Science.gov

Sample records for induces loop structures

  1. Crowding-Induced Structural Alterations of Random-Loop Chromosome Model

    NASA Astrophysics Data System (ADS)

    Kim, Jun Soo; Backman, Vadim; Szleifer, Igal

    2011-04-01

    We investigate structural alterations of random-loop polymers due to changes in the crowding condition, as a model to study environmental effects on the structure of chromosome subcompartments. The polymer structure is changed in a nonmonotonic fashion with an increasing density of crowders: condensed at small volume fractions; decondensed at high crowding volume fractions. The nonmonotonic behavior is a manifestation of the nontrivial distance dependence of the depletion interactions. We also show that crowding-induced structural alterations affect the access of binding proteins to the surface of polymer segments and are distinguished from structural changes due to the increased number of specific polymer loops.

  2. Human lactoferricin derived di-peptides deploying loop structures induce apoptosis specifically in cancer cells through targeting membranous phosphatidylserine.

    PubMed

    Riedl, Sabrina; Leber, Regina; Rinner, Beate; Schaider, Helmut; Lohner, Karl; Zweytick, Dagmar

    2015-11-01

    Host defense-derived peptides have emerged as a novel strategy for the development of alternative anticancer therapies. In this study we report on characteristic features of human lactoferricin (hLFcin) derivatives which facilitate specific killing of cancer cells of melanoma, glioblastoma and rhabdomyosarcoma compared with non-specific derivatives and the synthetic peptide RW-AH. Changes in amino acid sequence of hLFcin providing 9-11 amino acids stretched derivatives LF11-316, -318 and -322 only yielded low antitumor activity. However, the addition of the repeat (di-peptide) and the retro-repeat (di-retro-peptide) sequences highly improved cancer cell toxicity up to 100% at 20 μM peptide concentration. Compared to the complete parent sequence hLFcin the derivatives showed toxicity on the melanoma cell line A375 increased by 10-fold and on the glioblastoma cell line U-87mg by 2-3-fold. Reduced killing velocity, apoptotic blebbing, activation of caspase 3/7 and formation of apoptotic DNA fragments proved that the active and cancer selective peptides, e.g. R-DIM-P-LF11-322, trigger apoptosis, whereas highly active, though non-selective peptides, such as DIM-LF11-318 and RW-AH seem to kill rapidly via necrosis inducing membrane lyses. Structural studies revealed specific toxicity on cancer cells by peptide derivatives with loop structures, whereas non-specific peptides comprised α-helical structures without loop. Model studies with the cancer membrane mimic phosphatidylserine (PS) gave strong evidence that PS only exposed by cancer cells is an important target for specific hLFcin derivatives. Other negatively charged membrane exposed molecules as sialic acid, heparan and chondroitin sulfate were shown to have minor impact on peptide activity.

  3. Involvement of the V1/V2 variable loop structure in the exposure of human immunodeficiency virus type 1 gp120 epitopes induced by receptor binding.

    PubMed Central

    Wyatt, R; Moore, J; Accola, M; Desjardin, E; Robinson, J; Sodroski, J

    1995-01-01

    The binding of human immunodeficiency virus type 1 (HIV-1) to the cellular receptor CD4 has been suggested to induce conformational changes in the viral envelope glycoproteins that promote virus entry. Conserved, discontinuous epitopes on the HIV-1 gp120 glycoprotein recognized by the 17b, 48d, and A32 antibodies are preferentially exposed upon the binding of soluble CD4 (sCD4). The binding of the 17b and 48d antibodies to the gp120 glycoprotein can also be enhanced by the binding of the A32 antibody. Here we constructed HIV-1 gp120 mutants in which the variable segments of the V1/V2 and V3 structures were deleted, individually or in combination, while the 17b, 48d, and A32 epitopes were retained. The effects of the variable loop deletions on the function of the HIV-1 envelope glycoproteins and on the exposure of epitopes induced by sCD4 or A32 binding to the monomeric gp120 glycoprotein were examined. The variable-loop-deleted envelope glycoproteins were able to mediate virus entry, albeit at lower efficiencies than those of the wild-type glycoproteins. Thus, the V1/V2 and V3 variable sequences contribute to the efficiency of HIV-1 entry but are not absolutely required for the process. Neither the V1/V2 nor V3 loops were necessary for the increase in exposure of the 17b/48d epitopes induced by binding of the A32 monoclonal antibody. By contrast, induction of the 17b, 48d, and A32 epitopes by sCD4 binding apparently involves a movement of the V1/V2 loops, which in the absence of CD4 partially mask these epitopes on the native gp120 monomer. The results obtained with a mutant glycoprotein containing a deletion of the V1 loop alone indicated that the contribution of the V2 loop to these phenomena was more significant than that of the V1 sequences. These results suggest that the V1/V2 loops, which have been previously implicated in CD4-modulated, postattachment steps in HIV-1 entry, contribute to CD4-induced gp120 conformational changes detected by the 17b, 48d, and A

  4. Detection and Characterization of R Loop Structures.

    PubMed

    Boque-Sastre, Raquel; Soler, Marta; Guil, Sonia

    2017-01-01

    R loops are special three stranded nucleic acid structures that comprise a nascent RNA hybridized with the DNA template strand, leaving a non-template DNA single-stranded. More specifically, R loops form in vivo as G-rich RNA transcripts invade the DNA duplex and anneal to the template strand to generate an RNA:DNA hybrid, leaving the non-template, G-rich DNA strand in a largely single-stranded conformation (Aguilera and Garcia-Muse, Mol Cell 46:115-124, 2012).DNA-RNA hybrids are a natural occurrence within eukaryotic cells, with levels of these hybrids increasing at sites with high transcriptional activity, such as during transcription initiation, repression, and elongation. RNA-DNA hybrids influence genomic instability, and growing evidence points to an important role for R loops in active gene expression regulation (Ginno et al., Mol Cell 45, 814-825, 2012; Sun et al., Science 340: 619-621, 2013; Bhatia et al., Nature 511, 362-365, 2014). Analysis of the occurrence of such structures is therefore of increasing relevance and herein we describe methods for the in vivo and in vitro identification and characterization of R loops in mammalian systems.R loops (DNA:RNA hybrids and the associated single-stranded DNA) have been traditionally associated with threats to genome integrity, making some regions of the genome more prone to DNA-damaging and mutagenic agents. Initially considered to be rare byproducts of transcription, over the last decade accumulating evidence has pointed to a new view in which R loops form more frequently than previously thought. The R loop field has become an increasingly expanded area of research, placing these structures as a major threat to genome stability but also as potential regulators of gene expression. Special interest has arisen as they have also been linked to a variety of diseases, including neurological disorders and cancer, positioning them as potential therapeutic targets [5].

  5. RNase H enables efficient repair of R-loop induced DNA damage

    PubMed Central

    Amon, Jeremy D; Koshland, Douglas

    2016-01-01

    R-loops, three-stranded structures that form when transcripts hybridize to chromosomal DNA, are potent agents of genome instability. This instability has been explained by the ability of R-loops to induce DNA damage. Here, we show that persistent R-loops also compromise DNA repair. Depleting endogenous RNase H activity impairs R-loop removal in Saccharomyces cerevisiae, causing DNA damage that occurs preferentially in the repetitive ribosomal DNA locus (rDNA). We analyzed the repair kinetics of this damage and identified mutants that modulate repair. We present a model that the persistence of R-loops at sites of DNA damage induces repair by break-induced replication (BIR). This R-loop induced BIR is particularly susceptible to the formation of lethal repair intermediates at the rDNA because of a barrier imposed by RNA polymerase I. DOI: http://dx.doi.org/10.7554/eLife.20533.001 PMID:27938663

  6. Sequence–structure relationships in RNA loops: establishing the basis for loop homology modeling

    PubMed Central

    Schudoma, Christian; May, Patrick; Nikiforova, Viktoria; Walther, Dirk

    2010-01-01

    The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence–structure relationships in loops. Loops differing by <25% in sequence identity fold into very similar structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts. PMID:19923230

  7. Fast loop modeling for protein structures

    NASA Astrophysics Data System (ADS)

    Zhang, Jiong; Nguyen, Son; Shang, Yi; Xu, Dong; Kosztin, Ioan

    2015-03-01

    X-ray crystallography is the main method for determining 3D protein structures. In many cases, however, flexible loop regions of proteins cannot be resolved by this approach. This leads to incomplete structures in the protein data bank, preventing further computational study and analysis of these proteins. For instance, all-atom molecular dynamics (MD) simulation studies of structure-function relationship require complete protein structures. To address this shortcoming, we have developed and implemented an efficient computational method for building missing protein loops. The method is database driven and uses deep learning and multi-dimensional scaling algorithms. We have implemented the method as a simple stand-alone program, which can also be used as a plugin in existing molecular modeling software, e.g., VMD. The quality and stability of the generated structures are assessed and tested via energy scoring functions and by equilibrium MD simulations. The proposed method can also be used in template-based protein structure prediction. Work supported by the National Institutes of Health [R01 GM100701]. Computer time was provided by the University of Missouri Bioinformatics Consortium.

  8. The Fundamental Structure of Coronal Loops

    NASA Technical Reports Server (NTRS)

    Winebarger, Amy; Warren, Harry; Cirtain, Jonathan; Kobayashi, Ken; Korreck, Kelly; Golub, Leon; Kuzin, Sergey; Walsh, Robert; DePontieu, Bart; Title, Alan; Weber, Mark

    2012-01-01

    During the past ten years, solar physicists have attempted to infer the coronal heating mechanism by comparing observations of coronal loops with hydrodynamic model predictions. These comparisons often used the addition of sub ]resolution strands to explain the observed loop properties. On July 11, 2012, the High Resolution Coronal Imager (Hi ]C) was launched on a sounding rocket. This instrument obtained images of the solar corona was 0.2 ]0.3'' resolution in a narrowband EUV filter centered around 193 Angstroms. In this talk, we will compare these high resolution images to simultaneous density measurements obtained with the Extreme Ultraviolet Imaging Spectrograph (EIS) on Hinode to determine whether the structures observed with Hi ]C are resolved.

  9. Looping charged elastic rods: applications to protein-induced DNA loop formation.

    PubMed

    Cherstvy, A G

    2011-01-01

    We analyze looping of thin charged elastic filaments under applied torques and end forces, using the solution of linear elasticity theory equations. In application to DNA, we account for its polyelectrolyte character and charge renormalization, calculating electrostatic energies stored in the loops. We argue that the standard theory of electrostatic persistence is only valid when the loop's radius of curvature and close-contact distance are much larger than the Debye screening length. We predict that larger twist rates are required to trigger looping of charged rods as compared with neutral ones. We then analyze loop shapes formed on charged filaments of finite length, mimicking DNA looping by proteins with two DNA-binding domains. We find optimal loop shapes at different salt amounts, minimizing the sum of DNA elastic, DNA electrostatic, and protein elastic energies. We implement a simple model where intercharge repulsions do not affect the loop shape directly but can choose the energy-optimized shape from the allowed loop types. At low salt concentrations more open loops are favored due to enhanced repulsion of DNA charges, consistent with the results of computer simulations on formation of DNA loops by lac repressor. Then, we model the precise geometry of DNA binding by the lac tetramer and explore loop shapes, varying the confined DNA length and protein opening angle. The characteristics of complexes obtained, such as the total loop energy, stretching forces required to maintain its shape, and the reduction of electrostatic energy with increment of salt, are in good agreement with the outcomes of more elaborate numerical calculations for lac-repressor-induced DNA looping.

  10. Interferon-inducible ribonuclease ISG20 inhibits hepatitis B virus replication through directly binding to the epsilon stem-loop structure of viral RNA.

    PubMed

    Liu, Yuanjie; Nie, Hui; Mao, Richeng; Mitra, Bidisha; Cai, Dawei; Yan, Ran; Guo, Ju-Tao; Block, Timothy M; Mechti, Nadir; Guo, Haitao

    2017-04-01

    Hepatitis B virus (HBV) replicates its DNA genome through reverse transcription of a viral RNA pregenome. We report herein that the interferon (IFN) stimulated exoribonuclease gene of 20 KD (ISG20) inhibits HBV replication through degradation of HBV RNA. ISG20 expression was observed at basal level and was highly upregulated upon IFN treatment in hepatocytes, and knock down of ISG20 resulted in elevation of HBV replication and attenuation of IFN-mediated antiviral effect. The sequence element conferring the susceptibility of HBV RNA to ISG20-mediated RNA degradation was mapped at the HBV RNA terminal redundant region containing epsilon (ε) stem-loop. Furthermore, ISG20-induced HBV RNA degradation relies on its ribonuclease activity, as the enzymatic inactive form ISG20D94G was unable to promote HBV RNA decay. Interestingly, ISG20D94G retained antiviral activity against HBV DNA replication by preventing pgRNA encapsidation, resulting from a consequence of ISG20-ε interaction. This interaction was further characterized by in vitro electrophoretic mobility shift assay (EMSA) and ISG20 was able to bind HBV ε directly in absence of any other cellular proteins, indicating a direct ε RNA binding capability of ISG20; however, cofactor(s) may be required for ISG20 to efficiently degrade ε. In addition, the lower stem portion of ε is the major ISG20 binding site, and the removal of 4 base pairs from the bottom portion of ε abrogated the sensitivity of HBV RNA to ISG20, suggesting that the specificity of ISG20-ε interaction relies on both RNA structure and sequence. Furthermore, the C-terminal Exonuclease III (ExoIII) domain of ISG20 was determined to be responsible for interacting with ε, as the deletion of ExoIII abolished in vitro ISG20-ε binding and intracellular HBV RNA degradation. Taken together, our study sheds light on the underlying mechanisms of IFN-mediated HBV inhibition and the antiviral mechanism of ISG20 in general.

  11. An Antibody Loop Replacement Design Feasibility Study and a Loop-Swapped Dimer Structure

    SciTech Connect

    Clark, L.; Boriack-Sjodin, P; Day, E; Eldredge, J; Fitch, C; Jarpe, M; Miller, S; Li, Y; Simon, K; van Vlijmen, H

    2009-01-01

    A design approach was taken to investigate the feasibility of replacing single complementarity determining region (CDR) antibody loops. This approach may complement simpler mutation-based strategies for rational antibody design by expanding conformation space. Enormous crystal structure diversity is available, making CDR loops logical targets for structure-based design. A detailed analysis for the L1 loop shows that each loop length takes a distinct conformation, thereby allowing control on a length scale beyond that accessible to simple mutations. The L1 loop in the anti-VLA1 antibody was replaced with the L2 loop residues longer in an attempt to add an additional hydrogen bond and fill space on the antibody-antigen interface. The designs expressed well, but failed to improve affinity. In an effort to learn more, one design was crystallized and data were collected at 1.9 {angstrom} resolution. The designed L1 loop takes the qualitatively desired conformation; confirming that loop replacement by design is feasible. The crystal structure also shows that the outermost loop (residues Leu51-Ser68) is domain swapped with another monomer. Tryptophan fluorescence measurements were used to monitor unfolding as a function of temperature and indicate that the loop involved in domain swapping does not unfold below 60C. The domain-swapping is not directly responsible for the affinity loss, but is likely a side-effect of the structural instability which may contribute to affinity loss. A second round of design was successful in eliminating the dimerization through mutation of a residue (Leu51Ser) at the joint of the domain-swapped loop.

  12. Structure Prediction of RNA Loops with a Probabilistic Approach

    PubMed Central

    Li, Jun; Zhang, Jian; Wang, Jun; Li, Wenfei; Wang, Wei

    2016-01-01

    The knowledge of the tertiary structure of RNA loops is important for understanding their functions. In this work we develop an efficient approach named RNApps, specifically designed for predicting the tertiary structure of RNA loops, including hairpin loops, internal loops, and multi-way junction loops. It includes a probabilistic coarse-grained RNA model, an all-atom statistical energy function, a sequential Monte Carlo growth algorithm, and a simulated annealing procedure. The approach is tested with a dataset including nine RNA loops, a 23S ribosomal RNA, and a large dataset containing 876 RNAs. The performance is evaluated and compared with a homology modeling based predictor and an ab initio predictor. It is found that RNApps has comparable performance with the former one and outdoes the latter in terms of structure predictions. The approach holds great promise for accurate and efficient RNA tertiary structure prediction. PMID:27494763

  13. Two-base DNA hairpin-loop structures in vivo.

    PubMed Central

    Davison, A; Leach, D R

    1994-01-01

    In vitro studies have revealed that DNA hairpin-loops usually contain four unpaired bases. However, a small subset of sequences can form two-base loops. We have previously described an in vivo assay that is sensitive to tight loop formation and have set out to test whether DNA sequences known to form two-base loops in vitro also form tight loops in vivo. It is shown that the sequences 5'dCNNG and 5'dTNNA behave as predicted if they favour two-base loop formation in vivo, a result that is consistent with previously described in vitro studies. The ability of specific DNA sequences to form tight loops in vivo has implications for their potential to form transient structures involved in gene regulation, recombination and mutagenesis. PMID:7971265

  14. Mining protein loops using a structural alphabet and statistical exceptionality

    PubMed Central

    2010-01-01

    Background Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. Results We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 Å). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a

  15. Automated event generation for loop-induced processes

    SciTech Connect

    Hirschi, Valentin; Mattelaer, Olivier

    2015-10-22

    We present the first fully automated implementation of cross-section computation and event generation for loop-induced processes. This work is integrated in the MadGraph5_aMC@NLO framework. We describe the optimisations implemented at the level of the matrix element evaluation, phase space integration and event generation allowing for the simulation of large multiplicity loop-induced processes. Along with some selected differential observables, we illustrate our results with a table showing inclusive cross-sections for all loop-induced hadronic scattering processes with up to three final states in the SM as well as for some relevant 2 → 4 processes. Furthermore, many of these are computed here for the first time.

  16. Automated event generation for loop-induced processes

    DOE PAGES

    Hirschi, Valentin; Mattelaer, Olivier

    2015-10-22

    We present the first fully automated implementation of cross-section computation and event generation for loop-induced processes. This work is integrated in the MadGraph5_aMC@NLO framework. We describe the optimisations implemented at the level of the matrix element evaluation, phase space integration and event generation allowing for the simulation of large multiplicity loop-induced processes. Along with some selected differential observables, we illustrate our results with a table showing inclusive cross-sections for all loop-induced hadronic scattering processes with up to three final states in the SM as well as for some relevant 2 → 4 processes. Furthermore, many of these are computed heremore » for the first time.« less

  17. Active region coronal loops - Structural and variability

    NASA Technical Reports Server (NTRS)

    Haisch, Bernhard M.; Strong, Keith T.; Harrison, Richard A.; Gary, G. A.

    1988-01-01

    X-ray images of a pair of active region loops are studied which show significant, short time-scale variability in the line fluxes of O VIII, Ne IX, and Mg XI and in the 3.5-11.5 keV soft X-ray bands. Vector magnetograms and high-resolution UV images were used to model the three-dimensional characteristics of the loops. X-ray light curves were generated spanning four consecutive orbits for both loops individually, and light curves of the loop tops and brightest points were also generated. The largest variations involve flux changes of up to several hundred percent on time scales of 10 minutes. No significant H-alpha flare activity is reported, and loop temperatures remain in the four to six million K range. The decay phases of the light curves indicate radiative cooling, inhibition of conduction, and some type of 'continued heating' due to ongoing, underlying activity at the microflare level.

  18. Observation of Nonlinear Looped Band Structure of Bose-Einstein condensates in an optical lattice

    NASA Astrophysics Data System (ADS)

    Goldschmidt, Elizabeth; Koller, Silvio; Brown, Roger; Wyllie, Robert; Wilson, Ryan; Porto, Trey

    2016-05-01

    We study experimentally the stability of excited, interacting states of bosons in a double-well optical lattice in regimes where the nonlinear interactions are expected to induce ``swallow-tail'' looped band structure. By carefully preparing different initial coherent states and observing their subsequent decay, we observe distinct decay rates, which provide direct evidence for multi-valued band structure. The double well lattice both stabilizes the looped band structure and allows for dynamic preparation of different initial states, including states within the loop structure. We confirm our state preparation procedure with dynamic Gross-Pitaevskii calculations. The excited loop states are found to be more stable than dynamically unstable ground states, but decay faster than expected based on a mean-field stability calculation, indicating the importance of correlations beyond a mean-field description. Now at Georgia Tech Research Institute.

  19. FINE STRUCTURES AND OVERLYING LOOPS OF CONFINED SOLAR FLARES

    SciTech Connect

    Yang, Shuhong; Zhang, Jun; Xiang, Yongyuan

    2014-10-01

    Using the Hα observations from the New Vacuum Solar Telescope at the Fuxian Solar Observatory, we focus on the fine structures of three confined flares and the issue why all the three flares are confined instead of eruptive. All the three confined flares take place successively at the same location and have similar morphologies, so can be termed homologous confined flares. In the simultaneous images obtained by the Solar Dynamics Observatory, many large-scale coronal loops above the confined flares are clearly observed in multi-wavelengths. At the pre-flare stage, two dipoles emerge near the negative sunspot, and the dipolar patches are connected by small loops appearing as arch-shaped Hα fibrils. There exists a reconnection between the small loops, and thus the Hα fibrils change their configuration. The reconnection also occurs between a set of emerging Hα fibrils and a set of pre-existing large loops, which are rooted in the negative sunspot, a nearby positive patch, and some remote positive faculae, forming a typical three-legged structure. During the flare processes, the overlying loops, some of which are tracked by activated dark materials, do not break out. These direct observations may illustrate the physical mechanism of confined flares, i.e., magnetic reconnection between the emerging loops and the pre-existing loops triggers flares and the overlying loops prevent the flares from being eruptive.

  20. Transcription-coupled nucleotide excision repair factors promote R-loop-induced genome instability.

    PubMed

    Sollier, Julie; Stork, Caroline Townsend; García-Rubio, María L; Paulsen, Renee D; Aguilera, Andrés; Cimprich, Karlene A

    2014-12-18

    R-loops, consisting of an RNA-DNA hybrid and displaced single-stranded DNA, are physiological structures that regulate various cellular processes occurring on chromatin. Intriguingly, changes in R-loop dynamics have also been associated with DNA damage accumulation and genome instability; however, the mechanisms underlying R-loop-induced DNA damage remain unknown. Here we demonstrate in human cells that R-loops induced by the absence of diverse RNA processing factors, including the RNA/DNA helicases Aquarius (AQR) and Senataxin (SETX), or by the inhibition of topoisomerase I, are actively processed into DNA double-strand breaks (DSBs) by the nucleotide excision repair endonucleases XPF and XPG. Surprisingly, DSB formation requires the transcription-coupled nucleotide excision repair (TC-NER) factor Cockayne syndrome group B (CSB), but not the global genome repair protein XPC. These findings reveal an unexpected and potentially deleterious role for TC-NER factors in driving R-loop-induced DNA damage and genome instability.

  1. Transcription-coupled nucleotide excision repair factors promote R-loop-induced genome instability

    PubMed Central

    Sollier, Julie; Stork, Caroline Townsend; García-Rubio, María L.; Paulsen, Renee D.; Aguilera, Andrés; Cimprich, Karlene A.

    2014-01-01

    Summary R-loops, consisting of an RNA-DNA hybrid and displaced single-stranded DNA, are physiological structures that regulate various cellular processes occurring on chromatin. Intriguingly, changes in R-loop dynamics have also been associated with DNA damage accumulation and genome instability, however the mechanisms underlying R-loop induced DNA damage remain unknown. Here we demonstrate in human cells that R-loops induced by the absence of diverse RNA processing factors, including the RNA/DNA helicases Aquarius (AQR) and Senataxin (SETX), or by the inhibition of topoisomerase I, are actively processed into DNA double-strand breaks (DSBs) by the nucleotide excision repair endonucleases XPF and XPG. Surprisingly, DSB formation requires the transcription-coupled nucleotide excision repair (TC-NER) factor Cockayne syndrome group B (CSB), but not the global genome repair protein XPC. These findings reveal an unexpected and potentially deleterious role for TC-NER factors in driving R-loop-induced DNA damage and genome instability. PMID:25435140

  2. LINE-OF-SIGHT SHELL STRUCTURE OF THE CYGNUS LOOP

    SciTech Connect

    Uchida, Hiroyuki; Tsunemi, Hiroshi; Katsuda, Satoru; Kimura, Masashi; Kosugi, Hiroko; Takahashi, Hiroaki

    2009-11-10

    We conducted a comprehensive study on the shell structure of the Cygnus Loop using 41 observation data obtained by the Suzaku and the XMM-Newton satellites. To investigate the detailed plasma structure of the Cygnus Loop, we divided our fields of view into 1042 box regions. From the spectral analysis, the spectra obtained from the limb of the Loop are well fitted by the single-component non-equilibrium ionization plasma model. On the other hand, the spectra obtained from the inner regions are well fitted by the two-component model. As a result, we confirmed that the low-temperature and high-temperature components originated from the surrounding interstellar matter (ISM) and the ejecta of the Loop, respectively. From the best-fit results, we showed a flux distribution of the ISM component. The distribution clearly shows the limb-brightening structure, and we found out some low-flux regions. Among them, the south blowout region has the lowest flux. We also found other large low-flux regions at slightly west and northeast from the center. We estimated the former thin shell region to be approx1.{sup 0}3 in diameter and concluded that there exists a blowout along the line of sight in addition to the south blowout. We also calculated the emission measure distribution of the ISM component and showed that the Cygnus Loop is far from the result obtained by a simple Sedov evolution model. From the results, we support that the Cygnus Loop originated from a cavity explosion. The emission measure distribution also suggests that the cavity-wall density is higher in the northeast than that in the southwest. These results suggest that the thickness of the cavity wall surrounding the Cygnus Loop is not uniform.

  3. THERMAL STRUCTURE OF CORONAL LOOPS AS SEEN WITH NORIKURA CORONAGRAPH

    SciTech Connect

    Prasad, S. Krishna; Singh, Jagdev; Ichimoto, K.

    2013-03-10

    The thermal structure of a coronal loop, both along and across the loop, is vital in determining the exact plasma heating mechanism. High-resolution spectroscopic observations of the off-limb corona were made using the 25 cm Norikura coronagraph, located at Norikura, Japan. Observations on a number of days were made simultaneously in four forbidden iron emission lines, namely, the [Fe XI] 7892 A line, the [Fe XIII] 10747 A and 10798 A lines, and the [Fe XIV] 5303 A line and on some days made only in the [Fe XI] 7892 A and [Fe X] 6374 A lines. Using temperature sensitive emission line ratios [Fe XIV] 5303 A/[Fe XIII] 10747 A and [Fe XI] 7892 A/[Fe X] 6374 A, we compute the electron temperatures along 18 different loop structures observed on different days. We find a significant negative temperature gradient in all of the structures observed in Fe XIV and Fe XIII and a positive temperature gradient in the structures observed in Fe XI and Fe X. Combining these results with the previous investigations by Singh and his collaborators, we infer that the loop tops, in general, appear hotter when observed in colder lines and colder when observed in relatively hotter lines as compared to their coronal foot points. We suggest that this contrasting trend observed in the temperature variation along the loop structures can be explained by a gradual interaction of different temperature plasma. The exact mechanism responsible for this interaction must be investigated further and has the potential to constrain loop heating models.

  4. Closed-loop control of flow-induced cavity oscillations

    NASA Astrophysics Data System (ADS)

    Song, Qi

    Flow-induced cavity oscillations are a coupled flow-acoustic problem in which the inherent closed-loop system dynamics can lead to large unsteady pressure levels in and around the cavity, resulting in both broadband noise and discrete tones. This problem exists in many practical environments, such as landing gear bays and weapon delivery systems on aircraft, and automobile sunroofs and windows. Researchers in both fluid dynamics and controls have been working on this problem for more than fifty years. This is because not only is the physical nature of this problem rich and complex, but also it has become a standard test bed for controller deign and implementation in flow control. The ultimate goal of this research is to minimize the cavity acoustic tones and the broadband noise level over a range of freestream Mach numbers. Although open-loop and closed-loop control methodologies have been explored extensively in recent years, there are still some issues that need to be studied further. For example, a low-order theoretical model suitable for controller design does not exist. Most recent flow-induced cavity models are based either on Rossiter's semi-expirical formula or a proper orthogonal decomposition (POD) based models. These models cannot be implemented in adaptive controller design directly. In addition, closed-loop control of high subsonic and supersonic flows remains an unexplored area. In order to achieve these objectives, an analytical system model is first developed in this research. This analytical model is a transfer function based model and it can be used as a potential model for controller design. Then, a MIMO system identification algorithm is derived and combined with the generalized prediction control (GPC) algorithm. The resultant integration of adaptive system ID and GPC algorithms can potentially track nonstationary cavity dynamics and reduce the flow-induced oscillations. A novel piezoelectric-driven synthetic jet actuator array is designed for

  5. Electrical resistance of complex two-dimensional structures of loops

    NASA Astrophysics Data System (ADS)

    Gomes, M. A. F.; Hora, R. R.; Brito, V. P.

    2011-06-01

    This work presents a study of the dc electrical resistance of a recently discovered hierarchical two-dimensional system which has a complex topology consisting of a distribution of disordered macroscopic loops with no characteristic size and a distribution of several types of contacts between loops. In addition to its intrinsic interest in the important context of low-dimensional systems and crumpled systems, the structures under study are of relevance in a number of areas including soft condensed matter and packing of DNA in viral capsids. In the particular case discussed here, the loops are made of layers of graphite with a height of tens of nanometers deposited on a substrate of cellulose. Experiments with these systems indicate an anomalous electrical resistance of sub-diffusive type. The results reported here are explained with scaling arguments and computer simulation. A comparison with the dc electrical properties of percolation clusters is made, and some other experimental issues as future prospects are commented.

  6. Structured Robust Loop shaping control for HIMAT System Using PSO

    NASA Astrophysics Data System (ADS)

    Kaitwanidvilai, Somyot; Jangwanitlert, Anuwat; Parnichkun, Manukid

    2009-01-01

    Robust loop shaping control is a feasible method for designing a robust controller; however, the controller designed by this method is complicated and difficult to implement practically. To overcome this problem, in this paper, a new design technique of a fixed-structure robust loop shaping controller for a highly maneuverable airplane, HIMAT, is proposed. The performance and robust stability conditions of the designed system satisfying H∞ loop shaping control are formulated as the objective function in the optimization problem. Particle Swarm Optimization (PSO) technique is adopted to solve this problem and to achieve the control parameters of the proposed controller. Simulation results demonstrate that the proposed approach is numerically efficient and leads to performance comparable to that of the other method.

  7. A conserved P-loop anchor limits the structural dynamics that mediate nucleotide dissociation in EF-Tu

    NASA Astrophysics Data System (ADS)

    Mercier, Evan; Girodat, Dylan; Wieden, Hans-Joachim

    2015-01-01

    The phosphate-binding loop (P-loop) is a conserved sequence motif found in mononucleotide-binding proteins. Little is known about the structural dynamics of this region and its contribution to the observed nucleotide binding properties. Understanding the underlying design principles is of great interest for biomolecular engineering applications. We have used rapid-kinetics measurements in vitro and molecular dynamics (MD) simulations in silico to investigate the relationship between GTP-binding properties and P-loop structural dynamics in the universally conserved Elongation Factor (EF) Tu. Analysis of wild type EF-Tu and variants with substitutions at positions in or adjacent to the P-loop revealed a correlation between P-loop flexibility and the entropy of activation for GTP dissociation. The same variants demonstrate more backbone flexibility in two N-terminal amino acids of the P-loop during force-induced EF-Tu.GTP dissociation in Steered Molecular Dynamics simulations. Amino acids Gly18 and His19 are involved in stabilizing the P-loop backbone via interactions with the adjacent helix C. We propose that these P-loop/helix C interactions function as a conserved P-loop anchoring module and identify the presence of P-loop anchors within several GTPases and ATPases suggesting their evolutionary conservation.

  8. A conserved P-loop anchor limits the structural dynamics that mediate nucleotide dissociation in EF-Tu.

    PubMed

    Mercier, Evan; Girodat, Dylan; Wieden, Hans-Joachim

    2015-01-08

    The phosphate-binding loop (P-loop) is a conserved sequence motif found in mononucleotide-binding proteins. Little is known about the structural dynamics of this region and its contribution to the observed nucleotide binding properties. Understanding the underlying design principles is of great interest for biomolecular engineering applications. We have used rapid-kinetics measurements in vitro and molecular dynamics (MD) simulations in silico to investigate the relationship between GTP-binding properties and P-loop structural dynamics in the universally conserved Elongation Factor (EF) Tu. Analysis of wild type EF-Tu and variants with substitutions at positions in or adjacent to the P-loop revealed a correlation between P-loop flexibility and the entropy of activation for GTP dissociation. The same variants demonstrate more backbone flexibility in two N-terminal amino acids of the P-loop during force-induced EF-Tu · GTP dissociation in Steered Molecular Dynamics simulations. Amino acids Gly18 and His19 are involved in stabilizing the P-loop backbone via interactions with the adjacent helix C. We propose that these P-loop/helix C interactions function as a conserved P-loop anchoring module and identify the presence of P-loop anchors within several GTPases and ATPases suggesting their evolutionary conservation.

  9. Structural studies on an internal loop from a hairpin ribozyme

    SciTech Connect

    Cai, Z.; SantaLucia, J. Jr.; Tinoco, I. Jr.

    1994-12-01

    Ribozymes, RNA enzymes, catalyze site-specific RNA cleavage and ligation reactions. We are studying the three-dimensional structure of a hairpin ribozyme derived from the minus strand of tobacco ring spot virus satellite RNA ((-)sTRSV), which has been engineering to specifically cleave the HIV-1 RNA. The minimum structure for the catalytic reaction involves a 50-nucleotide ribozyme and a 14-nucleotide substrate. The proposed secondary structure of the ribozyme-substrate complex consists of four short helices separated by two internal loops. The relatively large size (64-nucleotide) of the ribozyme-substrate complex presents formidable problems in solving the structure using NMR. Therefore we are studying smaller structural subunits of the complex. We are determining the high resolution structure of the symmetric internal loop involving the cleavage site and the flanking helices. One strand of the internal loop was selectively {sup 13}C-labeled at C8 of each purine and C6 of each pyrimidine. By using {sup 13}C-edited two-dimensional NMR, the proton NOESY spectrum was greatly simplified. This allowed unambiguous sequential proton resonance assignments along each strand. Three-dimensional {sup 1}-{sup 13}C HMQC-NOESY was used to further facilitate resonance assignments. We are also enzymatically synthesizing the entire 50-nucleotide ribozyme and will combine it with the {sup 13}C-labeled substrate. Through comparison of the NOE connectivities of the labeled nucleotides from the internal loop alone with those from the entire complex, the differences between the two structures can be elucidated.

  10. Predicting loop-helix tertiary structural contacts in RNA pseudoknots.

    PubMed

    Cao, Song; Giedroc, David P; Chen, Shi-Jie

    2010-03-01

    Tertiary interactions between loops and helical stems play critical roles in the biological function of many RNA pseudoknots. However, quantitative predictions for RNA tertiary interactions remain elusive. Here we report a statistical mechanical model for the prediction of noncanonical loop-stem base-pairing interactions in RNA pseudoknots. Central to the model is the evaluation of the conformational entropy for the pseudoknotted folds with defined loop-stem tertiary structural contacts. We develop an RNA virtual bond-based conformational model (Vfold model), which permits a rigorous computation of the conformational entropy for a given fold that contains loop-stem tertiary contacts. With the entropy parameters predicted from the Vfold model and the energy parameters for the tertiary contacts as inserted parameters, we can then predict the RNA folding thermodynamics, from which we can extract the tertiary contact thermodynamic parameters from theory-experimental comparisons. These comparisons reveal a contact enthalpy (DeltaH) of -14 kcal/mol and a contact entropy (DeltaS) of -38 cal/mol/K for a protonated C(+)*(G-C) base triple at pH 7.0, and (DeltaH = -7 kcal/mol, DeltaS = -19 cal/mol/K) for an unprotonated base triple. Tests of the model for a series of pseudoknots show good theory-experiment agreement. Based on the extracted energy parameters for the tertiary structural contacts, the model enables predictions for the structure, stability, and folding pathways for RNA pseudoknots with known or postulated loop-stem tertiary contacts from the nucleotide sequence alone.

  11. Leading logarithmic contribution to the second-order lamb shift induced by the loop-after-loop diagram.

    PubMed

    Yerokhin, V A

    2001-03-05

    The contribution of order alpha(2)(Zalpha)(6)ln (3)(Zalpha)(-2) to the ground-state Lamb shift in hydrogen induced by the loop-after-loop diagram is evaluated analytically. An additional contribution of this order is found compared to the previous calculation by Karshenboim [Sov. Phys. JETP 76, 541 (1993)]. As a result, agreement is achieved for this correction between different numerical and analytical methods.

  12. Collider study on the loop-induced dark matter mediation

    NASA Astrophysics Data System (ADS)

    Tsai, Yuhsin

    2016-06-01

    Collider experiments are one of the most promising ways to constrain Dark Matter (DM) interactions. For DM couplings involving light mediators, especially for the loop-mediated interactions, a meaningful interpretation of the results requires to go beyond effective field theory. In this note we discuss the study of the magnetic dipole interacting DM, focusing on a model with anarchic dark flavor structure. By including the momentum-dependent form factors that mediate the coupling - given by the Dark Penguin - in collider processes, we study bounds from monophoton, diphoton, and non-pointing photon searches at the LHC. We also compare our results to constraints from the direct detection experiments.

  13. Conformational Sampling in Template-Free Protein Loop Structure Modeling: An Overview

    PubMed Central

    Li, Yaohang

    2013-01-01

    Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a “mini protein folding problem” under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the approaches of sampling loop conformation space, which is a critical step to obtain high resolution models in template-free methods. We review the potential energy functions for loop modeling, loop buildup mechanisms to satisfy geometric constraints, and loop conformation sampling algorithms. The recent loop modeling results are also summarized. PMID:24688696

  14. Band-structure loops and multistability in cavity QED

    NASA Astrophysics Data System (ADS)

    Prasanna Venkatesh, B.; Larson, J.; O'Dell, D. H. J.

    2011-06-01

    We calculate the band structure of ultracold atoms located inside a laser-driven optical cavity. For parameters where the atom-cavity system exhibits bistability, the atomic band structure develops loop structures akin to the ones predicted for Bose-Einstein condensates in ordinary (noncavity) optical lattices. However, in our case the nonlinearity derives from the cavity back-action rather than from direct interatomic interactions. We find both bi- and tristable regimes associated with the lowest band, and show that the multistability we observe can be analyzed in terms of swallowtail catastrophes. Dynamic and energetic stability of the mean-field solutions is also discussed, and we show that the bistable solutions have, as expected, one unstable and two stable branches. The presence of loops in the atomic band structure has important implications for proposals concerning Bloch oscillations of atoms inside optical cavities [Peden , Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.80.043803 80, 043803 (2009); Prasanna Venkatesh , Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.80.063834 80, 063834 (2009)].

  15. Discrete state model and accurate estimation of loop entropy of RNA secondary structures.

    PubMed

    Zhang, Jian; Lin, Ming; Chen, Rong; Wang, Wei; Liang, Jie

    2008-03-28

    Conformational entropy makes important contribution to the stability and folding of RNA molecule, but it is challenging to either measure or compute conformational entropy associated with long loops. We develop optimized discrete k-state models of RNA backbone based on known RNA structures for computing entropy of loops, which are modeled as self-avoiding walks. To estimate entropy of hairpin, bulge, internal loop, and multibranch loop of long length (up to 50), we develop an efficient sampling method based on the sequential Monte Carlo principle. Our method considers excluded volume effect. It is general and can be applied to calculating entropy of loops with longer length and arbitrary complexity. For loops of short length, our results are in good agreement with a recent theoretical model and experimental measurement. For long loops, our estimated entropy of hairpin loops is in excellent agreement with the Jacobson-Stockmayer extrapolation model. However, for bulge loops and more complex secondary structures such as internal and multibranch loops, we find that the Jacobson-Stockmayer extrapolation model has large errors. Based on estimated entropy, we have developed empirical formulae for accurate calculation of entropy of long loops in different secondary structures. Our study on the effect of asymmetric size of loops suggest that loop entropy of internal loops is largely determined by the total loop length, and is only marginally affected by the asymmetric size of the two loops. Our finding suggests that the significant asymmetric effects of loop length in internal loops measured by experiments are likely to be partially enthalpic. Our method can be applied to develop improved energy parameters important for studying RNA stability and folding, and for predicting RNA secondary and tertiary structures. The discrete model and the program used to calculate loop entropy can be downloaded at http://gila.bioengr.uic.edu/resources/RNA.html.

  16. Formation and evolution of structure in loop cosmology.

    PubMed

    Bojowald, Martin; Kagan, Mikhail; Singh, Parampreet; Hernández, Hector H; Skirzewski, Aureliano

    2007-01-19

    Inhomogeneous cosmological perturbation equations are derived in loop quantum gravity, taking into account corrections, in particular, in gravitational parts. This provides a framework for calculating the evolution of modes in structure formation scenarios related to inflationary or bouncing models. Applications here are corrections to the Newton potential and to the evolution of large scale modes which imply nonconservation of curvature perturbations possibly noticeable in a running spectral index. These effects are sensitive to quantization procedures and test the characteristic behavior of correction terms derived from quantum gravity.

  17. SELF-ORGANIZED BRAIDING AND THE STRUCTURE OF CORONAL LOOPS

    SciTech Connect

    Berger, Mitchell A.; Asgari-Targhi, Mahboubeh E-mail: m.asgari@ucl.ac.u

    2009-11-01

    The Parker model for heating of the solar corona involves reconnection of braided magnetic flux elements. Much of this braiding is thought to occur at as yet unresolved scales, for example, braiding of threads within an extreme-ultraviolet or X-ray loop. However, some braiding may be still visible at scales accessible to TRACE or Hinode. We suggest that attempts to estimate the amount of braiding at these scales must take into account the degree of coherence of the braid structure. In this paper, we examine the effect of reconnection on the structure of a braided magnetic field. We demonstrate that simple models of braided magnetic fields which balance the input of topological structure with reconnection evolve to a self-organized critical state. An initially random braid can become highly ordered, with coherence lengths obeying power-law distributions. The energy released during reconnection also obeys a power law. Our model gives more frequent (but smaller) energy releases nearer to the ends of a coronal loop.

  18. Porous Foam Based Wick Structures for Loop Heat Pipes

    NASA Technical Reports Server (NTRS)

    Silk, Eric A.

    2012-01-01

    As part of an effort to identify cost efficient fabrication techniques for Loop Heat Pipe (LHP) construction, NASA Goddard Space Flight Center's Cryogenics and Fluids Branch collaborated with the U.S. Naval Academy s Aerospace Engineering Department in Spring 2012 to investigate the viability of carbon foam as a wick material within LHPs. The carbon foam was manufactured by ERG Aerospace and machined to geometric specifications at the U.S. Naval Academy s Materials, Mechanics and Structures Machine Shop. NASA GSFC s Fractal Loop Heat Pipe (developed under SBIR contract #NAS5-02112) was used as the validation LHP platform. In a horizontal orientation, the FLHP system demonstrated a heat flux of 75 Watts per square centimeter with deionized water as the working fluid. Also, no failed start-ups occurred during the 6 week performance testing period. The success of this study validated that foam can be used as a wick structure. Furthermore, given the COTS status of foam materials this study is one more step towards development of a low cost LHP.

  19. Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions.

    PubMed

    Najibi, Seyed Morteza; Maadooliat, Mehdi; Zhou, Lan; Huang, Jianhua Z; Gao, Xin

    2017-01-01

    Recently, the study of protein structures using angular representations has attracted much attention among structural biologists. The main challenge is how to efficiently model the continuous conformational space of the protein structures based on the differences and similarities between different Ramachandran plots. Despite the presence of statistical methods for modeling angular data of proteins, there is still a substantial need for more sophisticated and faster statistical tools to model the large-scale circular datasets. To address this need, we have developed a nonparametric method for collective estimation of multiple bivariate density functions for a collection of populations of protein backbone angles. The proposed method takes into account the circular nature of the angular data using trigonometric spline which is more efficient compared to existing methods. This collective density estimation approach is widely applicable when there is a need to estimate multiple density functions from different populations with common features. Moreover, the coefficients of adaptive basis expansion for the fitted densities provide a low-dimensional representation that is useful for visualization, clustering, and classification of the densities. The proposed method provides a novel and unique perspective to two important and challenging problems in protein structure research: structure-based protein classification and angular-sampling-based protein loop structure prediction.

  20. Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops.

    PubMed

    Phan, Andy; Mailey, Katherine; Sakai, Jessica; Gu, Xiaobo; Schroeder, Susan J

    2017-02-17

    Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased towards small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with more than 6 nucleotides that occur frequently in viral RNA. This paper presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Protonated cytosine and uracil base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with more than 6 nucleotides are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2x2 have been measured (Mathews 2004). These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites.

  1. Volumetric contributions of loop regions of G-quadruplex DNA to the formation of the tertiary structure.

    PubMed

    Takahashi, Shuntaro; Sugimoto, Naoki

    2017-02-06

    DNA guanine-quadruplexes (G-quadruplexes) are unique DNA structures formed by guanine-rich sequences. The loop regions of G-quadruplexes play key roles in stability and topology of G-quadruplexes. Here, we investigated volumetric changes induced by pressure in the folding of the G-quadruplex formed by the thrombin binding aptamer (TBA) with mutations within the loop regions. The change of partial molar volume in the transition from coil to G-quadruplex, ∆Vtr, of TBA with a mutation from T to A in the 5' most loop (TBA T3A) was 75.5cm(3)mol(-1), which was larger than that of TBA (54.6cm(3)mol(-1)). TBA with a G to T mutation in the central loop (TBA G8T) had thermal stability similar to TBA T3A but a smaller ∆Vtr of 41.1cm(3)mol(-1). In the presence of poly(ethylene)glycol 200 (PEG200), ∆Vtr values were 14.7cm(3)mol(-1) for TBA T3A and 13.2cm(3)mol(-1) for TBA G8T. These results suggest that the two mutations destabilize the G-quadruplex structure differently. Thus, volumetric data obtained using pressure-based thermodynamic analyses provides information about the dynamics of the loop regions and the roles of loops in the stabilities and folding of G-quadruplex structures.

  2. Ab initio structure prediction of the antibody hypervariable H3 loop.

    PubMed

    Zhu, Kai; Day, Tyler

    2013-06-01

    Antibodies have the capability of binding a wide range of antigens due to the diversity of the six loops constituting the complementarity determining region (CDR). Among the six loops, the H3 loop is the most diverse in structure, length, and sequence identity. Prediction of the three-dimensional structures of antibodies, especially the CDR loops, is an important step in the computational design and engineering of novel antibodies for improved affinity and specificity. Although it has been demonstrated that the conformation of the five non-H3 loops can be accurately predicted by comparing their sequences against databases of canonical loop conformations, no such connection has been established for H3 loops. In this work, we present the results for ab initio structure prediction of the H3 loop using conformational sampling and energy calculations with the program Prime on a dataset of 53 loops ranging in length from 4 to 22 residues. When the prediction is performed in the crystal environment and including symmetry mates, the median backbone root mean square deviation (RMSD) is 0.5 Å to the crystal structure, with 91% of cases having an RMSD of less than 2.0 Å. When the prediction is performed in a noncrystallographic environment, where the scaffold is constructed by swapping the H3 loops between homologous antibodies, 70% of cases have an RMSD below 2.0 Å. These results show promise for ab initio loop predictions applied to modeling of antibodies.

  3. Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics

    PubMed Central

    Pasi, Marco; Lavery, Richard

    2016-01-01

    DNA loop formation on nucleosomes is strongly implicated in chromatin remodeling and occurs spontaneously in nucleosomes subjected to superhelical stress. The nature of such loops depends crucially on the balance between DNA deformation and DNA interaction with the nucleosome core. Currently, no high-resolution structural data on these loops exist. Although uniform rod models have been used to study loop size and shape, these models make assumptions concerning DNA mechanics and DNA–core binding. We present here atomic-scale molecular dynamics simulations for two different loop sizes. The results point to the key role of localized DNA kinking within the loops. Kinks enable the relaxation of DNA bending strain to be coupled with improved DNA–core interactions. Kinks lead to small, irregularly shaped loops that are asymmetrically positioned with respect to the nucleosome core. We also find that loop position can influence the dynamics of the DNA segments at the extremities of the nucleosome. PMID:27098037

  4. Short loop length and high thermal stability determine genomic instability induced by G-quadruplex-forming minisatellites

    PubMed Central

    Piazza, Aurèle; Adrian, Michael; Samazan, Frédéric; Heddi, Brahim; Hamon, Florian; Serero, Alexandre; Lopes, Judith; Teulade-Fichou, Marie-Paule; Phan, Anh Tuân; Nicolas, Alain

    2015-01-01

    G-quadruplexes (G4) are polymorphic four-stranded structures formed by certain G-rich nucleic acids, with various biological roles. However, structural features dictating their formation and/or functionin vivo are unknown. InS. cerevisiae, the pathological persistency of G4 within the CEB1 minisatellite induces its rearrangement during leading-strand replication. We now show that several other G4-forming sequences remain stable. Extensive mutagenesis of the CEB25 minisatellite motif reveals that only variants with very short (≤ 4 nt) G4 loops preferentially containing pyrimidine bases trigger genomic instability. Parallel biophysical analyses demonstrate that shortening loop length does not change the monomorphic G4 structure of CEB25 variants but drastically increases its thermal stability, in correlation with thein vivo instability. Finally, bioinformatics analyses reveal that the threat for genomic stability posed by G4 bearing short pyrimidine loops is conserved inC. elegans and humans. This work provides a framework explanation for the heterogeneous instability behavior of G4-forming sequencesin vivo, highlights the importance of structure thermal stability, and questions the prevailing assumption that G4 structures with short or longer loops are as likely to formin vivo. PMID:25956747

  5. Interaction of irradiation-induced prismatic dislocation loops with free surfaces in tungsten

    NASA Astrophysics Data System (ADS)

    Fikar, Jan; Gröger, Roman; Schäublin, Robin

    2017-02-01

    The prismatic dislocation loops appear in metals as a result of high-energy irradiation. Understanding their formation and interaction is important for quantification of irradiation-induced deterioration of mechanical properties. Characterization of dislocation loops in thin foils is commonly made using transmission electron microscopy (TEM), but the results are inevitably influenced by the proximity of free surfaces. The prismatic loops are attracted to free surfaces by image forces. Depending on the type, size and depth of the loop in the foil, they can escape to the free surface, thus invalidating TEM observations and conclusions. In this article small prismatic hexagonal and circular dislocation loops in tungsten with the Burgers vectors 1/2 < 1 1 1 > and < 1 0 0 > are studied by molecular statics simulations using three embedded atom method (EAM) potentials. The calculated image forces are compared to known elastic solutions. A particular attention is paid to the critical stress to move edge dislocations. The escape of the loop to the free surface is quantified by a combination of atomistic simulations and elastic calculations. For example, for the 1/2 < 1 1 1 > loop with diameter 7.4 nm in a 55 nm thick foil we calculated that about one half of the loops will escape to the free surface. This implies that TEM observations detect only approx. 50% of the loops that were originally present in the foil.

  6. Myotonic Dystrophy Type 1 RNA Crystal Structures Reveal Heterogeneous 1×1 Nucleotide UU Internal Loop Conformations⊥

    PubMed Central

    Kumar, Amit; Park, HaJeung; Fang, Pengfei; Parkesh, Raman; Guo, Min; Nettles, Kendall W.; Disney, Matthew D.

    2011-01-01

    RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5′CUG/3′GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures are disclosed of a model DM1 triplet repeating construct, 5′r(UUGGGC(CUG)3GUCC)2, refined to 2.20 Å and 1.52 Å resolution. Here, differences in orientation of the 5′ dangling UU end between the two structures induce changes in the backbone groove width, which reveals that non-canonical 1×1 nucleotide UU internal loops can display an ensemble of pairing conformations. In the 2.20 Å structure, CUGa, the 5′UU forms one hydrogen-bonded pairs with a 5′UU of a neighboring helix in the unit cell to form a pseudo-infinite helix. The central 1×1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1×1 nucleotide UU internal loops each form a one hydrogen-bonded pair. In the 1.52 Å structure, CUGb, the 5′ UU dangling end is tucked into the major groove of the duplex. While the canonical paired bases show no change in base pairing, in CUGb the terminal 1×1 nucleotide UU internal loops form now two hydrogen-bonded pairs. Thus, the shift in major groove induced by the 5′UU dangling end alters non-canonical base patterns. Collectively, these structures indicate that 1×1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands. PMID:21988728

  7. Myotonic dystrophy type 1 RNA crystal structures reveal heterogeneous 1 × 1 nucleotide UU internal loop conformations.

    PubMed

    Kumar, Amit; Park, HaJeung; Fang, Pengfei; Parkesh, Raman; Guo, Min; Nettles, Kendall W; Disney, Matthew D

    2011-11-15

    RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5'CUG/3'GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures of a model DM1 triplet repeating construct, 5'r[UUGGGC(CUG)(3)GUCC](2), refined to 2.20 and 1.52 Å resolution are disclosed. Here, differences in the orientation of the 5' dangling UU end between the two structures induce changes in the backbone groove width, which reveals that noncanonical 1 × 1 nucleotide UU internal loops can display an ensemble of pairing conformations. In the 2.20 Å structure, CUGa, the 5' UU forms a one hydrogen-bonded pair with a 5' UU of a neighboring helix in the unit cell to form a pseudoinfinite helix. The central 1 × 1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1 × 1 nucleotide UU internal loops each form a one-hydrogen bond pair. In the 1.52 Å structure, CUGb, the 5' UU dangling end is tucked into the major groove of the duplex. While the canonically paired bases show no change in base pairing, in CUGb the terminal 1 × 1 nucleotide UU internal loops now form two hydrogen-bonded pairs. Thus, the shift in the major groove induced by the 5' UU dangling end alters noncanonical base patterns. Collectively, these structures indicate that 1 × 1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands.

  8. Inhibitory loop robustly induces anticipated synchronization in neuronal microcircuits

    NASA Astrophysics Data System (ADS)

    Matias, Fernanda S.; Gollo, Leonardo L.; Carelli, Pedro V.; Mirasso, Claudio R.; Copelli, Mauro

    2016-10-01

    We investigate the synchronization properties between two excitatory coupled neurons in the presence of an inhibitory loop mediated by an interneuron. Dynamic inhibition together with noise independently applied to each neuron provide phase diversity in the dynamics of the neuronal motif. We show that the interplay between the coupling strengths and the external noise controls the phase relations between the neurons in a counterintuitive way. For a master-slave configuration (unidirectional coupling) we find that the slave can anticipate the master, on average, if the slave is subject to the inhibitory feedback. In this nonusual regime, called anticipated synchronization (AS), the phase of the postsynaptic neuron is advanced with respect to that of the presynaptic neuron. We also show that the AS regime survives even in the presence of unbalanced bidirectional excitatory coupling. Moreover, for the symmetric mutually coupled situation, the neuron that is subject to the inhibitory loop leads in phase.

  9. A modular perspective of protein structures: application to fragment based loop modeling.

    PubMed

    Fernandez-Fuentes, Narcis; Fiser, Andras

    2013-01-01

    Proteins can be decomposed into supersecondary structure modules. We used a generic definition of supersecondary structure elements, so-called Smotifs, which are composed of two flanking regular secondary structures connected by a loop, to explore the evolution and current variety of structure building blocks. Here, we discuss recent observations about the saturation of Smotif geometries in protein structures and how it opens new avenues in protein structure modeling and design. As a first application of these observations we describe our loop conformation modeling algorithm, ArchPred that takes advantage of Smotifs classification. In this application, instead of focusing on specific loop properties the method narrows down possible template conformations in other, often not homologous structures, by identifying the most likely supersecondary structure environment that cradles the loop. Beyond identifying the correct starting supersecondary structure geometry, it takes into account information of fit of anchor residues, sterical clashes, match of predicted and observed dihedral angle preferences, and local sequence signal.

  10. Hairpin loop structure of African swine fever virus DNA.

    PubMed Central

    González, A; Talavera, A; Almendral, J M; Viñuela, E

    1986-01-01

    The ends of African swine fever virus genome are formed by a 37 nucleotide-long hairpin loop composed, almost entirely, of incompletely paired A and T residues. The loops at each DNA end were present in two equimolar forms that, when compared in opposite polarities, were inverted and complementary (flip-flop), as in the case of poxvirus DNA. The hairpin loops of African swine fever and vaccinia virus DNAs had no homology, but both DNAs had a 16 nucleotide-long sequence, close to the hairpin loops, with an homology of about 80%. An analysis of African swine fever virus replicating DNA showed head-to-head and tail-to-tail linked molecules that may be replicative intermediates. Images PMID:3763393

  11. Systematic U(1 ) B - L extensions of loop-induced neutrino mass models with dark matter

    NASA Astrophysics Data System (ADS)

    Ho, Shu-Yu; Toma, Takashi; Tsumura, Koji

    2016-08-01

    We study the gauged U(1 ) B - L extensions of the models for neutrino masses and dark matter. In this class of models, tiny neutrino masses are radiatively induced through the loop diagrams, while the origin of the dark matter stability is guaranteed by the remnant of the gauge symmetry. Depending on how the lepton number conservation is violated, these models are systematically classified. We present complete lists for the one-loop Z2 and the two-loop Z3 radiative seesaw models as examples of the classification. The anomaly cancellation conditions in these models are also discussed.

  12. Structural and Functional Studies on the Marburg Virus GP2 Fusion Loop.

    PubMed

    Liu, Nina; Tao, Yisong; Brenowitz, Michael D; Girvin, Mark E; Lai, Jonathan R

    2015-10-01

    Marburg virus (MARV) and the ebolaviruses belong to the family Filoviridae (the members of which are filoviruses) that cause severe hemorrhagic fever. Infection requires fusion of the host and viral membranes, a process that occurs in the host cell endosomal compartment and is facilitated by the envelope glycoprotein fusion subunit, GP2. The N-terminal fusion loop (FL) of GP2 is a hydrophobic disulfide-bonded loop that is postulated to insert and disrupt the host endosomal membrane during fusion. Here, we describe the first structural and functional studies of a protein corresponding to the MARV GP2 FL. We found that this protein undergoes a pH-dependent conformational change, as monitored by circular dichroism and nuclear magnetic resonance. Furthermore, we report that, under low pH conditions, the MARV GP2 FL can induce content leakage from liposomes. The general aspects of this pH-dependent structure and lipid-perturbing behavior are consistent with previous reports on Ebola virus GP2 FL. However, nuclear magnetic resonance studies in lipid bicelles and mutational analysis indicate differences in structure exist between MARV and Ebola virus GP2 FL. These results provide new insight into the mechanism of MARV GP2-mediated cell entry.

  13. The NMR Structure of an Internal Loop from 23S Ribosomal RNA Differs from its Structure in Crystals of 50S Ribosomal Subunits

    PubMed Central

    Shankar, Neelaabh; Kennedy, Scott D.; Chen, Gang; Krugh, Thomas R.; Turner, Douglas H.

    2014-01-01

    Internal loops play an important role in structure and folding of RNA and in RNA recognition by other molecules such as proteins and ligands. An understanding of internal loops with propensities to form a particular structure will help predict RNA structure, recognition, and function. The structures of internal loops 5'1009CUAAG10133'3'1168GAAGC11645' and 5'998CUAAG10023'3'1157GAAGC11535' from helix 40 of the large subunit rRNA in Deinococcus radiodurans and Escherichia coli, respectively, are phylogenetically conserved, suggesting functional relevance. The energetics and NMR solution structure of the loop were determined in the duplex, 5'1GGCUAAGAC93'3'18CCGAAGCUG105' The internal loop forms a different structure in solution than in the crystal structures of the ribosomal subunits. In particular, the crystal structures have a bulged out adenine at the equivalent of position A15 and a reverse Hoogsteen UA pair (trans Watson-Crick/Hoogsteen UA) at the equivalent of U4 and A14, whereas the solution structure has a single hydrogen bond UA pair (cis Watson-Crick/sugar edge A15U4) between U4 and A15 and a sheared AA pair (trans Hoogsteen/sugar edge A14A5) between A5 and A14. There is cross-strand stacking between A6 and A14 (A6/A14/A15 stacking pattern) in the NMR structure. All three structures have a sheared GA pair (trans Hoogsteen/sugar edge A6G13) at the equivalent of A6 and G13. The internal loop has contacts with ribosomal protein L20 and other parts of the RNA in the crystal structures. These contacts presumably provide the free energy to rearrange the base pairing in the loop. Evidently, molecular recognition of this internal loop involves induced fit binding, which could confer several advantages. The predicted thermodynamic stability of the loop agrees with the experimental value, even though the thermodynamic model assumes a Watson–Crick UA pair. PMID:17002278

  14. Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction.

    PubMed

    Zhu, Kai; Day, Tyler; Warshaviak, Dora; Murrett, Colleen; Friesner, Richard; Pearlman, David

    2014-08-01

    We present the blinded prediction results in the Second Antibody Modeling Assessment (AMA-II) using a fully automatic antibody structure prediction method implemented in the programs BioLuminate and Prime. We have developed a novel knowledge based approach to model the CDR loops, using a combination of sequence similarity, geometry matching, and the clustering of database structures. The homology models are further optimized with a physics-based energy function (VSGB2.0), which improves the model quality significantly. H3 loop modeling remains the most challenging task. Our ab initio loop prediction performs well for the H3 loop in the crystal structure context, and allows improved results when refining the H3 loops in the context of homology models. For the 10 human and mouse derived antibodies in this assessment, the average RMSDs for the homology model Fv and framework regions are 1.19 Å and 0.74 Å, respectively. The average RMSDs for five non-H3 CDR loops range from 0.61 Å to 1.05 Å, and the H3 loop average RMSD is 2.91 Å using our knowledge-based loop prediction approach. The ab initio H3 loop predictions yield an average RMSD of 1.28 Å when performed in the context of the crystal structure and 2.67 Å in the context of the homology modeled structure. Notably, our method for predicting the H3 loop in the crystal structure environment ranked first among the seven participating groups in AMA-II, and our method made the best prediction among all participants for seven of the ten targets.

  15. Heavy ion irradiation induced dislocation loops in AREVA's M5® alloy

    NASA Astrophysics Data System (ADS)

    Hengstler-Eger, R. M.; Baldo, P.; Beck, L.; Dorner, J.; Ertl, K.; Hoffmann, P. B.; Hugenschmidt, C.; Kirk, M. A.; Petry, W.; Pikart, P.; Rempel, A.

    2012-04-01

    Pressurized water reactor (PWR) Zr-based alloy structural materials show creep and growth under neutron irradiation as a consequence of the irradiation induced microstructural changes in the alloy. A better scientific understanding of these microstructural processes can improve simulation programs for structural component deformation and simplify the development of advanced deformation resistant alloys. As in-pile irradiation leads to high material activation and requires long irradiation times, the objective of this work was to study whether ion irradiation is an applicable method to simulate typical PWR neutron damage in Zr-based alloys, with AREVA's M5® alloy as reference material. The irradiated specimens were studied by electron backscatter diffraction (EBSD), positron Doppler broadening spectroscopy (DBS) and in situ transmission electron microscopy (TEM) at different dose levels and temperatures. The irradiation induced microstructure consisted of - and -type dislocation loops with their characteristics corresponding to typical neutron damage in Zr-based alloys; it can thus be concluded that heavy ion irradiation under the chosen conditions is an excellent method to simulate PWR neutron damage.

  16. Structure of Staphylococcal Enterotoxin E in Complex with TCR Defines the Role of TCR Loop Positioning in Superantigen Recognition.

    PubMed

    Rödström, Karin E J; Regenthal, Paulina; Lindkvist-Petersson, Karin

    2015-01-01

    T cells are crucial players in cell-mediated immunity. The specificity of their receptor, the T cell receptor (TCR), is central for the immune system to distinguish foreign from host antigens. Superantigens are bacterial toxins capable of inducing a toxic immune response by cross-linking the TCR and the major histocompatibility complex (MHC) class II and circumventing the antigen specificity. Here, we present the structure of staphylococcal enterotoxin E (SEE) in complex with a human T cell receptor, as well as the unligated T cell receptor structure. There are clear structural changes in the TCR loops upon superantigen binding. In particular, the HV4 loop moves to circumvent steric clashes upon complex formation. In addition, a predicted ternary model of SEE in complex with both TCR and MHC class II displays intermolecular contacts between the TCR α-chain and the MHC, suggesting that the TCR α-chain is of importance for complex formation.

  17. Global structure of curves from generalized unitarity cut of three-loop diagrams

    NASA Astrophysics Data System (ADS)

    Hauenstein, Jonathan D.; Huang, Rijun; Mehta, Dhagash; Zhang, Yang

    2015-02-01

    This paper studies the global structure of algebraic curves defined by generalized unitarity cut of four-dimensional three-loop diagrams with eleven propagators. The global structure is a topological invariant that is characterized by the geometric genus of the algebraic curve. We use the Riemann-Hurwitz formula to compute the geometric genus of algebraic curves with the help of techniques involving convex hull polytopes and numerical algebraic geometry. Some interesting properties of genus for arbitrary loop orders are also explored where computing the genus serves as an initial step for integral or integrand reduction of three-loop amplitudes via an algebraic geometric approach.

  18. Fields induced by three-dimensional dislocation loops in anisotropic magneto-electro-elastic bimaterials

    NASA Astrophysics Data System (ADS)

    Han, Xueli; Pan, Ernie; Sangghaleh, Ali

    2013-08-01

    The coupled elastic, electric and magnetic fields produced by an arbitrarily shaped three-dimensional dislocation loop in general anisotropic magneto-electro-elastic (MEE) bimaterials are derived. First, we develop line-integral expressions for the fields induced by a general dislocation loop. Then, we obtain analytical solutions for the fields, including the extended Peach-Koehler force, due to some useful dislocation segments such as straight line and elliptic arc. The present solutions contain the piezoelectric, piezomagnetic and purely elastic solutions as special cases. As numerical examples, the fields induced by a square and an elliptic dislocation loop in MEE bimaterials are studied. Our numerical results show the coupling effects among different fields, along with various interesting features associated with the dislocation and interface.

  19. Thermodynamics of DNA Loops with Long-Range Correlated Structural Disorder

    NASA Astrophysics Data System (ADS)

    Vaillant, C.; Audit, B.; Arnéodo, A.

    2005-08-01

    We study the influence of a structural disorder on the thermodynamical properties of 2D-elastic chains submitted to mechanical/topological constraint as loops. The disorder is introduced via a spontaneous curvature whose distribution along the chain presents either no correlation or long-range correlations (LRC). The equilibrium properties of the one-loop system are derived numerically and analytically for weak disorder. LRC are shown to favor the formation of small loop, larger the LRC, smaller the loop size. We use the mean first passage time formalism to show that the typical short time loop dynamics is superdiffusive in the presence of LRC. Potential biological implications on nucleosome positioning and dynamics in eukaryotic chromatin are discussed.

  20. Unresolved Fine-scale Structure in Solar Coronal Loop-tops

    NASA Astrophysics Data System (ADS)

    Scullion, E.; Rouppe van der Voort, L.; Wedemeyer, S.; Antolin, P.

    2014-12-01

    New and advanced space-based observing facilities continue to lower the resolution limit and detect solar coronal loops in greater detail. We continue to discover even finer substructures within coronal loop cross-sections, in order to understand the nature of the solar corona. Here, we push this lower limit further to search for the finest coronal loop substructures, through taking advantage of the resolving power of the Swedish 1 m Solar Telescope/CRisp Imaging Spectro-Polarimeter (CRISP), together with co-observations from the Solar Dynamics Observatory/Atmospheric Image Assembly (AIA). High-resolution imaging of the chromospheric Hα 656.28 nm spectral line core and wings can, under certain circumstances, allow one to deduce the topology of the local magnetic environment of the solar atmosphere where its observed. Here, we study post-flare coronal loops, which become filled with evaporated chromosphere that rapidly condenses into chromospheric clumps of plasma (detectable in Hα) known as a coronal rain, to investigate their fine-scale structure. We identify, through analysis of three data sets, large-scale catastrophic cooling in coronal loop-tops and the existence of multi-thermal, multi-stranded substructures. Many cool strands even extend fully intact from loop-top to footpoint. We discover that coronal loop fine-scale strands can appear bunched with as many as eight parallel strands within an AIA coronal loop cross-section. The strand number density versus cross-sectional width distribution, as detected by CRISP within AIA-defined coronal loops, most likely peaks at well below 100 km, and currently, 69% of the substructure strands are statistically unresolved in AIA coronal loops.

  1. Unresolved fine-scale structure in solar coronal loop-tops

    SciTech Connect

    Scullion, E.; Van der Voort, L. Rouppe; Wedemeyer, S.; Antolin, P.

    2014-12-10

    New and advanced space-based observing facilities continue to lower the resolution limit and detect solar coronal loops in greater detail. We continue to discover even finer substructures within coronal loop cross-sections, in order to understand the nature of the solar corona. Here, we push this lower limit further to search for the finest coronal loop substructures, through taking advantage of the resolving power of the Swedish 1 m Solar Telescope/CRisp Imaging Spectro-Polarimeter (CRISP), together with co-observations from the Solar Dynamics Observatory/Atmospheric Image Assembly (AIA). High-resolution imaging of the chromospheric Hα 656.28 nm spectral line core and wings can, under certain circumstances, allow one to deduce the topology of the local magnetic environment of the solar atmosphere where its observed. Here, we study post-flare coronal loops, which become filled with evaporated chromosphere that rapidly condenses into chromospheric clumps of plasma (detectable in Hα) known as a coronal rain, to investigate their fine-scale structure. We identify, through analysis of three data sets, large-scale catastrophic cooling in coronal loop-tops and the existence of multi-thermal, multi-stranded substructures. Many cool strands even extend fully intact from loop-top to footpoint. We discover that coronal loop fine-scale strands can appear bunched with as many as eight parallel strands within an AIA coronal loop cross-section. The strand number density versus cross-sectional width distribution, as detected by CRISP within AIA-defined coronal loops, most likely peaks at well below 100 km, and currently, 69% of the substructure strands are statistically unresolved in AIA coronal loops.

  2. Uptake inhibitors but not substrates induce protease resistance in extracellular loop two of the dopamine transporter.

    PubMed

    Gaffaney, Jon D; Vaughan, Roxanne A

    2004-03-01

    Changes in protease sensitivity of extracellular loop two (EL2) of the dopamine transporter (DAT) during inhibitor and substrate binding were examined using trypsin proteolysis and epitope-specific immunoblotting. In control rat striatal membranes, proteolysis of DAT in a restricted region of EL2 was produced by 0.001 to 10 microg/ml trypsin. However, in the presence of the dopamine uptake blockers [2-(diphenylmethoxyl) ethyl]-4-(3phenylpropyl) piperazine (GBR 12909), mazindol, 2beta-carbomethoxy-3beta-(4-flourophenyl)tropane (beta-CFT), nomifensine, benztropine, or (-)-cocaine, 100- to 1000-fold higher concentrations of trypsin were required to produce comparable levels of proteolysis. Protease resistance induced by ligands was correlated with their affinity for DAT binding, was not observed with Zn2+, (+)-cocaine, or inhibitors of norepinephrine or serotonin transporters, and was not caused by altered catalytic activity of trypsin. Together, these results support the hypothesis that the interaction of uptake inhibitors with DAT induces a protease-resistant conformation in EL2. In contrast, binding of substrates did not induce protease resistance in EL2, suggesting that substrates and inhibitors interact with DAT differently during binding. To assess the effects of EL2 proteolysis on DAT function, the binding and transport properties of trypsin-digested DAT were assayed with [3H]CFT and [3H]dopamine. Digestion decreased the Bmax for binding and the Vmax for uptake in amounts that were proportional to the extent of proteolysis, indicating that the structural integrity of EL2 is required for maintenance of both DAT binding and transport functions. Together this data provides novel information about inhibitor and substrate interactions at EL2, possibly relating the protease resistant DAT conformation to a mechanism of transport inhibition.

  3. A light-induced shortcut in the planktonic microbial loop

    NASA Astrophysics Data System (ADS)

    Ptacnik, Robert; Gomes, Ana; Royer, Sarah-Jeanne; Berger, Stella A.; Calbet, Albert; Nejstgaard, Jens C.; Gasol, Josep M.; Isari, Stamatina; Moorthi, Stefanie D.; Ptacnikova, Radka; Striebel, Maren; Sazhin, Andrey F.; Tsagaraki, Tatiana M.; Zervoudaki, Soultana; Altoja, Kristi; Dimitriou, Panagiotis D.; Laas, Peeter; Gazihan, Ayse; Martínez, Rodrigo A.; Schabhüttl, Stefanie; Santi, Ioulia; Sousoni, Despoina; Pitta, Paraskevi

    2016-07-01

    Mixotrophs combine photosynthesis with phagotrophy to cover their demands in energy and essential nutrients. This gives them a competitive advantage under oligotropihc conditions, where nutrients and bacteria concentrations are low. As the advantage for the mixotroph depends on light, the competition between mixo- and heterotrophic bacterivores should be regulated by light. To test this hypothesis, we incubated natural plankton from the ultra-oligotrophic Eastern Mediterranean in a set of mesocosms maintained at 4 light levels spanning a 10-fold light gradient. Picoplankton (heterotrophic bacteria (HB), pico-sized cyanobacteria, and small-sized flagellates) showed the fastest and most marked response to light, with pronounced predator-prey cycles, in the high-light treatments. Albeit cell specific activity of heterotrophic bacteria was constant across the light gradient, bacterial abundances exhibited an inverse relationship with light. This pattern was explained by light-induced top-down control of HB by bacterivorous phototrophic eukaryotes (PE), which was evidenced by a significant inverse relationship between HB net growth rate and PE abundances. Our results show that light mediates the impact of mixotrophic bacterivores. As mixo- and heterotrophs differ in the way they remineralize nutrients, these results have far-reaching implications for how nutrient cycling is affected by light.

  4. A light-induced shortcut in the planktonic microbial loop

    PubMed Central

    Ptacnik, Robert; Gomes, Ana; Royer, Sarah-Jeanne; Berger, Stella A.; Calbet, Albert; Nejstgaard, Jens C.; Gasol, Josep M.; Isari, Stamatina; Moorthi, Stefanie D.; Ptacnikova, Radka; Striebel, Maren; Sazhin, Andrey F.; Tsagaraki, Tatiana M.; Zervoudaki, Soultana; Altoja, Kristi; Dimitriou, Panagiotis D.; Laas, Peeter; Gazihan, Ayse; Martínez, Rodrigo A.; Schabhüttl, Stefanie; Santi, Ioulia; Sousoni, Despoina; Pitta, Paraskevi

    2016-01-01

    Mixotrophs combine photosynthesis with phagotrophy to cover their demands in energy and essential nutrients. This gives them a competitive advantage under oligotropihc conditions, where nutrients and bacteria concentrations are low. As the advantage for the mixotroph depends on light, the competition between mixo- and heterotrophic bacterivores should be regulated by light. To test this hypothesis, we incubated natural plankton from the ultra-oligotrophic Eastern Mediterranean in a set of mesocosms maintained at 4 light levels spanning a 10-fold light gradient. Picoplankton (heterotrophic bacteria (HB), pico-sized cyanobacteria, and small-sized flagellates) showed the fastest and most marked response to light, with pronounced predator-prey cycles, in the high-light treatments. Albeit cell specific activity of heterotrophic bacteria was constant across the light gradient, bacterial abundances exhibited an inverse relationship with light. This pattern was explained by light-induced top-down control of HB by bacterivorous phototrophic eukaryotes (PE), which was evidenced by a significant inverse relationship between HB net growth rate and PE abundances. Our results show that light mediates the impact of mixotrophic bacterivores. As mixo- and heterotrophs differ in the way they remineralize nutrients, these results have far-reaching implications for how nutrient cycling is affected by light. PMID:27404551

  5. Hydration structure of antithrombin conformers and water transfer during reactive loop insertion.

    PubMed Central

    Liang, J; McGee, M P

    1998-01-01

    The serine protease inhibitor antithrombin undergoes extensive conformational changes during functional interaction with its target proteases. Changes include insertion of the reactive loop region into a beta-sheet structure in the protein core. We explore the possibility that these changes are linked to water transfer. Volumes of water transferred during inhibition of coagulation factor Xa are compared to water-permeable volumes in the x-ray structure of two different antithrombin conformers. In one conformer, the reactive loop is largely exposed to solvent, and in the other, the loop is inserted. Hydration fingerprints of antithrombin (that is, water-permeable pockets) are analyzed to determine their location, volume, and size of access pores, using alpha shape-based methods from computational geometry. Water transfer during reactions is calculated from changes in rate with osmotic pressure. Hydration fingerprints prove markedly different in the two conformers. There is an excess of 61-76 water molecules in loop-exposed as compared to loop-inserted conformers. Quantitatively, rate increases with osmotic pressure are consistent with the transfer of 73 +/- 7 water molecules. This study demonstrates that conformational changes of antithrombin, including loop insertion, are linked to water transfer from antithrombin to bulk solution. It also illustrates the combined use of osmotic stress and analytical geometry as a new and effective tool for structure/function studies. PMID:9675160

  6. Getting in (and out of) the loop: regulating higher order telomere structures

    PubMed Central

    Luke-Glaser, Sarah; Poschke, Heiko; Luke, Brian

    2012-01-01

    The DNA at the ends of linear chromosomes (the telomere) folds back onto itself and forms an intramolecular lariat-like structure. Although the telomere loop has been implicated in the protection of chromosome ends from nuclease-mediated resection and unscheduled DNA repair activities, it potentially poses an obstacle to the DNA replication machinery during S-phase. Therefore, the coordinated regulation of telomere loop formation, maintenance, and resolution is required in order to establish a balance between protecting the chromosome ends and promoting their duplication prior to cell division. Until recently, the only factor known to influence telomere looping in human cells was TRF2, a component of the shelterin complex. Recent work in yeast and mouse cells has uncovered additional regulatory factors that affect the loop structure at telomeres. In the following “perspective” we outline what is known about telomere looping and highlight the latest results regarding the regulation of this chromosome end structure. We speculate about how the manipulation of the telomere loop may have therapeutic implications in terms of diseases associated with telomere dysfunction and uncontrolled proliferation. PMID:23226680

  7. F-actin structure destabilization and DNase I binding loop: fluctuations mutational cross-linking and electron microscopy analysis of loop states and effects on F-actin.

    PubMed

    Oztug Durer, Zeynep A; Diraviyam, Karthikeyan; Sept, David; Kudryashov, Dmitri S; Reisler, Emil

    2010-01-22

    The conformational dynamics of filamentous actin (F-actin) is essential for the regulation and functions of cellular actin networks. The main contribution to F-actin dynamics and its multiple conformational states arises from the mobility and flexibility of the DNase I binding loop (D-loop; residues 40-50) on subdomain 2. Therefore, we explored the structural constraints on D-loop plasticity at the F-actin interprotomer space by probing its dynamic interactions with the hydrophobic loop (H-loop), the C-terminus, and the W-loop via mutational disulfide cross-linking. To this end, residues of the D-loop were mutated to cysteines on yeast actin with a C374A background. These mutants showed no major changes in their polymerization and nucleotide exchange properties compared to wild-type actin. Copper-catalyzed disulfide cross-linking was investigated in equimolar copolymers of cysteine mutants from the D-loop with either wild-type (C374) actin or mutant S265C/C374A (on the H-loop) or mutant F169C/C374A (on the W-loop). Remarkably, all tested residues of the D-loop could be cross-linked to residues 374, 265, and 169 by disulfide bonds, demonstrating the plasticity of the interprotomer region. However, each cross-link resulted in different effects on the filament structure, as detected by electron microscopy and light-scattering measurements. Disulfide cross-linking in the longitudinal orientation produced mostly no visible changes in filament morphology, whereas the cross-linking of D-loop residues >45 to the H-loop, in the lateral direction, resulted in filament disruption and the presence of amorphous aggregates on electron microscopy images. A similar aggregation was also observed upon cross-linking the residues of the D-loop (>41) to residue 169. The effects of disulfide cross-links on F-actin stability were only partially accounted for by the simulations of current F-actin models. Thus, our results present evidence for the high level of conformational plasticity in

  8. Structure of a cardiotoxic phospholipase A(2) from Ophiophagus hannah with the "pancreatic loop".

    PubMed

    Zhang, Hai-Long; Xu, Su-Juan; Wang, Qiu-Yan; Song, Shi-Ying; Shu, Yu-Yan; Lin, Zheng-Jiong

    2002-06-01

    The crystal structure of an acidic phospholipase A(2) from Ophiophagus hannah (king cobra) has been determined by molecular replacement at 2.6-A resolution to a crystallographic R factor of 20.5% (R(free)=23.3%) with reasonable stereochemistry. The venom enzyme contains an unusual "pancreatic loop." The conformation of the loop is well defined and different from those in pancreas PLA(2), showing its structural variability. This analysis provides the first structure of a PLA(2)-type cardiotoxin. The sites related to the cardiotoxic and myotoxic activities are explored and the oligomer observed in the crystalline state is described.

  9. Structural consequences of cutting a binding loop: two circularly permuted variants of streptavidin

    SciTech Connect

    Le Trong, Isolde; Chu, Vano; Xing, Yi; Lybrand, Terry P.; Stayton, Patrick S.; Stenkamp, Ronald E.

    2013-06-01

    The crystal structures of two circularly permuted streptavidins probe the role of a flexible loop in the tight binding of biotin. Molecular-dynamics calculations for one of the mutants suggests that increased fluctuations in a hydrogen bond between the protein and biotin are associated with cleavage of the binding loop. Circular permutation of streptavidin was carried out in order to investigate the role of a main-chain amide in stabilizing the high-affinity complex of the protein and biotin. Mutant proteins CP49/48 and CP50/49 were constructed to place new N-termini at residues 49 and 50 in a flexible loop involved in stabilizing the biotin complex. Crystal structures of the two mutants show that half of each loop closes over the binding site, as observed in wild-type streptavidin, while the other half adopts the open conformation found in the unliganded state. The structures are consistent with kinetic and thermodynamic data and indicate that the loop plays a role in enthalpic stabilization of the bound state via the Asn49 amide–biotin hydrogen bond. In wild-type streptavidin, the entropic penalties of immobilizing a flexible portion of the protein to enhance binding are kept to a manageable level by using a contiguous loop of medium length (six residues) which is already constrained by its anchorage to strands of the β-barrel protein. A molecular-dynamics simulation for CP50/49 shows that cleavage of the binding loop results in increased structural fluctuations for Ser45 and that these fluctuations destabilize the streptavidin–biotin complex.

  10. Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage

    PubMed Central

    Jiang, Fuguo; Taylor, David W.; Chen, Janice S.; Kornfeld, Jack E.; Zhou, Kaihong; Thompson, Aubri J.; Nogales, Eva; Doudna, Jennifer A.

    2016-01-01

    Bacterial adaptive immunity and genome engineering involving the CRISPR (clustered regularly interspaced short palindromic repeats)–associated (Cas) protein Cas9 begin with RNA-guided DNA unwinding to form an RNA-DNA hybrid and a displaced DNA strand inside the protein. The role of this R-loop structure in positioning each DNA strand for cleavage by the two Cas9 nuclease domains is unknown. We determine molecular structures of the catalytically active Streptococcus pyogenes Cas9 R-loop that show the displaced DNA strand located near the RuvC nuclease domain active site. These protein-DNA interactions, in turn, position the HNH nuclease domain adjacent to the target DNA strand cleavage site in a conformation essential for concerted DNA cutting. Cas9 bends the DNA helix by 30°, providing the structural distortion needed for R-loop formation. PMID:26841432

  11. Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage.

    PubMed

    Jiang, Fuguo; Taylor, David W; Chen, Janice S; Kornfeld, Jack E; Zhou, Kaihong; Thompson, Aubri J; Nogales, Eva; Doudna, Jennifer A

    2016-02-19

    Bacterial adaptive immunity and genome engineering involving the CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) protein Cas9 begin with RNA-guided DNA unwinding to form an RNA-DNA hybrid and a displaced DNA strand inside the protein. The role of this R-loop structure in positioning each DNA strand for cleavage by the two Cas9 nuclease domains is unknown. We determine molecular structures of the catalytically active Streptococcus pyogenes Cas9 R-loop that show the displaced DNA strand located near the RuvC nuclease domain active site. These protein-DNA interactions, in turn, position the HNH nuclease domain adjacent to the target DNA strand cleavage site in a conformation essential for concerted DNA cutting. Cas9 bends the DNA helix by 30°, providing the structural distortion needed for R-loop formation.

  12. Aggregation and secondary loop structure of oligonucleotides do not determine their ability to inhibit TLR9.

    PubMed

    Ashman, Robert F; Goeken, J Adam; Lenert, Petar S

    2011-08-01

    Toll-like receptor 9 (TLR9) is an endosomal DNA sensor that warns us of the presence of infectious danger and triggers a rapid pro-inflammatory response in dendritic cells, macrophages, and B cells. The consequences of uncontrolled TLR9 activation can be detrimental for the host, contributing to the pathogenesis of bacterial septic shock or autoimmune diseases, such as systemic lupus erythematosus. Therefore, we need to develop TLR9 antagonists. We and others have created inhibitory oligonucleotides (INH-ODN) that are capable of sequence-dependent inhibition of TLR9-induced activation in both human and mouse cells. However, it is not clear whether marked differences in INH-ODN activity related to base sequence derived from polymerization of INH-ODNs or their ability to complex with stimulatory CpG-oligonucleotides (ST-ODN). Furthermore, the 5' end of INH-ODNs may assume a particular loop configuration that may be needed for binding to a critical site on TLR9. Here, we show that 1) G-tetrads required for ODN stacking were compatible with INH-ODN activity but were not necessary; 2) there was no relationship between activity and self-association at endosomal pH; 3) there was no evidence for direct binding between ST-ODNs and INH-ODNs; 4) when a 3G sequence was disrupted, despite a preserved stem-loop formation, INH-ODN activity was abolished. These results support the conclusion that certain features of the primary linear sequence are critical for TLR9 inhibition, but changes in secondary structure or in ODN aggregation are irrelevant.

  13. A systematic classification of Plasmodium falciparum P-loop NTPases: structural and functional correlation

    PubMed Central

    Gangwar, Deepti; Kalita, Mridul K; Gupta, Dinesh; Chauhan, Virander S; Mohmmed, Asif

    2009-01-01

    Background The P-loop NTPases constitute one of the largest groups of globular protein domains that play highly diverse functional roles in most of the organisms. Even with the availability of nearly 300 different Hidden Markov Models representing the P-loop NTPase superfamily, not many P-loop NTPases are known in Plasmodium falciparum. A number of characteristic attributes of the genome have resulted into the lack of knowledge about this functionally diverse, but important class of proteins. Method In the study, protein sequences with characteristic motifs of NTPase domain (Walker A and Walker B) are computationally extracted from the P. falciparum database. A detailed secondary structure analysis, functional classification, phylogenetic and orthology studies of the NTPase domain of repertoire of 97 P. falciparum P-loop NTPases is carried out. Results Based upon distinct sequence features and secondary structure profile of the P-loop domain of obtained sequences, a cladistic classification is also conceded: nucleotide kinases and GTPases, ABC and SMC family, SF1/2 helicases, AAA+ and AAA protein families. Attempts are made to identify any ortholog(s) for each of these proteins in other Plasmodium sp. as well as its vertebrate host, Homo sapiens. A number of P. falciparum P-loop NTPases that have no homologue in the host, as well as those annotated as hypothetical proteins and lack any characteristic functional domain are identified. Conclusion The study suggests a strong correlation between sequence and secondary structure profile of P-loop domains and functional roles of these proteins and thus provides an opportunity to speculate the role of many hypothetical proteins. The study provides a methodical framework for the characterization of biologically diverse NTPases in the P. falciparum genome. The efforts made in the analysis are first of its kind; and the results augment to explore the functional role of many of these proteins from the parasite that could

  14. Loop-length-dependent SVM prediction of domain linkers for high-throughput structural proteomics.

    PubMed

    Ebina, Teppei; Toh, Hiroyuki; Kuroda, Yutaka

    2009-01-01

    The prediction of structural domains in novel protein sequences is becoming of practical importance. One important area of application is the development of computer-aided techniques for identifying, at a low cost, novel protein domain targets for large-scale functional and structural proteomics. Here, we report a loop-length-dependent support vector machine (SVM) prediction of domain linkers, which are loops separating two structural domains. (DLP-SVM is freely available at: http://www.tuat.ac.jp/ approximately domserv/cgi-bin/DLP-SVM.cgi.) We constructed three loop-length-dependent SVM predictors of domain linkers (SVM-All, SVM-Long and SVM-Short), and also built SVM-Joint, which combines the results of SVM-Short and SVM-Long into a single consolidated prediction. The performances of SVM-Joint were, in most aspects, the highest, with a sensitivity of 59.7% and a specificity of 43.6%, which indicated that the specificity and the sensitivity were improved by over 2 and 3% respectively, when loop-length-dependent characteristics were taken into account. Furthermore, the sensitivity and specificity of SVM-Joint were, respectively, 37.6 and 17.4% higher than those of a random guess, and also superior to those of previously reported domain linker predictors. These results indicate that SVMs can be used to predict domain linkers, and that loop-length-dependent characteristics are useful for improving SVM prediction performances.

  15. Sampling multiple scoring functions can improve protein loop structure prediction accuracy.

    PubMed

    Li, Yaohang; Rata, Ionel; Jakobsson, Eric

    2011-07-25

    Accurately predicting loop structures is important for understanding functions of many proteins. In order to obtain loop models with high accuracy, efficiently sampling the loop conformation space to discover reasonable structures is a critical step. In loop conformation sampling, coarse-grain energy (scoring) functions coupling with reduced protein representations are often used to reduce the number of degrees of freedom as well as sampling computational time. However, due to implicitly considering many factors by reduced representations, the coarse-grain scoring functions may have potential insensitivity and inaccuracy, which can mislead the sampling process and consequently ignore important loop conformations. In this paper, we present a new computational sampling approach to obtain reasonable loop backbone models, so-called the Pareto optimal sampling (POS) method. The rationale of the POS method is to sample the function space of multiple, carefully selected scoring functions to discover an ensemble of diversified structures yielding Pareto optimality to all sampled conformations. The POS method can efficiently tolerate insensitivity and inaccuracy in individual scoring functions and thereby lead to significant accuracy improvement in loop structure prediction. We apply the POS method to a set of 4-12-residue loop targets using a function space composed of backbone-only Rosetta and distance-scale finite ideal-gas reference (DFIRE) and a triplet backbone dihedral potential developed in our lab. Our computational results show that in 501 out of 502 targets, the model sets generated by POS contain structure models are within subangstrom resolution. Moreover, the top-ranked models have a root mean square deviation (rmsd) less than 1 A in 96.8, 84.1, and 72.2% of the short (4-6 residues), medium (7-9 residues), and long (10-12 residues) targets, respectively, when the all-atom models are generated by local optimization from the backbone models and are ranked by our

  16. Propagation and localization of electromagnetic waves in quasiperiodic serial loop structures

    NASA Astrophysics Data System (ADS)

    Aynaou, H.; El Boudouti, E. H.; El Hassouani, Y.; Akjouj, A.; Djafari-Rouhani, B.; Vasseur, J.; Benomar, A.; Velasco, V. R.

    2005-11-01

    We study the propagation of electromagnetic waves in one-dimensional quasiperiodic photonic band gap structures made of serial loop structures separated by segments. Different quasiperiodic structures such as Fibonacci, Thue-Morse, Rudin-Shapiro, and double period are investigated with special focus on the Fibonacci structure. Depending on the lengths of the two arms constituting the loops, one can distinguish two particular cases. (i) There are symmetric loop structures, which are shown to be equivalent to impedance-modulated mediums. In this case, it is found that besides the existence of extended and forbidden modes, some narrow frequency bands appear as defect modes in the transmission spectrum inside the gaps. These modes are shown to be localized within only one of the two types of blocks constituting the structure. An analysis of the transmission phase time enables us to derive the group velocity as well as the density of states in these structures. In particular, the stop bands (localized modes) may give rise to unusual (strong normal) dispersion in the gaps, yielding fast (slow) group velocities above (below) the velocity of light. (ii) There are also asymmetric loop structures, where the loops play the role of resonators that may introduce transmission zeros and hence additional gaps unnoticed in the case of simple impedance-modulated mediums. A comparison of the transmission amplitude and phase time of Fibonacci systems with those of other quasiperiodic systems is also outlined. In particular, it was shown that these structures present similar behaviors in the transmission spectra inside the regions of extended modes, whereas they present different localized modes inside the gaps. Experiments and numerical calculations are in very good agreement.

  17. Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage.

    PubMed

    Stork, Caroline Townsend; Bocek, Michael; Crossley, Madzia P; Sollier, Julie; Sanz, Lionel A; Chédin, Frédéric; Swigut, Tomek; Cimprich, Karlene A

    2016-08-23

    The hormone estrogen (E2) binds the estrogen receptor to promote transcription of E2-responsive genes in the breast and other tissues. E2 also has links to genomic instability, and elevated E2 levels are tied to breast cancer. Here, we show that E2 stimulation causes a rapid, global increase in the formation of R-loops, co-transcriptional RNA-DNA products, which in some instances have been linked to DNA damage. We show that E2-dependent R-loop formation and breast cancer rearrangements are highly enriched at E2-responsive genomic loci and that E2 induces DNA replication-dependent double-strand breaks (DSBs). Strikingly, many DSBs that accumulate in response to E2 are R-loop dependent. Thus, R-loops resulting from the E2 transcriptional response are a significant source of DNA damage. This work reveals a novel mechanism by which E2 stimulation leads to genomic instability and highlights how transcriptional programs play an important role in shaping the genomic landscape of DNA damage susceptibility.

  18. Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage

    PubMed Central

    Stork, Caroline Townsend; Bocek, Michael; Crossley, Madzia P; Sollier, Julie; Sanz, Lionel A; Chédin, Frédéric; Swigut, Tomek; Cimprich, Karlene A

    2016-01-01

    The hormone estrogen (E2) binds the estrogen receptor to promote transcription of E2-responsive genes in the breast and other tissues. E2 also has links to genomic instability, and elevated E2 levels are tied to breast cancer. Here, we show that E2 stimulation causes a rapid, global increase in the formation of R-loops, co-transcriptional RNA-DNA products, which in some instances have been linked to DNA damage. We show that E2-dependent R-loop formation and breast cancer rearrangements are highly enriched at E2-responsive genomic loci and that E2 induces DNA replication-dependent double-strand breaks (DSBs). Strikingly, many DSBs that accumulate in response to E2 are R-loop dependent. Thus, R-loops resulting from the E2 transcriptional response are a significant source of DNA damage. This work reveals a novel mechanism by which E2 stimulation leads to genomic instability and highlights how transcriptional programs play an important role in shaping the genomic landscape of DNA damage susceptibility. DOI: http://dx.doi.org/10.7554/eLife.17548.001 PMID:27552054

  19. Application of phase-lock loops to periodic disturbance rejection in smart structures

    NASA Astrophysics Data System (ADS)

    Algrain, Marcelo C.; Ehlers, Douglas E.; Hardt, Steven L.

    1996-05-01

    This paper presents a simple, effective and economical system capable of suppressing periodic vibration (external or self induced) affecting a structure or payload. The approach used integrates piezoelectric materials/actuators, sensors, and low-cost electronics in a novel way. The key innovation is the use of phase-lock-loops (PLL) and switch capacitor filters (SCF) for the on-line identification, tracking and control of periodic vibration. This method concentrates its control action at those frequencies where periodic vibration is detected. Among the advantages of this approach are: it is conceptually simple, easily expandable and modular; the controller does not rely on a model of the structure, and it only needs some approximate notion of the frequency range where the periodic disturbances are expected to occur; it is robust and can be operated at high gain without loss of stability; it is not significantly affected by the presence of random vibration or sensor noise; and it can be implemented with inexpensive electronics. The effectiveness of this new approach was experimentally evaluated using a test unit consisting of a simple structure, accelerometers and Terfenol-D actuators. The structure was excited by driving one of the actuator with sinusoidal and random signals. The resulting periodic disturbances were measured using the accelerometers. The acceleration signals were passed though a bank of PLLs and associated SCFs to detect the fundamental frequency and harmonics. This information was used to drive another actuator that rejected the original disturbances, and attenuation levels as high as 30 dB were achieved.

  20. A phase-lock-loop-based control system for suppressing periodic vibration in smart structural systems

    NASA Astrophysics Data System (ADS)

    Algrain, Marcelo; Hardt, Steve; Ehlers, Douglas

    1997-02-01

    This paper presents a simple, effective and economical system capable of suppressing periodic vibration (external or self-induced) affecting a structure or payload. The approach used integrates piezoelectric materials/actuators, sensors and low-cost electronics in a novel way. The key innovation is the use of phase-lock loops (PLLs) and switch-capacitor filters (SCFs) for the on-line identification, tracking and control of periodic vibration. This method concentrates its control action at those frequencies where periodic vibration is detected. Among the advantages of this approach are the following: it is conceptually simple, easily expandable and modular; the controller does not rely on a model of the structure and it only needs some approximate notion of the frequency range where the periodic disturbances are expected to occur; it is robust and can be operated at high gain without loss of stability; it is not significantly affected by the presence of random vibration or sensor noise and it can be implemented with inexpensive electronics. The effectiveness of this new approach was experimentally evaluated using a test unit consisting of a simple structure, accelerometers and Terfenol-D actuators. The structure was excited by driving one of the actuators with sinusoidal and random signals. The resulting periodic disturbances were measured using the accelerometers. The acceleration signals were passed though a bank of PLLs and associated SCFs to detect the fundamental frequency and harmonics. This information was used to drive another actuator that rejected the original disturbances, and attenuation levels as high as 30 dB were achieved.

  1. Determination of the secondary structure of group II bulge loops using the fluorescent probe 2-aminopurine

    PubMed Central

    Dishler, Abigael L.; McMichael, Elizabeth L.; Serra, Martin J.

    2015-01-01

    Eleven RNA hairpins containing 2-aminopurine (2-AP) in either base-paired or single nucleotide bulge loop positions were optically melted in 1 M NaCl; and, the thermodynamic parameters ΔH°, ΔS°, ΔG°37, and TM for each hairpin were determined. Substitution of 2-AP for an A (adenosine) at a bulge position (where either the 2-AP or A is the bulge) in the stem of a hairpin, does not affect the stability of the hairpin. For group II bulge loops such as AA/U, where there is ambiguity as to which of the A residues is paired with the U, hairpins with 2-AP substituted for either the 5′ or 3′ position in the hairpin stem have similar stability. Fluorescent melts were performed to monitor the environment of the 2-AP. When the 2-AP was located distal to the hairpin loop on either the 5′ or 3′ side of the hairpin stem, the change in fluorescent intensity upon heating was indicative of an unpaired nucleotide. A database of phylogenetically determined RNA secondary structures was examined to explore the presence of naturally occurring bulge loops embedded within a hairpin stem. The distribution of bulge loops is discussed and related to the stability of hairpin structures. PMID:25805856

  2. The influence of the local sequence environment on RNA loop structures.

    PubMed

    Schudoma, Christian; Larhlimi, Abdelhalim; Walther, Dirk

    2011-07-01

    RNA folding is assumed to be a hierarchical process. The secondary structure of an RNA molecule, signified by base-pairing and stacking interactions between the paired bases, is formed first. Subsequently, the RNA molecule adopts an energetically favorable three-dimensional conformation in the structural space determined mainly by the rotational degrees of freedom associated with the backbone of regions of unpaired nucleotides (loops). To what extent the backbone conformation of RNA loops also results from interactions within the local sequence context or rather follows global optimization constraints alone has not been addressed yet. Because the majority of base stacking interactions are exerted locally, a critical influence of local sequence on local structure appears plausible. Thus, local loop structure ought to be predictable, at least in part, from the local sequence context alone. To test this hypothesis, we used Random Forests on a nonredundant data set of unpaired nucleotides extracted from 97 X-ray structures from the Protein Data Bank (PDB) to predict discrete backbone angle conformations given by the discretized η/θ-pseudo-torsional space. Predictions on balanced sets with four to six conformational classes using local sequence information yielded average accuracies of up to 55%, thus significantly better than expected by chance (17%-25%). Bases close to the central nucleotide appear to be most tightly linked to its conformation. Our results suggest that RNA loop structure does not only depend on long-range base-pairing interactions; instead, it appears that local sequence context exerts a significant influence on the formation of the local loop structure.

  3. The DE and FG loops of the HPV major capsid protein contribute to the epitopes of vaccine-induced cross-neutralising antibodies

    PubMed Central

    Bissett, Sara L.; Godi, Anna; Beddows, Simon

    2016-01-01

    The human papillomavirus (HPV) vaccines consist of major capsid protein (L1) virus-like particles (VLP) and are highly efficacious against the development of cervical cancer precursors attributable to oncogenic genotypes, HPV16 and HPV18. A degree of vaccine-induced cross-protection has also been demonstrated against genetically-related genotypes in the Alpha-7 (HPV18-like) and Alpha-9 (HPV16-like) species groups which is coincident with the detection of L1 cross-neutralising antibodies. In this study the L1 domains recognised by inter-genotype cross-neutralising antibodies were delineated. L1 crystallographic homology models predicted a degree of structural diversity between the L1 loops of HPV16 and the non-vaccine Alpha-9 genotypes. These structural predictions informed the design of chimeric pseudovirions with inter-genotype loop swaps which demonstrated that the L1 domains recognised by inter-genotype cross-neutralising antibodies comprise residues within the DE loop and the late region of the FG loop. These data contribute to our understanding of the L1 domains recognised by vaccine-induced cross-neutralising antibodies. Such specificities may play a critical role in vaccine-induced cross-protection. PMID:28004837

  4. Curcumin improves synaptic plasticity impairment induced by HIV-1gp120 V3 loop

    PubMed Central

    Shen, Ling-ling; Jiang, Ming-liang; Liu, Si-si; Cai, Min-chun; Hong, Zhong-qiu; Lin, Li-qing; Xing, Yan-yan; Chen, Gui-lin; Pan, Rui; Yang, Li-juan; Xu, Ying; Dong, Jun

    2015-01-01

    Curcumin has been shown to significantly improve spatial memory impairment induced by HIV-1 gp120 V3 in rats, but the electrophysiological mechanism remains unknown. Using extracellular microelectrode recording techniques, this study confirmed that the gp120 V3 loop could suppress long-term potentiation in the rat hippocampal CA1 region and synaptic plasticity, and that curcumin could antagonize these inhibitory effects. Using a Fura-2/AM calcium ion probe, we found that curcumin resisted the effects of the gp120 V3 loop on hippocampal synaptosomes and decreased Ca2+ concentration in synaptosomes. This effect of curcumin was identical to nimodipine, suggesting that curcumin improved the inhibitory effects of gp120 on synaptic plasticity, ameliorated damage caused to the central nervous system, and might be a potential neuroprotective drug. PMID:26199609

  5. Stem-loop structures of the repetitive DNA sequences located at human centromeres

    SciTech Connect

    Gupta, G.; Garcia, A.E.; Ratliff, R.; Moyzis, R.K.; Catasti, P.; Hong, Lin; Yau, P.; Bradbury, E.M. |

    1993-09-01

    The presence of the highly conserved repetitive DNA sequences in the human centromeres argues for a special role of these sequences in their biological functions - most likely achieved by the formation of unusual structures. This prompted us to carry out quantitative one- and two-dimensional nuclear magnetic resonance (lD/2D NMR) spectroscopy to determine the structural properties of the human centromeric repeats, d(AATGG){sub n.d}(CCATT){sub n}. The studies on centromeric DNAs reveal that the complementary sequence, d(AATGG){sub n.d}(CCATT){sub n}, adopts the usual Watson-Crick B-DNA duplex and the pyrimidine-rich d(CCATT){sub n} strand is essentially a random coil. However, the purine-rich d(AATGG){sub n} strand is shown to adopt unusual stem-loop structures for repeat lengths, n=2,3,4, and 6. In addition to normal Watson-Crick A{center_dot}T pairs, the stem-loop structures are stabilized by mismatch A{center_dot}G and G{center_dot}G pairs in the stem and G-G-A stacking in the loop. Stem-loop structures of d(AATGG)n are independently verified by gel electrophoresis and nuclease digestion studies. Thermal melting studies show that the DNA repeats, d(AATGG){sub n}, are as stable as the corresponding Watson-Crick duplex d(AATGG){sub n.d}(CCATT){sub n}. Therefore, the sequence d(AATGG){sub n} can, indeed, nucleate a stem-loop structure at little free-energy cost and if, during mitosis, they are located on the chromosome surface they can provide specific recognition sites for kinetochore function.

  6. Towards the use of Structural Loop Analysis to Study System Behaviour of Socio-Ecological Systems.

    NASA Astrophysics Data System (ADS)

    Abram, Joseph; Dyke, James

    2016-04-01

    Maintaining socio-ecological systems in desirable states is key to developing a growing economy, alleviating poverty and achieving a sustainable future. While the driving forces of an environmental system are often well known, the dynamics impacting these drivers can be hidden within a tangled structure of causal chains and feedback loops. A lack of understanding of a system's dynamic structure and its influence on a system's behaviour can cause unforeseen side-effects during model scenario testing and policy implementation. Structural Loop analysis of socio-ecological system models identifies dominant feedback structures during times of behavioural shift, allowing the user to monitor key influential drivers during model simulation. This work carries out Loop Eigenvalue Elasticity Analysis (LEEA) on three system dynamic models, exploring tipping points in lake systems undergoing eutrophication. The purpose is to explore the potential benefits and limitations of the technique in the field of socio-ecology. The LEEA technique shows promise for socio-ecological systems which undergo regime shifts or express oscillatory trends, but shows limited usefulness with large models. The results of this work highlight changes in feedback loop dominance, years prior to eutrophic tipping events in lake systems. LEEA could be used as an early warning signal to impending system changes, complementary to other known early warning signals. This approach could improve our understanding during critical times of a system's behaviour, changing how we approach model analysis and the way scenario testing and policy implementation are addressed in socio-ecological system models.

  7. Exploring the Structure-Function Loop Adaptability of a (β/α)(8)-Barrel Enzyme through Loop Swapping and Hinge Variability.

    PubMed

    Ochoa-Leyva, Adrián; Barona-Gómez, Francisco; Saab-Rincón, Gloria; Verdel-Aranda, Karina; Sánchez, Filiberto; Soberón, Xavier

    2011-08-05

    Evolution of proteins involves sequence changes that are frequently localized at loop regions, revealing their important role in natural evolution. However, the development of strategies to understand and imitate such events constitutes a challenge to design novel enzymes in the laboratory. In this study, we show how to adapt loop swapping as semiautonomous units of functional groups in an enzyme with the (β/α)(8)-barrel and how this functional adaptation can be measured in vivo. To mimic the natural mechanism providing loop variability in antibodies, we developed an overlap PCR strategy. This includes introduction of sequence diversity at two hinge residues, which connect the new loops with the rest of the protein scaffold, and we demonstrate that this is necessary for a successful exploration of functional sequence space. This design allowed us to explore the sequence requirements to functional adaptation of each loop replacement that may not be sampled otherwise. Libraries generated following this strategy were evaluated in terms of their folding competence and their functional proficiency, an observation that was formalized as a Structure-Function Loop Adaptability value. Molecular details about the function and structure of some variants were obtained by enzyme kinetics and circular dichroism. This strategy yields functional variants that retain the original activity at higher frequencies, suggesting a new strategy for protein engineering that incorporates a more divergent sequence exploration beyond that limited to point mutations. We discuss how this approach may provide insights into the mechanism of enzyme evolution and function.

  8. SOLAR CORONA LOOP STUDIES WITH THE ATMOSPHERIC IMAGING ASSEMBLY. I. CROSS-SECTIONAL TEMPERATURE STRUCTURE

    SciTech Connect

    Aschwanden, Markus J.; Boerner, Paul

    2011-05-10

    We present a first systematic study on the cross-sectional temperature structure of coronal loops using the six coronal temperature filters of the Atmospheric Imaging Assembly (AIA) instrument on the Solar Dynamics Observatory (SDO). We analyze a sample of 100 loop snapshots measured at 10 different locations and 10 different times in active region NOAA 11089 on 2010 July 24, 21:00-22:00 UT. The cross-sectional flux profiles are measured and a cospatial background is subtracted in six filters in a temperature range of T {approx} 0.5-16 MK, and four different parameterizations of differential emission measure (DEM) distributions are fitted. We find that the reconstructed DEMs consist predominantly of narrowband peak temperature components with a thermal width of {sigma}{sub log(T)} {<=} 0.11 {+-} 0.02, close to the temperature resolution limit of the instrument, consistent with earlier triple-filter analysis from the Transition Region and Coronal Explorer by Aschwanden and Nightingale and from EIS/Hinode by Warren et al. or Tripathi et al. We find that 66% of the loops could be fitted with a narrowband single-Gaussian DEM model, and 19% with a DEM consisting of two narrowband Gaussians (which mostly result from pairs of intersecting loops along the same line of sight). The mostly isothermal loop DEMs allow us also to derive an improved empirical response function of the AIA 94 A filter, which needs to be boosted by a factor of q{sub 94} = 6.7 {+-} 1.7 for temperatures at log (T) {approx}< 6.3. The main result of near-isothermal loop cross-sections is not consistent with the predictions of standard nanoflare scenarios, but can be explained by flare-like heating mechanisms that drive chromospheric evaporation and upflows of heated plasma coherently over loop cross-sections of w {approx} 2-4 Mm.

  9. Solar Corona Loop Studies with the Atmospheric Imaging Assembly. I. Cross-sectional Temperature Structure

    NASA Astrophysics Data System (ADS)

    Aschwanden, Markus J.; Boerner, Paul

    2011-05-01

    We present a first systematic study on the cross-sectional temperature structure of coronal loops using the six coronal temperature filters of the Atmospheric Imaging Assembly (AIA) instrument on the Solar Dynamics Observatory (SDO). We analyze a sample of 100 loop snapshots measured at 10 different locations and 10 different times in active region NOAA 11089 on 2010 July 24, 21:00-22:00 UT. The cross-sectional flux profiles are measured and a cospatial background is subtracted in six filters in a temperature range of T ≈ 0.5-16 MK, and four different parameterizations of differential emission measure (DEM) distributions are fitted. We find that the reconstructed DEMs consist predominantly of narrowband peak temperature components with a thermal width of σlog (T) <= 0.11 ± 0.02, close to the temperature resolution limit of the instrument, consistent with earlier triple-filter analysis from the Transition Region and Coronal Explorer by Aschwanden & Nightingale and from EIS/Hinode by Warren et al. or Tripathi et al. We find that 66% of the loops could be fitted with a narrowband single-Gaussian DEM model, and 19% with a DEM consisting of two narrowband Gaussians (which mostly result from pairs of intersecting loops along the same line of sight). The mostly isothermal loop DEMs allow us also to derive an improved empirical response function of the AIA 94 Å filter, which needs to be boosted by a factor of q 94 = 6.7 ± 1.7 for temperatures at log (T) <~ 6.3. The main result of near-isothermal loop cross-sections is not consistent with the predictions of standard nanoflare scenarios, but can be explained by flare-like heating mechanisms that drive chromospheric evaporation and upflows of heated plasma coherently over loop cross-sections of w ≈ 2-4 Mm.

  10. Domain Dynamics in Piezoresponse Force Spectroscopy: Quantitative Deconvolution and Hysteresis Loop Fine Structure

    SciTech Connect

    Bdikin, Igor; Kholkin, Andrei; Morozovska, A. N.; Svechnikov, S. V.; Kim, S.-H.; Kalinin, Sergei V

    2008-01-01

    Domain dynamics in the Piezoresponse Force Spectroscopy (PFS) experiment is studied using the combination of local hysteresis loop acquisition with simultaneous domain imaging. The analytical theory for PFS signal from domain of arbitrary cross-section and length is developed for the analysis of experimental data on Pb(Zr,Ti)O3 polycrystalline films. The results suggest formation of oblate domain at early stage of the nucleation and growth, consistent with efficient screening of depolarization field. The fine structure of the hysteresis loop is shown to be related to the observed jumps in the domain geometry during domain wall propagation (nanoscale Barkhausen jumps), indicative of strong domain-defect interactions.

  11. Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.

    PubMed

    Tran, Huyen Thi; Hong, Myoung Ki; Ngo, Ho Phuong Thuy; Huynh, Kim Hung; Ahn, Yeh Jin; Wang, Zhong; Kang, Lin Woo

    2016-01-01

    D-Alanyl-D-alanine is an essential precursor of bacterial peptidoglycan and is synthesized by D-alanine-D-alanine ligase (DDL) with hydrolysis of ATP; this reaction makes DDL an important drug target for the development of antibacterial agents. Five crystal structures of DDL from Yersinia pestis (YpDDL) were determined at 1.7-2.5 Å resolution: apo, AMP-bound, ADP-bound, adenosine 5'-(β,γ-imido)triphosphate-bound, and D-alanyl-D-alanine- and ADP-bound structures. YpDDL consists of three domains, in which four loops, loop 1, loop 2 (the serine loop), loop 3 (the ω-loop) and loop 4, constitute the binding sites for two D-alanine molecules and one ATP molecule. Some of them, especially the serine loop and the ω-loop, show flexible conformations, and the serine loop is mainly responsible for the conformational change in substrate nucleotide phosphates. Enzyme-kinetics assays were carried out for both the D-alanine and ATP substrates and a substrate-binding mechanism was proposed for YpDDL involving conformational changes of the loops.

  12. The use of R-looping for structural gene identification and mRNA purification.

    PubMed Central

    Woolford, J L; Rosbash, M

    1979-01-01

    A method is presented for the purification of mRNAs and the identification of structural gene sequences in recombinant DNA molecules. RNA is hybridized to double-stranded linear DNA such that R-loops are formed between most DNAs and their complementary RNA sequences. These R-loops are purified from unhybridized RNAs by gel filtration chromatography in the presence of a high concentration of salt. The complementary RNAs are released from the R-loops by heating, and are assayed by gel electrophoresis or cell free translation to determine their purity and to identify the proteins for which they code. We have demonstrated that recombinant DNAs containing sequences for abundant or moderately abundant mRNAs of Saccharomyces cerevisiae can be identified by this means. Images PMID:379820

  13. Experimental observations of the coupling between induced currents and mechanical motion in torsionally supported square loops and plates

    SciTech Connect

    Bialek, J.M.; Cargulia, G.J.; Ulrickson, M.; Knott, M.J.; Turner, L.R.; Wehrle, R.B.

    1986-11-01

    A series of experiments that were successfully conducted to investigate the coupling between induced currents and rigid body rotation in square loops and plates is presented. The experimental arrangement consisted of a conducting test piece, rigidly mounted in a nonconducting fixture that provided a controlled stiffness against rotation. Electric current were induced in the test loop/plate by pulsing a magnetic field oriented perpendicular to the test piece. This was done in the presence of a constant magnetic field oriented parallel to the loop/plate. The interaction of the induced currents and the background magnetic field produced a net torque about the axis of the test fixture. Measurements were made of the total current flowing around the test piece and the angular rotation versus time. The observed data exhibited the magnetic damping and magnetic stiffness effects that arise in coupled systems and agreed very well with the predicted responses for both the loops and plates.

  14. Behaviour of oscillations in loop structures above active regions

    NASA Astrophysics Data System (ADS)

    Kolobov, D. Y.; Kobanov, N. I.; Chelpanov, A. A.; Kochanov, A. A.; Anfinogentov, S. A.; Chupin, S. A.; Myshyakov, I. I.; Tomin, V. E.

    2015-12-01

    In this study we combine the multiwavelength ultraviolet-optical (Solar Dynamics Observatory, SDO) and radio (Nobeyama Radioheliograph, NoRH) observations to get further insight into space-frequency distribution of oscillations at different atmospheric levels of the Sun. We processed the observational data on NOAA 11711 active region and found oscillations propagating from the photospheric level through the transition region upward into the corona. The power maps of low-frequency (1-2 mHz) oscillations reproduce well the fan-like coronal structures visible in the Fe IX 171 Å line. High frequency oscillations (5-7 mHz) propagate along the vertical magnetic field lines and concentrate inside small-scale elements in the umbra and at the umbra-penumbra boundary. We investigated the dependence of the dominant oscillation frequency upon the distance from the sunspot barycentre to estimate inclination of magnetic tubes in higher levels of sunspots where it cannot be measured directly, and found that this angle is close to 40° above the umbra boundaries in the transition region.

  15. Flap loop of GluD2 binds to Cbln1 and induces presynaptic differentiation.

    PubMed

    Kuroyanagi, Tomoaki; Hirano, Tomoo

    2010-07-30

    Glutamate receptor delta2 (GluD2) is selectively expressed on the postsynaptic spines at parallel-fiber (PF)-Purkinje neuron (PN) synapses. GluD2 knockout mice show a reduced number of PF-PN synapses, suggesting that GluD2 is involved in synapse formation. Recent studies revealed that GluD2 induces presynaptic differentiation in a manner dependent on its N-terminal domain (NTD) through binding of Cbln1 secreted from cerebellar granule neurons. However, the underlying mechanism of the specific binding of the NTD to Cbln1 remains elusive. Here, we have identified the flap loop (Arg321-Trp339) in the NTD of GluD2 (GluD2-NTD) as a crucial region for the binding to Cbln1 and the induction of presynaptic differentiation. Both induction of presynaptic differentiation and binding of Cbln1 were abolished in the HEK cells expressing not wild-type GluD2 but GluD2 with mutations in the flap loop. Especially, single amino acid substitution of either Arg321 or Trp323 to alanine was sufficient to disable the GluD2 function. Finally, a homology model of GluD2-NTD suggested that the flap loop is located at the distal end, which appears consistent with an interaction with Cbln1 and a presynaptic varicosity.

  16. Predicting structure and stability for RNA complexes with intermolecular loop–loop base-pairing

    PubMed Central

    Cao, Song; Xu, Xiaojun; Chen, Shi-Jie

    2014-01-01

    RNA loop–loop interactions are essential for genomic RNA dimerization and regulation of gene expression. In this article, a statistical mechanics-based computational method that predicts the structures and thermodynamic stabilities of RNA complexes with loop–loop kissing interactions is described. The method accounts for the entropy changes for the formation of loop–loop interactions, which is a notable advancement that other computational models have neglected. Benchmark tests with several experimentally validated systems show that the inclusion of the entropy parameters can indeed improve predictions for RNA complexes. Furthermore, the method can predict not only the native structures of RNA/RNA complexes but also alternative metastable structures. For instance, the model predicts that the SL1 domain of HIV-1 RNA can form two different dimer structures with similar stabilities. The prediction is consistent with experimental observation. In addition, the model predicts two different binding sites for hTR dimerization: One binding site has been experimentally proposed, and the other structure, which has a higher stability, is structurally feasible and needs further experimental validation. PMID:24751648

  17. Ricin A-chain substrate specificity in RNA, DNA, and hybrid stem-loop structures.

    PubMed

    Amukele, Tim K; Schramm, Vern L

    2004-05-04

    Ricin toxin A-chain (RTA) is the catalytic subunit of ricin, a heterodimeric toxin from castor beans. Its ribosomal inactivating activity arises from depurination of a single adenine from position A(4324) in a GAGA tetraloop from 28S ribosomal RNA. Minimal substrate requirements are the GAGA tetraloop and stem of two or more base pairs. Depurination activity also occurs on stem-loop DNA with the same sequence, but with the k(cat) reduced 200-fold. Systematic variation of RNA 5'-G(1)C(2)G(3)C(4)[G(5)A(6)G(7)A(8)]G(9)C(10)G(11)C(12)-3' 12mers via replacement of each nucleotide in the tetraloop with a deoxynucleotide showed a 16-fold increase in k(cat) for A(6) --> dA(6) but reduced k(cat) up to 300-fold for the other sites. Methylation of individual 2'-hydroxyls in a similar experiment reduced k(cat) by as much as 3 x 10(-3)-fold. In stem-loop DNA, replacement of d[G(5)A(6)G(7)A(8)] with individual ribonucleotides resulted in small kinetic changes, except for the dA(6) --> A(6) replacement for which k(cat) decreased 6-fold. Insertion of d[G(5)A(6)G(7)A(8)] into an RNA stem-loop or G(5)A(6)G(7)A(8) into a DNA stem-loop reduced k(cat) by 30- and 5-fold, respectively. Multiple substitutions of deoxyribonucleotides into RNA stem-loops in one case (dG(5),dG(7)) decreased k(cat)/K(m) by 10(5)-fold, while a second change (dG(5),dA(8)) decreased k(cat) by 100-fold. Mapping these interactions on the structure of GAGA stem-loop RNA suggests that all the loop 2'-hydroxyl groups play a significant role in the action of ricin A-chain. Improved binding of RNA-DNA stem-loop hybrids provides a scaffold for inhibitor design. Replacing the adenosine of the RTA depurination site with deoxyadenosine in a small RNA stem-loop increased k(cat) 20-fold to 1660 min(-1), a value similar to RTA's k(cat) on intact ribosomes.

  18. Closed-Loop Performance Measures for Flight Controllers Subject to Neutron-Induced Upsets

    NASA Technical Reports Server (NTRS)

    Gray, W. Steven; Zhang, Hong; Gonzalex, Oscar R.

    2003-01-01

    It has been observed that atmospheric neutrons can produce single event upsets in digital flight control hardware. The phenomenon has been studied extensively at the chip level, and now system level experiments are underway. In this paper analytical closed-loop performance measures for the tracking error are developed for a plant that is stabilized by a recoverable computer system subject to neutron induced upsets. The underlying model is a Markov jump-linear system with process noise. The steady-state tracking error is expressed in terms of a generalized observability Gramian.

  19. Alteration of Sugar-Induced Conformational Changes of the Melibiose Permease by Mutating Arg141 in Loop 4-5

    PubMed Central

    León, Xavier; Leblanc, Gérard; Padrós, Esteve

    2009-01-01

    Abstract The melibiose permease (MelB) from Escherichia coli couples the uptake of melibiose to that of Na+, Li+, or H+. In this work, we applied attenuated total reflection Fourier transform infrared (ATR-FTIR) difference spectroscopy to obtain information about the structural changes involved in substrate interaction with the R141C mutant and with the wild-type MelB reacted with N-ethylmaleimide (NEM). These modified permeases have the ability to bind the substrates but fail to transport them. It is shown that the sugar-induced ATR-FTIR difference spectra of the R141C mutant are different from those corresponding to the Cys-less permease from which it is derived. There are alterations of peaks assigned to turns and β-structures located most likely in loop 4-5. In addition, and quite notably, a peak at 1659 cm−1, assigned to changes at the level of one α-helix subpopulation, disappears in the melibiose-induced difference spectrum in the presence of Na+, suggesting a reduction of the conformational change capacity of the mutated MelB. These helices may involve structural components that couple the cation- and sugar-binding sites. On the other hand, MelB-NEM difference spectra are proportionally less disrupted than the R141C ones. Hence, the transport cycle of these two permeases, modified at two different loops, is most likely impaired at a different stage. It is proposed that the R141C mutant leads to the generation of a partially defective ternary complex that is unable to catalyze the subsequent conformational change necessary for substrate translocation. PMID:19527646

  20. Loop structures in the 5' untranslated region and antisense RNA mediate pilE gene expression in Neisseria gonorrhoeae.

    PubMed

    Masters, Thao L; Wachter, Jenny; Hill, Stuart A

    2016-11-01

    Regulation of the Neisseria gonorrhoeae pilE gene is ill-defined. In this study, post-transcriptional effects on expression were assessed. In silico analysis predicts the formation of three putative stable stem-loop structures with favourable free energies within the 5' untranslated region of the pilE message. Using quantitative reverse transcriptase PCR analyses, we show that each loop structure forms, with introduced destabilizing stem-loop mutations diminishing loop stability. Utilizing a series of pilE translational fusions, deletion of either loop 1 or loop 2 caused a significant reduction of pilE mRNA resulting in reduced expression of the reporter gene. Consequently, the formation of the loops apparently protects the pilE transcript from degradation. Putative loop 3 contains the pilE ribosomal binding site. Consequently, its formation may influence translation. Analysis of a small RNA transcriptome revealed an antisense RNA being produced upstream of the pilE promoter that is predicted to hybridize across the 5' untranslated region loops. Insertional mutants were created where the antisense RNA is not transcribed. In these mutants, pilE transcript levels are greatly diminished, with any residual message apparently not being translated. Complementation of these insertion mutants in trans with the antisense RNA gene facilitates pilE translation yielding a pilus + phenotype. Overall, this study demonstrates a complex relationship between loop-dependent transcript protection and antisense RNA in modulating pilE expression levels.

  1. Determination of the acceleration region size in a loop-structured solar flare

    NASA Astrophysics Data System (ADS)

    Guo, J.; Emslie, A. G.; Kontar, E. P.; Benvenuto, F.; Massone, A. M.; Piana, M.

    2012-07-01

    Aims: To study the acceleration and propagation of bremsstrahlung-producing electrons in solar flares, we analyze the evolution of the flare loop size with respect to energy at a variety of times. A GOES M3.7 loop-structured flare starting around 23:55 on 2002 April 14 is studied in detail using Ramaty High Energy Solar Spectroscopic Imager (RHESSI) observations. Methods: We construct photon and mean-electron-flux maps in 2-keV energy bins by processing observationally-deduced photon and electron visibilities, respectively, through several image-processing methods: a visibility-based forward-fit (FWD) algorithm, a maximum entropy (MEM) procedure and the uv-smooth (UVS) approach. We estimate the sizes of elongated flares (i.e., the length and width of flaring loops) by calculating the second normalized moments of the intensity in any given map. Employing a collisional model with an extended acceleration region, we fit the loop lengths as a function of energy in both the photon and electron domains. Results: The resulting fitting parameters allow us to estimate the extent of the acceleration region which is between ~ 13 arcsec and ~19 arcsec. Both forward-fit and uv-smooth algorithms provide substantially similar results with a systematically better fit in the electron domain. Conclusions: The consistency of the estimates from these methods provides strong support that the model can reliably determine geometric parameters of the acceleration region. The acceleration region is estimated to be a substantial fraction (~1/2) of the loop extent, indicating that this dense flaring loop incorporates both acceleration and transport of electrons, with concurrent thick-target bremsstrahlung emission.

  2. SiV center photoluminescence induced by C=O termination in nanocrystalline diamond and graphite loops hybridized films

    NASA Astrophysics Data System (ADS)

    Mei, Yingshuang; Fan, Dong; Lu, Shaohua; Shen, Yaogen; Hu, Xiaojun

    2016-12-01

    We performed a series of thermal oxidation at different temperatures on nanocrystalline diamond (NCD) films to construct various surface termination states of NCD grains and investigated their effects on silicon-vacancy (SiV) photoluminescence (PL) at 738 nm. Experiments and first principles calculations show that the negative electron affinity surface induced by C-H bond termination quenches the SiV PL, while the positive electron affinity surface originating from C=O bond termination removes this quenching. Moreover, oxidation at 600 °C results in the transition from amorphous carbon to graphite loops with an interlayer space of 0.4 nm, so that NCD and graphite loops' hybridized structure is formed. This allows oxygen atoms to contact with inside NCD grains to form more C=O bonds on the surface, producing much larger positive electron affinity in the surface. It traps the excited state electrons, lets them scatter back to the ground state, and emits SiV PL. These results reveal that C=O bonds play a crucial role in SiV PL of NCD grains and well explain the experimentally observed quenching effect. A novel way by changing the surface termination states is proposed to control the PL of NCD grains with SiV centers for potential quantum information processing and biological sensing.

  3. The structure of the third intracellular loop of the muscarinic acetylcholine receptor M2 subtype.

    PubMed

    Ichiyama, Susumu; Oka, Yoshiaki; Haga, Kazuko; Kojima, Shuichi; Tateishi, Yukihiro; Shirakawa, Masahiro; Haga, Tatsuya

    2006-01-09

    We have examined whether the long third intracellular loop (i3) of the muscarinic acetylcholine receptor M2 subtype has a rigid structure. Circular dichroism (CD) and nuclear magnetic resonance spectra of M2i3 expressed in and purified from Escherichia coli indicated that M2i3 consists mostly of random coil. In addition, the differential CD spectrum between the M2 and M2deltai3 receptors, the latter of which lacks most of i3 except N- and C-terminal ends, gave no indication of secondary structure. These results suggest that the central part of i3 of the M2 receptor has a flexible structure.

  4. The basic helix-loop-helix transcription factor, Mist1, induces maturation of mouse fetal hepatoblasts

    PubMed Central

    Chikada, Hiromi; Ito, Keiichi; Yanagida, Ayaka; Nakauchi, Hiromitsu; Kamiya, Akihide

    2015-01-01

    Hepatic stem/progenitor cells, hepatoblasts, have a high proliferative ability and can differentiate into mature hepatocytes and cholangiocytes. Therefore, these cells are considered to be useful for regenerative medicine and drug screening for liver diseases. However, it is problem that in vitro maturation of hepatoblasts is insufficient in the present culture system. In this study, a novel regulator to induce hepatic differentiation was identified and the molecular function of this factor was examined in embryonic day 13 hepatoblast culture with maturation factor, oncostatin M and extracellular matrices. Overexpression of the basic helix-loop-helix type transcription factor, Mist1, induced expression of mature hepatocytic markers such as carbamoyl-phosphate synthetase1 and several cytochrome P450 (CYP) genes in this culture system. In contrast, Mist1 suppressed expression of cholangiocytic markers such as Sox9, Sox17, Ck19, and Grhl2. CYP3A metabolic activity was significantly induced by Mist1 in this hepatoblast culture. In addition, Mist1 induced liver-enriched transcription factors, CCAAT/enhancer-binding protein α and Hepatocyte nuclear factor 1α, which are known to be involved in liver functions. These results suggest that Mist1 partially induces mature hepatocytic expression and function accompanied by the down-regulation of cholangiocytic markers. PMID:26456005

  5. New insights into the structural bases of activation of Cys-loop receptors.

    PubMed

    Bouzat, Cecilia

    2012-01-01

    Neurotransmitter receptors of the Cys-loop superfamily mediate rapid synaptic transmission throughout the nervous system, and include receptors activated by ACh, GABA, glycine and serotonin. They are involved in physiological processes, including learning and memory, and in neurological disorders, and they are targets for clinically relevant drugs. Cys-loop receptors assemble either from five copies of one type of subunit, giving rise to homomeric receptors, or from several types of subunits, giving rise to heteromeric receptors. Homomeric receptors are invaluable models for probing fundamental relationships between structure and function. Receptors contain a large extracellular domain that carries the binding sites and a transmembrane region that forms the ion pore. How the structural changes elicited by agonist binding are propagated through a distance of 50Å to the ion channel gate is central to understanding receptor function. Depending on the receptor subtype, occupancy of either two, as in the prototype muscle nicotinic receptor, or three binding sites, as in homomeric receptors, is required for full activation. The conformational changes initiated at the binding sites are propagated to the gate through the interface between the extracellular and transmembrane domains. This region forms a network that relays structural changes from the binding site towards the pore, and also contributes to open channel lifetime and rate of desensitization. Thus, this coupling region controls the beginning and duration of a synaptic response. Here we review recent advances in the molecular mechanism by which Cys-loop receptors are activated with particular emphasis on homomeric receptors.

  6. The Effective Field Theory of Large Scale Structures at two loops

    SciTech Connect

    Carrasco, John Joseph M.; Foreman, Simon; Green, Daniel; Senatore, Leonardo E-mail: sfore@stanford.edu E-mail: senatore@stanford.edu

    2014-07-01

    Large scale structure surveys promise to be the next leading probe of cosmological information. It is therefore crucial to reliably predict their observables. The Effective Field Theory of Large Scale Structures (EFTofLSS) provides a manifestly convergent perturbation theory for the weakly non-linear regime of dark matter, where correlation functions are computed in an expansion of the wavenumber k of a mode over the wavenumber associated with the non-linear scale k{sub NL}. Since most of the information is contained at high wavenumbers, it is necessary to compute higher order corrections to correlation functions. After the one-loop correction to the matter power spectrum, we estimate that the next leading one is the two-loop contribution, which we compute here. At this order in k/k{sub NL}, there is only one counterterm in the EFTofLSS that must be included, though this term contributes both at tree-level and in several one-loop diagrams. We also discuss correlation functions involving the velocity and momentum fields. We find that the EFTofLSS prediction at two loops matches to percent accuracy the non-linear matter power spectrum at redshift zero up to k∼ 0.6 h Mpc{sup −1}, requiring just one unknown coefficient that needs to be fit to observations. Given that Standard Perturbation Theory stops converging at redshift zero at k∼ 0.1 h Mpc{sup −1}, our results demonstrate the possibility of accessing a factor of order 200 more dark matter quasi-linear modes than naively expected. If the remaining observational challenges to accessing these modes can be addressed with similar success, our results show that there is tremendous potential for large scale structure surveys to explore the primordial universe.

  7. Shark IgNAR antibody mimotopes target a murine immunoglobulin through extended CDR3 loop structures.

    PubMed

    Simmons, David P; Streltsov, Victor A; Dolezal, Olan; Hudson, Peter J; Coley, Andrew M; Foley, Michael; Proll, David F; Nuttall, Stewart D

    2008-04-01

    Mimotopes mimic the three-dimensional topology of an antigen epitope, and are frequently recognized by antibodies with affinities comparable to those obtained for the original antibody-antigen interaction. Peptides and anti-idiotypic antibodies are two classes of protein mimotopes that mimic the topology (but not necessarily the sequence) of the parental antigen. In this study, we combine these two classes by selecting mimotopes based on single domain IgNAR antibodies, which display exceptionally long CDR3 loop regions (analogous to a constrained peptide library) presented in the context of an immunoglobulin framework with adjacent and supporting CDR1 loops. By screening an in vitro phage-display library of IgNAR variable domains (V(NAR)s) against the target antigen monoclonal antibody MAb5G8, we obtained four potential mimotopes. MAb5G8 targets a linear tripeptide epitope (AYP) in the flexible signal sequence of the Plasmodium falciparum Apical Membrane Antigen-1 (AMA1), and this or similar motifs were detected in the CDR loops of all four V(NAR)s. The V(NAR)s, 1-A-2, -7, -11, and -14, were demonstrated to bind specifically to this paratope by competition studies with an artificial peptide and all showed enhanced affinities (3-46 nM) compared to the parental antigen (175 nM). Crystallographic studies of recombinant proteins 1-A-7 and 1-A-11 showed that the SYP motifs on these V(NAR)s presented at the tip of the exposed CDR3 loops, ideally positioned within bulge-like structures to make contact with the MAb5G8 antibody. These loops, in particular in 1-A-11, were further stabilized by inter- and intra- loop disulphide bridges, hydrogen bonds, electrostatic interactions, and aromatic residue packing. We rationalize the higher affinity of the V(NAR)s compared to the parental antigen by suggesting that adjacent CDR1 and framework residues contribute to binding affinity, through interactions with other CDR regions on the antibody, though of course definitive support of

  8. A low-cost DAC BIST structure using a resistor loop

    PubMed Central

    Jang, Jaewon; Kim, Heetae

    2017-01-01

    This paper proposes a new DAC BIST (digital-to-analog converter built-in self-test) structure using a resistor loop known as a DDEM ADC (deterministic dynamic element matching analog-to-digital converter). Methods for both switch reduction and switch effect reduction are proposed for solving problems related to area overhead and accuracy of the conventional DAC BIST. The proposed BIST modifies the length of each resistor in the resistor loop via a merging operation and reduces the number of switches and resistors. In addition, the effect of switches is mitigated using the proposed switch effect reduction method. The accuracy of the proposed BIST is demonstrated by the reduction in the switch effect. The experimental results show that the proposed BIST reduces resource usages and the mismatch error caused by the switches. PMID:28212421

  9. A low-cost DAC BIST structure using a resistor loop.

    PubMed

    Jang, Jaewon; Kim, Heetae; Kang, Sungho

    2017-01-01

    This paper proposes a new DAC BIST (digital-to-analog converter built-in self-test) structure using a resistor loop known as a DDEM ADC (deterministic dynamic element matching analog-to-digital converter). Methods for both switch reduction and switch effect reduction are proposed for solving problems related to area overhead and accuracy of the conventional DAC BIST. The proposed BIST modifies the length of each resistor in the resistor loop via a merging operation and reduces the number of switches and resistors. In addition, the effect of switches is mitigated using the proposed switch effect reduction method. The accuracy of the proposed BIST is demonstrated by the reduction in the switch effect. The experimental results show that the proposed BIST reduces resource usages and the mismatch error caused by the switches.

  10. Domain Dynamics in Piezoresponse Force Microscopy: Quantitative Deconvolution and Hysteresis Loop Fine Structure

    SciTech Connect

    Bdikin, Igor; Kholkin, Andrei; Morozovska, A. N.; Svechnikov, S. V.; Kim, S.-H.; Kalinin, Sergei V

    2008-01-01

    Domain dynamics in the Piezoresponse Force Spectroscopy (PFS) experiment is studied using the combination of local hysteresis loop acquisition with simultaneous domain imaging. The analytical theory for PFS signal from domain of arbitrary cross-section is developed and used for the analysis of experimental data on Pb(Zr,Ti)O3 polycrystalline films. The results suggest formation of oblate domain at early stage of the domain nucleation and growth, consistent with efficient screening of depolarization field within the material. The fine structure of the hysteresis loop is shown to be related to the observed jumps in the domain geometry during domain wall propagation (nanoscale Barkhausen jumps), indicative of strong domain-defect interactions.

  11. The structure of n-point one-loop open superstring amplitudes

    NASA Astrophysics Data System (ADS)

    Mafra, Carlos R.; Schlotterer, Oliver

    2014-08-01

    In this article we investigate one-loop amplitudes in maximally supersymmetric superstring theory. The non-anomalous part of the worldsheet integrand is presented for any number of massless open-string states. The polarization dependence is organized into the same BRST-invariant kinematic combinations which also govern the leading string correction to tree-level amplitudes. The dimensions of the bases for both the kinematics and the associated worldsheet integrals is found to be the unsigned Stirling number of first kind. We explain why the same combinatorial structures govern on the one hand finite one-loop amplitudes of equal helicity states in pure Yang-Mills theory and on the other hand the color tensors at order α'2 of the color-dressed tree amplitude.

  12. Polar structure of disclination loops in nematic liquid crystals probed by second-harmonic-light scattering.

    PubMed

    Pardaev, Shokir A; Williams, J C; Twieg, R J; Jakli, A; Gleeson, J T; Ellman, B; Sprunt, S

    2015-03-01

    Angle-resolved, second-harmonic-light scattering (SHLS) measurements are reported for three different classes of thermotropic nematic liquid crystals (NLCs): polar and nonpolar rodlike compounds and a bent-core compound. Results revealing well-defined scattering peaks are interpreted in terms of the electric polarization induced by distortions of the nematic orientational field ("flexopolarity") associated with inversion wall defects, nonsingular disclinations, analogous to Neel walls in ferromagnets, that often exhibit a closed loop morphology in NLCs. Analysis of the SHLS patterns based on this model provides a "proof-of-concept" for a potentially useful method to probe the flexopolar properties of NLCs.

  13. Origin of anomalous hysteresis loops induced by femtosecond laser pulses in GdFeCo amorphous films

    NASA Astrophysics Data System (ADS)

    Xu, Chudong; Chen, Zhifeng; Chen, Daxin; Zhou, Shiming; Lai, Tianshu

    2010-03-01

    A controllable pump-pulse-number magneto-optical Kerr technique combined with an initializing field scanning approach is developed to eliminate and identify memory and accumulation effects, respectively, from external field history and multiple pulse excitations. A series of anomalous loops of GdFeCo films are measured for different amount of pump pulses using this technique, revealing that serious memory and accumulation effects exist in continuous-pulse-pumped anomalous hysteresis loops which show illusory information of hot coercivity and degree of magnetization reversal. Single-pulse-induced anomalous loop reveals that the hot coercivity shown by continuous-pulse-pumped anomalous loops is not the minimum external field that drives real magneto-optical recording.

  14. Loop-induced charmless B decays and B-B¯ mixing

    NASA Astrophysics Data System (ADS)

    Eilam, G.; Gronau, M.

    1988-07-01

    We calculate the rate of the inclusive loop-induced process b-->d+... for three and four families using the constraint of B-B¯ mixing on the quark masses and mixings. We find that the level of background which this process provides to the tree-level b-->u+. . . decay may reach 10% if ||Vub/Vcb||=0.2 and may grow to about 40% if ||Vub/Vcb||=0.07. The branching ratio of b-->d+. . . may reach its highest level of 0.5% if ||Vub/Vcb||=0.2 and 0.1% if Vub=0. In the latter case b-->d+. . . cannot account by itself for the charmless baryonic modes observed recently by the ARGUS collaboration.

  15. Reinforced concrete structural corrosion monitoring using Hi-Bi photonic crystal fibres in a fiber loop structure

    NASA Astrophysics Data System (ADS)

    Bravo, M.; McCague, C.; Fabian, M.; Jaroszewicz, L.; Mergo, P.; Lopez-Amo, M.; Grattan, K. T. V.; Sun, T.

    2014-05-01

    A novel sensing approach has been developed for in-situ corrosion monitoring of steel in reinforced concrete structures, using a fibre loop interferometer sensor system based on a Hi-Bi photonic crystal fibre (PCF). To do so an accurate fibre alignment procedure has been implemented in order to improve the performance of the sensor system embedded into the concrete structure when it is subjected to an accelerated corrosion test. The positive results obtained have confirmed the effectiveness of such a sensor system for applications in structural health monitoring.

  16. Flow Induced Microvascular Network Formation of Therapeutic Relevant Arteriovenous (AV) Loop-Based Constructs in Response to Ionizing Radiation.

    PubMed

    Schmidt, Volker J; Covi, Jennifer M; Koepple, Christoph; Hilgert, Johannes G; Polykandriotis, Elias; Bigdeli, Amir K; Distel, Luitpold V; Horch, Raymund E; Kneser, Ulrich

    2017-02-15

    BACKGROUND The arteriovenous (AV) loop model enables axial vascularization to gain a functional microcirculatory system in tissue engineering constructs in vivo. These constructs might replace surgical flaps for the treatment of complex wounds in the future. Today, free flaps are often exposed to high-dose radiation after defect coverage, according to guideline-oriented treatment plans. Vascular response of AV loop-based constructs has not been evaluated after radiation, although it is of particular importance. It is further unclear whether the interposed venous AV loop graft is crucial for the induction of angiogenesis. MATERIAL AND METHODS We exposed the grafted vein to a single radiation dose of 2 Gy prior to loop construction to alter intrinsic and angio-inductive properties specifically within the graft. Vessel loops were embedded in a fibrin-filled chamber for 15 days and radiation-induced effects on flow-mediated vascularization were assessed by micro-CT and two-dimensional histological analysis. RESULTS Vessel amount was significantly impaired when an irradiated vein graft was used for AV loop construction. However, vessel growth and differentiation were still present. In contrast to vessel density, which was homogeneously diminished in constructs containing irradiated veins, vessel diameter was primarily decreased in the more peripheral regions. CONCLUSIONS Vascular luminal sprouts were significantly diminished in irradiated venous grafts, suggesting that the interposing vein constitutes a vital part of the AV loop model and is essential to initiate flow-mediate angiogenesis. These results add to the current understanding of AV loop-based neovascularization and suggest clinical implications for patients requiring combined AV loop-based tissue transfer and adjuvant radiotherapy.

  17. Flow Induced Microvascular Network Formation of Therapeutic Relevant Arteriovenous (AV) Loop-Based Constructs in Response to Ionizing Radiation

    PubMed Central

    Schmidt, Volker J.; Covi, Jennifer M.; Koepple, Christoph; Hilgert, Johannes G.; Polykandriotis, Elias; Bigdeli, Amir K.; Distel, Luitpold V.; Horch, Raymund E.; Kneser, Ulrich

    2017-01-01

    Background The arteriovenous (AV) loop model enables axial vascularization to gain a functional microcirculatory system in tissue engineering constructs in vivo. These constructs might replace surgical flaps for the treatment of complex wounds in the future. Today, free flaps are often exposed to high-dose radiation after defect coverage, according to guideline-oriented treatment plans. Vascular response of AV loop-based constructs has not been evaluated after radiation, although it is of particular importance. It is further unclear whether the interposed venous AV loop graft is crucial for the induction of angiogenesis. Material/Methods We exposed the grafted vein to a single radiation dose of 2 Gy prior to loop construction to alter intrinsic and angio-inductive properties specifically within the graft. Vessel loops were embedded in a fibrin-filled chamber for 15 days and radiation-induced effects on flow-mediated vascularization were assessed by micro-CT and two-dimensional histological analysis. Results Vessel amount was significantly impaired when an irradiated vein graft was used for AV loop construction. However, vessel growth and differentiation were still present. In contrast to vessel density, which was homogeneously diminished in constructs containing irradiated veins, vessel diameter was primarily decreased in the more peripheral regions. Conclusions Vascular luminal sprouts were significantly diminished in irradiated venous grafts, suggesting that the interposing vein constitutes a vital part of the AV loop model and is essential to initiate flow-mediate angiogenesis. These results add to the current understanding of AV loop-based neovascularization and suggest clinical implications for patients requiring combined AV loop-based tissue transfer and adjuvant radiotherapy. PMID:28199294

  18. Heat removal from bipolar transistor by loop heat pipe with nickel and copper porous structures.

    PubMed

    Nemec, Patrik; Smitka, Martin; Malcho, Milan

    2014-01-01

    Loop heat pipes (LHPs) are used in many branches of industry, mainly for cooling of electrical elements and systems. The loop heat pipe is a vapour-liquid phase-change device that transfers heat from evaporator to condenser. One of the most important parts of the LHP is the porous wick structure. The wick structure provides capillary force to circulate the working fluid. To achieve good thermal performance of LHP, capillary wicks with high permeability and porosity and fine pore radius are expected. The aim of this work was to develop porous structures from copper and nickel powder with different grain sizes. For experiment copper powder with grain size of 50 and 100 μm and nickel powder with grain size of 10 and 25 μm were used. Analysis of these porous structures and LHP design are described in the paper. And the measurements' influences of porous structures in LHP on heat removal from the insulated gate bipolar transistor (IGBT) have been made.

  19. Heat Removal from Bipolar Transistor by Loop Heat Pipe with Nickel and Copper Porous Structures

    PubMed Central

    Smitka, Martin; Malcho, Milan

    2014-01-01

    Loop heat pipes (LHPs) are used in many branches of industry, mainly for cooling of electrical elements and systems. The loop heat pipe is a vapour-liquid phase-change device that transfers heat from evaporator to condenser. One of the most important parts of the LHP is the porous wick structure. The wick structure provides capillary force to circulate the working fluid. To achieve good thermal performance of LHP, capillary wicks with high permeability and porosity and fine pore radius are expected. The aim of this work was to develop porous structures from copper and nickel powder with different grain sizes. For experiment copper powder with grain size of 50 and 100 μm and nickel powder with grain size of 10 and 25 μm were used. Analysis of these porous structures and LHP design are described in the paper. And the measurements' influences of porous structures in LHP on heat removal from the insulated gate bipolar transistor (IGBT) have been made. PMID:24959622

  20. Radiation Enhanced Absorption of Frank Loops by Nanovoids in Cu

    NASA Astrophysics Data System (ADS)

    Chen, Y.; Zhang, X.; Wang, J.

    2016-01-01

    Neutron and heavy ion irradiations generally induce voids in metallic materials, and continuous radiations typically result in void swelling and mechanical failure of the irradiated materials. Recent experiments showed that nanovoids in nanotwinned copper could act as sinks for radiation-induced Frank loops, significantly mitigating radiation damage. In this paper, we report on structural evolution of Frank loops under cascades and address the role of nanovoids in absorbing Frank loops in detail by using molecular dynamics simulations. Results show that a stand-alone Frank loop is stable under cascades. When Frank loops are adjacent to nanovoids, the diffusion of a group of atoms from the loop into nanovoids is accomplished via the formation and propagation of dislocation loops. The loop-nanovoid interactions result in the shrinkage of the nanovoids and the Frank loops.

  1. Radiation Enhanced Absorption of Frank Loops by Nanovoids in Cu

    SciTech Connect

    Chen, Youxing; Zhang, Xinghang; Wang, Jian

    2016-11-01

    Neutron and heavy ion irradiation generally induces voids in metallic materials, and continuous radiations typically result in void swelling and mechanical failure of the irradiated materials. Recent experiments showed that nanovoids in nanotwinned copper could act as sinks for radiation-induced Frank loops, significantly mitigating radiation damage [Y. Chen et al., Nat. Commun. 6:7036 (2015)]. In this paper, we report on structural evolution of Frank loops under cascades and address the role of nanovoids in absorbing Frank loops in detail by using molecular dynamics simulations. Results show that a stand-alone Frank loop is stable under cascades. When Frank loops are adjacent to nanovoids, the diffusion of a group of atoms from the loop into nanovoids is accomplished via the formation and propagation of dislocation loops. The loop-nanovoid interactions result in the shrinkage of the nanovoids and the Frank loops.

  2. Radiation Enhanced Absorption of Frank Loops by Nanovoids in Cu

    DOE PAGES

    Chen, Youxing; Zhang, Xinghang; Wang, Jian

    2016-11-01

    Neutron and heavy ion irradiation generally induces voids in metallic materials, and continuous radiations typically result in void swelling and mechanical failure of the irradiated materials. Recent experiments showed that nanovoids in nanotwinned copper could act as sinks for radiation-induced Frank loops, significantly mitigating radiation damage [Y. Chen et al., Nat. Commun. 6:7036 (2015)]. In this paper, we report on structural evolution of Frank loops under cascades and address the role of nanovoids in absorbing Frank loops in detail by using molecular dynamics simulations. Results show that a stand-alone Frank loop is stable under cascades. When Frank loops are adjacentmore » to nanovoids, the diffusion of a group of atoms from the loop into nanovoids is accomplished via the formation and propagation of dislocation loops. The loop-nanovoid interactions result in the shrinkage of the nanovoids and the Frank loops.« less

  3. Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications.

    PubMed

    Álvarez, Lucía; Lewis-Ballester, Ariel; Roitberg, Adrián; Estrin, Darío A; Yeh, Syun-Ru; Marti, Marcelo A; Capece, Luciana

    2016-05-17

    Human indoleamine 2,3-dioxygenase catalyzes the oxidative cleavage of tryptophan to N-formyl kynurenine, the initial and rate-limiting step in the kynurenine pathway. Additionally, this enzyme has been identified as a possible target for cancer therapy. A 20-amino acid protein segment (the JK loop), which connects the J and K helices, was not resolved in the reported hIDO crystal structure. Previous studies have shown that this loop undergoes structural rearrangement upon substrate binding. In this work, we apply a combination of replica exchange molecular dynamics simulations and site-directed mutagenesis experiments to characterize the structure and dynamics of this protein region. Our simulations show that the JK loop can be divided into two regions: the first region (JK loop(C)) displays specific and well-defined conformations and is within hydrogen bonding distance of the substrate, while the second region (JK loop(N)) is highly disordered and exposed to the solvent. The peculiar flexible nature of JK loop(N) suggests that it may function as a target for post-translational modifications and/or a mediator for protein-protein interactions. In contrast, hydrogen bonding interactions are observed between the substrate and Thr379 in the highly conserved "GTGG" motif of JK loop(C), thereby anchoring JK loop(C) in a closed conformation, which secures the appropriate substrate binding mode for catalysis. Site-directed mutagenesis experiments confirm the key role of this residue, highlighting the importance of the JK loop(C) conformation in regulating the enzymatic activity. Furthermore, the existence of the partially and totally open conformations in the substrate-free form suggests a role of JK loop(C) in controlling substrate and product dynamics.

  4. Three-dimensional flow structure and bed morphology in large elongate meander loops with different outer bank roughness characteristics

    NASA Astrophysics Data System (ADS)

    Konsoer, Kory M.; Rhoads, Bruce L.; Best, James L.; Langendoen, Eddy J.; Abad, Jorge D.; Parsons, Dan R.; Garcia, Marcelo H.

    2016-12-01

    Few studies have examined the three-dimensional flow structure and bed morphology within elongate loops of large meandering channels. The present study focuses on the spatial patterns of three-dimensional flow structure and bed morphology within two elongate meander loops and examines how differences in outer bank roughness influence near-bank flow characteristics. Three-dimensional velocities were measured during two different events - a near-bankfull flow and an overbank event. Detailed data on channel bathymetry and bed form geometry were obtained during a near-bankfull event. Flow structure within the loops is characterized by strong topographic steering by the point bar, by the development of helical motion associated with flow curvature, and by acceleration of flow where bedrock is exposed along the outer bank. Near-bank velocities during the overbank event are less than those for the near-bankfull flow, highlighting the strong influence of the point bar on redistribution of mass and momentum of the flow at subbankfull stages. Multiple outer bank pools are evident within the elongate meander loop with low outer bank roughness, but are not present in the loop with high outer bank roughness, which may reflect the influence of abundant large woody debris on near-bank velocity characteristics. The positions of pools within both loops can be linked to spatial variations in planform curvature. The findings indicate that flow structure and bed morphology in these large elongate loops is similar to that in small elongate loops, but differs somewhat from flow structure and bed morphology reported for experimental elongate loops.

  5. Dynamic response analysis of closed-loop control system for random intelligent truss structure under random forces

    NASA Astrophysics Data System (ADS)

    Gao, Wei; Chen, Jianjun; Zhou, Yabin; Cui, Mingtao

    2004-07-01

    Considering the randomness of structural damping, physical parameters of structural materials, geometric dimensions of active bars and passive bars, applied loads and control forces simultaneously, the problems of dynamic response analysis of closed-loop control system based on probability for the random intelligent truss structures are studied in this paper. The computational expressions of numerical characteristics of structural dynamic response of closed-loop control system are derived by means of the mode superposition method. Through the engineering examples, the influences of the randomness of them on structural dynamic response are inspected and some significant conclusions are obtained.

  6. Antagonist-induced conformational changes in dopamine transporter extracellular loop two involve residues in a potential salt bridge.

    PubMed

    Gaffaney, Jon D; Shetty, Madhur; Felts, Bruce; Pramod, Akula-Bala; Foster, James D; Henry, L Keith; Vaughan, Roxanne A

    2014-07-01

    Ligand-induced changes in the conformation of extracellular loop (EL) 2 in the rat (r) dopamine transporter (DAT) were examined using limited proteolysis with endoproteinase Asp-N and detection of cleavage products by epitope-specific immunoblotting. The principle N-terminal fragment produced by Asp-N was a 19kDa peptide likely derived by proteolysis of EL2 residue D174, which is present just past the extracellular end of TM3. Production of this fragment was significantly decreased by binding of cocaine and other uptake blockers, but was not affected by substrates or Zn(2+), indicating the presence of a conformational change at D174 that may be related to the mechanism of transport inhibition. DA transport activity and cocaine analog binding were decreased by Asp-N treatment, suggesting a requirement for EL2 integrity in these DAT functions. In a previous study we demonstrated that ligand-induced protease resistance also occurred at R218 on the C-terminal side of rDAT EL2. Here using substituted cysteine accessibility analysis of human (h) DAT we confirm cocaine-induced alterations in reactivity of the homologous R219 and identify conformational sensitivity of V221. Focused molecular modeling of D174 and R218 based on currently available Aquifex aeolicus leucine transporter crystal structures places these residues within 2.9Å of one another, suggesting their proximity as a structural basis for their similar conformational sensitivities and indicating their potential to form a salt bridge. These findings extend our understanding of DAT EL2 and its role in transport and binding functions.

  7. Immunophilins and HIV-1 V3 loop for structure-based anti-AIDS drug design.

    PubMed

    Andrianov, Alexander M

    2009-02-01

    The model of the structural complex of cyclophilin A (CycA) belonging to the immunophilins family with the HIV-MN gp120 V3 loop was generated, and the computer-aided design of the immunophilin-derived peptide able to mask the biologically crucial V3 segments was implemented. To this end, the following problems were solved: (i) the NMR-based conformational analysis of the HIV-MN V3 loop was put into effect, and its low energy structure fitting the input experimental observations was determined; (ii) molecular docking of this V3 structure with the X-ray conformation of CycA was carried out, and the energy refining the simulated structural complex was performed; (iii) the matrix of inter-atomic distances for the amino acids of the molecules forming part of the built over-molecular ensemble was computed, the types of interactions responsible for its stabilization were analyzed, and the CycA stretch, which accounts for the binding to V3, was identified; (iv) the most probable 3D structure for this stretch in the unbound state was predicted, and its collation with the X-ray structure for the corresponding site of CycA was performed; (v) the potential energy function and its constituents were studied for the structural complex generated by molecular docking of the V3 loop with the CycA peptide offering the virtual molecule that imitates the CycA segment, making a key contribution to the interactions of the native protein with the HIV-1 principal neutralizing determinant; (vi) as a result of the studies above, the designed molecule was shown to be capable of the efficacious blockading the functionally crucial V3 sites; and (vii) based on the joint analysis of the evidence obtained previously and in the present study, the composition of the peptide cocktail presenting the promising anti-AIDS pharmacological substance was developed. The molecules simulated here by molecular modeling methods may become the first representatives of a new class of the chemical compounds

  8. Structural delineation of stem-loop RNA binding by human TAF15 protein

    PubMed Central

    Kashyap, Maruthi; Ganguly, Akshay Kumar; Bhavesh, Neel Sarovar

    2015-01-01

    Human TATA binding protein associated factor 2 N (TAF15) and Fused in sarcoma (FUS) are nucleic acid binding proteins belonging to the conserved FET family of proteins. They are involved in diverse processes such as pre-mRNA splicing, mRNA transport, and DNA binding. The absence of information regarding the structural mechanism employed by the FET family in recognizing and discriminating their cognate and non-cognate RNA targets has hampered the attainment of consensus on modes of protein-RNA binding for this family. Our study provides a molecular basis of this RNA recognition using a combination of solution-state NMR spectroscopy, calorimetry, docking and molecular dynamics simulation. Analysis of TAF15-RRM solution structure and its binding with stem-loop RNA has yielded conclusive evidence of a non-canonical mode of RNA recognition. Rather than classical stacking interactions that occur across nitrogen bases and aromatic amino acids on ribonucleoprotein sites, moderate-affinity hydrogen bonding network between the nitrogen bases in the stem-loop RNA and a concave face on the RRM surface primarily mediate TAF15-RRM RNA interaction. We have compared the binding affinities across a set of single-stranded RNA oligonucleotides to conclusively establish that RNA binding is dependent upon structural elements in the RNA rather than sequence. PMID:26612539

  9. Structural and dynamic insights into the energetics of activation loop rearrangement in FGFR1 kinase

    NASA Astrophysics Data System (ADS)

    Klein, Tobias; Vajpai, Navratna; Phillips, Jonathan J.; Davies, Gareth; Holdgate, Geoffrey A.; Phillips, Chris; Tucker, Julie A.; Norman, Richard A.; Scott, Andrew D.; Higazi, Daniel R.; Lowe, David; Thompson, Gary S.; Breeze, Alexander L.

    2015-07-01

    Protein tyrosine kinases differ widely in their propensity to undergo rearrangements of the N-terminal Asp-Phe-Gly (DFG) motif of the activation loop, with some, including FGFR1 kinase, appearing refractory to this so-called `DFG flip'. Recent inhibitor-bound structures have unexpectedly revealed FGFR1 for the first time in a `DFG-out' state. Here we use conformationally selective inhibitors as chemical probes for interrogation of the structural and dynamic features that appear to govern the DFG flip in FGFR1. Our detailed structural and biophysical insights identify contributions from altered dynamics in distal elements, including the αH helix, towards the outstanding stability of the DFG-out complex with the inhibitor ponatinib. We conclude that the αC-β4 loop and `molecular brake' regions together impose a high energy barrier for this conformational rearrangement, and that this may have significance for maintaining autoinhibition in the non-phosphorylated basal state of FGFR1.

  10. Argos transcription is induced by the Drosophila EGF receptor pathway to form an inhibitory feedback loop.

    PubMed

    Golembo, M; Schweitzer, R; Freeman, M; Shilo, B Z

    1996-01-01

    Argos is a secreted molecule with an atypical EGF motif. It was recently shown to function as an inhibitor of the signaling triggered by the Drosophila EGF receptor (DER). In this work, we determine the contribution of Argos to the establishment of cell fates in the embryonic ventral ectoderm. Graded activation of DER is essential for patterning the ventral ectoderm. argos mutant embryos show expansion of ventral cell fates suggesting hyperactivation of the DER pathway. In the embryonic ventral ectoderm, argos is expressed in the ventralmost row of cells. We show that argos expression in the ventral ectoderm is induced by the DER pathway: argos is not expressed in DER mutant embryos, while it is ectopically expressed in the entire ventral ectoderm following ubiquitous activation of the DER pathway. argos expression appears to be triggered directly by the DER pathway, since induction can also be observed in cell culture, following activation of DER by its ligand, Spitz. Argos therefore functions in a sequential manner, to restrict the duration and level of DER signaling. This type of inhibitory feedback loop may represent a general paradigm for signaling pathways inducing diverse cell fates within a population of non-committed cells.

  11. Crystal Structures of Trypanosoma cruzi UDP-Galactopyranose Mutase Implicate Flexibility of the Histidine Loop in Enzyme Activation

    SciTech Connect

    Dhatwalia, Richa; Singh, Harkewal; Oppenheimer, Michelle; Sobrado, Pablo; Tanner, John J.

    2012-11-01

    Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. Here we report crystal structures of the galactofuranose biosynthetic enzyme UDP-galactopyranose mutase (UGM) from T. cruzi, which are the first structures of this enzyme from a protozoan parasite. UGM is an attractive target for drug design because galactofuranose is absent in humans but is an essential component of key glycoproteins and glycolipids in trypanosomatids. Analysis of the enzyme-UDP noncovalent interactions and sequence alignments suggests that substrate recognition is exquisitely conserved among eukaryotic UGMs and distinct from that of bacterial UGMs. This observation has implications for inhibitor design. Activation of the enzyme via reduction of the FAD induces profound conformational changes, including a 2.3 {angstrom} movement of the histidine loop (Gly60-Gly61-His62), rotation and protonation of the imidazole of His62, and cooperative movement of residues located on the si face of the FAD. Interestingly, these changes are substantially different from those described for Aspergillus fumigatus UGM, which is 45% identical to T. cruzi UGM. The importance of Gly61 and His62 for enzymatic activity was studied with the site-directed mutant enzymes G61A, G61P, and H62A. These mutations lower the catalytic efficiency by factors of 10-50, primarily by decreasing k{sub cat}. Considered together, the structural, kinetic, and sequence data suggest that the middle Gly of the histidine loop imparts flexibility that is essential for activation of eukaryotic UGMs. Our results provide new information about UGM biochemistry and suggest a unified strategy for designing inhibitors of UGMs from the eukaryotic pathogens.

  12. The LD loop as an important structural element required for transmission of the allosteric signal in the HtrA (DegP) protease from Escherichia coli.

    PubMed

    Figaj, Donata; Gieldon, Artur; Bartczak, Marlena; Koper, Tomasz; Zarzecka, Urszula; Lesner, Adam; Lipinska, Barbara; Skorko-Glonek, Joanna

    2016-09-01

    High-temperature requirement A (HtrA; DegP) from Escherichia coli, an important element of the extracytoplasmic protein quality-control system, is a member of the evolutionarily conserved family of serine proteases. The characteristic feature of this protein is its allosteric mode of activation. The regulatory loops, L3, L2, L1 and LD, play a crucial role in the transmission of the allosteric signal. Yet, the role of LD has not been fully elucidated. Therefore, we undertook a study to explain the role of the individual LD residues in inducing and maintaining the proteolytic activity of HtrA. We investigated the influence of amino acid substitutions located within the LD loop on the kinetics of a model substrate cleavage as well as on the dynamics of the oligomeric structure of HtrA. We found that the mutations that were expected to disturb the loop's structure and/or interactions with the remaining regulatory loops severely diminished the proteolytic activity of HtrA. The opposite effect, that is, increased activity, was observed for G174S substitution, which was predicted to strengthen the interactions mediated by LD. HtrAG174S protein had an equilibrium shifted toward the active enzyme and formed preferentially high-order oligomeric forms.

  13. The one-loop matter bispectrum in the Effective Field Theory of Large Scale Structures

    DOE PAGES

    Angulo, Raul E.; Foreman, Simon; Schmittfull, Marcel; ...

    2015-10-14

    With this study, given the importance of future large scale structure surveys for delivering new cosmological information, it is crucial to reliably predict their observables. The Effective Field Theory of Large Scale Structures (EFTofLSS) provides a manifestly convergent perturbative scheme to compute the clustering of dark matter in the weakly nonlinear regime in an expansion in k/kNL, where k is the wavenumber of interest and kNL is the wavenumber associated to the nonlinear scale. It has been recently shown that the EFTofLSS matches to 1% level the dark matter power spectrum at redshift zero up to k ≃ 0.3 hmore » Mpc–1 and k ≃ 0.6 h Mpc–1 at one and two loops respectively, using only one counterterm that is fit to data. Similar results have been obtained for the momentum power spectrum at one loop. This is a remarkable improvement with respect to former analytical techniques. Here we study the prediction for the equal-time dark matter bispectrum at one loop. We find that at this order it is sufficient to consider the same counterterm that was measured in the power spectrum. Without any remaining free parameter, and in a cosmology for which kNL is smaller than in the previously considered cases (σ8=0.9), we find that the prediction from the EFTofLSS agrees very well with N-body simulations up to k ≃ 0.25 h Mpc–1, given the accuracy of the measurements, which is of order a few percent at the highest k's of interest. While the fit is very good on average up to k ≃ 0.25 h Mpc–1, the fit performs slightly worse on equilateral configurations, in agreement with expectations that for a given maximum k, equilateral triangles are the most nonlinear.« less

  14. Stationary Vortex Loops Induced by Filament Interaction and Local Pinning in a Chemical Reaction-Diffusion System

    NASA Astrophysics Data System (ADS)

    Jiménez, Zulma A.; Steinbock, Oliver

    2012-08-01

    Scroll rings are three-dimensional excitation waves rotating around one-dimensional filament loops. In experiments with the Belousov-Zhabotinsky reaction we show that the collapse of these loops can be stopped by local pinning to only two unexcitable heterogeneities. The resulting vortices rotate around stationary but curved filaments. The absence of filament motion can be explained by repulsive interaction that counteracts the expected curvature-induced motion. The shape and key dependencies of the stationary filaments are well described by a curvature-flow model with additive interaction velocities that rapidly decrease with filament distance.

  15. X-ray crystal structure of MENT: evidence for functional loop-sheet polymers in chromatin condensation.

    PubMed

    McGowan, Sheena; Buckle, Ashley M; Irving, James A; Ong, Poh Chee; Bashtannyk-Puhalovich, Tanya A; Kan, Wan-Ting; Henderson, Kate N; Bulynko, Yaroslava A; Popova, Evgenya Y; Smith, A Ian; Bottomley, Stephen P; Rossjohn, Jamie; Grigoryev, Sergei A; Pike, Robert N; Whisstock, James C

    2006-07-12

    Most serpins are associated with protease inhibition, and their ability to form loop-sheet polymers is linked to conformational disease and the human serpinopathies. Here we describe the structural and functional dissection of how a unique serpin, the non-histone architectural protein, MENT (Myeloid and Erythroid Nuclear Termination stage-specific protein), participates in DNA and chromatin condensation. Our data suggest that MENT contains at least two distinct DNA-binding sites, consistent with its simultaneous binding to the two closely juxtaposed linker DNA segments on a nucleosome. Remarkably, our studies suggest that the reactive centre loop, a region of the MENT molecule essential for chromatin bridging in vivo and in vitro, is able to mediate formation of a loop-sheet oligomer. These data provide mechanistic insight into chromatin compaction by a non-histone architectural protein and suggest how the structural plasticity of serpins has adapted to mediate physiological, rather than pathogenic, loop-sheet linkages.

  16. Conformational sampling and structure prediction of multiple interacting loops in soluble and β-barrel membrane proteins using multi-loop distance-guided chain-growth Monte Carlo method

    PubMed Central

    Tang, Ke; Wong, Samuel W.K.; Liu, Jun S.; Zhang, Jinfeng; Liang, Jie

    2015-01-01

    Motivation: Loops in proteins are often involved in biochemical functions. Their irregularity and flexibility make experimental structure determination and computational modeling challenging. Most current loop modeling methods focus on modeling single loops. In protein structure prediction, multiple loops often need to be modeled simultaneously. As interactions among loops in spatial proximity can be rather complex, sampling the conformations of multiple interacting loops is a challenging task. Results: In this study, we report a new method called multi-loop Distance-guided Sequential chain-Growth Monte Carlo (M-DiSGro) for prediction of the conformations of multiple interacting loops in proteins. Our method achieves an average RMSD of 1.93 Å for lowest energy conformations of 36 pairs of interacting protein loops with the total length ranging from 12 to 24 residues. We further constructed a data set containing proteins with 2, 3 and 4 interacting loops. For the most challenging target proteins with four loops, the average RMSD of the lowest energy conformations is 2.35 Å. Our method is also tested for predicting multiple loops in β-barrel membrane proteins. For outer-membrane protein G, the lowest energy conformation has a RMSD of 2.62 Å for the three extracellular interacting loops with a total length of 34 residues (12, 12 and 10 residues in each loop). Availability and implementation: The software is freely available at: tanto.bioe.uic.edu/m-DiSGro. Contact: jinfeng@stat.fsu.edu or jliang@uic.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25861965

  17. Dual-Band Magnetic Loop Antenna with Monopolar Radiation Using Slot-Loaded Composite Right/Left-Handed Structures

    NASA Astrophysics Data System (ADS)

    Pyo, Seongmin; Lee, Min-Jae; Lee, Kyoung-Joo; Kim, Young-Sik

    A novel dual-band magnetic loop antenna is proposed using slot-loaded composite right/left-handed (SL-CRLH) structures. Since each radiating element consists of a symmetrically-array of unit-cells, a dual-band magnetic loop source is obtained with unchanged beam patterns. Simulations and measurements show its good radiation performance with monopole-like radiation patterns in both operating bands.

  18. Low-order design and high-order simulation of active closed-loop control for aerospace structures under construction

    NASA Technical Reports Server (NTRS)

    Balas, Mark J.

    1989-01-01

    Partially constructed/assembled structures in space are complicated enough but their dynamics will also be operating in closed-loop with feedback controllers. The dynamics of such structures are modeled by large-scale finite element models. The model dimension L is extremely large (approximately 10,000) while the numbers of actuators (M) and sensors (P) are small. The model parameters M(sub m) mass matrix, D(sub o) damping matrix, and K(sub o) stiffness matrix, are all symmetric and sparse (banded). Thus simulation of open-loop structure models of very large dimension can be accomplished by special integration techniques for sparse matrices. The problem of simulation of closed-loop control of such structures is complicated by the addition of controllers. Simulation of closed-loop controlled structures is an essential part of the controller design and evaluation process. Current research in the following areas is presented: high-order simulation of actively controlled aerospace structures; low-order controller design and SCI compensation for unmodeled dynamics; prediction of closed-loop stability using asymptotic eigenvalue series; and flexible robot manipulator control experiment.

  19. Structural-dynamical investigation of the ZnuA histidine-rich loop: involvement in zinc management and transport.

    PubMed

    Falconi, Mattia; Oteri, Francesco; Di Palma, Francesco; Pandey, Saurabh; Battistoni, Andrea; Desideri, Alessandro

    2011-02-01

    Comparative homology modelling techniques have been used to model the protein ZnuA from Salmonella enterica serovar Typhimurium using the 3D structure of the homologous protein from Escherichia coli. These two-domain proteins bind one Zn(2+) atom, with high affinity, in the inter-domain cleft and possess a histidine-rich loop in the N-terminal domain. Alternative structures of the ZnuA histidine-rich loop, never resolved by the X-ray diffraction method, have been modelled. A model of the apo form, one with the histidine-rich loop deleted and two alternative structures with a second zinc ion bound to the histidine-rich loop, have been generated. In all the modelled proteins, investigated through molecular dynamics simulation, the histidine-rich loop is highly mobile and its fluctuations are correlated to the ligand stability observed in the zinc sites. Based on the plasticity of the histidine-rich loop and its significant effects on protein mobility a possible role in the capture and/or transfer of the zinc ions has been suggested.

  20. Formation of large-scale structure from cosmic-string loops and cold dark matter

    NASA Technical Reports Server (NTRS)

    Melott, Adrian L.; Scherrer, Robert J.

    1987-01-01

    Some results from a numerical simulation of the formation of large-scale structure from cosmic-string loops are presented. It is found that even though G x mu is required to be lower than 2 x 10 to the -6th (where mu is the mass per unit length of the string) to give a low enough autocorrelation amplitude, there is excessive power on smaller scales, so that galaxies would be more dense than observed. The large-scale structure does not include a filamentary or connected appearance and shares with more conventional models based on Gaussian perturbations the lack of cluster-cluster correlation at the mean cluster separation scale as well as excessively small bulk velocities at these scales.

  1. Detection of Ligand‐induced Conformational Changes in the Activation Loop of Aurora‐A Kinase by PELDOR Spectroscopy

    PubMed Central

    Burgess, Selena G.; Grazia Concilio, Maria

    2016-01-01

    Abstract The structure of protein kinases has been extensively studied by protein crystallography. Conformational movement of the kinase activation loop is thought to be crucial for regulation of activity; however, in many cases the position of the activation loop in solution is unknown. Protein kinases are an important class of therapeutic target and kinase inhibitors are classified by their effect on the activation loop. Here, we report the use of pulsed electron double resonance (PELDOR) and site‐directed spin labeling to monitor conformational changes through the insertion of MTSL [S‐(1‐oxyl‐2,2,5,5‐tetramethyl‐2,5‐dihydro‐1 H‐pyrrol‐3‐yl)methyl methanesulfonothioate] on the dynamic activation loop and a stable site on the outer surface of the enzyme. The action of different ligands such as microtubule‐associated protein (TPX2) and inhibitors could be discriminated as well as their ability to lock the activation loop in a fixed conformation. This study provides evidence for structural adaptations that could be used for drug design and a methodological approach that has potential to characterize inhibitors in development. PMID:28032021

  2. The thermal structure of solar coronal loops and implications for physical models of coronae

    NASA Technical Reports Server (NTRS)

    Raymond, J. C.; Foukal, P.

    1982-01-01

    EUV spectra of three active region loops observed above the solar limb with the SO55 spectrometer on Skylab are analyzed. It is noted that the lengths, peak temperatures, and pressures of the loops are typical of the X-ray coronal loops to which static models have been applied. It is found that the physical parameters of the coronal loop plasma derived from EUV spectra and raster pictures are not well represented by the static models. Although the loops also contain a significant quantity of cool plasma, no physical reason is found to differentiate them from other active region loops of similar length, pressure, and temperature. Several line ratios in the loop spectrum suggest departures from ionization equilibrium caused by rapid cooling. The source of this cooling material is discussed with reference to several models of loop dynamics.

  3. Loop Heat Pipe Temperature Oscillation Induced by Gravity Assist and Reservoir Heating

    NASA Technical Reports Server (NTRS)

    Ku, Jentung; Garrison, Matthew; Patel, Deepak; Robinson, Franklin; Ottenstein, Laura

    2015-01-01

    The Laser Thermal Control System (LCTS) for the Advanced Topographic Laser Altimeter System (ATLAS) to be installed on NASA's Ice, Cloud, and Land Elevation Satellite (ICESat-2) consists of a constant conductance heat pipe and a loop heat pipe (LHP) with an associated radiator. During the recent thermal vacuum testing of the LTCS where the LHP condenser/radiator was placed in a vertical position above the evaporator and reservoir, it was found that the LHP reservoir control heater power requirement was much higher than the analytical model had predicted. Even with the control heater turned on continuously at its full power, the reservoir could not be maintained at its desired set point temperature. An investigation of the LHP behaviors found that the root cause of the problem was fluid flow and reservoir temperature oscillations, which led to persistent alternate forward and reversed flow along the liquid line and an imbalance between the vapor mass flow rate in the vapor line and liquid mass flow rate in the liquid line. The flow and temperature oscillations were caused by an interaction between gravity and reservoir heating, and were exacerbated by the large thermal mass of the instrument simulator which modulated the net heat load to the evaporator, and the vertical radiator/condenser which induced a variable gravitational pressure head. Furthermore, causes and effects of the contributing factors to flow and temperature oscillations intermingled.

  4. A linear control design structure to maintain loop properties during limit operation in a multi-nozzle turbofan engine

    NASA Technical Reports Server (NTRS)

    Mattern, Duane; Ouzts, Peter

    1991-01-01

    The implementation of multi-variable control systems on turbofan engines requires the use of limit protection to maintain safe engine operation. Since a turbofan engine typically encounters limits during transient operation, the use of a limit protection scheme that modifies the feedback loop may void the desired 'guarantees' associated with linear multi-variable control design methods, necessitating considerable simulation to validate the control with limit protection. An alternative control design structure is proposed that maintains the desired linear feedback properties when certain safety limits are encountered by moving the limit protection scheme outside of the feedback loop. This proposed structure is compared to a structure with a limit protection scheme that modifies the feedback loop properties. The two design structures are compared using both linear and nonlinear simulations. The evaluation emphasizes responses where the fan surge margin limit is encountered.

  5. A linear control design structure to maintain loop properties during limit operation in a multi-nozzle turbofan engine

    NASA Technical Reports Server (NTRS)

    Mattern, Duane; Ouzts, Peter

    1991-01-01

    The implementation of multi-variable control systems on turbofan engines requires the use of limit protection to maintain safe engine operation. Since a turbofan engine typically encounters limits during transient operation, the use of a limit protection scheme that modifies the feedback loop may void the desired 'guarantees' associated with linear multi-variable control design methods, necessitating considerable simulation to validate the control with limited protection. An alternative control design structure is proposed that maintains the desired linear feedback properties when certain safety limits are encountered by moving the limit protection scheme outside the feedback loop. This proposed structure is compared to a structure with a limit protection scheme that modifies the feedback loop properties. The two design structures are compared using both linear and nonlinear simulations. The evaluation emphasizes responses where the fan surge margin limit is encountered.

  6. Two aspects of one loop structure: Unitarity delay in the Standard Model and modular invariance in string theory

    SciTech Connect

    Ahn, C.

    1989-08-01

    We study two aspects of one loop structures in quantum field theories which describe two different areas of particle physics: the one loop unitarity behavior of the Standard Model of electroweak interactions and modular invariance of string model theory. Loop expansion has its importance in that it contains quantum fluctuations due to all physical states in the theory. Therefore, by studying the various models to one loop, we can understand how the contents of the theory can contribute to physically measurable quantities and how the consistency at quantum level restricts the physical states of the theory, as well. In the first half of the thesis, we study one loop corrections to the process {ital e}{sup +}{ital e}{sup {minus}} {yields} {ital W}{sup +}{ital W}{sup {minus}}. In this process, there is a delicate unitarity-saving cancellation between s-channel and t-channel tree level Feynman diagrams. If the one loop contribution due to heavy particles corrects the channels asymmetrically, the cancellation, hence unitarity, will be delayed up to the mass scale of these heavy particles. We refer to this phenomena as the unitarity delay effect. Due to this effect, cross section below these mass scales can have significant radiative corrections which may provide an appropriate window through which we can see the high energy structure of the Standard Model from relatively low energy experiments. In the second half, we will show how quantum consistency can restrict the physical states in string theory. 53 refs., 13 figs.

  7. Properties and Modeling of Unresolved Fine Structure Loops Observed in the Solar Transition Region by IRIS

    NASA Astrophysics Data System (ADS)

    Brooks, David H.; Reep, Jeffrey W.; Warren, Harry P.

    2016-08-01

    Recent observations from the Interface Region Imaging Spectrograph (IRIS) have discovered a new class of numerous low-lying dynamic loop structures, and it has been argued that they are the long-postulated unresolved fine structures (UFSs) that dominate the emission of the solar transition region. In this letter, we combine IRIS measurements of the properties of a sample of 108 UFSs (intensities, lengths, widths, lifetimes) with one-dimensional non-equilibrium ionization simulations, using the HYDRAD hydrodynamic model to examine whether the UFSs are now truly spatially resolved in the sense of being individual structures rather than being composed of multiple magnetic threads. We find that a simulation of an impulsively heated single strand can reproduce most of the observed properties, suggesting that the UFSs may be resolved, and the distribution of UFS widths implies that they are structured on a spatial scale of 133 km on average. Spatial scales of a few hundred kilometers appear to be typical for a range of chromospheric and coronal structures, and we conjecture that this could be an important clue for understanding the coronal heating process.

  8. A novel approach to segregate and identify functional loop regions in protein structures using their Ramachandran maps.

    PubMed

    Kumar, Mattaparthi Venkata Satish; Swaminathan, Rajaram

    2010-03-01

    The loops which connect or flank helices/sheets in protein structures are known to be functionally important. However, ironically they also belong to the part of protein whose structure is least accurately predicted. Here, a new method to isolate and analyze loop regions in protein structure is proposed using the spatial coordinates of the solved three-dimensional structure. The extent of dispersion among points of successive amino acid residues in the Ramachandran map of protein region is utilized to calculate the Mean Separation between these points in the Ramachandran Plot (MSRP). Based on analysis of 2935 protein secondary structure regions obtained using DSSP software, spanning a range from 2 to 64 residues, taken from a set of 170 proteins, it is shown that helices (MSRP < 17) and strands (MSRP < 64) stand effectively demarcated from the loop regions (MSRP > 130). Analysis of 43 DNA binding and 98 ligand binding proteins revealed several loop regions with clear change in MSRP subsequent to binding. The population of such loops correlated with the magnitude of backbone displacement in the protein subsequent to binding. Can changes in MSRP quantify the temporal oscillations in dihedral angles among structured/unstructured regions in proteins? Molecular dynamics simulations (10 ns) revealed that deviations in MSRP among different snapshots in the trajectory were at least twofold higher for unstructured proteins in comparison with ordered proteins. The above results validate the use of MSRP parameter as a tool to identify and investigate functionally active loops and unstructured regions in protein structures. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

  9. The one-loop matter bispectrum in the Effective Field Theory of Large Scale Structures

    SciTech Connect

    Angulo, Raul E.; Foreman, Simon; Senatore, Leonardo; Schmittfull, Marcel E-mail: sfore@stanford.edu E-mail: senatore@stanford.edu

    2015-10-01

    Given the importance of future large scale structure surveys for delivering new cosmological information, it is crucial to reliably predict their observables. The Effective Field Theory of Large Scale Structures (EFTofLSS) provides a manifestly convergent perturbative scheme to compute the clustering of dark matter in the weakly nonlinear regime in an expansion in k/k{sub NL}, where k is the wavenumber of interest and k{sub NL} is the wavenumber associated to the nonlinear scale. It has been recently shown that the EFTofLSS matches to 1% level the dark matter power spectrum at redshift zero up to k≅ 0.3 h Mpc{sup −1} and k≅ 0.6 h Mpc{sup −1} at one and two loops respectively, using only one counterterm that is fit to data. Similar results have been obtained for the momentum power spectrum at one loop. This is a remarkable improvement with respect to former analytical techniques. Here we study the prediction for the equal-time dark matter bispectrum at one loop. We find that at this order it is sufficient to consider the same counterterm that was measured in the power spectrum. Without any remaining free parameter, and in a cosmology for which k{sub NL} is smaller than in the previously considered cases (σ{sub 8}=0.9), we find that the prediction from the EFTofLSS agrees very well with N-body simulations up to k≅ 0.25 h Mpc{sup −1}, given the accuracy of the measurements, which is of order a few percent at the highest k's of interest. While the fit is very good on average up to k≅ 0.25 h Mpc{sup −1}, the fit performs slightly worse on equilateral configurations, in agreement with expectations that for a given maximum k, equilateral triangles are the most nonlinear.

  10. The one-loop matter bispectrum in the Effective Field Theory of Large Scale Structures

    SciTech Connect

    Angulo, Raul E.; Foreman, Simon; Schmittfull, Marcel; Senatore, Leonardo

    2015-10-14

    With this study, given the importance of future large scale structure surveys for delivering new cosmological information, it is crucial to reliably predict their observables. The Effective Field Theory of Large Scale Structures (EFTofLSS) provides a manifestly convergent perturbative scheme to compute the clustering of dark matter in the weakly nonlinear regime in an expansion in k/kNL, where k is the wavenumber of interest and kNL is the wavenumber associated to the nonlinear scale. It has been recently shown that the EFTofLSS matches to 1% level the dark matter power spectrum at redshift zero up to k ≃ 0.3 h Mpc–1 and k ≃ 0.6 h Mpc–1 at one and two loops respectively, using only one counterterm that is fit to data. Similar results have been obtained for the momentum power spectrum at one loop. This is a remarkable improvement with respect to former analytical techniques. Here we study the prediction for the equal-time dark matter bispectrum at one loop. We find that at this order it is sufficient to consider the same counterterm that was measured in the power spectrum. Without any remaining free parameter, and in a cosmology for which kNL is smaller than in the previously considered cases (σ8=0.9), we find that the prediction from the EFTofLSS agrees very well with N-body simulations up to k ≃ 0.25 h Mpc–1, given the accuracy of the measurements, which is of order a few percent at the highest k's of interest. While the fit is very good on average up to k ≃ 0.25 h Mpc–1, the fit performs slightly worse on equilateral configurations, in agreement with expectations that for a given maximum k, equilateral triangles are the most nonlinear.

  11. Removing the invariant salt bridge of parvalbumin increases flexibility in the AB-loop structure.

    PubMed

    Hoh, François; Cavé, Adrien; Strub, Marie Paule; Banères, Jean Louis; Padilla, André

    2009-08-01

    Parvalbumins (PVs) are calcium-buffer proteins that belong to the EF-hand family. Their N-terminal domain consists of two antiparallel helices A and B that make up a flat hydrophobic surface that is associated with the opposite side of the CD and EF binding sites. A single conserved Arg75-Glu81 salt bridge is buried in this hydrophobic interface. The structure of a rat PV mutant in which Arg75 was replaced by alanine was solved by molecular replacement. Unexpectedly, a large distance deviation of 7.8 A was observed for the AB loop but not for the residues that flank the R75A mutation. The thermal stability of the calcium-loaded form is lower (T(m) = 352.0 K; DeltaT(m) = -11.4 K) than that of the wild-type protein and the apo mutant is unfolded at room temperature. Weaker calcium or magnesium affinities were also measured for the R75A mutant (Ca(2+): K(1) = 4.21 x 10(7) M(-1), K(2) = 6.18 x 10(6) M(-1); Mg(2+): K(1) = 2.98 x 10(4) M(-1), K(2) = 3.09 x 10(3) M(-1)). Finally, comparison of the B factors showed an increase in the flexibility of the AB loop that is consistent with this region being more exposed to solvent in the mutant. The mutant structure therefore demonstrates the role of the salt bridge in attaching the nonbinding AB domain to the remaining protein core. Normal-mode analysis indeed indicated an altered orientation of the AB domain with regard to the CD-EF binding domains.

  12. Amplification activation loop between caspase-8 and -9 dominates artemisinin-induced apoptosis of ASTC-a-1 cells.

    PubMed

    Xiao, Fenglian; Gao, Weijie; Wang, Xiaoping; Chen, Tongsheng

    2012-06-01

    Although caspases have been demonstrated to be involved in artemisinin (ARTE)-induced apoptosis, their exact functions are not well understood. The aim of this report is to explore the roles of caspase-8, -9 and -3 during ARTE-induced apoptosis in human lung adenocarcinoma (ASTC-a-1) cells. ARTE treatment induces a rapid generation of reactive oxygen species (ROS), and ROS-dependent apoptosis as well as the activation of caspase-8, -9 and -3 via time- and dose-dependent fashion. Of upmost importance, inhibition of caspase-8 or -9, but not caspase-3, almost completely blocks the ARTE-induced not only activation of the caspase-8, -9 and -3 but also apoptosis. In addition, the apoptotic process triggered by ARTE does not involve the Bid cleavage, tBid translocation, significant loss of mitochondrial membrane potential and cytochrome c release from mitochondria. Moreover, silencing Bax/Bak does not prevent the ATRE-induced cell death as well as the activation of caspase-8, -9 and -3. Collectively, our data firstly demonstrate that ARTE triggers a ROS-mediated positive feedback amplification activation loop between caspase-8 and -9 independent of mitochondria, which dominantly mediated the ARTE-induced apoptosis via a caspase-3-independent apoptotic pathway in ASTC-a-1 cells. Our findings imply a potential to develop new derivatives from artemisinin to effectively initiate the amplification activation loop of caspases.

  13. Folding of a DNA Hairpin Loop Structure in Explicit Solvent Using Replica-Exchange Molecular Dynamics Simulations.

    SciTech Connect

    Kannan, Srinivasaraghavan; Zacharias, Martin W.

    2007-11-01

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Hairpin loop structures are common motifs in folded nucleic acids. The 59-GCGCAGC sequence in DNA forms a characteristic and stable trinucleotide hairpin loop flanked by a two basepair stem helix. To better understand the structure formation of this hairpin loop motif in atomic detail, we employed replica-exchange molecular dynamics (RexMD) simulations starting from a single-stranded DNA conformation. In two independent 36 ns RexMD simulations, conformations in very close agreement with the experimental hairpin structure were sampled as dominant conformations (lowest free energy state) during the final phase of the RexMDs (;35% at the lowest temperature replica). Simultaneous compaction and accumulation of folded structures were observed. Comparison of the GCA trinucleotides from early stages of the simulations with the folded topology indicated a variety of central loop conformations, but arrangements close to experiment that are sampled before the fully folded structure also appeared. Most of these intermediates included a stacking of the C2 and G3 bases, which was further stabilized by hydrogen bonding to the A5 base and a strongly bound water molecule bridging the C2 and A5 in the DNA minor groove. The simulations suggest a folding mechanism where these intermediates can rapidly proceed toward the fully folded hairpin and emphasize the importance of loop and stem nucleotide interactions for hairpin folding. In one simulation, a loop motif with G3 in syn conformation (dihedral flip at N-glycosidic bond) accumulated, resulting in a misfolded hairpin. Such conformations may correspond to long-lived trapped states that have been postulated to account for the folding kinetics of

  14. The role of salt concentration and magnesium binding in HIV-1 subtype-A and subtype-B kissing loop monomer structures.

    PubMed

    Kim, Taejin; Shapiro, Bruce A

    2013-01-01

    The subtype-B monomers of the human immunodeficiency virus type-1 (HIV-1) have experimentally been shown to dimerize at high salt concentration or in the presence of magnesium, while the dimerization of the subtype-A monomers requires magnesium binding at the G273 or G274 phosphate groups regardless of salt concentration. We used explicit solvent molecular dynamics (MD) simulations to investigate the conformational changes in subtype-A and -B monomers in different salt concentrations, and we found that our MD simulation results are consistent with those of experiments. At low salt concentration, hairpin loop structures of both subtypes were deformed and bases in the hairpin loop were turned inside. At high salt concentrations, the subtype-B monomer maintained the hairpin loop shape and most bases in the hairpin loop pointed out, while the subtype-A monomer showed a severe deformation. We also found that the flanking bases in the subtype-B stabilize the hairpin loop, while the flanking base G273 in the subtype-A caused a significant deformation. However, a bound magnesium ion at the G273 or G274 phosphate groups controlled the behavior of the G273 base and prevented the subtype-A monomer from deformation. We also applied restraints to both subtypes to examine the role of high salt concentration or magnesium binding. While restraints were applied, both subtypes at 0 M salt concentration maintained their shapes. However, when restraints were removed, they deformed significantly. Therefore, we suggest that the dimerization of both subtypes requires the proper conformation of the monomers which is induced by the appropriate salt strength and magnesium ion binding.

  15. Structures of apo IRF-3 and IRF-7 DNA binding domains: effect of loop L1 on DNA binding

    SciTech Connect

    De Ioannes, Pablo; Escalante, Carlos R.; Aggarwal, Aneel K.

    2013-11-20

    Interferon regulatory factors IRF-3 and IRF-7 are transcription factors essential in the activation of interferon-{beta} (IFN-{beta}) gene in response to viral infections. Although, both proteins recognize the same consensus IRF binding site AANNGAAA, they have distinct DNA binding preferences for sites in vivo. The X-ray structures of IRF-3 and IRF-7 DNA binding domains (DBDs) bound to IFN-{beta} promoter elements revealed flexibility in the loops (L1-L3) and the residues that make contacts with the target sequence. To characterize the conformational changes that occur on DNA binding and how they differ between IRF family members, we have solved the X-ray structures of IRF-3 and IRF-7 DBDs in the absence of DNA. We found that loop L1, carrying the conserved histidine that interacts with the DNA minor groove, is disordered in apo IRF-3 but is ordered in apo IRF-7. This is reflected in differences in DNA binding affinities when the conserved histidine in loop L1 is mutated to alanine in the two proteins. The stability of loop L1 in IRF-7 derives from a unique combination of hydrophobic residues that pack against the protein core. Together, our data show that differences in flexibility of loop L1 are an important determinant of differential IRF-DNA binding.

  16. Identification of an evolutionary conserved structural loop that is required for the enzymatic and biological function of tryptophan 2,3-dioxygenase

    PubMed Central

    Michels, Helen; Seinstra, Renée I.; Uitdehaag, Joost C. M.; Koopman, Mandy; van Faassen, Martijn; Martineau, Céline N.; Kema, Ido P.; Buijsman, Rogier; Nollen, Ellen A. A.

    2016-01-01

    The enzyme TDO (tryptophan 2,3-dioxygenase; TDO-2 in Caenorhabditis elegans) is a potential therapeutic target to cancer but is also thought to regulate proteotoxic events seen in the progression of neurodegenerative diseases. To better understand its function and develop specific compounds that target TDO we need to understand the structure of this molecule. In C. elegans we compared multiple different CRISPR/Cas9-induced tdo-2 deletion mutants and identified a motif of three amino acids (PLD) that is required for the enzymatic conversion of tryptophan to N-formylkynurenine. Loss of TDO-2’s enzymatic activity in PDL deletion mutants was accompanied by an increase in motility during aging and a prolonged lifespan, which is in line with the previously observed phenotypes induced by a knockdown of the full enzyme. Comparison of sequence structures suggests that blocking this motif might interfere with haem binding, which is essential for the enzyme’s activity. The fact that these three residues are situated in an evolutionary conserved structural loop of the enzyme suggests that the findings can be translated to humans. The identification of this specific loop region in TDO-2–essential for its catalytic function–will aid in the design of novel inhibitors to treat diseases in which the TDO enzyme is overexpressed or hyperactive. PMID:27995966

  17. Structural Insights Into Substrate Recognition by the Neurospora Varkud Satellite Ribozyme: Importance of U-Turns at the Kissing-Loop Junction

    PubMed Central

    2013-01-01

    Substrate recognition by the Neurospora Varkud satellite ribozyme depends on the formation of a magnesium-dependent kissing-loop interaction between the stem-loop I (SLI) substrate and stem-loop V (SLV) of the catalytic domain. From mutagenesis studies, it has been established that this I/V kissing-loop interaction involves three Watson–Crick base pairs and is associated with a structural rearrangement of the SLI substrate that facilitates catalysis. Here, we report the NMR structural characterization of this I/V kissing-loop using isolated stem-loops. NMR studies were performed on different SLI/SLV complexes containing a common SLV and shiftable, preshifted, or double-stranded SLI variants. These studies confirm the presence of three Watson–Crick base pairs at the kissing-loop junction and provide evidence for the structural rearrangement of shiftable SLI variants upon SLV binding. NMR structure determination of an SLI/SLV complex demonstrates that both the SLI and SLV loops adopt U-turn structures, which facilitates intermolecular Watson–Crick base pairing. Several other interactions at the I/V interface, including base triples and base stacking, help create a continuously stacked structure. These NMR studies provide a structural basis to understand the stability of the I/V kissing-loop interaction and lead us to propose a kinetic model for substrate activation in the VS ribozyme. PMID:24325625

  18. Structural insights into substrate recognition by the Neurospora Varkud satellite ribozyme: importance of U-turns at the kissing-loop junction.

    PubMed

    Bouchard, Patricia; Legault, Pascale

    2014-01-14

    Substrate recognition by the Neurospora Varkud satellite ribozyme depends on the formation of a magnesium-dependent kissing-loop interaction between the stem-loop I (SLI) substrate and stem-loop V (SLV) of the catalytic domain. From mutagenesis studies, it has been established that this I/V kissing-loop interaction involves three Watson-Crick base pairs and is associated with a structural rearrangement of the SLI substrate that facilitates catalysis. Here, we report the NMR structural characterization of this I/V kissing-loop using isolated stem-loops. NMR studies were performed on different SLI/SLV complexes containing a common SLV and shiftable, preshifted, or double-stranded SLI variants. These studies confirm the presence of three Watson-Crick base pairs at the kissing-loop junction and provide evidence for the structural rearrangement of shiftable SLI variants upon SLV binding. NMR structure determination of an SLI/SLV complex demonstrates that both the SLI and SLV loops adopt U-turn structures, which facilitates intermolecular Watson-Crick base pairing. Several other interactions at the I/V interface, including base triples and base stacking, help create a continuously stacked structure. These NMR studies provide a structural basis to understand the stability of the I/V kissing-loop interaction and lead us to propose a kinetic model for substrate activation in the VS ribozyme.

  19. Insights into the Structure, Correlated Motions, and Electrostatic Properties of Two HIV-1 gp120 V3 Loops

    PubMed Central

    Kieslich, Chris A.; Morikis, Dimitrios

    2012-01-01

    The V3 loop of the glycoprotein 120 (gp120) is a contact point for cell entry of HIV-1 leading to infection. Despite sequence variability and lack of specific structure, the highly flexible V3 loop possesses a well-defined role in recognizing and selecting cell-bound coreceptors CCR5 and CXCR4 through a mechanism of charge complementarity. We have performed two independent molecular dynamics (MD) simulations to gain insights into the dynamic character of two V3 loops with slightly different sequences, but significantly different starting crystallographic structures. We have identified highly populated trajectory-specific salt bridges between oppositely charged stem residues Arg9 and Glu25 or Asp29. The two trajectories share nearly identical correlated motions within the simulations, despite their different overall structures. High occupancy salt bridges play a key role in the major cross-correlated motions in both trajectories, and may be responsible for transient structural stability in preparation for coreceptor binding. In addition, the two V3 loops visit conformations with similarities in spatial distributions of electrostatic potentials, despite their inherent flexibility, which may play a role in coreceptor recognition. It is plausible that cooperativity between overall electrostatic potential, charged residue interactions, and correlated motions could be associated with a coreceptor selection and binding. PMID:23185486

  20. Mutation-induced loop opening and energetics for binding of tamiflu to influenza N8 neuraminidase.

    PubMed

    Kar, Parimal; Knecht, Volker

    2012-05-31

    Tamiflu, also known as oseltamivir (OTV), binds to influenza A neuraminidase (H5N1) with very high affinity (0.32 nM). However, this inhibitor binds to other neuraminidases as well. In the present work, a systematic computational study is performed to investigate the mechanism underlying the binding of oseltamivir to N8 neuraminidase (NA) in "open" and "closed" conformations of the 150-loop through molecular dynamics simulations and the popular and well established molecular mechanics Poisson-Boltzmann (MM-PBSA) free energy calculation method. Whereas the closed conformation is stable for wild type N8, it transforms into the open conformation for the mutants Y252H, H274Y, and R292K, indicating that bound to oseltamivir these mutants are preferentially in the open conformation. Our calculations show that the binding of wild type oseltamivir to the closed conformation of N8 neuraminidase is energetically favored compared to the binding to the open conformation. We observe water mediated binding of oseltamivir to the N8 neuraminidase in both conformations which is not seen in the case of binding of the same drug to the H5N1 neuraminidase. The decomposition of the binding free energy reveals the mechanisms underlying the binding and changes in affinity due to mutations. Considering the mutant N8 variants in the open conformation adopted during the simulations, we observe a significant loss in the size of the total binding free energy for the N8(Y252H)-OTV, N8(H274Y)-OTV, and N8(R292K)-OTV complexes compared to N8(WT)-OTV, mainly due to the decrease in the size of the intermolecular electrostatic energy. For R292K, an unfavorable shift in the van der Waals interactions also contributes to the drug resistance. The mutations cause a significant expansion in the active site cavity, increasing its solvent accessible surface compared to the crystal structures of both the open and closed conformations. Our study underscores the need to consider dynamics in rationalizing the

  1. Statistical characterization of the internal structure of noiselike pulses using a nonlinear optical loop mirror

    NASA Astrophysics Data System (ADS)

    Pottiez, O.; Paez-Aguirre, R.; Cruz, J. L.; Andrés, M. V.; Kuzin, E. A.

    2016-10-01

    In this work we study statistically the internal structure of noiselike pulses generated by a passively mode-locked fiber laser. For this purpose, we use a technique that allows estimating the distribution of the amplitudes of the sub-pulses in the bunch. The technique takes advantage of the fast response of the optical Kerr effect in a fiber nonlinear optical loop mirror (NOLM). It requires the measurement of the energy transfer characteristic of the pulses through the NOLM, and the numerical resolution of a system of nonlinear algebraic equations. The results yield a strongly asymmetric distribution, with a high-amplitude tail that is compatible with the existence of extreme-intensity sub-pulses in the bunch. Following the recent discovery of pulse-energy rogue waves and spectral rogue waves in the noiselike pulse regime, we propose a new way to look for extreme events in this particular mode of operation of mode-locked fiber lasers, and confirm that rogue wave generation is a key ingredient in the complex dynamics of these unconventional pulses.

  2. Structure of force networks in tapped particulate systems of disks and pentagons. I. Clusters and loops.

    PubMed

    Pugnaloni, Luis A; Carlevaro, C Manuel; Kramár, M; Mischaikow, K; Kondic, L

    2016-06-01

    The force network of a granular assembly, defined by the contact network and the corresponding contact forces, carries valuable information about the state of the packing. Simple analysis of these networks based on the distribution of force strengths is rather insensitive to the changes in preparation protocols or to the types of particles. In this and the companion paper [Kondic et al., Phys. Rev. E 93, 062903 (2016)10.1103/PhysRevE.93.062903], we consider two-dimensional simulations of tapped systems built from frictional disks and pentagons, and study the structure of the force networks of granular packings by considering network's topology as force thresholds are varied. We show that the number of clusters and loops observed in the force networks as a function of the force threshold are markedly different for disks and pentagons if the tangential contact forces are considered, whereas they are surprisingly similar for the network defined by the normal forces. In particular, the results indicate that, overall, the force network is more heterogeneous for disks than for pentagons. Such differences in network properties are expected to lead to different macroscale response of the considered systems, despite the fact that averaged measures (such as force probability density function) do not show any obvious differences. Additionally, we show that the states obtained by tapping with different intensities that display similar packing fraction are difficult to distinguish based on simple topological invariants.

  3. Repetitive formation and decay of current sheets in magnetic loops: An origin of diverse magnetic structures

    SciTech Connect

    Kumar, Dinesh; Bhattacharyya, R.; Smolarkiewicz, P. K.

    2015-01-15

    In this work, evolution of an incompressible, thermally homogeneous, infinitely conducting, viscous magnetofluid is numerically explored as the fluid undergoes repeated events of magnetic reconnection. The initial magnetic field is constructed by a superposition of two linear force-free fields and has similar morphology as the magnetic loops observed in the solar corona. The results are presented for computations with three distinct sets of footpoint geometries. To onset reconnection, we rely on numerical model magnetic diffusivity, in the spirit of implicit large eddy simulation. It is generally expected that in a high Lundquist number fluid, repeated magnetic reconnections are ubiquitous and hence can lead to a host of magnetic structures with considerable observational importance. In particular, the simulations presented here illustrate formations of magnetic islands, rotating magnetic helices and rising flux ropes—depending on the initial footpoint geometry but through the common process of repeated magnetic reconnections. Further, we observe the development of extended current sheets in two case studies, where the footpoint reconnections generate favorable dynamics.

  4. Regulative Loops, Step Loops and Task Loops

    ERIC Educational Resources Information Center

    VanLehn, Kurt

    2016-01-01

    This commentary suggests a generalization of the conception of the behavior of tutoring systems, which the target article characterized as having an outer loop that was executed once per task and an inner loop that was executed once per step of the task. A more general conception sees these two loops as instances of regulative loops, which…

  5. Possible use of spin-vortex-induced loop currents as qubits: A numerical simulation for two-qubit system

    NASA Astrophysics Data System (ADS)

    Wakaura, Hikaru; Koizumi, Hiroyasu

    2016-02-01

    We propose new qubits; they are nano-sized persistent loop currents called, the spin-vortex-induced loop currents (SVILCs), predicted to exist in hole doped cuprate superconductors in one of the proposed mechanisms of the cuprate superconductivity. In the SVILC theory for the cuprate superconductivity, the superconducting state arises when the network of SVILCs generates a macroscopic current as a collection of the loop currents. The predicted SVILC has a number of properties that are suitable for qubits: each SVILC is characterized by topological winding number, thus, expected to be robust against environmental perturbations; because of the smallness of their size, they can be assembled into a large qubit-number system in a small space. Energy levels of different current patterns of the SVILC system are split by an external inhomogeneous magnetic field, and they are used as qubit states. The quantum gate control is achieved by the Rabi oscillation using electric dipole transitions. We have calculated the transition dipole moments between different SVILC qubit states. Some of the calculated values are relatively large, around 10-30 C m. We have also performed a numerical simulation for the Glover's search algorithm using the two-qubit SVILC system. The search completes in a nanosecond order using the electromagnetic field with electric field amplitude 105 V/m. The present results indicate the quantum gate control capability of the SVILC qubits, and suggest the potentiality to satisfy DiVincenzo's criteria for quantum computers.

  6. Structure-function relationships of curaremimetic neurotoxin loop 2 and of a structurally similar segment of rabies virus glycoprotein in their interaction with the nicotinic acetylcholine receptor

    SciTech Connect

    Lentz, T.L. )

    1991-11-12

    Peptides corresponding to portions of curaremimetic neurotoxin loop 2 and to a structurally similar segment of rabies virus glycoprotein were synthetically modified in order to gain information on structure-function relationships of neurotoxin loop 2 interactions with the acetylcholine receptor. Binding of synthetic peptides to the acetylcholine receptor of Torpedo electric organ membranes was assessed by measuring their ability to inhibit the binding of {sup 125}I-{alpha}-bungarotoxin to the receptor. The peptides showing the highest affinity for the receptor were a peptide corresponding to the sequence of loop 2 (residues 25-44) of Ophiophagus hannah (king cobra) toxin b and the structurally similar segment of CVS rabies virus glycoprotein. These affinities were comparable to those of d-tubocurarine and suberyldicholine. These results demonstrate the importance of loop 2 in the neurotoxin interaction with the receptor. N- and C-terminal deletions of the loop 2 peptides and substitution of residues invariant or highly conserved among neurotoxins were performed in order to determine the role of individual residues in binding. Residues 25-40 are the most crucial in the interaction with the acetylcholine receptor. Since this region of the glycoprotein contains residues corresponding to all of the functionally invariant neurotoxin residues, it may interact with the acetylcholine receptor through a mechanism similar to that of the neurotoxins.

  7. Using the Theory of Elasticity to Model the Structure of DNA Loops

    NASA Astrophysics Data System (ADS)

    Balaeff, Alexander; Mahadevan, L.; Schulten, Klaus

    2000-03-01

    A fast computational method to study the conformation and energetics of short DNA loops is presented. The DNA is modeled as an electrically charged elastic rod. The ensemble of equilibrium conformations of the DNA loop, attainable for given boundary conditions, is generated as a set of numerical solutions to the equations of the Kirchhoff-Love theory of elasticity. The equations are augmented by electrostatic and van der Waals force terms. These modifications allow one to account for the DNA self-repulsion and to model the DNA loop interactions with other macromolecules, involved in a biomolecular system. We demonstrate the application of the method to the test system: the looped lac operon promoter of E. coli clamped by the repressor protein and stabilized by the catabolite gene activator protein. The developed coarse-grained modeling method provides the basis for multi-resolution modeling of protein-DNA complexes, e.g., in combination with all-atom molecular dynamics simulations.

  8. Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere

    NASA Technical Reports Server (NTRS)

    Kang, C.; Berger, I.; Lockshin, C.; Ratliff, R.; Moyzis, R.; Rich, A.

    1995-01-01

    In most metazoans, the telomeric cytosine-rich strand repeating sequence is d(TAACCC). The crystal structure of this sequence was solved to 1.9-A resolution. Four strands associate via the cytosine-containing parts to form a four-stranded intercalated structure held together by C.C+ hydrogen bonds. The base-paired strands are parallel to each other, and the two duplexes are intercalated into each other in opposite orientations. One TAA end forms a highly stabilized loop with the 5' thymine Hoogsteen-base-paired to the third adenine. The 5' end of this loop is in close proximity to the 3' end of one of the other intercalated cytosine strands. Instead of being entirely in a DNA duplex, this structure suggests the possibility of an alternative conformation for the cytosine-rich telomere strands.

  9. Characterization of strain-induced martensite phase in austenitic stainless steel using a magnetic minor-loop scaling relation

    SciTech Connect

    Kobayashi, Satoru; Saito, Atsushi; Takahashi, Seiki; Kamada, Yasuhiro; Kikuchi, Hiroaki

    2008-05-05

    We propose a combined magnetic method using a scaling power-law rule and initial permeability in magnetic minor hysteresis loops for characterization of ferromagnetic {alpha}{sup '} martensites in austenitic stainless steel. The scaling power law between the hysteresis loss and remanence is universal, being independent of volume fraction of strain-induced {alpha}{sup '} martensites. A coefficient of the power law largely decreases with volume fraction, while the initial permeability linearly increases, reflecting a change in the morphology and quantity of martensites, respectively. The present method is highly effective for integrity assessment of austenitic stainless steels because of the sensitivity and extremely low measurement field.

  10. Structures of native and complexed complement factor D: implications of the atypical His57 conformation and self-inhibitory loop in the regulation of specific serine protease activity.

    PubMed

    Jing, H; Babu, Y S; Moore, D; Kilpatrick, J M; Liu, X Y; Volanakis, J E; Narayana, S V

    1998-10-09

    Factor D is a serine protease essential for the activation of the alternative pathway of complement. The structures of native factor D and a complex formed with isatoic anhydride inhibitor were determined at resolution of 2.3 and 1.5 A, respectively, in an isomorphous monoclinic crystal form containing one molecule per asymmetric unit. The native structure was compared with structures determined previously in a triclinic cell containing two molecules with different active site conformations. The current structure shows greater similarity with molecule B in the triclinic cell, suggesting that this may be the dominant factor D conformation in solution. The major conformational differences with molecule A in the triclinic cell are located in four regions, three of which are close to the active site and include some of the residues shown to be critical for factor D catalytic activity. The conformational flexibility associated with these regions is proposed to provide a structural basis for the previously proposed substrate-induced reversible conformational changes in factor D. The high-resolution structure of the factor D/isatoic anhydride complex reveals the binding mode of the mechanism-based inhibitor. The higher specificity towards factor D over trypsin and thrombin is based on hydrophobic interactions between the inhibitor benzyl ring and the aliphatic side-chain of Arg218 that is salt bridged with Asp189 at the bottom of the primary specificity (S1) pocket. Comparison of factor D structural variants with other serine protease structures revealed the presence of a unique "self-inhibitory loop". This loop (214-218) dictates the resting-state conformation of factor D by (1) preventing His57 from adopting active tautomer conformation, (2) preventing the P1 to P3 residues of the substrate from forming anti-parallel beta-sheets with the non-specific substrate binding loop, and (3) blocking the accessibility of Asp189 to the positive1y charged P1 residue of the

  11. GABA(A) receptor M2-M3 loop secondary structure and changes in accessibility during channel gating.

    PubMed

    Bera, Amal K; Chatav, Maya; Akabas, Myles H

    2002-11-08

    The gamma-aminobutyric acid type A (GABA(A)) receptor M2-M3 loop structure and its role in gating were investigated using the substituted cysteine accessibility method. Residues from alpha(1)Arg-273 to alpha(1)Ile-289 were mutated to cysteine, one at a time. MTSET(+) or MTSES(-) reacted with all mutants from alpha(1)R273C to alpha(1)Y281C, except alpha(1)P277C, in the absence and presence of GABA. The MTSET(+) closed-state reaction rate was >1000 liters/mol-s at alpha(1)N274C, alpha(1)S275C, alpha(1)K278C, and alpha(1)Y281C and was <300 liters/mol-s at alpha(1)R273C, alpha(1)L276C, alpha(1)V279C, alpha(1)A280C, and alpha(1)A284C. These two groups of residues lie on opposite sides of an alpha-helix. The fast reacting group lies on a continuation of the M2 segment channel-lining helix face. This suggests that the M2 segment alpha-helix extends about two helical turns beyond alpha(1)N274 (20'), aligned with the extracellular ring of charge. At alpha(1)S275C, alpha(1)V279C, alpha(1)A280C, and alpha(1)A284C the reaction rate was faster in the presence of GABA. The reagents had no functional effect on the mutants from alpha(1)A282C to alpha(1)I289C, except alpha(1)A284C. Access may be sterically hindered possibly by close interaction with the extracellular domain. We suggest that the M2 segment alpha-helix extends beyond the predicted extracellular end of the M2 segment and that gating induces a conformational change in and/or around the N-terminal half of the M2-M3 loop. Implications for coupling ligand-evoked conformational changes in the extracellular domain to channel gating in the membrane-spanning domain are discussed.

  12. Contributions of Charged Residues in Structurally Dynamic Capsid Surface Loops to Rous Sarcoma Virus Assembly

    PubMed Central

    Heyrana, Katrina J.; Goh, Boon Chong; Nguyen, Tam-Linh N.; England, Matthew R.; Bewley, Maria C.; Schulten, Klaus

    2016-01-01

    ABSTRACT Extensive studies of orthoretroviral capsids have shown that many regions of the CA protein play unique roles at different points in the virus life cycle. The N-terminal domain (NTD) flexible-loop (FL) region is one such example: exposed on the outer capsid surface, it has been implicated in Gag-mediated particle assembly, capsid maturation, and early replication events. We have now defined the contributions of charged residues in the FL region of the Rous sarcoma virus (RSV) CA to particle assembly. Effects of mutations on assembly were assessed in vivo and in vitro and analyzed in light of new RSV Gag lattice models. Virus replication was strongly dependent on the preservation of charge at a few critical positions in Gag-Gag interfaces. In particular, a cluster of charges at the beginning of FL contributes to an extensive electrostatic network that is important for robust Gag assembly and subsequent capsid maturation. Second-site suppressor analysis suggests that one of these charged residues, D87, has distal influence on interhexamer interactions involving helix α7. Overall, the tolerance of FL to most mutations is consistent with current models of Gag lattice structures. However, the results support the interpretation that virus evolution has achieved a charge distribution across the capsid surface that (i) permits the packing of NTD domains in the outer layer of the Gag shell, (ii) directs the maturational rearrangements of the NTDs that yield a functional core structure, and (iii) supports capsid function during the early stages of virus infection. IMPORTANCE The production of infectious retrovirus particles is a complex process, a choreography of protein and nucleic acid that occurs in two distinct stages: formation and release from the cell of an immature particle followed by an extracellular maturation phase during which the virion proteins and nucleic acids undergo major rearrangements that activate the infectious potential of the virion. This

  13. Structural discrimination of robustness in transcriptional feedforward loops for pattern formation.

    PubMed

    Rodrigo, Guillermo; Elena, Santiago F

    2011-02-14

    Signaling pathways are interconnected to regulatory circuits for sensing the environment and expressing the appropriate genetic profile. In particular, gradients of diffusing molecules (morphogens) determine cell fate at a given position, dictating development and spatial organization. The feedforward loop (FFL) circuit is among the simplest genetic architectures able to generate one-stripe patterns by operating as an amplitude detection device, where high output levels are achieved at intermediate input ones. Here, using a heuristic optimization-based approach, we dissected the design space containing all possible topologies and parameter values of the FFL circuits. We explored the ability of being sensitive or adaptive to variations in the critical morphogen level where cell fate is switched. We found four different solutions for precision, corresponding to the four incoherent architectures, but remarkably only one mode for adaptiveness, the incoherent type 4 (I4-FFL). We further carried out a theoretical study to unveil the design principle for such structural discrimination, finding that the synergistic action and cooperative binding on the downstream promoter are instrumental to achieve absolute adaptive responses. Subsequently, we analyzed the robustness of these optimal circuits against perturbations in the kinetic parameters and molecular noise, which has allowed us to depict a scenario where adaptiveness, parameter sensitivity and noise tolerance are different, correlated facets of the robustness of the I4-FFL circuit. Strikingly, we showed a strong correlation between the input (environment-related) and the intrinsic (mutation-related) susceptibilities. Finally, we discussed the evolution of incoherent regulations in terms of multifunctionality and robustness.

  14. Structural Discrimination of Robustness in Transcriptional Feedforward Loops for Pattern Formation

    PubMed Central

    Rodrigo, Guillermo; Elena, Santiago F.

    2011-01-01

    Signaling pathways are interconnected to regulatory circuits for sensing the environment and expressing the appropriate genetic profile. In particular, gradients of diffusing molecules (morphogens) determine cell fate at a given position, dictating development and spatial organization. The feedforward loop (FFL) circuit is among the simplest genetic architectures able to generate one-stripe patterns by operating as an amplitude detection device, where high output levels are achieved at intermediate input ones. Here, using a heuristic optimization-based approach, we dissected the design space containing all possible topologies and parameter values of the FFL circuits. We explored the ability of being sensitive or adaptive to variations in the critical morphogen level where cell fate is switched. We found four different solutions for precision, corresponding to the four incoherent architectures, but remarkably only one mode for adaptiveness, the incoherent type 4 (I4-FFL). We further carried out a theoretical study to unveil the design principle for such structural discrimination, finding that the synergistic action and cooperative binding on the downstream promoter are instrumental to achieve absolute adaptive responses. Subsequently, we analyzed the robustness of these optimal circuits against perturbations in the kinetic parameters and molecular noise, which has allowed us to depict a scenario where adaptiveness, parameter sensitivity and noise tolerance are different, correlated facets of the robustness of the I4-FFL circuit. Strikingly, we showed a strong correlation between the input (environment-related) and the intrinsic (mutation-related) susceptibilities. Finally, we discussed the evolution of incoherent regulations in terms of multifunctionality and robustness. PMID:21340024

  15. Polarimetric fiber vibration sensor based on polarization-diversity loop structure

    NASA Astrophysics Data System (ADS)

    Park, Kyoungsoo; Kim, Young Suk; Jo, Songhyun; Lee, Yong Wook

    2015-07-01

    Here, we demonstrated a polarimetric fiber vibration sensor based on a polarization-diversity loop structure (PDLS) by using polarization-maintaining photonic crystal fiber (PM-PCF). The PDLS is composed of a polarization beam splitter, PM-PCF, and polarization controllers, forming a Sagnac birefringence interferometer (SBI) that has periodic interference spectra. When static strain is applied to PM-PCF used as a sensor head, spectral shift is observed in the output interference spectrum of the SBI of the sensor. If a monochromatic light source such as a laser diode is introduced into the SBI, the output optical power of the SBI is determined by its wavelength-dependent transmittance. If the wavelength of the light source is properly located at a spectral region where the transmittance of the SBI linearly varies, therefore, the magnitude of strain applied to PM-PCF can be found by observing the output voltage variation of a photodetector connected to the output port of the SBI. To investigate the vibration response of the proposed sensor with respect to various types of vibration, vibration diverse in the amplitude and frequency was applied to 8-cm-long PM-PCF by using a cylindrical piezoelectric transducer or a metal cantilever. First, vibration characteristics were examined for single frequency vibration in a range of 1-3000 Hz. Then, the sensor response to naturally damped vibration was explored. It was experimentally observed that the cut-off frequency was ~1900 Hz in the frequency response, and the peak value of the sensor output signal increased with the amount of impulse for naturally damped vibration.

  16. Induced-fit motion of a lid loop involved in catalysis in alginate lyase A1-III.

    PubMed

    Mikami, Bunzo; Ban, Mizuho; Suzuki, Sachiko; Yoon, Hye-Jin; Miyake, Osamu; Yamasaki, Masayuki; Ogura, Kohei; Maruyama, Yukie; Hashimoto, Wataru; Murata, Kousaku

    2012-09-01

    The structures of two mutants (H192A and Y246F) of a mannuronate-specific alginate lyase, A1-III, from Sphingomonas species A1 complexed with a tetrasaccharide substrate [4-deoxy-L-erythro-hex-4-ene-pyranosyluronate-(mannuronate)(2)-mannuronic acid] were determined by X-ray crystallography at around 2.2 Å resolution together with the apo form of the H192A mutant. The final models of the complex forms, which comprised two monomers (of 353 amino-acid residues each), 268-287 water molecules and two tetrasaccharide substrates, had R factors of around 0.17. A large conformational change occurred in the position of the lid loop (residues 64-85) in holo H192A and Y246F compared with that in apo H192A. The lid loop migrated about 14 Å from an open form to a closed form to interact with the bound tetrasaccharide and a catalytic residue. The tetrasaccharide was bound in the active cleft at subsites -3 to +1 as a substrate form in which the glycosidic linkage to be cleaved existed between subsites -1 and +1. In particular, the O(η) atom of Tyr68 in the closed lid loop forms a hydrogen bond to the side chain of a presumed catalytic residue, O(η) of Tyr246, which acts both as an acid and a base catalyst in a syn mechanism.

  17. Correlated particle and magnetic field observations of a large-scale magnetic loop structure behind an interplanetary shock

    NASA Technical Reports Server (NTRS)

    Sanderson, T. R.; Marsden, R. G.; Reinhard, R.; Wenzel, K.-P.; Smith, E. J.

    1983-01-01

    From a survey of observations on ISEE-3, an example of correlated particle and magnetic field observations of a large-scale magnetic loop structure is presented. Bidirectional proton fluxes were observed for a period of 40 hours in the energy range 35-1600 keV approximately 12 hours after the passage of the interplanetary shock of December 11, 1980, and directly after the passage of a discontinuity. For each of the eight logarithmically spaced energy channels, a three-dimensional anisotropy analysis reveals streaming along both directions of the magnetic field. The magnetic field rotated slowly but steadily through approximately 180 deg during this same 40-hour period; this is consistent with the existence of a large-scale loop with extent greater than 0.5 AU. The observations suggest that the particles are being injected into the loop sunward of the spacecraft; they appear as bidirectional fluxes in the outermost regions of the loop arising from a combination of focusing and near scatter-free transport.

  18. Structural Characterization of an LPA1 Second Extracellular Loop Mimetic with a Self-Assembling Coiled-Coil Folding Constraint.

    PubMed

    Young, John K; Clayton, Benjamin T; Kikonyogo, Alexandra; Pham, Truc-Chi T; Parrill, Abby L

    2013-01-29

    G protein-coupled receptor (GPCR) structures are of interest as a means to understand biological signal transduction and as tools for therapeutic discovery. The growing number of GPCR crystal structures demonstrates that the extracellular loops (EL) connecting the membrane-spanning helices show tremendous structural variability relative to the more structurally-conserved seven transmembrane α-helical domains. The EL of the LPA(1) receptor have not yet been conclusively resolved, and bear limited sequence identity to known structures. This study involved development of a peptide to characterize the intrinsic structure of the LPA(1) GPCR second EL. The loop was embedded between two helices that assemble into a coiled-coil, which served as a receptor-mimetic folding constraint (LPA(1)-CC-EL2 peptide). The ensemble of structures from multi-dimensional NMR experiments demonstrated that a robust coiled-coil formed without noticeable deformation due to the EL2 sequence. In contrast, the EL2 sequence showed well-defined structure only near its C-terminal residues. The NMR ensemble was combined with a computational model of the LPA(1) receptor that had previously been validated. The resulting hybrid models were evaluated using docking. Nine different hybrid models interacted with LPA 18:1 as expected, based on prior mutagenesis studies, and one was additionally consistent with antagonist affinity trends.

  19. Flow-induced structured phase in nonionic micellar solutions.

    PubMed

    Cardiel, Joshua J; Tonggu, Lige; de la Iglesia, Pablo; Zhao, Ya; Pozzo, Danilo C; Wang, Liguo; Shen, Amy Q

    2013-12-17

    In this work, we consider the flow of a nonionic micellar solution (precursor) through an array of microposts, with focus on its microstructural and rheological evolution. The precursor contains polyoxyethylene(20) sorbitan monooleate (Tween-80) and cosurfactant monolaurin (ML). An irreversible flow-induced structured phase (NI-FISP) emerges after the nonionic precursor flows through the hexagonal micropost arrays, when subjected to strain rates ~10(4) s(-1) and strain ~10(3). NI-FISP consists of close-looped micellar bundles and multiconnected micellar networks as evidenced by transmission electron microscopy (TEM) and cryo-electron microscopy (cryo-EM). We also conduct small-angle neutron scattering (SANS) measurements in both precursor and NI-FISP to illustrate the structural transition. We propose a potential mechanism for the NI-FISP formation that relies on the micropost arrays and the flow kinematics in the microdevice to induce entropic fluctuations in the micellar solution. Finally, we show that the rheological variation from a viscous precursor solution to a viscoelastic micellar structured phase is associated with the structural evolution from the precursor to NI-FISP.

  20. An adaptive and generalizable closed-loop system for control of medically induced coma and other states of anesthesia

    NASA Astrophysics Data System (ADS)

    Yang, Yuxiao; Shanechi, Maryam M.

    2016-12-01

    Objective. Design of closed-loop anesthetic delivery (CLAD) systems is an important topic, particularly for medically induced coma, which needs to be maintained for long periods. Current CLADs for medically induced coma require a separate offline experiment for model parameter estimation, which causes interruption in treatment and is difficult to perform. Also, CLADs may exhibit bias due to inherent time-variation and non-stationarity, and may have large infusion rate variations at steady state. Finally, current CLADs lack theoretical performance guarantees. We develop the first adaptive CLAD for medically induced coma, which addresses these limitations. Further, we extend our adaptive system to be generalizable to other states of anesthesia. Approach. We designed general parametric pharmacodynamic, pharmacokinetic and neural observation models with associated guidelines, and derived a novel adaptive controller. We further penalized large steady-state drug infusion rate variations in the controller. We derived theoretical guarantees that the adaptive system has zero steady-state bias. Using simulations that resembled real time-varying and noisy environments, we tested the closed-loop system for control of two different anesthetic states, burst suppression in medically induced coma and unconsciousness in general anesthesia. Main results. In 1200 simulations, the adaptive system achieved precise control of both anesthetic states despite non-stationarity, time-variation, noise, and no initial parameter knowledge. In both cases, the adaptive system performed close to a baseline system that knew the parameters exactly. In contrast, a non-adaptive system resulted in large steady-state bias and error. The adaptive system also resulted in significantly smaller steady-state infusion rate variations compared to prior systems. Significance. These results have significant implications for clinically viable CLAD design for a wide range of anesthetic states, with potential cost

  1. A divalent ion is crucial in the structure and dominant-negative function of ID proteins, a class of helix-loop-helix transcription regulators.

    PubMed

    Wong, Marie Vivian; Jiang, Sizun; Palasingam, Paaventhan; Kolatkar, Prasanna R

    2012-01-01

    Inhibitors of DNA binding and differentiation (ID) proteins, a dominant-negative group of helix-loop-helix (HLH) transcription regulators, are well-characterized key players in cellular fate determination during development in mammals as well as Drosophila. Although not oncogenes themselves, their upregulation by various oncogenic proteins (such as Ras, Myc) and their inhibitory effects on cell cycle proteins (such as pRb) hint at their possible roles in tumorigenesis. Furthermore, their potency as inhibitors of cellular differentiation, through their heterodimerization with subsequent inactivation of the ubiquitous E proteins, suggest possible novel roles in engineering induced pluripotent stem cells (iPSCs). We present the high-resolution 2.1Å crystal structure of ID2 (HLH domain), coupled with novel biochemical insights in the presence of a divalent ion, possibly calcium (Ca2+), in the loop of ID proteins, which appear to be crucial for the structure and activity of ID proteins. These new insights will pave the way for new rational drug designs, in addition to current synthetic peptide options, against this potent player in tumorigenesis as well as more efficient ways for stem cells reprogramming.

  2. Evidence for small-molecule-mediated loop stabilization in the structure of the isolated Pin1 WW domain

    SciTech Connect

    Mortenson, David E.; Kreitler, Dale F.; Yun, Hyun Gi; Gellman, Samuel H. Forest, Katrina T.

    2013-12-01

    Two structures of a small protein with a defined tertiary fold, the isolated Pin1 WW domain, have been determined via racemic crystallization with small-molecule additives. These additives, which are either racemic or achiral, appear to stabilize a dynamic loop region of the structure. The human Pin1 WW domain is a small autonomously folding protein that has been useful as a model system for biophysical studies of β-sheet folding. This domain has resisted previous attempts at crystallization for X-ray diffraction studies, perhaps because of intrinsic conformational flexibility that interferes with the formation of a crystal lattice. Here, the crystal structure of the human Pin1 WW domain has been obtained via racemic crystallization in the presence of small-molecule additives. Both enantiomers of a 36-residue variant of the Pin1 WW domain were synthesized chemically, and the l- and d-polypeptides were combined to afford diffracting crystals. The structural data revealed packing interactions of small carboxylic acids, either achiral citrate or a d,l mixture of malic acid, with a mobile loop region of the WW-domain fold. These interactions with solution additives may explain our success in crystallization of this protein racemate. Molecular-dynamics simulations starting from the structure of the Pin1 WW domain suggest that the crystal structure closely resembles the conformation of this domain in solution. The structural data presented here should provide a basis for further studies of this important model system.

  3. Structure of the Neisserial Outer Membrane Protein Opa60: Loop Flexibility Essential to Receptor Recognition and Bacterial Engulfment

    PubMed Central

    2015-01-01

    The structure and dynamics of Opa proteins, which we report herein, are responsible for the receptor-mediated engulfment of Neisseria gonorrheae or Neisseria meningitidis by human cells and can offer deep understanding into the molecular recognition of pathogen–host receptor interactions. Such interactions are vital to understanding bacterial pathogenesis as well as the mechanism of foreign body entry to a human cell, which may provide insights for the development of targeted pharmaceutical delivery systems. The size and dynamics of the extracellular loops of Opa60 required a hybrid refinement approach wherein membrane and distance restraints were used to generate an initial NMR structural ensemble, which was then further refined using molecular dynamics in a DMPC bilayer. The resulting ensemble revealed that the extracellular loops, which bind host receptors, occupy compact conformations, interact with each other weakly, and are dynamic on the nanosecond time scale. We predict that this conformational sampling is critical for enabling diverse Opa loop sequences to engage a common set of receptors. PMID:24813921

  4. A sandwich-type DNA electrochemical biosensor for hairpin-stem-loop structure based on multistep temperature-controlling method

    PubMed Central

    Hong, Guolin; Liu, Yinhuan; Chen, Wei; Weng, Shaohuang; Liu, Qicai; Liu, Ailin; Zheng, Daoxin; Lin, Xinhua

    2012-01-01

    A highly sensitive and selective method for amplified electrochemical detection for hairpin-stem-loop structured target sequences was developed based on the temperature regulation of DNA hybrids on a sandwich-type electrochemical DNA sensor. Multistep hybridization was applied to promote the hybridization efficiency of each section of sandwich structure. The results showed that both multistep and temperature-controlling hybridization techniques were both especially made to fabricate the sensor for the tendency of internal hybridization of target gene sequences. This strategy provides significantly enhanced hybridization efficiency and sequence specificity of electrochemical detection. PMID:23028223

  5. Collision-induced dissociation fragmentation inside disulfide C-terminal loops of natural non-tryptic peptides.

    PubMed

    Samgina, Tatiana Y; Vorontsov, Egor A; Gorshkov, Vladimir A; Artemenko, Konstantin A; Zubarev, Roman A; Ytterberg, Jimmy A; Lebedev, Albert T

    2013-07-01

    Collision-induced dissociation (CID) spectra of long non-tryptic peptides are usually quite complicated and rather difficult to interpret. Disulfide bond formed by two cysteine residues at C-terminus of frog skin peptides precludes one to determine sequence inside the forming loop. Thereby, chemical modification of S-S bonds is often used in "bottom up" sequencing approach. However, low-energy CID spectra of natural non-tryptic peptides with C-terminal disulfide cycle demonstrate an unusual fragmentation route, which may be used to elucidate the "hidden" C-terminal sequence. Low charge state protonated molecules experience peptide bond cleavage at the N-terminus of C-terminal cysteine. The forming isomeric acyclic ions serve as precursors for a series of b-type ions revealing sequence inside former disulfide cycle. The reaction is preferable for peptides with basic lysine residues inside the cycle. It may also be activated by acidic protons of Asp and Glu residues neighboring the loop. The observed cleavages may be quite competitive, revealing the sequence inside disulfide cycle, although S-S bond rupture does not occur in this case.

  6. Loop quantization

    SciTech Connect

    Nicolau, A.

    1988-10-01

    Loop unwinding is a known technique for reducing loop overhead, exposing parallelism, and increasing the efficiency of pipelining. Traditional loop unwinding is limited to the innermost loop in a group of nested loops and the amount of unwinding either is fixed or must be specified by the user, on a case by case basis. In this paper the authors present a general technique for automatically unwinding multiply nested loops, explain its advantages over other transformation techniques, and illustrate its practical effectiveness. Lopp Quantization could be beneficial by itself or coupled with other loop transformations.

  7. The Kinetics of Dislocation Loop Formation in Ferritic Alloys Through the Aggregation of Irradiation Induced Defects

    NASA Astrophysics Data System (ADS)

    Kohnert, Aaron Anthony

    The mechanical properties of materials are often degraded over time by exposure to irradiation environments, a phenomenon that has hindered the development of multiple nuclear reactor design concepts. Such property changes are the result of microstructural changes induced by the collision of high energy particles with the atoms in a material. The lattice defects generated in these recoil events migrate and interact to form extended damage structures. This study has used theoretical models based on the mean field chemical reaction rate theory to analyze the aggregation of isolated lattice defects into larger microstructural features that are responsible for long term property changes, focusing on the development of black dot damage in ferritic iron based alloys. The purpose of such endeavors is two-fold. Primarily, such models explain and quantify the processes through which these microstructures form. Additionally, models provide insight into the behavior and properties of the point defects and defect clusters which drive general microstructural evolution processes. The modeling effort presented in this work has focused on physical fidelity, drawing from a variety of sources of information to characterize the unobservable defect generation and agglomeration processes that give rise to the observable features reported in experimental data. As such, the models are based not solely on isolated point defect creation, as is the case with many older rate theory approaches, but instead on realistic estimates of the defect cluster population produced in high energy cascade damage events. Experimental assessments of the microstructural changes evident in transmission electron microscopy studies provide a means to measure the efficacy of the kinetic models. Using common assumptions of the mobility of defect clusters generated in cascade damage conditions, an unphysically high density of damage features develops at the temperatures of interest with a temperature dependence

  8. Viscoelastic phenomenology based structure assignment for closed-loop vibration control of a beam with sensors and actuators

    NASA Astrophysics Data System (ADS)

    Vadiraja, G. K.; Mahapatra, D. Roy

    2009-03-01

    In this paper we incorporate a novel approach to synthesize a class of closed-loop feedback control, based on the variational structure assignment. Properties of a viscoelastic system are used to design an active feedback controller for an undamped structural system with distributed sensor, actuator and controller. Wave dispersion properties of onedimensional beam system have been studied. Efficiency of the chosen viscoelastic model in enhancing damping and stability properties of one-dimensional viscoelastic bar have been analyzed. The variational structure is projected on a solution space of a closed-loop system involving a weakly damped structure with distributed sensor and actuator with controller. These assign the phenomenology based internal strain rate damping parameter of a viscoelastic system to the usual elastic structure but with active control. In the formulation a model of cantilever beam with non-collocated actuator and sensor has been considered. The formulation leads to the matrix identification problem of two dynamic stiffness matrices. The method has been simplified to obtain control system gains for the free vibration control of a cantilever beam system with collocated actuator-sensor, using quadratic optimal control and pole-placement methods.

  9. Structure-function relationships of curaremimetic neurotoxin loop 2 and of a structurally similar segment of rabies virus glycoprotein in their interaction with the nicotinic acetylcholine receptor.

    PubMed

    Lentz, T L

    1991-11-12

    Peptides corresponding to portions of curaremimetic neurotoxin loop 2 and to a structurally similar segment of rabies virus glycoprotein were synthetically modified in order to gain information on structure-function relationships of neurotoxin loop 2 interactions with the acetylcholine receptor. Binding of synthetic peptides to the acetylcholine receptor of Torpedo electric organ membranes was assessed by measuring their ability to inhibit the binding of 125I-alpha-bungarotoxin to the receptor. The peptides showing the highest affinity for the receptor were a peptide corresponding to the sequence of loop 2 (residues 25-44) of Ophiophagus hannah (king cobra) toxin b (IC50 = 5.7 x 10(-6) M) and the structurally similar segment (residues 173-203) of CVS rabies virus glycoprotein (IC50 = 2.6 x 10(-6) M). These affinities were comparable to those of d-tubocurarine (IC50 = 3.4 x 10(-6) M) and suberyldicholine (IC50 = 2.5 x 10(-6) M). These results demonstrate the importance of loop 2 in the neurotoxin interaction with the receptor. N- and C-terminal deletions of the loop 2 peptides and substitution of residues invariant or highly conserved among neurotoxins were performed in order to determine the role of individual residues in binding. Residues 25-40 are the most crucial in the interaction with the acetylcholine receptor. Modifications involving Lys-27, Trp-29, Phe-33, Arg-37, and Gly-38 reduced affinity of binding. R37D and F33T modifications reduced the affinity of alpha-bungarotoxin residues 28-40 by an order of magnitude. Arg-37 may correspond to the positively charged quaternary ammonium group and Phe-33 to the hydrophobic acetyl methyl group of acetylcholine.(ABSTRACT TRUNCATED AT 250 WORDS)

  10. Distance-Guided Forward and Backward Chain-Growth Monte Carlo Method for Conformational Sampling and Structural Prediction of Antibody CDR-H3 Loops.

    PubMed

    Tang, Ke; Zhang, Jinfeng; Liang, Jie

    2017-01-10

    Antibodies recognize antigens through the complementary determining regions (CDR) formed by six-loop hypervariable regions crucial for the diversity of antigen specificities. Among the six CDR loops, the H3 loop is the most challenging to predict because of its much higher variation in sequence length and identity, resulting in much larger and complex structural space, compared to the other five loops. We developed a novel method based on a chain-growth sequential Monte Carlo method, called distance-guided sequential chain-growth Monte Carlo for H3 loops (DiSGro-H3). The new method samples protein chains in both forward and backward directions. It can efficiently generate low energy, near-native H3 loop structures using the conformation types predicted from the sequences of H3 loops. DiSGro-H3 performs significantly better than another ab initio method, RosettaAntibody, in both sampling and prediction, while taking less computational time. It performs comparably to template-based methods. As an ab initio method, DiSGro-H3 offers satisfactory accuracy while being able to predict any H3 loops without templates.

  11. Dark-matter production through loop-induced processes at the LHC: the s-channel mediator case.

    PubMed

    Mattelaer, Olivier; Vryonidou, Eleni

    We show how studies relevant for mono-X searches at the LHC in simplified models featuring a dark-matter candidate and an s-channel mediator can be performed within the MadGraph5_aMC@NLO framework. We focus on gluon-initiated loop-induced processes, mostly relevant to the case where the mediator couples preferentially to third generation quarks and in particular to the top quark. Our implementation allows us to study signatures at hadron colliders involving missing transverse energy plus jets or plus neutral bosons ([Formula: see text]), possibly including the effects of extra radiation by multi-parton merging and matching to the parton shower.

  12. Production implementation of fully automated, closed loop cure control for advanced composite structures

    NASA Astrophysics Data System (ADS)

    Johnson, Sean A.; Roberts, Nancy K.

    Economic of advanced composite part production requires development and use of the most aggressive cure cycles possible without sacrificing quality. As cure cycles are shortened and heating rates increase, tolerance windows for process parameters become increasingly narrow. These factors are intensified by condensation curing systems which generate large amounts of volatiles. Management of the situation requires fully automated, closed loop process control and a fundamental understanding of the material system used for the application. No turnkey system for this application is currently available. General Dynamics Pomona Division (GD/PD) has developed an integrated closed loop control system which is now being proofed in production. Realization of this system will enable cure time reductions of nearly 50 percent, while increasing yield and maintaining quality.

  13. Distinct Second Extracellular Loop Structures of the Brain Cannabinoid CB1 Receptor: Implication in Ligand Binding and Receptor Function

    PubMed Central

    Shim, Joong-Youn; Rudd, James; Ding, Tomas T.

    2010-01-01

    The G-protein coupled receptor (GPCR) second extracellular loop (E2) is known to play an important role in receptor structure and function. The brain cannabinoid (CB1) receptor is unique in that it lacks the inter-loop E2 disulfide linkage to the transmembrane (TM) helical bundle, a characteristic of many GPCRs. Recent mutation studies of the CB1 receptor, however, suggest the presence of an alternative intra-loop disulfide bond between two E2 Cys residues. Considering the oxidation state of these Cys residues, we determine the molecular structures of the 17-residue E2 in the dithiol form (E2dithiol) and in the disulfide form (E2disulfide) of the CB1 receptor in a fully hydrated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer, employing a combination of simulated annealing (SA) and molecular dynamics (MD) simulation approaches. We characterize the CB1 receptor models with these two E2 forms, CB1(E2dithiol) and CB1(E2disulfide), by analyzing interaction energy, contact number, core crevice and cross-correlation. The results show that the distinct E2 structures interact differently with the TM helical bundle and uniquely modify the TM helical topology, suggesting that E2 plays a critical role in stabilizing receptor structure, regulating ligand binding, and ultimately modulating receptor activation. Further studies on the role of E2 of the CB1 receptor are warranted; particularly comparisons of the ligand-bound form with the present ligand-free form. PMID:21120862

  14. Plastic Changes in Human Motor Cortical Output Induced by Random but not Closed-Loop Peripheral Stimulation: the Curse of Causality

    PubMed Central

    Brown, Kenneth I.; Williams, Elizabeth R.; de Carvalho, Felipe; Baker, Stuart N.

    2016-01-01

    Previous work showed that repetitive peripheral nerve stimulation can induce plastic changes in motor cortical output. Triggering electrical stimulation of central structures from natural activity can also generate plasticity. In this study, we tested whether triggering peripheral nerve stimulation from muscle activity would likewise induce changes in motor output. We developed a wearable electronic device capable of recording electromyogram (EMG) and delivering electrical stimulation under closed-loop control. This allowed paired stimuli to be delivered over longer periods than standard laboratory-based protocols. We tested this device in healthy human volunteers. Motor cortical output in relaxed thenar muscles was first assessed via the recruitment curve of responses to contralateral transcranial magnetic stimulation. The wearable device was then configured to record thenar EMG and stimulate the median nerve at the wrist (intensity around motor threshold, rate ~0.66 Hz). Subjects carried out normal daily activities for 4–7 h, before returning to the laboratory for repeated recruitment curve assessment. Four stimulation protocols were tested (9–14 subjects each): No Stim, no stimuli delivered; Activity, stimuli triggered by EMG activity above threshold; Saved, stimuli timed according to a previous Activity session in the same subject; Rest, stimuli given when EMG was silent. As expected, No Stim did not modify the recruitment curve. Activity and Rest conditions produced no significant effects across subjects, although there were changes in some individuals. Saved produced a significant and substantial increase, with average responses 2.14 times larger at 30% stimulator intensity above threshold. We argue that unavoidable delays in the closed loop feedback, due mainly to central and peripheral conduction times, mean that stimuli in the Activity paradigm arrived too late after cortical activation to generate consistent plastic changes. By contrast, stimuli

  15. Plastic Changes in Human Motor Cortical Output Induced by Random but not Closed-Loop Peripheral Stimulation: the Curse of Causality.

    PubMed

    Brown, Kenneth I; Williams, Elizabeth R; de Carvalho, Felipe; Baker, Stuart N

    2016-01-01

    Previous work showed that repetitive peripheral nerve stimulation can induce plastic changes in motor cortical output. Triggering electrical stimulation of central structures from natural activity can also generate plasticity. In this study, we tested whether triggering peripheral nerve stimulation from muscle activity would likewise induce changes in motor output. We developed a wearable electronic device capable of recording electromyogram (EMG) and delivering electrical stimulation under closed-loop control. This allowed paired stimuli to be delivered over longer periods than standard laboratory-based protocols. We tested this device in healthy human volunteers. Motor cortical output in relaxed thenar muscles was first assessed via the recruitment curve of responses to contralateral transcranial magnetic stimulation. The wearable device was then configured to record thenar EMG and stimulate the median nerve at the wrist (intensity around motor threshold, rate ~0.66 Hz). Subjects carried out normal daily activities for 4-7 h, before returning to the laboratory for repeated recruitment curve assessment. Four stimulation protocols were tested (9-14 subjects each): No Stim, no stimuli delivered; Activity, stimuli triggered by EMG activity above threshold; Saved, stimuli timed according to a previous Activity session in the same subject; Rest, stimuli given when EMG was silent. As expected, No Stim did not modify the recruitment curve. Activity and Rest conditions produced no significant effects across subjects, although there were changes in some individuals. Saved produced a significant and substantial increase, with average responses 2.14 times larger at 30% stimulator intensity above threshold. We argue that unavoidable delays in the closed loop feedback, due mainly to central and peripheral conduction times, mean that stimuli in the Activity paradigm arrived too late after cortical activation to generate consistent plastic changes. By contrast, stimuli delivered

  16. A closed-loop synthetic gene circuit for the treatment of diet-induced obesity in mice

    PubMed Central

    Rössger, Katrin; Charpin-El-Hamri, Ghislaine; Fussenegger, Martin

    2013-01-01

    Diet-induced obesity is a lifestyle-associated medical condition that increases the risk of developing cardiovascular disease, type 2 diabetes and certain types of cancer. Here we report the design of a closed-loop genetic circuit that constantly monitors blood fatty acid levels in the setting of diet-associated hyperlipidemia and coordinates reversible and adjustable expression of the clinically licensed appetite-suppressing peptide hormone pramlintide. Grafting of the peroxisome proliferator-activated receptor-α onto the phloretin-responsive repressor TtgR produces a synthetic intracellular lipid-sensing receptor (LSR) that reversibly induces chimeric TtgR-specific promoters in a fatty acid-adjustable manner. Mice with diet-induced obesity in which microencapsulated cells engineered for LSR-driven expression of pramlintide are implanted show significant reduction in food consumption, blood lipid levels and body weight when put on a high-fat diet. Therapeutic designer circuits that monitor levels of pathologic metabolites and link these with the tailored expression of protein pharmaceuticals may provide new opportunities for the treatment of metabolic disorders. PMID:24281397

  17. Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg2+ Bound Structure in the Presence of Monovalent Ions

    PubMed Central

    2015-01-01

    The Varkud Satellite RNA contains a self-cleaving ribozyme that has been shown to function independently of its surroundings. This 160 nucleotide ribozyme adopts a catalytically active tertiary structure that includes a kissing hairpin complex formed by stem-loop I and stem-loop V (SLV). The five-nucleotide 5′-rUGACU loop of the isolated SLV has been shown to adopt a Mg2+-dependent U-turn structure by solution NMR. This U-turn hairpin is examined here by molecular dynamics simulations in the presence of monovalent and divalent ions. Simulations confirm on an all-atom level the hypotheses for the role of the Mg2+ ions in stabilizing the loop, as well as the role of the solvent exposed U700 base. Additionally, these simulations suggest the Mg2+-free stem-loop adopts a wide range of structures, including energetically favorable structures similar to the Mg2+-bound loop structure. We propose this structure is a “gatekeeper” or precursor to Mg2+ binding when those ions are present. PMID:26328924

  18. Quantum Structure of Field Theory and Standard Model Based on Infinity-Free Loop Regularization/renormalization

    NASA Astrophysics Data System (ADS)

    Wu, Yue-Liang

    2014-04-01

    To understand better the quantum structure of field theory and standard model in particle physics, it is necessary to investigate carefully the divergence structure in quantum field theories (QFTs) and work out a consistent framework to avoid infinities. The divergence has got us into trouble since developing quantum electrodynamics in 1930s. Its treatment via the renormalization scheme is satisfied not by all physicists, like Dirac and Feynman who have made serious criticisms. The renormalization group analysis reveals that QFTs can in general be defined fundamentally with the meaningful energy scale that has some physical significance, which motivates us to develop a new symmetry-preserving and infinity-free regularization scheme called loop regularization (LORE). A simple regularization prescription in LORE is realized based on a manifest postulation that a loop divergence with a power counting dimension larger than or equal to the space-time dimension must vanish. The LORE method is achieved without modifying original theory and leads the divergent Feynman loop integrals well-defined to maintain the divergence structure and meanwhile preserve basic symmetries of original theory. The crucial point in LORE is the presence of two intrinsic energy scales which play the roles of ultraviolet cutoff Mc and infrared cutoff μs to avoid infinities. As Mc can be made finite when taking appropriately both the primary regulator mass and number to be infinity to recover the original integrals, the two energy scales Mc and μs in LORE become physically meaningful as the characteristic energy scale and sliding energy scale, respectively. The key concept in LORE is the introduction of irreducible loop integrals (ILIs) on which the regularization prescription acts, which leads to a set of gauge invariance consistency conditions between the regularized tensor-type and scalar-type ILIs. An interesting observation in LORE is that the evaluation of ILIs with ultraviolet

  19. Quantum Structure of Field Theory and Standard Model Based on Infinity-Free Loop Regularization/renormalization

    NASA Astrophysics Data System (ADS)

    Wu, Yue-Liang

    2014-02-01

    To understand better the quantum structure of field theory and standard model in particle physics, it is necessary to investigate carefully the divergence structure in quantum field theories (QFTs) and work out a consistent framework to avoid infinities. The divergence has got us into trouble since developing quantum electrodynamics in 1930s. Its treatment via the renormalization scheme is satisfied not by all physicists, like Dirac and Feynman who have made serious criticisms. The renormalization group analysis reveals that QFTs can in general be defined fundamentally with the meaningful energy scale that has some physical significance, which motivates us to develop a new symmetry-preserving and infinity-free regularization scheme called loop regularization (LORE). A simple regularization prescription in LORE is realized based on a manifest postulation that a loop divergence with a power counting dimension larger than or equal to the space-time dimension must vanish. The LORE method is achieved without modifying original theory and leads the divergent Feynman loop integrals well-defined to maintain the divergence structure and meanwhile preserve basic symmetries of original theory. The crucial point in LORE is the presence of two intrinsic energy scales which play the roles of ultraviolet cutoff Mc and infrared cutoff μs to avoid infinities. As Mc can be made finite when taking appropriately both the primary regulator mass and number to be infinity to recover the original integrals, the two energy scales Mc and μs in LORE become physically meaningful as the characteristic energy scale and sliding energy scale, respectively. The key concept in LORE is the introduction of irreducible loop integrals (ILIs) on which the regularization prescription acts, which leads to a set of gauge invariance consistency conditions between the regularized tensor-type and scalar-type ILIs. An interesting observation in LORE is that the evaluation of ILIs with ultraviolet

  20. Gravitational steady states of solar coronal loops

    NASA Astrophysics Data System (ADS)

    Sugiyama, Linda E.; Asgari-Targhi, M.

    2017-02-01

    Coronal loops on the surface of the sun appear to consist of curved, plasma-confining magnetic flux tubes or "ropes," anchored at both ends in the photosphere. Toroidal loops carrying current are inherently unstable to expansion in the major radius due to toroidal-curvature-induced imbalances in the magnetic and plasma pressures. An ideal MHD analysis of a simple isolated loop with density and pressure higher than the surrounding corona, based on the theory of magnetically confined toroidal plasmas, shows that the radial force balance depends on the loop internal structure and varies over parameter space. It provides a unified picture of simple loop steady states in terms of the plasma beta βo, the inverse aspect ratio ɛ =a /Ro , and the MHD gravitational parameter G ̂≡g a /vA2 , all at the top of the loop, where g is the acceleration due to gravity, a the average minor radius, and vA the shear Alfvén velocity. In the high and low beta tokamak orderings, βo=2 noT /(Bo2/2 μo)˜ɛ1 and ɛ2 , that fit many loops, the solar gravity can sustain nonaxisymmetric steady states at G ̂˜ɛ βo that represent the maximum stable height. At smaller G ̂≤ɛ2βo , the loop is axisymmetric to leading order and stabilized primarily by the two fixed loop ends. Very low beta, nearly force-free, steady states with βo˜ɛ3 may also exist, with or without gravity, depending on higher order effects. The thin coronal loops commonly observed in solar active regions have ɛ ≃0.02 and fit the high beta steady states. G ̂ increases with loop height. Fatter loops in active regions that form along magnetic neutral lines and may lead to solar flares and Coronal Mass Ejections have ɛ ≃0.1 -0.2 and may fit the low beta ordering. Larger loops tend to have G ̂>ɛ βo and be unstable to radial expansion because the exponential hydrostatic reduction in the density at the loop-top reduces the gravitational force -ρG ̂ R ̂ below the level that balances expansion, in agreement with

  1. Aircraft propeller induced structure-borne noise

    NASA Technical Reports Server (NTRS)

    Unruh, James F.

    1989-01-01

    A laboratory-based test apparatus employing components typical of aircraft construction was developed that would allow the study of structure-borne noise transmission due to propeller induced wake/vortex excitation of in-wake structural appendages. The test apparatus was employed to evaluate several aircraft installation effects (power plant placement, engine/nacelle mass loading, and wing/fuselage attachment methods) and several structural response modifications for structure-borne noise control (the use of wing blocking mass/fuel, wing damping treaments, and tuned mechanical dampers). Most important was the development of in-flight structure-borne noise transmission detection techniques using a combination of ground-based frequency response function testing and in-flight structural response measurement. Propeller wake/vortex excitation simulation techniques for improved ground-based testing were also developed to support the in-flight structure-borne noise transmission detection development.

  2. Lipopolysaccharide induces the expression of an autocrine prolactin loop enhancing inflammatory response in monocytes

    PubMed Central

    2013-01-01

    Background Prolactin from pituitary gland helps maintain homeostasis but it is also released in immune cells where its function is not completely understood. Pleiotropic functions of prolactin (PRL) might be mediated by different isoforms of its receptor (PRLr). Methods The aim of this study was to investigate the relationship between the eventual synthesis of PRL and PRLr isoforms with the inflammatory response in monocytes. We used THP-1 and monocytes isolated from healthy subjects stimulated with lipopolysaccharide (LPS). Western blot, real time PCR and immunocytochemistry were performed to identify both molecules. The bioactivity of the PRL was assessed using a bioassay and ELISA to detect pro inflammatory cytokines. Results PRLr mRNA and PRL mRNA were synthesized in THP-1 monocytes activated with LPS with peaks of 300-fold and 130-fold, respectively. The long (100 kDa) and the intermediate (50 kDa) isoforms of PRLr and big PRL (60 kDa) were time-dependent upregulated for monocytes stimulated with LPS. This expression was confirmed in monocytes from healthy subjects. The PRLr intermediate isoform and the big PRL were found soluble in the culture media and later in the nucleus in THP-1 monocytes stimulated with LPS. Big PRL released by monocytes showed bioactivity in Nb2 Cells, and both PRL and PRLr, synthesized by monocytes were related with levels of nitrites and proinflammatory citokines. Conclusions Our results suggest the expression of a full-autocrine loop of PRL enhances the inflammatory response in activated monocytes. This response mediated by big PRL may contribute to the eradication of potential pathogens during innate immune response in monocytes but may also contribute to inflammatory disorders. PMID:23731754

  3. Experimental observations of the coupling between induced currents and mechanical motion in torsionally supported square loops and plates. Part 2. Data inventory

    SciTech Connect

    Weissenburger, D.W.; Bialek, J.M.; Cargulia, G.J.; Ulrickson, M.; Knott, M.J.; Turner, L.R.; Wehrle, R.B.

    1984-12-01

    A series of experiments was successfully conducted to investigate the coupling between induced currents and rigid body rotation in square loops and plates. The experiments were performed with the Fusion Electromagnetic Induction Experiment (FELIX) facility at the Argonne National Laboratory. The observed data exhibited the magnetic damping and magnetic stiffness effects ehich arise in coupled systems and agreed very well with previous analytic calculations.

  4. Enhancement of surface nonwettability by grafting loops.

    PubMed

    Pei, Han-Wen; Liu, Xiao-Li; Liu, Hong; Zhu, You-Liang; Lu, Zhong-Yuan

    2017-02-08

    We present a computer simulation study on the nonwettability of a flat surface tethered with deformable looped polymer chains. Two kinds of loops are studied: monodispersed loops (loops with the same length) and polydispersed loops (loops with different lengths). Both kinds of loops include two arrangements: with regularly tethered sites and with randomly tethered sites. Regularly grafted loops form typical grooves on the surface, while randomly grafted loops form a more rugged surface. For monodispersed loops, we analyze the factors that influence the nonwettability when varying the rigidity of the loops. The loops are divided into two categories based on their rigidity according to our previous analysis procedure (Phys. Chem. Chem. Phys., 2016, 18, 18767-18775): rigid loops and flexible loops. It is found that the loop can partially form a re-entrant-like structure, which is helpful to increase the nonwettability of the surface. The surfaces with grafted loops have increased nonwettability, especially those grafted with flexible chains. However, the contact angle on the loop structure cannot further increase for the rigid chains due to a large top layer density (Phys. Chem. Chem. Phys., 2016, 18, 18767-18775). For polydispersed loops, the contact angle is highly related to the rigidity of the long loops that contact the droplet. Different from monodispersed loops, the mechanism of the nonwettability of polydispersed loops is attributed to the supporting ability (rigidity) of long loops.

  5. Thermally induced all-optical inverter and dynamic hysteresis loops in graphene oxide dispersions.

    PubMed

    Melle, Sonia; Calderón, Oscar G; Egatz-Gómez, Ana; Cabrera-Granado, E; Carreño, F; Antón, M A

    2015-11-01

    We experimentally study the temporal dynamics of amplitude-modulated laser beams propagating through a water dispersion of graphene oxide sheets in a fiber-to-fiber U-bench. Nonlinear refraction induced in the sample by thermal effects leads to both phase reversing of the transmitted signals and dynamic hysteresis in the input-output power curves. A theoretical model including beam propagation and thermal lensing dynamics reproduces the experimental findings.

  6. Muscle enhancement using closed-loop electrical stimulation: volitional versus induced torque.

    PubMed

    Langzam, E; Nemirovsky, Y; Isakov, E; Mizrahi, J

    2007-06-01

    In cases of partial deficiency of muscle activation capacity, force augmentation can be achieved by hybrid activation, i.e., by combining electrical stimulation (ES) with volitional activation. In this activation modality the shares of the volitional and induced torques within the overall hybrid torque are unknown. The purpose of this study was to suggest a computational approach to parcel out the volitional and stimulation induced components of joint torque generated during combined voluntary and electrical activation of the Tibialis Anterior muscle (TA). For this purpose, isometric contraction of the TA was studied on 5 healthy subjects, using an activation protocol involving ES alone, volitional activation alone and hybrid activation. Ankle torque and TA EMG were measured. A computational algorithm was developed to dissociate the volitional from the overall torque, based on EMG filtering and on pre-measured calibration curves of volitional torque versus EMG. The results indicated that for a certain hybrid torque there is a linear decaying relationship between the induced torque and the volitional torque shares. Moreover, based on a defined enhancement ratio, the results indicate that within the range of stimulation intensities, there exist regions of increased facilitation, in which the stimulation efficiency is higher under combined compared to isolated conditions.

  7. Structural and functional properties of the membranotropic HIV-1 glycoprotein gp41 loop region are modulated by its intrinsic hydrophobic core.

    PubMed

    Qiu, Jiayin; Ashkenazi, Avraham; Liu, Shuwen; Shai, Yechiel

    2013-10-04

    The gp41 disulfide loop region switches from a soluble state to a membrane-bound state during the human immunodeficiency virus type 1 (HIV-1) envelope-mediated membrane fusion process. The loop possesses a hydrophobic core at the center of the region with an unusual basic residue (Lys-601). Furthermore, two loop core mutations, K601A and L602A, are found to inhibit HIV-1 infectivity while keeping wild type-like levels of the envelope, implying that they exert an inhibitory effect on gp41 during the membrane fusion event. Here, we investigated the mode of action of these mutations on the loop region. We show that the K601A mutation, but not the L602A mutation, abolished the binding of a loop-specific monoclonal antibody to a loop domain peptide. Additionally, the K601A, but not the L602A, impaired disulfide bond formation in the peptides. This was correlated with changes in the circular dichroism spectrum imposed by the K601A mutation. In the membrane, however, the L602A, but not the K601A, reduced the lipid mixing ability of the loop peptides, which was correlated with decreased α-helical content of the L602A mutant. The results suggest that the Lys-601 residue provides a moderate hydrophobicity level within the gp41 loop core that contributes to the proper structure and function of the loop inside and outside the membrane. Because basic residues are found between the loop Cys residues of several lentiviral fusion proteins, the findings may contribute to understanding the fusion mechanism of other viruses as well.

  8. The LA loop as an important regulatory element of the HtrA (DegP) protease from Escherichia coli: structural and functional studies.

    PubMed

    Figaj, Donata; Gieldon, Artur; Polit, Agnieszka; Sobiecka-Szkatula, Anna; Koper, Tomasz; Denkiewicz, Milena; Banecki, Bogdan; Lesner, Adam; Ciarkowski, Jerzy; Lipinska, Barbara; Skorko-Glonek, Joanna

    2014-05-30

    Bacterial HtrAs are serine proteases engaged in extracytoplasmic protein quality control and are required for the virulence of several pathogenic species. The proteolytic activity of HtrA (DegP) from Escherichia coli, a model prokaryotic HtrA, is stimulated by stressful conditions; the regulation of this process is mediated by the LA, LD, L1, L2, and L3 loops. The precise mechanism of action of the LA loop is not known due to a lack of data concerning its three-dimensional structure as well as its mode of interaction with other regulatory elements. To address these issues we generated a theoretical model of the three-dimensional structure of the LA loop as per the resting state of HtrA and subsequently verified its correctness experimentally. We identified intra- and intersubunit contacts that formed with the LA loops; these played an important role in maintaining HtrA in its inactive conformation. The most significant proved to be the hydrophobic interactions connecting the LA loops of the hexamer and polar contacts between the LA' (the LA loop on an opposite subunit) and L1 loops on opposite subunits. Disturbance of these interactions caused the stimulation of HtrA proteolytic activity. We also demonstrated that LA loops contribute to the preservation of the integrity of the HtrA oligomer and to the stability of the monomer. The model presented in this work explains the regulatory role of the LA loop well; it should also be applicable to numerous Enterobacteriaceae pathogenic species as the amino acid sequences of the members of this bacterial family are highly conserved.

  9. Contribution of intertwined loop to membrane association revealed by Zika virus full-length NS1 structure.

    PubMed

    Xu, Xiaoying; Song, Hao; Qi, Jianxun; Liu, Yuqian; Wang, Haiyuan; Su, Chao; Shi, Yi; Gao, George F

    2016-10-17

    The association of Zika virus (ZIKV) infections with microcephaly and neurological diseases has highlighted an emerging public health concern. Here, we report the crystal structure of the full-length ZIKV nonstructural protein 1 (NS1), a major host-interaction molecule that functions in flaviviral replication, pathogenesis, and immune evasion. Of note, a long intertwined loop is observed in the wing domain of ZIKV NS1, and forms a hydrophobic "spike", which can contribute to cellular membrane association. For different flaviviruses, the amino acid sequences of the "spike" are variable but their common characteristic is either hydrophobic or positively charged, which is a beneficial feature for membrane binding. Comparative studies with West Nile and Dengue virus NS1 structures reveal conserved features, but diversified electrostatic characteristics on both inner and outer faces. Our results suggest different mechanisms of flavivirus pathogenesis and should be considered during the development of diagnostic tools.

  10. The hypoxia-inducible miR-429 regulates hypoxia-inducible factor-1α expression in human endothelial cells through a negative feedback loop

    PubMed Central

    Bartoszewska, Sylwia; Kochan, Kinga; Piotrowski, Arkadiusz; Kamysz, Wojciech; Ochocka, Renata J.; Collawn, James F.; Bartoszewski, Rafal

    2015-01-01

    Hypoxia-inducible factors (HIFs) 1 and 2 are dimeric α/β transcription factors that regulate cellular responses to low oxygen. HIF-1 is induced first, whereas HIF-2 is associated with chronic hypoxia. To determine how HIF1A mRNA, the inducible subunit of HIF-1, is regulated during hypoxia, we followed HIF1A mRNA levels in primary HUVECs over 24 hours using quantitative PCR. HIF1A and VEGF A (VEGFA) mRNA, a transcriptional target of HIF-1, increased ∼2.5- and 8-fold at 2–4 hours, respectively. To determine how the mRNAs were regulated, we identified a microRNA (miRNA), miR-429, that destabilized HIF1A message and decreased VEGFA mRNA by inhibiting HIF1A. Target protector analysis, which interferes with miRNA-mRNA complex formation, confirmed that miR-429 targeted HIF1A message. Desferoxamine treatment, which inhibits the hydroxylases that promote HIF-1α protein degradation, stabilized HIF-1 activity during normoxic conditions and elevated miR-429 levels, demonstrating that HIF-1 promotes miR-429 expression. RNA-sequencing-based transcriptome analysis indicated that inhibition of miRNA-429 in HUVECs up-regulated 209 mRNAs, a number of which regulate angiogenesis. The results demonstrate that HIF-1 is in a negative regulatory loop with miR-429, that miR-429 attenuates HIF-1 activity by decreasing HIF1A message during the early stages of hypoxia before HIF-2 is activated, and this regulatory network helps explain the HIF-1 transition to HIF-2 during chronic hypoxia in endothelial cells.—Bartoszewska, S., Kochan, K., Piotrowski, A., Kamysz, W., Ochocka, R. J., Collawn, J. F., Bartoszewski, R. The hypoxia-inducible miR-429 regulates hypoxia hypoxia-inducible factor-1α expression in human endothelial cells through a negative feedback loop. PMID:25550463

  11. A Rapid, Manual Method to Map Coronal-Loop Structures of an Active Region Using Cubic Bézier Curves and Its Applications to Misalignment Angle Analysis

    NASA Astrophysics Data System (ADS)

    Gary, G. Allen; Hu, Qiang; Lee, Jong Kwan

    2014-03-01

    A rapid and flexible manual method is described that maps individual coronal loops of a 2D EUV image as Bézier curves using only four points per loop. Using the coronal loops as surrogates of magnetic-field lines, the mapping results restrict the magnetic-field models derived from extrapolations of magnetograms to those admissible and inadmissible via a fitness parameter. We outline explicitly how the coronal loops can be employed in constraining competing magnetic-field models by transforming 2D coronal-loop images into 3D field lines. The magnetic-field extrapolations must satisfy not only the lower boundary conditions of the vector field (the vector magnetogram) but also must have a set of field lines that satisfies the mapped coronal loops in the volume, analogous to an upper boundary condition. This method uses the minimization of the misalignment angles between the magnetic-field model and the best set of 3D field lines that match a set of closed coronal loops. The presented method is an important tool in determining the fitness of magnetic-field models for the solar atmosphere. The magnetic-field structure is crucial in determining the overall dynamics of the solar atmosphere.

  12. Comparing model-based adaptive LMS filters and a model-free hysteresis loop analysis method for structural health monitoring

    NASA Astrophysics Data System (ADS)

    Zhou, Cong; Chase, J. Geoffrey; Rodgers, Geoffrey W.; Xu, Chao

    2017-02-01

    The model-free hysteresis loop analysis (HLA) method for structural health monitoring (SHM) has significant advantages over the traditional model-based SHM methods that require a suitable baseline model to represent the actual system response. This paper provides a unique validation against both an experimental reinforced concrete (RC) building and a calibrated numerical model to delineate the capability of the model-free HLA method and the adaptive least mean squares (LMS) model-based method in detecting, localizing and quantifying damage that may not be visible, observable in overall structural response. Results clearly show the model-free HLA method is capable of adapting to changes in how structures transfer load or demand across structural elements over time and multiple events of different size. However, the adaptive LMS model-based method presented an image of greater spread of lesser damage over time and story when the baseline model is not well defined. Finally, the two algorithms are tested over a simpler hysteretic behaviour typical steel structure to quantify the impact of model mismatch between the baseline model used for identification and the actual response. The overall results highlight the need for model-based methods to have an appropriate model that can capture the observed response, in order to yield accurate results, even in small events where the structure remains linear.

  13. Robust Feedback Control of Flow Induced Structural Radiation of Sound

    NASA Technical Reports Server (NTRS)

    Heatwole, Craig M.; Bernhard, Robert J.; Franchek, Matthew A.

    1997-01-01

    A significant component of the interior noise of aircraft and automobiles is a result of turbulent boundary layer excitation of the vehicular structure. In this work, active robust feedback control of the noise due to this non-predictable excitation is investigated. Both an analytical model and experimental investigations are used to determine the characteristics of the flow induced structural sound radiation problem. The problem is shown to be broadband in nature with large system uncertainties associated with the various operating conditions. Furthermore the delay associated with sound propagation is shown to restrict the use of microphone feedback. The state of the art control methodologies, IL synthesis and adaptive feedback control, are evaluated and shown to have limited success for solving this problem. A robust frequency domain controller design methodology is developed for the problem of sound radiated from turbulent flow driven plates. The control design methodology uses frequency domain sequential loop shaping techniques. System uncertainty, sound pressure level reduction performance, and actuator constraints are included in the design process. Using this design method, phase lag was added using non-minimum phase zeros such that the beneficial plant dynamics could be used. This general control approach has application to lightly damped vibration and sound radiation problems where there are high bandwidth control objectives requiring a low controller DC gain and controller order.

  14. Germinal-center kinase-like kinase co-crystal structure reveals a swapped activation loop and C-terminal extension.

    PubMed

    Marcotte, Douglas; Rushe, Mia; M Arduini, Robert; Lukacs, Christine; Atkins, Kateri; Sun, Xin; Little, Kevin; Cullivan, Michael; Paramasivam, Murugan; Patterson, Thomas A; Hesson, Thomas; D McKee, Timothy; May-Dracka, Tricia L; Xin, Zhili; Bertolotti-Ciarlet, Andrea; Bhisetti, Govinda R; Lyssikatos, Joseph P; Silvian, Laura F

    2017-02-01

    Germinal-center kinase-like kinase (GLK, Map4k3), a GCK-I family kinase, plays multiple roles in regulating apoptosis, amino acid sensing, and immune signaling. We describe here the crystal structure of an activation loop mutant of GLK kinase domain bound to an inhibitor. The structure reveals a weakly associated, activation-loop swapped dimer with more than 20 amino acids of ordered density at the carboxy-terminus. This C-terminal PEST region binds intermolecularly to the hydrophobic groove of the N-terminal domain of a neighboring molecule. Although the GLK activation loop mutant crystallized demonstrates reduced kinase activity, its structure demonstrates all the hallmarks of an "active" kinase, including the salt bridge between the C-helix glutamate and the catalytic lysine. Our compound displacement data suggests that the effect of the Ser170Ala mutation in reducing kinase activity is likely due to its effect in reducing substrate peptide binding affinity rather than reducing ATP binding or ATP turnover. This report details the first structure of GLK; comparison of its activation loop sequence and P-loop structure to that of Map4k4 suggests ideas for designing inhibitors that can distinguish between these family members to achieve selective pharmacological inhibitors.

  15. The plasma structure of the north-east rim of the Cygnus Loop as observed with ASCA

    NASA Technical Reports Server (NTRS)

    Miyata, Emi; Tsunemi, Hiroshi; Pisarski, Ryszard; Kissel, Steve E.

    1994-01-01

    We present the first results from Advanced Satellite for Cosmology and Astrophysics (ASCAS) observations of the Cygnus Loop. A 22 min square of the north-east rim was observed. The imaging capability of ASCA permits clear indentification of the shock front structure. The energy resolving power of ASCA in the energy band between 0.5 keV to 10 keV reveals several emission lines from oxygen to silicon. The intensity ratio between the O VIII and O VII emission lines demonstrates that the plasma has not reached collisional ionization equilibrium. A nonequilibrium ionization model is applied to determine the gradients both in electron temperature T(sub e), and in electron density n(sub e). T(sub e) ranges from 0.22 keV at the shock front to 0.30 keV at 17 min inside the shock front. n(sub e) can be represented as a power law function of radius with an index of about 6 at an ambient gas density of 0.5 cm(exp -3). The plasma parameter n(sub e)t is about 2 x 10(exp 11) cm(exp -3), resulting in an age of about 20000 yr for the Loop.

  16. Reducing the two-loop large-scale structure power spectrum to low-dimensional, radial integrals

    NASA Astrophysics Data System (ADS)

    Schmittfull, Marcel; Vlah, Zvonimir

    2016-11-01

    Modeling the large-scale structure of the universe on nonlinear scales has the potential to substantially increase the science return of upcoming surveys by increasing the number of modes available for model comparisons. One way to achieve this is to model nonlinear scales perturbatively. Unfortunately, this involves high-dimensional loop integrals that are cumbersome to evaluate. Trying to simplify this, we show how two-loop (next-to-next-to-leading order) corrections to the density power spectrum can be reduced to low-dimensional, radial integrals. Many of those can be evaluated with a one-dimensional fast Fourier transform, which is significantly faster than the five-dimensional Monte-Carlo integrals that are needed otherwise. The general idea of this fast fourier transform perturbation theory method is to switch between Fourier and position space to avoid convolutions and integrate over orientations, leaving only radial integrals. This reformulation is independent of the underlying shape of the initial linear density power spectrum and should easily accommodate features such as those from baryonic acoustic oscillations. We also discuss how to account for halo bias and redshift space distortions.

  17. Bimodal loop-gap resonator

    NASA Astrophysics Data System (ADS)

    Piasecki, W.; Froncisz, W.; Hyde, James S.

    1996-05-01

    A bimodal loop-gap resonator for use in electron paramagnetic resonance (EPR) spectroscopy at S band is described. It consists of two identical one-loop-one-gap resonators in coaxial juxtaposition. In one mode, the currents in the two loops are parallel and in the other antiparallel. By introducing additional capacitors between the loops, the frequencies of the two modes can be made to coincide. Details are given concerning variable coupling to each mode, tuning of the resonant frequency of one mode to that of the other, and adjustment of the isolation between modes. An equivalent circuit is given and network analysis carried out both experimentally and theoretically. EPR applications are described including (a) probing of the field distributions with DPPH, (b) continuous wave (cw) EPR with a spin-label line sample, (c) cw electron-electron double resonance (ELDOR), (d) modulation of saturation, and (e) saturation-recovery (SR) EPR. Bloch induction experiments can be performed when the sample extends half way through the structure, but microwave signals induced by Mx and My components of magnetization cancel when it extends completely through. This latter situation is particularly favorable for SR, modulation of saturation, and ELDOR experiments, which depend on observing Mz indirectly using a second weak observing microwave source.

  18. Properties of a large-scale interplanetary loop structure as deduced from low-energy proton anisotropy and magnetic field measurements

    NASA Technical Reports Server (NTRS)

    Tranquille, C.; Sanderson, T. R.; Marsden, R. G.; Wenzel, K.-P.; Smith, E. J.

    1987-01-01

    Correlated particle and magnetic field measurements by the ISEE 3 spacecraft are presented for the loop structure behind the interplanetary traveling shock event of Nov. 12, 1978. Following the passage of the turbulent shock region, strong bidirectional streaming of low-energy protons is observed for approximately 6 hours, corresponding to a loop thickness of about 0.07 AU. This region is also characterized by a low relative variance of the magnetic field, a depressed proton intensity, and a reduction in the magnetic power spectral density. Using quasi-linear theory applied to a slab model, a value of 3 AU is derived for the mean free path during the passage of the closed loop. It is inferred from this observation that the proton regime associated with the loop structure is experiencing scatter-free transport and that either the length of the loop is approximately 3 AU between the sun and the earth or else the protons are being reflected at both ends of a smaller loop.

  19. Generation of a flare loop structure and ejection of magnetic flux from an erupting laboratory arched magnetic flux rope

    NASA Astrophysics Data System (ADS)

    Tripathi, S.; Gekelman, W. N.

    2011-12-01

    A laboratory plasma experiment has been built to generate an arched magnetic flux rope (AMFR) which is essentially an arch-shaped, current-carrying, magnetized plasma structure. Coronal loops and prominences are the main examples of solar AMFRs that frequently erupt and evolve into more energetic events such as flares and coronal mass ejections. Numerous small-scale AMFRs are also observed in the solar corona. In order to capture the important micro-physics of an erupting AMFR, the laboratory experiment has been designed by careful scaling of the solar plasma parameters. The laboratory AMFR (n ~ 1019 m-3, Te ~ 10 eV, L ~ 0.5 m) is produced using a LaB6 plasma source in presence of an arched vacuum magnetic field (B ~ 1 kG) and it evolves in a large magnetized plasma (1.0 m diameter, 4.5 m long, n ~ 1018 m-3, Te ~ 4 eV, B = 25-150 G). Two laser beams (1064 nm, ~0.5 J/pulse) strike movable carbon targets placed behind the electrodes to generate controlled plasma flows from the footpoints of the AMFR. The laser generated flows can mimic a variety of plasma flow conditions that exist on the sun and they can trigger the AMFR eruption by injecting dense plasma and magnetic flux in the AMFR. The experiment runs continuously with a 0.5 Hz repetition rate and is highly reproducible. Thus, several thousands of identical eruptions are routinely generated and evolution of the magnetic field, density, and plasma temperature is recorded in 3D with a high spatiotemporal resolution ( dx = 1 mm, dt= 20 ns) using movable diagnostic probes. Fast-camera images of the erupting AMFR demonstrate striking similarities between laboratory and solar plasma structures, most notably the observation of a flare-loop like structure following the eruption of the laboratory AMFR. The eruption of the AMFR can be initiated either by the laser generated intense flows or by the presence of a strong background magnetic field (B > 50 G ~ magnetic field at the leading edge of the AMFR). In both scenarios

  20. Artemisinin induces A549 cell apoptosis dominantly via a reactive oxygen species-mediated amplification activation loop among caspase-9, -8 and -3.

    PubMed

    Gao, Weijie; Xiao, Fenglian; Wang, Xiaoping; Chen, Tongsheng

    2013-10-01

    This report is designed to explore the roles of caspase-8, -9 and -3 in artemisinin (ARTE)-induced apoptosis in non-small cell lung cancer cells (A549 cells). ARTE induced reactive oxygen species (ROS)-mediated apoptosis in dose- and time-dependent fashion. Although ARTE treatment did not induce Bid cleavage and significant loss of mitochondrial membrane potential, it induced release of Smac and AIF but not cytochrome c from mitochondria, and silencing of Bak but not Bax significantly prevented ARTE-induced cytotoxicity. Moreover, ARTE treatment induced ROS-dependent activation of caspase-9, -8 and -3. Of the utmost importance, silencing or inhibiting any one of caspase-8, -9 and -3 almost completely prevented ARTE-induced activation of all the three caspases and remarkably abrogated the cytotoxicity of ARTE, suggesting that ARTE triggered an amplification activation loop among caspase-9, -8 and -3. Collectively, our data demonstrate that ARTE induces a ROS-mediated amplification activation loop among caspase-9, -8 and -3 to dominantly mediate the apoptosis of A549 cells.

  1. Functional probes of drug-receptor interactions implicated by structural studies: Cys-loop receptors provide a fertile testing ground.

    PubMed

    Van Arnam, Ethan B; Dougherty, Dennis A

    2014-08-14

    Structures of integral membrane receptors provide valuable models for drug-receptor interactions across many important classes of drug targets and have become much more widely available in recent years. However, it remains to be determined to what extent these images are relevant to human receptors in their biological context and how subtle issues such as subtype selectivity can be informed by them. The high precision structural modifications enabled by unnatural amino acid mutagenesis on mammalian receptors expressed in vertebrate cells allow detailed tests of predictions from structural studies. Using the Cys-loop superfamily of ligand-gated ion channels, we show that functional studies lead to detailed binding models that, at times, are significantly at odds with the structural studies on related invertebrate proteins. Importantly, broad variations in binding interactions are seen for very closely related receptor subtypes and for varying drugs at a given binding site. These studies highlight the essential interplay between structural studies and functional studies that can guide efforts to develop new pharmaceuticals.

  2. Phase transition and hysteresis loop in structured games with global updating

    NASA Astrophysics Data System (ADS)

    Wang, Wen-Xu; Lü, Jinhu; Chen, Guanrong; Hui, P. M.

    2008-04-01

    We present a global payoff-based strategy updating model for studying cooperative behavior of a networked population. We adopt the Prisoner’s Dilemma game and the snowdrift game as paradigms for characterizing the interactions among individuals. We investigate the model on regular, small-world, and scale-free networks, and find multistable cooperation states depending on the initial cooperator density. In particular for the snowdrift game on small-world and scale-free networks, there exist a discontinuous phase transition and hysteresis loops of cooperator density. We explain the observed properties by theoretical predictions and simulation results of the average number of neighbors of cooperators and defectors, respectively. Our work indicates that individuals with more neighbors have a trend to preserve their initial strategies, which has strong impacts on the strategy updating of individuals with fewer neighbors; while the fact that individuals with few neighbors have to become cooperators to avoid gaining the lowest payoff plays significant roles in maintaining and spreading of cooperation strategy.

  3. A stem-loop structure directs oskar mRNA to microtubule minus ends.

    PubMed

    Jambor, Helena; Mueller, Sandra; Bullock, Simon L; Ephrussi, Anne

    2014-04-01

    mRNA transport coupled with translational control underlies the intracellular localization of many proteins in eukaryotic cells. This is exemplified in Drosophila, where oskar mRNA transport and translation at the posterior pole of the oocyte direct posterior patterning of the embryo. oskar localization is a multistep process. Within the oocyte, a spliced oskar localization element (SOLE) targets oskar mRNA for plus end-directed transport by kinesin-1 to the posterior pole. However, the signals mediating the initial minus end-directed, dynein-dependent transport of the mRNA from nurse cells into the oocyte have remained unknown. Here, we show that a 67-nt stem-loop in the oskar 3' UTR promotes oskar mRNA delivery to the developing oocyte and that it shares functional features with the fs(1)K10 oocyte localization signal. Thus, two independent cis-acting signals, the oocyte entry signal (OES) and the SOLE, mediate sequential dynein- and kinesin-dependent phases of oskar mRNA transport during oogenesis. The OES also promotes apical localization of injected RNAs in blastoderm stage embryos, another dynein-mediated process. Similarly, when ectopically expressed in polarized cells of the follicular epithelium or salivary glands, reporter RNAs bearing the oskar OES are apically enriched, demonstrating that this element promotes mRNA localization independently of cell type. Our work sheds new light on how oskar mRNA is trafficked during oogenesis and the RNA features that mediate minus end-directed transport.

  4. Gallstone ileus inducing obstructive jaundice at the afferent loop of Roux-en-Y hepaticojejunostomy after bile duct cancer surgery: a case report.

    PubMed

    Lee, Hyun Gu; Hwang, Shin; Joo, Yo-Han; Cho, Yu-Jeong; Choi, Kyunghak

    2015-05-01

    The diagnosis of gallstone ileus is occasionally challenging due to the variability of its presentation. We herein present a very rare case of gallstone ileus inducing obstructive jaundice at the afferent loop of Roux-en-Y hepaticojejunostomy after 10 years of bile duct cancer surgery. We describe the case of a 74-year-old Korean woman with obstructive jaundice, treated conservatively. She showed severely impaired liver function test and obstructive jaundice. The computed tomography (CT) scan led to a diagnosis of very rare type of gallstones ileus at the afferent jejunal loop. Since the clinical manifestation was improved, we decided to observe her closely. On the next follow-up CT scan, the gallstone disappeared with mild distension of the afferent bowel loop, implicating spontaneous passage of the gallstone. She recovered and returned to normal life after 10 days of initiation of clinical manifestations. We presume that the gallstone may enter the afferent jejunal loop through the hepaticojejunostomy and later increase in size. The presence of narrow tract of intestine may facilitate the incidence of gallstone ileus. It appears to be the first report on this rare type of gallstone ileus inducing obstructive jaundice.

  5. Telomere targeting with a novel G-quadruplex-interactive ligand BRACO-19 induces T-loop disassembly and telomerase displacement in human glioblastoma cells

    PubMed Central

    Zhou, Guangtong; Liu, Xinrui; Li, Yunqian; Xu, Songbai; Ma, Chengyuan; Wu, Xinmin; Cheng, Ye; Yu, Zhiyun; Zhao, Gang; Chen, Yong

    2016-01-01

    Interference with telomerase and telomere maintenance is emerging as an attractive target for anticancer therapies. Ligand-induced stabilization of G-quadruplex formation by the telomeric DNA 3′-overhang inhibits telomerase from catalyzing telomeric DNA synthesis and from capping telomeric ends, making these ligands good candidates for chemotherapeutic purposes. BRACO-19 is one of the most effective and specific ligand for telomeric G4. It is shown here that BRACO-19 suppresses proliferation and reduces telomerase activity in human glioblastoma cells, paralleled by the displacement of telomerase from nuclear to cytoplasm. Meanwhile, BRACO-19 triggers extensive DNA damage response at telomere, which may result from uncapping and disassembly of telomeric T-loop structure, characterized by the formation of anaphase bridge and telomere fusion, as well as the release of telomere-binding protein from telomere. The resulting dysfunctional telomere ultimately provokes p53 and p21-mediated cell cycle arrest, apoptosis and senescence. Notably, normal primary astrocytes do not respond to the treatment of BRACO-19, suggesting the agent's good selectivity for cancer cells. These results reinforce the notion that G-quadruplex binding compounds can act as broad inhibitors of telomere-related processes and have potential as selective antineoplastic drugs for various tumors including malignant gliomas. PMID:26908447

  6. Strategies for recognition of stem-loop RNA structures by synthetic ligands: application to the HIV-1 frameshift stimulatory sequence.

    PubMed

    Palde, Prakash B; Ofori, Leslie O; Gareiss, Peter C; Lerea, Jaclyn; Miller, Benjamin L

    2010-08-26

    Production of the Gag-Pol polyprotein in human immunodeficiency virus (HIV) requires a -1 ribosomal frameshift, which is directed by a highly conserved RNA stem-loop. Building on our discovery of a set of disulfide-containing peptides that bind this RNA, we describe medicinal chemistry efforts designed to begin to understand the structure-activity relationships and RNA sequence-selectivity relationships associated with these compounds. Additionally, we have prepared analogues incorporating an olefin or saturated hydrocarbon bioisostere of the disulfide moiety, as a first step toward enhancing biostability. The olefin-containing compounds exhibit affinity comparable to the lead disulfide and, importantly, have no discernible toxicity when incubated with human fibroblasts at concentrations up to 1 mM.

  7. A stem–loop structure directs oskar mRNA to microtubule minus ends

    PubMed Central

    Jambor, Helena; Mueller, Sandra; Bullock, Simon L.; Ephrussi, Anne

    2014-01-01

    mRNA transport coupled with translational control underlies the intracellular localization of many proteins in eukaryotic cells. This is exemplified in Drosophila, where oskar mRNA transport and translation at the posterior pole of the oocyte direct posterior patterning of the embryo. oskar localization is a multistep process. Within the oocyte, a spliced oskar localization element (SOLE) targets oskar mRNA for plus end-directed transport by kinesin-1 to the posterior pole. However, the signals mediating the initial minus end-directed, dynein-dependent transport of the mRNA from nurse cells into the oocyte have remained unknown. Here, we show that a 67-nt stem–loop in the oskar 3′ UTR promotes oskar mRNA delivery to the developing oocyte and that it shares functional features with the fs(1)K10 oocyte localization signal. Thus, two independent cis-acting signals, the oocyte entry signal (OES) and the SOLE, mediate sequential dynein- and kinesin-dependent phases of oskar mRNA transport during oogenesis. The OES also promotes apical localization of injected RNAs in blastoderm stage embryos, another dynein-mediated process. Similarly, when ectopically expressed in polarized cells of the follicular epithelium or salivary glands, reporter RNAs bearing the oskar OES are apically enriched, demonstrating that this element promotes mRNA localization independently of cell type. Our work sheds new light on how oskar mRNA is trafficked during oogenesis and the RNA features that mediate minus end-directed transport. PMID:24572808

  8. Structure of a C. perfringens enterotoxin mutant in complex with a modified Claudin-2 extracellular loop 2.

    PubMed

    Yelland, Tamas S; Naylor, Claire E; Bagoban, Tannya; Savva, Christos G; Moss, David S; McClane, Bruce A; Blasig, Ingolf E; Popoff, M; Basak, Ajit K

    2014-09-09

    CPE (Clostridium perfringens enterotoxin) is the major virulence determinant for C. perfringens type-A food poisoning, the second most common bacterial food-borne illness in the UK and USA. After binding to its receptors, which include particular human claudins, the toxin forms pores in the cell membrane. The mature pore apparently contains a hexamer of CPE, claudin and, possibly, occludin. The combination of high binding specificity with cytotoxicity has resulted in CPE being investigated, with some success, as a targeted cytotoxic agent for oncotherapy. In this paper, we present the X-ray crystallographic structure of CPE in complex with a peptide derived from extracellular loop 2 of a modified, CPE-binding Claudin-2, together with high-resolution native and pore-formation mutant structures. Our structure provides the first atomic-resolution data on any part of a claudin molecule and reveals that claudin's CPE-binding fingerprint (NPLVP) is in a tight turn conformation and binds, as expected, in CPE's C-terminal claudin-binding groove. The leucine and valine residues insert into the binding groove while the first residue, asparagine, tethers the peptide via an interaction with CPE's aspartate 225 and the two prolines are required to maintain the tight turn conformation. Understanding the structural basis of the contribution these residues make to binding will aid in engineering CPE to target tumor cells.

  9. Distinct second extracellular loop structures of the brain cannabinoid CB(1) receptor: implication in ligand binding and receptor function.

    PubMed

    Shim, Joong-Youn; Rudd, James; Ding, Tomas T

    2011-02-01

    The G-protein-coupled receptor (GPCR) second extracellular loop (E2) is known to play an important role in receptor structure and function. The brain cannabinoid (CB(1)) receptor is unique in that it lacks the interloop E2 disulfide linkage to the transmembrane (TM) helical bundle, a characteristic of many GPCRs. Recent mutation studies of the CB(1) receptor, however, suggest the presence of an alternative intraloop disulfide bond between two E2 Cys residues. Considering the oxidation state of these Cys residues, we determine the molecular structures of the 17-residue E2 in the dithiol form (E2(dithiol)) and in the disulfide form (E2(disulfide)) of the CB(1) receptor in a fully hydrated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer, using a combination of simulated annealing and molecular dynamics simulation approaches. We characterize the CB(1) receptor models with these two E2 forms, CB(1)(E2(dithiol)) and CB(1)(E2(disulfide)), by analyzing interaction energy, contact number, core crevice, and cross correlation. The results show that the distinct E2 structures interact differently with the TM helical bundle and uniquely modify the TM helical topology, suggesting that E2 of the CB(1) receptor plays a critical role in stabilizing receptor structure, regulating ligand binding, and ultimately modulating receptor activation. Further studies on the role of E2 of the CB(1) receptor are warranted, particularly comparisons of the ligand-bound form with the present ligand-free form.

  10. Investigation of Deterioration Behavior of Hysteretic Loops in Nonlinear Static Procedure Analysis of Concrete Structures with Shear Walls

    SciTech Connect

    Ghodrati Amiri, G.; Amidi, S.; Khorasani, M.

    2008-07-08

    In the recent years, scientists developed the seismic rehabilitation of structures and their view points were changed from sufficient strength to the performance of structures (Performance Base Design) to prepare a safe design. Nonlinear Static Procedure analysis (NSP) or pushover analysis is a new method that is chosen for its speed and simplicity in calculations. 'Seismic Rehabilitation Code for Existing Buildings' and FEMA 356 considered this method. Result of this analysis is a target displacement that is the base of the performance and rehabilitation procedure of the structures. Exact recognition of that displacement could develop the workability of pushover analysis. In these days, Nonlinear Dynamic Analysis (NDP) is only method can exactly apply the seismic ground motions. In this case because it consumes time, costs very high and is more difficult than other methods, is not applicable as much as NSP. A coefficient used in NSP for determining the target displacement is C2 (Stiffness and Strength Degradations Coefficient) and is applicable for correcting the errors due to eliminating the stiffness and strength degradations in hysteretic loops. In this study it has been tried to analysis three concrete frames with shear walls by several accelerations that scaled according to FEMA 273 and FEMA 356. These structures were designed with Iranian 2800 standard (vers.3). Finally after the analyzing by pushover method and comparison results with dynamic analysis, calculated C2 was comprised with values in rehabilitation codes.

  11. Structure-guided Design and Immunological Characterization of Immunogens Presenting the HIV-1 gp120 V3 Loop on a CTB Scaffold

    SciTech Connect

    M Totrov; X Jiang; X Kong; S Cohen; C Krachmarov; A Salomon; C Williams; M Seaman; R Abagyan; et al.

    2011-12-31

    V3 loop is a major neutralizing determinant of the HIV-1 gp120. Using 3D structures of cholera toxin B subunit (CTB), complete V3 in the gp120 context, and V3 bound to a monoclonal antibody (mAb), we designed two V3-scaffold immunogen constructs (V3-CTB). The full-length V3-CTB presenting the complete V3 in a structural context mimicking gp120 was recognized by the large majority of our panel of 24 mAbs. The short V3-CTB presenting a V3 fragment in the conformation observed in the complex with the 447-52D Fab, exhibited high-affinity binding to this mAb. The immunogens were evaluated in rabbits using DNA-prime/protein-boost protocol. Boosting with the full-length V3-CTB induced high anti-V3 titers in sera that potently neutralize multiple HIV virus strains. The short V3-CTB was ineffective. The results suggest that very narrow antigenic profile of an immunogen is associated with poor Ab response. An immunogen with broader antigenic activity elicits robust Ab response.

  12. Vortex induced motion in compliant structures

    NASA Astrophysics Data System (ADS)

    Song, Arnold; Tuttman, Max; Breuer, Kenneth

    2008-11-01

    The coupling of the unsteady shedding of vortices from the leading and trailing edges of a flat plate can lead to large scale oscillations of a structure. Examples of these large motions abound in engineered structures (Traffic signs vibrating in the wind, wing flutter, chattering venetian blinds, etc.) and in nature (the rustling of leaves on a tree in the wind). In all of these examples, the efficiency of energy extraction from the flow to the structure increases dramatically as the vortex shedding and structural vibrations near resonance. As the motion becomes more exaggerated, the fluid-structure interaction becomes increasingly nonlinear as the motion of the plate becomes increasingly important to the vortex shedding dynamics. We present experimental results from two related systems tested in a low speed wind tunnel (using high-speed videography, PIV and hotwire anemometry) (i) a rectangular cantilevered flat plate free to bend and twist, and (ii) a flexible ribbon pinned at its two ends and exposed to the flow. In both systems, a rich phase map of vortex-induced vibrations is described in which both mechanisms for vortex shedding and structural vibration can be tuned independently using geometry, material properties and flow conditions.

  13. NMR structure and dynamics of the RNA-binding site for the histone mRNA stem-loop binding protein.

    PubMed Central

    DeJong, Eric S; Marzluff, William F; Nikonowicz, Edward P

    2002-01-01

    The 3' end of replication-dependent histone mRNAs terminate in a conserved sequence containing a stem-loop. This 26-nt sequence is the binding site for a protein, stem-loop binding protein (SLBP), that is involved in multiple aspects of histone mRNA metabolism and regulation. We have determined the structure of the 26-nt sequence by multidimensional NMR spectroscopy. There is a 16-nt stem-loop motif, with a conserved 6-bp stem and a 4-nt loop. The loop is closed by a conserved U.A base pair that terminates the canonical A-form stem. The pyrimidine-rich 4-nt loop, UUUC, is well organized with the three uridines stacking on the helix, and the fourth base extending across the major groove into the solvent. The flanking nucleotides at the base of the hairpin stem do not assume a unique conformation, despite the fact that the 5' flanking nucleotides are a critical component of the SLBP binding site. PMID:11871662

  14. Allosteric binding site in a Cys-loop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazine

    PubMed Central

    Nys, Mieke; Wijckmans, Eveline; Farinha, Ana; Yoluk, Özge; Andersson, Magnus; Brams, Marijke; Spurny, Radovan; Peigneur, Steve; Tytgat, Jan; Lindahl, Erik; Ulens, Chris

    2016-01-01

    Pentameric ligand-gated ion channels or Cys-loop receptors are responsible for fast inhibitory or excitatory synaptic transmission. The antipsychotic compound chlorpromazine is a widely used tool to probe the ion channel pore of the nicotinic acetylcholine receptor, which is a prototypical Cys-loop receptor. In this study, we determine the molecular determinants of chlorpromazine binding in the Erwinia ligand-gated ion channel (ELIC). We report the X-ray crystal structures of ELIC in complex with chlorpromazine or its brominated derivative bromopromazine. Unexpectedly, we do not find a chlorpromazine molecule in the channel pore of ELIC, but behind the β8–β9 loop in the extracellular ligand-binding domain. The β8–β9 loop is localized downstream from the neurotransmitter binding site and plays an important role in coupling of ligand binding to channel opening. In combination with electrophysiological recordings from ELIC cysteine mutants and a thiol-reactive derivative of chlorpromazine, we demonstrate that chlorpromazine binding at the β8–β9 loop is responsible for receptor inhibition. We further use molecular-dynamics simulations to support the X-ray data and mutagenesis experiments. Together, these data unveil an allosteric binding site in the extracellular ligand-binding domain of ELIC. Our results extend on previous observations and further substantiate our understanding of a multisite model for allosteric modulation of Cys-loop receptors. PMID:27791038

  15. Reovirus FAST Proteins Drive Pore Formation and Syncytiogenesis Using a Novel Helix-Loop-Helix Fusion-Inducing Lipid Packing Sensor.

    PubMed

    Read, Jolene; Clancy, Eileen K; Sarker, Muzaddid; de Antueno, Roberto; Langelaan, David N; Parmar, Hiren B; Shin, Kyungsoo; Rainey, Jan K; Duncan, Roy

    2015-06-01

    Pore formation is the most energy-demanding step during virus-induced membrane fusion, where high curvature of the fusion pore rim increases the spacing between lipid headgroups, exposing the hydrophobic interior of the membrane to water. How protein fusogens breach this thermodynamic barrier to pore formation is unclear. We identified a novel fusion-inducing lipid packing sensor (FLiPS) in the cytosolic endodomain of the baboon reovirus p15 fusion-associated small transmembrane (FAST) protein that is essential for pore formation during cell-cell fusion and syncytiogenesis. NMR spectroscopy and mutational studies indicate the dependence of this FLiPS on a hydrophobic helix-loop-helix structure. Biochemical and biophysical assays reveal the p15 FLiPS preferentially partitions into membranes with high positive curvature, and this partitioning is impeded by bis-ANS, a small molecule that inserts into hydrophobic defects in membranes. Most notably, the p15 FLiPS can be functionally replaced by heterologous amphipathic lipid packing sensors (ALPS) but not by other membrane-interactive amphipathic helices. Furthermore, a previously unrecognized amphipathic helix in the cytosolic domain of the reptilian reovirus p14 FAST protein can functionally replace the p15 FLiPS, and is itself replaceable by a heterologous ALPS motif. Anchored near the cytoplasmic leaflet by the FAST protein transmembrane domain, the FLiPS is perfectly positioned to insert into hydrophobic defects that begin to appear in the highly curved rim of nascent fusion pores, thereby lowering the energy barrier to stable pore formation.

  16. YghJ, the secreted metalloprotease of pathogenic E. coli induces hemorrhagic fluid accumulation in mouse ileal loop.

    PubMed

    Tapader, Rima; Bose, Dipro; Pal, Amit

    2017-04-01

    YghJ, also known as SslE (Secreted and surface associated lipoprotein) is a cell surface associated and secreted lipoprotein harbouring M60 metalloprotease domain. Though the gene is known to be conserved among both pathogenic and commensal Escherichia coli isolates, the expression and secretion of YghJ was found to be higher among diverse E. coli pathotypes. YghJ, secreted from intestinal pathogens such as enterotoxigenic E. coli (ETEC) and enteropathogenic E. coli (EPEC) has been demonstrated to possess mucinase activity and hence facilitates colonization of these enteric pathogens to intestinal epithelial cells. Importantly, YghJ is also reported to be secreted from extraintestinal pathogenic E. coli isolates. In our previous study we have shown that YghJ, purified from a neonatal septicemic E. coli isolate could trigger induction of various proinflammatory cytokines in vitro. This led us to investigate the role of YghJ in causing in vivo tissue hemorrhage. In the present study, we validate the earlier in vitro finding and have showed that YghJ can cause extensive tissue damage in mouse ileum and is also able to induce significant fluid accumulation in a dose dependent manner in a mouse ileal loop (MIL) assay. Hence, our present study not only confirms the pathogenic potential of YghJ in sepsis pathophysiology but also indicates the enterotoxic ability of YghJ which makes it an important virulence determinant of intestinal pathogenic E. coli.

  17. Dissecting the chemical interactions and substrate structural signatures governing RNA polymerase II trigger loop closure by synthetic nucleic acid analogues

    PubMed Central

    Xu, Liang; Butler, Kyle Vincent; Chong, Jenny; Wengel, Jesper; Kool, Eric T.; Wang, Dong

    2014-01-01

    The trigger loop (TL) of RNA polymerase II (Pol II) is a conserved structural motif that is crucial for Pol II catalytic activity and transcriptional fidelity. The TL remains in an inactive open conformation when the mismatched substrate is bound. In contrast, TL switches from an inactive open state to a closed active state to facilitate nucleotide addition upon the binding of the cognate substrate to the Pol II active site. However, a comprehensive understanding of the specific chemical interactions and substrate structural signatures that are essential to this TL conformational change remains elusive. Here we employed synthetic nucleotide analogues as ‘chemical mutation’ tools coupling with α-amanitin transcription inhibition assay to systematically dissect the key chemical interactions and structural signatures governing the substrate-coupled TL closure in Saccharomyces cerevisiae Pol II. This study reveals novel insights into understanding the molecular basis of TL conformational transition upon substrate binding during Pol II transcription. This synthetic chemical biology approach may be extended to understand the mechanisms of other RNA polymerases as well as other nucleic acid enzymes in future studies. PMID:24692664

  18. A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity

    SciTech Connect

    Breustedt, Daniel A.; Chatwell, Lorenz; Skerra, Arne

    2009-10-01

    The crystal structure of tear lipocalin determined in space group P2{sub 1} revealed large structural deviations from the previously solved X-ray structure in space group C2, especially in the loop region and adjoining parts of the β-barrel which give rise to the ligand-binding site. These findings illustrate a novel mechanism for promiscuity in ligand recognition by the lipocalin protein family. Tear lipocalin (TLC) with the bound artificial ligand 1,4-butanediol has been crystallized in space group P2{sub 1} with four protein molecules in the asymmetric unit and its X-ray structure has been solved at 2.6 Å resolution. TLC is a member of the lipocalin family that binds ligands with diverse chemical structures, such as fatty acids, phospholipids and cholesterol as well as microbial siderophores and the antibiotic rifampin. Previous X-ray structural analysis of apo TLC crystallized in space group C2 revealed a rather large bifurcated ligand pocket and a partially disordered loop region at the entrace to the cavity. Analysis of the P2{sub 1} crystal form uncovered major conformational changes (i) in β-strands B, C and D, (ii) in loops 1, 2 and 4 at the open end of the β-barrel and (iii) in the extended C-terminal segment, which is attached to the β-barrel via a disulfide bridge. The structural comparison indicates high conformational plasticity of the loop region as well as of deeper parts of the ligand pocket, thus allowing adaptation to ligands that differ vastly in size and shape. This illustrates a mechanism for promiscuity in ligand recognition which may also be relevant for some other physiologically important members of the lipocalin protein family.

  19. Crystal Structure of the Lactose Operon Repressor and Its Complexes with DNA and Inducer

    NASA Astrophysics Data System (ADS)

    Lewis, Mitchell; Chang, Geoffrey; Horton, Nancy C.; Kercher, Michele A.; Pace, Helen C.; Schumacher, Maria A.; Brennan, Richard G.; Lu, Ponzy

    1996-03-01

    The lac operon of Escherichia coli is the paradigm for gene regulation. Its key component is the lac repressor, a product of the lacI gene. The three-dimensional structures of the intact lac repressor, the lac repressor bound to the gratuitous inducer isopropyl-β-D-1-thiogalactoside (IPTG) and the lac repressor complexed with a 21-base pair symmetric operator DNA have been determined. These three structures show the conformation of the molecule in both the induced and repressed states and provide a framework for understanding a wealth of biochemical and genetic information. The DNA sequence of the lac operon has three lac repressor recognition sites in a stretch of 500 base pairs. The crystallographic structure of the complex with DNA suggests that the tetrameric repressor functions synergistically with catabolite gene activator protein (CAP) and participates in the quaternary formation of repression loops in which one tetrameric repressor interacts simultaneously with two sites on the genomic DNA.

  20. Plasticity of 150-Loop in Influenza Neuraminidase Explored by Hamiltonian Replica Exchange Molecular Dynamics Simulations

    PubMed Central

    Han, Nanyu; Mu, Yuguang

    2013-01-01

    Neuraminidase (NA) of influenza is a key target for antiviral inhibitors, and the 150-cavity in group-1 NA provides new insight in treating this disease. However, NA of 2009 pandemic influenza (09N1) was found lacking this cavity in a crystal structure. To address the issue of flexibility of the 150-loop, Hamiltonian replica exchange molecular dynamics simulations were performed on different groups of NAs. Free energy landscape calculated based on the volume of 150-cavity indicates that 09N1 prefers open forms of 150-loop. The turn A (residues 147–150) of the 150-loop is discovered as the most dynamical motif which induces the inter-conversion of this loop among different conformations. In the turn A, the backbone dynamic of residue 149 is highly related with the shape of 150-loop, thus can function as a marker for the conformation of 150-loop. As a contrast, the closed conformation of 150-loop is more energetically favorable in N2, one of group-2 NAs. The D147-H150 salt bridge is found having no correlation with the conformation of 150-loop. Instead the intimate salt bridge interaction between the 150 and 430 loops in N2 variant contributes the stabilizing factor for the closed form of 150-loop. The clustering analysis elaborates the structural plasticity of the loop. This enhanced sampling simulation provides more information in further structural-based drug discovery on influenza virus. PMID:23593372

  1. Closed coronal structures. V - Gasdynamic models of flaring loops and comparison with SMM observations

    NASA Technical Reports Server (NTRS)

    Peres, G.; Serio, S.; Vaiana, G.; Acton, L.; Leibacher, J.; Rosner, R.; Pallavicini, R.

    1983-01-01

    A time-dependent one-dimensional code incorporating energy, momentum and mass conservation equations, and taking the entire solar atmospheric structure into account, is used to investigate the hydrodynamic response of confined magnetic structures to strong heating perturbations. Model calculation results are compared with flare observations which include the light curves of spectral lines formed over a wide range of coronal flare temperatures, as well as determinations of Doppler shifts for the high temperature plasma. It is shown that the numerical simulation predictions are in good overall agreement with the observed flare coronal plasma evolution, correctly reproducing the temporal profile of X-ray spectral lines and their relative intensities. The predicted upflow velocities support the interpretation of the blueshifts as due to evaporation of chromospheric material.

  2. Defect Induced Electronic Structure of Uranofullerene

    PubMed Central

    Dai, Xing; Cheng, Cheng; Zhang, Wei; Xin, Minsi; Huai, Ping; Zhang, Ruiqin; Wang, Zhigang

    2013-01-01

    The interaction between the inner atoms/cluster and the outer fullerene cage is the source of various novel properties of endohedral metallofullerenes. Herein, we introduce an adatom-type spin polarization defect on the surface of a typical endohedral stable U2@C60 to predict the associated structure and electronic properties of U2@C61 based on the density functional theory method. We found that defect induces obvious changes in the electronic structure of this metallofullerene. More interestingly, the ground state of U2@C61 is nonet spin in contrast to the septet of U2@C60. Electronic structure analysis shows that the inner U atoms and the C ad-atom on the surface of the cage contribute together to this spin state, which is brought about by a ferromagnetic coupling between the spin of the unpaired electrons of the U atoms and the C ad-atom. This discovery may provide a possible approach to adapt the electronic structure properties of endohedral metallofullerenes. PMID:23439318

  3. Viscosity-dependent structural fluctuation of the M80-containing Ω-loop of horse ferrocytochrome c

    NASA Astrophysics Data System (ADS)

    Kumar, Rajesh; Jain, Rishu; Kumar, Rajesh

    2013-06-01

    To determine the effect of solvent viscosity on low-frequency local motions that control the slow changes in structural dynamics of proteins, we have studied the effects of solvent viscosity on the structural fluctuation of presumably the M80-containing Ω-loop by measuring the rate of thermally-driven CO-dissociation from a natively-folded carbonmonoxycytochrome c (NCO-state) in the 0.65-92.5 cP range of viscosity at pH 7.0. At low viscosities (⩽8 cP), the rate coefficient, kdiss for dissociation of CO from the NCO-state varies inversely with the viscosity, but saturates at high viscosities, suggesting that CO-dissociation reaction involves sequential stages that depend differently on solvent friction, i.e., solvent coupled and nonsolvent-coupled stages of the process. In the low viscosity regime (0.65 ⩽ ηs ⩽ 8.0 cP), the rate-viscosity data were fitted to modified Kramers model, kdiss = [A'/(σ + ηs)n]exp(-ΔG/RT), which produced internal friction, σ = 1.35 cP (±0.88), which suggests that the speed of CO-dissociation from NCO at ηs ⩽ 8.0 cP is controlled by internal friction.

  4. Impaired Acid Catalysis by Mutation of a Protein Loop Hinge Residue in a YopH Mutant Revealed by Crystal Structures

    SciTech Connect

    Brandao, T.; Robinson, H; Johnson, S; Hengge, A

    2009-01-01

    Catalysis by the Yersinia protein-tyrosine phosphatase YopH is significantly impaired by the mutation of the conserved Trp354 residue to Phe. Though not a catalytic residue, this Trp is a hinge residue in a conserved flexible loop (the WPD-loop) that must close during catalysis. To learn why this seemingly conservative mutation reduces catalysis by 2 orders of magnitude, we have solved high-resolution crystal structures for the W354F YopH in the absence and in the presence of tungstate and vanadate. Oxyanion binding to the P-loop in W354F is analogous to that observed in the native enzyme. However, the WPD-loop in the presence of oxyanions assumes a half-closed conformation, in contrast to the fully closed state observed in structures of the native enzyme. This observation provides an explanation for the impaired general acid catalysis observed in kinetic experiments with Trp mutants. A 1.4 Angstroms structure of the W354F mutant obtained in the presence of vanadate reveals an unusual divanadate species with a cyclic [VO]2 core, which has precedent in small molecules but has not been previously reported in a protein crystal structure.

  5. NMR structure of the noncytotoxic α-sarcin mutant Δ(7-22): The importance of the native conformation of peripheral loops for activity

    PubMed Central

    García-Mayoral, Ma Flor; García-Ortega, Lucia; Lillo, Ma Pilar; Santoro, Jorge; Martínez Del Pozo, Álvaro; Gavilanes, José G.; Rico, Manuel; Bruix, Marta

    2004-01-01

    The deletion mutant Δ(7-22) of α-sarcin, unlike its wild-type protein counterpart, lacks the specific ability to degrade rRNA in intact ribosomes and exhibits an increased unspecific ribonuclease activity and decreased interaction with lipid vesicles. In trying to shed light on these differences, we report here on the three-dimensional structure of the Δ(7-22) α-sarcin mutant using NMR methods. We also evaluated its dynamic properties on the basis of theoretical models and measured its correlation time (6.2 nsec) by time-resolved fluorescence anisotropy. The global fold characteristic of ribotoxins is preserved in the mutant. The most significant differences with respect to the α-sarcin structure are concentrated in (1) loop 2, (2) loop 3, which adopts a new orientation, and (3) loop 5, which shows multiple conformations and an altered dynamics. The interactions between loop 5 and the N-terminal hairpin are lost in the mutant, producing increased solvent accessibility of the active-site residues. The degree of solvent exposure of the catalytic His 137 is similar to that shown by His 92 in RNase T1. Additionally, the calculated order parameters of residues belonging to loop 5 in the mutant correspond to an internal dynamic behavior more similar to RNase T1 than α-sarcin. On the other hand, changes in the relative orientation of loop 3 move the lysine-rich region 111–114, crucial for substrate recognition, away from the active site. All of the structural and dynamic data presented here reveal that the mutant is a hybrid of ribotoxins and noncytotoxic ribonucleases, consistent with its biological properties. PMID:15044731

  6. Importance of lipid-pore loop interface for potassium channel structure and function.

    PubMed

    van der Cruijsen, Elwin A W; Nand, Deepak; Weingarth, Markus; Prokofyev, Alexander; Hornig, Sönke; Cukkemane, Abhishek Arun; Bonvin, Alexandre M J J; Becker, Stefan; Hulse, Raymond E; Perozo, Eduardo; Pongs, Olaf; Baldus, Marc

    2013-08-06

    Potassium (i.e., K(+)) channels allow for the controlled and selective passage of potassium ions across the plasma membrane via a conserved pore domain. In voltage-gated K(+) channels, gating is the result of the coordinated action of two coupled gates: an activation gate at the intracellular entrance of the pore and an inactivation gate at the selectivity filter. By using solid-state NMR structural studies, in combination with electrophysiological experiments and molecular dynamics simulations, we show that the turret region connecting the outer transmembrane helix (transmembrane helix 1) and the pore helix behind the selectivity filter contributes to K(+) channel inactivation and exhibits a remarkable structural plasticity that correlates to K(+) channel inactivation. The transmembrane helix 1 unwinds when the K(+) channel enters the inactivated state and rewinds during the transition to the closed state. In addition to well-characterized changes at the K(+) ion coordination sites, this process is accompanied by conformational changes within the turret region and the pore helix. Further spectroscopic and computational results show that the same channel domain is critically involved in establishing functional contacts between pore domain and the cellular membrane. Taken together, our results suggest that the interaction between the K(+) channel turret region and the lipid bilayer exerts an important influence on the selective passage of potassium ions via the K(+) channel pore.

  7. Structures induced by companions in galactic discs

    NASA Astrophysics Data System (ADS)

    Kyziropoulos, P. E.; Efthymiopoulos, C.; Gravvanis, G. A.; Patsis, P. A.

    2016-12-01

    Using N-body simulations, we study the structures induced on a galactic disc by repeated flybys of a companion in decaying eccentric orbit around the disc. Our system is composed of a stellar disc, bulge and live dark matter halo, and we study the system's dynamical response to a sequence of a companion's flybys, when we vary (i) the disc's temperature (parametrized by Toomre's Q-parameter) and (ii) the companion's mass and initial orbit. We use a new 3D Cartesian grid code: MAIN (Mesh-adaptive Approximate Inverse N-body solver). The main features of MAIN are reviewed, with emphasis on the use of a new Symmetric Factored Approximate Sparse Inverse matrix in conjunction with the multigrid method that allows the efficient solution of Poisson's equation in three space variables. We find that (i) companions need to be assigned initial masses in a rather narrow window of values in order to produce significant and more long-standing non-axisymmetric structures (bars and spirals) in the main galaxy's disc by the repeated flyby mechanism. (ii) A crucial phenomenon is the antagonism between companion-excited and self-excited modes on the disc. Values of Q > 1.5 are needed in order to allow for the growth of the companion-excited modes to prevail over the growth of the disc's self-excited modes. (iii) We give evidence that the companion-induced spiral structure is best represented by a density wave with pattern speed nearly constant in a region extending from the inner Lindblad resonance to a radius close to, but inside, corotation.

  8. Effects of T-loop modification on the PII-signalling protein: structure of uridylylated Escherichia coli GlnB bound to ATP.

    PubMed

    Palanca, Carles; Rubio, Vicente

    2017-03-26

    To adapt to environments with variable nitrogen sources and richness, the widely distributed homotrimeric PII signalling proteins bind their allosteric effectors ADP/ATP/2-oxoglutarate, and experience nitrogen-sensitive uridylylation of their flexible T-loops at Tyr51, regulating their interactions with effector proteins. To clarify whether uridylylation triggers a given T-loop conformation, we determined the crystal structure of the classical paradigm of PII protein, Escherichia coli GlnB (EcGlnB), in fully uridylylated form (EcGlnB-UMP3 ). This is the first structure of a postranslationally modified PII protein. This required recombinant production and purification of the uridylylating enzyme GlnD and its use for full uridylylation of large amounts of recombinantly produced pure EcGlnB. Unlike crystalline non-uridylylated EcGlnB, in which T-loops are fixed, uridylylation rendered the T-loop highly mobile because of loss of contacts mediated by Tyr51, with concomitant abolition of T-loop anchoring via Arg38 on the ATP site. This site was occupied by ATP, providing the first, long-sought snapshot of the EcGlnB-ATP complex, connecting ATP binding with T-loop changes. Inferences are made on the mechanisms of PII selectivity for ATP and of PII-UMP3 signalling, proposing a model for the architecture of the complex of EcGlnB-UMP3 with the uridylylation-sensitive PII target ATase (which adenylylates/deadenylylates glutamine synthetase [GS]) and with GS.

  9. A positive feedback loop between ROS and Mxi1-0 promotes hypoxia-induced VEGF expression in human hepatocellular carcinoma cells.

    PubMed

    Hu, Zhenzhen; Dong, Na; Lu, Dian; Jiang, Xiuqin; Xu, Jinjin; Wu, Zhiwei; Zheng, Datong; Wechsler, Daniel S

    2017-02-01

    VEGF expression induced by hypoxia plays a critical role in promoting tumor angiogenesis. However, the molecular mechanism that modulates VEGF expression under hypoxia is still poorly understood. In this study, we found that VEGF induction in hypoxic HepG2 cells is ROS-dependent. ROS mediates hypoxia-induced VEGF by upregulation of Mxi1-0. Furthermore, PI3K/AKT/HIF-1α signaling pathway is involved in ROS-mediated Mxi1-0 and VEGF expression in hypoxic HepG2 cells. Finally, Mxi1-0 could in turn regulate ROS generation in hypoxic HepG2 cells, creating a positive feedback loop. Taken together, this study demonstrate a positive regulatory feedback loop in which ROS mediates hypoxia-induced Mxi1-0 via activation of PI3K/AKT/HIF-1α pathway, events that in turn elevate ROS generation and promote hypoxia-induced VEGF expression. These findings could provide a rationale for designing new therapies based on inhibition of hepatocellular carcinoma (HCC) angiogenesis.

  10. Performance Comparison of BPL, EtherLoop and SHDSL technology performance on existing pilot cable circuits under the presence of induced voltage

    NASA Astrophysics Data System (ADS)

    Che, Y. X.; Ong, H. S.; Lai, L. C.; Karuppiah, S.; Ong, X. J.; Do, N. Q.

    2013-06-01

    Pilot cable is originally used for utility protection. Then, pilot cable is further utilized for SCADA communication with low frequency PSK modem in the early 1990. However, the quality of pilot cable communication drops recently. Pilot cable starts to deteriorate due to aging and other unknown factors. It is also believed that the presence of induced voltage causes interference to existing modem communication which operates at low frequency channel. Therefore, BPL (Broadband Power Line), EtherLoop and SHDSL (Symmetrical High-speed Digital Subscriber Line) modem technology are proposed as alternative communication solutions for pilot cable communication. The performance of the 3 selected technologies on existing pilot cable circuits under the presence of induced voltage are measured and compared. Total of 11 pilot circuits with different length and level of induced voltage influence are selected for modem testing. The performance of BPL, EtherLoop and SHDSL modem technology are measured by the delay, bandwidth, packet loss and the long term usability SCADA (Supervisory Control and Data Acquisition) application. The testing results are presented and discussed in this paper. The results show that the 3 selected technologies are dependent on distance and independent on the level of induced voltage.

  11. Assembly induced delaminations in composite structures

    NASA Technical Reports Server (NTRS)

    Goering, J.; Bohlmann, R.; Wanthal, S.; Kautz, E.; Neri, Lawrence M.

    1992-01-01

    Experimental and analytical studies of the development of delaminations around fastener holes in composite structures are presented. This type of delamination is known to occur in composite skins that are mechanically fastened to a poorly mating substructure. Results of an experimental study to determine the resistance of laminates to the initiation of assembly induced delaminations and the residual strength of assembly damaged coupons are presented for AS4/3501-6, IM7/8551-7A, and AS4/PEEK material systems. A survey of existing analytical models for predicting the residual strength and stability of delaminations is presented, and the development of a new model for predicting the initiation of delaminations around a fastener hole is outlined. The fastener hole damage initiation model utilizes a finite element based Fourier series solution, and is validated through comparisons of analytical and experimental results.

  12. Chromospheric magnetic field and density structure measurements using hard X-rays in a flaring coronal loop

    NASA Astrophysics Data System (ADS)

    Kontar, E. P.; Hannah, I. G.; MacKinnon, A. L.

    2008-10-01

    Aims: A novel method of using hard X-rays as a diagnostic for chromospheric density and magnetic structures is developed to infer sub-arcsecond vertical variation of magnetic flux tube size and neutral gas density. Methods: Using Reuven Ramaty High Energy Solar Spectroscopic Imager (RHESSI) X-ray data and the newly developed X-ray visibilities forward fitting technique we find the FWHM and centroid positions of hard X-ray sources with sub-arcsecond resolution (~0.2'') for a solar limb flare. We show that the height variations of the chromospheric density and the magnetic flux densities can be found with an unprecedented vertical resolution of ~150 km by mapping 18-250 keV X-ray emission of energetic electrons propagating in the loop at chromospheric heights of 400-1500 km. Results: Our observations suggest that the density of the neutral gas is in good agreement with hydrostatic models with a scale height of around 140 ± 30 km. FWHM sizes of the X-ray sources decrease with energy suggesting the expansion (fanning out) of magnetic flux tubes in the chromosphere with height. The magnetic scale height B(z)(dB/dz)-1 is found to be of the order of 300 km and a strong horizontal magnetic field is associated with noticeable flux tube expansion at a height of ~900 km.

  13. The P-loop region of Schlafen 3 acts within the cytosol to induce differentiation of human Caco-2 intestinal epithelial cells

    PubMed Central

    Chaturvedi, Lakshmishankar; Sun, Kelian; Walsh, Mary F.; Kuhn, Leslie A.; Basson, Marc D.

    2014-01-01

    Schlafen 3 (Slfn3) mediates rodent enterocyte differentiation in vitro and in vivo, required for intestinal function. Little is known about Schlafen protein structure-function relationships. To define the Slfn3 domain that promotes differentiation, we studied villin and sucrase isomaltase (SI) promoter activity in Slfn3-null human Caco-2BBE cells transfected with full-length rat Slfn3 DNA or truncated constructs. Confocal microscopy and Western blots showed that Slfn3 is predominantly cytosolic. Villin promoter activity, increased by wild type Slfn3, was further enhanced by adding a nuclear exclusion sequence, suggesting that Slfn3 does not affect transcription by direct nuclear action. We therefore sought to dissect the region in Slfn3 stimulating promoter activity. Since examination of the Slfn3 N-terminal region revealed sequences similar to both an aminopeptidase (App) and a divergent P-loop resembling those in NTPases, we initially divided Slfn3 into an N-terminal domain containing the App and P-loop regions, and a C-terminal region. Only the N-terminal construct stimulated promoter activity. Further truncation indicated that both the App and the smaller P-loop constructs enhanced promoter activity similarly to the N-terminal sequence. Point mutations within the N-terminal region (R128L, altering a critical active site residue in the App domain, and L212D, conserved in Schlafens but variable in P-loop proteins) did not affect activity. These results show that Slfn3 acts in the cytosol to trigger a secondary signal cascade that elicits differentiation marker expression and narrow the active domain to the third of the Slfn3 sequence homologous to P-loop NTPases, a first step in understanding its mechanism of action. PMID:25261706

  14. Binding Characteristics of Small Molecules that Mimic Nucleocapsid Protein-induced Maturation of Stem-loop-1 of HIV-1 RNA†

    PubMed Central

    Chung, Janet; Ulyanov, Nikolai B.; Guilbert, Christophe; Mujeeb, Anwer; James, Thomas L.

    2010-01-01

    As a retrovirus, the human immunodeficiency virus (HIV-1) packages two copies of the RNA genome as a dimer in the infectious virion. Dimerization is initiated at the dimer initiation site (DIS) which encompasses stem-loop 1 (SL1) in the 5’-UTR of the genome. Study of genomic dimerization has been facilitated by the discovery that short RNA fragments containing SL1 can dimerize spontaneously without any protein factors. Based on the palindromic nature of SL1, a kissing loop model has been proposed. First, a metastable kissing dimer is formed via standard Watson-Crick base pairs and then converted into a more stable extended dimer by the viral nucleocapsid protein (NCp7). This dimer maturation in vitro is believed to mimic initial steps in the RNA maturation in vivo, which is correlated with viral infectivity. We previously discovered a small molecule activator, Lys-Ala-7-amido-4-methylcoumarin (KA-AMC), which facilitates dimer maturation in vitro, and determined aspects of its structure-activity relationship. In this report, we present measurements of the binding affinity of the activators and characterization of their interactions with the SL1 RNA. Guanidinium groups and increasing positive charge on the side chain enhance affinity and activity, but features in the aromatic ring at least partially decouple affinity from activity. Although KA-AMC can bind to multiple structural motifs, NMR study showed KA-AMC preferentially binds to unique structural motifs, such as the palindromic loop and the G-rich internal loop in the SL1 RNA. NCp7 binds to SL1 only an order of magnitude tighter than the best small molecule ligand tested. The study presented here provides guidelines for design of superior small molecule binders to the SL1 RNA that have the potential of being developed as an antiviral by either interfering with SL1-NCp7 interaction at the packaging and/or maturation stages. PMID:20565056

  15. 2.0 A crystal structure of a four-domain segment of human fibronectin encompassing the RGD loop and synergy region.

    PubMed

    Leahy, D J; Aukhil, I; Erickson, H P

    1996-01-12

    We have determined the 2.0 A crystal structure of a fragment of human fibronectin encompassing the seventh through the RGD-containing tenth type III repeats (FN7-10). The structure reveals an extended rod-like molecule with a long axis of approximately 140 A and highly variable relationships between adjacent domains. An unusually small rotation between domains 9 and 10 creates a distinctive binding site, in which the RGD loop from domain 10 and the "synergy" region from domain 9 are on the same face of FN7-10 and thus easily accessible to a single integrin molecule. The cell-binding RGD loop is well-ordered in this structure and extends approximately 10 A away from the FN7-10 core.

  16. Comparison Between Self-Guided Langevin Dynamics and Molecular Dynamics Simulations for Structure Refinement of Protein Loop Conformations

    DTIC Science & Technology

    2011-01-01

    the shorter loops placed initially from a coarse- grained lattice model and the longer loops from an enumeration assembly method (the Loopy program...Å, a0 ¼ 1.2045, and a1 ¼ 0.1866. The hydrophobic cavitation energy term was approximated by a linear product of the sol- vent-exposed surface area... boundary should allow greater excursions on rugged conformational energy landscapes by increasing transmission probabilities across high potential-energy

  17. The 1.59Å resolution structure of the minor pseudopilin EpsH of Vibrio cholerae reveals a long flexible loop.

    PubMed

    Raghunathan, Kannan; Vago, Frank S; Grindem, David; Ball, Terry; Wedemeyer, William J; Bagdasarian, Michael; Arvidson, Dennis N

    2014-02-01

    The type II secretion complex exports folded proteins from the periplasm to the extracellular milieu. It is used by the pathogenic bacterium Vibrio cholerae to export several proteins, including its major virulence factor, cholera toxin. The pseudopilus is an essential component of the type II secretion system and likely acts as a piston to push the folded proteins across the outer membrane through the secretin pore. The pseudopilus is composed of the major pseudopilin, EpsG, and four minor pseudopilins, EpsH, EpsI, EpsJ and EpsK. We determined the x-ray crystal structure of the head domain of EpsH at 1.59Å resolution using molecular replacement with the previously reported EpsH structure, 2qv8, as the template. Three additional N-terminal amino acids present in our construct prevent an artifactual conformation of residues 160-166, present in one of the two monomers of the 2qv8 structure. Additional crystal contacts stabilize a long flexible loop comprised of residues 104-135 that is more disordered in the 2qv8 structure but is partially observed in our structure in very different positions for the two EpsH monomers in the asymmetric unit. In one of the conformations the loop is highly extended. Modeling suggests the highly charged loop is capable of contacting EpsG and possibly secreted protein substrates, suggesting a role in specificity of pseudopilus assembly or secretion function.

  18. Crystal structure and mutagenesis of a protein phosphatase-1:calcineurin hybrid elucidate the role of the beta12-beta13 loop in inhibitor binding.

    PubMed

    Maynes, Jason T; Perreault, Kathleen R; Cherney, Maia M; Luu, Hue Anh; James, Michael N G; Holmes, Charles F B

    2004-10-08

    Protein phosphatase-1 and protein phosphatase-2B (calcineurin) are eukaryotic serine/threonine phosphatases that share 40% sequence identity in their catalytic subunits. Despite the similarities in sequence, these phosphatases are widely divergent when it comes to inhibition by natural product toxins, such as microcystin-LR and okadaic acid. The most prominent region of non-conserved sequence between these phosphatases corresponds to the beta12-beta13 loop of protein phosphatase-1, and the L7 loop of toxin-resistant calcineurin. In the present study, mutagenesis of residues 273-277 of the beta12-beta13 loop of the protein phosphatase-1 catalytic subunit (PP-1c) to the corresponding residues in calcineurin (312-316), resulted in a chimeric mutant that showed a decrease in sensitivity to microcystin-LR, okadaic acid, and the endogenous PP-1c inhibitor protein inhibitor-2. A crystal structure of the chimeric mutant in complex with okadaic acid was determined to 2.0-A resolution. The beta12-beta13 loop region of the mutant superimposes closely with that of wild-type PP-1c bound to okadaic acid. Systematic mutation of each residue in the beta12-beta13 loop of PP-1c showed that a single amino acid change (C273L) was the most influential in mediating sensitivity of PP-1c to toxins. Taken together, these data indicate that it is an individual amino acid residue substitution and not a change in the overall beta12-beta13 loop conformation of protein phosphatase-1 that contributes to disrupting important interactions with inhibitors such as microcystin-LR and okadaic acid.

  19. Sphingosine-1-phosphate induced epithelial-mesenchymal transition of hepatocellular carcinoma via an MMP-7/syndecan-1/TGF-β autocrine loop

    PubMed Central

    Zeng, Ye; Yao, Xinghong; Chen, Li; Yan, Zhiping; Liu, Jingxia; Zhang, Yingying; Feng, Tang; Wu, Jiang; Liu, Xiaoheng

    2016-01-01

    Sphingosine-1-phosphate (S1P) induces epithelial–mesenchymal transition (EMT) in hepatocellular carcinoma (HCC). However, its underlying mechanism remains largely unknown. In the present study, we investigated the correlation between S1P and syndecan-1 in HCC, the molecular mechanism involved, as well as their roles in EMT of HCC. Results revealed a high serum S1P level presents in patients with HCC, which positively correlated with the serum syndecan-1 level. A significant inverse correlation existed between S1P1 and syndecan-1 in HCC tissues. S1P elicits activation of the PI3K/AKT signaling pathways via S1P1, which triggers HPSE, leading to increases in expression and activity of MMP-7 and leading to shedding and suppression of syndecan-1. The loss of syndecan-1 causes an increase in TGF-β1 production. The limited chronic increase in TGF-β1 can convert HCC cells into a mesenchymal phenotype via establishing an MMP-7/Syndecan-1/TGF-β autocrine loop. Finally, TGF-β1 and syndecan-1 are essential for S1P-induced epithelial to mesenchymal transition. Taken together, our study demonstrates that S1P induces advanced tumor phenotypes of HCC via establishing an MMP-7/syndecan-1/TGF-β1 autocrine loop, and implicates targetable S1P1-PI3K/AKT-HPSE-MMP-7 signaling axe in HCC metastasis. PMID:27556509

  20. miR-29b sensitizes multiple myeloma cells to bortezomib-induced apoptosis through the activation of a feedback loop with the transcription factor Sp1

    PubMed Central

    Amodio, N; Di Martino, M T; Foresta, U; Leone, E; Lionetti, M; Leotta, M; Gullà, A M; Pitari, M R; Conforti, F; Rossi, M; Agosti, V; Fulciniti, M; Misso, G; Morabito, F; Ferrarini, M; Neri, A; Caraglia, M; Munshi, N C; Anderson, K C; Tagliaferri, P; Tassone, P

    2012-01-01

    MicroRNAs (miRNAs) with tumor-suppressor potential might have therapeutic applications in multiple myeloma (MM) through the modulation of still undiscovered molecular pathways. Here, we investigated the effects of enforced expression of miR-29b on the apoptotic occurrence in MM and highlighted its role in the context of a new transcriptional loop that is finely tuned by the proteasome inhibitor bortezomib. In details, in vitro growth inhibition and apoptosis of MM cells was induced by either transient expression of synthetic miR-29b or its stable lentivirus-enforced expression. We identified Sp1, a transcription factor endowed with oncogenic activity, as a negative regulator of miR-29b expression in MM cells. Since Sp1 expression and functions are regulated via the 26S proteasome, we investigated the effects of bortezomib on miR-29b-Sp1 loop, showing that miR-29b levels were indeed upregulated by the drug. At the same time, the bortezomib/miR-29b combination produced significant pro-apoptotic effects. We also demonstrated that the PI3K/AKT pathway plays a major role in the regulation of miR-29b-Sp1 loop and induction of apoptosis in MM cells. Finally, MM xenografts constitutively expressing miR-29b showed significant reduction of their tumorigenic potential. Our findings indicate that miR-29b is involved in a regulatory loop amenable of pharmacologic intervention and modulates the anti-MM activity of bortezomib in MM cells. PMID:23190608

  1. Loop-to-loop coupling.

    SciTech Connect

    Warne, Larry Kevin; Lucero, Larry Martin; Langston, William L.; Salazar, Robert Austin; Coleman, Phillip Dale; Basilio, Lorena I.; Bacon, Larry Donald

    2012-05-01

    This report estimates inductively-coupled energy to a low-impedance load in a loop-to-loop arrangement. Both analytical models and full-wave numerical simulations are used and the resulting fields, coupled powers and energies are compared. The energies are simply estimated from the coupled powers through approximations to the energy theorem. The transmitter loop is taken to be either a circular geometry or a rectangular-loop (stripline-type) geometry that was used in an experimental setup. Simple magnetic field models are constructed and used to estimate the mutual inductance to the receiving loop, which is taken to be circular with one or several turns. Circuit elements are estimated and used to determine the coupled current and power (an equivalent antenna picture is also given). These results are compared to an electromagnetic simulation of the transmitter geometry. Simple approximate relations are also given to estimate coupled energy from the power. The effect of additional loads in the form of attached leads, forming transmission lines, are considered. The results are summarized in a set of susceptibility-type curves. Finally, we also consider drives to the cables themselves and the resulting common-to-differential mode currents in the load.

  2. Structure and variability of the Yucatan and loop currents along the slope and shelf break of the Yucatan channel and Campeche bank

    NASA Astrophysics Data System (ADS)

    Sheinbaum, Julio; Athié, Gabriela; Candela, Julio; Ochoa, José; Romero-Arteaga, Angélica

    2016-12-01

    Three years (2008-2011) of direct current measurements from a mooring array deployed at the western Yucatan Channel (defined west of 85.6°W) and along the eastern Campeche Bank captured the main characteristics of the Yucatan and Loop Currents and the eddies associated with them. The array was deployed to provide upstream conditions in support of the Loop Current Dynamics Experiment. A substantial portion (60-80%) of the variance at the mooring sections is related to horizontal shifts of the currents due to meanders and eddies. Time-frequency analysis indicates that the velocity time-series are "event dominated", with higher variability at low-frequencies (40-100 days or longer periods) but with a substantial contribution at higher frequencies (5-25 days periods) particularly strong from October to March. The vertical structure and time evolution of the eddy kinetic energy in a developing Campeche Bank cyclone suggest baroclinic instability dynamics are relevant for its development. Four Loop Current eddies (Cameron, Darwin, Ekman and Franklin) separated during 2008-2011. Ekman and Franklin were particularly dominated by a cyclone associated with a meander trough of the southward flowing branch of the Loop Current (Donohue et al., 2016a,b) and weaker Campeche Bank cyclones. For Cameron and Darwin, Campeche Bank cyclonic anomalies appear to be nearly as strong as the ones coming from the eastern side of the Loop Current. Eastward shifts of the Yucatan and Loop Currents observed over the sections appear to be linked to vorticity perturbations propagating from the Caribbean and precede several eddy detachments; their significance for the generation of Campeche Bank cyclones and eddy shedding remains to be determined. Time-series of Yucatan Current transport, vorticity fluctuations and Loop Current northward extension during the 3 deployment periods only depict positive correlation in two of them. Given the wide spectrum of variability, much more data are required to

  3. Suggestive Evidence for the Involvement of the Second Calcium and Surface Loop in Interfacial Binding: Monoclinci and Trigonal Crystal Structures of a Quadruple Mutant of Phospholipase A2

    SciTech Connect

    Sekar,K.; Yogavel, M.; Kanaujia, S.; Sharma, A.; Velmurugan, D.; Poi, M.; Dauter, Z.; Tsai, M.

    2006-01-01

    The crystal structures of the monoclinic and trigonal forms of the quadruple mutant K53,56,120,121M of recombinant bovine pancreatic phospholipase A{sub 2} (PLA{sub 2}) have been solved and refined at 1.9 and 1.1 Angstroms resolution, respectively. Interestingly, the monoclinic form reveals the presence of the second calcium ion. Furthermore, the surface-loop residues are ordered and the conformation of residues 62-66 is similar to that observed in other structures containing the second calcium ion. On the other hand, in the trigonal form the surface loop is disordered and the second calcium is absent. Docking studies suggest that the second calcium and residues Lys62 and Asp66 from the surface loop could be involved in the interaction with the polar head group of the membrane phospholipid. It is hypothesized that the two structures of the quadruple mutant, monoclinic and trigonal, represent the conformations of PLA2 at the lipid interface and in solution, respectively. A docked structure with a phospholipid molecule and with a transition-state analogue bound, one at the active site coordinating to the catalytic calcium and the other at the second calcium site, but both at the i-face, is presented.

  4. Structural integration in hypoxia-inducible factors

    SciTech Connect

    Wu, Dalei; Potluri, Nalini; Lu, Jingping; Kim, Youngchang; Rastinejad, Fraydoon

    2015-08-20

    The hypoxia-inducible factors (HIFs) coordinate cellular adaptations to low oxygen stress by regulating transcriptional programs in erythropoiesis, angiogenesis and metabolism. These programs promote the growth and progression of many tumours, making HIFs attractive anticancer targets. Transcriptionally active HIFs consist of HIF-alpha and ARNT (also called HIF-1 beta) subunits. Here we describe crystal structures for each of mouse HIF-2 alpha-ARNT and HIF-1 alpha-ARNT heterodimers in states that include bound small molecules and their hypoxia response element. A highly integrated quaternary architecture is shared by HIF-2 alpha-ARNT and HIF-1 alpha-ARNT, wherein ARNT spirals around the outside of each HIF-alpha subunit. Five distinct pockets are observed that permit small-molecule binding, including PAS domain encapsulated sites and an interfacial cavity formed through subunit heterodimerization. The DNA-reading head rotates, extends and cooperates with a distal PAS domain to bind hypoxia response elements. HIF-alpha mutations linked to human cancers map to sensitive sites that establish DNA binding and the stability of PAS domains and pockets.

  5. Flexibility of the P-loop of Pim-1 kinase: observation of a novel conformation induced by interaction with an inhibitor.

    PubMed

    Parker, Lorien J; Watanabe, Hisami; Tsuganezawa, Keiko; Tomabechi, Yuri; Handa, Noriko; Shirouzu, Mikako; Yuki, Hitomi; Honma, Teruki; Ogawa, Naoko; Nagano, Tetsuo; Yokoyama, Shigeyuki; Tanaka, Akiko

    2012-08-01

    The serine/threonine kinase Pim-1 is emerging as a promising target for cancer therapeutics. Much attention has recently been focused on identifying potential Pim-1 inhibitor candidates for the treatment of haematopoietic malignancies. The outcome of a rational drug-design project has recently been reported [Nakano et al. (2012), J. Med. Chem. 55, 5151-5156]. The report described the process of optimization of the structure-activity relationship and detailed from a medicinal chemistry perspective the development of a low-potency and nonselective compound initially identified from in silico screening into a potent, selective and metabolically stable Pim-1 inhibitor. Here, the structures of the initial in silico hits are reported and the noteworthy features of the Pim-1 complex structures are described. A particular focus was placed on the rearrangement of the glycine-rich P-loop region that was observed for one of the initial compounds, (Z)-7-(azepan-1-ylmethyl)-2-[(1H-indol-3-yl)methylidene]-6-hydroxy-1-benzofuran-3(2H)-one (compound 1), and was also found in all further derivatives. This novel P-loop conformation, which appears to be stabilized by an additional interaction with the β3 strand located above the binding site, is not usually observed in Pim-1 structures.

  6. Hepatitis C virus internal ribosome entry site RNA contains a tertiary structural element in a functional domain of stem–loop II

    PubMed Central

    Lyons, Alita J.; Lytle, J. Robin; Gomez, Jordi; Robertson, Hugh D.

    2001-01-01

    The internal ribosome entry site (IRES) of hepatitis C virus (HCV) RNA contains >300 bases of highly conserved 5′-terminal sequence, most of it in the uncapped 5′-untranslated region (5′-UTR) upstream from the single AUG initiator triplet at which translation of the HCV polyprotein begins. Although progress has been made in defining singularities like the RNA pseudoknot near this AUG, the sequence and structural features of the HCV IRES which stimulate accurate and efficient initiation of protein synthesis are only partially defined. Here we report that a region further upstream from the AUG, stem–loop II of the HCV IRES, also contains an element of local tertiary structure which we have detected using RNase H cleavage and have mapped using the singular ability of two bases therein to undergo covalent intra-chain crosslinking stimulated by UV light. This pre-existing element maps to two non-contiguous stretches of the HCV IRES sequence, residues 53–68 and 103–117. Several earlier studies have shown that the correct sequence between bases 45 and 70 of the HCV IRES stem–loop II domain is required for initiation of protein synthesis. Because features of local tertiary structure like the one we report here are often associated with protein binding, we propose that the HCV stem–loop II element is directly involved in IRES action. PMID:11410661

  7. Protein Loop Closure Using Orientational Restraints from NMR Data

    NASA Astrophysics Data System (ADS)

    Tripathy, Chittaranjan; Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

    Protein loops often play important roles in biological functions such as binding, recognition, catalytic activities and allosteric regulation. Modeling loops that are biophysically sensible is crucial to determining the functional specificity of a protein. A variety of algorithms ranging from robotics-inspired inverse kinematics methods to fragmentbased homology modeling techniques have been developed to predict protein loops. However, determining the 3D structures of loops using global orientational restraints on internuclear vectors, such as those obtained from residual dipolar coupling (RDC) data in solution Nuclear Magnetic Resonance (NMR) spectroscopy, has not been well studied. In this paper, we present a novel algorithm that determines the protein loop conformations using a minimal amount of RDC data. Our algorithm exploits the interplay between the sphero-conics derived from RDCs and the protein kinematics, and formulates the loop structure determination problem as a system of low-degree polynomial equations that can be solved exactly and in closed form. The roots of these polynomial equations, which encode the candidate conformations, are searched systematically, using efficient and provable pruning strategies that triage the vast majority of conformations, to enumerate or prune all possible loop conformations consistent with the data. Our algorithm guarantees completeness by ensuring that a possible loop conformation consistent with the data is never missed. This data-driven algorithm provides a way to assess the structural quality from experimental data with minimal modeling assumptions. We applied our algorithm to compute the loops of human ubiquitin, the FF Domain 2 of human transcription elongation factor CA150 (FF2), the DNA damage inducible protein I (DinI) and the third IgG-binding domain of Protein G (GB3) from experimental RDC data. A comparison of our results versus those obtained by using traditional structure determination protocols on the

  8. Evolution in a Braided Loop Ensemble

    NASA Video Gallery

    This braided loop has several loops near the 'base' that appear to be unwinding with significant apparent outflow. This is evidence of untwisting, and the braided structure also seeming to unwind w...

  9. Effects of the positive feedback loop in polymerization on the reaction-induced phase separation of polymer mixturesa)

    NASA Astrophysics Data System (ADS)

    Furubayashi, Y.; Kawakubo, R.; Nakanishi, H.; Norisuye, T.; Tran-Cong-Miyata, Q.

    2015-06-01

    Phase separation of mixtures composed of a guest polymer dissolved in monomer of a host polymer was induced by photopolymerization. From the polymerization kinetics, it was found that for the host polymer with the glass transition temperature (Tg) higher than the experimental temperature, the Trommsdorff-Norrish effect emerges, providing a method to terminate the phase separation at various intermediate stages of the process and thereby a variety of morphologies can be constructed. For the host polymers with (Tg) lower than the experimental temperature, the freezing process of morphology is not complete, leading to the secondary phase separation inside the domains already generated by the primary process. The kinetics of this secondary phase separation indicates that the peculiar morphology like "sunny-side-up egg"-like structures was generated via spinodal decomposition. The experimental results obtained in this study show that the competition between photopolymerization and phase separation can provide a useful method of materials design in the micro- and sub-micrometer scales.

  10. Flexibility of the P-loop of Pim-1 kinase: observation of a novel conformation induced by interaction with an inhibitor

    PubMed Central

    Parker, Lorien J.; Watanabe, Hisami; Tsuganezawa, Keiko; Tomabechi, Yuri; Handa, Noriko; Shirouzu, Mikako; Yuki, Hitomi; Honma, Teruki; Ogawa, Naoko; Nagano, Tetsuo; Yokoyama, Shigeyuki; Tanaka, Akiko

    2012-01-01

    The serine/threonine kinase Pim-1 is emerging as a promising target for cancer therapeutics. Much attention has recently been focused on identifying potential Pim-1 inhibitor candidates for the treatment of haematopoietic malignancies. The outcome of a rational drug-design project has recently been reported [Nakano et al. (2012 ▶), J. Med. Chem. 55, 5151–5156]. The report described the process of optimization of the structure–activity relationship and detailed from a medicinal chemistry perspective the development of a low-potency and nonselective compound initially identified from in silico screening into a potent, selective and metabolically stable Pim-1 inhibitor. Here, the structures of the initial in silico hits are reported and the noteworthy features of the Pim-1 complex structures are described. A particular focus was placed on the rearrangement of the glycine-rich P-loop region that was observed for one of the initial compounds, (Z)-7-(azepan-1-ylmethyl)-2-[(1H-indol-3-­yl)methylidene]-6-hydroxy-1-benzofuran-3(2H)-one (compound 1), and was also found in all further derivatives. This novel P-loop conformation, which appears to be stabilized by an additional interaction with the β3 strand located above the binding site, is not usually observed in Pim-1 structures. PMID:22869110

  11. Structural variation and functional importance of a D-loop–T-loop interaction in valine-accepting tRNA-like structures of plant viral RNAs

    PubMed Central

    de Smit, Maarten H.; Gultyaev, Alexander P.; Hilge, Mark; Bink, Hugo H. J.; Barends, Sharief; Kraal, Barend; Pleij, Cornelis W. A.

    2002-01-01

    Valine-accepting tRNA-like structures (TLSs) are found at the 3′ ends of the genomic RNAs of most plant viruses belonging to the genera Tymovirus, Furovirus, Pomovirus and Pecluvirus, and of one Tobamovirus species. Sequence alignment of these TLSs suggests the existence of a tertiary D-loop–T-loop interaction consisting of 2 bp, analogous to those in the elbow region of canonical tRNAs. The conserved G18·Ψ55 pair of regular tRNAs is found to covary in these TLSs between G·U (possibly also modified to G·Ψ) and A·G. We have mutated the relevant bases in turnip yellow mosaic virus (TYMV) and examined the mutants for symptom development on Chinese cabbage plants and for accumulation of genetic reversions. Development of symptoms is shown to rely on the presence of either A·G or G·U in the original mutants or in revertants. This finding supports the existence and functional importance of this tertiary interaction. The fact that only G·U and A·G are accepted at this position appears to result from steric and energetic limitations related to the highly compact nature of the elbow region. We discuss the implications of these findings for the various possible functions of the valine-accepting TLS. PMID:12364602

  12. LOOP IIId of the HCV IRES is essential for the structural rearrangement of the 40S-HCV IRES complex.

    PubMed

    Angulo, Jenniffer; Ulryck, Nathalie; Deforges, Jules; Chamond, Nathalie; Lopez-Lastra, Marcelo; Masquida, Benoît; Sargueil, Bruno

    2016-02-18

    As obligatory intracellular parasites, viruses rely on cellular machines to complete their life cycle, and most importantly they recruit the host ribosomes to translate their mRNA. The Hepatitis C viral mRNA initiates translation by directly binding the 40S ribosomal subunit in such a way that the initiation codon is correctly positioned in the P site of the ribosome. Such a property is likely to be central for many viruses, therefore the description of host-pathogen interaction at the molecular level is instrumental to provide new therapeutic targets. In this study, we monitored the 40S ribosomal subunit and the viral RNA structural rearrangement induced upon the formation of the binary complex. We further took advantage of an IRES viral mutant mRNA deficient for translation to identify the interactions necessary to promote translation. Using a combination of structure probing in solution and molecular modeling we establish a whole atom model which appears to be very similar to the one obtained recently by cryoEM. Our model brings new information on the complex, and most importantly reveals some structural rearrangement within the ribosome. This study suggests that the formation of a 'kissing complex' between the viral RNA and the 18S ribosomal RNA locks the 40S ribosomal subunit in a conformation proficient for translation.

  13. LOOP IIId of the HCV IRES is essential for the structural rearrangement of the 40S-HCV IRES complex

    PubMed Central

    Angulo, Jenniffer; Ulryck, Nathalie; Deforges, Jules; Chamond, Nathalie; Lopez-Lastra, Marcelo; Masquida, Benoît; Sargueil, Bruno

    2016-01-01

    As obligatory intracellular parasites, viruses rely on cellular machines to complete their life cycle, and most importantly they recruit the host ribosomes to translate their mRNA. The Hepatitis C viral mRNA initiates translation by directly binding the 40S ribosomal subunit in such a way that the initiation codon is correctly positioned in the P site of the ribosome. Such a property is likely to be central for many viruses, therefore the description of host-pathogen interaction at the molecular level is instrumental to provide new therapeutic targets. In this study, we monitored the 40S ribosomal subunit and the viral RNA structural rearrangement induced upon the formation of the binary complex. We further took advantage of an IRES viral mutant mRNA deficient for translation to identify the interactions necessary to promote translation. Using a combination of structure probing in solution and molecular modeling we establish a whole atom model which appears to be very similar to the one obtained recently by cryoEM. Our model brings new information on the complex, and most importantly reveals some structural rearrangement within the ribosome. This study suggests that the formation of a ‘kissing complex’ between the viral RNA and the 18S ribosomal RNA locks the 40S ribosomal subunit in a conformation proficient for translation. PMID:26626152

  14. A Homology Model Reveals Novel Structural Features and an Immunodominant Surface Loop/Opsonic Target in the Treponema pallidum BamA Ortholog TP_0326

    PubMed Central

    Luthra, Amit; Anand, Arvind; Hawley, Kelly L.; LeDoyt, Morgan; La Vake, Carson J.; Caimano, Melissa J.; Cruz, Adriana R.; Salazar, Juan C.

    2015-01-01

    ABSTRACT We recently demonstrated that TP_0326 is a bona fide rare outer membrane protein (OMP) in Treponema pallidum and that it possesses characteristic BamA bipartite topology. Herein, we used immunofluorescence analysis (IFA) to show that only the β-barrel domain of TP_0326 contains surface-exposed epitopes in intact T. pallidum. Using the solved structure of Neisseria gonorrhoeae BamA, we generated a homology model of full-length TP_0326. Although the model predicts a typical BamA fold, the β-barrel harbors features not described in other BamAs. Structural modeling predicted that a dome comprised of three large extracellular loops, loop 4 (L4), L6, and L7, covers the barrel's extracellular opening. L4, the dome's major surface-accessible loop, contains mainly charged residues, while L7 is largely neutral and contains a polyserine tract in a two-tiered conformation. L6 projects into the β-barrel but lacks the VRGF/Y motif that anchors L6 within other BamAs. IFA and opsonophagocytosis assay revealed that L4 is surface exposed and an opsonic target. Consistent with B cell epitope predictions, immunoblotting and enzyme-linked immunosorbent assay (ELISA) confirmed that L4 is an immunodominant loop in T. pallidum-infected rabbits and humans with secondary syphilis. Antibody capture experiments using Escherichia coli expressing OM-localized TP_0326 as a T. pallidum surrogate further established the surface accessibility of L4. Lastly, we found that a naturally occurring substitution (Leu593 → Gln593) in the L4 sequences of T. pallidum strains affects antibody binding in sera from syphilitic patients. Ours is the first study to employ a “structure-to-pathogenesis” approach to map the surface topology of a T. pallidum OMP within the context of syphilitic infection. IMPORTANCE Previously, we reported that TP_0326 is a bona fide rare outer membrane protein (OMP) in Treponema pallidum and that it possesses the bipartite topology characteristic of a BamA ortholog

  15. High glucose concentration induces the overexpression of transforming growth factor-beta through the activation of a platelet-derived growth factor loop in human mesangial cells.

    PubMed Central

    Di Paolo, S.; Gesualdo, L.; Ranieri, E.; Grandaliano, G.; Schena, F. P.

    1996-01-01

    High glucose concentration has been shown to induce the overexpression of transforming growth factor (TGF)-beta 1 mRNA and protein in different cell types, including murine mesangial cells, thus possibly accounting for the expansion of mesangial extracellular matrix observed in diabetic glomerulopathy. In the present study, we evaluated platelet-derived growth factor (PDGF) B-chain and PDGF-beta receptor gene expression in human mesangial cells (HMCs) exposed to different concentrations of glucose and then sought a possible relationship between a PDGF loop and the modulation of TGF-beta 1 expression. HMC [3H]thymidine incorporation was upregulated by 30 mmol/L glucose (HG) up to 24 hours, whereas it was significantly inhibited at later time points. Neutralizing antibodies to PDGF BB abolished the biphasic response to HG, whereas anti-TGF-beta antibodies reversed only the late inhibitory effect of hyperglycemic medium. HG induced an early and persistent increase of PDGF B-chain gene expression, as evaluated by reverse transcriptase polymerase chain reaction, whereas PDGF-beta receptor mRNA increased by twofold after 6 hours, thereafter declining at levels 70% lower than in controls after 24 hours. 125I-Labeled PDGF BB binding studies in HMCs exposed to HG for 24 hours confirmed the decrease of PDGF-beta receptor expression. TGF-beta 1-specific transcripts showed 43 and 78% increases after 24 and 48 hours of incubation in HG, respectively, which was markedly diminished by anti-PDGF BB neutralizing antibodies or suramin. We conclude that HG induces an early activation of a PDGF loop that, in turn, causes an increase of TGF-beta 1 gene expression, thus modulating both HMC proliferation and mesangial matrix production. Images Figure 2 Figure 3 Figure 4 Figure 5 PMID:8952542

  16. A novel hypoxia-induced miR-147a regulates cell proliferation through a positive feedback loop of stabilizing HIF-1α

    PubMed Central

    Wang, Fan; Zhang, Haoxiang; Xu, Naihan; Huang, Nunu; Tian, Caiming; Ye, Anlin; Hu, Guangnan; He, Jie; Zhang, Yaou

    2016-01-01

    ABSTRACT Hypoxia is a general event in solid tumor growth. Therefore, induced cellular responses by hypoxia are important for tumorigenesis and tumor growth. MicroRNAs (miRNAs) have recently emerged as important regulators of hypoxia induced cellular responses. Here we report that miR-147a is a novel and crucial hypoxia induced miRNA. HIF-1α up-regulates the expression of miR-147a, and miR-147a in turn stabilizes and accumulates HIF-1α protein via directly targeting HIF-3α, a dominant negative regulator of HIF-1α. Subsequent studies in xenograft mouse model reveal that miR-147a is capable of inhibiting tumor growth. Collectively, these data demonstrate a positive feedback loop between HIF-1α, miR-147a and HIF-3α, which provide a new insight into the mechanism of miR-147a induced cell proliferation arrest under hypoxia. PMID:27260617

  17. Open and closed cortico-subcortical loops: A neuro-computational account of access to consciousness in the distractor-induced blindness paradigm.

    PubMed

    Ebner, Christian; Schroll, Henning; Winther, Gesche; Niedeggen, Michael; Hamker, Fred H

    2015-09-01

    How the brain decides which information to process 'consciously' has been debated over for decades without a simple explanation at hand. While most experiments manipulate the perceptual energy of presented stimuli, the distractor-induced blindness task is a prototypical paradigm to investigate gating of information into consciousness without or with only minor visual manipulation. In this paradigm, subjects are asked to report intervals of coherent dot motion in a rapid serial visual presentation (RSVP) stream, whenever these are preceded by a particular color stimulus in a different RSVP stream. If distractors (i.e., intervals of coherent dot motion prior to the color stimulus) are shown, subjects' abilities to perceive and report intervals of target dot motion decrease, particularly with short delays between intervals of target color and target motion. We propose a biologically plausible neuro-computational model of how the brain controls access to consciousness to explain how distractor-induced blindness originates from information processing in the cortex and basal ganglia. The model suggests that conscious perception requires reverberation of activity in cortico-subcortical loops and that basal-ganglia pathways can either allow or inhibit this reverberation. In the distractor-induced blindness paradigm, inadequate distractor-induced response tendencies are suppressed by the inhibitory 'hyperdirect' pathway of the basal ganglia. If a target follows such a distractor closely, temporal aftereffects of distractor suppression prevent target identification. The model reproduces experimental data on how delays between target color and target motion affect the probability of target detection.

  18. Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states

    PubMed Central

    Baranowski, Maciej; Ołldziej, Stanisław; Scheraga, Harold A.; Liwo, Adam; Czaplewski, Cezary

    2013-01-01

    The UNited RESidue (UNRES) coarse-grained model of polypeptide chains, developed in our laboratory, enables us to carry out millisecond-scale molecular-dynamics simulations of large proteins effectively. It performs well in ab initio predictions of protein structure, as demonstrated in the last Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP10). However, the resolution of the simulated structure is too coarse, especially in loop regions, which results from insufficient specificity of the model of local interactions. To improve the representation of local interactions, in this work we introduced new side-chain-backbone correlation potentials, derived from a statistical analysis of loop regions of 4585 proteins. To obtain sufficient statistics, we reduced the set of amino-acid-residue types to five groups, derived in our earlier work on structurally optimized reduced alphabets, based on a statistical analysis of the properties of amino-acid structures. The new correlation potentials are expressed as one-dimensional Fourier series in the virtual-bond-dihedral angles involving side-chain centroids. The weight of these new terms was determined by a trial-and-error method, in which Multiplexed Replica Exchange Molecular Dynamics (MREMD) simulations were run on selected test proteins. The best average root-mean-square deviations (RMSDs) of the calculated structures from the experimental structures below the folding-transition temperatures were obtained with the weight of the new side-chain-backbone correlation potentials equal to 0.57. The resulting conformational ensembles were analyzed in detail by using the Weighted Histogram Analysis Method (WHAM) and Ward's minimum-variance clustering. This analysis showed that the RMSDs from the experimental structures dropped by 0.5 Å on average, compared to simulations without the new terms, and the deviation of individual residues in the loop region of the computed

  19. All Ca(2+)-binding loops of light-sensitive ctenophore photoprotein berovin bind magnesium ions: The spatial structure of Mg(2+)-loaded apo-berovin.

    PubMed

    Burakova, Ludmila P; Natashin, Pavel V; Malikova, Natalia P; Niu, Fengfeng; Pu, Mengchen; Vysotski, Eugene S; Liu, Zhi-Jie

    2016-01-01

    Light-sensitive photoprotein berovin accounts for a bright bioluminescence of ctenophore Beroe abyssicola. Berovin is functionally identical to the well-studied Ca(2+)-regulated photoproteins of jellyfish, however in contrast to those it is extremely sensitive to the visible light. Berovin contains three EF-hand Ca(2+)-binding sites and consequently belongs to a large family of the EF-hand Ca(2+)-binding proteins. Here we report the spatial structure of apo-berovin with bound Mg(2+) determined at 1.75Å. The magnesium ion is found in each functional EF-hand loop of a photoprotein and coordinated by oxygen atoms donated by the side-chain groups of aspartate, carbonyl groups of the peptide backbone, or hydroxyl group of serine with characteristic oxygen-Mg(2+) distances. As oxygen supplied by the side-chain of the twelfth residue of all Ca(2+)-binding loops participates in the magnesium ion coordination, it was suggested that Ca(2+)-binding loops of berovin belong to the mixed Ca(2+)/Mg(2+) rather than Ca(2+)-specific type. In addition, we report an effect of physiological concentration of Mg(2+) on bioluminescence of berovin (sensitivity to Ca(2+), rapid-mixed kinetics, light-sensitivity, thermostability, and apo-berovin conversion into active protein). The different impact of physiological concentration of Mg(2+) on berovin bioluminescence as compared to hydromedusan photoproteins was attributed to different affinities of the Ca(2+)-binding sites of these photoproteins to Mg(2+).

  20. Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism

    PubMed Central

    Guan, Hong-Hsiang; Yoshimura, Masato; Chuankhayan, Phimonphan; Lin, Chien-Chih; Chen, Nai-Chi; Yang, Ming-Chi; Ismail, Asma; Fun, Hoong-Kun; Chen, Chun-Jung

    2015-01-01

    ST50, an outer-membrane component of the multi-drug efflux system from Salmonella enterica serovar Typhi, is an obligatory diagnostic antigen for typhoid fever. ST50 is an excellent and unique diagnostic antigen with 95% specificity and 90% sensitivity and is used in the commercial diagnosis test kit (TYPHIDOTTM). The crystal structure of ST50 at a resolution of 2.98 Å reveals a trimer that forms an α-helical tunnel and a β-barrel transmembrane channel traversing the periplasmic space and outer membrane. Structural investigations suggest significant conformational variations in the extracellular loop regions, especially extracellular loop 2. This is the location of the most plausible antibody-binding domain that could be used to target the design of new antigenic epitopes for the development of better diagnostics or drugs for the treatment of typhoid fever. A molecule of the detergent n-octyl-β-D-glucoside is observed in the D-cage, which comprises three sets of Asp361 and Asp371 residues at the periplasmic entrance. These structural insights suggest a possible substrate transport mechanism in which the substrate first binds at the periplasmic entrance of ST50 and subsequently, via iris-like structural movements to open the periplasmic end, penetrates the periplasmic domain for efflux pumping of molecules, including poisonous metabolites or xenobiotics, for excretion outside the pathogen. PMID:26563565

  1. Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism.

    PubMed

    Guan, Hong-Hsiang; Yoshimura, Masato; Chuankhayan, Phimonphan; Lin, Chien-Chih; Chen, Nai-Chi; Yang, Ming-Chi; Ismail, Asma; Fun, Hoong-Kun; Chen, Chun-Jung

    2015-11-13

    ST50, an outer-membrane component of the multi-drug efflux system from Salmonella enterica serovar Typhi, is an obligatory diagnostic antigen for typhoid fever. ST50 is an excellent and unique diagnostic antigen with 95% specificity and 90% sensitivity and is used in the commercial diagnosis test kit (TYPHIDOT(TM)). The crystal structure of ST50 at a resolution of 2.98 Å reveals a trimer that forms an α-helical tunnel and a β-barrel transmembrane channel traversing the periplasmic space and outer membrane. Structural investigations suggest significant conformational variations in the extracellular loop regions, especially extracellular loop 2. This is the location of the most plausible antibody-binding domain that could be used to target the design of new antigenic epitopes for the development of better diagnostics or drugs for the treatment of typhoid fever. A molecule of the detergent n-octyl-β-D-glucoside is observed in the D-cage, which comprises three sets of Asp361 and Asp371 residues at the periplasmic entrance. These structural insights suggest a possible substrate transport mechanism in which the substrate first binds at the periplasmic entrance of ST50 and subsequently, via iris-like structural movements to open the periplasmic end, penetrates the periplasmic domain for efflux pumping of molecules, including poisonous metabolites or xenobiotics, for excretion outside the pathogen.

  2. Oxidative stress activates the TRPM2-Ca(2+)-CaMKII-ROS signaling loop to induce cell death in cancer cells.

    PubMed

    Wang, Qian; Huang, Lihong; Yue, Jianbo

    2016-12-20

    High intracellular levels of reactive oxygen species (ROS) cause oxidative stress that results in numerous pathologies, including cell death. Transient potential receptor melastatin-2 (TRPM2), a Ca(2+)-permeable cation channel, is mainly activated by intracellular adenosine diphosphate ribose (ADPR) in response to oxidative stress. Here we studied the role and mechanisms of TRPM2-mediated Ca(2+) influx on oxidative stress-induced cell death in cancer cells. We found that oxidative stress activated the TRPM2-Ca(2+)-CaMKII cascade to inhibit early autophagy induction, which ultimately led to cell death in TRPM2 expressing cancer cells. On the other hand, TRPM2 knockdown switched cells from cell death to autophagy for survival in response to oxidative stress. Moreover, we found that oxidative stress activated the TRPM2-CaMKII cascade to further induce intracellular ROS production, which led to mitochondria fragmentation and loss of mitochondrial membrane potential. In summary, our data demonstrated that oxidative stress activates the TRPM2-Ca(2+)-CaMKII-ROS signal loop to inhibit autophagy and induce cell death.

  3. Loop-bed combustion apparatus

    DOEpatents

    Shang, Jer-Yu; Mei, Joseph S.; Slagle, Frank D.; Notestein, John E.

    1984-01-01

    The present invention is directed to a combustion apparatus in the configuration of a oblong annulus defining a closed loop. Particulate coal together with a sulfur sorbent such as sulfur or dolomite is introduced into the closed loop, ignited, and propelled at a high rate of speed around the loop. Flue gas is withdrawn from a location in the closed loop in close proximity to an area in the loop where centrifugal force imposed upon the larger particulate material maintains these particulates at a location spaced from the flue gas outlet. Only flue gas and smaller particulates resulting from the combustion and innerparticle grinding are discharged from the combustor. This structural arrangement provides increased combustion efficiency due to the essentially complete combustion of the coal particulates as well as increased sulfur absorption due to the innerparticle grinding of the sorbent which provides greater particle surface area.

  4. Higher dimensional loop quantum cosmology

    NASA Astrophysics Data System (ADS)

    Zhang, Xiangdong

    2016-07-01

    Loop quantum cosmology (LQC) is the symmetric sector of loop quantum gravity. In this paper, we generalize the structure of loop quantum cosmology to the theories with arbitrary spacetime dimensions. The isotropic and homogeneous cosmological model in n+1 dimensions is quantized by the loop quantization method. Interestingly, we find that the underlying quantum theories are divided into two qualitatively different sectors according to spacetime dimensions. The effective Hamiltonian and modified dynamical equations of n+1 dimensional LQC are obtained. Moreover, our results indicate that the classical big bang singularity is resolved in arbitrary spacetime dimensions by a quantum bounce. We also briefly discuss the similarities and differences between the n+1 dimensional model and the 3+1 dimensional one. Our model serves as a first example of higher dimensional loop quantum cosmology and offers the possibility to investigate quantum gravity effects in higher dimensional cosmology.

  5. Detection of cystic structures using pulsed ultrasonically induced resonant cavitation

    NASA Technical Reports Server (NTRS)

    Bar-Cohen, Yoseph (Inventor); Kovach, John S. (Inventor)

    2002-01-01

    Apparatus and method for early detection of cystic structures indicative of ovarian and breast cancers uses ultrasonic wave energy at a unique resonance frequency for inducing cavitation in cystic fluid characteristic of cystic structures in the ovaries associated with ovarian cancer, and in cystic structures in the breast associated with breast cancer. Induced cavitation bubbles in the cystic fluid implode, creating implosion waves which are detected by ultrasonic receiving transducers attached to the abdomen of the patient. Triangulation of the ultrasonic receiving transducers enables the received signals to be processed and analyzed to identify the location and structure of the cyst.

  6. Random anisotropy induced by structural disorder

    NASA Astrophysics Data System (ADS)

    Martinez, B.; Labarta, A.; Badia, F.; Tejada, J.

    1992-02-01

    As a direct consequence of the structural disorder, inherent to the amorphous state, local electrostatic fields are highly irregular. Due to the interplay between those highly irregular local electrostatic fields and the aspherical 4f electron clouds of the rare earth atoms, local anisotropy axis, directed along directions that vary randomly in space, may be generated. These directions are determined by the local arrangement of atoms; therefore, some information about amorphous structure may be obtained through the study of the magnetization curve.

  7. Dynamic Aperture-based Solar Loop Segmentation

    NASA Technical Reports Server (NTRS)

    Lee, Jon Kwan; Newman, Timothy S.; Gary, G. Allen

    2006-01-01

    A new method to automatically segment arc-like loop structures from intensity images of the Sun's corona is introduced. The method constructively segments credible loop structures by exploiting the Gaussian-like shape of loop cross-sectional intensity profiles. The experimental results show that the method reasonably segments most of the well-defined loops in coronal images. The method is only the second published automated solar loop segmentation method. Its advantage over the other published method is that it operates independently of supplemental time specific data.

  8. A TNF receptor loop peptide mimic blocks RANK ligand-induced signaling, bone resorption, and bone loss.

    PubMed

    Aoki, Kazuhiro; Saito, Hiroaki; Itzstein, Cecile; Ishiguro, Masaji; Shibata, Tatsuya; Blanque, Roland; Mian, Anower Hussain; Takahashi, Mariko; Suzuki, Yoshifumi; Yoshimatsu, Masako; Yamaguchi, Akira; Deprez, Pierre; Mollat, Patrick; Murali, Ramachandran; Ohya, Keiichi; Horne, William C; Baron, Roland

    2006-06-01

    Activating receptor activator of NF-kappaB (RANK) and TNF receptor (TNFR) promote osteoclast differentiation. A critical ligand contact site on the TNFR is partly conserved in RANK. Surface plasmon resonance studies showed that a peptide (WP9QY) that mimics this TNFR contact site and inhibits TNF-alpha-induced activity bound to RANK ligand (RANKL). Changing a single residue predicted to play an important role in the interaction reduced the binding significantly. WP9QY, but not the altered control peptide, inhibited the RANKL-induced activation of RANK-dependent signaling in RAW 264.7 cells but had no effect on M-CSF-induced activation of some of the same signaling events. WP9QY but not the control peptide also prevented RANKL-induced bone resorption and osteoclastogenesis, even when TNFRs were absent or blocked. In vivo, where both RANKL and TNF-alpha promote osteoclastogenesis, osteoclast activity, and bone loss, WP9QY prevented the increased osteoclastogenesis and bone loss induced in mice by ovariectomy or low dietary calcium, in the latter case in both wild-type and TNFR double-knockout mice. These results suggest that a peptide that mimics a TNFR ligand contact site blocks bone resorption by interfering with recruitment and activation of osteoclasts by both RANKL and TNF.

  9. Ultrahigh and High Resolution Structures and Mutational Analysis of Monomeric Streptococcus pyogenes SpeB Reveal a Functional Role for the Glycine-rich C-terminal Loop

    SciTech Connect

    González-Páez, Gonzalo E.; Wolan, Dennis W.

    2012-09-05

    Cysteine protease SpeB is secreted from Streptococcus pyogenes and has been studied as a potential virulence factor since its identification almost 70 years ago. Here, we report the crystal structures of apo mature SpeB to 1.06 {angstrom} resolution as well as complexes with the general cysteine protease inhibitor trans-epoxysuccinyl-L-leucylamido(4-guanidino)butane and a novel substrate mimetic peptide inhibitor. These structures uncover conformational changes associated with maturation of SpeB from the inactive zymogen to its active form and identify the residues required for substrate binding. With the use of a newly developed fluorogenic tripeptide substrate to measure SpeB activity, we determined IC{sub 50} values for trans-epoxysuccinyl-L-leucylamido(4-guanidino)butane and our new peptide inhibitor and the effects of mutations within the C-terminal active site loop. The structures and mutational analysis suggest that the conformational movements of the glycine-rich C-terminal loop are important for the recognition and recruitment of biological substrates and release of hydrolyzed products.

  10. Ultrahigh and High Resolution Structures and Mutational Analysis of Monomeric Streptococcus pyogenes SpeB Reveal a Functional Role for the Glycine-rich C-terminal Loop

    PubMed Central

    González-Páez, Gonzalo E.; Wolan, Dennis W.

    2012-01-01

    Cysteine protease SpeB is secreted from Streptococcus pyogenes and has been studied as a potential virulence factor since its identification almost 70 years ago. Here, we report the crystal structures of apo mature SpeB to 1.06 Å resolution as well as complexes with the general cysteine protease inhibitor trans-epoxysuccinyl-l-leucylamido(4-guanidino)butane and a novel substrate mimetic peptide inhibitor. These structures uncover conformational changes associated with maturation of SpeB from the inactive zymogen to its active form and identify the residues required for substrate binding. With the use of a newly developed fluorogenic tripeptide substrate to measure SpeB activity, we determined IC50 values for trans-epoxysuccinyl-l-leucylamido(4-guanidino)butane and our new peptide inhibitor and the effects of mutations within the C-terminal active site loop. The structures and mutational analysis suggest that the conformational movements of the glycine-rich C-terminal loop are important for the recognition and recruitment of biological substrates and release of hydrolyzed products. PMID:22645124

  11. Verification of Loop Diagnostics

    NASA Technical Reports Server (NTRS)

    Winebarger, A.; Lionello, R.; Mok, Y.; Linker, J.; Mikic, Z.

    2014-01-01

    Many different techniques have been used to characterize the plasma in the solar corona: density-sensitive spectral line ratios are used to infer the density, the evolution of coronal structures in different passbands is used to infer the temperature evolution, and the simultaneous intensities measured in multiple passbands are used to determine the emission measure. All these analysis techniques assume that the intensity of the structures can be isolated through background subtraction. In this paper, we use simulated observations from a 3D hydrodynamic simulation of a coronal active region to verify these diagnostics. The density and temperature from the simulation are used to generate images in several passbands and spectral lines. We identify loop structures in the simulated images and calculate the loop background. We then determine the density, temperature and emission measure distribution as a function of time from the observations and compare with the true temperature and density of the loop. We find that the overall characteristics of the temperature, density, and emission measure are recovered by the analysis methods, but the details of the true temperature and density are not. For instance, the emission measure curves calculated from the simulated observations are much broader than the true emission measure distribution, though the average temperature evolution is similar. These differences are due, in part, to inadequate background subtraction, but also indicate a limitation of the analysis methods.

  12. Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops

    SciTech Connect

    Kwon, Young Do; Finzi, Andrés; Wu, Xueling; Dogo-Isonagie, Cajetan; Lee, Lawrence K.; Moore, Lucas R.; Schmidt, Stephen D.; Stuckey, Jonathan; Yang, Yongping; Zhou, Tongqing; Zhu, Jiang; Vicic, David A.; Debnath, Asim K.; Shapiro, Lawrence; Bewley, Carole A.; Mascola, John R.; Sodroski, Joseph G.; Kwong, Peter D.

    2013-03-04

    The HIV-1 envelope (Env) spike (gp120{sub 3}/gp41{sub 3}) undergoes considerable structural rearrangements to mediate virus entry into cells and to evade the host immune response. Engagement of CD4, the primary human receptor, fixes a particular conformation and primes Env for entry. The CD4-bound state, however, is prone to spontaneous inactivation and susceptible to antibody neutralization. How does unliganded HIV-1 maintain CD4-binding capacity and regulate transitions to the CD4-bound state? To define this mechanistically, we determined crystal structures of unliganded core gp120 from HIV-1 clades B, C, and E. Notably, all of these unliganded HIV-1 structures resembled the CD4-bound state. Conformational fixation with ligand selection and thermodynamic analysis of full-length and core gp120 interactions revealed that the tendency of HIV-1 gp120 to adopt the CD4-bound conformation was restrained by the V1/V2- and V3-variable loops. In parallel, we determined the structure of core gp120 in complex with the small molecule, NBD-556, which specifically recognizes the CD4-bound conformation of gp120. Neutralization by NBD-556 indicated that Env spikes on primary isolates rarely assume the CD4-bound conformation spontaneously, although they could do so when quaternary restraints were loosened. Together, the results suggest that the CD4-bound conformation represents a 'ground state' for the gp120 core, with variable loop and quaternary interactions restraining unliganded gp120 from 'snapping' into this conformation. A mechanism of control involving deformations in unliganded structure from a functionally critical state (e.g., the CD4-bound state) provides advantages in terms of HIV-1 Env structural diversity and resistance to antibodies and inhibitors, while maintaining elements essential for entry.

  13. Crystal structure of the lactose operon repressor and its complexes with DNA and inducer

    SciTech Connect

    Lewis, M.; Chang, G.; Horton, N.C.

    1996-03-01

    The lac operon of Escherichia coli is the paradigm for gene regulation. Its key component is the lac repressor a product of the lacl gene. The three-dimensional structures of the intact lac repressor, the lac repressor bound to the gratuitous inducer isopropyl-B-D-1thiogalactoside (IPTG) and the lac repressor complexed with a 21 base pair symmetric operator DNA have been determined. These three structures show the conformation of the molecule in both the induced and the repressed states and provide a framework for understanding a wealth of biochemical and genetic information. The DNA sequence of the lac operon has three lac repressor recognition sites in stretch of 500 base pairs. The crystallographic structure of the complex with DNA suggests that the tetrameric repressor functions synergistically with catabolite gene activator protein (CAP) and participates in the quarternary formation of repression loops in which one tetrameric repressor interacts simultaneously with two sites in the genomic DNA. 76 refs., 11 figs., 1 tab.

  14. Silica nanowire conjugated with loop-shaped oligonucleotides: A new structure to silence cysteine proteinase gene in Leishmania tropica.

    PubMed

    Bafghi, Ali Fatahi; Jebali, Ali; Daliri, Karim

    2015-12-01

    The main aim of this study was to evaluate the capability of silica nanowire conjugated with loop-shaped oligonucleotides (SNWCLSOs) to silence cysteine proteinase b (Cpb) gene in Leishmania (L) tropica. On the other hand, its toxicity on amastigotes and mouse peritoneal macrophages was evaluated by 5-diphenyl-tetrazolium bromide (MTT) assay. For control, two loop-shaped oligonucleotides (LSO) were considered. LSO1 and LSO2 were 5'-NH2-cccccaaaaaaaaaaaaaaaaaaaaaaaaaggggg-COOH-3' and LSO2: 5'-NH2-cccccttttttttttttttttttttttttttttttttttttttggggg-COOH-3', respectively. After 72 h incubation at 37 °C, AMSNW, LSO1, and LSO2 had no remarkable toxicity on L. tropica amastigote (2 × 10(5)/mL) and mouse peritoneal macrophages (2 × 10(5)/mL). In case of SNWCLSOs, they had high toxicity on L. tropica amastigote, but they had no effect on mouse peritoneal macrophages. At concentrations of 1, 10, and 25 μg/mL, AMSNW, LSO1 and LSO2 had no effect on the gene expression. But, at concentration of 50 and 100 μg/mL, decrease of gene expression was observed. In case of SNWCLSOs, they could dramatically decrease the gene expression. It could be concluded that since SNWCLSOs could silence Cpb gene with no remarkable toxicity, they are good choice for treat cutaneous leishmaniasis in future. As a new agent, it must be checked in vivo.

  15. Understanding the role of thermal fluctuations in DNA looping

    NASA Astrophysics Data System (ADS)

    Wilson, David P.; Lillian, Todd; Goyal, Sachin; Tkachenko, Alexei V.; Perkins, Noel C.; Meiners, Jens-Christian

    2007-06-01

    Protein-mediated DNA loop formation is an important biological process that regulates key functions such as transcription. We present a mechanical model for these DNA-protein complexes that can take effects of the DNA sequence such induced curvature into account. This model provides the equilibrium shape and elastic energy of the DNA loop, using boundary conditions from the protein crystal structure. We then construct a Hamiltonian for small perturbations of the DNA around the equilibrium shape, which in turn allows us to calculate the eigenmodes and the entropic contributions of the thermal fluctuations to the free energy of the DNA loop. Here we present computations related to the short wild-type lactose repressor loop of Escheria coli (E. coli), and find that the entropic contributions are significant and amount to up to 3.9 k BT of the free energy. We also show that this entropic contribution from the stiffening of the DNA loop depends strongly on the phase angle between the two operator sites, which adds to the known phasing effect of the elastic energy of the loop.

  16. Weak operator binding enhances simulated Lac repressor-mediated DNA looping.

    PubMed

    Colasanti, Andrew V; Grosner, Michael A; Perez, Pamela J; Clauvelin, Nicolas; Lu, Xiang-Jun; Olson, Wilma K

    2013-12-01

    The 50th anniversary of Biopolymers coincides closely with the like celebration of the discovery of the Escherichia coli (lac) lactose operon, a classic genetic system long used to illustrate the influence of biomolecular structure on function. The looping of DNA induced by the binding of the Lac repressor protein to sequentially distant operator sites on DNA continues to serve as a paradigm for understanding long-range genomic communication. Advances in analyses of DNA structures and in incorporation of proteins in computer simulations of DNA looping allow us to address long-standing questions about the role of protein-mediated DNA loop formation in transcriptional control. Here we report insights gained from studies of the sequence-dependent contributions of the natural lac operators to Lac repressor-mediated DNA looping. Novel superposition of the ensembles of protein-bound operator structures derived from NMR measurements reveals variations in DNA folding missed in conventional structural alignments. The changes in folding affect the predicted ease with which the repressor induces loop formation and the ways that DNA closes between the protein headpieces. The peeling of the auxiliary operators away from the repressor enhances the formation of loops with the 92-bp wildtype spacing and hints of a structural reason behind their weak binding.

  17. Dynamic Antagonism between Phytochromes and PIF Family Basic Helix-Loop-Helix Factors Induces Selective Reciprocal Responses to Light and Shade in a Rapidly Responsive Transcriptional Network in Arabidopsis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plants respond to shade-modulated light signals via phytochrome (phy)-induced adaptive changes, termed shade avoidance. To examine the roles of Phytochrome-Interacting basic helix-loop-helix Factors, PIF1, 3, 4, and 5, in relaying such signals to the transcriptional network, we compared the shade-re...

  18. [Aging and retrieval-induced forgetting of associatively structured lists].

    PubMed

    Matsuda, Takashi; Matsukawa, Junko

    2010-12-01

    Research on retrieval-induced forgetting has shown that remembering can cause forgetting of related information. This study examined whether such forgetting occurred for associatively structured lists and if aging influenced such forgetting. We compared retrieval-induced forgetting during a free recall test by using Deese/Roediger-McDermott (DRM) lists with an associative structure as the stimulus. Two age groups of young and old adult participants were tested. The results indicated that both age groups showed the same degree of retrieval-induced forgetting of the lists. These results suggest that the association between items causes retrieval-induced forgetting and that the inhibitory function of the association in retrieval-induced forgetting does not decline with age.

  19. Structural fluctuation of proteins induced by thermodynamic perturbation

    SciTech Connect

    Hirata, Fumio; Akasaka, Kazuyuki

    2015-01-28

    A theory to describe structural fluctuations of protein induced by thermodynamic perturbations, pressure, temperature, and denaturant, is proposed. The theory is formulated based on the three methods in the statistical mechanics: the generalized Langevin theory, the linear response theory, and the three dimensional interaction site model (3D-RISM) theory. The theory clarifies how the change in thermodynamic conditions, or a macroscopic perturbation, induces the conformational fluctuation, which is a microscopic property. The theoretical results are applied, on the conceptual basis, to explain the experimental finding by Akasaka et al., concerning the NMR experiment which states that the conformational change induced by pressure corresponds to structural fluctuations occurring in the ambient condition. A method to evaluate the structural fluctuation induced by pressure is also suggested by means of the 3D-RISM and the site-site Kirkwood-Buff theories.

  20. A Mutation within the Extended X Loop Abolished Substrate-induced ATPase Activity of the Human Liver ATP-binding Cassette (ABC) Transporter MDR3*

    PubMed Central

    Kluth, Marianne; Stindt, Jan; Dröge, Carola; Linnemann, Doris; Kubitz, Ralf; Schmitt, Lutz

    2015-01-01

    The human multidrug resistance protein 3 (MDR3/ABCB4) belongs to the ubiquitous family of ATP-binding cassette (ABC) transporters and is located in the canalicular membrane of hepatocytes. There it flops the phospholipids of the phosphatidylcholine (PC) family from the inner to the outer leaflet. Here, we report the characterization of wild type MDR3 and the Q1174E mutant, which was identified previously in a patient with progressive familial intrahepatic cholestasis type 3 (PFIC-3). We expressed different variants of MDR3 in the yeast Pichia pastoris, purified the proteins via tandem affinity chromatography, and determined MDR3-specific ATPase activity in the presence or absence of phospholipids. The ATPase activity of wild type MDR3 was stimulated 2-fold by liver PC or 1,2-dioleoyl-sn-glycero-3-phosphatidylethanolamine lipids. Furthermore, the cross-linking of MDR3 with a thiol-reactive fluorophore blocked ATP hydrolysis and exhibited no PC stimulation. Similarly, phosphatidylethanolamine, phosphatidylserine, and sphingomyelin lipids did not induce an increase of wild type MDR3 ATPase activity. The phosphate analogues beryllium fluoride and aluminum fluoride led to complete inhibition of ATPase activity, whereas orthovanadate inhibited exclusively the PC-stimulated ATPase activity of MDR3. The Q1174E mutation is located in the nucleotide-binding domain in direct proximity of the leucine of the ABC signature motif and extended the X loop, which is found in ABC exporters. Our data on the Q1174E mutant demonstrated basal ATPase activity, but PC lipids were incapable of stimulating ATPase activity highlighting the role of the extended X loop in the cross-talk of the nucleotide-binding domain and the transmembrane domain. PMID:25533467

  1. A mutation within the extended X loop abolished substrate-induced ATPase activity of the human liver ATP-binding cassette (ABC) transporter MDR3.

    PubMed

    Kluth, Marianne; Stindt, Jan; Dröge, Carola; Linnemann, Doris; Kubitz, Ralf; Schmitt, Lutz

    2015-02-20

    The human multidrug resistance protein 3 (MDR3/ABCB4) belongs to the ubiquitous family of ATP-binding cassette (ABC) transporters and is located in the canalicular membrane of hepatocytes. There it flops the phospholipids of the phosphatidylcholine (PC) family from the inner to the outer leaflet. Here, we report the characterization of wild type MDR3 and the Q1174E mutant, which was identified previously in a patient with progressive familial intrahepatic cholestasis type 3 (PFIC-3). We expressed different variants of MDR3 in the yeast Pichia pastoris, purified the proteins via tandem affinity chromatography, and determined MDR3-specific ATPase activity in the presence or absence of phospholipids. The ATPase activity of wild type MDR3 was stimulated 2-fold by liver PC or 1,2-dioleoyl-sn-glycero-3-phosphatidylethanolamine lipids. Furthermore, the cross-linking of MDR3 with a thiol-reactive fluorophore blocked ATP hydrolysis and exhibited no PC stimulation. Similarly, phosphatidylethanolamine, phosphatidylserine, and sphingomyelin lipids did not induce an increase of wild type MDR3 ATPase activity. The phosphate analogues beryllium fluoride and aluminum fluoride led to complete inhibition of ATPase activity, whereas orthovanadate inhibited exclusively the PC-stimulated ATPase activity of MDR3. The Q1174E mutation is located in the nucleotide-binding domain in direct proximity of the leucine of the ABC signature motif and extended the X loop, which is found in ABC exporters. Our data on the Q1174E mutant demonstrated basal ATPase activity, but PC lipids were incapable of stimulating ATPase activity highlighting the role of the extended X loop in the cross-talk of the nucleotide-binding domain and the transmembrane domain.

  2. Radiation-induced structural changes, 4

    NASA Astrophysics Data System (ADS)

    Hama, Yoshimasa; Matsuyama, Tomochika; Ogasawara, Masaaki

    1993-10-01

    This seminar was held for discussion on recent progress in experimental investigation of positron and its application to material science. Fundamental characteristics of positronium, measuring method, molecular structure of positronium, and its annihilation and reaction, in liquid phase positronium chemistry are reported. The nonthermal positrons (0.25-2.5 keV) are occurred in KURRI-LINAC, slow positrons are found out by moderating with solid xenon film. Positronium formation in insulating materials are reported. Positron lifetime and insulating rupture strength are measured with epoxy resin and fluororesin changing bridging density, experimental materials temperature, gamma ray dose Free-volume studies on polymer in multiphase systems are evaluated using the method of spin labeling, the molecular dynamics of polymer chains are discussed. The anisotropy diffusion process on structural relaxation of linear polymers are described, introducing the molecular dynamics simulation of polarization and stress relaxation of ferroelectric polymers.

  3. The Arabidopsis NAC transcription factor NTL4 participates in a positive feedback loop that induces programmed cell death under heat stress conditions.

    PubMed

    Lee, Sangmin; Lee, Hyo-Jun; Huh, Sung Un; Paek, Kyung-Hee; Ha, Jun-Ho; Park, Chung-Mo

    2014-10-01

    Programmed cell death (PCD) is an integral component of plant development and adaptation under adverse environmental conditions. Reactive oxygen species (ROS) are one of the most important players that trigger PCD in plants, and ROS-generating machinery is activated in plant cells undergoing PCD. The membrane-bound NAC transcription factor NTL4 has recently been proven to facilitate ROS production in response to drought stress in Arabidopsis. In this work, we show that NTL4 participates in a positive feedback loop that bursts ROS accumulation to modulate PCD under heat stress conditions. Heat stress induces NTL4 gene transcription and NTL4 protein processing. The level of hydrogen peroxide (H2O2) was elevated in 35S:4ΔC transgenic plants that overexpress a transcriptionally active nuclear NTL4 form but significantly reduced in NTL4-deficient ntl4 mutants under heat stress conditions. In addition, heat stress-induced cell death was accelerated in the 35S:4ΔC transgenic plants but decreased in the ntl4 mutants. Notably, H2O2 triggers NTL4 gene transcription and NTL4 protein processing under heat stress conditions. On the basis of these findings, we conclude that NTL4 modulates PCD through a ROS-mediated positive feedback control under heat stress conditions, possibly providing an adaptation strategy by which plants ensure their survival under extreme heat stress conditions.

  4. Metschnikowia Species Share a Pool of Diverse rRNA Genes Differing in Regions That Determine Hairpin-Loop Structures and Evolve by Reticulation

    PubMed Central

    Sipiczki, Matthias; Pfliegler, Walter P.; Holb, Imre J.

    2013-01-01

    Modern taxonomy of yeasts is mainly based on phylogenetic analysis of conserved DNA and protein sequences. By far the most frequently used sequences are those of the repeats of the chromosomal rDNA array. It is generally accepted that the rDNA repeats of a genome have identical sequences due to the phenomenon of sequence homogenisation and can thus be used for identification and barcoding of species. Here we show that the rDNA arrays of the type strains of Metschnikowia andauensis and M. fructicola are not homogenised. Both have arrays consisting of diverse repeats that differ from each other in the D1/D2 domains by up to 18 and 25 substitutions. The variable sites are concentrated in two regions that correspond to back-folding stretches of hairpin loops in the predicted secondary structure of the RNA molecules. The substitutions do not alter significantly the overall hairpin-loop structure due to wobble base pairing at sites of C-T transitions and compensatory mutations in the complementary strand of the hairpin stem. The phylogenetic and network analyses of the cloned sequences revealed that the repeats had not evolved in a vertical tree-like way but reticulation might have shaped the rDNA arrays of both strains. The neighbour-net analysis of all cloned sequences of the type strains and the database sequences of different strains further showed that these species share a continuous pool of diverse repeats that appear to evolve by reticulate evolution. PMID:23805311

  5. A small stem-loop structure of the Ebola virus trailer is essential for replication and interacts with heat-shock protein A8

    PubMed Central

    Sztuba-Solinska, Joanna; Diaz, Larissa; Kumar, Mia R.; Kolb, Gaëlle; Wiley, Michael R.; Jozwick, Lucas; Kuhn, Jens H.; Palacios, Gustavo; Radoshitzky, Sheli R.; J. Le Grice, Stuart F.; Johnson, Reed F.

    2016-01-01

    Ebola virus (EBOV) is a single-stranded negative-sense RNA virus belonging to the Filoviridae family. The leader and trailer non-coding regions of the EBOV genome likely regulate its transcription, replication, and progeny genome packaging. We investigated the cis-acting RNA signals involved in RNA–RNA and RNA–protein interactions that regulate replication of eGFP-encoding EBOV minigenomic RNA and identified heat shock cognate protein family A (HSC70) member 8 (HSPA8) as an EBOV trailer-interacting host protein. Mutational analysis of the trailer HSPA8 binding motif revealed that this interaction is essential for EBOV minigenome replication. Selective 2′-hydroxyl acylation analyzed by primer extension analysis of the secondary structure of the EBOV minigenomic RNA indicates formation of a small stem-loop composed of the HSPA8 motif, a 3′ stem-loop (nucleotides 1868–1890) that is similar to a previously identified structure in the replicative intermediate (RI) RNA and a panhandle domain involving a trailer-to-leader interaction. Results of minigenome assays and an EBOV reverse genetic system rescue support a role for both the panhandle domain and HSPA8 motif 1 in virus replication. PMID:27651462

  6. Mitochondrial D-loop analysis for uncovering the population structure and genetic diversity among the indigenous duck (Anas platyrhynchos) populations of India.

    PubMed

    Gaur, Uma; Tantia, Madhu Sudan; Mishra, Bina; Bharani Kumar, Settypalli Tirumala; Vijh, Ramesh Kumar; Chaudhury, Ashok

    2017-01-24

    The indigenous domestic duck (Anas platyrhynchos domestica) which is domesticated from Mallard (Anas platyrhynchos) contributes significantly to poor farming community in coastal and North Eastern regions of India. For conservation and maintenance of indigenous duck populations it is very important to know the existing genetic diversity and population structure. To unravel the population structure and genetic diversity among the five indigenous duck populations of India, the mitochondrial D-loop sequences of 120 ducks were analyzed. The sequence analysis by comparison of mtDNA D-loop region (470 bp) of five Indian duck populations revealed 25 mitochondrial haplotypes. Pairwise FST value among populations was 0.4243 (p < .01) and the range of nucleotide substitution per site (Dxy) between the five Indian duck populations was 0.00034-0.00555, and the net divergence (Da) was 0-0.00355. The phylogenetic analysis in the present study unveiled three clades. The analysis revealed genetic continuity among ducks of coastal region of the country which formed a separate group from the ducks of the inland area. Both coastal as well as the land birds revealed introgression of the out group breed Khaki Campbell, which is used for breed improvement programs in India. The observations revealed very less selection and a single matrilineal lineage of indigenous domestic ducks.

  7. A new moon-induced structure

    NASA Astrophysics Data System (ADS)

    Albers, N.; Sremcevic, M.; Esposito, L. W.

    2015-10-01

    Embedded moons are known to create an observable propeller-shaped structure in the surrounding ring which consists of a gap and kinematic wake. In the cases of Pan and Daphnis, the moons are sufficiently massive to open a circumferential gap - the Encke and Keeler gap, respectively. New results, however, reveal the existence of a previously unknown moonassociated structure found at the Encke and Keeler gap edges. By analyzing Cassini Ultraviolet Spectrometer (UVIS) High Speed Photometer (HSP) and Voyager 2 Photopolarimeter (PPS) occultations we found a few kilometer wide gaps located within a few kilometers of the ring edges. These transparent regions feature sharp edges and have so far been found exclusively downstream of the respective embedded moon. Gap characteristics for features found near the inner and outer Encke gap edges are consistent with each other. Two occultations with special observing geometries, one tracking and one double-star, allow to investigate spatial and temporal morphology of these gaps. Our preliminary results suggest that these structures are individual gaps with an aspect ratio of about 1:5 and may thus be about 10km long. Their existence offers another avenue in searching for embedded objects although our preliminary search did not produce examples apart from those reported here for Pan and Daphnis.

  8. Structural changes of linear DNA molecules induced by cisplatin

    SciTech Connect

    Liu, Zhiguo; Liu, Ruisi; Zhou, Zhen; Zu, Yuangang; Xu, Fengjie

    2015-02-20

    Interaction between long DNA molecules and activated cisplatin is believed to be crucial to anticancer activity. However, the exact structural changes of long DNA molecules induced by cisplatin are still not very clear. In this study, structural changes of long linear double-stranded DNA (dsDNA) and short single-stranded DNA (ssDNA) induced by activated cisplatin have been investigated by atomic force microscopy (AFM). The results indicated that long DNA molecules gradually formed network structures, beads-on-string structures and their large aggregates. Electrostatic and coordination interactions were considered as the main driving forces producing these novel structures. An interesting finding in this study is the beads-on-string structures. Moreover, it is worth noting that the beads-on-string structures were linked into the networks, which can be ascribed to the strong DNA–DNA interactions. This study expands our knowledge of the interactions between DNA molecules and cisplatin. - Highlights: • We investigate structural changes of dsDNA and ssDNA induced by cisplatin. • AFM results indicated long dsDNA formed network, beads-on-string and aggregates. • ssDNA can form very similar structures as those of long linear dsDNA. • A possible formation process of theses novel structure is proposed.

  9. Dismantling Structures and Equipment of the MR Reactor and its Loop Facilities at the National Research Center 'Kurchatov Institute' - 12051

    SciTech Connect

    Volkov, V.G.; Danilovich, A.S.; Zverkov, Yu. A.; Ivanov, O.P.; Kolyadin, V.I.; Lemus, A.V.; Muzrukova, V.D.; Pavlenko, V.I.; Semenov, S.G.; Fadin, S.Yu.; Shisha, A.D.; Chesnokov, A.V.

    2012-07-01

    In 2008 a design of decommissioning of research reactors MR and RFT has been developed in the National research Center 'Kurchatov institute'. The design has been approved by Russian State Authority in July 2009 year and has received the positive conclusion of ecological expertise. In 2009-2010 a preparation for decommissioning of reactors MR and RFT was spent. Within the frames of a preparation a characterization, sorting and removal of radioactive objects, including the irradiated fuel, from reactor storage facilities and pool have been executed. During carrying out of a preparation on removal of radioactive objects from reactor sluice pool water treating has been spent. For these purposes modular installation for clearing and processing of a liquid radioactive waste 'Aqua - Express' was used. As a result of works it was possible to lower volume activity of water on three orders in magnitude that has allowed improving essentially of radiating conditions in a reactor hall. Auxiliary systems of ventilation, energy and heat supplies, monitoring systems of radiating conditions of premises of the reactor and its loop-back installations are reconstructed. In 2011 the license for a decommissioning of the specified reactors has been received and there are begun dismantling works. Within the frames of works under the design the armature and pipelines are dismantled in a under floor space of a reactor hall where a moving and taking away pipelines of loop facilities and the first contour of the MR reactor were replaced. A dismantle of the main equipment of loop facility with the gas coolant has been spent. Technologies which were used on dismantle of the radioactive contaminated equipment are presented, the basic works on reconstruction of systems of maintenance of on the decommissioning works are described, the sequence of works on the decommissioning of reactors MR and RFT is shown. Dismantling works were carried out with application of means of a dust suppression that, in

  10. Structure dependent hydrogen induced etching features of graphene crystals

    NASA Astrophysics Data System (ADS)

    Thangaraja, Amutha; Shinde, Sachin M.; Kalita, Golap; Papon, Remi; Sharma, Subash; Vishwakarma, Riteshkumar; Sharma, Kamal P.; Tanemura, Masaki

    2015-06-01

    H2 induced etching of graphene is of significant interest to understand graphene growth process as well as to fabricate nanoribbons and various other structures. Here, we demonstrate the structure dependent H2 induced etching behavior of graphene crystals. We synthesized graphene crystals on electro-polished Cu foil by an atmospheric pressure chemical vapor deposition process, where some of the crystals showed hexagonal shaped snowflake-dendritic morphology. Significant differences in H2 induced etching behavior were observed for the snowflake-dendritic and regular graphene crystals by annealing in a gas mixture of H2 and Ar. The regular graphene crystals were etched anisotropically creating hexagonal holes with pronounced edges, while etching of all the dendritic crystals occurred from the branches of lobs creating symmetrical fractal structures. The etching behavior provides important clue of graphene nucleation and growth as well as their selective etching to fabricate well-defined structures for nanoelectronics.

  11. A new moon-induced structure

    NASA Astrophysics Data System (ADS)

    Albers, Nicole

    2014-11-01

    Cassini UVIS stellar occultations show prominent gaps within Saturn's ring located only a few km from the Encke and Keeler gap edges. These transparent regions feature sharp edges and measure a few km in radial width. Already the Voyager 2 PPS experiment registered such a gap near the inner Encke gap edge.All gaps identified so far have been found exclusively downstream of the embedded moons Pan and Daphnis, respectively. Interestingly, none has been observed at the inner Keeler gap edge, where temporal and spatial variability of the edge are still poorly understood and most likely driven by the Prometheus 32:31 ILR located nearby. There is evidence for a weak trend between radial width and relative azimuthal distance to the moon. Trends for features found near the inner and outer Encke gap edge are consistent with each other. Two occultations, one tracking and one double star occultation, allow to investigate spatial and temporal morphology of these gaps. Our preliminary results suggest that these structures are individual gaps with an aspect ratio of about 1:5 and may thus be about 10km long.Embedded moons are known to create observable structures - gaps and kinematic wakes - in the surrounding ring. While Pan and Daphnis are massive enough to open a circumferential gap, smaller objects create the propeller features. These new results, however, reveal the existence of a previously unknown and unpredicted moon-associated structure. Its existence offers another avenue in searching for embedded objects, although our preliminary search did not produce examples apart from those reported here for Pan and Daphnis.We acknowledge Tracy Becker for providing an initial list of positive detections. This work is supported by the Cassini project.

  12. Water Stream "Loop-the-Loop"

    ERIC Educational Resources Information Center

    Jefimenko, Oleg

    1974-01-01

    Discusses the design of a modified loop-the-loop apparatus in which a water stream is used to illustrate centripetal forces and phenomena of high-velocity hydrodynamics. Included are some procedures of carrying out lecture demonstrations. (CC)

  13. Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity

    SciTech Connect

    Manjasetty, Babu A.; Halavaty, Andrei S.; Luan, Chi-Hao; Osipiuk, Jerzy; Mulligan, Rory; Kwon, Keehwan; Anderson, Wayne F.; Joachimiak, Andrzej

    2016-04-01

    Multidrug transcription regulator AcrR from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 belongs to the tetracycline repressor family, one of the largest groups of bacterial transcription factors. The crystal structure of dimeric AcrR was determined and refined to 1.56 Å resolution. The tertiary and quaternary structures of AcrR are similar to those of its homologs. The multidrug binding site was identified based on structural alignment with homologous proteins and has a di(hydroxyethyl)ether molecule bound. Residues from helices a4 and a7 shape the entry into this binding site. The structure of AcrR reveals that the extended helical conformation of helix a4 is stabilized by the hydrogen bond between Glu67 (helix a4) and Gln130 (helix a7). Based on the structural comparison with the closest homolog structure, the Escherichia coli AcrR, we propose that this hydrogen bond is responsible for control of the loop-to-helix transition within helix a4. This local conformational switch of helix a4 may be a key step in accessing the multidrug binding site and securing ligands at the binding site. Solution smallmolecule binding studies suggest that AcrR binds ligands with their core chemical structure resembling the tetracyclic ring of cholesterol.

  14. Supersymmetric structure of the induced W gravities

    NASA Astrophysics Data System (ADS)

    Ader, Jean-Pierre; Biet, Franck; Noirot, Yves

    1999-03-01

    We derive the supersymmetric structure present in W-gravities which has been already observed in various contexts as Yang-Mills theory, topological field theories, bosonic string and chiral 0264-9381/16/3/029/img2-gravity. This derivation which is made in the geometrical framework of Zucchini, necessitates the introduction of an appropriate new basis of variables which replace the canonical fields and their derivatives. This construction is used, in the 0264-9381/16/3/029/img3-case, to deduce from the Chern-Simons action the Wess-Zumino-Polyakov action.

  15. Thermo-structural analysis of target assembly and back plate in the IFMIF/EVEDA lithium test loop

    NASA Astrophysics Data System (ADS)

    Watanabe, Kazuyoshi; Ida, Mizuho; Kondo, Hiroo; Miyashita, Makoto; Nakamura, Hiroo

    2011-10-01

    IFMIF is an accelerator-based intense neutron source for testing candidate materials for fusion reactors. The Engineering Validation and Engineering Design Activities (EVEDA) of IFMIF are in progress under the Broader Approach Agreement. In the EVEDA Li test loop, two types of target assemblies, "an integrated type target assembly without a back plate", made of SUS316L, and "a target assembly with replaceable bayonet back plate", made of F82H steel, will be evaluated. For these target assemblies, thermal stresses were evaluated using the ABAQUS code. As the permitted stress, the values of yield strengths at 300 °C were used. In the case of the integrated target assembly, the maximum thermal stress was below the allowed stress (164 MPa). However, in the case of the target assembly with the bayonet back plate, thermal insulation around the back plate should be necessary to reduce the thermal stress below the allowed value (455 MPa).

  16. Arsenic Induces p62 Expression to Form a Positive Feedback Loop with Nrf2 in Human Epidermal Keratinocytes: Implications for Preventing Arsenic-Induced Skin Cancer

    PubMed Central

    Shah, Palak; Trinh, Elaine; Qiang, Lei; Xie, Lishi; Hu, Wen-Yang; Prins, Gail S.; Pi, Jingbo; He, Yu-Ying

    2017-01-01

    Exposure to inorganic arsenic in contaminated drinking water poses an environmental public health threat for hundreds of millions of people in the US and around the world. Arsenic is a known carcinogen for skin cancer. However, the mechanism by which arsenic induces skin cancer remains poorly understood. Here, we have shown that arsenic induces p62 expression in an autophagy-independent manner in human HaCaT keratinocytes. In mouse skin, chronic arsenic exposure through drinking water increases p62 protein levels in the epidermis. Nrf2 is required for basal and arsenic-induced p62 up-regulation. p62 knockdown reduces arsenic-induced Nrf2 activity, and induces sustained p21 up-regulation. p62 induction is associated with increased proliferation in mouse epidermis. p62 knockdown had little effect on arsenic-induced apoptosis, while it decreased cell proliferation following arsenic treatment. Our findings indicate that arsenic induces p62 expression to regulate the Nrf2 pathway in human keratinocytes and suggest that targeting p62 may help prevent arsenic-induced skin cancer. PMID:28125038

  17. The solution structure of the pH-induced monomer of dynein light-chain LC8 from Drosophila.

    PubMed

    Makokha, Moses; Huang, Yuanpeng Janet; Montelione, Gaetano; Edison, Arthur S; Barbar, Elisar

    2004-03-01

    The structure of Drosophila LC8 pH-induced monomer has been determined by NMR spectroscopy using the program AutoStructure. The structure at pH 3 and 30 degrees C is similar to the individual subunits of mammalian LC8 dimer with the exception that a beta strand, which crosses between monomers to form an intersubunit beta-sheet in the dimer, is a flexible loop with turnlike conformations in the monomer. Increased flexibility in the interface region relative to the rest of the protein is confirmed by dynamic measurements based on (15)N relaxation. Comparison of the monomer and dimer structures indicates that LC8 is not a domain swapped dimer.

  18. Loop coupled resonator optical waveguides.

    PubMed

    Song, Junfeng; Luo, Lian-Wee; Luo, Xianshu; Zhou, Haifeng; Tu, Xiaoguang; Jia, Lianxi; Fang, Qing; Lo, Guo-Qiang

    2014-10-06

    We propose a novel coupled resonator optical waveguide (CROW) structure that is made up of a waveguide loop. We theoretically investigate the forbidden band and conduction band conditions in an infinite periodic lattice. We also discuss the reflection- and transmission- spectra, group delay in finite periodic structures. Light has a larger group delay at the band edge in a periodic structure. The flat band pass filter and flat-top group delay can be realized in a non-periodic structure. Scattering matrix method is used to calculate the effects of waveguide loss on the optical characteristics of these structures. We also introduce a tunable coupling loop waveguide to compensate for the fabrication variations since the coupling coefficient of the directional coupler in the loop waveguide is a critical factor in determining the characteristics of a loop CROW. The loop CROW structure is suitable for a wide range of applications such as band pass filters, high Q microcavity, and optical buffers and so on.

  19. Loop Quantum Cosmology.

    PubMed

    Bojowald, Martin

    2005-01-01

    Quantum gravity is expected to be necessary in order to understand situations where classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical space-time inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding space-time is then modified. One particular realization is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. Main effects are introduced into effective classical equations which allow to avoid interpretational problems of quantum theory. They give rise to new kinds of early universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function which allows to extend space-time beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of space-time arising in loop quantum gravity and its application to cosmology sheds new light on more general issues such as time.

  20. Loop Quantum Cosmology.

    PubMed

    Bojowald, Martin

    2008-01-01

    Quantum gravity is expected to be necessary in order to understand situations in which classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical spacetime inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding spacetime is then modified. One particular theory is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. The main effects are introduced into effective classical equations, which allow one to avoid the interpretational problems of quantum theory. They give rise to new kinds of early-universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function, which allows an extension of quantum spacetime beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of spacetime arising in loop quantum gravity and its application to cosmology sheds light on more general issues, such as the nature of time.

  1. Observations of loops and prominences

    NASA Technical Reports Server (NTRS)

    Strong, Keith T.

    1994-01-01

    We review recent observations by the Yohkoh-SXT (Soft X-ray Telescope) in collaboration with other spacecraft and ground-based observatories of coronal loops and prominences. These new results point to problems that SoHO will be able to address. With a unique combination of rapid-cadence digital imaging (greater than or equal to 32 s full-disk and greater than or equal to 2 s partial-frame images), high spatial resolution (greater than or equal to 2.5 arcsec pixels), high sensitivity (EM less than or equal to 10(exp 42) cm(exp -3)), a low-scatter mirror, and large dynamic range, SXT can observe a vast range of targets on the Sun. Over the first 21 months of Yohkoh operations SXT has taken over one million images of the corona and so is building up an invaluable long-term database on the large-scale corona and loop geometry. The most striking thing about the SXT images is the range of loop sizes and shapes. The active regions are a bright tangle of magnetic field lines, surrounded by a network of large-scale quiet-Sun loops stretching over distances in excess of 105 km. The cross-section of most loops seems to be constant. Loops displaying significant Gamma's are the exception, not the rule, implying the presence of widespread currents in the corona. All magnetic structures show changes. Time scales range from seconds to months. The question of how these structures are formed, become filled with hot plasma, and are maintained is still open. While we see the propagation of brightenings along the length of active-region loops and in X-ray jets with velocities of several hundred km/s, much higher velocities are seen in the quiet Sun. In XBP flares, for example, velocities of over 1000 km/s are common. Active-region loops seem to be in constant motion, moving slowly outward, carrying plasma with them. During flares, loops often produce localized brightenings at the base and later at the apex of the loop. Quiescent filaments and prominences have been observed regularly

  2. Shear induced structures in crystallizing cocoa butter

    NASA Astrophysics Data System (ADS)

    Mazzanti, Gianfranco; Guthrie, Sarah E.; Sirota, Eric B.; Marangoni, Alejandro G.; Idziak, Stefan H. J.

    2004-03-01

    Cocoa butter is the main structural component of chocolate and many cosmetics. It crystallizes in several polymorphs, called phases I to VI. We used Synchrotron X-ray diffraction to study the effect of shear on its crystallization. A previously unreported phase (phase X) was found and a crystallization path through phase IV under shear was observed. Samples were crystallized under shear from the melt in temperature controlled Couette cells, at final crystallization temperatures of 17.5^oC, 20^oC and 22.5^oC in Beamline X10A of NSLS. The formation of phase X was observed at low shear rates (90 s-1) and low crystallization temperature (17.5^oC), but was absent at high shear (720 s-1) and high temperature (20^oC). The d-spacing and melting point suggest that this new phase is a mixture rich on two of the three major components of cocoa butter. We also found that, contrary to previous reports, the transition from phase II to phase V can happen through the intermediate phase IV, at high shear rates and temperature.

  3. All three Ca[superscript 2+]-binding loops of photoproteins bind calcium ions: The crystal structures of calcium-loaded apo-aequorin and apo-obelin

    SciTech Connect

    Deng, Lu; Vysotski, Eugene S.; Markova, Svetlana V.; Liu, Zhi-Jie; Lee, John; Rose, John; Wang, Bi-Cheng

    2010-07-13

    The crystal structures of calcium-loaded apoaequorin and apo-obelin have been determined at resolutions 1.7 {angstrom} and 2.2 {angstrom}, respectively. A calcium ion is observed in each of the three EF-hand loops that have the canonical calcium-binding sequence, and each is coordinated in the characteristic pentagonal bipyramidal configuration. The calcium-loaded apo-proteins retain the same compact scaffold and overall fold as the unreacted photoproteins containing the bound substrate, 2-hydroperoxycoelenterazine, and also the same as the Ca{sup 2+}-discharged obelin bound with the product, coelenteramide. Nevertheless, there are easily discerned shifts in both helix and loop regions, and the shifts are not the same between the two proteins. It is suggested that these subtle shifts are the basis of the ability of these photoproteins to sense Ca{sup 2+} concentration transients and to produce their bioluminescence response on the millisecond timescale. A mechanism of intrastructural transmission of the calcium signal is proposed.

  4. The kissing-loop T-shaped structure translational enhancer of Pea enation mosaic virus can bind simultaneously to ribosomes and a 5' proximal hairpin.

    PubMed

    Gao, Feng; Gulay, Suna P; Kasprzak, Wojciech; Dinman, Jonathan D; Shapiro, Bruce A; Simon, Anne E

    2013-11-01

    The Pea enation mosaic virus (PEMV) 3' translational enhancer, known as the kissing-loop T-shaped structure (kl-TSS), binds to 40S subunits, 60S subunits, and 80S ribosomes, whereas the Turnip crinkle virus (TCV) TSS binds only to 60S subunits and 80S ribosomes. Using electrophoretic mobility gel shift assay (EMSA)-based competition assays, the kl-TSS was found to occupy a different site in the ribosome than the P-site-binding TCV TSS, suggesting that these two TSS employ different mechanisms for enhancing translation. The kl-TSS also engages in a stable, long-distance RNA-RNA kissing-loop interaction with a 12-bp 5'-coding-region hairpin that does not alter the structure of the kl-TSS as revealed by molecular dynamics simulations. Addition of the kl-TSS in trans to a luciferase reporter construct containing either wild-type or mutant 5' and 3' PEMV sequences suppressed translation, suggesting that the kl-TSS is required in cis to function, and both ribosome-binding and RNA interaction activities of the kl-TSS contributed to translational inhibition. Addition of the kl-TSS was more detrimental for translation than an adjacent eIF4E-binding 3' translational enhancer known as the PTE, suggesting that the PTE may support the ribosome-binding function of the kl-TSS. Results of in-line RNA structure probing, ribosome filter binding, and high-throughput selective 2'-hydroxyl acylation analyzed by primer extension (hSHAPE) of rRNAs within bound ribosomes suggest that kl-TSS binding to ribosomes and binding to the 5' hairpin are compatible activities. These results suggest a model whereby posttermination ribosomes/ribosomal subunits bind to the kl-TSS and are delivered to the 5' end of the genome via the associated RNA-RNA interaction, which enhances the rate of translation reinitiation.

  5. Catheterization of Intestinal Loops in Ruminants Does Not Adversely Affect Loop Function

    PubMed Central

    Inglis, G Douglas; Kastelic, John P; Uwiera, Richard R E

    2010-01-01

    Catheterized intestinal loops may be a valuable model to elucidate key components of the host response to various treatments within the small intestine of ruminants. We examined whether catheterizing ileal loops in sheep affected the overall health of animals and intestinal function, whether a bacterial treatment could be introduced into the loops through the catheters, and whether broad-spectrum antibiotics could sterilize the loops. Escherichia coli cells transformed to express the GFP gene were introduced readily into the loops through the catheters, and GFP E. coli cells were localized within the injected loops. Catheterized loops, interspaces, and intact ileum exhibited no abnormalities in tissue appearance or electrical resistance. Expression of the IFNγ, IL1α, IL4, IL6, IL12p40, IL18, TGFβ1, and TNFα cytokine genes did not differ significantly among the intact ileum, catheterized loops, and interspaces, nor did the expression of the gene for inducible nitric oxide synthase. Broad-spectrum antibiotics administered during surgery did not sterilize the loops or interspaces and did not substantively change the composition of the microbiota. However, antibiotics reduced the overall number of bacterial cells within the loop and the relative abundance of community constituents. We concluded that catheterization of intestinal loops did not adversely affect health or loop function in sheep. Furthermore, allowing animals to recover fully from surgery and to clear pharmaceuticals will remove any confounding effects due to these factors, making catheterized intestinal loops a feasible model for studying host responses in ruminants. PMID:21262134

  6. Fiber Loop Ringdown Sensor for Potential Real-Time Monitoring of Cracks in Concrete Structures: An Exploratory Study

    PubMed Central

    Sahay, Peeyush; Kaya, Malik; Wang, Chuji

    2013-01-01

    A fiber loop ringdown (FLRD) concrete crack sensor is described for the first time. A bare single mode fiber (SMF), without using other optical components or chemical coatings, etc., was utilized to construct the sensor head, which was driven by a FLRD sensor system. The performance of the sensor was evaluated on concrete bars with dimensions 20 cm × 5 cm × 5 cm, made in our laboratory. Cracks were produced manually and the responses of the sensor were recorded in terms of ringdown times. The sensor demonstrated detection of the surface crack width (SCW) of 0.5 mm, which leads to a theoretical SCW detection limit of 31 μm. The sensor's response to a cracking event is near real-time (1.5 s). A large dynamic range of crack detection ranging from a few microns (μm) to a few millimeters is expected from this sensor. With the distinct features, such as simplicity, temperature independence, near real-time response, high SCW detection sensitivity, and a large dynamic range, this FLRD crack sensor appears promising for detections of cracks when embedded in concrete. PMID:23344372

  7. Thermally-Induced Structural Disturbances of Rigid Panel Solar Arrays

    NASA Technical Reports Server (NTRS)

    Johnston, John D.; Thornton, Earl A.

    1997-01-01

    The performance of a significant number of spacecraft has been impacted negatively by attitude disturbances resulting from thermally-induced motions of flexible structures. Recent examples of spacecraft affected by these disturbances include the Hubble Space Telescope (HST) and the Upper Atmosphere Research Satellite (UARS). Thermally-induced structural disturbances occur as the result of rapid changes in thermal loading typically initiated as a satellite exits or enters the Earth's shadow. Temperature differences in flexible appendages give rise to structural deformations, which in turn result in disturbance torques reacting back on the spacecraft. Structures which have proven susceptible to these disturbances include deployable booms and solar arrays. This paper investigates disturbances resulting from thermally-induced deformations of rigid panel solar arrays. An analytical model for the thermal-structural response of the solar array and the corresponding disturbance torque are presented. The effect of these disturbances on the attitude dynamics of a simple spacecraft is then investigated using a coupled system of governing equations which includes the effects of thermally-induced deformations. Numerical results demonstrate the effect of varying solar array geometry on the dynamic response of the system.

  8. PATZ1 induces PP4R2 to form a negative feedback loop on IKK/NF-κB signaling in lung cancer

    PubMed Central

    Ho, Ming-Yi; Liang, Chi-Ming; Liang, Shu-Mei

    2016-01-01

    Activation of IKK enhances NF-κB signaling to facilitate cancer cell migration, invasion and metastasis. Here, we uncover the existence of a negative feedback loop of IKK. The transcription factor PATZ1 induces protein phosphatase-4 (PP4) regulatory subunit 2 (PP4R2) in an IKK-dependent manner. PP4R2 enhances the binding of PP4 to phosphorylated IKK to inactivate IKK/NF-κB signaling during sustained stimulation by cellular stimuli such as growth factors and inflammatory mediators. Matched pair studies reveal that primary lung cancers express more PATZ1 and PP4R2 than lymph node metastases in patients. Ectopic PATZ1 decreases invasion/colonization of lung cancers and prolongs the survival of xenograft mice. These effects of PATZ1 are reversed by downregulating PP4R2. Our results suggest that PATZ1 and PP4R2 provide negative feedback on IKK/NF-κB signaling to prevent cancer cells from over-stimulation from cellular stimuli; a decline in PATZ1 and PP4R2 is functionally associated with cancer migration/invasion and agents enhancing PATZ1 and PP4R2 are worth exploring to prevent invasion/metastasis of lung cancers. PMID:27391343

  9. M2 macrophages induce ovarian cancer cell proliferation via a heparin binding epidermal growth factor/matrix metalloproteinase 9 intercellular feedback loop

    PubMed Central

    Carroll, Molly J.; Kapur, Arvinder; Felder, Mildred; Patankar, Manish S.; Kreeger, Pamela K.

    2016-01-01

    In ovarian cancer, a high ratio of anti-inflammatory M2 to pro-inflammatory M1 macrophages correlates with poor patient prognosis. The mechanisms driving poor tumor outcome as a result of the presence of M2 macrophages in the tumor microenvironment remain unclear and are challenging to study with current techniques. Therefore, in this study we utilized a micro-culture device previously developed by our lab to model concentrated paracrine signaling in order to address our hypothesis that interactions between M2 macrophages and ovarian cancer cells induce tumor cell proliferation. Using the micro-culture device, we determined that co-culture with M2-differentiated primary macrophages or THP-1 increased OVCA433 proliferation by 10–12%. This effect was eliminated with epidermal growth factor receptor (EGFR) or heparin-bound epidermal growth factor (HB-EGF) neutralizing antibodies and HBEGF expression in peripheral blood mononuclear cells from ovarian cancer patients was 9-fold higher than healthy individuals, suggesting a role for HB-EGF in tumor progression. However, addition of HB-EGF at levels secreted by macrophages or macrophage-conditioned media did not induce proliferation to the same extent, indicating a role for other factors in this process. Matrix metalloproteinase-9, MMP-9, which cleaves membrane-bound HB-EGF, was elevated in co-culture and its inhibition decreased proliferation. Utilizing inhibitors and siRNA against MMP9 in each population, we determined that macrophage-secreted MMP-9 released HB-EGF from macrophages, which increased MMP9 in OVCA433, resulting in a positive feedback loop to drive HB-EGF release and increase proliferation in co-culture. Identification of multi-cellular interactions such as this may provide insight into how to most effectively control ovarian cancer progression. PMID:27888810

  10. Structure Formation in the Universe from Texture Induced Fluctuations

    NASA Astrophysics Data System (ADS)

    Durrer, Ruth; Zhou, Zhi-Hong

    1995-03-01

    We discuss structure formation with topological defects. First we present a partially new, local, and gauge invariant system of perturbation equations to treat microwave background and dark matter fluctuations induced by topological defects or any other type of seeds. We show that this system is well suited for numerical analysis of structure formation by applying it to the texture scenario. Our numerical results cover a larger dynamical range than previous investigations and are complementary to them since we use substantially different methods.

  11. Asymptotic 3-loop heavy flavor corrections to the charged current structure functions FLW+-W-(x ,Q2) and F2W+-W-(x ,Q2)

    NASA Astrophysics Data System (ADS)

    Behring, A.; Blümlein, J.; Falcioni, G.; De Freitas, A.; von Manteuffel, A.; Schneider, C.

    2016-12-01

    We derive the massive Wilson coefficients for the heavy flavor contributions to the nonsinglet charged current deep-inelastic scattering structure functions FLW+(x ,Q2)-FLW-(x ,Q2) and F2W+(x ,Q2)-F2W-(x ,Q2) in the asymptotic region Q2≫m2 to 3-loop order in quantum chromodynamics at general values of the Mellin variable N and the momentum fraction x . Besides the heavy quark pair production, also the single heavy flavor excitation s →c contributes. Numerical results are presented for the charm quark contributions, and consequences on the unpolarized Bjorken sum rule and Adler sum rule are discussed.

  12. Local and global ligand-induced changes in the structure of the GABA(A) receptor.

    PubMed

    Muroi, Yukiko; Czajkowski, Cynthia; Jackson, Meyer B

    2006-06-13

    Ligand-gated channels mediate synaptic transmission through conformational transitions triggered by the binding of neurotransmitters. These transitions are well-defined in terms of ion conductance, but their structural basis is poorly understood. To probe these changes in structure, GABA(A) receptors were expressed in Xenopus oocytes and labeled at selected sites with environment-sensitive fluorophores. With labels at two different residues in the alpha1 subunit in loop E of the GABA-binding pocket, GABA elicited fluorescence changes opposite in sign. This pattern of fluorescence changes is consistent with a closure of the GABA-binding cavity at the subunit interface. The competitive antagonist SR-95531 inverted this pattern of fluorescence change, but the noncompetitive antagonist picrotoxin failed to elicit optical signals. In response to GABA (but not SR-95531), labels at the homologous residues in the beta2 subunit showed the same pattern of fluorescence change as the alpha1-subunit labels, indicating a global transition with comparable movements in homologous regions of different subunits. Incorporation of the gamma2 subunit altered the fluorescence changes of alpha1-subunit labels and eliminated them in beta2-subunit labels. Thus, the ligand-induced structural changes in the GABA(A) receptor can extend over considerable distances or remain highly localized, depending upon subunit composition and ligand.

  13. Leukocyte integrin αLβ2 headpiece structures: The αI domain, the pocket for the internal ligand, and concerted movements of its loops.

    PubMed

    Sen, Mehmet; Springer, Timothy A

    2016-03-15

    High-resolution crystal structures of the headpiece of lymphocyte function-associated antigen-1 (integrin αLβ2) reveal how the αI domain interacts with its platform formed by the α-subunit β-propeller and β-subunit βI domains. The αLβ2 structures compared with αXβ2 structures show that the αI domain, tethered through its N-linker and a disulfide to a stable β-ribbon pillar near the center of the platform, can undergo remarkable pivoting and tilting motions that appear buffered by N-glycan decorations that differ between αL and αX subunits. Rerefined β2 integrin structures reveal details including pyroglutamic acid at the β2 N terminus and bending within the EGF1 domain. Allostery is relayed to the αI domain by an internal ligand that binds to a pocket at the interface between the β-propeller and βI domains. Marked differences between the αL and αX subunit β-propeller domains concentrate near the binding pocket and αI domain interfaces. Remarkably, movement in allostery in the βI domain of specificity determining loop 1 (SDL1) causes concerted movement of SDL2 and thereby tightens the binding pocket for the internal ligand.

  14. Leukocyte integrin αLβ2 headpiece structures: The αI domain, the pocket for the internal ligand, and concerted movements of its loops

    PubMed Central

    Sen, Mehmet; Springer, Timothy A.

    2016-01-01

    High-resolution crystal structures of the headpiece of lymphocyte function-associated antigen-1 (integrin αLβ2) reveal how the αI domain interacts with its platform formed by the α-subunit β-propeller and β-subunit βI domains. The αLβ2 structures compared with αXβ2 structures show that the αI domain, tethered through its N-linker and a disulfide to a stable β-ribbon pillar near the center of the platform, can undergo remarkable pivoting and tilting motions that appear buffered by N-glycan decorations that differ between αL and αX subunits. Rerefined β2 integrin structures reveal details including pyroglutamic acid at the β2 N terminus and bending within the EGF1 domain. Allostery is relayed to the αI domain by an internal ligand that binds to a pocket at the interface between the β-propeller and βI domains. Marked differences between the αL and αX subunit β-propeller domains concentrate near the binding pocket and αI domain interfaces. Remarkably, movement in allostery in the βI domain of specificity determining loop 1 (SDL1) causes concerted movement of SDL2 and thereby tightens the binding pocket for the internal ligand. PMID:26936951

  15. Flow-Induced Vibration of Circular Cylindrical Structures

    SciTech Connect

    Chen, Shoei-Sheng

    1985-06-01

    Flow-induced vibration is a term to denote those phenomena associated with the response of structures placed in or conveying fluid flow. More specifically, the terra covers those cases in which an interaction develops between fluid-dynamic forces and the inertia, damping or elastic forces in the structures. The study of these phenomena draws on three disciplines: (1) structural mechanics, (2) mechanical vibration, and (3) fluid dynamics. The vibration of circular cylinders subject to flow has been known to man since ancient times; the vibration of a wire at its natural frequency in response to vortex shedding was known in ancient Greece as aeolian tones. But systematic studies of the problem were not made until a century ago when Strouhal established the relationship between vortex shedding frequency and flow velocity for a given cylinder diameter. The early research in this area has beer summarized by Zdravkovich (1985) and Goldstein (1965). Flow-induced structural vibration has been experienced in numerous fields, including the aerospace industry, power generation/transmission (turbine blades, heat exchanger tubes, nuclear reactor components), civil engineering (bridges, building, smoke stacks), and undersea technology. The problems have usually been encountered or created accidentally through improper design. In most cases, a structural or mechanical component, designed to meet specific objectives, develops problems when the undesired effects of flow field have not been accounted for in the design. When a flow-induced vibration problem is noted in the design stage, the engineer has different options to eliminate the detrimental vibration. Unfortunately, in many situations, the problems occur after the components are already in operation; the "fix" usually is very costly. Flow-induced vibration comprises complex and diverse phenomena; subcritical vibration of nuclear fuel assemblies, galloping of transmission lines, flutter of pipes conveying fluid, and whirling

  16. A Small Molecule that Mimics the BB-Loop in the Toll/IL-1 Receptor Domain of MyD88 Attenuates Staphylococcal Enterotoxin B Induced Pro-Inflammatory Cytokine Production and Toxicity in Mice

    DTIC Science & Technology

    2011-06-01

    to allow the cells to swell. 50 µl of 10% Nonidet P - 40 was added to the cells and briefly centrifuged. The nuclear pellet was resuspended in...protein 10 (IP-10). A conserved sequence, (F/Y)-(V/L/I)-( P /G), called the BB- loop appears in the TIR domain of most members of the TLR/IL-1R family...from 7 structural analogs based on the tripeptide sequence of the BB-loop [(F/Y)-(V/L/I)-( P /G)] of the Toll/IL-1 receptor (TIR) domain binding

  17. Crystal structure of laser-induced subsurface modifications in Si

    DOE PAGES

    Verburg, P. C.; Smillie, L. A.; Römer, G. R. B. E.; ...

    2015-06-04

    Laser-induced subsurface modification of dielectric materials is a well-known technology. Applications include the production of optical components and selective etching. In addition to dielectric materials, the subsurface modification technology can be applied to silicon, by employing near to mid-infrared radiation. An application of subsurface modifications in silicon is laser-induced subsurface separation, which is a method to separate wafers into individual dies. Other applications for which proofs of concept exist are the formation of waveguides and resistivity tuning. However, limited knowledge is available about the crystal structure of subsurface modifications in silicon. In this paper, we investigate the geometry and crystalmore » structure of laser-induced subsurface modifications in monocrystalline silicon wafers. Finally, in addition to the generation of lattice defects, we found that transformations to amorphous silicon and Si-iii/Si-xii occur as a result of the laser irradiation.« less

  18. Crystal structure of laser-induced subsurface modifications in Si

    SciTech Connect

    Verburg, P. C.; Smillie, L. A.; Römer, G. R. B. E.; Haberl, B.; Bradby, J. E.; Williams, J. S.; Huis in ’t Veld, A. J.

    2015-06-04

    Laser-induced subsurface modification of dielectric materials is a well-known technology. Applications include the production of optical components and selective etching. In addition to dielectric materials, the subsurface modification technology can be applied to silicon, by employing near to mid-infrared radiation. An application of subsurface modifications in silicon is laser-induced subsurface separation, which is a method to separate wafers into individual dies. Other applications for which proofs of concept exist are the formation of waveguides and resistivity tuning. However, limited knowledge is available about the crystal structure of subsurface modifications in silicon. In this paper, we investigate the geometry and crystal structure of laser-induced subsurface modifications in monocrystalline silicon wafers. Finally, in addition to the generation of lattice defects, we found that transformations to amorphous silicon and Si-iii/Si-xii occur as a result of the laser irradiation.

  19. Laser-induced periodic surface structuring of biopolymers

    NASA Astrophysics Data System (ADS)

    Pérez, Susana; Rebollar, Esther; Oujja, Mohamed; Martín, Margarita; Castillejo, Marta

    2013-03-01

    We report here on a systematic study about the formation of laser-induced periodic surface structures (LIPSS) on biopolymers. Self-standing films of the biopolymers chitosan, starch and the blend of chitosan with the synthetic polymer poly (vinyl pyrrolidone), PVP, were irradiated in air with linearly polarized laser beams at 193, 213 and 266 nm, with pulse durations in the range of 6-17 ns. The laser-induced periodic surface structures were topographically characterized by atomic force microscopy and the chemical modifications induced by laser irradiation were inspected via Raman spectroscopy. Formation of LIPSS parallel to the laser polarization direction, with periods similar to the laser wavelength, was observed at efficiently absorbed wavelengths in the case of the amorphous biopolymer chitosan and its blend with PVP, while formation of LIPSS is prevented in the crystalline starch biopolymer.

  20. Behavior control in the sensorimotor loop with short-term synaptic dynamics induced by self-regulating neurons

    PubMed Central

    Toutounji, Hazem; Pasemann, Frank

    2014-01-01

    The behavior and skills of living systems depend on the distributed control provided by specialized and highly recurrent neural networks. Learning and memory in these systems is mediated by a set of adaptation mechanisms, known collectively as neuronal plasticity. Translating principles of recurrent neural control and plasticity to artificial agents has seen major strides, but is usually hampered by the complex interactions between the agent's body and its environment. One of the important standing issues is for the agent to support multiple stable states of behavior, so that its behavioral repertoire matches the requirements imposed by these interactions. The agent also must have the capacity to switch between these states in time scales that are comparable to those by which sensory stimulation varies. Achieving this requires a mechanism of short-term memory that allows the neurocontroller to keep track of the recent history of its input, which finds its biological counterpart in short-term synaptic plasticity. This issue is approached here by deriving synaptic dynamics in recurrent neural networks. Neurons are introduced as self-regulating units with a rich repertoire of dynamics. They exhibit homeostatic properties for certain parameter domains, which result in a set of stable states and the required short-term memory. They can also operate as oscillators, which allow them to surpass the level of activity imposed by their homeostatic operation conditions. Neural systems endowed with the derived synaptic dynamics can be utilized for the neural behavior control of autonomous mobile agents. The resulting behavior depends also on the underlying network structure, which is either engineered or developed by evolutionary techniques. The effectiveness of these self-regulating units is demonstrated by controlling locomotion of a hexapod with 18 degrees of freedom, and obstacle-avoidance of a wheel-driven robot. PMID:24904403

  1. Fast flux locked loop

    DOEpatents

    Ganther, Jr., Kenneth R.; Snapp, Lowell D.

    2002-09-10

    A flux locked loop for providing an electrical feedback signal, the flux locked loop employing radio-frequency components and technology to extend the flux modulation frequency and tracking loop bandwidth. The flux locked loop of the present invention has particularly useful application in read-out electronics for DC SQUID magnetic measurement systems, in which case the electrical signal output by the flux locked loop represents an unknown magnetic flux applied to the DC SQUID.

  2. The preprocessed doacross loop

    NASA Technical Reports Server (NTRS)

    Saltz, Joel H.; Mirchandaney, Ravi

    1990-01-01

    Dependencies between loop iterations cannot always be characterized during program compilation. Doacross loops typically make use of a-priori knowledge of inter-iteration dependencies to carry out required synchronizations. A type of doacross loop is proposed that allows the scheduling of iterations of a loop among processors without advance knowledge of inter-iteration dependencies. The method proposed for loop iterations requires that parallelizable preprocessing and postprocessing steps be carried out during program execution.

  3. OPE for super loops

    NASA Astrophysics Data System (ADS)

    Sever, Amit; Vieira, Pedro; Wang, Tianheng

    2011-11-01

    We extend the Operator Product Expansion for Null Polygon Wilson loops to the Mason-Skinner-Caron-Huot super loop dual to non MHV gluon amplitudes. We explain how the known tree level amplitudes can be promoted into an infinite amount of data at any loop order in the OPE picture. As an application, we re-derive all one loop NMHV six gluon amplitudes by promoting their tree level expressions. We also present some new all loops predictions for these amplitudes.

  4. Topological interactions between ring polymers: Implications for chromatin loops

    NASA Astrophysics Data System (ADS)

    Bohn, Manfred; Heermann, Dieter W.

    2010-01-01

    Chromatin looping is a major epigenetic regulatory mechanism in higher eukaryotes. Besides its role in transcriptional regulation, chromatin loops have been proposed to play a pivotal role in the segregation of entire chromosomes. The detailed topological and entropic forces between loops still remain elusive. Here, we quantitatively determine the potential of mean force between the centers of mass of two ring polymers, i.e., loops. We find that the transition from a linear to a ring polymer induces a strong increase in the entropic repulsion between these two polymers. On top, topological interactions such as the noncatenation constraint further reduce the number of accessible conformations of close-by ring polymers by about 50%, resulting in an additional effective repulsion. Furthermore, the transition from linear to ring polymers displays changes in the conformational and structural properties of the system. In fact, ring polymers adopt a markedly more ordered and aligned state than linear ones. The forces and accompanying changes in shape and alignment between ring polymers suggest an important regulatory function of such a topology in biopolymers. We conjecture that dynamic loop formation in chromatin might act as a versatile control mechanism regulating and maintaining different local states of compaction and order.

  5. Deceleration of arginine kinase refolding by induced helical structures.

    PubMed

    Li, Hai-Long; Zhou, Sheng-Mei; Park, Daeui; Jeong, Hyoung Oh; Chung, Hae Young; Yang, Jun-Mo; Meng, Fan-Guo; Hu, Wei-Jiang

    2012-04-01

    Arginine kinase (AK) is a key metabolic enzyme for keeping energy balance in invertebrates. Therefore, regulation of the enzymatic activity and the folding studies of AK from the various invertebrates have been the focus of investigation. We studied the effects of helical structures by using hexafluoroisopropanol (HFIP) on AK folding. Folding kinetic studies showed that the folding rates of the urea-denatured AKs were significantly decelerated after being induced in various concentrations of HFIP. AK lost its activity completely at concentrations greater than 60%. The results indicated that the HFIP-induced helical structures in the denatured state play a negative role in protein folding, and the helical structures induced in 5% (v/v) HFIP act as the most effective barrier against AK taking its native structure. The computational docking simulations (binding energies for -2.19 kcal/mol for AutoDock4.2 and -20.47 kcal/mol for Dock6.3) suggested that HFIP interacts with the several important residues that are predicted by both programs. The excessively pre-organized helical structures not only hampered the folding process, but also ultimately brought about changes in the three-dimensional conformation and biological function of AK.

  6. Loop Models from SOHO Observations

    NASA Astrophysics Data System (ADS)

    Landini, M.; Brković , A.; Landi, E.; Rüedi, I.; Solanki, S.

    1999-01-01

    The Coronal Diagnostic Spectrometer (CDS) on SOHO is a grazing/normal incidence spectrograph, aimed to produce stigmatic spectra of selected regions of the solar surface in six spectral windows of the extreme ultraviolet from 150 Å to 785 Å (Harrison et al. 1995). In the present work, CDS, EIT, MDI and Yohkoh observations of active region lops have been analyzed. These observations are part of JOP 54. CDS monochromatic images from lines at different temperatures have been co-aligned with EIT and MDI images, and loop structures have been clearly identified using Fe XVI emission lines. Density sensitive lines and lines from adjacent stages of ionization of Fe ions have been used to measure electron density and temperature along the loop length; these measurements have been used to determine the electron pressure along the loop and test the constant pressure assumption commonly used in loop modeling. The observations have been compared with a static, isobaric loop model (Landini and Monsignori Fossi 1975) assuming a temperature-constant heating function in the energy balance equation. Good agreement is found for the temperature distribution along the loop at the coronal level. The model pressure is somewhat higher than obtained from density sensitive line ratios.

  7. Structure of Trypanosoma brucei glutathione synthetase: Domain and loop alterations in the catalytic cycle of a highly conserved enzyme

    PubMed Central

    Fyfe, Paul K.; Alphey, Magnus S.; Hunter, William N.

    2010-01-01

    Glutathione synthetase catalyses the synthesis of the low molecular mass thiol glutathione from l-γ-glutamyl-l-cysteine and glycine. We report the crystal structure of the dimeric enzyme from Trypanosoma brucei in complex with the product glutathione. The enzyme belongs to the ATP-grasp family, a group of enzymes known to undergo conformational changes upon ligand binding. The T. brucei enzyme crystal structure presents two dimers in the asymmetric unit. The structure reveals variability in the order and position of a small domain, which forms a lid for the active site and serves to capture conformations likely to exist during the catalytic cycle. Comparisons with orthologous enzymes, in particular from Homo sapiens and Saccharomyces cerevisae, indicate a high degree of sequence and structure conservation in part of the active site. Structural differences that are observed between the orthologous enzymes are assigned to different ligand binding states since key residues are conserved. This suggests that the molecular determinants of ligand recognition and reactivity are highly conserved across species. We conclude that it would be difficult to target the parasite enzyme in preference to the host enzyme and therefore glutathione synthetase may not be a suitable target for antiparasitic drug discovery. PMID:20045436

  8. NMR structure of a 4 × 4 nucleotide RNA internal loop from an R2 retrotransposon: Identification of a three purine–purine sheared pair motif and comparison to MC-SYM predictions

    PubMed Central

    Lerman, Yelena V.; Kennedy, Scott D.; Shankar, Neelaabh; Parisien, Marc; Major, Francois; Turner, Douglas H.

    2011-01-01

    The NMR solution structure is reported of a duplex, 5′GUGAAGCCCGU/3′UCACAGGAGGC, containing a 4 × 4 nucleotide internal loop from an R2 retrotransposon RNA. The loop contains three sheared purine–purine pairs and reveals a structural element found in other RNAs, which we refer to as the 3RRs motif. Optical melting measurements of the thermodynamics of the duplex indicate that the internal loop is 1.6 kcal/mol more stable at 37°C than predicted. The results identify the 3RRs motif as a common structural element that can facilitate prediction of 3D structure. Known examples include internal loops having the pairings: 5′GAA/3′AGG, 5′GAG/3′AGG, 5′GAA/3′AAG, and 5′AAG/3′AGG. The structural information is compared with predictions made with the MC-Sym program. PMID:21778280

  9. Contributions of Cu-rich clusters, dislocation loops and nanovoids to the irradiation-induced hardening of Cu-bearing low-Ni reactor pressure vessel steels

    NASA Astrophysics Data System (ADS)

    Bergner, F.; Gillemot, F.; Hernández-Mayoral, M.; Serrano, M.; Török, G.; Ulbricht, A.; Altstadt, E.

    2015-06-01

    Dislocation loops, nanovoids and Cu-rich clusters (CRPs) are known to represent obstacles for dislocation glide in neutron-irradiated reactor pressure vessel (RPV) steels, but a consistent experimental determination of the respective obstacle strengths is still missing. A set of Cu-bearing low-Ni RPV steels and model alloys was characterized by means of SANS and TEM in order to specify mean size and number density of loops, nanovoids and CRPs. The obstacle strengths of these families were estimated by solving an over-determined set of linear equations. We have found that nanovoids are stronger than loops and loops are stronger than CRPs. Nevertheless, CRPs contribute most to irradiation hardening because of their high number density. Nanovoids were only observed for neutron fluences beyond typical end-of-life conditions of RPVs. The estimates of the obstacle strength are critically compared with reported literature data.

  10. Hyd5 gene-based detection of the major gushing-inducing Fusarium spp. in a loop-mediated isothermal amplification (LAMP) assay.

    PubMed

    Denschlag, Carla; Vogel, Rudi F; Niessen, Ludwig

    2012-06-01

    Fusarium graminearum and the closely related F. culmorum were found to be associated with over foaming of bottled beer (gushing) when contaminated brewing malt is used. The presence of highly surface active hydrophobins produced by these fungi upon growth on wheat or barley in the field or during malting may affect bubble formation and stability in gushing beers and other carbonated beverages. Aiming for a method for the rapid and user friendly analysis of unmalted and malted cereals during quality control in the brewing industry, a loop-mediated isothermal amplification (LAMP) assay for the detection of Fusarium spp. capable of producing the gushing inducing hydrophobin Hyd5p was set up. A set of primers was designed towards a 221 bp region within the hyd5 gene of F. culmorum. The LAMP product was verified by sequencing a 150 bp portion. Testing specificity with purified DNA from 99 different fungal species as well as barley and wheat showed that DNA synthesis only occurred during LAMP when DNA of the closely related species F. graminearum, F. culmorum, F. cerealis and F. lunulosporum were used as template. In-tube indirect detection of DNA amplification was applied using manganese-quenched calcein as fluorescence indicator for pyrophosphate produced during DNA synthesis. The assay had a detection limit of 0.74 pg of purified target DNA which corresponds 20 copy numbers per reaction within 30 minutes using a simple heating block. Analysis of Fusarium infected cereals revealed that the assay was able to detect F. graminearum at a level of 0.5% of infected grains in uninfected barley by analysis of surface washings without further sample preparation. Results show that the hyd5 based LAMP assay can be a rapid, useful and sensitive tool for quality control in the brewing and malting industry.

  11. Predictive lethal proarrhythmic risk evaluation using a closed-loop-circuit cell network with human induced pluripotent stem cells derived cardiomyocytes

    NASA Astrophysics Data System (ADS)

    Nomura, Fumimasa; Hattori, Akihiro; Terazono, Hideyuki; Kim, Hyonchol; Odaka, Masao; Sugio, Yoshihiro; Yasuda, Kenji

    2016-06-01

    For the prediction of lethal arrhythmia occurrence caused by abnormality of cell-to-cell conduction, we have developed a next-generation in vitro cell-to-cell conduction assay, i.e., a quasi in vivo assay, in which the change in spatial cell-to-cell conduction is quantitatively evaluated from the change in waveforms of the convoluted electrophysiological signals from lined-up cardiomyocytes on a single closed loop of a microelectrode of 1 mm diameter and 20 µm width in a cultivation chip. To evaluate the importance of the closed-loop arrangement of cardiomyocytes for prediction, we compared the change in waveforms of convoluted signals of the responses in the closed-loop circuit arrangement with that of the response of cardiomyocyte clusters using a typical human ether a go-go related gene (hERG) ion channel blocker, E-4031. The results showed that (1) waveform prolongation and fluctuation both in the closed loops and clusters increased depending on the E-4031 concentration increase. However, (2) only the waveform signals in closed loops showed an apparent temporal change in waveforms from ventricular tachycardia (VT) to ventricular fibrillation (VF), which is similar to the most typical cell-to-cell conductance abnormality. The results indicated the usefulness of convoluted waveform signals of a closed-loop cell network for acquiring reproducible results acquisition and more detailed temporal information on cell-to-cell conduction.

  12. Light-induced structural changes in a monomeric bacteriophytochrome

    PubMed Central

    Takala, Heikki; Niebling, Stephan; Berntsson, Oskar; Björling, Alexander; Lehtivuori, Heli; Häkkänen, Heikki; Panman, Matthijs; Gustavsson, Emil; Hoernke, Maria; Newby, Gemma; Zontone, Federico; Wulff, Michael; Menzel, Andreas; Ihalainen, Janne A.; Westenhoff, Sebastian

    2016-01-01

    Phytochromes sense red light in plants and various microorganism. Light absorption causes structural changes within the protein, which alter its biochemical activity. Bacterial phytochromes are dimeric proteins, but the functional relevance of this arrangement remains unclear. Here, we use time-resolved X-ray scattering to reveal the solution structural change of a monomeric variant of the photosensory core module of the phytochrome from Deinococcus radiodurans. The data reveal two motions, a bend and a twist of the PHY domain with respect to the chromophore-binding domains. Infrared spectroscopy shows the refolding of the PHY tongue. We conclude that a monomer of the phytochrome photosensory core is sufficient to perform the light-induced structural changes. This implies that allosteric cooperation with the other monomer is not needed for structural activation. The dimeric arrangement may instead be intrinsic to the biochemical output domains of bacterial phytochromes. PMID:27679804

  13. Structures of Receptor Complexes of a North American H7N2 Influenza Hemagglutinin with a Loop Deletion in the Receptor Binding Site

    SciTech Connect

    Yang, Hua; Chen, Li-Mei; Carney, Paul J.; Donis, Ruben O.; Stevens, James

    2012-02-21

    Human infections with subtype H7 avian influenza viruses have been reported as early as 1979. In 1996, a genetically stable 24-nucleotide deletion emerged in North American H7 influenza virus hemagglutinins, resulting in an eight amino acid deletion in the receptor-binding site. The continuous circulation of these viruses in live bird markets, as well as its documented ability to infect humans, raises the question of how these viruses achieve structural stability and functionality. Here we report a detailed molecular analysis of the receptor binding site of the North American lineage subtype H7N2 virus A/New York/107/2003 (NY107), including complexes with an avian receptor analog (3'-sialyl-N-acetyllactosamine, 3'SLN) and two human receptor analogs (6'-sialyl-N-acetyllactosamine, 6'SLN; sialyllacto-N-tetraose b, LSTb). Structural results suggest a novel mechanism by which residues Arg220 and Arg229 (H3 numbering) are used to compensate for the deletion of the 220-loop and form interactions with the receptor analogs. Glycan microarray results reveal that NY107 maintains an avian-type ({alpha}2-3) receptor binding profile, with only moderate binding to human-type ({alpha}2-6) receptor. Thus despite its dramatically altered receptor binding site, this HA maintains functionality and confirms a need for continued influenza virus surveillance of avian and other animal reservoirs to define their zoonotic potential.

  14. Shear Induced Structural Relaxation in a Supercooled Colloidal Liquid

    NASA Astrophysics Data System (ADS)

    Chen, Dandan; Semwogerere, Denis; Weeks, Eric R.

    2009-11-01

    Amorphous materials include many common products we use everyday, such as window glass, moisturizer, shaving cream and peanut butter. These materials have liquid-like disordered structure, but keep their shapes like a solid. The rheology of dense amorphous materials under large shear strain is not fully understood, partly due to the difficulty of directly viewing the microscopic details of such materials. We use a colloidal suspension to simulate amorphous materials, and study the shear- induced structural relaxation with fast confocal microscopy. We quantify the plastic rearrangements of the particles using standard analysis techniques based on the motion of the particles.

  15. Surface-induced structures in nematic liquid crystal colloids

    NASA Astrophysics Data System (ADS)

    Chernyshuk, S. B.; Tovkach, O. M.; Lev, B. I.

    2014-08-01

    We predict theoretically the existence of a class of colloidal structures in nematic liquid crystal (NLC) cells, which are induced by surface patterns on the plates of the cell (like cells with UV-irradiated polyamide surfaces using micron sized masks in front of the cell). These bulk structures arise from nonuniform boundary conditions for the director distortions at the confining surfaces. In particular, we demonstrate that quadrupole spherical particles (like spheres with boojums or Saturn-ring director configurations) form a square lattice inside a planar NLC cell, which has checkerboard patterns on both its plates.

  16. Hydrogen peroxide-induced structural alterations of RNAse A.

    PubMed

    Lasch, P; Petras, T; Ullrich, O; Backmann, J; Naumann, D; Grune, T

    2001-03-23

    Proteins exposed to oxidative stress are degraded via proteolytic pathways. In the present study, we undertook a series of in vitro experiments to establish a correlation between the structural changes induced by mild oxidation of the model protein RNase A and the proteolytic rate found upon exposure of the modified protein toward the isolated 20 S proteasome. Fourier transform infrared spectroscopy was used as a structure-sensitive probe. We report here strong experimental evidence for oxidation-induced conformational rearrangements of the model protein RNase A and, at the same time, for covalent modifications of amino acid side chains. Oxidation-related conformational changes, induced by H(2)O(2) exposure of the protein may be monitored in the amide I region, which is sensitive to changes in protein secondary structure. A comparison of the time- and H(2)O(2) concentration-dependent changes in the amide I region demonstrates a high degree of similarity to spectral alterations typical for temperature-induced unfolding of RNase A. In addition, spectral parameters of amino acid side chain marker bands (Tyr, Asp) revealed evidence for covalent modifications. Proteasome digestion measurements on oxidized RNase A revealed a specific time and H(2)O(2) concentration dependence; at low initial concentration of the oxidant, the RNase A turnover rate increases with incubation time and concentration. Based on these experimental findings, a correlation between structural alterations detected upon RNase A oxidation and proteolytic rates of RNase A is established, and possible mechanisms of the proteasome recognition process of oxidatively damaged proteins are discussed.

  17. Gravitationally induced particle production and its impact on structure formation

    NASA Astrophysics Data System (ADS)

    Nunes, Rafael C.

    2016-08-01

    In this paper we investigate the influence of a continuous particles creation processes on the linear and nonlinear matter clustering, and its consequences on the weak lensing effect induced by structure formation. We study the line of sight behavior of the contribution to the bispectrum signal at a given angular multipole l, showing that the scale where the nonlinear growth overcomes the linear effect depends strongly of particles creation rate.

  18. Structure of the partially unliganded met state of 400 kDa hemoglobin: insights into ligand-induced structural changes of giant hemoglobins.

    PubMed

    Numoto, Nobutaka; Nakagawa, Taro; Kita, Akiko; Sasayama, Yuichi; Fukumori, Yoshihiro; Miki, Kunio

    2008-10-01

    Recent crystallographic studies have revealed the structures of some invertebrate extracellular giant hemoglobins of 3,600 kDa or 400 kDa and their common quaternary structure of dodecameric subassembly composed of four kinds of globin subunits (A1, A2, B1, and B2). These results have provided insight into the mechanisms of their unique functional properties of oxygen binding and sulfide binding. All of these structures were solved with oxygenated or CO-liganded forms at low or moderate resolutions. We have determined the crystal structure of 400 kDa Hb from a polychaete Oligobrachia mashikoi at 1.95 A resolution. The electron densities at higher resolution confirm the existence of an isoform of the B1 subunit because of the inconsistency with the model that was built from the formerly known amino acid sequence. The brownish color of the crystals used in this study and the absorption spectrum from the dissolved crystals strongly indicated that the obtained structure was a ferric met state, whereas complete absence of electron density around the distal heme pockets were observed at the A2, B1, and B2 subunits. We concluded that the obtained structure was in unliganded met forms at three of four globin subunits in the 24mer assembly and in oxygenated forms at the remaining A1 subunits. The partially unliganded structure showed remarkable structural changes at the AB loop regions causing quaternary rearrangements of the EF-dimer structure. In contrast, few changes occurred at the interface regions composed of the E and F helices. These results suggest that the ligand-induced structural changes of Oligobrachia Hb are quite different from those of the well-studied mollusk Hb having the same EF-dimer structure. The structural rearrangements make the dodecameric subassembly form a tighter conformation than those of fully oxygenated or CO-liganded dodecamer structure.

  19. Telomeres thrown for a loop.

    PubMed

    Haber, James E

    2004-11-19

    A remarkable paper from the de Lange lab (Wang et al., 2004) in a recent issue of Cell reveals that homologous recombination can result in the abrupt shortening of telomeres in a process that appears to involve reciprocal crossing over within the t-loop structure that protects chromosome ends.

  20. Buckling-induced encapsulation of structured elastic shells under pressure

    PubMed Central

    Shim, Jongmin; Perdigou, Claude; Chen, Elizabeth R.; Bertoldi, Katia; Reis, Pedro M.

    2012-01-01

    We introduce a class of continuum shell structures, the Buckliball, which undergoes a structural transformation induced by buckling under pressure loading. The geometry of the Buckliball comprises a spherical shell patterned with a regular array of circular voids. In order for the pattern transformation to be induced by buckling, the possible number and arrangement of these voids are found to be restricted to five specific configurations. Below a critical internal pressure, the narrow ligaments between the voids buckle, leading to a cooperative buckling cascade of the skeleton of the ball. This ligament buckling leads to closure of the voids and a reduction of the total volume of the shell by up to 54%, while remaining spherical, thereby opening the possibility of encapsulation. We use a combination of precision desktop-scale experiments, finite element simulations, and scaling analyses to explore the underlying mechanics of these foldable structures, finding excellent qualitative and quantitative agreement. Given that this folding mechanism is induced by a mechanical instability, our Buckliball opens the possibility for reversible encapsulation, over a wide range of length scales. PMID:22451901

  1. Loop calculus for lattice gauge theories

    SciTech Connect

    Gambini, R.; Leal, L.; Trias, A.

    1989-05-15

    Hamiltonian calculations are performed using a loop-labeled basis where the full set of identities for the SU(/ital N/) gauge models has been incorporated. The loops are classified as clusterlike structures and the eigenvalue problem leads to a linear set of finite-difference equations easily amenable to numerical treatment. Encouraging results are reported for SU(2) at spatial dimension 2.

  2. Spring control of wire harness loops

    NASA Technical Reports Server (NTRS)

    Curcio, P. J.

    1979-01-01

    Negator spring control guides wire harness between movable and fixed structure. It prevents electrical wire harness loop from jamming or being severed as wire moves in response to changes in position of aircraft rudder. Spring-loaded coiled cable controls wire loop regardless of rudder movement.

  3. Coronal Loops: Observations and Modeling of Confined Plasma.

    PubMed

    Reale, Fabio

    Coronal loops are the building blocks of the X-ray bright solar corona. They owe their brightness to the dense confined plasma, and this review focuses on loops mostly as structures confining plasma. After a brief historical overview, the review is divided into two separate but not independent parts: the first illustrates the observational framework, the second reviews the theoretical knowledge. Quiescent loops and their confined plasma are considered and, therefore, topics such as loop oscillations and flaring loops (except for non-solar ones, which provide information on stellar loops) are not specifically addressed here. The observational section discusses the classification, populations, and the morphology of coronal loops, its relationship with the magnetic field, and the loop stranded structure. The section continues with the thermal properties and diagnostics of the loop plasma, according to the classification into hot, warm, and cool loops. Then, temporal analyses of loops and the observations of plasma dynamics, hot and cool flows, and waves are illustrated. In the modeling section, some basics of loop physics are provided, supplying fundamental scaling laws and timescales, a useful tool for consultation. The concept of loop modeling is introduced and models are divided into those treating loops as monolithic and static, and those resolving loops into thin and dynamic strands. More specific discussions address modeling the loop fine structure and the plasma flowing along the loops. Special attention is devoted to the question of loop heating, with separate discussion of wave (AC) and impulsive (DC) heating. Large-scale models including atmosphere boxes and the magnetic field are also discussed. Finally, a brief discussion about stellar coronal loops is followed by highlights and open questions.

  4. Multi-instrument observations of coronal loops

    NASA Astrophysics Data System (ADS)

    Scott, Jason Terrence

    This document exhibits results of analysis from data collected with multiple EUV satellites (SOHO, TRACE, STEREO, Hinode, and SDO). The focus is the detailed observation of coronal loops using multiple instruments, i.e. filter imagers and spectrometers. Techniques for comparing the different instruments and deriving loop parameters are demonstrated. Attention is given to the effects the different instruments may introduce into the data and their interpretation. The assembled loop parameters are compared to basic energy balance equations and scaling laws. Discussion of the blue-shifted, asymmetric, and line broadened spectral line profiles near the footpoints of coronal loops is made. The first quantitative analysis of the anti-correlation between intensity and spectral line broadening for isolated regions along loops and their footpoints is presented. A magnetic model of an active region shows where the separatrices meet the photospheric boundary. At the boundary, the spectral data reveal concentrated regions of increased blue-shifted outflows, blue wing asymmetry, and line broadening. This is found just outside the footpoints of bright loops. The intensity and line broadening in this region are anti-correlated. A comparison of the similarities in the spectroscopic structure near the footpoints of the arcade loops and more isolated loops suggests the notion of consistent structuring for the bright loops forming an apparent edge of an active region core.

  5. Loop-Loop Interactions Regulate KaiA-Stimulated KaiC Phosphorylation in the Cyanobacterial KaiABC Circadian Clock

    SciTech Connect

    Egli, Martin; Pattanayek, Rekha; Sheehan, Jonathan H.; Xu, Yao; Mori, Tetsuya; Smith, Jarrod A.; Johnson, Carl H.

    2013-01-25

    We found that the Synechococcus elongatus KaiA, KaiB, and KaiC proteins in the presence of ATP generate a post-translational oscillator that runs in a temperature-compensated manner with a period of 24 h. KaiA dimer stimulates phosphorylation of KaiC hexamer at two sites per subunit, T432 and S431, and KaiB dimers antagonize KaiA action and induce KaiC subunit exchange. Neither the mechanism of KaiA-stimulated KaiC phosphorylation nor that of KaiB-mediated KaiC dephosphorylation is understood in detail at present. We demonstrate here that the A422V KaiC mutant sheds light on the former mechanism. It was previously reported that A422V is less sensitive to dark pulse-induced phase resetting and has a reduced amplitude of the KaiC phosphorylation rhythm in vivo. A422 maps to a loop (422-loop) that continues toward the phosphorylation sites. By pulling on the C-terminal peptide of KaiC (A-loop), KaiA removes restraints from the adjacent 422-loop whose increased flexibility indirectly promotes kinase activity. We found in the crystal structure that A422V KaiC lacks phosphorylation at S431 and exhibits a subtle, local conformational change relative to wild-type KaiC. Molecular dynamics simulations indicate higher mobility of the 422-loop in the absence of the A-loop and mobility differences in other areas associated with phosphorylation activity between wild-type and mutant KaiCs. Finally, the A-loop–422-loop relay that informs KaiC phosphorylation sites of KaiA dimer binding propagates to loops from neighboring KaiC subunits, thus providing support for a concerted allosteric mechanism of phosphorylation.

  6. Characterization of flow-induced structures in carbon nanotube suspensions

    NASA Astrophysics Data System (ADS)

    Khalkhal, Fatemeh

    Carbon nanotubes (CNTs) are fibre-like nano-particles with many different applications. Due to their high specific surface area, high electric current density, thermal stability and excellent mechanical properties, they are used to reinforce physical properties of polymer matrices. The macroscopic properties of suspensions are inherited from their properties at micron and sub-micron scales. The suspensions structure can be easily influenced by many parameters such as the extent of external shear forces, the suspension concentration, temperature, the particles specifications, etc. This makes the study of the suspension structure a very challenging task and has been the subject of interest to many researchers. In this thesis, the structure of a model carbon nanotube suspension dispersed in an epoxy is studied by employing a set of rheological methods, scaling and fractal theories and a structural thixotropic model. The effect of flow history on linear viscoelastic properties of suspensions and the evolution of structure upon cessation of shear flow has been studied over a wide range of pre-shearing rates, concentration and temperature. The results of these analyses are as follows. The effect of flow history is more pronounced on the suspensions structure in dilute and semi-dilute concentration regimes. By pre-shearing at low rates, more inter-particle entanglements were induced, which resulted in reduction of rheological percolation thresholds. After cessation of shear flow, for dilute and semi-dilute suspensions, the formed metastable structures were distinguishable by different storage moduli, which were inversely related to the rate of pre-shearing. However, for the concentrated suspensions, the formed metastable structures had an approximately equal storage modulus regardless of the rate of the applied pre-shearing. It was shown that the rate of formation of these metastable structures was enhanced by increasing concentration. Furthermore, the rate of structure

  7. Mechanistic Insight into Bunyavirus-Induced Membrane Fusion from Structure-Function Analyses of the Hantavirus Envelope Glycoprotein Gc.

    PubMed

    Guardado-Calvo, Pablo; Bignon, Eduardo A; Stettner, Eva; Jeffers, Scott Allen; Pérez-Vargas, Jimena; Pehau-Arnaudet, Gerard; Tortorici, M Alejandra; Jestin, Jean-Luc; England, Patrick; Tischler, Nicole D; Rey, Félix A

    2016-10-01

    Hantaviruses are zoonotic viruses transmitted to humans by persistently infected rodents, giving rise to serious outbreaks of hemorrhagic fever with renal syndrome (HFRS) or of hantavirus pulmonary syndrome (HPS), depending on the virus, which are associated with high case fatality rates. There is only limited knowledge about the organization of the viral particles and in particular, about the hantavirus membrane fusion glycoprotein Gc, the function of which is essential for virus entry. We describe here the X-ray structures of Gc from Hantaan virus, the type species hantavirus and responsible for HFRS, both in its neutral pH, monomeric pre-fusion conformation, and in its acidic pH, trimeric post-fusion form. The structures confirm the prediction that Gc is a class II fusion protein, containing the characteristic β-sheet rich domains termed I, II and III as initially identified in the fusion proteins of arboviruses such as alpha- and flaviviruses. The structures also show a number of features of Gc that are distinct from arbovirus class II proteins. In particular, hantavirus Gc inserts residues from three different loops into the target membrane to drive fusion, as confirmed functionally by structure-guided mutagenesis on the HPS-inducing Andes virus, instead of having a single "fusion loop". We further show that the membrane interacting region of Gc becomes structured only at acidic pH via a set of polar and electrostatic interactions. Furthermore, the structure reveals that hantavirus Gc has an additional N-terminal "tail" that is crucial in stabilizing the post-fusion trimer, accompanying the swapping of domain III in the quaternary arrangement of the trimer as compared to the standard class II fusion proteins. The mechanistic understandings derived from these data are likely to provide a unique handle for devising treatments against these human pathogens.

  8. Pseudonoise code tracking loop

    NASA Technical Reports Server (NTRS)

    Laflame, D. T. (Inventor)

    1980-01-01

    A delay-locked loop is presented for tracking a pseudonoise (PN) reference code in an incoming communication signal. The loop is less sensitive to gain imbalances, which can otherwise introduce timing errors in the PN reference code formed by the loop.

  9. Structure and Property Changes in Self-Assembled Lubricin Layers Induced by Calcium Ion Interactions.

    PubMed

    Greene, George W; Thapa, Rajiv; Holt, Stephen A; Wang, Xiaoen; Garvey, Christopher J; Tabor, Rico F

    2017-03-14

    Lubricin (LUB) is a "mucin-like" glycoprotein found in synovial fluids and coating the cartilage surfaces of articular joints, which is now generally accepted as one of the body's primary boundary lubricants and antiadhesive agents. LUB's superior lubrication and antiadhesion are believed to derive from its unique interfacial properties by which LUB molecules adhere to surfaces (and biomolecules, such as hyaluronic acid and collagen) through discrete interactions localized to its two terminal end domains. These regionally specific interactions lead to self-assembly behavior and the formation of a well-ordered "telechelic" polymer brush structure on most substrates. Despite its importance to biological lubrication, detailed knowledge on the LUB's self-assembled brush structure is insufficient and derived mostly from indirect and circumstantial evidence. Neutron reflectometry (NR) was used to directly probe the self-assembled LUB layers, confirming the polymer brush architecture and resolving the degree of hydration and level of surface coverage. While attempting to improve the LUB contrast in the NR measurements, the LUB layers were exposed to a 20 mM solution of CaCl2, which resulted in a significant change in the polymer brush structural parameters consisting of a partial denaturation of the surface-binding end-domain regions, partial dehydration of the internal mucin-domain "loop", and collapse of the outer mucin-domain surface region. A series of atomic force microscopy measurements investigating the LUB layer surface morphology, mechanical properties, and adhesion forces in phosphate-buffered saline and CaCl2 solutions reveal that the structural changes induced by calcium ion interactions also significantly alter key properties, which may have implications to LUB's efficacy as a boundary lubricant and wear protector in the presence of elevated calcium ion concentrations.

  10. Thermally induced fracture for core-veneered dental ceramic structures.

    PubMed

    Zhang, Zhongpu; Guazzato, Massimiliano; Sornsuwan, Tanapon; Scherrer, Susanne S; Rungsiyakull, Chaiy; Li, Wei; Swain, Michael V; Li, Qing

    2013-09-01

    Effective and reliable clinical uses of dental ceramics necessitate an insightful analysis of the fracture behaviour under critical conditions. To better understand failure characteristics of porcelain veneered to zirconia core ceramic structures, thermally induced cracking during the cooling phase of fabrication is studied here by using the extended finite element method (XFEM). In this study, a transient thermal analysis of cooling is conducted first to determine the temperature distributions. The time-dependent temperature field is then imported to the XFEM model for viscoelastic thermomechanical analysis, which predicts thermally induced damage and cracking at different time steps. Temperature-dependent material properties are used in both transient thermal and thermomechanical analyses. Three typical ceramic structures are considered in this paper, namely bi-layered spheres, squat cylinders and dental crowns with thickness ratios of either 1:2 or 1:1. The XFEM fracture patterns exhibit good agreement with clinical observation and the in vitro experimental results obtained from scanning electron microscopy characterization. The study reveals that fast cooling can lead to thermal fracture of these different bi-layered ceramic structures, and cooling rate (in terms of heat transfer coefficient) plays a critical role in crack initiation and propagation. By exploring different cooling rates, the heat transfer coefficient thresholds of fracture are determined for different structures, which are of clear clinical implication.

  11. Complex nanoprecipitate structures induced by irradiation in immiscible alloy systems

    NASA Astrophysics Data System (ADS)

    Shu, Shipeng; Bellon, P.; Averback, R. S.

    2013-04-01

    We investigate the fundamentals of compositional patterning induced by energetic particle irradiation in model A-B substitutional binary alloys using kinetic Monte Carlo simulations. The study focuses on a type of nanostructure that was recently observed in dilute Cu-Fe and Cu-V alloys, where precipitates form within precipitates, a morphology that we term “cherry-pit” structures. The simulations show that the domain of stability of these cherry-pit structures depends on the thermodynamic and kinetic asymmetry between the A and B elements. In particular, both lower solubilities and diffusivities of A in B compared to those of B in A favor the stabilization of these cherry-pit structures for A-rich average compositions. The simulation results are rationalized by extending the analytic model introduced by Frost and Russell for irradiation-induced compositional patterning so as to include the possible formation of pits within precipitates. The simulations indicate also that the pits are dynamical structures that undergo nearly periodic cycles of nucleation, growth, and absorption by the matrix.

  12. Insertion of primary syncytium-inducing (SI) and non-SI envelope V3 loops in human immunodeficiency virus type 1 (HIV-1) LAI reduces neutralization sensitivity to autologous, but not heterologous, HIV-1 antibodies.

    PubMed Central

    Hogervorst, E; de Jong, J; van Wijk, A; Bakker, M; Valk, M; Nara, P; Goudsmit, J

    1995-01-01

    The aim of the study was to investigate the influence of V3 loops from naturally occurring viruses on the neutralization sensitivity of a molecularly cloned virus. A selection of well-defined syncytium-inducing (SI) and non-SI V3 loops of a single human immunodeficiency virus type 1-infected individual (H594) and the V3 regions of two SI laboratory strains were inserted in an infectious molecular clone of human immunodeficiency type 1 LAI. Neutralization was performed with a heterologous serum pool and autologous patient serum, using the virus reduction neutralization assay and peripheral blood lymphocytes as target cells. High sensitivity of the chimeric viruses containing the laboratory strain V3 regions to neutralization by H594 sequential sera as well as the heterologous serum pool was found. A statistically significant correlation between the sensitivities of these viruses was seen. In contrast, insertion of the primary isolate NSI and SI envelope V3 loops significantly reduced the neutralization by autologous serum but not by the heterologous serum pool. No correlation was found between the neutralization of the viruses with laboratory strain-derived V3 regions and the viruses with primary isolate V3 domains. We conclude that heterologous antibodies are able to neutralize infectious molecular clones with V3 loops of both SI and NSI viruses, regardless of whether they originated from laboratory strains or primary isolates. However, serum of patient H594 discriminated between the two types of viruses and showed reduced neutralization of the viruses with the autologous NSI and SI primary isolate V3 loops. These results indicated that the neutralization sensitivity of the viruses depended on the capacity of the V3 region to influence the conformation of the virus envelope. These V3-dependent conformational changes partially explain the neutralization sensitivity of laboratory strains and the relative neutralization resistance of primary isolates. PMID:7666535

  13. Crystal structure of type I ryanodine receptor amino-terminal [beta]-trefoil domain reveals a disease-associated mutation 'hot spot' loop

    SciTech Connect

    Amador, Fernando J.; Liu, Shuang; Ishiyama, Noboru; Plevin, Michael J.; Wilson, Aaron; MacLennan, David H.; Ikura, Mitsuhiko

    2009-12-01

    Muscle contraction and relaxation is regulated by transient elevations of myoplasmic Ca{sup 2+}. Ca{sup 2+} is released from stores in the lumen of the sarco(endo)plasmic reticulum (SER) to initiate formation of the Ca{sup 2+} transient by activation of a class of Ca{sup 2+} release channels referred to as ryanodine receptors (RyRs) and is pumped back into the SER lumen by Ca{sup 2+}-ATPases (SERCAs) to terminate the Ca{sup 2+} transient. Mutations in the type 1 ryanodine receptor gene, RYR1, are associated with 2 skeletal muscle disorders, malignant hyperthermia (MH), and central core disease (CCD). The evaluation of proposed mechanisms by which RyR1 mutations cause MH and CCD is hindered by the lack of high-resolution structural information. Here, we report the crystal structure of the N-terminal 210 residues of RyR1 (RyR{sub NTD}) at 2.5 {angstrom}. The RyR{sub NTD} structure is similar to that of the suppressor domain of type 1 inositol 1,4,5-trisphosphate receptor (IP3Rsup), but lacks most of the long helix-turn-helix segment of the 'arm' domain in IP3Rsup. The N-terminal {beta}-trefoil fold, found in both RyR and IP{sub 3}R, is likely to play a critical role in regulatory mechanisms in this channel family. A disease-associated mutation 'hot spot' loop was identified between strands 8 and 9 in a highly basic region of RyR1. Biophysical studies showed that 3 MH-associated mutations (C36R, R164C, and R178C) do not adversely affect the global stability or fold of RyRNTD, supporting previously described mechanisms whereby mutations perturb protein-protein interactions.

  14. The function and structural influence of selective relaxed constraint at functional intracellular loop3 of 5-HT(1A) serotonin-1 receptor family.

    PubMed

    Dass, J Febin Prabhu; Sudandiradoss, C

    2012-10-25

    Serotonin (5-HT) and its receptors have been involved in critical signal transduction mechanism and deregulation implicated in mood-related disorders. 5-HT activities are mediated through a family of transmembrane spanning serotonin receptors. Both within the family and species, 5-HT receptor protein sequence diversity and 7-transmembrane structural homogeneity have long been intriguing. In this study, we have analyzed the codon site constraint in 5-HT1 subclass receptors from 13 orthologous mammalian mRNA coding sequence. Further, the study was extended to computationally investigate the impact of non-synonymous sites with respect to function and structural significance through sequence homology algorithm and molecular dynamics simulation (MDS). Codon sites with significant posterior probability were observed in 5-HT(1A), 5-HT(1B) and 5-HT(1D) receptor indicating variations in site constraint within the 5-HT1 sub-class genes. In 5-HT(1A) receptor, seven sites were detected at the functional intracellular loop(3) (ICL(3)) with higher substitution rate through Codeml program. Sequence homology algorithm identifies that these sites were functionally tolerant within the mammals representing a selectively relaxed constraint at this domain. On the other hand, the root mean square deviation (rmsd) values from MDS suggest differences in structural conformation of ICL(3) models among the species. Specifically, the human ICL(3) model fluctuation was comparatively more stable than other species. Hence, we argue that these sites may have varying influence in G-proteins coupling and activation of effectors systems through downstream interacting accessory proteins of cell among the species. However, further experimental studies are required to elucidate the precise role and the seeming difference of these sites in 5-HT receptors between species.

  15. Self-condensation of a thiazole-peptide bearing a 21-membered loop into a library of giant macrocycles with multiple orthogonal loops.

    PubMed

    Singh, Yogendra; Hoang, Huy N; Flanagan, Bernadine; Fairlie, David P

    2006-03-16

    [reaction: see text] Tetrapeptide analogue H-[Glu-Ser-Lys(Thz)]-OH, containing a turn-inducing thiazole constraint, was used as a template to produce a 21-membered structurally characterized loop by linking Glu and Lys side chains with a Val-Ile dipeptide. This template was oligomerized in one pot to a library (cyclo-[1](n)(), n = 2-10) of giant symmetrical macrocycles (up to 120-membered rings), fused to 2-10 appended loops that were carried intact through multiple oligomerization (chain extension) and cyclization (chain terminating) reactions of the template. A three-dimensional solution structure for cyclo-[1](3) shows all three appended loops projecting from the same face of the macrocycle. This is a promising approach to separating peptide motifs over large distances.

  16. Diabetes as a case study of chronic disease management with a personalized approach: the role of a structured feedback loop.

    PubMed

    Ceriello, Antonio; Barkai, László; Christiansen, Jens Sandahl; Czupryniak, Leszek; Gomis, Ramon; Harno, Kari; Kulzer, Bernhard; Ludvigsson, Johnny; Némethyová, Zuzana; Owens, David; Schnell, Oliver; Tankova, Tsvetalina; Taskinen, Marja-Riitta; Vergès, Bruno; Weitgasser, Raimund; Wens, Johan

    2012-10-01

    As non-communicable or chronic diseases are a growing threat to human health and economic growth, political stakeholders are aiming to identify options for improved response to the challenges of prevention and management of non-communicable diseases. This paper is intended to contribute ideas on personalized chronic disease management which are based on experience with one major chronic disease, namely diabetes mellitus. Diabetes provides a pertinent case of chronic disease management with a particular focus on patient self-management. Despite advances in diabetes therapy, many people with diabetes still fail to achieve treatment targets thus remaining at risk of complications. Personalizing the management of diabetes according to the patient's individual profile can help in improving therapy adherence and treatment outcomes. This paper suggests using a six-step cycle for personalized diabetes (self-)management and collaborative use of structured blood glucose data. E-health solutions can be used to improve process efficiencies and allow remote access. Decision support tools and algorithms can help doctors in making therapeutic decisions based on individual patient profiles. Available evidence about the effectiveness of the cycle's constituting elements justifies expectations that the diabetes management cycle as a whole can generate medical and economic benefit.

  17. Light-induced structural phase behaviour of metal nanoparticle materials

    NASA Astrophysics Data System (ADS)

    Plech, A.; Kotaidis, V.; Wulff, M.; Dahmen, C.; von Plessen, G.

    2005-01-01

    We have investigated the structural dynamics of gold nanoparticles induced by femtosecond light excitation. Structure evolution in both embedded particles (glass matrix or liquid water suspension) and quasi-free particles adsorbed on a solid surface is analyzed. By use of stroboscopic laser pump- x-ray probe techniques the structural relaxations have been resolved on the 100 ps time scale at the European Synchrotron Radiation Facility. Several methods including powder scattering, liquid scattering and small angle scattering serve to resolve microscopic and mesoscopic length scales of the composite system. The thermal response includes the heating, lattice melting, explosive solvent evaporation and solvent cooling subsequent to the laser flash excitation. Nonthermal effects are observed with femtosecond excitation. They are attributed to ablation from the particle and particle explosion at strong nonequilibrium conditions. The observations can form a complete picture of the energy dissipation and phase transitions involved in nanoscale composites.

  18. Sonic-boom-induced building structure responses including damage.

    NASA Technical Reports Server (NTRS)

    Clarkson, B. L.; Mayes, W. H.

    1972-01-01

    Concepts of sonic-boom pressure loading of building structures and the associated responses are reviewed, and results of pertinent theoretical and experimental research programs are summarized. The significance of sonic-boom load time histories, including waveshape effects, are illustrated with the aid of simple structural elements such as beams and plates. Also included are discussions of the significance of such other phenomena as three-dimensional loading effects, air cavity coupling, multimodal responses, and structural nonlinearities. Measured deflection, acceleration, and strain data from laboratory models and full-scale building tests are summarized, and these data are compared, where possible, with predicted values. Damage complaint and claim experience due both to controlled and uncontrolled supersonic flights over communities are summarized with particular reference to residential, commercial, and historic buildings. Sonic-boom-induced building responses are compared with those from other impulsive loadings due to natural and cultural events and from laboratory simulation tests.

  19. Identifying structures in clouds of induced microseismic events

    SciTech Connect

    Fehler, M.; House, L.; Phillips, W.S.

    1997-07-01

    A method for finding improved relative locations of microearthquakes accompanying fluid production and injection is presented. The method is based on the assumption that the microearthquake locations are more clustered than found when events are located using conventional techniques. By allowing the rms misfit between measured arrival times and predicted arrival times to increase if events move closer together, the authors find that there is more structure in the pattern of seismic locations. The method is demonstrated using a dataset of microearthquakes induced by hydraulic fracturing. The authors find that structures found using relative arrival times of events having similar waveforms to find improved relative locations of events can also be recovered using the new inversion method but without the laborious repicking procedure. The method provides improved relative locations and hence, an improved image of the structure within the seismic zone that may allow for a better relation between microearthquake locations and zones of increased fluid permeability to be found.

  20. Sheep-urine-induced changes in soil microbial community structure.

    PubMed

    Nunan, Naoise; Singh, Brajesh; Reid, Eileen; Ord, Brian; Papert, Artemis; Squires, Julie; Prosser, Jim I; Wheatley, Ron E; McNicol, Jim; Millard, Peter

    2006-05-01

    Soil microbial communities play an important role in nutrient cycling and nutrient availability, especially in unimproved soils. In grazed pastures, sheep urine causes local changes in nutrient concentration which may be a source of heterogeneity in microbial community structure. In the present study, we investigated the effects of synthetic urine on soil microbial community structure, using physiological (community level physiological profiling, CLPP), biochemical (phospholipid fatty acid analysis, PLFA) and molecular (denaturing gradient gel electrophoresis, DGGE) fingerprinting methods. PLFA data suggested that synthetic urine treatment had no significant effect on total microbial (total PLFA), total bacterial or fungal biomass; however, significant changes in microbial community structure were observed with both PLFA and DGGE data. PLFA data suggested that synthetic urine induced a shift towards communities with higher concentrations of branched fatty acids. DGGE banding patterns derived from control and treated soils differed, due to a higher proportion of DNA sequences migrating only to the upper regions of the gel in synthetic urine-treated samples. The shifts in community structure measured by PLFA and DGGE were significantly correlated with one another, suggesting that both datasets reflected the same changes in microbial communities. Synthetic urine treatment preferentially stimulated the use of rhizosphere-C in sole-carbon-source utilisation profiles. The changes caused by synthetic urine addition accounted for only 10-15% of the total variability in community structure, suggesting that overall microbial community structure was reasonably stable and that changes were confined to a small proportion of the communities.

  1. Mutational analysis of three predicted 5'-proximal stem-loop structures in the genome of tick-borne encephalitis virus indicates different roles in RNA replication and translation

    SciTech Connect

    Rouha, Harald; Hoenninger, Verena M.; Thurner, Caroline; Mandl, Christian W.

    2011-08-15

    Flavivirus gene expression is modulated by RNA secondary structure elements at the terminal ends of the viral RNA molecule. For tick-borne encephalitis virus (TBEV), four stem-loop (SL) elements have been predicted in the first 180 nucleotides of the viral genome: 5'-SL1, 5'-SL2, 5'-SL3 and 5'-SL4. The last three of these appear to be unique to tick-borne flaviviruses. Here, we report their characterization by mutagenesis in a TBEV luciferase reporter system. By manipulating their thermodynamic properties, we found that an optimal stability of the 5'-SL2 is required for efficient RNA replication. 5'-SL3 formation is also important for viral RNA replication, but although it contains the viral start codon, its formation is dispensable for RNA translation. 5'-SL4 appears to facilitate both RNA translation and replication. Our data suggest that maintenance of the balanced thermodynamic stability of these SL elements is important for temporal regulation of its different functions.

  2. Composition and temperature-induced structural evolution in La, Sm, and Dy substituted BiFeO3 epitaxial thin films at morphotropic phase boundaries

    NASA Astrophysics Data System (ADS)

    Kan, Daisuke; Cheng, Ching-Jung; Nagarajan, Valanoor; Takeuchi, Ichiro

    2011-07-01

    Detailed structural investigations on the substitution-induced structural phase transition from the rhombohedral phase to an orthorhombic phase in (Bi,RE)FeO3 epitaxial thin films (RE = La, Sm, and Dy) grown on (100) SrTiO3 substrates are presented. X ray diffraction reveals that the unit cell dimensions of the orthorhombic phase are strongly dependent on the type of the RE dopant. For RE = La3+ ion, which has an ionic size comparable to the Bi3+ ion, the unit cell is found to be a0 × a0 × 2a0, where a0 is the pseudo-cubic lattice parameter. This is in contrast with the √2a0 × √2a0 × 2a0 unit cell for the case of smaller ionic radius RE (= Sm and Dy) elements. While clear double-hysteresis loops in the polarization versus electric-field curves due to field-induced transitions are observed for smaller ionic radius RE (= Sm and Dy), no signature of the double hysteresis loops is observed for the RE = La case across the structural boundary. We have also performed systematic tracking of the structural phases as functions of the RE composition and temperature, based on which we propose a phase diagram. This work reveals that the ionic size of the RE element plays a critical role in the evolution of the structural and functional properties of RE-substituted BiFeO3 thin film materials systems.

  3. Induced radioactivity of LDEF materials and structural components

    NASA Technical Reports Server (NTRS)

    Harmon, B. A.; Laird, C. E.; Fishman, G. J.; Parnell, T. A.; Camp, D. C.; Frederick, C. E.; Hurley, D. L.; Lindstrom, D. J.; Moss, C. E.; Reedy, R. C.; Reeves, J. H.; Smith, A. R.; Winn, W. G.; Benton, E. V.

    1996-01-01

    We present an overview of the Long Duration Exposure Facility (LDEF) induced activation measurements. The LDEF, which was gravity-gradient stabilized, was exposed to the low Earth orbit (LEO) radiation environment over a 5.8 year period. Retrieved activation samples and structural components from the spacecraft were analyzed with low and ultra-low background HPGe gamma spectrometry at several national facilities. This allowed a very sensitive measurement of long-lived radionuclides produced by proton- and neutron-induced reactions in the time-dependent, non-isotropic LEO environment. A summary of major findings from this study is given that consists of directionally dependent activation, depth profiles, thermal neutron activation, and surface beryllium-7 deposition from the upper atmosphere. We also describe a database of these measurements that has been prepared for use in testing radiation environmental models and spacecraft design.

  4. Double hysteresis loop induced by defect dipoles in ferroelectric Pb(Zr{sub 0.8}Ti{sub 0.2})O{sub 3} thin films

    SciTech Connect

    Pu Yunti; Zhu Jiliang; Zhu Xiaohong; Luo Yuansheng; Wang Mingsong; Li Xuhai; Liu Jing; Zhu Jianguo; Xiao Dingquan

    2011-02-15

    Pb(Zr{sub 0.8}Ti{sub 0.2})O{sub 3} (PZT80/20) thin films were deposited on the Pt(111)/Ti/SiO{sub 2}/Si(100) substrates by RF magnetron sputtering. Mainly perovskite crystalline phase with highly (202)-preferred orientation, determined by x-ray diffraction, was formed in the lead zirconate titanate (PZT)(80/20) thin films. Polarization measurements of the unannealed and aged films showed a clear double hysteresis loop. However, the double hysteresis loop phenomenon was greatly suppressed in the PZT thin films annealed under pure oxygen, and thus they exhibited larger remnant polarization (P{sub r} = 6.3 {mu}C/cm{sup 2}). The related mechanism for the appearance of constricted and double hysteresis loops was investigated to be associated with the realignment and disassociation of defect dipoles via oxygen octahedral rotations or oxygen vacancy diffusion. The butterfly-shaped C-V characteristic curve with a valley gave further evidence for double hysteresis loop characteristic in the unannealed and aged PZT thin films.

  5. Drosophila melanogaster kl-3 and kl-5 Y-loops harbor triple-stranded nucleic acids.

    PubMed

    Piergentili, Roberto; Mencarelli, Caterina

    2008-05-15

    Primary spermatocyte nuclei of Drosophila melanogaster contain three prominent lampbrush-like loops. The development of these structures has been associated with the transcription of three fertility factors located on the Y chromosome, named kl-5, kl-3 and ks-1. These loci have huge physical dimensions and contain extremely long introns. In addition, kl-3 and kl-5 were shown to encode two putative dynein subunits required for the correct assembly of the sperm axoneme. Here, we show that both the kl-5 and kl-3 loops are intensely decorated by monoclonal antibodies recognizing triple-stranded nucleic acids, and that each loop presents a peculiar molecular organization of triplex structures. Moreover, immunostaining of Drosophila hydei primary spermatocytes revealed that also in this species - which diverged from D. melanogaster 58 million years ago - Y-loops are decorated by anti-triplex antibodies, strongly suggesting a conserved role of loop-associated triplexes. Finally, we showed that in D. melanogaster wild-type lines that are raised at the non-permissive temperature of 31+/-0.5 degrees C (which is known to induce male sterility in flies) both the triplex immunostaining and the axonemal dynein heavy chains encoded by kl-3 and kl-5 are no longer detectable, which suggests a functional correlation between loop-associated triplexes, the presence of axonemal proteins and male fertility in fly.

  6. Structural Anisotropy and Orientation-Induced Casimir Repulsion in Fluids

    DTIC Science & Technology

    2011-05-10

    Physics , Lecture Notes in Physics , edited by D. A. R. Dalvit, P. W. Milonni, D. C. Roberts, and F. S. S. Rosa (Springer, New York) (in press). [53] A... PHYSICAL REVIEW A 83, 052503 (2011) Structural anisotropy and orientation-induced Casimir repulsion in fluids Alexander P. McCauley,1 F. S. S. Rosa...2,3 Alejandro W. Rodriguez,4,5 John D. Joannopoulos,1 D. A. R. Dalvit,3 and Steven G. Johnson4 1Department of Physics , Massachusetts Institute of

  7. Light-induced metastable structural changes in hydrogenated amorphous silicon

    SciTech Connect

    Fritzsche, H.

    1996-09-01

    Light-induced defects (LID) in hydrogenated amorphous silicon (a-Si:H) and its alloys limit the ultimate efficiency of solar panels made with these materials. This paper reviews a variety of attempts to find the origin of and to eliminate the processes that give rise to LIDs. These attempts include novel deposition processes and the reduction of impurities. Material improvements achieved over the past decade are associated more with the material`s microstructure than with eliminating LIDs. We conclude that metastable LIDs are a natural by-product of structural changes which are generally associated with non-radiative electron-hole recombination in amorphous semiconductors.

  8. Structures of a bi-functional Kunitz-type STI family inhibitor of serine and aspartic proteases: Could the aspartic protease inhibition have evolved from a canonical serine protease-binding loop?

    PubMed

    Guerra, Yasel; Valiente, Pedro A; Pons, Tirso; Berry, Colin; Rudiño-Piñera, Enrique

    2016-08-01

    Bi-functional inhibitors from the Kunitz-type soybean trypsin inhibitor (STI) family are glycosylated proteins able to inhibit serine and aspartic proteases. Here we report six crystal structures of the wild-type and a non-glycosylated mutant of the bifunctional inhibitor E3Ad obtained at different pH values and space groups. The crystal structures show that E3Ad adopts the typical β-trefoil fold of the STI family exhibiting some conformational changes due to pH variations and crystal packing. Despite the high sequence identity with a recently reported potato cathepsin D inhibitor (PDI), three-dimensional structures obtained in this work show a significant conformational change in the protease-binding loop proposed for aspartic protease inhibition. The E3Ad binding loop for serine protease inhibition is also proposed, based on structural similarity with a novel non-canonical conformation described for the double-headed inhibitor API-A from the Kunitz-type STI family. In addition, structural and sequence analyses suggest that bifunctional inhibitors of serine and aspartic proteases from the Kunitz-type STI family are more similar to double-headed inhibitor API-A than other inhibitors with a canonical protease-binding loop.

  9. Conserved stem-loop structures in the HIV-1 RNA region containing the A3 3' splice site and its cis-regulatory element: possible involvement in RNA splicing.

    PubMed

    Jacquenet, S; Ropers, D; Bilodeau, P S; Damier, L; Mougin, A; Stoltzfus, C M; Branlant, C

    2001-01-15

    The HIV-1 transcript is alternatively spliced to over 30 different mRNAs. Whether RNA secondary structure can influence HIV-1 RNA alternative splicing has not previously been examined. Here we have determined the secondary structure of the HIV-1/BRU RNA segment, containing the alternative A3, A4a, A4b, A4c and A5 3' splice sites. Site A3, required for tat mRNA production, is contained in the terminal loop of a stem-loop structure (SLS2), which is highly conserved in HIV-1 and related SIVcpz strains. The exon splicing silencer (ESS2) acting on site A3 is located in a long irregular stem-loop structure (SLS3). Two SLS3 domains were protected by nuclear components under splicing condition assays. One contains the A4c branch points and a putative SR protein binding site. The other one is adjacent to ESS2. Unexpectedly, only the 3' A residue of ESS2 was protected. The suboptimal A3 polypyrimidine tract (PPT) is base paired. Using site-directed mutagenesis and transfection of a mini-HIV-1 cDNA into HeLa cells, we found that, in a wild-type PPT context, a mutation of the A3 downstream sequence that reinforced SLS2 stability decreased site A3 utilization. This was not the case with an optimized PPT. Hence, sequence and secondary structure of the PPT may cooperate in limiting site A3 utilization.

  10. Dirac Loops in Carbon Allotropes

    NASA Astrophysics Data System (ADS)

    Mullen, Kieran; Uchoa, Bruno; Glatzhofer, D.

    2015-03-01

    We propose a family of structures that have ``Dirac loops'': closed lines in momentum space with Dirac-like quasiparticles, on which the density of states vanishes linearly with energy. The structures all possess the planar trigonal connectivity present in graphene, but are three dimensional. We discuss the consequences of their multiply-connected Fermi surface for transport, including the presence of three dimensional Integer Quantum Hall effect. In the presence of spin-orbit coupling, we show that those structures may have topological surface states. We discuss the feasibility of realizing the structures as an allotrope of carbon. Work supported by NSF Grants DMR-1310407 and DMR-1352604.

  11. Irradiation induced structural change in Mo2Zr intermetallic phase

    DOE PAGES

    Gan, J.; Keiser, Jr., D. D.; Miller, B. D.; ...

    2016-05-14

    The Mo2Zr phase has been identified as a major interaction product at the interface of U-10Mo and Zr. Transmission electron microscopy in-situ irradiation with Kr ions at 200 °C with doses up to 2.0E+16 ions/cm2 was carried out to investigate the radiation stability of the Mo2Zr. The Mo2Zr undergoes a radiation-induced structural change, from a large cubic (cF24) to a small cubic (cI2), along with an estimated 11.2% volume contraction without changing its composition. The structural change begins at irradiation dose below 1.0E+14 ions/cm2. Furthermore, the transformed Mo2Zr phase demonstrates exceptional radiation tolerance with the development of dislocations without bubblemore » formation.« less

  12. Collision induced ultraviolet structure in nitrogen radar REMPI spectra

    SciTech Connect

    McGuire, S. Miles, R.

    2014-12-28

    We present 2 + 2 radar REMPI measurements in molecular nitrogen under atmospheric conditions and observe a strong interference in the (1,0) vibrational band of the a{sup 1}Π{sub g} ← X{sup 1}Σ{sub g}{sup +} electronic manifold. The interference is suppressed by using circularly polarized light, permitting rotational analysis of the 2 + 2 radar REMPI spectrum. It is observed in pure nitrogen, though the structure varies with gas composition. The structure also varies with temperature and pressure. These results indicate that it is collision induced. We hypothesize that the source of the interference is a 3 + 1 REMPI process through the a{sup ″1}Σ{sub g}{sup +} electronic state.

  13. Field-induced structure of confined ferrofluid emulsion

    SciTech Connect

    Lawrence, E.M.; Ivey, M.L.; Flores, G.A.; Liu, J. . Dept. of Physics and Astronomy); Bibette, J. ); Richard, J. )

    1994-09-01

    Field-induced phase behavior of a confined monodisperse ferrofluid emulsion was studied using optical microscopy, light transmission, and static light scattering techniques. Upon application of magnetic field, randomly-dispersed magnetic emulsion droplets form solid structures at [lambda] = 1.5, where [lambda] is defines as the ratio of the dipole-dipole interaction energy to the thermal energy at room temperature. The new solid phase consists of either single droplet chains, columns, or worm-like clusters, depending on the volume fraction, cell thickness and rate of field application. For the column phase, an equilibrium structure of equally-sized and spaced columns was observed. The measurements taken for cell thickness 5[mu]m [<=] L [<=] 500 [mu]m and volume fraction 0.04 show the column spacing to be reasonably described by d = 1.49 L[sup 0.34].

  14. Understanding Gas-Induced Structural Deformation of ZIF-8.

    PubMed

    Ania, Conchi O; García-Pérez, E; Haro, M; Gutiérrez-Sevillano, J J; Valdés-Solís, T; Parra, J B; Calero, S

    2012-05-03

    ZIF-8 is a zeolitic imidazolate framework with very good thermal and chemical stability that opens up many applications that are not feasible by other metal-organic frameowrks (MOFs) and zeolites. Several works report the adsorption properties of ZIF-8 for strategic gases. However, despite the vast experimental corpus of data reported, there seems yet to be a dearth in the understanding of the gas adsorption properties. In this work we provide insights at a molecular level on the mechanisms governing the ZIF-8 structural deformation during molecular adsorption. We demonstrate that the ZIF-8 structural deformation during the adsorption of different molecules at cryogenic temperature goes beyond the gas-induced rotation of the imidazolate linkers. We combine experimental and simulation studies to demonstrate that this deformation is governed by the polarizability and molecular size and shape of the gases, and that the stepped adsorption behavior is defined by the packing arrangement of the guest inside the host.

  15. Sulfur-induced structural motifs on copper and gold surfaces

    SciTech Connect

    Walen, Holly

    2016-01-01

    The interaction of sulfur with copper and gold surfaces plays a fundamental role in important phenomena that include coarsening of surface nanostructures, and self-assembly of alkanethiols. Here, we identify and analyze unique sulfur-induced structural motifs observed on the low-index surfaces of these two metals. We seek out these structures in an effort to better understand the fundamental interactions between these metals and sulfur that lends to the stability and favorability of metal-sulfur complexes vs. chemisorbed atomic sulfur. The experimental observations presented here—made under identical conditions—together with extensive DFT analyses, allow comparisons and insights into factors that favor the existence of metal-sulfur complexes, vs. chemisorbed atomic sulfur, on metal terraces. We believe this data will be instrumental in better understanding the complex phenomena occurring between the surfaces of coinage metals and sulfur.

  16. Congestion Induced by the Structure of Multiplex Networks

    NASA Astrophysics Data System (ADS)

    Solé-Ribalta, Albert; Gómez, Sergio; Arenas, Alex

    2016-03-01

    Multiplex networks are representations of multilayer interconnected complex networks where the nodes are the same at every layer. They turn out to be good abstractions of the intricate connectivity of multimodal transportation networks, among other types of complex systems. One of the most important critical phenomena arising in such networks is the emergence of congestion in transportation flows. Here, we prove analytically that the structure of multiplex networks can induce congestion for flows that otherwise would be decongested if the individual layers were not interconnected. We provide explicit equations for the onset of congestion and approximations that allow us to compute this onset from individual descriptors of the individual layers. The observed cooperative phenomenon is reminiscent of Braess' paradox in which adding extra capacity to a network when the moving entities selfishly choose their route can in some cases reduce overall performance. Similarly, in the multiplex structure, the efficiency in transportation can unbalance the transportation loads resulting in unexpected congestion.

  17. The RPB2 Flap Loop of Human RNA Polymerase II Is Dispensable for Transcription Initiation and Elongation▿†

    PubMed Central

    Palangat, Murali; Grass, Jeffrey A.; Langelier, Marie-France; Coulombe, Benoit; Landick, Robert

    2011-01-01

    The flap domain of multisubunit RNA polymerases (RNAPs), also called the wall, forms one side of the RNA exit channel. In bacterial RNAP, the mobile part of the flap is called the flap tip and makes essential contacts with initiation and elongation factors. Cocrystal structures suggest that the orthologous part of eukaryotic RNAPII, called the flap loop, contacts transcription factor IIB (TFIIB), but the function of the flap loop has not been assessed. We constructed and tested a deletion of the flap loop in human RNAPII (subunit RPB2 Δ873-884) that removes the flap loop interaction interface with TFIIB. Genome-wide analysis of the distribution of the RNAPII with the flap loop deletion expressed in a human embryonic kidney cell line (HEK 293) revealed no effect of the flap loop on global transcription initiation, RNAPII occupancy within genes, or the efficiency of promoter escape and productive elongation. In vitro, the flap loop deletion had no effect on promoter binding, abortive initiation or promoter escape, TFIIS-stimulated transcript cleavage, or inhibition of transcript elongation by the complex of negative elongation factor (NELF) and 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole (DRB) sensitivity-inducing factor (DSIF). A modest effect on transcript elongation and pausing was suppressed by TFIIF. Although similar to the flap tip of bacterial RNAP, the RNAPII flap loop is not equivalently essential. PMID:21670157

  18. Detecting neutrino magnetic moments with conducting loops

    NASA Astrophysics Data System (ADS)

    Apyan, Aram; Apyan, Armen; Schmitt, Michael

    2008-02-01

    It is well established that neutrinos have mass, yet it is very difficult to measure those masses directly. Within the standard model of particle physics, neutrinos will have an intrinsic magnetic moment proportional to their mass. We examine the possibility of detecting the magnetic moment using a conducting loop. According to Faraday’s law of induction, a magnetic dipole passing through a conducting loop induces an electromotive force in the loop. We compute this electromotive force for neutrinos in several cases, based on a fully covariant formulation of the problem. We discuss prospects for a real experiment, as well as the possibility to test the relativistic formulation of intrinsic magnetic moments.

  19. Implantation-induced structural and surface modification of silica

    NASA Astrophysics Data System (ADS)

    Johnson, C. M.; Thompson, T. D.; Ridgway, M. C.; Gurarie, V.

    1998-05-01

    Ion irradiation of silica causes compaction of the substrate over the extent of the ion range and the resulting increase in refractive index has applications to optical waveguide fabrication. Several analytical techniques have been utilized to characterize implantation-induced structural and surface modifications of silica with the aim of yielding further insight into this technologically relevant process. Substrates of both fused silica and plasma-enhanced chemical vapor deposited silica-on-Si were implanted with C, Si or Ge ions at an energy of 5 MeV and a temperature of -196°C over a range of ion fluences. Compaction of the substrate was characterized as a function of ion dose with both standard profilometry and extended X-ray absorption fine structure (EXAFS). With the former, the extent of compaction was dependent on the silica density with a saturation of the compaction for all substrates at an ion fluence of ˜10 15/cm 2. With EXAFS, complementary information on implantation-induced effects at the atomic scale were determined to differentiate the influences of bond length and bond angle changes in the compaction process. No changes in nearest-neighbour bond length were observed following compaction. The condition of the substrate surface during ion implantation was recorded by in situ photography. Cracking of the surface, as a means of stress relief, was observed and thereafter, the evolution of the cracked surface was quantitatively characterized as a function of ion fluence.

  20. Structural and functional changes in human insulin induced by methylglyoxal.

    PubMed

    Jia, Xuming; Olson, Douglas J H; Ross, Andrew R S; Wu, Lingyun

    2006-07-01

    Elevated methylglyoxal (MG) levels have been reported in insulin-resistance syndrome. The present study investigated whether MG, a highly reactive metabolite of glucose, induced structural and functional changes of insulin. Incubation of human insulin with MG in vitro yielded MG-insulin adducts, as evidenced by additional peaks observed on mass spectrometric (MS) analysis of the incubates. Tandem MS analysis of insulin B-chain adducts confirmed attachment of MG at an arginine residue. [3H]-2-deoxyglucose uptake by 3T3-L1 adipocytes was significantly and concentration-dependently decreased after the treatment with MG-insulin adducts, in comparison with the effect of native insulin at the same concentrations. A significant decrease of glucose uptake induced by MG-insulin adducts was also observed in L8 skeletal muscle cells. MG alone had no effect on glucose uptake or the transcriptional expression of insulin receptor. Unlike native insulin, MG-insulin adducts did not inhibit insulin release from pancreatic beta-cells. The degradation of MG-insulin through liver cells was also decreased. In conclusion, MG modifies insulin by attaching to internal arginine residue in beta-chain of insulin. The formation of this MG-insulin adduct decreases insulin-mediated glucose uptake, impairs autocrine control of insulin secretion, and decreases insulin clearance. These structural and functional abnormalities of insulin molecule may contribute to the pathogenesis of insulin resistance.

  1. Mechanically Induced Intercellular Calcium Communication in Confined Endothelial Structures

    PubMed Central

    Junkin, Michael; Lu, Yi; Long, Juexuan; Deymier, Pierre A.; Hoying, James B.; Wong, Pak Kin

    2012-01-01

    Calcium signaling in the diverse vascular structures is regulated by a wide range of mechanical and biochemical factors to maintain essential physiological functions of the vasculature. To properly transmit information, the intercellular calcium communication mechanism must be robust against various conditions in the cellular microenvironment. Using plasma lithography geometric confinement, we investigate mechanically induced calcium wave propagation in networks of human umbilical vein endothelial cells organized. Endothelial cell networks with confined architectures were stimulated at the single cell level, including using capacitive force probes. Calcium wave propagation in the network was observed using fluorescence calcium imaging. We show that mechanically induced calcium signaling in the endothelial networks is dynamically regulated against a wide range of probing forces and repeated stimulations. The calcium wave is able to propagate consistently in various dimensions from monolayers to individual cell chains, and in different topologies from linear patterns to cell junctions. Our results reveal that calcium signaling provides a robust mechanism for cell-cell communication in networks of endothelial cells despite the diversity of the microenvironmental inputs and complexity of vascular structures. PMID:23267827

  2. Light Localization by Defects in Optically Induced Photonic Structures

    NASA Astrophysics Data System (ADS)

    Yang, Jianke; Wang, Xiaosheng; Wang, Jiandong; Chen, Zhigang

    In the past ten years, there has blossomed an interest in the study of collective behavior of wave propagation in periodic waveguide arrays and photonic lattices [1-3]. The unique bandgap structures of these periodic media, coupled with nonlinear effects, give rise to many types of novel soliton structures [1- 26]. On the other hand, it is well known that one of the unique and most interesting features of photonic band-gap structures is a fundamentally different way of waveguiding by defects in otherwise uniformly periodic structures. Such waveguiding has been demonstrated with an "air-hole" in photonic crystal fibers (PCF) for optical waves [27, 28], in an isolated defect in two-dimensional arrays of dielectric cylinders for microwaves [29-31], and recently in all-solid PCF with a lower-index core [32, 33]. In addition, laser emission based on photonic defect modes has been realized in a number of experiments [34-38]. In one-dimensional (1D) fabricated semiconductor waveguide arrays, previous experiments have investigated nonlinearity-induced escape from a defect state [39] and interactions of discrete solitons with structural defects [40] (see also [41]). Despite the above efforts, theoretical understanding on defect guiding was still limited, and experimental demonstrations of defect guiding was still scarce. In addition, when nonlinear effects are significant, how defect guiding is affected by nonlinearity is largely an open issue. Recently, in a series of theoretical and experimental studies, we optically induced 1D, 2D and ringlike photonic lattices with single-site negative defects in photorefractive crystals, and investigated their linear and nonlinear light guiding properties [42-48]. This work will be reviewed in this Chapter. In addition, we present the first experimental demonstration of nonlinear defect modes which undergoes nonlinear propagation through the defects. Our work not only has a direct link to technologically important systems of periodic

  3. Origin of the constricted hysteresis loop in cobalt ferrites revisited

    NASA Astrophysics Data System (ADS)

    Zhang, Hong-guo; Zhang, Yu-Jie; Wang, Weng-Hong; Wu, Guang-Heng

    2011-08-01

    A series of Co ferrites (Co xFe 3- xO 4 ( x=0-1)) were prepared using solid-state method in this work. The aging effect of their structures and constrictions of hysteresis loops under low magnetic field were investigated. It was found that during the aging process, the migration of trivalent (bivalent) ions between tetrahedral (A-site) and octahedral (B-site) coordination induced a shrinking of the lattice, which would expand again due to the precipitation of Fe 3+ after a much longer aging time. The first process caused a pronounced constriction of the loops, due to the uniaxial anisotropy led by this migration. The depression of constriction could attribute to both the expansion of lattice and the change of ionic ratios as a result of the second-phase-precipitation. The impacts of Co content, aging time and temperature upon the constriction were also discussed.

  4. REVIEWS OF TOPICAL PROBLEMS: Coronal magnetic loops

    NASA Astrophysics Data System (ADS)

    Zaitsev, Valerii V.; Stepanov, Alexander V.

    2008-11-01

    The goal of this review is to outline some new ideas in the physics of coronal magnetic loops, the fundamental structural elements of the atmospheres of the Sun and flaring stars, which are involved in phenomena such as stellar coronal heating, flare energy release, charged particle acceleration, and the modulation of optical, radio, and X-ray emissions. The Alfvén-Carlqvist view of a coronal loop as an equivalent electric circuit allows a good physical understanding of loop processes. Describing coronal loops as MHD-resonators explains various ways in which flaring emissions from the Sun and stars are modulated, whereas modeling them by magnetic mirror traps allows one to describe the dynamics and emission of high-energy particles. Based on these approaches, loop plasma and fast particle parameters are obtained and models for flare energy release and stellar corona heating are developed.

  5. Dihedral-like constructions of automorphic loops

    NASA Astrophysics Data System (ADS)

    Aboras, Mouna

    In this dissertation we study dihedral-like constructions of automorphic loops. Automorphic loops are loops in which all inner mappings are automorphisms. We start by describing a generalization of the dihedral construction for groups. Namely, if (G, +) is an abelian group, m > 1 and alpha ∈2 Aut(G), let Dih(m, G, alpha) on Zm x G be defined by. (i, u)(j, v) = (i + j, ((--1)ju + v)alpha ij). We prove that the resulting loop is automorphic if and only if m = 2 or (alpha2 = 1 and m is even) or (m is odd, alpha = 1 and exp(G) ≤ 2). In the last case, the loop is a group. The case m = 2 was introduced by Kinyon, Kunen, Phillips, and Vojtechovsky. We study basic structural properties of dihedral-like automorphic loops. We describe certain subloops, including: nucleus, commutant, center, associator subloop and derived subloop. We prove theorems for dihedral-like automorphic loops analogous to the Cauchy and Lagrange theorems for groups, and further we discuss the coset decomposition in dihedral-like automorphic loops. We show that two finite dihedral-like automorphic loops Dih( m, G, alpha) and Dih(m¯, G¯, [special character omitted]) are isomorphic if and only if m = m¯, G ≅ G¯ and alpha is conjugate to [special character omitted] in Aut(G). We describe the automorphism group of Q and its subgroup consisting of inner mappings of Q. Finally, due to the solution to the isomorphism problem, we are interested in studying conjugacy classes of automorphism groups of finite abelian groups. Then we describe all dihedral-like automorphic loops of order < 128 up to isomorphism. We conclude with a description of all dihedral-like automorphic loops of order < 64 up to isotopism.

  6. Structural coloration of metallic surfaces with micro/nano-structures induced by elliptical vibration texturing

    NASA Astrophysics Data System (ADS)

    Yang, Yang; Pan, Yayue; Guo, Ping

    2017-04-01

    Creating orderly periodic micro/nano-structures on metallic surfaces, or structural coloration, for control of surface apparent color and optical reflectivity has been an exciting research topic over the years. The direct applications of structural coloration include color marking, display devices, and invisibility cloak. This paper presents an efficient method to colorize metallic surfaces with periodic micro/nano-gratings using elliptical vibration texturing. When the tool vibration is coupled with a constant cutting velocity, controlled periodic ripples can be generated due to the overlapping tool trajectory. These periodic ripples with a wavelength near visible spectrum can act as micro-gratings to introduce iridescent colors. The proposed technique also provides a flexible method for color marking of metallic surfaces with arbitrary patterns and images by precise control of the spacing distance and orientation of induced micro/nano-ripples. Theoretical analysis and experimental results are given to demonstrate structural coloration of metals by a direct mechanical machining technique.

  7. Detection of radiation-induced changes in electrochemical properties of austenitic stainless steels using miniaturized specimens and the single-loop electrochemical potentiokinetic reactivation method

    SciTech Connect

    Inazumi, T.; Bell, G.E.C.; Kenik, E.A.; Kiuchi, K.

    1993-01-01

    Single-loop electrochemical potentiokinetic reactivation testing of miniaturized (TEM) specimens can provide reliable data comparable to data obtained with larger specimens. Significant changes in electrochemical properties (increased reactivation current and Flade potential) were detected for PCA and type 316 stainless steels irradiated at 200--420[degrees]C up to 7--9 dpa. Irradiations in the FFTF Materials Open Test Assembly and in the Oak Ridge Research Reactor are reported on. 45 figs., 5 tabs., 52 refs.

  8. Detection of radiation-induced changes in electrochemical properties of austenitic stainless steels using miniaturized specimens and the single-loop electrochemical potentiokinetic reactivation method

    SciTech Connect

    Inazumi, T.; Bell, G.E.C.; Kenik, E.A.; Kiuchi, K.

    1993-01-01

    Single-loop electrochemical potentiokinetic reactivation testing of miniaturized (TEM) specimens can provide reliable data comparable to data obtained with larger specimens. Significant changes in electrochemical properties (increased reactivation current and Flade potential) were detected for PCA and type 316 stainless steels irradiated at 200--420{degrees}C up to 7--9 dpa. Irradiations in the FFTF Materials Open Test Assembly and in the Oak Ridge Research Reactor are reported on. 45 figs., 5 tabs., 52 refs.

  9. Extending two Higgs doublet models for two-loop neutrino mass generation and one-loop neutrinoless double beta decay

    NASA Astrophysics Data System (ADS)

    Liu, Zhen; Gu, Pei-Hong

    2017-02-01

    We extend some two Higgs doublet models, where the Yukawa couplings for the charged fermion mass generation only involve one Higgs doublet, by two singlet scalars respectively carrying a singly electric charge and a doubly electric charge. The doublet and singlet scalars together can mediate a two-loop diagram to generate a tiny Majorana mass matrix of the standard model neutrinos. Remarkably, the structure of the neutrino mass matrix is fully determined by the symmetric Yukawa couplings of the doubly charged scalar to the right-handed leptons. Meanwhile, a one-loop induced neutrinoless double beta decay can arrive at a testable level even if the electron neutrino has an extremely small Majorana mass. We also study other experimental constraints and implications including some rare processes and Higgs phenomenology.

  10. Structural brain plasticity in Parkinson's disease induced by balance training.

    PubMed

    Sehm, Bernhard; Taubert, Marco; Conde, Virginia; Weise, David; Classen, Joseph; Dukart, Juergen; Draganski, Bogdan; Villringer, Arno; Ragert, Patrick

    2014-01-01

    We investigated morphometric brain changes in patients with Parkinson's disease (PD) that are associated with balance training. A total of 20 patients and 16 healthy matched controls learned a balance task over a period of 6 weeks. Balance testing and structural magnetic resonance imaging were performed before and after 2, 4, and 6 training weeks. Balance performance was re-evaluated after ∼20 months. Balance training resulted in performance improvements in both groups. Voxel-based morphometry revealed learning-dependent gray matter changes in the left hippocampus in healthy controls. In PD patients, performance improvements were correlated with gray matter changes in the right anterior precuneus, left inferior parietal cortex, left ventral premotor cortex, bilateral anterior cingulate cortex, and left middle temporal gyrus. Furthermore, a TIME × GROUP interaction analysis revealed time-dependent gray matter changes in the right cerebellum. Our results highlight training-induced balance improvements in PD patients that may be associated with specific patterns of structural brain plasticity. In summary, we provide novel evidence for the capacity of the human brain to undergo learning-related structural plasticity even in a pathophysiological disease state such as in PD.

  11. Laser-induced periodic surface structures, modeling, experiments, and applications

    NASA Astrophysics Data System (ADS)

    Römer, G. R. B. E.; Skolski, J. Z. P.; Oboňa, J. Vincenc; Ocelík, V.; de Hosson, J. T. M.; Huis in't Veld, A. J.

    2014-03-01

    Laser-induced periodic surface structures (LIPSSs) consist of regular wavy surface structures, or ripples, with amplitudes and periodicity in the sub-micrometer range. A summary of experimentally observed LIPSSs is presented, as well as our model explaining their possible origin. Linearly polarized continuous wave (cw) or pulsed laser light, at normal incidence, can produce LIPSSs with a periodicity close to the laser wavelength, and direction orthogonal to the polarization on the surface of the material. Ripples with a periodicity (much) smaller than the laser wavelength develop when applying laser pulses with ultra-short durations in the femtosecond and picosecond regime. The direction of these ripples is either parallel or orthogonal to the polarization direction. Finally, when applying numerous pulses, structures with periodicity larger than the laser wavelength can form, which are referred to as "grooves". The physical origin of LIPSSs is still under debate. The strong correlation of the ripple periodicity to the laser wavelength, suggests that their formation can be explained by an electromagnetic approach. Recent results from a numerical electromagnetic model, predicting the spatially modulated absorbed laser energy, are discussed. This model can explain the origin of several characteristics of LIPSSs. Finally, applications of LIPSSs will be discussed.

  12. Platinum-induced structural collapse in layered oxide polycrystalline films

    SciTech Connect

    Wang, Jianlin; Liu, Changhui; Huang, Haoliang; Fu, Zhengping; Peng, Ranran E-mail: yllu@ustc.edu.cn; Zhai, Xiaofang; Lu, Yalin E-mail: yllu@ustc.edu.cn

    2015-03-30

    Effect of a platinum bottom electrode on the SrBi{sub 5}Fe{sub 1−x}Co{sub x}Ti{sub 4}O{sub 18} layered oxide polycrystalline films was systematically studied. The doped cobalt ions react with the platinum to form a secondary phase of PtCoO{sub 2}, which has a typical Delafossite structure with a weak antiferromagnetism and an exceptionally high in-plane electrical conductivity. Formation of PtCoO{sub 2} at the interface partially consumes the cobalt dopant and leads to the structural collapsing from 5 to 4 layers, which was confirmed by X-ray diffraction and high resolution transmission electron microscopy measurements. Considering the weak magnetic contribution from PtCoO{sub 2}, the observed ferromagnetism should be intrinsic of the Aurivillius compounds. Ferroelectric properties were also indicated by the piezoresponse force microscopy. In this work, the platinum induced secondary phase at the interface was observed, which has a strong impact on Aurivillius structural configuration and thus the ferromagnetic and ferroelectric properties.

  13. Structural Basis for Inhibitor-Induced Aggregation of HIV Integrase

    PubMed Central

    Sherrill-Mix, Scott; Hwang, Young; Eilers, Grant; McDanal, Charlene; Wang, Ping; Temelkoff, David

    2016-01-01

    The allosteric inhibitors of integrase (termed ALLINIs) interfere with HIV replication by binding to the viral-encoded integrase (IN) protein. Surprisingly, ALLINIs interfere not with DNA integration but with viral particle assembly late during HIV replication. To investigate the ALLINI inhibitory mechanism, we crystallized full-length HIV-1 IN bound to the ALLINI GSK1264 and determined the structure of the complex at 4.4 Å resolution. The structure shows GSK1264 buried between the IN C-terminal domain (CTD) and the catalytic core domain. In the crystal lattice, the interacting domains are contributed by two different dimers so that IN forms an open polymer mediated by inhibitor-bridged contacts; the N-terminal domains do not participate and are structurally disordered. Engineered amino acid substitutions at the inhibitor interface blocked ALLINI-induced multimerization. HIV escape mutants with reduced sensitivity to ALLINIs commonly altered amino acids at or near the inhibitor-bound interface, and these substitutions also diminished IN multimerization. We propose that ALLINIs inhibit particle assembly by stimulating inappropriate polymerization of IN via interactions between the catalytic core domain and the CTD and that understanding the interface involved offers new routes to inhibitor optimization. PMID:27935939

  14. Laser induced formation of micro-rough structures

    NASA Astrophysics Data System (ADS)

    Singh, Rajiv K.; Fitz-Gerald, James M.

    1997-01-01

    Laser induced micro-rough structures (LIMS) are a by-product of laser ablation process and are created during multiple pulse irradiation on the surface of the material. Although LIMS have been found to be deleterious for the thin film deposition process, these surfaces have wide variety of applications in synthesis of adherent coatings in thermal expansion mismatched systems. Earlier models, based on interference effects of the laser beam, to explain the evolution of LIMS, are not consistent with the experimental results. Experiments were conducted on a wide variety of materials (e.g. SiC, alumina, YBaCuO superconductor, etc.) to understand the mechanisms for generation of the micro-rough structures. A novel model was developed to explain the characteristics of LIMS such as (i) feature orientation (ii) evolution of surface structures as a function of pulses, (iii) formation of LIMS within a energy window near ablation threshold and (iv) periodicity which is independent of the laser wavelength and incident angle.

  15. Formation of Chromosomal Domains by Loop Extrusion.

    PubMed

    Fudenberg, Geoffrey; Imakaev, Maxim; Lu, Carolyn; Goloborodko, Anton; Abdennur, Nezar; Mirny, Leonid A

    2016-05-31

    Topologically associating domains (TADs) are fundamental structural and functional building blocks of human interphase chromosomes, yet the mechanisms of TAD formation remain unclear. Here, we propose that loop extrusion underlies TAD formation. In this process, cis-acting loop-extruding factors, likely cohesins, form progressively larger loops but stall at TAD boundaries due to interactions with boundary proteins, including CTCF. Using polymer simulations, we show that this model produces TADs and finer-scale features of Hi-C data. Each TAD emerges from multiple loops dynamically formed through extrusion, contrary to typical illustrations of single static loops. Loop extrusion both explains diverse experimental observations-including the preferential orientation of CTCF motifs, enrichments of architectural proteins at TAD boundaries, and boundary deletion experiments-and makes specific predictions for the depletion of CTCF versus cohesin. Finally, loop extrusion has potentially far-ranging consequences for processes such as enhancer-promoter interactions, orientation-specific chromosomal looping, and compaction of mitotic chromosomes.

  16. A double-loop structure in the adaptive generalized predictive control algorithm for control of robot end-point contact force.

    PubMed

    Wen, Shuhuan; Zhu, Jinghai; Li, Xiaoli; Chen, Shengyong

    2014-09-01

    Robot force control is an essential issue in robotic intelligence. There is much high uncertainty when robot end-effector contacts with the environment. Because of the environment stiffness effects on the system of the robot end-effector contact with environment, the adaptive generalized predictive control algorithm based on quantitative feedback theory is designed for robot end-point contact force system. The controller of the internal loop is designed on the foundation of QFT to control the uncertainty of the system. An adaptive GPC algorithm is used to design external loop controller to improve the performance and the robustness of the system. Two closed loops used in the design approach realize the system׳s performance and improve the robustness. The simulation results show that the algorithm of the robot end-effector contacting force control system is effective.

  17. The 26 December 2001 Solar Eruptive Event Responsible for GLE63. II. Multi-Loop Structure of Microwave Sources in a Major Long-Duration Flare

    NASA Astrophysics Data System (ADS)

    Grechnev, V.; Uralov, A. M.; Kiselev, V. I.; Kochanov, A. A.

    2017-01-01

    Our analysis of the observations of the SOL2001-12-26 event, which was related to ground-level enhancement of cosmic-ray intensity GLE63, including microwave spectra and images from the Nobeyama Radioheliograph at 17 and 34 GHz, from the Siberian Solar Radio Telescope at 5.7 GHz, and from the Transition Region and Coronal Explorer in 1600 Å, has led to the following results: A flare ribbon overlapped with the sunspot umbra, which is typical of large particle events. Atypical were i) the long duration of the flare, which lasted more than one hour; ii) the moderate intensity of the microwave burst, which was about 104 sfu; iii) the low peak frequency of the gyrosynchrotron spectrum, which was about 6 GHz; and its insensitivity to the flux increase by more than one order of magnitude. This was accompanied by a nearly constant ratio of the flux emitted by the volume in the high-frequency part of the spectrum to its elevated low-frequency part determined by the area of the source. With the self-similarity of the spectrum, a similarity was observed between the moving microwave sources and the brightest parts of the flare ribbons in 1600 Å images. We compared the 17 GHz and 1600 Å images and confirm that the microwave sources were associated with multiple flare loops, whose footpoints appeared in the ultraviolet as intermittent bright kernels. To understand the properties of the event, we simulated its microwave emission using a system of several homogeneous gyrosynchrotron sources above the ribbons. The scatter between the spectra and the sizes of the individual sources is determined by the inhomogeneity of the magnetic field within the ribbons. The microwave flux is mainly governed by the magnetic flux passing through the ribbons and the sources. The apparent simplicity of the microwave structures is caused by a poorer spatial resolution and dynamic range of the microwave imaging. The results indicate that microwave manifestations of accelerated electrons correspond

  18. Laser-induced periodic surface structures: Fingerprints of light localization

    NASA Astrophysics Data System (ADS)

    Skolski, J. Z. P.; Römer, G. R. B. E.; Obona, J. V.; Ocelik, V.; Huis in't Veld, A. J.; de Hosson, J. Th. M.

    2012-02-01

    The finite-difference time-domain (FDTD) method is used to study the inhomogeneous absorption of linearly polarized laser radiation below a rough surface. The results are first analyzed in the frequency domain and compared to the efficacy factor theory of Sipe and coworkers. Both approaches show that the absorbed energy shows a periodic nature, not only in the direction orthogonal to the laser polarization, but also in the direction parallel to it. It is shown that the periodicity is not always close to the laser wavelength for the perpendicular direction. In the parallel direction, the periodicity is about λ/Re(ñ), with ñ being the complex refractive index of the medium. The space-domain FDTD results show a periodicity in the inhomogeneous energy absorption similar to the periodicity of the low- and high-spatial-frequency laser-induced periodic surface structures depending on the material's excitation.

  19. Endotoxin-Induced Structural Transformations in Liquid Crystalline Droplets

    NASA Astrophysics Data System (ADS)

    Lin, I.-Hsin; Miller, Daniel S.; Bertics, Paul J.; Murphy, Christopher J.; de Pablo, Juan J.; Abbott, Nicholas L.

    2011-06-01

    The ordering of liquid crystals (LCs) is known to be influenced by surfaces and contaminants. Here, we report that picogram per milliliter concentrations of endotoxin in water trigger ordering transitions in micrometer-size LC droplets. The ordering transitions, which occur at surface concentrations of endotoxin that are less than 10-5 Langmuir, are not due to adsorbate-induced changes in the interfacial energy of the LC. The sensitivity of the LC to endotoxin was measured to change by six orders of magnitude with the geometry of the LC (droplet versus slab), supporting the hypothesis that interactions of endotoxin with topological defects in the LC mediate the response of the droplets. The LC ordering transitions depend strongly on glycophospholipid structure and provide new designs for responsive soft matter.

  20. Interfacial patterns in magnetorheological fluids: Azimuthal field-induced structures

    NASA Astrophysics Data System (ADS)

    Dias, Eduardo O.; Lira, Sérgio A.; Miranda, José A.

    2015-08-01

    Despite their practical and academic relevance, studies of interfacial pattern formation in confined magnetorheological (MR) fluids have been largely overlooked in the literature. In this work, we present a contribution to this soft matter research topic and investigate the emergence of interfacial instabilities when an inviscid, initially circular bubble of a Newtonian fluid is surrounded by a MR fluid in a Hele-Shaw cell apparatus. An externally applied, in-plane azimuthal magnetic field produced by a current-carrying wire induces interfacial disturbances at the two-fluid interface, and pattern-forming structures arise. Linear stability analysis, weakly nonlinear theory, and a vortex sheet approach are used to access early linear and intermediate nonlinear time regimes, as well as to determine stationary interfacial shapes at fully nonlinear stages.

  1. Energy landscapes of dynamic ensembles of rolling triplet repeat bulge loops: implications for DNA expansion associated with disease states.

    PubMed

    Völker, Jens; Gindikin, Vera; Klump, Horst H; Plum, G Eric; Breslauer, Kenneth J

    2012-04-04

    DNA repeat domains can form ensembles of canonical and noncanonical states, including stable and metastable DNA secondary structures. Such sequence-induced structural diversity creates complex conformational landscapes for DNA processing pathways, including those triplet expansion events that accompany replication, recombination, and/or repair. Here we demonstrate further levels of conformational complexity within repeat domains. Specifically, we show that bulge loop structures within an extended repeat domain can form dynamic ensembles containing a distribution of loop positions, thereby yielding families of positional loop isomers, which we designate as "rollamers". Our fluorescence, absorbance, and calorimetric data are consistent with loop migration/translocation between sites within the repeat domain ("rollamerization"). We demonstrate that such "rollameric" migration of bulge loops within repeat sequences can invade and disrupt previously formed base-paired domains via an isoenthalpic, entropy-driven process. We further demonstrate that destabilizing abasic lesions alter the loop distributions so as to favor "rollamers" with the lesion positioned at the duplex/loop junction, sites where the flexibility of the abasic "universal hinge" relaxes unfavorable interactions and/or facilitates topological accommodation. Another strategic siting of an abasic site induces directed loop migration toward denaturing domains, a phenomenon that merges destabilizing domains. In the aggregate, our data reveal that dynamic ensembles within repeat domains profoundly impact the overall energetics of such DNA constructs as well as the distribution of states by which they denature/renature. These static and dynamic influences within triplet repeat domains expand the conformational space available for selection and targeting by the DNA processing machinery. We propose that such dynamic ensembles and their associated impact on DNA properties influence pathways that lead to DNA

  2. Deformation-induced dehydration structures in the Nankai accretionary prism

    NASA Astrophysics Data System (ADS)

    Famin, V.; Byrne, T.; Lewis, J. C.; Kanagawa, K.; Behrmann, J.; Iodp 314/315/316 Scientists, E.

    2008-12-01

    This study investigates the chemical changes caused by deformation in the hanging wall of a major, probably seismogenic thrust fault in the Kumano forearc basin, Nankai Trough. In cores from IODP Expedition 315 (site C0001), the clay sediments display numerous deformation structures including tilted beddings, decimeter scale faults and shear zones with normal or thrust offsets, and clusters of parallel curviplanar veins interpreted as earthquake-induced dewatering structures. Curviplanar veins are often observed to merge into small oblique shear zones with millimeter offsets, or to branch on larger shear zones with a ~30° angle. This suggests that some shear zones may form by the coalescence of veins. Curviplanar veins and shear zones appear darker than the surrounding clay at the macroscopic observation scale, and brighter and therefore denser under CT-scan imaging. At the micro-scale, clay has a preferred crystallographic orientation in the deformation structures and no preferred orientation outside. Electron probe micro-analysis reveals that the dark material has a higher sum of major elements (65-80 wt%), i.e. a lower volatile content (assumed to be mostly water) than the host sediment (50-60 wt%). All the major elements are equally enriched in proportion to the volatile depletion. Mass balance calculation indicates that a 20-30 wt% water loss is required to account for chemical change in the deformation microstructures. The water loss may be due to clay dehydration or to pore collapse. Shear zones are equally dehydrated as the curviplanar veins from the mass balance standpoint. In 1 m3 of sediment, a deformed volume of 1 % should produce about 6.2 L of water. Given the low permeability of the sediment, dehydration may increase the pore pressure and enhance further deformation. Deformation localization would be self-sustained by fluid overpressure, suggesting that dewatering veins may evolve into larger deformation structures after an earthquake.

  3. Quantitative Evaluation of Closed-Loop-Shaped Cardiomyocyte Network by Using Ring-Shaped Electrode

    NASA Astrophysics Data System (ADS)

    Nomura, Fumimasa; Kaneko, Tomoyuki; Hamada, Tomoyo; Hattori, Akihiro; Yasuda, Kenji

    2012-06-01

    Re-entry of excitation in the heart is one of the abnormal phenomena that causes lethal arrhythmia and is thought to be induced by the looped structure of the excitation conduction pathway. To evaluate the geometrical pattern dependence of electrophysiological results, we fabricated three models of cardiomyocyte networks and compared their beating frequencies (BFs), amplitudes of a depolarization peak, and field potential durations (FPDs). The set of different closed-loop-shaped network models from 3 to 8 mm in length showed the same BFs, amplitudes, and FPDs independent of their loop lengths, whereas the BFs and FPDs of 60 µm small clusters, and the FPDs of the 2 mm open-line-shaped network model were different from those of a closed-loop-shaped network model. These results indicate that the mm order larger size of clusters might create lower BFs, and the closed-loop-shaped model may generate longer FPDs. They also suggest the importance of spatial arrangement control of the cardoimyocyte community for reproducible measurement of electrophysiological properties of cardiomyocytes, especially control of the closed-loop formation, which might change the waveforms of FPDs depending on the difference in the geometry and conduction pathway of the cell network.

  4. Coherence in ultrafast laser-induced periodic surface structures

    NASA Astrophysics Data System (ADS)

    Zhang, Hao; Colombier, Jean-Philippe; Li, Chen; Faure, Nicolas; Cheng, Guanghua; Stoian, Razvan

    2015-11-01

    Ultrafast laser irradiation can trigger anisotropically structured nanoscaled gratinglike arrangements of matter, the laser-induced periodic surface structures (LIPSSs). We demonstrate here that the formation of LIPSS is intrinsically related to the coherence of the laser field. Employing several test materials that allow large optical excursions, we observe the effect of randomizing spatial phase in generating finite domains of ripples. Using three-dimensional finite-difference time-domain methods, we evaluate energy deposition patterns below a material's rough surface and show that modulated pattern, i.e., a spatially ordered electromagnetic solution, results from the coherent superposition of waves. By separating the field scattered from a surface rough topography from the total field, the inhomogeneous energy absorption problem is reduced to a simple interference equation. We further distinguish the contribution of the scattered near field and scattered far field on various types of inhomogeneous energy absorption features. It is found that the inhomogeneous energy absorption which could trigger the low-spatial-frequency LIPSSs (LSFLs) and high-spatial-frequency LIPSSs (HSFLs) of periodicity Λ >λ /Re(n ˜) are due to coherent superposition between the scattered far field (propagation) and the refracted field, while HSFLs of Λ <λ /Re(n ˜) are triggered by coherent superposition between the scattered near field (evanescent) and the refracted field. This is a general scenario that involves a topography-induced scattering phenomenon and stationary evanescent fields, being applied to two model case materials that exhibit large optical excursions upon excitation (W, Si) and nonplasmonic to plasmonic transitions. We indicate the occurrence of a general light interference phenomenon that does not necessarily involve wavelike surface plasmonic excitation. Finally, we discuss the role of interference field and scattered field on the enhancement of LIPSSs by

  5. Structural basis for constitutive activity and agonist-induced activation of the enteroendocrine fat sensor GPR119

    PubMed Central

    Engelstoft, M S; Norn, C; Hauge, M; Holliday, N D; Elster, L; Lehmann, J; Jones, R M; Frimurer, T M; Schwartz, T W

    2014-01-01

    Background and Purpose GPR119 is a Gαs-coupled 7TM receptor activated by endogenous lipids such as oleoylethanolamide (OEA) and by the dietary triglyceride metabolite 2-monoacylglycerol. GPR119 stimulates enteroendocrine hormone and insulin secretion. But despite massive drug discovery efforts in the field, very little is known about the basic molecular pharmacology of GPR119. Experimental Approach GPR119 receptor signalling was studied in transfected cells. Mutational mapping (30 mutations in 23 positions) was performed on residues required for ligand-independent and agonist-induced GPR119 activation (AR231453 and OEA). Novel Rosetta-based receptor modelling was applied, using a composite template approach with segments from different X-ray structures and fully flexible ligand docking. Key Results The increased signalling induced by increasing the cell surface expression of GPR119 in the absence of agonist and the inhibitory effect of two synthetic inverse agonists demonstrated that GRP119 signals with a high degree of constitutive activity through the Gαs pathway. The mutational maps for AR231453 and OEA were very similar and, surprisingly, also similar to the mutational map for residues affecting the constitutive signalling – albeit with key differences. Surprisingly, almost all residues in extracellular loop-2b were important for the constitutive activity. The molecular modelling and docking demonstrated that AR231453 binds in a ‘vertical’ pocket in between mutational hits reaching from the centre of the receptor out to extracellular loop-2b. Conclusions and Implications The high constitutive activity of GPR119 should be taken into account in future drug discovery efforts, which can now be guided by the detailed knowledge of the physiochemical properties of the extended ligand-binding pocket. PMID:25117266

  6. Effect of DNA looping on the induction kinetics of the lac operon.

    PubMed

    Narang, Atul

    2007-08-21

    The induction of the lac operon follows cooperative kinetics. The first mechanistic model of these kinetics is the de facto standard in the modeling literature [Yagil, G., Yagil, E., 1971. On the relation between effector concentration and the rate of induced enzyme synthesis. Biophys. J. 11, 11-17]. Yet, subsequent studies have shown that the model is based on incorrect assumptions. Specifically, the repressor is a tetramer with four (not two) inducer-binding sites, and the operon contains two auxiliary operators (in addition to the main operator). Furthermore, these structural features are crucial for the formation of DNA loops, the key determinants of lac repression and induction. Indeed, the repression is determined almost entirely (>95%) by the looped complexes [Oehler, S., Eismann, E.R., Krämer, H., Müller-Hill, B., 1990. The three operators of the lac operon cooperate in repression. EMBO J. 9(4), 973-979], and the pronounced cooperativity of the induction curve hinges upon the existence of the looped complexes [Oehler, S., Alberti, S., Müller-Hill, B., 2006. Induction of the lac promoter in the absence of DNA loops and the stoichiometry of induction. Nucleic Acids Res. 34(2), 606-612]. Here, we formulate a model of lac induction taking due account of the tetrameric structure of the repressor and the existence of looped complexes. We show that: (1) The kinetics are significantly more cooperative than those predicted by the Yagil and Yagil model. The cooperativity is higher because the formation of looped complexes is easily abolished by repressor-inducer binding. (2) The model provides good fits to the repression data for cells containing wild-type tetrameric or mutant dimeric repressor, as well as the induction curves for 6 different strains of Escherichia coli. It also implies that the ratios of certain looped and non-looped complexes are independent of inducer and repressor levels, a conclusion that can be rigorously tested by gel electrophoresis. (3

  7. Pirfenidone controls the feedback loop of the AT1R/p38 MAPK/renin-angiotensin system axis by regulating liver X receptor-α in myocardial infarction-induced cardiac fibrosis

    PubMed Central

    Li, Chunmei; Han, Rui; Kang, Le; Wang, Jianping; Gao, Yonglin; Li, Yanshen; He, Jie; Tian, Jingwei

    2017-01-01

    Pirfenidone (PFD), an anti-fibrotic small molecule drug, is used to treat fibrotic diseases, but its effects on myocardial infarction (MI)-induced cardiac fibrosis are unknown. The aim of this study was to determine the effects of PFD on MI-induced cardiac fibrosis and the possible underlying mechanisms in rats. After establishment of the model, animals were administered PFD by gavage for 4 weeks. During the development of MI-induced cardiac fibrosis, we found activation of a positive feedback loop between the angiotensin II type 1 receptor (AT1R)/phospho-p38 mitogen-activated protein kinase (p38 MAPK) pathway and renin-angiotensin system (RAS), which was accompanied by down-regulation of liver X receptor-α (LXR-α) expression. PFD attenuated body weight, heart weight, left ventricular weight, left ventricular systolic pressure, and ±dp/dtmax changes induced by MI, which were associated with a reduction in cardiac fibrosis, infarct size, and hydroxyproline concentration. Moreover, PFD inhibited the AT1R/p38 MAPK pathway, corrected the RAS imbalance [decreased angiotensin-converting enzyme (ACE), angiotensin II, and angiotensin II type 1 receptor expression, but increased ACE2 and angiotensin (1-7) activity and Mas expression] and strongly enhanced heart LXR-α expression. These results indicate that the cardioprotective effects of PFD may be due, in large part, to controlling the feedback loop of the AT1R/p38 MAPK/RAS axis by activation of LXR-α. PMID:28091615

  8. Electrical stimulation induces IL-6 in skeletal muscle through extracellular ATP by activating Ca2+ signals and an IL-6 autocrine loop

    PubMed Central

    Bustamante, Mario; Fernández-Verdejo, Rodrigo; Jaimovich, Enrique

    2014-01-01

    Interleukin-6 (IL-6) is an important myokine that is highly expressed in skeletal muscle cells upon exercise. We assessed IL-6 expression in response to electrical stimulation (ES) or extracellular ATP as a known mediator of the excitation-transcription mechanism in skeletal muscle. We examined whether the canonical signaling cascade downstream of IL-6 (IL-6/JAK2/STAT3) also responds to muscle cell excitation, concluding that IL-6 influences its own expression through a positive loop. Either ES or exogenous ATP (100 μM) increased both IL-6 expression and p-STAT3 levels in rat myotubes, a process inhibited by 100 μM suramin and 2 U/ml apyrase. ATP also evoked IL-6 expression in both isolated skeletal fibers and extracts derived from whole FDB muscles. ATP increased IL-6 release up to 10-fold. STAT3 activation evoked by ATP was abolished by the JAK2 inhibitor HBC. Blockade of secreted IL-6 with a neutralizing antibody or preincubation with the STAT3 inhibitor VIII reduced STAT3 activation evoked by extracellular ATP by 70%. Inhibitor VIII also reduced by 70% IL-6 expression evoked by ATP, suggesting a positive IL-6 loop. In addition, ATP increased up to 60% the protein levels of SOCS3, a negative regulator of the IL-6 signaling pathway. On the other hand, intracellular calcium chelation or blockade of IP3-dependent calcium signals abolished STAT3 phosphorylation evoked by either extracellular ATP or ES. These results suggest that expression of IL-6 in stimulated skeletal muscle cells is mediated by extracellular ATP and nucleotide receptors, involving IP3-dependent calcium signals as an early step that triggers a positive IL-6 autocrine loop. PMID:24518675

  9. Electrical stimulation induces IL-6 in skeletal muscle through extracellular ATP by activating Ca(2+) signals and an IL-6 autocrine loop.

    PubMed

    Bustamante, Mario; Fernández-Verdejo, Rodrigo; Jaimovich, Enrique; Buvinic, Sonja

    2014-04-15

    Interleukin-6 (IL-6) is an important myokine that is highly expressed in skeletal muscle cells upon exercise. We assessed IL-6 expression in response to electrical stimulation (ES) or extracellular ATP as a known mediator of the excitation-transcription mechanism in skeletal muscle. We examined whether the canonical signaling cascade downstream of IL-6 (IL-6/JAK2/STAT3) also responds to muscle cell excitation, concluding that IL-6 influences its own expression through a positive loop. Either ES or exogenous ATP (100 μM) increased both IL-6 expression and p-STAT3 levels in rat myotubes, a process inhibited by 100 μM suramin and 2 U/ml apyrase. ATP also evoked IL-6 expression in both isolated skeletal fibers and extracts derived from whole FDB muscles. ATP increased IL-6 release up to 10-fold. STAT3 activation evoked by ATP was abolished by the JAK2 inhibitor HBC. Blockade of secreted IL-6 with a neutralizing antibody or preincubation with the STAT3 inhibitor VIII reduced STAT3 activation evoked by extracellular ATP by 70%. Inhibitor VIII also reduced by 70% IL-6 expression evoked by ATP, suggesting a positive IL-6 loop. In addition, ATP increased up to 60% the protein levels of SOCS3, a negative regulator of the IL-6 signaling pathway. On the other hand, intracellular calcium chelation or blockade of IP3-dependent calcium signals abolished STAT3 phosphorylation evoked by either extracellular ATP or ES. These results suggest that expression of IL-6 in stimulated skeletal muscle cells is mediated by extracellular ATP and nucleotide receptors, involving IP3-dependent calcium signals as an early step that triggers a positive IL-6 autocrine loop.

  10. Protein-induced surface structuring in myelin membrane monolayers.

    PubMed

    Rosetti, Carla M; Maggio, Bruno

    2007-12-15

    Monolayers prepared from myelin conserve all the compositional complexity of the natural membrane when spread at the air-water interface. They show a complex pressure-dependent surface pattern that, on compression, changes from the coexistence of two liquid phases to a viscous fractal phase embedded in a liquid phase. We dissected the role of major myelin protein components, myelin basic protein (MBP), and Folch-Lees proteolipid protein (PLP) as crucial factors determining the structural dynamics of the interface. By analyzing mixtures of a single protein with the myelin lipids we found that MBP and PLP have different surface pressure-dependent behaviors. MBP stabilizes the segregation of two liquid phases at low pressures and becomes excluded from the film under compression, remaining adjacent to the interface. PLP, on the contrary, organizes a fractal-like pattern at all surface pressures when included in a monolayer of the protein-free myelin lipids but it remains mixed in the MBP-induced liquid phase. The resultant surface topography and dynamics is regulated by combined near to equilibrium and out-of-equilibrium effects. PLP appears to act as a surface skeleton for the whole components whereas MBP couples the structuring to surface pressure-dependent extrusion and adsorption processes.

  11. Structural modifications induced in dentin by femtosecond laser

    NASA Astrophysics Data System (ADS)

    Le, Quang-Tri; Bertrand, Caroline; Vilar, Rui

    2016-12-01

    The structural and chemical modifications induced in dentin by ultrafast laser ablation were studied. The laser experiments were performed with a Yb:KYW chirped-pulse-regenerative amplification laser system (560-fs pulse duration, 1030-nm radiation wavelength), fluences in the range 2 to 14 J/cm2, 1-kHz pulse repetition rate, and 5-mm/s scanning speed. The ablation surfaces were characterized by scanning electron microscopy and Fourier transform infrared spectroscopy. The ablation surfaces produced with 2 J/cm2 presented an irregular morphology with exposed dentinal tubules and no evidence of thermal effects. For 7 and 14 J/cm2, the ablation surfaces were covered by a layer of redeposited ablation debris, consisting mainly of amorphous calcium phosphate. This layer is weakly adherent to the underlying tissue and can be easily removed by ultrasonication, revealing a surface with a morphology similar to the one obtained with 2 J/cm2. The constitution of the dentin ablation surfaces is similar to the constitution of pristine dentin, showing that, within this fluence range, the laser treatment does not significantly modify the structure and constitution of dentin. The results achieved suggest an ablation mechanism where collagen is preferentially decomposed by the laser radiation, reducing the tissue cohesive strength and leading, ultimately, to its ablation.

  12. Structure-induced spin reorientation in magnetic nanostructures

    NASA Astrophysics Data System (ADS)

    Neumann, Alexander; Frauen, Axel; Vollmers, Julian; Meyer, Andreas; Oepen, Hans Peter

    2016-09-01

    We report on structuring-induced changes of the magnetic anisotropy of cylindrical nanostructures which are carved out of thin Pt/Co/Pt films. The magnetic properties of films and structures with a diameter of about 34 nm were investigated via magneto-optic Kerr effect. The magnetic anisotropy is determined for both films and nanostructures for varying Co thicknesses (0.5-7 nm). In general, the nanostructures exhibit larger perpendicular anisotropy than the films. On thickness increase of the Co layer two spin reorientation transitions at about 2.2 and 5 nm are found. At 2.2 nm the nanostructures exhibit the transition from perpendicular to in-plane orientation of magnetization while at 5 nm the reversed transition is found. The variation of the magnetic anisotropy of the Co nanostructures is not solely caused by the change of shape anisotropy. The net change, corrected for the shape, reveals a reduction of strain in the thinnest Co layers while the increase of the anisotropy of the nanostructures at higher Co thicknesses is caused by a transformation of the Co lattice from fcc to hcp.

  13. Mancozeb-induced behavioral deficits precede structural neural degeneration.

    PubMed

    Harrison Brody, A; Chou, Eunice; Gray, Janet M; Pokyrwka, Nancy J; Raley-Susman, Kathleen M

    2013-01-01

    Manganese-containing fungicides like Mancozeb have been associated with neurodegenerative conditions like Parkinson's disease. We examined the behavioral damage and differential neuronal vulnerability resulting from Mancozeb exposure using Caenorhabditis elegans, an important mid-trophic level soil organism that is also a powerful model for studying mechanisms of environmental pollutant-induced neurodegenerative disease. The dopamine-mediated swim to crawl locomotory transition behavior is exquisitely vulnerable to Mancozeb, with functional impairment preceding markers of neuronal structural damage. The damage is partially rescued in mutants lacking the divalent metal transporter, SMF-1, demonstrating that some, but not all, of the damage is mediated by manganese. Increasing concentrations of Mancozeb recruit additional behavioral dysfunction, notably serotonin-mediated egg-laying behavior, but without evident serotonergic neuronal structural damage. Thus, measurements of behavioral dysfunction are a sensitive early marker of fungicide toxicity that could be exploited to examine further mechanisms of neuron damage and possible therapeutic interventions. These results also provide important insight into the consequences of fungicide use on the ecological behavior of nematodes.

  14. A Systematic Investigation of Structure/Function Requirements for the Apolipoprotein A-I/Lecithin Cholesterol Acyltransferase Interaction Loop of High-density Lipoprotein.

    PubMed

    Gu, Xiaodong; Wu, Zhiping; Huang, Ying; Wagner, Matthew A; Baleanu-Gogonea, Camelia; Mehl, Ryan A; Buffa, Jennifer A; DiDonato, Anthony J; Hazen, Leah B; Fox, Paul L; Gogonea, Valentin; Parks, John S; DiDonato, Joseph A; Hazen, Stanley L

    2016-03-18

    The interaction of lecithin-cholesterol acyltransferase (LCAT) with apolipoprotein A-I (apoA-I) plays a critical role in high-density lipoprotein (HDL) maturation. We previously identified a highly solvent-exposed apoA-I loop domain (Leu(159)-Leu(170)) in nascent HDL, the so-called "solar flare" (SF) region, and proposed that it serves as an LCAT docking site (Wu, Z., Wagner, M. A., Zheng, L., Parks, J. S., Shy, J. M., 3rd, Smith, J. D., Gogonea, V., and Hazen, S. L. (2007) Nat. Struct. Mol. Biol. 14, 861-868). The stability and role of the SF domain of apoA-I in supporting HDL binding and activation of LCAT are debated. Here we show by site-directed mutagenesis that multiple residues within the SF region (Pro(165), Tyr(166), Ser(167), and Asp(168)) of apoA-I are critical for both LCAT binding to HDL and LCAT catalytic efficiency. The critical role for possible hydrogen bond interaction at apoA-I Tyr(166) was further supported using reconstituted HDL generated from apoA-I mutants (Tyr(166) → Glu or Asn), which showed preservation in both LCAT binding affinity and catalytic efficiency. Moreover, the in vivo functional significance of NO2-Tyr(166)-apoA-I, a specific post-translational modification on apoA-I that is abundant within human atherosclerotic plaque, was further investigated by using the recombinant protein generated from E. coli containing a mutated orthogonal tRNA synthetase/tRNACUA pair enabling site-specific insertion of the unnatural amino acid into apoA-I. NO2-Tyr(166)-apoA-I, after subcutaneous injection into hLCAT(Tg/Tg), apoA-I(-/-) mice, showed impaired LCAT activation in vivo, with significant reduction in HDL cholesteryl ester formation. The present results thus identify multiple structural features within the solvent-exposed SF region of apoA-I of nascent HDL essential for optimal LCAT binding and catalytic efficiency.

  15. A Systematic Investigation of Structure/Function Requirements for the Apolipoprotein A-I/Lecithin Cholesterol Acyltransferase Interaction Loop of High-density Lipoprotein*

    PubMed Central

    Gu, Xiaodong; Wu, Zhiping; Huang, Ying; Wagner, Matthew A.; Baleanu-Gogonea, Camelia; Mehl, Ryan A.; Buffa, Jennifer A.; DiDonato, Anthony J.; Hazen, Leah B.; Fox, Paul L.; Gogonea, Valentin; Parks, John S.; DiDonato, Joseph A.; Hazen, Stanley L.

    2016-01-01

    The interaction of lecithin-cholesterol acyltransferase (LCAT) with apolipoprotein A-I (apoA-I) plays a critical role in high-density lipoprotein (HDL) maturation. We previously identified a highly solvent-exposed apoA-I loop domain (Leu159–Leu170) in nascent HDL, the so-called “solar flare” (SF) region, and proposed that it serves as an LCAT docking site (Wu, Z., Wagner, M. A., Zheng, L., Parks, J. S., Shy, J. M., 3rd, Smith, J. D., Gogonea, V., and Hazen, S. L. (2007) Nat. Struct. Mol. Biol. 14, 861–868). The stability and role of the SF domain of apoA-I in supporting HDL binding and activation of LCAT are debated. Here we show by site-directed mutagenesis that multiple residues within the SF region (Pro165, Tyr166, Ser167, and Asp168) of apoA-I are critical for both LCAT binding to HDL and LCAT catalytic efficiency. The critical role for possible hydrogen bond interaction at apoA-I Tyr166 was further supported using reconstituted HDL generated from apoA-I mutants (Tyr166 → Glu or Asn), which showed preservation in both LCAT binding affinity and catalytic efficiency. Moreover, the in vivo functional significance of NO2-Tyr166-apoA-I, a specific post-translational modification on apoA-I that is abundant within human atherosclerotic plaque, was further investigated by using the recombinant protein generated from E. coli containing a mutated orthogonal tRNA synthetase/tRNACUA pair enabling site-specific insertion of the unnatural amino acid into apoA-I. NO2-Tyr166-apoA-I, after subcutaneous injection into hLCATTg/Tg, apoA-I−/− mice, showed impaired LCAT activation in vivo, with significant reduction in HDL cholesteryl ester formation. The present results thus identify multiple structural features within the solvent-exposed SF region of apoA-I of nascent HDL essential for optimal LCAT binding and catalytic efficiency. PMID:26797122

  16. The structure of a dual-specificity tyrosine phosphorylation-regulated kinase 1A-PKC412 complex reveals disulfide-bridge formation with the anomalous catalytic loop HRD(HCD) cysteine.

    PubMed

    Alexeeva, Marina; Åberg, Espen; Engh, Richard A; Rothweiler, Ulli

    2015-05-01

    Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a protein kinase associated with neuronal development and brain physiology. The DYRK kinases are very unusual with respect to the sequence of the catalytic loop, in which the otherwise highly conserved arginine of the HRD motif is replaced by a cysteine. This replacement, along with the proximity of a potential disulfide-bridge partner from the activation segment, implies a potential for redox control of DYRK family activities. Here, the crystal structure of DYRK1A bound to PKC412 is reported, showing the formation of the disulfide bridge and associated conformational changes of the activation loop. The DYRK kinases represent emerging drug targets for several neurological diseases as well as cancer. The observation of distinct activation states may impact strategies for drug targeting. In addition, the characterization of PKC412 binding offers new insights for DYRK inhibitor discovery.

  17. Mutations within a putative cysteine loop of the transmembrane protein of an attenuated immunodeficiency-inducing feline leukemia virus variant inhibit envelope protein processing.

    PubMed Central

    Burns, C C; Poss, M L; Thomas, E; Overbaugh, J

    1995-01-01

    A replication-defective feline leukemia virus molecular clone, 61B, has been shown to cause immunodeficiency in cats and cytopathicity in T cells after a long latency period when coinfected with a minimally pathogenic helper virus (J. Overbaugh, E. A. Hoover, J. I. Mullins, D. P. W. Burns, L. Rudensey, S. L. Quackenbush, V. Stallard, and P. R. Donahue, Virology 188:558-569, 1992). The long-latency phenotype of 61B has been mapped to four mutations in the extracellular domain of the envelope transmembrane protein, and we report here that these mutations cause a defect in envelope protein processing. Immunoprecipitation analyses demonstrated that the 61B gp85 envelope precursor was produced but that further processing to generate the surface protein (SU/gp70) and the transmembrane protein (TM/p15E) did not occur. The 61B precursor was not expressed on the cell surface and appeared to be retained in the endoplasmic reticulum or Golgi apparatus. Two of the four 61B-specific amino acid changes are located within a putative cysteine loop in a region of TM that is conserved among retroviruses. Introduction of these two amino acid changes into a replication-competent highly cytopathic virus resulted in the production of noninfectious virus that exhibited an envelope-protein-processing defect. This analysis suggests that mutations in a conserved region within a putative cysteine loop affect retroviral envelope protein maturation and viral infectivity. PMID:7884859

  18. Modeling loop entropy.

    PubMed

    Chirikjian, Gregory S

    2011-01-01

    Proteins fold from a highly disordered state into a highly ordered one. Traditionally, the folding problem has been stated as one of predicting "the" tertiary structure from sequential information. However, new evidence suggests that the ensemble of unfolded forms may not be as disordered as once believed, and that the native form of many proteins may not be described by a single conformation, but rather an ensemble of its own. Quantifying the relative disorder in the folded and unfolded ensembles as an entropy difference may therefore shed light on the folding process. One issue that clouds discussions of "entropy" is that many different kinds of entropy can be defined: entropy associated with overall translational and rotational Brownian motion, configurational entropy, vibrational entropy, conformational entropy computed in internal or Cartesian coordinates (which can even be different from each other), conformational entropy computed on a lattice, each of the above with different solvation and solvent models, thermodynamic entropy measured experimentally, etc. The focus of this work is the conformational entropy of coil/loop regions in proteins. New mathematical modeling tools for the approximation of changes in conformational entropy during transition from unfolded to folded ensembles are introduced. In particular, models for computing lower and upper bounds on entropy for polymer models of polypeptide coils both with and without end constraints are presented. The methods reviewed here include kinematics (the mathematics of rigid-body motions), classical statistical mechanics, and information theory.

  19. Multiprotein DNA Looping

    NASA Astrophysics Data System (ADS)

    Vilar, Jose M. G.; Saiz, Leonor

    2006-06-01

    DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve it analytically in the case of identical binding. We uncover a switchlike transition between looped and unlooped phases and identify the key parameters that control this transition. Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance.

  20. The Orbital Structure of a Tidally Induced Bar

    NASA Astrophysics Data System (ADS)

    Gajda, Grzegorz; Łokas, Ewa L.; Athanassoula, E.

    2016-10-01

    Orbits are the key building blocks of any density distribution, and their study helps us understand the kinematical structure and the evolution of galaxies. Here, we investigate orbits in a tidally induced bar of a dwarf galaxy, using an N-body simulation of an initially disky dwarf galaxy orbiting a Milky Way-like host. After the first pericenter passage, a tidally induced bar forms in the stellar component of the dwarf. The bar evolution is different than in isolated galaxies and our analysis focuses on the period before it buckles. We study the orbits in terms of their dominant frequencies, which we calculate in a Cartesian coordinate frame rotating with the bar. Apart from the well-known x1 orbits, we find many other types, mostly with boxy shapes of various degree of elongation. Some of them are also near-periodic, admitting frequency ratios of 4/3, 3/2, and 5/3. The box orbits have various degrees of vertical thickness but only a relatively small fraction of those have banana (i.e., smile/frown) or infinity-symbol shapes in the edge-on view. In the very center we also find orbits known from the potential of triaxial ellipsoids. The elongation of the orbits grows with distance from the center of the bar in agreement with the variation of the shape of the density distribution. Our classification of orbits leads to the conclusion that more than 80% of them have boxy shapes, while only 8% have shapes of classical x1 orbits.

  1. Empirical potential simulations of interstitial dislocation loops in uranium dioxide

    NASA Astrophysics Data System (ADS)

    Le Prioux, Arno; Fossati, Paul; Maillard, Serge; Jourdan, Thomas; Maugis, Philippe

    2016-10-01

    Stoichiometric circular shaped interstitial dislocation loop energies are calculated in stoichiometric UO2 by empirical potential simulation. The Burgers vector directions studied are <110> and <111>. The main structural properties of each type of interstitial dislocation loop are determined, including stacking fault energy. Defect energies are compared and a maximum size for stable <111> dislocation loops before transition to <110> dislocation loops is given. A model of dislocation loop energy based on elasticity theory is then fitted on the basis of these simulation results.

  2. Observing the Fine Structure of Loops through High-resolution Spectroscopic Observations of Coronal Rain with the CRISP Instrument at the Swedish Solar Telescope

    NASA Astrophysics Data System (ADS)

    Antolin, P.; Rouppe van der Voort, L.

    2012-02-01

    Observed in cool chromospheric lines, such as Hα or Ca II H, coronal rain corresponds to cool and dense plasma falling from coronal heights. Considered as a peculiar sporadic phenomenon of active regions, it has not received much attention since its discovery more than 40 years ago. Yet, it has been shown recently that a close relationship exists between this phenomenon and the coronal heating mechanism. Indeed, numerical simulations have shown that this phenomenon is most likely due to a loss of thermal equilibrium ensuing from a heating mechanism acting mostly toward the footpoints of loops. We present here one of the first high-resolution spectroscopic observations of coronal rain, performed with the CRisp Imaging Spectro Polarimeter (CRISP) instrument at the Swedish Solar Telescope. This work constitutes the first attempt to assess the importance of coronal rain in the understanding of the coronal magnetic field in active regions. With the present resolution, coronal rain is observed to literally invade the entire field of view. A large statistical set is obtained in which dynamics (total velocities and accelerations), shapes (lengths and widths), trajectories (angles of fall of the blobs), and thermodynamic properties (temperatures) of the condensations are derived. Specifically, we find that coronal rain is composed of small and dense chromospheric cores with average widths and lengths of ~310 km and ~710 km, respectively, average temperatures below 7000 K, displaying a broad distribution of falling speeds with an average of ~70 km s-1, and accelerations largely below the effective gravity along loops. Through estimates of the ion-neutral coupling in the blobs we show that coronal rain acts as a tracer of the coronal magnetic field, thus supporting the multi-strand loop scenario, and acts as a probe of the local thermodynamic conditions in loops. We further elucidate its potential in coronal heating. We find that the cooling in neighboring strands occurs

  3. OBSERVING THE FINE STRUCTURE OF LOOPS THROUGH HIGH-RESOLUTION SPECTROSCOPIC OBSERVATIONS OF CORONAL RAIN WITH THE CRISP INSTRUMENT AT THE SWEDISH SOLAR TELESCOPE

    SciTech Connect

    Antolin, P.; Rouppe van der Voort, L. E-mail: v.d.v.l.rouppe@astro.uio.no

    2012-02-01

    Observed in cool chromospheric lines, such as H{alpha} or Ca II H, coronal rain corresponds to cool and dense plasma falling from coronal heights. Considered as a peculiar sporadic phenomenon of active regions, it has not received much attention since its discovery more than 40 years ago. Yet, it has been shown recently that a close relationship exists between this phenomenon and the coronal heating mechanism. Indeed, numerical simulations have shown that this phenomenon is most likely due to a loss of thermal equilibrium ensuing from a heating mechanism acting mostly toward the footpoints of loops. We present here one of the first high-resolution spectroscopic observations of coronal rain, performed with the CRisp Imaging Spectro Polarimeter (CRISP) instrument at the Swedish Solar Telescope. This work constitutes the first attempt to assess the importance of coronal rain in the understanding of the coronal magnetic field in active regions. With the present resolution, coronal rain is observed to literally invade the entire field of view. A large statistical set is obtained in which dynamics (total velocities and accelerations), shapes (lengths and widths), trajectories (angles of fall of the blobs), and thermodynamic properties (temperatures) of the condensations are derived. Specifically, we find that coronal rain is composed of small and dense chromospheric cores with average widths and lengths of {approx}310 km and {approx}710 km, respectively, average temperatures below 7000 K, displaying a broad distribution of falling speeds with an average of {approx}70 km s{sup -1}, and accelerations largely below the effective gravity along loops. Through estimates of the ion-neutral coupling in the blobs we show that coronal rain acts as a tracer of the coronal magnetic field, thus supporting the multi-strand loop scenario, and acts as a probe of the local thermodynamic conditions in loops. We further elucidate its potential in coronal heating. We find that the cooling

  4. Radiation-Induced Topological Disorder in Irradiated Network Structures

    SciTech Connect

    Hobbs, Linn W.

    2002-12-21

    This report summarizes results of a research program investigating the fundamental principles underlying the phenomenon of topological disordering in a radiation environment. This phenomenon is known popularly as amorphization, but is more formally described as a process of radiation-induced structural arrangement that leads in crystals to loss of long-range translational and orientational correlations and in glasses to analogous alteration of connectivity topologies. The program focus has been on a set compound ceramic solids with directed bonding exhibiting structures that can be described as networks. Such solids include SiO2, Si3N4, SiC, which are of interest to applications in fusion energy production, nuclear waste storage, and device manufacture involving ion implantation or use in radiation fields. The principal investigative tools comprise a combination of experimental diffraction-based techniques, topological modeling, and molecular-dynamics simulations that have proven a rich source of information in the preceding support period. The results from the present support period fall into three task areas. The first comprises enumeration of the rigidity constraints applying to (1) more complex ceramic structures (such as rutile, corundum, spinel and olivine structures) that exhibit multiply polytopic coordination units or multiple modes of connecting such units, (2) elemental solids (such as graphite, silicon and diamond) for which a correct choice of polytope is necessary to achieve correct representation of the constraints, and (3) compounds (such as spinel and silicon carbide) that exhibit chemical disorder on one or several sublattices. With correct identification of the topological constraints, a unique correlation is shown to exist between constraint and amorphizability which demonstrates that amorphization occurs at a critical constraint loss. The second task involves the application of molecular dynamics (MD) methods to topologically-generated models

  5. Introduction to Loop Heat Pipes

    NASA Technical Reports Server (NTRS)

    Ku, Jentung

    2015-01-01

    This is the presentation file for the short course Introduction to Loop Heat Pipes, to be conducted at the 2015 Thermal Fluids and Analysis Workshop, August 3-7, 2015, Silver Spring, Maryland. This course will discuss operating principles and performance characteristics of a loop heat pipe. Topics include: 1) pressure profiles in the loop; 2) loop operating temperature; 3) operating temperature control; 4) loop startup; 4) loop shutdown; 5) loop transient behaviors; 6) sizing of loop components and determination of fluid inventory; 7) analytical modeling; 8) examples of flight applications; and 9) recent LHP developments.

  6. Turbomachinery Design Quality Checks to Avoid Friction Induced Structural Failure

    NASA Technical Reports Server (NTRS)

    Moore, Jerry H.

    1999-01-01

    A unique configuration of the P&W SSME Alternate Fuel Turbopump turbine disk/blade assembly, combined with a severe thermal environment, resulted in several structural anomalies that were driven by frictional contact forces. Understanding the mechanics of these problems provides new quality checks for future turbo machinery designs. During development testing in 1997 of the SSME alternate fuel turbopump at Stennis Space Center, several potentially serious problems surfaced with the turbine disk/blade assembly that had not been experienced in extensive earlier testing. Changes to the operational thermal environment were noted based on analytical prediction of modifications that affected performance and on stationary thermal measurements adjacent to the rotor assembly. A detailed structural investigation was required to reveal the mechanism of distress induced by the change. The turbine disk experienced cracking in several locations due to increased thermal gradient induced stress during start and shutdown transients. This was easily predictable using standard analysis procedures and expected once the thermal environment was characterized. What was not expected was the curling of a piston ring used for blade axial retention in the disk, indentation of the axial face of the blade attachment by a spacer separating the first and second stage blades, and most significantly, galling and cracking of the blade root attachment that could have resulted in blade release. Past experience, in gas turbine environments, set a precedent of never relying on friction for help and to evaluate it only in specific instances where it was obvious that it would degrade capability. In each of the three cases above, friction proved to be a determining factor that pushed the components into an unsatisfactory mode of operation. The higher than expected temperatures and rapid thermal transients combined with friction to move beyond past experience. The turbine disk/blade assembly configuration

  7. Mitotic chromosome compaction via active loop extrusion

    NASA Astrophysics Data System (ADS)

    Goloborodko, Anton; Imakaev, Maxim; Marko, John; Mirny, Leonid; MIT-Northwestern Team

    During cell division, two copies of each chromosome are segregated from each other and compacted more than hundred-fold into the canonical X-shaped structures. According to earlier microscopic observations and the recent Hi-C study, chromosomes are compacted into arrays of consecutive loops of ~100 kilobases. Mechanisms that lead to formation of such loop arrays are largely unknown. Here we propose that, during cell division, chromosomes can be compacted by enzymes that extrude loops on chromatin fibers. First, we use computer simulations and analytical modeling to show that a system of loop-extruding enzymes on a chromatin fiber self-organizes into an array of consecutive dynamic loops. Second, we model the process of loop extrusion in 3D and show that, coupled with the topo II strand-passing activity, it leads to robust compaction and segregation of sister chromatids. This mechanism of chromosomal condensation and segregation does not require additional proteins or specific DNA markup and is robust against variations in the number and properties of such loop extruding enzymes. Work at NU was supported by the NSF through Grants DMR-1206868 and MCB-1022117, and by the NIH through Grants GM105847 and CA193419. Work at MIT was supported by the NIH through Grants GM114190 R01HG003143.

  8. Resonant electrodynamic heating of stellar coronal loops: An LRC circuit analogue

    NASA Technical Reports Server (NTRS)

    Ionson, J. A.

    1980-01-01

    The electrodynamic coupling of stellar coronal loops to underlying beta velocity fields. A rigorous analysis revealed that the physics can be represented by a simple yet equivalent LRC circuit analogue. This analogue points to the existence of global structure oscillations which resonantly excite internal field line oscillations at a spatial resonance within the coronal loop. Although the width of this spatial resonance, as well as the induced currents and coronal velocity field, explicitly depend upon viscosity and resistivity, the resonant form of the generalized electrodynamic heating function is virtually independent of irreversibilities. This is a classic feature of high quality resonators that are externally driven by a broad band source of spectral power. Applications to solar coronal loops result in remarkable agreement with observations.

  9. Regular subwavelength surface structures induced by femtosecond laser pulses on stainless steel.

    PubMed

    Qi, Litao; Nishii, Kazuhiro; Namba, Yoshiharu

    2009-06-15

    In this research, we studied the formation of laser-induced periodic surface structures on the stainless steel surface using femtosecond laser pulses. A 780 nm wavelength femtosecond laser, through a 0.2 mm pinhole aperture for truncating fluence distribution, was focused onto the stainless steel surface. Under different experimental condition, low-spatial-frequency laser-induced periodic surface structures with a period of 526 nm and high-spatial-frequency laser-induced periodic surface structures with a period of 310 nm were obtained. The mechanism of the formation of laser-induced periodic surface structures on the stainless steel surface is discussed.

  10. Perturbation Theory at Eight Loops: Novel Structures and the Breakdown of Manifest Conformality in N =4 Supersymmetric Yang-Mills Theory

    NASA Astrophysics Data System (ADS)

    Bourjaily, Jacob L.; Heslop, Paul; Tran, Vuong-Viet

    2016-05-01

    We use the soft-collinear bootstrap to construct the 8-loop integrand for the 4-point amplitude and 4-stress-tensor correlation function in planar maximally supersymmetric Yang-Mills theory. Both have a unique representation in terms of planar, conformal integrands grouped according to a hidden symmetry discovered for correlation functions. The answer we find exposes a fundamental tension between manifest locality and planarity with manifest conformality not seen at lower loops. For the first time, the integrand must include terms that are finite even on-shell and terms that are divergent even off-shell (so-called pseudoconformal integrals). We describe these novelties and their consequences in this Letter, and we make the full correlator and amplitude available as part of the Supplemental Material.

  11. CD5 Binds to Interleukin-6 and Induces a Feed-Forward Loop with the Transcription Factor STAT3 in B Cells to Promote Cancer.

    PubMed

    Zhang, Chunyan; Xin, Hong; Zhang, Wang; Yazaki, Paul J; Zhang, Zhifang; Le, Keith; Li, Wenzhao; Lee, Heehyoung; Kwak, Larry; Forman, Stephen; Jove, Richard; Yu, Hua

    2016-04-19

    The participation of a specific subset of B cells and how they are regulated in cancer is unclear. Here, we demonstrate that the proportion of CD5(+) relative to interleukin-6 receptor α (IL-6Rα)-expressing B cells was greatly increased in tumors. CD5(+) B cells responded to IL-6 in the absence of IL-6Rα. IL-6 directly bound to CD5, leading to activation of the transcription factor STAT3 via gp130 and its downstream kinase JAK2. STAT3 upregulated CD5 expression, thereby forming a feed-forward loop in the B cells. In mouse tumor models, CD5(+) but not CD5(-) B cells promoted tumor growth. CD5(+) B cells also showed activation of STAT3 in multiple types of human tumor tissues. Thus, our findings demonstrate a critical role of CD5(+) B cells in promoting cancer.

  12. Femtosecond laser-induced periodic surface structures on silica

    SciTech Connect

    Hoehm, S.; Rosenfeld, A.; Krueger, J.; Bonse, J.

    2012-07-01

    The formation of laser-induced periodic surface structures (LIPSS) on two different silica polymorphs (single-crystalline synthetic quartz and commercial fused silica glass) upon irradiation in air with multiple linearly polarized single- and double-fs-laser pulse sequences ({tau} = 150 fs pulse duration, {lambda} = 800 nm center wavelength, temporal pulse separation {Delta}t < 40 ps) is studied experimentally and theoretically. Two distinct types of fs-LIPSS [so-called low-spatial-frequency LIPSS (LSFL) and high-spatial-frequency LIPSS (HSFL)] with different spatial periods and orientations were identified. Their appearance was characterized with respect to the experimental parameters peak laser fluence and number of laser pulses per spot. Additionally, the 'dynamics' of the LIPSS formation was addressed in complementary double-fs-pulse experiments with varying delays, revealing a characteristic change of the LSFL periods. The experimental results are interpreted on the basis of a Sipe-Drude model considering the carrier dependence of the optical properties of fs-laser excited silica. This new approach provides an explanation of the LSFL orientation parallel to the laser beam polarisation in silica - as opposed to the behaviour of most other materials.

  13. Degradation pattern of photosystem II reaction center protein D1 in intact leaves. The major photoinhibition-induced cleavage site in D1 polypeptide is located amino terminally of the DE loop.

    PubMed Central

    Kettunen, R; Tyystjärvi, E; Aro, E M

    1996-01-01

    Photoinhibition-induced degradation of the D1 protein of the photosystem II reaction center was studied in intact pumpkin (Cucurbita pepo L.) leaves. Photoinhibition was observed to cause the cleavage of the D1 protein at two distinct sites. The main cleavage generated an 18-kD N-terminal and a 20-kD C-terminal degradation fragment of the D1 protein. this cleavage site was mapped to be located clearly N terminally of the DE loop. The other, less-frequent cleavage occurred at the DE loop and produced the well-documented 23-kD, N-terminal D1 degradation product. Furthermore, the 23-kD, N-terminal D1 fragment appears to be phosphorylated and can be detected only under severe photoinhibition in vivo. Comparison of the D1 degradation pattern after in vivo photoinhibition to that after in vitro acceptor-side and donor-side photoinhibition, performed with isolated photosystem II core particles, gives indirect evidence in support of donor-side photoinhibition in intact leaves. PMID:8756500

  14. Explaining Warm Coronal Loops

    NASA Technical Reports Server (NTRS)

    Klimchuk, James A.; Karpen, Judy T.; Patsourakos, Spiros

    2008-01-01

    One of the great mysteries of coronal physics that has come to light in the last few years is the discovery that warn (- 1 INK) coronal loops are much denser than expected for quasi-static equilibrium. Both the excess densities and relatively long lifetimes of the loops can be explained with bundles of unresolved strands that are heated impulsively to very high temperatures. Since neighboring strands are at different stages of cooling, the composite loop bundle is multi-thermal, with the distribution of temperatures depending on the details of the "nanoflare storm." Emission hotter than 2 MK is predicted, but it is not clear that such emission is always observed. We consider two possible explanations for the existence of over-dense warm loops without corresponding hot emission: (1) loops are bundles of nanoflare heated strands, but a significant fraction of the nanoflare energy takes the form of a nonthermal electron beam rather then direct plasma heating; (2) loops are bundles of strands that undergo thermal nonequilibrium that results when steady heating is sufficiently concentrated near the footpoints. We present numerical hydro simulations of both of these possibilities and explore the observational consequences, including the production of hard X-ray emission and absorption by cool material in the corona.

  15. A feed-back regulatory loop between glycerol-3-phosphate and lipid transfer proteins DIR1 and AZI1 mediates azelaic acid-induced systemic immunity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Systemic acquired resistance (SAR), a highly desirable form of plant defense, provides broad-spectrum immunity against diverse pathogens. The recent identification of seemingly unrelated chemical inducers of SAR warrants an investigation of their mutual interrelationships. We show that SAR induced b...

  16. Irradiation-induced formation of nanocrystallites with C15 Laves phase structure in bcc iron.

    PubMed

    Marinica, M-C; Willaime, F; Crocombette, J-P

    2012-01-13

    A three-dimensional periodic structure is proposed for self-interstitial clusters in body-centered-cubic metals, as opposed to the conventional two-dimensional loop morphology. The underlying crystal structure corresponds to the C15 Laves phase. Using density functional theory and interatomic potential calculations, we demonstrate that in α-iron these C15 aggregates are highly stable and immobile and that they exhibit large antiferromagnetic moments. They form directly in displacement cascades, and they can grow by capturing self-interstitials. They thus constitute an important new element to account for when predicting the microstructural evolution of iron base materials under irradiation.

  17. Atomic Force Microscopy Studies on DNA Structural Changes Induced by Vincristine Sulfate and Aspirin

    NASA Astrophysics Data System (ADS)

    Zhu, Yi; Zeng, Hu; Xie, Jianming; Ba, Long; Gao, Xiang; Lu, Zuhong

    2004-04-01

    We report that atomic force microscopy (AFM) studies on structural variations of a linear plasmid DNA interact with various concentrations of vincristine sulfate and aspirin. The different binding images show that vincrinstine sulfate binding DNA chains caused some loops and cleavages of the DNA fragments, whereas aspirin interaction caused the width changes and conformational transition of the DNA fragments. Two different DNA structural alternations could be explained by the different mechanisms of the interactions with these two components. Our work indicates that the AFM is a powerful tool in studying the interaction between DNA and small molecules.

  18. Mechanistic Insight into Bunyavirus-Induced Membrane Fusion from Structure-Function Analyses of the Hantavirus Envelope Glycoprotein Gc

    PubMed Central

    Stettner, Eva; Jeffers, Scott Allen; Pérez-Vargas, Jimena; Pehau-Arnaudet, Gerard; Tortorici, M. Alejandra; Jestin, Jean-Luc; England, Patrick; Tischler, Nicole D.; Rey, Félix A.

    2016-01-01

    Hantaviruses are zoonotic viruses transmitted to humans by persistently infected rodents, giving rise to serious outbreaks of hemorrhagic fever with renal syndrome (HFRS) or of hantavirus pulmonary syndrome (HPS), depending on the virus, which are associated with high case fatality rates. There is only limited knowledge about the organization of the viral particles and in particular, about the hantavirus membrane fusion glycoprotein Gc, the function of which is essential for virus entry. We describe here the X-ray structures of Gc from Hantaan virus, the type species hantavirus and responsible for HFRS, both in its neutral pH, monomeric pre-fusion conformation, and in its acidic pH, trimeric post-fusion form. The structures confirm the prediction that Gc is a class II fusion protein, containing the characteristic β-sheet rich domains termed I, II and III as initially identified in the fusion proteins of arboviruses such as alpha- and flaviviruses. The structures also show a number of features of Gc that are distinct from arbovirus class II proteins. In particular, hantavirus Gc inserts residues from three different loops into the target membrane to drive fusion, as confirmed functionally by structure-guided mutagenesis on the HPS-inducing Andes virus, instead of having a single “fusion loop”. We further show that the membrane interacting region of Gc becomes structured only at acidic pH via a set of polar and electrostatic interactions. Furthermore, the structure reveals that hantavirus Gc has an additional N-terminal “tail” that is crucial in stabilizing the post-fusion trimer, accompanying the swapping of domain III in the quaternary arrangement of the trimer as compared to the standard class II fusion proteins. The mechanistic understandings derived from these data are likely to provide a unique handle for devising treatments against these human pathogens. PMID:27783711

  19. Miniature loops in the solar corona

    NASA Astrophysics Data System (ADS)

    Barczynski, K.; Peter, H.; Savage, S. L.

    2017-03-01

    Context. Magnetic loops filled with hot plasma are the main building blocks of the solar corona. Usually they have lengths of the order of the barometric scale height in the corona that is 50 Mm. Aims: Previously it has been suggested that miniature versions of hot loops exist. These would have lengths of only 1 Mm barely protruding from the chromosphere and spanning across just one granule in the photosphere. Such short loops are well established at transition region temperatures (0.1 MK), and we investigate if such miniature loops also exist at coronal temperatures (>1 MK). Methods: We used extreme UV (EUV) imaging observations from the High-resolution Coronal Imager (Hi-C) at an unprecedented spatial resolution of 0.3'' to 0.4''. Together with EUV imaging and magnetogram data from the Solar Dynamics Observatory (SDO) and X-Ray Telescope (XRT) data from Hinode we investigated the spatial, temporal and thermal evolution of small loop-like structures in the solar corona above a plage region close to an active region and compared this to a moss area within the active region. Results: We find that the size, motion and temporal evolution of the loop-like features are consistent with photospheric motions, suggesting a close connection to the photospheric magnetic field. Aligned magnetograms show that one of their endpoints is rooted at a magnetic concentration. Their thermal structure, as revealed together with the X-ray observations, shows significant differences to moss-like features. Conclusions: Considering different scenarios, these features are most probably miniature versions of hot loops rooted at magnetic concentrations at opposite sides of a granule in small emerging magnetic loops (or flux tubes).

  20. The importance of slow motions for protein functional loops.

    PubMed

    Skliros, Aris; Zimmermann, Michael T; Chakraborty, Debkanta; Saraswathi, Saras; Katebi, Ataur R; Leelananda, Sumudu P; Kloczkowski, Andrzej; Jernigan, Robert L

    2012-02-07

    Loops in proteins that connect secondary structures such as alpha-helix and beta-sheet, are often on the surface and may play a critical role in some functions of a protein. The mobility of loops is central for the motional freedom and flexibility requirements of active-site loops and may play a critical role for some functions. The structures and behaviors of loops have not been studied much in the context of the whole structure and its overall motions, especially how these might be coupled. Here we investigate loop motions by using coarse-grained structures (C(α) atoms only) to solve the motions of the system by applying Lagrange equations with elastic network models to learn about which loops move in an independent fashion and which move in coordination with domain motions, faster and slower, respectively. The normal modes of the system are calculated using eigen-decomposition of the stiffness matrix. The contribution of individual modes and groups of modes is investigated for their effects on all residues in each loop by using Fourier analyses. Our results indicate overall that the motions of functional sets of loops behave in similar ways as the whole structure. But overall only a relatively few loops move in coordination with the dominant slow modes of motion, and these are often closely related to function.

  1. Chromatin structure and ionizing-radiation-induced chromosome aberrations

    SciTech Connect

    Muehlmann-Diaz, M.C.

    1993-01-01

    The possible influence of chromatic structure or activity on chromosomal radiosensitivity was studied. A cell line was isolated which contained some 10[sup 5] copies of an amplified plasmid in a single large mosquito artificial chromosome (MAC). This chromosome was hypersensitive to DNase I. Its radiosensitivity was some three fold greater than normal mosquito chromosomes in the same cell. In cultured human cells irradiated during G[sub 0], the initial breakage frequency in chromosome 4, 19 and the euchromatic and heterochromatic portions of the Y chromosome were measured over a wide range of doses by inducing Premature Chromosome Condensation (PCC) immediately after irradiation with Cs-137 gamma rays. No evidence was seen that Y heterochromatin or large fragments of it remained unbroken. The only significant deviation from the expected initial breakage frequency per Gy per unit length of chromosome was that observed for the euchromatic portion of the Y chromosome, with breakage nearly twice that expected. The development of aberrations involving X and Y chromosomes at the first mitosis after irradation was also studied. Normal female cells sustained about twice the frequency of aberrations involving X chromosomes for a dose of 7.3 Gy than the corresponding male cells. Fibroblasts from individuals with supernumerary X chromosomes did not show any further increase in X aberrations for this dos. The frequency of aberrations involving the heterochromatic portion of the long arm of the Y chromosome was about what would be expected for a similar length of autosome, but the euchromatic portion of the Y was about 3 times more radiosensitive per unit length. 5-Azacytidine treatment of cultured human female fibroblasts or fibroblasts from a 49,XXXXY individual, reduced the methylation of cytosine residues in DNA, and resulted in an increased chromosomal radiosensitivity in general, but it did not increase the frequency of aberrations involving the X chromosomes.

  2. Oriented Connectivity-Based Method for Segmenting Solar Loops

    NASA Technical Reports Server (NTRS)

    Lee, J. K.; Newman, T. S.; Gary, G. A.

    2005-01-01

    A method based on oriented connectivity that can automatically segnient arc-like structures (solar loops) from intensity images of the Sun's corona is introduced. The method is a constructive approach that uses model-guided processing to enable extraction of credible loop structures. Since the solar loops are vestiges of the solar magnetic field, the model-guided processing exploits external estimates of this field s local orientations that are derived from a physical magnetic field model. Empirical studies of the method s effectiveness are also presented. The Oriented Connectivity- Based Method is the first automatic method for the segmentation of solar loops.

  3. Modulation of DNA loop lifetimes by the free energy of loop formation

    PubMed Central

    Chen, Yi-Ju; Johnson, Stephanie; Mulligan, Peter; Spakowitz, Andrew J.; Phillips, Rob

    2014-01-01

    Storage and retrieval of the genetic information in cells is a dynamic process that requires the DNA to undergo dramatic structural rearrangements. DNA looping is a prominent example of such a structural rearrangement that is essential for transcriptional regulation in both prokaryotes and eukaryotes, and the speed of such regulations affects the fitness of individuals. Here, we examine the in vitro looping dynamics of the classic Lac repressor gene-regulatory motif. We show that both loop association and loop dissociation at the DNA-repressor junctions depend on the elastic deformation of the DNA and protein, and that both looping and unlooping rates approximately scale with the looping J factor, which reflects the system’s deformation free energy. We explain this observation by transition state theory and model the DNA–protein complex as an effective worm-like chain with twist. We introduce a finite protein–DNA binding interaction length, in competition with the characteristic DNA deformation length scale, as the physical origin of the previously unidentified loop dissociation dynamics observed here, and discuss the robustness of this behavior to perturbations in several polymer parameters. PMID:25411314

  4. Decay-less kink oscillations in coronal loops

    NASA Astrophysics Data System (ADS)

    Anfinogentov, S.; Nisticò, G.; Nakariakov, V. M.

    2013-12-01

    Context. Kink oscillations of coronal loops in an off-limb active region are detected with the Imaging Assembly Array (AIA) instruments of the Solar Dynamics Observatory (SDO) at 171 Å. Aims: We aim to measure periods and amplitudes of kink oscillations of different loops and to determinate the evolution of the oscillation phase along the oscillating loop. Methods: Oscillating coronal loops were visually identified in the field of view of SDO/AIA and STEREO/EUVI-A: the loop length was derived by three-dimensional analysis. Several slits were taken along the loops to assemble time-distance maps. We identified oscillatory patterns and retrieved periods and amplitudes of the oscillations. We applied the cross-correlation technique to estimate the phase shift between oscillations at different segments of oscillating loops. Results: We found that all analysed loops show low-amplitude undamped transverse oscillations. Oscillation periods of loops in the same active region range from 2.5 to 11 min, and are different for different loops. The displacement amplitude is lower than 1 Mm. The oscillation phase is constant along each analysed loop. The spatial structure of the phase of the oscillations corresponds to the fundamental standing kink mode. We conclude that the observed behaviour is consistent with the empirical model in terms of a damped harmonic resonator affected by a non-resonant continuously operating external force. A movie is available in electronic form at http://www.aanda.org

  5. R loops: new modulators of genome dynamics and function.

    PubMed

    Santos-Pereira, José M; Aguilera, Andrés

    2015-10-01

    R loops are nucleic acid structures composed of an RNA-DNA hybrid and a displaced single-stranded DNA. Recently, evidence has emerged that R loops occur more often in the genome and have greater physiological relevance, including roles in transcription and chromatin structure, than was previously predicted. Importantly, however, R loops are also a major threat to genome stability. For this reason, several DNA and RNA metabolism factors prevent R-loop formation in cells. Dysfunction of these factors causes R-loop accumulation, which leads to replication stress, genome instability, chromatin alterations or gene silencing, phenomena that are frequently associated with cancer and a number of genetic diseases. We review the current knowledge of the mechanisms controlling R loops and their putative relationship with disease.

  6. eIF4B stimulates translation of long mRNAs with structured 5′ UTRs and low closed-loop potential but weak dependence on eIF4G

    PubMed Central

    Sen, Neelam Dabas; Zhou, Fujun; Harris, Michael S.; Ingolia, Nicholas T.

    2016-01-01

    DEAD-box RNA helicases eukaryotic translation initiation factor 4A (eIF4A) and Ded1 promote translation by resolving mRNA secondary structures that impede preinitiation complex (PIC) attachment to mRNA or scanning. Eukaryotic translation initiation factor 4B (eIF4B) is a cofactor for eIF4A but also might function independently of eIF4A. Ribosome profiling of mutants lacking eIF4B or with impaired eIF4A or Ded1 activity revealed that eliminating eIF4B reduces the relative translational efficiencies of many more genes than does inactivation of eIF4A, despite comparable reductions in bulk translation, and few genes display unusually strong requirements for both factors. However, either eliminating eIF4B or inactivating eIF4A preferentially impacts mRNAs with longer, more structured 5′ untranslated regions (UTRs). These findings reveal an eIF4A-independent role for eI