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Sample records for invariant chain fragment

  1. Single chain Fab (scFab) fragment

    PubMed Central

    Hust, Michael; Jostock, Thomas; Menzel, Christian; Voedisch, Bernd; Mohr, Anja; Brenneis, Mariam; Kirsch, Martina I; Meier, Doris; Dübel, Stefan

    2007-01-01

    Background The connection of the variable part of the heavy chain (VH) and and the variable part of the light chain (VL) by a peptide linker to form a consecutive polypeptide chain (single chain antibody, scFv) was a breakthrough for the functional production of antibody fragments in Escherichia coli. Being double the size of fragment variable (Fv) fragments and requiring assembly of two independent polypeptide chains, functional Fab fragments are usually produced with significantly lower yields in E. coli. An antibody design combining stability and assay compatibility of the fragment antigen binding (Fab) with high level bacterial expression of single chain Fv fragments would be desirable. The desired antibody fragment should be both suitable for expression as soluble antibody in E. coli and antibody phage display. Results Here, we demonstrate that the introduction of a polypeptide linker between the fragment difficult (Fd) and the light chain (LC), resulting in the formation of a single chain Fab fragment (scFab), can lead to improved production of functional molecules. We tested the impact of various linker designs and modifications of the constant regions on both phage display efficiency and the yield of soluble antibody fragments. A scFab variant without cysteins (scFabΔC) connecting the constant part 1 of the heavy chain (CH1) and the constant part of the light chain (CL) were best suited for phage display and production of soluble antibody fragments. Beside the expression system E. coli, the new antibody format was also expressed in Pichia pastoris. Monovalent and divalent fragments (DiFabodies) as well as multimers were characterised. Conclusion A new antibody design offers the generation of bivalent Fab derivates for antibody phage display and production of soluble antibody fragments. This antibody format is of particular value for high throughput proteome binder generation projects, due to the avidity effect and the possible use of common standard sera

  2. 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

  3. Thermally activated fragmentation of a homopolymer chain

    NASA Astrophysics Data System (ADS)

    Fugmann, Simon; Sokolov, Igor M.

    2011-03-01

    We consider the thermally activated fragmentation of a homopolymer chain, which can exhibit strongly non-Markovian behavior on the timescale of interest. In our model the dynamics of the intact chain is a Rouse one until a bond breaks and bond breakdown is considered as a first passage problem over a barrier to an absorbing boundary. Using the framework of the Wilemski-Fixman approximation we calculate activation times of individual bonds for free and grafted polymer chains. We show that these times crucially depend on the length of the chain and the location of the bond yielding a minimum at the free chain ends. Going beyond the Wilemski-Fixman approximation we show that a generalized form of the renewal equation for barrier crossings serves to improve the quantitative agreement between numerical simulations and analytical predictions. The authors thankfully acknowledge financial support by DFG within the SFB 555 research collaboration program.

  4. Single-Chain Fragment Variable Antibody Piezoimmunosensors

    PubMed Central

    Shen, Zhihong; Stryker, Gabrielle A.; Mernaugh, Ray L.; Yu, Lei; Yan, Heping; Zeng, Xiangqun

    2008-01-01

    In this paper, we describe a novel nonlabeled biosensor with high diagnostic potential for rapid and sensitive detection of antigens in complex biological samples. The biosensor comprises a piezoimmunosensor (PZ) displaying a specially constructed recombinant antibody on its surface. The recombinant single-chain fragment variable (scFv) antibody contained a cysteine within the linker amino acid sequence used to join the scFv variable heavy and light chains. The presence of cysteine induced the scFv construct to self-assemble as a densely packed rigid monolayer on the gold surface of a quartz crystal microbalance. scFv molecules in this self-assembled mono-layer (SAM) exhibited a defined orientation and high areal densities, with scFv-modified microbalance surfaces displaying 35 times as many variable antigen-binding sites per square centimeter as surfaces modified with whole antibody. Experimental data show that the scFv SAM PZ is superior to Fab fragment, Fab fragment containing a free sulfhydryl group (i.e., Fab-SH), and whole antibody PZs regarding sensitivity and specificity. Because of their small uniform size (MW ≈ 27000) and the ease with which they can be modified using genetic engineering, scFv’s have significant advantages over whole antibodies in microbalance biosensor systems. We demonstrate here that the use of scFv containing a cysteine within the scFv linker sequence (i.e., scFv-cys) for preparation of biosensor surfaces markedly increases the density of available antigen-binding sites, yielding a system that is highly selective, rapid, and capable of detecting low concentrations of antigens in complex samples. PMID:15679346

  5. Interfaces in the Ising quantum chain and conformal invariance

    NASA Astrophysics Data System (ADS)

    Zhang, De-Gang; Li, Bo-Zang; Zhao, Min-Guang

    1996-04-01

    The Ising quantum chain with multiple interfaces is solved exactly. The model is shown to be conformally invariant only for a commensurate configuration of the critical parameters. The spectra are generated by an irreducible oscillator representation of the shifted SO(2c) Kac-Moody algebra, where the central charge c is a discontinuous function of the critical parameters. The critical exponents associated with these interfaces are determined.

  6. Invariant Chain Complexes and Clusters as Platforms for MIF Signaling.

    PubMed

    Lindner, Robert

    2017-02-10

    Invariant chain (Ii/CD74) has been identified as a surface receptor for migration inhibitory factor (MIF). Most cells that express Ii also synthesize major histocompatibility complex class II (MHC II) molecules, which depend on Ii as a chaperone and a targeting factor. The assembly of nonameric complexes consisting of one Ii trimer and three MHC II molecules (each of which is a heterodimer) has been regarded as a prerequisite for efficient delivery to the cell surface. Due to rapid endocytosis, however, only low levels of Ii-MHC II complexes are displayed on the cell surface of professional antigen presenting cells and very little free Ii trimers. The association of Ii and MHC II has been reported to block the interaction with MIF, thus questioning the role of surface Ii as a receptor for MIF on MHC II-expressing cells. Recent work offers a potential solution to this conundrum: Many Ii-complexes at the cell surface appear to be under-saturated with MHC II, leaving unoccupied Ii subunits as potential binding sites for MIF. Some of this work also sheds light on novel aspects of signal transduction by Ii-bound MIF in B-lymphocytes: membrane raft association of Ii-MHC II complexes enables MIF to target Ii-MHC II to antigen-clustered B-cell-receptors (BCR) and to foster BCR-driven signaling and intracellular trafficking.

  7. Invariant Chain Complexes and Clusters as Platforms for MIF Signaling

    PubMed Central

    Lindner, Robert

    2017-01-01

    Invariant chain (Ii/CD74) has been identified as a surface receptor for migration inhibitory factor (MIF). Most cells that express Ii also synthesize major histocompatibility complex class II (MHC II) molecules, which depend on Ii as a chaperone and a targeting factor. The assembly of nonameric complexes consisting of one Ii trimer and three MHC II molecules (each of which is a heterodimer) has been regarded as a prerequisite for efficient delivery to the cell surface. Due to rapid endocytosis, however, only low levels of Ii-MHC II complexes are displayed on the cell surface of professional antigen presenting cells and very little free Ii trimers. The association of Ii and MHC II has been reported to block the interaction with MIF, thus questioning the role of surface Ii as a receptor for MIF on MHC II-expressing cells. Recent work offers a potential solution to this conundrum: Many Ii-complexes at the cell surface appear to be under-saturated with MHC II, leaving unoccupied Ii subunits as potential binding sites for MIF. Some of this work also sheds light on novel aspects of signal transduction by Ii-bound MIF in B-lymphocytes: membrane raft association of Ii-MHC II complexes enables MIF to target Ii-MHC II to antigen-clustered B-cell-receptors (BCR) and to foster BCR-driven signaling and intracellular trafficking. PMID:28208600

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

    SciTech Connect

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

    2006-09-15

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

  9. Sieving polymer synthesis by reversible addition fragmentation chain transfer polymerization.

    PubMed

    Nai, Yi Heng; Jones, Roderick C; Breadmore, Michael C

    2013-12-01

    Replaceable sieving polymers are the fundamental component for high resolution nucleic acids separation in CE. The choice of polymer and its physical properties play significant roles in influencing separation performance. Recently, reversible addition fragmentation chain transfer (RAFT) polymerization has been shown to be a versatile polymerization technique capable of yielding well defined polymers previously unattainable by conventional free radical polymerization. In this study, a high molecular weight PDMA at 765 000 gmol-1 with a PDI of 1.55 was successfully synthesized with the use of chain transfer agent - 2-propionic acidyl butyl trithiocarbonate (PABTC) in a multi-step sequential RAFT polymerization approach. This study represents the first demonstration of RAFT polymerization for synthesizing polymers with the molecular weight range suitable for high resolution DNA separation in sieving electrophoresis. Adjustment of pH in the reaction was found to be crucial for the successful RAFT polymerization of high molecular weight polymer as the buffered condition minimizes the effect of hydrolysis and aminolysis commonly associated with trithiocarbonate chain transfer agents. The separation efficiency of PABTC-PDMA was found to have marginally superior separation performance compared to a commercial PDMA formulation, POP™-CAP, of similar molecular weight range.

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

    NASA Astrophysics Data System (ADS)

    Semsarilar, Mona; Perrier, Sébastien

    2010-10-01

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

  11. Single-Chain Fragment Variable Passive Immunotherapies for Neurodegenerative Diseases

    PubMed Central

    Huang, Liang; Su, Xiaomin; Federoff, Howard J.

    2013-01-01

    Accumulation of misfolded proteins has been implicated in a variety of neurodegenerative diseases including prion diseases, Alzheimer’s disease (AD), Parkinson’s disease (PD), and Huntington’s disease (HD). In the past decade, single-chain fragment variable (scFv) -based immunotherapies have been developed to target abnormal proteins or various forms of protein aggregates including Aβ, SNCA, Htt, and PrP proteins. The scFvs are produced by fusing the variable regions of the antibody heavy and light chains, creating a much smaller protein with unaltered specificity. Because of its small size and relative ease of production, scFvs are promising diagnostic and therapeutic reagents for protein misfolded diseases. Studies have demonstrated the efficacy and safety of scFvs in preventing amyloid protein aggregation in preclinical models. Herein, we discuss recent developments of these immunotherapeutics. We review efforts of our group and others using scFv in neurodegenerative disease models. We illustrate the advantages of scFvs, including engineering to enhance misfolded conformer specificity and subcellular targeting to optimize therapeutic action. PMID:24048248

  12. A general model of invariant chain association with class II major histocompatibility complex proteins.

    PubMed Central

    Lee, C; McConnell, H M

    1995-01-01

    The binding of invariant chain to major histocompatibility complex (MHC) proteins is an important step in processing of MHC class II proteins and in antigen presentation. The question of how invariant chain can bind to all MHC class II proteins is central to understanding these processes. We have employed molecular modeling to predict the structure of class II-associated invariant chain peptide (CLIP)-MHC protein complexes and to ask whether the predicted mode of association could be general across all MHC class II proteins. CLIP fits identically into the MHC class II alleles HLA-DR3, I-Ak, I-Au, and I-Ad, with a consistent pattern of hydrogen bonds, contacts, and hydrophobic burial and without bad contacts. Our model predicts the burial of CLIP residues Met-91 and Met-99 in the deep P1 and P9 anchor pockets and other detailed interactions, which we have compared with available data. The predicted pattern of I-A allele-specific effects on CLIP binding is very similar to that observed experimentally by alanine-scanning mutations of CLIP. Together, these results indicate that CLIP may bind in a single, general way across products of MHC class II alleles. Images Fig. 1 Fig. 2 Fig. 3 PMID:7667280

  13. 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...

  14. The p35 human invariant chain in transgenic mice restores mature B cells in the absence of endogenous CD74.

    PubMed

    Genève, Laetitia; Ménard, Catherine; Labrecque, Nathalie; Thibodeau, Jacques

    2012-10-01

    The invariant chain (Ii; CD74) has pleiotropic functions and Ii-deficient mice show defects in MHC class II (MHC II) transport and B cell maturation. In humans, but not in mice, a minor Iip35 isoform of unknown function includes an endoplasmic reticulum-retention motif that is masked upon binding of MHC II molecules. To gain further insight into the roles of Ii in B cell homeostasis, we generated Iip35 transgenic mice (Tgp35) and bred these with mice deficient for Ii (Tgp35/mIiKO). Iip35 was shown to compete with mIi for the binding to I-A(b) . In addition, classical endosomal degradation products (p20/p10) and the class II-associated invariant chain peptide (CLIP) fragment were detected. Moreover, Iip35 favored the formation of compact peptide-MHC II complexes in the Tgp35/mIiKO mice. I-A(b) levels were restored at the plasma membrane of mature B cells but Iip35 affected the fine conformation of MHC II molecules as judged by the increased reactivity of the AF6-120.1 antibody in permeabilized cells. However, the human Iip35 cannot fully replace the endogenous Ii. Indeed, most immature B cells in the bone marrow and spleen of transgenic mice had reduced surface expression of MHC II molecules, demonstrating a dominant-negative effect of Iip35 in Tgp35 mice. Interestingly, while maturation to follicular B cells was normal, Iip35 expression appeared to reduce the proportions of marginal zone B cells. These results emphasize the importance of Ii in B cell homeostasis and suggest that Iip35 could have regulatory functions.

  15. 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.

  16. The amino acid sequences of the Fd fragments of two human γ heavy chains

    PubMed Central

    Press, E. M.; Hogg, N. M.

    1970-01-01

    The amino acid sequences of the Fd fragments of two human pathological immunoglobulins of the immunoglobulin G1 class are reported. Comparison of the two sequences shows that the heavy-chain variable regions are similar in length to those of the light chains. The existence of heavy chain variable region subgroups is also deduced, from a comparison of these two sequences with those of another γ 1 chain, Eu, a μ chain, Ou, and the partial sequence of a fourth γ 1 chain, Ste. Carbohydrate has been found to be linked to an aspartic acid residue in the variable region of one of the γ 1 chains, Cor. PMID:5449120

  17. Discovery of invariant T cells by next-generation sequencing of the human TCR α-chain repertoire.

    PubMed

    van Schaik, Barbera; Klarenbeek, Paul; Doorenspleet, Marieke; van Kampen, Antoine; Moody, D Branch; de Vries, Niek; Van Rhijn, Ildiko

    2014-11-15

    During infection and autoimmune disease, activation and expansion of T cells take place. Consequently, the TCR repertoire contains information about ongoing and past diseases. Analysis and interpretation of the human TCR repertoire are hampered by its size and stochastic variation and by the diversity of Ags and Ag-presenting molecules encoded by the MHC, but are highly desirable and would greatly impact fundamental and clinical immunology. A subset of the TCR repertoire is formed by invariant T cells. Invariant T cells express interdonor-conserved TCRs and recognize a limited set of Ags, presented by nonpolymorphic Ag-presenting molecules. Discovery of the three known invariant T cell populations has been a tedious and slow process, identifying them one by one. Because conservation of the TCR α-chain of invariant T cells is much higher than the β-chain, and because the TCR α-chain V gene segment TRAV1-2 is used by two of the three known invariant TCRs, we employed next-generation sequencing of TCR α-chains that contain the TRAV1-2 gene segment to identify 16 invariant TCRs shared among many blood donors. Frequency analysis of individual clones indicates these T cells are expanded in many donors, implying an important role in human immunity. This approach extends the number of known interdonor-conserved TCRs and suggests that many more exist and that these TCR patterns can be used to systematically evaluate human Ag exposure.

  18. Evaluation of Microbial Diversity in Wetland through Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism (RFLP)

    DTIC Science & Technology

    2006-06-01

    MICROBIAL DIVERSITY IN WETLANDS THROUGH POLYMERASE CHAIN REACTION ( PCR ) AND RESTRICTION FRAGMENT LENGTH POLYMORPHISM ( RFLP ) THESIS Presented to the...MICROBIAL DIVERSITY IN WETLANDS THROUGH POLYMERASE CHAIN REACTION ( PCR ) AND RESTRICTION FRAGMENT LENGTH POLYMORPHISM ( RFLP ) Gregory K. Joseph, B.A...AFIT/GES/ENV/06J-02 EVALUATION OF MICROBIAL DIVERSITY IN WETLANDS THROUGH POLYMERASE CHAIN REACTION ( PCR ) AND RESTRICTION FRAGMENT LENGTH

  19. Exposing the Specific Roles of the Invariant Chain Isoforms in Shaping the MHC Class II Peptidome.

    PubMed

    Fortin, Jean-Simon; Cloutier, Maryse; Thibodeau, Jacques

    2013-12-13

    The peptide repertoire (peptidome) associated with MHC class II molecules (MHCIIs) is influenced by the polymorphic nature of the peptide binding groove but also by cell-intrinsic factors. The invariant chain (Ii) chaperones MHCIIs, affecting their folding and trafficking. Recent discoveries relating to Ii functions have provided insights as to how it edits the MHCII peptidome. In humans, the Ii gene encodes four different isoforms for which structure-function analyses have highlighted common properties but also some non-redundant roles. Another layer of complexity arises from the fact that Ii heterotrimerizes, a characteristic that has the potential to affect the maturation of associated MHCIIs in many different ways, depending on the isoform combinations. Here, we emphasize the peptide editing properties of Ii and discuss the impact of the various isoforms on the MHCII peptidome.

  20. The segment of invariant chain that is critical for association with major histocompatibility complex class II molecules contains the sequence of a peptide eluted from class II polypeptides.

    PubMed Central

    Freisewinkel, I M; Schenck, K; Koch, N

    1993-01-01

    Major histocompatibility complex class II molecules present peptides from an extracellular source of antigens to CD4+ T lymphocytes. The class II-associated invariant chain affects this role of alpha and beta polypeptides by restriction of peptide loading to endocytic vesicles. Up to now no specific portion of the invariant chain has been defined as the class II binding site. We constructed recombinant invariant chain genes and inspected association of the mutant invariant chains with class II polypeptides. Here we demonstrate that an extracytoplasmic sequence of the invariant chain (aa 81-109) that is only 23 residues away from the transmembrane region is essential for contact with class II polypeptides, whereas the remaining C-terminal part is dispensable for binding. The sequence of invariant-chain-derived peptides that were eluted from class II molecules is contained in this segment and may define the class II binding site of the invariant chain. The membrane-proximal position of this region suggests that the invariant chain and invariant-chain-derived peptides isolated from class II molecules bind to a domain distinct from the class II pocket. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 PMID:8415765

  1. Autolysis of bovine enteropeptidase heavy chain: evidence of fragment 118-465 involvement in trypsinogen activation.

    PubMed

    Mikhailova, A G; Rumsh, L D

    1999-01-15

    Variations in bovine enteropeptidase (EP) activity were shown to result from autolysis caused by the loss of calcium ions; the cleavage sites were determined. The native enzyme preferred its natural substrate, trypsinogen (KM=2.4 microM), to the peptide and fusion protein substrates (KM=200 and 125 microM, respectively). On the other hand, the truncated enzyme composed of the C-terminal fragment 466-800 of EP heavy chain and intact light chain did not distinguish these substrates. The results suggest that the N-terminal fragment 118-465 of the enteropeptidase heavy chain contains a secondary substrate-binding site that interacts directly with trypsinogen.

  2. The invariant chain p35 isoform promotes formation of nonameric complexes with MHC II molecules.

    PubMed

    Cloutier, Maryse; Gauthier, Catherine; Fortin, Jean-Simon; Thibodeau, Jacques

    2014-07-01

    Four different isoforms of the human invariant chain (Ii) have been described (p33, p35, p41 and p43). These heterotrimerize in the endoplasmic reticulum (ER) before associating with MHC class II molecules (MHCIIs). However, the final stoichiometry of the Ii/MHCII complex remains debated. This is particularly interesting as both p35 and p43 include a di-arginine motif that requires masking by MHCII to allow ER egress. Here, to functionally address the requirement for stoichiometric interactions, we used a recombinant DR heterodimer bearing its own cytoplasmic di-lysine ER-retention motif (DRKKAA). When coexpressed with p33 and a control myc-tagged DR (DRmyc), DRKKAA was retained in the ER but had little impact on surface expression of DRmyc. However, when coexpressed with p35, DRKKAA restricted the surface expression of DRmyc, indicating that Ii trimers can be loaded with more than one MHCII. Similar results were obtained using HLA-DQ instead of DRmyc, showing that a single trimeric Ii scaffold can include distinct MHCII isotypes. Altogether, these results demonstrate that the subunit stoichiometry of oligomeric Ii/MHCII complexes is influenced by p35.

  3. 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...

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

    PubMed

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

    2013-10-15

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

  5. RECOMBINANT SINGLE CHAIN VARIABLE FRAGMENT ANTIBODIES (scFv) AGAINST Pro144-Leu155 FRAGMENT OF HUMAN PROTEIN C.

    PubMed

    Oliinyk, O S; Palyvoda, K O; Lugovskaya, N E; Kolibo, D V; Lugovskoy, E V; Komisarenko, S V

    2015-01-01

    The aim of this work was to obtain the recombinant single chain variable fragments of antibodies (scFv) against human protein C, the key component of blood anticoagulation system. For this purpose a peptide that mimics a Pro144-Leu155 sequence of protein C was synthesized and the murine immune scFv library against this peptide was constructed. The protein C specific scFv 9E were selected from the constructed library by the phage-display method. The scFv 9E dissociation constant was found to be 2∙10(-9) M. It was shown that scFv 9E were suitable for protein C detection by ELISA and Western blotting. Selected scFv could be further used for protein C investigation and for the development of quantitative methods for protein C detection in human blood.

  6. 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

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

    PubMed

    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; Bromme, Dieter

    2003-08-01

    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 alphabeta-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.

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

    SciTech Connect

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

    2013-10-15

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

  9. Construction of single-chain variable fragment antibodies against MCF-7 breast cancer cells.

    PubMed

    Zuhaida, A A; Ali, A M; Tamilselvan, S; Alitheen, N B; Hamid, M; Noor, A M; Yeap, S K

    2013-11-18

    A phage display library of single chain variable fragment (scFv) against MCF-7 breast cancer cells was constructed from C3A8 hybridoma cells. RNA from the C3A8 was isolated, cDNA was constructed, and variable heavy and light immunoglobulin chain gene region were amplified using PCR. The variable heavy and light chain gene regions were combined with flexible linker, linked to a pCANTAB 5E phagemid vector and electrophoresed into supE strain of Escherichia coli TG1 cells. Forty-eight clones demonstrated positive binding activity to MCF-7 breast cancer cell membrane fragments and the strongest of 48 clones was selected for analysis. The anti-MCF-7 library evaluated by SfiI and NotI digests demonstrated that anti-MCF-7 scFv antibodies possess individual patterns that should be able to recognize distinct human breast cancer cells. The C3A8 scFv, with an apparent molecular weight of 32 kDa, showed high homology (99%) with single chain antibody against rice stripe virus protein P20. In summary, the anti MCF-7 scFv antibody can be used for pretargeting breast cancer for clinical diagnosis of patients; it also has potential for therapeutic applications.

  10. Wavepacket delocalization, self-trapping and fragmentation in discrete chains with relaxing nonlinearity

    NASA Astrophysics Data System (ADS)

    Lima, R. P. A.; Gléria, Iram; Cícero, C. H.; Lyra, M. L.; de Moura, F. A. B. F.

    2017-03-01

    The discrete nonlinear Schrodinger equation (DNSE) describes wave phenomena in several physical contexts, ranging from electronic transport in crystalline chains to light propagation in nonlinear media and Bose-Einstein condensates. Here, we study the influence of the nonlinear response time on the temporal evolution of a wavepacket initially localized in a single site of a finite closed chain. Distinct long-time wavepacket distributions are identified as a function of the nonlinear strength χ and the characteristic relaxation time τ. Besides the more standard delocalized and self-trapped regimes, we report the occurrence of intermediate phases. In one of them the wavepacket self-focus in the opposite chain site. A phase with asymptotically fragmented wavepackets also develops. A crossover regime on which the ultimate wavepacket distribution is strongly dependent on the precise set of model parameters is also identified. We provide the full phase diagram related to the long-time wavepacket distribution in the (χ, τ) space.

  11. Selection of single chain variable fragments specific for the human-inducible costimulator using ribosome display.

    PubMed

    Pan, Yangbin; Mao, Weiping; Liu, Xuanxuan; Xu, Chong; He, Zhijuan; Wang, Wenqian; Yan, Hao

    2012-11-01

    We applied a ribosome display technique to a mouse single chain variable fragment (scFv) library to select scFvs specific for the inducible costimulator (ICOS). mRNA was isolated from the spleens of BALB/c mice immunized with ICOS protein. Heavy and κ chain genes (VH and κ) were amplified separately by reverse transcriptase polymerase chain reaction, and the anti-ICOS VH/κ chain ribosome display library was constructed with a special flexible linker by overlap extension PCR. The VH/κ chain library was transcribed and translated in vitro using a rabbit reticulocyte lysate system. Then, antibody-ribosome-mRNA complexes were produced and panned against ICOS protein under appropriate conditions. However, in order to isolate specific scFvs for ICOS, negative selection using CD28 was carried out before three rounds of positive selection on ICOS. After three rounds of panning, the selected scFv DNAs were cloned into pET43.1a and detected by SDS-PAGE. Then, enzyme-linked immunosorbent assay showed that we successfully constructed a native ribosome display library, and among seven clones, clone 5 had the highest affinity for the ICOS and low for the CD28. Anti-ICOS scFvs are assessed for binding specificity and affinity and may provide the potential for development of the humanized and acute and chronic allograft rejection.

  12. Stress relaxation via addition-fragmentation chain transfer in a thiol-ene photopolymerization

    PubMed Central

    Kloxin, Christopher J.; Scott, Timothy F.; Bowman, Christopher N.

    2009-01-01

    Allyl sulfide addition-fragmentation chain transfer was employed concurrently with the radical-mediated formation of a thiol-ene network to enable network adaptation and mitigation of polymerization-induced shrinkage stress. This result represents the first demonstration of simultaneous polymerization and network adaptation in covalently crosslinked networks with significant implications for the fabrication of low stress polymer networks. For comparison, analogous networks incorporating propyl sulfide moieties, incapable of addition-fragmentation, were synthesized and evaluated in parallel. At the highest irradiation intensity, the allyl sulfide-containing material demonstrated a more than 75% reduction in the final stress when compared with the propyl sulfide-containing material. Analysis of the conversion evolution revealed that allyl sulfide addition-fragmentation decreased the polymerization rate owing to thiyl radical sequestration. Slow consumption of the allyl sulfide functional group suggests that intramolecular homolytic substitution occurs by a step-wise, rather than concerted, mechanism. Simultaneous stress and conversion measurements demonstrated that the initial stress evolution was identical for both the allyl and propyl sulfide-containing materials but diverged after gelation. While addition-fragmentation chain transfer was found to occur throughout the polymerization, its effect on the stress evolution was concentrated towards the end of polymerization when network rearrangement becomes the dominant mechanism for stress relaxation. Even after the polymerization reaction was completed, the polymerization-induced shrinkage stress in the allyl sulfide-containing material continued to decrease, exhibiting a maximum in the stress evolution and demonstrating the potential for continuing, longer term stress relaxation. PMID:20160931

  13. Production of single chain Fab (scFab) fragments in Bacillus megaterium

    PubMed Central

    Jordan, Eva; Al-Halabi, Laila; Schirrmann, Thomas; Hust, Michael; Dübel, Stefan

    2007-01-01

    Background The demand on antigen binding reagents in research, diagnostics and therapy raises questions for novel antibody formats as well as appropriate production systems. Recently, the novel single chain Fab (scFab) antibody format combining properties of single chain Fv (scFv) and Fab fragments was produced in the Gram-negative bacterium Escherichia coli. In this study we evaluated the Gram-positive bacterium Bacillus megaterium for the recombinant production of scFab and scFvs in comparison to E. coli. Results The lysozyme specific D1.3 scFab was produced in B. megaterium and E. coli. The total yield of the scFab after purification obtained from the periplasmic fraction and culture supernatant of E. coli was slightly higher than that obtained from culture supernatant of B. megaterium. However, the yield of functional scFab determined by analyzing the antigen binding activity was equally in both production systems. Furthermore, a scFv fragment with specificity for the human C reactive protein was produced in B. megaterium. The total yield of the anti-CRP scFv produced in B. megaterium was slightly lower compared to E. coli, whereas the specific activity of the purified scFvs produced in B. megaterium was higher compared to E. coli. Conclusion B. megaterium allows the secretory production of antibody fragments including the novel scFab antibody format. The yield and quality of functional antibody fragment is comparable to the periplasmic production in E. coli. PMID:18042285

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  15. Polymerase chain reaction-restriction fragment length polymorphism analysis of a 16S rRNA gene fragment for authentication of four clam species.

    PubMed

    Fernandez, Alicia; García, Teresa; Gonzalez, Isabel; Asensio, Luis; Rodriguez, Miguel Angel; Hernández, Pablo E; Martin, Rosario

    2002-04-01

    Specific identification of four clam species, Ruditapes decussatus (grooved carpet shell), Venerupis pullastra (pullet carpet shell), Ruditapes philippinarum (Japanese carpet shell), and Venerupis rhomboides (yellow carpet shell), was achieved by polymerase chain reaction-restriction fragment length polymorphism analysis of a fragment of the mitochondrial 16S rRNA gene. Amplification of DNA isolated from the foot muscle produced fragments of 511 bp for V. pullastra, 523 bp for R. decussatus, 545 bp for R. philippinarum, and 502 bp for V. rhomboides. The restriction profiles obtained by agarose gel electrophoresis when amplicons were digested with endonucleases BsmAI and BsrI allowed unequivocal identification of the four clam species. This approach would be less costly, simpler, and quicker than conventional sequencing of polymerase chain reaction products followed by detailed comparison of individual sequences, especially when large numbers of samples need to be analyzed.

  16. 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.

  17. Human invariant chain isoform p35 restores thymic selection and antigen presentation in CD74-deficient mice.

    PubMed

    Genève, Laetitia; Chemali, Magali; Desjardins, Michel; Labrecque, Nathalie; Thibodeau, Jacques

    2012-10-01

    The invariant chain (Ii) has pleiotropic functions and is a key factor in antigen presentation. Ii associates with major histocompatibility complex class II molecules in the endoplasmic reticulum (ER) and targets the complex in the endocytic pathway to allow antigenic peptide loading. The human Iip35 isoform includes a cytoplasmic extension containing a di-arginine motif causing ER retention. This minor isoform does not exist in mice and its function in humans has not been thoroughly investigated. We have recently generated transgenic mice expressing Iip35 and these were crossed with Ii-deficient mice to generate animals (Tgp35/mIiKO) expressing exclusively the human isoform. In these mice, we show that Iip35 is expressed in antigen presenting cells and is inducible by interferon gamma (IFN-γ). Despite the low constitutive expression of the protein and some minor differences in the Vβ repertoire of Tgp35/mIiKO mice, Iip35 restored thymic selection of CD4(+) T cells and of invariant natural killer T cells. In vitro functional assays using purified primary macrophages treated with IFN-γ showed that Iip35 allows presentation of an Ii-dependent ovalbumin T-cell epitope. Altogether, our results suggest that Iip35 is functional and does not require co-expression of other isoforms for antigen presentation.

  18. Magnetization Plateau of the S = 1/2 Frustrated Heisenberg Chain with Period 3 Parity Invariant Exchange Modulation

    NASA Astrophysics Data System (ADS)

    Hida, K.; Affleck, I.

    The magnetization plateau of the S = 1/2 frustrated Heisenberg chain with period 3 parity invariant exchange modulation is investigated by the bosonization and numerical exact diagonalization method. The ground state phase diagram at 1/3 of the saturated magnetization is obtained. Among three degenerate \\uparrow\\uparrowdownarrow-type plateau states in the uniform chain, two of them (downarrow\\uparrow\\uparrowdownarrow\\uparrow\\uparrow\\cdots\\ and \\uparrowdownarrow\\uparrow\\uparrowdownarrow\\uparrow\\cdots\\ ) turned out to be robust against the period 3 exchange modulation which favors the bullet-bullet\\uparrowbullet-bullet\\uparrow\\cdots phase up to a critical value of the modulation amplitude (bullet-bullet = singlet dimer) resulting in the Z_2 symmetry broken phase. Another \\uparrow\\uparrowdownarrow-type state with \\uparrow\\uparrowdownarrow\\uparrow\\uparrowdownarrow\\cdots\\ configuration is stabilized for period 3 modulation with opposite sign. The transition between the bullet-bullet\\uparrowbullet-bullet\\uparrow\\cdots\\ -phase and Z_2-broken phase is the Ising transition and that between the \\uparrow\\uparrowdownarrow\\uparrow\\uparrowdownarrow\\cdots\\ -phase and Z_2 broken phase is the first order transition. The spin configuration in each phase is numerically verified by applying the local symmetry breaking field.

  19. Human single-chain variable fragment antibody inhibits macrophage migration inhibitory factor tautomerase activity.

    PubMed

    Tarasuk, Mayuri; Poungpair, Ornnuthchar; Ungsupravate, Duangporn; Bangphoomi, Kunan; Chaicumpa, Wanpen; Yenchitsomanus, Pa-Thai

    2014-03-01

    Macrophage migration inhibitory factor (MIF) is a pro-inflammatory cytokine, secreted from a variety of immune cells, that regulates innate and adaptive immune responses. Elevation of MIF levels in plasma correlates with the severity of inflammatory diseases in humans. Inhibition of MIF or its tautomerase activity ameliorates disease severity by reducing inflammatory responses. In this study, the human single-chain variable fragment (HuScFv) antibody specific to MIF was selected from the human antibody phage display library by using purified recombinant full-length human MIF (rMIF) as the target antigen. Monoclonal HuScFv was produced from phage-transformed bacteria and tested for their binding activities to rMIF by indirect enzyme-linked immunosorbent assay as well as to native MIF by western blot analysis and immunofluorescence assay. The HuScFv with highest binding signal to rMIF also inhibited the tautomerase activities of both rMIF and native MIF in human monoblastic leukemia (U937) cells in a dose-dependent manner. Mimotope searching and molecular docking concordantly demonstrated that the HuScFv interacted with Lys32 and Ile64 in the MIF tautomerase active site. To the best of our knowledge, this is the first study to focus on MIF-specific fully-human antibody fragment with a tautomerase-inhibitory effect that has potential to be developed as anti-inflammatory biomolecules for human use.

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

    PubMed

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

    2011-08-01

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

  1. 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

  2. Duplex microfluidic SERS detection of pathogen antigens with nanoyeast single-chain variable fragments.

    PubMed

    Wang, Yuling; Rauf, Sakandar; Grewal, Yadveer S; Spadafora, Lauren J; Shiddiky, Muhammad J A; Cangelosi, Gerard A; Schlücker, Sebastian; Trau, Matt

    2014-10-07

    Quantitative and accurate detection of multiple biomarkers would allow for the rapid diagnosis and treatment of diseases induced by pathogens. Monoclonal antibodies are standard affinity reagents applied for biomarkers detection; however, their production is expensive and labor-intensive. Herein, we report on newly developed nanoyeast single-chain variable fragments (NYscFv) as an attractive alternative to monoclonal antibodies, which offers the unique advantage of a cost-effective production, stability in solution, and target-specificity. By combination of surface-enhanced Raman scattering (SERS) microspectroscopy using glass-coated, highly purified SERS nanoparticle clusters as labels, with a microfluidic device comprising multiple channels, a robust platform for the sensitive duplex detection of pathogen antigens has been developed. Highly sensitive detection for individual Entamoeba histolytica antigen EHI_115350 (limit of detection = 1 pg/mL, corresponding to 58.8 fM) and EHI_182030 (10 pg/mL, corresponding 453 fM) with high specificity has been achieved, employing the newly developed corresponding NYscFv as probe in combination with SERS microspectroscopy at a single laser excitation wavelength. Our first report on SERS-based immunoassays using the novel NYscFv affinity reagent demonstrates the flexibility of NYscFv fragments as viable alternatives to monoclonal antibodies in a range of bioassay platforms and paves the way for further applications.

  3. Expression and production of llama variable heavy-chain antibody fragments (V(HH)s) by Aspergillus awamori.

    PubMed

    Joosten, Vivi; Gouka, Robin J; van den Hondel, Cees A M J J; Verrips, C Theo; Lokman, B Christien

    2005-01-01

    We report the expression and production of llama variable heavy-chain antibody fragments (V(HH)s) by Aspergillus awamori. Fragments encoding V(HH)s were cloned in a suitable Aspergillus expression vector and transformants secreting V(HH) fragments were analysed for integrated gene copy-numbers, mRNA levels and protein production. Functional V(HH)s were detected in the culture medium, indicating the feasibility of producing this type of protein in a fungal expression system. Secreted V(HH)s were subjected to (extracellular) degradation, which could be partially prevented by the addition of BSA to the culture medium.

  4. 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.

  5. Expression of recombinant antibody (single chain antibody fragment) in transgenic plant Nicotiana tabacum cv. Xanthi.

    PubMed

    Dobhal, S; Chaudhary, V K; Singh, A; Pandey, D; Kumar, A; Agrawal, S

    2013-12-01

    Plants offer an alternative inexpensive and convenient technology for large scale production of recombinant proteins especially recombinant antibodies (plantibodies). In this paper, we describe the expression of a model single chain antibody fragment (B6scFv) in transgenic tobacco. Four different gene constructs of B6scFv with different target signals for expression in different compartments of a tobacco plant cell with and without endoplasmic reticulum (ER) retention signal were used. Agrobacterium mediated plant transformation of B6scFv gene was performed with tobacco leaf explants and the gene in regenerated plants was detected using histochemical GUS assay and PCR. The expression of B6scFv gene was detected by western blotting and the recombinant protein was purified from putative transgenic tobacco plants using metal affinity chromatography. The expression level of recombinant protein was determined by indirect enzyme-linked immunosorbent assay. The highest accumulation of protein was found up to 3.28 % of the total soluble protein (TSP) in plants expressing B6scFv 1003 targeted to the ER, and subsequently expression of 2.9 % of TSP in plants expressing B6scFv 1004 (with target to apoplast with ER retention signal). In contrast, lower expression of 0.78 and 0.58 % of TSP was found in plants expressing antibody fragment in cytosol and apoplast, without ER retention signal. The described method/system could be used in the future for diverse applications including expression of other recombinant molecules in plants for immunomodulation, obtaining pathogen resistance against plant pathogens, altering metabolic pathways and also for the expression of different antibodies of therapeutic and diagnostic uses.

  6. 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.

  7. 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...

  8. Class II–Associated Invariant Chain Peptide Expression Represents a Novel Parameter for Flow Cytometric Detection of Acute Promyelocytic Leukemia

    PubMed Central

    van Luijn, Marvin M.; Westers, Theresia M.; Chamuleau, Martine E.D.; van Ham, S. Marieke; Ossenkoppele, Gert J.; van de Loosdrecht, Arjan A.

    2011-01-01

    Because of severe bleeding complications, patients with acute promyelocytic leukemia (APL) have to be treated with all-trans retinoic acid immediately following diagnosis. In addition to morphology, flow cytometry contributes to a rapid detection of APL according to phenotypic characteristics of leukemic cells. In some patients, these analyses are inconclusive or even contradictory to diagnosis. Previously, we showed the clinical and functional impact of class II–associated invariant chain peptide (CLIP) in acute myeloid leukemia (AML). This study focuses on the analysis of CLIP expression on leukemic cells to characterize HLA-DR–negative AML, including APL. We demonstrate exclusive and significant CLIP expression in all cases of typical and variant APL, as compared to other HLA-DR–negative non–APL-type AML. CLIP appears to be a highly sensitive and specific flow cytometric marker, resolving discrepant identification of both genetic subgroups. Our findings show the additive value of CLIP analysis for a fast and unequivocal recognition of APL by flow cytometry in conjunction with morphology. PMID:21907692

  9. Isolation of human single chain variable fragment antibodies against specific sperm antigens for immunocontraceptive development

    PubMed Central

    Samuel, A.S.; Naz, R.K.

    2008-01-01

    BACKGROUND Contraceptive vaccines can provide valuable alternatives to current methods of contraception. We describe here the development of sperm-reactive human single chain variable fragment (scFv) antibodies of defined sperm specificity for immunocontraception. METHODS Peripheral blood leukocytes (PBL) from antisperm antibody-positive immunoinfertile and vasectomized men were activated with human sperm antigens in vitro, and the complementary DNA prepared and PCR-amplified using primers based on all the variable regions of heavy and light chains of immunoglobulins. The scFv repertoire was cloned into pCANTAB5E vector to create a human scFv antibody library. RESULTS Panning of the library against specific sperm antigens yielded several clones, and the four strongest reactive were selected for further analysis. These clones had novel sequences with unique complementarity-determining regions. ScFv antibodies were expressed, purified and analyzed for human sperm reactivity and effect on human sperm function. AFA-1 and FAB-7 scFv antibodies both reacted with fertilization antigen-1 antigen, but against different epitopes. YLP20 antibody reacted with the expected human sperm protein of 48 ± 5 kDa. The fourth antibody, AS16, reacted with an 18 kDa sperm protein and seems to be a human homologue of the mouse monoclonal recombinant antisperm antibody that causes sperm agglutination. All these antibodies inhibited human sperm function. CONCLUSIONS This is the first study to report the use of phage display technology to obtain antisperm scFv antibodies of defined antigen specificity. These antibodies will find clinical applications in the development of novel immunocontraceptives, and specific diagnostics for immunoinfertility. PMID:18372255

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

    PubMed

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

    2014-09-01

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

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

    PubMed Central

    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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    Wang, Man; Zhang, Yan; Zhu, Jianguo

    2016-03-01

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

  14. Isolation and characterization of anti ROR1 single chain fragment variable antibodies using phage display technique.

    PubMed

    Aghebati-Maleki, Leili; Younesi, Vahid; Jadidi-Niaragh, Farhad; Baradaran, Behzad; Majidi, Jafar; Yousefi, Mehdi

    2017-01-01

    Receptor tyrosine kinase-like orphan receptor (ROR1) belongs to one of the families of receptor tyrosine kinases (RTKs). RTKs are involved in the various physiologic cellular functions including proliferation, migration, survival, signaling and differentiation. Several RTKs are deregulated in various cancers implying the targeting potential of these molecules in cancer therapy. ROR1 has recently been shown to be expressed in various types of cancer cells but not in normal adult cells. Hence a molecular inhibitor of extracellular domain of ROR1 that inhibits ROR1-cell surface interaction is of great therapeutic importance. In an attempt to develop molecular inhibitors of ROR1, we screened single chain variable fragment (scFv) phage display libraries, Tomlinson I + J, against one specific synthetic oligopeptide from extracellular domain of ROR1 and selected scFvs were characterized using various immunological techniques. Several ROR1 specific scFvs were selected following five rounds of panning procedure. The scFvs showed specific binding to ROR1 using immunological techniques. Our results demonstrate successful isolation and characterization of specific ROR1 scFvs that may have great therapeutic potential in cancer immunotherapy.

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

    PubMed

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

    2016-01-01

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

  16. 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.

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

    PubMed

    Hu, Guodong; Chen, L Y

    2010-12-01

    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, κlight chain, K(d)=11nM). The first set of in silico experiments are long time equilibration runs of scFv:drug complexes and of drug-free scFv both in the solution. They demonstrate how the solution structures of scFv deviate from its crystallographic form with or without drug molecules bound to it. 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 the 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 results.

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

    PubMed Central

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

    2011-01-01

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

  19. Exploiting cross-reactivity to neutralize two different scorpion venoms with one single chain antibody fragment.

    PubMed

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

    2011-02-25

    We report the optimization of a family of human single chain antibody fragments (scFv) for neutralizing two scorpion venoms. The parental scFv 3F recognizes the main toxins of Centruroides noxius Hoffmann (Cn2) and Centruroides suffusus suffusus (Css2), albeit with low affinity. This scFv was subjected to independent processes of directed evolution to improve its recognition toward Cn2 (Riaño-Umbarila, L., Juárez-González, V. R., Olamendi-Portugal, T., Ortíz-León, M., Possani, L. D., and Becerril, B. (2005) FEBS J. 272, 2591-2601) and Css2 (this work). Each evolved variant showed strong cross-reactivity against several toxins, and was capable of neutralizing Cn2 and Css2. Furthermore, each variant neutralized the whole venoms of the above species. As far as we know, this is the first report of antibodies with such characteristics. Maturation processes revealed key residue changes to attain expression, stability, and affinity improvements as compared with the parental scFv. Combination of these changes resulted in the scFv LR, which is capable of rescuing mice from severe envenomation by 3 LD(50) of freshly prepared whole venom of C. noxius (7.5 μg/20 g of mouse) and C. suffusus (26.25 μg/20 g of mouse), with surviving rates between 90 and 100%. Our research is leading to the formulation of an antivenom consisting of a discrete number of human scFvs endowed with strong cross-reactivity and low immunogenicity.

  20. Inhibiting angiogenesis with human single-chain variable fragment antibody targeting VEGF.

    PubMed

    Hosseini, Hossien; Rajabibazl, Masoumeh; Ebrahimizadeh, Walead; Dehbidi, Gholamreza Rafiei

    2015-01-01

    Vascular endothelial growth factor (VEGF) is a highly specific angiogenesis factor which has crucial roles in the angiogenesis of tumors. Anti-angiogenesis agents can inhibit growth and metastasis of tumor cells. Single-chain variable fragments (scFv) have the same affinity as whole antibodies and smaller size, thus result in more tissue permeability and higher production yield. In this research we aim to isolate a human scFv antibody against VEGF that inhibits angiogenesis. For that, we have used human scFv phage library to isolate a specific scFv antibody against binding site of VEGF. The human scFv phage library was amplified according to the manufacture protocol and panned against recombinant VEGF. ScFv antibody was isolated after five rounds of panning. Phage ELISA was used for detection of the highest affinity binder (HR6). Soluble HR6 scFv was expressed in non-suppressor strain of Escherichia coli HB2151 and purified using Ni-NTA chromatography. In vivo and in vitro function of the HR6 scFv was analyzed by chorioallantoic membrane assay and endothelial cell proliferation assay on VEGF stimulated HUVECs. Result of the cross reactivity showed that HR6 scFv specifically bounds to VEGF. The affinity was calculated to be 1.8×10(-7)M. HR6 could stop HUVEC proliferation in a dose dependent manner and anti-angiogenesis activity was observed using 10μg of HR6 in chorioallantoic membrane assay. In this work, we demonstrate that a HR6 scFv selected from human library phage display specifically blocks VEGF signaling, furthermore, this scFv has an anti-angiogenesis effect and because of its small size has more tissue diffusion. The HR6 antibody was isolated form a human library thus, it is not immunogenic for humans and could serve as a potential therapeutic agent in cancer.

  1. Isolation and characterization of anti c-met single chain fragment variable (scFv) antibodies.

    PubMed

    Qamsari, Elmira Safaie; Sharifzadeh, Zahra; Bagheri, Salman; Riazi-Rad, Farhad; Younesi, Vahid; Abolhassani, Mohsen; Ghaderi, Sepideh Safaei; Baradaran, Behzad; Somi, Mohammad Hossein; Yousefi, Mehdi

    2017-12-01

    The receptor tyrosine kinase (RTK) Met is the cell surface receptor for hepatocyte growth factor (HGF) involved in invasive growth programs during embryogenesis and tumorgenesis. There is compelling evidence suggesting important roles for c-Met in colorectal cancer proliferation, migration, invasion, angiogenesis, and survival. Hence, a molecular inhibitor of an extracellular domain of c-Met receptor that blocks c-Met-cell surface interactions could be of great thera-peutic importance. In an attempt to develop molecular inhibitors of c-Met, single chain variable fragment (scFv) phage display libraries Tomlinson I + J against a specific synthetic oligopeptide from the extracellular domain of c-Met receptor were screened; selected scFv were then characterized using various immune techniques. Three c-Met specific scFv (ES1, ES2, and ES3) were selected following five rounds of panning procedures. The scFv showed specific binding to c-Met receptor, and significantly inhibited proliferation responses of a human colorectal carcinoma cell line (HCT-116). Moreover, anti- apoptotic effects of selected scFv antibodies on the HCT-116 cell line were also evaluated using Annexin V/PI assays. The results demonstrated rates of apoptotic cell death of 46.0, 25.5, and 37.8% among these cells were induced by use of ES1, ES2, and ES3, respectively. The results demonstrated ability to successfully isolate/char-acterize specific c-Met scFv that could ultimately have a great therapeutic potential in immuno-therapies against (colorectal) cancers.

  2. 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.

  3. Functional CD1d and/or NKT cell invariant chain transcript in horse, pig, African elephant and guinea pig, but not in ruminants

    PubMed Central

    Looringh van Beeck, Frank A.; Reinink, Peter; Hermsen, Roel; Zajonc, Dirk M.; Laven, Marielle J.; Fun, Axel; Troskie, Milana; Schoemaker, Nico J.; Morar, Darshana; Lenstra, Johannes A.; Vervelde, Lonneke; Rutten, Victor P.M.G.; van Eden, Willem; Van Rhijn, Ildiko

    2009-01-01

    CD1d-restricted invariant natural killer T cells (NKT cells) have been well characterized in humans and mice, but it is unknown whether they are present in other species. Here we describe the invariant TCR α chain and the full length CD1d transcript of pig and horse. Molecular modeling predicts that porcine (po) invariant TCR α chain/poCD1d/α-GalCer and equine (eq) invariant TCR α chain/eqCD1d/α-GalCer form complexes that are highly homologous to the human complex. Since a prerequisite for the presence of NKT cells is the expression of CD1d protein, we performed searches for CD1D genes and CD1d transcripts in multiple species. Previously, cattle and guinea pig have been suggested to lack CD1D genes. The CD1D genes of European taurine cattle (Bos taurus) are known to be pseudogenes because of disrupting mutations in the start codon and in the donor splice site of the first intron. Here we show that the same mutations are found in six other ruminants: African buffalo, sheep, bushbuck, bongo, N’Dama cattle, and roe deer. In contrast, intact CD1d transcripts were found in guinea pig, African elephant, horse, rabbit, and pig. Despite the discovery of a highly homologous NKT/CD1d system in pig and horse, our data suggest that functional CD1D and CD1d-restricted NKT cells are not universally present in mammals. PMID:19185921

  4. 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.

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

    PubMed Central

    2013-01-01

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

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

    PubMed

    Gupta, Chetali; Washburn, Newell R

    2014-08-12

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

  7. Construction of eigenfunctions for a system of quantum minors of the monodromy matrix for an SL( n,ℂ)-invariant spin chain

    NASA Astrophysics Data System (ADS)

    Valinevich, P. A.; Derkachov, S. É.; Kulish, P. P.; Uvarov, E. M.

    2016-11-01

    We consider the problem of seeking the eigenvectors for a commuting family of quantum minors of the monodromy matrix for an SL(n,ℂ)-invariant inhomogeneous spin chain. The algebra generators and elements of the L-operator at each site of the chain are implemented as linear differential operators in the space of functions of n(n-1)/2 variables. In the general case, the representation of the sln(ℂ) algebra at each site is infinite-dimensional and belongs to the principal unitary series. We solve this problem using a recursive procedure with respect to the rank n of the algebra. We obtain explicit expressions for the eigenvalues and eigenvectors of the commuting family. We consider the particular cases n = 2 and n = 3 and also the limit case of the one-site chain in detail.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  9. Polymerase chain reaction-restriction fragment-length polymorphism method to distinguish Liriomyza huidobrensis from L. Langei (Diptera: Agromyzidae) applied to three recent leafminer invasions.

    PubMed

    Scheffer, S J; Wijesekara, A; Visser, D; Hallett, R H

    2001-10-01

    A molecular method is presented for differentiating the morphologically cryptic leafminers Liriomyza langei Frick and L. huidobrensis (Blanchard). This method requires polymerase chain reaction (PCR) amplification of a 1031-bp region of mitochondrial cytochrome oxidase DNA followed by restriction fragment analysis using the restriction enzymes SpeI and EcoRV. Spel cuts the mitochondrial fragment of L. langei into two fragments, but does not cut the L. huidobrensis fragment. EcoRV cuts the L. huidobrensis fragment into two fragments, but does not cut the L. langei fragment. This PCR-restriction fragment-length polymorphism (RFLP) method is faster and less costly than DNA sequencing,which is currently the only other way to differentiate these two species. We apply the method to samples from recently introduced leafminer populations in Sri Lanka, Canada, and South Africa and find that the invasive leafminer in all three locations is L. huidobrensis.

  10. 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 (V(H )and V(L)) 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 V(H) and V(L) 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.

  11. Preventing phage lysis of Lactococcus lactis in cheese production using a neutralizing heavy-chain antibody fragment from llama.

    PubMed

    Ledeboer, A M; Bezemer, S; de Hiaard, J J W; Schaffers, I M; Verrips, C T; van Vliet, C; Düsterhöft, E M; Zoon, P; Moineau, S; Frenken, L G J

    2002-06-01

    Bacteriophage infection is still a persistent problem in large dairy processes despite extensive studies over the last decades. Consequently, new methods are constantly sought to prevent phage infection. In this paper, we show that phage neutralizing heavy-chain antibody fragments, obtained from Camelidae and produced at a large scale in the generally regarded as safe microorganism Saccharomyces cerevisiae, can effectively be used to impede phage induced lysis during a cheese process. The growth inhibition of the cheese starter culture by 10(5) pfu/ml cheese-milk of the small isometric-headed 936-type phage p2 was prevented by the addition of only 0.1 microg/ml (7 nM) of the neutralizing antibody fragment. The use of such antibody fragments in cheese manufacturing are a realistic and interesting option because of the small amount of antibody fragments that are needed. Moreover the antibodies are produced in a food grade microorganism and can easily be isolated from the fermentation liquid in a pure and DNA free form.

  12. Polymerase chain reaction-restriction fragment length polymorphism analysis: a simple method for species identification in food.

    PubMed

    Meyer, R; Höfelein, C; Lüthy, J; Candrian, U

    1995-01-01

    The polymerase chain reaction (PCR) technique was applied to meat species identification in marinated and heat-treated or fermented products and to the differentiation of closely related species. DNA was isolated from meat samples by using a DNA-binding resin and was subjected to PCR analysis. Primers used were complementary to conserved areas of the vertebrate mitochondrial cytochrome b (cytb) gene and yielded a 359 base-pair (bp) fragment, including a variable 307 bp region. Restriction endonuclease analysis based on sequence data of those fragments was used for differentiation among species. Restriction fragment length polymorphisms (RFLPs) were detected when pig, cattle, wild boar, buffalo, sheep, goat, horse, chicken, and turkey amplicons were cut with AluI, RsaI, TaqI, and HinfI. Analysis of sausages indicates the applicability of this approach to food products containing meat from 3 different species. The PCR-RFLP analytical method detected pork in heated meat mixtures with beef at levels below 1%, and the method was confirmed with porcine- and bovine-specific PCR assays by amplifying fragments of their growth hormone genes. Inter- and intraspecific differences of more than 22 animal species with nearly unknown cytb DNA sequences, including hoofed mammals (ungulates), and poultry were determined with PCR-RFLP typing by using 20 different endonucleases. This typing method allowed the discrimination of game meats, including stag, roe deer, chamois, moose, reindeer, kangaroo, springbok, and other antelopes in marinated and heat-treated products.

  13. Development of competitive ELISA for the detection of bovine serum albumin using single-chain variable fragments.

    PubMed

    Liu, Yuan; Lin, Manman; Zhang, Xifeng; Hu, Xiaodan; Lin, Jieru; Hao, Jia; He, Dan; Zhang, Xiao; Xu, Chongxin; Zhong, Jianfeng; Xie, Yajing; Zhang, Cunzheng; Liu, Xianjin

    2017-05-15

    Soluble anti-bovine serum albumin (BSA) single-chain variable fragments (scFvs) were expressed in E. Coli. HB2151. The antigen-binding equilibrium dissociation constant of the scFvs was determined to be 2.9 × 10(-8) M by surface plasmon resonance analysis. A competitive ELISA for the detection of BSA was developed using the antibody fragment above. The limits of detection (I10) and I50 were 0.002 and 0.74 μg/ml respectively, with a recovery between 87.8 and 119.2% in spiked milk samples. The assay has the potential to be used to detect concentration of BSA in milk or other matrix instead of the ELISA based on traditional antibodies.

  14. Vaccination with recombinant whole heavy chain fragments of Clostridium botulinum Type C and D neurotoxins.

    PubMed

    Arimitsu, Hideyuki; Lee, Jae-Chul; Sakaguchi, Yoshihiko; Hayakawa, Yuji; Hayashi, Michiko; Nakaura, Miki; Takai, Hikaru; Lin, Song-Nan; Mukamoto, Masafumi; Murphy, Tom; Oguma, Keiji

    2004-05-01

    Mice and ducks were subcutaneously immunized with recombinant whole heavy (H) chains of Clostridium botulinum type C and D neurotoxins, which were expressed as glutathione S-transferase fusion proteins. In the case of mice, it was confirmed that two immunizations with type C- and D-H chains, 10 microg each time, significantly increased the specific antibodies against 100-kDa H chains of type C and D neurotoxins in an immunoblot analysis and an enzyme-linked immunosorbent assay, respectively. The mice immunized with type C- and D-H chains showed no symptoms of botulism when they were challenged with C- and D-16 S toxins at doses, given intraperitoneally, of up to 10(5) and 10(6) minmum lethal doses (MLD), respectively, per mouse. Ducks were immunized with a total of 100 microg of type C-H chain. The ducks also developed specific antibodies to the type C-H chain and showed significant protection against a challenge with 10(3) duck MLD of C-16 S toxin given intravenously. These results indicate that recombinant whole H chains can be used as an effective and safe vaccine for type C and D botulism in domestic animals.

  15. 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.

  16. Generation of a recombinant single-chain variable fragment (scFv) targeting 5-methyl-2'-deoxycytidine.

    PubMed

    Ohshima, Motohiro; Tadakuma, Tomomi; Hayashi, Hideki; Inoue, Kazuyuki; Itoh, Kunihiko

    2010-01-01

    We generated a single-chain variable fragment (scFv) against 5-methyl-2'-deoxycytidine (m(5)dCyd) using phage display technology. The heavy and light chain variable region genes were amplified by the polymerase chain reaction (PCR) from hybridoma cell line FMC9 and assembled as an scFv fragment with a flexible linker (Gly(4)-Ser)(3). The scFv DNA fragment was then cloned into pCANTAB-5E, and a phage displaying the scFv was produced. Antigen-positive phage clones were successfully selected by enzyme-linked immunosorbent assay (ELISA). The scFv was modified with FLAG and His tags for detection and purification. The scFv reacted strongly with m(5)dCyd and weakly with 5-methylcytidine (m(5)Cyd) but not with cytidine (Cyd) and 1-methyladenosine in a manner similar to the monoclonal antibody (MoAb). Although the specificities of scFv and MoAb were almost identical, the sensitivity of the scFv (IC(50) 0.054 microg/ml) was approximately 80 times higher than that of the parent MoAb (IC(50) 4.27 microg/ml), determined by inhibition ELISA. As a biochemical application of this scFv, we quantified the m(5)dCyd content of genomic DNA by enzymatic hydrolysis using inhibition ELISA. The cancer cell lines HeLa, HeLa S3 and MDA-MB-453 contained approximately 1% of the methylated DNA in total genomic DNA, as did peripheral blood cell genomic DNA from healthy volunteers, but HT29 and T-47D showed hypomethylation compared with the HeLa, HeLa S3 and MDA-MB-453 cell lines. The scFv generated here may be applicable to the assessment of cellular DNA methylation levels and is more sensitive than the MoAb.

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

    PubMed

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

    2011-04-26

    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 Cu(I) 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.

  18. Carprofen-imprinted monolith prepared by reversible addition-fragmentation chain transfer polymerization in room temperature ionic liquids.

    PubMed

    Ban, Lu; Han, Xu; Wang, Xian-Hua; Huang, Yan-Ping; Liu, Zhao-Sheng

    2013-10-01

    To obtain fast separation, ionic liquids were used as porogens first in combination with reversible addition-fragmentation chain transfer (RAFT) polymerization to prepare a new type of molecularly imprinted polymer (MIP) monolith. The imprinted monolithic column was synthesized using a mixture of carprofen (template), 4-vinylpyridine, ethylene glycol dimethacrylate, [BMIM]BF4, and chain transfer agent (CTA). Some polymerization factors, such as template-monomer molar ratio, the degree of crosslinking, the composition of the porogen, and the content of CTA, on the column efficiency and imprinting effect of the resulting MIP monolith were systematically investigated. Affinity screening of structurally similar compounds with the template can be achieved in 200 s on the MIP monolith due to high column efficiency (up to 12,070 plates/m) and good column permeability. Recognition mechanism of the imprinted monolith was also investigated.

  19. Invariant chain+ N2a neuroblastoma cells stably expressing the class II MHC transactivator CIITA fail to stimulate anti-tumor immunity.

    PubMed

    Rickard, Steve; Ono, Santa Jeremy

    2008-12-01

    A promising cancer treatment strategy involves stimulation of anti-tumor immune responses. CD4(+) T cell responses are particularly desirable, as they enhance CD8(+) T cell activity and provide immune memory. The major histocompatibility complex (MHC) class II transactivator CIITA can be used to stimulate expression of MHC II on tumor cells, thereby promoting CD4(+) T cell activation. In this study, N2a neuroblastoma cells were stably transfected with CIITA. N2aCIITA cells displayed increased expression of MHC I, MHC II and invariant chain; CD80 and CD86 were expressed by neither the parental N2a cells nor by the N2aCIITA cells. All mice injected with N2aCIITA cells developed tumors. Furthermore, no increase in the numbers of T cells, natural killer cells, macrophages, or eosinophils was observed in the spleens or tumors of mice injected with N2aCIITA cells, compared to tissues from mice injected with the parental N2a cells. This absence of an anti-tumor immune response despite MHC II expression is likely due to the presence of invariant chain, in support of the MHCII(+)/Ii(-) paradigm.

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

    PubMed Central

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

    1995-01-01

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

  1. Development of a hyperimmune anti-MUC-1 single chain antibody fragments phage display library for targeting breast cancer.

    PubMed

    Winthrop, M D; DeNardo, S J; DeNardo, G L

    1999-10-01

    Radioimmunotherapy (RIT) has demonstrated potential for improving clinical cancer therapy. Optimizing the approach has proven difficult thus far. Antibody phage display libraries provide unique molecules that could improve RIT. A phage display library of single chain antibody fragments (scFv) against the MUC-1 mucin molecule, which is expressed on 90% of human breast cancers, was produced from the spleen cells of MUC-1 hyperimmunized BALB/c mice. Increased serum IgG levels, 15 times baseline, were detected following the third immunization. RNA from the spleen cells was isolated, cDNA was made, and variable heavy and variable light immunoglobulin chain gene regions were amplified using PCR technology. The variable heavy and variable light chain gene regions were combined with a flexible linker, ligated into the pCANTAB 5E phagemid vector, and electroporated into TG1 Escherichia coli cells. A library of 10(7) initial colonies was compiled. Forty-six of 288 colonies screened for reactivity demonstrated binding to MUC-1-expressing MCF-7 breast cancer cell membrane fragments. Anti-MUC-1 library diversity evaluated by BstNI digest demonstrated that 52% of the anti-MUC-1 scFv binding MCF-7 possessed individual banding patterns representative of approximately 5 x 10(5) colonies likely able to recognize distinct epitopes present on MUC-1 positive human breast cancers. In summary, the anti-MUC-1 scFv antibody phage library contains diverse scFv molecules, which should provide unique characteristics and epitope recognition. These molecules will be used in the development of pretargeting RIT strategies designed to improve the clinical outcome of patients with breast cancer.

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

    SciTech Connect

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

    2015-07-20

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

  3. 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

  4. 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.

  5. ER egress of invariant chain isoform p35 requires direct binding to MHCII molecules and is inhibited by the NleA virulence factor of enterohaemorrhagic Escherichia coli.

    PubMed

    Cloutier, Maryse; Gauthier, Catherine; Fortin, Jean-Simon; Genève, Laetitia; Kim, Kyungho; Gruenheid, Samantha; Kim, Jinoh; Thibodeau, Jacques

    2015-04-01

    Four invariant chain (Ii) isoforms assist the folding and trafficking of human MHC class II (MHCIIs). The main isoforms, Iip33 and Iip35, assemble in the ER into homo- and/or hetero-trimers. The sequential binding of up to three MHCII αβ heterodimers to Ii trimers results in the formation of pentamers, heptamers and nonamers. MHCIIs are required to overcome the p35-encoded di-arginine (RxR) ER retention motif and to allow anterograde trafficking of the complex. Here, we show that inactivation of the RxR motif requires a direct cis interaction between p35 and the MHCII, precluding ER egress of some unsaturated Ii trimers. Interestingly, as opposed to MHCII/p33 complexes, those including p35 remained in the ER when co-expressed with the NleA protein of enterohaemorrhagic Escherichia coli. Taken together, our results demonstrate that p35 influences distinctively MHCII/Ii assembly and trafficking.

  6. 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

  7. 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

  8. 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.

  9. 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.

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

    PubMed

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

    2016-01-01

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

  11. 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.

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

    PubMed

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

    2016-06-03

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

  13. Factors affecting the production of a single-chain antibody fragment by Aspergillus awamori in a stirred tank reactor.

    PubMed

    Sotiriadis, A; Keshavarz, T; Keshavarz-Moore, E

    2001-01-01

    A recombinant strain of Aspergillus awamori expressing anti-lysozyme single chain antibody fragments (scFv), under the control of a xylanase promoter, was studied in order to investigate the impact of medium, induction regime and protease production on the expression of the product. Experiments with the time of induction showed that the optimum results are achieved when induction is started in the late exponential phase (21 h after inoculation) improving the titer of the product from 14.5 mg L(-1), obtained in the early exponential phase (7 h after inoculation), to 16.2 mg L(-1). A 100% increase of the carbon (fructose) and nitrogen (ammonium sulfate) sources in the growth medium resulted in an increase in product concentration from 16.2 to 108.9 mg L(-1) and an increase in maximum dry cell weight from 7.5 to 11.5 g L(-1). A 50% reduction in the concentration of the inducer resulted in an increase in the product yield from 10 mg g(-1) dry cell weight to 12 mg g(-1). Proteolytic enzymes were produced during the fermentation up to concentrations equivalent to 1.4 g L(-1) trypsin, but they had no detrimental effect on the concentration of the antibody fragment.

  14. Detection and differentiation of filarial parasites by universal primers and polymerase chain reaction-restriction fragment length polymorphism analysis.

    PubMed

    Nuchprayoon, Surang; Junpee, Alisa; Poovorawan, Yong; Scott, Alan L

    2005-11-01

    Filarial nematode parasites are a serious cause of morbidity in humans and animals. Identification of filarial infection using traditional morphologic criteria can be difficult and lead to misdiagnosis. We report on a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP)-based method to detect and differentiate a broad range of filarial species in a single PCR. The first internal transcribed spacer 1 (ITS1) along with the flanking 18S and 5.8S ribosomal DNA (rDNA) were isolated and cloned from Wuchereria bancrofti, Brugia malayi, and Brugia pahangi. Sequence analysis identified conserved sites in the 18S and 5.8S rDNA sequence that could be used as universal priming sites to generate ITS1-distinctive PCR products that were useful for distinguishing filariae at the genus level. The addition of a digestion of the ITS1 PCR product with the restriction endonuclease Ase I generated a fragment profile that allowed differentiation down to the species level for W. bancrofti, B. malayi, B. pahangi, Dirofilaria immitis, and D. repens. The PCR-RFLP of ITS1 rDNA will be useful in diagnosing and differentiating filarial parasites in human, animal reservoir hosts, and mosquito vectors in disease-endemic areas.

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

    PubMed

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

    2014-11-26

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

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

    PubMed Central

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

    2015-01-01

    The internal transcribed spacer (ITS) of ribosomal DNA has been used to confirm taxonomic classifications and define phylogenies in several plant species following sequencing or polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) techniques. In this study, co-dominant ITS PCR–RFLP molecular markers were produced in 30 Fagaceae individuals belonging to the Castanea, Fagus and Quercus genera in order to assess the potential of this technique for taxonomic discrimination and determination of phylogenies. The complete ITS region (ITS1-5.8S rRNA-ITS2) was amplified in most of the Fagaceae individuals as a single fragment of ∼700 bp. The ITS amplified products were digested with nine restriction enzymes, but only four (HaeIII, HpaII, TaqI and Sau96I) produced polymorphic/discriminative patterns. The total expected heterozygosity (HE) was 20.31 % and the gene diversity (I), 32.97 %. The ITS polymorphism was higher within the Quercus genus (85.3 %). The ITS PCR–RFLP markers clustered the Fagaceae species according to genus or infrageneric group (in the case of Quercus sp. individuals). Five oaks did not cluster in line with the adopted infrageneric classification, but three of these were grouped according to their actual ecological distributions. The ITS PCR–RFLP markers indicated their potential for phylogenetic studies since all Fagaceae individuals were discriminated according to genus, and most of the oaks were clustered according to infrageneric group or ecological area. PMID:25429047

  17. Comprehensive optimization of a single-chain variable domain antibody fragment as a targeting ligand for a cytotoxic nanoparticle.

    PubMed

    Zhang, Kathy; Geddie, Melissa L; Kohli, Neeraj; Kornaga, Tad; Kirpotin, Dmitri B; Jiao, Yang; Rennard, Rachel; Drummond, Daryl C; Nielsen, Ulrik B; Xu, Lihui; Lugovskoy, Alexey A

    2015-01-01

    Antibody-targeted nanoparticles have the potential to significantly increase the therapeutic index of cytotoxic anti-cancer therapies by directing them to tumor cells. Using antibodies or their fragments requires careful engineering because multiple parameters, including affinity, internalization rate and stability, all need to be optimized. Here, we present a case study of the iterative engineering of a single chain variable fragment (scFv) for use as a targeting arm of a liposomal cytotoxic nanoparticle. We describe the effect of the orientation of variable domains, the length and composition of the interdomain protein linker that connects VH and VL, and stabilizing mutations in both the framework and complementarity-determining regions (CDRs) on the molecular properties of the scFv. We show that variable domain orientation can alter cross-reactivity to murine antigen while maintaining affinity to the human antigen. We demonstrate that tyrosine residues in the CDRs make diverse contributions to the binding affinity and biophysical properties, and that replacement of non-essential tyrosines can improve the stability and bioactivity of the scFv. Our studies demonstrate that a comprehensive engineering strategy may be required to identify a scFv with optimal characteristics for nanoparticle targeting.

  18. Site-specific photobiotinylation of antibodies, light chains, and immunoglobulin fragments.

    PubMed

    Pavlinkova, G; Lou, D; Kohler, H

    2000-09-01

    The high affinity of biotin for avidin has been exploited for many antibody-based assays. This requires that biotin is covalently conjugated to the antibody molecule. Several chemically reactive biotinylation reagents are commercially available. Except for the attachment via sulfhydryl groups in the immunoglobulin (Ig) molecule, these reagents attach biotin randomly to various amino acid side chains. Although non-site-specific modification of antibodies does not interfere in most immunoassays, specific application and sensitive antibodies would benefit from site-specific biotinylation. Here we describe an affinity biotinylation technique based on a photoreactive biotin reagent. The design of this reaction was possible from the discovery of a conserved binding site in the variable Ig domain for nucleotides and nucleosides. The described photoaffinity biotinylation offers the advantages of ease, convenience, and production of a reproducible and defined biotinylated antibody preparation.

  19. Suppression of Aggrus/podoplanin-induced platelet aggregation and pulmonary metastasis by a single-chain antibody variable region fragment.

    PubMed

    Miyata, Kenichi; Takagi, Satoshi; Sato, Shigeo; Morioka, Hiroshi; Shiba, Kiyotaka; Minamisawa, Tamiko; Takami, Miho; Fujita, Naoya

    2014-12-01

    Almost all highly metastatic tumor cells possess high platelet aggregating abilities, thereby form large tumor cell-platelet aggregates in the microvasculature. Embolization of tumor cells in the microvasculature is considered to be the first step in metastasis to distant organs. We previously identified the platelet aggregation-inducing factor expressed on the surfaces of highly metastatic tumor cells and named as Aggrus. Aggrus was observed to be identical to the marker protein podoplanin (alternative names, T1α, OTS-8, and others). Aggrus is frequently overexpressed in several types of tumors and enhances platelet aggregation by interacting with the platelet receptor C-type lectin-like receptor 2 (CLEC-2). Here, we generated a novel single-chain antibody variable region fragment (scFv) by linking the variable regions of heavy and light chains of the neutralizing anti-human Aggrus monoclonal antibody MS-1 with a flexible peptide linker. Unfortunately, the generated KM10 scFv failed to suppress Aggrus-induced platelet aggregation in vitro. Therefore, we performed phage display screening and finally obtained a high-affinity scFv, K-11. K-11 scFv was able to suppress Aggrus-induced platelet aggregation in vitro. Moreover, K-11 scFv prevented the formation of pulmonary metastasis in vivo. These results suggest that K-11 scFv may be useful as metastasis inhibitory scFv and is expected to aid in the development of preclinical and clinical examinations of Aggrus-targeted cancer therapies.

  20. 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.

  1. 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.

  2. Expression, purification, and characterization of anti-plumbagin single-chain variable fragment antibody in Sf9 insect cell.

    PubMed

    Sakamoto, Seiichi; Taura, Futoshi; Tsuchihashi, Ryota; Putalun, Waraporn; Kinjo, Junei; Tanaka, Hiroyuki; Morimoto, Satoshi

    2010-12-01

    Plumbagin (PL; 5-hydroxy-2-methyl-1, 4-naphthoquinone) is an important secondary metabolite, mainly produced in the Plumbago zeylanica L. (Plumbaginaceae). A single-chain variable fragment (scFv) antibody, fusion of the variable regions of the heavy chain and light chain of immunoglobulin against PL (PL-scFv) was expressed by Bac-to-Bac Baculovirus Expression System using Spodoptera frugiperda (Sf9) insect cells and characterized to investigate potential use of PL-scFv as a tool for plant immunomodulation. Functional PL-scFv expressed in the Sf9 insect cells were purified using cation exchange chromatography followed by immobilized metal ion affinity chromatography (IMAC). The yields of the purified PL-scFv in the culture supernatant and Sf9 insect cells were 2.0 mg and 5.2 mg per 1 liter of Sf9 culture medium, respectively. Recombinant purified PL-scFv was then characterized by the indirect competitive enzyme-linked immunosorbent assay (ELISA). The cross-reactivity and sensitivity of PL-scFv expressed in Sf9 insect cells were compared with PL-scFv expressed in Escherichia coli and its parental anti-plumbagin monoclonal antibody (MAb 3A3) secreted from hybridoma cells. Intriguingly, the specificity of the PL-scFv expressed in Sf9 insect cells was found to be different from that expressed in E. coli and parental MAb 3A3, although the detectable level (0.2-25 μg/mL) was the same in ELISA using each antibody. Even more interestingly, the characteristics of PL-scFv, which have wide cross-reactivity against 1,4-napththoquinone, suggest its potential use as a tool for plant immunomodulation not only for breeding Plumbaginacea family containing PL but also for breeding other medicinal plants containing bioactive naphthoquinones.

  3. 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.

  4. Construction of a human functional single-chain variable fragment (scFv) antibody recognizing the malaria parasite Plasmodium falciparum.

    PubMed

    Wajanarogana, Sumet; Prasomrothanakul, Teerawat; Udomsangpetch, Rachanee; Tungpradabkul, Sumalee

    2006-04-01

    Falciparum malaria is one of the most deadly and profound human health problems around the tropical world. Antimalarial drugs are now considered to be a powerful treatment; however, there are drugs currently being used that are resistant to Plasmodium falciparum parasites spreading in different parts of the world. Although the protective immune response against intraerythrocytic stages of the falciparum malaria parasite is still not fully understood, immune antibodies have been shown to be associated with reduced parasite prevalence. Therefore antibodies of the right specificity present in adequate concentrations and affinity are reasonably effective in providing protection. In the present study, VH (variable domain of heavy chain) and VL (variable domain of light chain) were isolated from human blood lymphocytes of P. falciparum in one person who had high serum titre to RESA (ring-infected erythrocyte surface antigen). Equal amounts of VH and VL were assembled together with universal linker (G4S)3 to generate scFvs (single-chain variable fragments). The scFv antibodies were expressed with a phage system for the selection process. Exclusively, an expressed scFv against asynchronous culture of P. falciparum-infected erythrocytes was selected and characterized. Sequence analysis of selected scFv revealed that this clone could be classified into a VH family-derived germline gene (VH1) and Vkappa family segment (Vkappa1). Using an indirect immunofluorescence assay, we could show that soluble expressed scFv reacted with falciparum-infected erythrocytes. The results encourage the further study of scFvs for development as a potential immunotherapeutic agent.

  5. Production of a single-chain fragment of the murine anti-idiotypic antibody ACA125 as phage-displayed and soluble antibody by recombinant phage antibody technique.

    PubMed

    Schlebusch, H; Reinartz, S; Kaiser, R; Grünn, U; Wagner, U

    1997-02-01

    The F(ab')2 fragment of the murine monoclonal anti-idiotypic antibody ACA125 mimicking the tumor-associated antigen CA125 is used as a vaccine for the induction of an anti-tumoral immunity in patients with ovarian carcinoma. We tried to generate a single-chain fragment (ScFv) composed of ACA125 heavy- and light-chain variable domains connected by a polypeptide linker as an alternative to the corresponding F(ab')2 fragment. Heavy- and light-chain genes of antibody-producing mouse hybridoma cell line were amplified separately and assembled into a ScFv gene with linker DNA by the polymerase chain reaction (PCR). The ScFv gene was ligated into the phagemid vector pCANTAB5E, which allows the production of both phage-displayed and soluble ScFv. Transformed Escherichia coli TG1 cells were infected with M13K07 helper phage to yield recombinant phage, which display ScFv fragments as a g3p fusion protein on the surface of the filamentous phage M13. Recombinant phages could be selected by binding to the idiotypic antibody OC125 after one round of panning and directly used to reinfect E. coli TG1 cells. The E. coli nonsuppressor strain HB2151 was infected with an antigen-positive phage clone, previously screened by enzyme-linked immunosorbent assay (ELISA), to express soluble ScFv fragments. Functional soluble ScFv binding to the idiotypic antibody OC125 F(ab')2 could be detected in the bacterial periplasm by Western blot and ELISA. The variable heavy- and light-chain genes of the ACA125 ScFv fragment were further sequenced and compared with known antibody sequences.

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

    PubMed

    Kazuma, Soraya M; Cavalcante, Marcela F; Telles, Andréia E R; Maranhão, Andrea Queiroz; Abdalla, Dulcineia S P

    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(-).

  7. Secretion of an immunoreactive single-chain variable fragment antibody against mouse interleukin 6 by Lactococcus lactis.

    PubMed

    Shigemori, Suguru; Ihara, Masaki; Sato, Takashi; Yamamoto, Yoshinari; Nigar, Shireen; Ogita, Tasuku; Shimosato, Takeshi

    2017-01-01

    Interleukin 6 (IL-6) is an important pathogenic factor in development of various inflammatory and autoimmune diseases and cancer. Blocking antibodies against molecules associated with IL-6/IL-6 receptor signaling are an attractive candidate for the prevention or therapy of these diseases. In this study, we developed a genetically modified strain of Lactococcus lactis secreting a single-chain variable fragment antibody against mouse IL-6 (IL6scFv). An IL6scFv-secretion vector was constructed by cloning an IL6scFv gene fragment into a lactococcal secretion plasmid and was electroporated into L. lactis NZ9000 (NZ-IL6scFv). Secretion of recombinant IL6scFv (rIL6scFv) by nisin-induced NZ-IL6scFv was confirmed by western blotting and was optimized by tuning culture conditions. We found that rIL6scFv could bind to commercial recombinant mouse IL-6. This result clearly demonstrated the immunoreactivity of rIL6scFv. This is the first study to engineer a genetically modified strain of lactic acid bacteria (gmLAB) that produces a functional anti-cytokine scFv. Numerous previous studies suggested that mucosal delivery of biomedical proteins using gmLAB is an effective and low-cost way to treat various disorders. Therefore, NZ-IL6scFv may be an attractive tool for the research and development of new IL-6 targeting agents for various inflammatory and autoimmune diseases as well as for cancer.

  8. 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.

  9. The serine proteinase chain of human complement component C1s. Cyanogen bromide cleavage and N-terminal sequences of the fragments.

    PubMed Central

    Carter, P E; Dunbar, B; Fothergill, J E

    1983-01-01

    Human complement component C1s was purified from fresh blood by conventional methods of precipitation and chromatography. The single-chain zymogen form was activated by treatment with C1r. Reduction and carboxymethylation then allowed the light chain and heavy chain to be separated on DEAE-Sepharose CL-6B in 8 M-urea. Liquid-phase sequencing of the light chain determined 50 residues from the N-terminus. CNBr-cleavage fragments of the light chain were separated by high-pressure liquid chromatography on gel-permeation and reverse-phase columns. N-Terminal sequencing of these fragments determined the order of a further 138 residues, giving a total of 188 residues or about 75% of the light chain. Seven of these eight sequences could be readily aligned with the amino acid sequences of other serine proteinases. The typical serine proteinase active-site residues are clearly conserved in C1s, and the specificity-related side chain of the substrate-binding pocket is aspartic acid, as in trypsin, consistent with the proteolytic action of C1s on C4 at an arginine residue. Somewhat surprisingly, when the C1s sequence is compared with that of complement subcomponent C1r, the percentage difference (59%) is approximately the same as that found between the other mammalian serine proteinases (56-71%). PMID:6362661

  10. Isolation and characterization of recombinant single chain fragment variable anti-idiotypic antibody specific to Aspergillus fumigatus membrane protein.

    PubMed

    Krishnaswamy, Senthilkumar; Kabir, M Enamul; Rahman, M Mamunur; Miyamoto, Masahiko; Furuichi, Yasuhiro; Komiyama, Tadazumi

    2011-03-07

    Aspergillus fumigatus causes the highly lethal form of invasive aspergillosis (IA). In the present study to develop a novel anti-fungal drug for protection against invasive disease, we identified a single chain fragment variable (scFv) antibody (scFv AF1) by panning against A. fumigatus membrane fraction (AMF) or HM-1 killer toxin (HM-1) neutralizing monoclonal antibody (nmAb-KT) as antigen. The key step was elution of bound phages with phosphate buffered saline (PBS) at pH 7.0 containing AMF. The specificity of soluble scFv AF1 antibody to antigens was verified by ELISA, which specifically binds to both AMF and nmAb-KT. After nucleotide sequencing, clone expression and purification by HisTrap HP affinity column, scFv AF1 showed in vitro anti-fungal activity against A. fumigatus. By SPR analysis it showed high binding affinity to nmAb-KT (K(d)=5.22×10(-11) M). The method used to isolate scFv AF1 was a new method and we believe that it will be applicable to isolate the specific scFv against any kind of membrane protein of yeast or fungus.

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

    PubMed

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

    2015-07-01

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

  12. Distinguishing Heterodera filipjevi and H. avenae using polymerase chain reaction-restriction fragment length polymorphism and cyst morphology.

    PubMed

    Yan, Guiping; Smiley, Richard W

    2010-03-01

    The cereal cyst nematodes Heterodera filipjevi and H. avenae impede wheat production in the Pacific Northwest (PNW). Accurate identification of cyst nematode species and awareness of high population density in affected fields are essential for designing effective control measures. Morphological methods for differentiating these species are laborious. These species were differentiated using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) of internal transcribed spacer (ITS)-ribosomal (r)DNA with up to six restriction endonucleases (TaqI, HinfI, PstI, HaeIII, RsaI, and AluI). The method was validated by inspecting underbridge structures of cyst vulval cones. Grid soil sampling of an Oregon field infested by both species revealed that H. filipjevi was present at most of the infested grid sites but mixtures of H. avenae and H. filipjevi also occurred. These procedures also detected and differentiated H. filipjevi and H. avenae in soil samples from nearby fields in Oregon and H. avenae in samples from Idaho and Washington. Intraspecific polymorphism was not observed within H. filipjevi or PNW H. avenae populations based on the ITS-rDNA. However, intraspecific variation was observed between H. avenae populations occurring in the PNW and France. Methods described here will improve detection and identification efficiencies for cereal cyst nematodes in wheat fields.

  13. 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

  14. 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

  15. 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.

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

    SciTech Connect

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

    1990-06-01

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

  17. 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.

  18. 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.

  19. 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).

  20. 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.

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

    PubMed Central

    Miyaguchi, Hajime

    2016-01-01

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

  2. High production of llama variable heavy-chain antibody fragment (VHH) fused to various reader proteins by Aspergillus oryzae.

    PubMed

    Hisada, Hiromoto; Tsutsumi, Hiroko; Ishida, Hiroki; Hata, Yoji

    2013-01-01

    Llama variable heavy-chain antibody fragment (VHH) fused to four different reader proteins was produced and secreted in culture medium by Aspergillus oryzae. These fusion proteins consisted of N-terminal reader proteins, VHH, and a C-terminal his-tag sequence which facilitated purification using one-step his-tag affinity chromatography. SDS-PAGE analysis of the deglycosylated purified fusion proteins confirmed that the molecular weight of each corresponded to the expected sum of VHH and the respective reader proteins. The apparent high molecular weight reader protein glucoamylase (GlaB) was found to be suitable for efficient VHH production. The GlaB-VHH-His protein bound its antigen, human chorionic gonadotropin, and was detectable by a new ELISA-based method using a coupled assay with glucoamylase, glucose oxidase, peroxidase, maltose, and 3,3',5,5'-tetramethylbenzidine as substrates. Addition of potassium phosphate to the culture medium induced secretion of 0.61 mg GlaB-VHH-His protein/ml culture medium in 5 days.

  3. Scale invariance vs conformal invariance

    NASA Astrophysics Data System (ADS)

    Nakayama, Yu

    2015-03-01

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

  4. Sorting signals in the MHC class II invariant chain cytoplasmic tail and transmembrane region determine trafficking to an endocytic processing compartment

    PubMed Central

    1994-01-01

    Targeting of MHC class II molecules to the endocytic compartment where they encounter processed antigen is determined by the invariant chain (Ii). By analysis of Ii-transferrin receptor (TR) chimera trafficking, we have identified sorting signals in the Ii cytoplasmic tail and transmembrane region that mediate this process. Two non-tyrosine-based sorting signals in the Ii cytoplasmic tail were identified that mediate localization to plasma membrane clathrin-coated pits and promote rapid endocytosis. Leu7 and Ile8 were required for the activity of the signal most distal to the cell membrane whereas Pro15 Met16 Leu17 were important for the membrane-proximal signal. The same or overlapping non- tyrosine-based sorting signals are essential for delivery of Ii-TR chimeras, either by an intracellular route or via the plasma membrane, to an endocytic compartment where they are rapidly degraded. The Ii transmembrane region is also required for efficient delivery to this endocytic processing compartment and contains a signal distinct from the Ii cytoplasmic tail. More than 80% of the Ii-TR chimera containing the Ii cytoplasmic tail and transmembrane region is delivered directly to the endocytic pathway by an intracellular route, implying that the Ii sorting signals are efficiently recognized by sorting machinery located in the trans-Golgi. PMID:8034737

  5. The CLIP region of invariant chain plays a critical role in regulating major histocompatibility complex class II folding, transport, and peptide occupancy.

    PubMed

    Romagnoli, P; Germain, R N

    1994-09-01

    Invariant chain (Ii) contributes in a number of distinct ways to the proper functioning of major histocompatibility complex (MHC) class II molecules. These include promoting effective association and folding of newly synthesized MHC class II alpha and beta subunits, increasing transit of assembled heterodimers out of the endoplasmic reticulum (ER), inhibiting class II peptide binding, and facilitating class II movement to or accumulation in endosomes/lysosomes. Although the cytoplasmic tail of Ii makes a key contribution to the endocytic localization of class II, the relationship between the structure of Ii and its other diverse functions remains unknown. We show here that two thirds of the lumenal segment of Ii can be eliminated without affecting its contributions to the secretory pathway events of class II folding, ER to Golgi transport, or inhibition of peptide binding. These same experiments reveal that a short (25 residue) contiguous internal segment of Ii (the CLIP region), frequently found associated with purified MHC class II molecules, is critical for all three functions. Together with other recent findings, these results raise the possibility that the contributions of Ii to the early postsynthetic behavior of class II may depend on its interaction with the class II binding site. This would be consistent with the intracellular behavior of unoccupied MHC class I and class II molecules as incompletely folded proteins and imply a related structural basis for the similar contributions of Ii to class II and of short peptides to class I assembly and transport.

  6. 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.

  7. A polymerase chain reaction-restriction fragment length polymorphism method for screening ZNF804A gene polymorphism (rs1344706) in patients with schizophrenia: a significant association.

    PubMed

    Sazci, Ali; Ozel, Mavi Deniz; Ergul, Emel; Yildiz, Mustafa

    2012-03-01

    The original ZNF804A rs1344706 risk variant was identified through genome-wide association studies as a risk factor for schizophrenia. Follow-up studies involving meta-analysis have confirmed that rs1344706 is a risk factor for schizophrenia as well as bipolar disorders. We describe here a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method to genotype ZNF804A rs1344706 variant in patients with schizophrenia. We generated a 220 bp fragment through PCR and subsequently cleaved it by the restriction endonuclease BsaBI, creating two fragments of 114 and 106 bp. Upon change in the nucleotide from T to G, the 106 bp fragment is further cleaved by BsaBI, thus creating two fragments of 87 and 19 bp. As a result, when the 220 bp fragment is cleaved by BsaBI restriction endonuclease, the TT genotype yields two fragments of 114 and 106 bp, and TG genotype four fragments of 114, 106, 87, and 19 bp, and the GG genotype three fragments of 114, 87, and 19 bp. Thus, this is a simple, fast, and cost-effective method to genotype the ZNF804A rs1344706 risk variant. Using this method, we were able to replicate an association between ZNF804A rs1344706 variant and schizophrenia in a Turkish population. Stratification analysis of the population according to the gender showed an association that was statistically significant among overall schizophrenia and male schizophrenia and the risk T allele and TT genotype of the ZNF804A gene.

  8. One-step expression and purification of single-chain variable antibody fragment using an improved hexahistidine tag phagemid vector.

    PubMed

    Zhao, Qi; Chan, Yin-Wah; Lee, Susanna Sau-Tuen; Cheung, Wing-Tai

    2009-12-01

    Millions of candidate clones are commonly obtained following rounds of phage-displayed antibody library panning, and expression of those selected single-chain variable fragment (scFv) is required for secondary functional screening to identify positive clones. Large scale functional screening is often hampered by the time-consuming and labor-intensive subcloning of those candidate scFv clones into a bacterial expression vector carrying an affinity tag for scFv purification and detection. To overcome the limitations and to develop a multiplex approach, an improved hexahistidine tag phagemid vector was constructed for one-step scFv expression and purification. By using hexahistidine as an affinity tag, soluble scFvs can be rapidly and cost-effectively captured from Escherichia coli periplasmic extracts. For proof-of-concept, feasibility of the improved phagemid vector was examined against two scFvs, L17E4d targeting a cell surface antigen and L18Hh5 recognizing a monoclonal antibody (mAb). Using 1 ml of Ni-NTA agarose, 0.2-0.5 mg of soluble scFv was obtained from 1 L of bacteria culture, and the purified scFvs bound specifically to their target antigens with high affinity. Moreover, using two randomly selected hapten-specific scFv phage clones, it was demonstrated that the display of scFvs on phage surface was not affected by the hexahistidine affinity tag. These results suggest the improved phagemid vector allows the shuttle of phage-displayed antibody library panning and functional scFv production. Importantly, the improved phagemid vector can be easily adapted for multiplex screening.

  9. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) for rapid diagnosis of neonatal sepsis

    PubMed Central

    Rohit, Anusha; Maiti, Biswajit; Shenoy, Shalini; Karunasagar, Indrani

    2016-01-01

    Background & objectives: The difficulties in diagnosis of neonatal sepsis are due to varied clinical presentation, low sensitivity of blood culture which is considered the gold standard and empirical antibiotic usage affecting the outcome of results. Though polymerase chain reaction (PCR) based detection of bacterial 16S rRNA gene has been reported earlier, this does not provide identification of the causative agent. In this study, we used restriction fragment length polymorphism (RFLP) of amplified 16S rRNA gene to identify the organisms involved in neonatal sepsis and compared the findings with blood culture. Methods: Blood samples from 97 neonates were evaluated for diagnosis of neonatal sepsis using BacT/Alert (automated blood culture) and PCR-RFLP. Results: Bacterial DNA was detected by 16S rRNA gene PCR in 55 cases, while BacT/Alert culture was positive in 34 cases. Staphylococcus aureus was the most common organism detected with both methods. Klebsiella spp. was isolated from four samples by culture but was detected by PCR-RFLP in five cases while Acinetobacter spp. was isolated from one case but detected in eight cases by PCR-RFLP. The sensitivity of PCR was found to be 82.3 per cent with a negative predictive value of 85.7 per cent. Eighty of the 97 neonates had prior exposure to antibiotics. Interpretation & conclusions: The results of our study demonstrate that PCR-RFLP having a rapid turnaround time may be useful for the early diagnosis of culture negative neonatal sepsis. PMID:26997017

  10. Expression and characterization of a single-chain variable fragment against human LOX-1 in Escherichia coli and Brevibacillus choshinensis.

    PubMed

    Hu, Wei; Xiang, Jun-Yan; Kong, Ping; Liu, Ling; Xie, Qiuhong; Xiang, Hongyu

    2017-03-09

    The single-chain variable fragment (scFv) against lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) is a promising molecule for its potential use in the diagnosis and immunotherapy of atherosclerosis. Producing this scFv in several milligram amounts could be the starting point for further engineering and application of the scFv. In this study, the abundant expression of the anti-LOX-1 scFv was attempted using Escherichia coli (E. coli) and Brevibacillus choshinensis (B. choshinensis). The scFv had limited soluble yield in E. coli, but it was efficiently secreted by B. choshinensis. The optimized fermentation was determined using the Plackett-Burman screening design and the response surface methodology (RSM), under which the yield reached up to 1.5 g/L in a 5-L fermentor. Moreover, the properties of the scFvs obtained from the two expression systems were different. The antigen affinity, transition temperature and particle diameter size is 1.01E-07 M, 55.2 ± 0.3°C and 9.388 nm for the scFv expressed by B. choshinensis and 4.53E-07 M, 52.5 ± 0.3°C and 13.54 nm for the scFv expressed by E. coli. This study established an efficient scale-up production methodology for the anti-LOX-1 scFv, which will boost its use in LOX-1-based therapy.

  11. 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.

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

    PubMed

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

    2015-06-01

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

  13. 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.

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

    PubMed

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

    2015-12-01

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

  15. Transgenic tobacco plants expressing a dimeric single-chain variable fragment (scfv) antibody against Salmonella enterica serotype Paratyphi B.

    PubMed

    Makvandi-Nejad, Shokouh; McLean, Michael D; Hirama, Tomoko; Almquist, Kurt C; Mackenzie, C Roger; Hall, J Christopher

    2005-10-01

    Transgenic tobacco plants were produced that express an anti-Salmonella enterica single-chain variable fragment (scFv) antibody that binds to the lipopolysaccharide (LPS) of S. enterica Paratyphi B. The coding sequence of this scFv was optimized for expression in tobacco, synthesized and subsequently placed behind three different promoters: an enhanced tobacco constitutive ubiquitous promoter (EntCUP4), and single- and double-enhancer versions of the Cauliflower Mosaic Virus 35S promoter (CaMV 35S). These chimeric genes were introduced into Nicotiana tabacum cv. 81V9 by Agrobacterium-mediated transformation and 50 primary transgenic (T(0)) plants per construct were produced. Among these plants, 23 were selected for the ability to express active scFv as determined by enzyme-linked immunosorbent assay (ELISA) using S. enterica LPS as antigen. Expanded bed adsorption-immobilized metal affinity chromatography (EBA-IMAC) was used to purify 41.7 mug of scFv/g from leaf tissue. Gel filtration and surface plasmon resonance (SPR) analyses demonstrated that the purified scFv was active as a dimer or higher-order multimer. In order to identify T(1) plants suitable for development of homozygous lines with heritable scFv expression, kanamycin-resistance segregation analyses were performed to determine the number of T-DNA loci in each T(0) plant, and quantitative ELISA and immunoblot analyses were used to compare expression of active and total anti-Salmonella scFv, respectively, in the T(1) generation. As S. enterica causes millions of enteric fevers and hundreds of thousands of deaths worldwide each year, large-scale production and purification of this scFv will have potential for uses in diagnosis and detection, as a therapeutic agent, and in applications such as water system purification.

  16. 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.

  17. Efficient heterologous expression and secretion in Aspergillus oryzae of a llama variable heavy-chain antibody fragment V(HH) against EGFR.

    PubMed

    Okazaki, Fumiyoshi; Aoki, Jun-ichi; Tabuchi, Soichiro; Tanaka, Tsutomu; Ogino, Chiaki; Kondo, Akihiko

    2012-10-01

    We have constructed a filamentous fungus Aspergillus oryzae that secretes a llama variable heavy-chain antibody fragment (V(HH)) that binds specifically to epidermal growth factor receptor (EGFR) in a culture medium. A major improvement in yield was achieved by fusing the V(HH) with a Taka-amylase A signal sequence (sTAA) and a segment of 28 amino acids from the N-terminal region of Rhizopus oryzae lipase (N28). The yields of secreted, immunologically active anti-EGFR V(HH) reached 73.8 mg/1 in a Sakaguchi flask. The V(HH) fragments were released from the sTAA or N28 proteins by an indigenous A. oryzae protease during cultivation. The purified recombinant V(HH) fragment was specifically recognized and could bind to the EGFR with a high affinity.

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

    PubMed

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

    2009-03-01

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

  19. 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

    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

  20. HLA-DO increases bacterial superantigen binding to human MHC molecules by inhibiting dissociation of class II-associated invariant chain peptides.

    PubMed

    Pezeshki, Abdul Mohammad; Azar, Georges A; Mourad, Walid; Routy, Jean-Pierre; Boulassel, Mohamed-Rachid; Denzin, Lisa K; Thibodeau, Jacques

    2013-10-01

    HLA-DO (H2-O in mice) is an intracellular non-classical MHC class II molecule (MHCII). It forms a stable complex with HLA-DM (H2-M in mice) and shapes the MHC class II-associated peptide repertoire. Here, we tested the impact of HLA-DO and H2-O on the binding of superantigens (SAgs), which has been shown previously to be sensitive to the structural nature of the class II-bound peptides. We found that the binding of staphylococcal enterotoxin (SE) A and B, as well as toxic shock syndrome toxin 1 (TSST-1), was similar on the HLA-DO(+) human B cell lines 721.45 and its HLA-DO(-) counterpart. However, overexpressing HLA-DO in MHC class II(+) HeLa cells (HeLa-CIITA-DO) improved binding of SEA and TSST-1. Accordingly, knocking down HLA-DO expression using specific siRNAs decreased SEA and TSST-1 binding. We tested directly the impact of the class II-associated invariant chain peptide (CLIP), which dissociation from MHC class II molecules is inhibited by overexpressed HLA-DO. Loading of synthetic CLIP on HLA-DR(+) cells increased SEA and TSST-1 binding. Accordingly, knocking down HLA-DM had a similar effect. In mice, H2-O deficiency had no impact on SAgs binding to isolated splenocytes. Altogether, our results demonstrate that the sensitivity of SAgs to the MHCII-associated peptide has physiological basis and that the effect of HLA-DO on SEA and TSST-1 is mediated through the inhibition of CLIP release.

  1. 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

  2. Invariant death.

    PubMed

    Frank, Steven A

    2016-01-01

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

  3. Invariant death

    PubMed Central

    Frank, Steven A.

    2016-01-01

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

  4. Proteolysis of the class II-associated invariant chain generates a peptide binding site in intracellular HLA-DR molecules. Proc. Natl. Acad. Sci. USA. 1991. 88: 3150-3154.

    PubMed

    Roche, Paul A; Cresswell, Peter

    2011-08-01

    HLA-DR molecules are heterodimeric transmembrane glycoproteins that associate intracellularly with a polypeptide known as the invariant (I) chain. Shortly before expression of the HLA-DR αβ dimer on the cell surface, however the I chain is removed from the intracellular αβI complex by a mechanism thought to involve proteolysis . In this report, we show that treatment of purified αβI with the cysteine proteinase cathepsin B results in the specific proteolysis of the HLA-DR-associated I chain in vitro. As a consequence of this, the I chain is removed and free αβ dimers are released from αβI. Although αβI fails to bind an immunogenic peptide, the released αβ dimers acquire the ability to bind the peptide after proteolysis of the I chain. These results suggest that the I chain inhibits immunogenic peptide binding to αβI early during intracellular transport and demonstrate that proteolysis is likely to be the in vivo mechanism of I chain removal.

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

    PubMed

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

    2014-06-01

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

  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. 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.

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

    PubMed Central

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

    2014-01-01

    This research applied and evaluated a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using cytochrome b gene to detect pork contamination in meatballs from local markets in Surabaya and Yogyakarta regions, Indonesia. To confirm the effectiveness and specificity of this fragment, thirty nine DNA samples from different meatball shops were isolated and amplified, and then the PCR amplicon was digested by BseDI restriction enzyme to detect the presence of pork in meatballs. BseDI restriction enzyme was able to cleave porcine cytochrome b gene into two fragments (131 bp and 228 bp). Testing the meatballs from the local market showed that nine of twenty meatball shops in Yogyakarta region were detected to have pork contamination, but there was no pork contamination in meatball shops in Surabaya region. In conclusion, specific PCR amplification of cytochrome b gen and cleaved by BseDI restriction enzymes seems to be a powerful technique for the identification of pork presence in meatball because of its simplicity, specificity and sensitivity. Furthermore, pork contamination intended for commercial products of sausage, nugget, steak and meat burger can be checked. The procedure is also much cheaper than other methods based on PCR, immunodiffusion and other techniques that need expensive equipment. PMID:25178301

  9. 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

  10. Primary structure of the A chain of human complement-classical-pathway enzyme C1r. N-terminal sequences and alignment of autolytic fragments and CNBr-cleavage peptides.

    PubMed Central

    Gagnon, J; Arlaud, G J

    1985-01-01

    Activated human complement-classical-pathway enzyme C1r has previously been shown to undergo autolytic cleavages occurring in the A chain [Arlaud, Villiers, Chesne & Colomb (1980) Biochim. Biophys. Acta 616, 116-129]. Chemical analysis of the autolytic products confirms that the A chain undergoes two major cleavages, generating three fragments, which have now been isolated and characterized. The N-terminal alpha fragment (approx. 210 residues long) has a blocked N-terminus, as does the whole A chain, whereas N-terminal sequences of fragments beta and gamma (approx. 66 and 176 residues long respectively) do not, and their N-terminal sequences were determined. Fragments alpha, beta and gamma, which are not interconnected by disulphide bridges, are located in this order within C1r A chain. Fragment gamma is disulphide-linked to the B chain of C1r, which is C-terminal in the single polypeptide chain of precursor C1r. CNBr cleavage of C1r A chain yields seven major peptides, CN1b, CN4a, CN2a, CN1a, CN3, CN4b and CN2b, which were positioned in that order, on the basis of N-terminal sequences of the methionine-containing peptides generated from tryptic cleavage of the succinylated (3-carboxypropionylated) C1r A chain. About 60% of the sequence of C1r A chain (440-460 residues long) was determined, including the complete sequence of the C-terminal 95 residues. This region shows homology with the corresponding parts of plasminogen and chymotrypsinogen and, more surprisingly, with the alpha 1 chain of human haptoglobin 1-1, a serine proteinase homologue. PMID:2983658

  11. Taenia saginata: differential diagnosis of human taeniasis by polymerase chain reaction-restriction fragment length polymorphism assay.

    PubMed

    Nunes, Cáris Maroni; Dias, Ana Karina Kerche; Dias, Francisca Elda Ferreira; Aoki, Sérgio Moraes; de Paula, Henrique Borges; Lima, Luis Gustavo Ferraz; Garcia, José Fernando

    2005-08-01

    Speciation of Taenia in human stool is important because of their different clinical and epidemiological features. DNA analysis has recently become possible which overcomes the problems of differentiating human taeniid cestodes morphologically. In the present study, we evaluated PCR coupled to restriction fragment length polymorphism to differentiate Taenia solium from Taenia saginata eggs present in fecal samples from naturally infected patients. A different DraI-RFLP pattern: a two-band pattern (421 and 100 bp) for T. saginata and a three-band pattern (234, 188, and 99 bp) for T. solium was observed allowing the two species to be separated. The lower detection limit of the PCR-RFLP using a non-infected fecal sample prepared with a given number of T. saginata eggs was 34 eggs in 2 g stool sediment. The 521 bp mtDNA fragment was detected in 8 out of 12 Taenia sp. carriers (66.6%). Of these, three showed a T. solium pattern and five a T. saginata pattern.

  12. 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.

  13. Characterization of the native and denatured herceptin by enzyme linked immunosorbent assay and quartz crystal microbalance using a high-affinity single chain fragment variable recombinant antibody.

    PubMed

    Shang, Yuqin; Mernaugh, Ray; Zeng, Xiangqun

    2012-10-02

    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 a single chain fragment variable (scFv, designated 2B4) to a linear synthetic peptide representing Herceptin's heavy chain CDR3. Enzyme linked immunosorbent assays (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 amounts 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 × 10(13) 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 nonspecific binding events in assays. The potential theoretical and clinical implications of these results and the advantages of the use of QCM to characterize human therapeutic antibodies in samples are also discussed.

  14. 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.

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

    PubMed

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

    2016-01-01

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

  16. Analysis of T cell antigen receptor (TCR) expression by human peripheral blood CD4-8- alpha/beta T cells demonstrates preferential use of several V beta genes and an invariant TCR alpha chain

    PubMed Central

    1993-01-01

    CD4-CD8- (double negative [DN]) alpha/beta T cells are a largely uncharacterized subpopulation of unknown function. To investigate whether these cells are selected to recognize particular antigens or antigen-presenting molecules, DN alpha/beta T cells were purified from the peripheral blood of five normal donors and their T cell receptor (TCR) alpha and beta chains were examined. Random cloning of TCR alpha chains by single-sided polymerase chain reaction (PCR) amplification identified an invariant rearrangement between V alpha 24 and J alpha Q, with no N region diversity, which was expressed preferentially by DN alpha/beta T cells from all donors. Random cloning also identified a precise V alpha 7.2-J alpha (IGRJa14) rearrangement, with two variable amino acids encoded in the V-J junction, which was enriched in the DN alpha/beta T cell preparations from some, but not all, donors. Analysis of TCR beta chains by quantitative PCR amplification demonstrated that the expression of four V beta gene families, V beta 2, 8, 11, and 13, was markedly increased in these DN alpha/beta T cell preparations. The expression of particular TCRs by DN alpha/beta T cells from multiple donors indicates that these cells, or at least a subpopulation of cells with this phenotype, recognize a limited spectrum of antigens and suggests that they may use nonpolymorphic antigen-presenting molecules. PMID:8391057

  17. Single chain Fv fragment specific for human GM-CSF: selection and expression using a bacterial expression library.

    PubMed

    Tapryal, Suman; Pal Khasa, Yogender; Mukherjee, K J

    2010-10-01

    Single chain antibodies (scFvs) are replacing whole antibody molecules since they are easy to produce on large scale and amenable to genetic modifications. Here we report the development of an anti-human granulocyte macrophage colony-stimulating factor (hGM-CSF) scFv as an immunoassay bio-reagent, utilizing an easily scalable bacterial expression system. For this, the V(H) and V(L) gene repertoires were amplified from the immunoglobulin complementary DNA, derived from total RNA of mice splenocytes, pre-sensitized with the antigen. The scFv library was expressed under the strong T7 promoter in BL21 (DE3) Escherichia coli cells. Preliminary screening led to the selection of four potential candidates, which were later subjected to light chain shuffling. Cross-reactivity analysis involving the original and shuffled candidates resulted in the selection of one scFv (scFv196) with no cross-reactivity against E. coli antigens. The binding affinity of the scFv196 for hGM-CSF, measured by surface plasmon resonance, was found to be within the physiological range (K(D) =1.5 μM). The refolded scFv was also shown to recognize and bind the glycosylated antigen, a closer mimic of the physiological GM-CSF, potentiating its use in immunoassays. Expression studies using shake flasks suggested periplasmic export of the scFv196 protein.

  18. Molecular authentication of 21 Korean artemisia species (Compositae) by polymerase chain reaction-restriction fragment length polymorphism based on trnL-F region of chloroplast DNA.

    PubMed

    Lee, Jeong Hoon; Lee, Jei Wan; Sung, Jung Sook; Bang, Kyong Hwan; Moon, Sung Gi

    2009-11-01

    The present study describes the molecular authentication of 21 Korean Artemisia species using PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) technique based on the trnL-F sequences in chloroplast DNA. Five different banding patterns were generated from 21 Artemisia species using HinfI restriction enzyme. A. apiacea, A. keiskeana and A. sieversiana have specific banding patterns. The remaining 18 species had shared two banding patterns. Phylogenetic analysis based on trnL-F sequence variations showed results similar to PCR-RFLP banding patterns. It suggested that the trnL-F region does not have sufficient variations to identify the 21 Artemisia species. However, the specific banding patterns for A. apiacea, A. keiskeana and A. sieversiana can be utilized as a DNA marker for discriminating them from other Artemisia species. These markers will be also useful for developing A. apiacea, A. keiskeana and A. sieversiana into new medicine and food based on their efficacy.

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

    PubMed

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

    2009-02-01

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

  20. Mycobacterium avium restriction fragment length polymorphism-IS IS1245 and the simple double repetitive element polymerase chain reaction typing method to screen genetic diversity in Brazilian strains.

    PubMed

    Sequeira, Patrícia Carvalho de; Fonseca, Leila de Souza; Silva, Marlei Gomes da; Saad, Maria Helena Féres

    2005-11-01

    Simple double repetitive element polymerase chain reaction (MaDRE-PCR) and Pvu II-IS1245 restriction fragment length polymorphism (RFLP) typing methods were used to type 41 Mycobacterium avium isolates obtained from 14 AIDS inpatients and 10 environment and animals specimens identified among 53 mycobacteria isolated from 237 food, chicken, and pig. All environmental and animals strains showed orphan patterns by both methods. By MaDRE-PCR four patients, with multiple isolates, showed different patterns, suggesting polyclonal infection that was confirmed by RFLP in two of them. This first evaluation of MaDRE-PCR on Brazilian M. avium strains demonstrated that the method seems to be useful as simple and less expensive typing method for screening genetic diversity in M. avium strains on selected epidemiological studies, although with limitation on analysis identical patterns except for one band.

  1. Discrimination of seven Anopheles species from San Pedro de Uraba, Antioquia, Colombia, by polymerase chain reaction-restriction fragment length polymorphism analysis of its sequences.

    PubMed

    Zapata, Mario A; Cienfuegos, Astrid V; Quirós, Oscar I; Quiñones, Martha L; Luckhart, Shirley; Correa, Margarita M

    2007-07-01

    Accurate identification of anopheline species is essential for vector incrimination and implementation of appropriate control strategies. Several anopheline species are considered important malaria vectors in Colombia; however, species determination is complicated by cryptic morphology and intra-individual variation. We describe polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of internal transcribed spacer 2 (ITS2) sequences for differentiation of seven Anopheles species collected in a locality in Antioquia, Colombia, with high levels of malaria transmission. Each of these seven species can be identified by unique AluI PCR-RFLP restriction patterns. Comparisons of morphologic identification with molecular identification of voucher specimens confirmed species designation for 886 wild-caught anophelines. This new method can be used as a diagnostic tool for discrimination of anopheline species of medical importance in this region, some of which have overlapping morphologic characters and for conducting complementary studies where rapid and accurate identification of large numbers of specimens is needed.

  2. Generation and characterization of chicken-sourced single-chain variable fragments (scFvs) against porcine interferon-gamma (pIFN-γ).

    PubMed

    Chen, Hong-Xiu; He, Fan; Sun, Yuan; Luo, Yuzi; Qiu, Hua-Ji; Zhang, Xiao-Ying; Sutton, Brian J

    2015-01-01

    Development of chicken-sourced antibodies offers an alternative strategy for the development of highly specific antibodies against mammalian proteins with conserved epitopes due to the phylogenetic distance between avian and mammalian species. In this study, the single-chain variable fragments (scFvs) against porcine interferon-gamma was screened and characterized from a hyperimmunized chicken phage display library. The expressed soluble scFvs exhibited highly specific recognition of porcine interferon-gamma in ELISA, Western blot, and immunofluorescence staining assays. Results of the current study indicate that it is possible to develop scFv IgY antibodies to a mammalian interferon by using Biopanning technology. Furthermore, it also confirms that monoclonal avian IgY antibody technique could be applied as a promising tool to produce immunoglobulin molecules with high specificity and affinity towards conserved mammalian epitopes or antigens.

  3. 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

  4. Multi-fragment site-directed mutagenic overlap extension polymerase chain reaction as a competitive alternative to the enzymatic assembly method.

    PubMed

    Wäneskog, Marcus; Bjerling, Pernilla

    2014-01-01

    Methods for introducing multiple site-directed mutations are important experimental tools in molecular biology. Research areas that use these methods include the investigation of various protein modifications in cellular processes, modifying proteins for efficient recombinant expression, and the stabilization of mRNAs to allow for increased protein expression. Introducing multiple site-directed mutations is also an important tool in the field of synthetic biology. There are two main methods used in the assembling of fragments generated by mutagenic primers: enzymatic assembly and overlap extension polymerase chain reaction (OE-PCR). In this article, we present an improved OE-PCR method that can be used for the generation of large DNA fragments (up to 7.4 kb) where at least 13 changes can be introduced using a genomic template. The improved method is faster (due to fewer reaction steps) and more accurate (due to fewer PCR cycles), meaning that it can effectively compete with the enzymatic assembly method. Data presented here show that the site-directed mutations can be introduced anywhere between 50 and 1800 bp from each other. The method is highly reliable and predicted to be applicable to most DNA engineering when the introduction of multiple changes in a DNA sequence is required.

  5. T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids

    PubMed Central

    Nai, Yu-Shin; Chen, Tzu-Han; Huang, Yu-Feng; Midha, Mohit K.; Shiau, Hsin-Chieh; Shen, Chen-Yang; Chen, Chien-Jen; Yu, Alice L.; Chiu, Kuo Ping

    2017-01-01

    Body fluid DNA sequencing is a powerful noninvasive approach for the diagnosis of genetic defects, infectious agents and diseases. The success relies on the quantity and quality of the DNA samples. However, numerous clinical samples are either at low quantity or of poor quality due to various reasons. To overcome these problems, we have developed T oligo-primed polymerase chain reaction (TOP-PCR) for full-length nonselective amplification of minute quantity of DNA fragments. TOP-PCR adopts homogeneous “half adaptor” (HA), generated by annealing P oligo (carrying a phosphate group at the 5′ end) and T oligo (carrying a T-tail at the 3′ end), for efficient ligation to target DNA and subsequent PCR amplification primed by the T oligo alone. Using DNA samples from body fluids, we demonstrate that TOP-PCR recovers minute DNA fragments and maintains the DNA size profile, while enhancing the major molecular populations. Our results also showed that TOP-PCR is a superior method for detecting apoptosis and outperforms the method adopted by Illumina for DNA amplification. PMID:28094343

  6. T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids.

    PubMed

    Nai, Yu-Shin; Chen, Tzu-Han; Huang, Yu-Feng; Midha, Mohit K; Shiau, Hsin-Chieh; Shen, Chen-Yang; Chen, Chien-Jen; Yu, Alice L; Chiu, Kuo Ping

    2017-01-17

    Body fluid DNA sequencing is a powerful noninvasive approach for the diagnosis of genetic defects, infectious agents and diseases. The success relies on the quantity and quality of the DNA samples. However, numerous clinical samples are either at low quantity or of poor quality due to various reasons. To overcome these problems, we have developed T oligo-primed polymerase chain reaction (TOP-PCR) for full-length nonselective amplification of minute quantity of DNA fragments. TOP-PCR adopts homogeneous "half adaptor" (HA), generated by annealing P oligo (carrying a phosphate group at the 5' end) and T oligo (carrying a T-tail at the 3' end), for efficient ligation to target DNA and subsequent PCR amplification primed by the T oligo alone. Using DNA samples from body fluids, we demonstrate that TOP-PCR recovers minute DNA fragments and maintains the DNA size profile, while enhancing the major molecular populations. Our results also showed that TOP-PCR is a superior method for detecting apoptosis and outperforms the method adopted by Illumina for DNA amplification.

  7. Molecular characterization of Streptococcus suis strains by 16S–23S intergenic spacer polymerase chain reaction and restriction fragment length polymorphism analysis

    PubMed Central

    Le Devendec, Laëtitia; Gottschalk, Marcelo; Kobisch, Marylène

    2006-01-01

    Abstract We developed a new molecular method of typing Streptococcus suis based on polymerase chain reaction (PCR) amplification of a large fragment of rRNA genes, including a part of the 16S and 23S genes and the 16S–23S intergenic spacer region (ISR), followed by restriction fragment length polymorphism (RFLP) analysis with RsaI or MboII endonuclease. The 16S–23S ISRs of 5 S. suis isolates were sequenced and compared. Size and sequence polymorphisms were observed between the S735 reference strain and the 4 wild-type strains. The genetic relationships between 138 independent S. suis strains belonging to various serotypes, isolated from swine or human cases, were determined. The discriminatory power of the method was > 0.95, the threshold value for interpreting typing results with confidence (0.954 with RsaI and 0.984 with RsaI plus MboII). The in vitro reproducibility was 100%. The strains isolated from humans were less genetically diverse than the strains isolated from pigs. For the first time, 2 molecular patterns (R6, M9) were significantly associated with S. suis serotype 2 strains. This genetic tool could be valuable in distinguishing individual isolates of S. suis during epidemiologic investigations. PMID:16639941

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. Molecular characterization of a single-chain antibody variable fragment (scFv) specific for PspA from Streptococcus pneumoniae.

    PubMed

    Jang, ShinA; Kim, Gyuhee; Oh, Jihye; Lee, Seungyeop; Kim, Dongho; Kim, Kook-Han; Kim, Yong Ho; Rhee, Dong-Kwon; Lee, Sangho

    2017-01-01

    Streptococcus pneumoniae is a major infectious agent responsible for pneumonia, otitis media, sepsis and meningitis. Pneumococcal surface protein A (PspA) is a well-characterized virulence factor localized on the surface and a target for vaccine development. In this study, we screened a single-chain antibody variable fragment (scFv) using phage display from a human synthetic library to select a clone 2B11. Affinity (Kd) of 2B11 was measured to be 5 nM using biolayer interferometry. 2B11 exhibited a dose-dependent recognition of recombinant PspA with no cross-reactivity towards pneumococcal antigens. The epitope on PspA was defined to residues 231-242 by mutational analysis. Molecular docking analysis supported the experimentally determined epitope, suggesting that the helix spanning residues 231-242 can bind to 2B11 with residues in the CDR-H3 (complementarity determining region 3 in the heavy chain) actively participating in the molecular contacts. Comparison of 2B11 with a commercial PspA antibody revealed that 2B11 exhibited a better specificity towards recombinant PspA antigen. 2B11 was capable of detecting endogenous PspA from pneumococcal lysates with affinity similar to that of the commercial antibody. Our study provides a molecular tool for biosensors detecting pneumococcal diseases.

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

    PubMed

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

    2016-07-01

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

  14. 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.

  15. Preparation and characterization of anti-tissue factor single-chain variable fragment antibody for cancer diagnosis.

    PubMed

    Sato, Ryuta; Obonai, Toshifumi; Tsumura, Ryo; Tsumoto, Kouhei; Koga, Yoshikatsu; Yasunaga, Masahiro; Matsumura, Yasuhiro

    2014-12-01

    Tissue factor (TF), which serves as the initiator of the extrinsic blood coagulation cascade, has been found to be overexpressed in various solid tumors, especially brain tumors, pancreatic cancer, and gastric cancer. Overexpression of TF is considered to contribute to the high incidence of thrombotic complications and poor prognosis in patients with such cancers. Therefore, detection or targeting of TF may be a promising approach for the diagnosis and treatment of solid tumors that are known to overexpress the protein. Here, we used the recombinant DNA technology to develop an anti-TF single-chain Fv (scFv) of small size and high affinity for its target. The biochemical characteristics of the anti-TF scFv were evaluated using surface plasmon resonance (SPR) sensing and flow cytometry. The data obtained showed that the affinity of the anti-TF scFv was 2.04 × 10(-8) (KD), and that the protein showed significant binding to the cancer cells. Then, Alexa 647-labeled anti-TF scFv and anti-TF IgG were administered to mice bearing chemically induced spontaneous tumors. The maximum tumor to background ratios of anti-TF scFv and anti-TF IgG were obtained 3 and 24 h after the injections, respectively. This study indicates anti-TF scFv may be suitable as an imaging probe for the diagnosis of solid tumors.

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

    PubMed

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

    2015-01-15

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

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

    PubMed

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

    2011-04-01

    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 (111)In ((111)In-IL-M1), along with control non-targeted liposomes ((111)In-CL). Incubation of (111)In-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 (111)In-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 (111)In-IL-M1 in live xenograft animal models was verified by single photon emission computed tomography (SPECT/CT). In contrast, i.v. injection of (111)In-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.

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

    PubMed

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

    2014-01-01

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

  19. 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.

  20. 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...

  1. A Combinatory Antibody–Antigen Microarray Assay for High-Content Screening of Single-Chain Fragment Variable Clones from Recombinant Libraries

    PubMed Central

    Jansson, Bo; Stuhr-Hansen, Nicolai; Kovács, András; Welinder, Charlotte

    2016-01-01

    We have developed a combinatory antibody–antigen microarray for direct screening of multiple single-chain fragment variable (scFv) clones with no need for pre-purification or enrichment before screening. The straightforward workflow allows for early selection of binders to predefined peptide and glycopeptide targets. A capture antibody is contact printed on microarray slides, side by side with the antigens of interest. A large number of scFv clones, in supernatants, are printed on top of the capture antibody and the antigen in a “spot-on-spot” print. The printed scFv clones, which bind to the capture antibody, are detected using biotinylated antigen, while the binding of scFv clones to the printed antigen is detected through a mouse anti-tag antibody. Two different analyses are thus performed on the same slide, generating two kinds of information: one on the ability of an individual scFv clone to bind to the soluble form of the antigen, which may favour selection for higher affinity rather than avidity, while the other allows the identification of large numbers of clones, simultaneously, due to the binding of scFv clones to densely presented antigens, thus providing an overall increased hit rate. The functionality of the new screening approach was illustrated through the generation of antibodies against peptides from the chaperone complex Ku70/Ku80 and the GalNAcα-serine/threonine epitope on the IgA1 alpha chain hinge region. In total, 659 scFv clones were screened with a hit rate of approximately 20%. This approach allowed the identification of functional antibodies in both cases, illustrating the usefulness and capacity of this combinatory microarray screening technique for efficient analysis and validation of antibodies at an early stage of antibody generation. PMID:28002485

  2. Crystal structure of anti-polysialic acid antibody single chain Fv fragment complexed with octasialic acid: insight into the binding preference for polysialic acid.

    PubMed

    Nagae, Masamichi; Ikeda, Akemi; Hane, Masaya; Hanashima, Shinya; Kitajima, Ken; Sato, Chihiro; Yamaguchi, Yoshiki

    2013-11-22

    Polysialic acid is a linear homopolymer of α2-8-linked sialic acids attached mainly onto glycoproteins. Cell surface polysialic acid plays roles in cell adhesion and differentiation events in a manner that is often dependent on the degree of polymerization (DP). Anti-oligo/polysialic acid antibodies have DP-dependent antigenic specificity, and such antibodies are widely utilized in biological studies for detecting and distinguishing between different oligo/polysialic acids. A murine monoclonal antibody mAb735 has a unique preference for longer polymers of polysialic acid (DP >10), yet the mechanism of recognition at the atomic level remains unclear. Here, we report the crystal structure of mAb735 single chain variable fragment (scFv735) in complex with octasialic acid at 1.8 Å resolution. In the asymmetric unit, two scFv735 molecules associate with one octasialic acid. In both complexes of the unit, all the complementarity-determining regions except for L3 interact with three consecutive sialic acid residues out of the eight. A striking feature of the complex is that 11 ordered water molecules bridge the gap between antibody and ligand, whereas the direct antibody-ligand interaction is less extensive. The dihedral angles of the trisialic acid unit directly interacting with scFv735 are not uniform, indicating that mAb735 does not strictly favor the previously proposed helical conformation. Importantly, both reducing and nonreducing ends of the bound ligand are completely exposed to solvent. We suggest that mAb735 gains its apparent high affinity for a longer polysialic acid chain by recognizing every three sialic acid units in a paired manner.

  3. Sea bass (Dicentrarchus labrax) invariant chain and class II major histocompatibility complex: sequencing and structural analysis using 3D homology modelling.

    PubMed

    Silva, Daniela S P; Reis, Marta I R; Nascimento, Diana S; do Vale, Ana; Pereira, Pedro J B; dos Santos, Nuno M S

    2007-07-01

    The present manuscript reports for the first time the sequencing and characterisation of sea bass (sb) MHCII alpha and beta chains and Ii chain cDNAs as well as their expression analysis under resting state. 3D homology modelling, using crystal structures from mammalian orthologues, has been used to illustrate and support putative structural homologies of the sea bass counterparts. The sbIi cDNA consists of 96 bp of 5'-UTR, a 843 bp open reading frame (ORF) and 899 bp of 3'-UTR including a canonical polyadenylation signal 16 nucleotides before the polyadenylation tail. The ORF was translated into a 280 amino acid sequence, in which all characteristic domains found in the Ii p41 human form could be identified, including the cytoplasmic N-terminus domain, the transmembrane (TM) region, the CLIP domain, the trimerization domain and the thyroglobulin (Tg) type I domain. The trimerization and Tg domains of sbIi were successfully modelled using the human counterparts as templates. Four different sequences of each class II alpha and beta MHCII were obtained from a single fish, apparently not derived from a single locus. All the characteristic features of the MHCII chain structure could be identified in the predicted ORF of sea bass alpha and beta sequences, consisting of leader peptide (LP), alpha1/beta1 and alpha2/beta2 domains, connecting peptide and TM and cytoplasmic regions. Furthermore, independently of the HLA-DR crystal structure used as template in homology modelling, a similar predicted 3D structure and trimeric quaternary architecture was obtained for sbMHC, with major deviations occurring only within the sea bass MHCII alpha1 domain.

  4. Identification of phytophthora isolates to species level using restriction fragment length polymorphism analysis of a polymerase chain reaction-amplified region of mitochondrial DNA.

    PubMed

    Martin, Frank N; Tooley, Paul W

    2004-09-01

    ABSTRACT Polymerase chain reaction primers spanning the mitochondrially encoded coxI and II genes have been identified that were capable of amplifying target DNA from all 152 isolates of 31 species in the genus Phytophthora that were tested. Digestion of the amplicons with restriction enzymes generated species-specific restriction fragment length polymorphism banding profiles that were effective for isolate classification to a species level. Of the 24 species in which multiple isolates were examined, intraspecific polymorphisms were not observed for 16 species, while 5 species exhibited limited intraspecific polymorphism that could be explained by the addition/loss of a single restriction site. Intraspecific polymorphisms were observed for P. megakarya, P. megasperma, and P. syringae; however, these differences may be a reflection of the variation that exists in these species as reported in the literature. Although digestion with AluI alone could differentiate most species tested, single digests with a total of four restriction enzymes were used in this investigation to enhance the accuracy of the technique and minimize the effect of intraspecific variability on correct isolate identification. The use of the computer program BioNumerics simplified data analysis and identification of isolates. Successful template amplification was obtained with DNA recovered from hyphae using a boiling miniprep procedure, thereby reducing the time and materials needed for conducting this analysis.

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

    PubMed Central

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

    2011-01-01

    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 Å 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 β-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. PMID:21489992

  6. Expression and characterization of recombinant interleukin-21 receptor and its targeting single-chain variable fragment antibodies selected from a human phage display library.

    PubMed

    Wu, Qinhang; Zhang, Juan; Luo, Chen; Zhang, Tao; Wang, Tong; Wang, Min

    2012-10-01

    Interleukin-21 receptor (IL-21R) is widely expressed in lymphocytes, and plays an important role in immunological cell proliferation and cytokine production. The present study aims to express a recombinant extracellular domain of human IL-21R (rhIL-21R-ECD) with high yield, and to screen the anti-IL-21R single-chain variable fragments (scFvs) from a synthetic human phage display library. The rhIL-21R-ECD, being expressed mainly as insoluble inclusion bodies in Escherichia coli BL21 (DE3), was purified and refolded. ELISA analysis showed that the refolded rhIL-21R-ECD bound to its ligand IL-21 in a concentration-dependent manner. Using a phage display technique, anti-IL-21R scFvs were screened from a naïve human phage display library by biopanning. After four rounds of panning, positive clones were isolated, sequenced, and characterized. The clone with highest activity was designated as C2. Flow cytometry analysis showed that the scFv C2 could recognize IL-21R on Jurkat cells. Furthermore, proliferation assay revealed a concentration-dependent inhibitory effect of C2 on the Jurkat cell, with fifty percent inhibitory concentration (IC(50)) of 78 nM. A human scFv antibody C2 with a high binding specificity to IL-21R was isolated and characterized. The antibody showed a concentration-dependent inhibitory effect on Jurkat cell proliferation.

  7. 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

    2015-01-09

    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.

  8. 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.

  9. 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

  10. 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.

  11. A simple and rapid nested polymerase chain reaction-restriction fragment length polymorphism technique for differentiation of pathogenic and nonpathogenic Leptospira spp.

    PubMed

    Djadid, Navid Dinparast; Ganji, Zahra Faghanzadeh; Gouya, Mohammad Mehdi; Rezvani, Mahmood; Zakeri, Sedigheh

    2009-03-01

    A rapid and specific nested polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) has been developed to detect and differentiate pathogenic and nonpathogenic Leptospira spp. Leptospiral genomic DNA was extracted from suspected human sera using an improved method of standard phenol-chloroform, and specific primers have been used to amplify 16S ribosomal RNA from all pathogenic and nonpathogenic Leptospira spp. The PCR products of all nonpathogenic species were digested with ApoI enzyme, but not pathogenic. To evaluate this assay, we analyzed 283 serum samples collected from suspected patients with leptospirosis. Nested PCR assay confirmed that 42 (14.8%) of 283 samples harbored Leptospira infection, and RFLP assay confirmed 38 (90.5%) of 42 and 4 (9.5%) of 42 positive cases had pathogenic and nonpathogenic Leptospira spp., respectively. Based on sequencing results, Leptospira interrogans, Leptospira kirschneri, and Leptospira wolffii and nonpathogenic Leptospira biflexa and Leptospira genomospecies 3 have been detected among analyzed samples. The nested PCR-RFLP assay developed in this study fulfills this requirement in the early stage of infection.

  12. Polymerase chain reaction-restriction fragment length polymorphism of the rpoB gene for identification of Mycobacterium avium subsp. paratuberculosis and differentiation of Mycobacterium avium subspecies.

    PubMed

    Whang, Jake; Lee, Byung Soo; Choi, Go-Eun; Cho, Sang-Nae; Kil, Park Young; Collins, Michael T; Shin, Sung Jae

    2011-05-01

    Mycobacterial speciation by polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis (PRA) of the rpoB gene was evaluated for identification of Mycobacterium avium subsp. paratuberculosis (MAP) and other Mycobacterium avium complex (MAC) members to the species or subspecies level by comparison with conventional methods including hsp65 sequencing, high-performance liquid chromatography, and PCR for accepted species- or subspecies-specific genomic targets. A total of 185 type and clinical mycobacterial strains from humans, animals, and environments were tested. A 360-bp PCR product was subsequently digested with MspI, HaeIII, and SmaI restriction enzymes. The PRA using SmaI restriction showed a unique digestion pattern for MAP distinguishing it from other MAC members and other Mycobacterium spp. Moreover, HaeIII and MspI restriction of the rpoB gene enabled MAC-species and -subspecies discrimination. The rpoB-PRA using SmaI or MspI and HaeIII restriction of the rpoB gene is a simple, convenient, and reliable confirmatory assay for simultaneous identification of MAP and other MAC members.

  13. 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.

  14. Molecular identification of nine commercial flaffish species by polymerase chain reaction-restriction fragment length polymorphism analysis of a segment of the cytochrome b region.

    PubMed

    Sanjuan, Andrés; Comesaña, Angel S

    2002-06-01

    Commercial refrigerated or frozen flatfish fillets are sometimes mislabeled, and identification of these mislabeled products is necessary to prevent fraudulent substitution. Identification of nine commercial flatfish species (order Pleuronectiformes), Hippoglossus hippoglossus (halibut), Lepidorhombus boscii (four-spotted scaldfish), Lepidorhombus whiffiagonis (megrin), Platichthys flesus (flounder), Pleuronectes platessa (European plaice), Reinhardtius hippoglossoides (Greenland halibut), Scophthalmus maximus (turbot), Scophthalmus rhombus (brill), and Solea vulgaris (=Solea solea) (sole), was carried out on the basis of the amplification of a 486-bp segment of the mitochondrial genome (tRNA(Glu)/cytochrome b) by using the polymerase chain reaction (PCR) and universal primers. Sequences of PCR-amplified DNA from the flatfish species were used to select eight restriction enzymes (REs). The PCR products were cut with each RE, resulting in species-specific restriction fragment length polymorphism. Seven species groups could be identified by application of the single RE DdeI and six species groups by using HaeIII, HinfI, MaeI, or MboI. Different combinations of only a couple of these REs could unambiguously identify the nine flatfish species. Genetic polymorphisms of the target sequence were examined by comparison with previously published DNA sequences, and the results of this comparison confirmed the usefulness of this technique in distinguishing and genetically characterizing refrigerated or frozen pieces of these nine flatfish species.

  15. Structural basis of neutralization of the major toxic component from the scorpion Centruroides noxius Hoffmann by a human-derived single-chain antibody fragment.

    PubMed

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

    2011-06-10

    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 Å 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 β-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.

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

    PubMed

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

    2015-06-01

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

  17. Enhanced production of functional extracellular single chain variable fragment against HIV-1 matrix protein from Escherichia coli by sequential simplex optimization.

    PubMed

    Intachai, Kannaporn; Singboottra, Panthong; Leksawasdi, Noppol; Kasinrerk, Watchara; Tayapiwatana, Chatchai; Butr-Indr, Bordin

    2015-01-01

    The optimal culture condition for extracellular recombinant single chain variable fragment anti HIV-1 p17 protein (scFv anti-p17) production in Escherichia coli HB2151 was investigated by the sequential simplex optimization (SS) method. Five variable parameters were submitted in the fermentation process. The most favorable condition obtained from 19 independent experiments was as followed: 58 µM of IPTG induction to 1.7 OD600 nm at 25.5°C for 16 h with 202 rpm agitation rate. The amount of secreted scFv anti-p17 at the optimal condition was 38% higher than under the control condition. The binding activity of soluble extracellular scFv anti-p17 protein increased 95.5% and 73.2% in comparison with the control condition and non-optimized condition respectively. The soluble scFv anti-p17 from crude HB2151 lysated was subsequently purified by immobilized metal ion affinity chromatography (IMAC) with His-tag. The purified scFv anti-p17 was intact and retained its antigen-binding affinity against HIV-1 p17. We demonstrated that the sequential simplex optimization method was a key for exertion of high yield with fewer experimental requirements for acquiring of large scale secretory protein production.

  18. 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.

  19. Determination of integron frequency by a polymerase chain reaction-restriction fragment length polymorphism method in multidrug-resistant Escherichia coli, which causes urinary tract infections.

    PubMed

    Fallah, Fatemeh; Karimi, Abdollah; Goudarzi, Mehdi; Shiva, Farideh; Navidinia, Masoumeh; Jahromi, Mana Hadipour; Sajadi Nia, Raheleh Sadat

    2012-12-01

    The purpose of this study was to determine the presence of integrons in Escherichia coli, which cause urinary tract infections, and to define the association between integrons and antimicrobial susceptibility. Susceptibility of 200 isolates from urine samples of patients suffering from urinary tract infections to 13 antibiotics was determined by the Kirby-Bauer disk diffusion method. The existence of class1 and 2 integrons in resistant isolates was assessed by polymerase chain reaction-restriction fragment length polymorphism and sequencing. Antibiotic resistance patterns were observed as follows: amoxicillin 78%, tetracycline 76.1%, co-trimoxazole 67.7%, cephalotin 60%, nalidixic acid 57.4%, chloramphenicol 49%, gentamicin 46.4%, ceftazidim 38.1%, ciprofloxacin 36.2%, nitrofurantoin 33.5%, amikacin 32.1%, norfloxacin 36.1%, and imipenem 27.1%. Of 200 isolates, 155 (77.5%) were multidrug resistant (MDR). The existence of integrons was confirmed in 50.3% of isolates. Three class 1 integron types, aadA2 being the most frequently found, and four class 2 integron types are described. Significant association between resistance to gentamicin, co-trimoxazole, cephalotin, ceftazidim, imipenem, chloramphenicol, and nalidixic acid with the existence of integrons was observed. Multidrug resistance suggests that the strategy for treatment of patients with E.coli infections needs to be revised. Furthermore, it was shown that integrons may be partly responsible for multidrug resistance. Imipenem and norfloxacin were the most effective antibiotics against isolates.

  20. 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.

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

    PubMed

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

    2016-09-21

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

  2. 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.

  3. C terminal half fragment (50 kDa) of heavy chain components of Clostridium botulinum type C and D neurotoxins can be used as an effective vaccine.

    PubMed

    Lee, Jae-Chul; Hwang, Hyun-Jung; Sakaguchi, Yoshihiko; Yamamoto, Yumiko; Arimitsu, Hideyuki; Tsuji, Takao; Watanabe, Toshihiro; Ohyama, Tohru; Tsuchiya, Tomofusa; Oguma, Keiji

    2007-01-01

    Recombinant whole heavy chains (H, 100 kDa) and their N-terminal (Hn, 50 kDa) and C-terminal (Hc, 50 kDa) half fragments of Clostridium botulinum type C and D neurotoxins were expressed as glutathione S-transferase (GST) fusion proteins in Escherichia coli. GST eliminated-preparations of H (10 microg), Hn (5 microg), Hc (5 microg), or a mixture of Hn (5 microg) and Hc (5 microg) of types C and D were mixed with an equal volume of adjuvant, and then were twice injected into mice subcutaneously. After immunization, the mice were challenged with up to 10(6) the minimum lethal doses (MLD)/0.5 ml of C or D toxin, the type of which was same as that of the immunogens. All of the mice immunized with antigens except for Hn survived against 10(5) to 10(6) MLD/0.5 ml of the toxins, but the mice immunized with Hn were killed by 100 MLD/0.5 ml. The mice immunized with a mixture of C-Hc and D-Hc, each 5 microg, also showed a high level of resistance against both C and D toxins. Antibody levels immunized with GST fused-or GST eliminatedpreparation were quite similar. These results indicate that recombinant GST-fused Hc can be used as a safe and effective vaccine for type C and D botulism in animals. It also became clear that one time inoculation with a large amount of C-Hc or D-Hc, 100 microg, is useful for vaccine trials in mice.

  4. Soil pretreatment and fast cell lysis for direct polymerase chain reaction from forest soils for terminal restriction fragment length polymorphism analysis of fungal communities.

    PubMed

    Cheng, Fei; Hou, Lin; Woeste, Keith; Shang, Zhengchun; Peng, Xiaobang; Zhao, Peng; Zhang, Shuoxin

    Humic substances in soil DNA samples can influence the assessment of microbial diversity and community composition. Using multiple steps during or after cell lysis adds expenses, is time-consuming, and causes DNA loss. A pretreatment of soil samples and a single step DNA extraction may improve experimental results. In order to optimize a protocol for obtaining high purity DNA from soil microbiota, five prewashing agents were compared in terms of their efficiency and effectiveness in removing soil contaminants. Residual contaminants were precipitated by adding 0.6mL of 0.5M CaCl2. Four cell lysis methods were applied to test their compatibility with the pretreatment (prewashing+Ca(2+) flocculation) and to ultimately identify the optimal cell lysis method for analyzing fungal communities in forest soils. The results showed that pretreatment with TNP+Triton X-100+skim milk (100mM Tris, 100mM Na4P2O7, 1% polyvinylpyrrolidone, 100mM NaCl, 0.05% Triton X-100, 4% skim milk, pH 10.0) removed most soil humic contaminants. When the pretreatment was combined with Ca(2+) flocculation, the purity of all soil DNA samples was further improved. DNA samples obtained by the fast glass bead-beating method (MethodFGB) had the highest purity. The resulting DNA was successfully used, without further purification steps, as a template for polymerase chain reaction targeting fungal internal transcribed spacer regions. The results obtained by terminal restriction fragment length polymorphism analysis indicated that the MethodFGB revealed greater fungal diversity and more distinctive community structure compared with the other methods tested. Our study provides a protocol for fungal cell lysis in soil, which is fast, convenient, and effective for analyzing fungal communities in forest soils.

  5. Bicistronic expression plasmid encoding allergen and anti-IgE single chain variable fragment antibody as a novel DNA vaccine for allergy therapy and prevention.

    PubMed

    Bandbon Balenga, Nariman Aghaei; Thalhamer, Josef; Weiss, Richard

    2006-01-01

    Several approaches have been applied in order to alleviate the difficulties allergic patients are suffering from. Among them DNA vaccination and anti-IgE antibody have shown promising results. Herewith, a combination of both strategies is proposed to minimize IgE production while inducing high levels of blocking IgG and strong Th1 immune responses. A bicistronic expression plasmid including an internal ribosomal entry site (IRES) can express both, allergen and a single chain variable fragment (scFv) antibody against human IgE within antigen presenting cells (APCs) including B cells. Presentation of allergen derived peptides via MHC I and MHC II stimulates specific Th1 responses resulting in high levels of IFN-gamma and IgG. Anti-IgE scFv antibody binds to newly synthesized IgE molecules within B cell cytoplasm and also to free serum IgE, thereby inhibiting attachment of IgE to its receptors on basophils and mast cells. Also, IgE-anti-IgE complex functions as blocking antibody and neutralizes allergens entering the body. Additionally, anti-IgE scFv antibody binds to membrane bound IgE (mIgE) on B cells and interferes with IgE expression. Using assays, such as enzyme linked immunosorbent assay (ELISA), IgG and IgE production in response to this expression system can be evaluated. Also, rat basophil leukemia cell assay (using RBL-2H3 cells) can show the amount of functional IgE in sera as basophil mediator release is regarded as an indicator of the allergic hypersensitive reactions. The proposed approach may result in high levels of blocking IgG and low levels of IgE secretion from B cells. Additionally, it can inhibit activity of IgE in degranulation of basophils and mast cells.

  6. 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.

  7. Elongation of the C-terminal domain of an anti-amyloid β single-chain variable fragment increases its thermodynamic stability and decreases its aggregation tendency.

    PubMed

    Rivera-Hernández, Geovanny; Marin-Argany, Marta; Blasco-Moreno, Bernat; Bonet, Jaume; Oliva, Baldo; Villegas, Sandra

    2013-01-01

    Amyloid β (Aβ) immunotherapy is considered a promising approach to Alzheimer disease treatment. In contrast to the use of complete antibodies, administration of single-chain variable fragments (scFv) has not been associated with either meningoencephalitis or cerebral hemorrhage. ScFv-h3D6 is known to preclude cytotoxicity of the Aβ 1-42 peptide by removing its oligomers from the amyloid pathway. As is the case for other scFv molecules, the recombinant production of scFv-h3D6 is limited by its folding and stability properties. Here, we show that its urea-induced unfolding pathway is characterized by the presence of an intermediate state composed of the unfolded VL domain and the folded VH domain, which suggests the VL domain as a target for thermodynamic stability redesign. The modeling of the 3D structure revealed that the VL domain, located at the C-terminal of the molecule, was ending before its latest β-strand was completed. Three elongation mutants, beyond VL-K107, showed increased thermodynamic stability and lower aggregation tendency, as determined from urea denaturation experiments and Fourier-transform infrared spectroscopy, respectively. Because the mutants maintained the capability of removing Aβ-oligomers from the amyloid pathway, we expect these traits to increase the half-life of scFv-h3D6 in vivo and, consequently, to decrease the effective doses. Our results led to the improvement of a potential Alzheimer disease treatment and may be extrapolated to other class-I scFv molecules of therapeutic interest.

  8. Statistical models of brittle fragmentation

    NASA Astrophysics Data System (ADS)

    Åström, J. A.

    2006-06-01

    Recent developments in statistical models for fragmentation of brittle material are reviewed. The generic objective of these models is understanding the origin of the fragment size distributions (FSDs) that result from fracturing brittle material. Brittle fragmentation can be divided into two categories: (1) Instantaneous fragmentation for which breakup generations are not distinguishable and (2) continuous fragmentation for which generations of chronological fragment breakups can be identified. This categorization becomes obvious in mining industry applications where instantaneous fragmentation refers to blasting of rock and continuous fragmentation to the consequent crushing and grinding of the blasted rock fragments. A model of unstable cracks and crack-branch merging contains both of the FSDs usually related to instantaneous fragmentation: the scale invariant FSD with the power exponent (2-1/D) and the double exponential FSD which relates to Poisson process fragmentation. The FSDs commonly related to continuous fragmentation are: the lognormal FSD originating from uncorrelated breakup and the power-law FSD which can be modeled as a cascade of breakups. Various solutions to the generic rate equation of continuous fragmentation are briefly listed. Simulations of crushing experiments reveal that both cascade and uncorrelated fragmentations are possible, but that also a mechanism of maximizing packing density related to Apollonian packing may be relevant for slow compressive crushing.

  9. 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.

  10. 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.

  11. 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.

  12. Antitumor effects of ricin A chain immunotoxins prepared from intact antibodies and Fab' fragments on solid human Hodgkin's disease tumors in mice.

    PubMed

    Engert, A; Martin, G; Pfreundschuh, M; Amlot, P; Hsu, S M; Diehl, V; Thorpe, P

    1990-05-15

    Three monoclonal antibodies which strongly bind to Hodgkin and Reed-Sternberg cells and two corresponding Fab' fragments were linked to deglycosylated ricin A chain (dg A) to evaluate their potential as immunotoxins for the treatment of Hodgkin's disease. Two of the antibodies, Ber-H2 and HRS-3, were shown to bind to the same epitope on the CD30 antigen, whereas the third antibody, IRac, bound to a different antigen. None of the antibodies significantly cross-reacted with normal human tissues as judged by indirect immunofluorescence and immunoperoxidase analyses on frozen sections from 28 normal tissues. All three antibodies formed potent and specific immunotoxins. They inhibited protein synthesis of the L540 Hodgkin's disease cell line in vitro by 50% at concentrations of 1 x 10(-11) M for IRac.dgA, 9 x 10(-11) M for HRS-3.dgA, and 2 x 10(-10) M for Ber-H2.dgA. HRS-3 Fab' and IRac Fab' immunotoxins were 7.8- and 60-fold less cytotoxic, respectively, than their intact counterparts in vitro. In vivo, a single i.v. injection of a dose of Ber-H2.dgA, HRS-3.dgA, or IRac.dgA corresponding to 40% of the LD50 induced lasting complete remissions in 38, 44, and 50%, respectively, of mice with solid s.c. L540 tumors of 60 to 80 mm3 size (0.5-cm diameter). At equivalent dosage (40% of the LD50), the HRS-3 Fab'.dgA and the IRac Fab'.dgA both induced lasting complete remissions in 25% of the mice, although the HRS-3 Fab'.dgA was significantly superior to IRac Fab'.dgA at retarding tumor growth in the remaining animals. The effectiveness of the immunotoxins depended on the size of the tumor at the time of injection, since IRac.dgA treatment induced complete remissions in 100% of mice with small tumors (10 to 20 mm3, approximately 0.3 cm in diameter) but only 13% of mice with larger tumors of 400 to 600 mm3 (approximately 1 cm in diameter). Tumors which regrew after IRac.dgA treatment mainly consisted of antigen-deficient mutants having reduced sensitivity to IRac.dgA but normal

  13. Fragmentation of monoclonal antibodies

    PubMed Central

    Vlasak, Josef

    2011-01-01

    Fragmentation is a degradation pathway ubiquitously observed in proteins despite the remarkable stability of peptide bond; proteins differ only by how much and where cleavage occurs. The goal of this review is to summarize reports regarding the non-enzymatic fragmentation of the peptide backbone of monoclonal antibodies (mAbs). The sites in the polypeptide chain susceptible to fragmentation are determined by a multitude of factors. Insights are provided on the intimate chemical mechanisms that can make some bonds prone to cleavage due to the presence of specific side-chains. In addition to primary structure, the secondary, tertiary and quaternary structures have a significant impact in modulating the distribution of cleavage sites by altering local flexibility, accessibility to solvent or bringing in close proximity side chains that are remote in sequence. This review focuses on cleavage sites observed in the constant regions of mAbs, with special emphasis on hinge fragmentation. The mechanisms responsible for backbone cleavage are strongly dependent on pH and can be catalyzed by metals or radicals. The distribution of cleavage sites are different under acidic compared to basic conditions, with fragmentation rates exhibiting a minimum in the pH range 5–6; therefore, the overall fragmentation pattern observed for a mAb is a complex result of structural and solvent conditions. A critical review of the techniques used to monitor fragmentation is also presented; usually a compromise has to be made between a highly sensitive method with good fragment separation and the capability to identify the cleavage site. The effect of fragmentation on the function of a mAb must be evaluated on a case-by-case basis depending on whether cleavage sites are observed in the variable or constant regions, and on the mechanism of action of the molecule. PMID:21487244

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

    PubMed

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

    2014-10-01

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

  15. Enhanced and sustained CD8+ T cell responses with an adenoviral vector-based hepatitis C virus vaccine encoding NS3 linked to the MHC class II chaperone protein invariant chain.

    PubMed

    Mikkelsen, Marianne; Holst, Peter Johannes; Bukh, Jens; Thomsen, Allan Randrup; Christensen, Jan Pravsgaard

    2011-02-15

    Potent and broad cellular immune responses against the nonstructural (NS) proteins of hepatitis C virus (HCV) are associated with spontaneous viral clearance. In this study, we have improved the immunogenicity of an adenovirus (Ad)-based HCV vaccine by fusing NS3 from HCV (Strain J4; Genotype 1b) to the MHC class II chaperone protein invariant chain (Ii). We found that, after a single vaccination of C57BL/6 or BALB/c mice with Ad-IiNS3, the HCV NS3-specific CD8(+) T cell responses were significantly enhanced, accelerated, and prolonged compared with the vaccine encoding NS3 alone. The AdIiNS3 vaccination induced polyfunctional CD8(+) T cells characterized by coproduction of IFN-γ, TNF-α and IL-2, and this cell phenotype is associated with good viral control. The memory CD8(+) T cells also expressed high levels of CD27 and CD127, which are markers of long-term survival and maintenance of T cell memory. Functionally, the AdIiNS3-vaccinated mice had a significantly increased cytotoxic capacity compared with the AdNS3 group. The AdIiNS3-induced CD8(+) T cells protected mice from infection with recombinant vaccinia virus expressing HCV NS3 of heterologous 1b strains, and studies in knockout mice demonstrated that this protection was mediated primarily through IFN-γ production. On the basis of these promising results, we suggest that this vaccination technology should be evaluated further in the chimpanzee HCV challenge model.

  16. Conformal differential invariants

    NASA Astrophysics Data System (ADS)

    Kruglikov, Boris

    2017-03-01

    We compute the Hilbert polynomial and the Poincaré function counting the number of fixed jet-order differential invariants of conformal metric structures modulo local diffeomorphisms, and we describe the field of rational differential invariants separating generic orbits of the diffeomorphism pseudogroup action. This resolves the local recognition problem for conformal structures.

  17. 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.

  18. A population genetics study of Anopheles darlingi (Diptera: Culicidae) from Colombia based on random amplified polymorphic DNA-polymerase chain reaction and amplified fragment lenght polymorphism markers.

    PubMed

    González, Ranulfo; Wilkerson, Richard; Suárez, Marco Fidel; García, Felipe; Gallego, Gerardo; Cárdenas, Heiber; Posso, Carmen Elisa; Duque, Myriam Cristina

    2007-06-01

    The genetic variation and population structure of three populations of Anopheles darlingi from Colombia were studied using random amplified polymorphic markers (RAPDs) and amplified fragment length polymorphism markers (AFLPs). Six RAPD primers produced 46 polymorphic fragments, while two AFLP primer combinations produced 197 polymorphic fragments from 71 DNA samples. Both of the evaluated genetic markers showed the presence of gene flow, suggesting that Colombian An. darlingi populations are in panmixia. Average genetic diversity, estimated from observed heterozygosity, was 0.374 (RAPD) and 0.309 (AFLP). RAPD and AFLP markers showed little evidence of geographic separation between eastern and western populations; however, the F ST values showed high gene flow between the two western populations (RAPD: F ST = 0.029; Nm: 8.5; AFLP: F ST = 0.051; Nm: 4.7). According to molecular variance analysis (AMOVA), the genetic distance between populations was significant (RAPD:phiST = 0.084; AFLP:phiST = 0.229, P < 0.001). The F ST distances and AMOVAs using AFLP loci support the differentiation of the Guyana biogeographic province population from those of the Chocó-Magdalena. In this last region, Chocó and Córdoba populations showed the highest genetic flow.

  19. Development of a polymerase chain reaction-restriction fragment length polymorphism method for identification of the Fusarium genus using the transcription elongation factor-1α gene.

    PubMed

    Zarrin, Majid; Ganj, Farzaneh; Faramarzi, Sama

    2016-12-01

    Fusarium species are well-known plant pathogens and food contaminants that have also appeared as one of the most important groups of medically significant fungi. The sequences of the translation elongation factor (TEF)-1α gene have been broadly employed for species detection. A total of 50 strains of Fusarium spp., including environmental, clinical and reference isolates were used for the current study. The primer sets, Fu3f and Fu3r, were used to amplify an ~420-bp DNA fragment of the TEF-1α gene. Double digestion with two restriction enzymes, XhoI and SduI was used for discrimination of the Fusarium species in the TEF-1α gene fragment. Double digestion of the TEF-1α gene fragment from five clinically important Fusarium species were clearly differentiated from each other: The F. solani species complex, F. oxysporum species complex, F. verticillioides, F. proliferatum and F. fujikuroi. This method facilitates detection and enables verification of the Fusarium genus; therefore, it may be applied for disease control.

  20. Development of a polymerase chain reaction-restriction fragment length polymorphism method for identification of the Fusarium genus using the transcription elongation factor-1α gene

    PubMed Central

    Zarrin, Majid; Ganj, Farzaneh; Faramarzi, Sama

    2016-01-01

    Fusarium species are well-known plant pathogens and food contaminants that have also appeared as one of the most important groups of medically significant fungi. The sequences of the translation elongation factor (TEF)-1α gene have been broadly employed for species detection. A total of 50 strains of Fusarium spp., including environmental, clinical and reference isolates were used for the current study. The primer sets, Fu3f and Fu3r, were used to amplify an ~420-bp DNA fragment of the TEF-1α gene. Double digestion with two restriction enzymes, XhoI and SduI was used for discrimination of the Fusarium species in the TEF-1α gene fragment. Double digestion of the TEF-1α gene fragment from five clinically important Fusarium species were clearly differentiated from each other: The F. solani species complex, F. oxysporum species complex, F. verticillioides, F. proliferatum and F. fujikuroi. This method facilitates detection and enables verification of the Fusarium genus; therefore, it may be applied for disease control. PMID:28105337

  1. A novel anti-alpha-fetoprotein single-chain variable fragment displays anti-tumor effects in HepG2 cells as a single agent or in combination with paclitaxel.

    PubMed

    Ji, Xiaonan; Shen, Yanli; Sun, Hao; Gao, Xiangdong

    2016-08-01

    Human hepatocellular carcinoma (HCC) has a high rate of tumor recurrence and metastasis, resulting in shortened survival time. The function of alpha-fetoprotein (AFP) as a regulatory factor in the growth of HCC cells has been well defined. The aim of this study was to investigate the use of a novel AFP-specific single-chain variable fragment that blocked AFP and inhibited HCC cell growth. The results indicated that the anti-AFP single-chain variable fragment (scFv) induced growth inhibition of AFP-expressing HCC cell lines in vitro through induction of G1 cell cycle arrest and apoptosis. The mechanism of apoptosis probably involved with blocking AFP internalization and regulation of the PTEN/PI3K/Akt signaling network. Moreover, the anti-AFP-scFv also effectively sensitized the HepG2 cells to paclitaxel (PTX) at a lower concentration. The combination effect of PTX and anti-AFP-scFv displayed a synergistic effect on HepG2 cells both in vitro and in vivo. Our results demonstrated that targeting AFP by specific antibodies has potential immunotherapeutic efficacy in human HCC.

  2. 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

    Wang, Fengxue; Yan, Xijun; Chai, Xiuli; Zhang, Hailing; Zhao, Jianjun; Wen, Yongjun; Wu, Wei

    2011-02-27

    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.

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

    PubMed

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

    2016-01-01

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

  4. 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.

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

    SciTech Connect

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

    1987-05-01

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

  6. Cosmological disformal invariance

    SciTech Connect

    Domènech, Guillem; Sasaki, Misao; Naruko, Atsushi E-mail: naruko@th.phys.titech.ac.jp

    2015-10-01

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

  7. Explicit Krawtchouk moment invariants for invariant image recognition

    NASA Astrophysics Data System (ADS)

    Xiao, Bin; Zhang, Yanhong; Li, Linping; Li, Weisheng; Wang, Guoyin

    2016-03-01

    The existing Krawtchouk moment invariants are derived by a linear combination of geometric moment invariants. This indirect method cannot achieve perfect performance in rotation, scale, and translation (RST) invariant image recognition since the derivation of these invariants are not built on Krawtchouk polynomials. A direct method to derive RST invariants from Krawtchouk moments, named explicit Krawtchouk moment invariants, is proposed. The proposed method drives Krawtchouk moment invariants by algebraically eliminating the distorted (i.e., rotated, scaled, and translated) factor contained in the Krawtchouk moments of distorted image. Experimental results show that, compared with the indirect methods, the proposed approach can significantly improve the performance in terms of recognition accuracy and noise robustness.

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

    PubMed Central

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

    2009-01-01

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

  9. In search for graph invariants of chemical interes

    NASA Astrophysics Data System (ADS)

    Randić, Milan; Trinajstić, Nenad

    1993-12-01

    This article encourages readers to search for novel graph invariants that may be of potential interest in chemical applications of graph theory. It is also hoped that theoreticians, with their different backgrounds and different viewpoints, may identify or design novel graph invariants that have not yet been tested in chemistry and in this way enrich the pool of descriptors for use in studies of structure—property relationships. An outline of desirable attributes for graph invariants that have found use in chemistry is followed by a brief review of a selection of known ad hoc invariants. This continues with a description of families of structurally related invariants. We discuss some promising routes to construction of novel descriptors such as those based on consideration of graph fragments. A warning against useless and misleading descriptors is given. We end with a call for design of or verification of basis graphs.

  10. Development of a Multiplexed Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) Assay to Identify Common Members of the Subgenera Culex (Culex) and Culex (Phenacomyia) in Guatemala

    PubMed Central

    Kent, Rebekah J.; Deus, Stephen; Williams, Martin; Savage, Harry M.

    2010-01-01

    Morphological differentiation of mosquitoes in the subgenera Culex (Culex) and Culex (Phenacomyia) in Guatemala is difficult, with reliable identification ensured only through examination of larval skins from individually reared specimens and associated male genitalia. We developed a multiplexed polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay to identify common Cx. (Cux.) and Cx. (Phc.). Culex (Cux.) chidesteri, Cx. (Cux.) coronator, Cx. (Cux.) interrogator, Cx. (Cux.) quinquefasciatus, Cx. (Cux.) nigripalpus/Cx. (Cux.) thriambus, and Cx. (Phc.) lactator were identified directly with a multiplexed primer cocktail comprising a conserved forward primer and specific reverse primers targeting ribosomal DNA (rDNA). Culex nigripalpus and Cx. thriambus were differentiated by restriction digest of homologous amplicons. The assay was developed and optimized using well-characterized specimens from Guatemala and the United States and field tested with unknown material from Guatemala. This assay will be a valuable tool for mosquito identification in entomological and arbovirus ecology studies in Guatemala. PMID:20682869

  11. 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.

  12. 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

  13. Generalized scale invariant theories

    NASA Astrophysics Data System (ADS)

    Padilla, Antonio; Stefanyszyn, David; Tsoukalas, Minas

    2014-03-01

    We present the most general actions of a single scalar field and two scalar fields coupled to gravity, consistent with second-order field equations in four dimensions, possessing local scale invariance. We apply two different methods to arrive at our results. One method, Ricci gauging, was known to the literature and we find this to produce the same result for the case of one scalar field as a more efficient method presented here. However, we also find our more efficient method to be much more general when we consider two scalar fields. Locally scale invariant actions are also presented for theories with more than two scalar fields coupled to gravity and we explain how one could construct the most general actions for any number of scalar fields. Our generalized scale invariant actions have obvious applications to early Universe cosmology and include, for example, the Bezrukov-Shaposhnikov action as a subset.

  14. 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.

  15. A strategy for the generation of specific human antibodies by directed evolution and phage display. An example of a single-chain antibody fragment that neutralizes a major component of scorpion venom.

    PubMed

    Riaño-Umbarila, Lidia; Juárez-González, Victor Rivelino; Olamendi-Portugal, Timoteo; Ortíz-León, Mauricio; Possani, Lourival Domingos; Becerril, Baltazar

    2005-05-01

    This study describes the construction of a library of single-chain antibody fragments (scFvs) from a single human donor by individual amplification of all heavy and light variable domains (1.1 x 10(8) recombinants). The library was panned using the phage display technique, which allowed selection of specific scFvs (3F and C1) capable of recognizing Cn2, the major toxic component of Centruroides noxius scorpion venom. The scFv 3F was matured in vitro by three cycles of directed evolution. The use of stringent conditions in the third cycle allowed the selection of several improved clones. The best scFv obtained (6009F) was improved in terms of its affinity by 446-fold, from 183 nm (3F) to 410 pm. This scFv 6009F was able to neutralize 2 LD(50) of Cn2 toxin when a 1 : 10 molar ratio of toxin-to-antibody fragment was used. It was also able to neutralize 2 LD(50) of the whole venom. These results pave the way for the future generation of recombinant human antivenoms.

  16. 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

  17. Sequence comparison of pepsin-resistant segments of basement-membrane collagen alpha 1(IV) chains from bovine lens capsule and mouse tumour.

    PubMed Central

    Schuppan, D; Glanville, R W; Timpl, R; Dixit, S N; Kang, A H

    1984-01-01

    The C-terminal peptic fragment P1 (about 518 amino acid residues) of bovine lens-capsule collagen alpha 1(IV) chain was cleaved with CNBr and trypsin. The peptides were purified and characterized, allowing their ordering within the P1 fragment by comparison with a corresponding section of mouse collagen alpha 1(IV) chain [Schuppan, Glanville & Timpl (1982) Eur. J. Biochem. 123, 505-512]. About 67% of the sequence of bovine collagen fragment P1 was determined by Edman degradation. Comparison with the sequence of the corresponding mouse collagen fragment P1 showed 76% identity for positions Xaa and Yaa of the triplet structures Gly-Xaa-Yaa. Invariance was found for the positions of two non-triplet interruptions and of 3-hydroxyproline residues, pointing to the functional importance of these structures. PMID:6430279

  18. 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.

  19. Supersymmetric invariant theories

    NASA Astrophysics Data System (ADS)

    Esipova, S. R.; Lavrov, P. M.; Radchenko, O. V.

    2014-04-01

    We study field models for which a quantum action (i.e. the action appearing in the generating functional of Green functions) is invariant under supersymmetric transformations. We derive the Ward identity which is a direct consequence of this invariance. We consider a change of variables in functional integral connected with supersymmetric transformations when its parameter is replaced by a nilpotent functional of fields. Exact form of the corresponding Jacobian is found. We find restrictions on generators of supersymmetric transformations when a consistent quantum description of given field theories exists.

  20. Lack of coupling between secondary structure formation and collapse in a model polypeptide that mimics early folding intermediates, the F2 fragment of the Escherichia coli tryptophan-synthase beta chain.

    PubMed Central

    Gast, K.; Chaffotte, A. F.; Zirwer, D.; Guillou, Y.; Mueller-Frohne, M.; Cadieux, C.; Hodges, M.; Damaschun, G.; Goldberg, M. E.

    1997-01-01

    The isolated, 101-residue long C-terminal (so called F2) fragment of the beta chain from Escherichia coli tryptophan synthase was shown previously to fold into an ensemble of conformations that are condensed, to contain large amounts of highly dynamic secondary structures, and to behave as a good model of structured intermediates that form at the very early stages of protein folding. Here, solvent perturbations were used to investigate the forces that are involved in stabilizing the secondary structure (monitored by far-UV CD) and the condensation of the polypeptide chain (monitored by dynamic light scattering) in isolated F2. It was observed that neither the ionic strength, nor the pH (between 7 and 10), nor salts of the Hofmeister series affected the global secondary structure contents of F2, whereas some of these salts affected the collapse slightly. Addition of trifluoroethanol resulted in a large increase in both the amount of secondary structure and the Stokes radius of F2. Conversely, F2 became more condensed upon raising the temperature from 4 to 60 degrees C, whereas in this temperature range, the secondary structure undergoes significant melting. These observations lead to the conclusion that, in isolated F2, there is no coupling between the hydrophobic collapse and the secondary structure. This finding will be discussed in terms of early events in protein folding. PMID:9416607

  1. 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…

  2. Modular invariant inflation

    SciTech Connect

    Kobayashi, Tatsuo; Nitta, Daisuke; Urakawa, Yuko

    2016-08-08

    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 V{sub ht}, but it also has a non-negligible deviation from V{sub ht}. 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.

  3. 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.

  4. 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.

  5. Chameleon fragmentation

    SciTech Connect

    Brax, Philippe

    2014-02-01

    A scalar field dark energy candidate could couple to ordinary matter and photons, enabling its detection in laboratory experiments. Here we study the quantum properties of the chameleon field, one such dark energy candidate, in an ''afterglow'' experiment designed to produce, trap, and detect chameleon particles. In particular, we investigate the possible fragmentation of a beam of chameleon particles into multiple particle states due to the highly non-linear interaction terms in the chameleon Lagrangian. Fragmentation could weaken the constraints of an afterglow experiment by reducing the energy of the regenerated photons, but this energy reduction also provides a unique signature which could be detected by a properly-designed experiment. We show that constraints from the CHASE experiment are essentially unaffected by fragmentation for φ{sup 4} and 1/φ potentials, but are weakened for steeper potentials, and we discuss possible future afterglow experiments.

  6. 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.

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

    ERIC Educational Resources Information Center

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

    2008-01-01

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

  8. Clathrin heavy chain, light chain interactions.

    PubMed Central

    Winkler, F K; Stanley, K K

    1983-01-01

    Purified pig brain clathrin can be reversibly dissociated and separated into heavy chain trimers and light chains in the presence of non-denaturing concentrations of the chaotrope thiocyanate. The isolated heavy chain trimers reassemble into regular polygonal cage structures in the absence of light chains. The light chain fraction can be further resolved into its two components L alpha and L beta which give different one-dimensional peptide maps. Radiolabelled light chains bind with high affinity (KD < 10(-10) M) to heavy chain trimers, to heavy chain cages and to a 110,000 mol. wt. tryptic fragment of the heavy chain. Both light chains compete with each other and with light chains from other sources for the same binding sites on heavy chains and c.d. spectroscopy shows that the two pig brain light chains possess very similar structures. We conclude that light chains from different sources, despite some heterogeneity, have a highly conserved, high affinity binding site on the heavy chain but are not essential for the formation of regular cage structures. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 8. PMID:10872336

  9. Dimensional effects in dynamic fragmentation of brittle materials

    NASA Astrophysics Data System (ADS)

    Linna, R. P.; Åström, J. A.; Timonen, J.

    2005-07-01

    It has been shown previously that dynamic fragmentation of brittle D -dimensional objects in a D -dimensional space gives rise to a power-law contribution to the fragment-size distribution with a universal scaling exponent 2-1/D . We demonstrate that in fragmentation of two-dimensional brittle objects in three-dimensional space, an additional fragmentation mechanism appears, which causes scale-invariant secondary breaking of existing fragments. Due to this mechanism, the power law in the fragment-size distribution has now a scaling exponent of ˜1.17 .

  10. Invariance and Objectivity

    NASA Astrophysics Data System (ADS)

    Vollmer, Gerhard

    2010-10-01

    Scientific knowledge should not only be true, it should be as objective as possible. It should refer to a reality independent of any subject. What can we use as a criterion of objectivity? Intersubjectivity (i.e., intersubjective understandability and intersubjective testability) is necessary, but not sufficient. Other criteria are: independence of reference system, independence of method, non-conventionality. Is there some common trait? Yes, there is: invariance under some specified transformations. Thus, we say: A proposition is objective only if its truth is invariant against a change in the conditions under which it was formulated. We give illustrations from geometry, perception, neurobiology, relativity theory, and quantum theory. Such an objectivist position has many advantages.

  11. Convex Graph Invariants

    DTIC Science & Technology

    2010-12-02

    evaluating the function ΘP (A) for any fixed A,P is equivalent to solving the so-called Quadratic Assignment Problem ( QAP ), and thus we can employ various...tractable linear programming, spectral, and SDP relaxations of QAP [40, 11, 33]. In particular we discuss recent work [14] on exploiting group...symmetry in SDP relaxations of QAP , which is useful for approximately computing elementary convex graph invariants in many interesting cases. Finally in

  12. 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.

  13. 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.

  14. Time-reversal-based SU(2) x Sn scalar invariants as (Lie Algebraic) group measures: a structured overview of generalised democratic-recoupled, uniform non-Abelian [AX]n NMR spin systems, as abstract [Formula: see text] chain networks.

    PubMed

    Temme, F P

    2004-03-01

    The physics of dual group scalar invariants (SIs) as (Lie algebraic) group measures (L-GMs) and its significance to non-Abelian NMR spin systems motivates this overview of uniform general-2n [AX](2n) spin evolution, which represents an extensive addendum to Corio's earlier (essentially restricted) view of Abelian spin system SU(2)-based SI-cardinalities. The [Formula: see text] values in [J. Magn. Reson., 134 (1998) 131] arise from strictly linear recoupled time-reversal invariance (TRI) models. In contrast, here we discuss the physical significance of an alternative polyhedral combinatorics approach to democratic recoupling (DR), a property inherent in both the TRI and statistical sampling. Recognition of spin ensemble SIs as being L-GMs over isomorphic algebras is invaluable in many DR-based NMR problems. Various [AX]n model spin systems, including the [AX]3 bis odd-odd parity spin system, are examined as direct applications of these L-GM- and combinatorial-based SI ideas. Hence in place of /SI/=15 (implied by Corio's [Formula: see text] approach), the bis 3-fold spin system cardinality is seen now as constrained to a single invariant on an isomorphic product algebra under L-GMs, in accord with the subspectral analysis of Jones et al. [Canad. J. Chem., 43 (1965) 683]. The group projective ideas cited here for DR (as cf. to graph theoretic views) apply to highly degenerate non-Abelian problems. Over dual tensorial bases, they define models of spin dynamical evolution whose (SR) quasiparticle superboson carrier (sub)spaces are characterised by SIs acting as explicit auxiliary labels [Physica, A198 (1993) 245; J. Math. Chem., 31 (2002) 281]. A deeper [Formula: see text] network-based view of spin-alone space developed in Balasubramanian's work [J. Chem. Phys., 78 (1983) 6358] is especially important, (e.g.) in the study of spin waves [J. Math. Chem., 31 (2002) 363]. Beyond the specific NMR SIs derived here, there are DR applications where a sporadic, still higher, 2

  15. Fragmentation Processes

    NASA Astrophysics Data System (ADS)

    Whelan, Colm T.

    2012-12-01

    Preface; 1. Direct and resonant double-photoionization: from atoms to solids L. Avaldi and G. Stefani; 2. The application of propagation exterior complex scaling to atomic collisions P. L. Bartlett and A. T. Stelbovics; 3. Fragmentation of molecular-ion beams in intense ultra-short laser pulses I. Ben-Itzhak; 4. Atoms with one and two active electrons in strong laser fields I. A. Ivanov and A. S. Kheifets; 5. Experimental aspects of ionization studies by positron and positronium impact G. Laricchia, D. A. Cooke, Á. Kövér and S. J. Brawley; 6. (e,2e) spectroscopy using fragmentation processes J. Lower, M. Yamazaki and M. Takahashi; 7. A coupled pseudostate approach to the calculation of ion-atom fragmentation processes M. McGovern, H. R. J. Walters and C. T. Whelan; 8. Electron Impact Ionization using (e,2e) coincidence techniques from threshold to intermediate energies A. J. Murray; 9. (e,2e) processes on atomic inner shells C. T. Whelan; 10. Spin resolved atomic (e,2e) processes J. Lower and C. T. Whelan; Index.

  16. Binding of HIV-1 gp41-directed neutralizing and non-neutralizing fragment antibody binding domain (Fab) and single chain variable fragment (ScFv) antibodies to the ectodomain of gp41 in the pre-hairpin and six-helix bundle conformations.

    PubMed

    Louis, John M; Aniana, Annie; Lohith, Katheryn; Sayer, Jane M; Roche, Julien; Bewley, Carole A; Clore, G Marius

    2014-01-01

    We previously reported a series of antibodies, in fragment antigen binding domain (Fab) formats, selected from a human non-immune phage library, directed against the internal trimeric coiled-coil of the N-heptad repeat (N-HR) of HIV-1 gp41. Broadly neutralizing antibodies from that series bind to both the fully exposed N-HR trimer, representing the pre-hairpin intermediate state of gp41, and to partially-exposed N-HR helices within the context of the gp41 six-helix bundle. While the affinities of the Fabs for pre-hairpin intermediate mimetics vary by only 2 to 20-fold between neutralizing and non-neutralizing antibodies, differences in inhibition of viral entry exceed three orders of magnitude. Here we compare the binding of neutralizing (8066) and non-neutralizing (8062) antibodies, differing in only four positions within the CDR-H2 binding loop, in Fab and single chain variable fragment (ScFv) formats, to several pre-hairpin intermediate and six-helix bundle constructs of gp41. Residues 56 and 58 of the mini-antibodies are shown to be crucial for neutralization activity. There is a large differential (≥ 150-fold) in binding affinity between neutralizing and non-neutralizing antibodies to the six-helix bundle of gp41 and binding to the six-helix bundle does not involve displacement of the outer C-terminal helices of the bundle. The binding stoichiometry is one six-helix bundle to one Fab or three ScFvs. We postulate that neutralization by the 8066 antibody is achieved by binding to a continuum of states along the fusion pathway from the pre-hairpin intermediate all the way to the formation of the six-helix bundle, but prior to irreversible fusion between viral and cellular membranes.

  17. 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.

  18. Studies on the HLA-DRB1 genotypes in Japanese women with severe pre-eclampsia positive and negative for anticardiolipin antibody using a polymerase chain reaction-restriction fragment length polymorphism method.

    PubMed

    Takakuwa, K; Honda, K; Ishii, K; Hataya, I; Yasuda, M; Tanaka, K

    1999-12-01

    The human leukocyte antigen (HLA)-DR genotype was determined in 54 Japanese women with severe pre-eclampsia in order to elucidate the relationship between HLA-DR antigen systems and pre-eclampsia. The patients were divided into two groups according to positivity for the anticardiolipin antibody (ACA), i.e. one patient group negative for ACA (n = 41) and the other patient group positive for ACA (n = 13). The frequency of each HLA-DRB1 allele in both groups was compared with that in 81 normally fertile Japanese women who had not experienced pre-eclampsia. The genotypes of HLA-DR antigens were determined using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The frequency of DRB1*04 and DRB1*0403 in the patient group positive for the ACA was significantly higher compared with that in the group of normal fertile women (P< 0.05). The frequency of each HLA-DRB1 allele was not significantly different between patient group with pre-eclampsia negative for ACA and group of normal fertile women. These results suggest a difference in the immunogenetic background between the patient groups with severe pre-eclampsia positive and negative for the ACA.

  19. Characterization of nitrogen-fixing Paenibacillus species by polymerase chain reaction-restriction fragment length polymorphism analysis of part of genes encoding 16S rRNA and 23S rRNA and by multilocus enzyme electrophoresis.

    PubMed

    Coelho, Marcia Reed Rodrigues; von der Weid, Irene; Zahner, Viviane; Seldin, Lucy

    2003-05-28

    Forty-two strains representing the eight recognized nitrogen-fixing Paenibacillus species and 12 non-identified strains were examined by restriction fragment length polymorphism (RFLP) analysis of part of 16S and 23S rRNA genes amplified by polymerase chain reaction (PCR). Eleven different 16S rDNA genotypes were obtained from the combined data of RFLP analysis with four endonucleases and they were in agreement with the established taxonomic classification. Only one group of unclassified strains (Group I) was assigned in a separate genotype, suggesting they belong to a new species. Using the 23S PCR-RFLP method only six genotypes were detected, showing that this method is less discriminative than the 16S PCR-RFLP. Using the multilocus enzyme electrophoresis (MLEE) assay, the 48 strains tested could be classified into 35 zymovars. The seven enzymatic loci tested were polymorphic and the different profiles obtained among strains allowed the grouping of strains into 10 clusters. The PCR-RFLP methods together with the MLEE assay provide a rapid tool for the characterization and the establishment of the taxonomic position of isolates belonging to this nitrogen-fixing group, which shows a great potentiality in promoting plant growth.

  20. Selection of single chain variable fragments (scFv) against the glycoprotein antigen of the rabies virus from a human synthetic scFv phage display library and their fusion with the Fc region of human IgG1

    PubMed Central

    Ray, K; Embleton, M J; Jailkhani, B L; Bhan, M K; Kumar, R

    2001-01-01

    We have prepared human recombinant antibody molecules against the glycoprotein antigen of the rabies virus (GPRV) based on the single chain variable fragment (scFv) format. Anti-GPRV scFvs were selected from a human synthetic scFv phage display library with a repertoire of approximately 109 specificities. After three rounds of selection against the PV11 strain of the virus, 40% of the clones tested recognized the rabies antigen. Of the 20 positive clones that were sequenced, five distinct sequences were identified. These distinct scFvs were cloned into a mammalian expression vector carrying the human IgG1 Fc region. The specificity of the resulting scFv-Fc molecules for GPRV was established by ELISA, dot blot and western blot analyses and membrane immunofluorescence. Two of the scFv-Fc fusion proteins neutralized the PV11 strain in a standard in vivo neutralization assay where the virus was incubated with the scFv-Fc molecules before intracranial inoculation in mice. These anti-GPRV scFv-Fc molecules have the potential to be used as an alternative to the presently available HRIG, for use in post-exposure preventive treatment. PMID:11472431

  1. 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

  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 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

  3. Perspective Projection Invariants,

    DTIC Science & Technology

    1986-02-01

    ORGANIZATION NAME ANC ADDRESS 10. PROGRAM ELEMENT. PROJECT. TASK Artificial Inteligence Laboratory AREA & WORK UNIT NUMBERSO 545 Technology Square dCambridge...AD-AI67 793 PERSPECTIVE PROJECTION INVARIANTS(U) MASSACHUSETTS INST 1/1~ OF TECH CAMBRIDGE ARTIFICIAL INTELLIGENCE LAB VERRI ET AL, FEB 86 AI-M-832...0R020I4 661 SEC R TVC PAGE fjSr .W IlIII UI A 8 gT@OFTNS21 07 1 MASSACHUSETTS INSTITUTE OF TECHNOLOGY ARTIFICIAL INTELLIGENCE LABORATORY and CENTER

  4. Entanglement, Invariants, and Phylogenetics

    NASA Astrophysics Data System (ADS)

    Sumner, J. G.

    2007-10-01

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

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

    SciTech Connect

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

    2015-03-15

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

  6. Invariants from classical field theory

    SciTech Connect

    Diaz, Rafael; Leal, Lorenzo

    2008-06-15

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

  7. 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.

  8. Bifurcation from an invariant to a non-invariant attractor

    NASA Astrophysics Data System (ADS)

    Mandal, D.

    2016-12-01

    Switching dynamical systems are very common in many areas of physics and engineering. We consider a piecewise linear map that periodically switches between more than one different functional forms. We show that in such systems it is possible to have a border collision bifurcation where the system transits from an invariant attractor to a non-invariant attractor.

  9. 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.

  10. Site-specific conjugation of chain-terminal chelating polymers to Fab' fragments of anti-CEA mAb: effect of linkage type and polymer size on conjugate biodistribution in nude mice bearing human colorectal carcinoma.

    PubMed

    Slinkin, M A; Curtet, C; Sai-Maurel, C; Gestin, J F; Torchilin, V P; Chatal, J F

    1992-01-01

    Polylysine-based chelating polymers were used for site-specific modification of anti-CEA mAb Fab' fragments via their SH group distal to the antigen-binding site of the antibody molecule. Conjugation was performed using chain-terminal (pyridyldithio)propionate or 4-(p-maleimidophenyl)butyrate moieties to form reducible (S-S) or stable (S-C) bonds between a polymer and Fab' molecule, respectively. One S-S conjugate (S-S9) and two different S-C conjugates (S-C3 and S-C9) were prepared using 3- and 9-kDa molecular weight polymers. No significant loss of immunoreactivity was observed in solid-phase immunoassay, 90-95% of 111In-labeled conjugates being bound to CEA-coated Sepharose beads. After labeling with 111In, the conjugates had a specific radioactivity of 90-120 microCi/micrograms. Injected in nude mice bearing LS 174T carcinoma, the conjugates produced different biodistribution patterns. S-S9 was practically unable to accumulate in tumor and produced very rapid blood clearance of radioactivity and high uptake of radioactivity in liver, spleen, and especially kidneys (225% ID/g 24 h postinjection). S-C3 and S-C9 produced practically the same blood clearances (much slower than that of S-S9) and significant tumor uptake (9-10% ID/g at 24 h). S-C3 gave significantly lower radioactivity in spleen, skin, and bones, and cleared more rapidly from liver and kidneys. Renal uptake for S-C3 and S-C9 was rather high (45% ID/g at 24 h), but much lower than for S-S9.

  11. 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 Central

    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

    2016-01-01

    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

  12. Cross-neutralizing anti-HIV-1 human single chain variable fragments(scFvs) against CD4 binding site and N332 glycan identified from a recombinant phage library

    PubMed Central

    Khan, Lubina; Kumar, Rajesh; Thiruvengadam, Ramachandran; Parray, Hilal Ahmad; Makhdoomi, Muzamil Ashraf; Kumar, Sanjeev; Aggarwal, Heena; Mohata, Madhav; Hussain, Abdul Wahid; Das, Raksha; Varadarajan, Raghavan; Bhattacharya, Jayanta; Vajpayee, Madhu; Murugavel, K. G.; Solomon, Suniti; Sinha, Subrata; Luthra, Kalpana

    2017-01-01

    More than 50% of HIV-1 infection globally is caused by subtype_C viruses. Majority of the broadly neutralizing antibodies (bnAbs) targeting HIV-1 have been isolated from non-subtype_C infected donors. Mapping the epitope specificities of bnAbs provides useful information for vaccine design. Recombinant antibody technology enables generation of a large repertoire of monoclonals with diverse specificities. We constructed a phage recombinant single chain variable fragment (scFv) library with a diversity of 7.8 × 108 clones, using a novel strategy of pooling peripheral blood mononuclear cells (PBMCs) of six select HIV-1 chronically infected Indian donors whose plasma antibodies exhibited potent cross neutralization efficiency. The library was panned and screened by phage ELISA using trimeric recombinant proteins to identify viral envelope specific clones. Three scFv monoclonals D11, C11 and 1F6 selected from the library cross neutralized subtypes A, B and C viruses at concentrations ranging from 0.09 μg/mL to 100 μg/mL. The D11 and 1F6 scFvs competed with mAbs b12 and VRC01 demonstrating CD4bs specificity, while C11 demonstrated N332 specificity. This is the first study to identify cross neutralizing scFv monoclonals with CD4bs and N332 glycan specificities from India. Cross neutralizing anti-HIV-1 human scFv monoclonals can be potential candidates for passive immunotherapy and for guiding immunogen design. PMID:28332627

  13. Construction of human single-chain variable fragment antibodies of medullary thyroid carcinoma and single photon emission computed tomography/computed tomography imaging in tumor-bearing nude mice.

    PubMed

    Liu, Qiong; Pang, Hua; Hu, Xiaoli; Li, Wenbo; Xi, Jimei; Xu, Lu; Zhou, Jing

    2016-01-01

    Medullary thyroid carcinoma (MTC) is a rare tumor of the endocrine system with poor prognosis as it exhibits high resistance against conventional therapy. Recent studies have shown that monoclonal antibodies labeled with radionuclide have become important agents for diagnosing tumors. To elucidate whether single-chain fragment of variable (scFv) antibody labeled with 131I isotope is a potential imaging agent for diagnosing MTC. A human scFv antibody library of MTC using phage display technique was constructed with a capacity of 3x10(5). The library was panned with thyroid epithelial cell lines and MTC cell lines (TT). Western blotting and enzyme-linked immunosorbent assay (ELISA) were used to identify the biological characteristics of the panned scFv. Methyl thiazolyl tetrazolium (MTT) assay was also used to explore the optimal concentration of the TT cell proliferation inhibition rate. They were categorized into TT, SW480 and control groups using phosphate-buffered saline. Western blotting showed that molecular weight of scFv was 28 kDa, cell ELISA showed that the absorbance of TT cell group was significantly increased (P=0.000??) vs. the other three groups, and MTT assay showed that the inhibition rate between the two cell lines was statistically significantly different (P<0.05) when the concentration of scFv was 0.1, 1 and 10 µmol/l. The tumor uptake of 131I-scFv was visible at 12 h and clear image was obtained at 48 h using the single photon emission computed tomography. scFv rapidly and specifically target MTC cells, suggesting the potential of this antibody as an imaging agent for diagnosing MTC.

  14. 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.

  15. 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.

  16. 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

  17. Universal Dynamic Fragmentation in D Dimensions

    NASA Astrophysics Data System (ADS)

    Âström, J. A.; Ouchterlony, F.; Linna, R. P.; Timonen, J.

    2004-06-01

    A generic model is introduced for brittle fragmentation in D dimensions, and this model is shown to lead to a fragment-size distribution with two distinct components. In the small fragment-size limit a scale-invariant size distribution results from a crack branching-merging process. At larger sizes the distribution becomes exponential as a result of a Poisson process, which introduces a large-scale cutoff. Numerical simulations are used to demonstrate the validity of the distribution for D=2. Data from laboratory-scale experiments and large-scale quarry blastings of granitic gneiss confirm its validity for D=3. In the experiments the nonzero grain size of rock causes deviation from the ideal model distribution in the small-size limit. The size of the cutoff seems to diverge at the minimum energy sufficient for fragmentation to occur, but the scaling exponent is not universal.

  18. Trace Maps, Invariants, and Some of Their Applications

    NASA Astrophysics Data System (ADS)

    Baake, M.; Grimm, U.; Joseph, D.

    Trace maps of two-letter substitution rules are investigated with special emphasis on the underlying algebraic structure and on the existence of invariants. We illustrate the results with the generalized Fibonacci chains and show that the well-known Fricke character I(x, y, z)=x2+y2+z2-2xyz-1 is not the only type of invariant that can occur. We discuss several physical applications to electronic spectra including the gap-labeling theorem, to kicked two-level systems, and to the classical 1D Ising model with non-commuting transfer matrices.

  19. CATABOLIC ORIGIN OF A BENCE JONES PROTEIN FRAGMENT

    PubMed Central

    Cioli, D.; Baglioni, C.

    1968-01-01

    Gel filtration analysis of the urinary proteins of some patients with myeloma has shown the presence of "fragments" of Bence Jones proteins which correspond to the variable half of these proteins. Experiments have been carried out to establish the origin of a "fragment" observed in a patient who excreted a large amount of this protein. Labeled homologous Bence Jones protein has been injected into this and other control patients. Excretion of labeled "fragment" has been observed in all. Analysis by peptide mapping and radio-autography of this labeled "fragment" isolated from the urine showed that the invariable half of the Bence Jones protein was not excreted; it seemed thus likely that the invariable half was metabolized to small peptides and free amino acids. A labeled Bence Jones protein which was excreted without any accompanying "fragment" was injected into the patient who excreted large amounts of "fragment." No excretion of labeled "fragment" was observed. It was thus concluded that the property of being degraded to "fragment" is characteristic of some "fragile" Bence Jones proteins and is not determined by the patient. Incubation with serum or urine of the "fragile" Bence Jones protein failed to produce any "fragment." "Fragments" of Bence Jones proteins are thus most likely formed during excretion of these proteins through the kidney and are products of the catabolism of Bence Jones proteins. PMID:5666962

  20. Quadratic Generalized Scale Invariance

    NASA Astrophysics Data System (ADS)

    Lovejoy, S.; Schertzer, D.; Addor, J. B.

    Nearly twenty years ago, two of us argued that in order to account for the scaling strat- ification of the atmosphere, that an anisotropic "unified scaling model" of the atmo- sphere was required with elliptical dimension 23/9=2.555... "in between" the standard 3-D (small scale) and 2-D large scale model. This model was based on the formal- ism of generalized scale invariance (GSI). Physically, GSI is justified by arguing that various conserved fluxes (energy, buoyancy force variance etc.) should define the ap- propriate notion of scale. In a recent large scale satellite cloud image analysis, we directly confirmed this model by studying the isotropic (angle averaged) horizontal cloud statistics. Mathematically, GSI is based on a a group of scale changing opera- tors and their generators but to date, both analyses (primarily of cloud images) and nu- merical (multifractal) simulations, have been limited to the special case of linear GSI. This has shown that cloud texture can plausibly be associated with local linearizations. However realistic morphologies involve spatially avarying textures; the full non linear GSI is clearly necessary. In this talk, we first show that the observed angle averaged (multi)scaling statistics only give a realtively weak constraint on the nonlinear gner- ator: that the latter can be expressed by self-similar (isotropic) part, and a deviatoric part described (in two dimensions) by an arbitrary scalar potential which contains all the information about the cloud morphology. We then show (using a theorem due to Poincaré) how to reduce nonlinear GSI to linear GSI plus a nonlinear coordinate trans- formation numerically, using this to take multifractal GSI modelling to the next level of approximation: quadratic GSI. We show many examples of the coresponding simu- lations which include transitions from various morphologies (including cyclones) and we discuss the results in relation to satellite cloud images.

  1. Orthosymplectically invariant functions in superspace

    NASA Astrophysics Data System (ADS)

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

    2010-08-01

    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 Schrödinger 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. Baculovirus display of functional antibody Fab fragments.

    PubMed

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

    2015-08-01

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

  3. CPT violation implies violation of Lorentz invariance.

    PubMed

    Greenberg, O W

    2002-12-02

    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.

  4. Weyl invariance with a nontrivial mass scale

    SciTech Connect

    Álvarez, Enrique; González-Martín, Sergio

    2016-09-07

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

  5. Test of charge conjugation invariance.

    PubMed

    Nefkens, B M K; Prakhov, S; Gårdestig, A; Allgower, C E; Bekrenev, V; Briscoe, W J; Clajus, M; Comfort, J R; Craig, K; Grosnick, D; Isenhower, D; Knecht, N; Koetke, D; Koulbardis, A; Kozlenko, N; Kruglov, S; Lolos, G; Lopatin, I; Manley, D M; Manweiler, R; Marusić, A; McDonald, S; Olmsted, J; Papandreou, Z; Peaslee, D; Phaisangittisakul, N; Price, J W; Ramirez, A F; Sadler, M; Shafi, A; Spinka, H; Stanislaus, T D S; Starostin, A; Staudenmaier, H M; Supek, I; Tippens, W B

    2005-02-04

    We report on the first determination of upper limits on the branching ratio (BR) of eta decay to pi0pi0gamma and to pi0pi0pi0gamma. Both decay modes are strictly forbidden by charge conjugation (C) invariance. Using the Crystal Ball multiphoton detector, we obtained BR(eta-->pi0pi0gamma)<5 x 10(-4) at the 90% confidence level, in support of C invariance of isoscalar electromagnetic interactions of the light quarks. We have also measured BR(eta-->pi0pi0pi0gamma)<6 x 10(-5) at the 90% confidence level, in support of C invariance of isovector electromagnetic interactions.

  6. Invariants of broken discrete symmetries.

    PubMed

    Kalozoumis, P A; Morfonios, C; Diakonos, F K; Schmelcher, P

    2014-08-01

    The parity and Bloch theorems are generalized to the case of broken global symmetry. Local inversion or translation symmetries in one dimension are shown to yield invariant currents that characterize wave propagation. These currents map the wave function from an arbitrary spatial domain to any symmetry-related domain. Our approach addresses any combination of local symmetries, thus applying, in particular, to acoustic, optical, and matter waves. Nonvanishing values of the invariant currents provide a systematic pathway to the breaking of discrete global symmetries.

  7. Invariants of Broken Discrete Symmetries

    NASA Astrophysics Data System (ADS)

    Kalozoumis, P. A.; Morfonios, C.; Diakonos, F. K.; Schmelcher, P.

    2014-08-01

    The parity and Bloch theorems are generalized to the case of broken global symmetry. Local inversion or translation symmetries in one dimension are shown to yield invariant currents that characterize wave propagation. These currents map the wave function from an arbitrary spatial domain to any symmetry-related domain. Our approach addresses any combination of local symmetries, thus applying, in particular, to acoustic, optical, and matter waves. Nonvanishing values of the invariant currents provide a systematic pathway to the breaking of discrete global symmetries.

  8. DNA sequence from Cretaceous period bone fragments.

    PubMed

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

    1994-11-18

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

  9. Ground states for nonuniform periodic Ising chains.

    PubMed

    Martínez-Garcilazo, J P; Ramírez, C

    2015-04-01

    We generalize Morita's works [J. Phys. A 7, 289 (1974); J. Phys. A 7, 1613 (1974)] on ground states of Ising chains, for chains with a periodic structure and different spins, to any interaction order. The main assumption is translational invariance. The length of the irreducible blocks is a multiple of the period of the chain. If there is parity invariance, it restricts the length in general only in the diatomic case. There are degenerated states and under certain circumstances there could be nonregular ground states. We illustrate the results and give the ground state diagrams in several cases.

  10. Use of antibody fragments (Fv) in immunocytochemistry.

    PubMed

    Kleymann, G; Ostermeier, C; Heitmann, K; Haase, W; Michel, H

    1995-06-01

    We developed a novel antibody fragment (Fv) technique for localization and determination of the surface topology of membrane protein complexes by immunogold electron microscopy. Several hybridoma cell lines producing murine monoclonal antibodies (MAbs) raised against bacterial membrane proteins were established. The cDNAs coding for the variable domains of the MAbs were cloned and expressed in Escherichia coli. The engineered Fv fragments served as trifunctional adapter molecules. The Fv fragment binds to the epitope of the membrane protein. The Strep tag fused to the VH chain was used for one-step affinity purification of the Fv fragments. Immunological detection of the membrane protein-bound Fv fragments in electron microscopy was accomplished either via the Strep tag with colloidal gold-labeled streptavidin or via the c-myc tag, which was fused to the VL chain, in combination with the c-myc tag-specific antibody 9E10 and a colloidal gold-labeled secondary antibody. We examined four Fv fragments directed against the cytochrome c oxidase or the ubiquinol-cytochrome c oxidoreductase of Paracoccus denitrificans and bacteriorhodopsin of Halobacterium halobium to show that this method is generally applicable. In all cases the Fv fragments showed the same results as their corresponding parent antibodies in electron microscopic immunostaining and other applications.

  11. Algebraic invariants for homotopy types

    NASA Astrophysics Data System (ADS)

    Blanc, David

    1999-11-01

    We define a sequence of purely algebraic invariants - namely, classes in the Quillen cohomology of the [Pi]-algebra [pi][low asterisk]X - for distinguishing between different homotopy types of spaces. Another sequence of such cohomology classes allows one to decide whether a given abstract [Pi]-algebra can be realized as the homotopy [Pi]-algebra of a space.

  12. Galilean invariance in Lagrangian mechanics

    NASA Astrophysics Data System (ADS)

    Mohallem, J. R.

    2015-10-01

    The troublesome topic of Galilean invariance in Lagrangian mechanics is discussed in two situations: (i) A particular case involving a rheonomic constraint in uniform motion and (ii) the general translation of an entire system and the constants of motion involved. A widespread impropriety in most textbooks is corrected, concerning a condition for the equality h = E to hold.

  13. 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.

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

    Code of Federal Regulations, 2013 CFR

    2013-04-01

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

  15. Measurement invariance versus selection invariance: is fair selection possible?

    PubMed

    Borsboom, Denny; Romeijn, Jan-Willem; Wicherts, Jelte M

    2008-06-01

    This article shows that measurement invariance (defined in terms of an invariant measurement model in different groups) is generally inconsistent with selection invariance (defined in terms of equal sensitivity and specificity across groups). In particular, when a unidimensional measurement instrument is used and group differences are present in the location but not in the variance of the latent distribution, sensitivity and positive predictive value will be higher in the group at the higher end of the latent dimension, whereas specificity and negative predictive value will be higher in the group at the lower end of the latent dimension. When latent variances are unequal, the differences in these quantities depend on the size of group differences in variances relative to the size of group differences in means. The effect originates as a special case of Simpson's paradox, which arises because the observed score distribution is collapsed into an accept-reject dichotomy. Simulations show the effect can be substantial in realistic situations. It is suggested that the effect may be partly responsible for overprediction in minority groups as typically found in empirical studies on differential academic performance. A methodological solution to the problem is suggested, and social policy implications are discussed.

  16. Parton fragmentation functions

    NASA Astrophysics Data System (ADS)

    Metz, A.; Vossen, A.

    2016-11-01

    The field of fragmentation functions of light quarks and gluons is reviewed. In addition to integrated fragmentation functions, attention is paid to the dependence of fragmentation functions on transverse momenta and on polarization degrees of freedom. Higher-twist and di-hadron fragmentation functions are considered as well. Moreover, the review covers both theoretical and experimental developments in hadron production in electron-positron annihilation, deep-inelastic lepton-nucleon scattering, and proton-proton collisions.

  17. Cohomological invariants of central simple algebras

    NASA Astrophysics Data System (ADS)

    Merkurjev, A. S.

    2016-10-01

    We determine the indecomposable degree 3 cohomological invariants of tuples of central simple algebras with linear relations. Equivalently, we determine the degree 3 reductive cohomological invariants of all split semisimple groups of type A.

  18. Fragmentation Analysis - Fundamental Processes

    DTIC Science & Technology

    Wausau quartzite and anorthosite of 3.0 to 3.5 inch size were fragmented in this device. An analysis of the fragment distribution results of the drop...disc-shaped specimens of Wausau quartzite, anorthosite , and Felch marble were then fragmented with the impact pendulum device. Computer programs were

  19. Invariance in Measurement and Prediction Revisited

    ERIC Educational Resources Information Center

    Millsap, Roger E.

    2007-01-01

    Borsboom (Psychometrika, 71:425-440, 2006) noted that recent work on measurement invariance (MI) and predictive invariance (PI) has had little impact on the practice of measurement in psychology. To understand this contention, the definitions of MI and PI are reviewed, followed by results on the consistency between the two forms of invariance in…

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Proton spin: A topological invariant

    NASA Astrophysics Data System (ADS)

    Tiwari, S. C.

    2016-11-01

    Proton spin problem is given a new perspective with the proposition that spin is a topological invariant represented by a de Rham 3-period. The idea is developed generalizing Finkelstein-Rubinstein theory for Skyrmions/kinks to topological defects, and using non-Abelian de Rham theorems. Two kinds of de Rham theorems are discussed applicable to matrix-valued differential forms, and traces. Physical and mathematical interpretations of de Rham periods are presented. It is suggested that Wilson lines and loop operators probe the local properties of the topology, and spin as a topological invariant in pDIS measurements could appear with any value from 0 to ℏ 2, i.e. proton spin decomposition has no meaning in this approach.

  6. 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.

  7. [Invariants of the anthropometrical proportions].

    PubMed

    Smolianinov, V V

    2012-01-01

    In this work a general interpretation of a modulor as scales of segments proportions of anthropometrical modules (extremities and a body) is made. The objects of this study were: 1) to reason the idea of the growth modulor; 2) using the modern empirical data, to prove the validity of a principle of linear similarity for anthropometrical segments; 3) to specify the system of invariants for constitutional anthropometrics.

  8. Shift and Scale Invariant Preprocessor.

    DTIC Science & Technology

    1981-12-01

    1982 THESIS D V SHIFT AND SCALE INVARIANT ?PREPROCESSOR by Norman E. Huston, Jr. December 1981 0 Thesis Advisor: L. A. Wilson Approved for public...SCHOOL December 1981 Author: - . 4 ,/ A pp ro0ved by: rYY. ( Thesis Advisor Co-Ad isor Chairman, De artment of 4n n eing Dean of Science and...large range of problems/disciplines. Fields where it is particularly common include optical imagery, acoustic signal processing , radiology, radio

  9. Ii Chain Controls the Transport of Major Histocompatibility Complex Class II Molecules to and from Lysosomes

    PubMed Central

    Brachet, Valérie; Raposo, Graça; Amigorena, Sebastian; Mellman, Ira

    1997-01-01

    Major histocompatibility complex class II molecules are synthesized as a nonameric complex consisting of three αβ dimers associated with a trimer of invariant (Ii) chains. After exiting the TGN, a targeting signal in the Ii chain cytoplasmic domain directs the complex to endosomes where Ii chain is proteolytically processed and removed, allowing class II molecules to bind antigenic peptides before reaching the cell surface. Ii chain dissociation and peptide binding are thought to occur in one or more postendosomal sites related either to endosomes (designated CIIV) or to lysosomes (designated MIIC). We now find that in addition to initially targeting αβ dimers to endosomes, Ii chain regulates the subsequent transport of class II molecules. Under normal conditions, murine A20 B cells transport all of their newly synthesized class II I-Ab αβ dimers to the plasma membrane with little if any reaching lysosomal compartments. Inhibition of Ii processing by the cysteine/serine protease inhibitor leupeptin, however, blocked transport to the cell surface and caused a dramatic but selective accumulation of I-Ab class II molecules in lysosomes. In leupeptin, I-Ab dimers formed stable complexes with a 10-kD NH2-terminal Ii chain fragment (Ii-p10), normally a transient intermediate in Ii chain processing. Upon removal of leupeptin, Ii-p10 was degraded and released, I-Ab dimers bound antigenic peptides, and the peptide-loaded dimers were transported slowly from lysosomes to the plasma membrane. Our results suggest that alterations in the rate or efficiency of Ii chain processing can alter the postendosomal sorting of class II molecules, resulting in the increased accumulation of αβ dimers in lysosome-like MIIC. Thus, simple differences in Ii chain processing may account for the highly variable amounts of class II found in lysosomal compartments of different cell types or at different developmental stages. PMID:9105036

  10. 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.

  11. Disformal invariance of curvature perturbation

    SciTech Connect

    Motohashi, Hayato; White, Jonathan E-mail: jwhite@post.kek.jp

    2016-02-01

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

  12. 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

  13. 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.

  14. Scale invariance implies conformal invariance for the three-dimensional Ising model.

    PubMed

    Delamotte, Bertrand; Tissier, Matthieu; Wschebor, Nicolás

    2016-01-01

    Using the Wilson renormalization group, we show that if no integrated vector operator of scaling dimension -1 exists, then scale invariance implies conformal invariance. By using the Lebowitz inequalities, we prove that this necessary condition is fulfilled in all dimensions for the Ising universality class. This shows, in particular, that scale invariance implies conformal invariance for the three-dimensional Ising model.

  15. 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.

  16. 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

  17. 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.

  18. On asymptotically lacunary invariant statistical equivalent set sequences

    NASA Astrophysics Data System (ADS)

    Pancaroglu, Nimet; Nuray, Fatih; Savas, Ekrem

    2013-10-01

    In this paper, we define asymptotically invariant equivalence, strongly asymptotically invariant equivalence, asymptotically invariant statistical equivalence, asymptotically lacunary invariant statistical equivalence, strongly asymptotically lacunary invariant equivalence, asymptotically lacunary invariant equivalence (Wijsman sense) for sequences of sets. Also we investigate some relations between asymptotically lacunary invariant statistical equivalence and asymptotically invariant statistical equivalence for sequences of sets. We introduce some notions and theorems as follows, asymptotically lacunary invariant statistical equivalence, strongly asymptotically lacunary invariant equivalence, asymptotically lacunary invariant equivalence (Wijsman sense) for sequences of sets.

  19. 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.

  20. Invariant Quantities in Shear Flow

    NASA Astrophysics Data System (ADS)

    Baule, A.; Evans, R. M. L.

    2008-12-01

    The dynamics of systems out of thermal equilibrium is usually treated on a case-by-case basis without knowledge of fundamental and universal principles. We address this problem for a class of driven steady states, namely, those mechanically driven at the boundaries such as complex fluids under shear. From a nonequilibrium counterpart to detailed balance (NCDB) we derive a remarkably simple set of invariant quantities which remain unchanged when the system is driven. These new nonequilibrium relations are both exact and valid arbitrarily far from equilibrium. Furthermore, they enable the systematic calculation of transition rates in driven systems with state spaces of arbitrary connectivity.

  1. A Characterization of Invariant Connections

    NASA Astrophysics Data System (ADS)

    Hanusch, Maximilian

    2014-03-01

    Given a principal fibre bundle with structure group S and a fibre transitive Lie group G of automorphisms thereon, Wang's theorem identifies the invariant connections with certain linear maps ψ\\colon {g}→ {s}. In the present paper we prove an extension of this theorem that applies to the general situation where G acts non-transitively on the base manifold. We consider several special cases of the general theorem including the result of Harnad, Shnider and Vinet which applies to the situation where G admits only one orbit type. Along the way we give applications to loop quantum gravity.

  2. A Local Galilean Invariant Thermostat.

    PubMed

    Groot, Robert D

    2006-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  4. Interacting scale invariant but nonconformal field theories

    NASA Astrophysics Data System (ADS)

    Nakayama, Yu

    2017-03-01

    There is a dilemma in constructing interacting scale invariant Euclidean field theories that are not conformal invariant. On one hand, scale invariance without conformal invariance seems more generic by requiring only a smaller symmetry. On the other hand, the existence of a nonconserved current with exact scaling dimension d -1 in d dimensions seems to require extra fine-tuning. To understand the competition better, we explore some examples without the reflection positivity. We show that a theory of elasticity (also known as Riva-Cardy theory) coupled with massless fermions in d =4 -ɛ dimensions does not possess an interacting scale invariant fixed point except for an unstable (and unphysical) one with an infinite coefficient of compression. We do, however, find interacting scale invariant but nonconformal field theories in gauge fixed versions of the Banks-Zaks fixed points in d =4 dimensions.

  5. 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…

  6. Fragment Hazard Investigation Program

    DTIC Science & Technology

    1978-10-01

    53 Ballistic Density (k) ............................................. 53 Ejection A ngle (a...54 Ejection Velocity (V) ................................................. 54 DEVELOPMENT OF EMPIRICAL RELATION...5S 54 Fragment Weight Versus Gamma for Test QD-155-08 ......................... 56 55 Fragment Range Versus Ejection Angle as a Function of

  7. Fragmentation of fullerenes

    NASA Astrophysics Data System (ADS)

    Chancey, Ryan T.; Oddershede, Lene; Harris, Frank E.; Sabin, John R.

    2003-04-01

    We have performed classical molecular-dynamics simulations of the fragmentation collisions of neutral fullerenes (C24, C60, C100, and C240) with a hard wall. The interactions between the carbon atoms are modeled by a Tersoff potential and the position of each carbon atom at each time step is calculated using a sixth-order predictor-corrector method. The statistical distribution of the fragments depends on impact energy. At low energies, the fragment distribution appears symmetric, with both the large and small fragment distributions well fitted by an exponential function of the same exponent, the value of which decreases with impact energy. At intermediate energies, the distribution of the smallest fragments can be fitted equally well by a power law or an exponential function. At high impact energies, the entire fragmentation pattern is well described by a single exponential function, the exponent increasing with energy. The observed tendencies in fragment distributions as well as the obtained exponents are in agreement with experimental observations. The fragmentation behavior of the four investigated fullerenes is very similar, and it is noted that C60 appears to be the most stable.

  8. Galilei invariant technique for quantum system description

    SciTech Connect

    Kamuntavičius, Gintautas P.

    2014-04-15

    Problems with quantum systems models, violating Galilei invariance are examined. The method for arbitrary non-relativistic quantum system Galilei invariant wave function construction, applying a modified basis where center-of-mass excitations have been removed before Hamiltonian matrix diagonalization, is developed. For identical fermion system, the Galilei invariant wave function can be obtained while applying conventional antisymmetrization methods of wave functions, dependent on single particle spatial variables.

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

    PubMed

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

    2013-01-01

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

  10. 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).

  11. 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.

  12. Quantum groups with invariant integrals

    PubMed Central

    Van Daele, Alfons

    2000-01-01

    Quantum groups have been studied intensively for the last two decades from various points of view. The underlying mathematical structure is that of an algebra with a coproduct. Compact quantum groups admit Haar measures. However, if we want to have a Haar measure also in the noncompact case, we are forced to work with algebras without identity, and the notion of a coproduct has to be adapted. These considerations lead to the theory of multiplier Hopf algebras, which provides the mathematical tool for studying noncompact quantum groups with Haar measures. I will concentrate on the *-algebra case and assume positivity of the invariant integral. Doing so, I create an algebraic framework that serves as a model for the operator algebra approach to quantum groups. Indeed, the theory of locally compact quantum groups can be seen as the topological version of the theory of quantum groups as they are developed here in a purely algebraic context. PMID:10639115

  13. Asymptotic invariants of homotopy groups

    NASA Astrophysics Data System (ADS)

    Manin, Fedor

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

  14. Rotationally Invariant Holographic Tracking System

    NASA Astrophysics Data System (ADS)

    Lambert, James L.; Chao, Tien-Hsin; Gheen, Gregory; Johnston, Alan R.; Liu, Hua-Kuang

    1989-06-01

    A multi-channel holographic correlator has been constructed which can identify and track objects of a given shape across the input field independent of their in-plane rotation. This system, derived from the classic Vander Lugt correlator, incorporates a hololens to store an array of matched spatial filters (MSFs) on thermoplastic film. Each member of the MSF array is generated from a different incrementally rotated version of the training object. Rotational invariant tracking is achieved through superposition of the corresponding array of the correlations in the output plane. Real time tracking is accomplished by utilizing a liquid crystal light valve (LCLV) illuminated with a CRT to process video input signals. The system can be programmed to recognize different objects by recording the MSF array on re-usable thermoplastic film. Discussion of the system architecture and laboratory results are presented.

  15. Invariant Coordinates in Breakup Reactions

    NASA Astrophysics Data System (ADS)

    Skwira-Chalot, I.; Ciepał, I.; Kistryn, St.; Kozela, A.; Parol, W.; Stephan, E.

    2017-03-01

    Systematic experimental studies of few-nucleon systems expose various dynamical ingredients which play an important role in correct description of observables, such as three-nucleon force, Coulomb force and relativistic effects. A large set of existing experimental data for ^1H(d, p p)n reaction allows for systematic investigations of these dynamical effects, which vary with energy and appear with different strength in certain observables and phase space regions. Moreover, systematic comparisons with exact theoretical calculations, done in variables related to the system dynamics in a possibly direct ways is a very important tool to verify and improve the existing description of the nucleon interaction. Examples of experimental data for a breakup reaction, transformed to the variables based on Lorentz-invariants are compared with modern theoretical calculations.

  16. A Note on Invariant Observables

    NASA Astrophysics Data System (ADS)

    Lendelová, Katarína

    2006-05-01

    The ergodic theory and particularly the individual ergodic theorem were studied in many structures. Recently the individual ergodic theorem has been proved for MV-algebras of fuzzy sets (Riečan, 2000; Riečan and Neubrunn, 1997) and even in general MV-algebras (Jurečková, 2000). The notion of almost everywhere equality of observables was introduced by B. Riečan and M. Jurečková in Riečan and Jurečková (2005). They proved that the limit of Cesaro means is an invariant observable for P-observables. In this paper show that the assumption of P-observable can be omitted.

  17. Invariants of Boundary Link Cobordism

    NASA Astrophysics Data System (ADS)

    Sheiham, Desmond

    2001-10-01

    An n-dimensional μ-component boundary link is a codimension 2 embedding of spheres L=bigsqcup_{μ}S^n subset S^{n+2} such that there exist μ disjoint oriented embedded (n+1)-manifolds which span the components of L. An F_μ-link is a boundary link together with a cobordism class of such spanning manifolds. The F_μ-link cobordism group C_n(F_μ) is known to be trivial when n is even but not finitely generated when n is odd. Our main result is an algorithm to decide whether two odd-dimensional F_μ-links represent the same cobordism class in C_{2q-1}(F_μ) assuming q>1. We proceed to compute the isomorphism class of C_{2q-1}(F_μ), generalizing Levine's computation of the knot cobordism group C_{2q-1}(F_1). Our starting point is the algebraic formulation of Levine, Ko and Mio who identify C_{2q-1}(F_μ) with a surgery obstruction group, the Witt group G^{(-1)^q,μ}(Z) of μ-component Seifert matrices. We obtain a complete set of torsion-free invariants by passing from integer coefficients to complex coefficients and by applying the algebraic machinery of Quebbemann, Scharlau and Schulte. Signatures correspond to `algebraically integral' simple self-dual representations of a certain quiver (directed graph with loops). These representations, in turn, correspond to algebraic integers on an infinite disjoint union of real affine varieties. To distinguish torsion classes, we consider rational coefficients in place of complex coefficients, expressing G^{(-1)^q,μ}(Q) as an infinite direct sum of Witt groups of finite-dimensional division Q-algebras with involution. Numerical invariants of such Witt groups are available in the literature.

  18. 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.

  19. In muro fragmentation of the rhamnogalacturonan I backbone in potato (Solanum tuberosum L.) results in a reduction and altered location of the galactan and arabinan side-chains and abnormal periderm development.

    PubMed

    Oomen, Ronald J F J; Doeswijk-Voragen, Chantal H L; Bush, Maxwell S; Vincken, Jean-Paul; Borkhardt, Bernhard; van den Broek, Lambertus A M; Corsar, Julia; Ulvskov, Peter; Voragen, Alphons G J; McCann, Maureen C; Visser, Richard G F

    2002-05-01

    Rhamnogalacturonan (RG) I is a branched pectic polysaccharide in plant cell walls. Rhamnogalacturonan lyase (eRGL) from Aspergillus aculeatus is able to cleave the RG I backbone at specific sites. Transgenic potato (Solanum tuberosum L.) plants were made by the introduction of the gene encoding eRGL, under the control of the granule-bound starch synthase promoter. The eRGL protein was successfully expressed and translated into an active form, demonstrated by eRGL activity in the tuber extracts. The transgenic plants produced tubers with clear morphological alterations, including radial swelling of the periderm cells and development of intercellular spaces in the cortex. Sugar compositional analysis of the isolated cell walls showed a large reduction in galactosyl and arabinosyl residues in transgenic tubers. Immunocytochemical studies using the LM5 (galactan) and LM6 (arabinan) antibodies also showed a large reduction in galactan and arabinan side-chains of RG I. Most of the remaining LM5 epitopes were located in the expanded middle lamella at cell corners of eRGL tubers, which is in contrast to their normal location in the primary wall of wild type tubers. These data suggest that RG I has an important role in anchoring galactans and arabinans at particular regions in the wall and in normal development of the periderm.

  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. Universality in Fragmentation

    NASA Astrophysics Data System (ADS)

    Åström, J. A.; Holian, B. L.; Timonen, J.

    2000-04-01

    Fragmentation of a two-dimensional brittle solid by impact and ``explosion,'' and a fluid by ``explosion'' are all shown to become critical. The critical points appear at a nonzero impact velocity, and at infinite explosion duration, respectively. Within the critical regimes, the fragment-size distributions satisfy a scaling form qualitatively similar to that of the cluster-size distribution of percolation, but they belong to another universality class. Energy balance arguments give a correlation length exponent that is exactly one-half of its percolation value. A single crack dominates fragmentation in the slow-fracture limit, as expected.

  2. Evolution of transverse momentum dependent distribution and fragmentation functions

    NASA Astrophysics Data System (ADS)

    Henneman, A. A.; Boer, Daniël; Mulders, P. J.

    2002-01-01

    We use Lorentz invariance and the QCD equations of motion to study the evolution of functions that appear at leading order in a 1/ Q expansion in azimuthal asymmetries. This includes the evolution equation of the Collins fragmentation function. The moments of these functions are matrix elements of known twist two and twist three operators. We present the evolution in the large Nc limit, restricting to non-singlet for the chiral-even functions.

  3. 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…

  4. 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.

  5. Discernment of Invariants in Dynamic Geometry Environments

    ERIC Educational Resources Information Center

    Leung, Allen; Baccaglini-Frank, Anna; Mariotti, Maria Alessandra

    2013-01-01

    In this paper, we discuss discernment of invariants in dynamic geometry environments (DGE) based on a combined perspective that puts together the lens of variation and the maintaining dragging strategy developed previously by the authors. We interpret and describe a model of discerning invariants in DGE through types of variation awareness and…

  6. Invariant Ordering of Item-Total Regressions

    ERIC Educational Resources Information Center

    Tijmstra, Jesper; Hessen, David J.; van der Heijden, Peter G. M.; Sijtsma, Klaas

    2011-01-01

    A new observable consequence of the property of invariant item ordering is presented, which holds under Mokken's double monotonicity model for dichotomous data. The observable consequence is an invariant ordering of the item-total regressions. Kendall's measure of concordance "W" and a weighted version of this measure are proposed as measures for…

  7. Rejoinder: Continuing the Dialogue on Invariant Measurement

    ERIC Educational Resources Information Center

    Engelhard, George, Jr.

    2008-01-01

    The major purpose of my focus article was to stimulate discussion regarding the concept of invariant measurement. My intent was to provide a historical lens for considering how our views of invariant measurement have evolved over time through the work of three key measurement theorists: Guttman, Rasch, and Mokken. The commentators have offered a…

  8. 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.

  9. 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…

  10. Fragmentation in Biaxial Tension

    SciTech Connect

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

    2006-06-13

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

  11. Entanglement of several blocks in fermionic chains

    NASA Astrophysics Data System (ADS)

    Ares, Filiberto; Esteve, José G.; Falceto, Fernando

    2014-12-01

    In this paper we propose an expression for the entanglement entropy of several intervals in a stationary state of a free, translational invariant Hamiltonian in a fermionic chain. We check numerically the accuracy of our proposal and conjecture a formula for the asymptotic behavior of principal submatrices of a Toeplitz matrix.

  12. Falling chains

    NASA Astrophysics Data System (ADS)

    Wong, Chun Wa; Yasui, Kosuke

    2006-06-01

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

  13. 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

  14. Rotational Invariant Dimensionality Reduction Algorithms.

    PubMed

    Lai, Zhihui; Xu, Yong; Yang, Jian; Shen, Linlin; Zhang, David

    2016-06-30

    A common intrinsic limitation of the traditional subspace learning methods is the sensitivity to the outliers and the image variations of the object since they use the L₂ norm as the metric. In this paper, a series of methods based on the L₂,₁-norm are proposed for linear dimensionality reduction. Since the L₂,₁-norm based objective function is robust to the image variations, the proposed algorithms can perform robust image feature extraction for classification. We use different ideas to design different algorithms and obtain a unified rotational invariant (RI) dimensionality reduction framework, which extends the well-known graph embedding algorithm framework to a more generalized form. We provide the comprehensive analyses to show the essential properties of the proposed algorithm framework. This paper indicates that the optimization problems have global optimal solutions when all the orthogonal projections of the data space are computed and used. Experimental results on popular image datasets indicate that the proposed RI dimensionality reduction algorithms can obtain competitive performance compared with the previous L₂ norm based subspace learning algorithms.

  15. South Pole Lorentz Invariance Test

    NASA Astrophysics Data System (ADS)

    Hedges, Morgan; Smiciklas, Marc; Romalis, Michael

    2015-05-01

    Searches for Lorentz and CPT violation play an important role in testing current theories of space-time. To test one of the consequences of local Lorentz invariance we have performed a precision test of spatial isotropy at the Amundsen-Scott station near the geographic South Pole. This location provides the most isotropic environment available on Earth. The experiment is a rotating atomic-spin co-magnetometer which compares energy levels of 21Ne and Rubidium atoms as a function of direction. The experimental sensitivity obtained is more than an order of magnitude better than in previous such measurements, known as Hughes-Drever experiments. By operating the experiment at the Pole we are able to eliminate background signals due to the gyroscopic interactions of spins with Earth's rotation as well as diurnal environmental effects. Here we will present final results from the experiment's 2-year data collection period. This is the first precision atomic physics experiment performed at the Pole, and we will discuss the potential for future such measurements.

  16. South Pole Lorentz Invariance Test

    NASA Astrophysics Data System (ADS)

    Hedges, Morgan; Smiciklas, Marc; Romalis, Michael

    2015-04-01

    Tests of Lorentz and CPT symmetries are important because they form a cornerstone of quantum field theory and general relativity. To test one of the consequences of local Lorentz invariance we have performed a precision test of spatial isotropy at the Amundsen-Scott station near the geographic South Pole. This location provides the most isotropic environment available on Earth. We use an atomic spin co-magnetometer to compare energy levels in 21 Ne and Rubidium atoms as the apparatus rotates with respect to the cosmos. Our experimental sensitivity is more than an order of magnitude greater than in previous such measurements, known as Hughes-Drever experiments. By operating at the South Pole we eliminate background signals due to the gyroscopic interactions of spins with Earth's rotation as well as diurnal environmental effects. The experiment has finished a 2-year data collection period and we expect to present the final results at the meeting. This is the first precision atomic physics experiment performed at the Pole and we will discuss the potential for future such measurements.

  17. 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

  18. 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.

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

    DOE PAGES

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

    2016-02-19

    The classic method for mass determination in a SUSY-like cascade decay chain relies on measurements of the kinematic endpoints in the invariant mass distributions of suitable collections of visible decay products. However, the procedure is complicated by combinatorial ambiguities: e.g., the visible final state particles may be indistinguishable (as in the case of QCD jets), or one may not know the exact order in which they are emitted along the decay chain. In order to avoid such combinatorial ambiguities, we propose to treat the nal state particles fully democratically and consider the sorted set of the invariant masses of allmore » possible partitions of the visible particles in the decay chain. In particular, for a decay to N visible particles, one considers the sorted sets of all possible n-body invariant mass combinations (2≤ n≤ N) and determines the kinematic endpoint m(n,r)max of the distribution of the r-th largest n-body invariant mass m(n,r) for each possible value of n and r. For the classic example of a squark decay in supersymmetry, we provide analytical formulas for the interpretation of these endpoints in terms of the underlying physical masses. We point out that these measurements can be used to determine the structure of the decay topology, e.g., the number and position of intermediate on-shell resonances.« less

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

    SciTech Connect

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

    2016-02-19

    The classic method for mass determination in a SUSY-like cascade decay chain relies on measurements of the kinematic endpoints in the invariant mass distributions of suitable collections of visible decay products. However, the procedure is complicated by combinatorial ambiguities: e.g., the visible final state particles may be indistinguishable (as in the case of QCD jets), or one may not know the exact order in which they are emitted along the decay chain. In order to avoid such combinatorial ambiguities, we propose to treat the nal state particles fully democratically and consider the sorted set of the invariant masses of 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.

  1. Invariant variational structures on fibered manifolds

    NASA Astrophysics Data System (ADS)

    Krupka, Demeter

    2015-12-01

    The aim of this paper is to present a relatively complete theory of invariance of global, higher-order integral variational functionals in fibered spaces, as developed during a few past decades. We unify and extend recent results of the geometric invariance theory; new results on deformations of extremals are also included. We show that the theory can be developed by means of the general concept of invariance of a differential form in geometry, which does not require different ad hoc modifications. The concept applies to invariance of Lagrangians, source forms and Euler-Lagrange forms, as well as to extremals of the given variational functional. Equations for generators of invariance transformations of the Lagrangians and the Euler-Lagrange forms are characterized in terms of Lie derivatives. As a consequence of invariance, we derive the global Noether's theorem on existence of conserved currents along extremals, and discuss the meaning of conservation equations. We prove a theorem describing extremals, whose deformations by a vector field are again extremals. The general settings and structures we use admit extension of the global invariance theory to variational principles in physics, especially in field theory.

  2. 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.

  3. Invarient patterns in articulatory movements

    NASA Astrophysics Data System (ADS)

    Bonaventura, Patrizia

    2004-04-01

    The purpose of the reported study is to discover an effective method of characterizing movement patterns of the crucial articulator as the function of an abstract syllable magnitude and the adjacent boundary, and at the same time to investigate effects of prosodic control on utterance organization. In particular, the speed of movement when a flesh point on the tongue blade or the lower lip crosses a selected position relative to the occlusion plane is examined. The time of such crossing provides an effective measure of syllable timing and syllable duration according to previous work. In the present work, using a very limited vocabulary with only a few consonants and one vowel as the key speech materials, effects of contrastive emphasis on demisyllabic movement patterns were studied. The theoretical framework for this analysis is the C/D model of speech production in relation to the concept of an invariant part of selected articulatory movements. The results show evidence in favor of the existence of ``iceberg'' patterns, but a linear dependence of slope on the total excursion of the demisyllabic movement, instead of the approximate constancy of the threshold crossing speed as suggested in the original proposal of the iceberg, has been found. Accordingly, a revision of the original concept of iceberg, seems necessary. This refinement is consistent with the C/D model assumption on ``prominence control'' that the syllable magnitude determines the movement amplitude, accompanying directly related syllable duration change. In this assumption, the movement of a consonantal component should also be proportional to syllable magnitude. The results suggests, however, systematic outliers deviating from the linear dependence of movement speed on excursion. This deviation may be caused by the effect of the immediately following boundary, often referred to as phrase-final elongation. Thesis advisor: Osamu Fujimura Copies of this thesis written in English can be obtained from

  4. 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

  5. Ground states for nonuniform periodic Ising chains

    NASA Astrophysics Data System (ADS)

    Martínez-Garcilazo, J. P.; Ramírez, C.

    2015-04-01

    We generalize Morita's works [J. Phys. A 7, 289 (1974), 10.1088/0305-4470/7/2/014; J. Phys. A 7, 1613 (1974), 10.1088/0305-4470/7/13/015] on ground states of Ising chains, for chains with a periodic structure and different spins, to any interaction order. The main assumption is translational invariance. The length of the irreducible blocks is a multiple of the period of the chain. If there is parity invariance, it restricts the length in general only in the diatomic case. There are degenerated states and under certain circumstances there could be nonregular ground states. We illustrate the results and give the ground state diagrams in several cases.

  6. Numerical considerations in computing invariant subspaces

    SciTech Connect

    Dongarra, J.J. . Dept. of Computer Science Oak Ridge National Lab., TN ); Hammarling, S. ); Wilkinson, J.H. )

    1990-11-01

    This paper describes two methods for computing the invariant subspace of a matrix. The first involves using transformations to interchange the eigenvalues; the second involves direct computation of the vectors. 10 refs.

  7. Position, rotation, and intensity invariant recognizing method

    DOEpatents

    Ochoa, Ellen; Schils, George F.; Sweeney, Donald W.

    1989-01-01

    A method for recognizing the presence of a particular target in a field of view which is target position, rotation, and intensity invariant includes the preparing of a target-specific invariant filter from a combination of all eigen-modes of a pattern of the particular target. Coherent radiation from the field of view is then imaged into an optical correlator in which the invariant filter is located. The invariant filter is rotated in the frequency plane of the optical correlator in order to produce a constant-amplitude rotational response in a correlation output plane when the particular target is present in the field of view. Any constant response is thus detected in the output The U.S. Government has rights in this invention pursuant to Contract No. DE-AC04-76DP00789 between the U.S. Department of Energy and AT&T Technologies, Inc.

  8. 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.

  9. Testing Lorentz invariance of dark matter

    SciTech Connect

    Blas, Diego; Ivanov, Mikhail M.; Sibiryakov, Sergey E-mail: mm.ivanov@physics.msu.ru

    2012-10-01

    We study the possibility to constrain deviations from Lorentz invariance in dark matter (DM) with cosmological observations. Breaking of Lorentz invariance generically introduces new light gravitational degrees of freedom, which we represent through a dynamical timelike vector field. If DM does not obey Lorentz invariance, it couples to this vector field. We find that this coupling affects the inertial mass of small DM halos which no longer satisfy the equivalence principle. For large enough lumps of DM we identify a (chameleon) mechanism that restores the inertial mass to its standard value. As a consequence, the dynamics of gravitational clustering are modified. Two prominent effects are a scale dependent enhancement in the growth of large scale structure and a scale dependent bias between DM and baryon density perturbations. The comparison with the measured linear matter power spectrum in principle allows to bound the departure from Lorentz invariance of DM at the per cent level.

  10. Recognizing 3D Object Using Photometric Invariant.

    DTIC Science & Technology

    1995-02-01

    model and the data space coordinates, using centroid invariance of corresponding groups of feature positions. Tests are given to show the stability and...positions in the model and the data space coordinates, using centroid invariance of corresponding groups of feature positions. Tests are given to show the...ognizing 3D objects. In our testing , it took only 0.2 seconds to derive corresponding positions in the model and the image for natural pictures. 2

  11. 'Breaking' position-invariant object recognition.

    PubMed

    Cox, David D; Meier, Philip; Oertelt, Nadja; DiCarlo, James J

    2005-09-01

    While it is often assumed that objects can be recognized irrespective of where they fall on the retina, little is known about the mechanisms underlying this ability. By exposing human subjects to an altered world where some objects systematically changed identity during the transient blindness that accompanies eye movements, we induced predictable object confusions across retinal positions, effectively 'breaking' position invariance. Thus, position invariance is not a rigid property of vision but is constantly adapting to the statistics of the environment.

  12. Invariant distributions on compact homogeneous spaces

    SciTech Connect

    Gorbatsevich, V V

    2013-12-31

    In this paper, we study distributions on compact homogeneous spaces, including invariant distributions and also distributions admitting a sub-Riemannian structure. We first consider distributions of dimension 1 and 2 on compact homogeneous spaces. After this, we study the cases of compact homogeneous spaces of dimension 2, 3, and 4 in detail. Invariant distributions on simply connected compact homogeneous spaces are also treated. Bibliography: 18 titles.

  13. Invariants of Fokker-Planck equations

    NASA Astrophysics Data System (ADS)

    Abe, Sumiyoshi

    2017-02-01

    A weak invariant of a stochastic system is defined in such a way that its expectation value with respect to the distribution function as a solution of the associated Fokker-Planck equation is constant in time. A general formula is given for time evolution of the fluctuations of the invariant. An application to the problem of share price in finance is illustrated. It is shown how this theory makes it possible to reduce the growth rate of the fluctuations.

  14. 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.

  15. Jet mass dependence of fragmentation in positron-proton collisions

    NASA Astrophysics Data System (ADS)

    Urmossy, K.

    2017-02-01

    We propose the characterization of fragmentation functions by the energy fraction tilde{x} a hadron takes away from the energy of the jet measured in the frame co-moving with the jet. Besides, we propose the usage of the jet mass as the fragmentation scale tilde{Q}. We show that these two Lorentz-invariant variables emerge naturally in a microcanonical ensemble with conserved four-momentum. Then, we construct a statistical hadronisation model, in which, two features of the hadronic final states in various high-energy reactions (power law spectra and negative-binomial multiplicity distributions) can be connected simply. Finally, we analyse the scale dependence of the parameters of the model (power of the spectrum and mean energy per hadron) in the φ3 theory. Fitting fragmentation functions in diffractive positron-proton collisions, we obtain a prediction for the jet mass dependence of the hadron multiplicity distribution inside jets.

  16. The invariances of power law size distributions.

    PubMed

    Frank, Steven A

    2016-01-01

    Size varies. Small things are typically more frequent than large things. The logarithm of frequency often declines linearly with the logarithm of size. That power law relation forms one of the common patterns of nature. Why does the complexity of nature reduce to such a simple pattern? Why do things as different as tree size and enzyme rate follow similarly simple patterns? Here I analyze such patterns by their invariant properties. For example, a common pattern should not change when adding a constant value to all observations. That shift is essentially the renumbering of the points on a ruler without changing the metric information provided by the ruler. A ruler is shift invariant only when its scale is properly calibrated to the pattern being measured. Stretch invariance corresponds to the conservation of the total amount of something, such as the total biomass and consequently the average size. Rotational invariance corresponds to pattern that does not depend on the order in which underlying processes occur, for example, a scale that additively combines the component processes leading to observed values. I use tree size as an example to illustrate how the key invariances shape pattern. A simple interpretation of common pattern follows. That simple interpretation connects the normal distribution to a wide variety of other common patterns through the transformations of scale set by the fundamental invariances.

  17. The invariances of power law size distributions

    PubMed Central

    Frank, Steven A.

    2016-01-01

    Size varies. Small things are typically more frequent than large things. The logarithm of frequency often declines linearly with the logarithm of size. That power law relation forms one of the common patterns of nature. Why does the complexity of nature reduce to such a simple pattern? Why do things as different as tree size and enzyme rate follow similarly simple patterns? Here I analyze such patterns by their invariant properties. For example, a common pattern should not change when adding a constant value to all observations. That shift is essentially the renumbering of the points on a ruler without changing the metric information provided by the ruler. A ruler is shift invariant only when its scale is properly calibrated to the pattern being measured. Stretch invariance corresponds to the conservation of the total amount of something, such as the total biomass and consequently the average size. Rotational invariance corresponds to pattern that does not depend on the order in which underlying processes occur, for example, a scale that additively combines the component processes leading to observed values. I use tree size as an example to illustrate how the key invariances shape pattern. A simple interpretation of common pattern follows. That simple interpretation connects the normal distribution to a wide variety of other common patterns through the transformations of scale set by the fundamental invariances. PMID:27928497

  18. 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.

  19. The Fragmentation of Learning.

    ERIC Educational Resources Information Center

    Downes, Stephen

    2001-01-01

    Information and communication technologies, especially the Internet, have vastly increased access to information and educational opportunities. Steadily increasing consumer demand is driving the development of online educational materials. The end result may be a "fragmentation" of learning involving multiple learning providers and delivery modes,…

  20. Structural assessment of glycyl mutations in invariantly conserved motifs.

    PubMed

    Prakash, Tulika; Sandhu, Kuljeet Singh; Singh, Nitin Kumar; Bhasin, Yasha; Ramakrishnan, C; Brahmachari, Samir K

    2007-11-15

    Motifs that are evolutionarily conserved in proteins are crucial to their structure and function. In one of our earlier studies, we demonstrated that the conserved motifs occurring invariantly across several organisms could act as structural determinants of the proteins. We observed the abundance of glycyl residues in these invariantly conserved motifs. The role of glycyl residues in highly conserved motifs has not been studied extensively. Thus, it would be interesting to examine the structural perturbations induced by mutation in these conserved glycyl sites. In this work, we selected a representative set of invariant signature (IS) peptides for which both the PDB structure and mutation information was available. We thoroughly analyzed the conformational features of the glycyl sites and their local interactions with the surrounding residues. Using Ramachandran angles, we showed that the glycyl residues occurring in these IS peptides, which have undergone mutation, occurred more often in the L-disallowed as compared with the L-allowed region of the Ramachandran plot. Short range contacts around the mutation site were analyzed to study the steric effects. With the results obtained from our analysis, we hypothesize that any change of activity arising because of such mutations must be attributed to the long-range interaction(s) of the new residue if the glycyl residue in the IS peptide occurred in the L-allowed region of the Ramachandran plot. However, the mutation of those conserved glycyl residues that occurred in the L-disallowed region of the Ramachandran plot might lead to an altered activity of the protein as a result of an altered conformation of the backbone in the immediate vicinity of the glycyl residue, in addition to long range effects arising from the long side chains of the new residue. Thus, the loss of activity because of mutation in the conserved glycyl site might either relate to long range interactions or to local perturbations around the site

  1. Invariant natural killer T cell-based immunotherapy for cancer.

    PubMed

    Motohashi, Shinichiro; Nakayama, Toshinori

    2009-01-01

    Human Valpha24 invariant natural killer T (iNKT) cells are a distinct lymphocyte population, characterized by an invariant T-cell receptor Valpha24 chain paired mainly with Valpha11. Valpha24 iNKT cells are activated by a glycolipid ligand - alpha-galactosylceramide - and produce a large amount of Th1 and Th2 cytokines, thereby modulating the function of other cells. iNKT cells have the capability to control a wide variety of immune responses, including antitumor immunity. Abnormalities in the number and function of Valpha24 iNKT cells have been observed in patients with malignant diseases accompanied with a poor clinical outcome. Therefore, therapeutic strategies that focused on the restoration of Valpha24 iNKT cell population and function would be a reasonable rationale for the treatment of cancer. In this article, the progress to date in the clinical studies of iNKT cell-based immunotherapy is briefly reviewed and the role of Valpha24 iNKT cells in cancer immunotherapy is highlighted.

  2. Dealing with Reflection Invariance in Bayesian Factor Analysis.

    PubMed

    Erosheva, Elena A; Curtis, S McKay

    2017-03-13

    This paper considers the reflection unidentifiability problem in confirmatory factor analysis (CFA) and the associated implications for Bayesian estimation. We note a direct analogy between the multimodality in CFA models that is due to all possible column sign changes in the matrix of loadings and the multimodality in finite mixture models that is due to all possible relabelings of the mixture components. Drawing on this analogy, we derive and present a simple approach for dealing with reflection in variance in Bayesian factor analysis. We recommend fitting Bayesian factor analysis models without rotational constraints on the loadings-allowing Markov chain Monte Carlo algorithms to explore the full posterior distribution-and then using a relabeling algorithm to pick a factor solution that corresponds to one mode. We demonstrate our approach on the case of a bifactor model; however, the relabeling algorithm is straightforward to generalize for handling multimodalities due to sign invariance in the likelihood in other factor analysis models.

  3. 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.

  4. Fragmentation of Fractal Random Structures

    NASA Astrophysics Data System (ADS)

    Elçi, Eren Metin; Weigel, Martin; Fytas, Nikolaos G.

    2015-03-01

    We analyze the fragmentation behavior of random clusters on the lattice under a process where bonds between neighboring sites are successively broken. Modeling such structures by configurations of a generalized Potts or random-cluster model allows us to discuss a wide range of systems with fractal properties including trees as well as dense clusters. We present exact results for the densities of fragmenting edges and the distribution of fragment sizes for critical clusters in two dimensions. Dynamical fragmentation with a size cutoff leads to broad distributions of fragment sizes. The resulting power laws are shown to encode characteristic fingerprints of the fragmented objects.

  5. One-electron oxidation of 2-(4-methoxyphenyl)-2-methylpropanoic and 1-(4-methoxyphenyl)cyclopropanecarboxylic acids in aqueous solution. the involvement of radical cations and the influence of structural effects and pH on the side-chain fragmentation reactivity.

    PubMed

    Bietti, Massimo; Capone, Alberto

    2008-01-18

    A product and time-resolved kinetic study on the one-electron oxidation of 2-(4-methoxyphenyl)-2-methylpropanoic acid (2), 1-(4-methoxyphenyl)cyclopropanecarboxylic acid (3), and of the corresponding methyl esters (substrates 4 and 5, respectively) has been carried out in aqueous solution. With 2, no direct evidence for the formation of an intermediate radical cation 2*+ but only of the decarboxylated 4-methoxycumyl radical has been obtained, indicating either that 2*+ is not formed or that its decarboxylation is too fast to allow detection under the experimental conditions employed (k > 1 x 10(7) s(-1)). With 3, oxidation leads to the formation of the corresponding radical cation 3*+ or radical zwitterion -3*+ depending on pH. At pH 1.0 and 6.7, 3*+ and -3*+ have been observed to undergo decarboxylation as the exclusive side-chain fragmentation pathway with rate constants k = 4.6 x 10(3) and 2.3 x 10(4) s(-1), respectively. With methyl esters 4 and 5, direct evidence for the formation of the corresponding radical cations 4*+ and 5*+ has been obtained. Both radical cations have been observed to display a very low reactivity and an upper limit for their decay rate constants has been determined as k < 10(3) s(-1). Comparison between the one-electron oxidation reactions of 2 and 3 shows that the replacement of the C(CH3)2 moiety with a cyclopropyl group determines a decrease in decarboxylation rate constant of more than 3 orders of magnitude. This large difference in reactivity has been qualitatively explained in terms of three main contributions: substrate oxidation potential, stability of the carbon-centered radical formed after decarboxylation, and stereoelectronic effects. In basic solution, -3*+ and 5*+ have been observed to react with -OH in a process that is assigned to the -OH-induced ring-opening of the cyclopropane ring, and the corresponding second-order rate constants (k-OH) have been obtained. With -3*+, competition between decarboxylation and -OH

  6. Invariants for time-dependent Hamiltonian systems.

    PubMed

    Struckmeier, J; Riedel, C

    2001-08-01

    An exact invariant is derived for n-degree-of-freedom Hamiltonian systems with general time-dependent potentials. The invariant is worked out in two equivalent ways. In the first approach, we define a special Ansatz for the invariant and determine its time-dependent coefficients. In the second approach, we perform a two-step canonical transformation of the initially time-dependent Hamiltonian to a time-independent one. The invariant is found to contain a function of time f(2)(t), defined as a solution of a linear third-order differential equation whose coefficients depend in general on the explicitly known configuration space trajectory that follows from the system's time evolution. It is shown that the invariant can be interpreted as the time integral of an energy balance equation. Our result is applied to a one-dimensional, time-dependent, damped non-linear oscillator, and to a three-dimensional system of Coulomb-interacting particles that are confined in a time-dependent quadratic external potential. We finally show that our results can be used to assess the accuracy of numerical simulations of time-dependent Hamiltonian systems.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. Feedback network with space invariant coupling.

    PubMed

    Häusler, G; Lange, E

    1990-11-10

    Processing images by a neural network means performing a repeated sequence of operations on the images. The sequence consists of a general linear transformation and a nonlinear mapping of pixel intensities. The general (shift variant) linear transformation is time consuming for large images if done with a serial computer. A shift invariant linear transformation can be implemented much easier by fast Fourier transform or optically, but the shift invariant transform has fewer degrees of freedom because the coupling matrix is Toeplitz. We present a neural convolution network with shift invariant coupling that nevertheless exhibits autoassociative restoration of distorted images. Besides the simple implementation, the network has one more advantage: associative recall does not depend on object position.

  12. 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.

  13. 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.

  14. 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

  15. Scale Invariant Gravity - a Simple Formulation

    NASA Astrophysics Data System (ADS)

    Wesson, P. S.

    1981-09-01

    Using the Cosmological Principle as justification, it is suggested that the scale-invariant theory of gravity be based on a Conspiracy Hypothesis (CH). The CH says: The matter parameters of a system (mass, density, pressure, etc.), the "constants" of physics and the coordinates occur together in dimensionless combinations (η-numbers) in which the components may vary but in such a manner that the variations conspire to keep the -numbers constant. This hypothesis yields a formulation of the scale-invariant theory that is simpler than other versions of it in which the Newtonian gravitational parameter G is treated as a field variable (Dirac, Hoyle/Narlikar, Canuto et al.). This simple formulation of scale-invariant gravity agrees with a recent reformulation of the (Perfect) Cosmological Principle. It also agrees with observations that have been made to date, and the equations suggest several new tests that can possibly be carried out.

  16. Learning invariant face recognition from examples.

    PubMed

    Müller, Marco K; Tremer, Michael; Bodenstein, Christian; Würtz, Rolf P

    2013-05-01

    Autonomous learning is demonstrated by living beings that learn visual invariances during their visual experience. Standard neural network models do not show this sort of learning. On the example of face recognition in different situations we propose a learning process that separates learning of the invariance proper from learning new instances of individuals. The invariance is learned by a set of examples called model, which contains instances of all situations. New instances are compared with these on the basis of rank lists, which allow generalization across situations. The result is also implemented as a spike-time-based neural network, which is shown to be robust against disturbances. The learning capability is demonstrated by recognition experiments on a set of standard face databases.

  17. 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.

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

    PubMed Central

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

    2012-01-01

    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 NO2− 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 NO2− 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. PMID:21953257

  19. 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.

  20. An invariance theorem in acoustic scattering theory

    NASA Astrophysics Data System (ADS)

    Ha-Duong, T.

    1996-10-01

    Karp's theorem states that if the far-field pattern corresponding to the scattering of a time-harmonic acoustic plane wave by a sound-soft obstacle is invariant under the group of orthogonal transformations in 0266-5611/12/5/007/img1 (rotations in 0266-5611/12/5/007/img2), then the scatterer is a sphere (circle). The theorem is generalized to the case where the invariant group of the far field pattern is only a subgroup of the orthogonal group, and for a class of mixed boundary conditions.

  1. 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.

  2. On adiabatic invariant in generalized Galileon theories

    SciTech Connect

    Ema, Yohei; Jinno, Ryusuke; Nakayama, Kazunori; Mukaida, Kyohei E-mail: jinno@hep-th.phys.s.u-tokyo.ac.jp E-mail: kazunori@hep-th.phys.s.u-tokyo.ac.jp

    2015-10-01

    We consider background dynamics of generalized Galileon theories in the context of inflation, where gravity and inflaton are non-minimally coupled to each other. In the inflaton oscillation regime, the Hubble parameter and energy density oscillate violently in many cases, in contrast to the Einstein gravity with minimally coupled inflaton. However, we find that there is an adiabatic invariant in the inflaton oscillation regime in any generalized Galileon theory. This adiabatic invariant is useful in estimating the expansion law of the universe and also the particle production rate due to the oscillation of the Hubble parameter.

  3. 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.

  4. 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.

  5. Some cosmological consequences of Weyl invariance

    SciTech Connect

    Alvarez, Enrique; González-Martín, Sergio; Herrero-Valea, Mario E-mail: sergio.gonzalez.martin@csic.es

    2015-03-01

    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.

  6. Galilean invariant resummation schemes of cosmological perturbations

    NASA Astrophysics Data System (ADS)

    Peloso, Marco; Pietroni, Massimo

    2017-01-01

    Many of the methods proposed so far to go beyond Standard Perturbation Theory break invariance under time-dependent boosts (denoted here as extended Galilean Invariance, or GI). This gives rise to spurious large scale effects which spoil the small scale predictions of these approximation schemes. By using consistency relations we derive fully non-perturbative constraints that GI imposes on correlation functions. We then introduce a method to quantify the amount of GI breaking of a given scheme, and to correct it by properly tailored counterterms. Finally, we formulate resummation schemes which are manifestly GI, discuss their general features, and implement them in the so called Time-Flow, or TRG, equations.

  7. Invariant measures on multimode quantum Gaussian states

    NASA Astrophysics Data System (ADS)

    Lupo, C.; Mancini, S.; De Pasquale, A.; Facchi, P.; Florio, G.; Pascazio, S.

    2012-12-01

    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.

  8. 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.

  9. 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

  10. 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.

  11. Invariant Discretization Schemes Using Evolution-Projection Techniques

    NASA Astrophysics Data System (ADS)

    Bihlo, Alexander; Nave, Jean-Christophe

    2013-08-01

    Finite difference discretization schemes preserving a subgroup of the maximal Lie invariance group of the one-dimensional linear heat equation are determined. These invariant schemes are constructed using the invariantization procedure for non-invariant schemes of the heat equation in computational coordinates. We propose a new methodology for handling moving discretization grids which are generally indispensable for invariant numerical schemes. The idea is to use the invariant grid equation, which determines the locations of the grid point at the next time level only for a single integration step and then to project the obtained solution to the regular grid using invariant interpolation schemes. This guarantees that the scheme is invariant and allows one to work on the simpler stationary grids. The discretization errors of the invariant schemes are established and their convergence rates are estimated. Numerical tests are carried out to shed some light on the numerical p! roperties of invariant discretization schemes using the proposed evolution-projection strategy.

  12. 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.

  13. Influence of the germline sequence on the thermodynamic stability and fibrillogenicity of human lambda 6 light chains.

    PubMed

    del Pozo Yauner, Luis; Ortiz, Ernesto; Sánchez, Rosalba; Sánchez-López, Rosana; Güereca, Leopoldo; Murphy, Charles L; Allen, Amy; Wall, Jonathan S; Fernández-Velasco, D Alejandro; Solomon, Alan; Becerril, Baltazar

    2008-08-01

    Light chain-associated amyloidosis is a fatal disease characterized by the aggregation and pathologic deposition of monoclonal light chain-related fragments as amyloid fibrils in organs or tissues throughout the body. Notably, it has been observed that proteins encoded by the lambda variable light chain (V(L)) gene segment 6a are invariably associated with amyloid deposition; however, the contribution of the gene to this phenomenon has not been established. In this regard, we have determined the thermodynamic stability and kinetics of in vitro fibrillogenesis of a recombinant (r) V(L) protein, designated 6aJL2, which contains the predicted sequences encoded by the 6a and JL2 germline genes. Additionally, we studied a 6a mutant (6aJL2-Arg25Gly), that is present in approximately 25% of all amyloid-associated lambda6 light chains. Remarkably, the wild-type 6aJL2 protein was more stable than were all known amyloidogenic kappa and lambda light chains for which stability parameters are available; more importantly, it was even more so (and less fibrillogenic) than the only clinically proven nonamyloidogenic lambda6 protein, Jto. Conversely, the mutated 6aJL2-R25G molecule was considerably less stable and more fibrillogenic than was the native 6aJL2. Our data indicate that the propensity of lambda6 light chains to form amyloid can not be attributed to thermodynamic instability of the germline-encoded Vlambda6 domain, but rather, is dependent on sequence alterations that render such proteins amyloidogenic.

  14. Fragmentation of random trees

    NASA Astrophysics Data System (ADS)

    Kalay, Z.; Ben-Naim, E.

    2015-01-01

    We study fragmentation of a random recursive tree into a forest by repeated removal of nodes. The initial tree consists of N nodes and it is generated by sequential addition of nodes with each new node attaching to a randomly-selected existing node. As nodes are removed from the tree, one at a time, the tree dissolves into an ensemble of separate trees, namely, a forest. We study statistical properties of trees and nodes in this heterogeneous forest, and find that the fraction of remaining nodes m characterizes the system in the limit N\\to ∞ . We obtain analytically the size density {{φ }s} of trees of size s. The size density has power-law tail {{φ }s}˜ {{s}-α } with exponent α =1+\\frac{1}{m}. Therefore, the tail becomes steeper as further nodes are removed, and the fragmentation process is unusual in that exponent α increases continuously with time. We also extend our analysis to the case where nodes are added as well as removed, and obtain the asymptotic size density for growing trees.

  15. Fragmentation of random trees

    NASA Astrophysics Data System (ADS)

    Kalay, Ziya; Ben-Naim, Eli

    2015-03-01

    We investigate the fragmentation of a random recursive tree by repeated removal of nodes, resulting in a forest of disjoint trees. The initial tree is generated by sequentially attaching new nodes to randomly chosen existing nodes until the tree contains N nodes. As nodes are removed, one at a time, the tree dissolves into an ensemble of separate trees, namely a forest. We study the statistical properties of trees and nodes in this heterogeneous forest. In the limit N --> ∞ , we find that the system is characterized by a single parameter: the fraction of remaining nodes m. We obtain analytically the size density ϕs of trees of size s, which has a power-law tail ϕs ~s-α , with exponent α = 1 + 1 / m . Therefore, the tail becomes steeper as further nodes are removed, producing an unusual scaling exponent that increases continuously with time. Furthermore, we investigate the fragment size distribution in a growing tree, where nodes are added as well as removed, and find that the distribution for this case is much narrower.

  16. Chain Sampling

    DTIC Science & Technology

    1972-08-01

    35609 Advanced Techniques Branch Plans and Programs Analysis Division Directorate for Product Assurance U. S. Army Missile Command Redstone Arsenal...Ray Heathcock Advanced Techniques Branch Plans and Programs Analysis Division Directorate for Product Assurance U. S. Army Missile Command...for Product Assurance has established a rather unique computer program for handling a variety of chain sampling schemes and is available for

  17. Scale invariance, conformality, and generalized free fields

    SciTech Connect

    Dymarsky, Anatoly; Farnsworth, Kara; Komargodski, Zohar; Luty, Markus A.; Prilepina, Valentina

    2016-02-16

    This paper addresses the question of whether there are 4D Lorentz invariant unitary quantum fi eld theories with scale invariance but not conformal invariance. We present an important loophole in the arguments of Luty-Polchinski-Rattazzi and Dymarsky-Komargodski-Schwimmer-Theisen that is the trace of the energy-momentum tensor T could be a generalized free field. In this paper we rule out this possibility. The key ingredient is the observation that a unitary theory with scale but not conformal invariance necessarily has a non-vanishing anomaly for global scale transformations. We show that this anomaly cannot be reproduced if T is a generalized free field 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). Finally, despite the invalidity of the general argument of FLP, some of the techniques turn out to be useful in the present context.

  18. Constitutive laws, tensorial invariance and chocolate cake

    NASA Astrophysics Data System (ADS)

    Rundle, John B.; Passman, S. L.

    1982-04-01

    Although constitutive modeling is a well-established branch of mathematics which has found wide industrial application, geophysicists often do not take full advantage of its known results. We present a synopsis of the theory of constitutive modeling, couched in terms of the ‘simple material’, which has been extensively studied and is complex enough to include most of the correct models proposed to describe the behavior of geological materials. Critical in the development of the theory are various invariance requirements, the principal ones being coordinate invariance, peer group invariance (isotropy), and frame-indifference. Each places distinet restrictions on constitutive equations. A noncomprehensive list of properly invariant and commonly used constitutive equations is given. To exemplify use of the equations, we consider two problems in detail: steady extension, which models the commonly performed constant strain rate triaxial test, and simple shearing. We note that each test is so restricted kinematically that only the most trivial aspects of material behavior are manifested in these tests, no matter how complex the material. Furthermore, the results of one test do not generally determine the results of the other.

  19. 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.

  20. 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…

  1. 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.

  2. Scale invariance, conformality, and generalized free fields

    DOE PAGES

    Dymarsky, Anatoly; Farnsworth, Kara; Komargodski, Zohar; ...

    2016-02-16

    This paper addresses the question of whether there are 4D Lorentz invariant unitary quantum fi eld theories with scale invariance but not conformal invariance. We present an important loophole in the arguments of Luty-Polchinski-Rattazzi and Dymarsky-Komargodski-Schwimmer-Theisen that is the trace of the energy-momentum tensor T could be a generalized free field. In this paper we rule out this possibility. The key ingredient is the observation that a unitary theory with scale but not conformal invariance necessarily has a non-vanishing anomaly for global scale transformations. We show that this anomaly cannot be reproduced if T is a generalized free field unlessmore » the theory also contains a dimension-2 scalar operator. In the special case where such an operator is present it can be used to redefine ("improve") the energy-momentum tensor, and we show that there is at least one energy-momentum tensor that is not a generalized free field. In addition, we emphasize that, in general, large momentum limits of correlation functions cannot be understood from the leading terms of the coordinate space OPE. This invalidates a recent argument by Farnsworth-Luty-Prilepina (FLP). Finally, despite the invalidity of the general argument of FLP, some of the techniques turn out to be useful in the present context.« less

  3. 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…

  4. Gauge-invariant hydrogen-atom Hamiltonian

    SciTech Connect

    Sun Weimin; Wang Fan; Chen Xiangsong; Lue Xiaofu

    2010-07-15

    For quantum mechanics of a charged particle in a classical external electromagnetic field, there is an apparent puzzle that the matrix element of the canonical momentum and Hamiltonian operators is gauge dependent. A resolution to this puzzle was recently provided by us [X.-S. Chen et al., Phys. Rev. Lett. 100, 232002 (2008)]. Based on the separation of the electromagnetic potential into pure-gauge and gauge-invariant parts, we have proposed a new set of momentum and Hamiltonian operators which satisfy both the requirement of gauge invariance and the relevant commutation relations. In this paper we report a check for the case of the hydrogen-atom problem: Starting from the Hamiltonian of the coupled electron, proton, and electromagnetic field, under the infinite proton mass approximation, we derive the gauge-invariant hydrogen-atom Hamiltonian and verify explicitly that this Hamiltonian is different from the Dirac Hamiltonian, which is the time translation generator of the system. The gauge-invariant Hamiltonian is the energy operator, whose eigenvalue is the energy of the hydrogen atom. It is generally time dependent. In this case, one can solve the energy eigenvalue equation at any specific instant of time. It is shown that the energy eigenvalues are gauge independent, and by suitably choosing the phase factor of the time-dependent eigenfunction, one can ensure that the time-dependent eigenfunction satisfies the Dirac equation.

  5. Invariant functionals in higher-spin theory

    NASA Astrophysics Data System (ADS)

    Vasiliev, M. A.

    2017-03-01

    A new construction for gauge invariant functionals in the nonlinear higher-spin theory is proposed. Being supported by differential forms closed by virtue of the higher-spin equations, invariant functionals are associated with central elements of the higher-spin algebra. In the on-shell AdS4 higher-spin theory we identify a four-form conjectured to represent the generating functional for 3d boundary correlators and a two-form argued to support charges for black hole solutions. Two actions for 3d boundary conformal higher-spin theory are associated with the two parity-invariant higher-spin models in AdS4. The peculiarity of the spinorial formulation of the on-shell AdS3 higher-spin theory, where the invariant functional is supported by a two-form, is conjectured to be related to the holomorphic factorization at the boundary. The nonlinear part of the star-product function F* (B (x)) in the higher-spin equations is argued to lead to divergencies in the boundary limit representing singularities at coinciding boundary space-time points of the factors of B (x), which can be regularized by the point splitting. An interpretation of the RG flow in terms of proposed construction is briefly discussed.

  6. Neutrinos as Probes of Lorentz Invariance

    DOE PAGES

    Díaz, Jorge S.

    2014-01-01

    Neutrinos can be used to search for deviations from exact Lorentz invariance. The worldwide experimental program in neutrino physics makes these particles a remarkable tool to search for a variety of signals that could reveal minute relativity violations. This paper reviews the generic experimental signatures of the breakdown of Lorentz symmetry in the neutrino sector.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. Protein fragment reconstruction using various modeling techniques

    NASA Astrophysics Data System (ADS)

    Boniecki, Michal; Rotkiewicz, Piotr; Skolnick, Jeffrey; Kolinski, Andrzej

    2003-11-01

    Recently developed reduced models of proteins with knowledge-based force fields have been applied to a specific case of comparative modeling. From twenty high resolution protein structures of various structural classes, significant fragments of their chains have been removed and treated as unknown. The remaining portions of the structures were treated as fixed - i.e., as templates with an exact alignment. Then, the missed fragments were reconstructed using several modeling tools. These included three reduced types of protein models: the lattice SICHO (Side Chain Only) model, the lattice CABS (Cα + Cβ + Side group) model and an off-lattice model similar to the CABS model and called REFINER. The obtained reduced models were compared with more standard comparative modeling tools such as MODELLER and the SWISS-MODEL server. The reduced model results are qualitatively better for the higher resolution lattice models, clearly suggesting that these are now mature, competitive and complementary (in the range of sparse alignments) to the classical tools of comparative modeling. Comparison between the various reduced models strongly suggests that the essential ingredient for the sucessful and accurate modeling of protein structures is not the representation of conformational space (lattice, off-lattice, all-atom) but, rather, the specificity of the force fields used and, perhaps, the sampling techniques employed. These conclusions are encouraging for the future application of the fast reduced models in comparative modeling on a genomic scale.

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. A Mini-Library of Sequenced Human DNA Fragments: Linking Bench Experiments with Informatics

    ERIC Educational Resources Information Center

    Dalgleish, Raymond; Shanks, Morag E.; Monger, Karen; Butler, Nicola J.

    2012-01-01

    We describe the development of a mini-library of human DNA fragments for use in an enquiry-based learning (EBL) undergraduate practical incorporating "wet-lab" and bioinformatics tasks. In spite of the widespread emergence of the polymerase chain reaction (PCR), the cloning and analysis of DNA fragments in "Escherichia coli"…

  18. The Largest Fragment of a Homogeneous Fragmentation Process

    NASA Astrophysics Data System (ADS)

    Kyprianou, Andreas; Lane, Francis; Mörters, Peter

    2017-03-01

    We show that in homogeneous fragmentation processes the largest fragment at time t has size e^{-t Φ '(overline{p})}t^{-3/2 (log Φ )'(overline{p})+o(1)}, where Φ is the Lévy exponent of the fragmentation process, and overline{p} is the unique solution of the equation (log Φ )'(bar{p})=1/1+bar{p}. We argue that this result is in line with predictions arising from the classification of homogeneous fragmentation processes as logarithmically correlated random fields.

  19. Chain Gang

    NASA Technical Reports Server (NTRS)

    2006-01-01

    6 August 2006 This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows a chain of clustered and battered craters. These were formed by secondary impact. That is, somewhere to the south (beyond the bottom of this image), a large impact crater formed. When this occurred, material ejected from the crater was thrown tens to hundreds of kilometers away. This material then impacted the martian surface, forming clusters and chains of smaller craters.

    Location near: 15.8oN, 35.6oW Image width: 3 km (1.9 mi) Illumination from: upper left Season: Northern Spring

  20. 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

  1. Jet quenching and gluon to hadron fragmentation function in non-equilibrium QCD at RHIC and LHC

    NASA Astrophysics Data System (ADS)

    Nayak, Gouranga C.

    2017-01-01

    Theoretical understanding of the observed jet quenching measurements at RHIC and LHC is challenging in QCD because it requires understanding of parton to hadron fragmentation function in non-equilibrium QCD. In this paper, by using closed-time path integral formalism, we derive the gauge invariant definition of the gluon to hadron fragmentation function in non-equilibrium QCD which is consistent with factorization theorem in non-equilibrium QCD from first principles.

  2. Perturbative and gauge invariant treatment of gravitational wave memory

    NASA Astrophysics Data System (ADS)

    Bieri, Lydia; Garfinkle, David

    2014-04-01

    We present a perturbative treatment of gravitational wave memory. The coordinate invariance of Einstein's equations leads to a type of gauge invariance in perturbation theory. As with any gauge invariant theory, results are more clear when expressed in terms of manifestly gauge invariant quantities. Therefore we derive all our results from the perturbed Weyl tensor rather than the perturbed metric. We derive gravitational wave memory for the Einstein equations coupled to a general energy-momentum tensor that reaches null infinity.

  3. Binary stars - Formation by fragmentation

    NASA Technical Reports Server (NTRS)

    Boss, Alan P.

    1988-01-01

    Theories of binary star formation by capture, separate nuclei, fission and fragmentation are compared, assessing the success of theoretical attempts to explain the observed properties of main-sequence binary stars. The theory of formation by fragmentation is examined, discussing the prospects for checking the theory against observations of binary premain-sequence stars. It is concluded that formation by fragmentation is successful at explaining many of the key properties of main-sequence binary stars.

  4. Species–fragmented area relationship

    PubMed Central

    Hanski, Ilkka; Zurita, Gustavo A.; Bellocq, M. Isabel; Rybicki, Joel

    2013-01-01

    The species–area relationship (SAR) gives a quantitative description of the increasing number of species in a community with increasing area of habitat. In conservation, SARs have been used to predict the number of extinctions when the area of habitat is reduced. Such predictions are most needed for landscapes rather than for individual habitat fragments, but SAR-based predictions of extinctions for landscapes with highly fragmented habitat are likely to be biased because SAR assumes contiguous habitat. In reality, habitat loss is typically accompanied by habitat fragmentation. To quantify the effect of fragmentation in addition to the effect of habitat loss on the number of species, we extend the power-law SAR to the species–fragmented area relationship. This model unites the single-species metapopulation theory with the multispecies SAR for communities. We demonstrate with a realistic simulation model and with empirical data for forest-inhabiting subtropical birds that the species–fragmented area relationship gives a far superior prediction than SAR of the number of species in fragmented landscapes. The results demonstrate that for communities of species that are not well adapted to live in fragmented landscapes, the conventional SAR underestimates the number of extinctions for landscapes in which little habitat remains and it is highly fragmented. PMID:23858440

  5. 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.

  6. 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…

  7. 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.

  8. 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.

  9. Fast forward to the classical adiabatic invariant

    NASA Astrophysics Data System (ADS)

    Jarzynski, Christopher; Deffner, Sebastian; Patra, Ayoti; Subaşı, Yiǧit

    2017-03-01

    We show how the classical action, an adiabatic invariant, can be preserved under nonadiabatic conditions. Specifically, for a time-dependent Hamiltonian H =p2/2 m +U (q ,t ) in one degree of freedom, and for an arbitrary choice of action I0, we construct a so-called fast-forward potential energy function VFF(q ,t ) that, when added to H , guides all trajectories with initial action I0 to end with the same value of action. We use this result to construct a local dynamical invariant J (q ,p ,t ) whose value remains constant along these trajectories. We illustrate our results with numerical simulations. Finally, we sketch how our classical results may be used to design approximate quantum shortcuts to adiabaticity.

  10. Adiabatic invariance with first integrals of motion.

    PubMed

    Adib, Artur B

    2002-10-01

    The construction of a microthermodynamic formalism for isolated systems based on the concept of adiabatic invariance is an old but seldom appreciated effort in the literature, dating back at least to P. Hertz [Ann. Phys. (Leipzig) 33, 225 (1910)]. An apparently independent extension of such formalism for systems bearing additional first integrals of motion was recently proposed by Hans H. Rugh [Phys. Rev. E 64, 055101 (2001)], establishing the concept of adiabatic invariance even in such singular cases. After some remarks in connection with the formalism pioneered by Hertz, it will be suggested that such an extension can incidentally explain the success of a dynamical method for computing the entropy of classical interacting fluids, at least in some potential applications where the presence of additional first integrals cannot be ignored.

  11. Testing CPT Invariance with Antiprotonic Helium Atoms

    SciTech Connect

    Horvath, Dezso

    2008-08-08

    The structure of matter is related to symmetries at every level of study. CPT symmetry is one of the most important laws of field theory: it states the invariance of physical properties when one simultaneously changes the signs of the charge and of the spatial and time coordinates of free elementary particles. Although in general opinion CPT symmetry is not violated in Nature, there are theoretical attempts to develop CPT-violating models. The Antiproton Decelerator at CERN has been built to test CPT invariance. The ASACUSA experiment compares the properties of particles and antiparticles by studying the antiprotonic helium atom via laser spectroscopy and measuring the mass, charge and magnetic moment of the antiproton as compared to those of the proton.

  12. 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.

  13. Remarks on holography with broken Lorentz invariance

    NASA Astrophysics Data System (ADS)

    Gordeli, Ivan; Koroteev, Peter

    2009-12-01

    Recently a family of solutions of Einstein equations in backgrounds with broken Lorentz invariance was found. We show that the gravitational solution recently obtained by Kachru et al. is a part of the former solution which was derived earlier in the framework of extra-dimensional theories. We show how the energy-momentum and Einstein tensors are related and establish a correspondence between parameters which govern Lorentz invariance violation. Then we demonstrate that scaling behavior of two point correlation functions of local operators in scalar field theory is reproduced correctly for two cases with critical values of scaling parameters. Therefore, we complete the dictionary of “tree-level” duality for all known solutions of the bulk theory. In the end we speculate on relations between renormalization group flow of a boundary theory and asymptotic behavior of gravitational solutions in the bulk.

  14. Elastic wave invariants for acoustic emission

    NASA Astrophysics Data System (ADS)

    Pardee, W. J.

    1981-07-01

    It is shown that there are four conserved properties of an elastic wave in an infinite isotropic plate: the energy, the two components of wave momentum parallel to the surface, and wave angular momentum normal to the surface. All four invariants are volume integrals of quadratic functions of the spatial (Eulerian) coordinates. The canonical energy-momentum density tensor and the orbital, spin, and total angular momentum density tensors are constructed and sufficient conditions for their conservation are demonstrated. A procedure for measuring the wave momentum of a surface wave is proposed. It is argued that these invariants are likely to be particularly useful characterizations of acoustic emission, e.g., from a growing crack. Experimental tests are proposed, and possible applications to practical monitoring problems described.

  15. Invariant metrics, contractions and nonlinear matrix equations

    NASA Astrophysics Data System (ADS)

    Lee, Hosoo; Lim, Yongdo

    2008-04-01

    In this paper we consider the semigroup generated by the self-maps on the open convex cone of positive definite matrices of translations, congruence transformations and matrix inversion that includes symplectic Hamiltonians and show that every member of the semigroup contracts any invariant metric distance inherited from a symmetric gauge function. This extends the results of Bougerol for the Riemannian metric and of Liverani-Wojtkowski for the Thompson part metric. A uniform upper bound of the Lipschitz contraction constant for a member of the semigroup is given in terms of the minimum eigenvalues of its determining matrices. We apply this result to a variety of nonlinear equations including Stein and Riccati equations for uniqueness and existence of positive definite solutions and find a new convergence analysis of iterative algorithms for the positive definite solution depending only on the least contraction coefficient for the invariant metric from the spectral norm.

  16. Invariant measures for singular hyperbolic attractors

    SciTech Connect

    Sataev, Evgueni A

    2010-05-11

    This paper continues the author's previous paper, where strong unstable spaces were constructed for a singular hyperbolic attractor. In this paper the existence of local strongly unstable manifolds and invariant measures of Sinai-Bowen-Ruelle type is established. The properties of such measures are studied. It is proved that the number of ergodic components is finite and the set of periodic trajectories is dense. Bibliography: 34 titles.

  17. Neutrino velocity and local Lorentz invariance

    NASA Astrophysics Data System (ADS)

    Cardone, Fabio; Mignani, Roberto; Petrucci, Andrea

    2015-09-01

    We discuss the possible violation of local Lorentz invariance (LLI) arising from a faster-than-light neutrino speed. A toy calculation of the LLI violation parameter δ, based on the (disclaimed) OPERA data, suggests that the values of δ are determined by the interaction involved, and not by the energy range. This hypothesis is further corroborated by the analysis of the more recent results of the BOREXINO, LVD and ICARUS experiments.

  18. Global invariants in ideal magnetohydrodynamic turbulence

    SciTech Connect

    Shebalin, John V.

    2013-10-15

    Magnetohydrodynamic (MHD) turbulence is an important though incompletely understood factor affecting the dynamics of many astrophysical, geophysical, and technological plasmas. As an approximation, viscosity and resistivity may be ignored, and ideal MHD turbulence may be investigated by statistical methods. Incompressibility is also assumed and finite Fourier series are used to represent the turbulent velocity and magnetic field. The resulting model dynamical system consists of a set of independent Fourier coefficients that form a canonical ensemble described by a Gaussian probability density function (PDF). This PDF is similar in form to that of Boltzmann, except that its argument may contain not just the energy multiplied by an inverse temperature, but also two other invariant integrals, the cross helicity and magnetic helicity, each multiplied by its own inverse temperature. However, the cross and magnetic helicities, as usually defined, are not invariant in the presence of overall rotation or a mean magnetic field, respectively. Although the generalized form of the magnetic helicity is known, a generalized cross helicity may also be found, by adding terms that are linear in the mean magnetic field and angular rotation vectors, respectively. These general forms are invariant even in the presence of overall rotation and a mean magnetic field. We derive these general forms, explore their properties, examine how they extend the statistical theory of ideal MHD turbulence, and discuss how our results may be affected by dissipation and forcing.

  19. Data series embedding and scale invariant statistics.

    PubMed

    Michieli, I; Medved, B; Ristov, S

    2010-06-01

    Data sequences acquired from bio-systems such as human gait data, heart rate interbeat data, or DNA sequences exhibit complex dynamics that is frequently described by a long-memory or power-law decay of autocorrelation function. One way of characterizing that dynamics is through scale invariant statistics or "fractal-like" behavior. For quantifying scale invariant parameters of physiological signals several methods have been proposed. Among them the most common are detrended fluctuation analysis, sample mean variance analyses, power spectral density analysis, R/S analysis, and recently in the realm of the multifractal approach, wavelet analysis. In this paper it is demonstrated that embedding the time series data in the high-dimensional pseudo-phase space reveals scale invariant statistics in the simple fashion. The procedure is applied on different stride interval data sets from human gait measurements time series (Physio-Bank data library). Results show that introduced mapping adequately separates long-memory from random behavior. Smaller gait data sets were analyzed and scale-free trends for limited scale intervals were successfully detected. The method was verified on artificially produced time series with known scaling behavior and with the varying content of noise. The possibility for the method to falsely detect long-range dependence in the artificially generated short range dependence series was investigated.

  20. Time-warp-invariant neuronal processing.

    PubMed

    Gütig, Robert; Sompolinsky, Haim

    2009-07-01

    Fluctuations in the temporal durations of sensory signals constitute a major source of variability within natural stimulus ensembles. The neuronal mechanisms through which sensory systems can stabilize perception against such fluctuations are largely unknown. An intriguing instantiation of such robustness occurs in human speech perception, which relies critically on temporal acoustic cues that are embedded in signals with highly variable duration. Across different instances of natural speech, auditory cues can undergo temporal warping that ranges from 2-fold compression to 2-fold dilation without significant perceptual impairment. Here, we report that time-warp-invariant neuronal processing can be subserved by the shunting action of synaptic conductances that automatically rescales the effective integration time of postsynaptic neurons. We propose a novel spike-based learning rule for synaptic conductances that adjusts the degree of synaptic shunting to the temporal processing requirements of a given task. Applying this general biophysical mechanism to the example of speech processing, we propose a neuronal network model for time-warp-invariant word discrimination and demonstrate its excellent performance on a standard benchmark speech-recognition task. Our results demonstrate the important functional role of synaptic conductances in spike-based neuronal information processing and learning. The biophysics of temporal integration at neuronal membranes can endow sensory pathways with powerful time-warp-invariant computational capabilities.

  1. Invariance algorithms for processing NDE signals

    NASA Astrophysics Data System (ADS)

    Mandayam, Shreekanth; Udpa, Lalita; Udpa, Satish S.; Lord, William

    1996-11-01

    Signals that are obtained in a variety of nondestructive evaluation (NDE) processes capture information not only about the characteristics of the flaw, but also reflect variations in the specimen's material properties. Such signal changes may be viewed as anomalies that could obscure defect related information. An example of this situation occurs during in-line inspection of gas transmission pipelines. The magnetic flux leakage (MFL) method is used to conduct noninvasive measurements of the integrity of the pipe-wall. The MFL signals contain information both about the permeability of the pipe-wall and the dimensions of the flaw. Similar operational effects can be found in other NDE processes. This paper presents algorithms to render NDE signals invariant to selected test parameters, while retaining defect related information. Wavelet transform based neural network techniques are employed to develop the invariance algorithms. The invariance transformation is shown to be a necessary pre-processing step for subsequent defect characterization and visualization schemes. Results demonstrating the successful application of the method are presented.

  2. On local invariants of singular symplectic forms

    NASA Astrophysics Data System (ADS)

    Domitrz, Wojciech

    2017-04-01

    We find a complete set of local invariants of singular symplectic forms with the structurally stable Martinet hypersurface on a 2 n-dimensional manifold. In the C-analytic category this set consists of the Martinet hypersurface Σ2, the restriction of the singular symplectic form ω to TΣ2 and the kernel of ω n - 1 at the point p ∈Σ2. In the R-analytic and smooth categories this set contains one more invariant: the canonical orientation of Σ2. We find the conditions to determine the kernel of ω n - 1 at p by the other invariants. In dimension 4 we find sufficient conditions to determine the equivalence class of a singular symplectic form-germ with the structurally smooth Martinet hypersurface by the Martinet hypersurface and the restriction of the singular symplectic form to it. We also study the singular symplectic forms with singular Martinet hypersurfaces. We prove that the equivalence class of such singular symplectic form-germ is determined by the Martinet hypersurface, the canonical orientation of its regular part and the restriction of the singular symplectic form to its regular part if the Martinet hypersurface is a quasi-homogeneous hypersurface with an isolated singularity.

  3. Against relative timing invariance in movement kinematics.

    PubMed

    Burgess-Limerick, R; Neal, R J; Abernethy, B

    1992-05-01

    The kinematics of stair climbing were examined to test the assertion that relative timing is an invariant feature of human gait. Six male and four female subjects were video-recorded (at 60 Hz) while they climbed a flight of stairs 10 times at each of three speeds. Each gait cycle was divided into three segments by the maximum and minimum angular displacement of the left knee and left foot contact. Gentner's (1987) analysis methods were applied to the individual subject data to determine whether the duration of the segments remained a fixed proportion of gait cycle duration across changes in stair-climbing speed. A similar analysis was performed using knee velocity maxima to partition the gait cycle. Regardless of how the gait cycle was divided, relative timing was not found to remain strictly invariant across changes in speed. This conclusion is contrary to previous studies of relative timing that involved less conservative analysis but is consistent with the wider gait literature. Strict invariant relative timing may not be a fundamental feature of movement kinematics.

  4. Global invariants in ideal magnetohydrodynamic turbulence

    NASA Astrophysics Data System (ADS)

    Shebalin, John V.

    2013-10-01

    Magnetohydrodynamic (MHD) turbulence is an important though incompletely understood factor affecting the dynamics of many astrophysical, geophysical, and technological plasmas. As an approximation, viscosity and resistivity may be ignored, and ideal MHD turbulence may be investigated by statistical methods. Incompressibility is also assumed and finite Fourier series are used to represent the turbulent velocity and magnetic field. The resulting model dynamical system consists of a set of independent Fourier coefficients that form a canonical ensemble described by a Gaussian probability density function (PDF). This PDF is similar in form to that of Boltzmann, except that its argument may contain not just the energy multiplied by an inverse temperature, but also two other invariant integrals, the cross helicity and magnetic helicity, each multiplied by its own inverse temperature. However, the cross and magnetic helicities, as usually defined, are not invariant in the presence of overall rotation or a mean magnetic field, respectively. Although the generalized form of the magnetic helicity is known, a generalized cross helicity may also be found, by adding terms that are linear in the mean magnetic field and angular rotation vectors, respectively. These general forms are invariant even in the presence of overall rotation and a mean magnetic field. We derive these general forms, explore their properties, examine how they extend the statistical theory of ideal MHD turbulence, and discuss how our results may be affected by dissipation and forcing.

  5. 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.

  6. Thermodynamical string fragmentation

    NASA Astrophysics Data System (ADS)

    Fischer, Nadine; Sjöstrand, Torbjörn

    2017-01-01

    The observation of heavy-ion-like behaviour in pp collisions at the LHC suggests that more physics mechanisms are at play than traditionally assumed. The introduction e.g. of quark-gluon plasma or colour rope formation can describe several of the observations, but as of yet there is no established paradigm. In this article we study a few possible modifications to the Pythia event generator, which describes a wealth of data but fails for a number of recent observations. Firstly, we present a new model for generating the transverse momentum of hadrons during the string fragmentation process, inspired by thermodynamics, where heavier hadrons naturally are suppressed in rate but obtain a higher average transverse momentum. Secondly, close-packing of strings is taken into account by making the temperature or string tension environment-dependent. Thirdly, a simple model for hadron rescattering is added. The effect of these modifications is studied, individually and taken together, and compared with data mainly from the LHC. While some improvements can be noted, it turns out to be nontrivial to obtain effects as big as required, and further work is called for.

  7. 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.

  8. Fragment screening and HIV therapeutics.

    PubMed

    Bauman, Joseph D; Patel, Disha; Arnold, Eddy

    2012-01-01

    Fragment screening has proven to be a powerful alternative to traditional methods for drug discovery. Biophysical methods, such as X-ray crystallography, NMR spectroscopy, and surface plasmon resonance, are used to screen a diverse library of small molecule compounds. Although compounds identified via this approach have relatively weak affinity, they provide a good platform for lead development and are highly efficient binders with respect to their size. Fragment screening has been utilized for a wide range of targets, including HIV-1 proteins. Here, we review the fragment screening studies targeting HIV-1 proteins using X-ray crystallography or surface plasmon resonance. These studies have successfully detected binding of novel fragments to either previously established or new sites on HIV-1 protease and reverse transcriptase. In addition, fragment screening against HIV-1 reverse transcriptase has been used as a tool to better understand the complex nature of ligand binding to a flexible target.

  9. Fragmentation functions in nuclear media

    NASA Astrophysics Data System (ADS)

    Sassot, Rodolfo; Stratmann, Marco; Zurita, Pia

    2010-03-01

    We perform a detailed phenomenological analysis of how well hadronization in nuclear environments can be described in terms of effective fragmentation functions. The medium modified fragmentation functions are assumed to factorize from the partonic scattering cross sections and evolve in the hard scale in the same way as the standard or vacuum fragmentation functions. Based on precise data on semi-inclusive deep-inelastic scattering off nuclei and hadron production in deuteron-gold collisions, we extract sets of effective fragmentation functions for pions and kaons at next-to-leading order accuracy. The obtained sets provide a rather accurate description of the kinematical dependence of the analyzed cross sections and are found to differ significantly from standard fragmentation functions both in shape and magnitude. Our results support the notion of factorization and universality in the studied nuclear environments, at least in an effective way and within the precision of the available data.

  10. Renormalization group invariants in the MSSM and its extensions

    NASA Astrophysics Data System (ADS)

    Demir, Durmus A.

    2005-11-01

    We derive one-loop renormalization group (RG) invariant observables and analyze their phenomenological implications in the MSSM and its μ problem solving extensions, U(1)' model and NMSSM. We show that there exist several RG invariants in the gauge, Yukawa and soft-breaking sectors of each model. In general, RG invariants are highly useful for projecting experimental data to messenger scale, for revealing correlations among the model parameters, and for probing the mechanism that breaks supersymmetry. The Yukawa couplings and trilinear soft terms in U(1)' model and NMSSM do not form RG invariants though there exist approximate invariants in low tan β domain. In the NMSSM, there are no invariants that contain the Higgs mass-squareds. We provide a comparative analysis of RG invariants in all three models and analyze their model-building and phenomenological implications by a number of case studies.

  11. Watson-Crick pairing, the Heisenberg group and Milnor invariants.

    PubMed

    Gadgil, Siddhartha

    2009-07-01

    We study the secondary structure of RNA determined by Watson-Crick pairing without pseudo-knots using Milnor invariants of links. We focus on the first non-trivial invariant, which we call the Heisenberg invariant. The Heisenberg invariant, which is an integer, can be interpreted in terms of the Heisenberg group as well as in terms of lattice paths. We show that the Heisenberg invariant gives a lower bound on the number of unpaired bases in an RNA secondary structure. We also show that the Heisenberg invariant can predict allosteric structures for RNA. Namely, if the Heisenberg invariant is large, then there are widely separated local maxima (i.e., allosteric structures) for the number of Watson-Crick pairs found.

  12. Do scale-invariant fluctuations imply the breaking of de Sitter invariance?

    NASA Astrophysics Data System (ADS)

    Youssef, A.

    2013-01-01

    The quantization of the massless minimally coupled (mmc) scalar field in de Sitter spacetime is known to be a non-trivial problem due to the appearance of strong infrared (IR) effects. In particular, the scale-invariance of the CMB power-spectrum - certainly one of the most successful predictions of modern cosmology - is widely believed to be inconsistent with a de Sitter invariant mmc two-point function. Using a Cesaro-summability technique to properly define an otherwise divergent Fourier transform, we show in this Letter that de Sitter symmetry breaking is not a necessary consequence of the scale-invariant fluctuation spectrum. We also generalize our result to the tachyonic scalar fields, i.e. the discrete series of representations of the de Sitter group, that suffer from similar strong IR effects.

  13. High Efficiency Hydrodynamic DNA Fragmentation in a Bubbling System

    PubMed Central

    Li, Lanhui; Jin, Mingliang; Sun, Chenglong; Wang, Xiaoxue; Xie, Shuting; Zhou, Guofu; van den Berg, Albert; Eijkel, Jan C. T.; Shui, Lingling

    2017-01-01

    DNA fragmentation down to a precise fragment size is important for biomedical applications, disease determination, gene therapy and shotgun sequencing. In this work, a cheap, easy to operate and high efficiency DNA fragmentation method is demonstrated based on hydrodynamic shearing in a bubbling system. We expect that hydrodynamic forces generated during the bubbling process shear the DNA molecules, extending and breaking them at the points where shearing forces are larger than the strength of the phosphate backbone. Factors of applied pressure, bubbling time and temperature have been investigated. Genomic DNA could be fragmented down to controllable 1–10 Kbp fragment lengths with a yield of 75.30–91.60%. We demonstrate that the ends of the genomic DNAs generated from hydrodynamic shearing can be ligated by T4 ligase and the fragmented DNAs can be used as templates for polymerase chain reaction. Therefore, in the bubbling system, DNAs could be hydrodynamically sheared to achieve smaller pieces in dsDNAs available for further processes. It could potentially serve as a DNA sample pretreatment technique in the future. PMID:28098208

  14. High Efficiency Hydrodynamic DNA Fragmentation in a Bubbling System

    NASA Astrophysics Data System (ADS)

    Li, Lanhui; Jin, Mingliang; Sun, Chenglong; Wang, Xiaoxue; Xie, Shuting; Zhou, Guofu; van den Berg, Albert; Eijkel, Jan C. T.; Shui, Lingling

    2017-01-01

    DNA fragmentation down to a precise fragment size is important for biomedical applications, disease determination, gene therapy and shotgun sequencing. In this work, a cheap, easy to operate and high efficiency DNA fragmentation method is demonstrated based on hydrodynamic shearing in a bubbling system. We expect that hydrodynamic forces generated during the bubbling process shear the DNA molecules, extending and breaking them at the points where shearing forces are larger than the strength of the phosphate backbone. Factors of applied pressure, bubbling time and temperature have been investigated. Genomic DNA could be fragmented down to controllable 1–10 Kbp fragment lengths with a yield of 75.30–91.60%. We demonstrate that the ends of the genomic DNAs generated from hydrodynamic shearing can be ligated by T4 ligase and the fragmented DNAs can be used as templates for polymerase chain reaction. Therefore, in the bubbling system, DNAs could be hydrodynamically sheared to achieve smaller pieces in dsDNAs available for further processes. It could potentially serve as a DNA sample pretreatment technique in the future.

  15. High Efficiency Hydrodynamic DNA Fragmentation in a Bubbling System.

    PubMed

    Li, Lanhui; Jin, Mingliang; Sun, Chenglong; Wang, Xiaoxue; Xie, Shuting; Zhou, Guofu; van den Berg, Albert; Eijkel, Jan C T; Shui, Lingling

    2017-01-18

    DNA fragmentation down to a precise fragment size is important for biomedical applications, disease determination, gene therapy and shotgun sequencing. In this work, a cheap, easy to operate and high efficiency DNA fragmentation method is demonstrated based on hydrodynamic shearing in a bubbling system. We expect that hydrodynamic forces generated during the bubbling process shear the DNA molecules, extending and breaking them at the points where shearing forces are larger than the strength of the phosphate backbone. Factors of applied pressure, bubbling time and temperature have been investigated. Genomic DNA could be fragmented down to controllable 1-10 Kbp fragment lengths with a yield of 75.30-91.60%. We demonstrate that the ends of the genomic DNAs generated from hydrodynamic shearing can be ligated by T4 ligase and the fragmented DNAs can be used as templates for polymerase chain reaction. Therefore, in the bubbling system, DNAs could be hydrodynamically sheared to achieve smaller pieces in dsDNAs available for further processes. It could potentially serve as a DNA sample pretreatment technique in the future.

  16. Nonsinglet kaon fragmentation function from e{sup +}e{sup -} kaon production

    SciTech Connect

    Albino, Simon; Christova, Ekaterina

    2010-05-01

    We perform fits to the available charged and neutral kaon-production data in e{sup +}+e{sup -{yields}}K+X, K=K{sup {+-},} and K{sub S}{sup 0}, and determine the nonsinglet combination of kaon fragmentation functions D{sub u}{sup K{+-}-}D{sub d}{sup K{+-}}in a model independent way and without any correlations to the other fragmentation functions. Only nuclear isospin invariance is assumed. Working with nonsinglets allows us to include the data at very low momentum fractions, which have so far been excluded in global fits, and to perform a first next-next-to leading order fit to fragmentation functions. We find that the kaon nonsinglet fragmentation function at large z is larger than that obtained by the other collaborations from global fit analysis and differs significantly at low z.

  17. Conservation law for massive scale-invariant photons in Weyl-invariant gravity

    NASA Astrophysics Data System (ADS)

    Shukla, Aradhya; Abhinav, Kumar; Panigrahi, Prasanta K.

    2016-12-01

    It is demonstrated that a Stückelberg-type gauge theory, coupled to the scalar-tensor theory of gravity, is invariant under both gauge and Weyl transformations. Unlike the pure Stückelberg theory, this coupled Lagrangian has a genuine Weyl symmetry, with a non-vanishing current. The above is true in the Jordan frame, whereas in the Einstein frame, the same theory manifests as Proca theory in presence of pure gravity. It is found that broken scale invariance leads to simultaneous spontaneous breaking of the gauge symmetry.

  18. Driven fragmentation of granular gases.

    PubMed

    Cruz Hidalgo, Raúl; Pagonabarraga, Ignacio

    2008-06-01

    The dynamics of homogeneously heated granular gases which fragment due to particle collisions is analyzed. We introduce a kinetic model which accounts for correlations induced at the grain collisions and analyze both the kinetics and relevant distribution functions these systems develop. The work combines analytical and numerical studies based on direct simulation Monte Carlo calculations. A broad family of fragmentation probabilities is considered, and its implications for the system kinetics are discussed. We show that generically these driven materials evolve asymptotically into a dynamical scaling regime. If the fragmentation probability tends to a constant, the grain number diverges at a finite time, leading to a shattering singularity. If the fragmentation probability vanishes, then the number of grains grows monotonously as a power law. We consider different homogeneous thermostats and show that the kinetics of these systems depends weakly on both the grain inelasticity and driving. We observe that fragmentation plays a relevant role in the shape of the velocity distribution of the particles. When the fragmentation is driven by local stochastic events, the long velocity tail is essentially exponential independently of the heating frequency and the breaking rule. However, for a Lowe-Andersen thermostat, numerical evidence strongly supports the conjecture that the scaled velocity distribution follows a generalized exponential behavior f(c) approximately exp(-cn) , with n approximately 1.2 , regarding less the fragmentation mechanisms.

  19. Transformation invariant on-line target recognition.

    PubMed

    Iftekharuddin, Khan M

    2011-06-01

    Transformation invariant automatic target recognition (ATR) has been an active research area due to its widespread applications in defense, robotics, medical imaging and geographic scene analysis. The primary goal for this paper is to obtain an on-line ATR system for targets in presence of image transformations, such as rotation, translation, scale and occlusion as well as resolution changes. We investigate biologically inspired adaptive critic design (ACD) neural network (NN) models for on-line learning of such transformations. We further exploit reinforcement learning (RL) in ACD framework to obtain transformation invariant ATR. We exploit two ACD designs, such as heuristic dynamic programming (HDP) and dual heuristic dynamic programming (DHP) to obtain transformation invariant ATR. We obtain extensive statistical evaluations of proposed on-line ATR networks using both simulated image transformations and real benchmark facial image database, UMIST, with pose variations. Our simulations show promising results for learning transformations in simulated images and authenticating out-of plane rotated face images. Comparing the two on-line ATR designs, HDP outperforms DHP in learning capability and robustness and is more tolerant to noise. The computational time involved in HDP is also less than that of DHP. On the other hand, DHP achieves a 100% success rate more frequently than HDP for individual targets, and the residual critic error in DHP is generally smaller than that of HDP. Mathematical analyses of both our RL-based on-line ATR designs are also obtained to provide a sufficient condition for asymptotic convergence in a statistical average sense.

  20. Improving fragmentation of poorly fragmenting peptides and phosphopeptides during collision-induced dissociation by malondialdehyde modification of arginine residues.

    PubMed

    Leitner, Alexander; Foettinger, Alexandra; Lindner, Wolfgang

    2007-07-01

    Despite significant technological and methodological advancements in peptide sequencing by mass spectrometry, analyzing peptides that exhibit only poor fragmentation upon collision-induced dissociation (CID) remains a challenge. A major cause for unfavorable fragmentation is insufficient proton 'mobility' due to charge localization at strongly basic sites, in particular, the guanidine group of arginine. We have recently demonstrated that the conversion of the guanidine group of the arginine side chain by malondialdehyde (MDA) is a convenient tool to reduce the basicity of arginine residues and can have beneficial effects for peptide fragmentation. In the present work, we have focused on peptides that typically yield incomplete sequence information in CID-MS/MS experiments. Energy-resolved tandem MS experiments were carried out on angiotensins and arginine-containing phosphopeptides to study in detail the influence of the modification step on the fragmentation process. MDA modification dramatically improved the fragmentation behavior of peptides that exhibited only one or two dominant cleavages in their unmodified form. Neutral loss of phosphoric acid from phosphopeptides carrying phosphoserine and threonine residues was significantly reduced in favor of a higher abundance of fragment ions. Complementary experiments were carried out on three different instrumental platforms (triple-quadrupole, 3D ion trap, quadrupole-linear ion trap hybrid) to ascertain that the observation is a general effect.

  1. Native-state hydrogen-exchange studies of a fragment complex can provide structural information about the isolated fragments

    PubMed Central

    Chakshusmathi, G.; Ratnaparkhi, Girish S.; Madhu, P. K.; Varadarajan, R.

    1999-01-01

    Ordered protein complexes are often formed from partially ordered fragments that are difficult to structurally characterize by conventional NMR and crystallographic techniques. We show that concentration-dependent hydrogen exchange studies of a fragment complex can provide structural information about the solution structures of the isolated fragments. This general methodology can be applied to any bimolecular or multimeric system. The experimental system used here consists of Ribonuclease S, a complex of two fragments of Ribonuclease A. Ribonuclease S and Ribonuclease A have identical three-dimensional structures but exhibit significant differences in their dynamics and stability. We show that the apparent large dynamic differences between Ribonuclease A and Ribonuclease S are caused by small amounts of free fragments in equilibrium with the folded complex, and that amide exchange rates in Ribonuclease S can be used to determine corresponding rates in the isolated fragments. The studies suggest that folded RNase A and the RNase S complex exhibit very similar dynamic behavior. Thus cleavage of a protein chain at a single site need not be accompanied by a large increase in flexibility of the complex relative to that of the uncleaved protein. PMID:10393919

  2. A Note on Invariant Temporal Functions

    NASA Astrophysics Data System (ADS)

    Müller, Olaf

    2016-07-01

    The purpose of this article is to present a result on the existence of Cauchy temporal functions invariant by the action of a compact group of conformal transformations in arbitrary globally hyperbolic manifolds. Moreover, the previous results about the existence of Cauchy temporal functions with additional properties on arbitrary globally hyperbolic manifolds are unified in a very general theorem. To make the article more accessible for non-experts, and in the lack of an appropriate single reference for the Lorentzian geometry background of the result, the latter is provided in an introductory section.

  3. Light-bending tests of Lorentz invariance

    SciTech Connect

    Tso, Rhondale; Bailey, Quentin G.

    2011-10-15

    Classical light-bending is investigated for weak gravitational fields in the presence of hypothetical local Lorentz violation. Using an effective field theory framework that describes general deviations from local Lorentz invariance, we derive a modified deflection angle for light passing near a massive body. The results include anisotropic effects not present for spherical sources in General Relativity as well as Weak Equivalence Principle violation. We develop an expression for the relative deflection of two distant stars that can be used to analyze data in past and future solar-system observations. The measurement sensitivities of such tests to coefficients for Lorentz violation are discussed.

  4. Visual Distinctness Determined by Partially Invariant Features

    DTIC Science & Technology

    2000-03-01

    DISTINCTNESS DETERMINED BY PARTIALLY INVARIANT FEATURES. J.A. Garcia, J. Fdez-Valdivia Departamento de Ciencias de la Computacion e I.A. Univ. de Granada...E.T.S. de Ingenieria Informatica. 18071 Granada. Spain E-mail: jagsadecsai.ugr.es, J.Fdez-Valdivia@decsai.ugr.es Xose R. Fdez-Vidal Departamento de... Fisica Aplicada. Univ. de Santiago de Compostela. Facultad de Fisica . 15706 Santiago de Compostela. Spain E-mail: faxose@usc.es Rosa Rodriguez-Sanchez

  5. Gauge invariant actions for string models

    SciTech Connect

    Banks, T.

    1986-06-01

    String models of unified interactions are elegant sets of Feynman rules for the scattering of gravitons, gauge bosons, and a host of massive excitations. The purpose of these lectures is to describe the progress towards a nonperturbative formulation of the theory. Such a formulation should make the geometrical meaning of string theory manifest and explain the many ''miracles'' exhibited by the string Feynman rules. There are some new results on gauge invariant observables, on the cosmological constant, and on the symmetries of interacting string field theory. 49 refs.

  6. Thermodynamic Entropy as a Noether Invariant.

    PubMed

    Sasa, Shin-Ichi; Yokokura, Yuki

    2016-04-08

    We study a classical many-particle system with an external control represented by a time-dependent extensive parameter in a Lagrangian. We show that thermodynamic entropy of the system is uniquely characterized as the Noether invariant associated with a symmetry for an infinitesimal nonuniform time translation t→t+ηℏβ, where η is a small parameter, ℏ is the Planck constant, β is the inverse temperature that depends on the energy and control parameter, and trajectories in the phase space are restricted to those consistent with quasistatic processes in thermodynamics.

  7. Thermodynamic Entropy as a Noether Invariant

    NASA Astrophysics Data System (ADS)

    Sasa, Shin-ichi; Yokokura, Yuki

    2016-04-01

    We study a classical many-particle system with an external control represented by a time-dependent extensive parameter in a Lagrangian. We show that thermodynamic entropy of the system is uniquely characterized as the Noether invariant associated with a symmetry for an infinitesimal nonuniform time translation t →t +η ℏβ , where η is a small parameter, ℏ is the Planck constant, β is the inverse temperature that depends on the energy and control parameter, and trajectories in the phase space are restricted to those consistent with quasistatic processes in thermodynamics.

  8. Invariant mass spectroscopy of halo nuclei

    SciTech Connect

    Nakamura, Takashi

    2008-11-11

    We have applied the invariant mass spectroscopy to explore the low-lying exited states of halo nuclei at intermediate energies around 70 MeV/nucleon at RIKEN. As examples, we show here the results of Coulomb breakup study for {sup 11}Li using the Pb target, as well as breakup reactions of {sup 14}Be with p and C targets. The former study revealed a strong Coulomb breakup cross section reflecting the large enhancement of E1 strength at low excitation energies (soft E1 excitation). The latter revealed the observation of the first 2{sup +} state in {sup 14}Be.

  9. Parabolic Refined Invariants and Macdonald Polynomials

    NASA Astrophysics Data System (ADS)

    Chuang, Wu-yen; Diaconescu, Duiliu-Emanuel; Donagi, Ron; Pantev, Tony

    2015-05-01

    A string theoretic derivation is given for the conjecture of Hausel, Letellier and Rodriguez-Villegas on the cohomology of character varieties with marked points. Their formula is identified with a refined BPS expansion in the stable pair theory of a local root stack, generalizing previous work of the first two authors in collaboration with Pan. Haiman's geometric construction for Macdonald polynomials is shown to emerge naturally in this context via geometric engineering. In particular this yields a new conjectural relation between Macdonald polynomials and refined local orbifold curve counting invariants. The string theoretic approach also leads to a new spectral cover construction for parabolic Higgs bundles in terms of holomorphic symplectic orbifolds.

  10. Origin of gauge invariance in string theory

    NASA Technical Reports Server (NTRS)

    Horowitz, G. T.; Strominger, A.

    1986-01-01

    A first quantization of the space-time embedding Chi exp mu and the world-sheet metric rho of the open bosonic string. The world-sheet metric rho decouples from S-matrix elements in 26 dimensions. This formulation of the theory naturally includes 26-dimensional gauge transformations. The gauge invariance of S-matrix elements is a direct consequence of the decoupling of rho. Second quantization leads to a string field Phi(Chi exp mu, rho) with a gauge-covariant equation of motion.

  11. Superluminality in dilatationally invariant generalized Galileon theories

    NASA Astrophysics Data System (ADS)

    Kolevatov, R. S.

    2015-12-01

    We consider small perturbations about homogeneous backgrounds in dilatationally invariant Galileon models. The issues we address are stability (absence of ghosts and gradient instabilities) and superluminality. We show that in the Minkowski background, it is possible to construct the Lagrangian in such a way that any homogeneous Galileon background solution is stable and small perturbations about it are subluminal. On the other hand, in the case of Friedmann-Lemaitre-Robertson-Walker (FLRW) backgrounds, for any Lagrangian functions there exist homogeneous background solutions to the Galileon equation of motion and time dependence of the scale factor, such that the stability conditions are satisfied, but the Galileon perturbations propagate with superluminal speed.

  12. Dijet invariant mass spectrum at CDF

    SciTech Connect

    Incagli, M. )

    1992-11-01

    A summary of QCD results obtained using the dijet invariant mass spectrum d[sigma]/dM[sub jj] is presented. The spectrum is compared with QCD Leader Order and with the recently published Next to Leading Order calculations. A limit on the scale of an eventual quark compositness can be set at [Lambda]=1300 GeV. Limits on the production of new particles, decaying hadronically, are presented, too. Axigluons are ruled out in the mass range [240, 640] GeV, for a theory with N=10 strong interacting fermions, and in the two windows [260, 280] GeV and [450, 550] GeV, for N=20.

  13. Higher helicity invariants and solar dynamo

    NASA Astrophysics Data System (ADS)

    Sokolov, D. D.; Illarionov, E. A.; Akhmet'ev, P. M.

    2017-01-01

    Modern models of nonlinear dynamo saturation in celestial bodies (specifically, on the Sun) are largely based on the consideration of the balance of magnetic helicity. This physical variable has also a topological meaning: it is associated with the linking coefficient of magnetic tubes. In addition to magnetic helicity, magnetohydrodynamics has a number of topological integrals of motion (the so-called higher helicity moments). We have compared these invariants with magnetic helicity properties and concluded that they can hardly serve as nonlinear constraints on dynamo action.

  14. Are there p-adic knot invariants?

    NASA Astrophysics Data System (ADS)

    Morozov, A. Yu.

    2016-04-01

    We suggest using the Hall-Littlewood version of the Rosso-Jones formula to define the germs of p-adic HOMFLY-PT polynomials for torus knots [ m, n] as coefficients of superpolynomials in a q-expansion. In this form, they have at least the [ m, n] ↔ [ n, m] topological invariance. This opens a new possibility to interpret superpolynomials as p-adic deformations of HOMFLY polynomials and poses a question of generalizing to other knot families, which is a substantial problem for several branches of modern theory.

  15. Gauge Invariance of Thermal Transport Coefficients

    NASA Astrophysics Data System (ADS)

    Ercole, Loris; Marcolongo, Aris; Umari, Paolo; Baroni, Stefano

    2016-10-01

    Thermal transport coefficients are independent of the specific microscopic expression for the energy density and current from which they can be derived through the Green-Kubo formula. We discuss this independence in terms of a kind of gauge invariance resulting from energy conservation and extensivity, and demonstrate it numerically for a Lennard-Jones fluid, where different forms of the microscopic energy density lead to different time correlation functions for the heat flux, all of them, however, resulting in the same value for the thermal conductivity.

  16. 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.

  17. Computational and Experimental Determination of Fragmentation for Naturally Fragmenting Warheads

    DTIC Science & Technology

    1981-05-01

    Table Page I Chemical analysis of Armco iron and HF-I steel ....................... 3 2 Summary of tensile-pull measurements for transverse-direction...ntered) REPORT DOCUMENTATION PAGE - E-EFORE COMTLETING FORM I REPORT NUMBER 2 GOVT ACCESSION NO. 3 RECIPIENT’S CATALOG NUMBERNSWC TR 80-238 4 TITLE (and...Sulbtitle) S TYPE OF REPORT & PERIOD COVERED COMPUTATIONAL AND EXPERIMENTAL 1 Final DETERMINATION OF FRAGMENTATION FOR NATURALLY FRAGMENTING WARHEADS

  18. Antigen specificity of invariant natural killer T-cells.

    PubMed

    Birkholz, Alysia M; Kronenberg, Mitchell

    2015-12-01

    Natural killer T-cells, with an invariant T-cell antigen receptor α-chain (iNKT cells), are unique and conserved subset of lymphocytes capable of altering the immune system through their rapid and potent cytokine responses. They are reactive to lipid antigens presented by the CD1d molecule, an antigen-presenting molecule that is not highly polymorphic. iNKT cell responses frequently involve mixtures of cytokines that work against each other, and therefore attempts are underway to develop synthetic antigens that elicit only strong interferon-gamma (IFNγ) or only strong interleukin-4 responses but not both. Strong IFNγ responses may correlate with tighter binding to CD1d and prolonged stimulation of iNKT cells, and this may be useful for vaccine adjuvants and for stimulating anti-tumor responses. iNKT cells are self-reactive although the structure of the endogenous antigen is controversial. By contrast, bacterial and fungal lipids that engage the T-cell receptor and activate IFNγ from iNKT cells have been identified from both pathogenic and commensal organisms and the responses are in some cases highly protective from pathogens in mice. It is possible that the expanding knowledge of iNKT cell antigens and iNKT cell activation will provide the basis for therapies for patients suffering from infectious and immune diseases and cancer.

  19. Sequence-specific fragmentation of matrix-assisted laser-desorbed protein/peptide ions.

    PubMed

    Brown, R S; Lennon, J J

    1995-11-01

    By utilizing delayed pulsed ion extraction of ions generated via the matrix-assisted laser desorption/ionization (MALDI) technique, fast (< 320 ns) metastable ion fragmentation is observed for both peptide and protein analytes in the ion source of a linear time-of-flight mass spectrometer. Small peptides such as the oxidized B chain of bovine insulin exhibit fragmentation at the amide linking bond between peptide residues. Overlapping sequence information is provided by fragmentation from both the C- and N-terminal ends of the peptide (cn-, yn-, and z*n-type fragment ions). Larger proteins can also exhibit a wealth of sequence specific fragment ions in favorable cases. One example is cytochrome c, which undergoes substantial (approximately 80%) fast fragmentation at the amide bonds along the amino acid backbone of the protein. Only amide bond cleavages initiating from the C-terminal end (cn fragments) are observed. The observed fragmentation pattern provides a significant amount of potential sequence information for these molecules. External mass calibration of the intact protonated molecular ions is demonstrated with mass accuracies typically around 100 ppm. Mass accuracies for the observed fragment ions ranged from +/- 0.20 Da for the smaller peptides studied (i.e., oxidized B chain of bovine insulin) to +/- 0.38 Da for the largest protein studied (cytochrome c), based upon the known sequences.

  20. Depleted Uranium Test Range Fragment Reclamation

    DTIC Science & Technology

    1982-07-01

    fragment drying was necessary in order to obtain adequate vacuum levels in the VIR furnaces . e. Vacuujm Induction Remelting Fragments and Casting...Acid Pickle and Water Rinse .... ........ 2 d. Drying the Fragments .... ............... 2 e. Vacuum Induction Remelting Fragments and Casting...feasibility of reclaiming test range fragments by vacuum induction remelting (VIR). The technical direction of Phase 11 was highly dependent upon the