial DNA markers and the polymerase chain reaction-restriction fragment length polymorphism technique.

    PubMed

    Santos, S A; Bronzato, A R; Moreira, B M T; Araujo, K F; Ronqui, L; Mangolin, C A; Toledo, V A A; Ruvolo-Takasusuki, M C C

    2015-10-21

    The Meliponinae are important pollinators of plant species, and one of the most managed species is Tetragonisca angustula. Initially, two subspecies were identified in T. angustula: T. angustula angustula and T. angustula fiebrigi. Subsequently, T. a. fiebrigi was considered a species, based on the coloration of its mesepisternum. The objective of the present study was to obtain genetic markers that could differentiate the two species by amplifying regions of mitochondrial DNA and conducting polymerase chain reaction-restriction fragment length polymorphism analysis. Worker bees were collected in three Brazilian states: Paraná (Maringá, Altônia, and Foz do Iguaçu), São Paulo (Dracena, São Carlos, and Santa Cruz do Rio Pardo), and Rondônia (Ariquemes). Ten pairs of insect heterologous primers were tested and four were used (primer pair 1, ND2 and COI; primer pair 2, COI; primer pair 8, 16S and 12S; and primer pair 9, COII). For the restriction analysis, 13 enzymes were tested: EcoRI, EcoRV, HindIII, HinfI, RsaI, PstI, XbaI, HaeIII, ClaI, XhoI, BglII, PvuII, and ScaI. Markers were obtained (primer pair 8 cleaved with EcoRV and XbaI and primer pair 9 cleaved with HaeIII, RsaI, and XbaI) that enabled matrilineage identification in the nests studied, which confirmed that hybridization could occur between both Tetragonisca species. The beginning of speciation was probably recent, and secondary contact has resulted in crosses between T. angustula females and T. fiebrigi males. Because of this hybridization, it would be appropriate to consider them as two subspecies of T. angustula.

  8. Anti-CD20 single chain variable antibody fragment-apolipoprotein A-I chimera containing nanodisks promote targeted bioactive agent delivery to CD20-positive lymphomas.

    PubMed

    Crosby, Natasha M; Ghosh, Mistuni; Su, Betty; Beckstead, Jennifer A; Kamei, Ayako; Simonsen, Jens B; Luo, Bing; Gordon, Leo I; Forte, Trudy M; Ryan, Robert O

    2015-08-01

    A fusion protein comprising an α-CD20 single chain variable fragment (scFv) antibody, a spacer peptide, and human apolipoprotein (apo) A-I was constructed and expressed in Escherichia coli. The lipid interaction properties intrinsic to apoA-I as well as the antigen recognition properties of the scFv were retained by the chimera. scFv•apoA-I was formulated into nanoscale reconstituted high-density lipoprotein particles (termed nanodisks; ND) and incubated with cultured cells. α-CD20 scFv•apoA-I ND bound to CD20-positive non-Hodgkins lymphoma (NHL) cells (Ramos and Granta) but not to CD20-negative T lymphocytes (i.e., Jurkat). Binding to NHL cells was partially inhibited by pre-incubation with rituximab, a monoclonal antibody directed against CD20. Confocal fluorescence microscopy analysis of Granta cells following incubation with α-CD20 scFv•apoA-I ND formulated with the intrinsically fluorescent hydrophobic polyphenol, curcumin, revealed α-CD20 scFv•apoA-I localizes to the cell surface, while curcumin off-loads and gains entry to the cell. Compared to control incubations, viability of cultured NHL cells was decreased upon incubation with α-CD20 scFv•apoA-I ND harboring curcumin. Thus, formulation of curcumin ND with α-CD20 scFv•apoA-I as the scaffold component confers cell targeting and enhanced bioactive agent delivery, providing a strategy to minimize toxicity associated with chemotherapeutic agents.

  9. Anti-CD20 single chain variable antibody fragment-apolipoprotein A-I chimera containing nanodisks promote targeted bioactive agent delivery to CD20-positive lymphomas.

    PubMed

    Crosby, Natasha M; Ghosh, Mistuni; Su, Betty; Beckstead, Jennifer A; Kamei, Ayako; Simonsen, Jens B; Luo, Bing; Gordon, Leo I; Forte, Trudy M; Ryan, Robert O

    2015-08-01

    A fusion protein comprising an α-CD20 single chain variable fragment (scFv) antibody, a spacer peptide, and human apolipoprotein (apo) A-I was constructed and expressed in Escherichia coli. The lipid interaction properties intrinsic to apoA-I as well as the antigen recognition properties of the scFv were retained by the chimera. scFv•apoA-I was formulated into nanoscale reconstituted high-density lipoprotein particles (termed nanodisks; ND) and incubated with cultured cells. α-CD20 scFv•apoA-I ND bound to CD20-positive non-Hodgkins lymphoma (NHL) cells (Ramos and Granta) but not to CD20-negative T lymphocytes (i.e., Jurkat). Binding to NHL cells was partially inhibited by pre-incubation with rituximab, a monoclonal antibody directed against CD20. Confocal fluorescence microscopy analysis of Granta cells following incubation with α-CD20 scFv•apoA-I ND formulated with the intrinsically fluorescent hydrophobic polyphenol, curcumin, revealed α-CD20 scFv•apoA-I localizes to the cell surface, while curcumin off-loads and gains entry to the cell. Compared to control incubations, viability of cultured NHL cells was decreased upon incubation with α-CD20 scFv•apoA-I ND harboring curcumin. Thus, formulation of curcumin ND with α-CD20 scFv•apoA-I as the scaffold component confers cell targeting and enhanced bioactive agent delivery, providing a strategy to minimize toxicity associated with chemotherapeutic agents. PMID:25994015

  10. In vivo detection of amyloid-β deposits using heavy chain antibody fragments in a transgenic mouse model for Alzheimer's disease.

    PubMed

    Nabuurs, Rob J A; Rutgers, Kim S; Welling, Mick M; Metaxas, Athanasios; de Backer, Maaike E; Rotman, Maarten; Bacskai, Brian J; van Buchem, Mark A; van der Maarel, Silvère M; van der Weerd, Louise

    2012-01-01

    This study investigated the in vivo properties of two heavy chain antibody fragments (V(H)H), ni3A and pa2H, to differentially detect vascular or parenchymal amyloid-β deposits characteristic for Alzheimer's disease and cerebral amyloid angiopathy. Blood clearance and biodistribution including brain uptake were assessed by bolus injection of radiolabeled V(H)H in APP/PS1 mice or wildtype littermates. In addition, in vivo specificity for Aβ was examined in more detail with fluorescently labeled V(H)H by circumventing the blood-brain barrier via direct application or intracarotid co-injection with mannitol. All V(H)H showed rapid renal clearance (10-20 min). Twenty-four hours post-injection (99m)Tc-pa2H resulted in a small yet significant higher cerebral uptake in the APP/PS1 animals. No difference in brain uptake were observed for (99m)Tc-ni3A or DTPA((111)In)-pa2H, which lacked additional peptide tags to investigate further clinical applicability. In vivo specificity for Aβ was confirmed for both fluorescently labeled V(H)H, where pa2H remained readily detectable for 24 hours or more after injection. Furthermore, both V(H)H showed affinity for parenchymal and vascular deposits, this in contrast to human tissue, where ni3A specifically targeted only vascular Aβ. Despite a brain uptake that is as yet too low for in vivo imaging, this study provides evidence that V(H)H detect Aβ deposits in vivo, with high selectivity and favorable in vivo characteristics, making them promising tools for further development as diagnostic agents for the distinctive detection of different Aβ deposits. PMID:22675537

  11. In Vivo Detection of Amyloid-β Deposits Using Heavy Chain Antibody Fragments in a Transgenic Mouse Model for Alzheimer's Disease

    PubMed Central

    Welling, Mick M.; Metaxas, Athanasios; de Backer, Maaike E.; Rotman, Maarten; Bacskai, Brian J.; van Buchem, Mark A.; van der Maarel, Silvère M.; van der Weerd, Louise

    2012-01-01

    This study investigated the in vivo properties of two heavy chain antibody fragments (VHH), ni3A and pa2H, to differentially detect vascular or parenchymal amyloid-β deposits characteristic for Alzheimer's disease and cerebral amyloid angiopathy. Blood clearance and biodistribution including brain uptake were assessed by bolus injection of radiolabeled VHH in APP/PS1 mice or wildtype littermates. In addition, in vivo specificity for Aβ was examined in more detail with fluorescently labeled VHH by circumventing the blood-brain barrier via direct application or intracarotid co-injection with mannitol. All VHH showed rapid renal clearance (10–20 min). Twenty-four hours post-injection 99mTc-pa2H resulted in a small yet significant higher cerebral uptake in the APP/PS1 animals. No difference in brain uptake were observed for 99mTc-ni3A or DTPA(111In)-pa2H, which lacked additional peptide tags to investigate further clinical applicability. In vivo specificity for Aβ was confirmed for both fluorescently labeled VHH, where pa2H remained readily detectable for 24 hours or more after injection. Furthermore, both VHH showed affinity for parenchymal and vascular deposits, this in contrast to human tissue, where ni3A specifically targeted only vascular Aβ. Despite a brain uptake that is as yet too low for in vivo imaging, this study provides evidence that VHH detect Aβ deposits in vivo, with high selectivity and favorable in vivo characteristics, making them promising tools for further development as diagnostic agents for the distinctive detection of different Aβ deposits. PMID:22675537

  12. Expression of a single-chain variable-fragment antibody against a Fusarium virguliforme toxin peptide enhances tolerance to sudden death syndrome in transgenic soybean plants.

    PubMed

    Brar, Hargeet K; Bhattacharyya, Madan K

    2012-06-01

    Plants do not produce antibodies. However, plants can correctly assemble functional antibody molecules encoded by mammalian antibody genes. Many plant diseases are caused by pathogen toxins. One such disease is the soybean sudden death syndrome (SDS). SDS is a serious disease caused by the fungal pathogen Fusarium virguliforme. The pathogen, however, has never been isolated from diseased foliar tissues. Thus, one or more toxins produced by the pathogen have been considered to cause foliar SDS. One of these possible toxins, FvTox1, was recently identified. We investigated whether expression of anti-FvTox1 single-chain variable-fragment (scFv) antibody in transgenic soybean can confer resistance to foliar SDS. We have created two scFv antibody genes, Anti-FvTox1-1 and Anti-FvTox1-2, encoding anti-FvTox1 scFv antibodies from RNAs of a hybridoma cell line that expresses mouse monoclonal anti-FvTox1 7E8 antibody. Both anti-FvTox1 scFv antibodies interacted with an antigenic site of FvTox1 that binds to mouse monoclonal anti-FvTox1 7E8 antibody. Binding of FvTox1 by the anti-FvTox1 scFv antibodies, expressed in either Escherichia coli or transgenic soybean roots, was initially verified on nitrocellulose membranes. Expression of anti-FvTox1-1 in stable transgenic soybean plants resulted in enhanced foliar SDS resistance compared with that in nontransgenic control plants. Our results suggest that i) FvTox1 is an important pathogenicity factor for foliar SDS development and ii) expression of scFv antibodies against pathogen toxins could be a suitable biotechnology approach for protecting crop plants from toxin-induced diseases.

  13. Quantitative real-time polymerase chain reaction (qRT-PCR) restriction fragment length polymorphism (RFLP) method for monitoring highly conserved transgene expression during gene therapy.

    PubMed

    Bruzzone, Carol M; Belcher, John D; Schuld, Nathan J; Newman, Kristal A; Vineyard, Julie; Nguyen, Julia; Chen, Chunsheng; Beckman, Joan D; Steer, Clifford J; Vercellotti, Gregory M

    2008-12-01

    Evaluation of the transfer efficiency of a rat heme oxygenase-1 (HO-1) transgene into mice requires differentiation of rat and mouse HO-1. However, rat and mouse HO-1 have 94% homology; antibodies and enzyme activity cannot adequately distinguish HO-1. We designed a quantitative real-time polymerase chain reaction (qRT-PCR) method to monitor HO-1 transcription relative to a housekeeping gene, GAPDH. The ratio of rat and mouse HO-1 mRNA could be estimated through restriction fragment length polymorphism (RFLP) analysis of the PCR products. In vitro, murine AML12 hepatocytes were transfected with rat HO-1. After 40 h, the total HO-1 mRNA was enriched 2-fold relative to control cells, and rat HO-1 comprised 84% of HO-1 cDNA. In vivo, the rat HO-1 transgene was cloned into a Sleeping Beauty transposase (SB-Tn) construct and was injected hydrodynamically into a mouse model of sickle cell disease (SCD). After 21 days, there was a 32% enrichment of HO-1 mRNA relative to control mice and the rat transgene comprised 88% of HO-1 cDNA. After 21 days, HO-1 protein expression in liver was increased 2.5-fold. In summary, qRT-PCR RFLP is a useful and reliable method to differentiate the transgene from host gene transcription, especially when the host and transgene protein are identical or highly homologous. This method has translational applications to the design, delivery, and monitoring of gene-therapy vectors. PMID:19059164

  14. Cross-Neutralization Activity of Single-Chain Variable Fragment (scFv) Derived from Anti-V3 Monoclonal Antibodies Mediated by Post-Attachment Binding.

    PubMed

    Maruta, Yasuhiro; Kuwata, Takeo; Tanaka, Kazuki; Alam, Muntasir; Valdez, Kristel Paola Ramirez; Egami, Yoshika; Suwa, Yoshiaki; Morioka, Hiroshi; Matsushita, Shuzo

    2016-09-21

    The V3 loop in the envelope (Env) of HIV-1 is one of the major targets of neutralizing antibodies. However, this antigen is hidden inside the Env trimer in most isolates and is fully exposed only during CD4-gp120 interaction. Thus, primary HIV-1 isolates are relatively resistant to anti-V3 antibodies because IgG is too large to access the V3 loop. To overcome this obstacle, we constructed single-chain variable fragments (scFvs) from anti-V3 monoclonal antibodies 0.5γ, 5G2, and 16G6. Enhanced neutralization by 0.5γ and 5G2 scFvs was observed in strains resistant to their IgG counterparts. Neutralization coverage by 0.5γ scFv reached up to 90% of the tested viruses (tier 2 and 3 classes). The temperature-regulated neutralization assay revealed that extensive cross-neutralization of 0.5γ scFv can be explained by post-attachment neutralization. Neutralization assay involving viruses carrying an inter-subunit disulfide bond (SOS virus) showed that the neutralization-susceptible timeframe after attachment was 60 to 120 min. These results indicate that the scFvs efficiently access the V3 loop and subsequently neutralize HIV-1, even after virus attachment to the target cells. Based on its broad and potent neutralizing activity, further development of anti-V3 scFv for therapeutic and preventive strategies is warranted.

  15. Successful engineering of a highly potent single-chain variable-fragment (scFv) bispecific antibody to target disialoganglioside (GD2) positive tumors

    PubMed Central

    Cheng, Ming; Santich, Brian H.; Xu, Hong; Ahmed, Mahiuddin; Huse, Morgan; Cheung, Nai-Kong V.

    2016-01-01

    ABSTRACT Engineering potent bispecific antibodies from single-chain variable fragments (scFv) remains difficult due to the inherent instability and insufficient binding of scFv's compared to their parental immunoglobulin format. Previously, we described a scFv-based bispecific antibody (scBA) against disialoganglioside (GD2) based on the anti-GD2 murine 5F11-scFv and the anti-CD3 huOKT3-scFv (5F11-scBA). In this study, we substituted the 5F11-scFv with the higher affinity (13-fold) hu3F8-scFv to form hu3F8-scBA. With this modification, hu3F8-scBA redirected T cells to kill GD2(+) cancer cell lines with up to 5,000-fold higher potency (femtomolar EC50) compared with 5F11-scBA (picomolar EC50) in cytotoxicity assays, even against target cells with low GD2 densities. Furthermore, hu3F8-scBA induced stronger T-cell activation than 5F11-scBA, as measured by Ca2+ flux and cytokine release. Additionally, in vivo, hu3F8-scBA suppressed tumor growth and prolonged mice survival much more effectively than 5F11-scBA, in both neuroblastoma and melanoma xenograft models. We conclude that the functional properties of scBA's can be increased substantially by relatively modest increases in antigen affinity. PMID:27471647

  16. Selection of single chain variable fragment (scFv) antibodies from a hyperimmunized phage display library for the detection of the antibiotic monensin.

    PubMed

    Makvandi-Nejad, Shokouh; Sheedy, Claudia; Veldhuis, Linda; Richard, Gabrielle; Hall, J Christopher

    2010-08-31

    Concerns over the occurrence of the veterinary antibiotic monensin (MW 671Da) in animal food products and water have given rise to the need for a sensitive and rapid detection method. In this study, four monensin-specific single chain variable fragments (scFvs) were isolated from a hyperimmunized phage-displayed library originating from splenocytes of a mouse immunized with monensin conjugated to bovine serum albumin (BSA). The coding sequences of the scFvs were engineered in the order 5'-V(L)-linker-V(H)-3', where the linker encodes for Gly(10)Ser(7)Arg. Three rounds of selection were performed against monensin conjugated to chicken ovalbumin (OVA) and keyhole limpet hemocyanin (KLH), alternately. In the third round of selection, two different strategies, which differed in the number of washes and the concentration of the coating conjugates, were used to select for specific binders to monensin. A total of 376 clones from round two and three were screened for their specific binding to monensin conjugates and positive clones were sequenced. It was found that 80% of clones from round three contained a stop codon. After removing the stop codon by site-directed mutagenesis, ten binders with different amino acid sequences were subcloned into the vector pMED2 for soluble expression in Escherichia coli HB2151. Four of these scFvs bound to free monensin as determined using competitive fluorescence polarization assays (C-FPs). IC(50) values ranged from 0.031 and 231 microM. A cross-reactivity assay against salinomycin, lasalocid A, kanamycin and ampicillin revealed that the two best binders were highly specific to monensin.

  17. Expression of a single-chain variable-fragment antibody against a Fusarium virguliforme toxin peptide enhances tolerance to sudden death syndrome in transgenic soybean plants.

    PubMed

    Brar, Hargeet K; Bhattacharyya, Madan K

    2012-06-01

    Plants do not produce antibodies. However, plants can correctly assemble functional antibody molecules encoded by mammalian antibody genes. Many plant diseases are caused by pathogen toxins. One such disease is the soybean sudden death syndrome (SDS). SDS is a serious disease caused by the fungal pathogen Fusarium virguliforme. The pathogen, however, has never been isolated from diseased foliar tissues. Thus, one or more toxins produced by the pathogen have been considered to cause foliar SDS. One of these possible toxins, FvTox1, was recently identified. We investigated whether expression of anti-FvTox1 single-chain variable-fragment (scFv) antibody in transgenic soybean can confer resistance to foliar SDS. We have created two scFv antibody genes, Anti-FvTox1-1 and Anti-FvTox1-2, encoding anti-FvTox1 scFv antibodies from RNAs of a hybridoma cell line that expresses mouse monoclonal anti-FvTox1 7E8 antibody. Both anti-FvTox1 scFv antibodies interacted with an antigenic site of FvTox1 that binds to mouse monoclonal anti-FvTox1 7E8 antibody. Binding of FvTox1 by the anti-FvTox1 scFv antibodies, expressed in either Escherichia coli or transgenic soybean roots, was initially verified on nitrocellulose membranes. Expression of anti-FvTox1-1 in stable transgenic soybean plants resulted in enhanced foliar SDS resistance compared with that in nontransgenic control plants. Our results suggest that i) FvTox1 is an important pathogenicity factor for foliar SDS development and ii) expression of scFv antibodies against pathogen toxins could be a suitable biotechnology approach for protecting crop plants from toxin-induced diseases. PMID:22397408

  18. Close association of predominant genotype of herpes simplex virus type 1 with eczema herpeticum analyzed using restriction fragment length polymorphism of polymerase chain reaction.

    PubMed

    Yoshida, Masami; Umene, Kenichi

    2003-04-01

    Herpes simplex virus type 1 (HSV-1) strains belonging to the same genotype can possibly share biological properties and clinical manifestations common to the genotype. We classified previously 66 HSV-1 strains into 35 genotypes (F1-F35) using restriction fragment length polymorphism (RFLP) and F1 and F35 genotypes were revealed to be predominant [Arch. Virol. 13 (1993) 29]. It was found later that the F35 genotype seemed to be closely associated with eczema herpeticum [J. Med. Virol. 49 (1996) 329]. In the present study, a convenient method was developed for classification of two predominant genotypes by RFLP of polymerase chain reaction (RFLP-PCR). Using this method, genotypes of 21 strains isolated from eczema herpeticum were analyzed; seven of 21 strains (33.3%) were of F1 and five of 21 (23.8%) were of F35. Genotypes of 19 strains isolated from facial herpes other than eczema herpeticum were as follows; six of 19 (31.6%) strains were of F1 and one of 19 (5.3%) were of F35. Thus, strains belonging to F35 were appear to have been isolated more frequently from eczema herpeticum (5/21) than from facial herpes (1/19). These ratios showed a statistically significant difference. These results support the hypothesis that F35 strains is clearly associated with eczema herpeticum, in agreement with previous study. This is the first report of PCR-based approach for classification of HSV-1 strains into genotypes seeking an association of a genotype with clinical manifestation.

  19. Isolation and partial structural characterization of an equine fibrinogen CNBr fragment that exhibits immunologic cross-reactivity with an A alpha-chain cross-linking region of human fibrinogen.

    PubMed

    Sobel, J H; Thibodeau, C A; Kolks, M A; Canfield, R E

    1990-09-25

    Immunochemical studies of equine fibrinogen were conducted to characterize the structural basis for the immunologic cross-reactivity observed between human and equine A alpha chains when employing an antiserum to the 26K, human cyanogen bromide (CNBr) fragment, A alpha 241-476 (CNBr VIII). A 38K, equine CNBr fragment that reacts with this antiserum was isolated from CNBr-digested equine fibrinogen by Sephadex G-100 gel filtration. It was further purified by sequential hydrophobic chromatography on phenyl-Sepharose CL-4B, followed by reversed-phased (C-8) high-performance liquid chromatography (HPLC). NH2-Terminal analysis of the purified fragment, designated EqA alpha CNBr, identified one major sequence whose first three residues, E-L-E, were identical with those of human CNBr VIII. Tryptic and staphylococcal protease digests of the equine fragment were resolved by reversed-phase HPLC (C-4, C-18), and the separated components were characterized by amino acid analysis and automated Edman degradation. A total of 34 tryptic and 20 staph protease peptides yielded sequence information that permitted the alignment of 271 equine residues with residues A alpha 241-517 from the COOH-terminal two-thirds of the human A alpha chain so that 63% of the possible matches were identical. Other features of interest included (1) an amino acid substitution in which the methionine residue at A alpha 476 in the human A alpha chain was replaced by a valine residue, thus accounting, in part, for the larger EqA alpha CNBr fragment obtained from the equine molecule, and (2) a region of striking homology in which 36 successive residues, corresponding to A alpha 428-464 in the human A alpha chain, were identical in both species. These findings, together with available structural data for the COOH-terminal portion of the rat and bovine A alpha chains, indicate that the region corresponding to (human) A alpha 240-517 represents a conserved portion of the fibrinogen molecule. This may, in turn

  20. Invariance in the isoheptanes of petroleum

    SciTech Connect

    Mango, F.D.

    1987-07-31

    Four isoheptanes in petroleum display a remarkable invariance in a ratio of sums of concentrations. The isoheptanes are not at thermodynamic equilibrium, nor are they fixed to some constant composition. The four isomers display coherent change in relative amounts but maintain invariance in the ratio of sums. Within sets of genetically related petroleum samples, invariance reaches levels that approach the limits of their analytical precision. The invariance is inconsistent with a chemical origin that involves the thermal fragmentation of natural products or their derivatives. It suggests a reaction process at steady state, in which relative rates of product formation are constant. A mechanism is proposed in which the four isoheptanes are formed pairwise and sequentially through two intermediates in a catalytic process that operates at steady state. 13 references, 3 figures, 1 table.

  1. Chemiluminescence competitive indirect enzyme immunoassay for 20 fluoroquinolone residues in fish and shrimp based on a single-chain variable fragment.

    PubMed

    Tao, Xiaoqi; Chen, Min; Jiang, Haiyang; Shen, Jianzhong; Wang, Zhanhui; Wang, Xia; Wu, Xiaoping; Wen, Kai

    2013-09-01

    A chemiluminescent competitive indirect enzyme-linked immunosorbent assay, based on a mutant single-chain variable fragment (scFv), was developed to detect a broad range of fluoroquinolones (FQs) in fish and shrimp matrices. In this study, the best scFvC4A9H1_mut2 was adopted, which showed 10-fold improved affinity to sarafloxacin (SAR), difloxacin (DIF), and trovafloxacin (TRO), while the affinity to other FQs was fully inherited from wild-type scFvC4A9H1. In the optimized generic test, scFvC4A9H1_mut2 in combination with norfloxacin-ovalbumin conjugate and horseradish peroxidase-labeled anti-c-myc 9E10 antibody showed 50 % binding inhibition (IC50) at 0.12 μg kg(-1) for norfloxacin in buffer. Screening for the class of FQ antibiotics is accomplished using a simple, rapid extraction carried out with ethanol/acetic acid (99:1, v/v). This common extraction was able to detect 20 FQ residues such as s ciprofloxacin (CIP), danofloxacin, DIF, enoxacin, enrofloxacin (ENR), fleroxacin, amifloxacin, flumequine, levofloxacin, lomefloxacin hydrochloride, marbofloxacin, norfloxacin (NOR), ofloxacin, orbifloxacin, pazufloxacin, pefloxacin-d5 (PEF), prulifloxacin, SAR, sparfloxacin, and TRO in fish and shrimp. The limit of detection (LOD) for NOR was 0.2 μg kg(-1) and the LODs for CIP and ENR were all <0.2 μg kg(-1). Values of LODs inferred from the cross-reactivity data will range from approximately 0.23 μg kg(-1) for PEF to 2.1 μg kg(-1) for TRO. Field fish and shrimp samples were analyzed and compared to the results obtained from liquid chromatography tandem mass spectrometric method. All five instances (from 0.25 to 15.6 μg kg(-1)) in which FQs were present at concentrations near or above the assay LOD were identified as positive by the newly developed assay, demonstrating the usefulness of this assay as a screening tool.

  2. Invariance and neural nets.

    PubMed

    Barnard, E; Casasent, D

    1991-01-01

    Application of neural nets to invariant pattern recognition is considered. The authors study various techniques for obtaining this invariance with neural net classifiers and identify the invariant-feature technique as the most suitable for current neural classifiers. A novel formulation of invariance in terms of constraints on the feature values leads to a general method for transforming any given feature space so that it becomes invariant to specified transformations. A case study using range imagery is used to exemplify these ideas, and good performance is obtained.

  3. Ligation-based assembly for constructing mouse synthetic scFv libraries by chain shuffling with in vivo-amplified VH and VL fragments.

    PubMed

    Nishi, Michiru; Jian, Nan; Yamamoto, Keiko; Seto, Haruyo; Nishida, Yuichi; Tonoyama, Yasuhiro; Shimizu, Nobuyoshi; Nishi, Yoshisuke

    2014-10-01

    In vitro assembly of two or three PCR fragments using primers is a common method of constructing scFv fragments for display on the surface of phage. However, mismatch annealing often occurs during in this step, leading to cloning and display of incomplete Fab or scFv fragments. To overcome this limitation, we developed a ligation-based two-fragment assembly (LTFA) protocol that involved separately cloning VH and Vκ fragments into the high-copy-number plasmid pUC18. The VH and Vκ fragments had randomized complementarity-determining region 3 (CDR3) and were joined with a peptidyl linker composed of (G4S)3. Using this approach, complete sequences of scFv fragments were successfully constructed, and the sequencing of 83 scFv clones revealed that none of the sequences, including the linker region, contained deletions or mutations. In contrast, linker sequences generated using a conventional two-fragment PCR assembly (TFPA) protocol often contained sequence anomalies, including large truncations. Using the LTFA protocol, a final library size of 1.0×10(8)cfu was achieved. Examination of the amino acid profiles of the generated scFv fragments within the randomized regions introduced using degenerate codons did not detect any bias from that expected based on stochastic distribution. After several cycles of panning with this library, antigen-specific scFvs against two reference antigens, hen egg lysozyme and streptavidin were detected. In addition, scFvs with specificity against peptidyl antigens in the loop region of the Medaka ortholog of human C6orf89, which encodes a histone deacetylase enhancer that interacts with the bombesin receptor, were also obtained. The LTFA protocol developed here is robust and allows for the easy construction of integral scFv fragments compared with conventional TFPA. Utilizing LTFA, other CDRs can be readily combined. This approach also allows for the in vitro maturation of scFv fragments by separately introducing randomization in CDRs or

  4. Nonequilibrium invariant measure under heat flow.

    PubMed

    Delfini, Luca; Lepri, Stefano; Livi, Roberto; Politi, Antonio

    2008-09-19

    We provide an explicit representation of the nonequilibrium invariant measure for a chain of harmonic oscillators with conservative noise in the presence of stationary heat flow. By first determining the covariance matrix, we are able to express the measure as the product of Gaussian distributions aligned along some collective modes that are spatially localized with power-law tails. Numerical studies show that such a representation applies also to a purely deterministic model, the quartic Fermi-Pasta-Ulam chain.

  5. Short report: A new polymerase chain reaction-restriction fragment length polymorphism method to identify Anopheles arabiensis from An. gambiae and its two molecular forms from degraded DNA templates or museum samples.

    PubMed

    Santolamazza, Federica; Della Torre, Alessandra; Caccone, Adalgisa

    2004-06-01

    We present a polymerase chain reaction-restriction fragment length polymorphism method to simultaneously distinguish the two Anopheles gambiae M and S molecular forms and Anopheles arabiensis. This method uses different diagnostic sites than previously published methods, and it is based on the amplification of a smaller ribosomal DNA fragment. We have tested this protocol in a variety of samples from different geographic regions and various ages of preservation to ascertain the robustness of this protocol over a wide geographic window and on DNA templates of poor quality. This procedure is as efficient as previous ones in discriminating An. arabiensis from the two taxa in An gambiae s.s. However, it performs better than others on poor quality templates such as the ones from museum collections, and poorly stored field collected material. However, it must be noted that it does not allow the simultaneous discrimination of all the species in the An. gambiae complex.

  6. Lorentz invariance with an invariant energy scale.

    PubMed

    Magueijo, João; Smolin, Lee

    2002-05-13

    We propose a modification of special relativity in which a physical energy, which may be the Planck energy, joins the speed of light as an invariant, in spite of a complete relativity of inertial frames and agreement with Einstein's theory at low energies. This is accomplished by a nonlinear modification of the action of the Lorentz group on momentum space, generated by adding a dilatation to each boost in such a way that the Planck energy remains invariant. The associated algebra has unmodified structure constants. We also discuss the resulting modifications of field theory and suggest a modification of the equivalence principle which determines how the new theory is embedded in general relativity.

  7. Assembly of an R3N5(2-) chain by cycloaddition of a hydrazinediide and an azide at zirconium and its thermal fragmentation.

    PubMed

    Gehrmann, Thorsten; Lloret Fillol, Julio; Wadepohl, Hubert; Gade, Lutz H

    2009-01-01

    Breaking the chain: Reaction of a zirconium hydrazinediide with organoazides gives 2-pentazene-1,4-diyl complexes, such as [Zr(N(2) (TBS)N(py)){N(Ad)N(3)NPh(2)}] (C gray, N blue, Si green, Zr turquoise), by formal [2+3] cycloaddition. Bonding within the N(5) chain is investigated using density functional calculations. These complexes thermally eject N(2) to give side-on bonded diazenides.

  8. A translation invariant bipolaron in the Holstein model and superconductivity.

    PubMed

    Lakhno, Victor

    2016-01-01

    Large-radius translation invariant (TI) bipolarons are considered in a one-dimensional Holstein molecular chain. Criteria of their stability are obtained. The energy of a translation invariant bipolaron is shown to be lower than that of a bipolaron with broken symmetry. The results obtained are applied to the problem of superconductivity in 1D-systems. It is shown that TI-bipolaron mechanism of Bose-Einstein condensation can support superconductivity even for infinite chain.

  9. A translation invariant bipolaron in the Holstein model and superconductivity.

    PubMed

    Lakhno, Victor

    2016-01-01

    Large-radius translation invariant (TI) bipolarons are considered in a one-dimensional Holstein molecular chain. Criteria of their stability are obtained. The energy of a translation invariant bipolaron is shown to be lower than that of a bipolaron with broken symmetry. The results obtained are applied to the problem of superconductivity in 1D-systems. It is shown that TI-bipolaron mechanism of Bose-Einstein condensation can support superconductivity even for infinite chain. PMID:27547652

  10. The primary fibrin polymerization pocket: Three-dimensional structure of a 30-kDa C-terminal γ chain fragment complexed with the peptide Gly-Pro-Arg-Pro

    PubMed Central

    Pratt, K. P.; Côté, H. C. F.; Chung, D. W.; Stenkamp, R. E.; Davie, E. W.

    1997-01-01

    After vascular injury, a cascade of serine protease activations leads to the conversion of the soluble fibrinogen molecule into fibrin. The fibrin monomers then polymerize spontaneously and noncovalently to form a fibrin gel. The primary interaction of this polymerization reaction is between the newly exposed N-terminal Gly-Pro-Arg sequence of the α chain of one fibrin molecule and the C-terminal region of a γ chain of an adjacent fibrin(ogen) molecule. In this report, the polymerization pocket has been identified by determining the crystal structure of a 30-kDa C-terminal fragment of the fibrin(ogen) γ chain complexed with the peptide Gly-Pro-Arg-Pro. This peptide mimics the N terminus of the α chain of fibrin. The conformational change in the protein upon binding the peptide is subtle, with electrostatic interactions primarily mediating the association. This is consistent with biophysical experiments carried out over the last 50 years on this fundamental polymerization reaction. PMID:9207064

  11. Prevalence of Borrelia burgdorferi species and identification of Borrelia valaisiana in questing Ixodes ricinus in the Lyon region of France as determined by polymerase chain reaction-restriction fragment length polymorphism.

    PubMed

    Quessada, T; Martial-Convert, F; Arnaud, S; Leudet De La Vallee, H; Gilot, B; Pichot, J

    2003-03-01

    Many cases of Lyme borreliosis have been reported over the years in the region of Lyon, France. The identification and prevalence of Borrelia burgdorferi sensu lato in Ixodes ricinus were investigated by polymerase chain reaction (PCR) of the flagellin gene and restriction fragment length polymorphism (RFLP) analysis. Questing Ixodes ricinus larvae, nymphs and adults were collected by the flagging method from deciduous forests in four areas in the Lyon region of France between October 1994 and September 1995 and in June 1998. The overall prevalence of Borrelia burgdorferi sensu lato was 13.2% (91/688). No significant differences in prevalence were observed between the different stages and sex of the ixodids or between collection areas. The majority of infections were simple infections (82.4%; 75/91), most of which were due to Borrelia afzelii (41.4%), while coinfections (12.1%) were predominantly (54.5%) a combination of Borrelia valaisiana and Borrelia garinii. No tick was infected with more than two borrelial species, nor was Borrelia lusitaniae identified. The Borrelia valaisiana species was detected for the first time in France, confirming its widespread presence in Europe. This study confirms that the surroundings of Lyon are risk areas for contracting Lyme disease and that no particular clinical manifestations predominate due to the heterogeneous distribution of Borrelia genospecies. Moreover, the polymerase chain reaction restriction fragment length polymorphism analysis is a rapid and easy method for genotyping of Borrelia species.

  12. Differentiation of canine distemper virus isolates in fur animals from various vaccine strains by reverse transcription-polymerase chain reaction-restriction fragment length polymorphism according to phylogenetic relations in china

    PubMed Central

    2011-01-01

    In order to effectively identify the vaccine and field strains of Canine distemper virus (CDV), a new differential diagnostic test has been developed based on reverse transcription-polymerase chain reaction (RT-PCR) and restriction fragment length polymorphism (RFLP). We selected an 829 bp fragment of the nucleoprotein (N) gene of CDV. By RFLP analysis using BamHI, field isolates were distinguishable from the vaccine strains. Two fragments were obtained from the vaccine strains by RT-PCR-RFLP analysis while three were observed in the field strains. An 829 nucleotide region of the CDV N gene was analyzed in 19 CDV field strains isolated from minks, raccoon dogs and foxes in China between 2005 and 2007. The results suggest this method is precise, accurate and efficient. It was also determined that three different genotypes exist in CDV field strains in fur animal herds of the north of China, most of which belong to Asian type. Mutated field strains, JSY06-R1, JSY06-R2 and JDH07-F1 also exist in Northern China, but are most closely related to the standard virulent strain A75/17, designated in Arctic and America-2 genetype in the present study, respectively. PMID:21352564

  13. Multiparameter optimization method and enhanced production of secreted recombinant single-chain variable fragment against the HIV-1 P17 protein from Escherichia coli by fed-batch fermentation.

    PubMed

    Paopang, Porntip; Kasinrerk, Watchara; Tayapiwatana, Chatchai; Seesuriyachan, Phisit; Butr-Indr, Bordin

    2016-01-01

    The single-chain fragment variable (scFv) was used to produce a completely functional antigen-binding fragment in bacterial systems. The advancements in antibody engineering have simplified the method of producing Fv fragments and made it more efficient and generally relevant. In a previous study, the scFv anti HIV-1 P17 protein was produced by a batch production system, optimized by the sequential simplex optimization method. This study continued that work in order to enhance secreted scFv production by fed-batch cultivation, which supported high volumetric productivity and provided a large amount of scFvs for diagnostic and therapeutic research. The developments in cell culture media and process parameter settings were required to realize the maximum production of cells. This study investigated the combined optimization methods, Plackett-Burman design (PBD) and sequential simplex optimization, with the aim of optimize feed medium. Fed-batch cultivation with an optimal feeding rate was determined. The result demonstrated that a 20-mL/hr feeding rate of the optimized medium can increase cell growth, total protein production, and scFv anti-p17 activity by 4.43, 1.48, and 6.5 times more than batch cultivation, respectively. The combined optimization method demonstrated novel power tools for the optimization strategy of multiparameter experiments.

  14. Immunoglobulin light chains, glycosaminoglycans and amyloid.

    SciTech Connect

    Stevens, F. J.; Kisilevsky, R.; Biosciences Division; Queen's Univ.

    2000-03-01

    Immunoglobulin light chains are the precursor proteins for fibrils that are formed during primary amyloidosis and in amyloidosis associated with multiple myeloma. As found for the approximately 20 currently described forms of focal, localized, or systemic amyloidoses, light chain-related fibrils extracted from physiological deposits are invariably associated with glycosaminoglycans, predominantly heparan sulfate. Other amyloid-related proteins are either structurally normal, such as g2-microglobulin and islet amyloid polypeptide, fragments of normal proteins such as serum amyloid A protein or the precursor protein of the g peptide involved in Alzheimer's disease, or are inherited forms of single amino acid variants of a normal protein such as found in the familial forms of amyloid associated with transthyretin. In contrast, the primary structures of light chains involved in fibril formation exhibit extensive mutational diversity rendering some proteins highly amyloidogenic and others non-pathological. The interactions between light chains and glycosaminoglycans are also affected by amino acid variation and may influence the clinical course of disease by enhancing fibril stability and contributing to resistance to protease degradation. Relatively little is currently known about the mechanisms by which glycosaminoglycans interact with light chains and light-chain fibrils. It is probable that future studies of this uniquely diverse family of proteins will continue o shed light on the processes of amyloidosis, and contribute as well to a greater understanding of the normal physiological roles of glycosaminoglycans.

  15. Chain-amplified photochemical fragmentation of N-alkoxypyridinium salts: proposed reaction of alkoxyl radicals with pyridine bases to give pyridinyl radicals.

    PubMed

    Shukla, Deepak; Adiga, Shashishekar P; Ahearn, Wendy G; Dinnocenzo, Joseph P; Farid, Samir

    2013-03-01

    Photoinduced electron transfer to N-alkoxypyridiniums, which leads to N–O bond cleavage and alkoxyl radical formation, is highly chain amplified in the presence of a pyridine base such as lutidine. Density functional theory calculations support a mechanism in which the alkoxyl radicals react with lutidine via proton-coupled electron transfer (PCET) to produce lutidinyl radicals (BH•). A strong electron donor, BH• is proposed to reduce another alkoxypyridinium cation, leading to chain amplification, with quantum yields approaching 200. Kinetic data and calculations support the formation of a second, stronger reducing agent: a hydrogen-bonded complex between BH• and another base molecule (BH•···B). Global fitting of the quantum yield data for the reactions of four pyridinium salts (4-phenyl and 4-cyano with N-methoxy and N-ethoxy substituents) led to a consistent set of kinetic parameters. The chain nature of the reaction allowed rate constants to be determined from steady-state kinetics and independently determined chain-termination rate constants. The rate constant of the reaction of CH3O• with lutidine to form BH•, k1, is ~6 × 10(6) M(–1) s(–1); that of CH3CH2O• is ~9 times larger. Reaction of CD3O• showed a deuterium isotope effect of ~6.5. Replacing lutidine by 3-chloropyridine, a weaker base, decreases k1 by a factor of ~400.

  16. Collagen chains detected by western blotting using a /sup 125/I-labeled 45K fragment of fibronectin (45K FN)

    SciTech Connect

    Ristagno, R.; Heimer, R.; Fishman, A.P.; Sampson, P.M.

    1987-05-01

    The objective was to improve the sensitivity and specificity of detection of unlabeled collagen chains in biologic fluids. Chains of Types I,II,III,IV and XI (1..cap alpha..2..cap alpha..3..cap alpha..) collagen were separated by SDS PAGE. Their complete transfer to nitrocellulose was obtained by electrophoresis for 16 h at 150 mA with 10 mM Tris, 117 mM glycine, 100 mM cysteine, 0.1% SDS and 10% methanol. The 45K FN was prepared by chymotryptic digestion of fibronectin adsorbed to gelatin-Sepharose, followed by elution with 1.2 M urea, 1 M Tris-NaCl, pH 8.3 and iodination. When exposed to the nitrocellulose transblot at pH 9.5 and 4/sup 0/C, 45K FN did not react with IgG, fibrinogen, myosin, albumin or carbonic anhydrase. These proteins interfere in the assay under conditions of lower pH and higher temperature. The autoradiographs of the transblots were evaluated by densitometry and reflected results also obtained by dot blotting, that chains of collagen Types I,II,III were detectable at 4 ng and those of collagen Type IV at 12 ng. Generally, ..cap alpha..,BETA, and ..gamma.. chains were detectable. The 45K FN reacted equally with ..cap alpha..1(I) and ..cap alpha..2(I), but for Type XI the 1..cap alpha.. chain had considerably more reactivity than 2..cap alpha.. or 3..cap alpha... As the 45K FN was specific for collagens added to plasma, the authors method appears useful for qualitative and quantitative assays of unlabeled collagens in biologic fluids.

  17. Cosmological disformal invariance

    NASA Astrophysics Data System (ADS)

    Domènech, Guillem; Naruko, Atsushi; Sasaki, Misao

    2015-10-01

    The invariance of physical observables under disformal transformations is considered. It is known that conformal transformations leave physical observables invariant. However, whether it is true for disformal transformations is still an open question. In this paper, it is shown that a pure disformal transformation without any conformal factor is equivalent to rescaling the time coordinate. Since this rescaling applies equally to all the physical quantities, physics must be invariant under a disformal transformation, that is, neither causal structure, propagation speed nor any other property of the fields are affected by a disformal transformation itself. This fact is presented at the action level for gravitational and matter fields and it is illustrated with some examples of observable quantities. We also find the physical invariance for cosmological perturbations at linear and high orders in perturbation, extending previous studies. Finally, a comparison with Horndeski and beyond Horndeski theories under a disformal transformation is made.

  18. Structural features of T cell receptor variable regions that enhance domain stability and enable expression as single-chain VαVβ fragments

    PubMed Central

    Richman, Sarah A.; Aggen, David H.; Dossett, Michelle L.; Donermeyer, David L.; Allen, Paul M.; Greenberg, Philip D.; Kranz, David M.

    2009-01-01

    The variable (V) domains of antibodies and T cell receptors (TCRs) share sequence homology and striking structural similarity. Single-chain antibody V domain constructs (scFv) are routinely expressed in a variety of heterologous systems, both for production of soluble protein as well as for in vitro engineering. In contrast, single-chain T cell receptor V domain constructs (scTCR) are prone to aggregation and misfolding and are refractory to display on phage or yeast in their wild-type form. However, through random mutagenesis and yeast display engineering, it has been possible to isolate scTCR mutants that are properly folded and displayed on the yeast surface. These displayed mutants can serve not only as a scaffold for further engineering but also as scTCR variants that exhibit favorable biophysical properties in E. coli expression. Thus, a more comprehensive understanding of the V domain mutations that allowed display would be beneficial. Our goal here was to identify generalizable patterns of important mutations that can be applied to different TCRs. We compared five different scTCRs, four from mice and one from a human, for yeast surface display. Analysis of a collection of mutants revealed four distinct regions of TCR V domains that were most important for enabling surface expression: the Vα-Vβ interface, the HV4 of Vβ, and the region of the Vα and Vβ domains normally apposed against the constant (C) domains. Consistent with the role of the V-C interface in surface display, reconstitution of this interface, by including the constant domains of each chain, allowed V domain display and αβ chain association on the yeast surface, thus providing an alternative TCR scaffold. However, the surface levels of TCR achieved with engineered scTCR mutants were superior to that of the VαCα/VβCβ constructs. Therefore, we describe further optimization of the current strategy for surface display of the single-chain format in order to facilitate yeast display

  19. Characterization of the Native and Denatured Herceptin by ELISA and QCM using a High-Affinity Single Chain Fragment Variable (scFv) Recombinant Antibody

    PubMed Central

    Shang, Yuqin; Mernaugh, Ray

    2012-01-01

    Herceptin/Trastuzumab is a humanized IgG1κ light chain antibody used to treat some forms of breast cancer. A phage-displayed recombinant antibody library was used to obtain an scFv (designated 2B4) to a linear synthetic peptide representing Herceptin’s heavy chain CDR3. ELISAs and piezoimmunosensor/quartz crystal microbalance (QCM) assays were used to characterize 2B4-binding activity to both native and heat denatured Herceptin. The 2B4 scFv specifically bound to heat denatured Herceptin in a concentration dependent manner over a wide (35–220.5 nM) dynamic range. Herceptin denatures and forms significant amount of aggregates when heated. UV-Vis characterization confirms that Herceptin forms aggregates as the temperature used to heat Herceptin increases. QCM affinity assay shows that binding stoichiometry between 2B4 scFv and Herceptin follows a 1:2 relationship proving that 2B4 scFv binds strongly to the dimers of heat denatured Herceptin aggregates and exhibits an affinity constant of 7.17 × 1013 M−2. The 2B4-based QCM assay was more sensitive than the corresponding ELISA. Combining QCM with ELISA can be used to more fully characterize non-specific binding events in assays. The potential theoretical and clinical implications of these results and the advantages of using QCM to characterize human therapeutic antibodies in samples are also discussed. PMID:22934911

  20. Construction and characterization of DNA vaccines encoding the single-chain variable fragment of the anti-idiotype antibody 1A7 mimicking the tumor-associated antigen disialoganglioside GD2.

    PubMed

    Zeytin, H E; Tripathi, P K; Bhattacharya-Chatterjee, M; Foon, K A; Chatterjee, S K

    2000-11-01

    Anti-idiotype antibody, 1A7, functionally mimics the tumor-associated antigen disialoganglioside GD2, which is overexpressed on the surface of a number of neuroectodermal tumors such as melanoma, neuroblastoma, soft tissue sarcoma, and small cell carcinoma of the lung. Immunization of mice with 1A7 generated the production of anti-GD2 antibodies. In a phase I clinical trial, immunization of patients with 1A7, mixed with the adjuvant QS21, demonstrated that 1A7 could act as a surrogate antigen for GD2 and induce strong humoral immune responses in advanced stage melanoma patients. DNA vaccines have recently been shown to invoke humoral as well as cellular responses in injected hosts against the transgene product. To evaluate the efficiency of DNA vaccines encoding anti-idiotype antibodies, we constructed expression plasmids encoding the variable heavy (VH) and variable light (VL) chains of 1A7. The plasmids were made in two configurations, expressing either the VH (pc1A7VHLnVL) or the VL (pc1A7VLLnVH) chain of 1A7 at the amino terminus, linked together by a 15-amino acid linker (Ln). In vitro transcription/translation assays and transfection of CHO-K1 cells with the plasmids demonstrated that a approximately 30-kDa protein was expressed by both configurations of the single-chain variable fragment. This protein can be specifically precipitated by monoclonal anti-GD2 antibody, 14G2a. Following intramuscular injection in mice, the plasmids were detectable in the injected tissues for at least 3 months and the injected plasmids actively transcribed the single-chain variable fragment 1A7 gene at the injected site. A single, intramuscular immunization of a group of C57BL/6 mice with pc1A7VLLnVH in phosphate-buffered saline induced humoral immune responses against 1A7 as well as GD2, the nominal antigen. Multiple immunizations, however, were required to elicit stronger immune responses. PMID:11129285

  1. Isolation of Coxiella burnetii by a centrifugation shell-vial assay from ticks collected in Cyprus: detection by nested polymerase chain reaction (PCR) and by PCR-restriction fragment length polymorphism analyses.

    PubMed

    Spyridaki, Ioanna; Psaroulaki, Anna; Loukaides, Fidias; Antoniou, Maria; Hadjichristodolou, Christos; Tselentis, Yannis

    2002-01-01

    Ticks are the principal vectors and reservoirs of Coxiella burnetii. The identification of isolates is necessary for understanding the clinical diversity of Q fever in different geographic areas. This is the first report of isolation of C. burnetii from ticks by the shell-vial assay and by nested polymerase chain reaction (PCR) assay for the detection of this pathogen in ticks. Of 141 ticks collected in Cyprus (Rhipicephalus sanguineus and Hyalloma spp.), 10% were found to be infected with C. burnetii. Three ticks were positive by hemolymph test, and 11 triturated ticks were positive by nested PCR. Three isolates were obtained by the centrifugation shell-vial technique. Analysis by PCR, then restriction fragment length polymorphism showed that the 3 Cyprus isolates had identical restriction profiles to reference strains Nine Mile and Q212. The methods described are useful in studying the epidemiology and ecology of C. burnetii. PMID:12135275

  2. 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

  3. Specific single chain variable fragment (ScFv) antibodies to angiotensin II AT(2) receptor: evaluation of the angiotensin II receptor expression in normal and tumor-bearing mouse lung.

    PubMed

    Tamura, Masaaki; Yan, Heping; Zegarra-Moro, Ofelia; Edl, Jennifer; Oursler, Stephanie; Chard-Bergstrom, Cindy; Andrews, Gordon; Kanehira, Tsutomu; Takekoshi, Susumu; Mernaugh, Ray

    2008-08-01

    To gain insight into the mechanism by which angiotensin II type 2 receptor (AT(2)) regulates carcinogen-induced lung tumorigenesis, we have newly developed anti-AT(2) single chain variable fragment (ScFv) antibodies using a rodent phage-displayed recombinant antibody library with various peptide fragments of the receptor protein, and investigated the expression of the AT(2) receptor protein. The specificity of the antibodies was verified using AT(2) over-expressing COS-7 cells and AT(2) naturally expressing PC12W cells. In control wild type mouse lung, a stronger immunoreactivity was observed in bronchial epithelial cells. A moderate immunoreactivity was detected in pulmonary vascular walls and vascular endothelial cells. In the lungs possessing tobacco-specific nitrosamine (NNK)-induced tumors, significantly increased AT(2) and AT(1 )immunostaining was observed in adenomatous lesions. These data suggest that the increase in both receptors' expression in the alveolar epithelial cells may be accompanied with the onset of NNK-induced tumorigenesis and hence play important roles in lung tumorigenesis.

  4. Specific Single Chain Variable Fragment (ScFv) Antibodies to Angiotensin II AT2 Receptor: Evaluation of the Angiotensin II Receptor Expression in Normal and Tumor-bearing Mouse Lung

    PubMed Central

    Tamura, Masaaki; Yan, Heping; Zegarra-Moro, Ofelia; Edl, Jennifer; Oursler, Stephanie; Chard-Bergstrom, Cindy; Andrews, Gordon; Kanehira, Tsutomu; Takekoshi, Susumu; Mernaugh, Ray

    2010-01-01

    Summary To gain insight into the mechanism by which angiotensin II type 2 receptor (AT2) regulates carcinogen-induced lung tumorigenesis, we have newly developed anti-AT2 single chain variable fragment (ScFv) antibodies using a rodent phage-displayed recombinant antibody library with various peptide fragments of the receptor protein, and investigated the expression of the AT2 receptor protein. The specificity of the antibodies was verified using AT2 over-expressing COS-7 cells and AT2 naturally expressing PC12W cells. In control wild type mouse lung, a stronger immunoreactivity was observed in bronchial epithelial cells. A moderate immunoreactivity was detected in pulmonary vascular walls and vascular endothelial cells. In the lungs possessing tobacco-specific nitrosamine (NNK)-induced tumors, significantly increased AT2 and AT1 immunostaining was observed in adenomatous lesions. These data suggest that the increase in both receptors' expression in the alveolar epithelial cells may be accompanied with the onset of NNK-induced tumorigenesis and hence play important roles in lung tumorigenesis. PMID:18438736

  5. Aromatic Anchor at an Invariant Hormone-Receptor Interface

    PubMed Central

    Pandyarajan, Vijay; Smith, Brian J.; Phillips, Nelson B.; Whittaker, Linda; Cox, Gabriella P.; Wickramasinghe, Nalinda; Menting, John G.; Wan, Zhu-li; Whittaker, Jonathan; Ismail-Beigi, Faramarz; Lawrence, Michael C.; Weiss, Michael A.

    2014-01-01

    Crystallographic studies of insulin bound to fragments of the insulin receptor have recently defined the topography of the primary hormone-receptor interface. Here, we have investigated the role of PheB24, an invariant aromatic anchor at this interface and site of a human mutation causing diabetes mellitus. An extensive set of B24 substitutions has been constructed and tested for effects on receptor binding. Although aromaticity has long been considered a key requirement at this position, MetB24 was found to confer essentially native affinity and bioactivity. Molecular modeling suggests that this linear side chain can serve as an alternative hydrophobic anchor at the hormone-receptor interface. These findings motivated further substitution of PheB24 by cyclohexanylalanine (Cha), which contains a nonplanar aliphatic ring. Contrary to expectations, [ChaB24]insulin likewise exhibited high activity. Furthermore, its resistance to fibrillation and the rapid rate of hexamer disassembly, properties of potential therapeutic advantage, were enhanced. The crystal structure of the ChaB24 analog, determined as an R6 zinc-stabilized hexamer at a resolution of 1.5 Å, closely resembles that of wild-type insulin. The nonplanar aliphatic ring exhibits two chair conformations with partial occupancies, each recapitulating the role of PheB24 at the dimer interface. Together, these studies have defined structural requirements of an anchor residue within the B24-binding pocket of the insulin receptor; similar molecular principles are likely to pertain to insulin-related growth factors. Our results highlight in particular the utility of nonaromatic side chains as probes of the B24 pocket and suggest that the nonstandard Cha side chain may have therapeutic utility. PMID:25305014

  6. Genotypic characterization of Indian isolates of infectious bursal disease virus strains by reverse transcription-polymerase chain reaction combined with restriction fragment length polymorphism analysis.

    PubMed

    Priyadharsini, C V; Senthilkumar, T M A; Raja, P; Kumanan, K

    2016-03-01

    The reverse transcription PCR (RT-PCR) combined with restriction fragment length polymorphism (RFLP) is used for the differentiation of classical virulent (cv), virulent (v) and very virulent (vv) strains of infectious bursal disease virus (IBDV) isolates from chicken bursal tissues in southern states of India. In the present study, six different isolates (MB11, HY12, PY12, BGE14, VCN14 and NKL14) of IBDV strains were subjected for genotyping along with vaccine virus (Georgia, intermediate strain) using RT-PCR for amplification of a 743 bp sequence in the hypervariable region of VP2 gene followed by restriction enzyme digestion with 5 different restriction enzymes (BspMI, SacI, HhaI, StuI and SspI). The RT-PCR products obtained from vvIBDV strains were digested by SspI enzyme except PY12, BGE14 and MB11 isolates. The SacI digested the isolate MB11, PY12 and the vaccine strain, but it did not cleave the very virulent isolates of IBDV. HhaI cleaved all the isolates with different restriction profile patterns. StuI digested all the vvIBDV isolates and BspMI was not able to differentiate field isolates from vaccine strain. Though RT-PCR combined with RFLP is a genotypic method, further confirmation of serotypes to distinguish the vvIBDV from cvIBDV has to be carried out using pathogenicity studies.

  7. Scale invariance in biophysics

    NASA Astrophysics Data System (ADS)

    Stanley, H. Eugene

    2000-06-01

    In this general talk, we offer an overview of some problems of interest to biophysicists, medical physicists, and econophysicists. These include DNA sequences, brain plaques in Alzheimer patients, heartbeat intervals, and time series giving price fluctuations in economics. These problems have the common feature that they exhibit features that appear to be scale invariant. Particularly vexing is the problem that some of these scale invariant phenomena are not stationary-their statistical properties vary from one time interval to the next or form one position to the next. We will discuss methods, such as wavelet methods and multifractal methods, to cope with these problems. .

  8. Theoretical studies on interactions between low energy electrons and protein-DNA fragments: valence anions of AT-amino acids side chain complexes.

    PubMed

    Szyperska, Anna; Gajewicz, Agnieszka; Mazurkiewicz, Kamil; Leszczynski, Jerzy; Rak, Janusz

    2011-11-21

    Electron attachment to trimeric complexes that mimic most frequent hydrogen bonding interactions between an amino acid side chain (AASC) and the Watson-Crick (WC) 9-methyladenine-1-methylthymine (MAMT) base pair has been studied at the B3LYP/6-31++G(d,p) level of theory. Although the neutral trimers will not occur in the gas phase due to unfavorable free energy of stabilization (G(stab)) they should form a protein-DNA complex where entropy changes related to formation of such a complex will more than balance its disadvantageous G(stab). The most stable neutrals possess an identical pattern of hydrogen bonds (HBs). In addition, the proton-acceptor (N7) and proton-donor (N10) atoms of adenine involved in those HBs are located in the main groove of DNA. All neutral structures support the adiabatically stable valence anions in which the excess electron is localized on a π* orbital of thymine. The vertical detachment energies (VDEs) of anions corresponding to the most stable neutrals are substantially smaller than that of the isolated WC MAMT base pair. Hence, electron transfer from the anionic thymine to the phosphate group and as a consequence formation of a single strand break (SSB) should proceed more efficiently in a protein-dsDNA complex than in the naked dsDNA as far as electron attachment to thymine is concerned.

  9. Riemann quasi-invariants

    SciTech Connect

    Pokhozhaev, Stanislav I

    2011-06-30

    The notion of Riemann quasi-invariants is introduced and their applications to several conservation laws are considered. The case of nonisentropic flow of an ideal polytropic gas is analysed in detail. Sufficient conditions for gradient catastrophes are obtained. Bibliography: 16 titles.

  10. Modular invariant inflation

    NASA Astrophysics Data System (ADS)

    Kobayashi, Tatsuo; Nitta, Daisuke; Urakawa, Yuko

    2016-08-01

    Modular invariance is a striking symmetry in string theory, which may keep stringy corrections under control. In this paper, we investigate a phenomenological consequence of the modular invariance, assuming that this symmetry is preserved as well as in a four dimensional (4D) low energy effective field theory. As a concrete setup, we consider a modulus field T whose contribution in the 4D effective field theory remains invariant under the modular transformation and study inflation drived by T. The modular invariance restricts a possible form of the scalar potenntial. As a result, large field models of inflation are hardly realized. Meanwhile, a small field model of inflation can be still accomodated in this restricted setup. The scalar potential traced during the slow-roll inflation mimics the hilltop potential Vht, but it also has a non-negligible deviation from Vht. Detecting the primordial gravitational waves predicted in this model is rather challenging. Yet, we argue that it may be still possible to falsify this model by combining the information in the reheating process which can be determined self-completely in this setup.

  11. Idiographic Measurement Invariance?

    ERIC Educational Resources Information Center

    Willoughby, Michael T.; Sideris, John

    2007-01-01

    In this article, the authors comment on Nesselroade, Gerstorf, Hardy, and Ram's efforts (this issue) to grapple with the challenge of accommodating idiographic assessment as it pertains to measurement invariance (MI). Although the authors are in complete agreement with the motivation for Nesselroade et al.'s work, the authors have concerns about…

  12. Magma Fragmentation

    NASA Astrophysics Data System (ADS)

    Gonnermann, Helge M.

    2015-05-01

    Magma fragmentation is the breakup of a continuous volume of molten rock into discrete pieces, called pyroclasts. Because magma contains bubbles of compressible magmatic volatiles, decompression of low-viscosity magma leads to rapid expansion. The magma is torn into fragments, as it is stretched into hydrodynamically unstable sheets and filaments. If the magma is highly viscous, resistance to bubble growth will instead lead to excess gas pressure and the magma will deform viscoelastically by fracturing like a glassy solid, resulting in the formation of a violently expanding gas-pyroclast mixture. In either case, fragmentation represents the conversion of potential energy into the surface energy of the newly created fragments and the kinetic energy of the expanding gas-pyroclast mixture. If magma comes into contact with external water, the conversion of thermal energy will vaporize water and quench magma at the melt-water interface, thus creating dynamic stresses that cause fragmentation and the release of kinetic energy. Lastly, shear deformation of highly viscous magma may cause brittle fractures and release seismic energy.

  13. Adiabatic invariance of oscillons/I -balls

    NASA Astrophysics Data System (ADS)

    Kawasaki, Masahiro; Takahashi, Fuminobu; Takeda, Naoyuki

    2015-11-01

    Real scalar fields are known to fragment into spatially localized and long-lived solitons called oscillons or I -balls. We prove the adiabatic invariance of the oscillons/I -balls for a potential that allows periodic motion even in the presence of non-negligible spatial gradient energy. We show that such a potential is uniquely determined to be the quadratic one with a logarithmic correction, for which the oscillons/I -balls are absolutely stable. For slightly different forms of the scalar potential dominated by the quadratic one, the oscillons/I -balls are only quasistable, because the adiabatic charge is only approximately conserved. We check the conservation of the adiabatic charge of the I -balls in numerical simulation by slowly varying the coefficient of logarithmic corrections. This unambiguously shows that the longevity of oscillons/I -balls is due to the adiabatic invariance.

  14. Measurement Invariance versus Selection Invariance: Is Fair Selection Possible?

    ERIC Educational Resources Information Center

    Borsman, Denny; Romeijn, Jan-Willem; Wicherts, Jelte M.

    2008-01-01

    This article shows that measurement invariance (defined in terms of an invariant measurement model in different groups) is generally inconsistent with selection invariance (defined in terms of equal sensitivity and specificity across groups). In particular, when a unidimensional measurement instrument is used and group differences are present in…

  15. Fragmentation of parton jets at small x

    SciTech Connect

    Kirschner, R.

    1985-08-01

    The parton fragmentation function is calculated in the region of small x in the doubly logarithmic approximation of QCD. For this, the method of separating the softest particle, which has hitherto been applied only in the Regge kinematic region, is developed. Simple arguments based on unitarity and gauge invariance are used to derive the well known condition of ordering of the emission angles.

  16. DNA vaccines targeting heavy chain C-terminal fragments of Clostridium botulinum neurotoxin serotypes A, B, and E induce potent humoral and cellular immunity and provide protection from lethal toxin challenge.

    PubMed

    Scott, Veronica L; Villarreal, Daniel O; Hutnick, Natalie A; Walters, Jewell N; Ragwan, Edwin; Bdeir, Khalil; Yan, Jian; Sardesai, Niranjan Y; Finnefrock, Adam C; Casimiro, Danilo R; Weiner, David B

    2015-01-01

    Botulinum neurotoxins (BoNTs) are deadly, toxic proteins produced by the bacterium Clostridium botulinum that can cause significant diseases in humans. The use of the toxic substances as potential bioweapons has raised concerns by the Centers for Disease Control and Prevention and the United States Military. Currently, there is no licensed vaccine to prevent botulinum intoxication. Here we present an immunogenicity study to evaluate the efficacy of novel monovalent vaccines and a trivalent cocktail DNA vaccine targeting the heavy chain C-terminal fragments of Clostridium botulinum neurotoxin serotypes A, B, and E. These synthetic DNA vaccines induced robust humoral and polyfunctional CD4(+) T-cell responses which fully protected animals against lethal challenge after just 2 immunizations. In addition, naïve animals administered immunized sera mixed with the lethal neurotoxin were 100% protected against intoxication. The data demonstrate the protective efficacy induced by a combinative synthetic DNA vaccine approach. This study has importance for the development of vaccines that provide protective immunity against C. botulinum neurotoxins and other toxins.

  17. The identification and differentiation of the Candida parapsilosis complex species by polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer region of the rDNA

    PubMed Central

    Barbedo, Leonardo Silva; Figueiredo-Carvalho, Maria Helena Galdino; Muniz, Mauro de Medeiros; Zancopé-Oliveira, Rosely Maria

    2016-01-01

    Currently, it is accepted that there are three species that were formerly grouped under Candida parapsilosis: C. para- psilosis sensu stricto, Candida orthopsilosis, andCandida metapsilosis. In fact, the antifungal susceptibility profiles and distinct virulence attributes demonstrate the differences in these nosocomial pathogens. An accurate, fast, and economical identification of fungal species has been the main goal in mycology. In the present study, we searched sequences that were available in the GenBank database in order to identify the complete sequence for the internal transcribed spacer (ITS)1-5.8S-ITS2 region, which is comprised of the forward and reverse primers ITS1 and ITS4. Subsequently, an in silico polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was performed to differentiate the C. parapsilosis complex species. Ninety-eight clinical isolates from patients with fungaemia were submitted for analysis, where 59 isolates were identified as C. parapsilosis sensu stricto, 37 were identified as C. orthopsilosis, and two were identified as C. metapsilosis. PCR-RFLP quickly and accurately identified C. parapsilosis complex species, making this method an alternative and routine identification system for use in clinical mycology laboratories. PMID:27074256

  18. Efficient silkworm expression of single-chain variable fragment antibody against ginsenoside Re using Bombyx mori nucleopolyhedrovirus bacmid DNA system and its application in enzyme-linked immunosorbent assay for quality control of total ginsenosides.

    PubMed

    Sakamoto, Seiichi; Pongkitwitoon, Benyakan; Nakamura, Seiko; Maenaka, Katsumi; Tanaka, Hiroyuki; Morimoto, Satoshi

    2010-09-01

    A single-chain variable fragment (scFv) antibody against ginsenoside Re (G-Re) have been successfully expressed in the silkworm larvae using Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid DNA system. The baculovirus donor vector for expression of scFv against G-Re (GRe-scFv) was constructed to contain honeybee melittin signal sequence to accelerate secretion of the recombinant GRe-scFv into the haemolymph of silkworm larvae. Functional recombinant GRe-scFv was purified by cation exchange chromatography followed by immobilized metal ion affinity chromatography. The yield of purified GRe-scFv was 6.5 mg per 13 silkworm larvae, which is equivalent to 650 mg/l of the haemolymph, exhibiting extremely higher yield than that expressed in Escherichia coli (1.7 mg/l of culture medium). It was revealed from characterization that GRe-scFv retained similar characteristic of the parental monoclonal antibody (MAb) against G-Re (MAb-4G10), making it possible to develop indirect competitive enzyme-linked immunosorbent assay (icELISA) for quality control of total ginsenosides in various ginsengs. The detectable range for calibration of G-Re by developed icELISA shows 0.05-10 microg/ml. These results clearly suggested that the silkworm expression system is quite useful for the expression of functional scFv that frequently required time- and cost-consuming re-folding when it expressed in E. coli. PMID:20592135

  19. DNA vaccines targeting heavy chain C-terminal fragments of Clostridium botulinum neurotoxin serotypes A, B, and E induce potent humoral and cellular immunity and provide protection from lethal toxin challenge

    PubMed Central

    Scott, Veronica L; Villarreal, Daniel O; Hutnick, Natalie A; Walters, Jewell N; Ragwan, Edwin; Bdeir, Khalil; Yan, Jian; Sardesai, Niranjan Y; Finnefrock, Adam C; Casimiro, Danilo R; Weiner, David B

    2015-01-01

    Botulinum neurotoxins (BoNTs) are deadly, toxic proteins produced by the bacterium Clostridium botulinum that can cause significant diseases in humans. The use of the toxic substances as potential bioweapons has raised concerns by the Centers for Disease Control and Prevention and the United States Military. Currently, there is no licensed vaccine to prevent botulinum intoxication. Here we present an immunogenicity study to evaluate the efficacy of novel monovalent vaccines and a trivalent cocktail DNA vaccine targeting the heavy chain C-terminal fragments of Clostridium botulinum neurotoxin serotypes A, B, and E. These synthetic DNA vaccines induced robust humoral and polyfunctional CD4+ T-cell responses which fully protected animals against lethal challenge after just 2 immunizations. In addition, naïve animals administered immunized sera mixed with the lethal neurotoxin were 100% protected against intoxication. The data demonstrate the protective efficacy induced by a combinative synthetic DNA vaccine approach. This study has importance for the development of vaccines that provide protective immunity against C. botulinum neurotoxins and other toxins. PMID:26158319

  20. The identification and differentiation of the Candida parapsilosis complex species by polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer region of the rDNA.

    PubMed

    Barbedo, Leonardo Silva; Figueiredo-Carvalho, Maria Helena Galdino; Muniz, Mauro de Medeiros; Zancopé-Oliveira, Rosely Maria

    2016-04-01

    Currently, it is accepted that there are three species that were formerly grouped under Candida parapsilosis: C. para- psilosis sensu stricto, Candida orthopsilosis, and Candida metapsilosis. In fact, the antifungal susceptibility profiles and distinct virulence attributes demonstrate the differences in these nosocomial pathogens. An accurate, fast, and economical identification of fungal species has been the main goal in mycology. In the present study, we searched sequences that were available in the GenBank database in order to identify the complete sequence for the internal transcribed spacer (ITS)1-5.8S-ITS2 region, which is comprised of the forward and reverse primers ITS1 and ITS4. Subsequently, an in silico polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was performed to differentiate the C. parapsilosis complex species. Ninety-eight clinical isolates from patients with fungaemia were submitted for analysis, where 59 isolates were identified as C. parapsilosis sensu stricto, 37 were identified as C. orthopsilosis, and two were identified as C. metapsilosis. PCR-RFLP quickly and accurately identified C. parapsilosis complex species, making this method an alternative and routine identification system for use in clinical mycology laboratories.

  1. Cell bank characterization and fermentation optimization for production of recombinant heavy chain C-terminal fragment of botulinum neurotoxin serotype E (rBoNTE(H(c)): antigen E) by Pichia pastoris.

    PubMed

    Sinha, Jayanta; Inan, Mehmet; Fanders, Sarah; Taoka, Shinichi; Gouthro, Mark; Swanson, Todd; Barent, Rick; Barthuli, Ardis; Loveless, Bonnie M; Smith, Leonard A; Smith, Theresa; Henderson, Ian; Ross, John; Meagher, Michael M

    2007-01-10

    A process was developed for production of a candidate vaccine antigen, recombinant C-terminal heavy chain fragment of the botulinum neurotoxin serotype E, rBoNTE(H(c)) in Pichia pastoris. P. pastoris strain GS115 was transformed with the rBoNTE(H(c)) gene inserted into pHILD4 Escherichia coli-P. pastoris shuttle plasmid. The clone was characterized for genetic stability, copy number, and BoNTE(H(c)) sequence. Expression of rBoNTE(H(c)) from the Mut(+) HIS4 clone was confirmed in the shake-flask, prior to developing a fed-batch fermentation process at 5 and 19 L scale. The fermentation process consists of a glycerol growth phase in batch and fed-batch mode using a defined medium followed by a glycerol/methanol transition phase for adaptation to growth on methanol and a methanol induction phase resulting in the production of rBoNTE(H(c)). Specific growth rate, ratio of growth to induction phase, and time of induction were critical for optimal rBoNTE(H(c)) production and minimal proteolytic degradation. A computer-controlled exponential growth model was used for process automation and off-gas analysis was used for process monitoring. The optimized process had an induction time of 9 h on methanol and produced up to 3 mg of rBoNTE(H(c)) per gram wet cell mass as determined by HPLC and Western blot analysis.

  2. Expression of V(H)-linker-V(L) orientation-dependent single-chain Fv antibody fragment derived from hybridoma 2E6 against aflatoxin B1 in Escherichia coli.

    PubMed

    Liu, Aiping; Ye, Yang; Chen, Weifeng; Wang, Xiaohong; Chen, Fusheng

    2015-02-01

    Aflatoxin B1 (AFB1) is a toxic secondary metabolic product, which threatens human and animal health. Antibody is a key factor for immunoassay against toxic stuff like AFB1, and single-chain Fv antibody fragment (scFv) has become a popular format of genetically engineered antibody. In this study, four hybridoma cell lines against AFB1 were obtained, and then scFvs 2E6 derived from hybridoma cell line 2E6 were constructed in different V(H)/V(L) orientations. Subsequently, scFvs 2E6 were expressed in E. coli BL21(DE3) mainly in the form of inclusion body. SDS-PAGE, Western blot and ELISA were employed to characterize scFvs 2E6. The results revealed that the yield of inclusion body of scFvs 2E6 in either V(H)/V(L) orientation was similar; however, only the scFv in V(H)-linker-V(L) orientation showed anti-AFB1 bioactivity after refolding. The present study underscores the importance of choosing optimal V(H)/V(L) orientation for scFv construction, and scFv may be favorable for immunoassays in food industry. PMID:25540048

  3. Gauge invariant quantum cosmology

    NASA Technical Reports Server (NTRS)

    Berger, Beverly K.

    1987-01-01

    The study of boundary conditions, the Hamiltonian constraint, reparameterization-invariance, and quantum dynamics, is presently approached by means of the path-integral quantization of minisuperspace models. The separation of the wave functions for expansion and contraction by the Feynman boundary conditions is such that there can be no interference between them. This is implemented by the choice of a contour in the complex plane, in order to define the phase of the square-root Arnowitt, Deser, and Misner (1960) Hamiltonian for expansion, collapse, and the classically forbidden region.

  4. Entanglement, Invariants, and Phylogenetics

    NASA Astrophysics Data System (ADS)

    Sumner, J. G.

    2007-10-01

    This thesis develops and expands upon known techniques of mathematical physics relevant to the analysis of the popular Markov model of phylogenetic trees required in biology to reconstruct the evolutionary relationships of taxonomic units from biomolecular sequence data. The techniques of mathematical physics are plethora and have been developed for some time. The Markov model of phylogenetics and its analysis is a relatively new technique where most progress to date has been achieved by using discrete mathematics. This thesis takes a group theoretical approach to the problem by beginning with a remarkable mathematical parallel to the process of scattering in particle physics. This is shown to equate to branching events in the evolutionary history of molecular units. The major technical result of this thesis is the derivation of existence proofs and computational techniques for calculating polynomial group invariant functions on a multi-linear space where the group action is that relevant to a Markovian time evolution. The practical results of this thesis are an extended analysis of the use of invariant functions in distance based methods and the presentation of a new reconstruction technique for quartet trees which is consistent with the most general Markov model of sequence evolution.

  5. Wall-crossing invariants: from quantum mechanics to knots

    SciTech Connect

    Galakhov, D. E-mail: galakhov@physics.rutgers.edu; Mironov, A. Morozov, A.

    2015-03-15

    We offer a pedestrian-level review of the wall-crossing invariants. The story begins from the scattering theory in quantum mechanics where the spectrum reshuffling can be related to permutations of S-matrices. In nontrivial situations, starting from spin chains and matrix models, the S-matrices are operatorvalued and their algebra is described in terms of R- and mixing (Racah) U-matrices. Then the Kontsevich-Soibelman (KS) invariants are nothing but the standard knot invariants made out of these data within the Reshetikhin-Turaev-Witten approach. The R and Racah matrices acquire a relatively universal form in the semiclassical limit, where the basic reshufflings with the change of moduli are those of the Stokes line. Natural from this standpoint are matrices provided by the modular transformations of conformal blocks (with the usual identification R = T and U = S), and in the simplest case of the first degenerate field (2, 1), when the conformal blocks satisfy a second-order Shrödinger-like equation, the invariants coincide with the Jones (N = 2) invariants of the associated knots. Another possibility to construct knot invariants is to realize the cluster coordinates associated with reshufflings of the Stokes lines immediately in terms of check-operators acting on solutions of the Knizhnik-Zamolodchikov equations. Then the R-matrices are realized as products of successive mutations in the cluster algebra and are manifestly described in terms of quantum dilogarithms, ultimately leading to the Hikami construction of knot invariants.

  6. Invariants from classical field theory

    SciTech Connect

    Diaz, Rafael; Leal, Lorenzo

    2008-06-15

    We introduce a method that generates invariant functions from perturbative classical field theories depending on external parameters. By applying our methods to several field theories such as Abelian BF, Chern-Simons, and two-dimensional Yang-Mills theory, we obtain, respectively, the linking number for embedded submanifolds in compact varieties, the Gauss' and the second Milnor's invariant for links in S{sup 3}, and invariants under area-preserving diffeomorphisms for configurations of immersed planar curves.

  7. Correlation functions in conformal invariant stochastic processes

    NASA Astrophysics Data System (ADS)

    Alcaraz, Francisco C.; Rittenberg, Vladimir

    2015-11-01

    We consider the problem of correlation functions in the stationary states of one-dimensional stochastic models having conformal invariance. If one considers the space dependence of the correlators, the novel aspect is that although one considers systems with periodic boundary conditions, the observables are described by boundary operators. From our experience with equilibrium problems one would have expected bulk operators. Boundary operators have correlators having critical exponents being half of those of bulk operators. If one studies the space-time dependence of the two-point function, one has to consider one boundary and one bulk operators. The Raise and Peel model has conformal invariance as can be shown in the spin 1/2 basis of the Hamiltonian which gives the time evolution of the system. This is an XXZ quantum chain with twisted boundary condition and local interactions. This Hamiltonian is integrable and the spectrum is known in the finite-size scaling limit. In the stochastic base in which the process is defined, the Hamiltonian is not local anymore. The mapping into an SOS model, helps to define new local operators. As a byproduct some new properties of the SOS model are conjectured. The predictions of conformal invariance are discussed in the new framework and compared with Monte Carlo simulations.

  8. Form factors in quantum integrable models with GL(3)-invariant R-matrix

    NASA Astrophysics Data System (ADS)

    Pakuliak, S.; Ragoucy, E.; Slavnov, N. A.

    2014-04-01

    We study integrable models solvable by the nested algebraic Bethe ansatz and possessing GL(3)-invariant R-matrix. We obtain determinant representations for form factors of off-diagonal entries of the monodromy matrix. These representations can be used for the calculation of form factors and correlation functions of the XXX SU(3)-invariant Heisenberg chain.

  9. Purification optimization for a recombinant single-chain variable fragment against type 1 insulin-like growth factor receptor (IGF-1R) by using design of experiment (DoE).

    PubMed

    Song, Yong-Hong; Sun, Xue-Wen; Jiang, Bo; Liu, Ji-En; Su, Xian-Hui

    2015-12-01

    Design of experiment (DoE) is a statistics-based technique for experimental design that could overcome the shortcomings of traditional one-factor-at-a-time (OFAT) approach for protein purification optimization. In this study, a DoE approach was applied for optimizing purification of a recombinant single-chain variable fragment (scFv) against type 1 insulin-like growth factor receptor (IGF-1R) expressed in Escherichia coli. In first capture step using Capto L, a 2-level fractional factorial analysis and successively a central composite circumscribed (CCC) design were used to identify the optimal elution conditions. Two main effects, pH and trehalose, were identified, and high recovery (above 95%) and low aggregates ratio (below 10%) were achieved at the pH range from 2.9 to 3.0 with 32-35% (w/v) trehalose added. In the second step using cation exchange chromatography, an initial screening of media and elution pH and a following CCC design were performed, whereby the optimal selectivity of the scFv was obtained on Capto S at pH near 6.0, and the optimal conditions for fulfilling high DBC and purity were identified as pH range of 5.9-6.1 and loading conductivity range of 5-12.5 mS/cm. Upon a further gel filtration, the final purified scFv with a purity of 98% was obtained. Finally, the optimized conditions were verified by a 20-fold scale-up experiment. The purities and yields of intermediate and final products all fell within the regions predicted by DoE approach, suggesting the robustness of the optimized conditions. We proposed that the DoE approach described here is also applicable in production of other recombinant antibody constructs.

  10. A Discussion of Population Invariance

    ERIC Educational Resources Information Center

    Brennan, Robert L.

    2008-01-01

    The discussion here covers five articles that are linked in the sense that they all treat population invariance. This discussion of population invariance is a somewhat broader treatment of the subject than simply a discussion of these five articles. In particular, occasional reference is made to publications other than those in this issue. The…

  11. Invariant Measures for Cherry Flows

    NASA Astrophysics Data System (ADS)

    Saghin, Radu; Vargas, Edson

    2013-01-01

    We investigate the invariant probability measures for Cherry flows, i.e. flows on the two-torus which have a saddle, a source, and no other fixed points, closed orbits or homoclinic orbits. In the case when the saddle is dissipative or conservative we show that the only invariant probability measures are the Dirac measures at the two fixed points, and the Dirac measure at the saddle is the physical measure. In the other case we prove that there exists also an invariant probability measure supported on the quasi-minimal set, we discuss some situations when this other invariant measure is the physical measure, and conjecture that this is always the case. The main techniques used are the study of the integrability of the return time with respect to the invariant measure of the return map to a closed transversal to the flow, and the study of the close returns near the saddle.

  12. Physical Invariants of Intelligence

    NASA Technical Reports Server (NTRS)

    Zak, Michail

    2010-01-01

    A program of research is dedicated to development of a mathematical formalism that could provide, among other things, means by which living systems could be distinguished from non-living ones. A major issue that arises in this research is the following question: What invariants of mathematical models of the physics of systems are (1) characteristic of the behaviors of intelligent living systems and (2) do not depend on specific features of material compositions heretofore considered to be characteristic of life? This research at earlier stages has been reported, albeit from different perspectives, in numerous previous NASA Tech Briefs articles. To recapitulate: One of the main underlying ideas is to extend the application of physical first principles to the behaviors of living systems. Mathematical models of motor dynamics are used to simulate the observable physical behaviors of systems or objects of interest, and models of mental dynamics are used to represent the evolution of the corresponding knowledge bases. For a given system, the knowledge base is modeled in the form of probability distributions and the mental dynamics is represented by models of the evolution of the probability densities or, equivalently, models of flows of information. At the time of reporting the information for this article, the focus of this research was upon the following aspects of the formalism: Intelligence is considered to be a means by which a living system preserves itself and improves its ability to survive and is further considered to manifest itself in feedback from the mental dynamics to the motor dynamics. Because of the feedback from the mental dynamics, the motor dynamics attains quantum-like properties: The trajectory of the physical aspect of the system in the space of dynamical variables splits into a family of different trajectories, and each of those trajectories can be chosen with a probability prescribed by the mental dynamics. From a slightly different perspective

  13. Stabilization of antibody fragments in adverse environments.

    PubMed

    Dooley, H; Grant, S D; Harris, W J; Porter, A J

    1998-08-01

    Antibody fragments have the potential to be used as sensitive and specific binding agents in a broad range of industrial applications. Genetic manipulation has been used to design a series of antibody fragment configurations with a flexible linker and/or a disulphide bond between the heavy chain and light chain of an antibody fragment against the herbicide atrazine. The thermostability and stability to a range of denaturants, polar and non-polar solvents, surfactants and proteases have been compared. It has been found that a novel antibody fragment construct (STAB: stabilized antibody) containing both a flexible linker and a disulphide bond can be effectively produced and shows greatly improved stability in these diverse environments. These STABs should be useful in environmental diagnostics and remediation, and may provide a generic approach for stabilizing antibody fragments in formulations containing detergents and penetrants for topical application in the pharmaceutical and cosmetic industries.

  14. The NJL Model for Quark Fragmentation Functions

    SciTech Connect

    T. Ito, W. Bentz, I. Cloet, A W Thomas, K. Yazaki

    2009-10-01

    A description of fragmentation functions which satisfy the momentum and isospin sum rules is presented in an effective quark theory. Concentrating on the pion fragmentation function, we first explain the reason why the elementary (lowest order) fragmentation process q → qπ is completely inadequate to describe the empirical data, although the “crossed” process π → qq describes the quark distribution functions in the pion reasonably well. Then, taking into account cascade-like processes in a modified jet-model approach, we show that the momentum and isospin sum rules can be satisfied naturally without introducing any ad-hoc parameters. We present numerical results for the Nambu-Jona-Lasinio model in the invariant mass regularization scheme, and compare the results with the empirical parametrizations. We argue that this NJL-jet model provides a very useful framework to calculate the fragmentation functions in an effective chiral quark theory.

  15. Shaping propagation invariant laser beams

    NASA Astrophysics Data System (ADS)

    Soskind, Michael; Soskind, Rose; Soskind, Yakov

    2015-11-01

    Propagation-invariant structured laser beams possess several unique properties and play an important role in various photonics applications. The majority of propagation invariant beams are produced in the form of laser modes emanating from stable laser cavities. Therefore, their spatial structure is limited by the intracavity mode formation. We show that several types of anamorphic optical systems (AOSs) can be effectively employed to shape laser beams into a variety of propagation invariant structured fields with different shapes and phase distributions. We present a propagation matrix approach for designing AOSs and defining mode-matching conditions required for preserving propagation invariance of the output shaped fields. The propagation matrix approach was selected, as it provides a more straightforward approach in designing AOSs for shaping propagation-invariant laser beams than the alternative technique based on the Gouy phase evolution, especially in the case of multielement AOSs. Several practical configurations of optical systems that are suitable for shaping input laser beams into a diverse variety of structured propagation invariant laser beams are also presented. The laser beam shaping approach was applied by modeling propagation characteristics of several input laser beam types, including Hermite-Gaussian, Laguerre-Gaussian, and Ince-Gaussian structured field distributions. The influence of the Ince-Gaussian beam semifocal separation parameter and the azimuthal orientation between the input laser beams and the AOSs onto the resulting shape of the propagation invariant laser beams is presented as well.

  16. Invariant manifolds and global bifurcations.

    PubMed

    Guckenheimer, John; Krauskopf, Bernd; Osinga, Hinke M; Sandstede, Björn

    2015-09-01

    Invariant manifolds are key objects in describing how trajectories partition the phase spaces of a dynamical system. Examples include stable, unstable, and center manifolds of equilibria and periodic orbits, quasiperiodic invariant tori, and slow manifolds of systems with multiple timescales. Changes in these objects and their intersections with variation of system parameters give rise to global bifurcations. Bifurcation manifolds in the parameter spaces of multi-parameter families of dynamical systems also play a prominent role in dynamical systems theory. Much progress has been made in developing theory and computational methods for invariant manifolds during the past 25 years. This article highlights some of these achievements and remaining open problems. PMID:26428557

  17. Invariant manifolds and global bifurcations.

    PubMed

    Guckenheimer, John; Krauskopf, Bernd; Osinga, Hinke M; Sandstede, Björn

    2015-09-01

    Invariant manifolds are key objects in describing how trajectories partition the phase spaces of a dynamical system. Examples include stable, unstable, and center manifolds of equilibria and periodic orbits, quasiperiodic invariant tori, and slow manifolds of systems with multiple timescales. Changes in these objects and their intersections with variation of system parameters give rise to global bifurcations. Bifurcation manifolds in the parameter spaces of multi-parameter families of dynamical systems also play a prominent role in dynamical systems theory. Much progress has been made in developing theory and computational methods for invariant manifolds during the past 25 years. This article highlights some of these achievements and remaining open problems.

  18. Invariant manifolds and global bifurcations

    NASA Astrophysics Data System (ADS)

    Guckenheimer, John; Krauskopf, Bernd; Osinga, Hinke M.; Sandstede, Björn

    2015-09-01

    Invariant manifolds are key objects in describing how trajectories partition the phase spaces of a dynamical system. Examples include stable, unstable, and center manifolds of equilibria and periodic orbits, quasiperiodic invariant tori, and slow manifolds of systems with multiple timescales. Changes in these objects and their intersections with variation of system parameters give rise to global bifurcations. Bifurcation manifolds in the parameter spaces of multi-parameter families of dynamical systems also play a prominent role in dynamical systems theory. Much progress has been made in developing theory and computational methods for invariant manifolds during the past 25 years. This article highlights some of these achievements and remaining open problems.

  19. Generating maps, invariant manifolds, conjugacy

    NASA Astrophysics Data System (ADS)

    Chaperon, Marc

    2015-01-01

    The idea of generating functions and maps is presented, first in global symplectic geometry and then in the theory of invariant manifolds, as introduced by McGehee and Sander in 1996. Their result on the stable manifold theorem is generalised and simplified; the proofs no longer use any functional analysis. Then comes an original "non-autonomous" version of the previous results, yielding-besides Pesin's invariant laminations-seemingly unrelated results on invariant manifolds and conjugacies, presented in the end after a basic example.

  20. Preparation of the Fv fragment from a short-chain mouse IgG2a anti-dansyl monoclonal antibody and use of selectively deuterated Fv analogues for two-dimensional sup 1 H NMR analyses fo the antigen-antibody interactions

    SciTech Connect

    Takahashi, Hideo; Igarashi, Takako; Shimada, Ichio; Arata, Yoji )

    1991-03-19

    The Fv fragment, a univalent antigen-binding unit with a molecular weight of 25,000, has successfully been prepared in high yield by limited proteolysis with clostripain of a short-chain mouse IgG2a anti-dansyl monoclonal antibody in which the entire C{sub H}1 domain is deleted. The Fv fragment obtained is stable at room temperature and retains its full antigen-binding capability. It has been shown that selective deuterium labeling of the Fv fragment, which is half the size of the Fab fragment, provides {sup 1}H NMR spectral data at a sufficient resolution for a detailed structural analysis of the antigen-combining site. NOESY spectra of an Fv analogue, in which all aromatic protons except for His C2{prime}-H and Tyr C3{prime},5{prime}-H had been deuterated, were measured in the presence of varying amounts of dansyl-L-lysine. On the basis of the NOESY data obtained, it was possible to assign all the ring proton resonances for the dansly group that is bound to the Fv fragment. It was also possible to obtain information about His and Tyr residues of the Fv fragment in the absence and presence of the antigen. On the basis of the NMR data obtained, the authors have shown that at least two Tyr residues along with one of the amide groups are directly involved in antigen binding. The mode of interaction of the dansyl ring with these residues in the Fv fragment has briefly been discussed.

  1. Hidden scale invariance of metals

    NASA Astrophysics Data System (ADS)

    Hummel, Felix; Kresse, Georg; Dyre, Jeppe C.; Pedersen, Ulf R.

    2015-11-01

    Density functional theory (DFT) calculations of 58 liquid elements at their triple point show that most metals exhibit near proportionality between the thermal fluctuations of the virial and the potential energy in the isochoric ensemble. This demonstrates a general "hidden" scale invariance of metals making the condensed part of the thermodynamic phase diagram effectively one dimensional with respect to structure and dynamics. DFT computed density scaling exponents, related to the Grüneisen parameter, are in good agreement with experimental values for the 16 elements where reliable data were available. Hidden scale invariance is demonstrated in detail for magnesium by showing invariance of structure and dynamics. Computed melting curves of period three metals follow curves with invariance (isomorphs). The experimental structure factor of magnesium is predicted by assuming scale invariant inverse power-law (IPL) pair interactions. However, crystal packings of several transition metals (V, Cr, Mn, Fe, Nb, Mo, Ta, W, and Hg), most post-transition metals (Ga, In, Sn, and Tl), and the metalloids Si and Ge cannot be explained by the IPL assumption. The virial-energy correlation coefficients of iron and phosphorous are shown to increase at elevated pressures. Finally, we discuss how scale invariance explains the Grüneisen equation of state and a number of well-known empirical melting and freezing rules.

  2. Crater chains on Mercury

    NASA Astrophysics Data System (ADS)

    Shevchenko, V.; Skobeleva, T.

    After discovery of disruption comet Shoemaker-Levy 9 into fragment train before it's collision with Jupiter there was proposed that linear crater chains on the large satellites of Jupiter and on the Moon are impact scars of past tidally disrupted comets.It's known that radar images have revealed the possible presence of water ice deposits in polar regions of Mercury. Impacts by a few large comets seem to provide the best explanation for both the amount and cleanliness of the ice deposits on Mercury because they have a larger volatile content that others external sources, for example, asteroid. A number of crater chains on the surface of Mercury are most likely the impact tracks of "fragment trains" of comets tidally disrupted by Sun or by Mercury and are not secondary craters. Mariner 10 image set (the three Mariner 10 flybys in 1974-1975) was used to recognize the crater chains these did not associate with secondary crater ejecta from observed impact structures. As example, it can be shown such crater chain located near crater Imhotep and crater Ibsen (The Kuiper Quadrangle of Mercury). Resolution of the Mariner 10 image is about 0.54 km/pixel. The crater chain is about 50 km long. It was found a similar crater chain inside large crater Sophocles (The Tolstoj Quadrangle of Mercury). The image resolution is about 1.46 km/pixel. The chain about 50 km long is located in northen part of the crater. Image resolution limits possibility to examine the form of craters strongly. It seems the craters in chains have roughly flat floor and smooth form. Most chain craters are approximately circular. It was examined many images from the Mariner 10 set and there were identified a total 15 crater chains and were unable to link any of these directly to any specific large crater associated with ejecta deposits. Chain craters are remarkably aligned. All distinguished crater chains are superposed on preexisting formations. A total of 127 craters were identified in the 15 recognized

  3. CPT violation implies violation of Lorentz invariance.

    PubMed

    Greenberg, O W

    2002-12-01

    A interacting theory that violates CPT invariance necessarily violates Lorentz invariance. On the other hand, CPT invariance is not sufficient for out-of-cone Lorentz invariance. Theories that violate CPT by having different particle and antiparticle masses must be nonlocal. PMID:12484997

  4. Weyl invariance with a nontrivial mass scale

    NASA Astrophysics Data System (ADS)

    Álvarez, Enrique; González-Martín, Sergio

    2016-09-01

    A theory with a mass scale and yet Weyl invariant is presented. The theory is not invariant under all diffeomorphisms but only under transverse ones. This is the reason why Weyl invariance does not imply scale invariance in a free falling frame. Physical implications of this framework are discussed.

  5. CPT violation implies violation of Lorentz invariance.

    PubMed

    Greenberg, O W

    2002-12-01

    A interacting theory that violates CPT invariance necessarily violates Lorentz invariance. On the other hand, CPT invariance is not sufficient for out-of-cone Lorentz invariance. Theories that violate CPT by having different particle and antiparticle masses must be nonlocal.

  6. Baculovirus display of functional antibody Fab fragments.

    PubMed

    Takada, Shinya; Ogawa, Takafumi; Matsui, Kazusa; Suzuki, Tasuku; Katsuda, Tomohisa; Yamaji, Hideki

    2015-08-01

    The generation of a recombinant baculovirus that displays antibody Fab fragments on the surface was investigated. A recombinant baculovirus was engineered so that the heavy chain (Hc; Fd fragment) of a mouse Fab fragment was expressed as a fusion to the N-terminus of baculovirus gp64, while the light chain of the Fab fragment was simultaneously expressed as a secretory protein. Following infection of Sf9 insect cells with the recombinant baculovirus, the culture supernatant was analyzed by enzyme-linked immunosorbent assay using antigen-coated microplates and either an anti-mouse IgG or an anti-gp64 antibody. A relatively strong signal was obtained in each case, showing antigen-binding activity in the culture supernatant. In western blot analysis of the culture supernatant using the anti-gp64 antibody, specific protein bands were detected at an electrophoretic mobility that coincided with the molecular weight of the Hc-gp64 fusion protein as well as that of gp64. Flow cytometry using a fluorescein isothiocyanate-conjugated antibody specific to mouse IgG successfully detected the Fab fragments on the surface of the Sf9 cells. These results suggest that immunologically functional antibody Fab fragments can be displayed on the surface of baculovirus particles, and that a fluorescence-activated cell sorter with a fluorescence-labeled antigen can isolate baculoviruses displaying specific Fab fragments. This successful baculovirus display of antibody Fab fragments may offer a novel approach for the efficient selection of specific antibodies.

  7. Altered specificity of single-chain antibody fragments bound to pandemic H1N1-2009 influenza virus after conversion of the phage-bound to the soluble form

    PubMed Central

    2012-01-01

    Background In 2009, a novel influenza A/H1N1 virus (H1N1pdm) quickly spread worldwide and co-circulated with then-existing seasonal H1N1 virus (sH1N1). Distinguishing between these 2 viruses was necessary to better characterize the epidemiological properties of the emergent virus, including transmission patterns, pathogenesis, and anti-influenza drug resistance. This situation prompted us to develop a point-of-care virus differentiation system before entering the 2009–2010 influenza season. Aiming to establish H1N1pdm-specific detection tools rapidly, we employed phage display libraries to select H1N1pdm-specific single-chain variable fragments (scFvs). Findings Human single-fold scFv libraries (Tomlinson I + J) underwent selection for the ability to bind H1N1pdm virus particles. Three rounds of panning brought 1152 phage-bound scFvs, of which 58 clones reacted with H1N1pdm specifically or preferentially over sH1N1 in an enzyme-linked immunosorbent assay (ELISA). After conversion of the scFvs to soluble form, 7 clones demonstrating high/stable expression were finally obtained. However, all the soluble scFvs except No. 29 were found to have lost their specificity/preference for H1N1pdm in ELISA. The specificity/preference of No. 29 was also confirmed by immunofluorescence assay and immunoprecipitation, and the viral nucleoprotein was identified by ELISA as its target protein. The change in specificity associated with scFv conversion from phage-bound to soluble form could be due to loss of phage scaffold pIII protein, which likely provides structural support for the scFv antigen-binding site. It is also possible that the similar antigenic properties of H1N1pdm and sH1N1 led to the observed alterations in scFv specificity. Discussion Using a phage display library, we obtained 7 soluble scFv clones reactive against H1N1pdm; however, only 1 showed specificity/preference toward H1N1pdm. Our results confirmed that using phage display libraries was highly

  8. Human immunoglobulin subclasses. Partial amino acid sequence of the constant region of a γ4 chain

    PubMed Central

    Pink, J. R. L.; Buttery, S. H.; De Vries, G. M.; Milstein, C.

    1970-01-01

    The heavy chain of a human myeloma protein (Vin) belonging to the γ4 subclass was subjected to tryptic digestion after reduction and carboxymethylation. Cyanogen bromide fragments were also prepared and all 19 tryptic peptides that account for one of them (the Fc-like fragment) were studied. Selected peptic peptides were isolated and provided evidence for the order of 15 of the tryptic peptides. In addition the sequence of two large peptic peptides derived from two sections of the molecule including all the interchain bridges is presented. Comparison with published data on other chains allows us to propose a sequence of γ4 chains that extends from just before the presumed starting point of the invariable region (at about residue 113) to the C-terminal end of the chain (approx. residue 446), except for a section of about 50 residues. The results of the comparison suggest that the immunoglobulin subclasses have a recent independent evolutionary origin in different species. Implications for complement fixation and for the evolutionary origin of antibody diversity are also discussed. PMID:4192699

  9. Topological invariants in Fermi systems with time-reversal invariance

    NASA Astrophysics Data System (ADS)

    Avron, J. E.; Sadun, L.; Segert, J.; Simon, B.

    1988-09-01

    We discuss topological invariants for Fermi systems that have time-reversal invariance. The TKN2 integers (first Chern numbers) are replaced by second Chern numbers, and Berry's phase becomes a unit quaternion, or equivalently an element of SU(2). The canonical example playing much the same role as spin (1/2 in a magnetic field is spin (3/2 in a quadrupole electric field. In particular, the associated bundles are nontrivial and have +/-1 second Chern number. The connection that governs the adiabatic evolution coincides with the symmetric SU(2) Yang-Mills instanton.

  10. Critical phenomena of invariant circles

    SciTech Connect

    Hu, B.; Shi, J. ); Kim, S. )

    1991-04-15

    Some novel critical phenomena are discovered in a class of nonanalytic twist maps. It is found that the degree of inflection {ital z} plays a role reminiscent of that of dimensionality in phase transitions with {ital z}=2 and 3 corresponding to the lower and upper critical dimensions, respectively. Moreover, recurrence of invariant circles has also been observed. An inverse residue criterion,'' complementary to the residue criterion'' for the determination of the disappearance point, is introduced to determine the reappearance point of invariant circles.

  11. DNA sequence from Cretaceous period bone fragments.

    PubMed

    Woodward, S R; Weyand, N J; Bunnell, M

    1994-11-18

    DNA was extracted from 80-million-year-old bone fragments found in strata of the Upper Cretaceous Blackhawk Formation in the roof of an underground coal mine in eastern Utah. This DNA was used as the template in a polymerase chain reaction that amplified and sequenced a portion of the gene encoding mitochondrial cytochrome b. These sequences differ from all other cytochrome b sequences investigated, including those in the GenBank and European Molecular Biology Laboratory databases. DNA isolated from these bone fragments and the resulting gene sequences demonstrate that small fragments of DNA may survive in bone for millions of years.

  12. Fragment-Based Screen against HIV Protease

    PubMed Central

    Perryman, A. L.; Zhang, Q.; Soutter, H. H.; Rosenfeld, R.; McRee, D. E.; Olson, A. J.; Elder, J. E.; Stout, C. D.

    2009-01-01

    We have employed a fragment-based screen against wild-type (NL4-3) HIV protease (PR) using the Active Sight fragment library and X-ray crystallography. The experiments reveal two new binding sites for small molecules. PR was co-crystallized with fragments, or crystals were soaked in fragment solutions, using five crystal forms, and 378 data sets were collected to 2.3-1.3 Å resolution. Fragment binding induces a distinct conformation and specific crystal form of TL-3 inhibited PR during co-crystallization. One fragment, 2-methylcyclohexanol, binds in the ‘exo site’ adjacent to the Gly16Gly17Gln18 loop where the amide of Gly17 is a specific hydrogen bond donor, and hydrophobic contacts occur with the side chains of Lys14 and Leu63. Another fragment, indole-6-carboxylic acid, binds on the ‘outside/top of the flap’ via hydrophobic contacts with Trp42, Pro44, Met46, and Lys55, a hydrogen bond with Val56, and a salt-bridge with Arg57. 2-acetyl-benzothiophene also binds at this site. This study is the first fragment-based crystallographic screen against HIV PR, and the first time that fragments were screened against an inhibitor-bound drug target to search for compounds that both bind to novel sites and stabilize the inhibited conformation of the target. PMID:20659109

  13. Fragment-based screen against HIV protease.

    PubMed

    Perryman, Alexander L; Zhang, Qing; Soutter, Holly H; Rosenfeld, Robin; McRee, Duncan E; Olson, Arthur J; Elder, John E; Stout, C David

    2010-03-01

    We have employed a fragment-based screen against wild-type (NL4-3) HIV protease (PR) using the Active Sight fragment library and X-ray crystallography. The experiments reveal two new binding sites for small molecules. PR was co-crystallized with fragments, or crystals were soaked in fragment solutions, using five crystal forms, and 378 data sets were collected to 2.3-1.3 A resolution. Fragment binding induces a distinct conformation and specific crystal form of TL-3 inhibited PR during co-crystallization. One fragment, 2-methylcyclohexanol, binds in the 'exo site' adjacent to the Gly(16)Gly(17)Gln(18)loop where the amide of Gly(17)is a specific hydrogen bond donor, and hydrophobic contacts occur with the side chains of Lys(14)and Leu(63). Another fragment, indole-6-carboxylic acid, binds on the 'outside/top of the flap' via hydrophobic contacts with Trp(42), Pro(44), Met(46), and Lys(55), a hydrogen bond with Val(56), and a salt-bridge with Arg(57). 2-acetyl-benzothiophene also binds at this site. This study is the first fragment-based crystallographic screen against HIV PR, and the first time that fragments were screened against an inhibitor-bound drug target to search for compounds that both bind to novel sites and stabilize the inhibited conformation of the target.

  14. Scale invariance and superfluid turbulence

    NASA Astrophysics Data System (ADS)

    Sen, Siddhartha; Ray, Koushik

    2013-11-01

    We construct a Schroedinger field theory invariant under local spatial scaling. It is shown to provide an effective theory of superfluid turbulence by deriving, analytically, the observed Kolmogorov 5/3 law and to lead to a Biot-Savart interaction between the observed filament excitations of the system as well.

  15. Invariant Spin in the Proton

    SciTech Connect

    Thomas, Anthony

    2008-11-01

    We discuss recent theoretical progress in understanding the distribution of spin and orbital angular momentum in the proton. Particular attention is devoted to the effect of QCD evolution and to the distinction between "chiral" and "invariant" spin. This is particularly significant with respect to the possible presence of polarized strange quarks.

  16. Invariant Spin in the Proton

    SciTech Connect

    Thomas, Anthony W.

    2008-10-13

    We discuss recent theoretical progress in understanding the distribution of spin and orbital angular momentum in the proton. Particular attention is devoted to the effect of QCD evolution and to the distinction between 'chiral' and 'invariant' spin. This is particularly significant with respect to the possible presence of polarized strange quarks.

  17. Identity from classical invariant theory

    SciTech Connect

    Stein, P.R.

    1982-01-01

    A simple derivation is given of a well-known relation involving the so-called Cayley Operator of classical invariant theory. The proof is induction-free and independent of Capelli's identity; it makes use only of a known-theorem in the theory of determinants and some elementary combinatorics.

  18. Scale invariance of parity-invariant three-dimensional QED

    NASA Astrophysics Data System (ADS)

    Karthik, Nikhil; Narayanan, Rajamani

    2016-09-01

    We present numerical evidences using overlap fermions for a scale-invariant behavior of parity-invariant three-dimensional QED with two flavors of massless two-component fermions. Using finite-size scaling of the low-lying eigenvalues of the massless anti-Hermitian overlap Dirac operator, we rule out the presence of a bilinear condensate and estimate the mass anomalous dimension. The eigenvectors associated with these low-lying eigenvalues suggest critical behavior in the sense of a metal-insulator transition. We show that there is no mass gap in the scalar and vector correlators in the infinite-volume theory. The vector correlator does not acquire an anomalous dimension. The anomalous dimension associated with the long-distance behavior of the scalar correlator is consistent with the mass anomalous dimension.

  19. 21 CFR 866.5540 - Immunoglobulin G (Fd fragment specific) immunological test system.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... fragment) of the heavy chain (a subunit) of the immunoglobulin antibody molecule in serum. Measurement of immunoglobulin G Fd fragments aids in the diagnosis of plasma antibody-forming cell abnormalities....

  20. The solar system's invariable plane

    NASA Astrophysics Data System (ADS)

    Souami, D.; Souchay, J.

    2012-07-01

    Context. The dynamics of solar system objects, such as dwarf planets and asteroids, has become a well-established field of celestial mechanics in the past thirty years, owing to the improvements that have been made in observational techniques and numerical studies. In general, the ecliptic is taken as the reference plane in these studies, although there is no dynamical reason for doing so. In contrast, the invariable plane as originally defined by Laplace, seems to be a far more natural choice. In this context, the latest study of this plane dates back to Burkhardt. Aims: We define and determine the orientation of the invariable plane of the solar system with respect to both the ICRF and the equinox-ecliptic of J2000.0, and evaluate the accuracy of our determination. Methods: Using the long-term numerical ephemerides DE405, DE406, and INPOP10a over their entire available time span, we computed the total angular momentum of the solar system, as well as the individual contribution to it made by each of the planets, the dwarf planets Pluto and Ceres, and the two asteroids Pallas and Vesta. We then deduced the orientation of the invariable plane from these ephemerides. Results: We update the previous results on the determination of the orientation of the invariable plane with more accurate data, and a more complete analysis of the problem, taking into account the effect of the dwarf planet (1) Ceres as well as two of the biggest asteroids, (4) Vesta and (2) Pallas. We show that the inclusion of these last three bodies significantly improves the accuracy of determination of the invariable plane, whose orientation over a 100 y interval does not vary more than 0.1 mas in inclination, and 0.3 mas in longitude of the ascending node. Moreover, we determine the individual contributions of each body to the total angular momentum of the solar system, as well as the inclination and longitude of the node with respect to this latter plane. Conclusions: Owing to the high accuracy

  1. Emerging universe from scale invariance

    SciTech Connect

    Del Campo, Sergio; Herrera, Ramón; Guendelman, Eduardo I.; Labraña, Pedro E-mail: guendel@bgu.ac.il E-mail: plabrana@ubiobio.cl

    2010-06-01

    We consider a scale invariant model which includes a R{sup 2} term in action and show that a stable ''emerging universe'' scenario is possible. The model belongs to the general class of theories, where an integration measure independent of the metric is introduced. To implement scale invariance (S.I.), a dilaton field is introduced. The integration of the equations of motion associated with the new measure gives rise to the spontaneous symmetry breaking (S.S.B) of S.I. After S.S.B. of S.I. in the model with the R{sup 2} term (and first order formalism applied), it is found that a non trivial potential for the dilaton is generated. The dynamics of the scalar field becomes non linear and these non linearities are instrumental in the stability of some of the emerging universe solutions, which exists for a parameter range of the theory.

  2. Quantum mechanics from invariance principles

    NASA Astrophysics Data System (ADS)

    Moldoveanu, Florin

    2015-07-01

    Quantum mechanics is an extremely successful theory of nature and yet it lacks an intuitive axiomatization. In contrast, the special theory of relativity is well understood and is rooted into natural or experimentally justified postulates. Here we introduce an axiomatization approach to quantum mechanics which is very similar to special theory of relativity derivation. The core idea is that a composed system obeys the same laws of nature as its components. This leads to a Jordan-Lie algebraic formulation of quantum mechanics. The starting assumptions are minimal: the laws of nature are invariant under time evolution, the laws of nature are invariant under tensor composition, the laws of nature are relational, together with the ability to define a physical state (positivity). Quantum mechanics is singled out by a fifth experimentally justified postulate: nature violates Bell's inequalities.

  3. Anisotropic invariance in minisuperspace models

    NASA Astrophysics Data System (ADS)

    Chagoya, Javier; Sabido, Miguel

    2016-06-01

    In this paper we introduce invariance under anisotropic transformations to cosmology. This invariance is one of the key ingredients of the theory of quantum gravity at a Lifshitz point put forward by Hořava. We find that this new symmetry in the minisuperspace introduces characteristics to the model that can be relevant in the ultraviolet regime. For example, by canonical quantization we find a Schrödinger-type equation which avoids the problem of frozen time in quantum cosmology. For simple cases we obtain solutions to this quantum equation in a Kantowski–Sachs (KS) minisuperspace. At the classical level, we study KS and Friedmann–Robertson–Walker cosmologies, obtaining modifications to the solutions of general relativity that can be relevant in the early Universe.

  4. Anisotropic invariance in minisuperspace models

    NASA Astrophysics Data System (ADS)

    Chagoya, Javier; Sabido, Miguel

    2016-06-01

    In this paper we introduce invariance under anisotropic transformations to cosmology. This invariance is one of the key ingredients of the theory of quantum gravity at a Lifshitz point put forward by Hořava. We find that this new symmetry in the minisuperspace introduces characteristics to the model that can be relevant in the ultraviolet regime. For example, by canonical quantization we find a Schrödinger-type equation which avoids the problem of frozen time in quantum cosmology. For simple cases we obtain solutions to this quantum equation in a Kantowski-Sachs (KS) minisuperspace. At the classical level, we study KS and Friedmann-Robertson-Walker cosmologies, obtaining modifications to the solutions of general relativity that can be relevant in the early Universe.

  5. Geometry-invariant resonant cavities

    PubMed Central

    Liberal, I.; Mahmoud, A. M.; Engheta, N.

    2016-01-01

    Resonant cavities are one of the basic building blocks in various disciplines of science and technology, with numerous applications ranging from abstract theoretical modelling to everyday life devices. The eigenfrequencies of conventional cavities are a function of their geometry, and, thus, the size and shape of a resonant cavity is selected to operate at a specific frequency. Here we demonstrate theoretically the existence of geometry-invariant resonant cavities, that is, resonators whose eigenfrequencies are invariant with respect to geometrical deformations of their external boundaries. This effect is obtained by exploiting the unusual properties of zero-index metamaterials, such as epsilon-near-zero media, which enable decoupling of the temporal and spatial field variations in the lossless limit. This new class of resonators may inspire alternative design concepts, and it might lead to the first generation of deformable resonant devices. PMID:27010103

  6. Boosting Shift-Invariant Features

    NASA Astrophysics Data System (ADS)

    Hörnlein, Thomas; Jähne, Bernd

    This work presents a novel method for training shift-invariant features using a Boosting framework. Features performing local convolutions followed by subsampling are used to achieve shift-invariance. Other systems using this type of features, e.g. Convolutional Neural Networks, use complex feed-forward networks with multiple layers. In contrast, the proposed system adds features one at a time using smoothing spline base classifiers. Feature training optimizes base classifier costs. Boosting sample-reweighting ensures features to be both descriptive and independent. Our system has a lower number of design parameters as comparable systems, so adapting the system to new problems is simple. Also, the stage-wise training makes it very scalable. Experimental results show the competitiveness of our approach.

  7. Holographic multiverse and conformal invariance

    SciTech Connect

    Garriga, Jaume; Vilenkin, Alexander E-mail: vilenkin@cosmos.phy.tufts.edu

    2009-11-01

    We consider a holographic description of the inflationary multiverse, according to which the wave function of the universe is interpreted as the generating functional for a lower dimensional Euclidean theory. We analyze a simple model where transitions between inflationary vacua occur through bubble nucleation, and the inflating part of spacetime consists of de Sitter regions separated by thin bubble walls. In this model, we present some evidence that the dual theory is conformally invariant in the UV.

  8. Disformal invariance of curvature perturbation

    NASA Astrophysics Data System (ADS)

    Motohashi, Hayato; White, Jonathan

    2016-02-01

    We show that under a general disformal transformation the linear comoving curvature perturbation is not identically invariant, but is invariant on superhorizon scales for any theory that is disformally related to Horndeski's theory. The difference between disformally related curvature perturbations is found to be given in terms of the comoving density perturbation associated with a single canonical scalar field. In General Relativity it is well-known that this quantity vanishes on superhorizon scales through the Poisson equation that is obtained on combining the Hamiltonian and momentum constraints, and we confirm that a similar result holds for any theory that is disformally related to Horndeski's scalar-tensor theory so long as the invertibility condition for the disformal transformation is satisfied. We also consider the curvature perturbation at full nonlinear order in the unitary gauge, and find that it is invariant under a general disformal transformation if we assume that an attractor regime has been reached. Finally, we also discuss the counting of degrees of freedom in theories disformally related to Horndeski's.

  9. Similarity, invariance, and musical variation.

    PubMed

    McAdams, S; Matzkin, D

    2001-06-01

    Perceptual similarity underlies a number of important psychological properties of musical materials, including perceptual invariance under transformation, categorization, recognition, and the sense of familiarity. Mental processes involved in the perception of musical similarity may be an integral part of the functional logic of music composition and thus underly important aspects of musical experience. How much and in what ways can musical materials be varied and still be considered as perceptually related or as belonging to the same category? The notions of musical material, musical variation, perceptual similarity and invariance, and form-bearing dimensions are considered in this light. Recent work on similarity perception has demonstrated that the transformation space for a given musical material is limited by several factors ranging from degree of match of the values of auditory attributes of the events composing the sequences to their relations of various levels of abstraction and to the degree that the transformation respects the grammar of the musical system within which the material was composed. These notions and results are considered in the light of future directions of research, particularly concerning the role of similarity and invariance in the understanding of musical form during listening.

  10. Conformal Invariance of Graphene Sheets.

    PubMed

    Giordanelli, I; Posé, N; Mendoza, M; Herrmann, H J

    2016-03-10

    Suspended graphene sheets exhibit correlated random deformations that can be studied under the framework of rough surfaces with a Hurst (roughness) exponent 0.72 ± 0.01. Here, we show that, independent of the temperature, the iso-height lines at the percolation threshold have a well-defined fractal dimension and are conformally invariant, sharing the same statistical properties as Schramm-Loewner evolution (SLEκ) curves with κ = 2.24 ± 0.07. Interestingly, iso-height lines of other rough surfaces are not necessarily conformally invariant even if they have the same Hurst exponent, e.g. random Gaussian surfaces. We have found that the distribution of the modulus of the Fourier coefficients plays an important role on this property. Our results not only introduce a new universality class and place the study of suspended graphene membranes within the theory of critical phenomena, but also provide hints on the long-standing question about the origin of conformal invariance in iso-height lines of rough surfaces.

  11. Elementary examples of adiabatic invariance

    NASA Astrophysics Data System (ADS)

    Crawford, Frank S.

    1990-04-01

    Simple classical one-dimensional systems subject to adiabatic (gradual) perturbations are examined. The first examples are well known: the adiabatic invariance of the product Eτ of energy E and period τ for the simple pendulum and for the simple harmonic oscillator. Next, the adiabatic invariants of the vertical bouncer are found—a ball bouncing elastically from the floor of a rising elevator having slowly varying velocity and acceleration. These examples lead to consideration of adiabatic invariance for one-dimensional systems with potentials of the form V=axn, with a=a(t) slowly varying in time. Then, the horizontal bouncer is considered—a mass sliding on a smooth floor, bouncing back and forth between two impenetrable walls, one of which is slowly moving. This example is generalized to a particle in a bound state of a general potential with one slowly moving ``turning point.'' Finally, circular motion of a charged particle in a magnetic field slowly varying in time under three different configurations is considered: (a) a free particle in a uniform field; (b) a free particle in a nonuniform ``betatron'' field; and (c) a particle constrained to a circular orbit in a uniform field.

  12. Similarity, invariance, and musical variation.

    PubMed

    McAdams, S; Matzkin, D

    2001-06-01

    Perceptual similarity underlies a number of important psychological properties of musical materials, including perceptual invariance under transformation, categorization, recognition, and the sense of familiarity. Mental processes involved in the perception of musical similarity may be an integral part of the functional logic of music composition and thus underly important aspects of musical experience. How much and in what ways can musical materials be varied and still be considered as perceptually related or as belonging to the same category? The notions of musical material, musical variation, perceptual similarity and invariance, and form-bearing dimensions are considered in this light. Recent work on similarity perception has demonstrated that the transformation space for a given musical material is limited by several factors ranging from degree of match of the values of auditory attributes of the events composing the sequences to their relations of various levels of abstraction and to the degree that the transformation respects the grammar of the musical system within which the material was composed. These notions and results are considered in the light of future directions of research, particularly concerning the role of similarity and invariance in the understanding of musical form during listening. PMID:11458867

  13. Hidden structures of knot invariants

    NASA Astrophysics Data System (ADS)

    Sleptsov, Alexey

    2014-11-01

    We discuss a connection of HOMFLY polynomials with Hurwitz covers and represent a generating function for the HOMFLY polynomial of a given knot in all representations as Hurwitz partition function, i.e. the dependence of the HOMFLY polynomials on representation R is naturally captured by symmetric group characters (cut-and-join eigenvalues). The genus expansion and the loop expansion through Vassiliev invariants explicitly demonstrate this phenomenon. We study the genus expansion and discuss its properties. We also consider the loop expansion in details. In particular, we give an algorithm to calculate Vassiliev invariants, give some examples and discuss relations among Vassiliev invariants. Then we consider superpolynomials for torus knots defined via double affine Hecke algebra. We claim that the superpolynomials are not functions of Hurwitz type: symmetric group characters do not provide an adequate linear basis for their expansions. Deformation to superpolynomials is, however, straightforward in the multiplicative basis: the Casimir operators are beta-deformed to Hamiltonians of the Calogero-Moser-Sutherland system. Applying this trick to the genus and Vassiliev expansions, we observe that the deformation is fully straightforward only for the thin knots. Beyond the family of thin knots additional algebraically independent terms appear in the Vassiliev expansions. This can suggest that the superpolynomials do in fact contain more information about knots than the colored HOMFLY and Kauffman polynomials.

  14. Conformal Invariance of Graphene Sheets

    PubMed Central

    Giordanelli, I.; Posé, N.; Mendoza, M.; Herrmann, H. J.

    2016-01-01

    Suspended graphene sheets exhibit correlated random deformations that can be studied under the framework of rough surfaces with a Hurst (roughness) exponent 0.72 ± 0.01. Here, we show that, independent of the temperature, the iso-height lines at the percolation threshold have a well-defined fractal dimension and are conformally invariant, sharing the same statistical properties as Schramm-Loewner evolution (SLEκ) curves with κ = 2.24 ± 0.07. Interestingly, iso-height lines of other rough surfaces are not necessarily conformally invariant even if they have the same Hurst exponent, e.g. random Gaussian surfaces. We have found that the distribution of the modulus of the Fourier coefficients plays an important role on this property. Our results not only introduce a new universality class and place the study of suspended graphene membranes within the theory of critical phenomena, but also provide hints on the long-standing question about the origin of conformal invariance in iso-height lines of rough surfaces. PMID:26961723

  15. Selectable fragmentation warhead

    SciTech Connect

    Bryan, C.S.; Paisley, D.L.; Montoya, N.I.; Stahl, D.B.

    1992-12-31

    This report discusses a selectable fragmentation warhead which is capable of producing a predetermined number of fragments from a metal plate, and accelerating the fragments toward a target. A first explosive located adjacent to the plate is detonated at selected number of points by laser-driven slapper detonators. In one embodiment, a smoother-disk and a second explosive, located adjacent to the first explosive, serve to increase acceleration of the fragments toward a target. The ability to produce a selected number of fragments allows for effective destruction of a chosen target.

  16. Selectable fragmentation warhead

    DOEpatents

    Bryan, Courtney S.; Paisley, Dennis L.; Montoya, Nelson I.; Stahl, David B.

    1993-01-01

    A selectable fragmentation warhead capable of producing a predetermined number of fragments from a metal plate, and accelerating the fragments toward a target. A first explosive located adjacent to the plate is detonated at selected number of points by laser-driven slapper detonators. In one embodiment, a smoother-disk and a second explosive, located adjacent to the first explosive, serve to increase acceleration of the fragments toward a target. The ability to produce a selected number of fragments allows for effective destruction of a chosen target.

  17. SHARP ENTRYWISE PERTURBATION BOUNDS FOR MARKOV CHAINS

    PubMed Central

    THIEDE, ERIK; VAN KOTEN, BRIAN; WEARE, JONATHAN

    2015-01-01

    For many Markov chains of practical interest, the invariant distribution is extremely sensitive to perturbations of some entries of the transition matrix, but insensitive to others; we give an example of such a chain, motivated by a problem in computational statistical physics. We have derived perturbation bounds on the relative error of the invariant distribution that reveal these variations in sensitivity. Our bounds are sharp, we do not impose any structural assumptions on the transition matrix or on the perturbation, and computing the bounds has the same complexity as computing the invariant distribution or computing other bounds in the literature. Moreover, our bounds have a simple interpretation in terms of hitting times, which can be used to draw intuitive but rigorous conclusions about the sensitivity of a chain to various types of perturbations. PMID:26491218

  18. Shape invariant potentials in higher dimensions

    SciTech Connect

    Sandhya, R.; Sree Ranjani, S.; Kapoor, A.K.

    2015-08-15

    In this paper we investigate the shape invariance property of a potential in one dimension. We show that a simple ansatz allows us to reconstruct all the known shape invariant potentials in one dimension. This ansatz can be easily extended to arrive at a large class of new shape invariant potentials in arbitrary dimensions. A reformulation of the shape invariance property and possible generalizations are proposed. These may lead to an important extension of the shape invariance property to Hamiltonians that are related to standard potential problems via space time transformations, which are found useful in path integral formulation of quantum mechanics.

  19. On the question of adiabatic invariants

    NASA Astrophysics Data System (ADS)

    Mitropol'Skii, Iu. A.

    Some aspects of the construction of adiabadic invariants for dynamic systems with a single degree of freedom are discussed. Adiabatic invariants are derived using classical principles and the method proposed by Djukic (1981). The discussion covers an adiabatic invariant for a dynamic system with slowly varying parameters; derivation of an expression for an adiabatic invariant by the Djukic method for a second-order equation with a variable mass; and derivation of an expression for the adiabatic invariant for a nearly integrable differential equation.

  20. VLSI implementation of moment invariants for automated inspection

    NASA Astrophysics Data System (ADS)

    Armstrong, G. A.; Simpson, M. L.; Bouldin, D. W.

    This paper describes the design of a very large scale integration (VLSI) application specific integrated circuit (ASIC) for use in automated inspection. The inspection scheme uses Hu and Maitra's algorithms for moment invariants. A prototype design was generated that resolved the long delay time of the multiplier by custom designing adder cells based on the Manchester carry chain. The prototype ASIC is currently being fabricated in 2.0-micron CMOS technology and has been simulated at 20 MHz. The final ASICs will be used in parallel at the board level to achieve the 230 MOPs necessary to perform the moment invariant algorithms in real time on 512 by 512 pixel images with 256 grey scales.

  1. Universality of fragment shapes

    PubMed Central

    Domokos, Gábor; Kun, Ferenc; Sipos, András Árpád; Szabó, Tímea

    2015-01-01

    The shape of fragments generated by the breakup of solids is central to a wide variety of problems ranging from the geomorphic evolution of boulders to the accumulation of space debris orbiting Earth. Although the statistics of the mass of fragments has been found to show a universal scaling behavior, the comprehensive characterization of fragment shapes still remained a fundamental challenge. We performed a thorough experimental study of the problem fragmenting various types of materials by slowly proceeding weathering and by rapid breakup due to explosion and hammering. We demonstrate that the shape of fragments obeys an astonishing universality having the same generic evolution with the fragment size irrespective of materials details and loading conditions. There exists a cutoff size below which fragments have an isotropic shape, however, as the size increases an exponential convergence is obtained to a unique elongated form. We show that a discrete stochastic model of fragmentation reproduces both the size and shape of fragments tuning only a single parameter which strengthens the general validity of the scaling laws. The dependence of the probability of the crack plan orientation on the linear extension of fragments proved to be essential for the shape selection mechanism. PMID:25772300

  2. Universality of fragment shapes.

    PubMed

    Domokos, Gábor; Kun, Ferenc; Sipos, András Árpád; Szabó, Tímea

    2015-01-01

    The shape of fragments generated by the breakup of solids is central to a wide variety of problems ranging from the geomorphic evolution of boulders to the accumulation of space debris orbiting Earth. Although the statistics of the mass of fragments has been found to show a universal scaling behavior, the comprehensive characterization of fragment shapes still remained a fundamental challenge. We performed a thorough experimental study of the problem fragmenting various types of materials by slowly proceeding weathering and by rapid breakup due to explosion and hammering. We demonstrate that the shape of fragments obeys an astonishing universality having the same generic evolution with the fragment size irrespective of materials details and loading conditions. There exists a cutoff size below which fragments have an isotropic shape, however, as the size increases an exponential convergence is obtained to a unique elongated form. We show that a discrete stochastic model of fragmentation reproduces both the size and shape of fragments tuning only a single parameter which strengthens the general validity of the scaling laws. The dependence of the probability of the crack plan orientation on the linear extension of fragments proved to be essential for the shape selection mechanism. PMID:25772300

  3. Fragmentation properties of metals

    SciTech Connect

    Grady, D.E.; Kipp, M.E.

    1996-06-01

    In the present study we are developing an experimental fracture material property test method specific to dynamic fragmentation. Spherical test samples of the metals of interest are subjected to controlled impulsive stress loads by acceleration to high velocities with a light-gas launcher facility and subsequent normal impact on thin plates. Motion, deformation and fragmentation of the test samples are diagnosed with multiple flash radiography methods. The impact plate materials are selected to be transparent to the x-ray method so that only test metal material is imaged. Through a systematic series of such tests, both strain-to-failure and fragmentation resistance properties are determined through this experimental method. Fragmentation property data for several steels, copper, aluminum, tantalum and titanium have been obtained to date. Aspects of the dynamic data have been analyzed with computational methods to achieve a better understanding of the processes leading to failure and fragmentation, and to test an existing computational fragmentation model.

  4. Quantum Weyl invariance and cosmology

    NASA Astrophysics Data System (ADS)

    Dabholkar, Atish

    2016-09-01

    Equations for cosmological evolution are formulated in a Weyl invariant formalism to take into account possible Weyl anomalies. Near two dimensions, the renormalized cosmological term leads to a nonlocal energy-momentum tensor and a slowly decaying vacuum energy. A natural generalization to four dimensions implies a quantum modification of Einstein field equations at long distances. It offers a new perspective on time-dependence of couplings and naturalness with potentially far-reaching consequences for the cosmological constant problem, inflation, and dark energy.

  5. Relativistic chaos is coordinate invariant.

    PubMed

    Motter, Adilson E

    2003-12-01

    The noninvariance of Lyapunov exponents in general relativity has led to the conclusion that chaos depends on the choice of the space-time coordinates. Strikingly, we uncover the transformation laws of Lyapunov exponents under general space-time transformations and we find that chaos, as characterized by positive Lyapunov exponents, is coordinate invariant. As a result, the previous conclusion regarding the noninvariance of chaos in cosmology, a major claim about chaos in general relativity, necessarily involves the violation of hypotheses required for a proper definition of the Lyapunov exponents. PMID:14683170

  6. Vector spaces, invariance, and camouflage

    NASA Astrophysics Data System (ADS)

    Arsenault, Henri H.; Garcia-Martinez, Pascuala

    2004-12-01

    We present a method based on an orthonormal vector space basis representation to detect camouflaged targets in natural environments. Because the method is intensity invariant we detect camouflage targets independently of the illumination conditions. The detection technique does not require knowing the exact camouflage pattern, but only the class of patterns (foliage, netting, woods...). We used nonlinear filtering based on the calculation of several correlations. Moreover, the nonlinearity of the filtering process allows a high discrimination against false targets. Several experiments confirm the target detectability where strong camouflage might delude even human viewers.

  7. Invariant metrics for Hamiltonian systems

    SciTech Connect

    Rangarajan, G. ); Dragt, A.J. ); Neri, F. )

    1991-05-01

    In this paper, invariant metrics are constructed for Hamiltonian systems. These metrics give rise to norms on the space of homeogeneous polynomials of phase-space variables. For an accelerator lattice described by a Hamiltonian, these norms characterize the nonlinear content of the lattice. Therefore, the performance of the lattice can be improved by minimizing the norm as a function of parameters describing the beam-line elements in the lattice. A four-fold increase in the dynamic aperture of a model FODO cell is obtained using this procedure. 7 refs.

  8. Limit cycles and conformal invariance

    NASA Astrophysics Data System (ADS)

    Fortin, Jean-François; Grinstein, Benjamín; Stergiou, Andreas

    2013-01-01

    There is a widely held belief that conformal field theories (CFTs) require zero beta functions. Nevertheless, the work of Jack and Osborn implies that the beta functions are not actually the quantites that decide conformality, but until recently no such behavior had been exhibited. Our recent work has led to the discovery of CFTs with nonzero beta functions, more precisely CFTs that live on recurrent trajectories, e.g., limit cycles, of the beta-function vector field. To demonstrate this we study the S function of Jack and Osborn. We use Weyl consistency conditions to show that it vanishes at fixed points and agrees with the generator Q of limit cycles on them. Moreover, we compute S to third order in perturbation theory, and explicitly verify that it agrees with our previous determinations of Q. A byproduct of our analysis is that, in perturbation theory, unitarity and scale invariance imply conformal invariance in four-dimensional quantum field theories. Finally, we study some properties of these new, "cyclic" CFTs, and point out that the a-theorem still governs the asymptotic behavior of renormalization-group flows.

  9. Invariant imbedding in two dimensions

    SciTech Connect

    Faber, V.; Seth, D.L.; Wing, G.M.

    1988-01-01

    J. Corones has noted that the doubling and addition formulas of invariant imbedding can be extended conceptually to very general situations. All that is needed is a black box ''process'' with n ''ports.'' The /ital i/th port has vector input I/sub i/ and vector output J/sub i/. Addition formulas result when two or more of these processes are joined together to form a new process in some regular way. For example, four congruent squares can be juxtaposed to form a larger square. At each join, the output of one process becomes the input of the other and vice versa. (We always suppose the join to occur at one or more ports.) Addition formulas result from the combination of these shared quantities. Corones has thus pointed out that invariant imbedding is not, as is sometimes asserted, an inherently one-dimensional (1-D) method, but works conceptually in any number of dimensions; some previous work that is conceptually along these lines, with references to other such works, can be found in Refs. 2-4. The details can, of course, become very complicated. We shall show that the method is computationally feasible for certain two-dimensional (2-D) problems. To conform to the thrust of these proceedings, we shall usually phrase our discussions in terms of transport theory rather than speaking of more abstract processes. 7 refs., 13 figs.

  10. A Local Galilean Invariant Thermostat.

    PubMed

    Groot, Robert D

    2006-05-01

    The thermostat introduced recently by Stoyanov and Groot (J. Chem. Phys. 2005, 122, 114112) is analyzed for inhomogeneous systems. This thermostat has one global feature, because the mean temperature used to drive the system toward equilibrium is a global average. The consequence is that the thermostat locally conserves energy rather than temperature. Thus, local temperature variations can be long-lived, although they do average out by thermal diffusion. To obtain a faster local temperature equilibration, a truly local thermostat must be introduced. To conserve momentum and, hence, to simulate hydrodynamic interactions, the thermostat must be Galilean invariant. Such a local Galilean invariant thermostat is studied here. It is shown that, by defining a local temperature on each particle, the ensemble is locally isothermal. The local temperature is obtained from a local square velocity average around each particle. Simulations on the ideal gas show that this local Nosé-Hoover algorithm has a similar artifact as dissipative particle dynamics:  the ideal gas pair correlation function is slightly distorted. This is attributed to the fact that the thermostat compensates fluctuations that are natural within a small cluster of particles. When the cutoff range rc for the square velocity average is increased, systematic errors decrease proportionally to rc(-)(3/2); hence, the systematic error can be made arbitrary small.

  11. Sequential generation of polynomial invariants and N-body non-local correlations

    NASA Astrophysics Data System (ADS)

    Sharma, S. Shelly; Sharma, N. K.

    2016-09-01

    We report an inductive process that allows for sequential construction of local unitary invariant polynomials of state coefficients for multipartite quantum states. The starting point can be a physically meaningful invariant of a smaller part of the system. The process is applied to construct a chain of invariants that quantify non-local N-way correlations in an N-qubit pure state. It also yields the invariants to quantify the sum of N-way and (N-1)-way correlations. Analytic expressions for four-way and three-way correlation quantifiers for four-qubit states, as well as, five-way and four-way correlation quantifiers for five-qubit pure states are given.

  12. Blocking monocyte transmigration in in vitro system by an anti-CD99 human antibody in single chain fragment variable (scFv) format. Efficient large scale purification of biological active scFv from inclusion bodies in E. coli expression system

    PubMed Central

    Moricoli, Diego; Muller, William A.; Carbonella, Damiano Cosimo; Balducci, Maria Cristina; Dominici, Sabrina; Fiori, Valentina; Watson, Richard; Weber, Evan; Cianfriglia, Maurizio; Scotlandi, Katia; Magnani, Mauro

    2015-01-01

    Migration of leukocytes into a site of inflammation involves several steps mediated by various families of adhesion molecules. CD99 play a significant role in transendothelial migration (TEM) of leukocytes. Inhibition of TEM by specific monoclonal antibody (mAb) can provide a potent therapeutic approach to treating inflammatory conditions. However, the therapeutic utilization of whole IgG can lead to an inappropriate activation of Fc receptor-expressing cells inducing serious adverse side effects due to cytokine release. In this regard, specific recombinant antibody in single chain variable fragments (scFvs) originated by phage library may offer a solution by affecting TEM function in a safe clinical context. However, this consideration requires large scale production of functional scFv antibodies under GMP conditions and hence, the absence of toxic reagents utilized for the solubilization and refolding steps of inclusion bodies that may discourage industrial application of these antibody fragments. In order to apply the scFv anti-CD99 named C7A in a clinical setting we herein describe an efficient and large scale production of the antibody fragments expressed in E.coli as insoluble protein avoiding gel filtration chromatography approach, and laborious refolding step pre- and post-purification. Using differential salt elution which is a simple, reproducible and effective procedure we are able to separate scFv in monomer format from aggregates. The purified scFv antibody C7A exhibits inhibitory activity comparable to an antagonistic conventional mAb, thus providing an excellent agent for blocking CD99 signalling. Thanks to the original purification protocol that can be extended to other scFvs that are expressed as inclusion bodies in bacterial systems, the scFv anti-CD99 C7A herein described represents the first step towards the construction of new antibody therapeutic. PMID:24798881

  13. A new and improved method based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) for the determination of A1298C mutation in the methylenetetrahydrofolate reductase (MTHFR) gene.

    PubMed

    Machnik, Grzegorz; Zapala, Malgorzata; Pelc, Ewa; Gasecka-Czapla, Monika; Kaczmarczyk, Grzegorz; Okopien, Boguslaw

    2013-01-01

    Intracellular folate homeostasis and metabolism is regulated by numerous genes. Among them, 5,10-methylenetetrahydrofolate reductase (MTHFR) is of special interest because of its involvement in regulation of the homocysteine level in the body as a result of folate metabolism. Moreover, some studies demonstrated that the homocysteine plasma level in individuals may be influenced by polymorphisms present in the MTHFR gene. Two common, clinically relevant mutations have been described: MTHFR C677T and MTHFR A1298C. Although several laboratory techniques allow genotyping of both polymorphisms, PCR-RFLP analysis is simple to perform, relatively cheap, and thus one of the most utilized. In the case of A1298C, the PCR-RFLP technique that utilizes MboII endonuclease class II requires an acrylamide gel electrophoresis, since agarose gel electrophoresis is unable to resolve short deoxyribonucleic acid (DNA) fragments after restriction digestion. Agarose gel electrophoresis is commonly preferred over that of acrylamide. To resolve this inconvenience, a novel PCR-RFLP, AjuI-based method to genotype A1298C alleles has been developed that can be performed on standard agarose gel.

  14. Adiabatic and diabatic invariants in ion-molecule reactions.

    PubMed

    Lorquet, J C

    2009-12-28

    A point charge interacting with a dipole (either induced or permanent) constitutes a completely integrable dynamical subsystem characterized by three first integrals of the motion (E, p(phi), and either l(2) or a Hamilton-Jacobi separation constant beta). An ion-molecule reaction (capture or fragmentation) can be seen as an interaction between such a subsystem and a bath of oscillators. This interaction is a perturbation that destroys some of the first integrals. However, the perturbation depends on the separation between the fragments and the destruction is gradual. The mathematical simplicity of the long-range electrostatic interaction potential leads to useful simplifications. A first-order perturbation treatment based on the structured and regular nature of the multipole expansion is presented. The separating integrals valid in the asymptotic limit are found to subsist at intermediate distances, although in a weaker form. As the reaction coordinate decreases, i.e., as the fragments approach, the asymptotic range is followed by an outer region where (i) the azimuthal momentum p(phi) remains a constant of the motion; (ii) the square angular momentum l(2) or the separation constant beta transform into a diabatic invariant in regions of phase space characterized by a high value of the translational momentum p(r); (iii) for low values of p(r), it is advantageous to use the action integral contour integral(p(theta)d theta), which is an adiabatic invariant. The conditions under which an effective potential obtained by adding centrifugal repulsion to an electrostatic attractive term can be validly constructed are specified. In short, the dynamics of ion-molecule interactions is still regular in parts of phase space corresponding to a range of the reaction coordinate where the interaction potential deviates from its asymptotic shape. PMID:20059072

  15. Multiple-invariance esprit for DOA estimation

    NASA Astrophysics Data System (ADS)

    Linczuk, Maciej

    2004-07-01

    We consider the problem of estimating the direction of arrival (DOA) of multiple sources in the presence of noise. First, we introduce a narrowband signal model disturbed by white, Gaussian noise. This signal is detected by Uniform Linear Antenna Array -- ULA. Next, we discuss some properties of this signal model and its cross correlation matrix. Using this properties we introduce SINGLE SHIFT INVARIANCE algorithm for DOA estimation: ESPRIT. Next, we describe an idea of MULTIPLE INVARIANCE algorithm based on MULTIPLE INVARIANCE ESPRIT. In the last section we examine some statistical properties of both algorithms: ESPRIT and MULTIPLE INVARIANCE ESPRIT.

  16. Learning Slowness in a Sparse Model of Invariant Feature Detection.

    PubMed

    Chandrapala, Thusitha N; Shi, Bertram E

    2015-07-01

    Primary visual cortical complex cells are thought to serve as invariant feature detectors and to provide input to higher cortical areas. We propose a single model for learning the connectivity required by complex cells that integrates two factors that have been hypothesized to play a role in the development of invariant feature detectors: temporal slowness and sparsity. This model, the generative adaptive subspace self-organizing map (GASSOM), extends Kohonen's adaptive subspace self-organizing map (ASSOM) with a generative model of the input. Each observation is assumed to be generated by one among many nodes in the network, each being associated with a different subspace in the space of all observations. The generating nodes evolve according to a first-order Markov chain and generate inputs that lie close to the associated subspace. This model differs from prior approaches in that temporal slowness is not an externally imposed criterion to be maximized during learning but, rather, an emergent property of the model structure as it seeks a good model of the input statistics. Unlike the ASSOM, the GASSOM does not require an explicit segmentation of the input training vectors into separate episodes. This enables us to apply this model to an unlabeled naturalistic image sequence generated by a realistic eye movement model. We show that the emergence of temporal slowness within the model improves the invariance of feature detectors trained on this input.

  17. Learning Slowness in a Sparse Model of Invariant Feature Detection.

    PubMed

    Chandrapala, Thusitha N; Shi, Bertram E

    2015-07-01

    Primary visual cortical complex cells are thought to serve as invariant feature detectors and to provide input to higher cortical areas. We propose a single model for learning the connectivity required by complex cells that integrates two factors that have been hypothesized to play a role in the development of invariant feature detectors: temporal slowness and sparsity. This model, the generative adaptive subspace self-organizing map (GASSOM), extends Kohonen's adaptive subspace self-organizing map (ASSOM) with a generative model of the input. Each observation is assumed to be generated by one among many nodes in the network, each being associated with a different subspace in the space of all observations. The generating nodes evolve according to a first-order Markov chain and generate inputs that lie close to the associated subspace. This model differs from prior approaches in that temporal slowness is not an externally imposed criterion to be maximized during learning but, rather, an emergent property of the model structure as it seeks a good model of the input statistics. Unlike the ASSOM, the GASSOM does not require an explicit segmentation of the input training vectors into separate episodes. This enables us to apply this model to an unlabeled naturalistic image sequence generated by a realistic eye movement model. We show that the emergence of temporal slowness within the model improves the invariance of feature detectors trained on this input. PMID:25973550

  18. Asymptotic invariants of homotopy groups

    NASA Astrophysics Data System (ADS)

    Manin, Fedor

    We study the homotopy groups of a finite CW complex X via constraints on the geometry of representatives of their elements. For example, one can measure the "size" of alpha ∈ pi n (X) by the optimal Lipschitz constant or volume of a representative. By comparing the geometrical structure thus obtained with the algebraic structure of the group, one can define functions such as growth and distortion in pin(X), analogously to the way that such functions are studied in asymptotic geometric group theory. We provide a number of examples and techniques for studying these invariants, with a special focus on spaces with few rational homotopy groups. Our main theorem characterizes those X in which all non-torsion homotopy classes are undistorted, that is, their volume distortion functions, and hence also their Lipschitz distortion functions, are linear.

  19. Selectable fragmentation warhead

    SciTech Connect

    Bryan, C.S.; Paisley, D.L.; Montoya, N.I.; Stahl, D.B.

    1993-07-20

    A selectable fragmentation warhead is described comprising: a case having proximal and distal ends; a fragmenting plate mounted in said distal end of said casing; first explosive means cast adjacent to said fragmenting plate for creating a predetermined number of fragments from said fragmenting plate; three or more first laser-driven slapper detonators located adjacent to said first explosive means for detonating said first explosive means in a predetermined pattern; smoother-disk means located adjacent to said first means for accelerating said fragments; second explosive means cast adjacent to said smoother-disk means for further accelerating said fragments; at least one laser-driven slapper detonators located in said second explosive means; a laser located in said proximal end of said casing; optical fibers connecting said laser to said first and second laser-driven slapper detonators; and optical switch means located in series with said optical fibers connected to said plurality of first laser-driven slapper detonators for blocking or passing light from said laser to said plurality of first laser-driven slapper detonators.

  20. Opaque rock fragments

    SciTech Connect

    Abhijit, B.; Molinaroli, E.; Olsen, J.

    1987-05-01

    The authors describe a new, rare, but petrogenetically significant variety of rock fragments from Holocene detrital sediments. Approximately 50% of the opaque heavy mineral concentrates from Holocene siliciclastic sands are polymineralic-Fe-Ti oxide particles, i.e., they are opaque rock fragments. About 40% to 70% of these rock fragments show intergrowth of hm + il, mt + il, and mt + hm +/- il. Modal analysis of 23,282 opaque particles in 117 polished thin sections of granitic and metamorphic parent rocks and their daughter sands from semi-arid and humid climates show the following relative abundances. The data show that opaque rock fragments are more common in sands from igneous source rocks and that hm + il fragments are more durable. They assume that equilibrium conditions existed in parent rocks during the growth of these paired minerals, and that the Ti/Fe ratio did not change during oxidation of mt to hm. Geothermometric determinations using electron probe microanalysis of opaque rock fragments in sand samples from Lake Erie and the Adriatic Sea suggest that these rock fragments may have equilibrated at approximately 900/sup 0/ and 525/sup 0/C, respectively.

  1. Auroral fragmentation into patches

    NASA Astrophysics Data System (ADS)

    Shiokawa, Kazuo; Hashimoto, Ayumi; Hori, Tomoaki; Sakaguchi, Kaori; Ogawa, Yasunobu; Donovan, Eric; Spanswick, Emma; Connors, Martin; Otsuka, Yuichi; Oyama, Shin-Ichiro; Nozawa, Satonori; McWilliams, Kathryn

    2014-10-01

    Auroral patches in diffuse auroras are very common features in the postmidnight local time. However, the processes that produce auroral patches are not yet well understood. In this paper we present two examples of auroral fragmentation which is the process by which uniform aurora is broken into several fragments to form auroral patches. These examples were observed at Athabasca, Canada (geomagnetic latitude: 61.7°N), and Tromsø, Norway (67.1°N). Captured in sequences of images, the auroral fragmentation occurs as finger-like structures developing latitudinally with horizontal-scale sizes of 40-100 km at ionospheric altitudes. The structures tend to develop in a north-south direction with speeds of 150-420 m/s without any shearing motion, suggesting that pressure-driven instability in the balance between the earthward magnetic-tension force and the tailward pressure gradient force in the magnetosphere is the main driving force of the auroral fragmentation. Therefore, these observations indicate that auroral fragmentation associated with pressure-driven instability is a process that creates auroral patches. The observed slow eastward drift of aurora during the auroral fragmentation suggests that fragmentation occurs in low-energy ambient plasma.

  2. Falling chains

    NASA Astrophysics Data System (ADS)

    Wong, Chun Wa; Yasui, Kosuke

    2006-06-01

    The one-dimensional fall of a folded chain with one end suspended from a rigid support and a chain falling from a resting heap on a table is studied. Because their Lagrangians contain no explicit time dependence, the falling chains are conservative systems. Their equations of motion are shown to contain a term that enforces energy conservation when masses are transferred between subchains. We show that Cayley's 1857 energy nonconserving solution for a chain falling from a resting heap is incorrect because it neglects the energy gained when a link leaves a subchain. The maximum chain tension measured by Calkin and March for the falling folded chain is given a simple if rough interpretation. Other aspects of the falling folded chain are briefly discussed.

  3. Established a new double antibodies sandwich enzyme-linked immunosorbent assay for detecting Bacillus thuringiensis (Bt) Cry1Ab toxin based single-chain variable fragments from a naïve mouse phage displayed library.

    PubMed

    Zhang, Xiao; Xu, Chongxin; Zhang, Cunzheng; Liu, Yuan; Xie, Yajing; Liu, Xianjin

    2014-04-01

    ScFvs are composed of the variable regions of the heavy and light chains via a short linker that maintain the specific antigen binding abilities of antibodies. In this study, we constructed a naïve mouse phage displayed library to generate scFvs against Cry1Ab toxin. After affinity panning, positive phage-scFvs were isolated, sequenced and characterized by ELISA. The best binding ability scFv-G9 was expressed and purified. SDS-PAGE indicated that the relative molecular mass of scFv was estimated at 28 kDa. The purified scFv-G9 was used to develop a new DAS-ELISA for detecting Cry1Ab toxin, within minimum detection limit of 0.008 μg mL(-1), a working range 0.018-6.23 μg mL(-1), and the linear curve displayed an acceptable correlation coefficient of 0.98. The cross-reactivity showed that scFv-G9 had strongly binding ability to Cry1Ac toxin, but not to Cry1B, Cry1C and Cry1F toxin. The average recoveries of Cry1Ab toxin from spiked leaf and rice samples were in the range 92.1-94.8%, and 91.6-98.6%, respectively, with a coefficient of variation (C.V) less than 5.0%. These results showed promising applications of scfv-G9 for detecting Cry1Ab toxin with new DAS-ELISA.

  4. Cross-National Invariance of Children's Temperament

    ERIC Educational Resources Information Center

    Benson, Nicholas; Oakland, Thomas; Shermis, Mark

    2009-01-01

    Measurement of temperament is an important endeavor with international appeal; however, cross-national invariance (i.e., equivalence of test scores across countries as established by empirical comparisons) of temperament tests has not been established in published research. This study examines the cross-national invariance of school-aged…

  5. Invariance or Noninvariance, that Is the Question

    ERIC Educational Resources Information Center

    Widaman, Keith F.; Grimm, Kevin J.

    2009-01-01

    Nesselroade, Gerstorf, Hardy, and Ram developed a new and interesting way to enforce invariance at the second-order level in P-technique models, while allowing first-order structure to stray from invariance. We discuss our concerns with this approach under the headings of falsifiability, the nature of manifest variables included in models, and…

  6. Multipartite invariant states. I. Unitary symmetry

    SciTech Connect

    Chruscinski, Dariusz; Kossakowski, Andrzej

    2006-06-15

    We propose a natural generalization of bipartite Werner and isotropic states to multipartite systems consisting of an arbitrary even number of d-dimensional subsystems (qudits). These generalized states are invariant under the action of local unitary operations. We study basic properties of multipartite invariant states and present necessary and sufficient separability criteria.

  7. Factorial invariance in multilevel confirmatory factor analysis.

    PubMed

    Ryu, Ehri

    2014-02-01

    This paper presents a procedure to test factorial invariance in multilevel confirmatory factor analysis. When the group membership is at level 2, multilevel factorial invariance can be tested by a simple extension of the standard procedure. However level-1 group membership raises problems which cannot be appropriately handled by the standard procedure, because the dependency between members of different level-1 groups is not appropriately taken into account. The procedure presented in this article provides a solution to this problem. This paper also shows Muthén's maximum likelihood (MUML) estimation for testing multilevel factorial invariance across level-1 groups as a viable alternative to maximum likelihood estimation. Testing multilevel factorial invariance across level-2 groups and testing multilevel factorial invariance across level-1 groups are illustrated using empirical examples. SAS macro and Mplus syntax are provided.

  8. Geometric invariance of compressible turbulent boundary layers

    NASA Astrophysics Data System (ADS)

    Bi, Wei-Tao; Wu, Bin; She, Zhen-Su; Hussain, Fazle

    2015-11-01

    A symmetry based approach is applied to analyze the mean velocity and temperature fields of compressible, flat plate turbulent boundary layers (CTBL). A Reynolds stress length scale and a turbulent heat flux length scale are identified to possess the same defect scaling law in the CTBL bulk, which is solely owing to the constraint of the wall to the geometry of the wall-attached eddies, but invariant to compressibility and wall heat transfer. This invariance is called the geometric invariance of CTBL eddies and is likely the origin of the Mach number invariance of Morkovin's hypothesis, as well as the similarity of energy and momentum transports. A closure for the turbulent transport by using the invariant lengths is attainted to predict the mean velocity and temperature profiles in the CTBL bulk- superior to the van Driest transformation and the Reynolds analogy based relations for its sound physics and higher accuracy. Additionally, our approach offers a new understanding of turbulent Prandtl number.

  9. Fragment capture device

    DOEpatents

    Payne, Lloyd R.; Cole, David L.

    2010-03-30

    A fragment capture device for use in explosive containment. The device comprises an assembly of at least two rows of bars positioned to eliminate line-of-sight trajectories between the generation point of fragments and a surrounding containment vessel or asset. The device comprises an array of at least two rows of bars, wherein each row is staggered with respect to the adjacent row, and wherein a lateral dimension of each bar and a relative position of each bar in combination provides blockage of a straight-line passage of a solid fragment through the adjacent rows of bars, wherein a generation point of the solid fragment is located within a cavity at least partially enclosed by the array of bars.

  10. Fragmentation in Biaxial Tension

    SciTech Connect

    Campbell, G H; Archbold, G C; Hurricane, O A; Miller, P L

    2006-06-13

    We have carried out an experiment that places a ductile stainless steel in a state of biaxial tension at a high rate of strain. The loading of the ductile metal spherical cap is performed by the detonation of a high explosive layer with a conforming geometry to expand the metal radially outwards. Simulations of the loading and expansion of the metal predict strain rates that compare well with experimental observations. A high percentage of the HE loaded material was recovered through a soft capture process and characterization of the recovered fragments provided high quality data, including uniform strain prior to failure and fragment size. These data were used with a modified fragmentation model to determine a fragmentation energy.

  11. Enantioselective total synthesis of callipeltoside A: two approaches to the macrolactone fragment

    PubMed Central

    Evans, David A.; Burch, Jason D.; Hu, Essa; Jaeschke, Georg

    2012-01-01

    The enantioselective total synthesis of callipeltoside A is described. Two syntheses of the macrolactone subunit are included: the first relies upon an Ireland–Claisen rearrangement to generate the trisubstituted olefin geometry and the second utilizes an enantioselective vinylogous aldol reaction for this purpose. Enantioselective syntheses of the sugar and chlorocyclopropane side chain fragments are also disclosed. The relative and absolute stereochemistry of this natural product was determined by fragment coupling with the two enantiomers of the side chain fragment. PMID:22859865

  12. Stereo Correspondence Using Moment Invariants

    NASA Astrophysics Data System (ADS)

    Premaratne, Prashan; Safaei, Farzad

    Autonomous navigation is seen as a vital tool in harnessing the enormous potential of Unmanned Aerial Vehicles (UAV) and small robotic vehicles for both military and civilian use. Even though, laser based scanning solutions for Simultaneous Location And Mapping (SLAM) is considered as the most reliable for depth estimation, they are not feasible for use in UAV and land-based small vehicles due to their physical size and weight. Stereovision is considered as the best approach for any autonomous navigation solution as stereo rigs are considered to be lightweight and inexpensive. However, stereoscopy which estimates the depth information through pairs of stereo images can still be computationally expensive and unreliable. This is mainly due to some of the algorithms used in successful stereovision solutions require high computational requirements that cannot be met by small robotic vehicles. In our research, we implement a feature-based stereovision solution using moment invariants as a metric to find corresponding regions in image pairs that will reduce the computational complexity and improve the accuracy of the disparity measures that will be significant for the use in UAVs and in small robotic vehicles.

  13. The Evolution of Grain Size Distribution in Explosive Rock Fragmentation - Sequential Fragmentation Theory Revisited

    NASA Astrophysics Data System (ADS)

    Scheu, B.; Fowler, A. C.

    2015-12-01

    Fragmentation is a ubiquitous phenomenon in many natural and engineering systems. It is the process by which an initially competent medium, solid or liquid, is broken up into a population of constituents. Examples occur in collisions and impacts of asteroids/meteorites, explosion driven fragmentation of munitions on a battlefield, as well as of magma in a volcanic conduit causing explosive volcanic eruptions and break-up of liquid drops. Besides the mechanism of fragmentation the resulting frequency-size distribution of the generated constituents is of central interest. Initially their distributions were fitted empirically using lognormal, Rosin-Rammler and Weibull distributions (e.g. Brown & Wohletz 1995). The sequential fragmentation theory (Brown 1989, Wohletz at al. 1989, Wohletz & Brown 1995) and the application of fractal theory to fragmentation products (Turcotte 1986, Perfect 1997, Perugini & Kueppers 2012) attempt to overcome this shortcoming by providing a more physical basis for the applied distribution. Both rely on an at least partially scale-invariant and thus self-similar random fragmentation process. Here we provide a stochastic model for the evolution of grain size distribution during the explosion process. Our model is based on laboratory experiments in which volcanic rock samples explode naturally when rapidly depressurized from initial pressures of several MPa to ambient conditions. The physics governing this fragmentation process has been successfully modelled and the observed fragmentation pattern could be numerically reproduced (Fowler et al. 2010). The fragmentation of these natural rocks leads to grain size distributions which vary depending on the experimental starting conditions. Our model provides a theoretical description of these different grain size distributions. Our model combines a sequential model of the type outlined by Turcotte (1986), but generalized to cater for the explosive process appropriate here, in particular by

  14. Using sorted invariant mass variables to evade combinatorial ambiguities in cascade decays

    DOE PAGES

    Kim, Doojin; Matchev, Konstantin T.; Park, Myeonghun

    2016-02-19

    The classic method for mass determination in a SUSY-like cascade decay chain relies on measurements of the kinematic endpoints in the invariant mass distributions of suitable collections of visible decay products. However, the procedure is complicated by combinatorial ambiguities: e.g., the visible final state particles may be indistinguishable (as in the case of QCD jets), or one may not know the exact order in which they are emitted along the decay chain. In order to avoid such combinatorial ambiguities, we propose to treat the nal state particles fully democratically and consider the sorted set of the invariant masses of allmore » possible partitions of the visible particles in the decay chain. In particular, for a decay to N visible particles, one considers the sorted sets of all possible n-body invariant mass combinations (2≤ n≤ N) and determines the kinematic endpoint m(n,r)max of the distribution of the r-th largest n-body invariant mass m(n,r) for each possible value of n and r. For the classic example of a squark decay in supersymmetry, we provide analytical formulas for the interpretation of these endpoints in terms of the underlying physical masses. We point out that these measurements can be used to determine the structure of the decay topology, e.g., the number and position of intermediate on-shell resonances.« less

  15. Feedback-Driven Dynamic Invariant Discovery

    NASA Technical Reports Server (NTRS)

    Zhang, Lingming; Yang, Guowei; Rungta, Neha S.; Person, Suzette; Khurshid, Sarfraz

    2014-01-01

    Program invariants can help software developers identify program properties that must be preserved as the software evolves, however, formulating correct invariants can be challenging. In this work, we introduce iDiscovery, a technique which leverages symbolic execution to improve the quality of dynamically discovered invariants computed by Daikon. Candidate invariants generated by Daikon are synthesized into assertions and instrumented onto the program. The instrumented code is executed symbolically to generate new test cases that are fed back to Daikon to help further re ne the set of candidate invariants. This feedback loop is executed until a x-point is reached. To mitigate the cost of symbolic execution, we present optimizations to prune the symbolic state space and to reduce the complexity of the generated path conditions. We also leverage recent advances in constraint solution reuse techniques to avoid computing results for the same constraints across iterations. Experimental results show that iDiscovery converges to a set of higher quality invariants compared to the initial set of candidate invariants in a small number of iterations.

  16. Invariant variational structures on fibered manifolds

    NASA Astrophysics Data System (ADS)

    Krupka, Demeter

    2015-12-01

    The aim of this paper is to present a relatively complete theory of invariance of global, higher-order integral variational functionals in fibered spaces, as developed during a few past decades. We unify and extend recent results of the geometric invariance theory; new results on deformations of extremals are also included. We show that the theory can be developed by means of the general concept of invariance of a differential form in geometry, which does not require different ad hoc modifications. The concept applies to invariance of Lagrangians, source forms and Euler-Lagrange forms, as well as to extremals of the given variational functional. Equations for generators of invariance transformations of the Lagrangians and the Euler-Lagrange forms are characterized in terms of Lie derivatives. As a consequence of invariance, we derive the global Noether's theorem on existence of conserved currents along extremals, and discuss the meaning of conservation equations. We prove a theorem describing extremals, whose deformations by a vector field are again extremals. The general settings and structures we use admit extension of the global invariance theory to variational principles in physics, especially in field theory.

  17. Observation of magnetic fragmentation in spin ice

    NASA Astrophysics Data System (ADS)

    Petit, S.; Lhotel, E.; Canals, B.; Ciomaga Hatnean, M.; Ollivier, J.; Mutka, H.; Ressouche, E.; Wildes, A. R.; Lees, M. R.; Balakrishnan, G.

    2016-08-01

    Fractionalized excitations that emerge from a many-body system have revealed rich physics and concepts, from composite fermions in two-dimensional electron systems, revealed through the fractional quantum Hall effect, to spinons in antiferromagnetic chains and, more recently, fractionalization of Dirac electrons in graphene and magnetic monopoles in spin ice. Even more surprising is the fragmentation of the degrees of freedom themselves, leading to coexisting and a priori independent ground states. This puzzling phenomenon was recently put forward in the context of spin ice, in which the magnetic moment field can fragment, resulting in a dual ground state consisting of a fluctuating spin liquid, a so-called Coulomb phase, on top of a magnetic monopole crystal. Here we show, by means of neutron scattering measurements, that such fragmentation occurs in the spin ice candidate Nd2Zr2O7. We observe the spectacular coexistence of an antiferromagnetic order induced by the monopole crystallization and a fluctuating state with ferromagnetic correlations. Experimentally, this fragmentation manifests itself through the superposition of magnetic Bragg peaks, characteristic of the ordered phase, and a pinch point pattern, characteristic of the Coulomb phase. These results highlight the relevance of the fragmentation concept to describe the physics of systems that are simultaneously ordered and fluctuating.

  18. Multiperiod Maximum Loss is time unit invariant.

    PubMed

    Kovacevic, Raimund M; Breuer, Thomas

    2016-01-01

    Time unit invariance is introduced as an additional requirement for multiperiod risk measures: for a constant portfolio under an i.i.d. risk factor process, the multiperiod risk should equal the one period risk of the aggregated loss, for an appropriate choice of parameters and independent of the portfolio and its distribution. Multiperiod Maximum Loss over a sequence of Kullback-Leibler balls is time unit invariant. This is also the case for the entropic risk measure. On the other hand, multiperiod Value at Risk and multiperiod Expected Shortfall are not time unit invariant. PMID:27563531

  19. Comment on ``Pairing interaction and Galilei invariance''

    NASA Astrophysics Data System (ADS)

    Arias, J. M.; Gallardo, M.; Gómez-Camacho, J.

    1999-05-01

    A recent article by Dussel, Sofia, and Tonina studies the relation between Galilei invariance and dipole energy weighted sum rule (EWSR). The authors find that the pairing interaction, which is neither Galilei nor Lorentz invariant, produces big changes in the EWSR and in effective masses of the nucleons. They argue that these effects of the pairing force could be realistic. In this Comment we stress the validity of Galilei invariance to a very good approximation in this context of low-energy nuclear physics and show that the effective masses and the observed change in the EWSR for the electric dipole operator relative to its classical value are compatible with this symmetry.

  20. Callisto Crater Chain Mosaic

    NASA Technical Reports Server (NTRS)

    1997-01-01

    This mosaic of three images shows an area within the Valhalla region on Jupiter's moon, Callisto. North is to the top of the mosaic and the Sun illuminates the surface from the left. The smallest details that can be discerned in this picture are knobs and small impact craters about 160 meters (175 yards) across. The mosaic covers an area approximately 45 kilometers (28 miles) across. It shows part of a prominent crater chain located on the northern part of the Valhalla ring structure.

    Crater chains can form from the impact of material ejected from large impacts (forming secondary chains) or by the impact of a fragmented projectile, perhaps similar to the Shoemaker-Levy 9 cometary impacts into Jupiter in July 1994. It is believed this crater chain was formed by the impact of a fragmented projectile. The images which form this mosaic were obtained by the solid state imaging system aboard NASA's Galileo spacecraft on Nov. 4, 1996 (Universal Time).

    Launched in October 1989, Galileo entered orbit around Jupiter on December 7, 1995. The spacecraft's mission is to conduct detailed studies of the giant planet, its largest moons and the Jovian magnetic environment. The Jet Propulsion Laboratory, Pasadena, CA manages the mission for NASA's Office of Space Science, Washington, DC.

    This image and other images and data received from Galileo are posted on the World Wide Web Galileo mission home page at http://galileo.jpl.nasa.gov. Background information and educational context for the images can be found at http:// www.jpl.nasa.gov/galileo/sepo.

  1. Invarient patterns in articulatory movements

    NASA Astrophysics Data System (ADS)

    Bonaventura, Patrizia

    2004-04-01

    The purpose of the reported study is to discover an effective method of characterizing movement patterns of the crucial articulator as the function of an abstract syllable magnitude and the adjacent boundary, and at the same time to investigate effects of prosodic control on utterance organization. In particular, the speed of movement when a flesh point on the tongue blade or the lower lip crosses a selected position relative to the occlusion plane is examined. The time of such crossing provides an effective measure of syllable timing and syllable duration according to previous work. In the present work, using a very limited vocabulary with only a few consonants and one vowel as the key speech materials, effects of contrastive emphasis on demisyllabic movement patterns were studied. The theoretical framework for this analysis is the C/D model of speech production in relation to the concept of an invariant part of selected articulatory movements. The results show evidence in favor of the existence of ``iceberg'' patterns, but a linear dependence of slope on the total excursion of the demisyllabic movement, instead of the approximate constancy of the threshold crossing speed as suggested in the original proposal of the iceberg, has been found. Accordingly, a revision of the original concept of iceberg, seems necessary. This refinement is consistent with the C/D model assumption on ``prominence control'' that the syllable magnitude determines the movement amplitude, accompanying directly related syllable duration change. In this assumption, the movement of a consonantal component should also be proportional to syllable magnitude. The results suggests, however, systematic outliers deviating from the linear dependence of movement speed on excursion. This deviation may be caused by the effect of the immediately following boundary, often referred to as phrase-final elongation. Thesis advisor: Osamu Fujimura Copies of this thesis written in English can be obtained from

  2. Heavy fragment radioactivities

    SciTech Connect

    Price, P.B.

    1987-12-10

    This recently discovered mode of radioactive decay, like alpha decay and spontaneous fission, is believed to involve tunneling through the deformation-energy barrier between a very heavy nucleus and two separated fragments the sum of whose masses is less than the mass of the parent nucleus. In all known cases the heavier of the two fragments is close to doubly magic /sup 208/Pb, and the lighter fragment has even Z. Four isotopes of Ra are known to emit /sup 14/C nuclei; several isotopes of U as well as /sup 230/Th and /sup 231/Pa emit Ne nuclei; and /sup 234/U exhibits four hadronic decay modes: alpha decay, spontaneous fission, Ne decay and Mg decay.

  3. Okazaki fragment metabolism.

    PubMed

    Balakrishnan, Lata; Bambara, Robert A

    2013-02-01

    Cellular DNA replication requires efficient copying of the double-stranded chromosomal DNA. The leading strand is elongated continuously in the direction of fork opening, whereas the lagging strand is made discontinuously in the opposite direction. The lagging strand needs to be processed to form a functional DNA segment. Genetic analyses and reconstitution experiments identified proteins and multiple pathways responsible for maturation of the lagging strand. In both prokaryotes and eukaryotes the lagging-strand fragments are initiated by RNA primers, which are removed by a joining mechanism involving strand displacement of the primer into a flap, flap removal, and then ligation. Although the prokaryotic fragments are ~1200 nucleotides long, the eukaryotic fragments are much shorter, with lengths determined by nucleosome periodicity. The prokaryotic joining mechanism is simple and efficient. The eukaryotic maturation mechanism involves many enzymes, possibly three pathways, and regulation that can shift from high efficiency to high fidelity.

  4. Allogenous tooth fragment reattachment

    PubMed Central

    Maitin, Nitin; Maitin, Shipra; Rastogi, Khushboo; Bhushan, Rajarshi

    2013-01-01

    Coronal fractures of the anterior teeth are a common form of dental trauma and its sequelae may impair the establishment and accomplishment of an adequate treatment plan. Among the various treatment options, reattachment of a crown fragment obtained from a previously extracted tooth is a conservative treatment that should be considered for crown fractures of anterior teeth. This article reports reattachment of an allogenous tooth fragment in a fractured maxillary lateral incisor in a 38-year-old patient. It is suggested that allogenous reattachment in a fractured anterior tooth serves to be a better alternative and should be further researched. Aesthetic and functional rehabilitation of a fractured complicated anterior crown using allogenous tooth fragment is a better alternative to other more conventional treatment options. PMID:23845684

  5. IMPACT fragmentation model developments

    NASA Astrophysics Data System (ADS)

    Sorge, Marlon E.; Mains, Deanna L.

    2016-09-01

    The IMPACT fragmentation model has been used by The Aerospace Corporation for more than 25 years to analyze orbital altitude explosions and hypervelocity collisions. The model is semi-empirical, combining mass, energy and momentum conservation laws with empirically derived relationships for fragment characteristics such as number, mass, area-to-mass ratio, and spreading velocity as well as event energy distribution. Model results are used for several types of analysis including assessment of short-term risks to satellites from orbital altitude fragmentations, prediction of the long-term evolution of the orbital debris environment and forensic assessments of breakup events. A new version of IMPACT, version 6, has been completed and incorporates a number of advancements enabled by a multi-year long effort to characterize more than 11,000 debris fragments from more than three dozen historical on-orbit breakup events. These events involved a wide range of causes, energies, and fragmenting objects. Special focus was placed on the explosion model, as the majority of events examined were explosions. Revisions were made to the mass distribution used for explosion events, increasing the number of smaller fragments generated. The algorithm for modeling upper stage large fragment generation was updated. A momentum conserving asymmetric spreading velocity distribution algorithm was implemented to better represent sub-catastrophic events. An approach was developed for modeling sub-catastrophic explosions, those where the majority of the parent object remains intact, based on estimated event energy. Finally, significant modifications were made to the area-to-mass ratio distribution to incorporate the tendencies of different materials to fragment into different shapes. This ability enabled better matches between the observed area-to-mass ratios and those generated by the model. It also opened up additional possibilities for post-event analysis of breakups. The paper will discuss

  6. Topological invariants and renormalization of Lorenz maps

    NASA Astrophysics Data System (ADS)

    Silva, Luis; Sousa Ramos, J.

    2002-02-01

    We prove that the invariants of the topological semiconjugation of Lorenz maps with β-transformations remains constant on the renormalization archipelagoes and analyze how the dynamics on the archipelagoes depends on its structure.

  7. Position, rotation, and intensity invariant recognizing method

    DOEpatents

    Ochoa, Ellen; Schils, George F.; Sweeney, Donald W.

    1989-01-01

    A method for recognizing the presence of a particular target in a field of view which is target position, rotation, and intensity invariant includes the preparing of a target-specific invariant filter from a combination of all eigen-modes of a pattern of the particular target. Coherent radiation from the field of view is then imaged into an optical correlator in which the invariant filter is located. The invariant filter is rotated in the frequency plane of the optical correlator in order to produce a constant-amplitude rotational response in a correlation output plane when the particular target is present in the field of view. Any constant response is thus detected in the output The U.S. Government has rights in this invention pursuant to Contract No. DE-AC04-76DP00789 between the U.S. Department of Energy and AT&T Technologies, Inc.

  8. Scattering matrix invariants of Floquet topological insulators

    NASA Astrophysics Data System (ADS)

    Fulga, I. C.; Maksymenko, M.

    2016-02-01

    Similar to static systems, periodically driven systems can host a variety of topologically nontrivial phases. Unlike the case of static Hamiltonians, the topological indices of bulk Floquet bands may fail to describe the presence and robustness of edge states, prompting the search for new invariants. We develop a unified description of topological phases and their invariants in driven systems by using scattering theory. We show that scattering matrix invariants correctly describe the topological phase, even when all bulk Floquet bands are trivial. Additionally, we use scattering theory to introduce and analyze new periodically driven phases, such as weak topological Floquet insulators, for which invariants were previously unknown. We highlight some of their similarities with static systems, including robustness to disorder, as well as some of the features unique to driven systems, showing that the weak phase may be destroyed by breaking translational symmetry not in space, but in time.

  9. On Lorentz invariants in relativistic magnetic reconnection

    NASA Astrophysics Data System (ADS)

    Yang, Shu-Di; Wang, Xiao-Gang

    2016-08-01

    Lorentz invariants whose nonrelativistic correspondences play important roles in magnetic reconnection are discussed in this paper. Particularly, the relativistic invariant of the magnetic reconnection rate is defined and investigated in a covariant two-fluid model. Certain Lorentz covariant representations for energy conversion and magnetic structures in reconnection processes are also investigated. Furthermore, relativistic measures for topological features of reconnection sites, particularly magnetic nulls and separatrices, are analyzed.

  10. Galilean invariance at quantum Hall edge

    NASA Astrophysics Data System (ADS)

    Moroz, Sergej; Hoyos, Carlos; Radzihovsky, Leo

    2015-05-01

    We construct the theory of a chiral Luttinger liquid that lives on the boundary of a Galilean invariant quantum Hall fluid. In contrast to previous studies, Galilean invariance of the total (bulk plus edge) theory is guaranteed. We consider electromagnetic response at the edge and calculate momentum- and frequency-dependent electric conductivity and argue that its experimental measurement can provide a new means to determine the "shift" and bulk Hall viscosity.

  11. Computer calculation of Witten's 3-manifold invariant

    NASA Astrophysics Data System (ADS)

    Freed, Daniel S.; Gompf, Robert E.

    1991-10-01

    Witten's 2+1 dimensional Chern-Simons theory is exactly solvable. We compute the partition function, a topological invariant of 3-manifolds, on generalized Seifert spaces. Thus we test the path integral using the theory of 3-manifolds. In particular, we compare the exact solution with the asymptotic formula predicted by perturbation theory. We conclude that this path integral works as advertised and gives an effective topological invariant.

  12. Invariant distributions on compact homogeneous spaces

    SciTech Connect

    Gorbatsevich, V V

    2013-12-31

    In this paper, we study distributions on compact homogeneous spaces, including invariant distributions and also distributions admitting a sub-Riemannian structure. We first consider distributions of dimension 1 and 2 on compact homogeneous spaces. After this, we study the cases of compact homogeneous spaces of dimension 2, 3, and 4 in detail. Invariant distributions on simply connected compact homogeneous spaces are also treated. Bibliography: 18 titles.

  13. Completion of autobuilt protein models using a database of protein fragments

    SciTech Connect

    Cowtan, Kevin

    2012-04-01

    Two developments in the process of automated protein model building in the Buccaneer software are described: the use of a database of protein fragments in improving the model completeness and the assembly of disconnected chain fragments into complete molecules. Two developments in the process of automated protein model building in the Buccaneer software are presented. A general-purpose library for protein fragments of arbitrary size is described, with a highly optimized search method allowing the use of a larger database than in previous work. The problem of assembling an autobuilt model into complete chains is discussed. This involves the assembly of disconnected chain fragments into complete molecules and the use of the database of protein fragments in improving the model completeness. Assembly of fragments into molecules is a standard step in existing model-building software, but the methods have not received detailed discussion in the literature.

  14. Four motional invariants in axisymmetric tori equilibria

    SciTech Connect

    A ring gren, O.; Moiseenko, V.E.

    2006-05-15

    In addition to the standard set ({epsilon},{mu},p{sub {phi}}) of three invariants in axisymmetric tori, there exists a fourth independent radial drift invariant I{sub r}. For confined particles, the net radial drift has to be zero, whereby the drift orbit average I{sub r}= of the gyro center radial Clebsch coordinate is constant. To lowest order in the banana width, the radial invariant is the gyro center radial coordinate r{sub 0}(x,v), and to this order the gyro center moves on a magnetic flux surface. The gyro center orbit projected on the (r,z) plane determines the radial invariant and first order banana width corrections to I{sub r} are calculated. The radial drift invariant exists for trapped as well as passing particles. The new invariant is applied to construct Vlasov equilibria, where the magnetic field satisfies a generalized Grad-Shafranov equation with a poloidal plasma current and a bridge to ideal magnetohydrodynamic equilibria is found. For equilibria with sufficiently small banana widths and radial drift excursions, the approximation I{sub r}{approx_equal}r{sub 0}(x,v) can be used for the equilibrium state.

  15. Shift-invariant target in allocation problems.

    PubMed

    Mandal, Saumen; Biswas, Atanu

    2014-07-10

    We provide a template for finding target allocation proportions in optimal allocation designs where the target will be invariant for both shifts in location and scale of the response distributions. One possible application of such target allocation proportions is to carry out a response-adaptive allocation. While most of the existing designs are invariant for any change in scale of the underlying distributions, they are not location invariant in most of the cases. First, we indicate this serious flaw in the existing literature and illustrate how this lack of location invariance makes the performance of the designs very poor in terms of allocation for any drastic change in location, such as the changes from degrees centigrade to degrees Fahrenheit. We illustrate that unless a target allocation is location invariant, it might lead to a completely irrelevant and useless target for allocation. Then we discuss how such location invariance can be achieved for general continuous responses. We illustrate the proposed method using some real clinical trial data. We also indicate the possible extension of the procedure for more than two treatments at hand and in the presence of covariates.

  16. Target fragmentation in radiobiology

    NASA Technical Reports Server (NTRS)

    Wilson, John W.; Cucinotta, Francis A.; Shinn, Judy L.; Townsend, Lawrence W.

    1993-01-01

    Nuclear reactions in biological systems produce low-energy fragments of the target nuclei seen as local high events of linear energy transfer (LET). A nuclear-reaction formalism is used to evaluate the nuclear-induced fields within biosystems and their effects within several biological models. On the basis of direct ionization interaction, one anticipates high-energy protons to have a quality factor and relative biological effectiveness (RBE) of unity. Target fragmentation contributions raise the effective quality factor of 10 GeV protons to 3.3 in reasonable agreement with RBE values for induced micronuclei in bean sprouts. Application of the Katz model indicates that the relative increase in RBE with decreasing exposure observed in cell survival experiments with 160 MeV protons is related solely to target fragmentation events. Target fragment contributions to lens opacity given an RBE of 1.4 for 2 GeV protons in agreement with the work of Lett and Cox. Predictions are made for the effective RBE for Harderian gland tumors induced by high-energy protons. An exposure model for lifetime cancer risk is derived from NCRP 98 risk tables, and protraction effects are examined for proton and helium ion exposures. The implications of dose rate enhancement effects on space radiation protection are considered.

  17. Fragment Separator ACCULINNA-2

    SciTech Connect

    Krupko, S. A.; Fomichev, A. S.; Chudoba, V.; Daniel, A. V.; Golovkov, M. S.; Gorshkov, V. A.; Oganessian, Yu. Ts.; Sidorchuk, S. I.; Slepnev, R. S.; Stepantsov, S. V.; Ter-Akopian, G. M.; Wolski, R.; Grigorenko, L. V.; Tarasov, O. B.; Ershov, S. N.; Lukyanov, V. K.; Danilin, B. V.; Korsheninnikov, A. A.; Goldberg, V. Z.; Mukha, I. G.

    2010-04-30

    Project of a new in-flight fragment separator is proposed as a part of the third generation DRIBs facilities in Dubna. As compared to the existing separator ACCULINNA, beam intensity should be increased by a factor 10-15, the beam quality improved and the RIB assortment should broaden considerably at ACCULINNA-2. Research program and structure are outlined for the new instrument.

  18. Comment on diquark fragmentation

    SciTech Connect

    Fredriksson, S.; Larsson, T.

    1983-07-01

    We discuss diquark fragmentation and suggest that a spectator uu system in deep-inelastic lepton-nucleon scattering has a larger breakup probability than a ud system. The reason for this is argued to be that half of the leftover ud systems are in bound (ud)/sub 0/ diquark configurations, while no such bound uu diquarks exist.

  19. On gauge-invariant and phase-invariant spinor analysis. II

    NASA Astrophysics Data System (ADS)

    Buchdahl, H. A.

    1992-01-01

    Granted customary definitions, the operations of juggling indices and covariant differentiation do not commute with one another in a Weyl space. The same noncommutativity obtains in the spinor calculus of Infeld and van der Waerden. Gauge-invariant and phase-invariant calculations therefore tend to be rather cumbersome. Here, a modification of the definition of covariant derivative leads immediately to a manifestly gauge-invariant and phase-invariant version of Weyl-Cartan space and of the two-spinor calculus associated with it in which the metric tensor and the metric spinor are both covariant constant.

  20. A sampling approach for protein backbone fragment conformations.

    PubMed

    Yu, J Y; Zhang, W

    2013-01-01

    In protein structure prediction, backbone fragment bias information can narrow down the conformational space of the whole polypeptide chain significantly. Unlike existing methods that use fragments as building blocks, the paper presents a probabilistic sampling approach for protein backbone torsion angles by modelling angular correlation of (phi, psi) with a directional statistics distribution. Given a protein sequence and secondary structure information, this method samples backbone fragments conformations by using a backtrack sampling algorithm for the hidden Markov model with multiple inputs and a single output. The proposed approach is applied to a fragment library, and some well-known structural motifs are sampled very well on the optimal path. Computational results show that the method can help to obtain native-like backbone fragments conformations. PMID:23777175

  1. Model of the Newtonian cosmology: Symmetries, invariant and partially invariant solutions

    NASA Astrophysics Data System (ADS)

    Klebanov, I.; Startsun, O.; Ivanov, S.

    2016-10-01

    Symmetry group of the equation system of ideal nonrelativistic self-gravitating fluid with zero pressure is calculated. Submodel invariant under the subgroup of rotations SO(3) is built and symmetry group of the factorsystem is calculated. A particular analytical invariant solution of the factorsystem is obtained.

  2. Cryobiology of coral fragments.

    PubMed

    Hagedorn, Mary; Farrell, Ann; Carter, Virginia L

    2013-02-01

    Around the world, coral reefs are dying due to human influences, and saving habitat alone may not stop this destruction. This investigation focused on the biological processes that will provide the first steps in understanding the cryobiology of whole coral fragments. Coral fragments are a partnership of coral tissue and endosymbiotic algae, Symbiodinium sp., commonly called zooxanthellae. These data reflected their separate sensitivities to chilling and a cryoprotectant (dimethyl sulfoxide) for the coral Pocillopora damicornis, as measured by tissue loss and Pulse Amplitude Modulated fluorometry 3weeks post-treatment. Five cryoprotectant treatments maintained the viability of the coral tissue and zooxanthellae at control values (1M dimethyl sulfoxide at 1.0, 1.5 and 2.0h exposures, and 1.5M dimethyl sulfoxide at 1.0 and 1.5h exposures, P>0.05, ANOVA), whereas 2M concentrations did not (P<0.05, ANOVA). A seasonal response to chilling was observed in the coral tissue, but not in the zooxanthellae. During the winter when the fragments were chilled, the coral tissue remained relatively intact (∼25% loss) post-treatment, but the zooxanthellae numbers in the tissue declined after 5min of chilling (P<0.05, ANOVA). However, in the late spring, coral tissue (∼75% loss) and zooxanthellae numbers declined in response to chilling alone (P<0.05, ANOVA). When a cryoprotectant (1M dimethyl sulfoxide) was used in concert with chilling it protected the coral against tissue loss after 45min of cryoprotectant exposure (P>0.05, ANOVA), but it did not protect against the loss of zooxanthellae (P<0.05, ANOVA). The zooxanthellae are the most sensitive element in the coral fragment complex and future cryopreservation protocols must be guided by their greater sensitivity.

  3. Local and gauge invariant observables in gravity

    NASA Astrophysics Data System (ADS)

    Khavkine, Igor

    2015-09-01

    It is well known that general relativity (GR) does not possess any non-trivial local (in a precise standard sense) and diffeomorphism invariant observable. We propose a generalized notion of local observables, which retain the most important properties that follow from the standard definition of locality, yet is flexible enough to admit a large class of diffeomorphism invariant observables in GR. The generalization comes at a small price—that the domain of definition of a generalized local observable may not cover the entire phase space of GR and two such observables may have distinct domains. However, the subset of metrics on which generalized local observables can be defined is in a sense generic (its open interior is non-empty in the Whitney strong topology). Moreover, generalized local gauge invariant observables are sufficient to separate diffeomorphism orbits on this admissible subset of the phase space. Connecting the construction with the notion of differential invariants gives a general scheme for defining generalized local gauge invariant observables in arbitrary gauge theories, which happens to agree with well-known results for Maxwell and Yang-Mills theories.

  4. Defending the beauty of the Invariance Principle

    NASA Astrophysics Data System (ADS)

    Barkana, Itzhak

    2014-01-01

    Customary stability analysis methods for nonlinear nonautonomous systems seem to require a strict condition of uniform continuity. Although extensions of LaSalle's Invariance Principle to nonautonomous systems that mitigate this condition have been available for a long time, they have remained surprisingly unknown or open to misinterpretations. The large scope of the Principle might have misled the prospective users and its application to Control problems has been received with amazing yet clear uneasiness. Counterexamples have been used in order to claim that the Invariance Principle cannot be applied to nonlinear nonautonomous systems. Because the original formulation of the Invariance Principle still imposes conditions that are not necessarily needed, this paper presents a new Invariance Principle that further mitigates previous conditions and thus further expands the scope of stability analysis. A brief comparative review of various alternatives to stability analysis of nonautonomous nonlinear systems and their implications is also presented in order to illustrate that thorough analysis of same examples may actually confirm the efficiency of the Invariance Principle approach when dealing with stability of nonautonomous nonlinear systems problems that may look difficult or even unsolvable otherwise.

  5. Dimensional Analysis Using Toric Ideals: Primitive Invariants

    PubMed Central

    Atherton, Mark A.; Bates, Ronald A.; Wynn, Henry P.

    2014-01-01

    Classical dimensional analysis in its original form starts by expressing the units for derived quantities, such as force, in terms of power products of basic units etc. This suggests the use of toric ideal theory from algebraic geometry. Within this the Graver basis provides a unique primitive basis in a well-defined sense, which typically has more terms than the standard Buckingham approach. Some textbook examples are revisited and the full set of primitive invariants found. First, a worked example based on convection is introduced to recall the Buckingham method, but using computer algebra to obtain an integer matrix from the initial integer matrix holding the exponents for the derived quantities. The matrix defines the dimensionless variables. But, rather than this integer linear algebra approach it is shown how, by staying with the power product representation, the full set of invariants (dimensionless groups) is obtained directly from the toric ideal defined by . One candidate for the set of invariants is a simple basis of the toric ideal. This, although larger than the rank of , is typically not unique. However, the alternative Graver basis is unique and defines a maximal set of invariants, which are primitive in a simple sense. In addition to the running example four examples are taken from: a windmill, convection, electrodynamics and the hydrogen atom. The method reveals some named invariants. A selection of computer algebra packages is used to show the considerable ease with which both a simple basis and a Graver basis can be found. PMID:25436774

  6. Fragmentation of cancer cells

    NASA Astrophysics Data System (ADS)

    Vanapalli, Siva; Kamyabi, Nabiollah

    Tumor cells have to travel through blood capillaries to be able to metastasize and colonize in distant organs. Among the numerous cells that are shed by the primary tumor, very few survive in circulation. In vivo studies have shown that tumor cells can undergo breakup at microcapillary junctions affecting their survival. It is currently unclear what hydrodynamic and biomechanical factors contribute to fragmentation and moreover how different are the breakup dynamics of highly and weakly metastatic cells. In this study, we use microfluidics to investigate flow-induced breakup of prostate and breast cancer cells. We observe several different modes of breakup of cancer cells, which have striking similarities with breakup of viscous drops. We quantify the breakup time and find that highly metastatic cancer cells take longer to breakup than lowly metastatic cells suggesting that tumor cells may dynamically modify their deformability to avoid fragmentation. We also identify the role that cytoskeleton and membrane plays in the breakup process. Our study highlights the important role that tumor cell fragmentation plays in cancer metastasis. Cancer Prevention and Research Institute of Texas.

  7. Fracture, failure, and fragmentation

    SciTech Connect

    Dienes, J.K.

    1984-01-01

    Though continuum descriptions of material behavior are useful for many kinds of problems, particularly those involving plastic flow, a more general approach is required when the failure is likely to involve growth and coalescence of a large number of fractures, as in fragmentation. Failures of this kind appear frequently in rapid dynamic processes such as those resulting from impacts and explosions, particularly in the formation of spall fragments. In the first part of this paper an approach to formulating constitutive relations that accounts for the opening, shear and growth of an ensemble of cracks is discussed. The approach also accounts for plastic flow accompanying fragmentation. The resulting constitutive relations have been incorporated into a Lagrangean computer program. In the second part of this paper a theoretical approach to coalescence is described. The simplest formulation makes use of a linear Liouville equation, with crack growth limited by the mean free path of cracks, assumed constant. This approach allows for an anisotropic distribution of cracks. An alternative approach is also described in which the decrease of the mean free path with increasing crack size is accounted for, but the crack distribution is assumed isotropic. A reduction of the governing Liouville equation to an ordinary differential equation of third order is possible, and the result can be used to determine how mean-free-path decreases with increasing crack size.

  8. Markov Chain Monte Carlo and Irreversibility

    NASA Astrophysics Data System (ADS)

    Ottobre, Michela

    2016-06-01

    Markov Chain Monte Carlo (MCMC) methods are statistical methods designed to sample from a given measure π by constructing a Markov chain that has π as invariant measure and that converges to π. Most MCMC algorithms make use of chains that satisfy the detailed balance condition with respect to π; such chains are therefore reversible. On the other hand, recent work [18, 21, 28, 29] has stressed several advantages of using irreversible processes for sampling. Roughly speaking, irreversible diffusions converge to equilibrium faster (and lead to smaller asymptotic variance as well). In this paper we discuss some of the recent progress in the study of nonreversible MCMC methods. In particular: i) we explain some of the difficulties that arise in the analysis of nonreversible processes and we discuss some analytical methods to approach the study of continuous-time irreversible diffusions; ii) most of the rigorous results on irreversible diffusions are available for continuous-time processes; however, for computational purposes one needs to discretize such dynamics. It is well known that the resulting discretized chain will not, in general, retain all the good properties of the process that it is obtained from. In particular, if we want to preserve the invariance of the target measure, the chain might no longer be reversible. Therefore iii) we conclude by presenting an MCMC algorithm, the SOL-HMC algorithm [23], which results from a nonreversible discretization of a nonreversible dynamics.

  9. Set-based corral control in stochastic dynamical systems: Making almost invariant sets more invariant

    PubMed Central

    Forgoston, Eric; Billings, Lora; Yecko, Philip; Schwartz, Ira B.

    2011-01-01

    We consider the problem of stochastic prediction and control in a time-dependent stochastic environment, such as the ocean, where escape from an almost invariant region occurs due to random fluctuations. We determine high-probability control-actuation sets by computing regions of uncertainty, almost invariant sets, and Lagrangian coherent structures. The combination of geometric and probabilistic methods allows us to design regions of control, which provide an increase in loitering time while minimizing the amount of control actuation. We show how the loitering time in almost invariant sets scales exponentially with respect to the control actuation, causing an exponential increase in loitering times with only small changes in actuation force. The result is that the control actuation makes almost invariant sets more invariant. PMID:21456830

  10. Fragmentation under the Scaling Symmetry and Turbulent Cascade with Intermittency

    NASA Technical Reports Server (NTRS)

    Gorokhovski, M.

    2003-01-01

    Fragmentation plays an important role in a variety of physical, chemical, and geological processes. Examples include atomization in sprays, crushing of rocks, explosion and impact of solids, polymer degradation, etc. Although each individual action of fragmentation is a complex process, the number of these elementary actions is large. It is natural to abstract a simple 'effective' scenario of fragmentation and to represent its essential features. One of the models is the fragmentation under the scaling symmetry: each breakup action reduces the typical length of fragments, r (right arrow) alpha r, by an independent random multiplier alpha (0 < alpha < 1), which is governed by the fragmentation intensity spectrum q(alpha), integral(sup 1)(sub 0) q(alpha)d alpha = 1. This scenario has been proposed by Kolmogorov (1941), when he considered the breakup of solid carbon particle. Describing the breakup as a random discrete process, Kolmogorov stated that at latest times, such a process leads to the log-normal distribution. In Gorokhovski & Saveliev, the fragmentation under the scaling symmetry has been reviewed as a continuous evolution process with new features established. The objective of this paper is twofold. First, the paper synthesizes and completes theoretical part of Gorokhovski & Saveliev. Second, the paper shows a new application of the fragmentation theory under the scale invariance. This application concerns the turbulent cascade with intermittency. We formulate here a model describing the evolution of the velocity increment distribution along the progressively decreasing length scale. The model shows that when the turbulent length scale gets smaller, the velocity increment distribution has central growing peak and develops stretched tails. The intermittency in turbulence is manifested in the same way: large fluctuations of velocity provoke highest strain in narrow (dissipative) regions of flow.

  11. Gauge-invariant massive BF models

    NASA Astrophysics Data System (ADS)

    Bizdadea, Constantin; Saliu, Solange-Odile

    2016-02-01

    Consistent interactions that can be added to a free, Abelian gauge theory comprising a BF model and a finite set of massless real scalar fields are constructed from the deformation of the solution to the master equation based on specific cohomological techniques. Under the hypotheses of analyticity in the coupling constant, Lorentz covariance, spacetime locality, and Poincaré invariance, supplemented with the requirement of the preservation of the number of derivatives on each field with respect to the free theory, we see that the deformation procedure leads to two classes of gauge-invariant interacting theories with a mass term for the BF vector field A_{μ } with U(1) gauge invariance. In order to derive this result we have not used the Higgs mechanism based on spontaneous symmetry breaking.

  12. Lorentz invariance in chiral kinetic theory.

    PubMed

    Chen, Jing-Yuan; Son, Dam T; Stephanov, Mikhail A; Yee, Ho-Ung; Yin, Yi

    2014-10-31

    We show that Lorentz invariance is realized nontrivially in the classical action of a massless spin-1/2 particle with definite helicity. We find that the ordinary Lorentz transformation is modified by a shift orthogonal to the boost vector and the particle momentum. The shift ensures angular momentum conservation in particle collisions and implies a nonlocality of the collision term in the Lorentz-invariant kinetic theory due to side jumps. We show that 2/3 of the chiral-vortical effect for a uniformly rotating particle distribution can be attributed to the magnetic moment coupling required by the Lorentz invariance. We also show how the classical action can be obtained by taking the classical limit of the path integral for a Weyl particle. PMID:25396362

  13. Gauge-Invariant Formulation of Circular Dichroism.

    PubMed

    Raimbault, Nathaniel; de Boeij, Paul L; Romaniello, Pina; Berger, J A

    2016-07-12

    Standard formulations of magnetic response properties, such as circular dichroism spectra, are plagued by gauge dependencies, which can lead to unphysical results. In this work, we present a general gauge-invariant and numerically efficient approach for the calculation of circular dichroism spectra from the current density. First we show that in this formulation the optical rotation tensor, the response function from which circular dichroism spectra can be obtained, is independent of the origin of the coordinate system. We then demonstrate that its trace is independent of the gauge origin of the vector potential. We also show how gauge invariance can be retained in practical calculations with finite basis sets. As an example, we explain how our method can be applied to time-dependent current-density-functional theory. Finally, we report gauge-invariant circular dichroism spectra obtained using the adiabatic local-density approximation. The circular dichroism spectra we thus obtain are in good agreement with experiment. PMID:27295541

  14. Scale without conformal invariance at three loops

    NASA Astrophysics Data System (ADS)

    Fortin, Jean-François; Grinstein, Benjamín; Stergiou, Andreas

    2012-08-01

    We carry out a three-loop computation that establishes the existence of scale without conformal invariance in dimensional regularization with the MS scheme in unitary theories in d = 4 - ɛ spacetime dimensions. We also comment on the effects of scheme changes in theories with many couplings, as well as in theories that live on non-conformal scale-invariant renormalization group trajectories. Stability properties of such trajectories are analyzed, revealing both attractive and repulsive directions in a specific example. We explain how our results are in accord with those of Jack & Osborn on a c-theorem in d = 4 (and d = 4 - ɛ) dimensions. Finally, we point out that limit cycles with turning points are unlike limit cycles with continuous scale invariance.

  15. The Grassmannian origin of dual superconformal invariance

    NASA Astrophysics Data System (ADS)

    Arkani-Hamed, Nima; Cachazo, Freddy; Cheung, Clifford

    2010-03-01

    A dual formulation of the S Matrix for mathcal {N} = 4 SYM has recently been presented, where all leading singularities of n-particle N k-2MHV amplitudes are given as an integral over the Grassmannian G( k, n), with cyclic symmetry, parity and superconformal invariance manifest. In this short note we show that the dual superconformal invariance of this object is also manifest. The geometry naturally suggests a partial integration and simple change of variable to an integral over G( k - 2, n). This change of variable precisely corresponds to the mapping between usual momentum variables and the “momentum twistors” introduced by Hodges, and yields an elementary derivation of the momentumtwistor space formula very recently presented by Mason and Skinner, which is manifestly dual superconformal invariant. Thus the G( k, n) Grassmannian formulation allows a direct understanding of all the important symmetries of mathcal {N} = 4 SYM scattering amplitudes.

  16. Gauge-invariant decomposition of nucleon spin

    SciTech Connect

    Wakamatsu, M.

    2010-06-01

    We investigate the relation between the known decompositions of the nucleon spin into its constituents, thereby clarifying in what respect they are common and in what respect they are different essentially. The decomposition recently proposed by Chen et al. can be thought of as a nontrivial generalization of the gauge-variant Jaffe-Manohar decomposition so as to meet the gauge-invariance requirement of each term of the decomposition. We however point out that there is another gauge-invariant decomposition of the nucleon spin, which is closer to the Ji decomposition, while allowing the decomposition of the gluon total angular momentum into the spin and orbital parts. After clarifying the reason why the gauge-invariant decomposition of the nucleon spin is not unique, we discuss which decomposition is more preferable from an experimental viewpoint.

  17. Modular categories and 3-manifold invariants

    SciTech Connect

    Tureav, V.G. )

    1992-06-01

    The aim of this paper is to give a concise introduction to the theory of knot invariants and 3-manifold invariants which generalize the Jones polynomial and which may be considered as a mathematical version of the Witten invariants. Such a theory was introduced by N. Reshetikhin and the author on the ground of the theory of quantum groups. here we use more general algebraic objects, specifically, ribbon and modular categories. Such categories in particular arise as the categories of representations of quantum groups. The notion of modular category, interesting in itself, is closely related to the notion of modular tensor category in the sense of G. Moore and N. Seiberg. For simplicity we restrict ourselves in this paper to the case of closed 3-manifolds.

  18. Rainbow gravity and scale-invariant fluctuations

    NASA Astrophysics Data System (ADS)

    Amelino-Camelia, Giovanni; Arzano, Michele; Gubitosi, Giulia; Magueijo, João

    2013-08-01

    We reexamine a recently proposed scenario where the deformed dispersion relations associated with a flow of the spectral dimension to a UV value of 2 leads to a scale-invariant spectrum of cosmological fluctuations, without the need for inflation. In that scenario Einstein gravity was assumed. The theory displays a wavelength-dependent speed of light but by transforming to a suitable “rainbow frame” this feature can be removed, at the expense of modifying gravity. We find that the ensuing rainbow gravity theory is such that gravity switches off at high energy (or at least leads to a universal conformal coupling). This explains why the fluctuations are scale invariant on all scales: there is no horizon scale as such. For dispersion relations that do not lead to exact scale invariance we find instead esoteric inflation in the rainbow frame. We argue that these results shed light on the behavior of gravity under the phenomenon of dimensional reduction.

  19. Relaxing Lorentz invariance in general perturbative anomalies

    SciTech Connect

    Salvio, A.

    2008-10-15

    We analyze the role of Lorentz symmetry in the perturbative nongravitational anomalies for a single family of fermions. The theory is assumed to be translational-invariant, power-counting renormalizable and based on a local action, but is allowed to have general Lorentz violating operators. We study the conservation of global and gauge currents associated with general internal symmetry groups and find, by using a perturbative approach, that Lorentz symmetry does not participate in the clash of symmetries that leads to the anomalies. We first analyze the triangle graphs and prove that there are regulators for which the anomalous part of the Ward identities exactly reproduces the Lorentz-invariant case. Then we show, by means of a regulator independent argument, that the anomaly cancellation conditions derived in Lorentz-invariant theories remain necessary ingredients for anomaly freedom.

  20. Loewner Chains

    NASA Astrophysics Data System (ADS)

    Bauer, Michel; Bernard, Denis

    These lecture notes on 2D growth processes are divided in two parts. The first part is a non-technical introduction to stochastic Loewner evolutions (SLEs). Their relationship with 2D critical interfaces is illustrated using numerical simulations. Schramm's argument mapping conformally invariant interfaces to SLEs is explained. The second part is a more detailed introduction to the mathematically challenging problems of 2D growth processes such as Laplacian growth, diffusion limited aggregation (DLA), etc. Their description in terms of dynamical conformal maps, with discrete or continuous time evolution, is recalled. We end with a conjecture based on possible dendritic anomalies which, if true, would imply that the Hele-Shaw problem and DLA are in different universality classes.

  1. A Cholera Conjugate Vaccine Containing O-specific Polysaccharide (OSP) of V. cholerae O1 Inaba and Recombinant Fragment of Tetanus Toxin Heavy Chain (OSP:rTTHc) Induces Serum, Memory and Lamina Proprial Responses against OSP and Is Protective in Mice

    PubMed Central

    Eckhoff, Grace; Charles, Richelle C.; Alam, Mohammad Murshid; Sultana, Tania; Rashu, Md. Rasheduzzaman; Berger, Amanda; Gonzalez-Escobedo, Geoffrey; Mandlik, Anjali; Bhuiyan, Taufiqur Rahman; Leung, Daniel T.; LaRocque, Regina C.; Harris, Jason B.; Calderwood, Stephen B.; Qadri, Firdausi; Vann, W. F.; Kováč, Pavol; Ryan, Edward T.

    2015-01-01

    Background Vibrio cholerae is the cause of cholera, a severe watery diarrhea. Protection against cholera is serogroup specific. Serogroup specificity is defined by the O-specific polysaccharide (OSP) component of lipopolysaccharide (LPS). Methodology Here we describe a conjugate vaccine for cholera prepared via squaric acid chemistry from the OSP of V. cholerae O1 Inaba strain PIC018 and a recombinant heavy chain fragment of tetanus toxin (OSP:rTTHc). We assessed a range of vaccine doses based on the OSP content of the vaccine (10-50 μg), vaccine compositions varying by molar loading ratio of OSP to rTTHc (3:1, 5:1, 10:1), effect of an adjuvant, and route of immunization. Principle Findings Immunized mice developed prominent anti-OSP and anti-TT serum IgG responses, as well as vibriocidal antibody and memory B cell responses following intramuscular or intradermal vaccination. Mice did not develop anti-squarate responses. Intestinal lamina proprial IgA responses targeting OSP occurred following intradermal vaccination. In general, we found comparable immune responses in mice immunized with these variations, although memory B cell and vibriocidal responses were blunted in mice receiving the highest dose of vaccine (50 μg). We found no appreciable change in immune responses when the conjugate vaccine was administered in the presence or absence of immunoadjuvant alum. Administration of OSP:rTTHc resulted in 55% protective efficacy in a mouse survival cholera challenge model. Conclusion We report development of an Inaba OSP:rTTHc conjugate vaccine that induces memory responses and protection against cholera in mice. Development of an effective cholera conjugate vaccine that induces high level and long-term immune responses against OSP would be beneficial, especially in young children who respond poorly to polysaccharide antigens. PMID:26154421

  2. The invariable plane of the solar system

    NASA Astrophysics Data System (ADS)

    Souami, D.; Souchay, J.

    2012-04-01

    The invariable plane of the solar system is defined as the plane perpendicular to the total angular momentum of the system and passing through its centre of mass. The idea of using the invariable plane as a reference plane in the study of the dynamics of solar system bodies goes back at least to Laplace [3]. The latest study on this plane dates back to Burkhardt [2]. The aim of this work is to determine at best the orientation of the invariable plane with respect to both the ICRS and the equinox-ecliptic of J2000.0, and to evaluate the accuracy of its determination. Such a determination is of fundamental interest in the topic of solar system studies, as suggested by the WGCCRE 2009 [1] for the determination of planet's and satellites' rotational elements. Using the long-term numerical ephemerides DE405, DE406 [6] and INPOP10a[4] over their entire available time span, we compute the total angular momentum of the solar system, as well as the individual contribution of each planet. We then deduce the orientation of the invariable plane for each ephemeris, and establish their relative differences. Preliminary results can be found in [5]. Here we update them with more accurate data, and a more complete analysis of the problem, taking into account the effect of the dwarf planet (1) Ceres as well as two of the biggest asteroids, (4) Vesta and (2) Pallas. Moreover, we give the orbital elements (inclination, longitude of the ascending node) with respect to the invariable plane. As given its accuracy of determination, and its fundamental dynamical meaning, the invariable plane provides a permanent natural reference plane that should be used when studying solar system dynamics, instead of the ecliptic. Thus, we recommend referring to it when working on long-term dynamics.

  3. Some cosmological consequences of Weyl invariance

    SciTech Connect

    Alvarez, Enrique; González-Martín, Sergio; Herrero-Valea, Mario

    2015-03-19

    We examine some Weyl invariant cosmological models in the framework of generalized dilaton gravity, in which the action is made of a set of N conformally coupled scalar fields. It will be shown that when the FRW ansatz for the spacetime metric is assumed, the Ward identity for conformal invariance guarantees that the gravitational equations hold whenever the scalar fields EM do so. It follows that any scale factor can solve the theory provided a non-trivial profile for a dilaton field. In particular, accelerated expansion is a natural solution to the full set of equations.

  4. On adiabatic invariant in generalized Galileon theories

    SciTech Connect

    Ema, Yohei; Jinno, Ryusuke; Nakayama, Kazunori; Mukaida, Kyohei E-mail: jinno@hep-th.phys.s.u-tokyo.ac.jp E-mail: kazunori@hep-th.phys.s.u-tokyo.ac.jp

    2015-10-01

    We consider background dynamics of generalized Galileon theories in the context of inflation, where gravity and inflaton are non-minimally coupled to each other. In the inflaton oscillation regime, the Hubble parameter and energy density oscillate violently in many cases, in contrast to the Einstein gravity with minimally coupled inflaton. However, we find that there is an adiabatic invariant in the inflaton oscillation regime in any generalized Galileon theory. This adiabatic invariant is useful in estimating the expansion law of the universe and also the particle production rate due to the oscillation of the Hubble parameter.

  5. Affine Invariant Character Recognition by Progressive Removing

    NASA Astrophysics Data System (ADS)

    Iwamura, Masakazu; Horimatsu, Akira; Niwa, Ryo; Kise, Koichi; Uchida, Seiichi; Omachi, Shinichiro

    Recognizing characters in scene images suffering from perspective distortion is a challenge. Although there are some methods to overcome this difficulty, they are time-consuming. In this paper, we propose a set of affine invariant features and a new recognition scheme called “progressive removing” that can help reduce the processing time. Progressive removing gradually removes less feasible categories and skew angles by using multiple classifiers. We observed that progressive removing and the use of the affine invariant features reduced the processing time by about 60% in comparison to a trivial one without decreasing the recognition rate.

  6. An invariance theorem in acoustic scattering theory

    NASA Astrophysics Data System (ADS)

    Ha-Duong, T.

    1996-10-01

    Karp's theorem states that if the far-field pattern corresponding to the scattering of a time-harmonic acoustic plane wave by a sound-soft obstacle is invariant under the group of orthogonal transformations in 0266-5611/12/5/007/img1 (rotations in 0266-5611/12/5/007/img2), then the scatterer is a sphere (circle). The theorem is generalized to the case where the invariant group of the far field pattern is only a subgroup of the orthogonal group, and for a class of mixed boundary conditions.

  7. Scaling theory of {{{Z}}_{2}} topological invariants

    NASA Astrophysics Data System (ADS)

    Chen, Wei; Sigrist, Manfred; Schnyder, Andreas P.

    2016-09-01

    For inversion-symmetric topological insulators and superconductors characterized by {{{Z}}2} topological invariants, two scaling schemes are proposed to judge topological phase transitions driven by an energy parameter. The scaling schemes renormalize either the phase gradient or the second derivative of the Pfaffian of the time-reversal operator, through which the renormalization group flow of the driving energy parameter can be obtained. The Pfaffian near the time-reversal invariant momentum is revealed to display a universal critical behavior for a great variety of models examined.

  8. Cosmological constant in scale-invariant theories

    SciTech Connect

    Foot, Robert; Kobakhidze, Archil; Volkas, Raymond R.

    2011-10-01

    The incorporation of a small cosmological constant within radiatively broken scale-invariant models is discussed. We show that phenomenologically consistent scale-invariant models can be constructed which allow a small positive cosmological constant, providing certain relation between the particle masses is satisfied. As a result, the mass of the dilaton is generated at two-loop level. Another interesting consequence is that the electroweak symmetry-breaking vacuum in such models is necessarily a metastable ''false'' vacuum which, fortunately, is not expected to decay on cosmological time scales.

  9. Invariant measures on multimode quantum Gaussian states

    SciTech Connect

    Lupo, C.; Mancini, S.; De Pasquale, A.; Facchi, P.; Florio, G.; Pascazio, S.

    2012-12-15

    We derive the invariant measure on the manifold of multimode quantum Gaussian states, induced by the Haar measure on the group of Gaussian unitary transformations. To this end, by introducing a bipartition of the system in two disjoint subsystems, we use a parameterization highlighting the role of nonlocal degrees of freedom-the symplectic eigenvalues-which characterize quantum entanglement across the given bipartition. A finite measure is then obtained by imposing a physically motivated energy constraint. By averaging over the local degrees of freedom we finally derive the invariant distribution of the symplectic eigenvalues in some cases of particular interest for applications in quantum optics and quantum information.

  10. Ground and satellite observations of auroral fragmentation into patches

    NASA Astrophysics Data System (ADS)

    Shiokawa, Kazuo; Nishi, Katsuki

    2016-07-01

    We review characteristic auroral fragmentation which is the process by which uniform aurora is broken into several fragments to form auroral patches, based on the all-sky camera observations at Tromsoe, Norway and THEMIS chain in Canada. The auroral fragmentation occurs as finger-like structures developing predominantly in meridional direction with speeds of several tens m/s and scale sizes of several tens kilometers without any shearing motion. These features suggest that pressure-driven instability in the balance between the earthward magnetic-tension force and the tailward pressure gradient force in the magnetosphere is the main driving force of the auroral fragmentation. Thus, these observations indicate that auroral fragmentation associated with pressure-driven instability is a process that creates auroral patches. Auroral fragmentation is seen from midnight to dawn local time and usually appears at the beginning of the substorm recovery phase, near the low latitude boundary of the auroral region. One example of plasma and magnetic field observations by the THEMIS satellite in the conjugate magnetosphere shows diamagnetic anti-phase variations of magnetic and plasma pressures with time scales of several to tens minutes associated with the auroral fragmentation. This observation also supports the idea of pressure-driven instability to cause the auroral fragmentation into patches.

  11. A T-matrix theory of galactic heavy-ion fragmentation

    NASA Technical Reports Server (NTRS)

    Norbury, J. W.; Townsend, L. W.; Deutchman, P. A.

    1985-01-01

    The theory of galactic heavy ion fragmentation is furthered by incorporating a T matrix approach into the description of the three step process of abrasion, ablation, and final state interations. The connection between this T matrix and the interaction potential is derived. For resonant states, the substitution of complex energies for real energies in the transition rate is formerly justified for up to third order processes. The previously developed abrasion-ablation fragmentation theory is rederived from first principles and is shown to result from time ordering, classical probability, and zero width resonance approximations. Improvements in the accuracy of the total fragmentation cross sections require an alternative to the latter two approximations. A Lorentz invariant differential abrasion-ablation cross section is derived which explicitly includes the previously derived abrasion total cross sections. It is demonstrated that spectral and angular distributions can be obtained from the general Lorentz invariant form.

  12. Virtual fragment preparation for computational fragment-based drug design.

    PubMed

    Ludington, Jennifer L

    2015-01-01

    Fragment-based drug design (FBDD) has become an important component of the drug discovery process. The use of fragments can accelerate both the search for a hit molecule and the development of that hit into a lead molecule for clinical testing. In addition to experimental methodologies for FBDD such as NMR and X-ray Crystallography screens, computational techniques are playing an increasingly important role. The success of the computational simulations is due in large part to how the database of virtual fragments is prepared. In order to prepare the fragments appropriately it is necessary to understand how FBDD differs from other approaches and the issues inherent in building up molecules from smaller fragment pieces. The ultimate goal of these calculations is to link two or more simulated fragments into a molecule that has an experimental binding affinity consistent with the additive predicted binding affinities of the virtual fragments. Computationally predicting binding affinities is a complex process, with many opportunities for introducing error. Therefore, care should be taken with the fragment preparation procedure to avoid introducing additional inaccuracies.This chapter is focused on the preparation process used to create a virtual fragment database. Several key issues of fragment preparation which affect the accuracy of binding affinity predictions are discussed. The first issue is the selection of the two-dimensional atomic structure of the virtual fragment. Although the particular usage of the fragment can affect this choice (i.e., whether the fragment will be used for calibration, binding site characterization, hit identification, or lead optimization), general factors such as synthetic accessibility, size, and flexibility are major considerations in selecting the 2D structure. Other aspects of preparing the virtual fragments for simulation are the generation of three-dimensional conformations and the assignment of the associated atomic point charges

  13. New Scalings in Nuclear Fragmentation

    SciTech Connect

    Bonnet, E.; Bougault, R.; Galichet, E.; Gagnon-Moisan, F.; Guinet, D.; Lautesse, P.; Marini, P.; Parlog, M.

    2010-10-01

    Fragment partitions of fragmenting hot nuclei produced in central and semiperipheral collisions have been compared in the excitation energy region 4-10 MeV per nucleon where radial collective expansion takes place. It is shown that, for a given total excitation energy per nucleon, the amount of radial collective energy fixes the mean fragment multiplicity. It is also shown that, at a given total excitation energy per nucleon, the different properties of fragment partitions are completely determined by the reduced fragment multiplicity (i.e., normalized to the source size). Freeze-out volumes seem to play a role in the scalings observed.

  14. Fragmentation function measurements at Belle

    SciTech Connect

    Seidl, Ralf; Vossen, Anselm; Leitgab, Martin; Grosse-Perdekamp, Matthias; Giordano, Francesca; Ogawa, Akio

    2011-12-14

    The precision measurement of fragmentation functions is an important requirement to study the spin structure of the nucleon. Unpolarized fragmentation functions at reasonably low scale and high fractional energy are necessary to complement the measurements mostly performed at LEP in order to obtain high enough precision for measurements at semi-inclusive DIS experiments and at RHIC. Those can be obtained from the abundant data collected with the Belle detector at the e{sup +}e{sup -} collider KEKB. In addition one can cleanly measure the transversely polarized fragmentation functions such as the Collins fragmentation function and the interference fragmentation functions. Both have been obtained with great precision at Belle.

  15. Understanding Parameter Invariance in Unidimensional IRT Models

    ERIC Educational Resources Information Center

    Rupp, Andre A.; Zumbo, Bruno D.

    2006-01-01

    One theoretical feature that makes item response theory (IRT) models those of choice for many psychometric data analysts is parameter invariance, the equality of item and examinee parameters from different examinee populations or measurement conditions. In this article, using the well-known fact that item and examinee parameters are identical only…

  16. Scale invariance, conformality, and generalized free fields

    NASA Astrophysics Data System (ADS)

    Dymarsky, Anatoly; Farnsworth, Kara; Komargodski, Zohar; Luty, Markus A.; Prilepina, Valentina

    2016-02-01

    This paper addresses the question of whether there are 4D Lorentz invariant unitary quantum field theories with scale invariance but not conformal invariance. An important loophole in the arguments of Luty-Polchinski-Rattazzi and Dymarsky-Komargodski-Schwimmer-Theisen is that trace of the energy-momentum tensor T could be a generalized free field. In this paper we rule out this possibility. The key ingredient is the observation that a unitary theory with scale but not conformal invariance necessarily has a non-vanishing anomaly for global scale transformations. We show that this anomaly cannot be reproduced if T is a generalized free field unless the theory also contains a dimension-2 scalar operator. In the special case where such an operator is present it can be used to redefine ("improve") the energy-momentum tensor, and we show that there is at least one energy-momentum tensor that is not a generalized free field. In addition, we emphasize that, in general, large momentum limits of correlation functions cannot be understood from the leading terms of the coordinate space OPE. This invalidates a recent argument by Farnsworth-Luty-Prilepina (FLP). Despite the invalidity of the general argument of FLP, some of the techniques turn out to be useful in the present context.

  17. Position, rotation, and intensity invariant recognizing method

    DOEpatents

    Ochoa, E.; Schils, G.F.; Sweeney, D.W.

    1987-09-15

    A method for recognizing the presence of a particular target in a field of view which is target position, rotation, and intensity invariant includes the preparing of a target-specific invariant filter from a combination of all eigen-modes of a pattern of the particular target. Coherent radiation from the field of view is then imaged into an optical correlator in which the invariant filter is located. The invariant filter is rotated in the frequency plane of the optical correlator in order to produce a constant-amplitude rotational response in a correlation output plane when the particular target is present in the field of view. Any constant response is thus detected in the output plane to determine whether a particular target is present in the field of view. Preferably, a temporal pattern is imaged in the output plane with a optical detector having a plurality of pixels and a correlation coefficient for each pixel is determined by accumulating the intensity and intensity-square of each pixel. The orbiting of the constant response caused by the filter rotation is also preferably eliminated either by the use of two orthogonal mirrors pivoted correspondingly to the rotation of the filter or the attaching of a refracting wedge to the filter to remove the offset angle. Detection is preferably performed of the temporal pattern in the output plane at a plurality of different angles with angular separation sufficient to decorrelate successive frames. 1 fig.

  18. Invariant algebraic surfaces for a virus dynamics

    NASA Astrophysics Data System (ADS)

    Valls, Claudia

    2015-08-01

    In this paper, we provide a complete classification of the invariant algebraic surfaces and of the rational first integrals for a well-known virus system. In the proofs, we use the weight-homogeneous polynomials and the method of characteristic curves for solving linear partial differential equations.

  19. Neutrinos as Probes of Lorentz Invariance

    DOE PAGES

    Díaz, Jorge S.

    2014-01-01

    Neutrinos can be used to search for deviations from exact Lorentz invariance. The worldwide experimental program in neutrino physics makes these particles a remarkable tool to search for a variety of signals that could reveal minute relativity violations. This paper reviews the generic experimental signatures of the breakdown of Lorentz symmetry in the neutrino sector.

  20. Invariant of dynamical systems: A generalized entropy

    SciTech Connect

    Meson, A.M.; Vericat, F. |

    1996-09-01

    In this work the concept of entropy of a dynamical system, as given by Kolmogorov, is generalized in the sense of Tsallis. It is shown that this entropy is an isomorphism invariant, being complete for Bernoulli schemes. {copyright} {ital 1996 American Institute of Physics.}

  1. Broken Scale Invariance and Anomalous Dimensions

    DOE R&D Accomplishments Database

    Wilson, K. G.

    1970-05-01

    Mack and Kastrup have proposed that broken scale invariance is a symmetry of strong interactions. There is evidence from the Thirring model and perturbation theory that the dimensions of fields defined by scale transformations will be changed by the interaction from their canonical values. We review these ideas and their consequences for strong interactions.

  2. Harrison-Zeldovich spectrum from conformal invariance

    SciTech Connect

    Rubakov, V.A.

    2009-09-01

    We show that flat spectrum of small perturbations of field(s) is generated in a simple way in a theory of multi-component scalar field provided this theory is conformally invariant, it has some global symmetry and the quartic potential is negative. We suggest a mechanism of converting these field perturbations into adiabatic scalar perturbations with flat spectrum.

  3. A Discussion of Population Invariance of Equating

    ERIC Educational Resources Information Center

    Petersen, Nancy S.

    2008-01-01

    This article discusses the five studies included in this issue. Each article addressed the same topic, population invariance of equating. They all used data from major standardized testing programs, and they all used essentially the same statistics to evaluate their results, namely, the root mean square difference and root expected mean square…

  4. Scale invariance, conformality, and generalized free fields

    DOE PAGES

    Dymarsky, Anatoly; Farnsworth, Kara; Komargodski, Zohar; Luty, Markus A.; Prilepina, Valentina

    2016-02-16

    This paper addresses the question of whether there are 4D Lorentz invariant unitary quantum fi eld theories with scale invariance but not conformal invariance. We present an important loophole in the arguments of Luty-Polchinski-Rattazzi and Dymarsky-Komargodski-Schwimmer-Theisen that is the trace of the energy-momentum tensor T could be a generalized free field. In this paper we rule out this possibility. The key ingredient is the observation that a unitary theory with scale but not conformal invariance necessarily has a non-vanishing anomaly for global scale transformations. We show that this anomaly cannot be reproduced if T is a generalized free field unlessmore » the theory also contains a dimension-2 scalar operator. In the special case where such an operator is present it can be used to redefine ("improve") the energy-momentum tensor, and we show that there is at least one energy-momentum tensor that is not a generalized free field. In addition, we emphasize that, in general, large momentum limits of correlation functions cannot be understood from the leading terms of the coordinate space OPE. This invalidates a recent argument by Farnsworth-Luty-Prilepina (FLP). Finally, despite the invalidity of the general argument of FLP, some of the techniques turn out to be useful in the present context.« less

  5. Scale invariant density perturbations from cyclic cosmology

    NASA Astrophysics Data System (ADS)

    Frampton, Paul Howard

    2016-04-01

    It is shown how quantum fluctuations of the radiation during the contraction era of a comes back empty (CBE) cyclic cosmology can provide density fluctuations which re-enter the horizon during the subsequent expansion era and at lowest order are scale invariant, in a Harrison-Zel’dovich-Peebles sense. It is necessary to be consistent with observations of large scale structure.

  6. Multipartite invariant states. II. Orthogonal symmetry

    SciTech Connect

    Chruscinski, Dariusz; Kossakowski, Andrzej

    2006-06-15

    We construct a class of multipartite states possessing orthogonal symmetry. This new class contains multipartite states which are invariant under the action of local unitary operations introduced in our preceding paper [Phys. Rev. A 73, 062314 (2006)]. We study basic properties of multipartite symmetric states: separability criteria and multi-PPT conditions.

  7. Invariance Properties for General Diagnostic Classification Models

    ERIC Educational Resources Information Center

    Bradshaw, Laine P.; Madison, Matthew J.

    2016-01-01

    In item response theory (IRT), the invariance property states that item parameter estimates are independent of the examinee sample, and examinee ability estimates are independent of the test items. While this property has long been established and understood by the measurement community for IRT models, the same cannot be said for diagnostic…

  8. Fragment oriented molecular shapes.

    PubMed

    Hain, Ethan; Camacho, Carlos J; Koes, David Ryan

    2016-05-01

    Molecular shape is an important concept in drug design and virtual screening. Shape similarity typically uses either alignment methods, which dynamically optimize molecular poses with respect to the query molecular shape, or feature vector methods, which are computationally less demanding but less accurate. The computational cost of alignment can be reduced by pre-aligning shapes, as is done with the Volumetric-Aligned Molecular Shapes (VAMS) method. Here, we introduce and evaluate fragment oriented molecular shapes (FOMS), where shapes are aligned based on molecular fragments. FOMS enables the use of shape constraints, a novel method for precisely specifying molecular shape queries that provides the ability to perform partial shape matching and supports search algorithms that function on an interactive time scale. When evaluated using the challenging Maximum Unbiased Validation dataset, shape constraints were able to extract significantly enriched subsets of compounds for the majority of targets, and FOMS matched or exceeded the performance of both VAMS and an optimizing alignment method of shape similarity search. PMID:27085751

  9. Evolution of Particle Size Distributions in Fragmentation Over Time

    NASA Astrophysics Data System (ADS)

    Charalambous, C. A.; Pike, W. T.

    2013-12-01

    We present a new model of fragmentation based on a probabilistic calculation of the repeated fracture of a particle population. The resulting continuous solution, which is in closed form, gives the evolution of fragmentation products from an initial block, through a scale-invariant power-law relationship to a final comminuted powder. Models for the fragmentation of particles have been developed separately in mainly two different disciplines: the continuous integro-differential equations of batch mineral grinding (Reid, 1965) and the fractal analysis of geophysics (Turcotte, 1986) based on a discrete model with a single probability of fracture. The first gives a time-dependent development of the particle-size distribution, but has resisted a closed-form solution, while the latter leads to the scale-invariant power laws, but with no time dependence. Bird (2009) recently introduced a bridge between these two approaches with a step-wise iterative calculation of the fragmentation products. The development of the particle-size distribution occurs with discrete steps: during each fragmentation event, the particles will repeatedly fracture probabilistically, cascading down the length scales to a final size distribution reached after all particles have failed to further fragment. We have identified this process as the equivalent to a sequence of trials for each particle with a fixed probability of fragmentation. Although the resulting distribution is discrete, it can be reformulated as a continuous distribution in maturity over time and particle size. In our model, Turcotte's power-law distribution emerges at a unique maturation index that defines a regime boundary. Up to this index, the fragmentation is in an erosional regime with the initial particle size setting the scaling. Fragmentation beyond this index is in a regime of comminution with rebreakage of the particles down to the size limit of fracture. The maturation index can increment continuously, for example under

  10. Global invariant methods for object recognition

    NASA Astrophysics Data System (ADS)

    Stiller, Peter F.

    2001-11-01

    The general problem of single-view recognition is central to man image understanding and computer vision tasks; so central, that it has been characterized as the holy grail of computer vision. In previous work, we have shown how to approach the general problem of recognizing three dimensional geometric configurations (such as arrangements of lines, points, and conics) from a single two dimensional view, in a manner that is view independent. Our methods make use of advanced mathematical techniques from algebraic geometry, notably the theory of correspondences, and a novel equivariant geometric invariant theory. The machinery gives us a way to understand the relationship that exists between the 3D geometry and its residual in a 2D image. This relationship is shown to be a correspondence in the technical sense of algebraic geometry. Exploiting this, one can compute a set of fundamental equations in 3D and 2D invariants which generate the ideal of the correspondence, and which completely describe the mutual 3D/2D constraints. We have chosen to call these equations object/image equations. They can be exploited in a number of ways. For example, from a given 2D configuration, we can determine a set of non-linear constraints on the geometric invariants of a 3D configurations capable of imaging to the given 2D configuration (features on an object), we can derive a set of equations that constrain the images of that object; helping us to determine if that particular object appears in various images. One previous difficulty has been that the usual numerical geometric invariants get expressed as rational functions of the geometric parameters. As such they are not always defined. This leads to degeneracies in algorithms based on these invariants. We show how to replace these invariants by certain toric subvarieties of Grassmannians where the object/image equations become resultant like expressions for the existence of a non- trivial intersection of these subvarieties with

  11. Energetics and dynamics of the fragmentation reactions of protonated peptides containing methionine sulfoxide or aspartic acid via energy- and time-resolved surface induced dissociation.

    PubMed

    Lioe, Hadi; Laskin, Julia; Reid, Gavin E; O'Hair, Richard A J

    2007-10-25

    The surface-induced dissociation (SID) of six model peptides containing either methionine sulfoxide or aspartic acid (GAILM(O)GAILR, GAILM(O)GAILK, GAILM(O)GAILA, GAILDGAILR, GAILDGAILK, and GAILDGAILA) have been studied using a specially configured Fourier transform ion-cyclotron resonance mass spectrometer (FT-ICR MS). In particular, we have investigated the energetics and dynamics associated with (i) preferential cleavage of the methionine sulfoxide side chain via the loss of CH3SOH (64 Da), and (ii) preferential cleavage of the amide bond C-terminal to aspartic acid. The role of proton mobility in these selective bond cleavage reactions was examined by changing the C-terminal residue of the peptide from arginine (nonmobile proton conditions) to lysine (partially mobile proton conditions) to alanine (mobile proton conditions). Time- and energy-resolved fragmentation efficiency curves (TFECs) reveal that selective cleavages due to the methionine sulfoxide and aspartic acid residues are characterized by slow fragmentation kinetics. RRKM modeling of the experimental data suggests that the slow kinetics is associated with large negative entropy effects and these may be due to the presence of rearrangements prior to fragmentation. It was found that the Arrhenius pre-exponential factor (A) for peptide fragmentations occurring via selective bond cleavages are 1-2 orders of magnitude lower than nonselective peptide fragmentation reactions, while the dissociation threshold (E0) is relatively invariant. This means that selective bond cleavage is kinetically disfavored compared to nonselective amide bond cleavage. It was also found that the energetics and dynamics for the preferential loss of CH3SOH from peptide ions containing methionine sulfoxide are very similar to selective C-terminal amide bond cleavage at the aspartic acid residue. These results suggest that while preferential cleavage can compete with amide bond cleavage energetically, dynamically, these processes

  12. Energetics and Dynamics of the Fragmentation Reactions of Protonated Peptides Containing Methionine Sulfoxide or Aspartic Acid via Energy- and Time-Resolved Surface Induced Dissociation

    SciTech Connect

    Lioe, Hadi; Laskin, Julia; Reid, Gavin E.; O'Hair, Richard Aj

    2007-10-25

    The surface-induced dissociation (SID) of six model peptides containing either methionine sulfoxide or aspartic acid (GAILM(O)GAILR, GAILM(O)GAILK, GAILM(O)GAILA, GAILDGAILR, GAILDGAILK, and GAILDGAILA) have been studied using a specially configured Fourier transform ion-cyclotron resonance mass spectrometer (FT-ICR MS). In particular, we have investigated the energetics and dynamics associated with (i) preferential cleavage of the methionine sulfoxide side chain via the loss of CH3SOH (64Da), and (ii) preferential cleavage of the amide bond C-terminal to aspartic acid. The role of proton mobility on these selective bond cleavage reactions was examined by changing the C-terminal residue of the peptide from arginine (non-mobile proton conditions) to lysine (partially-mobile proton conditions) to alanine (mobile proton conditions). Time- and energy-resolved fragmentation efficiency curves (TFEC) reveals that selective cleavages due to the methionine sulfoxide and aspartic acid residues are characterized by slow fragmentation kinetics. RRKM modeling of the experimental data suggests that the slow kinetics is associated with large negative entropy effects and these may be due to the presence of rearrangements prior to fragmentation. It was found that the Arrhenius pre-exponential factor (A) for peptide fragmentations occurring via selective bond cleavages are 1–2 orders of magnitude lower than non-selective peptide fragmentation reactions, while the dissociation threshold (E0) is relatively invariant. This means that selective bond cleavage is kinetically disfavored compared to non-selective amide bond cleavage. It was also found that the energetics and dynamics for the preferential loss of CH3SOH from peptide ions containing methionine sulfoxide are very similar to selective C-terminal amide bond cleavage at the aspartic acid residue. These results suggest that while preferential cleavage can compete with amide bond cleavage energetically, dynamically, these

  13. Dimensional analysis using toric ideals: primitive invariants.

    PubMed

    Atherton, Mark A; Bates, Ronald A; Wynn, Henry P

    2014-01-01

    Classical dimensional analysis in its original form starts by expressing the units for derived quantities, such as force, in terms of power products of basic units [Formula: see text] etc. This suggests the use of toric ideal theory from algebraic geometry. Within this the Graver basis provides a unique primitive basis in a well-defined sense, which typically has more terms than the standard Buckingham approach. Some textbook examples are revisited and the full set of primitive invariants found. First, a worked example based on convection is introduced to recall the Buckingham method, but using computer algebra to obtain an integer [Formula: see text] matrix from the initial integer [Formula: see text] matrix holding the exponents for the derived quantities. The [Formula: see text] matrix defines the dimensionless variables. But, rather than this integer linear algebra approach it is shown how, by staying with the power product representation, the full set of invariants (dimensionless groups) is obtained directly from the toric ideal defined by [Formula: see text]. One candidate for the set of invariants is a simple basis of the toric ideal. This, although larger than the rank of [Formula: see text], is typically not unique. However, the alternative Graver basis is unique and defines a maximal set of invariants, which are primitive in a simple sense. In addition to the running example four examples are taken from: a windmill, convection, electrodynamics and the hydrogen atom. The method reveals some named invariants. A selection of computer algebra packages is used to show the considerable ease with which both a simple basis and a Graver basis can be found. PMID:25436774

  14. Complex-linear invariants of biochemical networks.

    PubMed

    Karp, Robert L; Pérez Millán, Mercedes; Dasgupta, Tathagata; Dickenstein, Alicia; Gunawardena, Jeremy

    2012-10-21

    The nonlinearities found in molecular networks usually prevent mathematical analysis of network behaviour, which has largely been studied by numerical simulation. This can lead to difficult problems of parameter determination. However, molecular networks give rise, through mass-action kinetics, to polynomial dynamical systems, whose steady states are zeros of a set of polynomial equations. These equations may be analysed by algebraic methods, in which parameters are treated as symbolic expressions whose numerical values do not have to be known in advance. For instance, an "invariant" of a network is a polynomial expression on selected state variables that vanishes in any steady state. Invariants have been found that encode key network properties and that discriminate between different network structures. Although invariants may be calculated by computational algebraic methods, such as Gröbner bases, these become computationally infeasible for biologically realistic networks. Here, we exploit Chemical Reaction Network Theory (CRNT) to develop an efficient procedure for calculating invariants that are linear combinations of "complexes", or the monomials coming from mass action. We show how this procedure can be used in proving earlier results of Horn and Jackson and of Shinar and Feinberg for networks of deficiency at most one. We then apply our method to enzyme bifunctionality, including the bacterial EnvZ/OmpR osmolarity regulator and the mammalian 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase glycolytic regulator, whose networks have deficiencies up to four. We show that bifunctionality leads to different forms of concentration control that are robust to changes in initial conditions or total amounts. Finally, we outline a systematic procedure for using complex-linear invariants to analyse molecular networks of any deficiency.

  15. Chain Gang

    NASA Technical Reports Server (NTRS)

    2006-01-01

    6 August 2006 This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows a chain of clustered and battered craters. These were formed by secondary impact. That is, somewhere to the south (beyond the bottom of this image), a large impact crater formed. When this occurred, material ejected from the crater was thrown tens to hundreds of kilometers away. This material then impacted the martian surface, forming clusters and chains of smaller craters.

    Location near: 15.8oN, 35.6oW Image width: 3 km (1.9 mi) Illumination from: upper left Season: Northern Spring

  16. Phage Display and Peptide Mapping of an Immunoglobulin Light Chain Fibril-Related Conformational Epitope†

    PubMed Central

    O’Nuallain, Brian; Allen, Amy; Ataman, Demet; Weiss, Deborah T.; Solomon, Alan; Wall, Jonathan S.

    2008-01-01

    Amyloid fibrils and partially unfolded intermediates can be distinguished serologically from native amyloidogenic precursor proteins or peptides. In this regard, we previously had reported that mAb 11-1F4, generated by immunizing mice with a thermally denatured variable domain (VL) fragment of the human κ4 Bence Jones protein Len, bound to a non-native conformational epitope located within the N-terminal 18 residues of fibrillar, as well as partially denatured, Ig light chains (O’Nuallain B. et al. (2006) Biochemistry 46, 1240–247). To define further the antibody binding site, we used random peptide phage display and epitope mapping of VL Len using wild-type and alanine-mutated Len peptides where it was shown that the antibody epitope was reliant on up to 10 of the first 15 residues of protein Len. Comparison of Vκ and Vλ N-terminal germline consensus sequences with protein Len and 11-1F4-binding phages indicated that this antibody’s cross-reactivity with light chains was related to an invariant proline at position(s) 7 and/or 8, bulky hydrophobic residues at positions 11 and 13, and additionally, to the ability to accommodate amino acid diversity at positions 1–4. Sequence alignments of the phage peptides revealed a central proline, often flanked by aromatic residues. Taken together, these results have provided evidence for the structural basis of the specificity of 11-1F4 for both κ and λ light chain fibrils. We posit that the associated binding site involves a rare type VI β-turn or touch-turn that is anchored by a cis-proline residue. The identification of an 11-1F4-related mimotope should facilitate development of pan-light chain fibril-reactive antibodies that could be used in the diagnosis and treatment of patients with AL amyloidosis. PMID:17944486

  17. A Mini-Library of Sequenced Human DNA Fragments: Linking Bench Experiments with Informatics

    ERIC Educational Resources Information Center

    Dalgleish, Raymond; Shanks, Morag E.; Monger, Karen; Butler, Nicola J.

    2012-01-01

    We describe the development of a mini-library of human DNA fragments for use in an enquiry-based learning (EBL) undergraduate practical incorporating "wet-lab" and bioinformatics tasks. In spite of the widespread emergence of the polymerase chain reaction (PCR), the cloning and analysis of DNA fragments in "Escherichia coli" remains a fundamental…

  18. 21 CFR 866.5540 - Immunoglobulin G (Fd fragment specific) immunological test system.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Immunoglobulin G (Fd fragment specific) immunological test system. 866.5540 Section 866.5540 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... fragment) of the heavy chain (a subunit) of the immunoglobulin antibody molecule in serum. Measurement...

  19. 21 CFR 866.5540 - Immunoglobulin G (Fd fragment specific) immunological test system.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Immunoglobulin G (Fd fragment specific) immunological test system. 866.5540 Section 866.5540 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... fragment) of the heavy chain (a subunit) of the immunoglobulin antibody molecule in serum. Measurement...

  20. 21 CFR 866.5540 - Immunoglobulin G (Fd fragment specific) immunological test system.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Immunoglobulin G (Fd fragment specific) immunological test system. 866.5540 Section 866.5540 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... fragment) of the heavy chain (a subunit) of the immunoglobulin antibody molecule in serum. Measurement...

  1. 21 CFR 866.5540 - Immunoglobulin G (Fd fragment specific) immunological test system.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Immunoglobulin G (Fd fragment specific) immunological test system. 866.5540 Section 866.5540 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... fragment) of the heavy chain (a subunit) of the immunoglobulin antibody molecule in serum. Measurement...

  2. Scale invariant texture descriptors for classifying celiac disease

    PubMed Central

    Hegenbart, Sebastian; Uhl, Andreas; Vécsei, Andreas; Wimmer, Georg

    2013-01-01

    Scale invariant texture recognition methods are applied for the computer assisted diagnosis of celiac disease. In particular, emphasis is given to techniques enhancing the scale invariance of multi-scale and multi-orientation wavelet transforms and methods based on fractal analysis. After fine-tuning to specific properties of our celiac disease imagery database, which consists of endoscopic images of the duodenum, some scale invariant (and often even viewpoint invariant) methods provide classification results improving the current state of the art. However, not each of the investigated scale invariant methods is applicable successfully to our dataset. Therefore, the scale invariance of the employed approaches is explicitly assessed and it is found that many of the analyzed methods are not as scale invariant as they theoretically should be. Results imply that scale invariance is not a key-feature required for successful classification of our celiac disease dataset. PMID:23481171

  3. Food-chain length and adaptive foraging.

    PubMed

    Kondoh, Michio; Ninomiya, Kunihiko

    2009-09-01

    Food-chain length, the number of feeding links from the basal species to the top predator, is a key characteristic of biological communities. However, the determinants of food-chain length still remain controversial. While classical theory predicts that food-chain length should increase with increasing resource availability, empirical supports of this prediction are limited to those from simple, artificial microcosms. A positive resource availability-chain length relationship has seldom been observed in natural ecosystems. Here, using a theoretical model, we show that those correlations, or no relationships, may be explained by considering the dynamic food-web reconstruction induced by predator's adaptive foraging. More specifically, with foraging adaptation, the food-chain length becomes relatively invariant, or even decreases with increasing resource availability, in contrast to a non-adaptive counterpart where chain length increases with increasing resource availability; and that maximum chain length more sharply decreases with resource availability either when species richness is higher or potential link number is larger. The interactive effects of resource availability, adaptability and community complexity may explain the contradictory effects of resource availability in simple microcosms and larger ecosystems. The model also explains the recently reported positive effect of habitat size on food-chain length as a result of increased species richness and/or decreased connectance owing to interspecific spatial segregation.

  4. Chapter 4 embedded metal fragments.

    PubMed

    Kalinich, John F; Vane, Elizabeth A; Centeno, Jose A; Gaitens, Joanna M; Squibb, Katherine S; McDiarmid, Melissa A; Kasper, Christine E

    2014-01-01

    The continued evolution of military munitions and armor on the battlefield, as well as the insurgent use of improvised explosive devices, has led to embedded fragment wounds containing metal and metal mixtures whose long-term toxicologic and carcinogenic properties are not as yet known. Advances in medical care have greatly increased the survival from these types of injuries. Standard surgical guidelines suggest leaving embedded fragments in place, thus individuals may carry these retained metal fragments for the rest of their lives. Nursing professionals will be at the forefront in caring for these wounded individuals, both immediately after the trauma and during the healing and rehabilitation process. Therefore, an understanding of the potential health effects of embedded metal fragment wounds is essential. This review will explore the history of embedded fragment wounds, current research in the field, and Department of Defense and Department of Veterans Affairs guidelines for the identification and long-term monitoring of individuals with embedded fragments.

  5. Frozen reaction fronts in steady flows: A burning-invariant-manifold perspective

    NASA Astrophysics Data System (ADS)

    Mahoney, John R.; Li, John; Boyer, Carleen; Solomon, Tom; Mitchell, Kevin A.

    2015-12-01

    The dynamics of fronts, such as chemical reaction fronts, propagating in two-dimensional fluid flows can be remarkably rich and varied. For time-invariant flows, the front dynamics may simplify, settling in to a steady state in which the reacted domain is static, and the front appears "frozen." Our central result is that these frozen fronts in the two-dimensional fluid are composed of segments of burning invariant manifolds, invariant manifolds of front-element dynamics in x y θ space, where θ is the front orientation. Burning invariant manifolds (BIMs) have been identified previously as important local barriers to front propagation in fluid flows. The relevance of BIMs for frozen fronts rests in their ability, under appropriate conditions, to form global barriers, separating reacted domains from nonreacted domains for all time. The second main result of this paper is an understanding of bifurcations that lead from a nonfrozen state to a frozen state, as well as bifurcations that change the topological structure of the frozen front. Although the primary results of this study apply to general fluid flows, our analysis focuses on a chain of vortices in a channel flow with an imposed wind. For this system, we present both experimental and numerical studies that support the theoretical analysis developed here.

  6. Frozen reaction fronts in steady flows: A burning-invariant-manifold perspective.

    PubMed

    Mahoney, John R; Li, John; Boyer, Carleen; Solomon, Tom; Mitchell, Kevin A

    2015-12-01

    The dynamics of fronts, such as chemical reaction fronts, propagating in two-dimensional fluid flows can be remarkably rich and varied. For time-invariant flows, the front dynamics may simplify, settling in to a steady state in which the reacted domain is static, and the front appears "frozen." Our central result is that these frozen fronts in the two-dimensional fluid are composed of segments of burning invariant manifolds, invariant manifolds of front-element dynamics in xyθ space, where θ is the front orientation. Burning invariant manifolds (BIMs) have been identified previously as important local barriers to front propagation in fluid flows. The relevance of BIMs for frozen fronts rests in their ability, under appropriate conditions, to form global barriers, separating reacted domains from nonreacted domains for all time. The second main result of this paper is an understanding of bifurcations that lead from a nonfrozen state to a frozen state, as well as bifurcations that change the topological structure of the frozen front. Although the primary results of this study apply to general fluid flows, our analysis focuses on a chain of vortices in a channel flow with an imposed wind. For this system, we present both experimental and numerical studies that support the theoretical analysis developed here. PMID:26764802

  7. Binary stars - Formation by fragmentation

    NASA Technical Reports Server (NTRS)

    Boss, Alan P.

    1988-01-01

    Theories of binary star formation by capture, separate nuclei, fission and fragmentation are compared, assessing the success of theoretical attempts to explain the observed properties of main-sequence binary stars. The theory of formation by fragmentation is examined, discussing the prospects for checking the theory against observations of binary premain-sequence stars. It is concluded that formation by fragmentation is successful at explaining many of the key properties of main-sequence binary stars.

  8. Multigroup Confirmatory Factor Analysis: Locating the Invariant Referent Sets

    ERIC Educational Resources Information Center

    French, Brian F.; Finch, W. Holmes

    2008-01-01

    Multigroup confirmatory factor analysis (MCFA) is a popular method for the examination of measurement invariance and specifically, factor invariance. Recent research has begun to focus on using MCFA to detect invariance for test items. MCFA requires certain parameters (e.g., factor loadings) to be constrained for model identification, which are…

  9. Testing Factorial Invariance in Multilevel Data: A Monte Carlo Study

    ERIC Educational Resources Information Center

    Kim, Eun Sook; Kwok, Oi-man; Yoon, Myeongsun

    2012-01-01

    Testing factorial invariance has recently gained more attention in different social science disciplines. Nevertheless, when examining factorial invariance, it is generally assumed that the observations are independent of each other, which might not be always true. In this study, we examined the impact of testing factorial invariance in multilevel…

  10. Breaking scale invariance with quantum gravity

    SciTech Connect

    Amendola, L.; Occhionero, F.; Saez, D. )

    1990-02-01

    It is argued that the closed, nonsingular cosmological model of Starobinsky (1980) allows a self-consistent, albeit schematic, description of the history of the universe from its beginning to now and even provides, given a suitable scenario, the possibility of breaking in a natural way the scale invariance of the perturbation spectrum. A double inflationary scenario is specified in detail to explain the anomalous power observed in the large-scale astronomical structures by assuming that the first inflation is driven by quantum gravity and that the second inflation is driven by the usual inflation. An example of a power spectrum where the scale invariance has been broken and extra power is put above 10 Mpc is presented. The model is now compatible with the observed upper limits from the large angular scale isotropy of the microwave background. 52 refs.

  11. Testing CPT Invariance with Antiprotonic Helium Atoms

    SciTech Connect

    Horvath, Dezso

    2008-08-08

    The structure of matter is related to symmetries at every level of study. CPT symmetry is one of the most important laws of field theory: it states the invariance of physical properties when one simultaneously changes the signs of the charge and of the spatial and time coordinates of free elementary particles. Although in general opinion CPT symmetry is not violated in Nature, there are theoretical attempts to develop CPT-violating models. The Antiproton Decelerator at CERN has been built to test CPT invariance. The ASACUSA experiment compares the properties of particles and antiparticles by studying the antiprotonic helium atom via laser spectroscopy and measuring the mass, charge and magnetic moment of the antiproton as compared to those of the proton.

  12. Localized, partially space-invariant filtering

    NASA Astrophysics Data System (ADS)

    Zalevsky, Zeev; Mendlovic, David; Caulfield, John H.

    1997-02-01

    In cases in which the image-to-image spatial variability of the input pattern changes with the spatial location, a localized-filtering method should be used for pattern recognition. Localized space-invariant filtering is investigated, and its improved recognition abilities are demonstrated with the recognition of fingerprints. The motivation for the investigated implementation is related to the fact that a person never presses his finger on a surface with equal pressure. This variation results in different amounts of spatial shifting being required from the optical processor in different regions of the fingerprint. A two-region mathematical model for representing the human finger is presented and investigated by use of localized space-invariant filtering by means of a computer.

  13. Monopoles, Abelian projection, and gauge invariance

    SciTech Connect

    Bonati, Claudio; Di Giacomo, Adriano; Lepori, Luca; Pucci, Fabrizio

    2010-04-15

    A direct connection is proved between the non-Abelian Bianchi Identities (NABI's) and the Abelian Bianchi identities for the 't Hooft tensor. As a consequence, the existence of a nonzero magnetic current is related to the violation of the NABI's and is a gauge-invariant property. The construction allows us to show that not all Abelian projections can be used to expose monopoles in lattice configurations: each field configuration with nonzero magnetic charge identifies its natural projection, up to gauge transformations which tend to unity at large distances. It is shown that the so-called maximal-Abelian gauge is a legitimate choice. It is also proven, starting from the NABI, that monopole condensation is a physical gauge-invariant phenomenon, independent of the choice of the Abelian projection.

  14. Hidden invariance of the free classical particle

    SciTech Connect

    Garcia, S. )

    1994-06-01

    A formalism describing the dynamics of classical and quantum systems from a group theoretical point of view is presented. We apply it to the simple example of the classical free particle. The Galileo group [ital G] is the symmetry group of the free equations of motion. Consideration of the free particle Lagrangian semi-invariance under [ital G] leads to a larger symmetry group, which is a central extension of the Galileo group by the real numbers. We study the dynamics associated with this group, and characterize quantities like Noether invariants and evolution equations in terms of group geometric objects. An extension of the Galileo group by [ital U](1) leads to quantum mechanics.

  15. Scale-invariant geometric random graphs.

    PubMed

    Xie, Zheng; Rogers, Tim

    2016-03-01

    We introduce and analyze a class of growing geometric random graphs that are invariant under rescaling of space and time. Directed connections between nodes are drawn according to influence zones that depend on node position in space and time, mimicking the heterogeneity and increased specialization found in growing networks. Through calculations and numerical simulations we explore the consequences of scale invariance for geometric random graphs generated this way. Our analysis reveals a dichotomy between scale-free and Poisson distributions of in- and out-degree, the existence of a random number of hub nodes, high clustering, and unusual percolation behavior. These properties are similar to those of empirically observed web graphs. PMID:27078369

  16. Revisiting R-invariant direct gauge mediation

    NASA Astrophysics Data System (ADS)

    Chiang, Cheng-Wei; Harigaya, Keisuke; Ibe, Masahiro; Yanagida, Tsutomu T.

    2016-03-01

    We revisit a special model of gauge mediated supersymmetry breaking, the " R-invariant direct gauge mediation." We pay particular attention to whether the model is consistent with the minimal model of the μ-term, i.e., a simple mass term of the Higgs doublets in the superpotential. Although the incompatibility is highlighted in view of the current experimental constraints on the superparticle masses and the observed Higgs boson mass, the minimal μ-term can be consistent with the R-invariant gauge mediation model via a careful choice of model parameters. We derive an upper limit on the gluino mass from the observed Higgs boson mass. We also discuss whether the model can explain the 3 σ excess of the Z + jets + E T miss events reported by the ATLAS collaboration.

  17. Symmetric form-invariant dual Pearcey beams.

    PubMed

    Ren, Zhijun; Fan, Changjiang; Shi, Yile; Chen, Bo

    2016-08-01

    We introduce another type of Pearcey beam, namely, dual Pearcey (DP) beams, based on the Pearcey function of catastrophe theory. DP beams are experimentally generated by applying Fresnel diffraction of bright elliptic rings. Form-invariant Bessel distribution beams can be regarded as a special case of DP beams. Subsequently, the basic propagation characteristics of DP beams are identified. DP beams are the result of the interference of two half DP beams instead of two classical Pearcey beams. Moreover, we also verified that half DP beams (including special-case parabolic-like beams) generated by half elliptical rings (circular rings) are a new member of the family of form-invariant beams. PMID:27505650

  18. Natural inflation with hidden scale invariance

    NASA Astrophysics Data System (ADS)

    Barrie, Neil D.; Kobakhidze, Archil; Liang, Shelley

    2016-05-01

    We propose a new class of natural inflation models based on a hidden scale invariance. In a very generic Wilsonian effective field theory with an arbitrary number of scalar fields, which exhibits scale invariance via the dilaton, the potential necessarily contains a flat direction in the classical limit. This flat direction is lifted by small quantum corrections and inflation is realised without need for an unnatural fine-tuning. In the conformal limit, the effective potential becomes linear in the inflaton field, yielding to specific predictions for the spectral index and the tensor-to-scalar ratio, being respectively: ns - 1 ≈ - 0.025 (N⋆/60)-1 and r ≈ 0.0667 (N⋆/60)-1, where N⋆ ≈ 30- 65 is a number of efolds during observable inflation. This predictions are in reasonable agreement with cosmological measurements. Further improvement of the accuracy of these measurements may turn out to be critical in falsifying our scenario.

  19. Hiding Lorentz invariance violation with MOND

    SciTech Connect

    Sanders, R. H.

    2011-10-15

    Horava-Lifshitz gravity is an attempt to construct a renormalizable theory of gravity by breaking the Lorentz invariance of the gravitational action at high energies. The underlying principle is that Lorentz invariance is an approximate symmetry and its violation by gravitational phenomena is somehow hidden to present limits of observational precision. Here I point out that a simple modification of the low-energy limit of Horava-Lifshitz gravity in its nonprojectable form can effectively camouflage the presence of a preferred frame in regions where the Newtonian gravitational field gradient is higher than cH{sub 0}; this modification results in the phenomenology of modified Newtonian dynamics (MOND) at lower accelerations. As a relativistic theory of MOND, this modified Horava-Lifshitz theory presents several advantages over its predecessors.

  20. Scale-invariant breaking of conformal symmetry

    NASA Astrophysics Data System (ADS)

    Dymarsky, Anatoly; Zhiboedov, Alexander

    2015-10-01

    Known examples of unitary relativistic scale but not conformal-invariant field theories (SFTs) can be embedded into conventional conformal field theories (CFTs). We show that any SFT which is a subsector of a unitary CFT is a free theory. Our discussion applies to an arbitrary number of spacetime dimensions and explains triviality of known SFTs in four spacetime dimensions. We comment on examples of unitary SFTs which are not captured by our construction.

  1. Neutrino velocity and local Lorentz invariance

    NASA Astrophysics Data System (ADS)

    Cardone, Fabio; Mignani, Roberto; Petrucci, Andrea

    2015-09-01

    We discuss the possible violation of local Lorentz invariance (LLI) arising from a faster-than-light neutrino speed. A toy calculation of the LLI violation parameter δ, based on the (disclaimed) OPERA data, suggests that the values of δ are determined by the interaction involved, and not by the energy range. This hypothesis is further corroborated by the analysis of the more recent results of the BOREXINO, LVD and ICARUS experiments.

  2. OSRI: a rotationally invariant binary descriptor.

    PubMed

    Xu, Xianwei; Tian, Lu; Feng, Jianjiang; Zhou, Jie

    2014-07-01

    Binary descriptors are becoming widely used in computer vision field because of their high matching efficiency and low memory requirements. Since conventional approaches, which first compute a floating-point descriptor then binarize it, are computationally expensive, some recent efforts have focused on directly computing binary descriptors from local image patches. Although these binary descriptors enable a significant speedup in processing time, their performances usually drop a lot due to orientation estimation errors and limited description abilities. To address these issues, we propose a novel binary descriptor based on the ordinal and spatial information of regional invariants (OSRIs) over a rotation invariant sampling pattern. Our main contributions are twofold: 1) each bit in OSRI is computed based on difference tests of regional invariants over pairwise sampling-regions instead of difference tests of pixel intensities commonly used in existing binary descriptors, which can significantly enhance the discriminative ability and 2) rotation and illumination changes are handled well by ordering pixels according to their intensities and gradient orientations, meanwhile, which is also more reliable than those methods that resort to a reference orientation for rotation invariance. Besides, a statistical analysis of discriminative abilities of different parts in the descriptor is conducted to design a cascade filter which can reject nonmatching descriptors at early stages by comparing just a small portion of the whole descriptor, further reducing the matching time. Extensive experiments on four challenging data sets (Oxford, 53 Objects, ZuBuD, and Kentucky) show that OSRI significantly outperforms two state-of-the-art binary descriptors (FREAK and ORB). The matching performance of OSRI with only 512 bits is also better than the well-known floating-point descriptor SIFT (4K bits) and is comparable with the state-of-the-art floating-point descriptor MROGH (6K bits

  3. Tests of Lorentz invariance using hydrogen molecules

    SciTech Connect

    Mueller, Holger; Herrmann, Sven; Saenz, Alejandro; Peters, Achim; Laemmerzahl, Claus

    2004-10-01

    We discuss the consequences of Lorentz violation (as expressed within the Lorentz-violating extension of the standard model) for the hydrogen molecule, which represents a generic model of a molecular binding. Lorentz-violating shifts of electronic, vibrational and rotational energy levels, and of the internuclear distance are calculated. This offers the possibility of obtaining improved bounds on Lorentz invariance by experiments using molecules.

  4. Invariance algorithms for processing NDE signals

    NASA Astrophysics Data System (ADS)

    Mandayam, Shreekanth; Udpa, Lalita; Udpa, Satish S.; Lord, William

    1996-11-01

    Signals that are obtained in a variety of nondestructive evaluation (NDE) processes capture information not only about the characteristics of the flaw, but also reflect variations in the specimen's material properties. Such signal changes may be viewed as anomalies that could obscure defect related information. An example of this situation occurs during in-line inspection of gas transmission pipelines. The magnetic flux leakage (MFL) method is used to conduct noninvasive measurements of the integrity of the pipe-wall. The MFL signals contain information both about the permeability of the pipe-wall and the dimensions of the flaw. Similar operational effects can be found in other NDE processes. This paper presents algorithms to render NDE signals invariant to selected test parameters, while retaining defect related information. Wavelet transform based neural network techniques are employed to develop the invariance algorithms. The invariance transformation is shown to be a necessary pre-processing step for subsequent defect characterization and visualization schemes. Results demonstrating the successful application of the method are presented.

  5. Permutation-invariant distance between atomic configurations.

    PubMed

    Ferré, Grégoire; Maillet, Jean-Bernard; Stoltz, Gabriel

    2015-09-14

    We present a permutation-invariant distance between atomic configurations, defined through a functional representation of atomic positions. This distance enables us to directly compare different atomic environments with an arbitrary number of particles, without going through a space of reduced dimensionality (i.e., fingerprints) as an intermediate step. Moreover, this distance is naturally invariant through permutations of atoms, avoiding the time consuming associated minimization required by other common criteria (like the root mean square distance). Finally, the invariance through global rotations is accounted for by a minimization procedure in the space of rotations solved by Monte Carlo simulated annealing. A formal framework is also introduced, showing that the distance we propose verifies the property of a metric on the space of atomic configurations. Two examples of applications are proposed. The first one consists in evaluating faithfulness of some fingerprints (or descriptors), i.e., their capacity to represent the structural information of a configuration. The second application concerns structural analysis, where our distance proves to be efficient in discriminating different local structures and even classifying their degree of similarity.

  6. Spectrally Invariant Approximation within Atmospheric Radiative Transfer

    NASA Technical Reports Server (NTRS)

    Marshak, A.; Knyazikhin, Y.; Chiu, J. C.; Wiscombe, W. J.

    2011-01-01

    Certain algebraic combinations of single scattering albedo and solar radiation reflected from, or transmitted through, vegetation canopies do not vary with wavelength. These spectrally invariant relationships are the consequence of wavelength independence of the extinction coefficient and scattering phase function in vegetation. In general, this wavelength independence does not hold in the atmosphere, but in cloud-dominated atmospheres the total extinction and total scattering phase function vary only weakly with wavelength. This paper identifies the atmospheric conditions under which the spectrally invariant approximation can accurately describe the extinction and scattering properties of cloudy atmospheres. The validity of the assumptions and the accuracy of the approximation are tested with 1D radiative transfer calculations using publicly available radiative transfer models: Discrete Ordinate Radiative Transfer (DISORT) and Santa Barbara DISORT Atmospheric Radiative Transfer (SBDART). It is shown for cloudy atmospheres with cloud optical depth above 3, and for spectral intervals that exclude strong water vapor absorption, that the spectrally invariant relationships found in vegetation canopy radiative transfer are valid to better than 5%. The physics behind this phenomenon, its mathematical basis, and possible applications to remote sensing and climate are discussed.

  7. Permutation-invariant distance between atomic configurations

    SciTech Connect

    Ferré, Grégoire; Maillet, Jean-Bernard; Stoltz, Gabriel

    2015-09-14

    We present a permutation-invariant distance between atomic configurations, defined through a functional representation of atomic positions. This distance enables us to directly compare different atomic environments with an arbitrary number of particles, without going through a space of reduced dimensionality (i.e., fingerprints) as an intermediate step. Moreover, this distance is naturally invariant through permutations of atoms, avoiding the time consuming associated minimization required by other common criteria (like the root mean square distance). Finally, the invariance through global rotations is accounted for by a minimization procedure in the space of rotations solved by Monte Carlo simulated annealing. A formal framework is also introduced, showing that the distance we propose verifies the property of a metric on the space of atomic configurations. Two examples of applications are proposed. The first one consists in evaluating faithfulness of some fingerprints (or descriptors), i.e., their capacity to represent the structural information of a configuration. The second application concerns structural analysis, where our distance proves to be efficient in discriminating different local structures and even classifying their degree of similarity.

  8. The Drosophila Clathrin Heavy Chain Gene: Clathrin Function Is Essential in a Multicellular Organism

    PubMed Central

    Bazinet, C.; Katzen, A. L.; Morgan, M.; Mahowald, A. P.; Lemmon, S. K.

    1993-01-01

    The clathrin heavy chain (HC) is the major structural polypeptide of the cytoplasmic surface lattice of clathrin-coated pits and vesicles. As a genetic approach to understanding the role of clathrin in cellular morphogenesis and developmental signal transduction, a clathrin heavy chain (Chc) gene of Drosophila melanogaster has been identified by a combination of molecular and classical genetic approaches. Using degenerate primers based on mammalian and yeast clathrin HC sequences, a small fragment of the HC gene was amplified from genomic Drosophila DNA by the polymerase chain reaction. Genomic and cDNA clones from phage libraries were isolated and analyzed using this fragment as a probe. The amino acid sequence of the Drosophila clathrin HC deduced from cDNA sequences is 80%, 57% and 49% identical, respectively, with the mammalian, Dictyostelium and yeast HCs. Hybridization in situ to larval polytene chromosomes revealed a single Chc locus at position 13F2 on the X chromosome. A 13-kb genomic Drosophila fragment including the Chc transcription unit was reintroduced into the Drosophila genome via P element-mediated germline transformation. This DNA complemented a group of EMS-induced lethal mutations mapping to the same region of the X chromosome, thus identifying the Chc complementation group. Mutant individuals homozygous or hemizygous for the Chc(1), Chc(2) or Chc(3) alleles developed to a late stage of embryogenesis, but failed to hatch to the first larval stage. A fourth allele, Chc(4), exhibited polyphasic lethality, with a significant number of homozygous and hemizygous offspring surviving to adulthood. Germline clonal analysis of Chc mutant alleles indicated that the three tight lethal alleles were autonomous cell-lethal mutations in the female germline. In contrast, Chc(4) germline clones were viable at a rate comparable to wild type, giving rise to viable adult progeny. However, hemizygous Chc(4) males were invariably sterile. The sterility was

  9. Passive estimation of the waveguide invariant per pair of modes.

    PubMed

    Le Gall, Yann; Bonnel, Julien

    2013-08-01

    In many oceanic waveguides, acoustic propagation is characterized by a parameter called waveguide invariant. This property is used in many passive and active sonar applications where knowledge of the waveguide invariant value is required. The waveguide invariant is classically considered as scalar but several studies show that it is better modeled by a distribution because of its dependence on frequency and mode pairs. This paper presents a new method for estimating the waveguide invariant distribution. Using the noise radiated by a distant ship and a single hydrophone, the proposed methodology allows estimating the waveguide invariant for each pair of modes in shallow water. Performance is evaluated on simulated data.

  10. Scope and applications of translation invariant wavelets to image registration

    NASA Technical Reports Server (NTRS)

    Chettri, Samir; LeMoigne, Jacqueline; Campbell, William

    1997-01-01

    The first part of this article introduces the notion of translation invariance in wavelets and discusses several wavelets that have this property. The second part discusses the possible applications of such wavelets to image registration. In the case of registration of affinely transformed images, we would conclude that the notion of translation invariance is not really necessary. What is needed is affine invariance and one way to do this is via the method of moment invariants. Wavelets or, in general, pyramid processing can then be combined with the method of moment invariants to reduce the computational load.

  11. Invariance of bipartite separability and PPT-probabilities over Casimir invariants of reduced states

    NASA Astrophysics Data System (ADS)

    Slater, Paul B.

    2016-09-01

    Milz and Strunz (J Phys A 48:035306, 2015) recently studied the probabilities that two-qubit and qubit-qutrit states, randomly generated with respect to Hilbert-Schmidt (Euclidean/flat) measure, are separable. They concluded that in both cases, the separability probabilities (apparently exactly 8/33 in the two-qubit scenario) hold constant over the Bloch radii ( r) of the single-qubit subsystems, jumping to 1 at the pure state boundaries (r=1). Here, firstly, we present evidence that in the qubit-qutrit case, the separability probability is uniformly distributed, as well, over the generalized Bloch radius ( R) of the qutrit subsystem. While the qubit (standard) Bloch vector is positioned in three-dimensional space, the qutrit generalized Bloch vector lives in eight-dimensional space. The radii variables r and R themselves are the lengths/norms (being square roots of quadratic Casimir invariants) of these ("coherence") vectors. Additionally, we find that not only are the qubit-qutrit separability probabilities invariant over the quadratic Casimir invariant of the qutrit subsystem, but apparently also over the cubic one—and similarly the case, more generally, with the use of random induced measure. We also investigate two-qutrit (3 × 3) and qubit- qudit (2 × 4) systems—with seemingly analogous positive partial transpose-probability invariances holding over what has been termed by Altafini the partial Casimir invariants of these systems.

  12. Analysis of Peptidoglycan Fragment Release.

    PubMed

    Schaub, Ryan E; Lenz, Jonathan D; Dillard, Joseph P

    2016-01-01

    Most bacteria break down a significant portion of their cell wall peptidoglycan during each round of growth and cell division. This process generates peptidoglycan fragments of various sizes that can either be imported back into the cytoplasm for recycling or released from the cell. Released fragments have been shown to act as microbe-associated molecular patterns for the initiation of immune responses, as triggers for the initiation of mutualistic host-microbe relationships, and as signals for cell-cell communication in bacteria. Characterizing these released peptidoglycan fragments can, therefore, be considered an important step in understanding how microbes communicate with other organisms in their environments. In this chapter, we describe methods for labeling cell wall peptidoglycan, calculating the rate at which peptidoglycan is turned over, and collecting released peptidoglycan to determine the abundance and species of released fragments. Methods are described for both the separation of peptidoglycan fragments by size-exclusion chromatography and further detailed analysis by HPLC.

  13. Fragment Screening and HIV Therapeutics

    PubMed Central

    Bauman, Joseph D.; Patel, Disha; Arnold, Eddy

    2013-01-01

    Fragment screening has proven to be a powerful alternative to traditional methods for drug discovery. Biophysical methods, such as X-ray crystallography, NMR spectroscopy, and surface plasmon resonance, are used to screen a diverse library of small molecule compounds. Although compounds identified via this approach have relatively weak affinity, they provide a good platform for lead development and are highly efficient binders with respect to their size. Fragment screening has been utilized for a wide-range of targets, including HIV-1 proteins. Here, we review the fragment screening studies targeting HIV-1 proteins using X-ray crystallography or surface plasmon resonance. These studies have successfully detected binding of novel fragments to either previously established or new sites on HIV-1 protease and reverse transcriptase. In addition, fragment screening against HIV-1 reverse transcriptase has been used as a tool to better understand the complex nature of ligand binding to a flexible target. PMID:21972022

  14. Fragment-based drug design.

    PubMed

    Feyfant, Eric; Cross, Jason B; Paris, Kevin; Tsao, Désirée H H

    2011-01-01

    Fragment-based drug design (FBDD), which is comprised of both fragment screening and the use of fragment hits to design leads, began more than 15 years ago and has been steadily gaining in popularity and utility. Its origin lies on the fact that the coverage of chemical space and the binding efficiency of hits are directly related to the size of the compounds screened. Nevertheless, FBDD still faces challenges, among them developing fragment screening libraries that ensure optimal coverage of chemical space, physical properties and chemical tractability. Fragment screening also requires sensitive assays, often biophysical in nature, to detect weak binders. In this chapter we will introduce the technologies used to address these challenges and outline the experimental advantages that make FBDD one of the most popular new hit-to-lead process. PMID:20981527

  15. Golgi fragmentation in amyotrophic lateral sclerosis, an overview of possible triggers and consequences

    PubMed Central

    Sundaramoorthy, Vinod; Sultana, Jessica M.; Atkin, Julie D.

    2015-01-01

    Amyotrophic Lateral Sclerosis (ALS) is an invariably fatal neurodegenerative disorder, which specifically targets motor neurons in the brain, brain stem and spinal cord. Whilst the etiology of ALS remains unknown, fragmentation of the Golgi apparatus is detected in ALS patient motor neurons and in animal/cellular disease models. The Golgi is a highly dynamic organelle that acts as a dispatching station for the vesicular transport of secretory/transmembrane proteins. It also mediates autophagy and maintains endoplasmic reticulum (ER) and axonal homeostasis. Both the trigger for Golgi fragmentation and the functional consequences of a fragmented Golgi apparatus in ALS remain unclear. However, recent evidence has highlighted defects in vesicular trafficking as a pathogenic mechanism in ALS. This review summarizes the evidence describing Golgi fragmentation in ALS, with possible links to other disease processes including cellular trafficking, ER stress, defective autophagy, and axonal degeneration. PMID:26578862

  16. Nonsinglet kaon fragmentation function from e{sup +}e{sup -} kaon production

    SciTech Connect

    Albino, Simon; Christova, Ekaterina

    2010-05-01

    We perform fits to the available charged and neutral kaon-production data in e{sup +}+e{sup -{yields}}K+X, K=K{sup {+-},} and K{sub S}{sup 0}, and determine the nonsinglet combination of kaon fragmentation functions D{sub u}{sup K{+-}-}D{sub d}{sup K{+-}}in a model independent way and without any correlations to the other fragmentation functions. Only nuclear isospin invariance is assumed. Working with nonsinglets allows us to include the data at very low momentum fractions, which have so far been excluded in global fits, and to perform a first next-next-to leading order fit to fragmentation functions. We find that the kaon nonsinglet fragmentation function at large z is larger than that obtained by the other collaborations from global fit analysis and differs significantly at low z.

  17. Antibody elbow angles are influenced by their light chain class

    SciTech Connect

    Stanfield, R; Zemla, A; Wilson, I; Rupp, B

    2006-01-12

    We have examined the elbow angles for 365 different Fab fragments, and observe that Fabs with lambda light chains have adopted a wider range of elbow angles than their kappa-chain counterparts, and that the lambda light chain Fabs are frequently found with very large (>195{sup o}) elbow angles. This apparent hyperflexibility of lambda-chain Fabs may be due to an insertion in their switch region, which is one residue longer than in kappa chains, with glycine occurring most frequently at the insertion position. A new, web-based computer program that was used to calculate the Fab elbow angles is also described.

  18. Methods for Assessing Item, Step, and Threshold Invariance in Polytomous Items Following the Partial Credit Model

    ERIC Educational Resources Information Center

    Penfield, Randall D.; Myers, Nicholas D.; Wolfe, Edward W.

    2008-01-01

    Measurement invariance in the partial credit model (PCM) can be conceptualized in several different but compatible ways. In this article the authors distinguish between three forms of measurement invariance in the PCM: step invariance, item invariance, and threshold invariance. Approaches for modeling these three forms of invariance are proposed,…

  19. Invariant quantities of a nondepolarizing Mueller matrix.

    PubMed

    Gil, José J; José, Ignacio San

    2016-07-01

    Orthogonal Mueller matrices can be considered as corresponding either to retarders or to generalized transformations of the polarization basis for the representation of Stokes vectors, so that they constitute the only type of Mueller matrices that preserve the degree of polarization and the intensity of any partially polarized input Stokes vector. The physical quantities that remain invariant when a nondepolarizing Mueller matrix is transformed through its product by different types of orthogonal Mueller matrices are identified and interpreted, providing a better knowledge of the information contained in a nondepolarizing Mueller matrix. PMID:27409687

  20. A Note on Invariant Temporal Functions

    NASA Astrophysics Data System (ADS)

    Müller, Olaf

    2016-07-01

    The purpose of this article is to present a result on the existence of Cauchy temporal functions invariant by the action of a compact group of conformal transformations in arbitrary globally hyperbolic manifolds. Moreover, the previous results about the existence of Cauchy temporal functions with additional properties on arbitrary globally hyperbolic manifolds are unified in a very general theorem. To make the article more accessible for non-experts, and in the lack of an appropriate single reference for the Lorentzian geometry background of the result, the latter is provided in an introductory section.

  1. Gauge Invariance of Thermal Transport Coefficients

    NASA Astrophysics Data System (ADS)

    Ercole, Loris; Marcolongo, Aris; Umari, Paolo; Baroni, Stefano

    2016-10-01

    Thermal transport coefficients are independent of the specific microscopic expression for the energy density and current from which they can be derived through the Green-Kubo formula. We discuss this independence in terms of a kind of gauge invariance resulting from energy conservation and extensivity, and demonstrate it numerically for a Lennard-Jones fluid, where different forms of the microscopic energy density lead to different time correlation functions for the heat flux, all of them, however, resulting in the same value for the thermal conductivity.

  2. Origin of gauge invariance in string theory

    NASA Technical Reports Server (NTRS)

    Horowitz, G. T.; Strominger, A.

    1986-01-01

    A first quantization of the space-time embedding Chi exp mu and the world-sheet metric rho of the open bosonic string. The world-sheet metric rho decouples from S-matrix elements in 26 dimensions. This formulation of the theory naturally includes 26-dimensional gauge transformations. The gauge invariance of S-matrix elements is a direct consequence of the decoupling of rho. Second quantization leads to a string field Phi(Chi exp mu, rho) with a gauge-covariant equation of motion.

  3. Gauge invariant actions for string models

    SciTech Connect

    Banks, T.

    1986-06-01

    String models of unified interactions are elegant sets of Feynman rules for the scattering of gravitons, gauge bosons, and a host of massive excitations. The purpose of these lectures is to describe the progress towards a nonperturbative formulation of the theory. Such a formulation should make the geometrical meaning of string theory manifest and explain the many ''miracles'' exhibited by the string Feynman rules. There are some new results on gauge invariant observables, on the cosmological constant, and on the symmetries of interacting string field theory. 49 refs.

  4. Are there p-adic knot invariants?

    NASA Astrophysics Data System (ADS)

    Morozov, A. Yu.

    2016-04-01

    We suggest using the Hall-Littlewood version of the Rosso-Jones formula to define the germs of p-adic HOMFLY-PT polynomials for torus knots [ m, n] as coefficients of superpolynomials in a q-expansion. In this form, they have at least the [ m, n] ↔ [ n, m] topological invariance. This opens a new possibility to interpret superpolynomials as p-adic deformations of HOMFLY polynomials and poses a question of generalizing to other knot families, which is a substantial problem for several branches of modern theory.

  5. Invariant mass spectroscopy of halo nuclei

    SciTech Connect

    Nakamura, Takashi

    2008-11-11

    We have applied the invariant mass spectroscopy to explore the low-lying exited states of halo nuclei at intermediate energies around 70 MeV/nucleon at RIKEN. As examples, we show here the results of Coulomb breakup study for {sup 11}Li using the Pb target, as well as breakup reactions of {sup 14}Be with p and C targets. The former study revealed a strong Coulomb breakup cross section reflecting the large enhancement of E1 strength at low excitation energies (soft E1 excitation). The latter revealed the observation of the first 2{sup +} state in {sup 14}Be.

  6. The axion mass in modular invariant supergravity

    SciTech Connect

    Butter, Daniel; Gaillard, Mary K.

    2005-02-09

    When supersymmetry is broken by condensates with a single condensing gauge group, there is a nonanomalous R-symmetry that prevents the universal axion from acquiring a mass. It has been argued that, in the context of supergravity, higher dimension operators will break this symmetry and may generate an axion mass too large to allow the identification of the universal axion with the QCD axion. We show that such contributions to the axion mass are highly suppressed in a class of models where the effective Lagrangian for gaugino and matter condensation respects modular invariance (T-duality).

  7. Fragmentation and densities of meteoroids

    NASA Technical Reports Server (NTRS)

    Babadzhanov, Pulat B.

    1992-01-01

    Photographic observations of meteors carried out in Dushanbe by the method of instantaneous exposure have shown clearly that meteoroids entering the Earth's atmosphere are subjected to different types of fragmentation. The quasi-continuous fragmentation of meteoroids is mostly widespread. Using the physical theory of meteors which takes into account the quasi-continuous fragmentation of meteoroids and on the basis of light curves of meteors the densities of meteoroids of different streams have been determined. The results enable us to conclude that the densities of meteoroids are over an order of magnitude higher than they have been assumed before. Moreover they are close to the densities of carbonaceous and ordinary chondrites.

  8. Velocity fluctuations of fission fragments

    NASA Astrophysics Data System (ADS)

    Llanes-Estrada, Felipe J.; Carmona, Belén Martínez; Martínez, Jose L. Muñoz

    2016-02-01

    We propose event by event velocity fluctuations of nuclear fission fragments as an additional interesting observable that gives access to the nuclear temperature in an independent way from spectral measurements and relates the diffusion and friction coefficients for the relative fragment coordinate in Kramers-like models (in which some aspects of fission can be understood as the diffusion of a collective variable through a potential barrier). We point out that neutron emission by the heavy fragments can be treated in effective theory if corrections to the velocity distribution are needed.

  9. Geometric local invariants and pure three-qubit states

    SciTech Connect

    Williamson, Mark S.; Ericsson, Marie; Johansson, Markus; Sjoeqvist, Erik; Sudbery, Anthony; Vedral, Vlatko; Wootters, William K.

    2011-06-15

    We explore a geometric approach to generating local SU(2) and SL(2,C) invariants for a collection of qubits inspired by lattice gauge theory. Each local invariant or ''gauge'' invariant is associated with a distinct closed path (or plaquette) joining some or all of the qubits. In lattice gauge theory, the lattice points are the discrete space-time points, the transformations between the points of the lattice are defined by parallel transporters, and the gauge invariant observable associated with a particular closed path is given by the Wilson loop. In our approach the points of the lattice are qubits, the link transformations between the qubits are defined by the correlations between them, and the gauge invariant observable, the local invariants associated with a particular closed path, are also given by a Wilson looplike construction. The link transformations share many of the properties of parallel transporters, although they are not undone when one retraces one's steps through the lattice. This feature is used to generate many of the invariants. We consider a pure three-qubit state as a test case and find we can generate a complete set of algebraically independent local invariants in this way; however, the framework given here is applicable to generating local unitary invariants for mixed states composed of any number of d-level quantum systems. We give an operational interpretation of these invariants in terms of observables.

  10. Entanglement entropy in quantum spin chains with broken reflection symmetry

    SciTech Connect

    Kadar, Zoltan; Zimboras, Zoltan

    2010-09-15

    We investigate the entanglement entropy of a block of L sites in quasifree translation-invariant spin chains concentrating on the effect of reflection-symmetry breaking. The Majorana two-point functions corresponding to the Jordan-Wigner transformed fermionic modes are determined in the most general case; from these, it follows that reflection symmetry in the ground state can only be broken if the model is quantum critical. The large L asymptotics of the entropy are calculated analytically for general gauge-invariant models, which have, until now, been done only for the reflection-symmetric sector. Analytical results are also derived for certain nongauge-invariant models (e.g., for the Ising model with Dzyaloshinskii-Moriya interaction). We also study numerically finite chains of length N with a nonreflection-symmetric Hamiltonian and report that the reflection symmetry of the entropy of the first L spins is violated but the reflection-symmetric Calabrese-Cardy formula is recovered asymptotically. Furthermore, for noncritical reflection-symmetry-breaking Hamiltonians, we find an anomaly in the behavior of the saturation entropy as we approach the critical line. The paper also provides a concise but extensive review of the block-entropy asymptotics in translation-invariant quasifree spin chains with an analysis of the nearest-neighbor case and the enumeration of the yet unsolved parts of the quasifree landscape.

  11. Casimir invariants for systems undergoing collective motion

    SciTech Connect

    Bishop, C. Allen; Byrd, Mark S.; Wu Lianao

    2011-06-15

    Dicke states are an important class of states which exhibit collective behavior in many-body systems. They are interesting because (1) the decay rates of these states can be quite different from a set of independently evolving particles and (2) a particular class of these states are decoherence-free or noiseless with respect to a set of errors. These noiseless states, or more generally subsystems, avoid certain types of errors in quantum-information-processing devices. Here we provide a method for determining a set of transformations of these states which leave the states in their subsystems but still enable them to evolve in particular ways. For subsystems of particles undergoing collective motions, these transformations can be calculated by using essentially the same construction which is used to determine the famous Casimir invariants for quantum systems. Such invariants can be used to determine a complete set of commuting observables for a class of Dicke states as well as to identify possible logical operations for decoherence-free-noiseless subsystems. Our method is quite general and provides results for cases where the constituent particles have more than two internal states.

  12. Rotational invariant visual object extraction and understanding

    NASA Astrophysics Data System (ADS)

    Ternovskiy, Igor V.; Jannson, Tomasz P.

    2000-08-01

    In this paper, we discuss a novel method, base don singularity representation, for integrating a rotational invariant visual object extraction and understanding technique. This new compression method applies Arnold's Differential Mapping Singularities Theory in the context of 3D object projection onto the 2D image plane. It takes advantage of the fact that object edges can be interpreted in terms of singularities, which can be described by simple polynomials. We discuss the relationship between traditional approaches, including wavelet transform and differential mapping singularities theory or catastrophe theory (CT) in the context of image understanding and rotational invariant object extraction and compression. CT maps 3D surfaces with exact results to construct an image-compression algorithm based on an expanded set of operations. This set includes shift, scaling rotation, and homogeneous nonlinear transformations. This approach permits the mathematical description of a ful set of singularities that describes edges and other specific points of objects. The edges and specific points are the products of mapping smooth 3D surfaces, which can be described by a simple set of polynomials that are suitable for image compression and ATR.

  13. Noise-assisted estimation of attractor invariants

    NASA Astrophysics Data System (ADS)

    Restrepo, Juan F.; Schlotthauer, Gastón

    2016-07-01

    In this article, the noise-assisted correlation integral (NCI) is proposed. The purpose of the NCI is to estimate the invariants of a dynamical system, namely the correlation dimension (D ), the correlation entropy (K2), and the noise level (σ ). This correlation integral is induced by using random noise in a modified version of the correlation algorithm, i.e., the noise-assisted correlation algorithm. We demonstrate how the correlation integral by Grassberger et al. and the Gaussian kernel correlation integral (GCI) by Diks can be thought of as special cases of the NCI. A third particular case is the U -correlation integral proposed herein, from which we derived coarse-grained estimators of the correlation dimension (DmU), the correlation entropy (KmU), and the noise level (σmU). Using time series from the Henon map and the Mackey-Glass system, we analyze the behavior of these estimators under different noise conditions and data lengths. The results show that the estimators DmU and σmU behave in a similar manner to those based on the GCI. However, for the calculation of K2, the estimator KmU outperforms its GCI-based counterpart. On the basis of the behavior of these estimators, we have proposed an automatic algorithm to find D ,K2, and σ from a given time series. The results show that by using this approach, we are able to achieve statistically reliable estimations of those invariants.

  14. Lorentz invariant dark-spinor and inflation

    SciTech Connect

    Basak, Abhishek; Bhatt, Jitesh R. E-mail: jeet@prl.res.in

    2011-06-01

    We investigate the possibility of the inflation driven by a Lorentz invariant non-standard spinor field. As these spinors are having dominant interaction via gravitational field only, they are considered as Dark Spinors. We study how these dark-spinors can drive the inflation and investigate the cosmological (scalar) perturbations generated by them. Though the dark-spinors obey a Klein-Gordon like equation, the underlying theory of the cosmological perturbations is far more complex than the theories which are using a canonical scalar field. For example the sound speed of the perturbations is not a constant but varies with time. We find that in order to explain the observed value of the spectral-index n{sub s} one must have upper bound on the values of the background NSS-field. The tensor to scalar ratio remains as small as that in the case of canonical scalar field driven inflation because the correction to tensor spectrum due to NSS is required to be very small. In addition we discuss the relationship of results with previous results obtained by using the Lorentz invariance violating theories.

  15. Are face representations depth cue invariant?

    PubMed

    Dehmoobadsharifabadi, Armita; Farivar, Reza

    2016-06-01

    The visual system can process three-dimensional depth cues defining surfaces of objects, but it is unclear whether such information contributes to complex object recognition, including face recognition. The processing of different depth cues involves both dorsal and ventral visual pathways. We investigated whether facial surfaces defined by individual depth cues resulted in meaningful face representations-representations that maintain the relationship between the population of faces as defined in a multidimensional face space. We measured face identity aftereffects for facial surfaces defined by individual depth cues (Experiments 1 and 2) and tested whether the aftereffect transfers across depth cues (Experiments 3 and 4). Facial surfaces and their morphs to the average face were defined purely by one of shading, texture, motion, or binocular disparity. We obtained identification thresholds for matched (matched identity between adapting and test stimuli), non-matched (non-matched identity between adapting and test stimuli), and no-adaptation (showing only the test stimuli) conditions for each cue and across different depth cues. We found robust face identity aftereffect in both experiments. Our results suggest that depth cues do contribute to forming meaningful face representations that are depth cue invariant. Depth cue invariance would require integration of information across different areas and different pathways for object recognition, and this in turn has important implications for cortical models of visual object recognition. PMID:27271993

  16. Fragmentation of drying paint layers

    NASA Astrophysics Data System (ADS)

    Bakos, Katinka; Dombi, András; Járai-Szabó, Ferenc; Néda, Zoltán

    2013-11-01

    Fragmentation of thin layers of drying granular materials on a frictional surface are studied both by experiments and computer simulations. Besides a qualitative description of the fragmentation phenomenon, the dependence of the average fragment size as a function of the layer thickness is thoroughly investigated. Experiments are done using a special nail polish, which forms characteristic crack structures during drying. In order to control the layer thickness, we diluted the nail polish in acetone and evaporated in a controlled manner different volumes of this solution on glass surfaces. During the evaporation process we managed to get an instable paint layer, which formed cracks as it dried out. In order to understand the obtained structures a previously developed spring-block model was implemented in a three-dimensional version. The experimental and simulation results proved to be in excellent qualitative and quantitative agreement. An earlier suggested scaling relation between the average fragment size and the layer thickness is reconfirmed.

  17. Calculus fragmentation in laser lithotripsy.

    PubMed

    Welch, A J; Kang, H W; Lee, H; Teichman, J M H

    2004-03-01

    The intracorporeal treatment of urinary calculi with lasers is presented, which describes laser-calculus interactions associated with lithotripsy. Reliable fragmentation of calculi with diverse compositions and minimal collateral tissue damage are primarily contingent upon laser parameters (wavelength, pulse duration, and pulse energy) and physical properties of calculi (optical, mechanical, and chemical). The pulse duration governs the dominant mechanism in calculi fragmentation, which is either photothermal or photoacoustical/photomechanical. Lasers with long pulse durations (i.e. > tens of micros) induce a temperature rise in the laser-affected zone with minimal acoustic waves; material is removed by means of vaporization, melting, mechanical stress, and/or chemical decomposition. Short-pulsed laser ablation (i.e. < 10 micros), on the other hand, produces shock waves, and the resultant mechanical energy fragments calculi. Work continues throughout the world to evaluate the feasibility of advanced lasers in lithotripsy and to optimize laser parameters and light delivery systems pertinent to efficient fragmentation of calculi.

  18. A vast amount of various invariant tori in the Nosé-Hoover oscillator.

    PubMed

    Wang, Lei; Yang, Xiao-Song

    2015-12-01

    This letter restudies the Nosé-Hoover oscillator. Some new averagely conservative regions are found, each of which is filled with different sequences of nested tori with various knot types. Especially, the dynamical behaviors near the border of "chaotic region" and conservative regions are studied showing that there exist more complicated and thinner invariant tori around the boundaries of conservative regions bounded by tori. Our results suggest an infinite number of island chains in a "chaotic sea" for the Nosé-Hoover oscillator.

  19. A vast amount of various invariant tori in the Nosé-Hoover oscillator

    SciTech Connect

    Wang, Lei; Yang, Xiao-Song

    2015-12-15

    This letter restudies the Nosé-Hoover oscillator. Some new averagely conservative regions are found, each of which is filled with different sequences of nested tori with various knot types. Especially, the dynamical behaviors near the border of “chaotic region” and conservative regions are studied showing that there exist more complicated and thinner invariant tori around the boundaries of conservative regions bounded by tori. Our results suggest an infinite number of island chains in a “chaotic sea” for the Nosé-Hoover oscillator.

  20. A vast amount of various invariant tori in the Nosé-Hoover oscillator

    NASA Astrophysics Data System (ADS)

    Wang, Lei; Yang, Xiao-Song

    2015-12-01

    This letter restudies the Nosé-Hoover oscillator. Some new averagely conservative regions are found, each of which is filled with different sequences of nested tori with various knot types. Especially, the dynamical behaviors near the border of "chaotic region" and conservative regions are studied showing that there exist more complicated and thinner invariant tori around the boundaries of conservative regions bounded by tori. Our results suggest an infinite number of island chains in a "chaotic sea" for the Nosé-Hoover oscillator.

  1. QGP and Modified Jet Fragmentation

    SciTech Connect

    Wang, Xin-Nian

    2005-04-18

    Recent progresses in the study of jet modification in hotmedium and their consequences in high-energy heavy-ion collisions are reviewed. In particular, I will discuss energy loss for propagating heavy quarks and the resulting modified fragmentation function. Medium modification of the parton fragmentation function due to quark recombination are formulated within finite temperature field theory and their implication on the search for deconfined quark-gluon plasma is also discussed.

  2. The classical Korteweg capillarity system: geometry and invariant transformations

    NASA Astrophysics Data System (ADS)

    Rogers, C.; Schief, W. K.

    2014-08-01

    A class of invariant transformations is presented for the classical Korteweg capillarity system. The invariance is an extension of a kind originally introduced in an anisentropic gasdynamics context. In a particular instance, application of the invariant transformation leads to a deformed one-parameter class of Kármán-Tsien-type capillarity laws associated with a deformation of an integrable nonlinear Schrödinger-type equation which incorporates a de Broglie-Bohm potential. The latter and another integrable case associated with the classical Boussinesq equation may be linked to the motion of curves in Euclidean and projective space so that both the invariant transformation and the Galilean invariance of the capillarity system may be interpreted in a geometric and soliton-theoretic manner. The work is set in the broader context of other connections of invariant transformations in gasdynamics with soliton theory.

  3. Studies on the characteristic and activity of low-molecular fragments from zymosan.

    PubMed

    Gao, Yang; Jiang, Ruizhi; Qie, Jing; Chen, Yinghong; Xu, Duoduo; Liu, Wei; Gao, Qipin

    2012-11-01

    Zymosan was hydrolysed with HCl and fractionated by ultrafiltration and dialysis to obtain water-soluble fragments A, B and C. Physical and chemical analyses showed that these fractions are composed primarily of glucose and have molecular weights of 8 kDa, 5 kDa and 2 kDa, respectively. A glycosidic linkage analysis indicated that they are mainly composed of β-1,3-glucans. Fragment A, which has the highest molecular weight, contains approximately 30% β-1,6-linked glucans, but fragment C is almost entirely composed of linear β-1,3-glucan chains. The anti-chronic atrophic gastritis activity experiments showed that fragment A has significant activity, the activity of zymosan is quite low and the activities of fragments B and C are in between those of fragment A and zymosan.

  4. Metric Ranking of Invariant Networks with Belief Propagation

    SciTech Connect

    Tao, Changxia; Ge, Yong; Song, Qinbao; Ge, Yuan; Omitaomu, Olufemi A

    2014-01-01

    The management of large-scale distributed information systems relies on the effective use and modeling of monitoring data collected at various points in the distributed information systems. A promising approach is to discover invariant relationships among the monitoring data and generate invariant networks, where a node is a monitoring data source (metric) and a link indicates an invariant relationship between two monitoring data. Such an invariant network representation can help system experts to localize and diagnose the system faults by examining those broken invariant relationships and their related metrics, because system faults usually propagate among the monitoring data and eventually lead to some broken invariant relationships. However, at one time, there are usually a lot of broken links (invariant relationships) within an invariant network. Without proper guidance, it is difficult for system experts to manually inspect this large number of broken links. Thus, a critical challenge is how to effectively and efficiently rank metrics (nodes) of invariant networks according to the anomaly levels of metrics. The ranked list of metrics will provide system experts with useful guidance for them to localize and diagnose the system faults. To this end, we propose to model the nodes and the broken links as a Markov Random Field (MRF), and develop an iteration algorithm to infer the anomaly of each node based on belief propagation (BP). Finally, we validate the proposed algorithm on both realworld and synthetic data sets to illustrate its effectiveness.

  5. Binary optical filters for scale invariant pattern recognition

    NASA Technical Reports Server (NTRS)

    Reid, Max B.; Downie, John D.; Hine, Butler P.

    1992-01-01

    Binary synthetic discriminant function (BSDF) optical filters which are invariant to scale changes in the target object of more than 50 percent are demonstrated in simulation and experiment. Efficient databases of scale invariant BSDF filters can be designed which discriminate between two very similar objects at any view scaled over a factor of 2 or more. The BSDF technique has considerable advantages over other methods for achieving scale invariant object recognition, as it also allows determination of the object's scale. In addition to scale, the technique can be used to design recognition systems invariant to other geometric distortions.

  6. The metrizability problem for Lorentz-invariant affine connections

    NASA Astrophysics Data System (ADS)

    Urban, Zbyněk; Volná, Jana

    2016-07-01

    The invariant metrizability problem for affine connections on a manifold, formulated by Tanaka and Krupka for connected Lie groups actions, is considered in the particular cases of Lorentz and Poincaré (inhomogeneous Lorentz) groups. Conditions under which an affine connection on the open submanifold ℝ × (ℝ3\\{(0, 0, 0)}) of the Euclidean space ℝ4 coincides with the Levi-Civita connection of some SO(3, 1), respectively (ℝ4 × sSO(3, 1))-invariant metric field are studied. We give complete description of metrizable Lorentz-invariant connections. Explicit solutions (metric fields) of the invariant metrizability equations are found and their properties are discussed.

  7. Fragmentation Pathways in the Uracil Radical Cation

    SciTech Connect

    Zhou, Congyi; Matsika, Spiridoula; Kotur, Marija; Weinacht, Thomas C.

    2012-08-24

    We investigate pathways for fragmentation in the uracil radical cation using ab initio electronic structure calculations. We focus on the main fragments produced in pump–probe dissociative ionization experiments. These are fragments with mass to charge ratios (m/z) of 69, 28, 41, and 42. Barriers to dissociation along the ground ionic surface are reported, which provide an estimate of the energetic requirements for the production of the main fragments. Finally, direct and sequential fragmentation mechanisms have been analyzed, and it is concluded that sequential fragmentation after production of fragment with m/z 69 is the dominant mechanism for the production of the smaller fragments.

  8. Bacterial expression and purification of recombinant bovine Fab fragments.

    PubMed

    O'Brien, Philippa M; Maxwell, Gavin; Campo, M Saveria

    2002-02-01

    We have previously described a recombinant phagemid expression vector, pComBov, designed for the production of native sequence bovine monoclonal antibodies (mAb) generated by antibody phage display. Bovine mAb Fab fragments isolated from libraries constructed using pComBov in Escherichia coli strain XL1-Blue, which is routinely used for antibodies expressed on the surface of phage, were expressed at very low yields. Therefore, a study was undertaken to determine optimal growth conditions for maximal expression of bovine Fab fragments in E. coli. By varying the E. coli strain, and the temperature and length of the culture growth, we were able to substantially increase the yield of soluble Fab fragments. A high yield of Fab fragments was found in the culture growth medium, which enabled us to devise a rapid and simple single-step method for the purification of native (nondenatured) Fabs based on immobilized metal affinity chromatography against a six-histidine amino acid carboxyl-terminal extension of the heavy-chain constant region. Using these methods we were able to express and purify antigen-specific bovine Fab fragments from E. coli. PMID:11812221

  9. Spiking Models for Level-Invariant Encoding

    PubMed Central

    Brette, Romain

    2012-01-01

    Levels of ecological sounds vary over several orders of magnitude, but the firing rate and membrane potential of a neuron are much more limited in range. In binaural neurons of the barn owl, tuning to interaural delays is independent of level differences. Yet a monaural neuron with a fixed threshold should fire earlier in response to louder sounds, which would disrupt the tuning of these neurons. How could spike timing be independent of input level? Here I derive theoretical conditions for a spiking model to be insensitive to input level. The key property is a dynamic change in spike threshold. I then show how level invariance can be physiologically implemented, with specific ionic channel properties. It appears that these ingredients are indeed present in monaural neurons of the sound localization pathway of birds and mammals. PMID:22291634

  10. Multivariate dice recognition using invariant features

    NASA Astrophysics Data System (ADS)

    Hsu, Gee-Sern; Peng, Hsiao-Chia; Yeh, Shang-Min; Lin, Chyi-Yeu

    2013-04-01

    A system is proposed for automatic reading of the number of dots on dice in general table game settings. Different from previous dice recognition systems that recognize dice of a specific color using a single top-view camera in an enclosure with controlled settings, the proposed one uses multiple cameras to recognize dice of various colors and under uncontrolled conditions. It is composed of three modules. Module-1 locates the dice using the gradient-conditioned color segmentation, proposed, to segment dice of arbitrary colors from the background. Module-2 exploits the local invariant features good for building homographies, giving a solution to segment the top faces of the dice. To identify the dots on the segmented top faces, a maximally stable extremal region detector is embedded in module-3 for its consistency in locating the dot region. Experiments show that the proposed system performs satisfactorily in various test conditions.

  11. Spiking models for level-invariant encoding.

    PubMed

    Brette, Romain

    2011-01-01

    Levels of ecological sounds vary over several orders of magnitude, but the firing rate and membrane potential of a neuron are much more limited in range. In binaural neurons of the barn owl, tuning to interaural delays is independent of level differences. Yet a monaural neuron with a fixed threshold should fire earlier in response to louder sounds, which would disrupt the tuning of these neurons. How could spike timing be independent of input level? Here I derive theoretical conditions for a spiking model to be insensitive to input level. The key property is a dynamic change in spike threshold. I then show how level invariance can be physiologically implemented, with specific ionic channel properties. It appears that these ingredients are indeed present in monaural neurons of the sound localization pathway of birds and mammals. PMID:22291634

  12. Onboard Image Registration from Invariant Features

    NASA Technical Reports Server (NTRS)

    Wang, Yi; Ng, Justin; Garay, Michael J.; Burl, Michael C

    2008-01-01

    This paper describes a feature-based image registration technique that is potentially well-suited for onboard deployment. The overall goal is to provide a fast, robust method for dynamically combining observations from multiple platforms into sensors webs that respond quickly to short-lived events and provide rich observations of objects that evolve in space and time. The approach, which has enjoyed considerable success in mainstream computer vision applications, uses invariant SIFT descriptors extracted at image interest points together with the RANSAC algorithm to robustly estimate transformation parameters that relate one image to another. Experimental results for two satellite image registration tasks are presented: (1) automatic registration of images from the MODIS instrument on Terra to the MODIS instrument on Aqua and (2) automatic stabilization of a multi-day sequence of GOES-West images collected during the October 2007 Southern California wildfires.

  13. Invariant conserved currents in generalized gravity

    NASA Astrophysics Data System (ADS)

    Obukhov, Yuri N.; Portales-Oliva, Felipe; Puetzfeld, Dirk; Rubilar, Guillermo F.

    2015-11-01

    We study conservation laws for gravity theories invariant under general coordinate transformations. The class of models under consideration includes Einstein's general relativity theory as a special case as well as its generalizations to non-Riemannian spacetime geometry and nonminimal coupling. We demonstrate that an arbitrary vector field on the spacetime manifold generates a current density that is conserved under certain conditions, and find the expression of the corresponding superpotential. For a family of models including nonminimal coupling between geometry and matter, we discuss in detail the differential conservation laws and the conserved quantities defined in terms of covariant multipole moments. We show that the equations of motion for the multipole moments of extended microstructured test bodies lead to conserved quantities that are closely related to the conserved currents derived in the field-theoretic framework.

  14. Hydrodynamic approach to boost invariant free streaming

    NASA Astrophysics Data System (ADS)

    Calzetta, E.

    2015-08-01

    We consider a family of exact boost invariant solutions of the transport equation for free-streaming massless particles, where the one-particle distribution function is defined in terms of a function of a single variable. The evolution of second and third moments of the one-particle distribution function [the second moment being the energy momentum tensor (EMT) and the third moment the nonequilibrium current (NEC)] depends only on two moments of that function. Given those two moments, we show how to build a nonlinear hydrodynamic theory which reproduces the early time evolution of the EMT and the NEC. The structure of these theories may give insight on nonlinear hydrodynamic phenomena on short time scales.

  15. Kahler stabilized, modular invariant heterotic string models

    SciTech Connect

    Gaillard, Mary K.; Gaillard, Mary K.; Nelson, Brent D.

    2007-03-19

    We review the theory and phenomenology of effective supergravity theories based on orbifold compactifications of the weakly-coupled heterotic string. In particular, we consider theories in which the four-dimensional theory displays target space modular invariance and where the dilatonic mode undergoes Kahler stabilization. A self-contained exposition of effective Lagrangian approaches to gaugino condensation and heterotic string theory is presented, leading to the development of the models of Binétruy, Gaillard and Wu. Various aspects of the phenomenology of this class of models are considered. These include issues of supersymmetry breaking and superpartner spectra, the role of anomalous U(1) factors, issues of flavor and R-parity conservation, collider signatures, axion physics, and early universe cosmology. For the vast majority of phenomenological considerations the theories reviewed here compare quite favorably to other string-derived models in the literature. Theoretical objections to the framework and directions for further research are identified and discussed.

  16. Truesdell invariance in relativistic electromagnetic fields

    NASA Astrophysics Data System (ADS)

    Walwadkar, B. B.; Virkar, K. V.

    1984-01-01

    The Truesdell derivative of a contravariant tensor fieldX ab is defined with respect to a null congruencel a analogous to the Truesdell stress rate in classical continuum mechanics. The dynamical consequences of the Truesdell invariance with respect to a timelike vectoru a of the stress-energy tensor characterizing a charged perfect fluid with null conductivity are the conservation of pressure (p), charged density (e) an expansion-free flow, constancy of the Maxwell scalars, and vanishing spin coefficientsα+¯β = ¯σ - λ = τ = 0 (assuming freedom conditionsk = λ = ɛ ψ + ¯γ = 0). The electromagnetic energy momentum tensor for the special subcases of Ruse-Synge classification for typesA andB are described in terms of the spin coefficients introduced by Newman-Penrose.

  17. Rotationally invariant ensembles of integrable matrices

    NASA Astrophysics Data System (ADS)

    Yuzbashyan, Emil A.; Shastry, B. Sriram; Scaramazza, Jasen A.

    2016-05-01

    We construct ensembles of random integrable matrices with any prescribed number of nontrivial integrals and formulate integrable matrix theory (IMT)—a counterpart of random matrix theory (RMT) for quantum integrable models. A type-M family of integrable matrices consists of exactly N -M independent commuting N ×N matrices linear in a real parameter. We first develop a rotationally invariant parametrization of such matrices, previously only constructed in a preferred basis. For example, an arbitrary choice of a vector and two commuting Hermitian matrices defines a type-1 family and vice versa. Higher types similarly involve a random vector and two matrices. The basis-independent formulation allows us to derive the joint probability density for integrable matrices, similar to the construction of Gaussian ensembles in the RMT.

  18. Bacterial phenotype identification using Zernike moment invariants

    NASA Astrophysics Data System (ADS)

    Bayraktar, Bulent; Banada, Padmapriya P.; Hirleman, E. Daniel; Bhunia, Arun K.; Robinson, J. Paul; Rajwa, Bartek

    2006-02-01

    Pathogenic bacterial contamination in food products is costly to the public and to industry. Traditional methods for detection and identification of major food-borne pathogens such as Listeria monocytogenes typically take 3-7 days. Herein, the use of optical scattering for rapid detection, characterization, and identification of bacteria is proposed. Scatter patterns produced by the colonies are recognized without the need to use any specific model of light scattering on biological material. A classification system was developed to characterize and identify the scatter patterns obtained from colonies of various species of Listeria. The proposed classification algorithm is based on Zernike moment invariants (features) calculated from the scatter images. It has also been demonstrated that even a simplest approach to multivariate analysis utilizing principal component analysis paired with clustering or linear discriminant analysis can be successfully used to discriminate and classify feature vectors computed from the bacterial scatter patterns.

  19. Conformally invariant fractals and potential theory

    PubMed

    Duplantier

    2000-02-14

    The multifractal (MF) distribution of the electrostatic potential near any conformally invariant fractal boundary, like a critical O(N) loop or a Q-state Potts cluster, is solved in two dimensions. The dimension &fcirc;(straight theta) of the boundary set with local wedge angle straight theta is &fcirc;(straight theta) = pi / straight theta-25-c / 12 (pi-straight theta)(2) / straight theta(2pi-straight theta), with c the central charge of the model. As a corollary, the dimensions D(EP) of the external perimeter and D(H) of the hull of a Potts cluster obey the duality equation (D(EP)-1) (D(H)-1) = 1 / 4. A related covariant MF spectrum is obtained for self-avoiding walks anchored at cluster boundaries.

  20. Orthogonal wavelet moments and their multifractal invariants

    NASA Astrophysics Data System (ADS)

    Uchaev, Dm. V.; Uchaev, D. V.; Malinnikov, V. A.

    2015-02-01

    This paper introduces a new family of moments, namely orthogonal wavelet moments (OWMs), which are orthogonal realization of wavelet moments (WMs). In contrast to WMs with nonorthogonal kernel function, these moments can be used for multiresolution image representation and image reconstruction. The paper also introduces multifractal invariants (MIs) of OWMs which can be used instead of OWMs. Some reconstruction tests performed with noise-free and noisy images demonstrate that MIs of OWMs can also be used for image smoothing, sharpening and denoising. It is established that the reconstruction quality for MIs of OWMs can be better than corresponding orthogonal moments (OMs) and reduces to the reconstruction quality for the OMs if we use the zero scale level.