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Sample records for invariant chain fragment

  1. Inhibition of peptide binding to DR molecules by a leupeptin-induced invariant chain fragment.

    PubMed

    Demotz, S; Danieli, C; Wallny, H J; Majdic, O

    1994-08-01

    Loading of peptides onto DR molecules was studied by characterizing precursors of the mature peptide-DR complexes expressed at the surface of B cells. Since invariant chain (Ii) prevents binding of peptides by DR molecules, it was speculated that analysis of complexes between DR heterodimers and proteolytic fragments of Ii offers the possibility to examine how DR molecules and peptides assemble. Using a procedure combining a two-step affinity chromatography and gel filtration, we isolated from leupeptin-treated B cells complexes between DR molecules and N-terminal Ii fragments previously called "leupeptin-induced polypeptides" (LIP; Blum and Cresswell, 1988, Proc. natn. Acad. Sci. U.S.A. 85, 3975-3979). It was observed that the most prominent LIP fragment has a relative molecular mass (M(r)) of 16 kDa. In addition, we show that this polypeptide species does not bear N-linked glycans, indicating that this fragment does not extend beyond residue 129 of Ii. Similarly to DR alpha beta heterodimers associated with the full length 33 and 35 kDa Ii forms, DR alpha beta heterodimers associated with LIP fragments are unstable in sodium dodecyl sulfate (SDS) at ambient temperature, whereas mature DR alpha beta heterodimers are resistant to dissociation with SDS. These results are indirect evidence that LIP-DR complexes are devoid of bound peptides. This possibility was supported by showing that LIP-DR complexes fail to bind a radioiodinated tetanus toxin peptide (125I-p2), while DR molecules, which are spontaneously released from complexes with LIP fragments, bind the labeled peptide. These results demonstrate that association with LIP fragments is sufficient to prevent binding of peptides by DR molecules. This notion was further documented by showing that binding of 125I-p2 on DR heterodimers is inhibited by preparations of LIP fragment. By contrast, a soluble recombinant fragment corresponding to the extracytoplasmic region of Ii did not block 125I-p2 binding. The results

  2. Release of DR molecules from complexes with invariant chain through the formation of a C-terminal 25 kDa invariant chain fragment.

    PubMed

    Demotz, S; Danieli, C

    1993-12-01

    To investigate how class II major histocompatibility complex (MHC) molecules are released from complexes with invariant chain (Ii), we studied a 25 kDa Ii fragment (p25) detected by Western blotting in affinity chromatographed DR preparations. The p25 species corresponds to the non-transmembrane, C-terminal Ii fragment 107-232. It was determined by gel filtration chromatography that the p25 fragment has a relative molecular mass (M(r)) of 46 kDa, indicating that this Ii fragment is present as dimers in B cell lysate. Two independent approaches were followed to demonstrate that generation of the p25 fragment takes place shortly before, or concomitantly to, loading of class II MHC molecules with antigen fragments. First, it was shown that a fraction of the p25 molecules is resistant to endoglycosidase H digestion, indicating that the p25 polypeptide can exit the endoplasmic reticulum (ER) and is transported at least to the cis-Golgi compartment. Second, treatment of class II MHC-positive B cells with leupeptin blocks the formation of p25, further indicating that this Ii fragment is generated in the endosomal compartment. The role of the p25 Ii species in the assembly of complexes between peptides and DR molecules was then investigated. While the p25 fragment was totally unable to prevent binding of a synthetic tetanus toxin peptide to DR molecules, the full-length Ii species (p33/35) effectively inhibited peptide binding, indicating that, by contrast with the p33/35 species, the p25 fragment does not occlude the peptide binding site of DR molecules. We concluded that the p25 fragment, which is produced by proteolytic cleavage at the N-terminal side of Methionine 107, has a decreased affinity for DR molecules as compared with the p33/35 species. Dissociation of the p25 fragment from DR molecules exposes the peptide binding site, which is thus made accessible for antigen fragments. This model of the complexes between DR and antigen fragments proposes that a stretch of

  3. Invariant object recognition based on extended fragments.

    PubMed

    Bart, Evgeniy; Hegdé, Jay

    2012-01-01

    Visual appearance of natural objects is profoundly affected by viewing conditions such as viewpoint and illumination. Human subjects can nevertheless compensate well for variations in these viewing conditions. The strategies that the visual system uses to accomplish this are largely unclear. Previous computational studies have suggested that in principle, certain types of object fragments (rather than whole objects) can be used for invariant recognition. However, whether the human visual system is actually capable of using this strategy remains unknown. Here, we show that human observers can achieve illumination invariance by using object fragments that carry the relevant information. To determine this, we have used novel, but naturalistic, 3-D visual objects called "digital embryos." Using novel instances of whole embryos, not fragments, we trained subjects to recognize individual embryos across illuminations. We then tested the illumination-invariant object recognition performance of subjects using fragments. We found that the performance was strongly correlated with the mutual information (MI) of the fragments, provided that MI value took variations in illumination into consideration. This correlation was not attributable to any systematic differences in task difficulty between different fragments. These results reveal two important principles of invariant object recognition. First, the subjects can achieve invariance at least in part by compensating for the changes in the appearance of small local features, rather than of whole objects. Second, the subjects do not always rely on generic or pre-existing invariance of features (i.e., features whose appearance remains largely unchanged by variations in illumination), and are capable of using learning to compensate for appearance changes when necessary. These psychophysical results closely fit the predictions of earlier computational studies of fragment-based invariant object recognition. PMID:22936910

  4. Extensive Adiabatic Invariants for Nonlinear Chains

    NASA Astrophysics Data System (ADS)

    Giorgilli, Antonio; Paleari, Simone; Penati, Tiziano

    2012-09-01

    We look for extensive adiabatic invariants in nonlinear chains in the thermodynamic limit. Considering the quadratic part of the Klein-Gordon Hamiltonian, by a linear change of variables we transform it into a sum of two parts in involution. At variance with the usual method of introducing normal modes, our constructive procedure allows us to exploit the complete resonance, while keeping the extensive nature of the system. Next we construct a nonlinear approximation of an extensive adiabatic invariant for a perturbation of the discrete nonlinear Schrödinger model. The fluctuations of this quantity are controlled via Gibbs measure estimates independent of the system size, for a large set of initial data at low specific energy. Finally, by numerical calculations we show that our adiabatic invariant is well conserved for times much longer than predicted by our first order theory, with fluctuation much smaller than expected according to standard statistical estimates.

  5. 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

  6. 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

  7. Invariants of nonlinearity in the phononic characteristics of granular chains.

    PubMed

    Ganesh, R; Gonella, S

    2014-08-01

    In this work, we analyze the phononic characteristics of wave motion in precompressed monoatomic and diatomic granular chains, with emphasis on the evolving spatial features of wave packets. A Taylor series expansion of the governing equations is considered to approximate the granular chain with the Fermi-Pasta-Ulam chain. Within this approximation, the envelope modulation of the first-order features of the wave profile is monitored and the characteristics of this modulation are determined by studying the evolution of one of the distinctive features of the spatial profile. A set of constants that describe the quantitative effects of nonlinearity on the response are determined for monoatomic and diatomic chains and interpreted as invariants of quadratic nonlinearity. The universality of these invariants is verified by constructing inverse problems to estimate the contact power law from the wave response of granular chains with arbitrary nonlinear force interaction. The imposed power law is recovered exactly from numerical simulations for a number of considered scenarios, paving the way for inverse characterization of nonlinearity from experimental data. PMID:25215841

  8. Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps

    NASA Astrophysics Data System (ADS)

    Uricaru, Raluca; Mancheron, Alban; Rivals, Eric

    Chaining fragments is a crucial step in genome alignment. Existing chaining algorithms compute a maximum weighted chain with no overlaps allowed between adjacent fragments. In practice, using local alignments as fragments, instead of MEMs, generates frequent overlaps between fragments, due to combinatorial reasons and biological factors, i.e. variable tandem repeat structures that differ in number of copies between genomic sequences. In this paper, in order to raise this limitation, we formulate a novel definition of a chain, allowing overlaps proportional to the fragments lengths, and exhibit an efficient algorithm for computing such a maximum weighted chain. We tested our algorithm on a dataset composed of 694 genome couples and accounted for significant improvements in terms of coverage, while keeping the running times below reasonable limits.

  9. 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.

  10. 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.

  11. '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.

  12. Entanglement properties of correlated random spin chains and similarities with conformally invariant systems

    NASA Astrophysics Data System (ADS)

    Getelina, João C.; Alcaraz, Francisco C.; Hoyos, José A.

    2016-01-01

    We study the Rényi entanglement entropy and the Shannon mutual information for a class of spin-1/2 quantum critical XXZ chains with random coupling constants which are partially correlated. In the XX case, distinctly from the usual uncorrelated random case where the system is governed by an infinite-disorder fixed point, the correlated-disorder chain is governed by finite-disorder fixed points. Surprisingly, we verify that, although the system is not conformally invariant, the leading behavior of the Rényi entanglement entropies are similar to those of the clean (no randomness) conformally invariant system. In addition, we compute the Shannon mutual information among subsystems of our correlated-disorder quantum chain and verify the same leading behavior as the n =2 Rényi entanglement entropy. This result extends a recent conjecture concerning the same universal behavior of these quantities for conformally invariant quantum chains. For the generic spin-1/2 quantum critical XXZ case, the true asymptotic regime is identical to that in the uncorrelated disorder case. However, these finite-disorder fixed points govern the low-energy physics up to a very long crossover length scale, and the same results as in the XX case apply. Our results are based on exact numerical calculations and on a numerical strong-disorder renormalization group.

  13. 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

  14. 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...

  15. Burning invariant manifolds for propagating fronts in a chain of vortices

    NASA Astrophysics Data System (ADS)

    Solomon, Tom; Kingsbury, Mark; Mahoney, John; Mitchell, Kevin

    2011-11-01

    We present experimental studies of the behavior of reaction fronts in a chain of alternating vortices. The flow is produced by a magnetohydrodynamic forcing technique, and the fronts are produced by the ferroin-catalyzed Belousov-Zhabotinsky chemical reaction. We introduce burning invariant manifolds (BIMs) which act as barriers to front propagation, similar to the role played by invariant manifolds as barriers to passive transport in two-dimensional flows. Unlike manifolds for passive transport, though, BIMs are one-sided barriers, passing either left- or right-going fronts but blocking the other. We show how the BIMs can be measured experimentally for both time-independent and time-periodic flows. The experimental results are compared to simulations based on a simplified numerical model of the flow. Supported by NSF Grants DMR-0703635, DMR-1004744, PHY-0552790 and PHY-0748828.

  16. Intracellular transport of MHC class II and associated invariant chain in antigen presenting cells from AP-3-deficient mocha mice.

    PubMed

    Sevilla, L M; Richter, S S; Miller, J

    2001-06-15

    MHC class II-restricted antigen presentation requires trafficking of newly synthesized class II-invariant chain complexes from the trans-Golgi network to endosomal, peptide-loading compartments. This transport is mediated by dileucine-like motifs within the cytosolic tail of the invariant chain. Although these signals have been well characterized, the cytosolic proteins that interact with these dileucine signals and mediate Golgi sorting and endosomal transport have not been identified. Recently, an adaptor complex, AP-3, has been identified that interacts with dileucine motifs and mediates endosomal/lysosomal transport in yeast, Drosophila, and mammals. In this report, we have assessed class II-invariant chain trafficking in a strain of mice (mocha) which lacks expression of AP-3. Our studies demonstrate that the lack of AP-3 does not affect the kinetics of invariant chain degradation, the route of class II-invariant chain transport, or the rate and extent of class II-peptide binding as assessed by the generation of SDS-stable dimers. The possible role of other known or unknown adaptor complexes in class II-invariant chain transport is discussed. PMID:11520080

  17. Topological invariants in the study of a chaotic food chain system

    NASA Astrophysics Data System (ADS)

    Duarte, Jorge; Januário, Cristina; Martins, Nuno

    2008-06-01

    The study of ecological systems has generated deep interest in exploring the complexity of chaotic food chains. The role of chaos in ecosystems is not entirely understood. One approach to have a better comprehension of ecological chaos is by analyzing it in mathematical models of basic food chains. In this article it is considered a classical chaotic food chain model from the literature. We use the theory of symbolic dynamics to study the topological entropy and the parameter space ordering of kneading sequences associated with one-dimensional maps that reproduce significant aspects of the model dynamics. The topological entropy allows us to distinguish different chaotic states in some realistic system parameter region. Another numerical invariant is introduced in order to characterize isentropic dynamics. Studying a set of maps with the same topological entropy, we exhibit numerical results about the relation between the second topological invariant and each of the control parameters in consideration. This work provides an illustration of how our understanding of ecological models can be enhanced by the theory of symbolic dynamics.

  18. Interaction of Human Immunodeficiency Virus Type 2 Vpx and Invariant Chain

    PubMed Central

    Pancio, Heather A.; Vander Heyden, Nancy; Kosuri, Kavitha; Cresswell, Peter; Ratner, Lee

    2000-01-01

    Vpx is a virion-associated protein of human immunodeficiency virus type 2 (HIV-2) and simian immunodeficiency viruses. The yeast two-hybrid system was used to identify invariant chain (Ii) as a cellular protein that interacts with HIV-2 Vpx. Vpx-Ii interaction was confirmed in cell-free reactions using bacterially expressed glutathione S-transferase fusion proteins and by coimmunoprecipitation in transfected and infected cells. In chronically infected cells expressing Vpx, Ii levels were markedly decreased, presumably due to enhanced degradation. These findings suggest that Vpx may disrupt major histocompatibility complex class II antigen presentation. PMID:10846101

  19. Complete amino acid sequence of globin chains and biological activity of fragmented crocodile hemoglobin (Crocodylus siamensis).

    PubMed

    Srihongthong, Saowaluck; Pakdeesuwan, Anawat; Daduang, Sakda; Araki, Tomohiro; Dhiravisit, Apisak; Thammasirirak, Sompong

    2012-08-01

    Hemoglobin, α-chain, β-chain and fragmented hemoglobin of Crocodylus siamensis demonstrated both antibacterial and antioxidant activities. Antibacterial and antioxidant properties of the hemoglobin did not depend on the heme structure but could result from the compositions of amino acid residues and structures present in their primary structure. Furthermore, thirteen purified active peptides were obtained by RP-HPLC analyses, corresponding to fragments in the α-globin chain and the β-globin chain which are mostly located at the N-terminal and C-terminal parts. These active peptides operate on the bacterial cell membrane. The globin chains of Crocodylus siamensis showed similar amino acids to the sequences of Crocodylus niloticus. The novel amino acid substitutions of α-chain and β-chain are not associated with the heme binding site or the bicarbonate ion binding site, but could be important through their interactions with membranes of bacteria. PMID:22648692

  20. The intramembrane protease SPPL2a promotes B cell development and controls endosomal traffic by cleavage of the invariant chain

    PubMed Central

    Schneppenheim, Janna; Dressel, Ralf; Hüttl, Susann; Lüllmann-Rauch, Renate; Engelke, Michael; Dittmann, Kai; Wienands, Jürgen; Eskelinen, Eeva-Liisa; Hermans-Borgmeyer, Irm; Fluhrer, Regina; Saftig, Paul

    2013-01-01

    Regulated intramembrane proteolysis is a central cellular process involved in signal transduction and membrane protein turnover. The presenilin homologue signal-peptide-peptidase-like 2a (SPPL2a) has been implicated in the cleavage of type 2 transmembrane proteins. We show that the invariant chain (li, CD74) of the major histocompatability class II complex (MHCII) undergoes intramembrane proteolysis mediated by SPPL2a. B lymphocytes of SPPL2a−/− mice accumulate an N-terminal fragment (NTF) of CD74, which severely impairs membrane traffic within the endocytic system and leads to an altered response to B cell receptor stimulation, reduced BAFF-R surface expression, and accumulation of MHCII in transitional developmental stage T1 B cells. This results in significant loss of B cell subsets beyond the T1 stage and disrupted humoral immune responses, which can be recovered by additional ablation of CD74. Hence, we provide evidence that regulation of CD74-NTF levels by SPPL2a is indispensable for B cell development and function by maintaining trafficking and integrity of MHCII-containing endosomes, highlighting SPPL2a as a promising pharmacological target for depleting and/or modulating B cells. PMID:23267015

  1. 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

  2. The multifaceted roles of the invariant chain CD74--More than just a chaperone.

    PubMed

    Schröder, Bernd

    2016-06-01

    The invariant chain (CD74) is well known for its essential role in antigen presentation by mediating assembly and subcellular trafficking of the MHCII complex. Beyond this, CD74 has also been implicated in a number of processes independent of MHCII. These include the regulation of endosomal trafficking, cell migration and cellular signalling as surface receptor of the pro-inflammatory cytokine macrophage migration inhibitory factor (MIF). In several forms of cancer, CD74 is up-regulated and associated with enhanced proliferation and metastatic potential. In this review, an overview of the diverse biological functions of the CD74 protein is provided with a particular focus on how these may be regulated. In particular, proteolysis of CD74 will be discussed as a central mechanism to control the actions of this important protein at different levels. PMID:27033518

  3. 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.

  4. 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

  5. Molecular characterization and tissue-specific expression of invariant chain isoform in Muscovy Duck (Cairina moschata).

    PubMed

    Liu, S J; Chen, F F; Wu, C; Ni, Q S; Yu, W Y

    2014-01-01

    Invariant chain (Ii) isoform, through its thyroglobulin-like (Tg) domain, inhibits cysteine proteases during antigen presentation in vertebrates. In birds, the Ii of Muscovy Duck (MDIi) has 2 forms: MDIi-1 and MDIi-2 (MDIi isoform). To understand the genetic information and expression characteristics of MDIi-2, polymerase chain reaction, and bioinformatic analysis were performed for MDIi-2 from healthy adult Muscovy Duck. The full-length MDIi-2 cDNA sequence was found to be 1377-base pairs, encoding a 285-amino acid protein. MDIi-2 contains 63 amino acids with an insertion sequence in the Tg domain. MDIi-2 shares high identity (72.51-94.74%) with the same protein in other birds. The Tg domain of MDIi-2 is highly conserved and showed relatively high identity (96.83%) among all tested birds. The molecular structure of the Tg domain supports this conservation. MDIi-2 expression was measured in various tissues using real-time quantitative polymerase chain reaction. Similar to MDIi-1, MDIi-2 was detected in all tissues but at different levels. Higher expression level was observed in the spleen, intestinal mucosa, and bursa stipe (bursa of Fabricius stipe) than in other tissues. This suggests that MDIi-2, like MDIi-1, plays an essential role in all tissues and that its differential expression may be related to its functions in these tissues. The coexistence of 2 MDIi isoforms indicates that their functions are correlated in Muscovy Duck. This study improves the understanding of poultry immunology and may be used to improve measures to protect Muscovy Duck from disease. PMID:25366788

  6. Deficiency of Antigen Presenting Cell Invariant Chain Reduces Atherosclerosis in Mice

    PubMed Central

    Sun, Jiusong; Hartvigsen, Karsten; Chou, Meng-Yun; Zhang, Yadong; Sukhova, Galina K.; Zhang, Jie; Lopez-Ilasaca, Marco; Diehl, Cody J.; Yakov, Niva; Harats, Dror; George, Jacob; Witztum, Joseph L.; Libby, Peter; Ploegh, Hidde; Shi, Guo-Ping

    2010-01-01

    Background Adaptive and innate immunity play important roles in atherogenesis. Invariant chain (CD74) mediates antigen presenting cell (APC) antigen presentation and T cell activation. This study tested the hypothesis that CD74-deficient mice have reduced numbers of active T cells and resist atherogenesis. Methods and Results In low-density lipoprotein receptor-deficient mice (Ldlr−/−), CD74 deficiency (Ldlr−/−Cd74−/−) significantly reduced atherosclerosis and CD25+ activated T cells in the atheromata. While Ldlr−/−Cd74−/− mice had decreased levels of plasma IgG1, IgG2b, and IgG2c against malondialdehyde-modified LDL (MDA-LDL), presumably due to impaired APC function, Ldlr−/−Cd74−/− mice showed higher levels of anti-MDA-LDL IgM and IgG3. After immunization with MDA-LDL, Ldlr−/−Cd74−/− mice had lower levels of all anti-MDA-LDL immunoglobulin (Ig) isotypes compared with Ldlr−/− mice. As anticipated, only Ldlr−/− splenocytes responded to in vitro stimulation with MDA-LDL, producing Th1/Th2 cytokines. Heat shock protein-65 (HSP65) immunization enhanced atherogenesis in Ldlr−/− mice, but Ldlr−/−Cd74−/− mice remained protected. Compared with Ldlr−/− mice, Ldlr−/−Cd74−/− mice had higher anti-MDA-LDL autoantibody titers, fewer lesion CD25+ activated T cells, impaired release of Th1/Th2 cytokines from APC after HSP65-stimulation, and reduced levels of all plasma anti-HSP65 Ig isotypes. Cytofluorimetry of splenocytes and peritoneal cavity cells of MDA-LDL- or HSP65-immunized mice showed increased percentages of autoantibody-producing marginal zone-B and B-1 cells in Ldlr−/−Cd74−/− mice compared to Ldlr−/− mice. Conclusion Invariant chain deficiency in Ldlr−/− mice reduced atherosclerosis. This finding was associated with an impaired adaptive immune response to disease-specific antigens. Concomitantly, there occurred an unexpected increase in the number of innate-like peripheral B-1 cell

  7. 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.

  8. Role of antigen presenting cell invariant chain in the development of hepatic steatosis in mouse model.

    PubMed

    Mishra, Alaknanda; Iyer, Srikanth; Kesarwani, Ashwani; Baligar, Prakash; Arya, Satya Pal; Arindkar, Shailendra; Kumar, M J Mahesh; Upadhyay, Pramod; Majumdar, Subeer S; Nagarajan, Perumal

    2016-08-15

    The role of Invariant chain (CD74 or Ii) in antigen presentation via Antigen Presenting Cells (APC), macrophage recruitment as well as survival, T cell activation and B cell differentiation has been well recognized. However, the aspect of CD74 which is involved in the development of hepatic steatosis and the pathways through which it acts remain to be studied. In this study, we investigated the role of CD74 in the inflammatory pathway and its contribution to development of hepatic steatosis. For this, wild type C57BL/6J and CD74 deficient mice (Ii(-/-) mice) were fed with high fat high fructose (HFHF) diet for 12 weeks. Chronic consumption of this feed did not develop hepatic steatosis, glucose intolerance or change in the level of immune cells in Ii(-/-) mice. Moreover, there was relatively delayed expression of genes involved in development of non alcoholic fatty liver disease (NAFLD) in HFHF fed Ii(-/-) mice as compared to that of C57BL/6J phenotype. Taken together, the data suggest that HFHF diet fed Ii(-/-) mice fail to develop hepatic steatosis, suggesting that Ii mediated pathways play a vital role in the initiation and propagation of liver inflammation. PMID:27371158

  9. 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

  10. Production and characterization of a single chain variable fragment (scFv) for the mycotoxin deoxynivalenol

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Deoxynivalenol (DON)is a mycotoxin produced by certain fungi that infest cereal grains worldwide. A hybridoma cell line producing a monoclonal antibody (Mab) recognizing DON was used as the starting point in the development of a recombinant single chain variable fragment (scFv) antibody. The scFv wa...

  11. 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.

  12. 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

  13. 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

  14. Aberrant immunoglobulin synthesis in light chain amyloidosis. Free light chain and light chain fragment production by human bone marrow cells in short-term tissue culture.

    PubMed Central

    Buxbaum, J

    1986-01-01

    Bone marrow cells obtained from 14 patients with light chain amyloid (AL) deposition were examined by biosynthetic labeling techniques. These analyses identified free monoclonal light chain (L-chain) synthesis even in those patients whose serum or urine contained no M protein or free L-chains or only an intact M protein. The experiments also identified a subset of patients whose plasma cells synthesized polypeptides bearing constant region antigenic determinants that migrated more rapidly than intact L-chains on polyacrylamide gels. Since most AL fibrils contain L-chain fragments rather than intact L-chains, these studies suggested that the genesis of the fibril components may reflect aberrant synthesis, proteolytic processing, or both. We also noted that in some individuals the pattern of Ig synthesis normalized after several courses of cytotoxic therapy. Thus, we could use bone marrow Ig synthesis as a sensitive biochemical parameter for monitoring therapy. Finally, the presence of aberrant synthetic products in these clones raised questions about their origin with respect to the normal processes of transcription, translation, and posttranslational modification in Ig-producing cells. Images PMID:3091637

  15. Cathepsin V is involved in the degradation of invariant chain in human thymus and is overexpressed in myasthenia gravis

    PubMed Central

    Tolosa, Eva; Li, Weijie; Yasuda, Yoshiyuki; Wienhold, Wolfgang; Denzin, Lisa K.; Lautwein, Alfred; Driessen, Christoph; Schnorrer, Petra; Weber, Ekkehard; Stevanovic, Stefan; Kurek, Raffael; Melms, Arthur; Brömme, Dieter

    2003-01-01

    Stepwise degradation of the invariant chain (Ii) is required for the binding of antigenic peptides to MHC class II molecules. Cathepsin (Cat) L in the murine thymus and Cat S in peripheral APCs have both been implicated in the last step of Ii degradation that gives rise to the class II–associated invariant chain peptides (CLIP). Cat V has been recently described as highly homologous to Cat L and exclusively expressed in human thymus and testis, but with no mouse orthologue. We report that Cat V is the dominant cysteine protease in cortical human thymic epithelial cells, while Cat L and Cat S seem to be restricted to dendritic and macrophage-like cells. Active Cat V in thymic lysosomal preparations was demonstrated by active-site labeling. Recombinant Cat V was capable of converting Ii into CLIP efficiently, suggesting that Cat V is the protease that controls the generation of αβ-CLIP complexes in the human thymus, in analogy to Cat L in mouse. Comparison of Cat V expression between thymi from patients with myasthenia gravis and healthy controls revealed a significantly higher expression level in the pathological samples, suggesting a potential involvement of this protease in the immunopathogenesis of myasthenia gravis, an autoimmune disease almost invariably associated with thymic pathology. PMID:12925692

  16. Engineered single-chain variable fragment antibody for immunodiagnosis of groundnut bud necrosis virus infection.

    PubMed

    Maheshwari, Yogita; Vijayanandraj, S; Jain, R K; Mandal, Bikash

    2015-05-01

    Few studies have been done on engineered antibodies for diagnosis of tospovirus infections. The present study was undertaken to develop a single-chain variable fragment (scFv) for specific diagnosis of infection by groundnut bud necrosis virus (GBNV), the most prevalent serogroup IV tospovirus in India. Heavy chain (372 nucleotide [nt]) and light chain (363 nt) variable region clones obtained from a hybridoma were used to make an scFv construct that expressed a ~29-kDa protein in E. coli. The scFv specifically detected GBNV in field samples of cowpea, groundnut, mung bean, and tomato, and it did not recognize watermelon bud necrosis virus, a close relative of GBNV belonging to tospovirus serogroup IV. This study for the first time demonstrated the application of a functional scFv against a serogroup-IV tospovirus. PMID:25698103

  17. Interplaying roles of native topology and chain length in marginally cooperative and noncooperative folding of small protein fragments

    NASA Astrophysics Data System (ADS)

    Badasyan, Artem; Liu, Zhirong; Chan, Hue Sun

    Coarse-grained chain simulations were used to study fragments of two homologous proteins of the peripheral subunit-binding domain (PSBD) family, Bacillus stearothermophilus PSBD (E3BD) and Escherichia coli 2-oxo-glutarate dehydrogenase PSBD (BBL). To ascertain a robust rank order of folding cooperativity, native-centric intraprotein interactions were modeled by (i) a common Gō;-like potential, and (ii) native-centric potentials with desolvation barriers or (iii) many-body terms. Homologous proteins can possess substantially different folding cooperativity. Consistent with experiment, our calculations indicated that E3BD fragments fold more cooperatively than BBL fragments of approximately the same chain length. For a given fragment, native contacts deduced from Protein Data Bank structures can vary significantly depending on the number of residues that the structure encompasses in addition to those of the fragment itself, resulting in variation in model folding cooperativity predicted using different native contact sets for the same fragment. This observation underscores that folding cooperativity of these fragments can be extremely sensitive to change in chain length. Thus, a ˜40-residue protein fragment's folding cooperativity, or lack thereof, does not necessarily imply essentially identical behaviors for super- or sub-fragments with only several residues more, or less, than the given fragment. Ramifications for experimental investigations of downhill folding are discussed.

  18. Structurally Diverse Mitochondrial Branched Chain Aminotransferase (BCATm) Leads with Varying Binding Modes Identified by Fragment Screening.

    PubMed

    Borthwick, Jennifer A; Ancellin, Nicolas; Bertrand, Sophie M; Bingham, Ryan P; Carter, Paul S; Chung, Chun-Wa; Churcher, Ian; Dodic, Nerina; Fournier, Charlène; Francis, Peter L; Hobbs, Andrew; Jamieson, Craig; Pickett, Stephen D; Smith, Sarah E; Somers, Donald O'N; Spitzfaden, Claus; Suckling, Colin J; Young, Robert J

    2016-03-24

    Inhibitors of mitochondrial branched chain aminotransferase (BCATm), identified using fragment screening, are described. This was carried out using a combination of STD-NMR, thermal melt (Tm), and biochemical assays to identify compounds that bound to BCATm, which were subsequently progressed to X-ray crystallography, where a number of exemplars showed significant diversity in their binding modes. The hits identified were supplemented by searching and screening of additional analogues, which enabled the gathering of further X-ray data where the original hits had not produced liganded structures. The fragment hits were optimized using structure-based design, with some transfer of information between series, which enabled the identification of ligand efficient lead molecules with micromolar levels of inhibition, cellular activity, and good solubility. PMID:26938474

  19. Latex agglutination test based on single-chain Fv recombinant antibody fragment.

    PubMed

    Golchin, M; Khalili-Yazdi, A; Karamouzian, M; Abareghi, A

    2012-01-01

    Recombinant antibodies have been proposed as invaluable tools for various therapeutic and diagnostic purposes. Here, we describe the development of a novel latex agglutination test (LAT) using single-chain Fv recombinant antibody fragment for the detection of K99(+) enterotoxigenic Escherichia coli strains. For the production of a single-chain Fv antibody fragment (scFv) against the major colonization factor (FanC) of K99 antigen, the scFv gene was integrated into a bacterial expression vector under the control of T7 promoter. After high-level expression of soluble scFv (approximately 50 mg/l) in flask cultivation of E. coli DE3 and purification, scFv was immobilized on different latex particles, and then, these sensitized beads were used in LAT. Results obtained with our latex reagents revealed that the recombinant antibody-coated particles were able to give a good agglutination signal with purified antigen, intact cells displaying this protein and clinical specimens. The strength of agglutination of scFv-coated beads for antigen was comparable to that of polyclonal anti-K99-coated particles. However, the assay proved to be simple and rapid, similar to conventional LATs, and owing to more convenient and economical production of recombinant antibodies, they can be considered as a useful reagent for replacing monoclonal antibodies in LATs. PMID:21916915

  20. Polymerase chain reaction-restriction fragment length polymorphism authentication of raw meats from game birds.

    PubMed

    Rojas, María; González, Isabel; Fajardo, Violeta; Martín, Irene; Hernández, Pablo E; García, Teresa; Martín, Rosario

    2008-01-01

    Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis has been applied to the identification of meats from quail (Coturnix coturnix), pheasant (Phasianus colchicus), red-legged partridge (Alectoris rufa), guinea fowl (Numida meleagris), capercaillie (Tetrao urogallus), Eurasian woodcock (Scolopax rusticola), woodpigeon (Columba palumbus), and song thrush (Turdus philomelos). PCR amplification was performed using a set of primers flanking a conserved region of approximately 720 base pairs (bp) from the mitochondrial 12S rRNA gene. Restriction site analysis based on sequence data from this DNA fragment permitted the selection of AluI and BfaI endonucleases for species identification. The restriction profiles obtained when amplicons were digested with the chosen enzymes allowed the unequivocal identification of all game bird species analyzed. However, the use of the PCR-RFLP technique described is limited to raw meat authentication. It is not suitable for cooked products because thermal treatment strongly accelerates DNA degradation leading to difficulties in amplifying the 720 bp fragment. PMID:19202803

  1. 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. PMID:8207055

  2. Substrate determinants of signal peptide peptidase-like 2a (SPPL2a)-mediated intramembrane proteolysis of the invariant chain CD74.

    PubMed

    Hüttl, Susann; Helfrich, Felix; Mentrup, Torben; Held, Sebastian; Fukumori, Akio; Steiner, Harald; Saftig, Paul; Fluhrer, Regina; Schröder, Bernd

    2016-05-15

    The presenilin homologue signal peptide peptidase-like 2a (SPPL2a) is an intramembrane protease of lysosomes/late endosomes which cleaves type II transmembrane proteins. We recently identified CD74, the invariant chain of the MHCII complex, as the first in vivo validated substrate of this protease. In endosomal compartments, CD74 undergoes sequential proteolysis leading to the generation of a membrane-bound N-terminal fragment (NTF) that requires cleavage by SPPL2a for its turnover. In SPPL2a(-/-) mice, this fragment accumulates in B-cells and significantly disturbs their maturation and functionality. To date, the substrate requirements of the protease SPPL2a have not been investigated. In the present study, we systematically analysed the molecular determinants of CD74 with regard to the intramembrane cleavage by SPPL2a. Using domain-exchange experiments, we demonstrate that the intracellular domain (ICD) of CD74 can be substituted without affecting cleavability by SPPL2a. Based on IP-MS analysis of the cleavage product, we report identification of the primary SPPL2a cleavage site between Y52 and F53 within the CD74 transmembrane segment. Furthermore, systematic alanine-scanning mutagenesis of the transmembrane and membrane-proximal parts of the CD74 NTF has been performed. We show that none of the analysed determinants within the CD74 NTF including the residues flanking the primary cleavage site are absolutely essential for SPPL2a cleavage. Importantly, we found that alanine substitution of helix-destabilizing glycines within the transmembrane segment and distinct residues within the luminal membrane-proximal segment led to a reduced efficiency of SPPL2a-mediated processing. Therefore we propose that elements within the transmembrane segment and the luminal juxtamembrane domain facilitate intramembrane proteolysis of CD74 by SPPL2a. PMID:26987812

  3. Counting solutions of the Bethe equations of the quantum group invariant open XXZ chain at roots of unity

    NASA Astrophysics Data System (ADS)

    Gainutdinov, Azat M.; Hao, Wenrui; Nepomechie, Rafael I.; Sommese, Andrew J.

    2015-12-01

    We consider the {U}q{sl}(2)-invariant open spin-1/2 XXZ quantum spin chain of finite length N. For the case that q is a root of unity, we propose a formula for the number of admissible solutions of the Bethe ansatz equations in terms of dimensions of irreducible representations of the Temperley-Lieb algebra; and a formula for the degeneracies of the transfer matrix eigenvalues in terms of dimensions of tilting {U}q{sl}(2)-modules. These formulas include corrections that appear if two or more tilting modules are spectrum-degenerate. For the XX case (q={{{e}}}{{i}π /2}), we give explicit formulas for the number of admissible solutions and degeneracies. We also consider the cases of generic q and the isotropic (q\\to 1) limit. Numerical solutions of the Bethe equations up to N = 8 are presented. Our results are consistent with the Bethe ansatz solution being complete.

  4. [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

  5. Fusion protein of single-chain variable domain fragments for treatment of myasthenia gravis

    PubMed Central

    Li, Fangfang; Meng, Fanping; Jin, Quanxin; Sun, Changyuan; Li, Yingxin; Li, Honghua; Jin, Songzhu

    2014-01-01

    Single-chain variable domain fragment (scFv) 637 is an antigen-specific scFv of myasthenia gravis. In this study, scFv and human serum albumin genes were conjugated and the fusion protein was expressed in Pichia pastoris. The affinity of scFv-human serum albumin fusion protein to bind to acetylcholine receptor at the neuromuscular junction of human intercostal muscles was detected by immunofluorescence staining. The ability of the fusion protein to block myasthenia gravis patient sera binding to acetylcholine receptors and its stability in healthy serum were measured by competitive ELISA. The results showed that the inhibition rate was 2.0-77.4%, and the stability of fusion protein in static healthy sera was about 3 days. This approach suggests the scFv-human serum albumin is a potential candidate for specific immunosuppressive therapy of myasthenia gravis. PMID:25206900

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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...

  11. Development of an Immunoassay for Chloramphenicol Based on the Preparation of a Specific Single-Chain Variable Fragment Antibody.

    PubMed

    Du, Xin-Jun; Zhou, Xiao-Nan; Li, Ping; Sheng, Wei; Ducancel, Frédéric; Wang, Shuo

    2016-04-13

    Specific antibodies are essential for the immune detection of small molecule contaminants. In the present study, the heavy and light variable regions (VH and VL) of the immunoglobulin genes from a hybridoma secreting a chloramphenicol (CAP)-specific monoclonal antibody (mAb) were cloned and sequenced. In addition, the light and heavy chains obtained from the monoclonal antibody were separated using SDS-PAGE and analyzed using Orbitrap mass spectrometry. The results of DNA sequencing and mass spectrometry analysis were compared, and the VH and VL chains specific for CAP were determined and used to construct a single-chain variable fragment (scFv). This fragment was recombinantly expressed as a soluble scFv-alkaline phosphatase fusion protein and used to develop a direct competitive ELISA. Compared with the parent mAb, scFv exhibits lower sensitivity but better food matrix resistance. This work highlights the application of engineered antibodies for CAP detection. PMID:27003441

  12. Optimization of a single-chain antibody fragment overexpression in Escherichia coli using response surface methodology.

    PubMed

    Akbari, V; Sadeghi, H Mir Mohammad; Jafarian-Dehkordi, A; Chou, C Perry; Abedi, D

    2015-01-01

    Human epidermal growth factor receptor (HER) family plays an important role in various types of cancers. As a result, antibodies against HER and the mechanism of antigen-antibody binding action are under active investigation. We previously constructed a single-chain variable fragment (ScFv) against HER2, i.e. anti-Her2 ScFv, for expressing in the Escherichia coli. In the present study, we report the optimization of anti-Her2 ScFv expression in an E. coli host of BL21 (DE3) pLysS using response surface methodology based on tuning of three cultivation variables, including isopropyl-beta-D-thiogalactopyranoside (IPTG) concentration, temperature and post-induction time. A model for protein expression according to the Box-Behnken design predicted a maximal anti-Her2 ScFv expression at 37 °C, a post-induction time of 10.45 h and 0.75 mM IPTG. In addition, strategies based on inclusion body isolation and affinity chromatography were applied to purify anti-Her2 ScFv. The purity of the final product for inclusion bodies isolation and purification by Ni-NTA resin were 70 % and 95 %, respectively. The solubilization of the inclusion bodies was carried out using two denaturant agents, guanidine hydrochloride and urea. The present study showed that guanidine hydrochloride was more effective than urea in solubilizing the inclusion bodies. PMID:26430460

  13. Affinity improvement by fine tuning of single-chain variable fragment against aflatoxin B1.

    PubMed

    Min, Won-Ki; Na, Kang-In; Yoon, Jung-Hyun; Heo, Yoon-Jee; Lee, Daesang; Kim, Sung-Gun; Seo, Jin-Ho

    2016-10-15

    Aflatoxin B1 (AFB1) produced in Aspergillus flavus is a major hepatocarcinogen found in foods and feed. For effective immunological detection of AFB1 at low concentrations, the development of high affinity antibody for AFB1 is required. Previously, an affinity-maturated single-chain variable fragment containing 6 mutations (scFv-M37) was isolated from an artificial mutagenic library, which showed a 9-fold higher affinity than its wild type scFv. In this study, the effect of the 6 mutated residues on the affinity improvement was characterized using surface plasmon resonance analysis, which identified a deleterious mutation (VH-A110T) located on a framework region of the scFv-M37. The back mutation of VH-A110T resulted in a 3.2-fold affinity improvement, which was attributed to decrease of dissociation rate constant (kd) in interaction between AFB1 and the back mutant scFv. The biophysical analyses using circular dichroism and gel filtration revealed that the back mutation of VH-A110T caused a subtle conformational change of the scFv toward tighter binding to AFB1. PMID:27173568

  14. 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

  15. [Preparation of epitope imprinted particles for transferrin recognition by reversible addition fragmentation chain transfer strategy].

    PubMed

    Li, Qinran; Yang, Kaiguang; Li, Senwu; Liu, Jianxi; Zhang, Lihua; Liang, Zhen; Zhang, Yukui

    2014-10-01

    A kind of novel epitope surface imprinted particles was prepared by the reversible addition fragmentation chain transfer (RAFT) strategy. The epitope of transferrin, N-terminal peptide of the protein with nine amino acid residues, was chosen as the template and immobi- lized with covalent interaction on the surface of silica particles through the truss arm glutaraldehyde. The living/controlled polymerization was initialed by 2,2'-azobisisobutyronitrile (AIBN) at 70 °C in the solution of N,N-dimethylformamide, with the regulation by triothioester agent 2-(dodecylthiocarbonothioylthio)-2-methylpropanoic acid. Methacrylic acid and 2-hydroxyethyl methacrylate were chosen as the functional monomers and N, N-methylenebisacrylamide was chosen as the cross-linker in this polymerization. For this material, the binding capacity of the nine residue peptide could reach 2.36 mg/g with the imprinting factor (IF) of 1.89, while that for transferrin could reach 4.98 mg/g with IF of 1.61. The equilibrium could be achieved in 120 min for the transferrin recognition. In multi-protein competitive recognition, the imprinted factor of transferrin was the highest in the mixture of transferrin and other competitive proteins, such as cytochrome C and β-lactoglobulin. The results indicated that these epitope surface imprinted particles with RAFT strategy could recognize not only the nine residue peptide but also the transferrin with good selectivity, high binding capacity and fast mass transfer. PMID:25739262

  16. In silico experiments of single-chain antibody fragment against drugs of abuse

    PubMed Central

    Hu, Guodong; Chen, L. Y.

    2010-01-01

    SUMMARY Three sets of in silico experiments have been conducted to elucidate the binding mechanics of two drugs, (+)-methamphetamine (METH) and amphetamine (AMP) to the single-chain variable fragment (scFv) recently engineered from anti-METH monoclonal antibody mAb6H4 (IgG, κ light chain, Kd = 11nM). The first set of in silico experiments are long time equilibration runs of scFv:drug complexes and of drug-free scFv both in solution. They demonstrate how the solution structures of scFv deviate from its crystallographic form with or without drug molecules bound to it. And they lead to the prediction that the Arrhenius activation barrier is nearly zero for transitions from the dissociated state to the bound state. The second set of in silico experiments are nonequilibrium dynamics of pulling the drug molecules out of the binding pocket of scFv and the equilibration runs for drugs to fall back into binding pocket. They demonstrate that extra water molecules (in addition to the two crystallographic waters) exist inside the binding pocket, underneath the drug molecules. These extra waters must have been evaporated from the binding pockets during the crystallization process of the in vitro experiments of structural determination. The third set of in silico experiments are nonequilibrium steered molecular dynamics simulations to determine the absolute binding free energies of METH and AMP to scFv. The center-of-mass of a drug molecule (METH or AMP) is steered (pulled) towards (forward) and away from (reverse) the binding site, sampling forward and reverse pulling paths. Mechanic work is measured along the pulling paths. The work measurements are averaged through the Brownian dynamics fluctuation dissipation theorem to produce the free-energy profiles of the scFv:drug complexes as a function of the drug-scFv separation. These experiments lead to the theoretical prediction of absolute binding energies of METH and AMP that are in agreement with the in vitro experimental

  17. Novel human single chain antibody fragments that are rapidly interalizing effectively target epithelioid and sarcomatoid mesotheliomas

    PubMed Central

    Iyer, Arun K.; Lan, Xiaoli; Zhu, Xiaodong; Su, Yang; Feng, Jinjin; Zhang, Xiaoju; Gao, Dongwei; Seo, Youngho; VanBrocklin, Henry F.; Broaddus, V. Courtney; Liu, Bin; He, Jiang

    2011-01-01

    Human antibodies targeting all subtypes of mesothelioma could be useful to image and treat this deadly disease. Here we report tumor targeting of a novel internalizing human single chain antibody fragment (scFv) labeled with 99mTc (99mTc-M40) in murine models of mesothelioma of both epithelioid (M28) and sarcomatoid (VAMT-1) origins. 99mTc-M40 was taken up rapidly and specifically by both subtype tumor cells in vitro, with 68–92% internalized within 1h. The specificity of binding was evidenced by blocking (up to 95%) with 10-fold excess of unlabeled M40. In animal studies, tumors of both subtypes were clearly visualized by SPECT/CT as early as 1h post-injection of 99mTc-M40. Tumor uptake measured as percent of injected dose per gram tissue (%ID/g) at 3h was 4.38 and 5.84 for M28 and VAMT-1 tumors respectively, significantly greater than all organs or tissues studied (liver, 2.62%ID/g; other organs or tissues <1.7%ID/g), except the kidneys (130.7%ID/g), giving tumor-to-blood ratios of 5:1 and 7:1 and tumor-to-muscle ratios of 45:1 and 60:1, for M28 and VAMT-1 respectively. The target-mediated uptake was confirmed by a nearly 70% reduction in tumor activity following administration of 10-fold excess of unlabeled scFv. Taken together, these results indicate that M40 can rapidly and specifically target epithelioid and sarcomatoid tumor cells, demonstrating the potential of this agent as a versatile targeting ligand for imaging and therapy of all subtypes of mesothelioma. PMID:21447742

  18. 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

  19. DR alpha beta dimers released from complexes with invariant chain fail to stimulate alloreactive T cell clones.

    PubMed

    Demotz, S

    1993-09-01

    To demonstrate that DR alpha beta dimers still complexed to invariant chain (Ii) have not yet acquired peptides recognized by alloreactive T cells, complexes between DR molecules and Ii isolated from Epstein-Barr-virus (EBV)-transformed B cells were analyzed by affinity chromatography and gel filtration. First, it was shown that DR/Ii complexes inserted into artificial planar membranes (PM) failed to stimulate proliferative response of five alloreactive T cell clones and a polyclonal alloreactive T cell line, while PM bearing mature DR alpha beta dimers from the same EBV-B cells were stimulatory for the T cell clones and the T cell line. These findings indicate that either Ii inhibits binding of peptides to DR molecules or Ii hinders T cells recognition of peptide/DR complexes. Second, to discriminate between these two possibilities, DR alpha beta dimers, which were artificially released from complexes between DR molecules and Ii, were inserted into PM. These DR alpha beta dimers were devoid of alloreactive stimulatory capacity while fully capable of binding and presenting a tetanus toxin synthetic peptide to a specific T cell clone, indicating that DR molecules released from complexes with Ii are empty. This study, by showing that DR molecules bound to Ii do not bear peptides recognized by alloreactive T cells, supports the notion that association of Ii with class II major histocompatibility complex (MHC) molecules prevents premature peptide loading and hence favors encounter with peptides derived from proteins of the extracellular compartment. Since allogeneic class II MHC molecules released from complexes with Ii were not stimulatory for five out of five alloreactive T cell clones and a polyclonal alloreactive T cell line, these data also indicate that, in most cases, alloreactive T cells recognize ligands constituted by complexes between allogeneic class II MHC molecules and specific peptides which derive from the antigen-presenting cells themselves or serum

  20. 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

  1. 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

  2. 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

  3. Preparation and identification of a single-chain variable fragment antibody against Newcastle diseases virus F48E9.

    PubMed

    Li, Benqiang; Ye, Jiaxin; Lin, Yuan; Wang, Man; Zhu, Jianguo

    2014-10-15

    This article describes a proposed method for convenient and efficient detection of Newcastle diseases virus (NDV) that uses the fusion of single-chain variable fragment (scFv) and pOPE101 vector. In order to select the single chain variable fragment (scFv) against NDV F48E9, the total RNA was extracted from the spleen of immunized chicken, and then was converted into cDNA via the reverse transcription. The scFv was spliced by using splice-overlap extension polymerase chain reaction (SOE-PCR). The scFv gene was cloned into a pOPE101 vector and expressed in E. coli. Under the optimized conditions, antibody affinity was studied by indirect ELISA. One positive clone was selected by ELISA screening, named ZL.6. Based on the positive clone and the germline sequence, the results of sequence analysis showed that there are more variation in CDR of VH and VL. In addition, BHK21 cell culture was conducted to examine the potential antiviral activity of ZL.6. The experimental result demonstrated that ZL.6 was able to neutralize NDV F48E9 which infected BHK21 cells. So ZL.6 will be proved useful for further characterization of NDV as potential diagnostic tool and therapeutic agent. PMID:25183016

  4. 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. PMID:26325475

  5. The Discovery of in Vivo Active Mitochondrial Branched-Chain Aminotransferase (BCATm) Inhibitors by Hybridizing Fragment and HTS Hits.

    PubMed

    Bertrand, Sophie M; Ancellin, Nicolas; Beaufils, Benjamin; Bingham, Ryan P; Borthwick, Jennifer A; Boullay, Anne-Bénédicte; Boursier, Eric; Carter, Paul S; Chung, Chun-wa; Churcher, Ian; Dodic, Nerina; Fouchet, Marie-Hélène; Fournier, Charlène; Francis, Peter L; Gummer, Laura A; Herry, Kenny; Hobbs, Andrew; Hobbs, Clare I; Homes, Paul; Jamieson, Craig; Nicodeme, Edwige; Pickett, Stephen D; Reid, Iain H; Simpson, Graham L; Sloan, Lisa A; Smith, Sarah E; Somers, Donald O'N; Spitzfaden, Claus; Suckling, Colin J; Valko, Klara; Washio, Yoshiaki; Young, Robert J

    2015-09-24

    The hybridization of hits, identified by complementary fragment and high throughput screens, enabled the discovery of the first series of potent inhibitors of mitochondrial branched-chain aminotransferase (BCATm) based on a 2-benzylamino-pyrazolo[1,5-a]pyrimidinone-3-carbonitrile template. Structure-guided growth enabled rapid optimization of potency with maintenance of ligand efficiency, while the focus on physicochemical properties delivered compounds with excellent pharmacokinetic exposure that enabled a proof of concept experiment in mice. Oral administration of 2-((4-chloro-2,6-difluorobenzyl)amino)-7-oxo-5-propyl-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile 61 significantly raised the circulating levels of the branched-chain amino acids leucine, isoleucine, and valine in this acute study. PMID:26090771

  6. Biodegradable Multiblock Poly[N-(2-hydroxypropyl)methacrylamide] via Reversible Addition-Fragmentation Chain Transfer Polymerization and Click Chemistry

    PubMed Central

    Luo, Kui; Yang, Jiyuan; Kopečková, Pavla; Kopeček, Jindřich

    2011-01-01

    A new bifunctional chain transfer agent (CTA) containing alkyne end groups was designed, synthesized and used for direct synthesis of clickable telechelic polymers. Good control of reversible addition-fragmentation chain transfer (RAFT) polymerization of N-(2-hydroxypropyl)methacrylamide (HPMA) was achieved by using the new CTA, as indicated by a linear increase of number average molecular weight (Mn) with conversion and low polydispersity (PDI) (<1.1). In particular, enzymatically degradable multiblock HPMA polymers were readily prepared by subsequent reaction with αω, -diazido oligopeptide (GFLG) sequence via CuI catalyzed alkyne-azide cycloaddition. Upon exposure of high molecular weight fractions of multiblock polyHPMA to papain or cathepsin B, the polymer was degraded into segments of molecular weight and narrow polydispersity similar to those of the initial telechelic polyHPMA. PMID:21552355

  7. Purification of single-chain antibody fragments exploiting pH-gradients in simulated moving bed chromatography.

    PubMed

    Martínez Cristancho, Carlos Andrés; Seidel-Morgenstern, Andreas

    2016-02-19

    This paper deals with the theoretical design and experimental validation of an affinity-based continuous multi-column chromatography process for the purification of single-chain Fragment variable (scFv) antibodies. An open-loop 3-zone pH-gradient simulated moving bed (SMB) process was investigated exploiting the highly specific affinity of metal ions toward histidine-tagged recombinant proteins. The separation problem was simplified by considering the cell culture supernatant as a pseudo-binary mixture. The influence of mobile phase pH on the adsorption isotherm parameters was estimated by the inverse method using recorded pH-gradient batch elution profiles. Suitable operating parameters for the SMB process were identified using an equilibrium stage model and subsequently validated in a lab-scale SMB unit. Finally, the performance of the pH-gradient SMB process was compared against a non-optimized batch process. Biologically active single-chain Fragment variable antibody formats were purified continuously with 9% more recovery, 11 times more productivity (576 mg of purified scFv per day and liter stationary phase in SMB) and enriched by a factor of 2.5 compared to those obtained in the non-optimized batch process. PMID:26810806

  8. Toward in vivo imaging of heart disease using a radiolabeled single-chain Fv fragment targeting tenascin-C.

    PubMed

    Kobayashi, Norihiro; Odaka, Kenichi; Uehara, Tomoya; Imanaka-Yoshida, Kyoko; Kato, Yoshinori; Oyama, Hiroyuki; Tadokoro, Hiroyuki; Akizawa, Hiromichi; Tanada, Shuji; Hiroe, Michiaki; Fukumura, Toshimitsu; Komuro, Issei; Arano, Yasushi; Yoshida, Toshimichi; Irie, Toshiaki

    2011-12-01

    Antibodies specific to a particular target molecule can be used as analytical reagents, not only for in vitro immunoassays but also for noninvasive in vivo imaging, e.g., immunoscintigraphies. In the latter case, it is important to reduce the size of antibody molecules in order to achieve suitable in vivo "diagnostic kinetics" and generate higher-resolution images. For these purposes, single-chain Fv fragments (scFvs; M(r) < 30 kDa) have greater potential than intact immunoglobulins (~150 kDa) or Fab (or Fab') fragments (~50 kDa). Our recent observation of enhanced tenascin-C (Tnc) expression at sites of cardiac repair after myocardial infarction prompted us to develop a radiolabeled scFv against Tnc for in vivo imaging of heart disease. We cloned the genes encoding the heavy and light chain variable domains of the mouse anti-Tnc monoclonal antibody 4F10, and combined them to create a single gene. The resulting scFv-4F10 gene was expressed in E. coli cells to produce soluble scFv proteins. scFv-4F10 has an affinity for Tnc (K(a) = 3.5 × 10(7) M(-1)), similar to the Fab fragment of antibody 4F10 (K(a) = 1.3 × 10(7) M(-1)) and high enough to be of practical use. A cysteine residue was then added to the C-terminus to achieve site-specific (111)In labeling via a chelating group. The resulting (111)In-labeled scFv was administered to a rat model of acute myocardial infarction. Biodistribution and quantitative autoradiographic studies indicated higher uptake of the radioactivity at the infarcted myocardium than the noninfarcted one. Single photon emission computed tomography (SPECT) provided in vivo cardiac images that coincided with the ex vivo observations. Our results will promote advances in diagnostic strategies for heart disease. PMID:22074352

  9. Enhanced Vaccine-Induced CD8+ T Cell Responses to Malaria Antigen ME-TRAP by Fusion to MHC Class II Invariant Chain

    PubMed Central

    Spencer, Alexandra J.; Cottingham, Matthew G.; Jenks, Jennifer A.; Longley, Rhea J.; Capone, Stefania; Colloca, Stefano; Folgori, Antonella; Cortese, Riccardo; Nicosia, Alfredo; Bregu, Migena; Hill, Adrian V. S.

    2014-01-01

    The orthodox role of the invariant chain (CD74; Ii) is in antigen presentation to CD4+ T cells, but enhanced CD8+ T cells responses have been reported after vaccination with vectored viral vaccines encoding a fusion of Ii to the antigen of interest. In this study we assessed whether fusion of the malarial antigen, ME-TRAP, to Ii could increase the vaccine-induced CD8+ T cell response. Following single or heterologous prime-boost vaccination of mice with a recombinant chimpanzee adenovirus vector, ChAd63, or recombinant modified vaccinia virus Ankara (MVA), higher frequencies of antigen-specific CD4+ and CD8+ T cells were observed, with the largest increases observed following a ChAd63-MVA heterologous prime-boost regimen. Studies in non-human primates confirmed the ability of Ii-fusion to augment the T cell response, where a 4-fold increase was maintained up to 11 weeks after the MVA boost. Of the numerous different approaches explored to increase vectored vaccine induced immunogenicity over the years, fusion to the invariant chain showed a consistent enhancement in CD8+ T cell responses across different animal species and may therefore find application in the development of vaccines against human malaria and other diseases where high levels of cell-mediated immunity are required. PMID:24945248

  10. Injectable formulations for an intravitreal sustained-release application of a novel single-chain VEGF antibody fragment.

    PubMed

    Asmus, Lutz R; Grimshaw, John P A; Richle, Philipp; Eicher, Barbara; Urech, David M; Gurny, Robert; Möller, Michael

    2015-09-01

    Sustained-release formulations of a single-chain anti-VEGF-A antibody fragment were investigated in vitro toward their potential use for intravitreal applications. The hydrophobic polyester hexylsubstituted poly(lactic acid) (hexPLA) was selected as the sustained-release excipient for its biodegradability and semi-solid aggregate state, allowing an easy and mild formulation procedure. The lyophilized antibody fragment ESBA903 was micronized and incorporated into the liquid polymer matrix by cryo-milling, forming homogeneous and injectable suspensions. The protein showed excellent compatibility with the hexPLA polymer and storage stability at 4°C for 10 weeks. Additionally, hexPLA shielded the incorporated active substance from the surrounding medium, resulting in a better stability of ESBA903 inside the polymer than after its release in the buffer solution. Formulations of ESBA903 with hexPLA having drug loadings between 1.25% and 5.0% and polymer molecular weights of 1500 g/mol, 2500 g/mol, 3500 g/mol and 5000 g/mol were investigated regarding their in vitro release. All formulations except with the highest molecular weight formed spherical depots in aqueous buffer solutions and released the antibody fragment for at least 6-14 weeks. The polymer viscosity derived from the molecular weight strongly influenced the release rate, while the drug loading had minor influence, allowing customization of the release profile and the daily drug release. Size exclusion chromatography and SDS-PAGE revealed that the antibody fragment structure was kept intact during incorporation and release from the liquid matrix. Furthermore, the released protein monomer maintained its high affinity to human VEGF-A, as measured by surface plasmon resonance analysis. Formulations of ESBA903 in hexPLA meet the basic needs to be used for intravitreal sustained-release applications in age-related macular degeneration treatment. PMID:25779352

  11. In situ gastrointestinal protection against anthrax edema toxin by single-chain antibody fragment producing lactobacilli

    PubMed Central

    2011-01-01

    Background Anthrax is caused by the bacterium Bacillus anthracis and is regarded as one of the most prominent bioterrorism threats. Anthrax toxicity is induced by the tripartite toxin complex, composed of the receptor-binding anthrax protective antigen and the two enzymatic subunits, lethal factor and edema factor. Recombinant lactobacilli have previously been used to deliver antibody fragments directed against surface epitopes of a variety of pathogens, including Streptococcus mutans, Porphyromonas gingivalis, and rotavirus. Here, we addressed whether or not anthrax toxins could be targeted and neutralised in the gastrointestinal tract by lactobacilli producing recombinant antibody fragments as a model system for toxin neutralisation in the gastrointestinal lumen. Results The neutralising anti-PA scFv, 1H, was expressed in L. paracasei as a secreted protein, a cell wall-anchored protein or both secreted and wall-anchored protein. Cell wall display on lactobacilli and PA binding of the anchored constructs was confirmed by flow cytometry analysis. Binding of secreted or attached scFv produced by lactobacilli to PA were verified by ELISA. Both construct were able to protect macrophages in an in vitro cytotoxicity assay. Finally, lactobacilli producing the cell wall attached scFv were able to neutralise the activity of anthrax edema toxin in the GI tract of mice, in vivo. Conclusion We have developed lactobacilli expressing a neutralising scFv fragment against the PA antigen of the anthrax toxin, which can provide protection against anthrax toxins both in vitro and in vivo. Utilising engineered lactobacilli therapeutically for neutralising toxins in the gastrointestinal tract can potential be expanded to provide protection against a range of additional gastrointestinal pathogens. The ability of lactobacilli to colonise the gastrointestinal tract may allow the system to be used both prophylactically and therapeutically. PMID:22185669

  12. Linker peptide and affinity tag for detection and purification of single-chain Fv fragments.

    PubMed

    Küttner, Gabriele; Giessmann, Elke; Wessner, Helga; Scholz, Christa; Reinhardt, Dina; Winkler, Karsten; Marx, Uwe; Höhne, Wolfgang

    2004-05-01

    The peptide tag GATPQDLNTML, corresponding to amino acids 46-56 of the human immunodeficiency virus type 1 (HIV-1) capsid protein p24, is the linear epitope of the murine monoclonal antibody CB4-1. This antibody shows high affinity (KD = 1.8 x 10(-8) M) to the free epitope peptide in solution. The original p24 peptide tag and mutant derivatives were fused to the C terminus of a single-chain antibody (scFv) and characterized with respect to sensitivity in Western blot analyses and behavior in purification procedures using affinity chromatography. The p24 tag also proved to be a suitable alternative to the (Gly4Ser)3 linker commonly used to connect single-chain antibody variable regions derived from a heavy (VH) and light chain (VL). Binding of CB4-1 antibody to the p24 tag was not hampered when the tag was located internally in the protein sequence, and the specific antigen affinity of the scFv was only slightly reduced. All scFv variants were solubly expressed in Escherichia coli and could be purified from the periplasm. Our results highlight the p24 tag as a useful tool for purifying and detecting recombinantly expressed scFvs. PMID:15152607

  13. 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. PMID:27352873

  14. 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

  15. 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

  16. Preparation and Identification of a Single-chain Variable Fragment Antibody Against Canine Distemper Virus.

    PubMed

    Yi, Li; Cheng, Shipeng

    2015-08-01

    The variable regions of the heavy chain (VH) and light chain (VL) were amplified by RT-PCR from the hybridoma 1N8, which secretes the monoclonal antibody against CDV N protein (aa 277-471). The VL and VH amplicons were combined using SOE-PCR by a 12 amino acid flexible linker (SSGGGGSGGGGS), which produced the scFv gene (named scFv/1N8). After sequence analysis, the scFv/1N8 gene was cloned into the prokaryotic expression vector PET32a with a His-tag. The recombinant scFv/1N8 protein was successfully expressed in recombinant Escherichia coli by IPTG induction. Moreover, the binding activity and specificity of the scFv were determined by indirect ELISA (His-tag) and competitive ELISA. The recombinant scFv/1N8 protein reported here will provide some basis for further antiviral drug research based on the scFv molecule. PMID:26301925

  17. 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

  18. Construction of Recombinant Single Chain Variable Fragment (ScFv) Antibody Against Superantigen for Immunodetection Using Antibody Phage Display Technology.

    PubMed

    Singh, Pawan Kumar; Agrawal, Ranu; Kamboj, D V; Singh, Lokendra

    2016-01-01

    Superantigens are a class of antigens that bind to the major histocompatibility complex class (MHC) II and T-cell receptor (TCR) and cause the nonspecific activation of T cells, resulting in a massive release of pro-inflammatory mediators. They are produced by the gram-positive organisms Staphylococcus aureus and Streptococcus pyogenes, and by a variety of other microbes such as viruses and mycoplasma, and cause toxic shock syndrome (TSS) and even death in some cases. The immunodetection of superantigens is difficult due to the polyclonal activation of T-cells leading to nonspecific antibody production. The production of recombinant monoclonal antibodies against superantigens can solve this problem and are far better than polyclonal antibodies in terms of detection. Here, we describe the construction of recombinant single chain variable fragments (ScFv) antibodies against superantigens with specific reference to SEB (staphylococcal enterotoxin B) using antibody phage display technology. PMID:26676049

  19. 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

  20. 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.

  1. Familial mutations in fibrinogen Aα (FGA) chain identified in renal amyloidosis increase in vitro amyloidogenicity of FGA fragment.

    PubMed

    Sivalingam, Vishwanath; Patel, Basant K

    2016-08-01

    Amyloidoses are clinical disorders where deposition of β-sheet rich, misfolded protein aggregates called amyloid occurs in vital organs like brain, kidney, liver or heart etc. Aggregation of several proteins such as immunoglobulin light chain, fibrinogen Aα chain (FGA) and lysozyme have been found to be associated with renal amyloidosis. Fibrinogen amyloidosis (AFib) is predominantly familial and is associated with the deposition of mutant FGA amyloid, primarily in kidneys. Over ten substitution and frame-shift mutations in FGA have been identified from AFib patients. Whether wild-type FGA is also involved in AFib is yet unknown. The affected tissues from AFib patients usually show ∼10 kDA peptide from C-terminal 80 amino acid residues of mutant FGA. Notably, this region also encompasses all known disease-related mutations. Whether these point mutations increase the amyloidogenicity of FGA leading to disease progression, have not been studied yet. Here, we have investigated the role of two disease-related mutations in affecting amyloidogenic propensity of an FGA(496-581) fragment. We found that at physiological pH, the wild-type FGA(496-581) fragment remains monomeric, whereas its E540V mutant forms amyloid-like fibrils as observed by AFM. Also, FGA(496-581) harbouring another familial mutation, R554L, converts in vitro into globular, β-sheet rich aggregates, showing amyloid-like properties. These findings suggest that familial mutations in FGA may have role in renal amyloidosis via enhanced amyloid formation. PMID:27126074

  2. 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

  3. 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. PMID:26209665

  4. 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

  5. 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

  6. Fast atoms and negative chain-cluster fragments from laser-induced Coulomb explosions in a super-fluid film of ultra-dense deuterium D(-1)

    NASA Astrophysics Data System (ADS)

    Andersson, Patrik U.; Holmlid, Leif

    2012-10-01

    Fragments from laser-induced Coulomb explosions (CE) in a thin super-fluid film of ultra-dense deuterium D(-1) on a vertical surface are now observed by both negative and positive time-of-flight mass spectrometry. The so-called normal phase of the super-fluid is probably associated with D4 clusters and gives only neutral atomic fragments with a kinetic energy from the CE of 945 eV. The super-fluid phase is associated with long chain clusters D2N with N deuteron pairs and gives cluster fragments by CE mainly with a kinetic energy of 315 eV from the central cleavage in a neutral, positive or negative form. This indicates that the chain clusters are standing perpendicularly to the surface. The fragment charge state is influenced by the external field, which indicates efficient charge transfer processes.

  7. 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

  8. An assay for the detection of grapevine leafroll-associated virus 3 using a single-chain fragment variable antibody.

    PubMed

    Cogotzi, Laura; Giampetruzzi, Annalisa; Nölke, Greta; Orecchia, Martin; Elicio, Vito; Castellano, Maria Antonietta; Martelli, Giovanni P; Fischer, Rainer; Schillberg, Stefan; Saldarelli, Pasquale

    2009-01-01

    Grapevine leafroll-associated virus 3 (GLRaV-3) is a major pathogen of grapevine. A previously described single-chain fragment variable (scFv) antibody (scFvLR3), directed against the coat protein (CP) of GLRaV-3, was expressed in Escherichia coli and used to develop a diagnostic ELISA kit. The antibody was fused to the light chain constant domain of human immunoglobulin to create the bivalent reagent C(L)-LR3, which was purified from the periplasmic fraction, giving a yield of ~5 mg/l. The sensitivity of the reagent against recombinant GLRaV-3 CP was 0.1 ng. The sensitivity, specificity and durability of the reagent was similar to a commercial kit. The C(L)-LR3 showed a weak cross-reaction in immune electron microscopy assays to GLRaV-1 and -7, but not with the phylogenetically more distant GLRaV-2. A fully recombinant kit was developed with the inclusion of a recombinant GLRaV-3 CP expressed in bacteria, thus avoiding problems associated with virus propagation and purification. This system represents a rapid, simple, sensitive and standardized diagnostic protocol for GLRaV-3 detection. PMID:19082687

  9. Neutralization Analysis of a Chicken Single-Chain Variable Fragment Derived from an Immune Antibody Library Against Infectious Bronchitis Virus.

    PubMed

    Lin, Yuan; Li, Benqiang; Ye, Jiaxin; Wang, Man; Wang, Jianhua; Zhang, Ying; Zhu, Jianguo

    2015-09-01

    Avian infectious bronchitis virus (IBV), which is prevalent in many countries causing severe economic loss to the poultry industry, causes infectious bronchitis (IB) in birds. Recombinant single-chain variable fragments (scFvs) have been proven to effectively inhibit many viruses, both in vitro and in vivo, and they could be a potential diagnostic and therapeutic reagent to control IB. In this study, six anti-IBV chicken scFvs, ZL.10, ZL.64, ZL.78, ZL.80, ZL.138, and ZL.256, were obtained by screening random clones from an immune antibody library. An analysis of nucleotide sequences revealed that they represented distinctive genetic sequences and greatly varied in complementarity-determining region three of the heavy chain. Neutralization tests showed that ZL.10, which bound the S1 protein in western blots, inhibited the formation of syncytia in Vero cells 48 h post IBV infection and decreased the transcriptional level of nucleoprotein mRNA to 17.2%, while the other five scFvs, including ZL.78 and ZL.256, that bound the N protein did not. In conclusion, the results suggested that specific and neutralizing chicken scFvs against IBV, which can be safe and economical antibody reagents, can be produced in vitro through prokaryotic expression. PMID:26090700

  10. Production of a soluble single-chain variable fragment antibody against okadaic acid and exploration of its specific binding.

    PubMed

    He, Kuo; Zhang, Xiuyuan; Wang, Lixia; Du, Xinjun; Wei, Dong

    2016-06-15

    Okadaic acid is a lipophilic marine algal toxin commonly responsible for diarrhetic shellfish poisoning (DSP). Outbreaks of DSP have been increasing and are of worldwide public health concern; therefore, there is a growing demand for more rapid, reliable, and economical analytical methods for the detection of this toxin. In this study, anti-okadaic acid single-chain variable fragment (scFv) genes were prepared by cloning heavy and light chain genes from hybridoma cells, followed by fusion of the chains via a linker peptide. An scFv-pLIP6/GN recombinant plasmid was constructed and transformed into Escherichia coli for expression, and the target scFv was identified with IC-CLEIA (chemiluminescent enzyme immunoassay). The IC15 was 0.012 ± 0.02 μg/L, and the IC50 was 0.25 ± 0.03 μg/L. The three-dimensional structure of the scFv was simulated with computer modeling, and okadaic acid was docked to the scFv model to obtain a putative structure of the binding complex. Two predicted critical amino acids, Ser32 and Thr187, were then mutated to verify this theoretical model. Both mutants exhibited significant loss of binding activity. These results help us to understand this specific scFv-antigen binding mechanism and provide guidance for affinity maturation of the antibody in vitro. The high-affinity scFv developed here also has potential for okadaic acid toxin detection. PMID:26772159

  11. 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.

  12. The MHC Class II-Associated Invariant Chain Interacts with the Neonatal Fcγ Receptor and Modulates Its Trafficking to Endosomal/Lysosomal Compartments1

    PubMed Central

    Ye, Lilin; Liu, Xindong; Rout, Subrat N.; Li, Zili; Yan, Yongqi; Lu, Li; Kamala, Tirumalai; Nanda, Navreet K.; Song, Wenxia; Samal, Siba K.; Zhu, Xiaoping

    2009-01-01

    The neonatal Fc receptor for IgG (FcRn) transfers maternal IgG to the offspring and protects IgG from degradation. The FcRn resides in an acidic intracellular compartment, allowing it to bind IgG. In this study, we found the association of FcRn and invariant chain (Ii). The interaction was initiated within the endoplasmic reticulum by Ii binding to either the FcRn H chain alone or FcRn H chain-β2-microglobulin complex and appeared to be maintained throughout the endocytic pathway. The CLIP in Ii was not required for FcRn-Ii association. The interaction was also detected in IFN-γ-treated THP-1, epithelial and endothelial cells, and immature mouse DCs. A truncated FcRn without the cytoplasmic tail was unable to traffic to early endosomes; however, its location in early endosomes was restored by Ii expression. FcRn was also detected in the late endosome/lysosome only in the presence of Ii or on exposure to IFN-γ. In immature human or mouse DCs, FcRn was barely detected in the late endosome/lysosome in the absence of Ii. Furthermore, the cytoplasmic tail of Ii conferred tailless FcRn to route to both the early endosome and late endosome/lysosome in a hybrid molecule. Because the FcRn is expressed in macrophages and DCs or epithelial and endothelial cells where Ii is induced under inflammation and infection, these results reveal the complexity of FcRn trafficking in which Ii is capable of expanding the boundary of FcRn trafficking. Taken together, the intracellular trafficking of FcRn is regulated by its intrinsic sorting information and/or an interaction with Ii chain. PMID:18684948

  13. Novel Dental Restorative Materials having Low Polymerization Shrinkage Stress via Stress Relaxation by Addition-Fragmentation Chain Transfer

    PubMed Central

    Park, Hee Young; Kloxin, Christopher J.; Abuelyaman, Ahmed S.; Oxman, Joe D.; Bowman, Christopher N.

    2012-01-01

    Objectives To produce a reduced stress dental restorative material while simultaneously maintaining excellent mechanical properties, we have incorporated an allyl sulfide functional group into norbornene-methacrylate comonomer resins. We hypothesize that the addition-fragmentation chain transfer (AFCT) enabled by the presence of the allyl sulfide relieves stress in these methacrylate-based systems while retaining excellent mechanical properties owing to the high glass transition temperature of norbornene-containing resins. Methods An allyl sulfide-containing dinorbornene was stoichiometrically formulated with a ring-containing allyl sulfide-possessing methacrylate. To evaluate the stress relaxation effect as a function of the allyl sulfide concentration, a propyl sulfide-based dinorbornene, not capable of addition-fragmentation, was also formulated with the methacrylate monomer. Shrinkage stress, the glass transition temperature and the elastic modulus were all measured. The composite flexural strength and modulus were also measured. ANOVA (CI 95%) was conducted to determine differences between the means. Results Increasing the allyl sulfide content in the resin dramatically reduces the final stress in the norbornene-methacrylate systems. Both norbornene-methacrylate resins demonstrated almost zero stress (more than 96% stress reduction) compared with the conventional BisGMA/TEGDMA 70/30 wt% control. Mechanical properties of the allyl sulfide-based dental composites were improved to the point of being statistically indistinguishable from the control BisGMA-TEGDMA by changing the molar ratio between the methacrylate and norbornene functionalities. Significance The allyl sulfide-containing norbornene-methacrylate networks possessed super-ambient Tg, and demonstrated significantly lower shrinkage stress when compared with the control (BisGMA/TEGDMA 70 to 30 wt%). Although additional development remains, these low stress materials exhibit excellent mechanical

  14. Production and characterization of a biotinylated single-chain variable fragment antibody for detection of parathion-methyl.

    PubMed

    Wang, Huimin; Zhao, Fengchun; Han, Xiao; Yang, Zhengyou

    2016-10-01

    In this article, we reported the development of a biotinylated single-chain variable fragment (scFv) antibody based indirect competitive enzyme-linked immunosorbent assay (IC-ELISA) for parathion-methyl (PM) detection. Firstly, a phage display library was generated using a pre-immunized BALB/C mouse against a specific hapten of PM. After four rounds of panning, the scFv gene fragments were transferred into a secreted expression vector. Then, the scFv antibodies were secreted expressed and screened by IC-ELISA against PM. The selected scFv antibody was fused with a biotin acceptor domain (BAD) and inserted into pET-28a(+) vector for high-level expression in Escherichia coli BL2 (DE3). After optimizing expression conditions, the scFv-BAD antibody was expressed as a soluble protein and biotinylated in vitro by the E. coli biotin ligase (BirA). Subsequently, the biotinylated scFv-BAD antibody was purified with a high yield of 59.2 ± 3.7 mg/L of culture, and was characterized by SDS-PAGE and western blotting. Finally, based on the biotinylated scFv-BAD, a sensitive IC-ELISA for detection of PM was developed, and the 50% inhibition value (IC50) of PM was determined as 14.5 ng/mL, with a limit of detection (LOD, IC10) of 0.9 ng/mL. Cross-reactivity (CR) studies revealed that the scFv antibody showed desirable specificity for PM. PMID:27181246

  15. Cloning and expression of an anti-LDL(-) single-chain variable fragment, and its inhibitory effect on experimental atherosclerosis

    PubMed Central

    Kazuma, Soraya M; Cavalcante, Marcela F; Telles, Andréia ER; Maranhão, Andrea Queiroz; Abdalla, Dulcineia SP

    2013-01-01

    The in vivo modified forms of low-density lipoprotein (LDL) are important for the formation of foam cells and as mediators of the immuno-inflammatory process involved in the progression of atherosclerosis. Electronegative LDL, LDL(-), is a LDL subfraction with pro-inflammatory properties that is present in human blood. To investigate possible atheroprotective effects, an anti-LDL(-) single-chain variable fragment (scFv) was expressed in the methylotrophic yeast Pichia pastoris and its activity was evaluated in vitro against macrophages and in experimental atherosclerosis in Ldlr-/-mice. The recombinant 2C7 scFv was produced in a yield of 9.5 mg of protein/L. The specificity and affinity of purified 2C7 scFv against LDL(-) was confirmed by ELISA. To assess the activity of 2C7 scFv on foam cell formation, RAW 264.7 macrophages were exposed to LDL(-) in the presence or absence of 2C7 scFv. The 2C7 scFv inhibited the uptake of LDL(-) by macrophages in a dose-dependent manner, and internalization of LDL(-) by these cells was found to be mediated by the CD36 and CD14 receptor. In addition, compared with untreated cells, lipid accumulation in macrophages was decreased, and the expression of Cd36, Tlr-4 and Cox-2 was downregulated in macrophages treated with 2C7 scFv. Importantly, compared with untreated mice, the treatment of Ldlr-/- mice with 2C7 scFv decreased the atherosclerotic lesion area at the aortic sinus. In conclusion, our data show that 2C7 scFv inhibits foam cell formation and atherosclerotic plaque development by modulating the expression of genes relevant to atherogenesis. These results encourage further use of this antibody fragment in the development of new therapeutic strategies that neutralize the pro-atherogenic effects of LDL(-). PMID:23924793

  16. Single Chain Variable Fragment Against Aβ Expressed in Baculovirus Inhibits Abeta Fibril Elongation and Promotes its Disaggregation

    PubMed Central

    Fang, Fang; Song, Lin-Lin; Jiao, Yue-Ying; Wang, He; Peng, Xiang-Lei; Zheng, Yan-Peng; Wang, Jun; He, Jin-Sheng; Hung, Tao

    2015-01-01

    Alzheimer’s disease (AD) is the most common form of age-related dementia, and the most urgent problem is that it is currently incurable. Amyloid-β (Aβ) peptide is believed to play a major role in the pathogenesis of AD. We previously reported that an Aβ N-terminal amino acid targeting monoclonal antibody (MAb), A8, inhibits Aβ fibril formation and has potential as an immunotherapy for AD based on a mouse model. To further study the underlying mechanisms, we tested our hypothesis that the single chain fragment variable (scFv) without the Fc fragment is capable of regulating either Aβ aggregation or disaggregation in vitro. Here, a model of cell-free Aβ “on-pathway” aggregation was established and identified using PCR, Western blot, ELISA, transmission electron microscopy (TEM) and thioflavin T (ThT) binding analyses. His-tagged A8 scFvs was cloned and solubly expressed in baculovirus. Our data demonstrated that the Ni-NTA agarose affinity-purified A8 scFv inhibited the forward reaction of “on-pathway” aggregation and Aβ fibril maturation. The effect of A8 scFv on Aβ fibrillogenesis was markedly more significant when administered at the start of the Aβ folding reaction. Furthermore, the results also showed that pre-formed Aβ fibrils could be disaggregated via incubation with purified A8 scFv, which suggested that A8 scFv is involved in the reverse reaction of Aβ aggregation. Therefore, A8 scFv was capable of both inhibiting fibrillogenesis and disaggregating matured fibrils. Our present study provides valuable insight into the regulators of ultrastructural dynamics of cell-free “on-pathway” Aβ aggregation and will assist in the development of therapeutic strategies for AD. PMID:25919299

  17. 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

  18. Genetic fusion of single-chain variable fragments to partial spider silk improves target detection in micro- and nanoarrays.

    PubMed

    Thatikonda, Naresh; Delfani, Payam; Jansson, Ronnie; Petersson, Linn; Lindberg, Diana; Wingren, Christer; Hedhammar, My

    2016-03-01

    Immobilizing biomolecules with retained functionality and stability on solid supports is crucial for generation of sensitive immunoassays. However, upon use of conventional immobilization strategies, a major portion of the biomolecules (e.g. antibodies) frequently tends to lose their bioactivity. In this study, we describe a procedure to immobilize human single-chain variable fragment (scFv) via genetic fusion to partial spider silk, which have a high tendency to adhere to solid supports. Two scFvs, directed towards serum proteins, were genetically fused to partial spider silk proteins and expressed as silk fusion proteins in E. coli. Antigen binding ability of scFvs attached to a partial silk protein denoted RC was investigated using microarray analysis, whereas scFvs fused to the NC silk variant were examined using nanoarrays. Results from micro- and nanoarrays confirmed the functionality of scFvs attached to both RC and NC silk, and also for binding of targets in crude serum. Furthermore, the same amount of added scFv gives higher signal intensity when immobilized via partial spider silk compared to when immobilized alone. Together, the results suggest that usage of scFv-silk fusion proteins in immunoassays could improve target detection, in the long run enabling novel biomarkers to be detected in crude serum proteomes. PMID:26470853

  19. Phase analysis in single-chain variable fragment production by recombinant Pichia pastoris based on proteomics combined with multivariate statistics.

    PubMed

    Fujiki, Yuya; Kumada, Yoichi; Kishimoto, Michimasa

    2015-08-01

    The proteomics technique, which consists of two-dimensional gel electrophoresis (2-DE), peptide mass fingerprinting (PMF), gel image analysis, and multivariate statistics, was applied to the phase analysis of a fed-batch culture for the production of a single-chain variable fragment (scFv) of an anti-C-reactive protein (CRP) antibody by Pichia pastoris. The time courses of the fed-batch culture were separated into three distinct phases: the growth phase of the batch process, the growth phase of the fed-batch process, and the production phase of the fed-batch process. Multivariate statistical analysis using 2-DE gel image analysis data clearly showed the change in the culture phase and provided information concerning the protein expression, which suggested a metabolic change related to cell growth and production during the fed-batch culture. Furthermore, specific proteins, such as alcohol oxidase, which is strongly related to scFv expression, and proteinase A, which could biodegrade scFv in the latter phases of production, were identified via the PMF method. The proteomics technique provided valuable information about the effect of the methanol concentration on scFv production. PMID:25636980

  20. 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). PMID:25322256

  1. A chimera of green fluorescent protein with single chain variable fragment antibody against ginsenosides for fluorescence-linked immunosorbent assay.

    PubMed

    Sakamoto, Seiichi; Tanizaki, Yusuke; Pongkitwitoon, Benyakan; Tanaka, Hiroyuki; Morimoto, Satoshi

    2011-05-01

    A chimera of green fluorescent protein extracted from Aequorea coerulescens (AcGFP), a mutant that has been codon optimized for mammalian expression, with single-chain variable fragment (scFv) antibody against ginsenoside Re (GRe-scFv), named fluobody, has been successfully expressed in Escherichia coli (E. coli) to develop simple, speedy, and sensitive fluorescence-linked immunosorbent assay (FLISA). Two chimera proteins were constructed to contain GRe-scFv at the C-terminus of AcGFP (C-fluobody) and at the N-terminus of AcGFP (N-fluobody). These fluobodies were then purified by ion metal affinity chromatography and refolded by stepwise dialysis. The characterization of both fluobodies revealed that C-fluobody was found to be appropriate probe for FLISA as compare with N-fluobody. Furthermore, improvement of limit of detection (LOD) was observed in FLISA using C-fluobody (10 ng/mL) due to its strong fluorescence intensity of AcGFP compared with conventional enzyme-linked immunosorbent assay (ELISA) using parental monoclonal antibody against ginsenoside Re (G-Re), MAb-4G10 (100 ng/mL). Since some steps required in ELISA can be avoided in this present FLISA, speedy and sensitive immunoassay also could be performed using fluobody instead of monoclonal antibody and scFv. PMID:21277981

  2. 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

  3. Gamma radiation induced synthesis of poly(N-isopropylacrylamide) mediated by Reversible Addition-Fragmentation Chain Transfer (RAFT) process

    NASA Astrophysics Data System (ADS)

    Kiraç, Feyza; Güven, Olgun

    2015-07-01

    Poly(N-isopropylacrylamide) (PNiPAAm) is synthesized by gamma radiation induced Reversible Addition-Fragmentation Chain Transfer (RAFT) polymerization. The monomer is polymerized in the presence of two different trithiocarbonate-based RAFT agents i.e., Cyanomethyldodecyltrithiocarbonate (CDTC) and 2-(Dodecylthiocarbonothioylthio)-2-methylpropionic acid (DMPA) in dimethylformamide (DMF) at room temperature under nitrogen atmosphere. Number-average molecular weights (Mn) and dispersities of the polymers were determined by Size Exclusion Chromatography (SEC). Dispersities (Ɖ) of the resulting polymers are narrow, i.e., Ɖ≤1.18, indicating the occurrence of well-controlled polymerization via radiation induced RAFT process. %Conversion is determined by gravimetric method and also confirmed by Proton Nuclear Magnetic Resonance (1H-NMR) Spectroscopy. By selecting proper [Monomer]/[RAFT] ratio and controlling conversion it is possible to synthesize PNiPAAm in the molecular weight range of 2400-72400 with extremely low molecular weight distributions with the anticipation of preparing corresponding size-controlled nanogels. The phase transition of PNiPAAm with low dispersity synthesized by RAFT is sharper than PNiPAAm synthesized by free radical polymerization.

  4. 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. PMID:24936911

  5. Single chain antibody fragment with serine protease inhibitory property capable of neutralizing toxicity of Trimeresurus mucrosquamatus venom.

    PubMed

    Lee, Yu-Ching; Chen, Wang-Chuan; Liang, Meng-Huei; Lee, Chi-Hsin; Tsai, Keng-Chang; Chiang, Jen-Ron; Chiang, Liao-Chun; Chen, Chi-Ching; Chang, Chang-Yu; Lee, Ching-Hsiao; Leu, Sy-Jye; Yang, Yi-Yuan

    2015-05-01

    Trimeresurus mucrosquamatus (TM) is one of majorities of snake envenomation with necrotic and hemorrhagic toxin in Taiwan. In this study, chickens were used as an alternative animal model for immunization with TM venom. Using phage display technology to process four rounds of panning, selected single chain variable fragments (scFv) could specifically recognize TM venom proteins, which were later identified as a group of homogeneous venom serine protease. The specific scFv antibodies showed various inhibitory effects on sheep RBC lysis induced by TM venom using an indirect hemolytic assay in vitro. In addition, the survival times of mice were extended to certain degrees when treated with these scFv antibodies individually or in a combination. To elucidate the inhibitory mechanism, we used molecular modeling to build up the serine protease structure to simulate the possible interactions with scFv antibodies. The results suggested that the CDR-loop of the scFv antibodies (3S10 or 4S1) might bind at the 99-loop of venom serine protease so as to affect substrate access due to the partial collapse of the subsite S2 and the partial movement of the subsite S4. It is hoped these chicken-derived antibodies could be applied to develop diagnostic and therapeutic agents against snakebites. PMID:25769957

  6. 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

  7. Molecular Epidemiology of Leptospirosis in Northern Iran by Nested Polymerase Chain Reaction/Restriction Fragment Length Polymorphism and Sequencing Methods

    PubMed Central

    Zakeri, Sedigheh; Sepahian, Neda; Afsharpad, Mandana; Esfandiari, Behzad; Ziapour, Peyman; Djadid, Navid D.

    2010-01-01

    This study was conducted to investigate the prevalence of Leptospira species in Mazandaran Province of Iran by using nested polymerase chain reaction (PCR)/restriction fragment length polymorphism (RFLP) methods and sequencing analysis. Blood samples (n = 119) were collected from humans suspected of having leptospirosis from different parts of the province in 2007. By using an indirect immunofluorescent antibody test (IFAT), we determined that 35 (29.4%) of 119 suspected cases had leptospiral antibody titers ≥ 1:80, which confirmed the diagnosis of leptospirosis. Nested PCR assay also determined that 60 (50.4%) of 119 samples showed Leptospira infection. Furthermore, 44 (73.3%) of 60 confirmed leptospirosis amplified products were subjected to sequencing analysis. Sequence alignment identified L. interrogans, L. kirschneri, and L. wolffii species. All positive cases diagnosed by IFAT or PCR were in patients who reported contact with animals, high-risk occupational activities, and exposure to contaminated water. Therefore, it is important to increase attention about this disease among physicians and to strengthen laboratory capacity for its diagnosis in infected patients in Iran. PMID:20439973

  8. CD176 single-chain variable antibody fragment inhibits the adhesion of cancer cells to endothelial cells and hepatocytes.

    PubMed

    Liu, Jiangnan; Yi, Bin; Zhang, Zhe; Cao, Yi

    2016-06-01

    CD176 (Thomsen-Friedenreich antigen) is a tumor-associated carbohydrate epitope (glycotope) functionally involved in blood spread and liver metastasis of cancer cells by mediating the adhesion of cancer cells to endothelial cells and hepatocytes, respectively. CD176 could be a promising target for antitumor immunotherapy. We applied B lymphocytes obtained from mice immunized with CD176 antigen and constructed a phage display library. A positive clone of CD176 single-chain variable antibody fragment (scFv) was successfully screened from this library. The CD176 scFv was expressed in Escherichia coli and purified. The purified scFv can bind to the natural CD176 expressed on the surface of cancer cells. Furthermore, the CD176 scFv inhibits the adhesion of CD176(+) cancer cells to endothelial cells and hepatocytes. This CD176 scFv provides a basis for future development of recombinant CD176-specific antibodies that can be used in therapeutic application. PMID:27090911

  9. An improved polymerase chain reaction-restriction fragment length polymorphism assay for the detection of a PON2 gene polymorphism

    PubMed Central

    DUAN, XIAORAN; YANG, YONGLI; WANG, TUANWEI; FENG, XIAOLEI; YAO, WU; YAN, ZHEN; WANG, WEI

    2016-01-01

    In recent research, it has been shown that there have been variants of rs12026 within the paraoxonase 2 (PON2) gene, which have been associated with cardiovascular disease, cerebrovascular disease, diabetes and other diseases. The isochizomers, such as the BsoFI enzyme, required for the detection of this polymorphism are expensive. Therefore, an improved and less expensive polymerase chain reaction (PCR)-restriction fragment length polymorphism method was established for the detection of the single-nucleotide polymorphism rs12026 in the exon 5 of chromosome 7 of the human PON2 gene using the method of amplification-created restriction site. Subsequent to assessing 302 individuals, the genotype frequencies were 68.9% for CC, 29.8% for CG and 1.3% for GG, and the allelic frequencies were 83.8% for C and 16.2% for G. The PCR results were confirmed by DNA sequencing. The χ2 test showed that the genotype and allele frequencies of PON2-148 do not deviate from Hardy-Weinberg equilibrium, and the sequences of amplified products were consistent with the sequence published in GenBank with the exception of a mismatched base. PMID:27330753

  10. Anti-Aβ single-chain variable fragment antibodies exert synergistic neuroprotective activities in Drosophila models of Alzheimer's disease.

    PubMed

    Fernandez-Funez, Pedro; Zhang, Yan; Sanchez-Garcia, Jonatan; de Mena, Lorena; Khare, Swati; Golde, Todd E; Levites, Yona; Rincon-Limas, Diego E

    2015-11-01

    Both active and passive immunotherapy protocols decrease insoluble amyloid-ß42 (Aß42) peptide in animal models, suggesting potential therapeutic applications against the main pathological trigger in Alzheimer's disease (AD). However, recent clinical trials have reported no significant benefits from humanized anti-Aß42 antibodies. Engineered single-chain variable fragment antibodies (scFv) are much smaller and can easily penetrate the brain, but identifying the most effective scFvs in murine AD models is slow and costly. We show here that scFvs against the N- and C-terminus of Aß42 (scFv9 and scFV42.2, respectively) that decrease insoluble Aß42 in CRND mice are neuroprotective in Drosophila models of Aß42 and amyloid precursor protein neurotoxicity. Both scFv9 and scFv42.2 suppress eye toxicity, reduce cell death in brain neurons, protect the structural integrity of dendritic terminals in brain neurons and delay locomotor dysfunction. Additionally, we show for the first time that co-expression of both anti-Aß scFvs display synergistic neuroprotective activities, suggesting that combined therapies targeting distinct Aß42 epitopes can be more effective than targeting a single epitope. Overall, we demonstrate the feasibility of using Drosophila as a first step for characterizing neuroprotective anti-Aß scFvs in vivo and identifying scFv combinations with synergistic neuroprotective activities. PMID:26253732

  11. Targeting Prostate Cancer Cells In Vivo Using a Rapidly Internalizing Novel Human Single-Chain Antibody Fragment

    PubMed Central

    He, Jiang; Wang, Yong; Feng, Jinjin; Zhu, Xiaodong; Lan, Xiaoli; Iyer, Arun K.; Zhang, Niu; Seo, Youngho; VanBrocklin, Henry F.; Liu, Bin

    2010-01-01

    Human antibodies targeting prostate cancer cell surface epitopes may be useful for imaging and therapy. The objective of this study was to evaluate the tumor targeting of an internalizing human antibody fragment, a small-size platform, to provide high contrast in a mouse model of human prostate carcinoma. Methods A prostate tumor-targeting single-chain antibody fragment (scFv), UA20, along with a nonbinding control scFv, N3M2, were labeled with 99mTc and evaluated for binding and rapid internalization into human prostate tumor cells in vitro and tumor homing in vivo using xenograft models. For the in vitro studies, the labeled UA20 scFv was incubated at 37°C for 1 h with metastatic prostate cancer cells (DU145) to assess the total cellular uptake versus intracellular uptake. For the animal studies, labeled UA20 and N3M2 scFvs were administered to athymic mice implanted subcutaneously with DU145 cells. Mice were imaged with small-animal SPECT/CT with concomitant biodistribution at 1 and 3 h after injection. Results The UA20 scFv was labeled in 55%–65% yield and remained stable in phosphate buffer within 24 h. The labeled UA20 scFv was taken up specifically by prostate tumor cells. Internalization was rapid, because incubation at 37°C for less than 1 h resulted in 93% internalization of total cell-associated scFvs. In animal studies, SPECT/CT showed significant tumor uptake as early as 1 h after injection. At 3 h after injection, tumor uptake was 4.4 percentage injected dose per gram (%ID/g), significantly greater than all organs or tissues studied (liver, 2.7 %ID/g; other organs or tissues, <1 %ID/g), except the kidneys (81.4 %ID/g), giving tumor-to-blood and tumor-to-muscle ratios of 12:1 and 70:1, respectively. In contrast, the control antibody exhibited a tumor uptake of only 0.26 %ID/g, similar to that of muscle and fat. Tumor-specific targeting was evidenced by reduced tumor uptake of nearly 70% on administration of a 10-fold excess of unlabeled UA20 sc

  12. 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. PMID:24128692

  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. PMID:25757566

  14. Screening, expression, and characterization of an anti-human oxidized low-density lipoprotein single-chain variable fragment.

    PubMed

    Kumano-Kuramochi, Miyuki; Fujimura, Takashi; Komba, Shiro; Maeda-Yamamoto, Mari; Machida, Sachiko

    2016-09-01

    Increased levels of oxidized low-density lipoprotein (OxLDL) in the blood circulation are correlated with atherosclerosis. Monoclonal antibody-based detection systems have been reported for OxLDL. We identified novel single-chain variable fragments (scFvs) having affinity for human OxLDL and related ligands. We constructed an scFv library from nonimmunized human spleen mRNA. Two types (γ+κ and μ+λ) of scFv phage libraries were enriched by biopanning, and five scFv clones with affinity for OxLDL were identified. The γκ5 scFv, which showed the highest affinity for OxLDL, was cloned into pET-22b(+) and expressed in Escherichia coli BL21(DE3). γκ5, expressed as an inclusion body in BL21(DE3), was refolded and purified. The specificity and sensitivity of γκ5 were analyzed using enzyme-linked immunosorbent assays (ELISAs). The γκ5 scFv showed affinity for OxLDL and acetylated LDL. The sensitivity of γκ5 to low concentrations (1-2 μg/mL) of OxLDL was higher than that to AcLDL and LDL. Finally, we developed a sandwich ELISA using γκ5 and CTLD14 (a lectin-like OxLDL receptor-1 ligand recognition region), which allowed specific detection of OxLDL at a level below 0.1 μg/mL. Our results indicated that the γκ5 scFv was a promising molecule for the detection of modified LDL at very low concentrations. PMID:27038672

  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. Fusion to the Lysosome Targeting Signal of the Invariant Chain Alters the Processing and Enhances the Immunogenicity of HIV-1 Reverse Transcriptase

    PubMed Central

    Starodubova, E. S.; Isaguliants, M. G.; Kuzmenko, Y. V.; Latanova, A. A.; Krotova, O. A.; Karpov, V. L.

    2014-01-01

    Intracellular processing of the antigen encoded by a DNA vaccine is one of the key steps in generating an immune response. Immunization with DNA constructs targeted to the endosomal-lysosomal compartments and to the MHC class II pathway can elicit a strong immune response. Herein, the weakly immunogenic reverse transcriptase of HIV-1 was fused to the minimal lysosomal targeting motif of the human MHC class II invariant chain. The motif fused to the N-terminus shifted the enzyme intracellular localization and accelerated its degradation. Degradation of the chimeric protein occurred predominantly in the lysosomal compartment. BALB/c mice immunized with the plasmid encoding the chimeric protein demonstrated an enhanced immune response, in the form of an increased antigen-specific production of Th1 cytokines, INF-γ and IL-2, by mouse splenocytes. Moreover, the majority of the splenocytes secreted both cytokines; i.e., were polyfunctional. These findings suggest that retargeting of the antigen to the lysosomes enhances the immune response to DNA vaccine candidates with low intrinsic immunogenicity. PMID:24772328

  17. 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

  18. 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

  19. Negative effects of a disulfide bond mismatch in anti-rabies G protein single-chain antibody variable fragment FV57.

    PubMed

    Duan, Ye; Gu, Tiejun; Zhang, Xizhen; Jiang, Chunlai; Yuan, Ruosen; Li, Zhuang; Wang, Dandan; Chen, Xiaoxu; Wu, Chunlai; Chen, Yan; Wu, Yongge; Kong, Wei

    2014-06-01

    Rabies virus (RV) causes a fatal infectious disease requiring efficient post-exposure prophylaxis (PEP), which includes a rabies vaccine and rabies immunoglobulin (RIG). The single-chain antibody variable fragment (scFv), a small engineered antibody fragment derived from an antibody variable heavy chain and light chain, has the potential to replace the current application of RIG. In previous studies, we constructed and evaluated an anti-rabies virus G protein scFv (FV57) based on the monoclonal antibody CR57. Of the five cysteines in FV57, four are linked in intra-chain disulfide bonds (Cys-VH28/Cys-VH98 and Cys-VL16/Cys-VL84), and one is free (Cys-VL85). However, the thiol in Cys-VL85 neighboring Cys-VL84 in the CDR3 of the light chain is likely to mismatch with the thiol in Cys-VL16 during the renaturing process. In order to study effects of the mismatched disulfide bond, Cys-VL85 and Cys-VL84 of FV57 were mutated to serine to construct mutants FV57(VL85S) and FV57(VL84S). Furthermore, the disulfide bonds in the light chain of FV57, FV57(VL85S) and FV57(VL84S) were deleted by mutating Cys-VL16 to serine. All mutants were prepared and evaluated along with the original FV57. The results indicated that the mismatched disulfide bond of FV57 linking the light chain FR1 and CDR3 would confer deleterious negative effects on its activity against RV, likely due to spatial hindrance in the light chain CDR3. Moreover, avoidance of the disulfide bond mismatch provided an additional 30% protective efficacy against RV infection in the mouse RV challenge model. Thus, modifications of FV57 to eliminate the disulfide bond mismatch may provide a candidate therapeutic agent for effective PEP against rabies. PMID:24598312

  20. Restricted access chiral stationary phase synthesized via reversible addition-fragmentation chain-transfer polymerization for direct analysis of biological samples by high performance liquid chromatography.

    PubMed

    Song, Wen-Jun; Wei, Ji-Ping; Wang, Su-Ying; Wang, Huai-Song

    2014-06-17

    Novel hydrophilic microparticles containing β-cyclodextrin (β-CD) were prepared via one-pot synthesis using reversible addition-fragmentation chain-transfer (RAFT) precipitation polymerization, a "controlled/living" radical polymerization technique. The polymerization was initiated by hydrophilic macromolecular chain-transfer agent [poly(2-hydroxyethyl methacrylate), PHEMA]. The hydrophilic PHEMA on the surface of microparticles can well improve their surface hydrophilicity and lead to their biological compatibility. As chiral restricted access material (RAM), the hydrophilic microparticles can be used for determination of enantiomers in biological samples with direct injection via HPLC analysis. PMID:24890695

  1. Chemical fragmentation by o-iodosobenzoic acid of. cap alpha. -chain of histidine decarboxylase from Micrococcus sp. n. at tryptophan residues

    SciTech Connect

    Alekseeva, E.A.; Grebenshchikova, O.G.; Prozorovskii, V.N.

    1987-02-10

    The carboxymethylated ..cap alpha..-chain of histidine decarboxylase from Micrococcus sp. n., which contains four tryptophan residues, was cleaved by o-iodosobenzoic acid. Five fragments were isolated in homogeneous form by means of gel filtration on Sephadex, rechromatography, and high-voltage paper electrophoresis. The molecular weight, amino acid composition, and N-terminal amino acid sequence were determined for all the peptides isolated.

  2. 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 Central

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

    2015-01-01

    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

  3. 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

  4. The anti-CD74 humanized monoclonal antibody, milatuzumab, which targets the invariant chain of MHC II complexes, alters B-cell proliferation, migration, and adhesion molecule expression

    PubMed Central

    2012-01-01

    Introduction Targeting CD74 as the invariant chain of major histocompatibility complexes (MHC) became possible by the availability of a specific humanized monoclonal antibody, milatuzumab, which is under investigation in patients with hematological neoplasms. CD74 has been reported to regulate chemo-attractant migration of macrophages and dendritic cells, while the role of CD74 on peripheral naïve and memory B cells also expressing CD74 remains unknown. Therefore, the current study addressed the influence of milatuzumab on B-cell proliferation, chemo-attractant migration, and adhesion molecule expression. Methods Surface expression of CD74 on CD27- naïve and CD27+ memory B cells as well as other peripheral blood mononuclear cells (PBMCs) obtained from normals, including the co-expression of CD44, CXCR4, and the adhesion molecules CD62L, β7-integrin, β1-integrin and CD9 were studied after binding of milatuzumab using multicolor flow cytometry. The influence of the antibody on B-cell proliferation and migration was analyzed in vitro in detail. Results In addition to monocytes, milatuzumab also specifically bound to human peripheral B cells, with a higher intensity on CD27+ memory versus CD27- naïve B cells. The antibody reduced B-cell proliferation significantly but moderately, induced enhanced spontaneous and CXCL12-dependent migration together with changes in the expression of adhesion molecules, CD44, β7-integrin and CD62L, mainly of CD27- naïve B cells. This was independent of macrophage migration-inhibitory factor as a ligand of CD74/CD44 complexes. Conclusions Milatuzumab leads to modestly reduced proliferation, alterations in migration, and adhesion molecule expression preferentially of CD27- naïve B cells. It thus may be a candidate antibody for the autoimmune disease therapy by modifying B cell functions. PMID:22404985

  5. 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

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

    PubMed Central

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

    2014-01-01

    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. PMID:24821056

  7. Comparison of detection platforms and post-polymerase chain reaction DNA purification methods for use in conjunction with Cleavase fragment length polymorphism analysis.

    PubMed

    Sander, T; Olson, S; Hall, J; Siebert, M; Grooms, K; Heisler, L; de Arruda, M; Neri, B

    1999-06-01

    The removal of impurities and contaminants from PCR-amplified fragments is important for mutation detection methods which identify mutations based on shifts in electrophoretic mobility. This is particularly critical for assays and detection methods which use target DNA that is labeled prior to analysis and electrophoretic detection. We examined several procedures for purifying DNA amplified by the polymerase chain reaction (PCR) and their use in conjunction with a novel DNA scanning method, the Cleavase fragment length polymorphism (CFLP)* assay. In this study, a 480 bp DNA fragment, fluorescently labeled on the 5'-end of one strand, was amplified and subjected to various widely used purification procedures, including several commercially available clean-up kits. We demonstrate that visualization of the fluorescent label, as opposed to simple ethidium bromide staining, reveals the presence of considerable levels of labeled, truncated, amplification products. The various procedures were evaluated on the basis of their ability to remove these unwanted DNA fragments as well as on the degree to which they inhibited or promoted the CFLP reaction. Several procedures are recommended for use with CFLP analysis, including isopropanol precipitation, gel excision, and several commercially available spin columns. Concurrently, we evaluated (compared) a number of commonly used visualization platforms, including fluorescence imaging, chemiluminescence, and post-electrophoretic staining, for the ability to detect CFLP pattern changes. The advantages and disadvantages of different methods are discussed and amounts of DNA to be used for CFLP analysis on different detection platforms are recommended. PMID:10380752

  8. Distinction of deep versus superficial clinical and nonclinical isolates of Trichosporon beigelii by isoenzymes and restriction fragment length polymorphisms of rDNA generated by polymerase chain reaction.

    PubMed Central

    Kemker, B J; Lehmann, P F; Lee, J W; Walsh, T J

    1991-01-01

    Fifteen clinical and environmental strains of Trichosporon beigelii were analyzed for similarities by using morphological features, biochemical profiles based on carbon compound assimilation and uric acid utilization, isoenzyme electrophoresis, and restriction fragment length polymorphisms of a segment of genes coding for rRNA expanded with the polymerase chain reaction. The findings suggest that strains that cause invasive disease are distinct from the superficial and the nonclinical isolates and that isolates from the skin and mucosae represent a number of different organisms, including some environmental forms. The study shows that T. beigelii is a complex of genetically distinct organisms and that more than one type is found in clinical samples. Images PMID:1684798

  9. Identification of raw and heat-processed meats from game bird species by polymerase chain reaction-restriction fragment length polymorphism of the mitochondrial D-loop region.

    PubMed

    Rojas, M; González, I; Fajardo, V; Martín, I; Hernández, P E; García, T; Martín, R

    2009-03-01

    Polymerase chain reaction-RFLP analysis has been applied to the identification of meats from quail (Coturnix coturnix), pheasant (Phasianus colchicus), red-legged partridge (Alectoris rufa), chukar partridge (Alectoris chukar), guinea fowl (Numida meleagris), capercaillie (Tetrao urogallus), Eurasian woodcock (Scolopax rusticola), and woodpigeon (Columba palumbus). Polymerase chain reaction amplification was carried out using a set of primers flanking a conserved region of approximately 310 bp from the mitochondrial D-loop region. Restriction site analysis based on sequence data from this DNA fragment permitted the selection of HinfI, MboII, and Hpy188III endonucleases for species identification. The restriction profiles obtained when amplicons were digested with the chosen enzymes allowed the unequivocal identification of all game bird species analyzed. Consistent results were obtained with both raw and heat-processed meats. PMID:19211540

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. Isolation and characterization of Ts19 Fragment II, a new long-chain potassium channel toxin from Tityus serrulatus venom.

    PubMed

    Cerni, Felipe Augusto; Pucca, Manuela Berto; Amorim, Fernanda Gobbi; de Castro Figueiredo Bordon, Karla; Echterbille, Julien; Quinton, Loïc; De Pauw, Edwin; Peigneur, Steve; Tytgat, Jan; Arantes, Eliane Candiani

    2016-06-01

    Ts19 Fragment II (Ts19 Frag-II) was first isolated from the venom of the scorpion Tityus serrulatus (Ts). It is a protein presenting 49 amino acid residues, three disulfide bridges, Mr 5534Da and was classified as a new member of class (subfamily) 2 of the β-KTxs, the second one described for Ts scorpion. The β-KTx family is composed by two-domain peptides: N-terminal helical domain (NHD), with cytolytic activity, and a C-terminal CSαβ domain (CCD), with Kv blocking activity. The extensive electrophysiological screening (16 Kv channels and 5 Nav channels) showed that Ts19 Frag-II presents a specific and significant blocking effect on Kv1.2 (IC50 value of 544±32nM). However, no cytolytic activity was observed with this toxin. We conclude that the absence of 9 amino acid residues from the N-terminal sequence (compared to Ts19 Frag-I) is responsible for the absence of cytolytic activity. In order to prove this hypothesis, we synthesized the peptide with these 9 amino acid residues, called Ts19 Frag-III. As expected, Ts19 Frag-III showed to be cytolytic and did not block the Kv1.2 channel. The post-translational modifications of Ts19 and its fragments (I-III) are also discussed here. A mechanism of post-translational processing (post-splitting) is suggested to explain Ts19 fragments production. In addition to the discovery of this new toxin, this report provides further evidence for the existence of several compounds in the scorpion venom contributing to the diversity of the venom arsenal. PMID:26116782

  15. 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

  16. Surface protein imprinted core-shell particles for high selective lysozyme recognition prepared by reversible addition-fragmentation chain transfer strategy.

    PubMed

    Li, Qinran; Yang, Kaiguang; Liang, Yu; Jiang, Bo; Liu, Jianxi; Zhang, Lihua; Liang, Zhen; Zhang, Yukui

    2014-12-24

    A novel kind of lysozyme (Lys) surface imprinted core-shell particles was synthesized by reversible addition-fragmentation chain transfer (RAFT) strategy. With controllable polymer shell chain length, such particles showed obviously improved selectivity for protein recognition. After the RAFT initial agent and template protein was absorbed on silica particles, the prepolymerization solution, with methacrylic acid and 2-hydroxyethyl methacrylate as the monomers, and N,N'-methylenebis(acrylamide) as the cross-linker, was mixed with the silica particles, and the polymerization was performed at 40 °C in aqueous phase through the oxidation-reduction initiation. Ater polymerization, with the template protein removal and destroying dithioester groups with hexylamine, the surface Lyz imprinted particles were obtained with controllable polymer chain length. The binding capacity of the Lys imprinted particles could reach 5.6 mg protein/g material, with the imprinting factor (IF) as 3.7, whereas the IF of the control material prepared without RAFT strategy was only 1.6. The absorption equilibrium could be achieved within 60 min. Moreover, Lys could be selectively recognized by the imprinted particles from both a four-proteins mixture and egg white sample. All these results demonstrated that these particles prepared by RAFT strategy are promising to achieve the protein recognition with high selectivity. PMID:25434676

  17. 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

  18. Discrimination among thermophilic Campylobacter species by polymerase chain reaction amplification of 23S rRNA gene fragments.

    PubMed Central

    Eyers, M; Chapelle, S; Van Camp, G; Goossens, H; De Wachter, R

    1993-01-01

    By comparing nucleic acid sequences determined for one of the most variable areas of 23S rRNA genes of 23 Campylobacter strains, we were able to identify regions specific for thermophilic Campylobacter strains. Oligonucleotide primers corresponding to these unique regions were synthesized and used in the polymerase chain reaction. One primer pair selectively detected all thermophilic Campylobacter species, while four other primer pairs allowed discrimination among the thermophilic species Campylobacter coli, Campylobacter jejuni subsp. jejuni, Campylobacter lari, and Campylobacter upsaliensis. All primer sets were tested successfully on a large number of clinical isolates. Images PMID:7508460

  19. 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

  20. 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. PMID:27157441

  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. 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

  3. 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

  4. 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. PMID:26166178

  5. Single-chain Fv fragment antibodies selected from an intrabody library as effective mono- or bivalent reagents for in vitro protein detection.

    PubMed

    Desplancq, Dominique; Rinaldi, Anne-Sophie; Stoessel, Audrey; Sibler, Annie-Paule; Busso, Didier; Oulad-Abdelghani, Mustapha; Van Regenmortel, Marc H; Weiss, Etienne

    2011-06-30

    In spite of their many potential applications, recombinant antibody molecules selected by phage display are rarely available commercially, one reason being the absence of robust bacterial expression systems that yield sufficient quantities of reagents for routine applications. We previously described the construction and validation of an intrabody library that allows the selection of single-chain Fv (scFv) fragments solubly expressed in the cytoplasm. Here, we show that it is possible to obtain monomeric scFvs binding specifically to human papillomavirus type 16 E6 and cellular gankyrin oncoproteins in quantities higher than 0.5 g/L of shake-flask culture in E. coli cytoplasm after auto-induction. In addition, stable bivalent scFvs of increased avidity were produced by tagging the scFvs with the dimeric glutathione-S-transferase enzyme (GST). These minibody-like molecules were further engineered by fusion with green fluorescent protein (GFPuv), leading to high yield of functional bivalent fluorescent antibody fragments. Our results demonstrate that scFvs selected from an intrabody library can be engineered into cost-effective bivalent reagents suitable for many biomedical and industrial applications. PMID:21501618

  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

    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 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

  8. 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

  9. 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

  10. 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

  11. Magnetite magnetosome and fragmental chain formation of Magnetospirillum magneticum AMB-1: transmission electron microscopy and magnetic observations

    NASA Astrophysics Data System (ADS)

    Li, Jinhua; Pan, Yongxin; Chen, Guanjun; Liu, Qingsong; Tian, Lanxiang; Lin, Wei

    2009-04-01

    Stable single-domain (SD) magnetite formed intracellularly by magnetotactic bacteria is of fundamental interest in sedimentary and environmental magnetism. In this study, we studied the time course of magnetosome growth and magnetosome chain formation (0-96 hr) in Magnetospirillum magneticum AMB-1 by transmission electron microscopy (TEM) observation and rock magnetism. The initial non-magnetic cells were microaerobically batch cultured at 26 °C in a modified magnetic spirillum growth medium. TEM observations indicated that between 20 and 24 hr magnetosome crystals began to mineralize simultaneously at multiple sites within the cell body, followed by a phase of rapid growth lasting up to 48 hr cultivation. The synthesized magnetosomes were found to be assembled into 3-5 subchains, which were linearly aligned along the long axis of the cell, supporting the idea that magnetosome vesicles were linearly anchored to the inner membrane of cell. By 96 hr cultivation, 14 cubo-octahedral magnetosome crystals in average with a mean grain size of ~44.5 nm were formed in a cell. Low-temperature (10-300 K) thermal demagnetization, room-temperature hysteresis loops and first-order reversal curves (FORCs) were conducted on whole cell samples. Both coercivity (4.7-18.1 mT) and Verwey transition temperature (100-106 K) increase with increasing cultivation time length, which can be explained by increasing grain size and decreasing non-stoichiometry of magnetite, respectively. Shapes of hysteresis loops and FORCs indicated each subchain behaving as an `ideal' uniaxial SD particle and extremely weak magnetostatic interaction fields between subchains. Low-temperature thermal demagnetization of remanence demonstrated that the Moskowitz test is valid for such linear subchain configurations (e.g. δFC/δZFC > 2.0), implying that the test is applicable to ancient sediments where magnetosome chains might have been broken up into short chains due to disintegration of the organic scaffold

  12. SCEDS: protein fragments for molecular replacement in Phaser

    PubMed Central

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

    2013-01-01

    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 Cα 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. PMID:24189233

  13. Selection and Characterization of Single Chain Antibody Fragments Specific for Hsp90 as a Potential Cancer Targeting Molecule

    PubMed Central

    Petters, Edyta; Sokolowska-Wedzina, Aleksandra; Otlewski, Jacek

    2015-01-01

    Heat shock proteins play an essential role in facilitating malignant transformation and they have been recognized as important factors in human cancers. One of the key elements of the molecular chaperones machinery is Hsp90 and it has recently become a target for anticancer therapeutic approaches. The potential and importance of Hsp90-directed agents becomes apparent when one realizes that disruption of Hsp90 function may influence over 200 oncogenic client proteins. Here, we described the selection and characterization of Hsp90-specific antibody fragments from commercially available Tomlinson I and J phage display libraries. The affinities of Hsp90-binding scFv variants were measured using SPR method. Then, based on the best clone selected, we performed the affinity maturation procedure and obtained valuable Hsp90-specific clones. The selected binders were expressed and applied for immunostaining, ELISA and SPR analysis using model cancer cell lines. All performed experiments confirmed the ability of selected antibodies to interact with the Hsp90. Therefore, the presented Hsp90-specific scFv, might be a starting point for the development of a novel antibody-based strategy targeting cancer. PMID:26307975

  14. Selection and Characterization of Single Chain Antibody Fragments Specific for Hsp90 as a Potential Cancer Targeting Molecule.

    PubMed

    Petters, Edyta; Sokolowska-Wedzina, Aleksandra; Otlewski, Jacek

    2015-01-01

    Heat shock proteins play an essential role in facilitating malignant transformation and they have been recognized as important factors in human cancers. One of the key elements of the molecular chaperones machinery is Hsp90 and it has recently become a target for anticancer therapeutic approaches. The potential and importance of Hsp90-directed agents becomes apparent when one realizes that disruption of Hsp90 function may influence over 200 oncogenic client proteins. Here, we described the selection and characterization of Hsp90-specific antibody fragments from commercially available Tomlinson I and J phage display libraries. The affinities of Hsp90-binding scFv variants were measured using SPR method. Then, based on the best clone selected, we performed the affinity maturation procedure and obtained valuable Hsp90-specific clones. The selected binders were expressed and applied for immunostaining, ELISA and SPR analysis using model cancer cell lines. All performed experiments confirmed the ability of selected antibodies to interact with the Hsp90. Therefore, the presented Hsp90-specific scFv, might be a starting point for the development of a novel antibody-based strategy targeting cancer. PMID:26307975

  15. Expression and characterization of a functional single-chain variable fragment (scFv) protein recognizing MCF7 breast cancer cells in E. coli cytoplasm.

    PubMed

    Mahgoub, Ilham Omer

    2012-08-01

    Single-chain variable fragment (scFv) is one of the most common antibody forms. This report describes the expression of the scFv gene as a soluble protein in Origami DE3 cytoplasm. The purified scFv recognized the epidermal growth factor receptor (EGFRvIII) on the surface of MCF-7 cells. The scFv protein was purified in soluble form at a concentration of 10 mg/l, and the scFv protein activity and specificity were characterized using several immunological assays. The purified scFv protein showed specific binding to MCF-7 cells, evidenced by a band of 68 kDa in Western blot analysis, and immunofluorescence clearly proved that the scFv antibody recognized the EGFRvIII antigen epitopes. Furthermore, 53 % of the MCF-7 cells were bound to scFv protein, as measured by flow cytometry analysis. This study demonstrated that the Origami DE3 expression system can produce single-chain antibodies in active form for later use in gene therapy and vaccine production. PMID:22552770

  16. Improved fluoroquinolone detection in ELISA through engineering of a broad-specific single-chain variable fragment binding simultaneously to 20 fluoroquinolones.

    PubMed

    Wen, Kai; Nölke, Greta; Schillberg, Stefan; Wang, Zhanhui; Zhang, Suxia; Wu, Congming; Jiang, Haiyang; Meng, Hui; Shen, Jianzhong

    2012-07-01

    Fluoroquinolones (FQs) are a group of synthetic, broad-spectrum antibacterial agents. Due to its extensive use in animal industry and aquaculture, residues of these antibiotics and the emergence of bacteria resistant to FQs have become a major public health issue. To prepare a generic antibody capable of recognizing nearly all FQs, a single-chain variable fragment (scFv) was generated from the murine hybridoma cells C49H1 producing a FQ-specific monoclonal antibody. This scFv was characterized by indirect competitive enzyme-linked immunosorbent assay (ciELISA), and it showed identical binding properties to parental monoclonal antibody: it was capable of recognizing 17 of 20 targeted FQs below maximum residue limits, except for sarafloxacin (SAR), difloxacin (DIF), and trovafloxacin (TRO) which are highly concerned members in the FQs family. In order to broaden the specificity of this scFv to SAR and its analogues (DIF and TRO), protein homology modeling and antibody-ligands docking analysis were employed to identify the potential key amino acid residues involved in hapten antibody. A mutagenesis phage display library was generated by site directed mutagenesis randomizing five aminoacid residues in the third heavy-chain complementarity determining region. After one round of panning against biotinylated norfloxacin (NOR) and four rounds of panning against biotinylated SAR, scFv variants we screened showed up to 10-fold improved IC(50) against SAR, DIF, and TRO in ciELISA while the specificity against other FQs was fully retained. PMID:22549819

  17. 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

  18. 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

  19. Chemistry of enol ethers. LXXXIII. Synthesis and investigation of penta- and hexacarbocyanine dyes containing cyclic fragments in the polymethine chain

    SciTech Connect

    Makin, S.M.; Shavrygina, O.A.; Boiko, T.N.; Monich, N.V.; Pomogaev, A.I.

    1988-09-20

    4,6-Dimethylene- and 4,6-trimethylene-1,1,3,7,9-4,8-nonadienes were obtained by the reaction of 2,4-dimethylene- and 2,4-trimethylene-1,1,5,7-tetraethoxy-2,6-heptadienes with vinyl ethyl ether. Treatment of the products with N-methylaniline in an acidic medium gave the corresponding nonamethine salts. Condensation of the latter with 2-methyl-3-ethylbenzothiazolium iodide led to thiapentacarbocyanine dyes having symmetrically arranged di- and trimethylene bridges between the meta atoms of the polymethine chain. The reaction of glutaconaldehyde acetal with the cyclic 1-alkoxy-1,3-dienes led to the synthesis of 2,4-dimethylene- and 2,4-trimethylene-1,1,5,9,9-pentaalkoxy-2,6-nonadienes, from the thiapentacarbocyanines with an unsymmetrical arrangement of the dimethylene and trimethylene bridges were obtained through the respective nonamethine salts. A thiahexacarbocyanine dye containing a trimethylene bridge was synthesized from the undercamethine salt obtained from the product from the reaction of 1,1,5,9,9-pentamethoxy-2,4-trimethylene-2,6-nonadiene with vinyl ethyl ether.

  20. Effect of linker length between variable domains of single chain variable fragment antibody against daidzin on its reactivity.

    PubMed

    Yusakul, Gorawit; Sakamoto, Seiichi; Pongkitwitoon, Benyakan; Tanaka, Hiroyuki; Morimoto, Satoshi

    2016-07-01

    The peptide linker between variable domains of heavy (VH) and light (VL) chains is one of important factors that influence the characteristics of scFv, including binding activity and specificity against target antigen. The scFvs against daidzin (DZ-scFvs) with different linker lengths were constructed in the format of VH-(GGGGS)n-VL (n = 1, 3, 5, and 7). They were expressed in the hemolymph of silkworm larvae using the Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid DNA system, and their reactivity against daidzin and related compounds were evaluated using an indirect competitive enzyme-linked immunosorbent assay (icELISA), which is applicable for quantitative analysis of daidzin. The results showed that the reactivity of scFvs against daidzin was increased, whereas specificity slightly decreased when their peptide linker was lengthened. These results suggested that the linker length of DZ-scFvs contributes to its reactivity. In addition, the results emphasize that the linker length could control the reactivity of DZ-scFvs. PMID:27116996

  1. The effect of internalizing human single chain antibody fragment on liposome targeting to epithelioid and sarcomatoid mesothelioma

    PubMed Central

    Iyer, Arun K.; Su, Yang; Feng, Jinjin; Lan, Xiaoli; Zhu, Xiaodong; Liu, Yue; Gao, Dongwei; Seo, Youngho; VanBrocklin, Henry F.; Broaddus, V. Courtney; Liu, Bin; He, Jiang

    2011-01-01

    Immunoliposomes (ILs) anchored with internalizing human antibodies capable of targeting all subtypes of mesothelioma can be useful for targeted imaging and therapy of this malignant disease. The objectives of this study were to evaluate both the in vitro and in vivo tumor targeted internalization of novel internalizing human single chain antibody (scFv) anchored ILs on both epithelioid (M28) and sarcomatoid (VAMT-1) subtypes of human mesothelioma. ILs were prepared by post-insertion of mesothelioma-targeting human scFv (M1) onto preformed liposomes and radiolabeled with 111In (111In-IL-M1), along with control non-targeted liposomes (111In-CL). Incubation of 111In-IL-M1 with M28, VAMT-1, and a control non-tumorigenic cell-line (BPH-1) at 37°C for 24 h revealed efficient binding and rapid internalization of ILs into both subtypes of tumor cells but not into the BPH-1 cells; internalization accounted for approximately 81-94% of total cell accumulation in mesothelioma cells compared to 37-55% in control cells. In tumor bearing mice intravenous (i.v.) injection of 111In-IL-M1 led to remarkable tumor accumulation: 4 % and 4.7% injected dose per gram (% ID/g) for M28 and VAMT-1 tumors, respectively, 48 h after injection. Furthermore, tumor uptake of 111In-IL-M1 in live xenograft animal models was verified by single photon emission computed tomography (SPECT/CT). In contrast, i.v. injection of 111In-CL in tumor-bearing mice revealed very low uptake in both subtypes of mesothelioma, 48 h after injection. In conclusion, M1 scFv-anchored ILs showed selective tumor targeting and rapid internalization into both epithelioid and sarcomatoid subtypes of human mesothelioma, demonstrating its potential as a promising vector for enhanced tumor drug targeting. PMID:21255833

  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. Improved soluble expression of a single-chain antibody fragment in E. coli for targeting CA125 in epithelial ovarian cancer.

    PubMed

    Sharma, Sai Kiran; Suresh, Mavanur R; Wuest, Frank R

    2014-10-01

    Production of antibody fragments in heterologous hosts such as Escherichiacoli provides a unique and cost-effective method to develop engineered vectors for tumor targeting. A single-chain Fragment variable (scFv) of the murine monoclonal antibody MAb-B43.13 targeting CA125 in epithelial ovarian cancer was previously developed, expressed, purified and proposed as a functional targeting entity for biomedical applications. However, the yields from its soluble expression in heterologous systems were very low for any practical use in preclinical translational research; leave alone the defeated objective of convenient and cost-effective production. In the present work, the anti-CA125 scFv gene was re-organized and sub-cloned into pET-22b(+) vector to be in frame with the pelB leader peptide for periplasmic localization and C-terminal hexa-histidine tag to facilitate downstream purification. Six variants of the scFv were constructed to investigate the impact of variable domain orientations, inter-domain peptide linker sequences and codon optimization on the soluble expression of the scFv using Rosetta 2(DE3) as the E. coli host supplemented with tRNAs for rare codons. Expression in shake flask cultures under the control of an inducible T7 promoter and subsequent purification by cobalt based immobilized metal affinity chromatography yielded differential amounts of high purity scFv for all constructs. Here, we report up to 14-fold increase in the soluble expression of the scFv primarily as a result of codon optimization with minor effects from inter-domain peptide linkers and variable domain orientation in the anti-CA125 scFv molecule. All the scFv constructs expressed and purified were found to be immunoreactive for in vitro targeting of CA125 antigen. PMID:25079010

  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. Efficient expression of single chain variable fragment antibody against paclitaxel using the Bombyx mori nucleopolyhedrovirus bacmid DNA system and its characterizations.

    PubMed

    Yusakul, Gorawit; Sakamoto, Seiichi; Tanaka, Hiroyuki; Morimoto, Satoshi

    2016-07-01

    A single chain variable fragment (scFv), the smallest unit of functional recombinant antibody, is an attractive format of recombinant antibodies for various applications due to its small fragment and possibility of genetic engineering. Hybridoma clone 3A3 secreting anti-paclitaxel monoclonal antibody was used to construct genes encoding its variable domains of heavy (VH) and light (VL) chains. The VH and VL domains were linked to be the PT-scFv3A3 using flexible peptide linker in a format of VH-(GGGGS)5-VL. The PT-scFv3A3 was primarily expressed using the pET28a(+) vector in the Escherichia coli system, and was then further expressed by using the Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid DNA system. Interestingly, the reactivity of PT-scFv3A3 expressed in the hemolymph of B. mori using the BmNPV bacmid DNA system was much higher than that expressed in the E. coli system. Using indirect competitive enzyme-linked immunosorbent assay (icELISA), the PT-scFv3A3 (B. mori) reacted not only with immobilized paclitaxel, but also with free paclitaxel in a concentration-dependent manner, with the linear range of free paclitaxel between 0.156 and 5.00 µg/ml. The PT-scFv3A3 (B. mori) exhibited less cross-reactivity (%) than its parental MAb clone 3A3 against paclitaxel-related compounds, including docetaxel (31.1 %), 7-xylosyltaxol (22.1 %), baccatin III (<0.68 %), 10-deacetylbaccatin III (<0.68 %), 1-hydroxybaccatin I (<0.68 %), and 1-acetoxy-5-deacetylbaccatin I (<0.68 %). With the exception of cephalomannine, the cross-reactivity was slightly increased to 8.50 %. The BmNPV bacmid DNA system was a highly efficient expression system of active PT-scFv3A3, which is applicable for PT-scFv3A3-based immunoassay of paclitaxel. In addition, the PT-scFv3A3 can be applied to evaluate its neutralizing property of paclitaxel or docetaxel toxicity. PMID:26940321

  6. Production of a recombinant anti-human CD4 single-chain variable-fragment antibody using phage display technology and its expression in Escherichia coli.

    PubMed

    Babaei, Arash; Zarkesh-Esfahani, Sayyed Hamid; Gharagozloo, Marjan

    2011-05-01

    Single-chain variable fragment (scFv) is a fusion protein of the variable regions of the heavy (VH) and light (VL) chains of immunoglobulin, connected with a short linker peptide of 10 to about 20 amino acids. In this study, the scFv of a monoclonal antibody against the third domain of human CD4 was cloned from OKT4 hybridoma cells using the phage display technique and produced in E. coli. The expression, production, and purification of anti-CD4 scFv were tested using SDS-PAGE and Western blot, and the specificity of anti-CD4 scFv was examined using ELISA. A 31 kDa recombinant anti-CD4 scFv was expressed and produced in bacteria, which was confirmed by SDS-PAGE and Western blot assays. Sequence analysis proved the ScFv structure of the construct. It was able to bind to CD4 in quality ELISA assay. The canonical structure of anti-CD4 scFv antibody was obtained using the SWISS_MODEL bioinformatics tool for comparing with the scFv general structure. To the best of our knowledge, this is the first report for generating scFv against human CD4 antigen. Engineered anti-CD4 scFv could be used in immunological studies, including fluorochrome conjugation, bispecific antibody production, bifunctional protein synthesis, and other genetic engineering manipulations. Since the binding site of our product is domain 3 (D3) of the CD4 molecule and different from the CD4 immunological main domain, including D1 and D2, further studies are needed to evaluate the anti-CD4 scFv potential for diagnostic and therapeutic applications. PMID:21617352

  7. 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. PMID:26179100

  8. Overproduction of anti-Tn antibody MLS128 single-chain Fv fragment in Escherichia coli cytoplasm using a novel pCold-PDI vector.

    PubMed

    Subedi, Ganesh P; Satoh, Tadashi; Hanashima, Shinya; Ikeda, Akemi; Nakada, Hiroshi; Sato, Reiko; Mizuno, Mamoru; Yuasa, Noriyuki; Fujita-Yamaguchi, Yoko; Yamaguchi, Yoshiki

    2012-03-01

    Overproduction of recombinant proteins in Escherichia coli is often hampered by their failure to fold correctly, leading to their accumulation within inclusion bodies. To overcome the problem, a variety of techniques aimed at soluble expression have been developed including low temperature expression and/or fusion of soluble tags and chaperones. However, a general protocol for bacterial expression of disulfide bond-containing proteins has hitherto not been established. Single chain Fv fragments (scFvs) are disulfide bond-containing proteins often difficult to express in soluble forms in E. coli. We here examine in detail the E. coli expression of a scFv originating from an anti-carbohydrate MLS128 antibody as a model system. We combine three techniques: (1) tagging scFv with thioredoxin, DsbC and protein disulfide isomerase (PDI), (2) expressing the proteins at low temperature using the pCold vector system, and (3) using Origami E. coli strains with mutations in the thioredoxin reductase and glutathione reductase genes. We observed a high expression level of soluble MLS128-scFv in the Origami strain only when PDI is used as a tag. The recombinant protein retains full binding activity towards synthetic carbohydrate antigens. The developed "pCold-PDI" vector has potential for overproduction of other scFvs and disulfide-containing proteins in the Origami strains. PMID:22245752

  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. 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

  11. 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

  12. Rapid diagnosis and genotyping of Leishmania isolates from cutaneous and visceral leishmaniasis by microcapillary cultivation and polymerase chain reaction-restriction fragment length polymorphism of miniexon region.

    PubMed

    Serin, Mehmet S; Daglioglu, Kenan; Bagirova, Melahat; Allahverdiyev, Adil; Uzun, Soner; Vural, Zeynep; Kayar, Begum; Tezcan, Seda; Yetkin, Mesut; Aslan, Gonul; Emekdas, Gurol; Koksal, Fatih

    2005-11-01

    We have performed a combination of microcapillary cultivation method and restriction fragment length polymorphism (RFLP) analysis of amplified products by 1 single PCR of miniexon region of Leishmania for molecular diagnosis and genotyping of different Leishmania species isolated from cutaneous leishmaniasis (CL) and visceral leishmaniasis. We have analyzed 10 microcapillary cultivated isolates from cutaneous cases and 5 microcapillary cultivated isolates from visceral cases (totally 15) by polymerase chain reaction-RFLP (PCR-RFLP). Of 10 isolates, 3 (30%) were genotyped as Leishmania infantum and 7 (70%) of 10 isolates were genotyped as Leishmania tropica from the microcapillary cultivated isolates of cutaneous cases. On the other hand, all 5 isolates (100%) were genotyped as L. infantum from microcapillary cultivated visceral cases. Our most interesting finding is the presence of 3 L. infantum isolates in CL cases without kala-azar history. Therefore, we suggest that further investigations must be done about this subject. On the other hand, we suggest the combination of microcapillary culture method and PCR-RFLP of miniexon region of leishmaniae can be used in routine laboratory experimentation because of their simple, cheap, and rapid benefits (within a week), whereas other different approaches offer a multitude of valid taxonomic characters for species identification. PMID:16249065

  13. Development of Fok-I based nested polymerase chain reaction-restriction fragment length polymorphism analysis for detection of hepatitis B virus X region V5M mutation

    PubMed Central

    Kim, Hong; Hong, Seok-Hyun; Lee, Seoung-Ae; Gong, Jeong-Ryeol; Kim, Bum-Joon

    2015-01-01

    AIM: To develop a Fok-I nested polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis (PRA) method for the detection of hepatitis B virus X region (HBx) V5M mutation. METHODS: Nested PCR was applied into DNAs from 198 chronic patients at 2 different stages [121 patients with hepatocellular carcinoma (HCC) and 77 carrier patients]. To identify V5M mutants, digestion of nested PCR amplicons by the restriction enzyme Fok-I (GGA TGN9↓) was done. For size comparison, the enzyme-treated products were analyzed by electrophoresis on 2.5% agarose gels, stained with ethidium bromide, and visualized on a UV transilluminator. RESULTS: The assay enabled the identification of 69 patients (sensitivity of 34.8%; 46 HCC patients and 23 carrier patients). Our data also showed that V5M prevalence in HCC patients was significantly higher than in carrier patients (47.8%, 22/46 patients vs 0%, 0/23 patients, P < 0.001), suggesting that HBxAg V5M mutation may play a pivotal role in HCC generation in chronic patients with genotype C infections. CONCLUSION: The Fok-I nested PRA developed in this study is a reliable and cost-effective method to detect HBxAg V5M mutation in chronic patients with genotype C2 infection. PMID:26715821

  14. Targeting human immunodeficiency virus type 1 reverse transcriptase by intracellular expression of single-chain variable fragments to inhibit early stages of the viral life cycle.

    PubMed Central

    Shaheen, F; Duan, L; Zhu, M; Bagasra, O; Pomerantz, R J

    1996-01-01

    Novel molecular approaches to inhibit human immunodeficiency virus type 1 (HIV-1) infection have received increasing attention because of the lack of effective antiviral drug therapies in vivo. We now demonstrate that cells can be intracellularly immunized by cytoplasmic expression of single-chain variable antibody fragments (SFv) which bind to the HIV-1 reverse transcriptase (RT) enzyme. The expression of anti-RT SFv in T-lymphocytic cells specifically neutralizes the RT activity in the preintegration stage and affects the reverse transcription process, an early event of the HIV-1 life cycle. Blocking the virus at these early stages dramatically decreased HIV-1 propagation, as well as the HIV-1-induced cytopathic effects in susceptible human T lymphocytes, by impeding the formation of the proviral DNA. These data also demonstrate that intracellular, complete SFvs may gain access to viral proteins of the HIV-1 preintegration complex. These SFvs will provide a tool with which to better understand the molecular mechanisms involved in restricting viral replication in HIV-1-infected cells. PMID:8648670

  15. 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. PMID:26524628

  16. 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

  17. 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

  18. Virus-Like Particles Displaying Recombinant Short-Chain Fragment Region and Interleukin 2 for Targeting Colon Cancer Tumors and Attracting Macrophages.

    PubMed

    Deo, Vipin Kumar; Kato, Tatsuya; Park, Enoch Y

    2016-05-01

    Functionalized virus-like particles (VLPs) can target with specificity as drug delivery systems and can attract macrophages for the destruction of cancer cells. Here, the group antigen capsid protein from the Rous sarcoma virus was used to prepare VLPs, functionalized by displaying glycol-inositol phosphate-anchored recombinant single chain fragment variable (rscFv) and hemagglutinin transmembrane region anchored recombinant human interleukin-2 (rhIL2) (designated as VLP-rscFv-rhIL2s) in silkworms. The rscFv specifically binds the tumor-associated glycoprotein 72 that is expressed at the surface of colon cancer cells. VLP-rscFv-rhIL2 was affinity purified and had a smooth particle size with a diameter of 50 nm. Calcein-AM-packaged VLP-rscFv-rhIL2s successfully targeted cancer cells as a model for drug delivery system. VLP-rscFv-rhIL2 bound with colon cancer cells that attracted macrophages (human monocytic cell line-1 cells) in chemotaxis chamber assays compared with negative controls. The macrophages secreted tumor necrosis factor-α, a cytokine that is necessary to destroy cancer cells. These results demonstrate the potential of VLP-rscFv-rhIL2 as an intelligent nano biomaterial that is capable of attracting macrophages. PMID:27037014

  19. 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

  20. Thermally conductive, electrically insulating and melt-processable polystyrene/boron nitride nanocomposites prepared by in situ reversible addition fragmentation chain transfer polymerization.

    PubMed

    Huang, Xingyi; Wang, Shen; Zhu, Ming; Yang, Ke; Jiang, Pingkai; Bando, Yoshio; Golberg, Dmitri; Zhi, Chunyi

    2015-01-01

    Thermally conductive and electrically insulating polymer/boron nitride (BN) nanocomposites are highly attractive for various applications in many thermal management fields. However, so far most of the preparation methods for polymer/BN nanocomposites have usually caused difficulties in the material post processing. Here, an in situ grafting approach is designed to fabricate thermally conductive, electrically insulating and post-melt processable polystyrene (PS)/BN nanosphere (BNNS) nanocomposites by initiating styrene (St) on the surface functionalized BNNSs via reversible addition fragmentation chain transfer polymerization. The nanocomposites exhibit significantly enhanced thermal conductivity. For example, at a St/BN feeding ratio of 5:1, an enhancement ratio of 1375% is achieved in comparison with pure PS. Moreover, the dielectric properties of the nanocomposites show a desirable weak dependence on frequency, and the dielectric loss tangent of the nanocomposites remains at a very low level. More importantly, the nanocomposites can be subjected to multiple melt processing to form different shapes. Our method can become a universal approach to prepare thermally conductive, electrically insulating and melt-processable polymer nanocomposites with diverse monomers and nanofillers. PMID:25493655

  1. Thermally conductive, electrically insulating and melt-processable polystyrene/boron nitride nanocomposites prepared by in situ reversible addition fragmentation chain transfer polymerization

    NASA Astrophysics Data System (ADS)

    Huang, Xingyi; Wang, Shen; Zhu, Ming; Yang, Ke; Jiang, Pingkai; Bando, Yoshio; Golberg, Dmitri; Zhi, Chunyi

    2015-01-01

    Thermally conductive and electrically insulating polymer/boron nitride (BN) nanocomposites are highly attractive for various applications in many thermal management fields. However, so far most of the preparation methods for polymer/BN nanocomposites have usually caused difficulties in the material post processing. Here, an in situ grafting approach is designed to fabricate thermally conductive, electrically insulating and post-melt processable polystyrene (PS)/BN nanosphere (BNNS) nanocomposites by initiating styrene (St) on the surface functionalized BNNSs via reversible addition fragmentation chain transfer polymerization. The nanocomposites exhibit significantly enhanced thermal conductivity. For example, at a St/BN feeding ratio of 5:1, an enhancement ratio of 1375% is achieved in comparison with pure PS. Moreover, the dielectric properties of the nanocomposites show a desirable weak dependence on frequency, and the dielectric loss tangent of the nanocomposites remains at a very low level. More importantly, the nanocomposites can be subjected to multiple melt processing to form different shapes. Our method can become a universal approach to prepare thermally conductive, electrically insulating and melt-processable polymer nanocomposites with diverse monomers and nanofillers.

  2. Application of adaptive DO-stat feeding control to Pichia pastoris X33 cultures expressing a single chain antibody fragment (scFv).

    PubMed

    Ferreira, A R; Ataíde, F; von Stosch, M; Dias, J M L; Clemente, J J; Cunha, A E; Oliveira, R

    2012-11-01

    In this study, fed-batch cultures of a Pichia pastoris strain constitutively expressing a single chain antibody fragment (scFv) under the control of the glyceraldehyde-3-phosphate dehydrogenase (GAP) promoter were performed in a pilot 50 L bioreactor. Due to the very high cell density achieved within the first 75 h, typically between 140 and 160 g-DCW/L of dry cell weight (DCW), most of the scFv is produced under hard oxygen transfer limitation. To improve scFv productivity, a direct adaptive dissolved oxygen (DO)-stat feeding controller that maximizes glycerol feeding under the constraint of available oxygen transfer capacity was developed and applied to this process. The developed adaptive controller enabled to maximize glycerol feeding through the regulation of DO concentration between 3 and 5 % of saturation, thereby improving process productivity. Set-point convergence dynamics are characterized by a fast response upon large perturbations to DO, followed by a slower but very robust convergence in the vicinity of the boundary with almost imperceptible overshoot. Such control performance enabled operating closer to the 0 % boundary for longer periods of time when compared to a traditional proportional-integral-derivative algorithm, which tends to destabilize with increasing cell density. PMID:22610694

  3. 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

  4. Expression of anti-tumor necrosis factor alpha (TNFα) single-chain variable fragment (scFv) in Spirodela punctata plants transformed with Agrobacterium tumefaciens.

    PubMed

    Balaji, Parthasarathy; Satheeshkumar, P K; Venkataraman, Krishnan; Vijayalakshmi, M A

    2016-05-01

    Therapeutic antibodies against tumor necrosis factor alpha (TNFα) have been considered effective for some of the autoimmune diseases such as rheumatoid arthritis, Crohn's diseases, and so on. But associated limitations of the current therapeutics in terms of cost, availability, and immunogenicity have necessitated the need for alternative candidates. Single-chain variable fragment (scFv) can negate the limitations tagged with the anti-TNFα therapeutics to a greater extent. In the present study, Spirodela punctata plants were transformed with anti-TNFα through in planta transformation using Agrobacterium tumefaciens strain, EHA105. Instead of cefotaxime, garlic extract (1 mg/mL) was used to remove the agrobacterial cells after cocultivation. To the best of our knowledge, this report shows for the first time the application of plant extracts in transgenic plant development. 95% of the plants survived screening under hygromycin. ScFv cDNA integration in the plant genomic DNA was confirmed at the molecular level by PCR. The transgenic protein expression was followed up to 10 months. Expression of scFv was confirmed by immunodot blot. Protein expression levels of up to 6.3% of total soluble protein were observed. β-Glucuronidase and green fluorescent protein expressions were also detected in the antibiotic resistant plants. The paper shows the generation of transgenic Spirodela punctuata plants through in planta transformation. PMID:25786575

  5. 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.

  6. Homotopy invariance of η-invariants

    PubMed Central

    Weinberger, Shmuel

    1988-01-01

    Intersection homology and results related to the higher signature problem are applied to show that certain combinations of η-invariants of the signature operator are homotopy invariant in various circumstances. PMID:16593961

  7. Potent and broad neutralizing activity of a single chain antibody fragment against cell-free and cell-associated HIV-1

    PubMed Central

    Borges, Andrew Rosa; Ptak, Roger G; Wang, Yanping; Dimitrov, Antony S; Alam, S. Munir; Wieczorek, Lindsay; Bouma, Peter; Fouts, Timothy; Jiang, Shibo; Polonis, Victoria R; Haynes, Barton F; Quinnan, Gerald V; Montefiori, David C; Dimitrov, Dimiter S

    2010-01-01

    Several human monoclonal antibodies (hmAbs) exhibit relatively potent and broad neutralizing activity against HIV-1, but there has not been much success in using them as potential therapeutics. We have previously hypothesized and demonstrated that small engineered antibodies can target highly conserved epitopes that are not accessible by full-size antibodies. However, their potency has not been comparatively evaluated with known HIV-1-neutralizing hmAbs against large panels of primary isolates. We report here the inhibitory activity of an engineered single chain antibody fragment (scFv), m9, against several panels of primary HIV-1 isolates from group M (clades A–G) using cell-free and cell-associated virus in cell line-based assays. M9 was much more potent than scFv 17b, and more potent than or comparable to the best-characterized broadly neutralizing hmAbs IgG1 b12, 2G12, 2F5 and 4e10. It also inhibited cell-to-cell transmission of HIV-1 with higher potency than enfuvirtide (t-20, Fuzeon). M9 competed with a sulfated CCR5 N-terminal peptide for binding to gp120-CD4 complex, suggesting an overlapping epitope with the coreceptor binding site. M9 did not react with phosphatidylserine (pS) and cardiolipin (CL), nor did it react with a panel of autoantigens in an antinuclear autoantibody (ANA) assay. We further found that escape mutants resistant to m9 did not emerge in an immune selection assay. these results suggest that m9 is a novel anti-HIV-1 candidate with potential therapeutic or prophylactic properties, and its epitope is a new target for drug or vaccine development. PMID:20305395

  8. The antitumor efficacy of a novel adenovirus-mediated anti-p21Ras single chain fragment variable antibody on human cancers in vitro and in vivo.

    PubMed

    Yang, Ju-Lun; Pan, Xin-Yan; Zhao, Wen-Xing; Hu, Qi-Chan; Ding, Feng; Feng, Qiang; Li, Gui-Yun; Luo, Ying

    2016-03-01

    Activated ras genes are found in a large number of human tumors, and therefore are one of important targets for cancer therapy. This study investigated the antitumor effects of a novel single chain fragment variable antibody (scFv) against ras protein, p21Ras. The anti-p21Ras scFv gene was constructed by phage display library from hybridoma KGHR1, and then subcloned into replication-defective adenovirus vector to obtain recombinant adenovirus KGHV100. Human tumor cell lines with high expression of p21Ras SW480, MDA-MB‑231, OVCAR-3, BEL-7402, as well as tumor cell line with low expression of p21Ras, SKOV3, were employed to investigate antitumor effects in vitro and in vivo. Fluorescence microscopy demonstrated that KGHV100 was able to express intracellularly anti-p21Ras scFv antibody in cultured tumor cells and in transplantation tumor cells. MTT, Transwell, colony formation, and flow cytometry analysis showed that KGHV100 led to significant growth arrest in tumor cells with high p21Ras expression, and induced G0/G1 cell cycle arrest in the studied tumor cell lines. In vivo, KGHV100 significantly inhibited tumor growth following intratumoral injection, and the survival rates of the mice were higher than the control group. These results indicate that the adenovirus-mediated intracellular expression of the novel anti-p21Ras scFv exerted strong antitumoral effects, and may be a potential method for therapy of cancers with p21Ras overexpression. PMID:26780944

  9. Expression and purification of a human anti-cyclin D1 single-chain variable fragment antibody AD5 and its characterization.

    PubMed

    Wu, Yan; Zou, Desheng; Cao, Yuhua; Yao, Nannan; Wang, Junye; Wang, Wenhan; Jiang, Hongyu; Li, Guiying

    2013-12-01

    Cyclin D1 plays an important role in cell cycle progression. Increasing evidence indicates that cyclin D1 is overexpressed in the majority of tumor cells and has become a potential target for tumor therapy. However, little research has been done on the specific inhibition of cyclin D1 for cancer therapy. With the rapid development of the phage display antibody library technique, single-chain variable fragment (scFv) antibodies have emerged, which have tremendous application prospects in cancer therapy and diagonosis. In this study, a human scFv binding specifically to cyclin D1 (AD5) that was derived from a human semi-synthetic scFv phage library was expressed in the soluble form in Escherichia coli (E. coli) HB2151 cells. To characterize AD5, soluble AD5 was purified successfully through ammonium sulfate precipitation and affinity chromatography from the culture supernatant of AD5/HB2151. ELISA assay revealed that purified soluble AD5 could specifically bind to human recombinant cyclin D1 with approximately (1.19±0.056) x 107 M-1 affinity constant and showed approximately 52% competitive inhibition with the anti-cyclin D1 polyclonal antibody for binding to cyclin D1 in vitro. These results suggest that the scFv antibody against cyclin D1 may be a novel potential tool for targeting cyclin D1 in cancer therapy and diagnosis. PMID:24127128

  10. 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. PMID:20600077

  11. 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

  12. 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

  13. Characterization of infectious laryngotracheitis virus isolates from the US by polymerase chain reaction and restriction fragment length polymorphism of multiple genome regions.

    PubMed

    Oldoni, Ivomar; García, Maricarmen

    2007-04-01

    Infectious laryngotracheitis (ILT) is an acute viral respiratory disease, primarily of chickens. Economic losses attributable to ILT affect many poultry-producing areas throughout the United States (US) and the world. Despite efforts to control the disease by vaccination, prolonged epidemics of ILT remain a threat to the poultry industry. Earlier epidemiological and molecular evidence indicated that outbreaks in the US are caused by vaccine-related strains. In this study, polymerase chain reaction and restriction fragment polymorphism (PCR-RFLP) of four genome regions was utilized to characterize 25 isolates from commercial poultry and backyard flocks from the US. Combinations of PCR-RFLP patterns classified the ILT virus isolates into nine groups. Backyard flock isolates were categorized in three separate groups. The ILT virus US Department of Agriculture (USDA) reference strain and the tissue culture origin (TCO) vaccine strain were categorized into two separate groups. Twenty-two isolates from commercial poultry were categorized into four groups: one group, of six isolates, showed patterns identical to the chicken embryo origin (CEO) vaccines; a second group, of nine isolates, differed in only one pattern from the CEO vaccines; a third group, of two isolates, differed in only one pattern from the TCO vaccine; a fourth group, of five isolates, differed in six and nine patterns from the CEO and TCO vaccines, respectively. Results obtained from this study clearly demonstrated that most of the commercial poultry isolates (17 of 22 isolates) were closely related to the vaccine strains. However, isolates different to the vaccine strains were also identified in commercial poultry. PMID:17479379

  14. Characterization of infectious laryngotracheitis virus (ILTV) isolates from commercial poultry by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP).

    PubMed

    Oldoni, Ivomar; Rodríguez-Avila, Andrés; Riblet, Sylva; García, Maricarmen

    2008-03-01

    Infectious laryngotracheitis (ILT) is a highly contagious, acute respiratory disease of chickens, of worldwide distribution, that affects growth and egg production and leads to significant economic losses during periodic outbreaks of the disease. Live attenuated vaccines (chicken embryo origin [CEO] and tissue-culture origin [TCO]) have been widely used to control the disease in the United States. It is believed that most of the outbreaks in the United States are caused by vaccine-related isolates that persist in the field and spill over into naïve poultry populations. The objective of this study was to utilize the previously developed polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) analysis to genotype recent ILT virus (ILTV) isolates from commercial poultry. Forty-six samples were collected during January 2006 to April 2007 from five poultry production regions of the United States and were characterized within PCR-RFLP groups III-VI. Sixty-three percent of the samples analyzed were categorized as closely related to the vaccine strains (groups III-V), whereas 33% were categorized as group VI viruses that differed in six and nine PCR-RFLP patterns from the CEO and TCO vaccines; a mixture of group IV and V viruses was detected in two samples (4%). In general, groups V and VI were the most prevalent viruses, found in 52% and 33% of the samples tested respectively. Both types of viruses were detected in vaccinated and nonvaccinated flocks. Although genetically different, both viruses produced severe disease in the field. PMID:18459297

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. APPLICATION OF POLYMERASE CHAIN REACTION (PCR) AND PCR BASED RESTRICTION FRAGMENT LENGTH POLYMORPHISM FOR DETECTION AND IDENTIFICATION OF DERMATOPHYTES FROM DERMATOLOGICAL SPECIMENS

    PubMed Central

    Bagyalakshmi, R; Senthilvelan, B; Therese, K L; Murugusundram, S; Madhavan, H N

    2008-01-01

    Objective: To develop and optimize polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) targeting 18S rDNA and internal transcribed spacer (ITS) region of fungi for rapid detection and identification of dermatophytes. Materials and Methods: Two PCR-RFLP methods targeting 18S rDNA and ITS regions of fungi were optimized using standard and laboratory isolates of dermatophytes and other fungi. Sixty-eight dermatological clinical specimens (nail clippings (56), material obtained from blisters (8), hair root (2), scraping from scaly plaque of foot (1) and skin scraping (1) collected by the dermatologist were subjected to both the optimized PCR-RFLP and conventional mycological (smear and culture) methods. Results: PCRs targeting 18S rDNA and the ITS region were sensitive to detect 10 picograms and 1 femtogram of T. rubrum DNA, respectively. PCR targeting 18S rDNA was specific for dermatophytes and subsequent RFLP identified them to species level. PCR-RFLP targeting the ITS region differentiated dermatophytes from other fungi with identification to species level. Among the 68 clinical specimens tested, both PCR-RFLP methods revealed the presence of dermatophytes in 27 cases (39.7%), whereas culture revealed the same only in 2 cases (7.40%), increasing the clinical sensitivity by 32.3%. Among 20 smear positive specimens, both PCR-RFLP methods detected dermatophytes in 12 (17.6%). Both the methods detected the presence of dermatophytes in 13 (19.11%) smear and culture negative specimens, increasing the clinical sensitivity by 36.1%. Conclusion: PCR-RFLP methods targeting 18S rDNA and the ITS regions of fungi were specific and highly sensitive for detection and speciation of dermatophytes. PMID:19967012

  1. A preliminary trial using multi-target polymerase chain reaction (multiplex PCR) and restriction fragment length polymorphism (PCR-RFLP) on the same feedstuffs to detect tissues of animal origin.

    PubMed

    Colombo, F; Marchisio, E; Trezzi, I E; Peri, V; Pinotti, L; Baldi, A; Soncini, G

    2004-08-01

    A preliminary study using multi-target polymerase chain reaction (multiplex PCR) and restriction fragment length polymorphism (PCR-RFLP) was done on the same feedstuffs to detect animal tissues. The results of the two methods differ somewhat: PCR-RFLP did not detect any signal in any sample, but multiplex PCR detected a signal in one sample. These findings could be a basis for further investigations. PMID:15509020

  2. 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. PMID:23842902

  3. Generalizing twisted gauge invariance

    SciTech Connect

    Duenas-Vidal, Alvaro; Vazquez-Mozo, Miguel A.

    2009-05-01

    We discuss the twisting of gauge symmetry in noncommutative gauge theories and show how this can be generalized to a whole continuous family of twisted gauge invariances. The physical relevance of these twisted invariances is discussed.

  4. CCAAT-binding factor NF-Y and RFX are required for in vivo assembly of a nucleoprotein complex that spans 250 base pairs: the invariant chain promoter as a model.

    PubMed Central

    Linhoff, M W; Wright, K L; Ting, J P

    1997-01-01

    The events that lead to promoter accessibility within chromatin are not completely understood. The invariant chain (Ii) promoter was used as a model to determine the contribution of different DNA-binding factors in establishing occupancy of a complex promoter. Gamma interferon induction of the Ii promoter requires the cooperation of multiple cis elements including distal S, X, and Y/CCAAT elements along with proximal GC and Y/CCAAT elements. The heteromeric transcription factor NF-Y binds to both Y/CCAAT elements. Genomic footprinting was used to analyze in vivo protein-DNA contacts for integrated Ii promoters bearing mutations in each element. The results reveal a hierarchy of transcription factor loading with NF-Y binding to the distal Y/CCAAT element being required for establishing protein-DNA interactions over the entire 250 bp analyzed. Mutation of the X box disrupts binding primarily at the adjacent Y/CCAAT element along with a lesser effect on GC box binding. Importantly, this finding is verified with a cell line which lacks a functional X-box-binding factor, RFX, providing physiological validity for the strategy described here. Mutation of both the S element and the GC box results in either no or little effect on transcription factor binding. However, mutation of the proximal Y/CCAAT element disrupts binding to the adjacent GC box and partially reduces binding in the distal S/X/Y domain. The crucial role for NF-Y in establishing promoter occupancy may be related to its histone fold motif, the essential component for assembling nucleosome-like structures. PMID:9234716

  5. Invariant turbulence models

    NASA Astrophysics Data System (ADS)

    Bihlo, Alexander; Dos Santos Cardoso-Bihlo, Elsa Maria; Nave, Jean-Christophe; Popovych, Roman

    2012-11-01

    Various subgrid-scale closure models break the invariance of the Euler or Navier-Stokes equations and thus violate the geometric structure of these equations. A method is shown which allows one to systematically derive invariant turbulence models starting from non-invariant turbulence models and thus to correct artificial symmetry-breaking. The method is illustrated by finding invariant hyperdiffusion schemes to be applied in the two-dimensional turbulence problem.

  6. 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.

  7. Synthesis of (E)-4-Bromo-3-methoxybut-3-en-2-one, the Key Fragment in the Polyhydroxylated Chain Common to Oscillariolide and Phormidolides A-C.

    PubMed

    Gil, Alejandro; Lamariano-Merketegi, Janire; Lorente, Adriana; Albericio, Fernando; Álvarez, Mercedes

    2016-05-17

    The terminal bromomethoxydiene (BMD) moiety of the polyhydroxylated chain present in phormidolides and oscillariolides has been synthesized for first time. Several strategies for the stereoselective synthesis of the 4-bromo-3-methoxybut-3-en-2-ones are described. Furthermore, a preliminary study to successfully introduce the BMD within the polyol chain and the fatty acid allowed us to corroborate the end structure of the polyol. PMID:26998826

  8. A non-reducing terminal fragment from tracheal cartilage keratan sulphate chains contains alpha (2-3)-linked N-acetylneuraminic acid.

    PubMed Central

    Dickenson, J M; Huckerby, T N; Nieduszynski, I A

    1991-01-01

    Keratan sulphate chains were isolated from bovine tracheal ring cartilage (15-18-month-old animals) after papain digestion of the tissue followed by ethanol fractionation, chondroitinase ABC digestion and alkaline borohydride reduction. The keratan sulphate chains were further purified by anion-exchange chromatography on a Pharmacia Mono-Q column in order to remove any contaminating chondroitin sulphate and O-linked oligosaccharides. The chains were then treated with keratanase and the digest was subjected to alkaline borohydride reduction, producing oligosaccharides with galactitol at their reducing ends. The reduced digest was chromatographed on a Nucleosil 5 SB anion-exchange column and individual oligosaccharides were isolated. One of these, oligosaccharide (I), was shown by 500 MHz 1H-n.m.r. spectroscopy to have the following structure: NeuAc alpha 2-3Gal beta 1-4GlcNAc(6SO4) beta 1-3Gal-ol (I) The structure of this oligosaccharide shows that keratan sulphate chains from bovine tracheal ring cartilage may be terminated with N-acetylneuraminic acid linked alpha (2-3) to an unsulphated galactose. Keratan sulphate chains were also isolated from bovine femoral head cartilage (15-18-month-old animals) using an identical protocol, but with keratanase which was subsequently shown to have sialidase activity. This yielded oligosaccharide (II), the unsialyated version of (I): Gal beta 1-4GlcNAc(6SO4) beta 1-3Gal-ol (II). PMID:1910336

  9. 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.

  10. 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

  11. 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

    2016-04-01

    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. PMID:25831436

  12. Form factors in SU(3)-invariant integrable models

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  13. 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. PMID:23181705

  14. 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

  15. Positive selection of invariant V alpha 14+ T cells by non-major histocompatibility complex-encoded class I-like molecules expressed on bone marrow-derived cells.

    PubMed Central

    Adachi, Y; Koseki, H; Zijlstra, M; Taniguchi, M

    1995-01-01

    V alpha 14+ T cells are a unique subset expressing an invariant T-cell antigen receptor alpha chain encoded by V alpha 14 and J alpha 281 gene fragments with a 1-nt N region. Most invariant V alpha 14+ T cells develop in extrathymic organs, independent of thymus, and expand at a high frequency in various mouse strains regardless of major histocompatibility complex (MHC) haplotype. In this paper, we show that the positive selection of invariant V alpha 14+ T cells requires a beta 2-microglobulin-associated MHC class I-like molecule not linked to the MHC on chromosome 17. This was determined by linkage analysis on DNA from recombinant mice generated by crossing a C57BL/6 mouse with a wild mouse, Mus musculus molossinus, that is negative for invariant V alpha 14 TCR expression. However, the peptide transporter TAP1 is not necessary for positive selection of invariant V alpha 14+ T cells, indicating the direct recognition of the MHC class I-like molecule without peptide by the invariant V alpha 14 TCR. Further, experiments with bone marrow-chimeric mice show that invariant V alpha 14+ T cells in the periphery are selected by bone marrow cells, suggesting a unique lineage of V alpha 14+ T cells differentiated through a selection process distinct from that of conventional alpha beta TCR+ T cells. Images Fig. 1 Fig. 2 Fig. 3 PMID:7862661

  16. 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

  17. 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

  18. 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

  19. Expression, purification and characterization of a human single-chain Fv antibody fragment fused with the Fc of an IgG1 targeting a rabies antigen in Pichia pastoris.

    PubMed

    Wang, Ding-ding; Su, Man-man; Sun, Yan; Huang, Shu-lin; Wang, Ju; Yan, Wei-qun

    2012-11-01

    Because the demand for rabies post exposure prophylaxis (PEP) treatment has increased exponentially in recent years, the limited supply of human and equine rabies immunoglobulin (HRIG and ERIG) has failed to provide an adequate amount of the required passive immune component in PEP in countries where canine rabies is endemic. The replacement of HRIG and ERIG with a potentially cheaper and efficacious alternative biological for the treatment of rabies in humans, therefore, remains a high priority. In this study, we set out to assess a human single-chain Fv antibody fragment fused with the Fc of an IgG1 targeting a rabies antigen to develop a product that can be used as a component of the PEP cocktail. We cloned the ScFv fragment from a human ScFv library that was established previously and inserted this fragment into the expression vector pPICZαC/Fc. An active recombinant ScFv-Fc fusion protein was successfully expressed in Pichia pastoris. The production of ScFv-Fc was optimized and scaled up in an 80L fermentor with yields exceeding 60mg/L. The ScFv-Fc protein was purified to more than 95% purity using a two-step scheme: ammonium sulfate fractionation and Protein A Sepharose CL-4B. The ScFv-Fc fusion protein neutralized rabies virus in a standard in vivo neutralization assay in which the virus was incubated with the ScFv-Fc molecules before intracranial inoculation in mice. Our results suggest that functional antibodies can be produced in P. pastoris and that ScFv-Fc fusion proteins have the potential to serve as therapeutic candidates. PMID:22982755

  20. 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. PMID:12005620

  1. Photoinduced electron transfer double fragmentation. An oxygen-mediated radical chain process in the cofragmentation of aminopinacol donors with organic halides

    SciTech Connect

    Chen, L.; Farahat, M.S.; Gan, H.; Whitten, D.G.; Farid, S. |

    1995-06-14

    We reprot an investigation in which excited states of amino pinacols 1-3 are reacted with the halides CCl{sub 4}, benzyl bromide, and p-cyanobenzyl bromide. Interesting results from this study include the finding that low-to-moderate quantum efficiencies for reaction are observed when the reactions are carried out under degassed conditions, indicating that the halide radical anions must survive long enough within the initial ion pair formed in the quenching step to undergo considerable return electron transfer. More strikingly we find that for certain pinacol-halide combinations reaction in aerared solutions leads to much higher efficiencies, which can be attributed to a chain reaction involving oxygen capture of a primary radical product. 25 refs., 1 fig., 1 tab.

  2. 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. PMID:26982465

  3. Aggregation of β-amyloid fragments

    NASA Astrophysics Data System (ADS)

    Meinke, Jan H.; Hansmann, Ulrich H. E.

    2007-01-01

    The authors study the folding and aggregation of six chains of the β-amyloid fragment 16-22 using Monte Carlo simulations. While the isolated fragment prefers a helical form at room temperature, in the system of six interacting fragments one observes both parallel and antiparallel β sheets below a crossover temperature Tx≈420K. The antiparallel sheets have lower energy and are therefore more stable. Above the nucleation temperature the aggregate quickly dissolves into widely separated, weakly interacting chains.

  4. Molecularly imprinted polymer coated solid-phase microextraction fiber prepared by surface reversible addition-fragmentation chain transfer polymerization for monitoring of Sudan dyes in chilli tomato sauce and chilli pepper samples.

    PubMed

    Hu, Xiaogang; Fan, Yanan; Zhang, Yi; Dai, Guimei; Cai, Quanling; Cao, Yujuan; Guo, Changjuan

    2012-06-20

    Surface reversible addition-fragmentation chain transfer (RAFT) polymerization method was firstly applied to the preparation of molecularly imprinted polymer (MIP) coated silicon solid-phase microextraction (SPME) fibers. With Sudan I as template, an ultra-thin MIP coating with about 0.55-μm thickness was obtained with homogeneous structure and controlled composition, due to the controllable radical growing and chain propagation in surface RAFT polymerization. The MIP-coated fibers were found with enhanced selectivity coefficients (3.0-6.5) to Sudan I-IV dyes in contrast with those reported in our previous work. Furthermore, the ultra-thin thickness of MIP coating was helpful to the effective elution of template and fast adsorption/desorption kinetics, so only about 18 min was needed for MIP-coated SPME operation. The detection limits of 21-55 ng L(-1) were achieved for four Sudan dyes, when MIP-coated SPME was coupled with liquid chromatography (LC) and mass spectrometry (MS) detection. The MIP-coated SPME-LC-MS/MS method was tested for the monitoring of ultra trace Sudan dyes in spiked chilli tomato sauce and chilli pepper samples, and high enrichment effect, remarkable matrix peaks-removing capability, and consequent high sensitivities were achieved to four Sudan dyes. PMID:22652263

  5. Engineering of a recombinant trivalent single-chain variable fragment antibody directed against rabies virus glycoprotein G with improved neutralizing potency.

    PubMed

    Turki, Imène; Hammami, Akil; Kharmachi, Habib; Mousli, Mohamed

    2014-02-01

    Human and equine rabies immunoglobulins are currently available for passive immunization against rabies. However, these are hampered by the limited supply and some drawbacks. Advances in antibody engineering have led to overcome issues of clinical applications and to improve the protective efficacy. In the present study, we report the generation of a trivalent single-chain Fv (scFv50AD1-Fd), that recognizes the rabies virus glycoprotein, genetically fused to the trimerization domain of the bacteriophage T4 fibritin, termed 'foldon' (Fd). scFv50AD1-Fd was expressed as soluble recombinant protein in bacterial periplasmic space and purified through affinity chromatography. The molecular integrity and stability were analyzed by polyacrylamide gradient-gel electrophoresis, size-exclusion chromatography and incubation in human sera. The antigen-binding properties of the trimeric scFv were analyzed by direct and competitive-ELISA. Its apparent affinity constant was estimated at 1.4 ± 0.25 × 10(9)M(-1) and was 75-fold higher than its monovalent scFv (1.9 ± 0.68 × 10(7)M(-1)). The scFv50AD1-Fd neutralized rabies virus in a standard in vitro and in vivo neutralization assay. We showed a high neutralization activity up to 75-fold compared with monovalent format and the WHO standard serum. The gain in avidity resulting from multivalency along with an improved biological activity makes the trivalent scFv50AD1-Fd construct an important reagent for rabies protection. The antibody engineering approach presented here may serve as a strategy for designing a new generation of anti-rabies for passive immunotherapy. PMID:24091293

  6. 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

  7. Fragmentation pathways of polymer ions.

    PubMed

    Wesdemiotis, Chrys; Solak, Nilüfer; Polce, Michael J; Dabney, David E; Chaicharoen, Kittisak; Katzenmeyer, Bryan C

    2011-01-01

    Tandem mass spectrometry (MS/MS) is increasingly applied to synthetic polymers to characterize chain-end or in-chain substituents, distinguish isobaric and isomeric species, and determine macromolecular connectivities and architectures. For confident structural assignments, the fragmentation mechanisms of polymer ions must be understood, as they provide guidelines on how to deduce the desired information from the fragments observed in MS/MS spectra. This article reviews the fragmentation pathways of synthetic polymer ions that have been energized to decompose via collisionally activated dissociation (CAD), the most widely used activation method in polymer analysis. The compounds discussed encompass polystyrenes, poly(2-vinyl pyridine), polyacrylates, poly(vinyl acetate), aliphatic polyester copolymers, polyethers, and poly(dimethylsiloxane). For a number of these polymers, several substitution patterns and architectures are considered, and questions regarding the ionization agent and internal energy of the dissociating precursor ions are also addressed. Competing and consecutive dissociations are evaluated in terms of the structural insight they provide about the macromolecular structure. The fragmentation pathways of the diverse array of polymer ions examined fall into three categories, viz. (1) charge-directed fragmentations, (2) charge-remote rearrangements, and (3) charge-remote fragmentations via radical intermediates. Charge-remote processes predominate. Depending on the ionizing agent and the functional groups in the polymer, the incipient fragments arising by pathways (1)-(3) may form ion-molecule complexes that survive long enough to permit inter-fragment hydrogen atom, proton, or hydride transfers. PMID:20623599

  8. Lorentz invariance in shape dynamics

    NASA Astrophysics Data System (ADS)

    Carlip, S.; Gomes, Henrique

    2015-01-01

    Shape dynamics is a reframing of canonical general relativity in which time reparametrization invariance is ‘traded’ for a local conformal invariance. We explore the emergence of Lorentz invariance in this model in three contexts: as a maximal symmetry, an asymptotic symmetry and a local invariance.

  9. C-terminal fragment of tetanus toxin heavy chain activates Akt and MEK/ERK signalling pathways in a Trk receptor-dependent manner in cultured cortical neurons.

    PubMed Central

    Gil, Carles; Chaib-Oukadour, Imane; Aguilera, José

    2003-01-01

    Previous publications from our group [Gil, Chaib, Pelliccioni and Aguilera (2000) FEBS Lett. 481, 177-182; Gil, Chaib, Blasi and Aguilera (2001) Biochem. J. 356, 97-103] have reported the activation, in rat brain synaptosomes, of several phosphoproteins, such as neurotrophin tyrosine kinase (Trk) A receptor, phospholipase Cgamma-1, protein kinase C (PKC) isoforms and extracellular-signal-regulated kinases 1 and 2 (ERK-1/2). In the present study, we examined, by means of phospho-specific antibodies, the activation of the signalling cascades involving neurotrophin Trk receptor, Akt kinase and ERK pathway, in cultured cortical neurons from foetal rat brain, by tetanus toxin (TeTx) as well as by the C-terminal part of its heavy chain (H(C)-TeTx). TeTx and H(C)-TeTx induce fast and transient phosphorylation of Trk receptor at Tyr(674) and Tyr(675), but not at Tyr(490), although the potency of TeTx in this action was higher when compared with H(C)-TeTx action. Moreover, H(C)-TeTx and TeTx also induced phosphorylation of Akt (at Ser(473) and Thr(308)) and of ERK-1/2 (Thr(202)/Tyr(204)), in a time- and concentration-dependent manner. The detection of TeTx- and H(C)-TeTx-induced phosphorylation at Ser(9) of glycogen synthase kinase 3beta confirms Akt activation. In the extended analysis of the ERK pathway, phosphorylation of the Raf, mitogen-activated protein kinase kinase (MEK)-1/2 and p90Rsk kinases and phosphorylation of the transcription factor cAMP-response-element-binding protein were detected. The use of tyrphostin AG879, an inhibitor of Trk receptors, demonstrates their necessary participation in the H(C)-TeTx-induced activation of Akt and ERK pathways, as well as in the phosphorylation of phospholipase Cgamma-1. Furthermore, both pathways are totally dependent on phosphatidylinositol 3-kinase action, and they are independent of PKC action, as assessed using wortmannin and Ro-31-8220 as inhibitors. The activation of PKC isoforms was determined by their translocation

  10. 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.

  11. Lattice invariants for knots

    SciTech Connect

    Janse Van Rensburg, E.J.

    1996-12-31

    The geometry of polygonal knots in the cubic lattice may be used to define some knot invariants. One such invariant is the minimal edge number, which is the minimum number of edges necessary (and sufficient) to construct a lattice knot of given type. In addition, one may also define the minimal (unfolded) surface number, and the minimal (unfolded) boundary number; these are the minimum number of 2-cells necessary to construct an unfolded lattice Seifert surface of a given knot type in the lattice, and the minimum number of edges necessary in a lattice knot to guarantee the existence of an unfolded lattice Seifert surface. In addition, I derive some relations amongst these invariants. 8 refs., 5 figs., 2 tabs.

  12. Reparametrization invariant collinear operators

    SciTech Connect

    Marcantonini, Claudio; Stewart, Iain W.

    2009-03-15

    In constructing collinear operators, which describe the production of energetic jets or energetic hadrons, important constraints are provided by reparametrization invariance (RPI). RPI encodes Lorentz invariance in a power expansion about a collinear direction, and connects the Wilson coefficients of operators at different orders in this expansion to all orders in {alpha}{sub s}. We construct reparametrization invariant collinear objects. The expansion of operators built from these objects provides an efficient way of deriving RPI relations and finding a minimal basis of operators, particularly when one has an observable with multiple collinear directions and/or soft particles. Complete basis of operators is constructed for pure glue currents at twist-4, and for operators with multiple collinear directions, including those appearing in e{sup +}e{sup -}{yields}3 jets, and for pp{yields}2 jets initiated via gluon fusion.

  13. Invariance in vowel systems.

    PubMed

    Funabashi, Masatoshi

    2015-05-01

    This study applies information geometry of normal distribution to model Japanese vowels on the basis of the first and second formants. The distribution of Kullback-Leibler (KL) divergence and its decomposed components were investigated to reveal the statistical invariance in the vowel system. The results suggest that although significant variability exists in individual KL divergence distributions, the population distribution tends to converge into a specific log-normal distribution. This distribution can be considered as an invariant distribution for the standard-Japanese speaking population. Furthermore, it was revealed that the mean and variance components of KL divergence are linearly related in the population distribution. The significance of these invariant features is discussed. PMID:25994716

  14. Performance Assessment of the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Method for Rapid Detection of Susceptibility to Ethambutol and Molecular Prediction of Extensively Drug-resistant Tuberculosis in Clinical Isolates of Mycobacterium tuberculosis

    PubMed Central

    Arjomandzadegan, M; Nazari, R; Zolfaghari, MR; Taherahmadi, M; Sadrnia, M; Titov, LP; Ahmadi, A; Shojapoor, M

    2015-01-01

    ABSTRACT Introduction: The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was employed for rapid detection of ethambutol (EMB) resistant clinical isolates of Mycobacterium tuberculosis. Materials and Methods: From 182 clinical isolates of M tuberculosis collected from different regions, 103 strains were entered in the investigation. DNA was extracted by Chelex 100 method and PCR was performed using specific primers for embB gene. Polymerase chain reaction products were digested with HaeIII and NlaII restriction endonucleases and the patterns of restriction fragments were analysed. Some randomly selected samples were sequenced. Results: Out of 103 studied strains, 52 were resistant to EMB. The cases of secondary tuberculosis were 53 (51.50 ± 1.77%), and primary cases 50 (48.50 ± 1.77%; p > 0.05). From 63 extensively drug-resistant (XDR), pre-XDR and multidrug-resistant (MDR) isolates, 27 (87%), 18 (81.8%) and 7 (70%) strains were resistant to EMB, respectively. Results of PCR-RFLP method showed that from 27R EMB XDR isolates, 13 (sensitivity 48% with CI: 0.307, 0.66 and specificity 100%), from 18R EMB pre-XDR strains, 4 (sensitivity 22% with CI: 0.09, 0.45 and specificity 100%) and of 7R EMB MDR, 2 (sensitivity 28% with CI: 0.082, 0.64 and specificity 100%) had mutation in ATG-Met codon 306. Results of sequencing were concordant with RFLP method. Overall, sensitivity of the molecular method was 36.5% (CI: 0.09, 0.45) and specificity 100%. None of the 40 pansusceptible strains was embB306 mutants. Extensively drug-resistant strains had a higher proportion of embB306 mutants (43%) than pre-XDR and MDR isolates (odds ratio 6.78; p < 0.001). Conclusion: Fast detection of susceptibility to EMB drug is possible by PCR-RFLP. The embB306 locus is a candidate marker for rapid prediction of high resistance of MDR and XDR forms to anti-tuberculosis drugs using this method. PMID:26624582

  15. 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. .

  16. Gauge invariants and bosonization

    NASA Astrophysics Data System (ADS)

    Kijowski, J.; Rudolph, G.; Rudolph, M.

    1998-12-01

    We present some results, which are part of our program of analyzing gauge theories with fermions in terms of local gauge invariant fields. In a first part the classical Dirac-Maxwell system is discussed. Next we develop a procedure which leads to a reduction of the functional integral to an integral over (bosonic) gauge invariant fields. We apply this procedure to the case of QED and the Schwinger model. In a third part we go some steps towards an analysis of the considered models. We construct effective (quantum) field theories which can be used to calculate vacuum expectation values of physical quantities.

  17. 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.

  18. Forest Fragmentation

    EPA Science Inventory

    This indicator describes forest fragmentation in the contiguous United States circa 2001. This information provides a broad, recent picture of the spatial pattern of the nation’s forests and the extent to which they are being broken into smaller patches and pierced or interspe...

  19. 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.

  20. 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…

  1. 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.

  2. High-density IgE recognition of the major grass pollen allergen Phl p 1 revealed with single-chain IgE antibody fragments obtained by combinatorial cloning.

    PubMed

    Madritsch, Christoph; Gadermaier, Elisabeth; Roder, Uwe W; Lupinek, Christian; Valenta, Rudolf; Flicker, Sabine

    2015-03-01

    The timothy grass pollen allergen Phl p 1 belongs to the group 1 of highly cross-reactive grass pollen allergens with a molecular mass of ∼25-30 kDa. Group 1 allergens are recognized by >95% of grass pollen allergic patients. We investigated the IgE recognition of Phl p 1 using allergen-specific IgE-derived single-chain variable Ab fragments (IgE-ScFvs) isolated from a combinatorial library constructed from PBMCs of a grass pollen-allergic patient. IgE-ScFvs reacted with recombinant Phl p 1 and natural group 1 grass pollen allergens. Using synthetic Phl p 1-derived peptides, the binding sites of two ScFvs were mapped to the N terminus of the allergen. In surface plasmon resonance experiments they showed comparable high-affinity binding to Phl p 1 as a complete human IgE-derived Ab recognizing the allergens' C terminus. In a set of surface plasmon resonance experiments simultaneous allergen recognition of all three binders was demonstrated. Even in the presence of the three binders, allergic patients' polyclonal IgE reacted with Phl p 1, indicating high-density IgE recognition of the Phl p 1 allergen. Our results show that multiple IgE Abs can bind with high density to Phl p 1, which may explain the high allergenic activity and sensitizing capacity of this allergen. PMID:25637023

  3. Co-expression of Dsb proteins enables soluble expression of a single-chain variable fragment (scFv) against human type 1 insulin-like growth factor receptor (IGF-1R) in E. coli.

    PubMed

    Sun, Xue-Wen; Wang, Xiao-Hua; Yao, Yan-Bing

    2014-12-01

    Type 1 insulin-like growth factor receptor (IGF-1R) is a promising therapeutic target for cancer treatment. A single-chain variable fragment (scFv) against human IGF-1R forms inclusion body when expressed in periplasmic space of E. coli routinely. Here, we described that co-expression of appropriate disulfide bonds (Dsb) proteins known to catalyze the formation and isomerization of Dsb can markedly recover the soluble expression of target scFv in E. coli. A 50 % recovery in solubility of the scFv was observed upon co-expression of DsbC alone, and a maximum solubility (80 %) was obtained when DsbA and DsbC were co-expressed in combination. Furthermore, the soluble scFv present full antigen-binding activity with IGF-1R, suggesting its correct folding. This study also suggested that the selection of Dsb proteins should be tested case-by-case if the approach of co-expression of Dsb system is adopted to address the problem of insoluble expression of proteins carrying Dsb. PMID:25256416

  4. 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

  5. Preparation of a bifunctional pyrazosulfuron-ethyl imprinted polymer with hydrophilic external layers by reversible addition-fragmentation chain transfer polymerization and its application in the sulfonylurea residue analysis.

    PubMed

    Yang, Meixian; Zhang, Yingying; Lin, Shen; Yang, Xinlin; Fan, Zhijin; Yang, Lixia; Dong, Xiangchao

    2013-09-30

    A new bifunctional pyrazosulfuron-ethyl imprinted polymer was synthesized by the combination of molecular imprinting technology and living radical polymerization. In the synthesis, the pyrazosulfuron-ethyl imprinted polymer was obtained by the reversible addition-fragmentation chain transfer (RAFT) precipitation polymerization followed by grafting poly(glyceryl monomethacrylate) (pGMMA) by the post-RAFT polymerization. In this research, we used polyethylene glycol (PEG) as the polymeric porogen in order to increase the porosity of the material which is a new porogen application in the precipitation polymerization. The imprinted polymer has selectivity for the template and ability of humic acids exclusion which has shown the merits of molecularly imprinted polymers and restricted access materials. An online solid-phase extraction/HPLC method for the analysis of three sulfonylurea residues in soil samples has been developed and validated. The recovery of 81-99% in the spiked levels of 40-200 μg kg(-1) was obtained and the limit of detection (LOD) and limit of quantification (LOQ) were less than 4.8 and 15.9 μg kg(-1) respectively. The results demonstrated that this bifunctional material can be used for the efficient pyrazosulfuron-ethyl extraction in the sulfonylurea residue analysis from environmental samples. PMID:23953454

  6. High-Density IgE Recognition of the Major Grass Pollen Allergen Phl p 1 Revealed with Single-Chain IgE Antibody Fragments Obtained by Combinatorial Cloning

    PubMed Central

    Madritsch, Christoph; Gadermaier, Elisabeth; Roder, Uwe W.; Lupinek, Christian; Valenta, Rudolf; Flicker, Sabine

    2015-01-01

    The timothy grass pollen allergen Phl p 1 belongs to the group 1 of highly cross-reactive grass pollen allergens with a molecular mass of ~25–30 kDa. Group 1 allergens are recognized by >95% of grass pollen allergic patients. We investigated the IgE recognition of Phl p 1 using allergen-specific IgE-derived single-chain variable Ab fragments (IgE-ScFvs) isolated from a combinatorial library constructed from PBMCs of a grass pollen–allergic patient. IgE-ScFvs reacted with recombinant Phl p 1 and natural group 1 grass pollen allergens. Using synthetic Phl p 1–derived peptides, the binding sites of two ScFvs were mapped to the N terminus of the allergen. In surface plasmon resonance experiments they showed comparable high-affinity binding to Phl p 1 as a complete human IgE-derived Ab recognizing the allergens’ C terminus. In a set of surface plasmon resonance experiments simultaneous allergen recognition of all three binders was demonstrated. Even in the presence of the three binders, allergic patients’ polyclonal IgE reacted with Phl p 1, indicating high-density IgE recognition of the Phl p 1 allergen. Our results show that multiple IgE Abs can bind with high density to Phl p 1, which may explain the high allergenic activity and sensitizing capacity of this allergen. PMID:25637023

  7. 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

  8. 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. PMID:17010465

  9. 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

  10. 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

  11. 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.

  12. View Invariant Gait Recognition

    NASA Astrophysics Data System (ADS)

    Seely, Richard D.; Goffredo, Michela; Carter, John N.; Nixon, Mark S.

    Recognition by gait is of particular interest since it is the biometric that is available at the lowest resolution, or when other biometrics are (intentionally) obscured. Gait as a biometric has now shown increasing recognition capability. There are many approaches and these show that recognition can achieve excellent performance on current large databases. The majority of these approaches are planar 2D, largely since the early large databases featured subjects walking in a plane normal to the camera view. To extend deployment capability, we need viewpoint invariant gait biometrics. We describe approaches where viewpoint invariance is achieved by 3D approaches or in 2D. In the first group, the identification relies on parameters extracted from the 3D body deformation during walking. These methods use several video cameras and the 3D reconstruction is achieved after a camera calibration process. On the other hand, the 2D gait biometric approaches use a single camera, usually positioned perpendicular to the subject’s walking direction. Because in real surveillance scenarios a system that operates in an unconstrained environment is necessary, many of the recent gait analysis approaches are orientated toward view-invariant gait recognition.

  13. Single-chain antibody-fragment M6P-1 possesses a mannose 6-phosphate monosaccharide-specific binding pocket that distinguishes N-glycan phosphorylation in a branch-specific manner†.

    PubMed

    Blackler, Ryan J; Evans, Dylan W; Smith, David F; Cummings, Richard D; Brooks, Cory L; Braulke, Thomas; Liu, Xinyu; Evans, Stephen V; Müller-Loennies, Sven

    2016-02-01

    The acquisition of mannose 6-phosphate (Man6P) on N-linked glycans of lysosomal enzymes is a structural requirement for their transport from the Golgi apparatus to lysosomes mediated by the mannose 6-phosphate receptors, 300 kDa cation-independent mannose 6-phosphate receptor (MPR300) and 46 kDa cation-dependent mannose 6-phosphate receptor (MPR46). Here we report that the single-chain variable domain (scFv) M6P-1 is a unique antibody fragment with specificity for Man6P monosaccharide that, through an array-screening approach against a number of phosphorylated N-glycans, is shown to bind mono- and diphosphorylated Man6 and Man7 glycans that contain terminal αMan6P(1 → 2)αMan(1 → 3)αMan. In contrast to MPR300, scFv M6P-1 does not bind phosphodiesters, monophosphorylated Man8 or mono- or diphosphorylated Man9 structures. Single crystal X-ray diffraction analysis to 2.7 Å resolution of Fv M6P-1 in complex with Man6P reveals that specificity and affinity is achieved via multiple hydrogen bonds to the mannose ring and two salt bridges to the phosphate moiety. In common with both MPRs, loss of binding was observed for scFv M6P-1 at pH values below the second pKa of Man6P (pKa = 6.1). The structures of Fv M6P-1 and the MPRs suggest that the change of the ionization state of Man6P is the main driving force for the loss of binding at acidic lysosomal pH (e.g. lysosome pH ∼ 4.6), which provides justification for the evolution of a lysosomal enzyme transport pathway based on Man6P recognition. PMID:26503547

  14. A strategy for high-level expression of a single-chain variable fragment against TNFα by subcloning antibody variable regions from the phage display vector pCANTAB 5E into pBV220.

    PubMed

    Yang, Tao; Yang, Lijun; Chai, Weiran; Li, Renke; Xie, Jun; Niu, Bo

    2011-03-01

    A phage display single-chain variable fragment (scFv) library against TNFα was constructed using a recombinant phage antibody system (RPAS). The cloned scFv gene was introduced into the phage display vector pCANTAB 5E and expressed in Escherichia coli (E. coli) with a yield of up to 0.15 mg/l of total protein. With the attempt to improve the expression level of TNF-scFv, a strategy was established for subcloning the scFv gene from pCANTAB 5E into the plasmid pBV220. Under the control of a highly efficient tandem P(R)P(L) promoter system, scFv production was increased to 30% of total protein as inclusion bodies. After extraction from the cell pellet by sonication, the inclusion bodies were solubilized and denatured in the presence of 8M urea. Purification of denatured scFv was performed using nickel column chromatography followed by renaturation. The purity and activity of the refolded scFv were confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), Western blotting and by an enzyme-linked immunoabsorbent assay (ELISA). The results reveal that the overall yield of bioactive TNF-scFv from E. coli flask cultures was more than 45 mg/l culture medium and 15 mg/g wet weight cells. The renatured scFv exhibited binding activity similarly to soluble scFv. In conclusion we developed a method to over-express TNF-scFv, which have biological function after purification and renaturation. PMID:20951213

  15. 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. PMID:26297993

  16. Perturbative fragmentation

    SciTech Connect

    Kopeliovich, B. Z.; Pirner, H.-J.; Potashnikova, I. K.; Schmidt, Ivan; Tarasov, A. V.

    2008-03-01

    The Berger model of perturbative fragmentation of quarks to pions is improved by providing an absolute normalization and keeping all terms in a (1-z) expansion, which makes the calculation valid at all values of fractional pion momentum z. We also replace the nonrelativistic wave function of a loosely bound pion by the more realistic procedure of projecting to the light-cone pion wave function, which in turn is taken from well known models. The full calculation does not confirm the (1-z){sup 2} behavior of the fragmentation function (FF) predicted in [E. L. Berger, Z. Phys. C 4, 289 (1980); Phys. Lett. 89B, 241 (1980] for z>0.5, and only works at very large z>0.95, where it is in reasonable agreement with phenomenological FFs. Otherwise, we observe quite a different z-dependence which grossly underestimates data at smaller z. The disagreement is reduced after the addition of pions from decays of light vector mesons, but still remains considerable. The process dependent higher twist terms are also calculated exactly and found to be important at large z and/or p{sub T}.

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    Galakhov, D.; Mironov, A.; Morozov, A.

    2015-03-01

    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.

  19. 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.

  20. The relation between the waveguide invariant and array invariant.

    PubMed

    Song, H C; Cho, Chomgun

    2015-08-01

    The waveguide invariant β is based on the dependence of group speed on phase speed and summarizes the robust interference phenomenon in the range-frequency plane. Over the last decade the elegant approach has been utilized for various applications including passive source ranging. Separately, the array invariant approach [Lee and Makris, J. Acoust. Soc. Am. 119, 336-351 (2006)] has been proposed for a robust source-range estimator from beam-time intensity data using either a horizontal or vertical array. In this paper, it is shown that the array invariant can be derived from the waveguide invariant theory assuming β=1. PMID:26328705

  1. Aggregation of beta-amyloid fragments.

    PubMed

    Meinke, Jan H; Hansmann, Ulrich H E

    2007-01-01

    The authors study the folding and aggregation of six chains of the beta-amyloid fragment 16-22 using Monte Carlo simulations. While the isolated fragment prefers a helical form at room temperature, in the system of six interacting fragments one observes both parallel and antiparallel beta sheets below a crossover temperature T(x) approximately equal to 420 K. The antiparallel sheets have lower energy and are therefore more stable. Above the nucleation temperature the aggregate quickly dissolves into widely separated, weakly interacting chains. PMID:17212510

  2. 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.

  3. 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.

  4. The algebraic Bethe ansatz for scalar products in SU(3)-invariant integrable models

    NASA Astrophysics Data System (ADS)

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

    2012-10-01

    We study SU(3)-invariant integrable models solvable by a nested algebraic Bethe ansatz. We obtain a determinant representation for the particular case of scalar products of Bethe vectors. This representation can be used for the calculation of form factors and correlation functions of the XXX SU(3)-invariant Heisenberg chain.

  5. 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.

  6. Tractors, mass, and Weyl invariance

    NASA Astrophysics Data System (ADS)

    Gover, A. R.; Shaukat, A.; Waldron, A.

    2009-05-01

    Deser and Nepomechie established a relationship between masslessness and rigid conformal invariance by coupling to a background metric and demanding local Weyl invariance, a method which applies neither to massive theories nor theories which rely upon gauge invariances for masslessness. We extend this method to describe massive and gauge invariant theories using Weyl invariance. The key idea is to introduce a new scalar field which is constant when evaluated at the scale corresponding to the metric of physical interest. This technique relies on being able to efficiently construct Weyl invariant theories. This is achieved using tractor calculus—a mathematical machinery designed for the study of conformal geometry. From a physics standpoint, this amounts to arranging fields in multiplets with respect to the conformal group but with novel Weyl transformation laws. Our approach gives a mechanism for generating masses from Weyl weights. Breitenlohner-Freedman stability bounds for Anti-de Sitter theories arise naturally as do direct derivations of the novel Weyl invariant theories given by Deser and Nepomechie. In constant curvature spaces, partially massless theories—which rely on the interplay between mass and gauge invariance—are also generated by our method. Another simple consequence is conformal invariance of the maximal depth partially massless theories. Detailed examples for spins s⩽2 are given including tractor and component actions, on-shell and off-shell approaches and gauge invariances. For all spins s⩾2 we give tractor equations of motion unifying massive, massless, and partially massless theories.

  7. Isotope Labeling Study of Retinal Chromophore Fragmentation.

    PubMed

    Musbat, Lihi; Nihamkin, Maria; Ytzhak, Shany; Hirshfeld, Amiram; Friedman, Noga; Dilger, Jonathan M; Sheves, Mordechai; Toker, Yoni

    2016-04-28

    Previous studies have shown that the gas-phase fragmentation of the retinal chromophore after S0-S1 photoexcitation results in a prominent fragment of mass 248 which cannot be explained by the cleavage of any single bond along the polyene chain. It was therefore theorized that the fragmentation mechanism involves a series of isomerizations and cyclization processes, and two mechanisms for these processes were suggested. Here we used isotope labeling MS-MS to provide conclusive support for the fragmentation mechanism suggested by Coughlan et al. (J. Phys. Chem. Lett. 2014, 5, 3195). PMID:27046667

  8. "Diabodies": small bivalent and bispecific antibody fragments.

    PubMed Central

    Holliger, P; Prospero, T; Winter, G

    1993-01-01

    Bivalent and bispecific antibodies and their fragments have immense potential for practical application. Here we describe the design of small antibody fragments with two antigen-binding sites. The fragments comprise a heavy-chain variable domain (VH) connected to a light-chain variable domain (VL) on the same polypeptide chain (VH-VL). By using a linker that is too short to allow pairing between the two domains on the same chain, the domains are forced to pair with the complementary domains of another chain and create two antigen-binding sites. As indicated by a computer graphic model of the dimers, the two pairs of domains can pack together with the antigen-binding sites pointing in opposite directions. The dimeric antibody fragments, or "diabodies," can be designed for bivalent or bispecific interactions. Starting from the monoclonal antibodies NQ11.7.22 (NQ11) and D1.3 directed against the hapten phenyloxazolone and hen egg lysozyme, respectively, we built bivalent fragments (VHNQ11-VLNQ11)2 and (VHD1.3-VLD1.3)2 and bispecific fragments VHNQ11-VLD1.3 and VHD1.3-VLNQ11. The fragments were expressed by secretion from bacteria and shown to bind specifically to the hapten and/or antigen. Those with 5- and 15-residue linkers had similar binding affinities to the parent antibodies, but a fragment with the VH domain joined directly to the VL domain was found to have slower dissociation kinetics and an improved affinity for hapten. Diabodies offer a ready means of constructing small bivalent and bispecific antibody fragments in bacteria. Images Fig. 1 Fig. 3 PMID:8341653

  9. The scale invariant generator technique for quantifying anisotropic scale invariance

    NASA Astrophysics Data System (ADS)

    Lewis, G. M.; Lovejoy, S.; Schertzer, D.; Pecknold, S.

    1999-11-01

    Scale invariance is rapidly becoming a new paradigm for geophysics. However, little attention has been paid to the anisotropy that is invariably present in geophysical fields in the form of differential stratification and rotation, texture and morphology. In order to account for scaling anisotropy, the formalism of generalized scale invariance (GSI) was developed. Until now there has existed only a single fairly ad hoc GSI analysis technique valid for studying differential rotation. In this paper, we use a two-dimensional representation of the linear approximation to generalized scale invariance, to obtain a much improved technique for quantifying anisotropic scale invariance called the scale invariant generator technique (SIG). The accuracy of the technique is tested using anisotropic multifractal simulations and error estimates are provided for the geophysically relevant range of parameters. It is found that the technique yields reasonable estimates for simulations with a diversity of anisotropic and statistical characteristics. The scale invariant generator technique can profitably be applied to the scale invariant study of vertical/horizontal and space/time cross-sections of geophysical fields as well as to the study of the texture/morphology of fields.

  10. 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

  11. 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.

  12. 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…

  13. Entanglements in polymer networks: two-state invariant

    NASA Astrophysics Data System (ADS)

    Müller-Nedebock, Kristian

    2001-03-01

    At the time of crosslinking of polymer chains, entanglements of these chains become permanent features of the resulting network. In a statistical physics formulation these constraints on the polymers can be dealt with by inclusion of invariants for the entangled states of chains. Analytical results are presented based upon an extension of a variational formalism for mechanical properties of entangled gels with a two-state invariant by Edwards and Müller-Nedebock (J. Phys. A: Math. Gen.32 3301 (1999)). Apart from showing Mooney-Rivlin-like behaviour of the reduced stress the theory is applied to olympic gels and discussed in the context of the limitations due to the approximations in this approach.

  14. 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.

  15. 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

  16. Differential invariants and operators of invariant differentiation of the projectable action of Lie groups

    NASA Astrophysics Data System (ADS)

    Goncharovskii, M. M.; Shirokov, I. V.

    2015-05-01

    We describe the relation between operators of invariant differentiation and invariant operators on orbits of Lie group actions. We propose a new effective method for finding differential invariants and operators of invariant differentiation and present examples.

  17. 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

  18. 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.

  19. 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

  20. Impact fragmentation of aluminum reactive materials

    NASA Astrophysics Data System (ADS)

    Hooper, Joseph P.

    2012-08-01

    We report the fragmentation of brittle, granular aluminum spheres following high velocity impact (0.5-2.0 km/s) on thin steel plates. These spheres, machined from isostatically pressed aluminum powder, represent a prototypical metallic reactive material. The fragments generated by the impacts are collected in a soft-catch apparatus and analyzed down to a length scale of 44μm. With increasing velocity, there is a transition from an exponential Poisson-process fragment distribution with a characteristic length scale to a power-law behavior indicative of scale-invariance. A normalized power-law distribution with a finite size cutoff is introduced and used to analyze the number and mass distributions of the recovered fragments. At high impact velocities, the power-law behavior dominates the distribution and the power-law exponent is identical to the universal value for brittle fragmentation discussed in recent works. The length scale at which the power-law behavior decays is consistent with the idea that the length of side microbranches or damage zones from primary cracks is governing this cutoff. The transition in fragment distribution at high strain-rates also implies a significant increase in small fragments that can rapidly combust in an ambient atmosphere.

  1. Orthosymplectically invariant functions in superspace

    SciTech Connect

    Coulembier, K.; De Bie, H.; Sommen, F.

    2010-08-15

    The notion of spherically symmetric superfunctions as functions invariant under the orthosymplectic group is introduced. This leads to dimensional reduction theorems for differentiation and integration in superspace. These spherically symmetric functions can be used to solve orthosymplectically invariant Schroedinger equations in superspace, such as the (an)harmonic oscillator or the Kepler problem. Finally, the obtained machinery is used to prove the Funk-Hecke theorem and Bochner's relations in superspace.

  2. 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.

  3. Rotation invariant moments and transforms for geometrically invariant image watermarking

    NASA Astrophysics Data System (ADS)

    Singh, Chandan; Ranade, Sukhjeet K.

    2013-01-01

    We present invariant image watermarking based on a recently introduced set of polar harmonic transforms and angular radial transforms and their comparative analysis with state-of-art approaches based on Zernike moments and pseudo-Zernike moments (ZMs/PZMs). Similar to ZMs/PZMs, these transforms provide rotation invariance and resilience to noise while mitigating inherent limitations like numerical instability and computational cost at high order of moments. These characteristics motivate us to design invariant transform-based invariant image watermarking schemes that can withstand various intentional or unintentional attacks, handle large bitcarriers, and work in a limited computing environment. A comparative performance evaluation of watermarking systems regarding critical parameters like visual imperceptibility, embedding capacity, and watermark robustness against geometric transformations, common signal processing distortions, and Stirmark attacks is performed along with the empirical analysis of various inherent properties of transforms and moments such as magnitude invariance, reconstruction capabilities, and computational complexity to investigate relationships between the performance of watermarking schemes and inherent properties of transforms.

  4. 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

  5. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and amplification refractory mutation system (ARMS) analyses of medicinally used Rheum species and their application for identification of Rhei Rhizoma.

    PubMed

    Yang, Dong-Ye; Fushimi, Hirotoshi; Cai, Shao-Qing; Komatsu, Katsuko

    2004-05-01

    Previously, we have determined marker nucleotides on the chloroplast matK gene to identify Rheum palmatum, R. tanguticum and R. officinale used as Rhei Rhizoma officially. In the present study, we further developed a convenient and efficient identification method on the basis of marker nucleotides with Amplification Refractory Mutation System analysis. On the basis of the nucleotide substitutions at positions 367 and 937 among the three species on the matK gene, at each position two kinds of reverse primers with complementary 3'-terminal nucleotides were designed. Upon PCR amplification using three sets of primers and template DNA from each species, one or two fragments (202 bp or/and 770 bp) were detected. As the resultant three fragment profiles were species-specific, the procedure enabled us to classify the botanic origins of 22 drug samples of Rhei Rhizoma. PMID:15133241

  6. Invariants of triangular Lie algebras

    NASA Astrophysics Data System (ADS)

    Boyko, Vyacheslav; Patera, Jiri; Popovych, Roman

    2007-07-01

    Triangular Lie algebras are the Lie algebras which can be faithfully represented by triangular matrices of any finite size over the real/complex number field. In the paper invariants ('generalized Casimir operators') are found for three classes of Lie algebras, namely those which are either strictly or non-strictly triangular, and for so-called special upper triangular Lie algebras. Algebraic algorithm of Boyko et al (2006 J. Phys. A: Math. Gen.39 5749 (Preprint math-ph/0602046)), developed further in Boyko et al (2007 J. Phys. A: Math. Theor.40 113 (Preprint math-ph/0606045)), is used to determine the invariants. A conjecture of Tremblay and Winternitz (2001 J. Phys. A: Math. Gen.34 9085), concerning the number of independent invariants and their form, is corroborated.

  7. Abelian link invariants and homology

    SciTech Connect

    Guadagnini, Enore; Mancarella, Francesco

    2010-06-15

    We consider the link invariants defined by the quantum Chern-Simons field theory with compact gauge group U(1) in a closed oriented 3-manifold M. The relation of the Abelian link invariants with the homology group of the complement of the links is discussed. We prove that, when M is a homology sphere or when a link--in a generic manifold M--is homologically trivial, the associated observables coincide with the observables of the sphere S{sup 3}. Finally, we show that the U(1) Reshetikhin-Turaev surgery invariant of the manifold M is not a function of the homology group only, nor a function of the homotopy type of M alone.

  8. Synthesis and crystal structures of the new metal-rich ternary borides Ni{sub 12}AlB{sub 8}, Ni{sub 12}GaB{sub 8} and Ni{sub 10.6}Ga{sub 0.4}B{sub 6}-examples for the first B{sub 5} zig-zag chain fragment

    SciTech Connect

    Ade, Martin; Kotzott, Dominik; Hillebrecht, Harald

    2010-08-15

    Single crystals of the new borides Ni{sub 12}AlB{sub 8}, and Ni{sub 10.6}Ga{sub 0.4}B{sub 6} were synthesized from the elements and characterized by XRD and EDXS measurements. The crystal structures were refined on the basis of single crystal data. Ni{sub 12}AlB{sub 8} (oC252, Cmce, a=10.527(2), b=14.527(2), c=14.554(2) A, Z=12, 1350 reflections, 127 parameters, R{sub 1}(F)=0.0284, wR{sub 2}(F{sup 2})=0.0590) represents a new structure type with isolated B atoms and B{sub 5} fragments of a B-B zig-zag chain. Because the pseudotetragonal metric crystals are usually twinned. Ni{sub 10.6}Ga{sub 0.4}B{sub 6} (oP68, Pnma, a=12.305(2), b=2.9488(6), c=16.914(3) A, Z=4, 1386 reflections, 86 parameters, R{sub 1}(F)=0.0394, wR{sub 2}(F{sup 2})=0.104) is closely related to binary Ni borides. The structure contains B-B zig-zag chains and isolated B atoms. Ni{sub 12}GaB{sub 8} is isotypical to the Al-compound (a=10.569(4), b=14.527(4) and c=14.557(5) A). - Graphical abstract: Pentameric B{sub 5}-units are longest fragments of a B-B zig-zag chain ever characterized in a boride. They are found in the structures of Ni{sub 12}AlB{sub 8} and Ni{sub 12}GaB{sub 8}. The compounds are formed on annealing boron-rich {tau}-borides like Ni{sub 20}AlB{sub 14}.

  9. 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

  10. Bak-Sneppen Type Models and Coagulation-Fragmentation Processes

    NASA Astrophysics Data System (ADS)

    Grinfeld, M.

    2008-09-01

    We suggest a construction that allows us to bring methods of denumerable Markov chain theory and coagulation-fragmentation processes to bear on the question of locating the threshold in Bak-Sneppen type models.

  11. 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.

  12. Link invariants of electromagnetic fields.

    PubMed

    von Bodecker, Hanno; Hornig, Gunnar

    2004-01-23

    The cross-helicity integral is known in fluid dynamics and plasma physics as a topological invariant which measures the mutual linkage of two divergence-free vector fields, e.g., magnetic fields, on a three-dimensional domain. Generalizing this concept, a new topological invariant is found which measures the mutual linkage of three closed two-forms, e.g., electromagnetic fields, on a four-dimensional domain. The integral is shown to detect a separation of the cross helicity between two of the fields with the help of the third field. It can be related to the triple linking number known in knot theory. Furthermore, it is shown that the well-known three-dimensional cross helicity and the new four-dimensional invariant are the first two examples of a series of topological invariants which are defined by n-1 field strengths F=dA on a simply connected n-dimensional manifold M(n). PMID:14753856

  13. 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.

  14. Measuring polynomial invariants of multiparty quantum states

    SciTech Connect

    Leifer, M.S.; Linden, N.; Winter, A.

    2004-05-01

    We present networks for directly estimating the polynomial invariants of multiparty quantum states under local transformations. The structure of these networks is closely related to the structure of the invariants themselves and this lends a physical interpretation to these otherwise abstract mathematical quantities. Specifically, our networks estimate the invariants under local unitary (LU) transformations and under stochastic local operations and classical communication (SLOCC). Our networks can estimate the LU invariants for multiparty states, where each party can have a Hilbert space of arbitrary dimension and the SLOCC invariants for multiqubit states. We analyze the statistical efficiency of our networks compared to methods based on estimating the state coefficients and calculating the invariants.

  15. 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.

  16. 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.

  17. Rotation Invariant Vortices for Flow Visualization.

    PubMed

    Günther, Tobias; Schulze, Maik; Theisel, Holger

    2016-01-01

    We propose a new class of vortex definitions for flows that are induced by rotating mechanical parts, such as stirring devices, helicopters, hydrocyclones, centrifugal pumps, or ventilators. Instead of a Galilean invariance, we enforce a rotation invariance, i.e., the invariance of a vortex under a uniform-speed rotation of the underlying coordinate system around a fixed axis. We provide a general approach to transform a Galilean invariant vortex concept to a rotation invariant one by simply adding a closed form matrix to the Jacobian. In particular, we present rotation invariant versions of the well-known Sujudi-Haimes, Lambda-2, and Q vortex criteria. We apply them to a number of artificial and real rotating flows, showing that for these cases rotation invariant vortices give better results than their Galilean invariant counterparts. PMID:26390472

  18. 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

  19. 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

  20. 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

  1. Universality of fragment shapes

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    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.

  2. SLOCC invariants for multipartite mixed states

    NASA Astrophysics Data System (ADS)

    Jing, Naihuan; Li, Ming; Li-Jost, Xianqing; Zhang, Tinggui; Fei, Shao-Ming

    2014-05-01

    We construct a nontrivial set of invariants for any multipartite mixed states under the stochastic local operations and classical communication symmetry. These invariants are given by hyperdeterminants and independent of basis change. In particular, a family of d2 invariants for arbitrary d-dimensional even partite mixed states are explicitly given.

  3. Measuring Scale Invariance between and within Subjects.

    ERIC Educational Resources Information Center

    Benson, Jeri; Hocevar, Dennis

    The present paper represents a demonstration of how LISREL V can be used to investigate scale invariance (1) across time (its relationship to test-retest reliability), and (2) across groups. Five criteria were established to test scale invariance across time and four criteria were established to test scale invariance across groups. Using the…

  4. Supergravity with broken Lorentz invariance

    NASA Astrophysics Data System (ADS)

    Marakulin, A. O.; Sibiryakov, S. M.

    Incompatibility of the principles of quantum field theory with general relativity is one of the most important problems in modern theoretical physics. A potential way out of this situation consists in restricting the domain of validity of some basic postulates of general relativity and abandoning them at high energy scales. A promising approach to quantization of gravity based on abandoning the Lorentz invariance has been proposed by Horava. The low-energy limit of the Horava theory, called khrono-metric model, presents a special case of the Einstein-aether gravity. In the latter model violation of the Lorentz invariance is described by the time-like vector field um with unit norm (umum = -1) called aether that minimally couples to the Einstein-Hilbert action for gravity.

  5. 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.

  6. Geometry-invariant resonant cavities

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    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.

  7. 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

  8. 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.

  9. 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.

  10. Permutation-invariant quantum codes

    NASA Astrophysics Data System (ADS)

    Ouyang, Yingkai

    2014-12-01

    A quantum code is a subspace of a Hilbert space of a physical system chosen to be correctable against a given class of errors, where information can be encoded. Ideally, the quantum code lies within the ground space of the physical system. When the physical model is the Heisenberg ferromagnet in the absence of an external magnetic field, the corresponding ground space contains all permutation-invariant states. We use techniques from combinatorics and operator theory to construct families of permutation-invariant quantum codes. These codes have length proportional to t2; one family of codes perfectly corrects arbitrary weight t errors, while the other family of codes approximately correct t spontaneous decay errors. The analysis of our codes' performance with respect to spontaneous decay errors utilizes elementary matrix analysis, where we revisit and extend the quantum error correction criterion of Knill and Laflamme, and Leung, Chuang, Nielsen and Yamamoto.

  11. Invariance of the Noether charge

    NASA Astrophysics Data System (ADS)

    Silagadze, Z. K.

    2016-01-01

    Surprisingly, an interesting property of the Noether charge that it is by itself invariant under the corresponding symmetry transformation is never discussed in quantum field theory or classical mechanics textbooks we have checked. This property is also almost never mentioned in articles devoted to Noether’s theorem. Nevertheless, to prove this property in the context of Lagrangian formalism is not quite trivial and the proof, outlined in this article, can constitute an useful and interesting exercise for students.

  12. 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.

  13. 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

  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. Inflationary quasiscale-invariant attractors

    NASA Astrophysics Data System (ADS)

    Rinaldi, Massimiliano; Vanzo, Luciano; Zerbini, Sergio; Venturi, Giovanni

    2016-01-01

    In a series of recent papers Kallosh, Linde, and collaborators provide a unified description of single-field inflation with several types of potentials ranging from power law to supergravity, in terms of just one parameter α . These so-called α attractors predict a spectral index ns and a tensor-to-scalar ratio r , which are fully compatible with the latest Planck data. The only common feature of all α attractors is a noncanonical kinetic term with a pole, and a potential analytic around the pole. In this paper, starting from the same Einstein frame with a noncanonical scalar kinetic energy, we explore the case of nonanalytic potentials. We find the functional form that corresponds to quasiscale-invariant gravitational models in the Jordan frame characterized by a universal relation between r and ns that fits the observational data but is clearly distinct from the one of the α attractors. It is known that the breaking of the exact classical scale invariance in the Jordan frame can be attributed to one-loop corrections. Therefore we conclude that there exists a class of nonanalytic potentials in the noncanonical Einstein frame that is physically equivalent to a class of models in the Jordan frame, with scale invariance softly broken by one-loop quantum corrections.

  16. Conformal Invariance of Graphene Sheets.

    PubMed

    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

  17. 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.

  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. Production of antibody fragments in Escherichia coli.

    PubMed

    Katsuda, Tomohisa; Sonoda, Hiroyuki; Kumada, Yoichi; Yamaji, Hideki

    2012-01-01

    Escherichia coli is a host widely used in the industrial production of recombinant proteins. However, the expression of heterologous proteins in E. coli often encounters the formation of inclusion bodies, which are insoluble and nonfunctional protein aggregates. For the successful production of antibody fragments, which includes single-chain variable fragments (scFvs), we describe here the modification of linker, signal, and Shine-Dalgarno (SD) sequences, the coexpression of cytoplasmic and periplasmic chaperones, and a method for fed-batch cultivation with exponential feed. PMID:22907360

  20. Facile Synthesis of Thiol-terminated Poly(styrene-ran-vinyl phenol) (PSVPh) Copolymers via Reversible Addition-Fragmentation Chain Transfer (RAFT) Polymerization and Their Use in the Synthesis of Gold Nanoparticles with Controllable Hydrophilicity

    SciTech Connect

    Lee, Chang-Uk; Roy, Debashish; Dadmun, Mark D

    2010-01-01

    A facile approach to prepare thiol-terminated poly(styrene-ran-vinyl phenol) (PSVPh) copolymers and PSVPh-coated gold nanoparticles is reported with the goal of creating stabilizing ligands for nanoparticles with controlled hydrophilicity. Dithioester-terminated poly(styrene-ran-acetoxystyrene) copolymers were synthesized via RAFT polymerization using cumyl dithiobenzoate as a chain transfer agent. These copolymers were converted to thiol-terminated PSVPh copolymers by a one step hydrazinolysis reaction using hydrazine hydrate to simultaneously convert dithioester-terminal and acetoxypendant groups to thiol-terminal and hydroxyl-pendant groups, respectively. Spectroscopic observations including NMR and IR confirm end- and pendant-group conversion. PSVPh-coated gold nanoparticles were synthesized in the presence of a mixture of thiol-terminated PSVPh and PSVPh copolymers containing disulfides as stabilizing ligands in a water/toluene, two-phase system. The size and size distribution of core gold nanoparticles were determined by TEM and image analysis. The hydrodynamic radius of PSVPh-coated gold nanoparticles was also determined by dynamic light scattering experiment, which confirms the particle analysis by TEM. This procedure provides a facile technique to control the polarity and hydrophilicity of metal nanoparticle surfaces and could prove critical in advancing the control of nanoparticle placement in biological and hierarchically ordered systems, such as diblock copolymers.

  1. Fragments and Coherence

    ERIC Educational Resources Information Center

    Watson, Anne

    2008-01-01

    Can teachers contact the inner coherence of mathematics while working in a context fragmented by always-new objectives, criteria, and initiatives? How, more importantly, can learners experience the inner coherence of mathematics while working in a context fragmented by testing, modular curricular, short-term learning objectives, and lessons that…

  2. Fluctuations in nuclear fragmentation

    SciTech Connect

    Aranda, A.; Dorso, C.O.; Furci, V.; Lopez, J.A.

    1995-12-01

    Heavy ion collisions can be used to study the thermodynamics of hot and dense nuclear matter only if the initial mass and energy fluctuations that lead to fragmentation are of thermal origin and survive the disassembly process. If this is the case, the observed fragment multiplicity should be directly related to those initial fluctuations and to the conditions of temperature and density causing them. The feasibility of this scenario is demonstrated with a molecular dynamics study of the evolution of mass and energy fluctuations, and fluctuations of the phase-space density. First, it is verified that the fluctuations leading to fragmentation are indeed early ones. Second, it is determined that different initial conditions of density and temperature can indeed produce varying final fragment multiplicities. The {rho}-{ital T} plane is mapped to the fragment multiplicity with good precision. This mapping should be easily reproducible with existing experimental data.

  3. About Thinning Invariant Partition Structures

    NASA Astrophysics Data System (ADS)

    Starr, Shannon; Vermesi, Brigitta; Wei, Ang

    2012-08-01

    Bernoulli- p thinning has been well-studied for point processes. Here we consider three other cases: (1) sequences ( X 1, X 2,…); (2) gaps of such sequences ( X n+1- X 1) n∈ℕ; (3) partition structures. For the first case we characterize the distributions which are simultaneously invariant under Bernoulli- p thinning for all p∈(0,1]. Based on this, we make conjectures for the latter two cases, and provide a potential approach for proof. We explain the relation to spin glasses, which is complementary to important previous work of Aizenman and Ruzmaikina, Arguin, and Shkolnikov.

  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. Fractal Fragmentation triggered by meteor impact: The Ries Crater (Germany)

    NASA Astrophysics Data System (ADS)

    Paredes Marino, Joali; Perugini, Diego; Rossi, Stefano; Kueppers, Ulrich

    2015-04-01

    meteor impact occurred as a scale- invariant process. We hypothesize that fractal fragmentation of impact melts occurred shortly after melt generation, as a consequence of the high strain rate suffered by the melts upon radial ejection from the point of the impact. In particular, the high strain rate may have induced the melt to cross the glass transition domain. The result is that the melt does not deform viscously as a high-Schmidt number fluid, but undergoes fragile fragmentation. This hypothesis might explain a series of feature observed on outcrop, such as cuspate terminations of melt fragments (a typical feature of fragile rheology).

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. Stratification of gallstone fragments: the key to more effective fragmentation.

    PubMed

    Alderfer, J T; Laufer, I; Wisniewski, F; Malet, P F

    1992-04-01

    During previous experiments with in vitro fragmentation in a simulated gallbladder, we noticed that stone fragments tended to stratify with the dust and smaller fragments settled to the dependent portion, while the larger fragments settled on top. We reviewed the oral cholecystogram (OCG) of 10 patients examined 6 months following gallstone lithotripsy. In all cases with adequate visualization of stone fragments, the stratification phenomenon was observed. We hypothesized that adjusting the shock wave focus to target on these large fragments would improve the efficiency of fragmentation. To test this hypothesis, we fragmented three matched pairs of gallstones in vitro. For each pair, the stones were removed from the same gallbladder and the stone weights of the two stones were within 10%. The smaller member of each pair was fragmented using the "old method" with the focus on the fragment line. The larger stone was fragmented with the "new method" with the focus in the acoustic shadow deep to the echogenic line caused by the dust and small fragments in the dependent portion. The distribution of fragments was analyzed by passing the fragments through a series of filters. With the new method of targeting, the proportion of fragments less than 1.5 mm was doubled while the fragments greater than 5 mm were eliminated. The new method of targeting, taking into account the stratification of stone fragments, produces more effective fragmentation and should lead to more rapid clearance of fragments from the gallbladder. PMID:10149180

  12. Extended Krein-Adler theorem for the translationally shape invariant potentials

    NASA Astrophysics Data System (ADS)

    Gomez-Ullate, David; Grandati, Yves; Milson, Robert

    2014-04-01

    Considering successive extensions of primary translationally shape invariant potentials, we enlarge the Krein-Adler theorem to mixed chains of state adding and state-deleting Darboux-Bäcklund transformations. It allows us to establish novel bilinear Wronskian and determinantal identities for classical orthogonal polynomials.

  13. 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

  14. 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.

  15. 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

  16. Wilson loop invariants from WN conformal blocks

    NASA Astrophysics Data System (ADS)

    Alekseev, Oleg; Novaes, Fábio

    2015-12-01

    Knot and link polynomials are topological invariants calculated from the expectation value of loop operators in topological field theories. In 3D Chern-Simons theory, these invariants can be found from crossing and braiding matrices of four-point conformal blocks of the boundary 2D CFT. We calculate crossing and braiding matrices for WN conformal blocks with one component in the fundamental representation and another component in a rectangular representation of SU (N), which can be used to obtain HOMFLY knot and link invariants for these cases. We also discuss how our approach can be generalized to invariants in higher-representations of WN algebra.

  17. Invariant length of a cosmic string

    NASA Astrophysics Data System (ADS)

    Anderson, Malcolm R.

    1990-06-01

    The world sheet of a cosmic string is characterized by a function l, invariant under both coordinate and gauge transformations, which can be interpreted as the ``invariant length'' of the string. In flat space, l reduces to the invariant length of Vachaspati and Vilenkin, and gives an upper bound for the actual length of the string, and a lower bound for its energy, as measured by any inertial observer. In curved spacetime, time variations in the invariant length divide naturally into two parts: one due to the tidal tensor at points exterior to the world sheet and one due to the tidal tensor at points on the world sheet itself.

  18. 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.

  19. Fracture tooth fragment reattachment

    PubMed Central

    Maitin, Nitin; Maitin, Shipra Nangalia; 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 is a conservative treatment that should be considered for crown fractures of anterior teeth. This clinical case reports the management of two coronal tooth fracture cases that were successfully treated using tooth fragment reattachment using glass-fibre-reinforced composite post. PMID:23853012

  20. Invariants of DNA genomic signals

    NASA Astrophysics Data System (ADS)

    Cristea, Paul Dan A.

    2005-02-01

    For large scale analysis purposes, the conversion of genomic sequences into digital signals opens the possibility to use powerful signal processing methods for handling genomic information. The study of complex genomic signals reveals large scale features, maintained over the scale of whole chromosomes, that would be difficult to find by using only the symbolic representation. Based on genomic signal methods and on statistical techniques, the paper defines parameters of DNA sequences which are invariant to transformations induced by SNPs, splicing or crossover. Re-orienting concatenated coding regions in the same direction, regularities shared by the genomic material in all exons are revealed, pointing towards the hypothesis of a regular ancestral structure from which the current chromosome structures have evolved. This property is not found in non-nuclear genomic material, e.g., plasmids.

  1. Sequence-invariant state machines

    NASA Astrophysics Data System (ADS)

    Whitaker, Sterling R.; Manjunath, Shamanna K.; Maki, Gary K.

    1991-08-01

    A synthesis method and an MOS VLSI architecture are presented to realize sequential circuits that have the ability to implement any state machine having N states and m inputs, regardless of the actual sequence specified in the flow table. The design method utilizes binary tree structured (BTS) logic to implement regular and dense circuits. The desired state sequence can be hardwired with power supply connections or can be dynamically reallocated if stored in a register. This allows programmable VLSI controllers to be designed with a compact size and performance approaching that of dedicated logic. Results of ICV implementations are reported and an example sequence-invariant state machine is contrasted with implementations based on traditional methods.

  2. Scale invariance in road networks

    NASA Astrophysics Data System (ADS)

    Kalapala, Vamsi; Sanwalani, Vishal; Clauset, Aaron; Moore, Cristopher

    2006-02-01

    We study the topological and geographic structure of the national road networks of the United States, England, and Denmark. By transforming these networks into their dual representation, where roads are vertices and an edge connects two vertices if the corresponding roads ever intersect, we show that they exhibit both topological and geographic scale invariance. That is, we show that for sufficiently large geographic areas, the dual degree distribution follows a power law with exponent 2.2⩽α⩽2.4 , and that journeys, regardless of their length, have a largely identical structure. To explain these properties, we introduce and analyze a simple fractal model of road placement that reproduces the observed structure, and suggests a testable connection between the scaling exponent α and the fractal dimensions governing the placement of roads and intersections.

  3. 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.

  4. 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

  5. Stepwise assembling of polypeptide chain energy distributions.

    PubMed

    Jacchieri, S G

    2001-03-01

    The principles and application of conformational analysis software that makes use of a new algorithm are described. It is known that the existence of a local energy minimum in the energy landscape is in general related to the clustering of polypeptide chain conformations near that energy value or, in other words, to a high density of states. A criterion based on this principle is part of an algorithm employed to select subsets of polypeptide chain conformations in broad energy ranges. Chain fragments belonging to these subsets are then combined to build larger polypeptide chains and the corresponding energy distributions. The functionality of the various operations employed in the process is described and the FORTRAN 77 source code that defines the algorithm is listed. The methodology is illustrated with a calculation involving three chain fragments belonging to the cellular prion protein (PrP(C)). PMID:11219430

  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. Renormalization for breakup of invariant tori

    NASA Astrophysics Data System (ADS)

    Apte, A.; Wurm, A.; Morrison, P. J.

    2005-01-01

    We present renormalization group operators for the breakup of invariant tori with winding numbers that are quadratic irrationals. We find the simple fixed points of these operators and interpret the map pairs with critical invariant tori as critical fixed points. Coordinate transformations on the space of maps relate these fixed points, and also induce conjugacies between the corresponding operators.

  8. Lorentz invariance in loop quantum gravity

    NASA Astrophysics Data System (ADS)

    Pullin, Jorge; Rastgoo, Saeed; Gambini, Rodolfo

    2011-04-01

    We reconsider the argument of Collins, Perez, Sudarsky, Urrutia and Vucetich concerning violations of Lorentz invariance in the context of loop quantum gravity. We show that even if one introduces a lattice that violates Lorentz invariance at the Planck scale, this does not translate itself into large violations that would conflict with experiment.

  9. Gauge theories in terms of invariants

    NASA Astrophysics Data System (ADS)

    Kijowski, J.; Rudolph, G.; Rudolph, M.

    1997-12-01

    We discuss some aspects of our programme of investigating gauge theories (with fermions) in terms of local gauge invariant quantities. In the first part, the functional integral for quantum electrodynamics is discussed within our formulation. Next, the algebra of Grassmann algebra-valued invariants for one-flavour chromodynamics is investigated and, finally, the functional integral for this theory is derived within our framework.

  10. 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…

  11. Invariants of sets of linear varieties.

    PubMed Central

    Huang, R Q

    1990-01-01

    A minimal set of generators of the ring of invariants for four linear subspaces of dimension n in a vector space of dimension 2n is computed, using the symbolic method introduced by Grosshans et al. [Grosshans, F., Rota, G.-C. & Stein, J. A. (1987) Invariant Theory and Superalgebras (Am. Math. Soc., Providence, RI)]. PMID:11607086

  12. Rotation-invariant of Quantum Gross Laplacian

    SciTech Connect

    Horrigue, Samah; Ouerdiane, Habib

    2010-05-04

    In this paper, we prove that the quantum Gross Laplacian denoted DELTA{sub QG} is a rotation-invariant operator. For this purpose, we use the Schwartz-Grothendieck kernel theorem and the characterization theorem of rotation-invariant distributions and operators.

  13. 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…

  14. 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.

  15. Gyro center invariant and associated diamagnetic current

    SciTech Connect

    Aaagren, O.; Moiseenko, V.; Johansson, C.; Savenko, N.

    2005-12-15

    The gyro center radial Clebsch coordinate r{sub 0} is an exact invariant in confining fields where the gyro center is restricted to move on a magnetic flux surface, and r{sub 0} could also be expected to be a useful approximating invariant in other confining magnetic fields. A radial drift invariant I{sub r} generalizes the invariance of r{sub 0} if there are oscillatory gyro center radial displacements off the magnetic surface. Expressions for r{sub 0}(x,v) and I{sub r}(x,v) are obtained for gyrating particles in the drift ordering. An exact energy integral is proven to exist for the first-order drift motion of the gyro center. The gyro center parallel motion is periodic with respect to a certain curve parameter {tau}{sub parallel} (the 'proper time' for the parallel motion) that deviates slightly, due to the slow perpendicular drift, from the ordinary time. A modification of the parallel invariant J{sub parallel} is derived which leads to an exact (not only adiabatic) invariant to first order. By using r{sub 0} in solutions of the Vlasov equation, it is demonstrated that the approximating gyro center invariant r{sub 0} determines the perpendicular plasma diamagnetic current. It is also shown that a fourth stationary motional invariant is required to calculate the parallel plasma current. Several systems with four time independent invariants are identified, and the general solution for straight cylindrical Vlasov equilibria with adiabatic particle motion is determined. A set ({epsilon},{mu},I{sub parallel},I{sub r}) of four invariants is proposed for adiabatic equilibria in general geometry, including systems where single valued flux surfaces may not exist.

  16. Using sorted invariant mass variables to evade combinatorial ambiguities in cascade decays

    NASA Astrophysics Data System (ADS)

    Kim, Doojin; Matchev, Konstantin T.; Park, Myeonghun

    2016-02-01

    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 final state particles fully democratically and consider the sorted set of the invariant masses of all 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.

  17. 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.

  18. Fragment screening: an introduction.

    PubMed

    Leach, Andrew R; Hann, Michael M; Burrows, Jeremy N; Griffen, Ed J

    2006-09-01

    There are clearly many different philosophies associated with adapting fragment screening into mainstream Drug Discovery Lead Generation strategies. Scientists at Astex, for instance, focus entirely on strategies involving use of X-ray crystallography and NMR. However, AstraZeneca uses a number of different fragment screening strategies. One approach is to screen a 2000 compound fragment set (with close to "lead-like" complexity) at 100 microM in parallel with every HTS such that the data are obtained on the entire screening collection at 10 microM plus the extra samples at 100 microM; this provides valuable compound potency data in a concentration range that is usually unexplored. The fragments are then screen-specific "privileged structures" that can be searched for in the rest of the HTS output and other databases as well as having synthesis follow-up. A typical workflow for a fragment screen within AstraZeneca is shown below (Figure 24) and highlights the desirability (particularly when screening >100 microM) for NMR and X-ray information to validate weak hits and give information on how to optimise them. In this chapter, we have provided an introduction to the theoretical and practical issues associated with the use of fragment methods and lead-likeness. Fragment-based approaches are still in an early stage of development and are just one of many interrelated techniques that are now used to identify novel lead compounds for drug development. Fragment based screening has some advantages, but like every other drug hunting strategy will not be universally applicable. There are in particular some practical challenges associated with fragment screening that relate to the generally lower level of potency that such compounds initially possess. Considerable synthetic effort has to be applied for post-fragment screening to build the sort of potency that would be expected to be found from a traditional HTS. However, if there are no low-hanging fruit in a screening

  19. 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

  20. 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.

  1. 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.

  2. Decay and fragmentation in an open Bose-Hubbard chain

    NASA Astrophysics Data System (ADS)

    Kordas, G.; Wimberger, S.; Witthaut, D.

    2013-04-01

    We analyze the decay of ultracold atoms from an optical lattice with loss from a single lattice site. If the initial state is dynamically stable, a suitable amount of dissipation can stabilize a Bose-Einstein condensate, such that it remains coherent even in the presence of strong interactions. A transition between two dynamical phases is observed if the initial state is dynamically unstable. This transition is analyzed here in detail. For strong interactions, the system relaxes to an entangled quantum state with remarkable statistical properties: The atoms bunch in a few “breathers” forming at random positions. Breathers at different positions are coherent, such that they can be used in precision quantum interferometry and other applications.

  3. 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

  4. Prevalence of the prothrombin G20210A mutation in the Irish populations: use of a novel polymerase chain reaction approach.

    PubMed

    Keenan, C; Livingstone, W J; White, B; Mynett-Johnson, L; Cusack, S; Lawler, M; Smith, O P

    2000-10-01

    The prothrombin G20210A polymorphism is associated with a threefold-increased risk of venous thrombosis. There is considerable variation in the reported prevalence of this polymorphism within normal populations, ranging from 0 to 6.5%. The prevalence within the Irish population has not been determined. A restriction fragment length polymorphism (RFLP)-based assay is commonly used for the detection of the prothrombin 20210A allele. This assay does not include a control restriction digest fragment and, consequently, failure of the enzyme activity or lack of addition of enzyme to the sample cannot be distinguished from wild-type prothrombin. We developed a RFLP-based assay, which incorporates an invariant digest site, resulting in the generation of a control digest fragment. Furthermore, we developed a nested polymerase chain reaction (PCR) method for the amplification and digestion of poor-quality or low-concentration DNA. In the Irish population studied, five of 385 (1.29%) were heterozygous and one patient was homozygous for the prothrombin 20210A polymorphism. This is the first reported data on an Irish or Celtic population and suggests that the allele frequency is similar to Anglo-Saxon populations. The nested PCR method successfully amplified and digested 100/100 (100%) of the archived samples; none of these samples could be analyzed by the standard single-round PCR method. In conclusion, nested PCR should be considered in the analysis of archived samples. Single-round PCR is appropriate for recently collected samples; however, an invariant control digest site should be incorporated in RFLP-based assays to validate the integrity of the digestion enzyme and limit the risk of false-negative results. PMID:11085288

  5. Fragmentation efficiencies of peptide ions following low energy collisional activation

    NASA Astrophysics Data System (ADS)

    Summerfield, Scott G.; Gaskell, Simon J.

    1997-11-01

    Low energy fragmentations of protonated peptides in the gas phase are generally attributed to charge-directed processes. The extent and location of peptide backbone fragmentation is accordingly influenced by the extent to which charge is sequestered on amino acid side-chains. We describe systematic studies of the efficiencies of decomposition of peptide ions to assess in particular the influence of the presence of basic amino acid residues and of the protonation state. In a set of analogues containing two arginine, two histidine or two lysine residues, the extent of fragmentation of [M + 2H]2+ ions decreases with increased basicity, reflecting decreased backbone protonation. The collisionally activated dissociation of multiply protonated melittin ions shows an increase in fragmentation efficiency with higher charge state (using activation conditions which are similar for each charge state). For a single charge state, acetylation of primary amine groups increases fragmentation efficiency, consistent with the reduction in basicity of lysine side-chains. Conversion of arginine residues to the less basic dimethylpyrimidylornithine, however, decreases fragmentation efficiency, suggesting more effective sequestering of ionizing protons; the effect may be attributable to a disfavouring of proton-bridged structures but this hypothesis requires further study. Preliminary data for the decompositions of [M- 2H]2- ions derived from peptides containing two acidic residues suggest that the sequestration of charge away from the backbone is again detrimental to efficient fragmentation. Apparently diagnostic cleavages adjacent to aspartic acid residues are observed.

  6. Lactobacillli expressing llama VHH fragments neutralise Lactococcus phages

    PubMed Central

    Hultberg, Anna; Tremblay, Denise M; de Haard, Hans; Verrips, Theo; Moineau, Sylvain; Hammarström, Lennart; Marcotte, Harold

    2007-01-01

    Background Bacteriophages infecting lactic acid bacteria (LAB) are widely acknowledged as the main cause of milk fermentation failures. In this study, we describe the surface-expression as well as the secretion of two functional llama heavy-chain antibody fragments, one binding to the major capsid protein (MCP) and the other to the receptor-binding proteins (RBP) of the lactococcal bacteriophage p2, by lactobacilli in order to neutralise lactococcal phages. Results The antibody fragment VHH5 that is directed against the RBP, was fused to a c-myc tag and expressed in a secreted form by a Lactobacillus strain. The fragment VHH2 that is binding to the MCP, was fused to an E-tag and anchored on the surface of the lactobacilli. Surface expression of VHH2 was confirmed by flow cytometry using an anti-E-tag antibody. Efficient binding of both the VHH2 and the secreted VHH5 fragment to the phage antigens was shown in ELISA. Scanning electron microscopy showed that lactobacilli expressing VHH2 anchored at their surface were able to bind lactococcal phages. A neutralisation assay also confirmed that the secreted VHH5 and the anchored VHH2 fragments prevented the adsorption of lactococcal phages to their host cells. Conclusion Lactobacilli were able to express functional VHH fragments in both a secreted and a cell surface form and reduced phage infection of lactococcal cells. Lactobacilli expressing llama heavy-chain antibody fragments represent a novel way to limit phage infection. PMID:17875214

  7. 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.

  8. Experimental breaking of an adiabatic invariant

    NASA Astrophysics Data System (ADS)

    Notte, J.; Fajans, J.; Chu, R.; Wurtele, J. S.

    1993-06-01

    When a cylindrical pure electron plasma is displaced from the center of the trap, it performs a bulk circular orbital motion known as the l=1 diocotron mode. The slow application of a perturbing potential to a patch on the trap wall distorts the orbit into a noncircular closed path. Experiments and a simple theoretical model indicate that the area by the loop is an adiabatic invariant. Detailed studies are made of the breaking of the invariant when perturbations are rapidly applied. When the perturbation is applied with discontinuous time derivatives, the invariant breaking greatly exceeds the predictions of the standard theory for smooth perturbations.

  9. 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

  10. Invariants of the local Clifford group

    SciTech Connect

    Nest, Maarten van den; Dehaene, Jeroen; Moor, Bart de

    2005-02-01

    We study the algebra of complex polynomials which remain invariant under the action of the local Clifford group under conjugation. Within this algebra, we consider the linear spaces of homogeneous polynomials degree by degree and construct bases for these vector spaces for each degree, thereby obtaining a generating set of polynomial invariants. Our approach is based on the description of Clifford operators in terms of linear operations over GF(2). Such a study of polynomial invariants of the local Clifford group is mainly of importance in quantum coding theory, in particular in the classification of binary quantum codes. Some applications in entanglement theory and quantum computing are briefly discussed as well.

  11. 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.

  12. 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.

  13. 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.

  14. Gauge invariance for a whole Abelian model

    SciTech Connect

    Chauca, J.; Doria, R.; Soares, W.

    2012-09-24

    Light invariance is a fundamental principle for physics be done. It generates Maxwell equations, relativity, Lorentz group. However there is still space for a fourth picture be developed which is to include fields with same Lorentz nature. It brings a new room for field theory. It says that light invariance does not work just to connect space and time but it also associates different fields with same nature. Thus for the ((1/2),(1/2)) representation there is a fields family {l_brace}A{sub {mu}I}{r_brace} to be studied. This means that given such fields association one should derive its corresponding gauge theory. This is the effort at this work. Show that there is a whole gauge theory to cover these fields relationships. Considering the abelian case, prove its gauge invariance. It yields the kinetic, massive, trilinear and quadrilinear gauge invariant terms.

  15. New Invariants in the Theory of Knots.

    ERIC Educational Resources Information Center

    Kauffman, Louis H.

    1988-01-01

    A diagrammatic approach to invariants of knots is the focus. Connections with graph theory, physics, and other topics are included, along with an explanation of how proofs of some old conjectures about alternating knots emerge from this work. (MNS)

  16. 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.

  17. 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.

  18. Convecting reference frames and invariant numerical models

    NASA Astrophysics Data System (ADS)

    Bihlo, Alexander; Nave, Jean-Christophe

    2014-09-01

    In the recent paper by Bernardini et al. [1] the discrepancy in the performance of finite difference and spectral models for simulations of flows with a preferential direction of propagation was studied. In a simplified investigation carried out using the viscous Burgers equation the authors attributed the poorer numerical results of finite difference models to a violation of Galilean invariance in the discretization and propose to carry out the computations in a reference frame moving with the bulk velocity of the flow. Here we further discuss this problem and relate it to known results on invariant discretization schemes. Non-invariant and invariant finite difference discretizations of Burgers equation are proposed and compared with the discretization using the remedy proposed by Bernardini et al.

  19. 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.

  20. Genuine multiparticle entanglement of permutationally invariant states

    NASA Astrophysics Data System (ADS)

    Novo, Leonardo; Moroder, Tobias; Gühne, Otfried

    2013-07-01

    We consider the problem of characterizing genuine multiparticle entanglement for permutationally invariant states using the approach of positive partial transpose mixtures. We show that the evaluation of this necessary biseparability criterion scales polynomially with the number of particles. In practice, it can be evaluated easily up to ten qubits and improves existing criteria significantly. Finally, we show that our approach solves the problem of characterizing genuine multiparticle entanglement for permutationally invariant three-qubit states.

  1. From scale invariance to Lorentz symmetry.

    PubMed

    Sibiryakov, Sergey

    2014-06-20

    It is shown that a unitary translationally invariant field theory in 1+1 dimensions, satisfying isotropic scale invariance, standard assumptions about the spectrum of states and operators, and the requirement that signals propagate with finite velocity, possesses an infinite dimensional symmetry given by one or a product of several copies of conformal algebra. In particular, this implies the presence of one or several Lorentz groups acting on the operator algebra of the theory. PMID:24996083

  2. Tests of Lorentz invariance with atomic clocks

    NASA Astrophysics Data System (ADS)

    Mohan, Lakshmi

    Lorentz invariance has been the cornerstone of special relativity. Recent theories have been proposed which suggest violations of Lorentz invariance. Experiments have been conducted using clocks that place the strictest limits on these theories. The thesis focuses on the Mansouri and Sexl formulation and I calculate using this framework the Doppler effect, Compton effect, Maxwell's equations, Hydrogen energy levels and other effects. I conclude the thesis by suggesting a possible method of testing my results using atomic clocks.

  3. 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.

  4. 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

  5. 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.

  6. Antiprotonic helium and CPT invariance

    NASA Astrophysics Data System (ADS)

    Hayano, Ryugo S.; Hori, Masaki; Horváth, Dezso; Widmann, Eberhard

    2007-12-01

    We review recent progress in the laser and microwave spectroscopy of antiprotonic helium atoms (\\barpHe^+ \\equiv \\rme^\\--\\barp - He^{++}) carried out at CERN's Antiproton Decelerator facility (AD). Laser transitions were here induced between Rydberg states (n, ell) and (n ± 1, ell - 1) of \\barpHe^+ (n ~ 40 and ell ≲ n - 1 being the principal and orbital angular momentum quantum numbers of the antiproton orbit). Successive refinements in the experimental techniques improved the fractional precision on the \\barpHe^+ frequencies from 3 parts in 106 to ~1 part in 108. These included a radiofrequency quadrupole decelerator, which reduced the energy of the antiprotons from 5.3 MeV (the energy of the beam emerging from AD) to ~100 keV. This enabled the production of \\barpHe^+ in ultra-low density targets, where collisional effects with other helium atoms are negligible. A continuous wave pulse-amplified dye laser, stabilized against a femtosecond optical frequency comb, was then used to measure the \\barpHe^+ frequencies with ppb-scale precision. This progress in the experimental field was matched by similar advances in computing methods for evaluating the expected transition frequencies in three-body QED calculations. The comparison of experimental (νexp) and theoretical (νth) frequencies for seven transitions in \\barp^4He^+ and five in \\barp^3 He^+ yielded an antiproton-to-electron mass ratio of m_\\bar p/m_{\\rme} = 1836.152\\,674(5) . This agrees with the known proton-to-electron mass ratio at the level of ~2 × 10-9. The experiment also set a limit on any CPT-violating difference between the antiproton and proton charges and masses, (Q_p - |Q_{\\barp}|)/Q_p \\sim (m_p - m_{\\barp})/m_p < 2 \\times 10^{-9} to a 90% confidence level. If on the other hand we assume the validity of the CPT invariance, the m_{\\barp}/m_{\\rme} result can be taken to be equal to mp/me. This can be used as an input to future adjustments of fundamental constants. The hyperfine

  7. Shielding and fragmentation studies.

    PubMed

    Zeitlin, C; Guetersloh, S; Heilbronn, L; Miller, J

    2005-01-01

    Radiation dosimetry for manned spaced missions depends on the ability to adequately describe the process of high-energy ion transport through many materials. Since the types of possible nuclear interactions are many and complex, transport models are used which depend upon a reliable source of experimental data. To expand the heavy ion database used in the models we have been measuring charge-changing cross sections and fragment production cross sections from heavy-ion interactions in various elementa targets. These include materials flown on space missions such as carbon and aluminium, as well as those important in radiation dosimetry such as hydrogen, nitrogen and water. Measuring heavy-ion fragmentation through these targets also gives us the ability to determine the effectiveness of new materials proposed for shielding such as graphite composites and polyethylene hybrids. Measurement without a target present gives an indication of the level of contamination of the primary beam, which is also important in radiobiology experiments. PMID:16604611

  8. 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.

  9. 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.

  10. Electroeluting DNA fragments.

    PubMed

    Zarzosa-Alvarez, Ana L; Sandoval-Cabrera, Antonio; Torres-Huerta, Ana L; Bermudez-Cruz, Rosa M

    2010-01-01

    Purified DNA fragments are used for different purposes in Molecular Biology and they can be prepared by several procedures. Most of them require a previous electrophoresis of the DNA fragments in order to separate the band of interest. Then, this band is excised out from an agarose or acrylamide gel and purified by using either: binding and elution from glass or silica particles, DEAE-cellulose membranes, "crush and soak method", electroelution or very often expensive commercial purification kits. Thus, selecting a method will depend mostly of what is available in the laboratory. The electroelution procedure allows one to purify very clean DNA to be used in a large number of applications (sequencing, radiolabeling, enzymatic restriction, enzymatic modification, cloning etc). This procedure consists in placing DNA band-containing agarose or acrylamide slices into sample wells of the electroeluter, then applying current will make the DNA fragment to leave the agarose and thus be trapped in a cushion salt to be recovered later by ethanol precipitation. PMID:20834225

  11. 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.

  12. Gas-Phase Fragmentation Analysis of Nitro-Fatty Acids

    NASA Astrophysics Data System (ADS)

    Bonacci, Gustavo; Asciutto, Eliana K.; Woodcock, Steven R.; Salvatore, Sonia R.; Freeman, Bruce A.; Schopfer, Francisco J.

    2011-09-01

    Nitro-fatty acids are electrophilic signaling mediators formed in increased amounts during inflammation by nitric oxide and nitrite-dependent redox reactions. A more rigorous characterization of endogenously-generated species requires additional understanding of their gas-phase induced fragmentation. Thus, collision induced dissociation (CID) of nitroalkane and nitroalkene groups in fatty acids were studied in the negative ion mode to provide mass spectrometric tools for their structural characterization. Fragmentation of nitroalkanes occurred mainly through loss of the NO{2/-} anion or neutral loss of HNO2. The CID of nitroalkenes proceeds via a more complex cyclization, followed by fragmentation to nitrile and aldehyde products. Gas-phase fragmentation of nitroalkene functional groups with additional γ or δ unsaturation occurred through a multiple step cyclization reaction process, leading to 5 and 6 member ring heterocyclic products and carbon chain fragmentation. Cyclization products were not obtained during nitroalkane fragmentation, highlighting the role of double bond π electrons during NO{2/-} rearrangements, stabilization and heterocycle formation. The proposed structures, mechanisms and products of fragmentation are supported by analysis of 13C and 15N labeled parent molecules, 6 different nitroalkene positional isomers, 6 nitroalkane positional isomers, accurate mass determinations at high resolution and quantum mechanics calculations. Multiple key diagnostic ion fragments were obtained through this analysis, allowing for the precise placement of double bonds and sites of fatty acid nitration, thus supporting an ability to predict nitro positions in biological samples.

  13. 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.

  14. 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.

  15. Statistical translation invariance protects a topological insulator from interactions

    NASA Astrophysics Data System (ADS)

    Milsted, A.; Seabra, L.; Fulga, I. C.; Beenakker, C. W. J.; Cobanera, E.

    2015-08-01

    We investigate the effect of interactions on the stability of a disordered, two-dimensional topological insulator realized as an array of nanowires or chains of magnetic atoms on a superconducting substrate. The Majorana zero-energy modes present at the ends of the wires overlap, forming a dispersive edge mode with thermal conductance determined by the central charge c of the low-energy effective field theory of the edge. We show numerically that, in the presence of disorder, the c =1 /2 Majorana edge mode remains delocalized up to extremely strong attractive interactions, while repulsive interactions drive a transition to a c =3 /2 edge phase localized by disorder. The absence of localization for strong attractive interactions is explained by a self-duality symmetry of the statistical ensemble of disorder configurations and of the edge interactions, originating from translation invariance on the length scale of the underlying mesoscopic array.

  16. Fragment-based lead design

    NASA Astrophysics Data System (ADS)

    Filz, O. A.; Poroikov, Vladimir V.

    2012-02-01

    State-of-the-art approaches to the fragment-based design of organic compounds with desired properties are considered. The review covers methods, which are used in different steps of the design, such as computational methods for fragment library design, experimental and computational methods for fragment discovery and methods for the generation of structures of organic compounds. Examples are given of drug candidates, which were constructed using the fragment-based approach. The bibliography includes 156 references.

  17. On the statistics of magnetotelluric rotational invariants

    NASA Astrophysics Data System (ADS)

    Chave, Alan D.

    2014-01-01

    The statistical properties of the Swift skew, the phase-sensitive skew and the WAL invariants I1-I7 and Q are examined through analytic derivation of their probability density functions and/or simulation based on a Gaussian model for the magnetotelluric response tensor. The WAL invariants I1-I2 are shown to be distributed as a folded Gaussian, and are statistically well behaved in the sense that all of their moments are defined. The probability density functions for Swift skew, phase-sensitive skew and the WAL invariants I3-I4, I7 and Q are derived analytically or by simulation, and are shown to have no moments of order 2 or more. Since their support is semi-infinite or infinite, they cannot be represented trigonometrically, and hence are inconsistent with a Mohr circle interpretation. By contrast, the WAL invariants I5-I6 are supported on [ - 1, 1], and are inferred to have a beta distribution based on analysis and simulation. Estimation of rotational invariants from data is described using two approaches: as the ratio of magnetotelluric responses that are themselves averages, and as averages of section-by-section estimates of the invariant. Confidence intervals on the former utilize either Fieller's theorem, which is preferred because it is capable of yielding semi-infinite or infinite confidence intervals, or the less accurate delta method. Because section-by-section averages of most of the rotational invariants are drawn from distributions with infinite variance, the classical central limit theorem does not pertain. Instead, their averaging is accomplished using the median in place of the mean for location and an order statistic model to bound the confidence interval of the median. An example using real data demonstrates that the ratio of averages approach has serious systematic bias issues that render the result physically inconsistent, while the average of ratios result is a smooth, physically interpretable function of period, and is the preferred approach.

  18. Discretely disordered photonic bandgap structures: a more accurate invariant measure calculation

    NASA Astrophysics Data System (ADS)

    Kissel, Glen J.

    2009-02-01

    In the one-dimensional optical analog to Anderson localization, a periodically layered medium has one or more parameters randomly disordered. Such a randomized system can be modeled by an infinite product of 2x2 random transfer matrices with the upper Lyapunov exponent of the matrix product identified as the localization factor (inverse localization length) for the model. The theorem of Furstenberg allows us, at least theoretically, to calculate this upper Lyapunov exponent. In Furstenberg's formula we not only integrate with respect to the probability measure of the random matrices, but also with respect to the invariant probability measure of the direction of the vector propagated by the random matrices. This invariant measure is difficult to find analytically, and, as a result, the most successful approach is to determine the invariant measure numerically. A Monte Carlo simulation which uses accumulated bin counts to track the direction of the propagated vector through a long chain of random matrices does a good job of estimating the invariant probability measure, but with a level of uncertainty. A potentially more accurate numerical technique by Froyland and Aihara obtains the invariant measure as a left eigenvector of a large sparse matrix containing probability values determined by the action of the random matrices on input vectors. We first apply these two techniques to a random Fibonacci sequence whose Lyapunov exponent was determined by Viswanath. We then demonstrate these techniques on a quarter-wave stack model with binary discrete disorder in layer thickness, and compare results to the continuously disordered counterpart.

  19. 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.

  20. 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

  1. 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

  2. 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.

  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. Tube Fragmentation of Multiple Materials

    SciTech Connect

    Thornhill, T. F.; Chhabildas, L. C.; Vogler, T. J.

    2006-07-28

    In the current study we are developing an experimental fracture material property test method specific to dynamic fragmentation. This test method allows the study of fracture fragmentation in a reproducible laboratory environment under well-controlled loading conditions. Motion and fragmentation of the specimen are diagnosed using framing camera, VISAR and soft recovery methods. Fragmentation properties of several steels, nitinol, tungsten alloy, copper, aluminum, and titanium have been obtained to date. The values for fragmentation toughness, and failure threshold will be reported, as well as effects in these values as the material strain-rate is varied through changes in wall thickness and impact conditions.

  5. Tube fragmentation of multiple materials.

    SciTech Connect

    Thornhill, Tom Finley, III; Vogler, Tracy John; Chhabildas, Lalit Chandra

    2003-07-01

    In the current study we are developing an experimental fracture material property test method specific to dynamic fragmentation. This test method allows the study of fracture fragmentation in a reproducible laboratory environment under well-controlled loading conditions. Motion and fragmentation of the specimen are diagnosed using framing camera, VISAR and soft recovery methods. Fragmentation properties of several steels, nitinol, tungsten alloy, copper, aluminum, and titanium have been obtained to date. The values for fragmentation toughness, and failure threshold will be reported, as well as effects in these values as the material strain-rate is varied through changes in wall thickness and impact conditions.

  6. 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.

  7. 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

  8. Fragmentation properties of jets produced in proton-antiproton collisions at radical S = 1. 8 TeV

    SciTech Connect

    Hubbard, B. . Dept. of Physics):)

    1989-11-01

    Jet fragmentation properties have been studied in collisions of protons and antiprotons at a center-of-mass energy of 1.8 TeV, using the Collider Detector at Fermilab (CDF). The fractional momentum distribution of charged particles within jets is presented and compared with Monte-Carlo predictions. With increasing di-jet invariant mass from 60 to 200 GeV/c{sup 2} the fragmentation is observed to soften as predicted by scale breaking effects in Quantum Chromodynamics (QCD). The charged multiplicity in the jet core is observed to rise with di-jet invariant mass. 57 refs.

  9. 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…

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 21 CFR 866.5540 - Immunoglobulin G (Fd fragment specific) immunological test system.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 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...

  15. Scaling behavior of fragment shapes.

    PubMed

    Kun, F; Wittel, F K; Herrmann, H J; Kröplin, B H; Måløy, K J

    2006-01-20

    We present an experimental and theoretical study of the shape of fragments generated by explosive and impact loading of closed shells. Based on high speed imaging, we have determined the fragmentation mechanism of shells. Experiments have shown that the fragments vary from completely isotropic to highly anisotropic elongated shapes, depending on the microscopic cracking mechanism of the shell. Anisotropic fragments proved to have a self-affine character described by a scaling exponent. The distribution of fragment shapes exhibits a power-law decay. The robustness of the scaling laws is illustrated by a stochastic hierarchical model of fragmentation. Our results provide a possible improvement of the representation of fragment shapes in models of space debris. PMID:16486594

  16. 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

  17. 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.

  18. Second-Order Invariants and Holography

    NASA Astrophysics Data System (ADS)

    Luongo, Orlando; Bonanno, Luca; Iannone, Gerardo

    2012-12-01

    Motivated by recent works on the role of the holographic principle in cosmology, we relate a class of second-order Ricci invariants to the IR cutoff characterizing the holographic dark energy density. The choice of second-order invariants provides an invariant way to account the problem of causality for the correct cosmological cutoff, since the presence of event horizons is not an a priori assumption. We find that these models work fairly well, by fitting the observational data, through a combined cosmological test with the use of SNeIa, BAO and CMB. This class of models is also able to overcome the fine-tuning and coincidence problems. Finally, to make a comparison with other recent models, we adopt the statistical tests AIC and BIC.

  19. Tests of Lorentz invariance: a 2013 update

    NASA Astrophysics Data System (ADS)

    Liberati, S.

    2013-07-01

    We present an updated review of Lorentz invariance tests in effective field theories (EFTs) in the matter as well as in the gravity sector. After a general discussion of the role of Lorentz invariance and a derivation of its transformations along the so-called von Ignatovski theorem, we present the dynamical frameworks developed within local EFT and the available constraints on the parameters governing the Lorentz breaking effects. In the end, we discuss two specific examples: the OPERA ‘affaire’ and the case of Hořava-Lifshitz gravity. The first case will serve as an example, and a caveat, of the practical application of the general techniques developed for constraining Lorentz invariance violation to a direct observation potentially showing these effects. The second case will show how the application of the same techniques to a specific quantum gravity scenario has far-reaching implications not foreseeable in a purely phenomenological EFT approach.

  20. 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.

  1. Manifestly diffeomorphism invariant classical Exact Renormalization Group

    NASA Astrophysics Data System (ADS)

    Morris, Tim R.; Preston, Anthony W. H.

    2016-06-01

    We construct a manifestly diffeomorphism invariant Wilsonian (Exact) Renor-malization Group for classical gravity, and begin the construction for quantum gravity. We demonstrate that the effective action can be computed without gauge fixing the diffeo-morphism invariance, and also without introducing a background space-time. We compute classical contributions both within a background-independent framework and by perturbing around a fixed background, and verify that the results are equivalent. We derive the exact Ward identities for actions and kernels and verify consistency. We formulate two forms of the flow equation corresponding to the two choices of classical fixed-point: the Gaussian fixed point, and the scale invariant interacting fixed point using curvature-squared terms. We suggest how this programme may completed to a fully quantum construction.

  2. Renormalization group invariant of lepton Yukawa couplings

    NASA Astrophysics Data System (ADS)

    Tsuyuki, Takanao

    2015-04-01

    By using quark Yukawa matrices only, we can construct renormalization invariants that are exact at the one-loop level in the standard model. One of them, Iq, is accidentally consistent with unity, even though quark masses are strongly hierarchical. We calculate a lepton version of the invariant Il for Dirac and Majorana neutrino cases and find that Il can also be close to unity. For the Dirac neutrino and inverted hierarchy case, if the lightest neutrino mass is 3.0 meV to 8.8 meV, an equality Iq=Il can be satisfied. These invariants are not changed even if new particles couple to the standard model particles, as long as those couplings are generation independent.

  3. 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

  4. Standard model with partial gauge invariance

    NASA Astrophysics Data System (ADS)

    Chkareuli, J. L.; Kepuladze, Z.

    2012-03-01

    We argue that an exact gauge invariance may disable some generic features of the Standard Model which could otherwise manifest themselves at high energies. One of them might be related to the spontaneous Lorentz invariance violation (SLIV), which could provide an alternative dynamical approach to QED and Yang-Mills theories with photon and non-Abelian gauge fields appearing as massless Nambu-Goldstone bosons. To see some key features of the new physics expected we propose partial rather than exact gauge invariance in an extended SM framework. This principle applied, in some minimal form, to the weak hypercharge gauge field B μ and its interactions, leads to SLIV with B field components appearing as the massless Nambu-Goldstone modes, and provides a number of distinctive Lorentz breaking effects. Being naturally suppressed at low energies they may become detectable in high energy physics and astrophysics. Some of the most interesting SLIV processes are considered in significant detail.

  5. 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

  6. Blurred image recognition by legendre moment invariants

    PubMed Central

    Zhang, Hui; Shu, Huazhong; Han, Guo-Niu; Coatrieux, Gouenou; Luo, Limin; Coatrieux, Jean-Louis

    2010-01-01

    Processing blurred images is a key problem in many image applications. Existing methods to obtain blur invariants which are invariant with respect to centrally symmetric blur are based on geometric moments or complex moments. In this paper, we propose a new method to construct a set of blur invariants using the orthogonal Legendre moments. Some important properties of Legendre moments for the blurred image are presented and proved. The performance of the proposed descriptors is evaluated with various point-spread functions and different image noises. The comparison of the present approach with previous methods in terms of pattern recognition accuracy is also provided. The experimental results show that the proposed descriptors are more robust to noise and have better discriminative power than the methods based on geometric or complex moments. PMID:19933003

  7. 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

  8. Low temperature chemical fragmentation of coal

    SciTech Connect

    Deno, N. C.; Curry, K.; Jones, A. D.; Minard, R.; Potter, T.; Rakitsky, W.; Wagner, K.; Yevak, R. J.

    1980-01-01

    Trifluoroperoxyacetic acid chemically fragments coals at 25 to 80/sup 0/. The reagent is so selective for oxidizing aromatic rings and is so inert towards benzylic hydrogen that isopropylbenzene, tetralin, indan, and dihydrophenanthrene have their benzene ring(s) totally destroyed without any evidence of oxidation at the benzylic hydrogen. The fragments contain more and different structural information relative to conventional oxidations with Mn VII, Cr VI, HNO/sub 3/, and O/sub 2/. These latter selectively oxidize benzylic hydrogen. Products from 37 selected coals show that 9,10-dihydroanthracene and 9,10-dihydrophenanthrene units are prominent features in most bituminous coals in accord with Given's structure of coal. Their frequency accounts for the fact that no continuous fused ring structure or graphite structure exists. The only simple alkyl substituent is methyl. Liquefaction (solvent refining) sharply increases the amount of arylmethyl and aromatic structure and causes the appearance of unsubstituted phenyl groups. Nitric acid degradations have been reinvestigated and are developed into a premier method for analyzing the amounts and lengths of linear alkane chains in coals. Generally the amounts of such chains represents 0 to 2% of the carbon in coal, but in one Utah coal they account for about 42% of the carbons.

  9. Measurement of Transverse Asymmetries from Interference Fragmentation at HERMES

    SciTech Connect

    Marco, Contalbrigo

    2007-06-13

    The HERMES experiment has measured for the first time single target-spin asymmetries in semi-inclusive two-pion production using a transversely polarized hydrogen target. These asymmetries are related to the product of two unknowns: the transversity distribution function and the interference fragmentation function. The measured asymmetries are found to be non-zero in the invariant mass range 0.51 GeV < M{pi}{pi} < 0.97 GeV, indicating that two-pion semi-inclusive deep-inelastic scattering can be used to probe transversity.

  10. 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.

  11. Scale-invariant geometric random graphs

    NASA Astrophysics Data System (ADS)

    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.

  12. On black hole spectroscopy via adiabatic invariance

    NASA Astrophysics Data System (ADS)

    Jiang, Qing-Quan; Han, Yan

    2012-12-01

    In this Letter, we obtain the black hole spectroscopy by combining the black hole property of adiabaticity and the oscillating velocity of the black hole horizon. This velocity is obtained in the tunneling framework. In particular, we declare, if requiring canonical invariance, the adiabatic invariant quantity should be of the covariant form Iadia = ∮pi dqi. Using it, the horizon area of a Schwarzschild black hole is quantized independently of the choice of coordinates, with an equally spaced spectroscopy always given by ΔA = 8 π lp2 in the Schwarzschild and Painlevé coordinates.

  13. 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.

  14. 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.

  15. 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.

  16. Approaching Moons from Resonance via Invariant Manifolds

    NASA Technical Reports Server (NTRS)

    Anderson, Rodney L.

    2012-01-01

    In this work, the approach phase from the final resonance of the endgame scenario in a tour design is examined within the context of invariant manifolds. Previous analyses have typically solved this problem either by using numerical techniques or by computing a catalog of suitable trajectories. The invariant manifolds of a selected set of libration orbits and unstable resonant orbits are computed here to serve as guides for desirable approach trajectories. The analysis focuses on designing an approach phase that may be tied into the final resonance in the endgame sequence while also targeting desired conditions at the moon.

  17. Five cases of alpha chain disease

    PubMed Central

    Doe, William F.; Henry, K.; Hobbs, J. R.; Jones, F. Avery; Dent, C. E.; Booth, C. C.

    1972-01-01

    Five patients suffering from alpha chain disease are described. Clinically the patients presented with clubbing and the symptoms of malabsorption. There was a characteristic, predominantly plasma cell infiltrate of the wall of the small intestine. Spread of the plasmacytosis beyond the small intestine to bone marrow (1), peripheral blood (1), and probably the nasopharyngeal lymphoid tissue (1) is described. Fragments of the heavy chain of IgA (alpha chain) were found in serum (5), urine (3), jejunal fluid (2), and saliva (1). The jejunal biopsy of one patient was shown to synthesize free alpha chain in tissue culture. A new and simple immunoselection technique for the identification of free alpha chain is described. Marked clinical remissions were achieved in two patients treated with intermittent cytotoxic and steroid therapy, and in a third patient who received intermittent cytotoxic therapy and tetracycline. ImagesFig. 1Fig. 2Fig. 3Fig. 4Fig. 5Fig. 6Fig. 7Fig. 8 PMID:4119805

  18. 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

  19. 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.

  20. BRST invariance in Coulomb gauge QCD

    NASA Astrophysics Data System (ADS)

    Andraši, A.; Taylor, J. C.

    2015-12-01

    In the Coulomb gauge, the Hamiltonian of QCD contains terms of order ħ2, identified by Christ and Lee, which are non-local but instantaneous. The question is addressed how do these terms fit in with BRST invariance. Our discussion is confined to the simplest, O(g4) , example.

  1. Permutation centralizer algebras and multimatrix invariants

    NASA Astrophysics Data System (ADS)

    Mattioli, Paolo; Ramgoolam, Sanjaye

    2016-03-01

    We introduce a class of permutation centralizer algebras which underly the combinatorics of multimatrix gauge-invariant observables. One family of such noncommutative algebras is parametrized by two integers. Its Wedderburn-Artin decomposition explains the counting of restricted Schur operators, which were introduced in the physics literature to describe open strings attached to giant gravitons and were subsequently used to diagonalize the Gaussian inner product for gauge invariants of two-matrix models. The structure of the algebra, notably its dimension, its center and its maximally commuting subalgebra, is related to Littlewood-Richardson numbers for composing Young diagrams. It gives a precise characterization of the minimal set of charges needed to distinguish arbitrary matrix gauge invariants, which are related to enhanced symmetries in gauge theory. The algebra also gives a star product for matrix invariants. The center of the algebra allows efficient computation of a sector of multimatrix correlators. These generate the counting of a certain class of bicoloured ribbon graphs with arbitrary genus.

  2. 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…

  3. 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.

  4. Rotation invariant features for wear particle classification

    NASA Astrophysics Data System (ADS)

    Arof, Hamzah; Deravi, Farzin

    1997-09-01

    This paper investigates the ability of a set of rotation invariant features to classify images of wear particles found in used lubricating oil of machinery. The rotation invariant attribute of the features is derived from the property of the magnitudes of Fourier transform coefficients that do not change with spatial shift of the input elements. By analyzing individual circular neighborhoods centered at every pixel in an image, local and global texture characteristics of an image can be described. A number of input sequences are formed by the intensities of pixels on concentric rings of various radii measured from the center of each neighborhood. Fourier transforming the sequences would generate coefficients whose magnitudes are invariant to rotation. Rotation invariant features extracted from these coefficients were utilized to classify wear particle images that were obtained from a number of different particles captured at different orientations. In an experiment involving images of 6 classes, the circular neighborhood features obtained a 91% recognition rate which compares favorably to a 76% rate achieved by features of a 6 by 6 co-occurrence matrix.

  5. 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.

  6. Note on gauge invariance and causal propagation

    NASA Astrophysics Data System (ADS)

    Henneaux, Marc; Rahman, Rakibur

    2013-09-01

    Interactions of gauge-invariant systems are severely constrained by several consistency requirements. One is the preservation of the number of gauge symmetries, another is causal propagation. For lower-spin fields, the emphasis is usually put on gauge invariance that happens to be very selective by itself. We demonstrate with an explicit example, however, that gauge invariance, albeit indispensable for constructing interactions, may not suffice as a consistency condition. The chosen example that exhibits this feature is the theory of a massless spin-3/2 field coupled to electromagnetism. We show that this system admits an electromagnetic background in which the spin-3/2 gauge field may move faster than light. Requiring causal propagation rules out otherwise allowed gauge-invariant couplings. This emphasizes the importance of causality analysis as an independent test for a system of interacting gauge fields. We comment on the implications of allowing new degrees of freedom and nonlocality in a theory, on higher-derivative gravity and Vasiliev’s higher-spin theories.

  7. 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.

  8. Parameter Invariance in the Rasch Model.

    ERIC Educational Resources Information Center

    Davison, Mark L.; Chen, Tsuey-Hwa

    This paper explores a logistic regression procedure for estimating item parameters in the Rasch model and testing the hypothesis of item parameter invariance across several groups/populations. Rather than using item responses directly, the procedure relies on "pseudo-paired comparisons" (PC) statistics defined over all possible pairs of items.…

  9. Neutrinos as Probes of Lorentz Invariance

    DOE PAGESBeta

    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.

  10. Testing local Lorentz invariance with gravitational waves

    NASA Astrophysics Data System (ADS)

    Kostelecký, V. Alan; Mewes, Matthew

    2016-06-01

    The effects of local Lorentz violation on dispersion and birefringence of gravitational waves are investigated. The covariant dispersion relation for gravitational waves involving gauge-invariant Lorentz-violating operators of arbitrary mass dimension is constructed. The chirp signal from the gravitational-wave event GW150914 is used to place numerous first constraints on gravitational Lorentz violation.

  11. 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…

  12. Chromaticity space for illuminant invariant recognition.

    PubMed

    Ratnasingam, Sivalogeswaran; McGinnity, T Martin

    2012-08-01

    In this paper an algorithm is proposed to extract two illuminant invariant chromaticity features from three image sensor responses. The algorithm extracts these chromaticity features at pixel level and therefore can perform well in scenes illuminated with non-uniform illuminant. An approach is proposed to use the algorithm with cameras of unknown sensitivity. The algorithm was tested for separability of perceptually similar colours under the International Commission on Illumination (CIE) standard illuminants and obtained a good performance. It was also tested for colour based object recognition by illuminating objects with typical indoor illuminants and obtained a better performance compared to other existing algorithms investigated in this paper. Finally, the algorithm was tested for skin detection invariant to illuminant, ethnic background and imaging device. In this investigation, daylight scenes under different weather conditions and scenes illuminated by typical indoor illuminants were used. The proposed algorithm gives a better skin detection performance compared to widely used standard colour spaces. Based on the results presented, the proposed illuminant invariant chromaticity space can be used for machine vision applications including illuminant invariant colour based object recognition and skin detection. PMID:22481826

  13. 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.}

  14. 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.

  15. 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.

  16. 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. PMID:25222538

  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. SCit: web tools for protein side chain conformation analysis.

    PubMed

    Gautier, R; Camproux, A-C; Tufféry, P

    2004-07-01

    SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit. PMID:15215438

  19. De novo design of drug-like molecules by a fragment-based molecular evolutionary approach.

    PubMed

    Kawai, Kentaro; Nagata, Naoya; Takahashi, Yoshimasa

    2014-01-27

    This paper describes a similarity-driven simple evolutionary approach to producing candidate molecules of new drugs. The aim of the method is to explore the candidates that are structurally similar to the reference molecule and yet somewhat different in not only peripheral chains but also their scaffolds. The method employs a known active molecule of our interest as a reference molecule which is used to navigate a huge chemical space. The reference molecule is also used to obtain seed fragments. An initial set of individual structures is prepared with the seed fragments and additional fragments using several connection rules. The fragment library is preferably prepared from a collection of known molecules related to the target of the reference molecule. Every fragment of the library can be used for fragment-based mutation. All the fragments are categorized into three classes; rings, linkers, and side chains. New individuals are produced by the crossover and the fragment-based mutation with the fragment library. Computer experiments with our own fragment library prepared from GPCR SARfari verified the feasibility of our approach to drug discovery. PMID:24372539

  20. 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

  1. Invariant visual object recognition: biologically plausible approaches.

    PubMed

    Robinson, Leigh; Rolls, Edmund T

    2015-10-01

    Key properties of inferior temporal cortex neurons are described, and then, the biological plausibility of two leading approaches to invariant visual object recognition in the ventral visual system is assessed to investigate whether they account for these properties. Experiment 1 shows that VisNet performs object classification with random exemplars comparably to HMAX, except that the final layer C neurons of HMAX have a very non-sparse representation (unlike that in the brain) that provides little information in the single-neuron responses about the object class. Experiment 2 shows that VisNet forms invariant representations when trained with different views of each object, whereas HMAX performs poorly when assessed with a biologically plausible pattern association network, as HMAX has no mechanism to learn view invariance. Experiment 3 shows that VisNet neurons do not respond to scrambled images of faces, and thus encode shape information. HMAX neurons responded with similarly high rates to the unscrambled and scrambled faces, indicating that low-level features including texture may be relevant to HMAX performance. Experiment 4 shows that VisNet can learn to recognize objects even when the view provided by the object changes catastrophically as it transforms, whereas HMAX has no learning mechanism in its S-C hierarchy that provides for view-invariant learning. This highlights some requirements for the neurobiological mechanisms of high-level vision, and how some different approaches perform, in order to help understand the fundamental underlying principles of invariant visual object recognition in the ventral visual stream. PMID:26335743

  2. Disorder and plasticity in the fragmentation of coatings

    NASA Astrophysics Data System (ADS)

    Handge, U. A.; Sokolov, I. M.; Blumen, A.

    2001-07-01

    Using a one-dimensional model that takes into account ideal plasticity of the surface layer, we investigate the fragmentation of thin coatings under uniaxial tension. The coating is modeled as a chain of plastically deforming elements that are connected via leaf springs to a uniformly stretched substrate. Each coating element can only withstand a maximum elongation, which is randomly distributed. From simulations of the fragmentation process we find that the average crack spacing scales with applied strain ɛ, i.e., ~ɛ-κ. Simulations and analytical arguments show that the scaling exponent κ depends on the disorder parameters of the model.

  3. Structural insight into MR1-mediated recognition of the mucosal associated invariant T cell receptor

    PubMed Central

    Reantragoon, Rangsima; Kjer-Nielsen, Lars; Patel, Onisha; Chen, Zhenjun; Illing, Patricia T.; Bhati, Mugdha; Kostenko, Lyudmila; Bharadwaj, Mandvi; Meehan, Bronwyn; Hansen, Ted H.; Godfrey, Dale I.

    2012-01-01

    Mucosal-associated invariant T (MAIT) cells express a semiinvariant αβ T cell receptor (TCR) that binds MHC class I–like molecule (MR1). However, the molecular basis for MAIT TCR recognition by MR1 is unknown. In this study, we present the crystal structure of a human Vα7.2Jα33-Vβ2 MAIT TCR. Mutagenesis revealed highly conserved requirements for the MAIT TCR–MR1 interaction across different human MAIT TCRs stimulated by distinct microbial sources. Individual residues within the MAIT TCR β chain were dispensable for the interaction with MR1, whereas the invariant MAIT TCR α chain controlled specificity through a small number of residues, which are conserved across species and located within the Vα-Jα regions. Mutagenesis of MR1 showed that only two residues, which were centrally positioned and on opposing sides of the antigen-binding cleft of MR1, were essential for MAIT cell activation. The mutagenesis data are consistent with a centrally located MAIT TCR–MR1 docking that was dominated by the α chain of the MAIT TCR. This candidate docking mode contrasts with that of the NKT TCR–CD1d-antigen interaction, in which both the α and β chain of the NKT TCR is required for ligation above the F′-pocket of CD1d. PMID:22412157

  4. Crater Chains

    NASA Technical Reports Server (NTRS)

    2003-01-01

    [figure removed for brevity, see original site]

    The large crater at the top of this THEMIS visible image has several other craters inside of it. Most noticeable are the craters that form a 'chain' on the southern wall of the large crater. These craters are a wonderful example of secondary impacts. They were formed when large blocks of ejecta from an impact crashed back down onto the surface of Mars. Secondaries often form radial patterns around the impact crater that generated them, allowing researchers to trace them back to their origin.

    Note: this THEMIS visual image has not been radiometrically nor geometrically calibrated for this preliminary release. An empirical correction has been performed to remove instrumental effects. A linear shift has been applied in the cross-track and down-track direction to approximate spacecraft and planetary motion. Fully calibrated and geometrically projected images will be released through the Planetary Data System in accordance with Project policies at a later time.

    NASA's Jet Propulsion Laboratory manages the 2001 Mars Odyssey mission for NASA's Office of Space Science, Washington, D.C. The Thermal Emission Imaging System (THEMIS) was developed by Arizona State University, Tempe, in collaboration with Raytheon Santa Barbara Remote Sensing. The THEMIS investigation is led by Dr. Philip Christensen at Arizona State University. Lockheed Martin Astronautics, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.

    Image information: VIS instrument. Latitude 19.3, Longitude 347.5 East (12.5 West). 19 meter/pixel resolution.

  5. What's hampering measurement invariance: detecting non-invariant items using clusterwise simultaneous component analysis

    PubMed Central

    De Roover, Kim; Timmerman, Marieke E.; De Leersnyder, Jozefien; Mesquita, Batja; Ceulemans, Eva

    2014-01-01

    The issue of measurement invariance is ubiquitous in the behavioral sciences nowadays as more and more studies yield multivariate multigroup data. When measurement invariance cannot be established across groups, this is often due to different loadings on only a few items. Within the multigroup CFA framework, methods have been proposed to trace such non-invariant items, but these methods have some disadvantages in that they require researchers to run a multitude of analyses and in that they imply assumptions that are often questionable. In this paper, we propose an alternative strategy which builds on clusterwise simultaneous component analysis (SCA). Clusterwise SCA, being an exploratory technique, assigns the groups under study to a few clusters based on differences and similarities in the component structure of the items, and thus based on the covariance matrices. Non-invariant items can then be traced by comparing the cluster-specific component loadings via congruence coefficients, which is far more parsimonious than comparing the component structure of all separate groups. In this paper we present a heuristic for this procedure. Afterwards, one can return to the multigroup CFA framework and check whether removing the non-invariant items or removing some of the equality restrictions for these items, yields satisfactory invariance test results. An empirical application concerning cross-cultural emotion data is used to demonstrate that this novel approach is useful and can co-exist with the traditional CFA approaches. PMID:24999335

  6. Localization and the invariant probability measure for a structural dynamic system

    NASA Astrophysics Data System (ADS)

    Kissel, Glen J.

    2009-03-01

    In the one-dimensional classical analogs to Anderson localization, whether optical, acoustical or structural dynamic, the periodic system has its periodicity disrupted by having one or more of its parameters randomly disordered. Such randomized systems can be modeled via an infinite product of random transfer matrices. In the case where the transfer matrices are 2x2, the upper (and positive) Lyapunov exponent of the random matrix product is identified as the localization factor (inverse localization length) for the disordered one-dimensional model. It is this localization factor which governs the confinement of energy transmission along the disordered system, and for which the localization phenomenon has been of interest. The theorem of Furstenberg for infinite products of random matrices allows us to calculate this upper Lyapunov exponent. In Furstenberg's master formula we integrate with respect to the probability measure of the random matrices, but also with respect to the invariant probability measure of the direction of the vector propagated by the long chain of random matrices. This invariant measure is difficult to find analytically, and, as a result, either an approximating assumption is frequently made, or, less frequently, the invariant measure is determined numerically. Here we calculate the invariant measure numerically using a Monte Carlo bin counting technique and then numerically integrate Furstenberg's formula to arrive at the localization factor for both continuous and discrete disorder of the mass. This result is cross checked with the (modified) Wolf algorithm.

  7. 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.

  8. 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

  9. Topological invariants of magnetic fields, and the effect of reconnections

    SciTech Connect

    Ruzmaikin, A. ); Akhmetiev, P. )

    1994-02-01

    Properties of the second-order topological invariant (the helicity) and the third-order topological invariant for the Borromean rings'' (three linked rings no two of which link each other) are discussed. A fourth-order topological invariant of ideal magnetohydrodynamics is constructed in an integral form. This invariant is determined by the properties of Seifert surfaces bounded by two coupled flux tubes. In particular, for the Whitehead link, it represents the fourth-order Sato--Levine invariant. The effect of reconnections on the topological invariants in the limit of small diffusivity is considered. In this limit the helicity is approximately conserved and the higher-order invariants decay rapidly under the action of diffusivity. The destruction of the higher-order invariants, however, creates helicity fluctuations.

  10. 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

  11. Local Unitary Invariant Spin-Squeezing in Multiqubit States

    NASA Astrophysics Data System (ADS)

    Divyamani, B. G.; Sudha; Usha Devi, A. R.

    2016-05-01

    We investiage Local Unitary Invariant Spin Squeezing (LUISS) in symmetric and non-symmetric multiqubit states. On developing an operational procedure to evaluate Local Unitary Invariant Spin Squeezing parameters, we explicitly evaluate these parameters for pure as well as mixed non-symmetric multiqubit states. We show that the existence of local unitary invariant version of Kitegawa-Ueda spin squeezing may not witness pairwise entanglement whereas the local unitary invariant analogue of Wineland spin squeezing necessarily implies pairwise entanglement.

  12. 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

  13. 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…

  14. 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…

  15. Possible universal quantum algorithms for generalized Turaev-Viro invariants

    NASA Astrophysics Data System (ADS)

    Vélez, Mario; Ospina, Juan

    2011-05-01

    An emergent trend in quantum computation is the topological quantum computation (TQC). Briefly, TQC results from the application of quantum computation with the aim to solve the problems of quantum topology such as topological invariants for knots and links (Jones polynomials, HOMFLY polynomials, Khovanov polynomials); topological invariants for graphs (Tutte polynomial and Bollobás-Riordan polynomial); topological invariants for 3-manifolds (Reshetiskin-Turaev, Turaev-Viro and Turaer-Viro-Ocneanu invariants) and topological invariants for 4-manifolds( Crane-Yetter invariants). In a few words, TQC is concerned with the formulation of quantum algorithms for the computation of these topological invariants in quantum topology. Given that one of the fundamental achievements of quantum topology was the discovery of strong connections between monoidal categories and 3-dimensional manifolds, in TQC is possible and necessary to exploit such connections with the purpose to formulate universal quantum algorithms for topological invariants of 3-manifolds. In the present work we make an exploration of such possibilities. Specifically we search for universal quantum algorithms for generalized Turaev-Viro invariants of 3-manifolds such as the Turaev-Viro-Ocneanu invariants, the Kashaev-Baseilhac-Benedetti invariants of 3-manifolds with links and the Geer-Kashaev-Turaev invariants of 3-manifolds with a link and a principal bundle. We also look for physical systems (three dimensional topological insulators and three-dimensional gravity) over which implement the resulting universal topological quantum algorithms.

  16. Permutation-invariant codes encoding more than one qubit

    NASA Astrophysics Data System (ADS)

    Ouyang, Yingkai; Fitzsimons, Joseph

    2016-04-01

    A permutation-invariant code on m qubits is a subspace of the symmetric subspace of the m qubits. We derive permutation-invariant codes that can encode an increasing amount of quantum information while suppressing leading-order spontaneous decay errors. To prove the result, we use elementary number theory with prior theory on permutation-invariant codes and quantum error correction.

  17. 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.

  18. Gauge-invariant approach to quark dynamics

    NASA Astrophysics Data System (ADS)

    Sazdjian, H.

    2016-02-01

    The main aspects of a gauge-invariant approach to the description of quark dynamics in the nonperturbative regime of quantum chromodynamics (QCD) are first reviewed. The role of the parallel transport operation in constructing gauge-invariant Green's functions is then presented, and the relevance of Wilson loops for the representation of the interaction is emphasized. Recent developments, based on the use of polygonal lines for the parallel transport operation, are presented. An integro-differential equation, obtained for the quark Green's function defined with a phase factor along a single, straight line segment, is solved exactly and analytically in the case of two-dimensional QCD in the large- N c limit. The solution displays the dynamical mass generation phenomenon for quarks, with an infinite number of branch-cut singularities that are stronger than simple poles.

  19. 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.

  20. Principles of Invariance in Radiative Transfer

    NASA Astrophysics Data System (ADS)

    Peraiah, A.

    1999-09-01

    We have reviewed the principle of invariance, its applications and its usefulness for obtaining the radiation field in semi-infinite and finite atmospheres. Various laws of scattering in dispersive media and the consequent radiation field are studied. The H-functions and X- and Y-functions in semi-infinite and finite media respectively are derived in a few cases. The Discrete Space Theory (DST) which is a general form of the Principle of Invariance is described. The method of addition of layers with general properties, is shown to describe all the properties of multiple scattering. A few examples of the application of DST such as polarization, line formation in expanding stellar atmospheres, etc., and a numerical analysis of DST are presented. Other developments in the theory of radiative transfer are briefly described.

  1. 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

  2. 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.

  3. Scale invariance in the spectral action

    SciTech Connect

    Chamseddine, Ali H.; Connes, Alain

    2006-06-15

    The arbitrary mass scale in the spectral action for the Dirac operator is made dynamical by introducing a dilaton field. We evaluate all the low-energy terms in the spectral action and determine the dilaton couplings. These results are applied to the spectral action of the noncommutative space defined by the standard model. We show that the effective action for all matter couplings is scale invariant, except for the dilaton kinetic term and Einstein-Hilbert term. The resulting action is almost identical to the one proposed for making the standard model scale invariant as well as the model for extended inflation and has the same low-energy limit as the Randall-Sundrum model. Remarkably, all desirable features with correct signs for the relevant terms are obtained uniquely and without any fine tuning.

  4. Mutation, Witten index, and quiver invariant

    NASA Astrophysics Data System (ADS)

    Kim, Heeyeon; Lee, Seung-Joo; Yi, Piljin

    2015-07-01

    We explore Seiberg-like dualities, or mutations, for quiver quantum mechanics in the context of wall-crossing. In contrast to higher dimensions, the 1d Seiberg-duality must be performed with much care. With fixed Fayet-Iliopoulos constants, at most two nodes can be mutated, one left and the other right, mapping a chamber of a quiver into a chamber of a mutated quiver. We delineate this complex pattern for triangle quivers and show how the Witten indices are preserved under such finely chosen mutations. On the other hand, the quiver invariants, or wall-crossing-safe part of supersymmetric spectra, mutate more straightforwardly, whereby a quiver is mapped to a quiver. The mutation rule that preserves the quiver invariant is different from the usual one, however, which we explore and confirm numerically.

  5. 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.

  6. Explicit travelling waves and invariant algebraic curves

    NASA Astrophysics Data System (ADS)

    Gasull, Armengol; Giacomini, Hector

    2015-06-01

    We introduce a precise definition of algebraic travelling wave solution of n-th order partial differential equations and prove that the only algebraic travelling waves solutions for the celebrated Fisher-Kolmogorov equation are the ones found in 1979 by Ablowitz and Zeppetella. This question is equivalent to study when an associated one-parameter family of planar ordinary differential systems has invariant algebraic curves.

  7. Conformally invariant wave equations for massless particles

    NASA Astrophysics Data System (ADS)

    McLennan, James A.

    1984-07-01

    The invariance of wave equations for massless particles under conformal transformations of space-time is briefly summarized. Particular attention is given to a recent paper by Bracken and Jessup in which it is claimed that results obtained by the author are in error. Their paper contains several misleading statements based on a misreading of the author's paper, and in addition an argument of theirs, intended to show error, is itself invalid. Their claims of error on the author's part are therefore unfounded.

  8. 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

  9. Permutation-invariant distance between atomic configurations

    NASA Astrophysics Data System (ADS)

    Ferré, Grégoire; Maillet, Jean-Bernard; Stoltz, Gabriel

    2015-09-01

    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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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. PMID:23927230

  15. Invariance of bipartite separability and PPT-probabilities over Casimir invariants of reduced states

    NASA Astrophysics Data System (ADS)

    Slater, Paul B.

    2016-05-01

    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.

  16. Fragmentation Function in Thermofield Dynamics

    NASA Astrophysics Data System (ADS)

    Ladrem, M.; Chekerker, M.; Khanna, F. C.; Santana, A. E.

    2013-04-01

    The fragmentation function at high energy experiments is introduced by using thermofield dynamics (TFD), a real-time finite-temperature quantum field formalism. Due to the structure of TFD, the results at T = 0 and T ≠ 0 are split in a direct way. As an application, we consider the temperature effect on the fragmentation function of a hadron leading to quark-antiquark pairs. Using a definition of Wilson-loop in real-time, we find that the fragmentation function decreases in magnitude with an increase in the temperature.

  17. 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.

  18. Composition of proteoglycan fragments from hyaline cartilage produced by granulocytes in a model of frustrated phagocytosis.

    PubMed

    Liszt, F; Schnittker-Schulze, K; Stuhlsatz, H W; Greiling, H

    1991-02-01

    An in vitro model of frustrated phagocytosis was developed in which granulocytes interact with well-defined slices of hyaline cartilage. The composition of the purified proteoglycan fragments released from the cartilage slices by N-formyl-methionyl-leucyl-phenylalanine-stimulated granulocytes was studied after 30, 60 and 90 min incubation time. It was shown that the proteoglycan fragments do not change their composition during incubation. The only change observed during incubation was an increase in the quantity of the fragments. The protein content of the proteoglycan fragments is 7.0-8.6%, corresponding to a peptide chain of 24-28 amino acids, and the relative molecular mass of the total fragment is Mr = 37,600-39,200. On average, each proteoglycan fragment contains two chondroitin sulphate chains (Mr = 22,000-22,400), every fourth fragment contains a keratan sulphate chain (Mr = 7000-7200) and every seventh to eighth contains an O-glycosidic oligosaccharide, whereas no N-glycosidic oligosaccharide could be detected. The results of the disaccharide analysis show that the galactosaminoglycan chains contain 76.2-83.6% chondroitin 4-sulphate, 12.9-19.4% chondroitin 6-sulphate, 3.5-3.8% chondroitin and no dermatan sulphate. Since composition and relative molecular mass of the chondroitin sulphate and keratan sulphate chains from the proteoglycan fragments resemble those of native proteoglycans, the conclusion may be drawn that the degeneration of the proteoglycans occurs by proteases that attack preferably the chondroitin sulphate-rich region of the core protein. This is the first inflammation model of joint destruction, which demonstrates the elution of soluble specific proteoglycan degradation products of defined size. PMID:1904780

  19. Second-Order Gauge Invariant Cosmological Perturbation Theory --- Einstein Equations in Terms of Gauge Invariant Variables ---

    NASA Astrophysics Data System (ADS)

    Nakamura, K.

    2007-01-01

    Following the general framework of the gauge invariant perturbation theory developed in the papers [K. Nakamura, Prog. Theor. Phys. 110 (2003), 723; ibid. 113 (2005), 481], we formulate second-order gauge invariant cosmological perturbation theory in a four-dimensional homogeneous isotropic universe. We consider perturbations both in the universe dominated by a single perfect fluid and in that dominated by a single scalar field. We derive all the components of the Einstein equations in the case that the first-order vector and tensor modes are negligible. All equations are derived in terms of gauge invariant variables without any gauge fixing. These equations imply that second-order vector and tensor modes may be generated due to the mode-mode coupling of the linear-order scalar perturbations. We also briefly discuss the main progress of this work through comparison with previous works.

  20. 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.