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Sample records for linker substructure common

  1. Towards optimization of the linker substructure common to transthyretin amyloidogenesis inhibitors using biochemical and structural studies

    PubMed Central

    Johnson, Steven M.; Connelly, Stephen; Wilson, Ian A.; Kelly, Jeffery W.

    2008-01-01

    To develop potent and highly selective transthyretin (TTR) amyloidogenesis inhibitors, it is useful to systematically optimize the three substructural elements that compose a typical TTR kinetic stabilizer: the two aryl rings and the linker joining them. Herein, we evaluated 40 bisaryl molecules based on 10 unique linker substructures to determine how these linkages influence inhibitor potency and selectivity. These linkers connect one unsubstituted aromatic ring to either a 3,5-X2 or a 3,5-X2-4-OH phenyl substructure (X=Br or CH3). Co-consideration of amyloid inhibition and ex vivo plasma TTR binding selectivity data reveal that direct connection of the two aryls, or linkage through non-polar E-olefin or –CH2CH2– substructures generates the most potent and selective TTR amyloidogenesis inhibitors exhibiting minimal undesirable binding to the thyroid hormone nuclear receptor or the COX-1 enzyme. Five high-resolution TTR•inhibitor crystal structures (1.4−1.8 Å) provide insight into why such linkers afford inhibitors with greater potency and selectivity. PMID:18811132

  2. Common substructure in otoacoustic emission spectra of land vertebrates

    NASA Astrophysics Data System (ADS)

    Manley, Geoffrey A.; Köppl, Christine; Bergevin, Christopher

    2015-12-01

    In humans, a similar spectral periodicity is found in all otoacoustic emission types and in threshold fine structure. This may reflect travelling wave phase and reflectance from "structural roughness" in the organ of Corti, or entrainment and suppressive interactions between emissions. To further understand these phenomena, we have examined spontaneous otoacoustic emission (SOAE) spectra in 9 lizard species and the barn owl and find a comparable periodicity. Importantly, the frequency spacing between SOAE peaks was independent of the physical spacing and of the frequency space constants in hearing organs. In 9 lizard species, median spectral gaps lay between 219 and 461 Hz, with no correlation to papillar length (0.3 to 2.1 mm). Similarly in much longer organs: In humans (35 mm), SOAE spectral gaps vary up to 220 Hz at 4 kHz; in the barn owl (11 mm), the median SOAE peak spacing was 395Hz. In the barn owl, a very large space constant between 5 and 10 kHz (5 mm/octave) contrasts with stable SOAE spacing between 1 and 11 kHz. Similar SOAE spectral gaps across all species suggests they represent a basic frequency grating revealing local phase-dependent interactions between active hair cells, a feature not determined by macro-structural anatomy. Emission spectral spacing is independent of cochlear length, of the frequency space constant, of the existence of travelling waves or of a tectorial membrane. Our data suggest that there are greater similarities between frequency selectivity reflected at the level of the hair cells' spontaneous mechanical output (OAEs) than there are at the level of the auditory nerve, where macro-structural anatomy links hair-cell activity differentially to the neural output. Apparently, all hair-cell arrays show a similar frequency substructure not directly replicated in neural tuning.

  3. Toward Optimization of the Second Aryl Substructure Common to Transthyretin Amyloidogenesis Inhibitors Using Biochemical and Structural Studies

    PubMed Central

    Johnson, Steven M.; Connelly, Stephen; Wilson, Ian A.; Kelly, Jeffery W.

    2009-01-01

    Transthyretin (TTR) amyloidogenesis inhibitors are typically composed of two aromatic rings and a linker. We have previously established optimal structures for one aromatic ring and the linker. Herein, we employ a suboptimal linker and an optimal aryl-X substructure to rank order the desirability of aryl-Z substructures–using a library of 56 N-(3,5-dibromo-4-hydroxyphenyl)benzamides. Co-consideration of amyloid inhibition potency and ex-vivo plasma TTR binding selectivity data reveal that 2,6; 2,5; 2; 3,4,5 and 3,5 aryls bearing small substituents generate the most potent and selective inhibitors, in descending order. These benzamides generally lack undesirable thyroid hormone receptor binding and COX-1 inhibition activity. Three high-resolution TTR•inhibitor crystal structures (1.31-1.35 Å) provide insight into why these inhibitors are potent and selective, enabling future structure-based design of TTR kinetic stabilizers. PMID:19191553

  4. Representing clusters using a maximum common edge substructure algorithm applied to reduced graphs and molecular graphs.

    PubMed

    Gardiner, Eleanor J; Gillet, Valerie J; Willett, Peter; Cosgrove, David A

    2007-01-01

    Chemical databases are routinely clustered, with the aim of grouping molecules which share similar structural features. Ideally, medicinal chemists are then able to browse a few representatives of the cluster in order to interpret the shared activity of the cluster members. However, when molecules are clustered using fingerprints, it may be difficult to decipher the structural commonalities which are present. Here, we seek to represent a cluster by means of a maximum common substructure based on the shared functionality of the cluster members. Previously, we have used reduced graphs, where each node corresponds to a generalized functional group, as topological molecular descriptors for virtual screening. In this work, we precluster a database using any clustering method. We then represent the molecules in a cluster as reduced graphs. By repeated application of a maximum common edge substructure (MCES) algorithm, we obtain one or more reduced graph cluster representatives. The sparsity of the reduced graphs means that the MCES calculations can be performed in real time. The reduced graph cluster representatives are readily interpretable in terms of functional activity and can be mapped directly back to the molecules to which they correspond, giving the chemist a rapid means of assessing potential activities contained within the cluster. Clusters of interest are then subject to a detailed R-group analysis using the same iterated MCES algorithm applied to the molecular graphs. PMID:17309248

  5. CLCA: maximum common molecular substructure queries within the MetRxn database.

    PubMed

    Kumar, Akhil; Maranas, Costas D

    2014-12-22

    The challenge of automatically identifying the preserved molecular moieties in a chemical reaction is referred to as the atom mapping problem. Reaction atom maps provide the ability to locate the fate of individual atoms across an entire metabolic network. Atom maps are used to track atoms in isotope labeling experiments for metabolic flux elucidation, trace novel biosynthetic routes to a target compound, and contrast entire pathways for structural homology. However, rapid computation of the reaction atom mappings remains elusive despite significant research. We present a novel substructure search algorithm, canonical labeling for clique approximation (CLCA), with polynomial run-time complexity to quickly generate atom maps for all the reactions present in MetRxn. CLCA uses number theory (i.e., prime factorization) to generate canonical labels or unique IDs and identify a bijection between the vertices (atoms) of two distinct molecular graphs. CLCA utilizes molecular graphs generated by combining atomistic information on reactions and metabolites from 112 metabolic models and 8 metabolic databases. CLCA offers improvements in run time, accuracy, and memory utilization over existing heuristic and combinatorial maximum common substructure (MCS) search algorithms. We provide detailed examples on the various advantages as well as failure modes of CLCA over existing algorithms. PMID:25412255

  6. O-xylosylation in a recombinant protein is directed at a common motif on glycine-serine linkers.

    PubMed

    Spencer, David; Novarra, Shabazz; Zhu, Liang; Mugabe, Sheila; Thisted, Thomas; Baca, Manuel; Depaz, Roberto; Barton, Christopher

    2013-11-01

    Glycine-serine (GS) linkers are commonly used in recombinant proteins to connect domains. Here, we report the posttranslational O-glycosylation of a GS linker in a novel fusion protein. The structure of the O-glycan moiety is a xylose-based core substituted with hexose and sulfated hexauronic acid residues. The total level of O-xylosylation was approximately 30% in the material expressed in HEK-293 cell lines. There was an approximate 10-fold reduction in O-xylosylation levels when the material was expressed in Chinese hamster ovary cell lines. Similar O-glycan structures have been reported for human urinary thrombomodulin and represent the initial building block for proteoglycans such as chondroitin sulfate and heparin. The sites of attachment, determined by electron transfer dissociation mass spectrometry, were localized to serine in the linker regions of the recombinant fusion protein. This attachment could be attributed, in part, to the inherent xylosyltransferase motif present in GS linkers. Elimination of the O-glycan moiety was achieved with modified linkers containing only glycine residues. The aggregation and fragmentation behavior of the GGG construct were comparable to the GSG-linked material during thermal stress. The O-xylosylation reported has implications for the manufacturing consistency of recombinant proteins containing GS linkers. PMID:24105735

  7. A relational extension of the notion of motifs: application to the common 3D protein substructures searching problem.

    PubMed

    Pisanti, Nadia; Soldano, Henry; Carpentier, Mathilde; Pothier, Joel

    2009-12-01

    The geometrical configurations of atoms in protein structures can be viewed as approximate relations among them. Then, finding similar common substructures within a set of protein structures belongs to a new class of problems that generalizes that of finding repeated motifs. The novelty lies in the addition of constraints on the motifs in terms of relations that must hold between pairs of positions of the motifs. We will hence denote them as relational motifs. For this class of problems, we present an algorithm that is a suitable extension of the KMR paradigm and, in particular, of the KMRC as it uses a degenerate alphabet. Our algorithm contains several improvements that become especially useful when-as it is required for relational motifs-the inference is made by partially overlapping shorter motifs, rather than concatenating them. The efficiency, correctness and completeness of the algorithm is ensured by several non-trivial properties that are proven in this paper. The algorithm has been applied in the important field of protein common 3D substructure searching. The methods implemented have been tested on several examples of protein families such as serine proteases, globins and cytochromes P450 additionally. The detected motifs have been compared to those found by multiple structural alignments methods. PMID:20047489

  8. Automated design of flexible linkers.

    PubMed

    Manion, Charles; Arlitt, Ryan; Campbell, Matthew I; Tumer, Irem; Stone, Rob; Greaney, P Alex

    2016-03-14

    This paper presents a method for the systematic and automated design of flexible organic linkers for construction of metal organic-frameworks (MOFs) in which flexibility, compliance, or other mechanically exotic properties originate at the linker level rather than from the framework kinematics. Our method couples a graph grammar method for systematically generating linker like molecules with molecular dynamics modeling of linkers' mechanical response. Using this approach we have generated a candidate pool of >59,000 hypothetical linkers. We screen linker candidates according to their mechanical behaviors under large deformation, and extract fragments common to the most performant candidate materials. To demonstrate the general approach to MOF design we apply our system to designing linkers for pressure switching MOFs-MOFs that undergo reversible structural collapse after a stress threshold is exceeded. PMID:26687337

  9. Antibodies directed to drug epitopes to investigate the structure of drug-protein photoadducts. Recognition of a common photobound substructure in tiaprofenic acid/ketoprofen cross-photoreactivity.

    PubMed

    Lahoz, A; Hernández, D; Miranda, M A; Pérez-Prieto, J; Morera, I M; Castell, J V

    2001-11-01

    Drug-induced photoallergy is an immune adverse reaction to the combined effect of drugs and light. From the mechanistic point of view, it first involves covalent binding of drug to protein resulting in the formation of a photoantigen. Hence, determination of the structures of drug-protein photoadducts is of great relevance to understand the molecular basis of photoallergy and cross-immunoreactivity among drugs. Looking for new strategies to investigate the covalent photobinding of drugs to proteins, we generated highly specific antibodies to drug chemical substructures. The availability of such antibodies has allowed us to discriminate between the different modes by which tiaprofenic acid (TPA), suprofen (SUP), and ketoprofen (KTP) photobind to proteins. The finding that the vast majority of the TPA photoadduct can be accounted for by means of antibody anti-benzoyl strongly supports the view that the drug binds preferentially via the thiophene ring, leaving the benzene ring more accessible. By contrast, selective recognition of SUP-protein photoadducts by antibody anti-thenoyl evidences a preferential coupling via the benzene ring leaving the thiophene moiety more distant from the protein matrix. In the case of KTP, photoadducts are exclusively recognized by antibody anti-benzoyl, indicating that the benzene ring is again more accessible. As a result of this research, we have been able to identify a common substructure that is present in TPA-albumin and KTP-albumin photoadducts. This is remarkable since, at a first sight, the greatest structural similarities can be found between TPA and SUP as they share the same benzoylthiophene chromophore. These findings can explain the previously reported observations of cross-reactivity to KTP (or TPA) in patients photosensitized to TPA (or KTP). PMID:11712905

  10. Substructural controller synthesis

    NASA Technical Reports Server (NTRS)

    Su, Tzu-Jeng; Craig, Roy R., Jr.

    1989-01-01

    A decentralized design procedure which combines substructural synthesis, model reduction, decentralized controller design, subcontroller synthesis, and controller reduction is proposed for the control design of flexible structures. The structure to be controlled is decomposed into several substructures, which are modeled by component mode synthesis methods. For each substructure, a subcontroller is designed by using the linear quadratic optimal control theory. Then, a controller synthesis scheme called Substructural Controller Synthesis (SCS) is used to assemble the subcontrollers into a system controller, which is to be used to control the whole structure.

  11. Jet Substructure Without Trees

    SciTech Connect

    Jankowiak, Martin; Larkoski, Andrew J.; /SLAC /Stanford U., ITP

    2011-08-19

    We present an alternative approach to identifying and characterizing jet substructure. An angular correlation function is introduced that can be used to extract angular and mass scales within a jet without reference to a clustering algorithm. This procedure gives rise to a number of useful jet observables. As an application, we construct a top quark tagging algorithm that is competitive with existing methods. In preparation for the LHC, the past several years have seen extensive work on various aspects of collider searches. With the excellent resolution of the ATLAS and CMS detectors as a catalyst, one area that has undergone significant development is jet substructure physics. The use of jet substructure techniques, which probe the fine-grained details of how energy is distributed in jets, has two broad goals. First, measuring more than just the bulk properties of jets allows for additional probes of QCD. For example, jet substructure measurements can be compared against precision perturbative QCD calculations or used to tune Monte Carlo event generators. Second, jet substructure allows for additional handles in event discrimination. These handles could play an important role at the LHC in discriminating between signal and background events in a wide variety of particle searches. For example, Monte Carlo studies indicate that jet substructure techniques allow for efficient reconstruction of boosted heavy objects such as the W{sup {+-}} and Z{sup 0} gauge bosons, the top quark, and the Higgs boson.

  12. Substructure system identification and synthesis

    NASA Technical Reports Server (NTRS)

    Su, Tzu-Jeng; Juang, Jer-Nan

    1993-01-01

    This paper explores the possibility of performing system identification at the substructure level and then synthesizing the results to obtain a mathematical model for the assembled structure. The study here shows that in order to enforce interface compatibility and equilibrium conditions to the substructure test data, it is necessary to place collocated actuator/sensor pair at every interface degree-of-freedom. Procedures for assembling substructure transfer function data, substructure state-space models, and substructure Markov parameters are presented. Testing difficulties and possible solutions are also discussed. A numerical simulation example is included to illustrate the proposed substructure synthesis methods.

  13. Chapter 6: Energy Storage in Cellulase Linker Peptides?

    SciTech Connect

    McCabe, C.; Zhao, X.; Adney, W. S.; Himmel, M. E.

    2010-01-01

    In this chapter, we discuss the use of molecular dynamics simulations and free-energy calculations to investigate the possible role the linker polypeptide, common to many cellulase enzymes, plays in the enzymatic hydrolysis of cellulose. In particular, we focus on the linker polypeptide from cellobiohydrolase I (CBH I) from Trichoderma reesei, which is one of the most active cellulase enzymes. CBH I is a multi-domain enzyme, consisting of a large catalytic domain containing an active site tunnel and a small cellulose binding module, which are joined together by a 27-amino-acid residue linker peptide. CBH I is believed to hydrolyze cellulose in a 'processive' manner; however, the exact mechanism of the depolymerization of cellulose by CBH I is not fully understood. It has been hypothesized that the flexible interdomain linker mediates a caterpillar-like motion that enables the enzyme to move along the cellodextrin strand. Although the linker polypeptide sequence is known, the spatial conformation adopted by the linker domain and its role in the hydrolysis process, if any, has yet to be determined. The simulation results obtained to date indicate that the CBH I linker's free energy is critically dependent on the existence of the cellulose substrate and the stretching/compression pathway adopted. In the presence of a cellulose surface, simulations suggest that the linker exhibits two stable states, which would support the hypothesis that the linker peptide has the capacity to store energy in a manner similar to a spring and facilitate a caterpillar-like motion.

  14. Rigid substructure search

    PubMed Central

    Shirvanyants, David; Alexandrova, Anastassia N.; Dokholyan, Nikolay V.

    2011-01-01

    Motivation: Identifying the location of binding sites on proteins is of fundamental importance for a wide range of applications, including molecular docking, de novo drug design, structure identification and comparison of functional sites. Here we present Erebus, a web server that searches the entire Protein Data Bank for a given substructure defined by a set of atoms of interest, such as the binding scaffolds for small molecules. The identified substructure contains atoms having the same names, belonging to same amino acids and separated by the same distances (within a given tolerance) as the atoms of the query structure. The accuracy of a match is measured by the root-mean-square deviation or by the normal weight with a given variance. Tests show that our approach can reliably locate rigid binding scaffolds of drugs and metal ions. Availability and Implementation: We provide this service through a web server at http://erebus.dokhlab.org. Contact: dokh@unc.edu PMID:21460026

  15. Transients by substructuring with DMAP

    NASA Technical Reports Server (NTRS)

    Butler, T. G.

    1978-01-01

    Automated substructuring in level 16 of NASTRAN was employed as a preface to the solution of a direct transient analysis. The DMAP ALTER statements written to adapt the substructuring for transient purposes are explained. Data recovery was accomplished with transfer functions. Proof of the success of the method is presented with an application to a missile structure.

  16. Design and characterization of structured protein linkers with differing flexibilities

    PubMed Central

    Klein, Joshua S.; Jiang, Siduo; Galimidi, Rachel P.; Keeffe, Jennifer R.; Bjorkman, Pamela J.

    2014-01-01

    Engineered fusion proteins containing two or more functional polypeptides joined by a peptide or protein linker are important for many fields of biological research. The separation distance between functional units can impact epitope access and the ability to bind with avidity; thus the availability of a variety of linkers with different lengths and degrees of rigidity would be valuable for protein design efforts. Here, we report a series of designed structured protein linkers incorporating naturally occurring protein domains and compare their properties to commonly used Gly4Ser repeat linkers. When incorporated into the hinge region of an immunoglobulin G (IgG) molecule, flexible Gly4Ser repeats did not result in detectable extensions of the IgG antigen-binding domains, in contrast to linkers including more rigid domains such as β2-microglobulin, Zn-α2-glycoprotein and tetratricopeptide repeats. This study adds an additional set of linkers with varying lengths and rigidities to the available linker repertoire, which may be useful for the construction of antibodies with enhanced binding properties or other fusion proteins. PMID:25301959

  17. Proposed definition of crystal substructure and substructural similarity

    NASA Astrophysics Data System (ADS)

    Yang, Lusann; Dacek, Stephen; Ceder, Gerbrand

    2014-08-01

    There is a clear need for a practical and mathematically rigorous description of local structure in inorganic compounds so that structures and chemistries can be easily compared across large data sets. Here a method for decomposing crystal structures into substructures is given, and a similarity function between those substructures is defined. The similarity function is based on both geometric and chemical similarity. This construction allows for large-scale data mining of substructural properties, and the analysis of substructures and void spaces within crystal structures. The method is validated via the prediction of Li-ion intercalation sites for the oxides. Tested on databases of known Li-ion-containing oxides, the method reproduces all Li-ion sites in an oxide with a maximum of 4 incorrect guesses 80% of the time.

  18. Surviving gas expulsion with substructure

    NASA Astrophysics Data System (ADS)

    Lee, Paweł L.; Goodwin, Simon P.

    2016-08-01

    We investigate the reaction of clumpy stellar distributions to gas expulsion. We show that regions containing highly unbound substructures/subclusters after gas expulsion can produce a significant final bound cluster. The key quantity in determining if a region is able to form a bound cluster is the global virial ratio, and so regions must be looked at as a whole rather than by an individual substructure/subclusters, when determining if they might survive as a bound cluster.

  19. Cellulase Linkers Are Optimized Based on Domain Type and Function: Insights from Sequence Analysis, Biophysical Measurements, and Molecular Simulation

    PubMed Central

    Sammond, Deanne W.; Payne, Christina M.; Brunecky, Roman; Himmel, Michael E.; Crowley, Michael F.; Beckham, Gregg T.

    2012-01-01

    Cellulase enzymes deconstruct cellulose to glucose, and are often comprised of glycosylated linkers connecting glycoside hydrolases (GHs) to carbohydrate-binding modules (CBMs). Although linker modifications can alter cellulase activity, the functional role of linkers beyond domain connectivity remains unknown. Here we investigate cellulase linkers connecting GH Family 6 or 7 catalytic domains to Family 1 or 2 CBMs, from both bacterial and eukaryotic cellulases to identify conserved characteristics potentially related to function. Sequence analysis suggests that the linker lengths between structured domains are optimized based on the GH domain and CBM type, such that linker length may be important for activity. Longer linkers are observed in eukaryotic GH Family 6 cellulases compared to GH Family 7 cellulases. Bacterial GH Family 6 cellulases are found with structured domains in either N to C terminal order, and similar linker lengths suggest there is no effect of domain order on length. O-glycosylation is uniformly distributed across linkers, suggesting that glycans are required along entire linker lengths for proteolysis protection and, as suggested by simulation, for extension. Sequence comparisons show that proline content for bacterial linkers is more than double that observed in eukaryotic linkers, but with fewer putative O-glycan sites, suggesting alternative methods for extension. Conversely, near linker termini where linkers connect to structured domains, O-glycosylation sites are observed less frequently, whereas glycines are more prevalent, suggesting the need for flexibility to achieve proper domain orientations. Putative N-glycosylation sites are quite rare in cellulase linkers, while an N-P motif, which strongly disfavors the attachment of N-glycans, is commonly observed. These results suggest that linkers exhibit features that are likely tailored for optimal function, despite possessing low sequence identity. This study suggests that cellulase

  20. Fatigue of fiberglass beam substructures

    SciTech Connect

    Mandell, J.F.; Combs, D.W.; Samborsky, D.D.

    1995-09-01

    Composite material beams representative of wind turbine blade substructure have been designed, fabricated, and tested under constant amplitude flexural fatigue loading. Beam stiffness, strength, and fatigue life are predicted based on detailed finite element analysis and the materials fatigue database developed using standard test coupons and special high frequency minicoupons.Beam results are in good agreement with predictions when premature adhesive and delamination failures are avoided in the load transfer areas. The results show that fiberglass substructures can be designed and fabricated to withstand maximum strain levels on the order of 8,000 microstrain for about 10{sup 6} cycles with proper structural detail design and the use of fatigue resistant laminate constructions. The study also demonstrates that the materials fatigue database and accurate analysis can be used to predict the fatigue life of composite substructures typical of blades.

  1. Substructure Search by Set Reduction

    ERIC Educational Resources Information Center

    Figueras, John

    1972-01-01

    The set reduction algorithm is based on set theory and Boolean algebra rather than the graph-theoretic approach. Time trials with a small file of organic chemical structures indicate that the algorithm can be economically used for substructure (or complete structure) sequential searches on a file containing 30,000-50,000 computer-coded structures.…

  2. Dynamic substructuring for shock spectrum analysis using component mode synthesis

    NASA Technical Reports Server (NTRS)

    Mcpheeters, Barton W.; Lev, Avivi; Bogert, Philip B.; Scavuzzo, Rudolph J.

    1988-01-01

    Component mode synthesis was used to analyze different types of structures with MSC NASTRAN. The theory and technique of using Multipoint Constraint Equations (MPCs) to connect substructures to each other or to a common foundation is presented. Computation of the dynamic response of the system from shack spectrum inputs was automated using the DMAP programming language of the MSC NASTRAN finite element code.

  3. A traceless photocleavable linker for the automated glycan assembly of carbohydrates with free reducing ends.

    PubMed

    Wilsdorf, M; Schmidt, D; Bartetzko, M P; Dallabernardina, P; Schuhmacher, F; Seeberger, P H; Pfrengle, F

    2016-08-01

    We report a traceless photocleavable linker for the automated glycan assembly of carbohydrates with free reducing ends. The reductive-labile functionality in the linker tolerates all commonly used reagents and protocols for automated glycan assembly, as demonstrated with the successful preparation of nine plant cell wall-related oligosaccharides, and is cleaved by hydrogenolysis. PMID:27463261

  4. Gene structure and molecular phylogeny of the linker chains from the giant annelid hexagonal bilayer hemoglobins.

    PubMed

    Chabasse, Christine; Bailly, Xavier; Sanchez, Sophie; Rousselot, Morgane; Zal, Franck

    2006-09-01

    Giant extracellular hexagonal bilayer hemoglobin (HBL-Hb), found only in annelids, is an approximately 3500-kDa heteropolymeric structure involved in oxygen transport. The HBL-Hbs are comprised of globin and linker chains, the latter being required for the assembly of the quaternary structure. The linker chains, varying in size from 225 to 283 amino acids, have a conserved cysteine-rich domain within their N-terminal moiety that is homologous to the cysteine-rich modules constituting the ligand binding domain of the low-density lipoprotein receptor (LDLR) protein family found in many metazoans. We have investigated the gene structure of linkers from Arenicola marina, Alvinella pompejana, Nereis diversicolor, Lumbricus terrestris, and Riftia pachyptila. We found, contrary to the results obtained earlier with linker genes from N. diversicolor and L. terrestris, that in all of the foregoing cases, the linker LDL-A module is flanked by two phase 1 introns, as in the human LDLR gene, with two more introns in the 3' side whose positions varied with the species. In addition, we obtained 13 linker cDNAs that have been determined experimentally or found in the EST database LumbriBASE. A molecular phylogenetic analysis of the linker primary sequences demonstrated that they cluster into two distinct families of linker proteins. We propose that the common gene ancestor to annelid linker genes exhibited a four-intron and five-exon structure and gave rise to the two families subsequent to a duplication event. PMID:16838215

  5. Development of Novel Quaternary Ammonium Linkers for Antibody-Drug Conjugates.

    PubMed

    Burke, Patrick J; Hamilton, Joseph Z; Pires, Thomas A; Setter, Jocelyn R; Hunter, Joshua H; Cochran, Julia H; Waight, Andrew B; Gordon, Kristine A; Toki, Brian E; Emmerton, Kim K; Zeng, Weiping; Stone, Ivan J; Senter, Peter D; Lyon, Robert P; Jeffrey, Scott C

    2016-05-01

    A quaternary ammonium-based drug-linker has been developed to expand the scope of antibody-drug conjugate (ADC) payloads to include tertiary amines, a functional group commonly present in biologically active compounds. The linker strategy was exemplified with a β-glucuronidase-cleavable auristatin E construct. The drug-linker was found to efficiently release free auristatin E (AE) in the presence of β-glucuronidase and provide ADCs that were highly stable in plasma. Anti-CD30 conjugates comprised of the glucuronide-AE linker were potent and immunologically specific in vitro and in vivo, displaying pharmacologic properties comparable with a carbamate-linked glucuronide-monomethylauristatin E control. The quaternary ammonium linker was then applied to a tubulysin antimitotic drug that contained an N-terminal tertiary amine that was important for activity. A glucuronide-tubulysin quaternary ammonium linker was synthesized and evaluated as an ADC payload, in which the resulting conjugates were found to be potent and immunologically specific in vitro, and displayed a high level of activity in a Hodgkin lymphoma xenograft. Furthermore, the results were superior to those obtained with a related tubulysin derivative containing a secondary amine N-terminus for conjugation using previously known linker technology. The quaternary ammonium linker represents a significant advance in linker technology, enabling stable conjugation of payloads with tertiary amine residues. Mol Cancer Ther; 15(5); 938-45. ©2016 AACR. PMID:26944920

  6. Stent linker effect in a porcine coronary restenosis model.

    PubMed

    Park, Jun-Kyu; Lim, Kyung Seob; Bae, In-Ho; Nam, Joung-Pyo; Cho, Jae Hwa; Choi, Changyong; Nah, Jae-Woon; Jeong, Myung Ho

    2016-01-01

    In this study, we aimed to evaluate the mechanical effects of different stent linker designs on in-stent restenosis in porcine coronary arteries. We fabricated stents with an open-cell structure composed of nine main cells and three linker structures in model 1 (I-type), model 2 (S-types) and model 3 (U-types)) as well as Model 4, which is similar to a commercial bare metal stent design. The stent cells were 70 mm thick and wide, with a common symmetrical wave pattern. As the radial force increased, the number of main cells increased and the length of linker decreased. Radial force was higher in model 1, with a linear I-linker, than in models with S- or U-linkers. The flexibility measured by three-point bending showed a force of 1.09 N in model 1, 0.35 N in model 2, 0.19 N in model 3, and 0.31 N in model 4. The recoil results were similar in all models except model 4 and were related to the shape of the main cells. The foreshortening results were related to linker shape, with the lowest foreshortening observed in model 3 (U-linker). Restenosis areas in the porcine restenosis model 4 weeks after implantation were 35.4 ± 8.39% (model 1), 30.4 ± 7.56% (model 2), 40.6 ± 9.87% (model 3) and 45.1 ± 12.33% (model 4). In-stent restenosis rates measured by intravascular ultrasound (IVUS) and micro-computed tomography (micro-CT) showed similar trends as percent area stenosis measured by micro-CT. Model 2, with optimized flexibility and radial force due to its S-linker, showed significantly reduced restenosis in the animal model compared to stents with different linker designs. These results suggest that the optimal stent structure has a minimum radial force for vascular support and maximum flexibility for vascular conformability. The importance of the effects of these differences in stent design and their potential relationship with restenosis remains to be determined. PMID:26318568

  7. Triple-layered QSAR studies on substituted 1,2,4-trioxanes as potential antimalarial agents: superiority of the quantitative pharmacophore-based alignment over common substructure-based alignment.

    PubMed

    Gupta, A K; Saxena, A K

    2013-01-01

    This study reports the utilization of three approaches - pharmacophore, CoMFA/CoMSIA and HQSAR studies - to identify the essential structural requirements in 3D chemical space for the modulation of the antimalarial activity of substituted 1,2,4-trioxanes. The superiority of quantitative pharmacophore-based alignment (QuantitativePBA) over global minima energy conformer-based alignment (GMCBA) has been reported in CoMFA and CoMSIA studies. The developed models showed good statistical significance in internal validation (q(2), group cross-validation and bootstrapping) and performed very well in predicting the antimalarial activity of test set compounds. Structural features in terms of their steric, electrostatic and hydrophobic interactions in 3D space have been found to be important for the antimalarial activity of substituted 1,2,4-trioxanes. Further, the HQSAR studies based on the same training and test set acted as an additional tool to find the sub-structural fingerprints of substituted 1,2,4-trioxanes for their antimalarial activity. Together, these studies may facilitate the design and discovery of new substituted 1,2,4-trioxanes with potent antimalarial activity. PMID:23194465

  8. Chemical substructure analysis in toxicology

    SciTech Connect

    Beauchamp, R.O. Jr.

    1990-12-31

    A preliminary examination of chemical-substructure analysis (CSA) demonstrates the effective use of the Chemical Abstracts compound connectivity file in conjunction with the bibliographic file for relating chemical structures to biological activity. The importance of considering the role of metabolic intermediates under a variety of conditions is illustrated, suggesting structures that should be examined that may exhibit potential activity. This CSA technique, which utilizes existing large files accessible with online personal computers, is recommended for use as another tool in examining chemicals in drugs. 2 refs., 4 figs.

  9. Mass Substructure in Abell 3128

    NASA Astrophysics Data System (ADS)

    McCleary, J.; dell'Antonio, I.; Huwe, P.

    2015-05-01

    We perform a detailed two-dimensional weak gravitational lensing analysis of the nearby (z = 0.058) galaxy cluster Abell 3128 using deep ugrz imaging from the Dark Energy Camera (DECam). We have designed a pipeline to remove instrumental artifacts from DECam images and stack multiple dithered observations without inducing a spurious ellipticity signal. We develop a new technique to characterize the spatial variation of the point-spread function that enables us to circularize the field to better than 0.5% and thereby extract the intrinsic galaxy ellipticities. By fitting photometric redshifts to sources in the observation, we are able to select a sample of background galaxies for weak-lensing analysis free from low-redshift contaminants. Photometric redshifts are also used to select a high-redshift galaxy subsample with which we successfully isolate the signal from an interloping z = 0.44 cluster. We estimate the total mass of Abell 3128 by fitting the tangential ellipticity of background galaxies with the weak-lensing shear profile of a Navarro-Frenk-White (NFW) halo and also perform NFW fits to substructures detected in the 2D mass maps of the cluster. This study yields one of the highest resolution mass maps of a low-z cluster to date and is the first step in a larger effort to characterize the redshift evolution of mass substructures in clusters.

  10. Some approaches to substructure coupling with damping

    NASA Technical Reports Server (NTRS)

    Craig, R. R., Jr.; Bachmeyer, R. C.; Howsman, T. G.

    1986-01-01

    Time-domain and frequency-domain methods for coupling substructures with general linear damping are discussed. A time-domain method is presented which employs a state variable representation of each substructure. Also presented is a method which employs frequency-domain coupling together with DFT and FFT transformations to obtain transient response solutions.

  11. Parallel Computational Environment for Substructure Optimization

    NASA Technical Reports Server (NTRS)

    Gendy, Atef S.; Patnaik, Surya N.; Hopkins, Dale A.; Berke, Laszlo

    1995-01-01

    Design optimization of large structural systems can be attempted through a substructure strategy when convergence difficulties are encountered. When this strategy is used, the large structure is divided into several smaller substructures and a subproblem is defined for each substructure. The solution of the large optimization problem can be obtained iteratively through repeated solutions of the modest subproblems. Substructure strategies, in sequential as well as in parallel computational modes on a Cray YMP multiprocessor computer, have been incorporated in the optimization test bed CometBoards. CometBoards is an acronym for Comparative Evaluation Test Bed of Optimization and Analysis Routines for Design of Structures. Three issues, intensive computation, convergence of the iterative process, and analytically superior optimum, were addressed in the implementation of substructure optimization into CometBoards. Coupling between subproblems as well as local and global constraint grouping are essential for convergence of the iterative process. The substructure strategy can produce an analytically superior optimum different from what can be obtained by regular optimization. For the problems solved, substructure optimization in a parallel computational mode made effective use of all assigned processors.

  12. Hydroquinone-pyrrole dyads with varied linkers.

    PubMed

    Huang, Hao; Karlsson, Christoffer; Strømme, Maria; Sjödin, Martin; Gogoll, Adolf

    2016-01-01

    A series of pyrroles functionalized in the 3-position with p-dimethoxybenzene via various linkers (CH2, CH2CH2, CH=CH, C≡C) has been synthesized. Their electronic properties have been deduced from (1)H NMR, (13)C NMR, and UV-vis spectra to detect possible interactions between the two aromatic subunits. The extent of conjugation between the subunits is largely controlled by the nature of the linker, with the largest conjugation found with the trans-ethene linker and the weakest with the aliphatic linkers. DFT calculations revealed substantial changes in the HOMO-LUMO gap that correlated with the extent of conjugation found experimentally. The results of this work are expected to open up for use of the investigated compounds as components of redox-active materials in sustainable, organic electrical energy storage devices. PMID:26877811

  13. Hydroquinone–pyrrole dyads with varied linkers

    PubMed Central

    Huang, Hao; Karlsson, Christoffer; Strømme, Maria; Sjödin, Martin

    2016-01-01

    Summary A series of pyrroles functionalized in the 3-position with p-dimethoxybenzene via various linkers (CH2, CH2CH2, CH=CH, C≡C) has been synthesized. Their electronic properties have been deduced from 1H NMR, 13C NMR, and UV–vis spectra to detect possible interactions between the two aromatic subunits. The extent of conjugation between the subunits is largely controlled by the nature of the linker, with the largest conjugation found with the trans-ethene linker and the weakest with the aliphatic linkers. DFT calculations revealed substantial changes in the HOMO–LUMO gap that correlated with the extent of conjugation found experimentally. The results of this work are expected to open up for use of the investigated compounds as components of redox-active materials in sustainable, organic electrical energy storage devices. PMID:26877811

  14. Substructure Main Bridge, River Piers A & V ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Substructure - Main Bridge, River Piers A & V - Huey P. Long Bridge, Spanning Mississippi River approximately midway between nine & twelve mile points upstream from & west of New Orleans, Jefferson, Jefferson Parish, LA

  15. Algebraic Sub-Structuring for Electromagnetic Applications

    SciTech Connect

    Yang, C.; Gao, W.G.; Bai, Z.J.; Li, X.Y.S.; Lee, L.Q.; Husbands, P.; Ng, E.G.; /LBL, Berkeley /UC, Davis /SLAC

    2006-06-30

    Algebraic sub-structuring refers to the process of applying matrix reordering and partitioning algorithms to divide a large sparse matrix into smaller submatrices from which a subset of spectral components are extracted and combined to form approximate solutions to the original problem. In this paper, they show that algebraic sub-structuring can be effectively used to solve generalized eigenvalue problems arising from the finite element analysis of an accelerator structure.

  16. Algebraic sub-structuring for electromagnetic applications

    SciTech Connect

    Yang, Chao; Gao, Weiguo; Bai, Zhaojun; Li, Xiaoye; Lee, Lie-Quan; Husbands, Parry; Ng, Esmond G.

    2004-09-14

    Algebraic sub-structuring refers to the process of applying matrix reordering and partitioning algorithms to divide a large sparse matrix into smaller submatrices from which a subset of spectral components are extracted and combined to form approximate solutions to the original problem. In this paper, we show that algebraic sub-structuring can be effectively used to solve generalized eigenvalue problems arising from the finite element analysis of an accelerator structure.

  17. A structural design decomposition method utilizing substructuring

    NASA Technical Reports Server (NTRS)

    Scotti, Stephen J.

    1994-01-01

    A new method of design decomposition for structural analysis and optimization is described. For this method, the structure is divided into substructures where each substructure has its structural response described by a structural-response subproblem, and its structural sizing determined from a structural-sizing subproblem. The structural responses of substructures that have rigid body modes when separated from the remainder of the structure are further decomposed into displacements that have no rigid body components, and a set of rigid body modes. The structural-response subproblems are linked together through forces determined within a structural-sizing coordination subproblem which also determines the magnitude of any rigid body displacements. Structural-sizing subproblems having constraints local to the substructures are linked together through penalty terms that are determined by a structural-sizing coordination subproblem. All the substructure structural-response subproblems are totally decoupled from each other, as are all the substructure structural-sizing subproblems, thus there is significant potential for use of parallel solution methods for these subproblems.

  18. Solid colloids with surface-mobile linkers.

    PubMed

    van der Meulen, Stef A J; Helms, Gesa; Dogterom, Marileen

    2015-06-17

    In this report we review the possibilities of using colloids with surface mobile linkers for the study of colloidal self-assembly processes. A promising route to create systems with mobile linkers is the use of lipid (bi-)layers. These lipid layers can be either used in the form of vesicles or as coatings for hard colloids and emulsion droplets. Inside the lipid bilayers molecules can be inserted via membrane anchors. Due to the fluidity of the lipid bilayer, the anchored molecules remain mobile. The use of different lipid mixtures even allows creating Janus-like particles that exhibit directional bonding if linkers are used which have a preference for a certain lipid phase. In nature mobile linkers can be found e.g. as receptors in cells. Therefore, towards the end of the review, we also briefly address the possibility of using colloids with surface mobile linkers as model systems to mimic cell-cell interactions and cell adhesion processes. PMID:25993272

  19. Singular behavior of jet substructure observables

    DOE PAGESBeta

    Larkoski, Andrew J.; Moult, Ian

    2016-01-20

    Jet substructure observables play a central role at the Large Hadron Collider for identifying the boosted hadronic decay products of electroweak scale resonances. The complete description of these observables requires understanding both the limit in which hard substructure is resolved, as well as the limit of a jet with a single hard core. In this paper we study in detail the perturbative structure of two prominent jet substructure observables, N-subjettiness and the energy correlation functions, as measured on background QCD jets. In particular, we focus on the distinction between the limits in which two-prong structure is resolved or unresolved. Dependingmore » on the choice of subjet axes, we demonstrate that at fixed order, N-subjettiness can manifest myriad behaviors in the unresolved region: smooth tails, end-point singularities, or singularities in the physical region. The energy correlation functions, by contrast, only have non-singular perturbative tails extending to the end point. We discuss the effect of hadronization on the various observables with Monte Carlo simulation and demonstrate that the modeling of these effects with non-perturbative shape functions is highly dependent on the N-subjettiness axes definitions. Lastly, our study illustrates those regions of phase space that must be controlled for high-precision jet substructure calculations, and emphasizes how such calculations can be facilitated by designing substructure observables with simple singular structures.« less

  20. Singular behavior of jet substructure observables

    NASA Astrophysics Data System (ADS)

    Larkoski, Andrew J.; Moult, Ian

    2016-01-01

    Jet substructure observables play a central role at the Large Hadron Collider for identifying the boosted hadronic decay products of electroweak scale resonances. The complete description of these observables requires understanding both the limit in which hard substructure is resolved, as well as the limit of a jet with a single hard core. In this paper we study in detail the perturbative structure of two prominent jet substructure observables, N -subjettiness and the energy correlation functions, as measured on background QCD jets. In particular, we focus on the distinction between the limits in which two-prong structure is resolved or unresolved. Depending on the choice of subjet axes, we demonstrate that at fixed order, N -subjettiness can manifest myriad behaviors in the unresolved region: smooth tails, end point singularities, or singularities in the physical region. The energy correlation functions, by contrast, only have nonsingular perturbative tails extending to the end point. We discuss the effect of hadronization on the various observables with Monte Carlo simulation and demonstrate that the modeling of these effects with nonperturbative shape functions is highly dependent on the N -subjettiness axes definitions. Our study illustrates those regions of phase space that must be controlled for high-precision jet substructure calculations, and emphasizes how such calculations can be facilitated by designing substructure observables with simple singular structures.

  1. Particle Substructure. A Common Theme of Discovery in this Century

    DOE R&D Accomplishments Database

    Panofsky, W. K. H.

    1984-02-01

    Some example of modern developments in particle physics are given which demonstrate that the fundamental rules of quantum mechanics, applied to all forces in nature as they became understood, have retained their validity. The well-established laws of electricity and magnetism, reformulated in terms of quantum mechanics, have exhibited a truly remarkable numerical agreement between theory and experiment over an enormous range of observation. As experimental techniques have grown from the top of a laboratory bench to the large accelerators of today, the basic components of experimentation have changed vastly in scale but only little in basic function. More important, the motivation of those engaged in this type of experimentation has hardly changed at all.

  2. Particel substructure. A common theme of discovery in this century

    SciTech Connect

    Panofsky, W.K.H.

    1984-02-01

    Some example of modern developments in particel physics are given which demonstrate that the fundamental rules of quantum mechanics, applied to all forces in nature as they became understood, have retained their validity. The well-established laws of electricity and magnetism, reformulated in terms of quantum mechanics, have exhibited a truly remarkable numerical agreement between theory and experiment over an enormous range of observation. As experimental techniques have grown from the top of a laboratory bench to the large accelerators of today, the basic components of experimentation have changed vastly in scale but only little in basic function. More important, the motivation of those engaged in this type of experimentation has hardly changed at all.

  3. Quantification of Substructure in Nearby Abell Clusters

    NASA Astrophysics Data System (ADS)

    Kriessler, J. R.; Beers, T. C.; Odewahn, S. C.

    1995-05-01

    Theory, as well as numerical simulations, suggests that Omega_o may be observationally constrained by the amount of substructure observed in present-day clusters of galaxies. We have therefore begun a study of the 116 Abell clusters with richness class greater than or equal to 1 and distance class less than or equal to 4, the so-called ``volume-limited'' sample of Hoessel, Gunn, & Thuan 1980 (ApJ 241, 486) to determine the prevalence of substructure in the clusters' projected galaxy positions. We use positions of galaxies identified by the Minnesota Automated Plate Scanner to obtain contour plots of the available clusters using an adaptive kernel routine. Significance of substructure is evaluated using the 2-D Lee test as well as a likelihood-ratio test on fits made with mixtures of two-dimensional gaussians. We also present nonparametric density profile estimates obtained with the program MAPEL (Merritt and Tremblay 1994, AJ 108, 514).

  4. THE ORIGIN OF THE VIRGO STELLAR SUBSTRUCTURE

    SciTech Connect

    Carlin, Jeffrey L.; Yam, William; Willett, Benjamin A.; Newberg, Heidi J.; Casetti-Dinescu, Dana I.; Girard, Terrence M.; Majewski, Steven R.

    2012-07-10

    We present three-dimensional space velocities of stars selected to be consistent with membership in the Virgo stellar substructure. Candidates were selected from SA 103, a single 40' Multiplication-Sign 40' field from our proper-motion (PM) survey in Kapteyn's Selected Areas (SAs), based on the PMs, Sloan Digital Sky Survey (SDSS) photometry, and follow-up spectroscopy of 215 stars. The signature of the Virgo substructure is clear in the SDSS color-magnitude diagram (CMD) centered on SA 103, and 16 stars are identified that have high Galactocentric-frame radial velocities (V{sub GSR} > 50 km s{sup -1}) and lie near the CMD locus of Virgo. The implied distance to the Virgo substructure from the candidates is 14 {+-} 3 kpc. We derive mean kinematics from these 16 stars, finding a radial velocity V{sub GSR} = 153 {+-} 22 km s{sup -1} and proper motions ({mu}{sub {alpha}}cos {delta}, {mu}{sub {delta}}) = (- 5.24, -0.91) {+-} (0.43, 0.46) mas yr{sup -1}. From the mean kinematics of these members, we determine that the Virgo progenitor was on an eccentric (e {approx} 0.8) orbit that recently passed near the Galactic center (pericentric distance R{sub p} {approx} 6 kpc). This destructive orbit is consistent with the idea that the substructure(s) in Virgo originated in the tidal disruption of a Milky Way satellite. N-body simulations suggest that the entire cloud-like Virgo substructure (encompassing the 'Virgo Overdensity' and the 'Virgo Stellar Stream') is likely the tidal debris remnant from a recently disrupted massive ({approx}10{sup 9} M{sub Sun }) dwarf galaxy. The model also suggests that some other known stellar overdensities in the Milky Way halo (e.g., the Pisces Overdensity and debris near NGC 2419 and SEGUE 1) are explained by the disruption of the Virgo progenitor.

  5. The Origin of the Virgo Stellar Substructure

    NASA Astrophysics Data System (ADS)

    Carlin, Jeffrey L.; Yam, William; Casetti-Dinescu, Dana I.; Willett, Benjamin A.; Newberg, Heidi J.; Majewski, Steven R.; Girard, Terrence M.

    2012-07-01

    We present three-dimensional space velocities of stars selected to be consistent with membership in the Virgo stellar substructure. Candidates were selected from SA 103, a single 40' × 40' field from our proper-motion (PM) survey in Kapteyn's Selected Areas (SAs), based on the PMs, Sloan Digital Sky Survey (SDSS) photometry, and follow-up spectroscopy of 215 stars. The signature of the Virgo substructure is clear in the SDSS color-magnitude diagram (CMD) centered on SA 103, and 16 stars are identified that have high Galactocentric-frame radial velocities (V GSR > 50 km s-1) and lie near the CMD locus of Virgo. The implied distance to the Virgo substructure from the candidates is 14 ± 3 kpc. We derive mean kinematics from these 16 stars, finding a radial velocity V GSR = 153 ± 22 km s-1 and proper motions (μαcos δ, μδ) = (- 5.24, -0.91) ± (0.43, 0.46) mas yr-1. From the mean kinematics of these members, we determine that the Virgo progenitor was on an eccentric (e ~ 0.8) orbit that recently passed near the Galactic center (pericentric distance Rp ~ 6 kpc). This destructive orbit is consistent with the idea that the substructure(s) in Virgo originated in the tidal disruption of a Milky Way satellite. N-body simulations suggest that the entire cloud-like Virgo substructure (encompassing the "Virgo Overdensity" and the "Virgo Stellar Stream") is likely the tidal debris remnant from a recently disrupted massive (~109 M ⊙) dwarf galaxy. The model also suggests that some other known stellar overdensities in the Milky Way halo (e.g., the Pisces Overdensity and debris near NGC 2419 and SEGUE 1) are explained by the disruption of the Virgo progenitor.

  6. Inverse substructure method for model updating of structures

    NASA Astrophysics Data System (ADS)

    Weng, Shun; Xia, Yong; Zhou, Xiao-Qing; Xu, You-Lin; Zhu, Hong-Ping

    2012-12-01

    Traditional model updating of large-scale structures is usually time-consuming because the global structural model needs to be repeatedly re-analyzed as a whole to match global measurements. This paper proposes a new substructural model updating method. The modal data measured on the global structure are disassembled to obtain the independent substructural dynamic flexibility matrices under force and displacement compatibility conditions. The method is extended to the case when the measurement is carried out at partial degrees-of-freedom of the structure. The extracted substructural flexibility matrices are then used as references for updating the corresponding substructural models. An orthogonal projector is employed on both the extracted substructural measurements and the substructural models to remove the rigid body modes of the free-free substructures. Compared with the traditional model updating at the global structure level, only the sub-models at the substructural level are re-analyzed in the proposed substructure-based model updating process, resulting in a rapid convergence of optimization. Moreover, only measurement on the local area corresponding to the concerned substructures is required, and those on other components can be avoided. The effectiveness and efficiency of the proposed substructuring method are verified through applications to a laboratory-tested frame structure and a large-scale 600 m tall Guangzhou New TV Tower. The present technique is referred to as the inverse substructuring model updating method as the measured global modal data are disassembled into the substructure level and then the updating is conducted on the substructures only. This differs from the substructuring model updating method previously proposed by the authors, in which the model updating is still conducted in the global level and the numerical global modal data are assembled from those of substructures. That can be referred to as the forward substructuring model

  7. Hadronic calorimeter shower size: Challenges and opportunities for jet substructure in the superboosted regime

    NASA Astrophysics Data System (ADS)

    Bressler, Shikma; Flacke, Thomas; Kats, Yevgeny; Lee, Seung J.; Perez, Gilad

    2016-05-01

    Hadrons have finite interaction size with dense material, a basic feature common to known forms of hadronic calorimeters (HCAL). We argue that substructure variables cannot use HCAL information to access the microscopic nature of jets much narrower than the hadronic shower size, which we call superboosted massive jets. It implies that roughly 15% of their transverse energy profile remains inaccessible due to the presence of long-lived neutral hadrons. This part of the jet substructure is also subject to order-one fluctuations. We demonstrate that the effects of the fluctuations are not reduced when a global correction to jet variables is applied. The above leads to fundamental limitations in the ability to extract intrinsic information from jets in the superboosted regime. The neutral fraction of a jet is correlated with its flavor. This leads to an interesting and possibly useful difference between superboosted W / Z / h / t jets and their corresponding backgrounds. The QCD jets that form the background to the signal superboosted jets might also be qualitatively different in their substructure as their mass might lie at or below the Sudakov mass peak. Finally, we introduce a set of zero-cone longitudinal jet substructure variables and show that while they carry information that might be useful in certain situations, they are not in general sensitive to the jet substructure.

  8. Statistics of substructures in dark matter haloes

    NASA Astrophysics Data System (ADS)

    Contini, E.; De Lucia, G.; Borgani, S.

    2012-03-01

    We study the amount and distribution of dark matter substructures within dark matter haloes, using a large set of high-resolution simulations ranging from group-size to cluster-size haloes, and carried out within a cosmological model consistent with Wilkinson Microwave Anisotropy Probe (WMAP) 7-year data. In particular, we study how the measured properties of subhaloes vary as a function of the parent halo mass, the physical properties of the parent halo and redshift. The fraction of halo mass in substructures increases with increasing mass: it is of the order of 5 per cent for haloes with M200˜ 1013 M⊙ and of the order of 10 per cent for the most massive haloes in our sample, with M200˜ 1015 M⊙. There is, however, a very large halo-to-halo scatter that can be explained only in part by a range of halo physical properties, e.g. concentration. At a given halo mass, less concentrated haloes contain significantly larger fractions of mass in substructures because of the reduced strength of tidal disruption. Most of the substructure mass is located at the outskirts of the parent haloes, in relatively few massive subhaloes. This mass segregation appears to become stronger at increasing redshift, and should reflect into a more significant mass segregation of the galaxy population at different cosmic epochs. When haloes are accreted on to larger structures, their mass is significantly reduced by tidal stripping. Haloes that are more massive at the time of accretion (these should host more luminous galaxies) are brought closer to the centre on shorter time-scales by dynamical friction, and therefore suffer a more significant stripping. The halo merger rate depends strongly on the environment with substructure in more massive haloes suffering more important mergers than their counterparts residing in less massive systems. This should translate into a different morphological mix for haloes of different mass.

  9. Linker Histones Incorporation Maintains Chromatin Fiber Plasticity

    PubMed Central

    Recouvreux, Pierre; Lavelle, Christophe; Barbi, Maria; Conde e Silva, Natalia; Le Cam, Eric; Victor, Jean-Marc; Viovy, Jean-Louis

    2011-01-01

    Genomic DNA in eukaryotic cells is organized in supercoiled chromatin fibers, which undergo dynamic changes during such DNA metabolic processes as transcription or replication. Indeed, DNA-translocating enzymes like polymerases produce physical constraints in vivo. We used single-molecule micromanipulation by magnetic tweezers to study the response of chromatin to mechanical constraints in the same range as those encountered in vivo. We had previously shown that under positive torsional constraints, nucleosomes can undergo a reversible chiral transition toward a state of positive topology. We demonstrate here that chromatin fibers comprising linker histones present a torsional plasticity similar to that of naked nucleosome arrays. Chromatosomes can undergo a reversible chiral transition toward a state of positive torsion (reverse chromatosome) without loss of linker histones. PMID:21641318

  10. The gamma-ray-flux PDF from galactic halo substructure

    NASA Astrophysics Data System (ADS)

    Lee, Samuel K.; Ando, Shin'ichiro; Kamionkowski, Marc

    2009-07-01

    One of the targets of the recently launched Fermi Gamma-ray Space Telescope is a diffuse gamma-ray background from dark-matter annihilation or decay in the Galactic halo. N-body simulations and theoretical arguments suggest that the dark matter in the Galactic halo may be clumped into substructure, rather than smoothly distributed. Here we propose the gamma-ray-flux probability distribution function (PDF) as a probe of substructure in the Galactic halo. We calculate this PDF for a phenomenological model of halo substructure and determine the regions of the substructure parameter space in which the PDF may be distinguished from the PDF for a smooth distribution of dark matter. In principle, the PDF allows a statistical detection of substructure, even if individual halos cannot be detected. It may also allow detection of substructure on the smallest microhalo mass scales, ~ M⊕, for weakly-interacting massive particles (WIMPs). Furthermore, it may also provide a method to measure the substructure mass function. However, an analysis that assumes a typical halo substructure model and a conservative estimate of the diffuse background suggests that the substructure PDF may not be detectable in the lifespan of Fermi in the specific case that the WIMP is a neutralino. Nevertheless, for a large range of substructure, WIMP annihilation, and diffuse background models, PDF analysis may provide a clear signature of substructure.

  11. Improving the Serum Stability of Site-Specific Antibody Conjugates with Sulfone Linkers

    PubMed Central

    2015-01-01

    Current routes for synthesizing antibody–drug conjugates commonly rely on maleimide linkers to react with cysteine thiols. However, thioether exchange with metabolites and serum proteins can compromise conjugate stability and diminish in vivo efficacy. We report the application of a phenyloxadiazole sulfone linker for the preparation of trastuzumab conjugates. This sulfone linker site-specifically labeled engineered cysteine residues in THIOMABs and improved antibody conjugate stability in human plasma at sites previously shown to be labile for maleimide conjugates. Similarly, sulfone conjugation with selenocysteine in an anti-ROR1 scFv-Fc improved human plasma stability relative to maleimide conjugation. Kinetically controlled labeling of a THIOMAB containing two cysteine substitutions was also achieved, offering a strategy for producing antibody conjugates with expanded valency. PMID:25099687

  12. Substructure coupling in the frequency domain

    NASA Technical Reports Server (NTRS)

    1985-01-01

    Frequency domain analysis was found to be a suitable method for determining the transient response of systems subjected to a wide variety of loads. However, since a large number of calculations are performed within the discrete frequency loop, the method loses it computational efficiency if the loads must be represented by a large number of discrete frequencies. It was also discovered that substructure coupling in the frequency domain work particularly well for analyzing structural system with a small number of interface and loaded degrees of freedom. It was discovered that substructure coupling in the frequency domain can lead to an efficient method of obtaining natural frequencies of undamped structures. It was also found that the damped natural frequencies of a system may be determined using frequency domain techniques.

  13. Practical applications of substructuring in shell dynamics

    SciTech Connect

    Sane, A.D.; Bitner, J.L.

    1982-01-01

    Transient dynamic stress analysis of large shell structures is often required in many industrial designs. The asymmetry features of the structure often require a full three dimensional analysis. The difficulties experienced in performing the dynamic analysis of such large and complex structures result from economic feasibility and limitations on the available computer core memory. Substructuring techniques provide a way of overcoming these difficulties. The advantages and features associated with substructuring methods are discussed in general terms. The technique is then applied to perform a transient dynamic analysis of a typical shell structure. The discussion of the example problem focused to highlight the economy, flexibility and the data handling aspects of this method. The example problem demonstrates that this method can be applied with success to a wide range of structural dynamic problems and results in significant cost savings.

  14. Substructure decoupling without using rotational DoFs: Fact or fiction?

    NASA Astrophysics Data System (ADS)

    D`Ambrogio, Walter; Fregolent, Annalisa

    2016-05-01

    In the framework of experimental dynamic substructuring, substructure decoupling consists in the identification of the dynamic behaviour of a structural subsystem, starting from the dynamic behaviour of both the assembled system and the residual subsystem (the known portion of the assembled system). On the contrary, substructure coupling identifies an assembled system starting from the component subsystems. The degrees of freedom (DoFs) of the assembled system can be partitioned into internal DoFs (not belonging to the couplings) and coupling DoFs. In substructure coupling, whenever coupling DoFs include rotational DoFs, the related rotational FRFs must be obtained experimentally. Does this requirement holds for substructure decoupling too, as it is commonly believed? Decoupling can be ideally accomplished by adding the negative of the residual subsystem to the assembled system (direct decoupling) and by enforcing compatibility and equilibrium at enough interface DoFs. Ideally, every DoF of the residual subsystem belongs to the interface between the assembled system and the residual subsystem. Hopefully, not all the coupling DoFs are necessary to enforce compatibility and equilibrium. This may allow us to skip coupling DoFs and specifically rotational DoFs. The goal of the paper is indeed to establish if rotational FRFs at coupling DoFs can be neglected in substructure decoupling. To this aim, after highlighting the possibility of avoiding the use of coupling DoFs from a theoretical standpoint, a test bed coupled through flexural and torsional DoFs is considered. Experimental results are presented and discussed.

  15. Composite Octet Searches with Jet Substructure

    SciTech Connect

    Bai, Yang; Shelton, Jessie; /Yale U.

    2012-02-14

    Many new physics models with strongly interacting sectors predict a mass hierarchy between the lightest vector meson and the lightest pseudoscalar mesons. We examine the power of jet substructure tools to extend the 7 TeV LHC sensitivity to these new states for the case of QCD octet mesons, considering both two gluon and two b-jet decay modes for the pseudoscalar mesons. We develop both a simple dijet search using only the jet mass and a more sophisticated jet substructure analysis, both of which can discover the composite octets in a dijet-like signature. The reach depends on the mass hierarchy between the vector and pseudoscalar mesons. We find that for the pseudoscalar-to-vector meson mass ratio below approximately 0.2 the simple jet mass analysis provides the best discovery limit; for a ratio between 0.2 and the QCD-like value of 0.3, the sophisticated jet substructure analysis has the best discovery potential; for a ratio above approximately 0.3, the standard four-jet analysis is more suitable.

  16. Star formation and substructure in galaxy clusters

    SciTech Connect

    Cohen, Seth A.; Hickox, Ryan C.; Wegner, Gary A.; Einasto, Maret; Vennik, Jaan

    2014-03-10

    We investigate the relationship between star formation (SF) and substructure in a sample of 107 nearby galaxy clusters using data from the Sloan Digital Sky Survey. Several past studies of individual galaxy clusters have suggested that cluster mergers enhance cluster SF, while others find no such relationship. The SF fraction in multi-component clusters (0.228 ± 0.007) is higher than that in single-component clusters (0.175 ± 0.016) for galaxies with M{sub r}{sup 0.1}<−20.5. In both single- and multi-component clusters, the fraction of star-forming galaxies increases with clustercentric distance and decreases with local galaxy number density, and multi-component clusters show a higher SF fraction than single-component clusters at almost all clustercentric distances and local densities. Comparing the SF fraction in individual clusters to several statistical measures of substructure, we find weak, but in most cases significant at greater than 2σ, correlations between substructure and SF fraction. These results could indicate that cluster mergers may cause weak but significant SF enhancement in clusters, or unrelaxed clusters exhibit slightly stronger SF due to their less evolved states relative to relaxed clusters.

  17. Mapping the Galactic Halo. VIII. Quantifying Substructure

    NASA Astrophysics Data System (ADS)

    Starkenburg, Else; Helmi, Amina; Morrison, Heather L.; Harding, Paul; van Woerden, Hugo; Mateo, Mario; Olszewski, Edward W.; Sivarani, Thirupathi; Norris, John E.; Freeman, Kenneth C.; Shectman, Stephen A.; Dohm-Palmer, R. C.; Frey, Lucy; Oravetz, Dan

    2009-06-01

    We have measured the amount of kinematic substructure in the Galactic halo using the final data set from the Spaghetti project, a pencil-beam high-latitude sky survey. Our sample contains 101 photometrically selected and spectroscopically confirmed giants with accurate distance, radial velocity, and metallicity information. We have developed a new clustering estimator: the "4distance" measure, which when applied to our data set leads to the identification of one group and seven pairs of clumped stars. The group, with six members, can confidently be matched to tidal debris of the Sagittarius dwarf galaxy. Two pairs match the properties of known Virgo structures. Using models of the disruption of Sagittarius in Galactic potentials with different degrees of dark halo flattening, we show that this favors a spherical or prolate halo shape, as demonstrated by Newberg et al. using the Sloan Digital Sky Survey data. One additional pair can be linked to older Sagittarius debris. We find that 20% of the stars in the Spaghetti data set are in substructures. From comparison with random data sets, we derive a very conservative lower limit of 10% to the amount of substructure in the halo. However, comparison to numerical simulations shows that our results are also consistent with a halo entirely built up from disrupted satellites, provided that the dominating features are relatively broad due to early merging or relatively heavy progenitor satellites.

  18. Spectroscopic study of the light-harvesting protein C-phycocyanin associated with colorless linker peptides

    SciTech Connect

    Pizarro, Shelly A.

    2000-05-12

    The phycobilisome (PBS) light-harvesting antenna is composed of chromophore-containing biliproteins and 'colorless' linker peptides and is structurally designed to support unidirectional transfer of excitation energy from the periphery of the PBS to its core. The linker peptides have a unique role in this transfer process by modulating the spectral properties of the associated biliprotein. There is only one three-dimensional structure of a biliprotein/linker complex available to date (APC/LC7.8) and the mechanism of interaction between these two proteins remains unknown. This study brings together a detailed spectroscopic characterization of C-Phycocyanin (PC)-linker complexes (isolated from Synechococcus sp. PCC 7002) with proteomic analysis of the linker amino acid sequences to produce a model for biliprotein/linker interaction. The amino acid sequences of the rod linkers [LR8.9, LR32.3 and LRC28.5] were examined to identify evolutionarily conserved regions important to either the structure or function of this protein family. Although there is not one common homologous site among all the linkers, there are strong trends across each separate subset (LC, LR and LRC) and the N-terminal segments of both LR32.3 and LRC28.5 display multiple regions of similarity with other linkers. Predictions of the secondary structure of LR32.3 and LRC28.5, and comparison to the crystal structure of LC7.8, further narrowed the candidates for interaction sites with the PC chromophores. Measurements of the absorption, fluorescence, CD and excitation anisotropy of PC trimer, PC/LR32.3, and PC/LRC28.5, document the spectroscopic effect of each linker peptide on the PC chromophores at a series of temperatures (298 to 77 K). Because LR32.3 and LRC28.5 modulate the PC trimer spectral properties in distinct manners, it suggests different chromophore-interaction mechanisms for each linker. The low temperature absorbance spectrum of the PC trimer is consistent with an excitonic coupling

  19. Phosphorylation of histone variant regions in chromatin: unlocking the linker?

    PubMed

    Green, G R

    2001-01-01

    Histone variants illuminate the behavior of chromatin through their unique structures and patterns of postsynthetic modification. This review examines the literature on heteromorphous histone structures in chromatin, structures that are primary targets for histone kinases and phosphatases in vivo. Special attention is paid to certain well-studied experimental systems: mammalian culture cells, chicken erythrocytes, sea urchin sperm, wheat sprouts, Tetrahymena, and budding yeast. A common theme emerges from these studies. Specialized, highly basic structures in histone variants promote chromatin condensation in a variety of developmental situations. Before, and sometimes after condensed chromatin is formed, the chromatin is rendered soluble by phosphorylation of the heteromorphous regions, preventing their interaction with linker DNA. A simple structural model accounting for histone variation and phosphorylation is presented. PMID:11467741

  20. Linker dependence of interfacial electron transfer rates in Fe(II)-polypyridine sensitized solar cells.

    PubMed

    Bowman, David N; Mukherjee, Sriparna; Barnes, Lyndsay J; Jakubikova, Elena

    2015-04-10

    Dye-sensitized solar cells (DSSCs) convert solar energy to electricity employing dye molecules attached to a semiconductor surface. Some of the most efficient DSSCs use Ru-based chromophores. Fe-based dyes represent a cheaper and more environmentally friendly alternative to these expensive and toxic dyes. The photoactive state of Fe-based chromophores responsible for charge-separation at the dye-semiconductor interface is, however, deactivated on a sub-picosecond time scale via the intersystem crossing (ISC) into a manifold of low-lying photo-inactive quintet states. Therefore, development of Fe-based dyes capable of fast interfacial electron transfer (IET) leading to efficient charge separation on a time scale competitive with the ISC events is important. This work investigates how linker groups anchoring a prototypical Fe-based dye [Fe(bpy-L)2(CN)2] (bpy = 2,2'-bipyridine, L = linker group) onto the TiO2 semiconductor surface influence the IET rates in the dye-semiconductor assemblies. Linker groups investigated include carboxylic acid, phosphonic acid, hydroxamate, catechol, and acetylacetonate. We employ time-dependent density functional theory (TD-DFT) to obtain absorption spectra of [Fe(bpy-L)2(CN)2] with each linker, and quantum dynamics simulations to investigate the IET rates between the dye and the (101) TiO2 anatase surface. For all attachments, TD-DFT calculations show similar absorption spectra with two main bands corresponding to the metal-to-ligand charge transfer transitions. The quantum dynamics simulations predict that the utilization of the hydroxamate linker instead of the commonly used carboxylic acid linker will lead to a more efficient IET and better photon-to-current conversion efficiencies in Fe(II)-polypyridine sensitized solar cells. PMID:25767105

  1. Linker dependence of interfacial electron transfer rates in Fe(II)-polypyridine sensitized solar cells

    NASA Astrophysics Data System (ADS)

    Bowman, David N.; Mukherjee, Sriparna; Barnes, Lyndsay J.; Jakubikova, Elena

    2015-04-01

    Dye-sensitized solar cells (DSSCs) convert solar energy to electricity employing dye molecules attached to a semiconductor surface. Some of the most efficient DSSCs use Ru-based chromophores. Fe-based dyes represent a cheaper and more environmentally friendly alternative to these expensive and toxic dyes. The photoactive state of Fe-based chromophores responsible for charge-separation at the dye-semiconductor interface is, however, deactivated on a sub-picosecond time scale via the intersystem crossing (ISC) into a manifold of low-lying photo-inactive quintet states. Therefore, development of Fe-based dyes capable of fast interfacial electron transfer (IET) leading to efficient charge separation on a time scale competitive with the ISC events is important. This work investigates how linker groups anchoring a prototypical Fe-based dye [Fe(bpy-L)2(CN)2] (bpy = 2,2‧-bipyridine, L = linker group) onto the TiO2 semiconductor surface influence the IET rates in the dye-semiconductor assemblies. Linker groups investigated include carboxylic acid, phosphonic acid, hydroxamate, catechol, and acetylacetonate. We employ time-dependent density functional theory (TD-DFT) to obtain absorption spectra of [Fe(bpy-L)2(CN)2] with each linker, and quantum dynamics simulations to investigate the IET rates between the dye and the (101) TiO2 anatase surface. For all attachments, TD-DFT calculations show similar absorption spectra with two main bands corresponding to the metal-to-ligand charge transfer transitions. The quantum dynamics simulations predict that the utilization of the hydroxamate linker instead of the commonly used carboxylic acid linker will lead to a more efficient IET and better photon-to-current conversion efficiencies in Fe(II)-polypyridine sensitized solar cells.

  2. Extraction of Substructural Flexibility from Global Frequencies and Mode Shapes

    SciTech Connect

    Alvin, K.F.; Park, K.C.

    1999-07-16

    A computational procedure for extracting substructure-by-substructure flexibility properties from global modal parameters is presented. The present procedure consists of two key features: an element-based direct flexibility method which uniquely determines the global flexibility without resorting to case-dependent redundancy selections; and, the projection of cinematically inadmissible modes that are contained in the iterated substructural matrices. The direct flexibility method is used as the basis of an inverse problem, whose goal is to determine substructural flexibilities given the global flexibility, geometrically-determined substructural rigid-body modes, and the local-to-global assembly operators. The resulting procedure, given accurate global flexibility, extracts the exact element-by-element substructural flexibilities for determinate structures. For indeterminate structures, the accuracy depends on the iteration tolerance limits. The procedure is illustrated using both simple and complex numerical examples, and appears to be effective for structural applications such as damage localization and finite element model reconciliation.

  3. Desmosine-Inspired Cross-Linkers for Hyaluronan Hydrogels

    NASA Astrophysics Data System (ADS)

    Hagel, Valentin; Mateescu, Markus; Southan, Alexander; Wegner, Seraphine V.; Nuss, Isabell; Haraszti, Tamás; Kleinhans, Claudia; Schuh, Christian; Spatz, Joachim P.; Kluger, Petra J.; Bach, Monika; Tussetschläger, Stefan; Tovar, Günter E. M.; Laschat, Sabine; Boehm, Heike

    2013-06-01

    We designed bioinspired cross-linkers based on desmosine, the cross-linker in natural elastin, to prepare hydrogels with thiolated hyaluronic acid. These short, rigid cross-linkers are based on pyridinium salts (as in desmosine) and can connect two polymer backbones. Generally, the obtained semi-synthetic hydrogels are form-stable, can withstand repeated stress, have a large linear-elastic range, and show strain stiffening behavior typical for biopolymer networks. In addition, it is possible to introduce a positive charge to the core of the cross-linker without affecting the gelation efficiency, or consequently the network connectivity. However, the mechanical properties strongly depend on the charge of the cross-linker. The properties of the presented hydrogels can thus be tuned in a range important for engineering of soft tissues by controlling the cross-linking density and the charge of the cross-linker.

  4. Traceless cross-linker for photocleavable bioconjugation.

    PubMed

    Wang, Rong; Yan, Funing; Qiu, Dengli; Jeong, Jae-Sun; Jin, Qiaoling; Kim, Tae-Young; Chen, Liaohai

    2012-04-18

    Photoresponsive bioconjugation empowers the development of novel methods for drug discovery, disease diagnosis, and high-throughput screening, among others. In this paper, we report on the characteristics of a traceless photocleavable cross-linker, di-6-(3-succinimidyl carbonyloxymethyl-4-nitro-phenoxy)-hexanoic acid disulfide diethanol ester (SCNE). The traceless feature and the biocompatibility of this photocleavable cross-linking reagent were corroborated. Consequently, we demonstrated its application in reversible phage particle immobilization that could provide a platform for direct single-phage screening. We also applied it in protein-photoprinting, where SCNE acts as a "photo-eraser" to remove the cross-linked protein molecules at a desired region in a simple, clean, and light-controllable fashion. We further demonstrated the two-tier atomic force microscopic (AFM) method that uses SCNE to carry out two subsequent AFM tasks in situ. The approach allows guided protein delivery and subsequent high-resolution imaging at the same local area, thus opening up the possibility of monitoring protein functions in live cells. The results imply that SCNE is a versatile cross-linker that can be used for a wide range of applications where photocleavage ensures clean and remote-controllable release of biological molecules from a substrate. PMID:22432929

  5. 5. DOWNSTREAM ELEVATION OF BRIDGE AND SUBSTRUCTURE (with graduated meter ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. DOWNSTREAM ELEVATION OF BRIDGE AND SUBSTRUCTURE (with graduated meter pole); VIEW TO NORTH-NORTHEAST. - Auwaiakeakua Bridge, Spanning Auwaiakekua Gulch at Mamalahoa Highway, Waikoloa, Hawaii County, HI

  6. Damage detection using the eigenparameter decomposition of substructural flexibility matrix

    NASA Astrophysics Data System (ADS)

    Weng, Shun; Zhu, Hong-Ping; Xia, Yong; Mao, Ling

    2013-01-01

    The crack or local damage on a structure reduces the stiffness of the structure, and thus leads to the modification of the dynamic properties. Damage detection is widely performed by comparing the initial modal data of the intact structure with those of the damaged structure. For a large-scale structure, the local damage usually introduces slight change to the global modal data, which makes the local damage difficult to be detected. This paper proposes a new substructuring method for the damage detection of a structure. The global structure is divided into manageable substructures. The modal data measured on the global structure are disassembled for obtaining the independent substructural dynamic flexibility matrices, under the force and displacement compatibility constraints. Thereafter, the substructural flexibility matrix is decomposed into its eigenvalues and eigenvectors to be used as the indicators for damage detection. Since the substructuring method concerns the local area by treating it as an independent structure, the substructural eigenparameters are more sensitive to the local damage than the global eigenparameters. The proposed substructuring method is firstly verified by a laboratory-tested portal frame structure. The location of the artificial cuts can be detected successfully by comparing the change of substructural eigenparameters. The proposed method is then applied to the 600 m tall Guangzhou New TV Tower. As compared with the global eigenparameters, the substructural eigenparameters bear larger changes caused by the local damage and thus are more sensitive to the local damage.

  7. CHEMTRAN and the Interconversion of Chemical Substructure Systems

    ERIC Educational Resources Information Center

    Granito, Charles E.

    1973-01-01

    The need for the interconversion of chemical substructure systems is discussed and CHEMTRAN, a new service, designed especially for creating interconversion programs, is introduced. (7 references) (Author)

  8. The Smad3 linker region contains a transcriptional activation domain.

    PubMed

    Wang, Guannan; Long, Jianyin; Matsuura, Isao; He, Dongming; Liu, Fang

    2005-02-15

    Transforming growth factor-beta (TGF-beta)/Smads regulate a wide variety of biological responses through transcriptional regulation of target genes. Smad3 plays a key role in TGF-beta/Smad-mediated transcriptional responses. Here, we show that the proline-rich linker region of Smad3 contains a transcriptional activation domain. When the linker region is fused to a heterologous DNA-binding domain, it activates transcription. We show that the linker region physically interacts with p300. The adenovirus E1a protein, which binds to p300, inhibits the transcriptional activity of the linker region, and overexpression of p300 can rescue the linker-mediated transcriptional activation. In contrast, an adenovirus E1a mutant, which cannot bind to p300, does not inhibit the linker-mediated transcription. The native Smad3 protein lacking the linker region is unable to mediate TGF-beta transcriptional activation responses, although it can be phosphorylated by the TGF-beta receptor at the C-terminal tail and has a significantly increased ability to form a heteromeric complex with Smad4. We show further that the linker region and the C-terminal domain of Smad3 synergize for transcriptional activation in the presence of TGF-beta. Thus our findings uncover an important function of the Smad3 linker region in Smad-mediated transcriptional control. PMID:15588252

  9. Robustness analysis applied to substructure controller synthesis

    NASA Technical Reports Server (NTRS)

    Gonzalez-Oberdoerffer, Marcelo F.; Craig, Roy R., Jr.

    1993-01-01

    The stability and robustness of the controlled system obtained via the substructure control synthesis (SCS) method of Su et al. (1990) were examined using a six-bay truss model, and employing an LQG control design method to obtain controllers for two separate structures. It is found that the assembled controller provides a stability in this instance. A qualitative assessment of the stability robustness of the system with controller designed with the SCS method is provided by obtaining a controller using the complete truss model and comparing the robustness of the corresponding closed-loop systems.

  10. Optimal numbers of residues in linkers of DNA polymerase I, T7 primase and DNA polymerase IV.

    PubMed

    Fu, Yi-Ben; Wang, Zhan-Feng; Wang, Peng-Ye; Xie, Ping

    2016-01-01

    DNA polymerase I (PolI), T7 primase and DNA polymerase IV (Dpo4) have a common feature in their structures that the two main domains are connected by an unstructured polypeptide linker. To perform their specific enzymatic activities, the enzymes are required to rearrange the position and orientation of one domain relative to the other into an active mode. Here, we show that the three enzymes share the same mechanism of the transition from the inert to active modes and use the minimum numbers of residues in their linkers to achieve the most efficient transitions. The transition time to the finally active mode is sensitively dependent on the stretched length of the linker in the finally active mode while is insensitive to the position and orientation in the initially inert state. Moreover, we find that for any enzyme whose two domains are connected by an unstructured flexible linker, the stretched length (L) of the linker in the finally active mode and the optimal number (Nopt) of the residues in the linker satisfy relation L ≈ αNopt, with α = 0.24-0.27 nm being a constant insensitive to the system. PMID:27364863

  11. Optimal numbers of residues in linkers of DNA polymerase I, T7 primase and DNA polymerase IV

    PubMed Central

    Fu, Yi-Ben; Wang, Zhan-Feng; Wang, Peng-Ye; Xie, Ping

    2016-01-01

    DNA polymerase I (PolI), T7 primase and DNA polymerase IV (Dpo4) have a common feature in their structures that the two main domains are connected by an unstructured polypeptide linker. To perform their specific enzymatic activities, the enzymes are required to rearrange the position and orientation of one domain relative to the other into an active mode. Here, we show that the three enzymes share the same mechanism of the transition from the inert to active modes and use the minimum numbers of residues in their linkers to achieve the most efficient transitions. The transition time to the finally active mode is sensitively dependent on the stretched length of the linker in the finally active mode while is insensitive to the position and orientation in the initially inert state. Moreover, we find that for any enzyme whose two domains are connected by an unstructured flexible linker, the stretched length (L) of the linker in the finally active mode and the optimal number (Nopt) of the residues in the linker satisfy relation L ≈ αNopt, with α = 0.24–0.27 nm being a constant insensitive to the system. PMID:27364863

  12. Substructurability: the effect of interface location on a real-time dynamic substructuring test

    PubMed Central

    Neild, S. A.; Lowenberg, M.; Szalai, R.; Krauskopf, B.

    2016-01-01

    A full-scale experimental test for large and complex structures is not always achievable. This can be due to many reasons, the most prominent one being the size limitations of the test. Real-time dynamic substructuring is a hybrid testing method where part of the system is modelled numerically and the rest of the system is kept as the physical test specimen. The numerical–physical parts are connected via actuators and sensors and the interface is controlled by advanced algorithms to ensure that the tested structure replicates the emulated system with sufficient accuracy. The main challenge in such a test is to overcome the dynamic effects of the actuator and associated controller, that inevitably introduce delay into the substructured system which, in turn, can destabilize the experiment. To date, most research concentrates on developing control strategies for stable recreation of the full system when the interface location is given a priori. Therefore, substructurability is mostly studied in terms of control. Here, we consider the interface location as a parameter and study its effect on the stability of the system in the presence of delay due to actuator dynamics and define substructurability as the system’s tolerance to delay in terms of the different interface locations. It is shown that the interface location has a major effect on the tolerable delays in an experiment and, therefore, careful selection of it is necessary. PMID:27616930

  13. Substructural QSAR approaches and topological pharmacophores.

    PubMed Central

    Franke, R; Huebel, S; Streich, W J

    1985-01-01

    For large and diverse data sets, simple QSAR methods based on linear and additive models can no longer be applied. In such cases topological methods using descriptors directly derivable from two-dimensional chemical structures provide a useful alternative. The results of such analyses can be used for lead optimization, to guide biological testing and even aid in the design of novel compounds. Various types of topological descriptors and algorithms are briefly discussed. Which of those is to be selected depends on the objective of the investigation and the properties of the data set. Two new methods, LOGANA and LOCON, are discussed in some more detail. With the help of these methods, substructural patterns ("topological pharmacophores") characteristic of compounds possessing a certain biological property can be evaluated. Both methods are designed in such a way that full use can be made of the data handling capacity of computers while maintaining an optimal impact of the experience of the researcher. They are model-free and do not require any mathematical knowledge. While LOGANA deals with semiquantitative or even qualitative biological data, LOCON can be applied to activity data on a continuous scale. The basic procedure in both cases consists in the stepwise combination of substructural descriptors by the logical operations "and," "or" and "not." With a simple example the utility of the methods is demonstrated. PMID:3905376

  14. Effects of the linker region on the structure and function of modular GH5 cellulases.

    PubMed

    Ruiz, Diego M; Turowski, Valeria R; Murakami, Mario T

    2016-01-01

    The association of glycosyl hydrolases with catalytically inactive modules is a successful evolutionary strategy that is commonly used by biomass-degrading microorganisms to digest plant cell walls. The presence of accessory domains in these enzymes is associated with properties such as higher catalytic efficiency, extension of the catalytic interface and targeting of the enzyme to the proper substrate. However, the importance of the linker region in the synergistic action of the catalytic and accessory domains remains poorly understood. Thus, this study examined how the inter-domain region affects the structure and function of modular GH5 endoglucanases, by using cellulase 5A from Bacillus subtilis (BsCel5A) as a model. BsCel5A variants featuring linkers with different stiffnesses or sizes were designed and extensively characterized, revealing that changes in flexibility or rigidity in this region differentially affect kinetic behavior. Regarding the linker length, we found that precise inter-domain spacing is required to enable efficient hydrolysis because excessively long or short linkers were equally detrimental to catalysis. Together, these findings identify molecular and structural features that may contribute to the rational design of chimeric and multimodular glycosyl hydrolases. PMID:27334041

  15. Effects of the linker region on the structure and function of modular GH5 cellulases

    PubMed Central

    Ruiz, Diego M.; Turowski, Valeria R.; Murakami, Mario T.

    2016-01-01

    The association of glycosyl hydrolases with catalytically inactive modules is a successful evolutionary strategy that is commonly used by biomass-degrading microorganisms to digest plant cell walls. The presence of accessory domains in these enzymes is associated with properties such as higher catalytic efficiency, extension of the catalytic interface and targeting of the enzyme to the proper substrate. However, the importance of the linker region in the synergistic action of the catalytic and accessory domains remains poorly understood. Thus, this study examined how the inter-domain region affects the structure and function of modular GH5 endoglucanases, by using cellulase 5A from Bacillus subtilis (BsCel5A) as a model. BsCel5A variants featuring linkers with different stiffnesses or sizes were designed and extensively characterized, revealing that changes in flexibility or rigidity in this region differentially affect kinetic behavior. Regarding the linker length, we found that precise inter-domain spacing is required to enable efficient hydrolysis because excessively long or short linkers were equally detrimental to catalysis. Together, these findings identify molecular and structural features that may contribute to the rational design of chimeric and multimodular glycosyl hydrolases. PMID:27334041

  16. Halo Substructure and the Power Spectrum

    NASA Astrophysics Data System (ADS)

    Zentner, Andrew R.; Bullock, James S.

    2003-11-01

    We present a semianalytic model to investigate the merger history, destruction rate, and survival probability of substructure in hierarchically formed dark matter halos and use it to study the substructure content of halos as a function of input primordial power spectrum. For a standard cold dark matter ``concordance'' cosmology (ΛCDM n=1, σ8=0.95) we successfully reproduce the subhalo velocity function and radial distribution profile seen in N-body simulations and determine that the rate of merging and disruption peaks ~10-12 Gyr in the past for Milky Way-like halos, while surviving substructures are typically accreted within the last ~0-8 Gyr. We explore power spectra with normalizations and spectral ``tilts'' spanning the ranges σ8~=1-0.65 and n~=1-0.8, and include a ``running-index'' model with dn/dlnk=-0.03 similar to the best-fit model discussed in the first-year Wilkinson Microwave Anisotropy Probe (WMAP) report. We investigate spectra with truncated small-scale power, including a broken-scale inflation model and three warm dark matter cases with mW=0.75-3.0 keV. We find that the mass fraction in substructure is relatively insensitive to the tilt and overall normalization of the primordial power spectrum. All of the CDM-type models yield projected substructure mass fractions that are consistent with, but on the low side, of published estimates from strong lens systems: f9=0.4%-1.5% (64th percentile) for subhalos smaller than 109 Msolar within projected cylinders of radius r<10 kpc. Truncated models produce significantly smaller fractions, f9=0.02%-0.2% for mW~=1 keV, and are disfavored by lensing estimates. This suggests that lensing and similar probes can provide a robust test of the CDM paradigm and a powerful constraint on broken-scale inflation/warm particle masses, including masses larger than the ~1 keV upper limits of previous studies. We compare our predicted subhalo velocity functions with the dwarf satellite population of the Milky Way. Assuming

  17. Kluyveromyces lactis genome harbours a functional linker histone encoding gene.

    PubMed

    Staneva, Dessislava; Georgieva, Milena; Miloshev, George

    2016-06-01

    Linker histones are essential components of chromatin in eukaryotes. Through interactions with linker DNA and nucleosomes they facilitate folding and maintenance of higher-order chromatin structures and thus delicately modulate gene activity. The necessity of linker histones in lower eukaryotes appears controversial and dubious. Genomic data have shown that Schizosaccharomyces pombe does not possess genes encoding linker histones while Kluyveromyces lactis has been reported to have a pseudogene. Regarding this controversy, we have provided the first direct experimental evidence for the existence of a functional linker histone gene, KlLH1, in K. lactis genome. Sequencing of KlLH1 from both genomic DNA and copy DNA confirmed the presence of an intact open reading frame. Transcription and splicing of the KlLH1 sequence as well as translation of its mRNA have been studied. In silico analysis revealed homology of KlLH1p to the histone H1/H5 protein family with predicted three domain structure characteristic for the linker histones of higher eukaryotes. This strongly proves that the yeast K. lactis does indeed possess a functional linker histone gene thus entailing the evolutionary preservation and significance of linker histones. The nucleotide sequences of KlLH1 are deposited in the GenBank under accession numbers KT826576, KT826577 and KT826578. PMID:27189369

  18. Substructuring and poroelastic modelling of the intervertebral disc.

    PubMed

    Swider, P; Pédrono, A; Ambard, D; Accadbled, F; Sales de Gauzy, J

    2010-05-01

    We proposed a substructure technique to predict the time-dependant response of biological tissue within the framework of a finite element resolution. Theoretical considerations in poroelasticity preceded the calculation of the sub-structured poroelastic matrix. The transient response was obtained using an exponential fitting method. We computed the creep response of an MRI 3D reconstructed L(5)-S(1) intervertebral disc of a scoliotic spine. The FE model was reduced from 10,000 degrees of freedom for the full 3D disc to only 40 degrees of freedom for the sub-structured model defined by 10 nodes attached to junction nodes located on both lower and upper surfaces of the disc. Comparisons of displacement fields were made between the full poroelastic FE model and the sub-structured model in three different loading conditions: compression, offset compression and torsion. Discrepancies in displacement were lower than 10% for the first time steps when time-dependant events were significant. The substructuring technique provided an exact solution in quasi-static behavior after pressure relaxation. Couplings between vertical and transversal displacements predicted by the reference FE model were well stored by the sub-structured model despite the drastic reduction of degrees of freedom. Finally, we demonstrated that substructuring was very efficient to reduce the size of numerical models while respecting the time-dependant behavior of the structure. This result highlighted the potential interest of substructure techniques in large-scale models of musculoskeletal structures. PMID:20170917

  19. Substructure synthesis method for simulating large molecular complexes

    PubMed Central

    Ming, Dengming; Kong, Yifei; Wu, Yinghao; Ma, Jianpeng

    2003-01-01

    This paper reports a computational method for describing the conformational flexibility of very large biomolecular complexes using a reduced number of degrees of freedom. It is called the substructure synthesis method, and the basic concept is to treat the motions of a given structure as a collection of those of an assemblage of substructures. The choice of substructures is arbitrary and sometimes quite natural, such as domains, subunits, or even large segments of biomolecular complexes. To start, a group of low-frequency substructure modes is determined, for instance by normal mode analysis, to represent the motions of the substructure. Next, a desired number of substructures are joined together by a set of constraints to enforce geometric compatibility at the interface of adjacent substructures, and the modes for the assembled structure can then be synthesized from the substructure modes by applying the Rayleigh–Ritz principle. Such a procedure is computationally much more desirable than solving the full eigenvalue problem for the whole assembled structure. Furthermore, to show the applicability to biomolecular complexes, the method is used to study F-actin, a large filamentous molecular complex involved in many cellular functions. The results demonstrate that the method is capable of studying the motions of very large molecular complexes that are otherwise completely beyond the reach of any conventional methods. PMID:12518058

  20. 8. Detail showing concrete abutment, showing substructure of bridge, specifically ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. Detail showing concrete abutment, showing substructure of bridge, specifically west side of arch and substructure. - Presumpscot Falls Bridge, Spanning Presumptscot River at Allen Avenue extension, 0.75 mile west of U.S. Interstate 95, Falmouth, Cumberland County, ME

  1. A Simple and Effective Cleavable Linker for Chemical Proteomics Applications*

    PubMed Central

    Yang, Yinliang; Hahne, Hannes; Kuster, Bernhard; Verhelst, Steven H. L.

    2013-01-01

    The study of metabolically labeled or probe-modified proteins is an important area in chemical proteomics. Isolation and purification of the protein targets is a necessary step before MS identification. The biotin-streptavidin system is widely used in this process, but the harsh denaturing conditions also release natively biotinylated proteins and non-selectively bound proteins. A cleavable linker strategy is a promising approach for solving this problem. Though several cleavable linkers have been developed and tested, an efficient, easily synthesized, and inexpensive cleavable linker is a desirable addition to the proteomics toolbox. Here, we describe the chemical proteomics application of a vicinal diol cleavable linker. Through easy-to-handle chemistry we incorporate this linker into an activity-based probe and a biotin alkyne tag amenable for bioorthogonal ligation. With these reagents, background protein identifications are significantly reduced relative to standard on-bead digestion. PMID:23028061

  2. Support Substructures: Support-Induced Part-Level Structural Representation.

    PubMed

    Huang, Shi-Sheng; Fu, Hongbo; Wei, Ling-Yu; Hu, Shi-Min

    2016-08-01

    In this work we explore a support-induced structural organization of object parts. We introduce the concept of support substructures, which are special subsets of object parts with support and stability. A bottom-up approach is proposed to identify such substructures in a support relation graph. We apply the derived high-level substructures to part-based shape reshuffling between models, resulting in nontrivial functionally plausible model variations that are difficult to achieve with symmetry-induced substructures by the state-of-the-art methods. We also show how to automatically or interactively turn a single input model to new functionally plausible shapes by structure rearrangement and synthesis, enabled by support substructures. To the best of our knowledge no single existing method has been designed for all these applications. PMID:26336128

  3. Mutations in Biosynthetic Enzymes for the Protein Linker Region of Chondroitin/Dermatan/Heparan Sulfate Cause Skeletal and Skin Dysplasias

    PubMed Central

    Mizumoto, Shuji; Yamada, Shuhei; Sugahara, Kazuyuki

    2015-01-01

    Glycosaminoglycans, including chondroitin, dermatan, and heparan sulfate, have various roles in a wide range of biological events such as cell signaling, cell proliferation, tissue morphogenesis, and interactions with various growth factors. Their polysaccharides covalently attach to the serine residues on specific core proteins through the common linker region tetrasaccharide, -xylose-galactose-galactose-glucuronic acid, which is produced through the stepwise addition of respective monosaccharides by four distinct glycosyltransferases. Mutations in the human genes encoding the glycosyltransferases responsible for the biosynthesis of the linker region tetrasaccharide cause a number of genetic disorders, called glycosaminoglycan linkeropathies, including Desbuquois dysplasia type 2, spondyloepimetaphyseal dysplasia, Ehlers-Danlos syndrome, and Larsen syndrome. This review focused on recent studies on genetic diseases caused by defects in the biosynthesis of the common linker region tetrasaccharide. PMID:26582078

  4. Mutations in Biosynthetic Enzymes for the Protein Linker Region of Chondroitin/Dermatan/Heparan Sulfate Cause Skeletal and Skin Dysplasias.

    PubMed

    Mizumoto, Shuji; Yamada, Shuhei; Sugahara, Kazuyuki

    2015-01-01

    Glycosaminoglycans, including chondroitin, dermatan, and heparan sulfate, have various roles in a wide range of biological events such as cell signaling, cell proliferation, tissue morphogenesis, and interactions with various growth factors. Their polysaccharides covalently attach to the serine residues on specific core proteins through the common linker region tetrasaccharide, -xylose-galactose-galactose-glucuronic acid, which is produced through the stepwise addition of respective monosaccharides by four distinct glycosyltransferases. Mutations in the human genes encoding the glycosyltransferases responsible for the biosynthesis of the linker region tetrasaccharide cause a number of genetic disorders, called glycosaminoglycan linkeropathies, including Desbuquois dysplasia type 2, spondyloepimetaphyseal dysplasia, Ehlers-Danlos syndrome, and Larsen syndrome. This review focused on recent studies on genetic diseases caused by defects in the biosynthesis of the common linker region tetrasaccharide. PMID:26582078

  5. Novel Polymer Linkers for Single Molecule AFM Force Spectroscopy

    PubMed Central

    Tong, Zenghan; Mikheikin, Andrey; Krasnoslobodtsev, Alexey; Lv, Zhengjian; Lyubchenko, Yuri L.

    2013-01-01

    Flexible polymer linkers play an important role in various imaging and probing techniques that require surface immobilization, including atomic force microscopy (AFM). In AFM force spectroscopy, polymer linkers are necessary for the covalent attachment of molecules of interest to the AFM tip and the surface. The polymer linkers tether the molecules and provide their proper orientation in probing experiments. Additionally, the linkers separate specific interactions from nonspecific short-range adhesion and serve as a reference point for the quantitative analysis of single molecule probing events. In this report, we present our results on the synthesis and testing of a novel polymer linker and the identification of a number of potential applications for its use in AFM force spectroscopy experiments. The synthesis of the linker is based on the well-developed phosphoramidate (PA) chemistry that allows the routine synthesis of linkers with predetermined lengths and PA composition. These linkers are homogeneous in length and can be terminated with various functional groups. PA linkers with different functional groups were synthesized and tested in experimental systems utilizing different immobilization chemistries. We probed interactions between complementary DNA oligonucleotides; DNA and protein complexes formed by the site-specific binding protein SfiI; and interactions between amyloid peptide (Aβ42). The results of the AFM force spectroscopy experiments validated the feasibility of the proposed approach for the linker design and synthesis. Furthermore, the properties of the tether (length, functional groups) can be adjusted to meet the specific requirements for different force spectroscopy experiments and system characteristics, suggesting that it could be used for a large number of various applications. PMID:23624104

  6. Characterization of T-Even Bacteriophage Substructures

    PubMed Central

    Cummings, Donald J.; Kusy, A. R.; Chapman, V. A.; DeLong, S. S.; Stone, K. R.

    1970-01-01

    T-even bacteriophages were grown and purified in bulk quantities. The protein coats were disrupted into their component substructures by treatment with 67% dimethyl sulfoxide (DMSO). Tail fibers and tubes were purified on glycerol-CsCl-D2O gradients and examined with respect to sedimentation properties, subunit molecular weights, amino acid composition, isoelectric points, and morphology. It was found that intact tail fibers had a sedimentation coefficient of 12 to 13S and that dissociated fibers consisted of three classes of proteins having molecular weights of 150 K ± 10, 42 K ± 4, and 28 K ± 3 daltons. A model was constructed in which the 150-K subunit folded back on itself twice to give a three-stranded rope. Each 150-K subunit then represented a half-fiber and it was proposed that the role of the 42- and 28-K subunits was to hold each half-fiber together as well as serve as a possible link with other substructures. Isoelectric point studies also indicated that there were three different proteins with pI values of 3.5, 5.7, and 8.0. Amino acid analyses indicated that fibers had a composition distinct from other phage substructures. In addition, a striking difference was noted in the content of tryptophan among the phages examined. T4B had three to five times more tryptophan than did T2L, T2H, T4D, and T6. Intact tail tubes had an S20,w of 31 to 38S and dissociated tubes consisted of three proteins of molecular weights 57 K ± 5, 38 K ± 4, and 25 K ± 3 daltons. Based on degradation studies with DMSO, it was proposed that these three proteins were arranged in a helical array yielding the tube structure. Isoelectric point studies indicated that there were three major proteins in the tube whose pI values were 5.1, 5.7, and 8.5. No significant differences were observed in the amino acid content of tubes obtained from all the T-even bacteriophages. Images PMID:5497900

  7. Structural requirements for the interdomain linker of alpha subunit of Escherichia coli RNA polymerase.

    PubMed

    Fujita, N; Endo, S; Ishihama, A

    2000-05-23

    The carboxy-terminal domain of the alpha subunit of Escherichia coli RNA polymerase, which is connected with the core part of RNA polymerase through a long flexible linker, plays decisive roles in transcription activation by directly interacting with a large number of transcription factors and upstream (UP) element DNA. Here we constructed a set of mutant RNA polymerases, each containing a mutant alpha subunit with an altered interdomain linker. Deletion of three amino acids from the linker exhibited 50% inhibition of cAMP receptor protein- (CRP-) dependent lac P1 transcription. Deletion of six amino acids completely knocked out the activity. Insertion of three amino acids did not affect the activity, whereas 40-60% inhibition was observed after insertion of one, two, or four amino acids. Substitution of 10 consecutive glycine residues resulted in nearly 90% reduction of the CRP-dependent activity, whereas 50% activity was retained after substitution of 10 proline residues or a sequence expected to form a strong alpha-helix. Essentially the same results were obtained with UP element-dependent rrnB P1 transcription. These observations altogether suggest that (i) sufficient length of the interdomain linker is required for transcription activation mediated by the alpha carboxy-terminal domain, (ii) the linker is not totally unstructured but has structural and torsional preferences to facilitate positioning of the carboxy-terminal domain to a proper location for the interaction with CRP and UP element, and (iii) CRP-dependent activation and UP element-dependent activation share a common intermediary state in which the positioning of the alpha carboxy-terminal domain is of primary importance. PMID:10821700

  8. A case of poor substructure diagnostics

    NASA Technical Reports Server (NTRS)

    Butler, Thomas G.

    1992-01-01

    The NASTRAN Manuals in the substructuring area are all geared toward instant success, but the solution paths are fraught with many traps for human error. Thus, the probability of suffering a fatal abort is high. In such circumstances, the necessity for diagnostics that are user friendly is paramount. This paper is written in the spirit of improving the diagnostics as well as the documentation in one area where the author felt he was backed into a blind corner as a result of his having committed a data oversight. This topic is aired by referring to an analysis of a particular structure. The structure, under discussion, used a number of local coordinate systems that simplified the preparation of input data. The principle features of this problem are introduced by reference to a series of figures.

  9. Exploring dark matter with Milky Way substructure.

    PubMed

    Kuhlen, Michael; Madau, Piero; Silk, Joseph

    2009-08-21

    The unambiguous detection of dark matter annihilation in our Galaxy would unravel one of the most outstanding puzzles in particle physics and cosmology. Recent observations have motivated models in which the annihilation rate is boosted by the Sommerfeld effect, a nonperturbative enhancement arising from a long-range attractive force. We applied the Sommerfeld correction to Via Lactea II, a high-resolution N-body simulation of a Milky Way-sized galaxy, to investigate the phase-space structure of the galactic halo. We found that the annihilation luminosity from kinematically cold substructure could be enhanced by orders of magnitude relative to previous calculations, leading to the prediction of gamma-ray fluxes from as many as several hundred dark clumps that should be detectable by the Fermi satellite. PMID:19608862

  10. Star-forming Substructure within Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Di Francesco, James

    2013-03-01

    Wide-field far-infrared/submillimeter continuum maps of molecular clouds by the Herschel Space Observatory GBS and HOBYS surveys are revealing the star-forming substructures that lead to star formation in dense gas. In particular, these maps have revealed the central role in clouds of filaments, likely formed through turbulent motions. These filaments appear to be non-isothermal and fragment into cores only when their column densities exceed a stability threshold. Organizations of filament networks suggest the relative role of turbulence and gravity can be traced in different parts of a cloud, and filament intersections may lead to larger amounts of mass flow that form the precursors of high-mass stars or clusters.

  11. Probabilistic Component Mode Synthesis of Nondeterministic Substructures

    NASA Technical Reports Server (NTRS)

    Brown, Andrew M.; Ferri, Aldo A.

    1996-01-01

    Standard methods of structural dynamic analysis assume that the structural characteristics are deterministic. Recognizing that these characteristics are actually statistical in nature researchers have recently developed a variety of methods that use this information to determine probabilities of a desired response characteristic, such as natural frequency, without using expensive Monte Carlo simulations. One of the problems in these methods is correctly identifying the statistical properties of primitive variables such as geometry, stiffness, and mass. We present a method where the measured dynamic properties of substructures are used instead as the random variables. The residual flexibility method of component mode synthesis is combined with the probabilistic methods to determine the cumulative distribution function of the system eigenvalues. A simple cantilever beam test problem is presented that illustrates the theory.

  12. The Sam68 nuclear body is composed of two RNase-sensitive substructures joined by the adaptor HNRNPL.

    PubMed

    Mannen, Taro; Yamashita, Seisuke; Tomita, Kozo; Goshima, Naoki; Hirose, Tetsuro

    2016-07-01

    The mammalian cell nucleus contains membraneless suborganelles referred to as nuclear bodies (NBs). Some NBs are formed with an architectural RNA (arcRNA) as the structural core. Here, we searched for new NBs that are built on unidentified arcRNAs by screening for ribonuclease (RNase)-sensitive NBs using 32,651 fluorescently tagged human cDNA clones. We identified 32 tagged proteins that required RNA for their localization in distinct nuclear foci. Among them, seven RNA-binding proteins commonly localized in the Sam68 nuclear body (SNB), which was disrupted by RNase treatment. Knockdown of each SNB protein revealed that SNBs are composed of two distinct RNase-sensitive substructures. One substructure is present as a distinct NB, termed the DBC1 body, in certain conditions, and the more dynamic substructure including Sam68 joins to form the intact SNB. HNRNPL acts as the adaptor to combine the two substructures and form the intact SNB through the interaction of two sets of RNA recognition motifs with the putative arcRNAs in the respective substructures. PMID:27377249

  13. Early dynamical evolution of substructured stellar clusters

    NASA Astrophysics Data System (ADS)

    Dorval, Julien; Boily, Christian

    2015-08-01

    It is now widely accepted that stellar clusters form with a high level of substructure (Kuhn et al. 2014, Bate 2009), inherited from the molecular cloud and the star formation process. Evidence from observations and simulations also indicate the stars in such young clusters form a subvirial system (Kirk et al. 2007, Maschberger et al. 2010). The subsequent dynamical evolution can cause important mass loss, ejecting a large part of the birth population in the field. It can also imprint the stellar population and still be inferred from observations of evolved clusters. Nbody simulations allow a better understanding of these early twists and turns, given realistic initial conditions. Nowadays, substructured, clumpy young clusters are usually obtained through pseudo-fractal growth (Goodwin et al. 2004) and velocity inheritance. Such models are visually realistics and are very useful, they are however somewhat artificial in their velocity distribution. I introduce a new way to create clumpy initial conditions through a "Hubble expansion" which naturally produces self consistent clumps, velocity-wise. A velocity distribution analysis shows the new method produces realistic models, consistent with the dynamical state of the newly created cores in hydrodynamic simulation of cluster formation (Klessen & Burkert 2000). I use these initial conditions to investigate the dynamical evolution of young subvirial clusters, up to 80000 stars. I find an overall soft evolution, with hierarchical merging leading to a high level of mass segregation. I investigate the influence of the mass function on the fate of the cluster, specifically on the amount of mass loss induced by the early violent relaxation. Using a new binary detection algorithm, I also find a strong processing of the native binary population.

  14. Flexible substructure online hybrid test system using conventional testing devices

    NASA Astrophysics Data System (ADS)

    Wang, Tao; Nakashima, Masayoshi

    2013-09-01

    This paper presents a substructure online hybrid test system that is extensible for geographically distributed tests. This system consists of a set of devices conventionally used for cyclic tests to load the tested substructures onto the target displacement or the target force. Due to their robustness and portability, individual sets of conventional loading devices can be transported and reconfigured to realize physical loading in geographically remote laboratories. Another appealing feature is the flexible displacement-force mixed control that is particularly suitable for specimens having large disparities in stiffness during various performance stages. To conduct a substructure online hybrid test, an extensible framework is developed, which is equipped with a generalized interface to encapsulate each substructure. Multiple tested substructures and analyzed substructures using various structural program codes can be accommodated within the single framework, simply interfaced with the boundary displacements and forces. A coordinator program is developed to keep the boundaries among all substructures compatible and equilibrated. An Internet-based data exchange scheme is also devised to transfer data among computers equipped with different software environments. A series of online hybrid tests are introduced, and the portability, flexibility, and extensibility of the online hybrid test system are demonstrated.

  15. Distant Galactic Halo Substructures Observed by the Palomar Transient Factory

    NASA Astrophysics Data System (ADS)

    Sesar, Branimir

    2013-01-01

    Characterization of Galactic halo substructures is important as their kinematic and chemical properties help constrain the properties of the Galactic dark matter halo, the formation history of the Milky Way, and the galaxy formation process in general. The best practical choice for finding distant halo substructures are pulsating RR Lyrae stars, due to their intrinsic brightness (M_V = 0.6 mag) and distinct light curves. I will present kinematic and chemical properties of two distant halo substructures that were traced using RR Lyrae stars observed by the Palomar Transient Factory. One of these substructures, located at 90 kpc from the Sun in the Cancer constellation, consists of two groups of RR Lyrae stars moving away from the Galaxy at ~80 and ~20 km/s, respectively. The second substructure is located at ~65 kpc from the Sun in the Hercules constellation. The kinematics of RR Lyrae stars tracing this substructure suggest a presence of 2 or 3 stellar streams extending in the similar direction on the sky. Due to their spatial extent, both of these substructures are clearly disrupted and would be very difficult to detect using tradiitonal techniques such as the color-magnitude diagram filtering.

  16. Tandem oligonucleotide synthesis using linker phosphoramidites

    PubMed Central

    Pon, Richard T.; Yu, Shuyuan

    2005-01-01

    Multiple oligonucleotides of the same or different sequence, linked end-to-end in tandem can be synthesized in a single automated synthesis. A linker phosphoramidite [R. T. Pon and S. Yu (2004) Nucleic Acids Res., 32, 623–631] is added to the 5′-terminal OH end of a support-bound oligonucleotide to introduce a cleavable linkage (succinic acid plus sulfonyldiethanol) and the 3′-terminal base of the new sequence. Conventional phosphoramidites are then used for the rest of the sequence. After synthesis, treatment with ammonium hydroxide releases the oligonucleotides from the support and cleaves the linkages between each sequence. Mixtures of one oligonucleotide with both 5′- and 3′-terminal OH ends and other oligonucleotides with 5′-phosphorylated and 3′-OH ends are produced, which are deprotected and worked up as a single product. Tandem synthesis can be used to make pairs of PCR primers, sets of cooperative oligonucleotides or multiple copies of the same sequence. When tandem synthesis is used to make two self-complementary sequences, double-stranded structures spontaneously form after deprotection. Tandem synthesis of oligonucleotide chains containing up to six consecutive 20mer (120 bases total), various trinucleotide codons and primer pairs for PCR, or self-complementary strands for in situ formation of double-stranded DNA fragments has been demonstrated. PMID:15814811

  17. Substructure System Identification for Finite Element Model Updating

    NASA Technical Reports Server (NTRS)

    Craig, Roy R., Jr.; Blades, Eric L.

    1997-01-01

    This report summarizes research conducted under a NASA grant on the topic 'Substructure System Identification for Finite Element Model Updating.' The research concerns ongoing development of the Substructure System Identification Algorithm (SSID Algorithm), a system identification algorithm that can be used to obtain mathematical models of substructures, like Space Shuttle payloads. In the present study, particular attention was given to the following topics: making the algorithm robust to noisy test data, extending the algorithm to accept experimental FRF data that covers a broad frequency bandwidth, and developing a test analytical model (TAM) for use in relating test data to reduced-order finite element models.

  18. Substructuring by Lagrange multipliers for solids and plates

    SciTech Connect

    Mandel, J.; Tezaur, R.; Farhat, C.

    1996-12-31

    We present principles and theoreretical foundation of a substructuring method for large structural problems. The algorithm is preconditioned conjugate gradients on a subspace for the dual problem. The preconditioning is proved asymptotically optimal and the method is shown to be parallel scalable, i.e., the condition number is bounded independently of the number of substructures. For plate problems, a special modification is needed that retains continuity of the displacement solution at substructure crosspoints, resulting in an asymptically optimal method. The results are confirmed by numerical experiments.

  19. Correlation among DNA Linker Length, Linker Histone Concentration, and Histone Tails in Chromatin.

    PubMed

    Luque, Antoni; Ozer, Gungor; Schlick, Tamar

    2016-06-01

    Eukaryotic cells condense their genetic material in the nucleus in the form of chromatin, a macromolecular complex made of DNA and multiple proteins. The structure of chromatin is intimately connected to the regulation of all eukaryotic organisms, from amoebas to humans, but its organization remains largely unknown. The nucleosome repeat length (NRL) and the concentration of linker histones (ρLH) are two structural parameters that vary among cell types and cell cycles; the NRL is the number of DNA basepairs wound around each nucleosome core plus the number of basepairs linking successive nucleosomes. Recent studies have found a linear empirical relationship between the variation of these two properties for different cells, but its underlying mechanism remains elusive. Here we apply our established mesoscale chromatin model to explore the mechanisms responsible for this relationship, by investigating chromatin fibers as a function of NRL and ρLH combinations. We find that a threshold of linker histone concentration triggers the compaction of chromatin into well-formed 30-nm fibers; this critical value increases linearly with NRL, except for long NRLs, where the fibers remain disorganized. Remarkably, the interaction patterns between core histone tails and chromatin elements are highly sensitive to the NRL and ρLH combination, suggesting a molecular mechanism that could have a key role in regulating the structural state of the fibers in the cell. An estimate of the minimized work and volume associated with storage of chromatin fibers in the nucleus further suggests factors that could spontaneously regulate the NRL as a function of linker histone concentration. Both the tail interaction map and DNA packing considerations support the empirical NRL/ρLH relationship and offer a framework to interpret experiments for different chromatin conditions in the cell. PMID:27276249

  20. Molecular Basis of Valine-Citrulline-PABC Linker Instability in Site-Specific ADCs and Its Mitigation by Linker Design.

    PubMed

    Dorywalska, Magdalena; Dushin, Russell; Moine, Ludivine; Farias, Santiago E; Zhou, Dahui; Navaratnam, Thayalan; Lui, Victor; Hasa-Moreno, Adela; Casas, Meritxell Galindo; Tran, Thomas-Toan; Delaria, Kathy; Liu, Shu-Hui; Foletti, Davide; O'Donnell, Christopher J; Pons, Jaume; Shelton, David L; Rajpal, Arvind; Strop, Pavel

    2016-05-01

    The degree of stability of antibody-drug linkers in systemic circulation, and the rate of their intracellular processing within target cancer cells are among the key factors determining the efficacy of antibody-drug conjugates (ADC) in vivo Previous studies demonstrated the susceptibility of cleavable linkers, as well as auristatin-based payloads, to enzymatic cleavage in rodent plasma. Here, we identify Carboxylesterase 1C as the enzyme responsible for the extracellular hydrolysis of valine-citrulline-p-aminocarbamate (VC-PABC)-based linkers in mouse plasma. We further show that the activity of Carboxylesterase 1C towards VC-PABC-based linkers, and consequently the stability of ADCs in mouse plasma, can be effectively modulated by small chemical modifications to the linker. While the introduced modifications can protect the VC-PABC-based linkers from extracellular cleavage, they do not significantly alter the intracellular linker processing by the lysosomal protease Cathepsin B. The distinct substrate preference of the serum Carboxylesterase 1C offers the opportunity to modulate the extracellular stability of cleavable ADCs without diminishing the intracellular payload release required for ADC efficacy. Mol Cancer Ther; 15(5); 958-70. ©2016 AACR. PMID:26944918

  1. Reactivity and applications of new amine reactive cross-linkers for mass spectrometric detection of protein-protein complexes.

    PubMed

    Bich, Claudia; Maedler, Stefanie; Chiesa, Katja; DeGiacomo, Fabio; Bogliotti, Nicolas; Zenobi, Renato

    2010-01-01

    Chemical cross-linking of proteins permits the stabilization of noncovalent complexes through introduction of covalent bonds. A crucial challenge is to find the fastest and most efficient cross-linkers in order to minimize reaction times and to handle delicate complexes. New cross-linkers were synthesized by introducing N-hydroxyphthalimide, hydroxybenzotriazole, and 1-hydroxy-7-azabenzotriazole as leaving groups instead of the commonly used N-hydroxysuccimidyl moiety. With the use of matrix-assisted laser desorption ionization (MALDI) mass spectrometry, these new cross-linkers were then compared with the commercially available disuccinimidyl suberate (DSS) for covalent stabilization of the gluthatione-S-transferase (GST) dimer and of an antibody-antigen complex. They showed a better efficiency, generated about 30% more cross-linked complex, and reacted about 10 times faster than DSS. The reaction with the GST dimer was utilized to get information about their reaction efficiency and kinetics. Their ability to stabilize only specific protein complexes was verified by incubating them with a mixture of the proteins GST and ubiquitin. Finally, the cross-linkers were incubated with synthetic peptides to study the selectivity of the binding with various amino acid side chains. Not only lysine but also tyrosine was found to react with the newly synthesized cross-linker containing 1-hydroxy-7-azabenzotriazole as the reactive group. PMID:19994840

  2. Creep induced substructures in titanium aluminide

    NASA Astrophysics Data System (ADS)

    Cerreta, Ellen Kathleen

    Many investigations have examined the creep properties of titanium aluminides. Attempts to classify observed behaviors with existing models for high temperature deformation have been met with limited success. Several researchers have shown that an understanding of substructural evolution in the early stages of the creep curve may offer insight into the mechanisms, which control the rate of deformation. Creep deformation has been shown to include twinning, recrystallization, grain boundary sliding, ordinary and super dislocation activity, and faulting depending on the microstructure of the alloy and testing conditions. However, the environments that these alloys are likely to be exposed to are not similar to the test conditions in the literature. Furthermore the emphasis of much of the research into this group of alloys has been on the effects of microstructure particularly, the volume fraction of lamellar phase and ternary elemental additions. With all of these studies little information is available on the deformation behavior of the gamma phase. The alloys in these studies are mostly composed of the gamma phase and yet its creep behavior is not well understood. For this reason single phase binary gamma titanium aluminides were investigated in this study. To understand the effects of aluminum, interstitial oxygen content, and stress on creep, five alloys of varying Al concentrations and interstitial oxygen contents were deformed at temperatures ranging from 700--800°C and at stresses of 150, 200, and 250MPa. Full creep curves were developed under these conditions and phenomenological parameters for creep were calculated from these data. Additional tests were interrupted during primary and secondary creep at 760°C. Specimens from the interrupted tests as well as from the as-processed materials were examined optically and by TEM. Creep data and the microscopy were analyzed in concert to determine rate-controlling mechanisms for creep. Evolution of the substructure

  3. Linker-mediated assembly of gold nanoparticles into multimeric motifs

    NASA Astrophysics Data System (ADS)

    Sikora, Mateusz; Szymczak, Piotr; Thompson, Damien; Cieplak, Marek

    2011-11-01

    We present a theoretical description of linker-mediated self-assembly of gold nanoparticles (Au-NP). Using mesoscale simulations with a coarse-grained model for the Au NPs and dirhenium-based linker molecules, we investigate the conditions under which large clusters can grow and construct a phase diagram that identifies favorable growth conditions in terms of floating and bound linker concentrations. The findings can be considered as generic, as we expect other NP-linker systems to behave in a qualitatively similar way. In particular, we also discuss the case of antibody-functionalised Au NPs connected by the C-reactive proteins (CRPs). We extract some general rules for NP linking that may aid the production of size- and shape-specific NP clusters for technology applications.

  4. Linker-mediated assembly of gold nanoparticles into multimeric motifs.

    PubMed

    Sikora, Mateusz; Szymczak, Piotr; Thompson, Damien; Cieplak, Marek

    2011-11-01

    We present a theoretical description of linker-mediated self-assembly of gold nanoparticles (Au-NP). Using mesoscale simulations with a coarse-grained model for the Au NPs and dirhenium-based linker molecules, we investigate the conditions under which large clusters can grow and construct a phase diagram that identifies favorable growth conditions in terms of floating and bound linker concentrations. The findings can be considered as generic, as we expect other NP-linker systems to behave in a qualitatively similar way. In particular, we also discuss the case of antibody-functionalised Au NPs connected by the C-reactive proteins (CRPs). We extract some general rules for NP linking that may aid the production of size- and shape-specific NP clusters for technology applications. PMID:21979426

  5. Linker-Mediated Self-Assembly Dynamics of Charged Nanoparticles.

    PubMed

    Lin, Guanhua; Chee, See Wee; Raj, Sanoj; Král, Petr; Mirsaidov, Utkur

    2016-08-23

    Using in situ liquid cell transmission electron microscopy (TEM), we visualized a stepwise self-assembly of surfactant-coated and hydrated gold nanoparticles (NPs) into linear chains or branched networks. The NP binding is facilitated by linker molecules, ethylenediammonium, which form hydrogen bonds with surfactant molecules of neighboring NPs. The observed spacing between bound neighboring NPs, ∼15 Å, matches the combined length of two surfactants and one linker molecule. Molecular dynamics simulations reveal that for lower concentrations of linkers, NPs with charged surfactants cannot be fully neutralized by strongly binding divalent linkers, so that NPs carry higher effective charges and tend to form chains, due to poor screening. The highly polar NP surfaces polarize and partly immobilize nearby water molecules, which promotes NPs binding. The presented experimental and theoretical approach allows for detail observation and explanation of self-assembly processes in colloidal nanosystems. PMID:27494560

  6. Linker histones in hormonal gene regulation.

    PubMed

    Vicent, G P; Wright, R H G; Beato, M

    2016-03-01

    In the present review, we summarize advances in our knowledge on the role of the histone H1 family of proteins in breast cancer cells, focusing on their response to progestins. Histone H1 plays a dual role in gene regulation by hormones, both as a structural component of chromatin and as a dynamic modulator of transcription. It contributes to hormonal regulation of the MMTV promoter by stabilizing a homogeneous nucleosome positioning, which reduces basal transcription whereas at the same time promoting progesterone receptor binding and nucleosome remodeling. These combined effects enhance hormone dependent gene transcription, which eventually requires H1 phosphorylation and displacement. Various isoforms of histone H1 have specific functions in differentiated breast cancer cells and compact nucleosomal arrays to different extents in vitro. Genome-wide studies show that histone H1 has a key role in chromatin dynamics of hormone regulated genes. A complex sequence of enzymatic events, including phosphorylation by CDK2, PARylation by PARP1 and the ATP-dependent activity of NURF, are required for H1 displacement and gene de-repression, as a prerequisite for further nucleosome remodeling. Similarly, during hormone-dependent gene repression a dedicated enzymatic mechanism controls H1 deposition at promoters by a complex containing HP1γ, LSD1 and BRG1, the ATPase of the BAF complex. Thus, a broader vision of the histone code should include histone H1, as the linker histone variants actively participate in the regulation of the chromatin structure. How modifications of the core histones tails affect H1 modifications and vice versa is one of the many questions that remains to be addressed to provide a more comprehensive view of the histone cross-talk mechanisms. PMID:26518266

  7. Functional Genomics Reveals Linkers Critical for Influenza Virus Polymerase

    PubMed Central

    Wang, Lulan; Wu, Aiping; Wang, Yao E.; Quanquin, Natalie; Li, Chunfeng; Wang, Jingfeng; Chen, Hsiang-Wen; Liu, Suyang; Liu, Ping; Zhang, Hong; Qin, F. Xiao-Feng

    2015-01-01

    ABSTRACT Influenza virus mRNA synthesis by the RNA-dependent RNA polymerase involves binding and cleavage of capped cellular mRNA by the PB2 and PA subunits, respectively, and extension of viral mRNA by PB1. However, the mechanism for such a dynamic process is unclear. Using high-throughput mutagenesis and sequencing analysis, we have not only generated a comprehensive functional map for the microdomains of individual subunits but also have revealed the PA linker to be critical for polymerase activity. This PA linker binds to PB1 and also forms ionic interactions with the PA C-terminal channel. Nearly all mutants with five-amino-acid insertions in the linker were nonviable. Our model further suggests that the PA linker plays an important role in the conformational changes that occur between stages that favor capped mRNA binding and cleavage and those associated with viral mRNA synthesis. IMPORTANCE The RNA-dependent RNA polymerase of influenza virus consists of the PB1, PB2, and PA subunits. By combining genome-wide mutagenesis analysis with the recently discovered crystal structure of the influenza polymerase heterotrimer, we generated a comprehensive functional map of the entire influenza polymerase complex. We identified the microdomains of individual subunits, including the catalytic domains, the interaction interfaces between subunits, and nine linkers interconnecting different domains. Interestingly, we found that mutants with five-amino-acid insertions in individual linkers were nonviable, suggesting the critical roles these linkers play in coordinating spatial relationships between the subunits. We further identified an extended PA linker that binds to PB1 and also forms ionic interactions with the PA C-terminal channel. PMID:26719244

  8. Linkers in the structural biology of protein–protein interactions

    PubMed Central

    Reddy Chichili, Vishnu Priyanka; Kumar, Veerendra; Sivaraman, J

    2013-01-01

    Linkers or spacers are short amino acid sequences created in nature to separate multiple domains in a single protein. Most of them are rigid and function to prohibit unwanted interactions between the discrete domains. However, Gly-rich linkers are flexible, connecting various domains in a single protein without interfering with the function of each domain. The advent of recombinant DNA technology made it possible to fuse two interacting partners with the introduction of artificial linkers. Often, independent proteins may not exist as stable or structured proteins until they interact with their binding partner, following which they gain stability and the essential structural elements. Gly-rich linkers have been proven useful for these types of unstable interactions, particularly where the interaction is weak and transient, by creating a covalent link between the proteins to form a stable protein–protein complex. Gly-rich linkers are also employed to form stable covalently linked dimers, and to connect two independent domains that create a ligand-binding site or recognition sequence. The lengths of linkers vary from 2 to 31 amino acids, optimized for each condition so that the linker does not impose any constraints on the conformation or interactions of the linked partners. Various structures of covalently linked protein complexes have been described using X-ray crystallography, nuclear magnetic resonance and cryo-electron microscopy techniques. In this review, we evaluate several structural studies where linkers have been used to improve protein quality, to produce stable protein–protein complexes, and to obtain protein dimers. PMID:23225024

  9. Substructure Main Bridge, Pier A Huey P. Long ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Substructure - Main Bridge, Pier A - Huey P. Long Bridge, Spanning Mississippi River approximately midway between nine & twelve mile points upstream from & west of New Orleans, Jefferson, Jefferson Parish, LA

  10. 98. DETAIL VIEW OF STORM DAMAGE AND EXPOSED SUBSTRUCTURE, NORTHWEST ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    98. DETAIL VIEW OF STORM DAMAGE AND EXPOSED SUBSTRUCTURE, NORTHWEST SIDE OF 4TH TEE, LOOKING WEST - Huntington Beach Municipal Pier, Pacific Coast Highway at Main Street, Huntington Beach, Orange County, CA

  11. 10. DETAIL OF BRIDGE SUBSTRUCTURE, SHOWING ORIGINAL CONNECTION WITH IRON ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    10. DETAIL OF BRIDGE SUBSTRUCTURE, SHOWING ORIGINAL CONNECTION WITH IRON PINS. VIEW LOOKING WEST FROM FACE OF EAST ABUTMENT. - Annisquam Bridge, Spanning Lobster Cove between Washington & River Streets, Gloucester, Essex County, MA

  12. Substructure view of the Young's Bay Bridge, view looking east, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Substructure view of the Young's Bay Bridge, view looking east, north side of the bascule trusswork - Old Young's Bay Bridge, Spanning Young's Bay at Milepoint 6.89 on Warrenton-Astoria Highway (Highway No. 9), Astoria, Clatsop County, OR

  13. EAGLE CREEK BRIDGE, EAST ELEVATION, SUBSTRUCTURE DETAIL LOOKING 333 DEGREES ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    EAGLE CREEK BRIDGE, EAST ELEVATION, SUBSTRUCTURE DETAIL LOOKING 333 DEGREES NORTH-NORTHWEST - Historic Columbia River Highway, Eagle Creek Bridge, Spanning Eagle Creek on Historic Columbia River Highway, Troutdale, Multnomah County, OR

  14. Detail view of Fanno Creek trestle, showing trestle substructure, view ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Detail view of Fanno Creek trestle, showing trestle substructure, view looking north - Oregon Electric Railroad, Fanno Creek Trestle, Garden Home to Wilsonville Segment, Milepost 34.7, Garden Home, Washington County, OR

  15. 22. VIEW OF FIXED SPAN SUBSTRUCTURE, EAST SPAN, SHOWING CANTILEVEREDBEAM ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    22. VIEW OF FIXED SPAN SUBSTRUCTURE, EAST SPAN, SHOWING CANTILEVERED-BEAM SIDEWALK SUPPORTS, LONGITUDINAL GIRDER AND TRANSVERSE ROADBED BEAMS, LOOKING SOUTHEAST - Congress Street Bascule Bridge, Spanning Fort Point Channel at Congress Street, Boston, Suffolk County, MA

  16. Substructure view illustrating the continuous concrete Tbeams, piers, sidewalk brackets ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Substructure view illustrating the continuous concrete T-beams, piers, sidewalk brackets and arched longitudinal beams - A Canal Bridge, Spanning the A Canal on Wall Street, Klamath Falls, Klamath County, OR

  17. 8. View of substructure showing the lower chord of the ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. View of substructure showing the lower chord of the Howe truss, flared board-and-batten siding, and pier configuration - Drift Creek Bridge, Spanning Drift Creek on Drift Creek County Road, Lincoln City, Lincoln County, OR

  18. 65. VIEW LOOKING UPSTREAM FROM FLUME SUBSTRUCTURE, SHOWING COLUMBIA IMPROVEMENT ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    65. VIEW LOOKING UPSTREAM FROM FLUME SUBSTRUCTURE, SHOWING COLUMBIA IMPROVEMENT COMPANY'S NEISSON CREEK SAWMILL. Print No. 177, November 1903 - Electron Hydroelectric Project, Along Puyallup River, Electron, Pierce County, WA

  19. Substructure Main Bridge, River Pier IV Huey P. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Substructure - Main Bridge, River Pier IV - Huey P. Long Bridge, Spanning Mississippi River approximately midway between nine & twelve mile points upstream from & west of New Orleans, Jefferson, Jefferson Parish, LA

  20. Substructure Main Bridge, River Piers I, II, III & ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Substructure - Main Bridge, River Piers I, II, III & IV - Huey P. Long Bridge, Spanning Mississippi River approximately midway between nine & twelve mile points upstream from & west of New Orleans, Jefferson, Jefferson Parish, LA

  1. 3. VIEW OF SOUTH FACE AND CONSTRUCTION DETAIL OF SUBSTRUCTURE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. VIEW OF SOUTH FACE AND CONSTRUCTION DETAIL OF SUBSTRUCTURE FROM NORTH BANK. RETAINING WALL OF GAUGING STATION IS VISIBLE IN BACKGROUND UNDER BRIDGE. - Old Happy Isles Bridge, Spanning Merced River on service road, Yosemite Village, Mariposa County, CA

  2. Linkers Having a Crucial Role in Antibody-Drug Conjugates.

    PubMed

    Lu, Jun; Jiang, Feng; Lu, Aiping; Zhang, Ge

    2016-01-01

    Antibody-drug conjugates (ADCs) comprised of a desirable monoclonal antibody, an active cytotoxic drug and an appropriate linker are considered to be an innovative therapeutic approach for targeted treatment of various types of tumors and cancers, enhancing the therapeutic parameter of the cytotoxic drug and reducing the possibility of systemic cytotoxicity. An appropriate linker between the antibody and the cytotoxic drug provides a specific bridge, and thus helps the antibody to selectively deliver the cytotoxic drug to tumor cells and accurately releases the cytotoxic drug at tumor sites. In addition to conjugation, the linkers maintain ADCs' stability during the preparation and storage stages of the ADCs and during the systemic circulation period. The design of linkers for ADCs is a challenge in terms of extracellular stability and intracellular release, and intracellular circumstances, such as the acid environment, the reducing environment and cathepsin, are considered as the catalysts to activate the triggers for initiating the cleavage of ADCs. This review discusses the linkers used in the clinical and marketing stages for ADCs and details the fracture modes of the linkers for the further development of ADCs. PMID:27089329

  3. Linkers Having a Crucial Role in Antibody–Drug Conjugates

    PubMed Central

    Lu, Jun; Jiang, Feng; Lu, Aiping; Zhang, Ge

    2016-01-01

    Antibody–drug conjugates (ADCs) comprised of a desirable monoclonal antibody, an active cytotoxic drug and an appropriate linker are considered to be an innovative therapeutic approach for targeted treatment of various types of tumors and cancers, enhancing the therapeutic parameter of the cytotoxic drug and reducing the possibility of systemic cytotoxicity. An appropriate linker between the antibody and the cytotoxic drug provides a specific bridge, and thus helps the antibody to selectively deliver the cytotoxic drug to tumor cells and accurately releases the cytotoxic drug at tumor sites. In addition to conjugation, the linkers maintain ADCs’ stability during the preparation and storage stages of the ADCs and during the systemic circulation period. The design of linkers for ADCs is a challenge in terms of extracellular stability and intracellular release, and intracellular circumstances, such as the acid environment, the reducing environment and cathepsin, are considered as the catalysts to activate the triggers for initiating the cleavage of ADCs. This review discusses the linkers used in the clinical and marketing stages for ADCs and details the fracture modes of the linkers for the further development of ADCs. PMID:27089329

  4. Linker histone variants control chromatin dynamics during early embryogenesis

    PubMed Central

    Saeki, Hideaki; Ohsumi, Keita; Aihara, Hitoshi; Ito, Takashi; Hirose, Susumu; Ura, Kiyoe; Kaneda, Yasufumi

    2005-01-01

    Complex transitions in chromatin structure produce changes in genome function during development in metazoa. Linker histones, the last component of nucleosomes to be assembled into chromatin, comprise considerably divergent subtypes as compared with core histones. In all metazoa studied, their composition changes dramatically during early embryogenesis concomitant with zygotic gene activation, leading to distinct functional changes that are still poorly understood. Here, we show that early embryonic linker histone B4, which is maternally expressed, is functionally different from somatic histone H1 in influencing chromatin structure and dynamics. We developed a chromatin assembly system with nucleosome assembly protein-1 as a linker histone chaperone. This assay system revealed that maternal histone B4 allows chromatin to be remodeled by ATP-dependent chromatin remodeling factor, whereas somatic histone H1 prevents this remodeling. Structural analysis shows that histone B4 does not significantly restrict the accessibility of linker DNA. These findings define the functional significance of developmental changes in linker histone variants. We propose a model that holds that maternally expressed linker histones are key molecules specifying nuclear dynamics with respect to embryonic totipotency. PMID:15821029

  5. The SNAP-25 Linker as an Adaptation Toward Fast Exocytosis

    PubMed Central

    Nagy, Gábor; Milosevic, Ira; Mohrmann, Ralf; Wiederhold, Katrin; Walter, Alexander M.

    2008-01-01

    The assembly of four soluble N-ethylmaleimide-sensitive factor attachment protein receptor domains into a complex is essential for membrane fusion. In most cases, the four SNARE-domains are encoded by separate membrane-targeted proteins. However, in the exocytotic pathway, two SNARE-domains are present in one protein, connected by a flexible linker. The significance of this arrangement is unknown. We characterized the role of the linker in SNAP-25, a neuronal SNARE, by using overexpression techniques in synaptosomal-associated protein of 25 kDa (SNAP-25) null mouse chromaffin cells and fast electrophysiological techniques. We confirm that the palmitoylated linker-cysteines are important for membrane association. A SNAP-25 mutant without cysteines supported exocytosis, but the fusion rate was slowed down and the fusion pore duration prolonged. Using chimeric proteins between SNAP-25 and its ubiquitous homologue SNAP-23, we show that the cysteine-containing part of the linkers is interchangeable. However, a stretch of 10 hydrophobic and charged amino acids in the C-terminal half of the SNAP-25 linker is required for fast exocytosis and in its absence the calcium dependence of exocytosis is shifted toward higher concentrations. The SNAP-25 linker therefore might have evolved as an adaptation toward calcium triggering and a high rate of execution of the fusion process, those features that distinguish exocytosis from other membrane fusion pathways. PMID:18579690

  6. The SEGUE K Giant Survey. III. Quantifying Galactic Halo Substructure

    NASA Astrophysics Data System (ADS)

    Janesh, William; Morrison, Heather L.; Ma, Zhibo; Rockosi, Constance; Starkenburg, Else; Xue, Xiang Xiang; Rix, Hans-Walter; Harding, Paul; Beers, Timothy C.; Johnson, Jennifer; Lee, Young Sun; Schneider, Donald P.

    2016-01-01

    We statistically quantify the amount of substructure in the Milky Way stellar halo using a sample of 4568 halo K giant stars at Galactocentric distances ranging over 5-125 kpc. These stars have been selected photometrically and confirmed spectroscopically as K giants from the Sloan Digital Sky Survey’s Sloan Extension for Galactic Understanding and Exploration project. Using a position-velocity clustering estimator (the 4distance) and a model of a smooth stellar halo, we quantify the amount of substructure in the halo, divided by distance and metallicity. Overall, we find that the halo as a whole is highly structured. We also confirm earlier work using blue horizontal branch (BHB) stars which showed that there is an increasing amount of substructure with increasing Galactocentric radius, and additionally find that the amount of substructure in the halo increases with increasing metallicity. Comparing to resampled BHB stars, we find that K giants and BHBs have similar amounts of substructure over equivalent ranges of Galactocentric radius. Using a friends-of-friends algorithm to identify members of individual groups, we find that a large fraction (˜33%) of grouped stars are associated with Sgr, and identify stars belonging to other halo star streams: the Orphan Stream, the Cetus Polar Stream, and others, including previously unknown substructures. A large fraction of sample K giants (more than 50%) are not grouped into any substructure. We find also that the Sgr stream strongly dominates groups in the outer halo for all except the most metal-poor stars, and suggest that this is the source of the increase of substructure with Galactocentric radius and metallicity.

  7. Using Network Methodology to Infer Population Substructure

    PubMed Central

    Prokopenko, Dmitry; Hecker, Julian; Silverman, Edwin; Nöthen, Markus M.; Schmid, Matthias; Lange, Christoph; Loehlein Fier, Heide

    2015-01-01

    One of the main caveats of association studies is the possible affection by bias due to population stratification. Existing methods rely on model-based approaches like structure and ADMIXTURE or on principal component analysis like EIGENSTRAT. Here we provide a novel visualization technique and describe the problem of population substructure from a graph-theoretical point of view. We group the sequenced individuals into triads, which depict the relational structure, on the basis of a predefined pairwise similarity measure. We then merge the triads into a network and apply community detection algorithms in order to identify homogeneous subgroups or communities, which can further be incorporated as covariates into logistic regression. We apply our method to populations from different continents in the 1000 Genomes Project and evaluate the type 1 error based on the empirical p-values. The application to 1000 Genomes data suggests that the network approach provides a very fine resolution of the underlying ancestral population structure. Besides we show in simulations, that in the presence of discrete population structures, our developed approach maintains the type 1 error more precisely than existing approaches. PMID:26098940

  8. Finding Nonoverlapping Substructures of a Sparse Matrix

    SciTech Connect

    Pinar, Ali; Vassilevska, Virginia

    2005-08-11

    Many applications of scientific computing rely on computations on sparse matrices. The design of efficient implementations of sparse matrix kernels is crucial for the overall efficiency of these applications. Due to the high compute-to-memory ratio and irregular memory access patterns, the performance of sparse matrix kernels is often far away from the peak performance on a modern processor. Alternative data structures have been proposed, which split the original matrix A into A{sub d} and A{sub s}, so that A{sub d} contains all dense blocks of a specified size in the matrix, and A{sub s} contains the remaining entries. This enables the use of dense matrix kernels on the entries of A{sub d} producing better memory performance. In this work, we study the problem of finding a maximum number of nonoverlapping dense blocks in a sparse matrix, which is previously not studied in the sparse matrix community. We show that the maximum nonoverlapping dense blocks problem is NP-complete by using a reduction from the maximum independent set problem on cubic planar graphs. We also propose a 2/3-approximation algorithm that runs in linear time in the number of nonzeros in the matrix. This extended abstract focuses on our results for 2x2 dense blocks. However we show that our results can be generalized to arbitrary sized dense blocks, and many other oriented substructures, which can be exploited to improve the memory performance of sparse matrix operations.

  9. Mass and Substructure in Dwarf Spheroidal Galaxies

    NASA Astrophysics Data System (ADS)

    Walker, Matthew G.

    2006-12-01

    I present results from a large spectroscopic survey of individual stars in dwarf spheroidal (dSph) galaxies, conducted using the Michigan/MIKE Fiber System (MMFS) at the Magellan Telescopes. dSph galaxies have come under intense scrutiny because they represent the lower extreme of the galaxy mass function, and thereby provide important constraints on models of structure formation. The proximity of the Milky Way's (MW's) dSph satellites allows us to study the resolved stellar populations of these systems in detail. Toward this end I have acquired MMFS spectra (5140-5180 Angstroms at resolution 20000) for more than 5000 stars in the MW dSphs Carina, Fornax, Sculptor, and Sextans. The spectra yield measurements of both radial velocity (median precision ± 1.8 km/s) and [Fe/H] metallicity (± 0.2 dex). I present radial velocity dispersion profiles for each dSph, as well as halo mass profiles derived using a variety of models and nonparametric estimation techniques. In some cases, the bulk stellar component is separable into populations following distinct distributions in position, kinematics, and chemistry, indicating a surprising level of complexity in these diminutive galaxies. Taking advantage of the fine spatial sampling of the MMFS data, I identify regions showing tentative evidence of localized chemo-dynamical substructure. This work is supported by grants from the National Science Foundation and the University of Michigan.

  10. The importance of the cosmic web and halo substructure for power spectra

    NASA Astrophysics Data System (ADS)

    Pace, Francesco; Manera, Marc; Bacon, David J.; Crittenden, Robert; Percival, Will J.

    2015-11-01

    In this work, we study the relevance of the cosmic web and substructures on the matter and lensing power spectra measured from halo mock catalogues extracted from the N-body simulations. Since N-body simulations are computationally expensive, it is common to use faster methods that approximate the dark matter field as a set of haloes. In this approximation, we replace mass concentrations in N-body simulations by a spherically symmetric Navarro-Frenk-White halo density profile. We also consider the full mass field as the sum of two distinct fields: dark matter haloes (M > 9 × 1012 M⊙ h-1) and particles not included into haloes. Mock haloes reproduce well the matter power spectrum, but underestimate the lensing power spectrum on large and small scales. For sources at zs = 1 the lensing power spectrum is underestimated by up to 40 per cent at ℓ ≈ 104 with respect to the simulated haloes. The large-scale effect can be alleviated by combining the mock catalogue with the dark matter distribution outside the haloes. In addition, to evaluate the contribution of substructures we have smeared out the intrahalo substructures in an N-body simulation while keeping the halo density profiles unchanged. For the matter power spectrum the effect of this smoothing is only of the order of 5 per cent, but for lensing substructures and ellipticity are much more important: for ℓ ≈ 104 modifications to the internal structure contribute to 30 per cent of the total spectrum. These findings have important implications in the way mock catalogues have to be created, suggesting that some approximate methods currently used for galaxy surveys will be inadequate for future weak lensing surveys.

  11. Effect of Interdomain Linker Length on an Antagonistic Folding-Unfolding Equilibrium between Two Protein Domains

    PubMed Central

    Cutler, Thomas A.; Mills, Brandon M.; Lubin, David J.; Chong, Lillian T.; Loh, Stewart N.

    2009-01-01

    Fusion of one protein domain with another is a common event in both evolution and protein engineering experiments. When insertion is at an internal site (e.g., a surface loop or turn), as opposed to one of the termini, conformational strain can be introduced into both domains. Strain is manifested by an antagonistic folding-unfolding equilibrium between the two domains, which we previously showed can be parameterized by a coupling free-energy term (ΔGX). The extent of strain is predicted to depend primarily on the ratio of the N-to-C distance of the guest protein to the distance between ends of the surface loop in the host protein. Here, we test that hypothesis by inserting ubiquitin (Ub) into the bacterial ribonuclease barnase (Bn), using peptide linkers from zero to 10 amino acids each. ΔGX values are determined by measuring the extent to which Co2+ binding to an engineered site on the Ub domain destabilizes the Bn domain. All-atom, unforced Langevin dynamics simulations are employed to gain structural insight into the mechanism of mechanically induced unfolding. Experimental and computational results find that the two domains are structurally and energetically uncoupled when linkers are long and that ΔGX increases with decreasing linker length. When the linkers are fewer than two amino acids, strain is so great that one domain unfolds the other. However, the protein is able to refold as dimers and higher-order oligomers. The likely mechanism is a three-dimensional domain swap of the Bn domain, which relieves conformational strain. The simulations suggest that an effective route to mechanical unfolding begins with disruption of the hydrophobic core of Bn near the Ub insertion site. PMID:19038264

  12. Substructure and Dynamics of the Fornax Cluster

    NASA Astrophysics Data System (ADS)

    Drinkwater, Michael J.; Gregg, Michael D.; Colless, Matthew

    2001-02-01

    We present the first dynamical analysis of a galaxy cluster to include a large fraction of dwarf galaxies. Our sample of 108 Fornax Cluster members measured with the UK Schmidt Telescope FLAIR-II spectrograph contains 55 dwarf galaxies (15.5>bJ>18.0 or -16>MB>-13.5). Hα emission shows that 36%+/-8% of the dwarfs are star forming, twice the fraction implied by morphological classifications. The total sample has a mean velocity of 1493+/-36 km s-1 and a velocity dispersion of 374+/-26 km s-1. The dwarf galaxies form a distinct population: their velocity dispersion (429+/-41 km s-1) is larger than that of the giants (308+/-30 km s-1) at the 98% confidence level. This suggests that the dwarf population is dominated by infalling objects whereas the giants are virialized. The Fornax system has two components, the main Fornax Cluster centered on NGC 1399 with cz=1478 km s-1 and σcz=370 km s-1 and a subcluster centered 3° to the southwest including NGC 1316 with cz=1583 km s-1 and σcz=377 km s-1. This partition is preferred over a single cluster at the 99% confidence level. The subcluster, a site of intense star formation, is bound to Fornax and probably infalling toward the cluster core for the first time. We discuss the implications of this substructure for distance estimates of the Fornax Cluster. We determine the cluster mass profile using the method of Diaferio, which does not assume a virialized sample. The mass within a projected radius of 1.4 Mpc is (7+/-2)×1013 Msolar, and the mass-to-light ratio is 300+/-100 Msolar/Lsolar. The mass is consistent with values derived from the projected mass virial estimator and X-ray measurements at smaller radii.

  13. SUBSTRUCTURE DEPLETION IN THE MILKY WAY HALO BY THE DISK

    SciTech Connect

    D'Onghia, Elena; Hernquist, Lars; Keres, Dusan; Springel, Volker

    2010-02-01

    We employ numerical simulations and simple analytical estimates to argue that dark matter substructures orbiting in the inner regions of the Galaxy can be efficiently destroyed by disk shocking, a dynamical process known to affect globular star clusters. We carry out a set of fiducial high-resolution collisionless simulations in which we adiabatically grow a disk, allowing us to examine the impact of the disk on the substructure abundance. We also track the orbits of dark matter satellites in high-resolution Aquarius simulations and analytically estimate the cumulative halo and disk-shocking effect. Our calculations indicate that the presence of a disk with only 10% of the total Milky Way mass can significantly alter the mass function of substructures in the inner parts of halos. This has important implications especially for the relatively small number of satellites seen within approx30 kpc of the Milky Way center, where disk shocking is expected to reduce the substructure abundance by a factor of 2 at 10{sup 9} M{sub sun} and a factor of 3 at 10{sup 7} M{sub sun}. The most massive subhalos with 10{sup 10} M{sub sun} survive even in the presence of the disk. This suggests that there is no inner missing satellite problem and calls into question whether these substructures can produce transient features in disks, like multi-armed spiral patterns. Also, the depletion of dark matter substructures through shocking on the baryonic structures of the disk and central bulge may aggravate the problem to fully account for the observed flux anomalies in gravitational lens systems, and significantly reduces the dark matter annihilation signal expected from nearby substructures in the inner halo.

  14. A study on the effects of linker flexibility on acid phosphatase PhoC-GFP fusion protein using a novel linker library.

    PubMed

    Huang, Ziliang; Li, Gang; Zhang, Chong; Xing, Xin-Hui

    2016-02-01

    Fusion strategy has been widely used to construct artificial multifunction proteins. The flexibility or rigidity of linkers between two fused partners is an important parameter that affects the function of fusion proteins. By combining the flexible unit GGGGS (F) and rigid unit EAAAK (R), ten linkers consisting of five elementary units that cover the fully rigid RRRRR linker to the fully flexible FFFFF linker were used to construct acid phosphatase-green fluorescence protein fusion protein (PhoC-GFP). By varying the linker flexibility in PhoC-GFPs, the relative specific activity of phosphotransferase and phosphatase varied from ∼19.0% to 100% and ∼9.35% to 100%, respectively. There exists an optimal linker capable of achieving the highest phosphotransferase/phosphatase activity and GFP fluorescence intensity. We found that the highest activities were achieved neither with the rigid RRRRR linker nor with the flexible FFFFF linker, but with the FFFRR linker. Linker flexibility could adjust the activity ratio between phosphotransferase and phosphatase and varied between ∼30% to 100%. PhoC-GFP with FRRRR linker achieved the highest relative specific phosphotransferase activity/relative specific phosphatase activity (T/P) value. Our results show that applying a linker library with controllable flexibility to the fusion proteins will be an efficient way to adjust the function of fusion enzymes. PMID:26777244

  15. Gamma-ray probes of dark matter substructure

    SciTech Connect

    Campbell, Sheldon

    2014-06-24

    The substructure content of dark matter halos is interesting because it can be affected by complex galaxy physics and dark matter particle physics. However, observing the small scale structure of dark matter is a challenge. The subhalo abundance (mass function, minimum mass) and morphology (density profile, subhalo shape, subsubstructure) contain information about complex astrophysics (halo formation processes) and new exotic fundamental physics (dark matter interactions). Indirect detection of dark matter annihilation radiation (DMAR) in gamma rays may be the most direct method for observing small scale structure. I outline the ways in which gamma rays may probe halo substructure. If substructure is bountiful, it may be responsible for the eventual discovery of DMAR, for instance in galaxy clusters or the diffuse gamma-ray background. Otherwise, the observation of DMAR in places without much substructure, such as the Galactic center, would lead to strict limits on the properties of small scale structure. Properties of the gamma-ray angular power spectrum will also provide information or constraints on Milky Way halo substructure.

  16. Substructure location and size effects on decentralized model updating

    NASA Astrophysics Data System (ADS)

    Dong, Xinjun; Zhu, Dapeng; Wang, Yang

    2015-04-01

    To improve the simulation accuracy of the finite-element (FE) model of an as-built structure, measurement data from the actual structure can be utilized for updating the model parameters, which is termed as FE model updating. During the past few decades, most efforts on FE model updating intend to update the entire structure model altogether, while using measurement data from sensors installed throughout the structure. When applied on large and complex structural models, the typical model updating approaches may fail due to computational challenges and convergence issues. In order to reduce the computational difficulty, this paper studies a decentralized FE model updating approach that intends to update one substructure at a time. The approach divides the entire structure into a substructure (currently being instrumented and updated) and the residual structure. The Craig-Bampton transform is adopted to condense the overall structural model. The optimization objective is formulated to minimize the modal dynamic residuals from the eigenvalue equations in structural dynamics involving natural frequencies and mode shapes. This paper investigates the effects of different substructure locations and sizes on updating performance. A space frame example, which is based on an actual pedestrian bridge on Georgia Tech campus, is used to study the substructure location and size effects. Keywords: substructure

  17. Quantifying the Significance of Substructure in Coronal Loops

    NASA Astrophysics Data System (ADS)

    McKeough, K. B. D.; Kashyap, V.; McKillop, S.

    2014-12-01

    A method to infer the presence of small-scale substructure in SDO/AIA (Atmospheric Imaging Assembly on the Solar Dynamics Observatory) images of coronal loops is developed. We can classify visible loop structure based on this propensity to show substructure which puts constraints on contemporary solutions to the coronal heating problem. The method uses the Bayesian algorithm Low-count Image Reconstruction and Analysis (LIRA) to infer the multi-scale component of the loops which describes deviations from a smooth model. The increase in contrast of features in this multi-scale component is determined using a statistic that estimates the sharpness across the image. Regions with significant substructure are determined using p-value upper bounds. We are able to locate substructure visible in Hi-C (High-Resolution Coronal Imager) data that are not salient features in the corresponding AIA image. Looking at coronal loops at different regions of the Sun (e.g., low-lying structure and loops in the upper corona) we are able to map where detectable substructure exists and thus the influence of the nanoflare heating process. We acknowledge support from AIA under contract SP02H1701R from Lockheed-Martin to SAO.

  18. On substructuring algorithms and solution techniques for the numerical approximation of partial differential equations

    NASA Technical Reports Server (NTRS)

    Gunzburger, M. D.; Nicolaides, R. A.

    1986-01-01

    Substructuring methods are in common use in mechanics problems where typically the associated linear systems of algebraic equations are positive definite. Here these methods are extended to problems which lead to nonpositive definite, nonsymmetric matrices. The extension is based on an algorithm which carries out the block Gauss elimination procedure without the need for interchanges even when a pivot matrix is singular. Examples are provided wherein the method is used in connection with finite element solutions of the stationary Stokes equations and the Helmholtz equation, and dual methods for second-order elliptic equations.

  19. Phenotypic variation of erythrocyte linker histone H1.c in a pheasant (Phasianus colchicus L.) population.

    PubMed

    Kowalski, Andrzej; Pa Yga, Jan; Górnicka-Michalska, Ewa; Bernacki, Zenon; Adamski, Marek

    2010-07-01

    Our goal was to characterize a phenotypic variation of the pheasant erythrocyte linker histone subtype H1.c. By using two-dimensional polyacrylamide gel electrophoresis three histone H1.c phenotypes were identified. The differently migrating allelic variants H1.c1 and H1.c2 formed either two homozygous phenotypes, c1 and c2, or a single heterozygous phenotype, c1c2. In the pheasant population screened, birds with phenotype c2 were the most common (frequency 0.761) while individuals with phenotype c1 were rare (frequency 0.043). PMID:21637419

  20. Shock induced deformation substructures in a copper bicrystal

    SciTech Connect

    Cao, Fang; Beyerlein, Irene J; Cerreta, Ellen K; Trujillo, Carl P; Gray Ill, George T; Sencer, Bulent H

    2008-01-01

    Controlled shock recovery experiments have been conducted to assess the role of shock pressure and orientation dependence on the substructure evolution of a [100]/[01{ovr 1}] copper bicrystal. Electron backscatter diffraction (EBSD) and transmission electron microscopy (TEM) were utilized to characterize orientation variation and substructure evolution of the post-shock specimens. Well defined dislocation cell structures were displayed in both grains and the average cell size was observed to decrease with increasing shock pressure. Twinning was occasionally observed in the 5 GPa shocked [100] grain and became the dominant substructure at higher shock pressure. The stress and directional dependence of twinning in the bicrystal was analyzed with consideration of the energetically favorable dissociation of dislocations into Shockley partials and the stress-orientation effect on the partial width. Moreover, a critical 'tear apart' stress is proposed and a good agreement is obtained between the calculated value and the experimental observations.

  1. EFFECT OF DARK MATTER HALO SUBSTRUCTURES ON GALAXY ROTATION CURVES

    SciTech Connect

    Roy, Nirupam

    2010-11-01

    In this paper, the effect of halo substructures on galaxy rotation curves is investigated using a simple model of dark matter clustering. A dark matter halo density profile is developed based only on the scale-free nature of clustering that leads to a statistically self-similar distribution of the substructures at the galactic scale. A semi-analytical method is used to derive rotation curves for such a clumpy dark matter density profile. It is found that the halo substructures significantly affect the galaxy velocity field. Based on the fractal geometry of the halo, this self-consistent model predicts a Navarro-Frenk-White-like rotation curve and a scale-free power spectrum of the rotation velocity fluctuations.

  2. Functional Group and Substructure Searching as a Tool in Metabolomics

    PubMed Central

    Kotera, Masaaki; McDonald, Andrew G.; Boyce, Sinéad; Tipton, Keith F.

    2008-01-01

    Background A direct link between the names and structures of compounds and the functional groups contained within them is important, not only because biochemists frequently rely on literature that uses a free-text format to describe functional groups, but also because metabolic models depend upon the connections between enzymes and substrates being known and appropriately stored in databases. Methodology We have developed a database named “Biochemical Substructure Search Catalogue” (BiSSCat), which contains 489 functional groups, >200,000 compounds and >1,000,000 different computationally constructed substructures, to allow identification of chemical compounds of biological interest. Conclusions This database and its associated web-based search program (http://bisscat.org/) can be used to find compounds containing selected combinations of substructures and functional groups. It can be used to determine possible additional substrates for known enzymes and for putative enzymes found in genome projects. Its applications to enzyme inhibitor design are also discussed. PMID:18253485

  3. Estimation of ADME properties with substructure pattern recognition.

    PubMed

    Shen, Jie; Cheng, Feixiong; Xu, You; Li, Weihua; Tang, Yun

    2010-06-28

    Over the past decade, absorption, distribution, metabolism, and excretion (ADME) property evaluation has become one of the most important issues in the process of drug discovery and development. Since in vivo and in vitro evaluations are costly and laborious, in silico techniques had been widely used to estimate ADME properties of chemical compounds. Traditional prediction methods usually try to build a functional relationship between a set of molecular descriptors and a given ADME property. Although traditional methods have been successfully used in many cases, the accuracy and efficiency of molecular descriptors must be concerned. Herein, we report a new classification method based on substructure pattern recognition, in which each molecule is represented as a substructure pattern fingerprint based on a predefined substructure dictionary, and then a support vector machine (SVM) algorithm is applied to build the prediction model. Therefore, a direct connection between substructures and molecular properties is built. The most important substructure patterns can be identified via the information gain analysis, which could help to interpret the models from a medicinal chemistry perspective. Afterward, this method was verified with two data sets, one for blood-brain barrier (BBB) penetration and the other for human intestinal absorption (HIA). The results demonstrated that the overall predictive accuracies of the best HIA model for the training and test sets were 98.5 and 98.8%, and the overall predictive accuracies of the best BBB model for the training and test sets were 98.8 and 98.4%, which confirmed the reliability of our method. In the additional validations, the predictive accuracies were 94 and 69.5% for the HIA and the BBB models, respectively. Moreover, some of the representative key substructure patterns which significantly correlated with the HIA and BBB penetration properties were also presented. PMID:20578727

  4. Linker histone protects linker DNA on only one side of the core particle and in a sequence-dependent manner

    PubMed Central

    An, Woojin; Leuba, Sanford H.; van Holde, Kensal; Zlatanova, Jordanka

    1998-01-01

    The protection against micrococcal nuclease digestion afforded to chromatosomal DNA by the presence of a linker histone (H1o) has been quantitatively measured in two reconstituted systems. We have used chromatosomes reconstituted at two distinct positions on a DNA fragment containing the 5S rRNA gene from Lytechinus variegatus and at a specific position on a sequence containing Gal4- and USF-binding sites. In all cases, we find asymmetric protection, with ≈20 bp protected on one side of the core particle and no protection on the other. We demonstrated through crosslinking experiments that the result is not due to any sliding of the histone core caused by either linker histone addition or micrococcal nuclease cleavage. Because the core particle is itself a symmetric object, the preferred asymmetric location of a linker histone must be dictated by unknown elements in the DNA sequence. PMID:9520377

  5. System for detecting substructure microfractures and method therefore

    NASA Technical Reports Server (NTRS)

    Parthasarathy, S. P.; Narasimhan, K. Y. (Inventor)

    1979-01-01

    Bursts of signals at different frequencies are induced into substructure, adjacent to a borehole. The return signals from each burst of signals are normalized to compensate for the attenuation, experienced by more distant return signals. The peak amplitudes of return signals, above a selected level, are cut off, and an average signal is produced from the normalized amplitude-limited return signals of each burst. The averaged signals of the return signals of all the signal bursts at the different frequencies are processed to provide a combined signal, whose amplitude is related to the microfracture density of the substructure adjacent to the borehole.

  6. A Robust Control Design Framework for Substructure Models

    NASA Technical Reports Server (NTRS)

    Lim, Kyong B.

    1994-01-01

    A framework for designing control systems directly from substructure models and uncertainties is proposed. The technique is based on combining a set of substructure robust control problems by an interface stiffness matrix which appears as a constant gain feedback. Variations of uncertainties in the interface stiffness are treated as a parametric uncertainty. It is shown that multivariable robust control can be applied to generate centralized or decentralized controllers that guarantee performance with respect to uncertainties in the interface stiffness, reduced component modes and external disturbances. The technique is particularly suited for large, complex, and weakly coupled flexible structures.

  7. A substructure coupling procedure applicable to general linear time-invariant dynamic systems

    NASA Technical Reports Server (NTRS)

    Howsman, T. G.; Craig, R. R., Jr.

    1984-01-01

    A substructure synthesis procedure applicable to structural systems containing general nonconservative terms is presented. In their final form, the nonself-adjoint substructure equations of motion are cast in state vector form through the use of a variational principle. A reduced-order mode for each substructure is implemented by representing the substructure as a combination of a small number of Ritz vectors. For the method presented, the substructure Ritz vectors are identified as a truncated set of substructure eigenmodes, which are typically complex, along with a set of generalized real attachment modes. The formation of the generalized attachment modes does not require any knowledge of the substructure flexible modes; hence, only the eigenmodes used explicitly as Ritz vectors need to be extracted from the substructure eigenproblem. An example problem is presented to illustrate the method.

  8. A substructure coupling procedure applicable to general linear time-invariant dynamic systems

    NASA Technical Reports Server (NTRS)

    Howsman, T. G.; Craig, R. R., Jr.

    1984-01-01

    A substructure synthesis procedure applicable to structural systems containing general nonconservative terms is presented. In their final form, the non-self-adjoint substructure equations of motion are cast in state vector form through the use of a variational principle. A reduced-order model for each substructure is implemented by representing the substructure as a combination of a small number of Ritz vectors. For the method presented, the substructure Ritz vectors are identified as a truncated set of substructure eigenmodes, which are typically complex, along with a set of generalized real attachment modes. The formation of the generalized attachment modes does not require any knowledge of the substructure flexible modes; hence, only the eigenmodes used explicitly as Ritz vectors need to be extracted from the substructure eigenproblem. An example problem is presented to illustrate the method.

  9. Synthesis of a novel photoactivatable glucosylceramide cross-linker.

    PubMed

    Budani, Monique; Mylvaganam, Murugesapillai; Binnington, Beth; Lingwood, Clifford

    2016-09-01

    The biosynthesis of glucosylceramide (GlcCer) is a key rate-limiting step in complex glycosphingolipid (GSL) biosynthesis. To further define interacting partners of GlcCer, we have made a cleavable, biotinylated, photoreactive GlcCer analog in which the reactive nitrene is closely apposed to the GlcCer head group, by substituting the native fatty acid with d, l-2-aminohexadecanoic acid. Two amino-GlcCer diastereomer cross-linkers (XLA and XLB) were generated. XLB proved an effective lactosylceramide (LacCer) synthase substrate while XLA was inhibitory. Both probes specifically bound and cross-linked the GlcCer binding protein, glycolipid transfer protein (GLTP), but not other GSL binding proteins (Shiga toxin and cholera toxin). GlcCer inhibited GLTP cross-linking. Both GlcCer cross-linkers competed with microsomal nitrobenzoxadiazole (NBD)-GlcCer anabolism to NBD-LacCer. GLTP showed marked, ATP-dependent enhancement of cell-free intact microsomal LacCer synthesis from endogenous or exogenous liposomal GlcCer, supporting a role in the transport/membrane translocation of cytosolic and extra-Golgi GlcCer. GLTP was specifically labeled by either XLA or XLB GlcCer cross-linker during this process, together with a (the same) small subset of microsomal proteins. These cross-linkers will serve to probe physiologically relevant GlcCer-interacting cellular proteins. PMID:27412675

  10. Cleavable carbamate linkers for controlled protein delivery from hydrogels.

    PubMed

    Hammer, Nadine; Brandl, Ferdinand P; Kirchhof, Susanne; Goepferich, Achim M

    2014-06-10

    The reversible attachment of proteins to polymers is one potential strategy to control protein release from hydrogels. In this study, we report the reversible attachment of lysozyme to poly(ethylene glycol) (PEG) by degradable carbamate linkers. Phenyl groups with different substituents were used to control the rate of carbamate hydrolysis and the resulting protein release. Sodium dodecyl sulfate polyacrylamide gel electrophoresis showed modification with 1-3 PEG chains per lysozyme molecule. Protein PEGylation and PEG chain elimination occurred without changes in secondary protein structure, as demonstrated by circular dichroism spectroscopy. The lytic activity of lysozyme was restored to 73.4±1.7%-92.5±1.2% during PEG chain elimination. Attached PEG chains were eliminated within 24h to 28days, depending on the used linker molecule. When formulated into hydrogels, a maximum of about 60% of the initial dose was released within 7days to 21days. Linker elimination occurs 'traceless', so that the protein is released in its native, unmodified form. Altogether, we believe that tethering proteins by degradable carbamate linkers is a promising strategy to control their release from hydrogels. PMID:24680687

  11. Tunable pH-Sensitive Linker for Controlled Release.

    PubMed

    Choy, Cindy J; Geruntho, Jonathan J; Davis, Austen L; Berkman, Clifford E

    2016-03-16

    We have developed a novel pH-sensitive linker based on a phosphoramidate scaffold that can be tuned to release amine-containing drug molecules at various pH values. The pH-triggered phosphoramidate-based linkers are responsive to pH alone and do not require intracellular enzymatic action to initiate drug release. Key to the pH-triggered amine release from these linkers is a proximal acidic group (e.g., pyridinium or carboxylic acid) to promote the hydrolysis of the phosphoramidate P-N bond, presumably through an intramolecular general-acid type mechanism. Phosphoramidate hydrolysis is largely governed by the pKa of the leaving amine (e.g., primary, secondary, aniline). However, the proximity of the neighboring pyridine group attenuates the stability of the P-N bond to hydrolysis, thus allowing for control over the release of an amine from the phosphoramidate center. Based on the model scaffolds examined, phosphoramidate-based linkers could be selected for particular properties for controlled-release applications such as amine type, stability under physiological conditions, or release rates at various pH values such as intracellular endosomal conditions. The tunability of the phosphoramidate scaffold is expected to find broad applicability in various controlled drug-release applications such as antibody or small-molecule drug conjugates, drug-eluting stents, prodrug activation, as well as intracellular trafficking studies in which pH changes can trigger the release of turn-on dyes. PMID:26886721

  12. Single-Crystal to Single-Crystal Linker Substitution, Linker Place Exchange, and Transmetalation Reactions in Interpenetrated Pillared-Bilayer Zinc(II) Metal-Organic Frameworks.

    PubMed

    De, Dinesh; Neogi, Subhadip; Sañudo, E Carolina; Bharadwaj, Parimal K

    2015-11-23

    A twofold interpenetrated pillared-bilayer framework, {[Zn3 (L)2 (L2 )(DMF)]⋅(18DMF)(6H2 O)}n (1), has been synthesized from the ligands tris(4'-carboxybiphenyl)amine (H3 L) and 1,2-bis(4-pyridyl)ethylene (L2 ). The structure contains [Zn3 (COO)6 ] secondary building units (SBUs), in which three Zn(II) ions are almost linear with carboxylate bridging. This framework undergoes reversible pillar linker substitution reactions at the terminal Zn(II) centers with three different dipyridyl linkers of different lengths to afford three daughter frameworks, 2-4. Frameworks 2-4 are interconvertible through reversible linker substitution reactions. Also, competitive linker-exchange experiments show preferential incorporation of linker L3 in the parent framework 1. The larger linker L5 does not undergo such substitution reactions and framework 5, which contains this linker, can be synthesized solvothermally as a twofold interpenetrated structure. Interestingly, when framework 5 is dipped in a solution of L3 in DMF, linker substitution takes place as before, but linker L5 now moves and diagonally binds two Zn(II) centers to afford 6 as a nonpenetrated single framework. This linker place exchange reaction is unprecedented. All of these reactions take place in a single-crystal to single-crystal (SC-SC) manner, and have been observed directly through X-ray crystallography. In addition, each 3D framework undergoes complete copper(II) transmetalation. PMID:26462612

  13. QUANTIFYING KINEMATIC SUBSTRUCTURE IN THE MILKY WAY'S STELLAR HALO

    SciTech Connect

    Xue Xiangxiang; Zhao Gang; Luo Ali; Rix, Hans-Walter; Bell, Eric F.; Koposov, Sergey E.; Kang, Xi; Liu, Chao; Yanny, Brian; Beers, Timothy C.; Lee, Young Sun; Bullock, James S.; Johnston, Kathryn V.; Morrison, Heather; Rockosi, Constance

    2011-09-01

    We present and analyze the positions, distances, and radial velocities for over 4000 blue horizontal-branch (BHB) stars in the Milky Way's halo, drawn from SDSS DR8. We search for position-velocity substructure in these data, a signature of the hierarchical assembly of the stellar halo. Using a cumulative 'close pair distribution' as a statistic in the four-dimensional space of sky position, distance, and velocity, we quantify the presence of position-velocity substructure at high statistical significance among the BHB stars: pairs of BHB stars that are close in position on the sky tend to have more similar distances and radial velocities compared to a random sampling of these overall distributions. We make analogous mock observations of 11 numerical halo formation simulations, in which the stellar halo is entirely composed of disrupted satellite debris, and find a level of substructure comparable to that seen in the actually observed BHB star sample. This result quantitatively confirms the hierarchical build-up of the stellar halo through a signature in phase (position-velocity) space. In detail, the structure present in the BHB stars is somewhat less prominent than that seen in most simulated halos, quite possibly because BHB stars represent an older sub-population. BHB stars located beyond 20 kpc from the Galactic center exhibit stronger substructure than at r{sub gc} < 20 kpc.

  14. Experimentally implementable criteria revealing substructures of genuine multipartite entanglement

    SciTech Connect

    Huber, Marcus; Schimpf, Hans; Gabriel, Andreas; Spengler, Christoph; Bruss, Dagmar; Hiesmayr, Beatrix C.

    2011-02-15

    We present a general framework that reveals substructures of genuine multipartite entanglement. Via simple inequalities it is possible to discriminate different sets of multipartite qubit states. These inequalities are beneficial regarding experimental examinations as only local measurements are required. Furthermore, the number of observables scales favorably with system size. In exemplary cases we demonstrate the noise resistance and discuss implementations.

  15. A Frequency-Domain Substructure System Identification Algorithm

    NASA Technical Reports Server (NTRS)

    Blades, Eric L.; Craig, Roy R., Jr.

    1996-01-01

    A new frequency-domain system identification algorithm is presented for system identification of substructures, such as payloads to be flown aboard the Space Shuttle. In the vibration test, all interface degrees of freedom where the substructure is connected to the carrier structure are either subjected to active excitation or are supported by a test stand with the reaction forces measured. The measured frequency-response data is used to obtain a linear, viscous-damped model with all interface-degree of freedom entries included. This model can then be used to validate analytical substructure models. This procedure makes it possible to obtain not only the fixed-interface modal data associated with a Craig-Bampton substructure model, but also the data associated with constraint modes. With this proposed algorithm, multiple-boundary-condition tests are not required, and test-stand dynamics is accounted for without requiring a separate modal test or finite element modeling of the test stand. Numerical simulations are used in examining the algorithm's ability to estimate valid reduced-order structural models. The algorithm's performance when frequency-response data covering narrow and broad frequency bandwidths is used as input is explored. Its performance when noise is added to the frequency-response data and the use of different least squares solution techniques are also examined. The identified reduced-order models are also compared for accuracy with other test-analysis models and a formulation for a Craig-Bampton test-analysis model is also presented.

  16. View of substructure of Sixth Street Bridge overcrossing of Los ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    View of substructure of Sixth Street Bridge overcrossing of Los Angeles River. Looking west. Note dark hole at lower with is access ramp to river channel seen in HAER CA-176-56 - Sixth Street Bridge, Spanning 101 Freeway at Sixth Street, Los Angeles, Los Angeles County, CA

  17. 7. General view of substructure of bridge, taken from hills ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    7. General view of substructure of bridge, taken from hills to northeast of bridge. Note old stone abutment under existing bridge, detailing of arch and abutments. - Presumpscot Falls Bridge, Spanning Presumptscot River at Allen Avenue extension, 0.75 mile west of U.S. Interstate 95, Falmouth, Cumberland County, ME

  18. Chemical Substructure Searching: Comparing Three Commercially Available Databases.

    ERIC Educational Resources Information Center

    Wagner, A. Ben

    1986-01-01

    Compares the differences in coverage and utility of three substructure databases--Chemical Abstracts, Index Chemicus, and Chemical Information System's Nomenclature Search System. The differences between Chemical Abstracts with two different vendors--STN International and Questel--are described and a summary guide for choosing between databases is…

  19. Cold Dark Matter Substructure and Galactic Disks I: Morphological Signatures of Hierarchical SatelliteAccretion

    SciTech Connect

    Kazantzidis, Stelios; Bullock, James S.; Zentner, Andrew R.; Kravtsov, Andrey V.; Moustakas, Leonidas A.

    2007-12-03

    We conduct a series of high-resolution, fully self-consistent dissipation less N-body simulations to investigate the cumulative effect of substructure mergers onto thin disk galaxies in the context of the {Lambda}CDM paradigm of structure formation. Our simulation campaign is based on a hybrid approach combining cosmological simulations and controlled numerical experiments. Substructure mass functions, orbital distributions, internal structures, and accretion times are culled directly from cosmological simulations of galaxy-sized cold dark matter (CDM) halos. We demonstrate that accretions of massive subhalos onto the central regions of host halos, where the galactic disk resides, since z {approx} 1 should be common occurrences. In contrast, extremely few satellites in present-day CDM halos are likely to have a significant impact on the disk structure. This is due to the fact that massive subhalos with small orbital pericenters that are most capable of strongly perturbing the disk become either tidally disrupted or suffer substantial mass loss prior to z = 0. One host halo merger history is subsequently used to seed controlled N-body experiments of repeated satellite impacts on an initially-thin Milky Way-type disk galaxy. These simulations track the effects of six dark matter substructures, with initial masses in the range {approx} (0.7-2) x 10{sup 10} M{sub {circle_dot}} ({approx} 20-60% of the disk mass), crossing the disk in the past {approx} 8 Gyr. We show that these accretion events produce several distinctive observational signatures in the stellar disk including: a long-lived, low-surface brightness, ring-like feature in the outskirts; a significant flare; a central bar; and faint filamentary structures that (spuriously) resemble tidal streams in configuration space. The final distribution of disk stars exhibits a complex vertical structure that is well-described by a standard 'thin-thick' disk decomposition, where the 'thick' disk component has emerged

  20. Peptide linkers for the assembly of semiconductor quantum dot bioconjugates

    NASA Astrophysics Data System (ADS)

    Boeneman, Kelly; Mei, Bing C.; Deschamps, Jeffrey R.; Delehanty, James B.; Mattoussi, Hedi; Medintz, Igor

    2009-02-01

    The use of semiconductor luminescent quantum dots for the labeling of biomolecules is rapidly expanding, however it still requires facile methods to attach functional globular proteins to biologically optimized quantum dots. Here we discuss the development of controlled variable length peptidyl linkers to attach biomolecules to poly(ethylene) glycol (PEG) coated quantum dots for both in vitro and in vivo applications. The peptides chosen, β-sheets and alpha helices are appended to polyhistidine sequences and this allows for control of the ratio of peptide bioconjugated to QD and the distance from QD to the biomolecule. Recombinant DNA engineering, bacterial peptide expression and Ni-NTA purification of histidine labeled peptides are utilized to create the linkers. Peptide length is confirmed by in vitro fluorescent resonance energy transfer (FRET).

  1. Fast antibody fragment motion: flexible linkers act as entropic spring

    DOE PAGESBeta

    Stingaciu, Laura R.; Ivanova, Oxana; Ohl, Michael; Biehl, Ralf; Richter, Dieter

    2016-03-29

    A flexible linker region between three fragments allows antibodies to adjust their binding sites to an antigen or receptor. Using Neutron Spin Echo Spectroscopy we observed fragment motion on a timescale of 7 ns with motional amplitudes of about 1 nm relative to each other. The mechanistic complexity of the linker region can be described by a spring model with Brownian motion of the fragments in a harmonic potential. Displacements, timescale, friction and force constant of the underlying dynamics are accessed. The force constant exhibits a similar strength to an entropic spring, with friction of the fragment matching the unboundmore » state. The observed fast motions are fluctuations in pre-existing equilibrium configurations. In conclusion, the Brownian motion of domains in a harmonic potential is the appropriate model to examine functional hinge motions dependent on the structural topology and highlights the role of internal forces and friction to function.« less

  2. Fast antibody fragment motion: flexible linkers act as entropic spring

    PubMed Central

    Stingaciu, Laura R.; Ivanova, Oxana; Ohl, Michael; Biehl, Ralf; Richter, Dieter

    2016-01-01

    A flexible linker region between three fragments allows antibodies to adjust their binding sites to an antigen or receptor. Using Neutron Spin Echo Spectroscopy we observed fragment motion on a timescale of 7 ns with motional amplitudes of about 1 nm relative to each other. The mechanistic complexity of the linker region can be described by a spring model with Brownian motion of the fragments in a harmonic potential. Displacements, timescale, friction and force constant of the underlying dynamics are accessed. The force constant exhibits a similar strength to an entropic spring, with friction of the fragment matching the unbound state. The observed fast motions are fluctuations in pre-existing equilibrium configurations. The Brownian motion of domains in a harmonic potential is the appropriate model to examine functional hinge motions dependent on the structural topology and highlights the role of internal forces and friction to function. PMID:27020739

  3. Fast antibody fragment motion: flexible linkers act as entropic spring.

    PubMed

    Stingaciu, Laura R; Ivanova, Oxana; Ohl, Michael; Biehl, Ralf; Richter, Dieter

    2016-01-01

    A flexible linker region between three fragments allows antibodies to adjust their binding sites to an antigen or receptor. Using Neutron Spin Echo Spectroscopy we observed fragment motion on a timescale of 7 ns with motional amplitudes of about 1 nm relative to each other. The mechanistic complexity of the linker region can be described by a spring model with Brownian motion of the fragments in a harmonic potential. Displacements, timescale, friction and force constant of the underlying dynamics are accessed. The force constant exhibits a similar strength to an entropic spring, with friction of the fragment matching the unbound state. The observed fast motions are fluctuations in pre-existing equilibrium configurations. The Brownian motion of domains in a harmonic potential is the appropriate model to examine functional hinge motions dependent on the structural topology and highlights the role of internal forces and friction to function. PMID:27020739

  4. Ringed Substructure and a Gap at 1 au in the Nearest Protoplanetary Disk

    NASA Astrophysics Data System (ADS)

    Andrews, Sean M.; Wilner, David J.; Zhu, Zhaohuan; Birnstiel, Tilman; Carpenter, John M.; Pérez, Laura M.; Bai, Xue-Ning; Öberg, Karin I.; Hughes, A. Meredith; Isella, Andrea; Ricci, Luca

    2016-04-01

    We present long baseline Atacama Large Millimeter/submillimeter Array (ALMA) observations of the 870 μm continuum emission from the nearest gas-rich protoplanetary disk, around TW Hya, that trace millimeter-sized particles down to spatial scales as small as 1 au (20 mas). These data reveal a series of concentric ring-shaped substructures in the form of bright zones and narrow dark annuli (1-6 au) with modest contrasts (5%-30%). We associate these features with concentrations of solids that have had their inward radial drift slowed or stopped, presumably at local gas pressure maxima. No significant non-axisymmetric structures are detected. Some of the observed features occur near temperatures that may be associated with the condensation fronts of major volatile species, but the relatively small brightness contrasts may also be a consequence of magnetized disk evolution (the so-called zonal flows). Other features, particularly a narrow dark annulus located only 1 au from the star, could indicate interactions between the disk and young planets. These data signal that ordered substructures on ˜au scales can be common, fundamental factors in disk evolution and that high-resolution microwave imaging can help characterize them during the epoch of planet formation.

  5. Application substructure model synthesis method on modeling of a space camera

    NASA Astrophysics Data System (ADS)

    Sun, De-wei; Tang, Tianjin; Wu, Yong-jian; Yang, Jia-wen

    2014-11-01

    Space infrared sensor must be assembled on a small satellite platform, so its whole mass and structure dimensions are strictly restricted by the satellite platform. The mechanical structure must be compacted, light, handy and reliable. Task of space infrared sensor structure system is to integrate each parts of system and provide a stable and reliable work platform for the whole body. The transfer functions of flexible object and base are analyzed by using mechanical impedance method and compared with stiffness models. It indicates that space infrared sensor must be considered the flexible body influence for transfer function on some certain conditions. Using second order Krylov method expresses multi-DOF flexible substructure, which combines with modal synthesis method to model and analyze two substructures connecting with springs and dampers. Compared with direct FEM arithmetic, it can improve the calculation efficiency and handle variable-rate stiffness and damping model or complex stiffness model of flexible connection, which is cannot do for common commercial FEM software.

  6. Simple models for rope substructure mechanics: application to electro-mechanical lifts

    NASA Astrophysics Data System (ADS)

    Herrera, I.; Kaczmarczyk, S.

    2016-05-01

    Mechanical systems modelled as rigid mass elements connected by tensioned slender structural members such as ropes and cables represent quite common substructures used in lift engineering and hoisting applications. Special interest is devoted by engineers and researchers to the vibratory response of such systems for optimum performance and durability. This paper presents simplified models that can be employed to determine the natural frequencies of systems having substructures of two rigid masses constrained by tensioned rope/cable elements. The exact solution for free un-damped longitudinal displacement response is discussed in the context of simple two-degree-of-freedom models. The results are compared and the influence of characteristics parameters such as the ratio of the average mass of the two rigid masses with respect to the rope mass and the deviation ratio of the two rigid masses with respect to the average mass is analyzed. This analysis gives criteria for the application of such simplified models in complex elevator and hoisting system configurations.

  7. Deformation behavior of a 16-8-2 GTA weld as influenced by its solidification substructure

    SciTech Connect

    Foulds, J.R.; Moteff, J.; Sikka, V.K.; McEnerney, J.W.

    1983-07-01

    Weldment sections from formed and welded type 316 stainless steel pipe are characterized with respect to some time-independent (tensile) and time-dependent (creep) mechanical properties at temperatures between 25/sup 0/C and 649/sup 0/C. The GTA weldment, welded with 16-8-2 filler metal, is sectioned from pipe in the formed + welded + solution annealed + straightened condition, as well as in the same condition with an additional re-solution treatment. Detailed room temperature microhardness measurements on these sections before and after reannealing enable a determination of the different recovery characteristics of weld and base metal. The observed stable weld metal solidification dislocation substructure in comparison with the base metal random dislocation structure, in fact, adequately explains weld/base metal elevated temperature mechanical behavior differences from this recovery characteristic standpoint. The weld metal substructure is the only parameter common to the variety of austenitic stainless steel welds exhibiting the consistent parent/weld metal deformation behavior differences described. As such, it must be considered the key to understanding weldment mechanical behavior.

  8. A Conserved Ectodomain-Transmembrane Domain Linker Motif Tunes the Allosteric Regulation of Cell Surface Receptors.

    PubMed

    Schmidt, Thomas; Ye, Feng; Situ, Alan J; An, Woojin; Ginsberg, Mark H; Ulmer, Tobias S

    2016-08-19

    In many families of cell surface receptors, a single transmembrane (TM) α-helix separates ecto- and cytosolic domains. A defined coupling of ecto- and TM domains must be essential to allosteric receptor regulation but remains little understood. Here, we characterize the linker structure, dynamics, and resulting ecto-TM domain coupling of integrin αIIb in model constructs and relate it to other integrin α subunits by mutagenesis. Cellular integrin activation assays subsequently validate the findings in intact receptors. Our results indicate a flexible yet carefully tuned ecto-TM coupling that modulates the signaling threshold of integrin receptors. Interestingly, a proline at the N-terminal TM helix border, termed NBP, is critical to linker flexibility in integrins. NBP is further predicted in 21% of human single-pass TM proteins and validated in cytokine receptors by the TM domain structure of the cytokine receptor common subunit β and its P441A-substituted variant. Thus, NBP is a conserved uncoupling motif of the ecto-TM domain transition and the degree of ecto-TM domain coupling represents an important parameter in the allosteric regulation of diverse cell surface receptors. PMID:27365391

  9. SUBSTRUCTURE IN THE STELLAR HALOS OF THE AQUARIUS SIMULATIONS

    SciTech Connect

    Helmi, Amina; Cooper, A. P.; Cole, S.; Frenk, C. S.; White, S. D. M.; Navarro, J. F.

    2011-05-20

    We characterize the substructure in the simulated stellar halos of Cooper et al. which were formed by the disruption of satellite galaxies within the cosmological N-body simulations of galactic halos of the Aquarius project. These stellar halos exhibit a wealth of tidal features: broad overdensities and very narrow faint streams akin to those observed around the Milky Way. The substructures are distributed anisotropically on the sky, a characteristic that should become apparent in the next generation of photometric surveys. The normalized RMS of the density of stars on the sky appears to be systematically larger for our halos compared with the value estimated for the Milky Way from main-sequence turnoff stars in the Sloan Digital Sky Survey. We show that this is likely to be due in part to contamination by faint QSOs and redder main-sequence stars, and might suggest that {approx}10% of the Milky Way halo stars have formed in situ.

  10. Synthesis of shuttle vehicle damping using substructure test results

    NASA Technical Reports Server (NTRS)

    Kana, D. D.; Huzar, S.

    1972-01-01

    An empirical method is developed for predicting the modal damping of a combined parallel-stage shuttle model by means of damping measurements performed on the individual substructures. Correlations are first determined for each component in terms of damping energy as a function of peak kinetic energy and modal amplitude. The results are then used to predict component damping energies corresponding to the respective kinetic energies and amplitudes that occur for the new modes of the combined system. Modal characteristics for the system, other than damping, are obtained by a real eigenvalue solution of dynamic equations developed by Hurty's procedure of substructures. System equations, which include component modal damping, are also solved by a complex eigenvalue approach for comparison with results of the empirical method.

  11. Fold Recognition Using Sequence Fingerprints of Protein Local Substructures

    SciTech Connect

    Kryshtafovych, A A; Hvidsten, T; Komorowski, J; Fidelis, K

    2003-06-04

    A protein local substructure (descriptor) is a set of several short non-overlapping fragments of the polypeptide chain. Each descriptor describes local environment of a particular residue and includes only those segments that are located in the proximity of this residue. Similar descriptors from the representative set of proteins were analyzed to reveal links between the substructures and sequences of their segments. Using detected sequence-based fingerprints specific geometrical conformations are assigned to new sequences. The ability of the approach to recognize correct SCOP folds was tested on 273 sequences from the 49 most popular folds. Good predictions were obtained in 85% of cases. No performance drop was observed with decreasing sequence similarity between target sequences and sequences from the training set of proteins.

  12. Fossil group origins. VII. Galaxy substructures in fossil systems

    NASA Astrophysics Data System (ADS)

    Zarattini, S.; Girardi, M.; Aguerri, J. A. L.; Boschin, W.; Barrena, R.; del Burgo, C.; Castro-Rodriguez, N.; Corsini, E. M.; D'Onghia, E.; Kundert, A.; Méndez-Abreu, J.; Sánchez-Janssen, R.

    2016-02-01

    Context. Fossil groups (FG) are expected to be the final product of galaxy merging within galaxy groups. In simulations, they are predicted to assemble their mass at high redshift. This early formation allows for the innermost M∗ galaxies to merge into a massive central galaxy. Then, they are expected to maintain their fossil status because of the few interactions with the large-scale structure. In this context, the magnitude gap between the two brightest galaxies of the system is considered a good indicator of its dynamical status. As a consequence, the systems with the largest gaps should be dynamically relaxed. Aims: In order to examine the dynamical status of these systems, we systematically analyze, for the first time, the presence of galaxy substructures in a sample of 12 spectroscopically-confirmed fossil systems with redshift z ≤ 0.25. Methods: We apply a number of tests to investigate the substructure in fossil systems in the two-dimensional space of projected positions out to R200. Moreover, for a subsample of five systems with at least 30 spectroscopically-confirmed members we also analyze the substructure in the velocity and in the three-dimensional velocity-position spaces. Additionally, we look for signs of recent mergers in the regions around the central galaxies. Results: We find that an important fraction of fossil systems show substructure. The fraction depends critically on the adopted test, since each test is more sensitive to a particular type of substructure. Conclusions: Our interpretation of the results is that fossil systems are not, in general, as relaxed as expected from simulations. Our sample of 12 spectroscopically-confirmed fossil systems need to be extended to compute an accurate fraction, but our conclusion is that this fraction is similar to the fraction of substructure detected in nonfossil clusters. This result points out that the magnitude gap alone is not a good indicator of the dynamical status of a system. However, the

  13. Towards an understanding of the correlations in jet substructure

    DOE PAGESBeta

    Adams, D.; Arce, A.; Asquith, L.; Backovic, M.; Barillari, T.; Berta, P.; Bertolini, D.; Buckley, A.; Butterworth, J.; Camacho Toro, R.  C.; et al

    2015-09-09

    Over the past decade, a large number of jet substructure observables have been proposed in the literature, and explored at the LHC experiments. Such observables attempt to utilize the internal structure of jets in order to distinguish those initiated by quarks, gluons, or by boosted heavy objects, such as top quarks and W bosons. This report, originating from and motivated by the BOOST2013 workshop, presents original particle-level studies that aim to improve our understanding of the relationships between jet substructure observables, their complementarity, and their dependence on the underlying jet properties, particularly the jet radius and jet transverse momentum. Thismore » is explored in the context of quark/gluon discrimination, boosted W boson tagging and boosted top quark tagging.« less

  14. Towards an understanding of the correlations in jet substructure

    SciTech Connect

    Adams, D.; Arce, A.; Asquith, L.; Backovic, M.; Barillari, T.; Berta, P.; Bertolini, D.; Buckley, A.; Butterworth, J.; Camacho Toro, R.  C.; Caudron, J.; Chien, Y. -T.; Cogan, J.; Cooper, B.; Curtin, D.; Debenedetti, C.; Dolen, J.; Eklund, M.; El Hedri, S.; Ellis, S.  D.; Embry, T.; Ferencek, D.; Ferrando, J.; Fleischmann, S.; Freytsis, M.; Giulini, M.; Han, Z.; Hare, D.; Harris, P.; Hinzmann, A.; Hoing, R.; Hornig, A.; Jankowiak, M.; Johns, K.; Kasieczka, G.; Kogler, R.; Lampl, W.; Larkoski, A.  J.; Lee, C.; Leone, R.; Loch, P.; Lopez Mateos, D.; Lou, H. K.; Low, M.; Maksimovic, P.; Marchesini, I.; Marzani, S.; Masetti, L.; McCarthy, R.; Menke, S.; Miller, D.  W.; Mishra, K.; Nachman, B.; Nef, P.; O’Grady, F.  T.; Ovcharova, A.; Picazio, A.; Pollard, C.; Potter-Landua, B.; Potter, C.; Rappoccio, S.; Rojo, J.; Rutherfoord, J.; Salam, G.  P.; Schabinger, R.  M.; Schwartzman, A.; Schwartz, M.  D.; Shuve, B.; Sinervo, P.; Soper, D.; Sosa Corral, D.  E.; Spannowsky, M.; Strauss, E.; Swiatlowski, M.; Thaler, J.; Thomas, C.; Thompson, E.; Tran, N.  V.; Tseng, J.; Usai, E.; Valery, L.; Veatch, J.; Vos, M.; Waalewijn, W.; Wacker, J.; Young, C.

    2015-09-09

    Over the past decade, a large number of jet substructure observables have been proposed in the literature, and explored at the LHC experiments. Such observables attempt to utilize the internal structure of jets in order to distinguish those initiated by quarks, gluons, or by boosted heavy objects, such as top quarks and W bosons. This report, originating from and motivated by the BOOST2013 workshop, presents original particle-level studies that aim to improve our understanding of the relationships between jet substructure observables, their complementarity, and their dependence on the underlying jet properties, particularly the jet radius and jet transverse momentum. This is explored in the context of quark/gluon discrimination, boosted W boson tagging and boosted top quark tagging.

  15. Substructure of the inner core of the Earth.

    PubMed Central

    Herndon, J M

    1996-01-01

    The rationale is disclosed for a substructure within the Earth's inner core, consisting of an actinide subcore at the center of the Earth, surrounded by a subshell composed of the products of nuclear fission and radioactive decay. Estimates are made as to possible densities, physical dimensions, and chemical compositions. The feasibility for self-sustaining nuclear fission within the subcore is demonstrated, and implications bearing on the structure and geodynamic activity of the inner core are discussed. PMID:11607625

  16. Galaxy Properties and Substructure in the Cluster Abell 160

    NASA Astrophysics Data System (ADS)

    Koontz, Craig; Pinkney, Jason

    2009-04-01

    We have developed a procedure for building a large catalog of cluster galaxies and their photometric properties as measured with CCDs. Our first case, Abell 160, is relatively nearby and redshifts exist for its brightest galaxies. We have mosaiced this cluster in R and V filters using a CCD imager on the 1.3-meter McGraw-Hill telescope. We fitted a world coordinate system to the images using the software ``WCStools,'' then used ``Source Extractor'' to extract sources from the images. We have created software for merging catalogs in such a way as to avoid double counting, to reject cosmic rays, and to combine redundant measurements. The software also corrects magnitude differences by comparing the mean difference and adding this to each individual catalog before merging it to a master catalog. The measured properties included in this study were magnitude, ellipticity, position angle, size, and color (V-R). We investigate the efficacy of our separation of galaxies and stars and find that it begins breaking down around R=19.0. We divide our master catalog into several subsamples for substructure analysis. For one subsample, we attempt to separate cluster members from foreground and background galaxies using the color-magnitude relation. We compare the results of substructure diagnostics for the subsamples. In future work, we will examine correlation of substructure with galaxy properties (especially color, size and morphology).

  17. Modal Substructuring of Geometrically Nonlinear Finite-Element Models

    DOE PAGESBeta

    Kuether, Robert J.; Allen, Matthew S.; Hollkamp, Joseph J.

    2016-02-01

    The efficiency of a modal substructuring method depends on the component modes used to reduce each subcomponent model. Methods such as Craig–Bampton have been used extensively to reduce linear finite-element models with thousands or even millions of degrees of freedom down orders of magnitude while maintaining acceptable accuracy. A novel reduction method is proposed here for geometrically nonlinear finite-element models using the fixed-interface and constraint modes of the linearized system to reduce each subcomponent model. The geometric nonlinearity requires an additional cubic and quadratic polynomial function in the modal equations, and the nonlinear stiffness coefficients are determined by applying amore » series of static loads and using the finite-element code to compute the response. The geometrically nonlinear, reduced modal equations for each subcomponent are then coupled by satisfying compatibility and force equilibrium. This modal substructuring approach is an extension of the Craig–Bampton method and is readily applied to geometrically nonlinear models built directly within commercial finite-element packages. The efficiency of this new approach is demonstrated on two example problems: one that couples two geometrically nonlinear beams at a shared rotational degree of freedom, and another that couples an axial spring element to the axial degree of freedom of a geometrically nonlinear beam. The nonlinear normal modes of the assembled models are compared with those of a truth model to assess the accuracy of the novel modal substructuring approach.« less

  18. Volume of hippocampal substructures in borderline personality disorder.

    PubMed

    Kreisel, Stefan Henner; Labudda, Kirsten; Kurlandchikov, Oleg; Beblo, Thomas; Mertens, Markus; Thomas, Christine; Rullkötter, Nina; Wingenfeld, Katja; Mensebach, Christoph; Woermann, Friedrich G; Driessen, Martin

    2015-03-30

    Borderline personality disorder (BPD) may be associated with smaller hippocampi in comparison to hippocampal size in controls. However, specific pathology in hippocampal substructures (i.e., head, body and tail) has not been sufficiently investigated. To address hippocampal structure in greater detail, we studied 39 psychiatric inpatients and outpatients with a DSM-IV diagnosis of BPD and 39 healthy controls. The hippocampus and its substructures were segmented manually on magnetic resonance imaging scans. The volumes of hippocampal substructures (and total hippocampal volume) did not differ between BPD patients and controls. Exploratory analysis suggests that patients with a lifetime history of posttraumatic stress disorder (PTSD) may have a significantly smaller hippocampus - affecting both the hippocampal head and body - in comparison to BPD patients without comorbid PTSD (difference in total hippocampal volume: -10.5%, 95%CI -2.6 to -18.5, significant). Also, patients fulfilling seven or more DSM-IV BPD criteria showed a hippocampal volume reduction, limited to the hippocampal head (difference in volume of the hippocampal head: -16.5%, 95%CI -6.1 to -26.8, significant). Disease heterogeneity in respect to, for example, symptom severity and psychiatric comorbidities may limit direct comparability between studies; the results presented here may reflect hippocampal volumes in patients who are "less" affected or they may simply be a chance finding. However, there is also the possibility that global effects of BPD on the hippocampus may have previously been overestimated. PMID:25624067

  19. Role of the Li(+) node in the Li-BH4 substructure of double-cation tetrahydroborates.

    PubMed

    Schouwink, Pascal; Smrčok, Lubomír; Černý, Radovan

    2014-10-01

    The phase diagram LiBH4-ABH4 (A = Rb,Cs) has been screened and revealed ten new compounds LiiAj(BH4)i+j (A = Rb, Cs), with i, j ranging between 1 and 3, representing eight new structure types amongst homoleptic borohydrides. An approach based on synchrotron X-ray powder diffraction to solve crystal structures and solid-state first principles calculations to refine atomic positions allows characterizing multi-phase ball-milled samples. The Li-BH4 substructure adopts various topologies as a function of the compound's Li content, ranging from one-dimensional isolated chains to three-dimensional networks. It is revealed that the Li(+) ion has potential as a surprisingly versatile cation participating in framework building with the tetrahydroborate anion BH4 as a linker, if the framework is stabilized by large electropositive counter-cations. This utility can be of interest when designing novel hydridic frameworks based on alkaline metals and will be of use when exploring the structural and coordination chemistry of light-metal systems otherwise subject to eutectic melting. PMID:25274521

  20. Construction of a linker library with widely controllable flexibility for fusion protein design.

    PubMed

    Li, Gang; Huang, Ziliang; Zhang, Chong; Dong, Bo-Jun; Guo, Ruo-Hai; Yue, Hong-Wei; Yan, Li-Tang; Xing, Xin-Hui

    2016-01-01

    Flexibility or rigidity of the linker between two fused proteins is an important parameter that affects the function of fusion proteins. In this study, we constructed a linker library with five elementary units based on the combination of the flexible (GGGGS) and the rigid (EAAAK) units. Molecular dynamics (MD) simulation showed that more rigid units in the linkers lead to more helical conformation and hydrogen bonds, and less distance fluctuation between the N- and C-termini of the linker. The diversity of linker flexibility of the linker library was then studied by fluorescence resonance energy transfer (FRET) of cyan fluorescent protein (CFP)-yellow fluorescent protein (YFP) fusion proteins, which showed that there is a wide range of distribution of the FRET efficiency. Dissipative particle dynamics (DPD) simulation of CFP-YFP with different linkers also gave identical results with that of FRET efficiency analysis, and we further found that the combination manner of the linker peptide had a remarkable effect on the orientation of CFP and YFP domains. Our studies demonstrated that the construction of the linker library with the widely controllable flexibility could provide appropriate linkers with the desirable characteristics to engineer the fusion proteins with the expected functions. PMID:26394862

  1. Characterization of the light-regulated operon encoding the phycoerythrin-associated linker proteins from the cyanobacterium Fremyella diplosiphon.

    PubMed Central

    Federspiel, N A; Grossman, A R

    1990-01-01

    Many biological processes in photosynthetic organisms can be regulated by light quantity or light quality or both. A unique example of the effect of specific wavelengths of light on the composition of the photosynthetic apparatus occurs in cyanobacteria that undergo complementary chromatic adaptation. These organisms alter the composition of their light-harvesting organelle, the phycobilisome, and exhibit distinct morphological features as a function of the wavelength of incident light. Fremyella diplosiphon, a filamentous cyanobacterium, responds to green light by activating transcription of the cpeBA operon, which encodes the pigmented light-harvesting component phycoerythrin. We have isolated and determined the complete nucleotide sequence of another operon, cpeCD, that encodes the linker proteins associated with phycoerythrin hexamers in the phycobilisome. The cpeCD operon is activated in green light and expressed as two major transcripts with the same 5' start site but differing 3' ends. Analysis of the kinetics of transcript accumulation in cultures of F. diplosiphon shifted from red light to green light and vice versa shows that the cpeBA and cpeCD operons are regulated coordinately. A common 17-base-pair sequence is found upstream of the transcription start sites of both operons. A comparison of the predicted amino acid sequences of the phycoerythrin-associated linker proteins CpeC and CpeD with sequences of other previously characterized rod linker proteins shows 49 invariant residues, most of which are in the amino-terminal half of the proteins. Images PMID:1694529

  2. The flexibility of modified-linker MIL-53 materials.

    PubMed

    Munn, Alexis S; Pillai, Renjith S; Biswas, Shyam; Stock, Norbert; Maurin, Guillaume; Walton, Richard I

    2016-03-14

    The flexibility of eight aluminium hydroxo terephthalates [Al(OH)(BDC-X)]·n(guest) (BDC = 1,4-benzene-dicarboxylate; X = -H, -CH3, -Cl, -Br, -NH2, -NO2, -(OH)2, -CO2H) crystallising in the MIL-53-type structure was investigated upon thermal dehydration of as-made samples, superhydration and methanol adsorption/desorption using in situ powder X-ray diffraction (PXRD). Profile fitting was used to determine lattice parameters as a function of time and/or temperature to describe their structural evolution. It has thus been shown that while methanol vapour adsorption induces an opening of all the modified frameworks, except the -NH2 material, superhydration only leads to open structures for Al-MIL-53-NO2, -Br and -(OH)2. All the MIL-53 solids, except Al-MIL-53-(OH)2 are present in the open structures upon thermal dehydration. In addition to the exploration of the breathing behavior of this MIL-53 series, the issue of disorder in the distribution of the functional groups between the organic linkers was explored. As a typical illustration, density functional theory calculations were carried out on different structures of Al-MIL-53-Cl, in which the distribution of -Cl within two adjacent BDC linkers is varied. The results show that the most energetically stable configuration leads to the best agreement with the experimental PXRD pattern. This observation supports that the distribution of the selected linker substituent in the functionalised solid is governed by energetics and that there is a preference for an ordering of this arrangement. PMID:26465320

  3. A traceless perfluoroalkylsulfonyl (PFS) linker for the deoxygenation of phenols.

    PubMed

    Pan, Y; Holmes, C P

    2001-08-23

    [reaction: see text]. The synthesis of a novel perfluoroalkylsulfonyl (PFS) fluoride is described for use as a traceless linker in solid-phase organic synthesis. Attachment to the resin and subsequent coupling of a phenol affords a stable arylsulfonate that behaves as a support-bound aryl triflate. Palladium-mediated reductive cleavage of a wide variety of phenols generated the parent arenes. The resin-bound aryl triflate was shown to be stable to reductive amination conditions, and the traceless synthesis of Meclizine is reported. PMID:11506630

  4. Increasing the Depth of Mass-Spectrometry-Based Structural Analysis of Protein Complexes through the Use of Multiple Cross-Linkers.

    PubMed

    Ding, Yue-He; Fan, Sheng-Bo; Li, Shuang; Feng, Bo-Ya; Gao, Ning; Ye, Keqiong; He, Si-Min; Dong, Meng-Qiu

    2016-04-19

    Chemical cross-linking of proteins coupled with mass spectrometry (CXMS) is a powerful tool to study protein folding and to map the interfaces between interacting proteins. The most commonly used cross-linkers in CXMS are BS(3) and DSS, which have similar structures and generate the same linkages between pairs of lysine residues in spatial proximity. However, there are cases where no cross-linkable lysine pairs are present at certain regions of a protein or at the interface of two interacting proteins. In order to find the cross-linkers that can best complement the performance of BS(3) and DSS, we tested seven additional cross-linkers that either have different spacer arm structures or that target different amino acids (BS(2)G, EGS, AMAS, GMBS, Sulfo-GMBS, EDC, and TFCS). Using BSA, aldolase, the yeast H/ACA protein complex, and E. coli 70S ribosomes, we showed that, in terms of providing structural information not obtained through the use of BS(3) and DSS, EGS and Sulfo-GMBS worked better than the other cross-linkers that we tested. EGS generated a large number of cross-links not seen with the other amine-specific cross-linkers, possibly due to its hydrophilic spacer arm. We demonstrate that incorporating the cross-links contributed by the EGS and amine-sulfhydryl cross-linkers greatly increased the accuracy of Rosetta in docking the structure of the yeast H/ACA protein complex. Given the improved depth of useful information it can provide, we suggest that the multilinker CXMS approach should be used routinely when the amount of a sample permits. PMID:27010980

  5. On the use of attachment modes in substructure coupling for dynamic analysis

    NASA Technical Reports Server (NTRS)

    Craig, R. R., Jr.; Chang, C.-J.

    1977-01-01

    Substructure coupling or component-mode synthesis may be employed in the solution of dynamics problems for complex structures. Although numerous substructure-coupling methods have been devised, little attention has been devoted to methods employing attachment modes. In the present paper the various mode sets (normal modes, constraint modes, attachment modes) are defined. A generalized substructure-coupling procedure is described. Those substructure-coupling methods which employ attachment modes are described in detail. One of these methods is shown to lead to results (e.g., system natural frequencies) comparable to or better than those obtained by the Hurty (1965) method.

  6. GLAST And Dark Matter Substructure in the Milky Way

    SciTech Connect

    Kuhlen, Michael; Diemand, Jurg; Madau, Piero; /UC, Santa Cruz, Astron. Astrophys. /Garching, Max Planck Inst.

    2011-11-29

    We discuss the possibility of GLAST detecting gamma-rays from the annihilation of neutralino dark matter in the Galactic halo. We have used 'Via Lactea', currently the highest resolution simulation of cold dark matter substructure, to quantify the contribution of subhalos to the annihilation signal. We present a simulated allsky map of the expected gamma-ray counts from dark matter annihilation, assuming standard values of particle mass and cross section. In this case GLAST should be able to detect the Galactic center and several individual subhalos. One of the most exciting discoveries that the Gamma-ray Large Area Space Telescope (GLAST) could make, is the detection of gamma-rays from the annihilation of dark matter (DM). Such a measurement would directly address one of the major physics problems of our time: the nature of the DM particle. Whether or not GLAST will actually detect a DM annihilation signal depends on both unknown particle physics and unknown astrophysics theory. Particle physics uncertainties include the type of particle (axion, neutralino, Kaluza-Klein particle, etc.), its mass, and its interaction cross section. From the astrophysical side it appears that DM is not smoothly distributed throughout the Galaxy halo, but instead exhibits abundant clumpy substructure, in the form of thousands of so-called subhalos. The observability of DM annihilation radiation originating in Galactic DM subhalos depends on their abundance, distribution, and internal properties. Numerical simulations have been used in the past to estimate the annihilation flux from DM substructure, but since the subhalo properties, especially their central density profile, which determines their annihilation luminosity, are very sensitive to numerical resolution, it makes sense to re-examine their contribution with higher resolution simulations.

  7. Tides, Interactions, and Fine-Scale Substructures in Galaxy Clusters

    NASA Astrophysics Data System (ADS)

    Conselice, Christopher J.; Gallagher, John S., III

    1999-01-01

    We present the results of a study on galaxy interactions, tides, and other processes that produce luminous fine-scale substructures in the galaxy clusters: Coma, Perseus, Abell 2199, AWM 3, and AWM 5. All unusual structures in these clusters can be categorized into seven morphologies: interacting galaxies, multiple galaxies (noninteracting), distorted galaxies, tailed galaxies, line galaxies, dwarf galaxy groups, and galaxy aggregates. The various morphologies are described, and a catalog is presented, of 248 objects in these five clusters along with color, and positional information obtained from CCD images taken with the WIYN 3.5 m telescope in broadband B and R filters. Distorted, interacting, and fine-scale substructures have a range of colors extending from blue objects with B-R~0 to redder colors at B-R~2.5. We also find that the structures with the most disturbed morphology have the bluest colors. In addition, the relative number distributions of these structures suggest that two separate classes of galaxy clusters exist: one dominated by distorted structures and the other dominated by galaxy associations. The Coma and Perseus clusters, respectively, are proposed as models for these types of clusters. These structures avoid the deep potentials of the dominant D or cD galaxies in the Coma and Perseus clusters, and tend to clump together. Possible mechanisms for the production of fine-scale substructure are reviewed and compared with observations of z~0.4 Butcher-Oemler clusters. We conclude, based on color, positional, and statistical data, that the most likely mechanism for the creation of these structures is through an interaction with the gravitational potential of the cluster, possibly coupled with effects of weak interactions with cluster ellipticals.

  8. Germline-specific H1 variants: the "sexy" linker histones.

    PubMed

    Pérez-Montero, Salvador; Carbonell, Albert; Azorín, Fernando

    2016-03-01

    The eukaryotic genome is packed into chromatin, a nucleoprotein complex mainly formed by the interaction of DNA with the abundant basic histone proteins. The fundamental structural and functional subunit of chromatin is the nucleosome core particle, which is composed by 146 bp of DNA wrapped around an octameric protein complex formed by two copies of each core histone H2A, H2B, H3, and H4. In addition, although not an intrinsic component of the nucleosome core particle, linker histone H1 directly interacts with it in a monomeric form. Histone H1 binds nucleosomes near the exit/entry sites of linker DNA, determines nucleosome repeat length and stabilizes higher-order organization of nucleosomes into the ∼30 nm chromatin fiber. In comparison to core histones, histone H1 is less well conserved through evolution. Furthermore, histone H1 composition in metazoans is generally complex with most species containing multiple variants that play redundant as well as specific functions. In this regard, a characteristic feature is the presence of specific H1 variants that replace somatic H1s in the germline and during early embryogenesis. In this review, we summarize our current knowledge about their structural and functional properties. PMID:25921218

  9. A Traceless Cross-linker for Photo-Cleavable Bioconjugation

    PubMed Central

    Wang, Rong; Yan, Funing; Qiu, Dengli; Jeong, Jae-Sun; Jin, Qiaoling; Kim, Tae-Young; Chen, Liaohai

    2012-01-01

    Photo-responsive bioconjugation empowers the development of novel methods for drug discovery, disease diagnosis, and high-throughput screening, among the others. In this paper, we report on the characteristics of a traceless photo-cleavable cross-linker, di 6-(3-succinimidyl carbonyloxymethyl-4-nitro-phenoxy)-hexanoic acid disulfide diethanol ester (SCNE). The traceless feature and the biocompatibility of this photo-cleavable cross-linking reagent were corroborated. Consequently, we demonstrated its application in reversible phage particle immobilization that could provide a platform for direct single phage screening. We also applied it in protein-photoprinting, where SCNE acts as a “photo-eraser” to remove the cross-linked protein molecules at a desired region in a simple, clean and light-controllable fashion. We further demonstrated the two-tier atomic force microscopic (AFM) method that uses SCNE to carry out two subsequent AFM tasks in situ. The approach allows guided protein delivery and subsequent high-resolution imaging at the same local area, thus opens up the possibility of monitoring protein functions in live cells. The results imply that SCNE is a versatile cross-linker that can be used for a wide range of applications where photo-cleavage ensures clean and remote-controllable release of biological molecules from a substrate. PMID:22432929

  10. Flexible Linker Modulates Glycosaminoglycan Affinity of Decorin Binding Protein A.

    PubMed

    Morgan, Ashli; Sepuru, Krishna Mohan; Feng, Wei; Rajarathnam, Krishna; Wang, Xu

    2015-08-18

    Decorin binding protein A (DBPA) is a glycosaminoglycan (GAG)-binding adhesin found on the surface of the bacterium Borrelia burgdorferi (B. burgdorferi), the causative agent of Lyme disease. DBPA facilitates bacterial adherence to extracellular matrices of human tissues and is crucial during the early stage of the infection process. Interestingly, DBPA from different strains (B31, N40, and PBr) show significant differences in GAG affinities, but the structural basis for the differences is not clear. In this study, we show that GAG affinity of N40 DBPA is modulated in part by flexible segments that control access to the GAG binding site, such that shortening of the linker leads to higher GAG affinity when analyzed using ELISA, gel mobility shift assay, solution NMR, and isothermal titration calorimetry. Our observation that GAG affinity differences among different B. burgdorferi strains can be attributed to a flexible linker domain regulating access to the GAG-binding domain is novel. It also provides a rare example of how neutral amino acids and dynamic segments in GAG binding proteins can have a large influence on GAG affinity and provides insights into why the number of basic amino acids in the GAG-binding site may not be the only factor determining GAG affinity of proteins. PMID:26223367

  11. GLAST and Dark Matter Substructure in the Milky Way

    SciTech Connect

    Kuhlen, Michael; Diemand, Juerg; Madau, Piero

    2007-07-12

    We discuss the possibility of GLAST detecting gamma-rays from the annihilation of neutralino dark matter in the Galactic halo. We have used ''Via Lactea'', currently the highest resolution simulation of cold dark matter substructure, to quantify the contribution of subhalos to the annihilation signal. We present a simulated allsky map of the expected gamma-ray counts from dark matter annihilation, assuming standard values of particle mass and cross section. In this case GLAST should be able to detect the Galactic center and several individual subhalos.

  12. Hierarchically Parallelized Constrained Nonlinear Solvers with Automated Substructuring

    NASA Technical Reports Server (NTRS)

    Padovan, Joe; Kwang, Abel

    1994-01-01

    This paper develops a parallelizable multilevel multiple constrained nonlinear equation solver. The substructuring process is automated to yield appropriately balanced partitioning of each succeeding level. Due to the generality of the procedure,_sequential, as well as partially and fully parallel environments can be handled. This includes both single and multiprocessor assignment per individual partition. Several benchmark examples are presented. These illustrate the robustness of the procedure as well as its capability to yield significant reductions in memory utilization and calculational effort due both to updating and inversion.

  13. Aligning graphs and finding substructures by a cavity approach

    NASA Astrophysics Data System (ADS)

    Bradde, S.; Braunstein, A.; Mahmoudi, H.; Tria, F.; Weigt, M.; Zecchina, R.

    2010-02-01

    We introduce a new distributed algorithm for aligning graphs or finding substructures within a given graph. It is based on the cavity method and is used to study the maximum-clique and the graph-alignment problems in random graphs. The algorithm allows to analyze large graphs and may find applications in fields such as computational biology. As a proof of concept we use our algorithm to align the similarity graphs of two interacting protein families involved in bacterial signal transduction, and to predict actually interacting protein partners between these families.

  14. Unexpected relationships of substructured populations in Chinese Locusta migratoria

    PubMed Central

    Zhang, De-Xing; Yan, Lu-Na; Ji, Ya-Jie; Hewitt, Godfrey M; Huang, Zu-Shi

    2009-01-01

    Background Highly migratory species are usually expected to have minimal population substructure because strong gene flow has the effect of homogenizing genetic variation over geographical populations, counteracting random drift, selection and mutation. The migratory locust Locusta migratoria belongs to a monotypic genus, and is an infamous pest insect with exceptional migratory ability – with dispersal documented over a thousand kilometers. Its distributional area is greater than that of any other locust or grasshopper, occurring in practically all the temperate and tropical regions of the eastern hemisphere. Consequently, minimal population substructuring is expected. However, in marked contrast to its high dispersal ability, three geographical subspecies have been distinguished in China, with more than nine being biologically and morphologically identified in the world. Such subspecies status has been under considerable debate. Results By multilocus microsatellite genotyping analysis, we provide ample genetic evidence for strong population substructure in this highly migratory insect that conforms to geography. More importantly, our genetic data identified an unexpected cryptic subdivision and demonstrated a strong affiliation of the East China locusts to those in Northwest/Northern China. The migratory locusts in China formed three distinct groups, viz. (1) the Tibetan group, comprising locusts from Tibet and nearby West China high mountain regions; this is congruent with the previously recognized Tibetan subspecies, L. m. tibetensis; (2) the South China group, containing locusts from the Hainan islands; this corresponds to the Southeast Asia oriental tropical subspecies L. m. manilensis; (3) the North China group, including locusts from the Northwest and Northern China (the Asiatic subspecies L. m. migratoria), Central China and Eastern China regions. Therefore, the traditional concept on Locusta subspecies status established from Uvarov in 1930s needs to be

  15. Convergence of a Substructuring Method with LaGrange Multipliers

    NASA Technical Reports Server (NTRS)

    Mandel, Jan; Tezaur, Radek

    1996-01-01

    We analyze the convergence of a substructuring iterative method with Lagrange multipliers, proposed recently by Farhat and Roux. The method decomposes finite element discretization of an elliptic boundary value problem into Neumann problems on the subdomains and a coarse problem for the subdomain nullspace components. For linear conforming elements and preconditioning by the Dirichlet problems on the subdomains, we prove the asymptotic bound on the condition number C(1 + log(H/h))(sup gamma), gamma = 2 or 3, where h is the characteristic element size and H is the subdomain size.

  16. Simulating and Synthesizing Substructures Using Neural Network and Genetic Algorithms

    NASA Technical Reports Server (NTRS)

    Liu, Youhua; Kapania, Rakesh K.; VanLandingham, Hugh F.

    1997-01-01

    The feasibility of simulating and synthesizing substructures by computational neural network models is illustrated by investigating a statically indeterminate beam, using both a 1-D and a 2-D plane stress modelling. The beam can be decomposed into two cantilevers with free-end loads. By training neural networks to simulate the cantilever responses to different loads, the original beam problem can be solved as a match-up between two subsystems under compatible interface conditions. The genetic algorithms are successfully used to solve the match-up problem. Simulated results are found in good agreement with the analytical or FEM solutions.

  17. The construction of preconditioners for elliptic problems by substructuring, IV

    SciTech Connect

    Bramble, J.H.; Pasciak, J.E.; Schatz, A.H.

    1987-06-01

    We consider the problem of solving the algebraic system of equations which result from the discretization of elliptic boundary value problems defined on three dimensional Euclidean space. We develop preconditioners for such systems based on substructuring (also known as domain decomposition). The resulting algorithms are well suited to emerging parallel computing architectures. We describe two techniques for developing these precondictioners. A theory for the analysis of the condition number for the resulting preconditioned system is given and the results of supporting numerical experiments are presented. 16 refs., 2 tabs.

  18. The construction of preconditioners for elliptic problems by substructuring, IV

    SciTech Connect

    Bramble, J.H.; Pasciak, J.E.; Schatz, A.H.

    1989-07-01

    We consider the problem of solving the algebraic system of equations which result from the discretization of elliptic boundary value problems defined on three-dimensional Euclidean space. We develop preconditioners for such systems based on substructuring (also known as domain decomposition). The resulting algorithms are well suited to emerging parallel computing architectures. We describe two techniques for developing these preconditioners. A theory for the analysis of the condition number for the resulting preconditioned system is given and the results of supporting numerical experiments are presented.

  19. Unlocking Dark Matter Physics out of Galactic Substructures

    NASA Astrophysics Data System (ADS)

    Cyr-Racine, Francis-Yan; Moustakas, Leonidas A.; Keeton, Charles R.

    2016-01-01

    Despite being ubiquitous throughout the Universe, the fundamental properties of dark matter remain a mystery. While dark matter physics plays little role in the current evolution of large-scale cosmic structures, it does have a major impact on small causal length scales. Studying the astrophysical structures that resulted from the gravitational collapse of fluctuations on these small scales can thus yield important clues about the physics of dark matter. Today, most of these structures are locked in deep inside the potential wells of galaxies, making the study of their properties difficult. Fortunately, due to fortuitous alignments between high-redshift bright sources and us, some of these galaxies act as spectacular strong gravitational lenses, allowing us to probe their inner structure. In this talk, we present a unified framework to extract information about the power spectrum of mass substructures inside lens galaxies. We determine which properties of mass substructures are most readily constrained by lensing data and forecast the constraining power of current and future observations.

  20. Jet substructures of boosted polarized hadronic top quarks

    NASA Astrophysics Data System (ADS)

    Kitadono, Yoshio; Li, Hsiang-nan

    2016-03-01

    We study jet substructures of a boosted polarized top quark, which undergoes the hadronic decay t →b u d ¯, in the perturbative QCD framework, focusing on the energy profile and the differential energy profile. These substructures are factorized into the convolution of a hard top-quark decay kernel with a bottom-quark jet function and a W -boson jet function, where the latter is further factorized into the convolution of a hard W -boson decay kernel with two light-quark jet functions. Computing the hard kernels to leading order in QCD and including the resummation effect in the jet functions, we show that the differential jet energy profile is a useful observable for differentiating the helicity of a boosted hadronic top quark: a right-handed top jet exhibits quick descent of the differential energy profile with the inner test cone radius r , which is attributed to the V -A structure of weak interaction and the dead-cone effect associated with the W -boson jet. The above helicity differentiation may help reveal the chiral structure of physics beyond the standard model at high energies.

  1. An Efficient Crankshaft Dynamic Analysis Using Substructuring with Ritz Vectors

    NASA Astrophysics Data System (ADS)

    MOURELATOS, Z. P.

    2000-11-01

    A structural analysis using dynamic substructuring with Ritz vectors is presented for predicting the dynamic response of an engine crankshaft, based on the finite-element method. A two-level dynamic substructuring is performed using a set of load-dependent Ritz vectors. The rotating crankshaft is properly coupled with the non-rotating, compliant engine block. The block compliance is represented by a distributed linear elastic foundation at each main bearing location. The stiffness of the elastic foundation can be different in the vertical and horizontal planes, thereby considering the anisotropy of the engine block compliance with respect to the crankshaft rotation. The analysis accounts for the kinematic non-linearity resulting from the crankangle-dependent circumferential contact location between each journal and the corresponding bore of the engine block. Crankshaft “bent” and block “misboring” effects due to manufacturing imperfections are considered in the analysis. The superior accuracy and reduced computational effort of the present method as compared with the equivalent superelement analysis in MSC/NASTRAN, are demonstrated using the free and forced vibrations of a slender cylindrical beam and free vibrations of a four-cylinder engine crankshaft. Subsequently, the accuracy of the present method in calculating the dynamic response of engine crankshafts is shown through comparisons between the analytical predictions and experimental results for the torsional vibrations of an in-line five cylinder engine and the bending vibrations of the crankshaft-flywheel assembly of a V6 engine.

  2. Toward quantitative proteomics of organ substructures: implications for renal physiology.

    PubMed

    Velic, Ana; Macek, Boris; Wagner, Carsten A

    2010-09-01

    Organs are complex structures that consist of multiple tissues with different levels of gene expression. To achieve comprehensive coverage and accurate quantitation data, organs ideally should be separated into morphologic and/or functional substructures before gene or protein expression analysis. However, because of complex morphology and elaborate isolation protocols, to date this often has been difficult to achieve. Kidneys are organs in which functional and morphologic subdivision is especially important. Each subunit of the kidney, the nephron, consists of more than 10 subsegments with distinct morphologic and functional characteristics. For a full understanding of kidney physiology, global gene and protein expression analyses have to be performed at the level of the nephron subsegments; however, such studies have been extremely rare to date. Here we describe the latest approaches in quantitative high-accuracy mass spectrometry-based proteomics and their application to quantitative proteomics studies of the whole kidney and nephron subsegments, both in human beings and in animal models. We compare these studies with similar studies performed on other organ substructures. We argue that the newest technologies used for preparation, processing, and measurement of small amounts of starting material are finally enabling global and subsegment-specific quantitative measurement of protein levels in the kidney and other organs. These new technologies and approaches are making a decisive impact on our understanding of the (patho)physiological processes at the molecular level. PMID:21044760

  3. Evolutionary correlation between linker histones and microtubular structures.

    PubMed

    Kaczanowski, S; Jerzmanowski, A

    2001-07-01

    Histones of the H1 group (linker histones) are abundant components of chromatin in eukaryotes, occurring on average at one molecule per nucleosome. The recent reports on the lack of a clear phenotypic effect of knock-out mutations as well as overexpression of histone H1 genes in different organisms have seriously undermined the long-held view that linker histones are essential for the basic functions of eukaryotic cells. In an attempt to resolve the paradox of an abundant conserved protein without a clear function, we re-examined the molecular and phylogenetic data on linker histones to see if they could reveal any correlation between the features of H1 and the functional or morphological characteristics of cells or organisms. Because of an earlier demonstration that in sea urchin the chromatin-type histone H1 is also found in the flagellar microtubules (Multigner et al. 1992), we focused on the correlation between the features of H1 and those of microtubular structures. A phylogenetic tree based on multiple alignment of over 100 available HI sequences suggests that the first divergence of the globular domain of H1 (GH1) resulted in branching into separate types characteristic for plants/Dictyostelium and for animals/ascomycetes, respectively. The GH1s of these two types differ by a short region (usually 5 amino acids) placed at a specific location within the C-terminal wing subdomain of GH1. Evolutionary analysis of the diversification of H1 mRNA into cell-cycle-dependent (polyA-) and independent (polyA+) forms showed a mosaic occurrence of these two forms in plants and animals, despite the fact that the H1 proteins of plants and animals belong to two well-distinguished groups. However, among organisms from both animal and plant kingdom, only those with H1 mRNA of a polyA- type have flagellated gametes. This correlation as well as the demonstration that in Volvox carteri the accumulation of polyA- mRNA of H1 occurs concurrently with the production of new flagella

  4. Resolving the chemical substructure of Orion-KL

    NASA Astrophysics Data System (ADS)

    Feng, S.; Beuther, H.; Henning, Th.; Semenov, D.; Palau, A.; Mills, E. A. C.

    2015-09-01

    Context. The Kleinmann-Low nebula in Orion (Orion-KL) is the nearest example of a high-mass star-forming environment. Studying the resolved chemical substructures of this complex region provides important insight into the chemistry of high-mass star-forming regions (HMSFRs), as it relates to their evolutionary states. Aims: The goal of this work is to resolve the molecular line emission from individual substructures of Orion-KL at high spectral and spatial resolution and to infer the chemical properties of the associated gas. Methods: We present a line survey of Orion-KL obtained from combined Submillimeter Array (SMA) interferometric and IRAM 30 m single-dish observations. Covering a 4 GHz bandwidth in total, this survey contains over 160 emission lines from 20 species (25 isotopologues), including 11 complex organic molecules (COMs). Spectra are extracted from individual substructures and the intensity-integrated distribution map for each species is provided. We then estimate the rotation temperature for each substructure, along with their molecular column densities and abundances. Results: For the first time, we complement 1.3 mm interferometric data with single-dish observations of the Orion-KL region and study small-scale chemical variations in this region. (1) We resolve continuum substructures on ~3'' angular scale. (2) We identify lines from the low-abundance COMs CH3COCH3 and CH3CH2OH, as well as tentatively detect CH3CHO and long carbon-chain molecules C6H and HC7N. (3) We find that while most COMs are segregated by type, peaking either towards the hotcore (e.g., nitrogen-bearing species) or the compact ridge (e.g., oxygen-bearing species like HCOOCH3 and CH3OCH3), the distributions of others do not follow this segregated structure (e.g., CH3CH2OH, CH3OH, CH3COCH3). (4) We find a second velocity component of HNCO, SO2, 34SO2, and SO lines, which may be associated with a strong shock event in the low-velocity outflow. (5) Temperatures and molecular

  5. The Tension between Organisational Sub-structures in Secondary Schools and Educational Reform.

    ERIC Educational Resources Information Center

    Imants, Jeroen; Sleegers, Peter; Witziers, Bob

    2001-01-01

    Explores how Dutch secondary schools can provide supportive working contexts that promote teacher learning, focusing on integration of two substructures (subject departments and student guidance units). Analyzes tensions between the substructures, summarizes insights into teacher learning communities, and discusses integrated teacher teams'…

  6. In Search of an Efficient Photoswitch for Functional RNA: Design Principles from a Microscopic Analysis of Azobenzene-linker-RNA Dynamics with Different Linkers.

    PubMed

    Mondal, Padmabati; Biswas, Mithun; Goldau, Thomas; Heckel, Alexander; Burghardt, Irene

    2015-08-27

    The design of optimal photoswitches to regulate nucleic acid functionality is a considerable challenge. Azobenzene switches that are covalently bound to the nucleic acid backbone are a paradigm example that has been studied using different types of linker species connecting the chromophore to the backbone. To support experimental efforts to construct optimal azobenzene-linker-RNA combinations, we introduce here a systematic approach for theoretical analysis, which provides criteria for the local embedding of the chromophore via a chosen linker. Using a local reference frame adapted to the chromophore, quantitative measures are provided for (i) the propensity of stacking in competition with a drift toward the minor or major groove, (ii) the tendency to disrupt the native hydrogen bond network, (iii) the structural flexibility of the chromophore-linker combination, and (iv) the correlations with the presence of a base in the opposite strand. Large differences in structural stability between the trans and cis forms of the azobenzene chromophore, according to these criteria, indicate good functionality and lead to significant differences in melting temperatures. In particular, a recently synthesized deoxyribose linker proves optimal within the set of azobenzene-linker-RNA combinations considered. PMID:26125118

  7. Linker Installation: Engineering Pore Environment with Precisely Placed Functionalities in Zirconium MOFs.

    PubMed

    Yuan, Shuai; Chen, Ying-Pin; Qin, Jun-Sheng; Lu, Weigang; Zou, Lanfang; Zhang, Qiang; Wang, Xuan; Sun, Xing; Zhou, Hong-Cai

    2016-07-20

    Precise placement of multiple functional groups in a highly ordered metal-organic framework (MOF) platform allows the tailoring of the pore environment, which is required for advanced applications. To realize this, we present a comprehensive study on the linker installation method, in which a stable MOF with coordinatively unsaturated Zr6 clusters was employed and linkers bearing different functional groups were postsynthetically installed. A Zr-MOF with inherent missing linker sites, namely, PCN-700, was initially constructed under kinetic control. Twelve linkers with different substituents were then designed to study their effect on MOF formation kinetics and therefore resulting MOF structures. Guided by the geometrical analysis, linkers with different lengths were installed into a parent PCN-700, giving rise to 11 new MOFs and each bearing up to three different functional groups in predefined positions. Systematic variation of the pore volume and decoration of pore environment were realized by linker installation, which resulted in synergistic effects including an enhancement of H2 adsorption capacities of up to 57%. In addition, a size-selective catalytic system for aerobic alcohol oxidation reaction is built in PCN-700 through linker installation, which shows high activity and tunable size selectivity. Altogether, these results exemplify the capability of the linker installation method in the pore environment engineering of stable MOFs with multiple functional groups, giving an unparalleled level of control. PMID:27345035

  8. Knowledge Linkers and the Flow of Educational Information. An Occasional Paper from ERIC at Stanford.

    ERIC Educational Resources Information Center

    Farr, Richard S.

    The flow of knowledge from researchers to users is aided by knowledge linkers who activate the interpersonal network of communication within the target audience. The linker enters this network by contacting (through periodicals, mass media, conventions, and directly) individuals in the audience who are more active than others (gatekeepers). Once…

  9. TA-Doc Linker Role. Draft. Documentation and Technical Assistance in Urban Schools.

    ERIC Educational Resources Information Center

    Holmes, Manford L.

    One of the aims of the Documentation and Technical Assistance (DTA) Project is to apply educational information that has been utilized for problem solving in one organization to other settings with their own unique characteristics. Within the staff of the DTA project, the position of Technical Assistance-Documentation Linker (TA-Doc Linker) was…

  10. Molecular design of light-harvesting photosensitizers: effect of varied linker conjugation on interfacial electron transfer.

    PubMed

    Jiang, Jianbing; Swierk, John R; Hedström, Svante; Matula, Adam J; Crabtree, Robert H; Batista, Victor S; Schmuttenmaer, Charles A; Brudvig, Gary W

    2016-07-28

    Interfacial electron transfer dynamics of a series of photosensitizers bound to TiO2via linkers of varying conjugation strength are explored by spectroscopic and computational techniques. Injection and recombination depend on the extent of conjugation in the linker, where the LUMO delocalization determines the injection dynamics but both the HOMO and HOMO-1 are involved in recombination. PMID:27364769

  11. Flexibility of C3h -Symmetrical Linkers in Tris-oligonucleotide-Based Tetrahedral Scaffolds.

    PubMed

    Panagiotidis, Christos; Kath-Schorr, Stephanie; von Kiedrowski, Günter

    2016-02-01

    Flexibility of tris-oligonucleotides is determined by the length of their connecting hydrocarbon chains. Tris-oligonucleotides are branched DNA building blocks with three oligonucleotide arms attached to a C3h -symmetrical linker core at these chains. Four tris-oligonucleotides hybridise into a tetrahedral nanocage by sequence-determined self-assembly. The influence of methylene, ethylene and propylene chains was studied by synthesising sets of tris-oligonucleotides and analysing the relative stability of the hybridisation products against digestion by mung bean nuclease by using gel electrophoresis. Linkers with ethylene chains showed sufficient flexibility, whereas methylene-chain linkers were too rigid. Tris-oligonucleotides based on the latter still formed tetrahedral scaffolds in intermixing experiments with linkers of higher flexibility. Thus, a new generation of versatile isocyanurate-based linkers was established. PMID:26593127

  12. Impact of linker strain and flexibility in the design of a fragment-based inhibitor

    PubMed Central

    Chung, Suhman; Parker, Jared B.; Bianchet, Mario; Amzel, L. Mario; Stivers, James T.

    2011-01-01

    The linking together of molecular fragments that bind to adjacent sites on an enzyme can lead to high affinity inhibitors. Ideally, this strategy would employ linkers that do not perturb the optimal binding geometries of the fragments and do not have excessive conformational flexibility that would increase the entropic penalty of binding. In reality, these aims are seldom realized due to limitations in linker chemistry. Here we systematically explore the energetic and structural effects of rigid and flexible linkers on the binding of a fragment-based inhibitor of human uracil DNA glycosylase. Analysis of the free energies of binding in combination with co-crystal structures shows that the flexibility and strain of a given linker can have a significant impact on binding affinity even when the binding fragments are optimally positioned. Such effects are not apparent from inspection of structures and underscore the importance of linker optimization in fragment-based drug discovery efforts. PMID:19396178

  13. Thermodynamic Insight in the High-Pressure Behavior of UiO-66: Effect of Linker Defects and Linker Expansion

    PubMed Central

    2016-01-01

    In this Article, we present a molecular-level understanding of the experimentally observed loss of crystallinity in UiO-66-type metal–organic frameworks, including the pristine UiO-66 to -68 as well as defect-containing UiO-66 materials, under the influence of external pressure. This goal is achieved by constructing pressure-versus-volume profiles at finite temperatures using a thermodynamic approach relying on ab initio derived force fields. On the atomic level, the phenomenon is reflected in a sudden drop in the number of symmetry operators for the crystallographic unit cell because of the disordered displacement of the organic linkers with respect to the inorganic bricks. For the defect-containing samples, a reduced mechanical stability is observed, however, critically depending on the distribution of these defects throughout the material, hence demonstrating the importance of judiciously characterizing defects in these materials. PMID:27594765

  14. Modeling of ion complexation and extraction using substructural molecular fragments

    PubMed

    Solov'ev; Varnek; Wipff

    2000-05-01

    A substructural molecular fragment (SMF) method has been developed to model the relationships between the structure of organic molecules and their thermodynamic parameters of complexation or extraction. The method is based on the splitting of a molecule into fragments, and on calculations of their contributions to a given property. It uses two types of fragments: atom/bond sequences and "augmented atoms" (atoms with their nearest neighbors). The SMF approach is tested on physical properties of C2-C9 alkanes (boiling point, molar volume, molar refraction, heat of vaporization, surface tension, melting point, critical temperature, and critical pressures) and on octanol/water partition coefficients. Then, it is applied to the assessment of (i) complexation stability constants of alkali cations with crown ethers and phosphoryl-containing podands, and of beta-cyclodextrins with mono- and 1,4-disubstituted benzenes, and (ii) solvent extraction constants for the complexes of uranyl cation by phosphoryl-containing ligands. PMID:10850791

  15. Effects of Magnetic Fields on Bar Substructures in Barred Galaxies

    NASA Astrophysics Data System (ADS)

    Kim, Woong-Tae

    2015-03-01

    To study the effects of magnetic fields on the properties of bar substructures, we run two-dimensional, ideal MHD simulations of barred galaxies under the influence of a non-axisymmetric bar potential. In the bar regions, magnetic fields reduce density compression in the dust-lane shocks, while removing angular momentum further from the gas at the shocks. This evidently results in a smaller and more distributed ring, and a larger mass inflows rate to the galaxy center in models with stronger magnetic fields. In the outer regions, an MHD dynamo due to the combined action of the bar potential and background shear operates, amplifying magnetic fields near the corotation resonance. In the absence of spiral arms, the amplified fields naturally shape into trailing magnetic arms with strong fields and low density. The reader is refereed to Kim & Stone (2012) for a detailed presentation of the simulation outcomes.

  16. Potent Oxazolidinone Antibacterials with Heteroaromatic C-Ring Substructure

    PubMed Central

    2013-01-01

    Novel oxazolidinone analogues bearing a condensed heteroaromatic ring as the C-ring substructure were synthesized as candidate antibacterial agents. Analogues 16 and 21 bearing imidazo[1,2-a]pyridine and 18 and 23 bearing [1,2,4]triazolo[1,5-a]pyridine as the C-ring had excellent in vitro antibacterial activities against methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecalis (VRE), and penicillin-resistant Streptococcus pneumoniae (PRSP). They also showed promising therapeutic effects in a mouse model of lethal infection. Preliminary safety data (inhibitory effects on cytochrome P450 isoforms and monoamine oxidases) were satisfactory. Further evaluation of 18 and 23 is ongoing. PMID:24900607

  17. Resolving the Chemical Substructure of Orion-KL

    NASA Astrophysics Data System (ADS)

    Feng, Siyi; Beuther, Henrik; Semenov, Dmitry; Henning, Thomas; Palau, Aina

    2013-07-01

    Context. The Kleinmann-Low nebula in Orion (Orion-KL) is the closest example of a high-mass star forming environment. Studying the resolved chemical structure of this complex region can provide important insight for relating the chemistry of high mass star forming regions with their evolutionary state. We present a line survey of Orion-KL obtained from the combined Submillimeter Array (SMA) and IRAM 30 m single-dish data. Covering 4 GHz bandwidth in total, this survey contains at least 160 emission lines from 27 chemical species. Aims. The goal of this work is to resolve the molecular line emission from individual substructure in Orion-KL at high spectral and spatial resolution, inferring the chemical properties of the associated gas. Methods. The spectra from different substructures are extracted and the intensity-integrated distribution maps for different molecules are imaged. We then calculate column densities, and abundances for each molecule in each identified substructure, assuming local thermal equilibrium (LTE), and that the lines are both optically thin and have uniform widths for all species. Results. By complementing interferometric data of the Orion-KL region with single-dish data to recover the short spacing information, we are able to study spatial abundance variations in this region for the first time. On one hand, at the spatial resolution of 4 arcsec, several substructures appear on the continuum map. The strongest emission from nitrogen-bearing molecules comes from the main hot core, which has chemistry typical of an active region, while sulfur-bearing and carbon monoxides have extended emission covering the cooler southern ridge and outflow regions. In contrast, the distribution of saturated complex organics is more complicated. Most of them peak at either the hot core (e.g., CH3OH) or the compact ridge (e.g., HCOOCH3), while others peak at intermediate positions between the hot core and the compact ridge (e.g., CH3CH2OH). But nevertheless, no

  18. Substructure drag effects and recrystallization textures in aluminium

    SciTech Connect

    Higginson, R.; Bate, P.

    1999-03-10

    Many important recrystallization texture components in metals such as aluminium originate from nuclei in which the mobile high-angle boundary exists prior to, or is formed in the early stages of, annealing. Nucleation can then occur by a process known as strain-induced boundary migration (SIBM). It is possible that this process will involve several growing subgrains, and the drag from that substructure can then have a significant effect. A simple model is used to demonstrate how changes in the overall driving force for recrystallization and Zener drag can affect recrystallization textures when SIBM is involved. This is discussed in relation to experimental observations and the evidence for this process is reviewed.

  19. Construction of preconditioners for elliptic problems by substructuring. I

    SciTech Connect

    Bramble, J.H.; Pasciak, J.E.; Schatz, A.H.

    1986-07-01

    We consider the problem of solving the algebraic system of equations which arise from the discretization of symmetric elliptic boundary value problems via finite element methods. A new class of preconditioners for the discrete system is developed based on substructuring (also known as domain decomposition). The resulting preconditioned algorithms are well suited to emerging parallel computing architectures. The proposed methods are applicable to problems on general domains involving differential operators with rather general coefficients. A basic theory for the analysis of the condition number of the preconditioned system (which determines the iterative convergence rate of the algorithm) is given. Techniques for applying the theory and algorithms to problems with irregular geometry are discussed and the results of extensive numerical experiments are reported.

  20. Population substructure in Cache County, Utah: the Cache County study

    PubMed Central

    2014-01-01

    Background Population stratification is a key concern for genetic association analyses. In addition, extreme homogeneity of ethnic origins of a population can make it difficult to interpret how genetic associations in that population may translate into other populations. Here we have evaluated the genetic substructure of samples from the Cache County study relative to the HapMap Reference populations and data from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Results Our findings show that the Cache County study is similar in ethnic diversity to the self-reported "Whites" in the ADNI sample and less homogenous than the HapMap CEU population. Conclusions We conclude that the Cache County study is genetically representative of the general European American population in the USA and is an appropriate population for conducting broadly applicable genetic studies. PMID:25078123

  1. Galaxy Properties and Substructure in the Cluster Abell 160

    NASA Astrophysics Data System (ADS)

    Koontz, Craig; Pinkney, Jason

    2008-10-01

    We continue development of a procedure for building a large catalog of cluster galaxies and their photometric properties, as measured with CCDs. Our first case, Abell 160, is relatively nearby and we have already obtained spectroscopic redshifts for its brightest galaxies. We have mosaiced this cluster in R and V filters using a CCD imager on the 1.3-meter McGraw-Hill telescope. For each CCD frame we fit a WCS (world coordinate system), remove bright cosmic rays, and extract sources using ``SExtractor.'' We create software for merging source catalogs in such a way as to reject residual cosmic rays and other invalid sources, and to combine redundant measurements without double counting. The measured properties include magnitude, ellipticity, position angle, size, and color (V-R). We compare our data to those of the HST (Hubble Space Telescope) and SDSS (Sloan Digital Sky Survey) archives to examine the accuracy of our star/galaxy separation and our color measurements. For our substructure investigation, we draw several subsamples of galaxies based on stellarity index, color (the color-magnitude relation), magnitude and velocity. The smallest subsample of spectroscopically confirmed members produces significant substructure signals from 1D (velocity) and 3D (x,y,velocity) diagnostics - a small, offset group may be the culprit. The 2D (x,y) diagnostics applied to the larger samples produce some significant statistics, the cause does not seem to be a large-scale merger, but perhaps several small groups. This is consistent with previous X-ray data showing X-ray emitting gas clumped around small groupings of galaxies.

  2. Cold Dark Matter Substructures in Early-type Galaxy Halos

    NASA Astrophysics Data System (ADS)

    Fiacconi, Davide; Madau, Piero; Potter, Doug; Stadel, Joachim

    2016-06-01

    We present initial results from the “Ponos” zoom-in numerical simulations of dark matter substructures in massive ellipticals. Two very highly resolved dark matter halos with M vir = 1.2 × 1013 {M}ȯ and M vir = 6.5 × 1012 {M}ȯ and different (“violent” versus “quiescent”) assembly histories have been simulated down to z = 0 in a ΛCDM cosmology with a total of 921,651,914 and 408,377,544 particles, respectively. Within the virial radius, the total mass fraction in self-bound M sub > 106 {M}ȯ subhalos at the present epoch is 15% for the violent host and 16.5% for the quiescent one. At z = 0.7, these fractions increase to 19% and 33%, respectively, as more recently accreted satellites are less prone to tidal destruction. In projection, the average fraction of surface mass density in substructure at a distance of R/R vir = 0.02 (˜5–10 kpc) from the two halo centers ranges from 0.6% to ≳2%, significantly higher than that measured in simulations of Milky Way-sized halos. The contribution of subhalos with M sub < 109 {M}ȯ to the projected mass fraction is between one-fifth and one-third of the total, with the smallest share found in the quiescent host. We assess the impact of baryonic effects via twin, lower-resolution hydrodynamical simulations that include metallicity-dependent gas cooling, star formation, and a delayed-radiative-cooling scheme for supernova feedback. Baryonic contraction produces a super-isothermal total density profile and increases the number of massive subhalos in the inner regions of the main host. The host density profiles and projected subhalo mass fractions appear to be broadly consistent with observations of gravitational lenses.

  3. Cold Dark Matter Substructures in Early-type Galaxy Halos

    NASA Astrophysics Data System (ADS)

    Fiacconi, Davide; Madau, Piero; Potter, Doug; Stadel, Joachim

    2016-06-01

    We present initial results from the “Ponos” zoom-in numerical simulations of dark matter substructures in massive ellipticals. Two very highly resolved dark matter halos with M vir = 1.2 × 1013 {M}ȯ and M vir = 6.5 × 1012 {M}ȯ and different (“violent” versus “quiescent”) assembly histories have been simulated down to z = 0 in a ΛCDM cosmology with a total of 921,651,914 and 408,377,544 particles, respectively. Within the virial radius, the total mass fraction in self-bound M sub > 106 {M}ȯ subhalos at the present epoch is 15% for the violent host and 16.5% for the quiescent one. At z = 0.7, these fractions increase to 19% and 33%, respectively, as more recently accreted satellites are less prone to tidal destruction. In projection, the average fraction of surface mass density in substructure at a distance of R/R vir = 0.02 (∼5–10 kpc) from the two halo centers ranges from 0.6% to ≳2%, significantly higher than that measured in simulations of Milky Way-sized halos. The contribution of subhalos with M sub < 109 {M}ȯ to the projected mass fraction is between one-fifth and one-third of the total, with the smallest share found in the quiescent host. We assess the impact of baryonic effects via twin, lower-resolution hydrodynamical simulations that include metallicity-dependent gas cooling, star formation, and a delayed-radiative-cooling scheme for supernova feedback. Baryonic contraction produces a super-isothermal total density profile and increases the number of massive subhalos in the inner regions of the main host. The host density profiles and projected subhalo mass fractions appear to be broadly consistent with observations of gravitational lenses.

  4. TGF-beta and HGF transmit the signals through JNK-dependent Smad2/3 phosphorylation at the linker regions.

    PubMed

    Mori, Shigeo; Matsuzaki, Koichi; Yoshida, Katsunori; Furukawa, Fukiko; Tahashi, Yoshiya; Yamagata, Hideo; Sekimoto, Go; Seki, Toshihito; Matsui, Hirofumi; Nishizawa, Mikio; Fujisawa, Jun-ichi; Okazaki, Kazuichi

    2004-09-23

    Although hepatocyte growth factor (HGF) can act synergistically or antagonistically with transforming growth factor-beta (TGF-beta) signaling, molecular mechanism of their crosstalk remains unknown. Using antibodies which selectively distinguished receptor-regulated Smads (R-Smads) phosphorylated at linker regions from those at C-terminal regions, we herein showed that either HGF or TGF-beta treatment of normal stomach-origin cells activated the JNK pathway, thereafter inducing endogenous R-Smads phosphorylation at linker regions. However, the phosphorylation at their C-terminal regions was not induced by HGF treatment. The activated JNK could directly phosphorylate R-Smads in vitro at the same sites that were phosphorylated in response to TGF-beta or HGF in vivo. Thus, the linker regions of R-Smads were the common phosphorylation sites for HGF and TGF-beta signaling pathways. The phosphorylation induced by simultaneous treatment with HGF and TGF-beta allowed R-Smads to associate with Smad4 and to translocate into the nucleus. JNK pathway involved HGF and TGF-beta-mediated infiltration potency since a JNK inhibitor SP600125 caused the reduction of invasive capacity induced by HGF and TGF-beta signals. Moreover, a combined treatment with HGF and TGF-beta led to a potent increase in plasminogen activator inhibitor type 1 transcriptional activity through Smad3 phosphorylation at the linker region. In contrast, HGF treatment reduced TGF-beta-dependent activation of p15INK4B promoter, in which Smad3 phosphorylation at the C-terminal region was involved. In conclusion, HGF and TGF-beta transmit the signals through JNK-mediated R-Smads phosphorylation at linker regions. PMID:15326485

  5. THE EFFECTS OF HALO-TO-HALO VARIATION ON SUBSTRUCTURE LENSING

    SciTech Connect

    Chen, Jacqueline; Koushiappas, Savvas M.; Zentner, Andrew R. E-mail: koushiappas@brown.edu

    2011-11-10

    We explore the halo-to-halo variation of dark matter (DM) substructure in galaxy-sized DM halos, focusing on its implications for strongly gravitational lensed systems. We find that the median value for projected substructure mass fractions within projected radii of 3% of the host halo virial radius is approximately f{sub sub} Almost-Equal-To 0.25%, but that the variance is large with a 95 percentile range of 0 {<=} f{sub sub} {<=} 1%. We quantify possible effects of substructure on quadruply imaged lens systems using the cusp relation and the simple statistic, R{sub cusp}. We estimate that the probability of obtaining the large values of the R{sub cusp} which have been observed from substructure effects is roughly {approx}10{sup -3} to {approx}10{sup -2}. We consider a variety of possible correlations between host halo properties and substructure properties in order to probe possible sample biases. In particular, low-concentration host DM halos have more large substructures and give rise to large values of R{sub cusp} more often. However, there is no known observational bias that would drive observed quadruply imaged quasars to be produced by low-concentration lens halos. Finally, we show that the substructure mass fraction is a relatively reliable predictor of the value of R{sub cusp}.

  6. Stability, Intracellular Delivery, and Release of siRNA from Chitosan Nanoparticles Using Different Cross-Linkers

    PubMed Central

    Abdul Ghafoor Raja, Maria; Katas, Haliza; Jing Wen, Thum

    2015-01-01

    Chitosan (CS) nanoparticles have been extensively studied for siRNA delivery; however, their stability and efficacy are highly dependent on the types of cross-linker used. To address this issue, three common cross-linkers; tripolyphosphate (TPP), dextran sulphate (DS) and poly-D-glutamic acid (PGA) were used to prepare siRNA loaded CS-TPP/DS/PGA nanoparticles by ionic gelation method. The resulting nanoparticles were compared with regard to their physicochemical properties including particle size, zeta potential, morphology, binding and encapsulation efficiencies. Among all the formulations prepared with different cross linkers, CS-TPP-siRNA had the smallest particle size (ranged from 127 ± 9.7 to 455 ± 12.9 nm) with zeta potential ranged from +25.1 ± 1.5 to +39.4 ± 0.5 mV, and high entrapment (>95%) and binding efficiencies. Similarly, CS-TPP nanoparticles showed better siRNA protection during storage at 4˚C and as determined by serum protection assay. TEM micrographs revealed the assorted morphology of CS-TPP-siRNA nanoparticles in contrast to irregular morphology displayed by CS-DS-siRNA and CS-PGA-siRNA nanoparticles. All siRNA loaded CS-TPP/DS/PGA nanoparticles showed initial burst release followed by sustained release of siRNA. Moreover, all the formulations showed low and concentration-dependent cytotoxicity with human colorectal cancer cells (DLD-1), in vitro. The cellular uptake studies with CS-TPP-siRNA nanoparticles showed successful delivery of siRNA within cytoplasm of DLD-1 cells. The results demonstrate that ionically cross-linked CS-TPP nanoparticles are biocompatible non-viral gene delivery system and generate a solid ground for further optimization studies, for example with regard to steric stabilization and targeting. PMID:26068222

  7. Protein inter-domain linker prediction using Random Forest and amino acid physiochemical properties

    PubMed Central

    2014-01-01

    Background Protein chains are generally long and consist of multiple domains. Domains are distinct structural units of a protein that can evolve and function independently. The accurate prediction of protein domain linkers and boundaries is often regarded as the initial step of protein tertiary structure and function predictions. Such information not only enhances protein-targeted drug development but also reduces the experimental cost of protein analysis by allowing researchers to work on a set of smaller and independent units. In this study, we propose a novel and accurate domain-linker prediction approach based on protein primary structure information only. We utilize a nature-inspired machine-learning model called Random Forest along with a novel domain-linker profile that contains physiochemical and domain-linker information of amino acid sequences. Results The proposed approach was tested on two well-known benchmark protein datasets and achieved 68% sensitivity and 99% precision, which is better than any existing protein domain-linker predictor. Without applying any data balancing technique such as class weighting and data re-sampling, the proposed approach is able to accurately classify inter-domain linkers from highly imbalanced datasets. Conclusion Our experimental results prove that the proposed approach is useful for domain-linker identification in highly imbalanced single- and multi-domain proteins. PMID:25521329

  8. Linker histone partial phosphorylation: effects on secondary structure and chromatin condensation.

    PubMed

    Lopez, Rita; Sarg, Bettina; Lindner, Herbert; Bartolomé, Salvador; Ponte, Inma; Suau, Pedro; Roque, Alicia

    2015-05-19

    Linker histones are involved in chromatin higher-order structure and gene regulation. We have successfully achieved partial phosphorylation of linker histones in chicken erythrocyte soluble chromatin with CDK2, as indicated by HPCE, MALDI-TOF and Tandem MS. We have studied the effects of linker histone partial phosphorylation on secondary structure and chromatin condensation. Infrared spectroscopy analysis showed a gradual increase of β-structure in the phosphorylated samples, concomitant to a decrease in α-helix/turns, with increasing linker histone phosphorylation. This conformational change could act as the first step in the phosphorylation-induced effects on chromatin condensation. A decrease of the sedimentation rate through sucrose gradients of the phosphorylated samples was observed, indicating a global relaxation of the 30-nm fiber following linker histone phosphorylation. Analysis of specific genes, combining nuclease digestion and qPCR, showed that phosphorylated samples were more accessible than unphosphorylated samples, suggesting local chromatin relaxation. Chromatin aggregation was induced by MgCl2 and analyzed by dynamic light scattering (DLS). Phosphorylated chromatin had lower percentages in volume of aggregated molecules and the aggregates had smaller hydrodynamic diameter than unphosphorylated chromatin, indicating that linker histone phosphorylation impaired chromatin aggregation. These findings provide new insights into the effects of linker histone phosphorylation in chromatin condensation. PMID:25870416

  9. Structurally diverse cyclisation linkers impose different backbone conformations in bicyclic peptides.

    PubMed

    Chen, Shiyu; Morales-Sanfrutos, Julia; Angelini, Alessandro; Cutting, Brian; Heinis, Christian

    2012-05-01

    Combinatorial libraries of structurally diverse peptide macrocycles offer a rich source for the development of high-affinity ligands to targets of interest. In this work we have developed linkers for the generation of genetically encoded bicyclic peptides and tested whether the peptides cyclised by them have significant variations in their backbone conformations. Two new cyclisation reagents, each containing three thiol-reactive groups, efficiently and selectively cyclised linear peptides containing three cysteine moieties. When the mesitylene linker of the bicyclic peptide PK15, a potent inhibitor of plasma kallikrein (K(i)=2 nM), was replaced by the new linkers, its inhibitory activity dropped by a factor of more than 1000, suggesting that the linkers impose different conformations on the peptide. Indeed, structural analysis by solution-state NMR revealed different NOE constraints in the three bicyclic peptides, indicating that these relatively small linkers at the centres of bicyclic peptide structures significantly influence the conformations of the peptides. These results demonstrate the prominent structural role of linkers in peptide macrocycles and suggest that application of different cyclisation linkers in a combinatorial fashion could be an attractive means to generate topologically diverse macrocycle libraries. PMID:22492661

  10. Glycosylated linkers in multimodular lignocellulose-degrading enzymes dynamically bind to cellulose.

    PubMed

    Payne, Christina M; Resch, Michael G; Chen, Liqun; Crowley, Michael F; Himmel, Michael E; Taylor, Larry E; Sandgren, Mats; Ståhlberg, Jerry; Stals, Ingeborg; Tan, Zhongping; Beckham, Gregg T

    2013-09-01

    Plant cell-wall polysaccharides represent a vast source of food in nature. To depolymerize polysaccharides to soluble sugars, many organisms use multifunctional enzyme mixtures consisting of glycoside hydrolases, lytic polysaccharide mono-oxygenases, polysaccharide lyases, and carbohydrate esterases, as well as accessory, redox-active enzymes for lignin depolymerization. Many of these enzymes that degrade lignocellulose are multimodular with carbohydrate-binding modules (CBMs) and catalytic domains connected by flexible, glycosylated linkers. These linkers have long been thought to simply serve as a tether between structured domains or to act in an inchworm-like fashion during catalytic action. To examine linker function, we performed molecular dynamics (MD) simulations of the Trichoderma reesei Family 6 and Family 7 cellobiohydrolases (TrCel6A and TrCel7A, respectively) bound to cellulose. During these simulations, the glycosylated linkers bind directly to cellulose, suggesting a previously unknown role in enzyme action. The prediction from the MD simulations was examined experimentally by measuring the binding affinity of the Cel7A CBM and the natively glycosylated Cel7A CBM-linker. On crystalline cellulose, the glycosylated linker enhances the binding affinity over the CBM alone by an order of magnitude. The MD simulations before and after binding of the linker also suggest that the bound linker may affect enzyme action due to significant damping in the enzyme fluctuations. Together, these results suggest that glycosylated linkers in carbohydrate-active enzymes, which are intrinsically disordered proteins in solution, aid in dynamic binding during the enzymatic deconstruction of plant cell walls. PMID:23959893

  11. Three-dimensional deformation analysis of two-phase dislocation substructures

    NASA Technical Reports Server (NTRS)

    Freed, Alan D.; Raj, S. V.; Walker, Kevin P.

    1992-01-01

    Three-dimensional deformation analysis of two-phase dislocation substructures was carried out, extending the Qian and Fan (1991) approach to 3D stress-strain fields by using the Budiansky and Wu (1962) criterion for strain compatibility between the 'hard' and 'soft' regions. The result is a rate-dependent viscoplastic theory, named the dislocation substructure viscoplasticity (DSV), which incorporates a self-consistent effect of dislocation substructure on material response. An algorithm developed for numerical implementation of the DSV theory is presented.

  12. Effect of load eccentricity and substructure deformation on ultimate strength of shuttle orbiter thermal protection system

    NASA Technical Reports Server (NTRS)

    Sawyer, J. W.

    1981-01-01

    The effect of load eccentricity and substructure deformation on the ultimate strength and stress displacement properties of the shuttle orbiter thermal protection system (TPS) was determined. The LI-900 Reusable Surface Insulation (RSI) tiles mounted on the .41 cm thick Strain Isolator Pad (SIP) were investigated. Substructure deformations reduce the ultimate strength of the SIP/tile TPS and increase the scatter in the ultimate strength data. Substructure deformations that occur unsymmetric to the tile can cause the tile to rotate when subjected to a uniform applied load. Load eccentricity reduces SIP/tile TPS ultimate strength and causes tile rotation.

  13. Jet Substructure: Boosting the Search for New Physics at the LHC

    NASA Astrophysics Data System (ADS)

    Thaler, Jesse

    2016-03-01

    Collisions at the Large Hadron Collider (LHC) are dominated by jets, collimated sprays of particles that are proxies for underlying quarks and gluons. With the remarkable performance of the ATLAS and CMS detectors, jets can now be characterized not just by their overall direction and energy but also by their substructure. In this talk, I highlight the ways that jet substructure has enhanced the search for new physics at the LHC, including recent excitement over a possible diboson excess. I also explain how theoretical studies of jet substructure have taught us surprising lessons about the nature of the strong force.

  14. Lecithin-Linker Microemulsion Gelatin Gels for Extended Drug Delivery

    PubMed Central

    Xuan, Xiao-Yue; Cheng, Yu-Ling; Acosta, Edgar

    2012-01-01

    This article introduces the formulation of alcohol-free, lecithin microemulsion-based gels (MBGs) prepared with gelatin as gelling agent. The influence of oil, water, lecithin and hydrophilic and lipophilic additives (linkers) on the rheological properties and appearance of these gels was systematically explored using ternary phase diagrams. Clear MBGs were obtained in regions of single phase microemulsions (μEs) at room temperature. Increasing the water content in the formulation increased the elastic modulus of the gels, while increasing the oil content had the opposite effect. The hydrophilic additive (PEG-6-caprylic/capric glycerides) was shown to reduce the elastic modulus of gelatin gels, particularly at high temperatures. In contrast to anionic (AOT) μEs, the results suggest that in lecithin (nonionic) μEs, the introduction of gelatin “dehydrates” the μE. Finally, when the transdermal transport of lidocaine formulated in the parent μE and the resulting MBG were compared, only a minor retardation in the loading and release of lidocaine was observed. PMID:24300183

  15. Impact of linker length on the activity of PROTACs

    PubMed Central

    Cyrus, Kedra; Wehenkel, Marie; Choi, Eun-Young; Han, Hyeong-Jun; Lee, Hyosung; Swanson, Hollie

    2013-01-01

    Conventional genetic approaches have provided a powerful tool in the study of proteins. However, these techniques often preclude selective manipulation of temporal and spatial protein functions, which is crucial for the investigation of dynamic cellular processes. To overcome these limitations, a small molecule-based novel technology termed “PROteolysis TArgeting ChimeraS (PROTACs)” has been developed, targeting proteins for degradation at the post-translational level. Despite the promising potential of PROTACs to serve as molecular probes of complex signaling pathways, their design has not been generalized for broad application. Here, we present the first generalized approach for PROTAC design by fine-tuning the distance between the two participating partner proteins, the E3 ubiquitin ligase and the target protein. As such, we took a chemical approach to create estrogen receptor (ER)-α targeting PROTACs with varying linker lengths and the loss of the ER in cultured cells was monitored via western blot and fluorometric analyses. We found a significant effect of chain length on PROTAC efficacy, and in this case, the optimum distance between the E3 recognition motif and the ligand was a 16 atom chain length. The information gathered from this experiment may offer a generalizable PROTAC design strategy to further the expansion of the PROTAC toolbox, opening new possibilities for the broad application of the PROTAC strategy in the study of multiple signaling pathways. PMID:20922213

  16. Impact of linker length on the activity of PROTACs.

    PubMed

    Cyrus, Kedra; Wehenkel, Marie; Choi, Eun-Young; Han, Hyeong-Jun; Lee, Hyosung; Swanson, Hollie; Kim, Kyung-Bo

    2011-02-01

    Conventional genetic approaches have provided a powerful tool in the study of proteins. However, these techniques often preclude selective manipulation of temporal and spatial protein functions, which is crucial for the investigation of dynamic cellular processes. To overcome these limitations, a small molecule-based novel technology termed "PROteolysis TArgeting ChimeraS (PROTACs)" has been developed, targeting proteins for degradation at the post-translational level. Despite the promising potential of PROTACs to serve as molecular probes of complex signaling pathways, their design has not been generalized for broad application. Here, we present the first generalized approach for PROTAC design by fine-tuning the distance between the two participating partner proteins, the E3 ubiquitin ligase and the target protein. As such, we took a chemical approach to create estrogen receptor (ER)-α targeting PROTACs with varying linker lengths and the loss of the ER in cultured cells was monitored via western blot and fluorometric analyses. We found a significant effect of chain length on PROTAC efficacy, and, in this case, the optimum distance between the E3 recognition motif and the ligand was a 16 atom chain length. The information gathered from this experiment may offer a generalizable PROTAC design strategy to further the expansion of the PROTAC toolbox, opening new possibilities for the broad application of the PROTAC strategy in the study of multiple signaling pathways. PMID:20922213

  17. Flexibility of NS5 Methyltransferase-Polymerase Linker Region Is Essential for Dengue Virus Replication

    PubMed Central

    Zhao, Yongqian; Soh, Tingjin Sherryl; Chan, Kitti Wing Ki; Fung, Sarah Suet Yin; Swaminathan, Kunchithapadam; Lim, Siew Pheng; Shi, Pei-Yong; Huber, Thomas; Lescar, Julien

    2015-01-01

    We examined the function of the conserved Val/Ile residue within the dengue virus NS5 interdomain linker (residues 263 to 272) by site-directed mutagenesis. Gly substitution or Gly/Pro insertion after the conserved residue increased the linker flexibility and created slightly attenuated viruses. In contrast, Pro substitution abolished virus replication by imposing rigidity in the linker and restricting NS5's conformational plasticity. Our biochemical and reverse genetics experiments demonstrate that NS5 utilizes conformational regulation to achieve optimum viral replication. PMID:26269182

  18. Direct detection of linker DNA bending in defined-length oligomers of chromatin.

    PubMed Central

    Yao, J; Lowary, P T; Widom, J

    1990-01-01

    Linker DNA, which connects between nucleosomes in chromatin, is short and, therefore, may be essentially straight and inflexible. We have carried out hydrodynamic and electron microscopic studies of dinucleosomes--fragments of chromatin containing just two nucleosomes--to test the ability of linker DNA to bend. We find that ionic conditions that stabilize the folding of long chromatin cause linker DNA in dinucleosomes to bend, bringing the two nucleosomes into contact. The results uphold a key prediction of the solenoid model of chromosome folding and suggest a mechanism by which proteins that are separated along the DNA can interact by direct contact. Images PMID:2217191

  19. New Structural-Dynamics Module for Offshore Multimember Substructures within the Wind Turbine Computer-Aided Engineering Tool FAST: Preprint

    SciTech Connect

    Song, H.; Damiani, R.; Robertson, A.; Jonkman, J.

    2013-08-01

    FAST, developed by the National Renewable Energy Laboratory (NREL), is a computer-aided engineering (CAE) tool for aero-hydro-servo-elastic analysis of land-based and offshore wind turbines. This paper discusses recent upgrades made to FAST to enable loads simulations of offshore wind turbines with fixed-bottom, multimember support structures (e.g., jackets and tripods, which are commonly used in transitional-depth waters). The main theory and strategies for the implementation of the multimember substructure dynamics module (SubDyn) within the new FAST modularization framework are introduced. SubDyn relies on two main engineering schematizations: 1) a linear frame finite-element beam (LFEB) model and 2) a dynamics system reduction via Craig-Bampton's method. A jacket support structure and an offshore system consisting of a turbine atop a jacket substructure were simulated to test the SubDyn module and to preliminarily assess results against results from a commercial finite-element code.

  20. Dark Halos and Substructure from Arcs & Einstein Rings

    NASA Astrophysics Data System (ADS)

    Koopmans, Leon

    2006-07-01

    statistically and individually the incidence of mass-substructure {with or without obvious luminous counter-parts such as dwarf galaxies}. Since dark-matter substructure could be more prevalent at higher redshift, both results provide a direct test of this prediction of the CDM hierarchical structure-formation model.

  1. Investigation of defect copper substructure disrupted in creep condition under the action of magnetic field

    NASA Astrophysics Data System (ADS)

    Konovalov, S. V.; Yaropolova, N. G.; Zaguyliaev1, D. V.; Gromov, V. E.; Ivanov, Yu F.; Komissarova, I. A.

    2015-09-01

    The defect substructure of M00b copper samples loaded up to disruption in creep condition both under and without the action of 0.35 T magnetic field is investigated in the paper. Material near the disrupted surface and at certain distances from it received the serious study. It has been ascertained that when copper disrupting without magnetic action on creep process the main type of dislocation substructure is the cellular one irrespectively of the distance to disruption surface. As the result of magnetic field influence on creep process the main type of dislocation substructure is replaced by the stripe-like one. The distinctive quantitative characteristics of dislocation substructures are observed. Moreover, a gradient behavior of the number of stress raisers has been revealed when moving away from disruption surface both in deformation conditions with and without a magnetic field.

  2. COLUMN DETAIL WITH SUBSTRUCTURE/STEEL BEAM/CONCRETE BEAM AT FIRST AVENUE ONRAMP. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    COLUMN DETAIL WITH SUBSTRUCTURE/STEEL BEAM/CONCRETE BEAM AT FIRST AVENUE ON-RAMP. TRIANGLE BUILDING AT RIGHT SIDE OF PHOTOGRAPH. - Alaskan Way Viaduct and Battery Street Tunnel, Seattle, King County, WA

  3. 20. Top 30/3. Plan of exposed substructure elevations. Wyoming ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    20. Top 30/3. Plan of exposed substructure elevations. - Wyoming Valley Flood Control System, Woodward Pumping Station, East of Toby Creek crossing by Erie-Lackawanna Railroad, Edwardsville, Luzerne County, PA

  4. Two Principles of Reticular Chemistry Uncovered in a Metal-Organic Framework of Heterotritopic Linkers and Infinite Secondary Building Units.

    PubMed

    Catarineu, Noelle R; Schoedel, Alexander; Urban, Philipp; Morla, Maureen B; Trickett, Christopher A; Yaghi, Omar M

    2016-08-31

    Structural diversity of metal-organic frameworks (MOFs) has been largely limited to linkers with at most two different types of coordinating groups. MOFs constructed from linkers with three or more nonidentical coordinating groups have not been explored. Here, we report a robust and porous crystalline MOF, Zn3(PBSP)2 or MOF-910, constructed from a novel linker PBSP (phenylyne-1-benzoate, 3-benzosemiquinonate, 5-oxidopyridine) bearing three distinct types of coordinative functionality. The MOF adopts a complex and previously unreported topology termed tto. Our study suggests that simple, symmetric linkers are not a necessity for formation of crystalline extended structures and that new, more complex topologies are attainable with irregular, heterotopic linkers. This work illustrates two principles of reticular chemistry: first, selectivity for helical over straight rod secondary building units (SBUs) is achievable with polyheterotopic linkers, and second, the pitch of the resulting helical SBUs may be fine-tuned based on the metrics of the polyheterotopic linker. PMID:27517606

  5. Composite materials with metal oxide attached to lead chalcogenide nanocrystal quantum dots with linkers

    DOEpatents

    Fuke, Nobuhiro; Koposov, Alexey Y; Sykora, Milan; Hoch, Laura

    2014-12-16

    Composite materials useful for devices such as photoelectrochemical solar cells include a substrate, a metal oxide film on the substrate, nanocrystalline quantum dots (NQDs) of lead sulfide, lead selenide, and lead telluride, and linkers that attach the NQDs to the metal oxide film. Suitable linkers preserve the 1s absorption peak of the NQDs. A suitable linker has a general structure A-B-C where A is a chemical group adapted for binding to a MO.sub.x and C is a chemical group adapted for binding to a NQD and B is a divalent, rigid, or semi-rigid organic spacer moiety. Other linkers that preserve the 1s absorption peak may also be used.

  6. Sequential Linker Installation: Precise Placement of Functional Groups in Multivariate Metal-Organic Frameworks

    SciTech Connect

    Yuan, S; Lu, WG; Chen, YP; Zhang, Q; Liu, TF; Feng, DW; Wang, X; Qin, JS; Zhou, HC

    2015-03-11

    A unique strategy, sequential linker installation (SLI), has been developed to construct multivariate MOFs with functional groups precisely positioned. PCN-700, a Zr-MOF with eight-connected Zr6O4(OH)(8)(H2O)(4) clusters, has been judiciously designed; the Zr-6 clusters in this MOF are arranged in such a fashion that, by replacement of terminal OH-/H2O ligands, subsequent insertion of linear dicarboxylate linkers is achieved. We demonstrate that linkers with distinct lengths and functionalities can be sequentially installed into PCN-700. Single-crystal to single-crystal transformation is realized so that the positions of the subsequently installed linkers are pinpointed via single-crystal X-ray diffraction analyses. This methodology provides a powerful tool to construct multivariate MOFs with precisely positioned functionalities in the desired proximity, which would otherwise be difficult to achieve.

  7. The Use of Aryl Hydrazide Linkers for the Solid Phase Synthesis of Chemically Modified Peptides

    SciTech Connect

    Woo, Y; Mitchell, A R; Camarero, J A

    2006-11-03

    Since Merrifield introduced the concept of solid phase synthesis in 1963 for the rapid preparation of peptides, a large variety of different supports and resin-linkers have been developed that improve the efficiency of peptide assembly and expand the myriad of synthetically feasible peptides. The aryl hydrazide is one of the most useful resin-linkers for the synthesis of chemically modified peptides. This linker is completely stable during Boc- and Fmoc-based solid phase synthesis and yet it can be cleaved under very mild oxidative conditions. The present article reviews the use of this valuable linker for the rapid and efficient synthesis of C-terminal modified peptides, head-to-tail cyclic peptides and lipidated peptides.

  8. Linker histones are not essential and affect chromatin condensation in vivo.

    PubMed

    Shen, X; Yu, L; Weir, J W; Gorovsky, M A

    1995-07-14

    We have (separately) disrupted all of the expressed macronuclear copies of the HHO gene encoding macronuclear histone H1 and of the micronuclear linker histone (MLH) gene encoding the protein MicLH in Tetrahymena thermophila. These disruptions are shown to eliminate completely the expression of each protein. Strains without either linker histone grow at normal rates and reach near-normal cell densities, demonstrating that linker histones are not essential for cell survival. Histone H1 knockout (delta H1) cells have enlarged DAPI-stained macronuclei and normal-sized micronuclei, while MicLH knockout (delta MicLH) cells have enlarged micronuclei and normal-sized macronuclei. delta MicLH cells undergo mitosis normally. However, the micronuclear mitotic chromosome structure is less condensed. These studies provide evidence that linker histones are nonessential and are involved in chromatin packaging and condensation in vivo. PMID:7606784

  9. Linker-Region Modified Derivatives of the Deoxyhypusine Synthase Inhibitor CNI-1493 Suppress HIV-1 Replication.

    PubMed

    Schröder, Marcus; Kolodzik, Adrian; Windshügel, Björn; Krepstakies, Marcel; Priyadarshini, Poornima; Hartjen, Philip; van Lunzen, Jan; Rarey, Matthias; Hauber, Joachim; Meier, Chris

    2016-02-01

    The inhibition of cellular factors that are involved in viral replication may be an important alternative to the commonly used strategy of targeting viral enzymes. The guanylhydrazone CNI-1493, a potent inhibitor of the deoxyhypusine synthase (DHS), prevents the activation of the cellular factor eIF-5A and thereby suppresses HIV replication and a number of other diseases. Here, we report on the design, synthesis and biological evaluation of a series of CNI-1493 analogues. The sebacoyl linker in CNI-1493 was replaced by different alkyl or aryl dicarboxylic acids. Most of the tested derivatives suppress HIV-1 replication efficiently in a dose-dependent manner without showing toxic side effects. The unexpected antiviral activity of the rigid derivatives point to a second binding mode as previously assumed for CNI-1493. Moreover, the chemical stability of CNI-1493 was analysed, showing a successive hydrolysis of the imino bonds. By molecular dynamics simulations, the behaviour of the parent CNI-1493 in solution and its interactions with DHS were investigated. PMID:26725082

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

    PubMed

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

    2004-05-01

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

  11. Common Space, Common Time, Common Work

    ERIC Educational Resources Information Center

    Shank, Melody J.

    2005-01-01

    The most valued means of support and learning cited by new teachers at Poland Regional High School in rural Maine are the collegial interactions that common workspace, common planning time, and common tasks make possible. The school has used these everyday structures to enable new and veteran teachers to converse about curricular and pedagogical…

  12. Chromatin fiber polymorphism triggered by variations of DNA linker lengths

    PubMed Central

    Collepardo-Guevara, Rosana; Schlick, Tamar

    2014-01-01

    Deciphering the factors that control chromatin fiber structure is key to understanding fundamental chromosomal processes. Although details remain unknown, it is becoming clear that chromatin is polymorphic depending on internal and external factors. In particular, different lengths of the linker DNAs joining successive nucleosomes (measured in nucleosome-repeat lengths or NRLs) that characterize different cell types and cell cycle stages produce different structures. NRL is also nonuniform within single fibers, but how this diversity affects chromatin fiber structure is not clear. Here we perform Monte Carlo simulations of a coarse-grained oligonucleosome model to help interpret fiber structure subject to intrafiber NRL variations, as relevant to proliferating cells of interphase chromatin, fibers subject to remodeling factors, and regulatory DNA sequences. We find that intrafiber NRL variations have a profound impact on chromatin structure, with a wide range of different architectures emerging (highly bent narrow forms, canonical and irregular zigzag fibers, and polymorphic conformations), depending on the NRLs mixed. This stabilization of a wide range of fiber forms might allow NRL variations to regulate both fiber compaction and selective DNA exposure. The polymorphic forms spanning canonical to sharply bent structures, like hairpins and loops, arise from large NRL variations and are surprisingly more compact than uniform NRL structures. They are distinguished by tail-mediated far-nucleosome interactions, in addition to the near-nucleosome interactions of canonical 30-nm fibers. Polymorphism is consistent with chromatin’s diverse biological functions and heterogeneous constituents. Intrafiber NRL variations, in particular, may contribute to fiber bending and looping and thus to distant communication in associated regulatory processes. PMID:24847063

  13. Statistics of magnification perturbations by substructure in the cold dark matter cosmological model

    SciTech Connect

    Rozo, Eduardo; Zentner, Andrew R.; Bertone, Gianfranco; Chen, Jacqueline; /KICP, Chicago /Chicago U., Astron. Astrophys. Ctr.

    2005-06-01

    We study the statistical properties of magnification perturbations by substructures in strong lensed systems using linear perturbation theory and an analytical substructure model including tidal truncation and a continuous substructure mass spectrum. We demonstrate that magnification perturbations are dominated by perturbers found within a tidal radius of an image, and that sizable magnification perturbations may arise from small, coherent contributions from several substructures within the lens halo. We find that the root-mean-square (rms) fluctuation of the magnification perturbation is {approx}10% to {approx}20% and both the average and rms perturbations are sensitive to the mass spectrum and density profile of the perturbers. Interestingly,we find that relative to a smooth model of the same mass, the average magnification in clumpy models is lower (higher) than that in smooth models for positive (negative) parity images. This is opposite from what is observed if one assumes that the image magnification predicted by the best-fit smooth model of a lens is a good proxy for what the observed magnification would have been if substructures were absent. While it is possible for this discrepancy to be resolved via nonlinear perturbers, we argue that a more likely explanation is that the assumption that the best-fit lens model is a good proxy for the magnification in the absence of substructure is not correct. We conclude that a better theoretical understanding of the predicted statistical properties of magnification perturbations by CDM substructure is needed in order to affirm that CDM substructures have been unambiguously detected.

  14. Application of Resin Transfer Molding to the Manufacture of Wind Turbine Blade Substructures. Final Report

    SciTech Connect

    Hedley, C. W.; Ritter, W. J.; Ashwill, T.

    2001-07-26

    The U.S. has generally lacked the capability for an iterative process of detailed structural design, manufacturing, and testing at the full blade level to achieve specific structural performance, cost, and weight targets. This project examined the effects that different composites processing methods had on the performance of representative blade substructures. In addition, the results of the testing of these substructures was used to validate NuMAD, the design tool developed at Sandia National Laboratories.

  15. Gravitational focusing and substructure effects on the rate modulation in direct dark matter searches

    SciTech Connect

    Nobile, Eugenio Del; Gelmini, Graciela B.; Witte, Samuel J.

    2015-08-21

    We study how gravitational focusing (GF) of dark matter by the Sun affects the annual and biannual modulation of the expected signal in non-directional direct dark matter searches, in the presence of dark matter substructure in the local dark halo. We consider the Sagittarius stream and a possible dark disk, and show that GF suppresses some, but not all, of the distinguishing features that would characterize substructure of the dark halo were GF neglected.

  16. A NEW METHOD TO QUANTIFY X-RAY SUBSTRUCTURES IN CLUSTERS OF GALAXIES

    SciTech Connect

    Andrade-Santos, Felipe; Lima Neto, Gastao B.; Lagana, Tatiana F.

    2012-02-20

    We present a new method to quantify substructures in clusters of galaxies, based on the analysis of the intensity of structures. This analysis is done in a residual image that is the result of the subtraction of a surface brightness model, obtained by fitting a two-dimensional analytical model ({beta}-model or Sersic profile) with elliptical symmetry, from the X-ray image. Our method is applied to 34 clusters observed by the Chandra Space Telescope that are in the redshift range z in [0.02, 0.2] and have a signal-to-noise ratio (S/N) greater than 100. We present the calibration of the method and the relations between the substructure level with physical quantities, such as the mass, X-ray luminosity, temperature, and cluster redshift. We use our method to separate the clusters in two sub-samples of high- and low-substructure levels. We conclude, using Monte Carlo simulations, that the method recuperates very well the true amount of substructure for small angular core radii clusters (with respect to the whole image size) and good S/N observations. We find no evidence of correlation between the substructure level and physical properties of the clusters such as gas temperature, X-ray luminosity, and redshift; however, analysis suggest a trend between the substructure level and cluster mass. The scaling relations for the two sub-samples (high- and low-substructure level clusters) are different (they present an offset, i.e., given a fixed mass or temperature, low-substructure clusters tend to be more X-ray luminous), which is an important result for cosmological tests using the mass-luminosity relation to obtain the cluster mass function, since they rely on the assumption that clusters do not present different scaling relations according to their dynamical state.

  17. Gap comparison between single crown and three-unit bridge zirconia substructures

    PubMed Central

    Charoenchitt, Masnisa; Asvanund, Chanavut

    2014-01-01

    PURPOSE To compare marginal and internal gaps of zirconia substructure of single crowns with those of three-unit fixed dental prostheses. MATERIALS AND METHODS Standardized Co-Cr alloy simulated second premolar and second molar abutments were fabricated and subsequently duplicated into type-III dental stone for working casts. After that, all zirconia substructures were made using Lava™ system. Marginal and internal gaps were measured in 2 planes (mesial-distal plane and buccal-palatal plane) at 5 locations: marginal opening (MO), chamfer area (CA), axial wall (AW), cusp tip (CT) and mid-occlusal (OA) using Replica technique. RESULTS There were significant differences between gaps at all locations. The mean ± SD of marginal gap in premolar was 43.6 ± 0.4 µm and 46.5 ± 0.5 µm for single crown and 3-unit bridge substructure respectively. For molar substructure the mean ± SD of marginal gap was 48.5 ± 0.4 µm and 52.6 ± 0.4 µm for single crown and 3-unit bridge respectively. The largest gaps were found at the occlusal area, which was 150.5 ± 0.5 µm and 154.5 ± 0.4 µm for single and 3-unit bridge premolar substructures respectively and 146.5 ± 0.4 µm and 211.5 ± 0.4 µm for single and 3-unit bridge molar substructure respectively. CONCLUSION Independent-samples t-test showed significant differences of gap in zirconia substructure between single crowns and three-unit bridge (P<.001). Therefore, the span length has the effect on the fit of zirconia substructure that is fabricated using CAD/CAM technique especially at the occlusal area. PMID:25177467

  18. Probing the substructure of f0(1370 )

    NASA Astrophysics Data System (ADS)

    Fariborz, Amir H.; Azizi, Azizollah; Asrar, Abdorreza

    2015-04-01

    Within an effective nonlinear chiral Lagrangian framework, the substructure of f0(1370 ) is studied. The investigation is conducted in the context of a global picture of scalar mesons in which the importance of the underlying connections among scalar mesons below and above 1 GeV is recognized and implemented. These connections are due to the mixings among various quark-antiquarks, four-quarks, and glue components and play a central role in understanding the properties of scalar mesons. Iterative Monte Carlo simulations are first performed on the 14-dimensional parameter space of the model and sets of points in this parameter space (the global sets) that give an overall agreement with all experimental data on mass spectrum, various decay widths, and decay ratios of all isosinglet scalar states below 2 GeV are determined. Then within each global set, subsets that give closest agreement for the properties of f0(1370 ) are studied. Unlike the properties of other isosinglet states that show a range of variation within each global set, it is found that there is a clear signal for f0(1370 ) to be predominantly a quark-antiquark state with a substantial s s ¯ component, together with small remnants of four-quark and glue components.

  19. A dimethacrylate cross-linker cleavable under thermolysis or alkaline hydrolysis conditions: synthesis, polymerization, and degradation.

    PubMed

    Elladiou, Marios; Patrickios, Costas S

    2016-02-11

    We develop a new platform based on 2,6-pyridinediethanol diesters for introducing polymer degradability under thermolysis or alkaline hydrolysis conditions, with the latter being rare in polymers. Such labile diesters can be cross-linkers, bifunctional initiators and inimers. We demonstrate the power of this platform through the synthesis of the 2,6-pyridinediethanol dimethacrylate cross-linker, its controlled (co)polymerization, and the thermal and hydrolytic cleavage of its (co)polymers. PMID:26803938

  20. Lecithin-linker formulations for self-emulsifying delivery of nutraceuticals.

    PubMed

    Chu, Jacquelene; Cheng, Yu-Ling; Rao, A Venketeshwer; Nouraei, Mehdi; Zarate-Muñoz, Silvia; Acosta, Edgar J

    2014-08-25

    Lecithin-linker microemulsions are formulations produced with soybean lecithin in combination with a highly lipophilic (lipophilic linker) and highly hydrophilic (hydrophilic linkers) surfactant-like additives. In this work, lecithin-linker systems were formulated to produce self-emulsifying delivery systems for β-carotene and β-sitosterol. The concentration of the lipophilic linker, sorbitan monooleate, was adjusted to minimize the formation of liquid crystals. The concentration of hydrophilic linkers, decaglyceryl caprylate/caprate and PEG-6-caprylic/capric glycerides, was gradually increased (scanned) until single phase clear microemulsions were obtained. For these scans, the oil (ethyl caprate) to water ratio was set to 1. The single phase, clear microemulsions were diluted with fed-state simulated intestinal fluid (FeSSIF) and produced stable emulsions, with drop sizes close to 200 nm. Using pseudo-ternary phase diagrams to evaluate the process of dilution of microemulsion preconcentrates (mixtures of oil, lecithin and linkers with little or no water) with FeSSIF, it was determined that self-emulsifying systems are obtained when the early stages of the dilution produce single phase microemulsions. If liquid crystals or multiple phase systems are obtained during those early stages, then the emulsification yields unstable emulsions with large drop sizes. An in vitro permeability study conducted using a Flow-Thru Dialyzer revealed that stable emulsions with drop sizes of 150-300 nm produce large and irreversible permeation of β-carotene to sheep intestine. On the other hand, unstable emulsions produced without the linker combination separated in the dialyzer chamber. PMID:24810240

  1. Modular construction of plasmids through ligation-free assembly of vector components with oligonucleotide linkers.

    PubMed

    Vroom, Jonathan A; Wang, Clifford L

    2008-06-01

    We have developed a modular method of plasmid construction that can join multiple DNA components in a single reaction. A nicking enzyme is used to create 5' and 3' overhangs on PCR-generated DNA components. Without the use of ligase or restriction enzymes, components are joined using oligonucleotide linkers that recognize the overhangs. By specifying the sequences of the linkers, desired components can be assembled in any combination and order to generate different plasmid vectors. PMID:18533903

  2. Combining allele frequency uncertainty and population substructure corrections in forensic DNA calculations.

    PubMed

    Cowell, Robert

    2016-07-01

    In forensic DNA calculations of relatedness of individuals and in DNA mixture analyses, at least two sources of uncertainty are present concerning the allele frequencies used for evaluating genotype probabilities when evaluating likelihoods. They are: (i) imprecision in the estimates of the allele frequencies in the population by using an inevitably finite database of DNA profiles to estimate them; and (ii) the existence of population substructure. Green and Mortera [6] showed that these effects may be taken into account individually using a common Dirichlet model within a Bayesian network formulation, but that when taken in combination this is not the case; however they suggested an approximation that could be used. Here we develop a slightly different approximation that is shown to be exact in the case of a single individual. We demonstrate the numerical closeness of the approximation using a published database of allele counts, and illustrate the effect of incorporating the approximation into calculations of a recently published statistical model of DNA mixtures. PMID:27231804

  3. Extreme Brightness Temperatures and Refractive Substructure in 3C273 with RadioAstron

    NASA Astrophysics Data System (ADS)

    Johnson, Michael D.; Kovalev, Yuri Y.; Gwinn, Carl R.; Gurvits, Leonid I.; Narayan, Ramesh; Macquart, Jean-Pierre; Jauncey, David L.; Voitsik, Peter A.; Anderson, James M.; Sokolovsky, Kirill V.; Lisakov, Mikhail M.

    2016-03-01

    Earth-space interferometry with RadioAstron provides the highest direct angular resolution ever achieved in astronomy at any wavelength. RadioAstron detections of the classic quasar 3C 273 on interferometric baselines up to 171,000 km suggest brightness temperatures exceeding expected limits from the “inverse-Compton catastrophe” by two orders of magnitude. We show that at 18 cm, these estimates most likely arise from refractive substructure introduced by scattering in the interstellar medium. We use the scattering properties to estimate an intrinsic brightness temperature of 7× {10}12 {{K}}, which is consistent with expected theoretical limits, but which is ˜15 times lower than estimates that neglect substructure. At 6.2 cm, the substructure influences the measured values appreciably but gives an estimated brightness temperature that is comparable to models that do not account for the substructure. At 1.35 {{cm}}, the substructure does not affect the extremely high inferred brightness temperatures, in excess of {10}13 {{K}}. We also demonstrate that for a source having a Gaussian surface brightness profile, a single long-baseline estimate of refractive substructure determines an absolute minimum brightness temperature, if the scattering properties along a given line of sight are known, and that this minimum accurately approximates the apparent brightness temperature over a wide range of total flux densities.

  4. Theoretical and software considerations for general dynamic analysis using multilevel substructured models

    NASA Technical Reports Server (NTRS)

    Schmidt, R. J.; Dodds, R. H., Jr.

    1985-01-01

    The dynamic analysis of complex structural systems using the finite element method and multilevel substructured models is presented. The fixed-interface method is selected for substructure reduction because of its efficiency, accuracy, and adaptability to restart and reanalysis. This method is extended to reduction of substructures which are themselves composed of reduced substructures. The implementation and performance of the method in a general purpose software system is emphasized. Solution algorithms consistent with the chosen data structures are presented. It is demonstrated that successful finite element software requires the use of software executives to supplement the algorithmic language. The complexity of the implementation of restart and reanalysis porcedures illustrates the need for executive systems to support the noncomputational aspects of the software. It is shown that significant computational efficiencies can be achieved through proper use of substructuring and reduction technbiques without sacrificing solution accuracy. The restart and reanalysis capabilities and the flexible procedures for multilevel substructured modeling gives economical yet accurate analyses of complex structural systems.

  5. Tuning the mechanosensitivity of a BK channel by changing the linker length.

    PubMed

    Zhao, Hucheng; Sokabe, Masahiro

    2008-08-01

    Some large-conductance Ca(2+) and voltage-activated K(+)(BK) channels are activated by membrane stretch. However, the mechanism of mechano-gating of the BK channels is still not well understood. Previous studies have led to the proposal that the linker-gating ring complex functions as a passive spring, transducing the force generated by intracellular Ca(2+) to the gate to open the channel. This raises the question as to whether membrane stretch is also transmitted to the gate of mechanosensitive (MS) BK channels via the linker-gating complex. To study this, we changed the linker length in the stretch-activated BK channel (SAKCaC), and examined the effect of membrane stretch on the gating of the resultant mutant channels. Shortening the linker increased, whereas extending the linker reduced, the channel mechanosensitivity both in the presence and in the absence of intracellular Ca(2+). However, the voltage and Ca(2+) sensitivities were not significantly altered by membrane stretch. Furthermore, the SAKCaC became less sensitive to membrane stretch at relatively high intracellular Ca(2+) concentrations or membrane depolarization. These observations suggest that once the channel is in the open-state conformation, tension on the spring is partially released and membrane stretch is less effective. Our results are consistent with the idea that membrane stretch is transferred to the gate via the linker-gating ring complex of the MS BK channels. PMID:18663377

  6. Novel regulation of Smad3 oligomerization and DNA binding by its linker domain.

    PubMed

    Vasilaki, Eleftheria; Siderakis, Manos; Papakosta, Paraskevi; Skourti-Stathaki, Konstantina; Mavridou, Sofia; Kardassis, Dimitris

    2009-09-01

    Smad proteins are key effectors of the transforming growth factor beta (TGFbeta) signaling pathway in mammalian cells. Smads are composed of two highly structured and conserved domains called Mad homology 1 (MH1) and 2 (MH2), which are linked together by a nonconserved linker region. The recent identification of phosphorylation sites and binding sites for ubiquitin ligases in the linker regions of TGFbeta and bone morphogenetic protein (BMP) receptor-regulated Smads suggested that the linker may contribute to the regulation of Smad function by facilitating cross-talks with other signaling pathways. In the present study, we have generated and characterized novel Smad3 mutants bearing individual substitutions of conserved and nonconserved amino acid residues within a previously described transcriptionally active linker fragment. Our analysis showed that the conserved linker amino acids glutamine 222 and proline 229 play important roles in Smad functions such as homo- and hetero-oligomerization, nuclear accumulation in response to TGFbeta stimulation, and DNA binding. Furthermore, a Smad3 mutant bearing a substitution of the nonconserved amino acid asparagine 218 to alanine displayed enhanced transactivation potential relative to wild type Smad3. Finally, Smad3 P229A inhibited TGFbeta signaling when overexpressed in mammalian cells. In conclusion, our data are in line with previous studies supporting an important regulatory role of the linker region of Smads in their function as key transducers of TGFbeta signaling. PMID:19645436

  7. Protein Disorder: Conformational Distribution of the Flexible Linker in a Chimeric Double Cellulase

    PubMed Central

    von Ossowski, Ingemar; Eaton, Julian T.; Czjzek, Mirjam; Perkins, Stephen J.; Frandsen, Torben P.; Schülein, Martin; Panine, Pierre; Henrissat, Bernard; Receveur-Bréchot, Veronique

    2005-01-01

    The structural properties of the linker peptide connecting the cellulose-binding module to the catalytic module in bimodular cellulases have been investigated by small-angle x-ray scattering. Since the linker and the cellulose-binding module are relatively small and cannot be readily detected separately, the conformation of the linker was studied by means of an artificial fusion protein, Cel6BA, in which an 88-residue linker connects the large catalytic modules of the cellulases Cel6A and Cel6B from Humicola insolens. Our data showed that Cel6BA is very elongated with a maximum dimension of 178 Å, but could not be described by a single conformation. Modeling of a series of Cel6BA conformers with interdomain separations ranging between 10 Å and 130 Å showed that good Guinier and P(r) profile fits were obtained by a weighted average of the scattering curves of all the models where the linker follows a nonrandom distribution, with a preference for the more compact conformers. These structural properties are likely to be essential for the function of the linker as a molecular spring between the two functional modules. Small-angle x-ray scattering therefore provides a unique tool to quantitatively analyze the conformational disorder typical of proteins described as natively unfolded. PMID:15653742

  8. Nuclear substructure reorganization during late stageerythropoiesis is selective and does not involve caspase cleavage ofmajor nuclear substructural proteins

    SciTech Connect

    Krauss, Sharon Wald; Lo, Annie J.; Short, Sarah A.; Koury, MarkJ.; Mohandas, Narla; Chasis, Joel Anne

    2005-04-06

    Enucleation, a rare feature of mammalian differentiation, occurs in three cell types: erythroblasts, lens epithelium and keratinocytes. Previous investigations suggest that caspase activation functions in lens epithelial and keratinocyte enucleation, as well as in early erythropoiesis encompassing BFU-E differentiation to proerythroblast. To determine whether caspase activation contributes to later erythropoiesis and whether nuclear substructures other than chromatin reorganize, we analyzed distributions of nuclear subcompartment proteins and assayed for caspase-induced cleavage of subcompartmental target proteins in mouse erythroblasts. We found that patterns of lamin B in the filamentous network interacting with both the nuclear envelope and DNA, nuclear matrix protein NuMA, and splicing factors Sm and SC35 persisted during nuclear condensation, consistent with effective transcription of genes expressed late in differentiation. Thus nuclear reorganization prior to enucleation is selective, allowing maintenance of critical transcriptional processes independent of extensive chromosomal reorganization. Consistent with these data, we found no evidence for caspase-induced cleavage of major nuclear subcompartment proteins during late erythropoiesis, in contrast to what has been observed in early erythropoiesis and in lens epithelial and keratinocyte differentiation. These findings imply that nuclear condensation and extrusion during terminal erythroid differentiation involve novel mechanisms that do not entail major activation of apoptotic machinery.

  9. Modulation of the Shaker K+Channel Gating Kinetics by the S3–S4 Linker

    PubMed Central

    Gonzalez, Carlos; Rosenman, Eduardo; Bezanilla, Francisco; Alvarez, Osvaldo; Latorre, Ramon

    2000-01-01

    In Shaker K+ channels depolarization displaces outwardly the positively charged residues of the S4 segment. The amount of this displacement is unknown, but large movements of the S4 segment should be constrained by the length and flexibility of the S3–S4 linker. To investigate the role of the S3–S4 linker in the ShakerH4Δ(6–46) (ShakerΔ) K+ channel activation, we constructed S3–S4 linker deletion mutants. Using macropatches of Xenopus oocytes, we tested three constructs: a deletion mutant with no linker (0 aa linker), a mutant containing a linker 5 amino acids in length, and a 10 amino acid linker mutant. Each of the three mutants tested yielded robust K+ currents. The half-activation voltage was shifted to the right along the voltage axis, and the shift was +45 mV in the case of the 0 aa linker channel. In the 0 aa linker, mutant deactivation kinetics were sixfold slower than in ShakerΔ. The apparent number of gating charges was 12.6 ± 0.6 eo in ShakerΔ, 12.7 ± 0.5 in 10 aa linker, and 12.3 ± 0.9 in 5 aa linker channels, but it was only 5.6 ± 0.3 eo in the 0 aa linker mutant channel. The maximum probability of opening (Pomax) as measured using noise analysis was not altered by the linker deletions. Activation kinetics were most affected by linker deletions; at 0 mV, the 5 and 0 aa linker channels' activation time constants were 89× and 45× slower than that of the ShakerΔ K+ channel, respectively. The initial lag of ionic currents when the prepulse was varied from −130 to −60 mV was 0.5, 14, and 2 ms for the 10, 5, and 0 aa linker mutant channels, respectively. These results suggest that: (a) the S4 segment moves only a short distance during activation since an S3–S4 linker consisting of only 5 amino acid residues allows for the total charge displacement to occur, and (b) the length of the S3–S4 linker plays an important role in setting ShakerΔ channel activation and deactivation kinetics. PMID:10653896

  10. Subnuclear distribution of the entire complement of linker histone variants in Arabidopsis thaliana.

    PubMed

    Ascenzi, R; Gantt, J S

    1999-11-01

    Linker histones (e.g. H1, H5, H1 degrees ) are thought to exert control on chromatin function by restricting nucleosomal dynamics. All higher eukaryotes possess a diverse family of linker histones, which may exhibit functional specialization. Arabidopsis thaliana apparently contains a minimal complement of linker histone structural variants and therefore is an ideal model for investigating functional differentiation among linker histones. Histones H1-1 and H1-2 are relatively similar proteins that are expressed in a wide variety of tissues and make up the majority of linker histone while H1-3 is a highly divergent minor variant protein that is induced by drought stress. We are interested in determining whether the in vivo distribution of each of these proteins also differs. To this end, we have produced subtype-specific antibodies and have localized each of the three proteins at the intranuclear and DNA sequence levels by indirect immunofluorescence and immunoprecipitation, respectively. Antibodies against linker histones H1-1 and H1-2 decorate nuclei in patterns very similar to 4',6-diamidino-2-phenylindole (DAPI) staining, but different than the staining pattern of total histones. In contrast, antibodies made against two regions of H1-3 bind to chromatin in a diffuse pattern distinct from the DAPI-staining pattern. We also describe a technique to determine the localization of plant linker histone variants along regions of chromatin, employing in vivo chemical DNA-protein cross-linking to preserve native associations followed by immunoprecipitation with subtype-specific antibodies. We use this technique to demonstrate that, in contrast to the major linker histones, H1-3 does not bind the repetitive sequences pAL1 and 5S rDNA. In addition, we show that linker histones are bound to the compacted nucleosomal arrays at the telomere but with reduced stoichiometry. Taken together, our results suggest that plants, as has been shown for animals, possess a variant linker

  11. Morphology parameters: substructure identification in X-ray galaxy clusters

    NASA Astrophysics Data System (ADS)

    Parekh, Viral; van der Heyden, Kurt; Ferrari, Chiara; Angus, Garry; Holwerda, Benne

    2015-03-01

    Context. In recent years multi-wavelength observations have shown the presence of substructures related to merging events in a large proportion of galaxy clusters. Clusters can be roughly grouped into two categories - relaxed and non-relaxed - and a proper characterisation of the dynamical state of these systems is crucial for both astrophysical and cosmological studies. Aims: In this paper we investigate the use of a number of morphological parameters (Gini, M20, concentration, asymmetry, smoothness, ellipticity, and Gini of the second-order moment, GM) introduced to automatically classify clusters as relaxed or dynamically disturbed systems. Methods: We apply our method to a sample of clusters at different redshifts extracted from the Chandra archive and investigate possible correlations between morphological parameters and other X-ray gas properties. Results: We conclude that a combination of the adopted parameters is a very useful tool for properly characterising the X-ray cluster morphology. According to our results, three parameters - Gini, M20, and concentration - are very promising for identifying cluster mergers. The Gini coefficient is a particularly powerful tool, especially at high redshift, because it is independent of the choice of the position of the cluster centre. We find that high Gini (>0.65), high concentration (>1.55), and low M20 (<-2.0) values are associated with relaxed clusters, while low Gini (<0.4), low concentration (<1.0), and high M20 (>-1.4) characterise dynamically perturbed systems. We also estimate the X-ray cluster morphological parameters in the case of radio loud clusters. Since they are in excellent agreement with previous analyses we confirm that diffuse intracluster radio sources are associated with major mergers. Appendix A is available in electronic form at http://www.aanda.org

  12. The Effects of Varying Cosmological Parameters on Halo Substructure

    NASA Astrophysics Data System (ADS)

    Dooley, Gregory A.; Griffen, Brendan F.; Zukin, Phillip; Ji, Alexander P.; Vogelsberger, Mark; Hernquist, Lars E.; Frebel, Anna

    2014-05-01

    We investigate how different cosmological parameters, such as those delivered by the WMAP and Planck missions, affect the nature and evolution of the dark matter halo substructure. We use a series of flat Λ cold dark matter cosmological N-body simulations of structure formation, each with a different power spectrum but with the same initial white noise field. Our fiducial simulation is based on parameters from the WMAP seventh year cosmology. We then systematically vary the spectral index, ns ; matter density, Ω M ; and normalization of the power spectrum, σ8, for seven unique simulations. Across these, we study variations in the subhalo mass function, mass fraction, maximum circular velocity function, spatial distribution, concentration, formation times, accretion times, and peak mass. We eliminate dependence of subhalo properties on host halo mass and average the values over many hosts to reduce variance. While the "same" subhalos from identical initial overdensity peaks in higher σ8, ns , and Ω m simulations accrete earlier and end up less massive and closer to the halo center at z = 0, the process of continuous subhalo accretion and destruction leads to a steady state distribution of these properties across all subhalos in a given host. This steady state mechanism eliminates cosmological dependence on all of the properties listed above except for subhalo concentration and V max, which remain greater for higher σ8, ns , and Ω m simulations, and subhalo formation time, which remains earlier. We also find that the numerical technique for computing the scale radius and the halo finder that were used can significantly affect the concentration-mass relationship as computed for a simulation.

  13. The effects of varying cosmological parameters on halo substructure

    SciTech Connect

    Dooley, Gregory A.; Griffen, Brendan F.; Ji, Alexander P.; Vogelsberger, Mark; Frebel, Anna; Zukin, Phillip; Hernquist, Lars E.

    2014-05-01

    We investigate how different cosmological parameters, such as those delivered by the WMAP and Planck missions, affect the nature and evolution of the dark matter halo substructure. We use a series of flat Λ cold dark matter cosmological N-body simulations of structure formation, each with a different power spectrum but with the same initial white noise field. Our fiducial simulation is based on parameters from the WMAP seventh year cosmology. We then systematically vary the spectral index, n{sub s} ; matter density, Ω {sub M}; and normalization of the power spectrum, σ{sub 8}, for seven unique simulations. Across these, we study variations in the subhalo mass function, mass fraction, maximum circular velocity function, spatial distribution, concentration, formation times, accretion times, and peak mass. We eliminate dependence of subhalo properties on host halo mass and average the values over many hosts to reduce variance. While the 'same' subhalos from identical initial overdensity peaks in higher σ{sub 8}, n{sub s} , and Ω {sub m} simulations accrete earlier and end up less massive and closer to the halo center at z = 0, the process of continuous subhalo accretion and destruction leads to a steady state distribution of these properties across all subhalos in a given host. This steady state mechanism eliminates cosmological dependence on all of the properties listed above except for subhalo concentration and V {sub max}, which remain greater for higher σ{sub 8}, n{sub s} , and Ω {sub m} simulations, and subhalo formation time, which remains earlier. We also find that the numerical technique for computing the scale radius and the halo finder that were used can significantly affect the concentration-mass relationship as computed for a simulation.

  14. A Genetic Screen and Transcript Profiling Reveal a Shared Regulatory Program for Drosophila Linker Histone H1 and Chromatin Remodeler CHD1

    PubMed Central

    Kavi, Harsh; Lu, Xingwu; Xu, Na; Bartholdy, Boris A.; Vershilova, Elena; Skoultchi, Arthur I.; Fyodorov, Dmitry V.

    2015-01-01

    Chromatin structure and activity can be modified through ATP-dependent repositioning of nucleosomes and posttranslational modifications of core histone tails within nucleosome core particles and by deposition of linker histones into the oligonucleosome fiber. The linker histone H1 is essential in metazoans. It has a profound effect on organization of chromatin into higher-order structures and on recruitment of histone-modifying enzymes to chromatin. Here, we describe a genetic screen for modifiers of the lethal phenotype caused by depletion of H1 in Drosophila melanogaster. We identify 41 mis-expression alleles that enhance and 20 that suppress the effect of His1 depletion in vivo. Most of them are important for chromosome organization, transcriptional regulation, and cell signaling. Specifically, the reduced viability of H1-depleted animals is strongly suppressed by ubiquitous mis-expression of the ATP-dependent chromatin remodeling enzyme CHD1. Comparison of transcript profiles in H1-depleted and Chd1 null mutant larvae revealed that H1 and CHD1 have common transcriptional regulatory programs in vivo. H1 and CHD1 share roles in repression of numerous developmentally regulated and extracellular stimulus-responsive transcripts, including immunity-related and stress response-related genes. Thus, linker histone H1 participates in various regulatory programs in chromatin to alter gene expression. PMID:25628309

  15. Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method

    PubMed Central

    Duhaime, Melissa B; Deng, Li; Poulos, Bonnie T; Sullivan, Matthew B

    2012-01-01

    Metagenomics generates and tests hypotheses about dynamics and mechanistic drivers in wild populations, yet commonly suffers from insufficient (< 1 ng) starting genomic material for sequencing. Current solutions for amplifying sufficient DNA for metagenomics analyses include linear amplification for deep sequencing (LADS), which requires more DNA than is normally available, linker-amplified shotgun libraries (LASLs), which is prohibitively low throughput, and whole-genome amplification, which is significantly biased and thus non-quantitative. Here, we adapt the LASL approach to next generation sequencing by offering an alternate polymerase for challenging samples, developing a more efficient sizing step, integrating a ‘reconditioning PCR’ step to increase yield and minimize late-cycle PCR artefacts, and empirically documenting the quantitative capability of the optimized method with both laboratory isolate and wild community viral DNA. Our optimized linker amplification method requires as little as 1 pg of DNA and is the most precise and accurate available, with G + C content amplification biases less than 1.5-fold, even for complex samples as diverse as a wild virus community. While optimized here for 454 sequencing, this linker amplification method can be used to prepare metagenomics libraries for sequencing with next-generation platforms, including Illumina and Ion Torrent, the first of which we tested and present data for here. PMID:22713159

  16. Thermodynamically Guided Synthesis of Mixed-Linker Zr-MOFs with Enhanced Tunability.

    PubMed

    Yuan, Shuai; Qin, Jun-Sheng; Zou, Lanfang; Chen, Ying-Pin; Wang, Xuan; Zhang, Qiang; Zhou, Hong-Cai

    2016-05-25

    Guided by thermodynamics, we have synthesized two mixed-linker zirconium-based metal-organic frameworks (Zr-MOFs), namely, PCN-133 and PCN-134. Both of them possess a layer-pillar structure, in which the connection between Zr6 clusters and primary BTB linkers form a (3,6)-connected kdg layer that is further extended into 3D frameworks by auxiliary DCDPS/TCPP linkers (BTB = benzene tribenzoate, DCDPS = 4,4'-dicarboxydiphenyl sulfone, TCPP = tetrakis(4-carboxyphenyl)porphyrin). PCN-134 demonstrates high porosity (N2 uptake of 717 cm(3)·g(-1) and BET surface area of 1946 cm(2)·g(-1)) and excellent chemical stability in aqueous solutions with pH values ranging from 0 to 13. More importantly, PCN-134 tolerates the partial absence of auxiliary linkers leading to structural defects during the assembly process while preserving its framework integrity. Furthermore, the defect density can be systematically controlled by tuning the occupancy of the auxiliary linker, which in turn affects the MOF properties. For instance, the dichromate uptake of PCN-134 is tuned by adjusting the BTB/TCPP ratios, which gives rise to an efficient dichromate absorbent when the TCPP molar ratio in linkers is set as 22%. In addition, the photocatalytic reduction of Cr(VI) in aqueous solution was also performed by PCN-134-22%TCPP which exhibits excellent catalytic activity. This work not only opens up a new synthetic route toward mixed-linker MOFs, but also provides tunable control of MOF defects and, in turn, the properties. PMID:27151517

  17. Common Schools for Common Education.

    ERIC Educational Resources Information Center

    Callan, Eamonn

    1995-01-01

    A vision of common education for citizens of a liberal democracy warrants faith in common schools as an instrument of social good. Some kinds of separate schooling are not inconsistent with common schooling and are even desirable. Equal respect, as defined by J. Rawls, is a basis for common education. (SLD)

  18. Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome.

    PubMed

    Öztürk, Mehmet Ali; Pachov, Georgi V; Wade, Rebecca C; Cojocaru, Vlad

    2016-08-19

    Linker histones are essential for DNA compaction in chromatin. They bind to nucleosomes in a 1:1 ratio forming chromatosomes. Alternative configurations have been proposed in which the globular domain of the linker histone H5 (gH5) is positioned either on- or off-dyad between the nucleosomal and linker DNAs. However, the dynamic pathways of chromatosome assembly remain elusive. Here, we studied the conformational plasticity of gH5 in unbound and off-dyad nucleosome-bound forms with classical and accelerated molecular dynamics simulations. We find that the unbound gH5 converts between open and closed conformations, preferring the closed form. However, the open gH5 contributes to a more rigid chromatosome and restricts the motion of the nearby linker DNA through hydrophobic interactions with thymidines. Moreover, the closed gH5 opens and reorients in accelerated simulations of the chromatosome. Brownian dynamics simulations of chromatosome assembly, accounting for a range of amplitudes of nucleosome opening and different nucleosome DNA sequences, support the existence of both on- and off-dyad binding modes of gH5 and reveal alternative, sequence and conformation-dependent chromatosome configurations. Taken together, these findings suggest that the conformational dynamics of linker histones and nucleosomes facilitate alternative chromatosome configurations through an interplay between induced fit and conformational selection. PMID:27270081

  19. Effect of Linker Structure on Salicylic Acid-Derived Poly(anhydride–esters)

    PubMed Central

    Prudencio, Almudena; Schmeltzer, Robert C.; Uhrich, Kathryn E.

    2013-01-01

    A series of salicylic acid-derived poly(anhydride–esters) were synthesized by melt polym erization methods, in which the structures of the molecule (“linker”) linking together the two salicylic acids were varied. To determine the relationship between the linker and the physical properties of the corresponding poly(anhydride–ester), several linkers were evaluated including linear aliphatic, aromatic, and aliphatic branched structures. For the linear aliphatic linkers, higher molecular weights were obtained with longer linear alkyl chains. The most sterically hindered linkers yielded lower molecular weight polymers. The thermal decomposition temperature increased with the alkyl chain length, but the glass transition temperature decreased, due to the enhanced flexibility of the polymer. The highest glass transition temperatures were obtained by using aromatic linkers as a result of increased π–π interactions. Water contact angles determined the relative hydrophobicity of the polymers, which correlated to hydrolytic degradation rates; i.e., the highest contact angle values yielded the slowest degrading polymers. PMID:23976793

  20. The measles virus phosphoprotein interacts with the linker domain of STAT1

    SciTech Connect

    Devaux, Patricia Priniski, Lauren; Cattaneo, Roberto

    2013-09-15

    The measles virus (MV) phosphoprotein (P) and V proteins block the interferon (IFN) response by impeding phosphorylation of the signal transducer and activator of transcription 1 (STAT1) by the Janus kinase 1 (JAK1). We characterized how STAT1 mutants interact with P and JAK1 phosphorylation. Certain mutants of the linker, the Src-homology 2 domain (SH2), or the transactivation domain had reduced or abolished phosphorylation through JAK1 after IFN treatment. Other mutants, mainly localized in the linker, failed to interact with P as documented by the lack of interference with nuclear translocation. Thus the functional footprint of P on STAT1 localizes mainly to the linker domain; there is also some overlap with the STAT1 phosphorylation functional footprint on the SH2 domain. Based on these observations, we discuss how the MV-P might operate to inhibit the JAK/STAT pathway. - Highlights: • Residue in the linker and SH2 domains of STAT1 are important for MV-P interaction. • Residue in the linker and SH2 domains of STAT1 are important for STAT1 phosphorylation. • Residues interferring with both functions have similar location on STAT1. • The viral P and V proteins may operate in concert to inhibit the JAK/STAT pathway.

  1. Mechanically Interlocked Linkers inside Metal-Organic Frameworks: Effect of Ring Size on Rotational Dynamics.

    PubMed

    Vukotic, V Nicholas; O'Keefe, Christopher A; Zhu, Kelong; Harris, Kristopher J; To, Christine; Schurko, Robert W; Loeb, Stephen J

    2015-08-01

    A series of metal-organic framework (MOF) materials has been prepared, each containing a mechanically interlocked molecule (MIM) as the linker and a copper(II) paddlewheel as the secondary building unit (SBU). The MIM linkers are [2]rotaxanes with varying sizes of crown ether macrocycles ([22]crown-6, 22C6; [24]crown-6, 24C6; [26]crown-6, 26C6; benzo[24]crown-6, B24C6) and an anilinium-based axle containing four carboxylate donor groups. Herein, the X-ray structures of MOFs UWCM-1 (no crown) and UWDM-1(22) are compared and demonstrate the effect of including a macrocycle around the axle of the linker. The rotaxane linkers are linear and result in nbo-type MOFs with void space that allows for motion of the interlocked macrocycle inside the MOF pores, while the macrocycle-free linker is bent and yields a MOF with a novel 12-connected bcc structure. Variable temperature (2)H solid-state nuclear magnetic resonance showed that the macrocycles in UWDM-1(22), UWDM-1(24), and UWDM-1(B24) undergo different degrees and rates of rotation depending on the size and shape of the macrocycle. PMID:26175343

  2. Formulation of an experimental substructure model using a Craig-Bampton based transmission simulator

    DOE PAGESBeta

    Kammer, Daniel C.; Allen, Matthew S.; Mayes, Randall L.

    2015-09-26

    An experimental–analytical substructuring is attractive when there is motivation to replace one or more system subcomponents with an experimental model. This experimentally derived substructure can then be coupled to finite element models of the rest of the structure to predict the system response. The transmission simulator method couples a fixture to the component of interest during a vibration test in order to improve the experimental model for the component. The transmission simulator is then subtracted from the tested system to produce the experimental component. This method reduces ill-conditioning by imposing a least squares fit of constraints between substructure modal coordinatesmore » to connect substructures, instead of directly connecting physical interface degrees of freedom. This paper presents an alternative means of deriving the experimental substructure model, in which a Craig–Bampton representation of the transmission simulator is created and subtracted from the experimental measurements. The corresponding modal basis of the transmission simulator is described by the fixed-interface modes, rather than free modes that were used in the original approach. Moreover, these modes do a better job of representing the shape of the transmission simulator as it responds within the experimental system, leading to more accurate results using fewer modes. The new approach is demonstrated using a simple finite element model based example with a redundant interface.« less

  3. Formulation of an experimental substructure model using a Craig-Bampton based transmission simulator

    SciTech Connect

    Kammer, Daniel C.; Allen, Matthew S.; Mayes, Randall L.

    2015-09-26

    An experimental–analytical substructuring is attractive when there is motivation to replace one or more system subcomponents with an experimental model. This experimentally derived substructure can then be coupled to finite element models of the rest of the structure to predict the system response. The transmission simulator method couples a fixture to the component of interest during a vibration test in order to improve the experimental model for the component. The transmission simulator is then subtracted from the tested system to produce the experimental component. This method reduces ill-conditioning by imposing a least squares fit of constraints between substructure modal coordinates to connect substructures, instead of directly connecting physical interface degrees of freedom. This paper presents an alternative means of deriving the experimental substructure model, in which a Craig–Bampton representation of the transmission simulator is created and subtracted from the experimental measurements. The corresponding modal basis of the transmission simulator is described by the fixed-interface modes, rather than free modes that were used in the original approach. Moreover, these modes do a better job of representing the shape of the transmission simulator as it responds within the experimental system, leading to more accurate results using fewer modes. The new approach is demonstrated using a simple finite element model based example with a redundant interface.

  4. An algebraic sub-structuring method for large-scale eigenvaluecalculation

    SciTech Connect

    Yang, C.; Gao, W.; Bai, Z.; Li, X.; Lee, L.; Husbands, P.; Ng, E.

    2004-05-26

    We examine sub-structuring methods for solving large-scalegeneralized eigenvalue problems from a purely algebraic point of view. Weuse the term "algebraic sub-structuring" to refer to the process ofapplying matrix reordering and partitioning algorithms to divide a largesparse matrix into smaller submatrices from which a subset of spectralcomponents are extracted and combined to provide approximate solutions tothe original problem. We are interested in the question of which spectralcomponentsone should extract from each sub-structure in order to producean approximate solution to the original problem with a desired level ofaccuracy. Error estimate for the approximation to the small esteigen pairis developed. The estimate leads to a simple heuristic for choosingspectral components (modes) from each sub-structure. The effectiveness ofsuch a heuristic is demonstrated with numerical examples. We show thatalgebraic sub-structuring can be effectively used to solve a generalizedeigenvalue problem arising from the simulation of an acceleratorstructure. One interesting characteristic of this application is that thestiffness matrix produced by a hierarchical vector finite elements schemecontains a null space of large dimension. We present an efficient schemeto deflate this null space in the algebraic sub-structuringprocess.

  5. Metrics for diagnosing negative mass and stiffness when uncoupling experimental and analytical substructures.

    SciTech Connect

    Allen, Matthew S.; Kammer, Daniel C.; Mayes, Randall Lee

    2010-10-01

    Recently, a new substructure coupling/uncoupling approach has been introduced, called Modal Constraints for Fixture and Subsystem (MCFS) [Allen, Mayes, & Bergman, Journal of Sound and Vibration, vol. 329, 2010]. This method reduces ill-conditioning by imposing constraints on substructure modal coordinates instead of the physical interface coordinates. The experimental substructure is tested in a free-free configuration, and the interface is exercised by attaching a flexible fixture. An analytical representation of the fixture is then used to subtract its effects in order to create an experimental model for the subcomponent of interest. However, it has been observed that indefinite mass and stiffness matrices can be obtained for the experimental substructure in some situations. This paper presents two simple metrics that can be used by the analyst to determine the cause of indefinite mass or stiffness matrices after substructure uncoupling. The metrics rank the experimental and fixture modes based upon their contribution to offending negative eigenvalues. Once the troublesome modes have been identified, they can be inspected and often reveal why the mass has become negative. Two examples are presented to demonstrate the metrics and to illustrate the physical phenomena that they reveal.

  6. Efficient substructure searching of large chemical libraries: the ABCD chemical cartridge.

    PubMed

    Agrafiotis, Dimitris K; Lobanov, Victor S; Shemanarev, Maxim; Rassokhin, Dmitrii N; Izrailev, Sergei; Jaeger, Edward P; Alex, Simson; Farnum, Michael

    2011-12-27

    Efficient substructure searching is a key requirement for any chemical information management system. In this paper, we describe the substructure search capabilities of ABCD, an integrated drug discovery informatics platform developed at Johnson & Johnson Pharmaceutical Research & Development, L.L.C. The solution consists of several algorithmic components: 1) a pattern mapping algorithm for solving the subgraph isomorphism problem, 2) an indexing scheme that enables very fast substructure searches on large structure files, 3) the incorporation of that indexing scheme into an Oracle cartridge to enable querying large relational databases through SQL, and 4) a cost estimation scheme that allows the Oracle cost-based optimizer to generate a good execution plan when a substructure search is combined with additional constraints in a single SQL query. The algorithm was tested on a public database comprising nearly 1 million molecules using 4,629 substructure queries, the vast majority of which were submitted by discovery scientists over the last 2.5 years of user acceptance testing of ABCD. 80.7% of these queries were completed in less than a second and 96.8% in less than ten seconds on a single CPU, while on eight processing cores these numbers increased to 93.2% and 99.7%, respectively. The slower queries involved extremely generic patterns that returned the entire database as screening hits and required extensive atom-by-atom verification. PMID:22035187

  7. DARK MATTER SUBSTRUCTURE DETECTION USING SPATIALLY RESOLVED SPECTROSCOPY OF LENSED DUSTY GALAXIES

    SciTech Connect

    Hezaveh, Yashar; Holder, Gilbert; Dalal, Neal; Kuhlen, Michael; Marrone, Daniel; Murray, Norman; Vieira, Joaquin

    2013-04-10

    We investigate how strong lensing of dusty, star-forming galaxies (DSFGs) by foreground galaxies can be used as a probe of dark matter halo substructure. We find that spatially resolved spectroscopy of lensed sources allows dramatic improvements to measurements of lens parameters. In particular, we find that modeling of the full, three-dimensional (angular position and radial velocity) data can significantly facilitate substructure detection, increasing the sensitivity of observables to lower mass subhalos. We carry out simulations of lensed dusty sources observed by early ALMA (Cycle 1) and use a Fisher matrix analysis to study the parameter degeneracies and mass detection limits of this method. We find that even with conservative assumptions, it is possible to detect galactic dark matter subhalos of {approx}10{sup 8} M{sub Sun} with high significance in most lensed DSFGs. Specifically, we find that in typical DSFG lenses, there is a {approx}55% probability of detecting a substructure with M > 10{sup 8} M{sub Sun} with more than 5{sigma} detection significance in each lens, if the abundance of substructure is consistent with previous lensing results. The full ALMA array, with its significantly enhanced sensitivity and resolution, should improve these estimates considerably. Given the sample of {approx}100 lenses provided by surveys such as the South Pole Telescope, our understanding of dark matter substructure in typical galaxy halos is poised to improve dramatically over the next few years.

  8. AN EXAMINATION OF THE OPTICAL SUBSTRUCTURE OF GALAXY CLUSTERS HOSTING RADIO SOURCES

    SciTech Connect

    Wing, Joshua D.; Blanton, Elizabeth L.

    2013-04-20

    Using radio sources from the Faint Images of the Radio Sky at Twenty-cm survey, and optical counterparts in the Sloan Digital Sky Survey, we have identified a large number of galaxy clusters. The radio sources within these clusters are driven by active galactic nuclei, and our cluster samples include clusters with bent, and straight, double-lobed radio sources. We also included a single-radio-component comparison sample. We examine these galaxy clusters for evidence of optical substructure, testing the possibility that bent double-lobed radio sources are formed as a result of large-scale cluster mergers. We use a suite of substructure analysis tools to determine the location and extent of substructure visible in the optical distribution of cluster galaxies, and compare the rates of substructure in clusters with different types of radio sources. We found no preference for significant substructure in clusters hosting bent double-lobed radio sources compared to those with other types of radio sources.

  9. Formulation of an experimental substructure model using a Craig-Bampton based transmission simulator

    NASA Astrophysics Data System (ADS)

    Kammer, Daniel C.; Allen, Mathew S.; Mayes, Randy L.

    2015-12-01

    Experimental-analytical substructuring is attractive when there is motivation to replace one or more system subcomponents with an experimental model. This experimentally derived substructure can then be coupled to finite element models of the rest of the structure to predict the system response. The transmission simulator method couples a fixture to the component of interest during a vibration test in order to improve the experimental model for the component. The transmission simulator is then subtracted from the tested system to produce the experimental component. The method reduces ill-conditioning by imposing a least squares fit of constraints between substructure modal coordinates to connect substructures, instead of directly connecting physical interface degrees of freedom. This paper presents an alternative means of deriving the experimental substructure model, in which a Craig-Bampton representation of the transmission simulator is created and subtracted from the experimental measurements. The corresponding modal basis of the transmission simulator is described by the fixed-interface modes, rather than free modes that were used in the original approach. These modes do a better job of representing the shape of the transmission simulator as it responds within the experimental system, leading to more accurate results using fewer modes. The new approach is demonstrated using a simple finite element model based example with a redundant interface.

  10. Common Cold

    MedlinePlus

    ... News & Events Volunteer NIAID > Health & Research Topics > Common Cold Skip Website Tools Website Tools Print this page ... Help people who are suffering from the common cold by volunteering for NIAID clinical studies on ClinicalTrials. ...

  11. Common Cold

    MedlinePlus

    ... coughing - everyone knows the symptoms of the common cold. It is probably the most common illness. In ... people in the United States suffer 1 billion colds. You can get a cold by touching your ...

  12. Assembly into chromatin and subtype-specific transcriptional effects of exogenous linker histones directly introduced into a living Physarum cell.

    PubMed

    Thiriet, C; Hayes, J J

    2001-03-01

    The apparent diversity of linker histone subtypes may be related to their specific roles in defining functional states of chromatin in vivo. We have developed a novel method to study constitutive peptides throughout the cell cycle and have demonstrated that an exogenous linker histone could be introduced into a living cell of the slime mold Physarum polycephalum. Here, we have used this method to assess the functional differences between three somatic linker histone subtypes in vivo, and to demonstrate the general applicability of this method. Exogenous linker histone proteins H1 degrees, H5 and H1 were directly absorbed into living cell segments of the naturally synchronous Physarum macroplasmodia at precise cell cycle stages. Fluorescence microscopy, native nucleoprotein gels and immunoblotting of nuclei and chromatin with subtype-specific antibodies revealed that exogenous linker histones were efficiently transported into nuclei and were integrated into chromatin. The immunoreactivity of a preparation of anti-H1 degrees antibodies that are blocked from binding to specific H1 degrees epitopes in native chromatin indicates that the exogenous linker histones were similarly associated into Physarum chromatin. Interestingly, linker histones were found to be less stably associated with Physarum chromatin during S-phase than during G(2)-phase. Furthermore, we show that exogenous linker histones incorporated in early G(2)-phase inhibited transcription and that the level of inhibition correlates with the apparent role of the linker histone subtype in regulating transcription in cells where it normally occurs. PMID:11181179

  13. Linker design for the modular assembly of multifunctional and targeted platinum(ii)-containing anticancer agents.

    PubMed

    Ding, S; Bierbach, U

    2016-08-16

    A versatile and efficient modular synthetic platform was developed for assembling multifunctional conjugates and targeted forms of platinum-(benz)acridines, a class of highly cytotoxic DNA-targeted hybrid agents. The synthetic strategy involved amide coupling between succinyl ester-modified platinum compounds (P1, P2) and a set of 11 biologically relevant primary and secondary amines (N1-N11). To demonstrate the feasibility and versatility of the approach, a structurally and functionally diverse range of amines was introduced. These include biologically active molecules, such as rucaparib (a PARP inhibitor), E/Z-endoxifen (an estrogen receptor antagonist), and a quinazoline-based tyrosine kinase inhibitor. Micro-scale reactions in Eppendorf tubes or on 96-well plates were used to screen for optimal coupling conditions in DMF solution with carbodiimide-, uronium-, and phosphonium-based compounds, as well as other common coupling reagents. Reactions with the phosphonium-based coupling reagent PyBOP produced the highest yields and gave the cleanest conversions. Furthermore, it was demonstrated that the chemistry can also be performed in aqueous media and is amenable to parallel synthesis based on multiple consecutive reactions in DMF in a "one-tube" format. In-line LC-MS was used to assess the stability of the conjugates in physiologically relevant buffers. Hydrolysis of the conjugates occurs at the ester moiety and is facilitated by the aquated metal moiety under low-chloride ion conditions. The rate of ester cleavage greatly depends on the nature of the amine component. Potential applications of the linker technology are discussed. PMID:27251881

  14. Synthesis and application of a new cleavable linker for "click"-based affinity chromatography.

    PubMed

    Landi, Felicetta; Johansson, Conny M; Campopiano, Dominic J; Hulme, Alison N

    2010-01-01

    A new chemically-cleavable linker has been synthesised for the affinity-independent elution of biomolecules by classical affinity chromatography. This azo-based linker is shown to couple efficiently with "click" derivatised ligands such as biotin propargyl amide through a copper(I)-catalysed Huisgen 1,3-dipolar cycloaddition reaction. Binding to Affi-Gel matrices displaying ligands coupled to the new linker is both efficient and selective. The captured material may be readily released from the resin upon treatment with sodium dithionite. These mild elution conditions have allowed for the efficient isolation of the affinity partner from complex protein mixtures such as those found in fetal bovine serum. PMID:20024132

  15. Wheat Gluten Blends with Maleic Anhydride-Functionalized Polyacrylate Cross-Linkers for Improved Properties.

    PubMed

    Diao, Cheng; Xia, Hongwei; Parnas, Richard S

    2015-10-14

    A family of polyacrylate-based cross-linkers was synthesized to maximize the toughness of high Tg, high modulus wheat gluten blends in the glassy state. Mechanical testing and damping measurements were conducted to provide an example where the work of fracture and strength of the blend substantially exceeds polystyrene while maintaining flexure stiffness in excess of 3 GPa. The new rubbery cross-linkers, polymethyl acrylate-co-maleic anhydride and polyethyl acrylate-co-maleic anhydride, improve WG mechanical properties and reduce water absorption simultaneously. MDSC, FTIR, HPLC, and NMR data confirmed the cross-linking reaction with wheat gluten. Flexural, DMA, and water absorption testing were carried out to characterize the property improvements. DMA was conducted to investigate the relationship between energy damping and mechanical property improvement. If the cross-linker damping temperature is close to the testing temperature, the entire sample exhibits high damping, toughness, and strength. PMID:26394179

  16. Development of a Multifunctional Benzophenone Linker for Peptide Stapling and Photoaffinity Labelling.

    PubMed

    Wu, Yuteng; Olsen, Lasse B; Lau, Yu Heng; Jensen, Claus Hatt; Rossmann, Maxim; Baker, Ysobel R; Sore, Hannah F; Collins, Súil; Spring, David R

    2016-04-15

    Photoaffinity labelling is a useful method for studying how proteins interact with ligands and biomolecules, and can help identify and characterise new targets for the development of new therapeutics. We present the design and synthesis of a novel multifunctional benzophenone linker that serves as both a photo-crosslinking motif and a peptide stapling reagent. Using double-click stapling, we attached the benzophenone to the peptide via the staple linker, rather than by modifying the peptide sequence with a photo-crosslinking amino acid. When applied to a p53-derived peptide, the resulting photoreactive stapled peptide was able to preferentially crosslink with MDM2 in the presence of competing protein. This multifunctional linker also features an extra alkyne handle for downstream applications such as pull-down assays, and can be used to investigate the target selectivity of stapled peptides. PMID:26919579

  17. Development of a Multifunctional Benzophenone Linker for Peptide Stapling and Photoaffinity Labelling

    PubMed Central

    Wu, Yuteng; Olsen, Lasse B.; Lau, Yu Heng; Jensen, Claus Hatt; Rossmann, Maxim; Baker, Ysobel R.; Sore, Hannah F.; Collins, Súil

    2016-01-01

    Abstract Photoaffinity labelling is a useful method for studying how proteins interact with ligands and biomolecules, and can help identify and characterise new targets for the development of new therapeutics. We present the design and synthesis of a novel multifunctional benzophenone linker that serves as both a photo‐crosslinking motif and a peptide stapling reagent. Using double‐click stapling, we attached the benzophenone to the peptide via the staple linker, rather than by modifying the peptide sequence with a photo‐crosslinking amino acid. When applied to a p53‐derived peptide, the resulting photoreactive stapled peptide was able to preferentially crosslink with MDM2 in the presence of competing protein. This multifunctional linker also features an extra alkyne handle for downstream applications such as pull‐down assays, and can be used to investigate the target selectivity of stapled peptides. PMID:26919579

  18. Smart linkers in polymer-drug conjugates for tumor-targeted delivery.

    PubMed

    Chang, Minglu; Zhang, Fang; Wei, Ting; Zuo, Tiantian; Guan, Yuanyuan; Lin, Guimei; Shao, Wei

    2016-07-01

    To achieve effective chemotherapy, many types of drug delivery systems have been developed for the specific environments in tumor tissues. Polymer-drug conjugates are increasingly used in tumor therapy due to several significant advantages over traditional delivery systems. In the fabrication of polymer-drug conjugates, a smart linker is an important component that joins two fragments or molecules together and can be cleared by a specific stimulus, which results in targeted drug delivery and controlled release. By regulating the conjugation between the drug and the nanocarriers, stimulus-sensitive systems based on smart linkers can offer high payloads, certified stability, controlled release and targeted delivery. In this review, we summarize the current state of smart linkers (e.g. disulfide, hydrazone, peptide, azo) used recently in various polymer-drug conjugate-based delivery systems with a primary focus on their sophisticated design principles and drug delivery mechanisms as well as in vivo processes. PMID:26560242

  19. Enhanced tumor retention of radioiodinated anti-epidermal growth factor receptor antibody using novel bifunctional iodination linker for radioimmunotherapy.

    PubMed

    Kim, Eun Jung; Kim, Byoung Soo; Choi, Dan Bee; Chi, Sung-Gil; Choi, Tae Hyun

    2016-06-01

    Radioimmunotherapy (RIT) uses an antibody labeled with a radionuclide to deliver cytotoxic radiation to a target tumor cells. Radioiodine is most commonly employed to prepare radiolabeled proteins (antibodies, peptides) for in vitro and in vivo applications. A major shortcoming of radioiodinated proteins prepared by direct labeling methods is their deiodination in vivo. For the preparation of more stable radioiodinated antibodies, we developed a new linker (N-(4-isothiocyanatobenzyl)-2-(3-(tributylstannyl)phenyl) acetamide (IBPA). This study evaluated the usefulness of IBPA as a linker for the stable radioiodinated internalizing antibody, cetuximab. Directly labeled cetuximab ([125I]-cetuximab) was prepared by the chloramine T method. To prepare indirectly labeled cetuximab using IBPA ([125I]-IBPA-cetuximab), IBPA was radioiodinated using chloramine-T to give N-(4-isothiocyanatobenzyl)-2-(3-[125I]phenyl)acetamide ([125I]‑IBPA), which was purified by high performance liquid chromatography. [125I]-IBPA was then conjugated to cetuximab. In vitro target binding and internalizing assays were performed in PC9, LS174T, and FaDu cell lines. In vivo planar images were obtained using an Inveon SPECT scanner 3, 24, 48, and 168 h after i.v. injection of [125I]-cetuximab or [125I]-IBPA-cetuximab in athymic mice bearing LS174T tumor xenografts. Specific binding and internalized radioactivity of [125I]-IBPA-cetuximab were higher than those of [125I]-cetuximab in PC9, LS174T, and FaDu cell lines. In planar images scant radioactivity was evident in thyroid glands after injection of [125I]-IBPA-cetuximab, while a high level of radioactivity was present in thyroid glands after injection of [125I]-cetuximab. Tumor uptake value of [125I]-IBPA-cetuximab was higher than that of [125I]-cetuximab for up to 168 h. [125I]-IBPA-cetuximab is stable and resistant to deiodination in vivo. IBPA is a promising bi-functional linker for radioiodination of internalizing monoclonal antibodies

  20. Enhanced tumor retention of radioiodinated anti-epidermal growth factor receptor antibody using novel bifunctional iodination linker for radioimmunotherapy

    PubMed Central

    KIM, EUN JUNG; KIM, BYOUNG SOO; CHOI, DAN BEE; CHI, SUNG-GIL; CHOI, TAE HYUN

    2016-01-01

    Radioimmunotherapy (RIT) uses an antibody labeled with a radionuclide to deliver cytotoxic radiation to a target tumor cells. Radioiodine is most commonly employed to prepare radiolabeled proteins (antibodies, peptides) for in vitro and in vivo applications. A major shortcoming of radioiodinated proteins prepared by direct labeling methods is their deiodination in vivo. For the preparation of more stable radioiodinated antibodies, we developed a new linker (N-(4-isothiocyanatobenzyl)-2-(3-(tributylstannyl)phenyl) acetamide (IBPA). This study evaluated the usefulness of IBPA as a linker for the stable radioiodinated internalizing antibody, cetuximab. Directly labeled cetuximab ([125I]-cetuximab) was prepared by the chloramine T method. To prepare indirectly labeled cetuximab using IBPA ([125I]-IBPA-cetuximab), IBPA was radioiodinated using chloramine-T to give N-(4-isothiocyanatobenzyl)-2-(3-[125I]phenyl)acetamide ([125I]-IBPA), which was purified by high performance liquid chromatography. [125I]-IBPA was then conjugated to cetuximab. In vitro target binding and internalizing assays were performed in PC9, LS174T, and FaDu cell lines. In vivo planar images were obtained using an Inveon SPECT scanner 3, 24, 48, and 168 h after i.v. injection of [125I]-cetuximab or [125I]-IBPA-cetuximab in athymic mice bearing LS174T tumor xenografts. Specific binding and internalized radioactivity of [125I]-IBPA-cetuximab were higher than those of [125I]-cetuximab in PC9, LS174T, and FaDu cell lines. In planar images scant radioactivity was evident in thyroid glands after injection of [125I]-IBPA-cetuximab, while a high level of radioactivity was present in thyroid glands after injection of [125I]-cetuximab. Tumor uptake value of [125I]-IBPA-cetuximab was higher than that of [125I]-cetuximab for up to 168 h. [125I]-IBPA-cetuximab is stable and resistant to deiodination in vivo. IBPA is a promising bi-functional linker for radioiodination of internalizing monoclonal antibodies for in

  1. Initial test results from FHWA project Dynamic Bridge Substructure Evaluation and Monitoring System

    NASA Astrophysics Data System (ADS)

    Aouad, Marwan F.; Olson, Larry D.; Liu, Ming

    1998-03-01

    The FHWA project 'Dynamic Bridge Substructure Evaluation and Monitoring System' was conceived to use dynamic characteristics of the bridge substructure to determine the condition of the foundation and to identify the type of the underground substructure (deep or shallow foundation). The determination of the foundation condition will be used to quantify losses in foundation stiffness caused by seismic and scour events. The dynamic characteristics of natural frequencies and mode shapes are extracted from the experimental data and compared with the computer simulation results. The computer simulations are based on a 3-D finite element modeling with Super-Soil-Structural (SSS) elements. The stiffness and mass of these Super-Soil-Structural elements are indicative of the foundation conditions which may be quantified by structural parameter identification techniques. Discussed in this paper are experimental test setups and initial test results for three kinds of foundation conditions at the Trinity River Bridge in Liberty County, Texas.

  2. Theory and Simulations of Refractive Substructure in Resolved Scatter-broadened Images

    NASA Astrophysics Data System (ADS)

    Johnson, Michael D.; Gwinn, Carl R.

    2015-06-01

    At radio wavelengths, scattering in the interstellar medium distorts the appearance of astronomical sources. Averaged over a scattering ensemble, the result is a blurred image of the source. However, Narayan & Goodman and Goodman & Narayan showed that for an incomplete average, scattering introduces refractive substructure in the image of a point source that is both persistent and wideband. We show that this substructure is quenched but not smoothed by an extended source. As a result, when the scatter-broadening is comparable to or exceeds the unscattered source size, the scattering can introduce spurious compact features into images. In addition, we derive efficient strategies to numerically compute realistic scattered images, and we present characteristic examples from simulations. Our results show that refractive substructure is an important consideration for ongoing missions at the highest angular resolutions, and we discuss specific implications for RadioAstron and the Event Horizon Telescope.

  3. Design studies for the transmission simulator method of experimental dynamic substructuring.

    SciTech Connect

    Mayes, Randall Lee; Arviso, Michael

    2010-05-01

    In recent years, a successful method for generating experimental dynamic substructures has been developed using an instrumented fixture, the transmission simulator. The transmission simulator method solves many of the problems associated with experimental substructuring. These solutions effectively address: (1) rotation and moment estimation at connection points; (2) providing substructure Ritz vectors that adequately span the connection motion space; and (3) adequately addressing multiple and continuous attachment locations. However, the transmission simulator method may fail if the transmission simulator is poorly designed. Four areas of the design addressed here are: (1) designating response sensor locations; (2) designating force input locations; (3) physical design of the transmission simulator; and (4) modal test design. In addition to the transmission simulator design investigations, a review of the theory with an example problem is presented.

  4. Cell biology of Smad2/3 linker region phosphorylation in vascular smooth muscle.

    PubMed

    Rezaei, Hossein B; Kamato, Danielle; Ansari, Ghazaleh; Osman, Narin; Little, Peter J

    2012-08-01

    The transforming growth factor (TGF)-β superfamily of ligands regulates a diverse set of cellular functions. Transforming growth factor-β induces its biological effects through Type I and Type II transmembrane receptors that have serine/threonine kinase activities and weak tyrosine kinase activity. In vascular smooth muscle, TGF-β binds to the TGF-β Type II receptor (TβRII) at the cell surface, recruiting the Type I receptor (TβRI) to form a heterocomplex. Consequently, after phosphorylation and activation of TβRI, the transcription factors receptor activated (R-) Smad2 and Smad3 are recruited and activated through phosphorylation of C terminal residues. Overall, Smad2/3 and co-Smad4 have similar structures consisting of three regions an N-terminal MH1 domain, a C-terminal MH2 domain and a central linker region. Phosphorylation of the Smad linker region appears to have an important role in the regulation of Smad activity and function. The mitogen-activated protein kinase (MAPK) family, CDK2, CDK4 and calcium-calmodulin dependent kinase are the main kinases that phosphorylate sites in the linker region. The role of the linker region includes enabling the formation of Smad homo-oligomers and provision of phosphorylation sites for MAPK and other kinases. In some instances, linker region phosphorylation regulates the inhibition of the nuclear translocation of Smads. In the present review, we describe TGF-β signalling through Smad2/3 and the importance of the linker region in the regulation and expression of genes induced by TGF-β superfamily ligands in the context of vascular smooth muscle. PMID:21883378

  5. The Centrosomal Linker and Microtubules Provide Dual Levels of Spatial Coordination of Centrosomes

    PubMed Central

    Panic, Marko; Hata, Shoji; Neuner, Annett; Schiebel, Elmar

    2015-01-01

    The centrosome is the principal microtubule organizing center in most animal cells. It consists of a pair of centrioles surrounded by pericentriolar material. The centrosome, like DNA, duplicates exactly once per cell cycle. During interphase duplicated centrosomes remain closely linked by a proteinaceous linker. This centrosomal linker is composed of rootletin filaments that are anchored to the centrioles via the protein C-Nap1. At the onset of mitosis the linker is dissolved by Nek2A kinase to support the formation of the bipolar mitotic spindle. The importance of the centrosomal linker for cell function during interphase awaits characterization. Here we assessed the phenotype of human RPE1 C-Nap1 knockout (KO) cells. The absence of the linker led to a modest increase in the average centrosome separation from 1 to 2.5 μm. This small impact on the degree of separation is indicative of a second level of spatial organization of centrosomes. Microtubule depolymerisation or stabilization in C-Nap1 KO cells dramatically increased the inter-centrosomal separation (> 8 μm). Thus, microtubules position centrosomes relatively close to one another in the absence of linker function. C-Nap1 KO cells had a Golgi organization defect with a two-fold expansion of the area occupied by the Golgi. When the centrosomes of C-Nap1 KO cells showed considerable separation, two spatially distinct Golgi stacks could be observed. Furthermore, migration of C-Nap1 KO cells was slower than their wild type RPE1 counterparts. These data show that the spatial organization of centrosomes is modulated by a combination of centrosomal cohesion and microtubule forces. Furthermore a modest increase in centrosome separation has major impact on Golgi organization and cell migration. PMID:26001056

  6. Pyrene-terminated phenylenethynylene rigid linkers anchored to metal oxide nanoparticles.

    PubMed

    Taratula, Olena; Rochford, Jonathan; Piotrowiak, Piotr; Galoppini, Elena; Carlisle, Rachael A; Meyer, Gerald J

    2006-08-17

    Phenylenethynylene (PE) rigid linkers (para and meta) were used to anchor pyrene to the surface of TiO2 (anatase) and ZrO2 nanoparticle thin films through the two COOH groups of an isophthalic acid (Ipa) unit. Four chromophore-linker models were studied in solution and bound. Two are novel meta-pyrene-PE linker systems: dimethyl 5-(3-(1-pyrenylethynyl)phenylethynyl)-isophthalate, carrying one pyrene, and dimethyl 5-(bis-3,5-(1-pyrenylethynyl)phenylethynyl)-isophthalate, carrying two. These were compared with para rigid-rods dimethyl 5-(1-pyrenylethynyl)isophthalate and dimethyl 5-(4-(1-pyrenylethynyl)phenylethynyl)-isophthalate, each carrying one pyrene but varying in length. The length of the PE linkers and the para or meta substitution influence the photophysical properties of the compounds. The extinction coefficient increased, and the long wavelength absorbance of the pyrene chromophore was shifted to the red with increasing conjugation. Compared to unsubstituted pyrene, the pyrene-linker systems were characterized by short fluorescence lifetimes (tau approximately 2 ns in tetrahydrofuran solutions), but quantum yields were close to unity. ZINDO/S CI calculations attribute this effect to a switching in the order of the two lowest-lying singlet states of pyrene. High surface coverages, approximately 10(-8) mol/cm2, and carboxylate binding modes on nanostructured TiO2 films were obtained in all cases. The appearance of a pyrene excimer emission on ZrO2, an insulator, indicates that the pyrene-linker system is closely packed (Py-Py < 4 A) on the surface. The fluorescence emission on TiO2 was completely quenched, consistent with quantitative and rapid electron injection into the semiconductor indicating that the pyrene excimer acts as a sensitizer. Photoelectrochemical studies in regenerative solar cells with I3-/I- as the redox mediator indicated near-quantitative conversion of absorbed photons into an electrical current. PMID:16898719

  7. Population substructure and control selection in genome-wide association studies.

    PubMed

    Yu, Kai; Wang, Zhaoming; Li, Qizhai; Wacholder, Sholom; Hunter, David J; Hoover, Robert N; Chanock, Stephen; Thomas, Gilles

    2008-01-01

    Determination of the relevance of both demanding classical epidemiologic criteria for control selection and robust handling of population stratification (PS) represents a major challenge in the design and analysis of genome-wide association studies (GWAS). Empirical data from two GWAS in European Americans of the Cancer Genetic Markers of Susceptibility (CGEMS) project were used to evaluate the impact of PS in studies with different control selection strategies. In each of the two original case-control studies nested in corresponding prospective cohorts, a minor confounding effect due to PS (inflation factor lambda of 1.025 and 1.005) was observed. In contrast, when the control groups were exchanged to mimic a cost-effective but theoretically less desirable control selection strategy, the confounding effects were larger (lambda of 1.090 and 1.062). A panel of 12,898 autosomal SNPs common to both the Illumina and Affymetrix commercial platforms and with low local background linkage disequilibrium (pair-wise r(2)<0.004) was selected to infer population substructure with principal component analysis. A novel permutation procedure was developed for the correction of PS that identified a smaller set of principal components and achieved a better control of type I error (to lambda of 1.032 and 1.006, respectively) than currently used methods. The overlap between sets of SNPs in the bottom 5% of p-values based on the new test and the test without PS correction was about 80%, with the majority of discordant SNPs having both ranks close to the threshold. Thus, for the CGEMS GWAS of prostate and breast cancer conducted in European Americans, PS does not appear to be a major problem in well-designed studies. A study using suboptimal controls can have acceptable type I error when an effective strategy for the correction of PS is employed. PMID:18596976

  8. An intrinsically disordered linker plays a critical role in bacterial cell division.

    PubMed

    Buske, P J; Mittal, Anuradha; Pappu, Rohit V; Levin, Petra Anne

    2015-01-01

    In bacteria, animals, fungi, and many single celled eukaryotes, division is initiated by the formation of a ring of cytoskeletal protein at the nascent division site. In bacteria, the tubulin-like GTPase FtsZ serves as the foundation for the cytokinetic ring. A conserved feature of FtsZ is an intrinsically disordered peptide known as the C-terminal linker. Chimeric experiments suggest the linker acts as a flexible boom allowing FtsZ to associate with the membrane through a conserved C-terminal domain and also modulates interactions both between FtsZ subunits and between FtsZ and modulatory proteins in the cytoplasm. PMID:25305578

  9. An N-sulfanylethylanilide-based traceable linker for enrichment and selective labelling of target proteins.

    PubMed

    Morisaki, Takuya; Denda, Masaya; Yamamoto, Jun; Tsuji, Daisuke; Inokuma, Tsubasa; Itoh, Kohji; Shigenaga, Akira; Otaka, Akira

    2016-05-25

    An N-sulfanylethylanilide-based traceable linker, developed to facilitate identification of target proteins of bioactive compounds, was introduced into an alkynylated target protein. Subsequent adsorption onto streptavidin beads allowed it to be treated with a cysteine-fluorophore conjugate in the presence of phosphate. This induced the N-S acyl transfer reaction of the N-sulfanylethylanilide unit. The subsequent native chemical ligation of the fluorophore resulted in cleavage of the linker for target elution and fluorescence labelling of the target, allowing it to be distinguished from non-target proteins. PMID:27146590

  10. Impact of metal-alkoxide functionalized linkers on H2 binding: A density functional study

    NASA Astrophysics Data System (ADS)

    Banu, Tahamida; Ghosh, Avik; Das, Abhijit K.

    2016-08-01

    The effect of metal-alkoxide functionalization of different organic linkers on the H2 binding is investigated employing DFT approach. While analyzing the H2 binding interaction of magnesium-alkoxide modified benzene, naphthalene, anthracene and pyrene linkers, we find their comparable affinity toward H2 molecules. Six-member alkoxide ring containing naphthalene and pyrene systems interact with the H2 molecules in a comparatively better way than their five-member analogues. AIM, NBO and LMO-EDA analyses have been performed to comprehend the bonding nature between Mg center and the H2 molecules. Polarization along with the charge transfer interactions play significant role in stabilizing the systems.

  11. An intrinsically disordered linker plays a critical role in bacterial cell division

    PubMed Central

    Buske, P. J.; Mittal, Anuradha; Pappu, Rohit V.; Levin, Petra Anne

    2014-01-01

    In bacteria, animals, fungi, and many single celled eukaryotes, division is initiated by the formation of a ring of cytoskeletal protein at the nascent division site. In bacteria, the tubulin-like GTPase FtsZ serves as the foundation for the cytokinetic ring. A conserved feature of FtsZ is an intrinsically disordered peptide known as the C-terminal linker. Chimeric experiments suggest the linker acts as a flexible boom allowing FtsZ to associate with the membrane through a conserved C-terminal domain and also modulates interactions both between FtsZ subunits and between FtsZ and modulatory proteins in the cytoplasm. PMID:25305578

  12. Substructure based modeling of nickel single crystals cycled at low plastic strain amplitudes

    NASA Astrophysics Data System (ADS)

    Zhou, Dong

    In this dissertation a meso-scale, substructure-based, composite single crystal model is fully developed from the simple uniaxial model to the 3-D finite element method (FEM) model with explicit substructures and further with substructure evolution parameters, to simulate the completely reversed, strain controlled, low plastic strain amplitude cyclic deformation of nickel single crystals. Rate-dependent viscoplasticity and Armstrong-Frederick type kinematic hardening rules are applied to substructures on slip systems in the model to describe the kinematic hardening behavior of crystals. Three explicit substructure components are assumed in the composite single crystal model, namely "loop patches" and "channels" which are aligned in parallel in a "vein matrix," and persistent slip bands (PSBs) connected in series with the vein matrix. A magnetic domain rotation model is presented to describe the reverse magnetostriction of single crystal nickel. Kinematic hardening parameters are obtained by fitting responses to experimental data in the uniaxial model, and the validity of uniaxial assumption is verified in the 3-D FEM model with explicit substructures. With information gathered from experiments, all control parameters in the model including hardening parameters, volume fraction of loop patches and PSBs, and variation of Young's modulus etc. are correlated to cumulative plastic strain and/or plastic strain amplitude; and the whole cyclic deformation history of single crystal nickel at low plastic strain amplitudes is simulated in the uniaxial model. Then these parameters are implanted in the 3-D FEM model to simulate the formation of PSB bands. A resolved shear stress criterion is set to trigger the formation of PSBs, and stress perturbation in the specimen is obtained by several elements assigned with PSB material properties a priori. Displacement increment, plastic strain amplitude control and overall stress-strain monitor and output are carried out in the user

  13. The usage of substructuring analyses in the Get Away Special (GAS) program

    NASA Technical Reports Server (NTRS)

    Ferragut, N. J.

    1982-01-01

    The use of automatic multi-stage substructing analysis is demonstrated for a hypothetical case of a GAS container supported by structural channels with a simulated experimental package inside the container. The GAS program purpose is stated and potential candidate structures to support experimental packages are discussed. The GAS container model and the substructuring analysis capabilities of NASTRAN make it possible to study the experiments inside the container as well as the design constraints resulting from the support structures holding the containers. The use of substructuring in the GAS program could be an important factor in increasing the number of flight opportunities.

  14. Substructure procedure for including tile flexibility in stress analysis of shuttle thermal protection system

    NASA Technical Reports Server (NTRS)

    Giles, G. L.

    1980-01-01

    A substructure procedure to include the flexibility of the tile in the stress analysis of the shuttle thermal protection system (TPS) is described. In this procedure, the TPS is divided into substructures of (1) the tile which is modeled by linear finite elements and (2) the SIP which is modeled as a nonlinear continuum. This procedure was applied for loading cases of uniform pressure, uniform moment, and an aerodynamic shock on various tile thicknesses. The ratios of through-the-thickness stresses in the SIP which were calculated using a flexible tile compared to using a rigid tile were found to be less than 1.05 for the cases considered.

  15. Dislocation substructure in NiAl single crystals deformed at ambient temperature

    SciTech Connect

    Shi, X.; Pollock, T.M.; Mahajan, S.; Arunachalam, V.S.

    1997-12-31

    Dislocation substructure in NiAl single crystals oriented for single slip and deformed at ambient temperature has been studied using weak-beam transmission electron microscopy. Deformation is localized in bands that consists mostly of near-edge dislocations, with an interspersion of a high density of elongated prismatic loops. Pure screw dislocations are not observed, but dislocations having zigzag configurations that are near-screw in orientation are present. A high density of jogs is observed on both near-edge and zigzag dislocation segments. The mechanisms for the development of this substructure are discussed, emphasizing the role of double cross slip and resulting glissile and sessile jogs of varying heights.

  16. Effect of temperature on the formation of creep substructure in sodium chloride single crystals

    NASA Technical Reports Server (NTRS)

    Raj, Sai V.; Pharr, George M.

    1992-01-01

    The effect of temperature on the substructure morphology and the cell and subgrain size was investigated experimentally in NaCl single crystals under creep in the temperature range 573-873 K. It is found that the effect of temperature on the cell and subgrain sizes is weak in comparison with the effect of stress. However, there was a qualitative change in the substructure morphology with temperature, with the cells and subgrains better defined at higher temperatures. The volume fraction of the cell boundaries decreased with increasing temperature, thereby indicating a refinement of the microstructure at higher temperatures.

  17. Parametric studies of stitching effectiveness for preventing substructure disbond

    NASA Technical Reports Server (NTRS)

    Flanagan, Gerry; Furrow, Keith

    1995-01-01

    A methodology is desired that will allow a designer to select appropriate amounts of through-thickness reinforcement needed to meet design requirements. The goal is to use a relatively simple analysis to minimize the amount of testing that needs to be performed, and to make test results from simple configurations applicable to more general structures. Using this methodology one should be able to optimize the selection of stitching materials, the weight of the yarn, and the stitching density. The analysis approach is to treat substructure disbond as a crack propagation problem. In this approach, the stitches have little influence until a delamination begins to grow. Once the delamination reaches, or extends beyond a stitch, the stitch serves to reduce the strain-energy-release-rate (G) at the crack tip for a given applied load. The reduced G can then be compared to the unstitched materials toughness to predict the load required to further extend the crack. The current model treats the stitch as a simple spring which responds to displacements in the vertical (through-thickness) direction. In concept, this approach is similar to that proposed by other authors. Test results indicate that the model should be refined to include the shearing stiffness of the stitch. The strain-energy-release-rate calculations are performed using a code which uses interconnected higher-order plates to model built-up composite cross-sections. When plates are stacked vertically, the interfacial tractions between the plates can be computed. The plate differential equations are solved in closed-form. The code, called SUBLAM, was developed as part of this section in one dimension. Because of this limitation, rows of stitches are treated as a two-dimensional sheet. The spring stiffness of a row of stitches can be estimated from the stitch material, weight, and density. As a practical and conservative approach, we can assume that the stitch is bonded until a crack passes the stitch location

  18. Clays, common

    USGS Publications Warehouse

    Virta, R.L.

    1998-01-01

    Part of a special section on the state of industrial minerals in 1997. The state of the common clay industry worldwide for 1997 is discussed. Sales of common clay in the U.S. increased from 26.2 Mt in 1996 to an estimated 26.5 Mt in 1997. The amount of common clay and shale used to produce structural clay products in 1997 was estimated at 13.8 Mt.

  19. Student Commons

    ERIC Educational Resources Information Center

    Gordon, Douglas

    2010-01-01

    Student commons are no longer simply congregation spaces for students with time on their hands. They are integral to providing a welcoming environment and effective learning space for students. Many student commons have been transformed into spaces for socialization, an environment for alternative teaching methods, a forum for large group meetings…

  20. Loop-linker PCR: an advanced PCR technique for genome walking.

    PubMed

    Trinh, Quoclinh; Shi, Hui; Xu, Wentao; Hao, Junran; Luo, Yunbo; Huang, Kunlun

    2012-10-01

    In this article, we developed a novel PCR method, termed loop-linker PCR, to isolate flanking sequences in transgenic crops. The novelty of this approach is its use of a stem-loop structure to design a loop-linker adapter. The adapter is designed to form a nick site when ligated with restricted DNA. This modification not only can prevent the self-ligation of adapters but also promotes the elongation of the 3' end of the loop-linker adapter to generate a stem-loop structure in the ligation products. Moreover, the suppressive effect of the stem-loop structure decreases nonspecific amplification and increases the success rate of the approach; all extension products will suppress exponential amplification except from the ligation product that contains the specific primer binding site. Using this method, 442, 1830, 107, and 512 bp left border flanking sequences were obtained from the transgenic maizes LY038, DAS-59122-7, Event 3272, and the transgenic soybean MON89788, respectively. The experimental results demonstrated that loop-linker PCR is an efficient, reliable, and cost-effective method for identifying flanking sequences in transgenic crops and could be applied for other genome walking applications. PMID:23008115

  1. A two-photon activatable amino acid linker for the induction of fluorescence.

    PubMed

    Friedrich, Felix; Klehs, Kathrin; Fichte, Manuela A H; Junek, Stephan; Heilemann, Mike; Heckel, Alexander

    2015-10-28

    A new one- and two-photon activatable fluorophore based on ATTO565 was developed using a photolabile linker that simultaneously acts as a quencher. It is especially interesting for protein and peptide applications because it can be incorporated by standard peptide chemistry. The application of the new fluorogenic construct in super-resolution microscopy of antibody conjugates is shown. PMID:26343765

  2. Technology Transfer and Utilization Methodology; Further Analysis of the Linker Concept.

    ERIC Educational Resources Information Center

    Jolly, James A.; Creighton, J. W.

    This study is based on a comparison of data from two independent studies of technology utilization and dissemination methodology that sought to identify the behavior characteristics of "linkers" and "stabilizers" and their relative existence within different groups of technical personnel. Hypothesis for this study is that the distribution of the…

  3. Conserved interdomain linker promotes phase separation of the multivalent adaptor protein Nck

    PubMed Central

    Banjade, Sudeep; Wu, Qiong; Mittal, Anuradha; Peeples, William B.; Pappu, Rohit V.; Rosen, Michael K.

    2015-01-01

    The organization of membranes, the cytosol, and the nucleus of eukaryotic cells can be controlled through phase separation of lipids, proteins, and nucleic acids. Collective interactions of multivalent molecules mediated by modular binding domains can induce gelation and phase separation in several cytosolic and membrane-associated systems. The adaptor protein Nck has three SRC-homology 3 (SH3) domains that bind multiple proline-rich segments in the actin regulatory protein neuronal Wiskott-Aldrich syndrome protein (N-WASP) and an SH2 domain that binds to multiple phosphotyrosine sites in the adhesion protein nephrin, leading to phase separation. Here, we show that the 50-residue linker between the first two SH3 domains of Nck enhances phase separation of Nck/N-WASP/nephrin assemblies. Two linear motifs within this element, as well as its overall positively charged character, are important for this effect. The linker increases the driving force for self-assembly of Nck, likely through weak interactions with the second SH3 domain, and this effect appears to promote phase separation. The linker sequence is highly conserved, suggesting that the sequence determinants of the driving forces for phase separation may be generally important to Nck functions. Our studies demonstrate that linker regions between modular domains can contribute to the driving forces for self-assembly and phase separation of multivalent proteins. PMID:26553976

  4. Novel nucleosomal particles containing core histones and linker DNA but no histone H1

    PubMed Central

    Cole, Hope A.; Cui, Feng; Ocampo, Josefina; Burke, Tara L.; Nikitina, Tatiana; Nagarajavel, V.; Kotomura, Naoe; Zhurkin, Victor B.; Clark, David J.

    2016-01-01

    Eukaryotic chromosomal DNA is assembled into regularly spaced nucleosomes, which play a central role in gene regulation by determining accessibility of control regions. The nucleosome contains ∼147 bp of DNA wrapped ∼1.7 times around a central core histone octamer. The linker histone, H1, binds both to the nucleosome, sealing the DNA coils, and to the linker DNA between nucleosomes, directing chromatin folding. Micrococcal nuclease (MNase) digests the linker to yield the chromatosome, containing H1 and ∼160 bp, and then converts it to a core particle, containing ∼147 bp and no H1. Sequencing of nucleosomal DNA obtained after MNase digestion (MNase-seq) generates genome-wide nucleosome maps that are important for understanding gene regulation. We present an improved MNase-seq method involving simultaneous digestion with exonuclease III, which removes linker DNA. Remarkably, we discovered two novel intermediate particles containing 154 or 161 bp, corresponding to 7 bp protruding from one or both sides of the nucleosome core. These particles are detected in yeast lacking H1 and in H1-depleted mouse chromatin. They can be reconstituted in vitro using purified core histones and DNA. We propose that these ‘proto-chromatosomes’ are fundamental chromatin subunits, which include the H1 binding site and influence nucleosome spacing independently of H1. PMID:26400169

  5. PROPERTIES OF CATALYTIC, LINKER AND CHITIN-BINDING DOMAINS OF INSECT CHITINASE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Manduca sexta (tobacco hornworm) chitinase is a glycoprotein that consists of an N-terminal catalytic domain, a Ser/Thr-rich linker region, and a C-terminal chitin-binding domain. To delineate the properties of these domains, we have generated truncated forms of chitinase, which were expressed in i...

  6. Assembly of bipolar microtubule structures by passive cross-linkers and molecular motors

    NASA Astrophysics Data System (ADS)

    Johann, D.; Goswami, D.; Kruse, K.

    2016-06-01

    During cell division, sister chromatids are segregated by the mitotic spindle, a bipolar assembly of interdigitating antiparallel polar filaments called microtubules. The spindle contains the midzone, a stable region of overlapping antiparallel microtubules, that is essential for maintaining bipolarity. Although a lot is known about the molecular players involved, the mechanism underlying midzone formation and maintenance is still poorly understood. We study the interaction of polar filaments that are cross-linked by molecular motors moving directionally and by passive cross-linkers diffusing along microtubules. Using a particle-based stochastic model, we find that the interplay of motors and passive cross-linkers can generate a stable finite overlap between a pair of antiparallel polar filaments. We develop a mean-field theory to study this mechanism in detail and investigate the influence of steric interactions between motors and passive cross-linkers on the overlap dynamics. In the presence of interspecies steric interactions, passive cross-linkers mimic the behavior of molecular motors and stable finite overlaps are generated even for non-cross-linking motors. Finally, we develop a mean-field theory for a bundle of aligned polar filaments and show that they can self-organize into a spindlelike pattern. Our work suggests possible ways as to how cells can generate spindle midzones and control their extensions.

  7. The Linker's Handbook for Curriculum Improvement Strategies. Volumes I, II, and III.

    ERIC Educational Resources Information Center

    Pennsylvania State Dept. of Education, Harrisburg. Bureau of Curriculum Services.

    This handbook is intended to aid in the implementation of the Pennsylvania School Improvement Program (PSIP), a curriculum improvement program. The PSIP model of curriculum improvement contains an intermediate unit (IU) linker (curriculum specialist) leading a school-level local action team (LAT) through a structured problem-solving approach to…

  8. MS2Analyzer: A Software for Small Molecule Substructure Annotations from Accurate Tandem Mass Spectra

    PubMed Central

    2015-01-01

    Systematic analysis and interpretation of the large number of tandem mass spectra (MS/MS) obtained in metabolomics experiments is a bottleneck in discovery-driven research. MS/MS mass spectral libraries are small compared to all known small molecule structures and are often not freely available. MS2Analyzer was therefore developed to enable user-defined searches of thousands of spectra for mass spectral features such as neutral losses, m/z differences, and product and precursor ions from MS/MS spectra in MSP/MGF files. The software is freely available at http://fiehnlab.ucdavis.edu/projects/MS2Analyzer/. As the reference query set, 147 literature-reported neutral losses and their corresponding substructures were collected. This set was tested for accuracy of linking neutral loss analysis to substructure annotations using 19 329 accurate mass tandem mass spectra of structurally known compounds from the NIST11 MS/MS library. Validation studies showed that 92.1 ± 6.4% of 13 typical neutral losses such as acetylations, cysteine conjugates, or glycosylations are correct annotating the associated substructures, while the absence of mass spectra features does not necessarily imply the absence of such substructures. Use of this tool has been successfully demonstrated for complex lipids in microalgae. PMID:25263576

  9. Major substructure in the M31 Outer Halo: the East Cloud

    NASA Astrophysics Data System (ADS)

    McMonigal, B.; Bate, N. F.; Conn, A. R.; Mackey, A. D.; Lewis, G. F.; Irwin, M. J.; Martin, N. F.; McConnachie, A. W.; Ferguson, A. M. N.; Ibata, R. A.; Huxor, A. P.

    2016-02-01

    We present the first detailed analysis of the East Cloud, a highly disrupted diffuse stellar substructure in the outer halo of M31. The core of the substructure lies at a projected distance of ˜100 kpc from the centre of M31 in the outer halo, with possible extensions reaching right into the inner halo. Using Pan-Andromeda Archaeological Survey photometry of red giant branch stars, we measure the distance, metallicity and brightness of the cloud. Using Hubble Space Telescope data, we independently measure the distance and metallicity to the two globular clusters coincident with the East Cloud core, PA-57 and PA-58, and find their distances to be consistent with the cloud. Four further globular clusters coincident with the substructure extensions are identified as potentially associated. Combining the analyses, we determine a distance to the cloud of 814^{+20}_{-9} kpc, a metallicity of [Fe/H] = -1.2 ± 0.1, and a brightness of MV = -10.7 ± 0.4 mag. Even allowing for the inclusion of the potential extensions, this accounts for less than 20 per cent of the progenitor luminosity implied by the luminosity-metallicity relation. Using the updated techniques developed for this analysis, we also refine our estimates of the distance and brightness of the South-West Cloud, a separate substructure analysed in the previous work in this series.

  10. VIEW OF BRIDGE SUBSTRUCTURE CONCRETE PIERS “III”, “II”, “I” AND ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    VIEW OF BRIDGE SUBSTRUCTURE CONCRETE PIERS “III”, “II”, “I” AND “A” AND SUPERSTRUCTURE MAIN BRIDGE, CANTILEVER THROUGH TRUSS CANTILEVER SECTION LOOKING SOUTH AND UP. - Huey P. Long Bridge, Spanning Mississippi River approximately midway between nine & twelve mile points upstream from & west of New Orleans, Jefferson, Jefferson Parish, LA

  11. VIEW OF BRIDGE SUBSTRUCTURE CONCRETE PIERS “II”, “III”, “1V” AND ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    VIEW OF BRIDGE SUBSTRUCTURE CONCRETE PIERS “II”, “III”, “1V” AND “V” AND SUPERSTRUCTURE MAIN BRIDGE CANTILEVER THROUGH TRUSS CANTILEVER SPAN AND SIMPLE THROUGH TRUSS SPAN LOOKING NORTHWEST AND UP. - Huey P. Long Bridge, Spanning Mississippi River approximately midway between nine & twelve mile points upstream from & west of New Orleans, Jefferson, Jefferson Parish, LA

  12. Exploring the reality of density substructures in the Palomar 5 stellar stream

    NASA Astrophysics Data System (ADS)

    Thomas, Guillaume F.; Ibata, R.; Famaey, B.; Martin, N. F.; Lewis, G. F.

    2016-08-01

    We present an analysis of the presence of substructures in the stellar stream of the Palomar 5 globular cluster, as derived from Sloan Digital Sky Survey data. Using a matched filter technique, we recover the positions and sizes of overdensities reported in previous studies. To explore the reality of these structures, we also create an artificial model of the stream, in which we construct a realistic background on top of which we add a perfectly smooth stream structure, taking into account the effects of photometric completeness and interstellar extinction. We find that the smooth artificial stream then shows similarly-pronounced substructures as the real structure. Interestingly, our best-fit N-body simulation does display real projected density variations linked to stellar epicyclic motions, but these become less significant when taking into account the SDSS star-count constraints. The substructures found when applying our matched filter technique to the N-body particles converted into observable stars are thus mostly unrelated to these epicyclic motions. This analysis suggests that the majority of the previously-detected substructures along the tidal tail of Palomar 5 are artefacts of observational inhomogeneities.

  13. 5. DETAIL OF SUBSTRUCTURE OF GEORGIA DOT BRIDGE NO. 145/01427/F/00050E ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. DETAIL OF SUBSTRUCTURE OF GEORGIA DOT BRIDGE NO. 145/01427/F/00050E INCLUDING TIMBER PILES AND CAPS AND STEEL I-BEAMS - Georgia DOT Bridge No. 145/01427/F/00050E, Spanning Long Cane Creek at County Road 29, Pine Lake, Harris County, GA

  14. Exploring the reality of density substructures in the Palomar 5 stellar stream

    NASA Astrophysics Data System (ADS)

    Thomas, Guillaume F.; Ibata, R.; Famaey, B.; Martin, N. F.; Lewis, G. F.

    2016-08-01

    We present an analysis of the presence of substructures in the stellar stream of the Palomar 5 globular cluster, as derived from Sloan Digital Sky Survey data. Using a matched filter technique, we recover the positions and sizes of overdensities reported in previous studies. To explore the reality of these structures, we also create an artificial model of the stream, in which we construct a realistic background on top of which we add a perfectly smooth stream structure, taking into account the effects of photometric completeness and interstellar extinction. We find that the smooth artificial stream then shows similarly pronounced substructures as the real structure. Interestingly, our best-fitting N-body simulation does display real projected density variations linked to stellar epicyclic motions, but these become less significant when taking into account the SDSS star-count constraints. The substructures found when applying our matched filter technique to the N-body particles converted into observable stars are thus mostly unrelated to these epicyclic motions. This analysis suggests that the majority of the previously detected substructures along the tidal tail of Palomar 5 are artefacts of observational inhomogeneities.

  15. Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search

    PubMed Central

    Alocci, Davide; Mariethoz, Julien; Horlacher, Oliver; Bolleman, Jerven T.; Campbell, Matthew P.; Lisacek, Frederique

    2015-01-01

    Resource description framework (RDF) and Property Graph databases are emerging technologies that are used for storing graph-structured data. We compare these technologies through a molecular biology use case: glycan substructure search. Glycans are branched tree-like molecules composed of building blocks linked together by chemical bonds. The molecular structure of a glycan can be encoded into a direct acyclic graph where each node represents a building block and each edge serves as a chemical linkage between two building blocks. In this context, Graph databases are possible software solutions for storing glycan structures and Graph query languages, such as SPARQL and Cypher, can be used to perform a substructure search. Glycan substructure searching is an important feature for querying structure and experimental glycan databases and retrieving biologically meaningful data. This applies for example to identifying a region of the glycan recognised by a glycan binding protein (GBP). In this study, 19,404 glycan structures were selected from GlycomeDB (www.glycome-db.org) and modelled for being stored into a RDF triple store and a Property Graph. We then performed two different sets of searches and compared the query response times and the results from both technologies to assess performance and accuracy. The two implementations produced the same results, but interestingly we noted a difference in the query response times. Qualitative measures such as portability were also used to define further criteria for choosing the technology adapted to solving glycan substructure search and other comparable issues. PMID:26656740

  16. A Computer Process for Substructure Searches on Compound Structures Ciphered in the IUPAC Notation

    ERIC Educational Resources Information Center

    Polton, D. J.

    1972-01-01

    Computer programs have been written which enable substructure searches to be carried out on a file of compounds ciphered using a modified version of the IUPAC (Dyson) notation. The search system outlined is to be linked with one which uses input from the chemical structure typewriter. (3 references) (Author)

  17. Substructure Evolution in Energetic-Driven Spherically Shock-Loaded Copper

    SciTech Connect

    Sinitsyna, L. M.; Novikov, S. A.; Gray, G. T. III; Cerreta, E.; Henrie, B.; Lopez, M.; Yablinsky, C.

    2006-07-28

    Post-shock-recovered metallurgical analysis of solid metal spheres shock loaded via spherical energetic(HE) loading provides a unique opportunity to quantify the substructure evolution in a material subjected to converging Taylor-wave (triangular-shock pulse) loading. In this paper detailed quantitative metallographic, orientation-imaging microscopy (OIM), and texture analysis is presented characterizing the gradient in substructure generated in Cu subjected to a spherical HE shock loading pulse at VNIIEF. The substructure in the recovered sphere is seen to include: 1) a spherical cavity generated in the center of the sphere due to shock-wave convergence and release, displaying ductile dimpled failure and no evidence of melting, 2) a gradient in deformation (slip and deformation twins) from the center outward to the surface, and 3) numerous shear cracks and/or spall planes. The substructure evolution is discussed relative to that previously observed in Cu shock prestrained via either 1-D triangular-shaped shockwave loading or 1-D square-topped pulse shock loading.

  18. Modelling and control issues of dynamically substructured systems: adaptive forward prediction taken as an example

    PubMed Central

    Tu, Jia-Ying; Hsiao, Wei-De; Chen, Chih-Ying

    2014-01-01

    Testing techniques of dynamically substructured systems dissects an entire engineering system into parts. Components can be tested via numerical simulation or physical experiments and run synchronously. Additional actuator systems, which interface numerical and physical parts, are required within the physical substructure. A high-quality controller, which is designed to cancel unwanted dynamics introduced by the actuators, is important in order to synchronize the numerical and physical outputs and ensure successful tests. An adaptive forward prediction (AFP) algorithm based on delay compensation concepts has been proposed to deal with substructuring control issues. Although the settling performance and numerical conditions of the AFP controller are improved using new direct-compensation and singular value decomposition methods, the experimental results show that a linear dynamics-based controller still outperforms the AFP controller. Based on experimental observations, the least-squares fitting technique, effectiveness of the AFP compensation and differences between delay and ordinary differential equations are discussed herein, in order to reflect the fundamental issues of actuator modelling in relevant literature and, more specifically, to show that the actuator and numerical substructure are heterogeneous dynamic components and should not be collectively modelled as a homogeneous delay differential equation. PMID:25104902

  19. Strategic Considerations in the Design of a Screening System for Substructure Searches of Chemical Structure Files

    ERIC Educational Resources Information Center

    Adamson, George W.; And Others

    1973-01-01

    A major problem in the design of screening systems for substructure searches of chemical structure files is the development of a methodology for selection of an optimal set of structural characteristics to act as screens. Distributions of several structural characteristics of the Chemical Abstracts Service Registry System are summarized. (13…

  20. Low Density Lipoprotein Receptor Class A Repeats Are O-Glycosylated in Linker Regions*

    PubMed Central

    Pedersen, Nis Borbye; Wang, Shengjun; Narimatsu, Yoshiki; Yang, Zhang; Halim, Adnan; Schjoldager, Katrine Ter-Borch Gram; Madsen, Thomas Daugbjerg; Seidah, Nabil G.; Bennett, Eric Paul; Levery, Steven B.; Clausen, Henrik

    2014-01-01

    The low density lipoprotein receptor (LDLR) is crucial for cholesterol homeostasis and deficiency in LDLR functions cause hypercholesterolemia. LDLR is a type I transmembrane protein that requires O-glycosylation for stable expression at the cell surface. It has previously been suggested that LDLR O-glycosylation is found N-terminal to the juxtamembrane region. Recently we identified O-glycosylation sites in the linker regions between the characteristic LDLR class A repeats in several LDLR-related receptors using the “SimpleCell” O-glycoproteome shotgun strategy. Herein, we have systematically characterized O-glycosylation sites on recombinant LDLR shed from HEK293 SimpleCells and CHO wild-type cells. We find that the short linker regions between LDLR class A repeats contain an evolutionarily conserved O-glycosylation site at position −1 of the first cysteine residue of most repeats, which in wild-type CHO cells is glycosylated with the typical sialylated core 1 structure. The glycosites in linker regions of LDLR class A repeats are conserved in LDLR from man to Xenopus and found in other homologous receptors. O-Glycosylation is controlled by a large family of polypeptide GalNAc transferases. Probing into which isoform(s) contributed to glycosylation of the linker regions of the LDLR class A repeats by in vitro enzyme assays suggested a major role of GalNAc-T11. This was supported by expression of LDLR in HEK293 cells, where knock-out of the GalNAc-T11 isoform resulted in the loss of glycosylation of three of four linker regions. PMID:24798328

  1. Common cold

    MedlinePlus

    ... are the most common reason that children miss school and parents miss work. Parents often get colds ... other children. A cold can spread quickly through schools or daycares. Colds can occur at any time ...

  2. Identification of population substructure among Jews using STR markers and dependence on reference populations included

    PubMed Central

    2010-01-01

    Background Detecting population substructure is a critical issue for association studies of health behaviors and other traits. Whether inherent in the population or an artifact of marker choice, determining aspects of a population's genetic history as potential sources of substructure can aid in design of future genetic studies. Jewish populations, among which association studies are often conducted, have a known history of migrations. As a necessary step in understanding population structure to conduct valid association studies of health behaviors among Israeli Jews, we investigated genetic signatures of this history and quantified substructure to facilitate future investigations of these phenotypes in this population. Results Using 32 autosomal STR markers and the program STRUCTURE, we differentiated between Ashkenazi (AJ, N = 135) and non-Ashkenazi (NAJ, N = 226) Jewish populations in the form of Northern and Southern geographic genetic components (AJ north 73%, south 23%, NAJ north 33%, south 60%). The ability to detect substructure within these closely related populations using a small STR panel was contingent on including additional samples representing major continental populations in the analyses. Conclusions Although clustering programs such as STRUCTURE are designed to assign proportions of ancestry to individuals without reference population information, when Jewish samples were analyzed in the absence of proxy parental populations, substructure within Jews was not detected. Generally, for samples with a given grandparental country of birth, STRUCTURE assignment values to Northern, Southern, African and Asian clusters agreed with mitochondrial DNA and Y-chromosomal data from previous studies as well as historical records of migration and intermarriage. PMID:20546593

  3. 1D coordination polymers with polychalcogenides as linkers between metal atoms

    SciTech Connect

    Kysliak, Oleksandr; Beck, Johannes

    2013-07-15

    The reactions of zinc metal with elemental selenium and selenium/sulfur mixtures in liquid ammonia or methylamine under solvothermal conditions in closed glass ampoules at 50 °C lead within some days specifically to [Zn(NH{sub 3}){sub 2}Se{sub 4}]{sub n} (1), [Zn(MeNH{sub 2}){sub 2}Se{sub 4}]{sub n} (2), [Zn(NH{sub 3}){sub 2}Se{sub 2.23}S{sub 1.77}]{sub n} (3). From MnCl{sub 2}, Rb{sub 2}Se and excess Se in n-butylamine [Mn({sup n}BuNH{sub 2}){sub 4}Se{sub 6}]{sub n} (4) is obtained after prolonged reaction time at ambient temperature. The compounds are sensitive towards air and loss of NH{sub 3} or the amine ligands. The crystal structures were determined by single crystal diffraction at low temperatures. As a common structural feature, all compounds represent 1D coordination polymers with polychalcogenide chains as linkers between the metal atoms and consist of infinite [M–Ch{sub m}–]{sub n} chains (M=Zn, Mn; Ch{sub m}=Se{sub 4}, (S/Se){sub 4}, Se{sub 6}). The Zn central atoms in 1–3 have tetrahedral coordination with two amine ligands, the Mn atoms in 4 have octahedral coordination with four amine ligands and cis position of the two Se atoms. Raman spectra of 1–3 show the stretching mode vibrations of the Ch{sub 4} groups. The observation of S–S, S–Se, and Se–Se vibration bands in the spectrum of 3 indicates the presence of mixed S/Se polyanions. An optical band gap of 1.86(5) eV was determined for 2 by diffuse reflectance spectroscopy. - Graphical abstract: The reaction of Zn and Se in liquid methylamine yields dark red [Zn(NH{sub 2}CH{sub 3})Se{sub 4}], a 1D coordination polymer consisting of helical Zn–Se{sub 4}–Zn– chains. - Highlights: • A series of 1D coordination polymers consisting of metal amine complexes concatenated by polychalcogenide ions is presented. • Syntheses were performed as solvothermal reactions in liquid ammonia, liquid methylamine and n-butylamine. • Crystal structures are dominated by helices [M–Ch{sub m

  4. Boosted objects and jet substructure at the LHC: Report of BOOST2012, held at IFIC Valencia, 23rd-27th of July 2012

    SciTech Connect

    Altheimer, A.

    2014-03-21

    This report of the BOOST2012 workshop presents the results of four working groups that studied key aspects of jet substructure. We discuss the potential of first-principle QCD calculations to yield a precise description of the substructure of jets and study the accuracy of state-of-the-art Monte Carlo tools. Limitations of the experiments’ ability to resolve substructure are evaluated, with a focus on the impact of additional (pile-up) proton proton collisions on jet substructure performance in future LHC operating scenarios. The final section summarizes the lessons learnt from jet substructure analyses in searches for new physics in the production of boosted top quarks.

  5. CyTargetLinker: A Cytoscape App to Integrate Regulatory Interactions in Network Analysis

    PubMed Central

    Kutmon, Martina; Kelder, Thomas; Mandaviya, Pooja; Evelo, Chris T. A.; Coort, Susan L.

    2013-01-01

    Introduction The high complexity and dynamic nature of the regulation of gene expression, protein synthesis, and protein activity pose a challenge to fully understand the cellular machinery. By deciphering the role of important players, including transcription factors, microRNAs, or small molecules, a better understanding of key regulatory processes can be obtained. Various databases contain information on the interactions of regulators with their targets for different organisms, data recently being extended with the results of the ENCODE (Encyclopedia of DNA Elements) project. A systems biology approach integrating our understanding on different regulators is essential in interpreting the regulation of molecular biological processes. Implementation We developed CyTargetLinker (http://projects.bigcat.unimaas.nl/cytargetlinker), a Cytoscape app, for integrating regulatory interactions in network analysis. Recently we released CyTargetLinker as one of the first apps for Cytoscape 3. It provides a user-friendly and flexible interface to extend biological networks with regulatory interactions, such as microRNA-target, transcription factor-target and/or drug-target. Importantly, CyTargetLinker employs identifier mapping to combine various interaction data resources that use different types of identifiers. Results Three case studies demonstrate the strength and broad applicability of CyTargetLinker, (i) extending a mouse molecular interaction network, containing genes linked to diabetes mellitus, with validated and predicted microRNAs, (ii) enriching a molecular interaction network, containing DNA repair genes, with ENCODE transcription factor and (iii) building a regulatory meta-network in which a biological process is extended with information on transcription factor, microRNA and drug regulation. Conclusions CyTargetLinker provides a simple and extensible framework for biologists and bioinformaticians to integrate different regulatory interactions into their network

  6. Aromatic fumaronitrile core-based donor-linker-acceptor-linker-donor (D-pi-A-pi-D) compounds: synthesis and photophysical properties.

    PubMed

    Panthi, Krishna; Adhikari, Ravi M; Kinstle, Thomas H

    2010-04-01

    A new class of aromatic fumaronitrile core-based compounds with different donors and linkers has been synthesized and well characterized. Compounds 1 and 2 have indole and 2-phenylindole groups as electron donors, respectively. Compounds 3 and 4 have a diphenylamino group as the electron donor, and compound 5 has a 3,6-di-tert-butylcarbazole group as an electron donor. These compounds absorb in the blue-to-green region and emit in the blue-to-red region depending on the electron donor, linker, and solvents. The quantum yields of fluorescence of these compounds in solution are measured and found to be moderate, but in solid states, they are high. These compounds display strong emission solvatochromism that is reflected by a large shift in their fluorescence emission maxima on changing the solvents. This change is accompanied by a successive decrease in fluorescence intensity. The fluorescence lifetimes of these compounds are measured in different solvent and found to vary from <1 to 7 ns. Optical switching of these compounds with solvents, concentration, and excitation energy have been studied. The correlation between the functional group and optical properties has been established to some extent. The ability of these compounds to function as colorimetric and luminescence pH sensors is demonstrated with color changes and luminescence switching upon the addition of trifluoroacetic acid. The potentiality of these compounds for application in optoelectronics has been optically assessed. PMID:20235549

  7. Improving corrosion resistance of post-tensioned substructures emphasizing high performance grouts

    NASA Astrophysics Data System (ADS)

    Schokker, Andrea Jeanne

    The use of post-tensioning in bridges can provide durability and structural benefits to the system while expediting the construction process. When post-tensioning is combined with precast elements, traffic interference can be greatly reduced through rapid construction. Post-tensioned concrete substructure elements such as bridge piers, hammerhead bents, and straddle bents have become more prevalent in recent years. Chloride induced corrosion of steel in concrete is one of the most costly forms of corrosion each year. Coastal substructure elements are exposed to seawater by immersion or spray, and inland bridges may also be at risk due to the application of deicing salts. Corrosion protection of the post-tensioning system is vital to the integrity of the structure because loss of post-tensioning can result in catastrophic failure. Documentation for durability design of the grout, ducts, and anchorage systems is very limited. The objective of this research is to evaluate the effectiveness of corrosion protection measures for post-tensioned concrete substructures by designing and testing specimens representative of typical substructure elements using state-of-the-art practices in aggressive chloride exposure environments. This was accomplished through exposure testing of twenty-seven large-scale beam specimens and ten large-scale column specimens. High performance grout for post-tensioning tendon injection was also developed through a series of fresh property tests, accelerated exposure tests, and a large-scale pumping test to simulate field conditions. A high performance fly ash grout was developed for applications with small vertical rises, and a high performance anti-bleed grout was developed for applications involving large vertical rises such as tall bridge piers. Long-term exposure testing of the beam and column specimens is ongoing, but preliminary findings indicate increased corrosion protection with increasing levels of post-tensioning, although traditional

  8. Chiral linker-bridged bis-N-heterocyclic carbenes: design, synthesis, palladium complexes, and catalytic properties.

    PubMed

    Zhang, Dao; He, Yu; Tang, Junkai

    2016-08-01

    A series of chiral bis(benzimidazolium) salts 10-19 with (1R,2R)-cyclohexene, (1R,2R)-diphenylethylene and (aR)-binaphthylene linkers have been designed and synthesized in 30-94% yield. Ten chiral bis(NHC) palladium complexes 20-28 have been synthesized and characterized by NMR, HRMS, elemental analysis and further confirmed by X-ray single crystal analysis. These bis(NHC)-Pd complexes showed obviously different catalytic properties in the asymmetric Suzuki-Miyaura coupling reactions. The (1R,2R)-cyclohexene-bridged bis(NHC)-Pd complex, (R,R)-23, achieved the highest yield of 90%, while complex (aR)-28, with a binaphthylene linker, showed the best enantioselectivity of 60 ee%. The structural analysis of these complexes suggested that such difference of catalytic performance has a close relationship with their coordination surroundings around metal centres. PMID:27230553

  9. Connecting two proteins using a fusion alpha helix stabilized by a chemical cross linker

    NASA Astrophysics Data System (ADS)

    Jeong, Woo Hyeon; Lee, Haerim; Song, Dong Hyun; Eom, Jae-Hoon; Kim, Sun Chang; Lee, Hee-Seung; Lee, Hayyoung; Lee, Jie-Oh

    2016-03-01

    Building a sophisticated protein nano-assembly requires a method for linking protein components in a predictable and stable structure. Most of the cross linkers available have flexible spacers. Because of this, the linked hybrids have significant structural flexibility and the relative structure between their two components is largely unpredictable. Here we describe a method of connecting two proteins via a `fusion α helix' formed by joining two pre-existing helices into a single extended helix. Because simple ligation of two helices does not guarantee the formation of a continuous helix, we used EY-CBS, a synthetic cross linker that has been shown to react selectively with cysteines in α-helices, to stabilize the connecting helix. Formation and stabilization of the fusion helix was confirmed by determining the crystal structures of the fusion proteins with and without bound EY-CBS. Our method should be widely applicable for linking protein building blocks to generate predictable structures.

  10. Engineering Cel7A carbohydrate binding module and linker for reduced lignin inhibition.

    PubMed

    Strobel, Kathryn L; Pfeiffer, Katherine A; Blanch, Harvey W; Clark, Douglas S

    2016-06-01

    Non-productive binding of cellulases to lignin inhibits enzymatic hydrolysis of biomass, increasing enzyme requirements and the cost of biofuels. This study used site-directed mutagenesis of the Trichoderma Cel7A carbohydrate binding module (CBM) and linker to investigate the mechanisms of adsorption to lignin and engineer a cellulase with increased binding specificity for cellulose. CBM mutations that added hydrophobic or positively charged residues decreased the specificity for cellulose, while mutations that added negatively charged residues increased the specificity. Linker mutations that altered predicted glycosylation patterns selectively impacted lignin affinity. Beneficial mutations were combined to generate a mutant with 2.5-fold less lignin affinity while fully retaining cellulose affinity. This mutant was uninhibited by added lignin during hydrolysis of Avicel and generated 40% more glucose than the wild-type enzyme from dilute acid-pretreated Miscanthus. Biotechnol. Bioeng. 2016;113: 1369-1374. © 2015 Wiley Periodicals, Inc. PMID:26616493

  11. Tunable capsule space: self-assembly of hemispherical cavitands with hydrogen-bonding linkers.

    PubMed

    Yamanaka, Masamichi; Ishii, Kei; Yamada, Yoshifumi; Kobayashi, Kenji

    2006-11-10

    Fine and/or drastic tuning of capsule space has been attained by alteration of the hydrogen-bonding linker and/or hemispherical cavitand, respectively. Two molecules of tetracarboxyl-cavitand 1 or tetrakis(4-carboxyphenyl)-cavitand 2 as a hemisphere and four molecules of 2-aminopyrimidine (2-AP) or tetrahydro-2-pyrimidinone (THP) as an equatorial hydrogen-bonding linker self-assemble into a capsule [(1)2.(2-AP)4] (3), [(1)2.(THP)4] (4), [(2)2.(2-AP)4] (5), or [(2)2.(THP)4] (6), respectively, via 16 hydrogen bonds. These capsules provide isolated nanospace and can encapsulate one guest molecule (7-13) in solution. Each capsule has a different cavity size and shows particular guest selectivity on the competitive encapsulation experiments. PMID:17081009

  12. Optical properties and sensing in plexcitonic nanocavities: from simple molecular linkers to molecular aggregate layers.

    PubMed

    Pérez-González, Olalla; Zabala, Nerea; Aizpurua, Javier

    2014-01-24

    We present a theoretical study of a metal-molecular aggregate hybrid system consisting of a strongly coupled dimer connected by molecules characterized by an excitonic transition. The plasmonic resonances of the metallic dimer interact with the molecular excitations giving rise to coupled plasmon-exciton states, so called plexcitons. We compare the differences in the optical response when the excitonic material is placed only as a linker in the plasmonic gap of the dimer and when the material is distributed as an aggregate layer covering the dimer entirely. We also explore the efficiency of plexcitons for localized surface plamon resonance (LSPR) sensing in both situations. The ordinary shift-based sensing is more efficient for dimers connected through molecular linkers, whereas intensity-based sensing is more effective when the molecular aggregate covers the entire nanostructure. These results can serve to design the chemistry of excitons around metallic nanoparticles. PMID:24346140

  13. Linking two DNA duplexes with a rigid linker for DNA nanotechnology.

    PubMed

    Tashiro, Ryu; Iwamoto, Masahiro; Morinaga, Hironobu; Emura, Tomoko; Hidaka, Kumi; Endo, Masayuki; Sugiyama, Hiroshi

    2015-08-18

    DNA has recently emerged as a promising material for the construction of nanosized architectures. Chemically modified DNA has been suggested to be an important component of such architectural building blocks. We have designed and synthesized a novel H-shaped DNA oligonucleotide dimer that is cross-linked with a structurally rigid linker composed of phenylene and ethynylene groups. A rotatable DNA unit was constructed through the self-assembly of this H-shaped DNA component and two complementary DNA oligonucleotides. In addition to the rotatable unit, a locked DNA unit containing two H-shaped DNA components was also constructed. As an example of an extended locked structure, a hexagonal DNA origami dimer and oligomer were constructed by using H-shaped DNA as linkers. PMID:26130712

  14. Application of linker technique to trap transiently interacting protein complexes for structural studies

    PubMed Central

    Reddy Chichili, Vishnu Priyanka; Kumar, Veerendra; Sivaraman, J.

    2016-01-01

    Protein-protein interactions are key events controlling several biological processes. We have developed and employed a method to trap transiently interacting protein complexes for structural studies using glycine-rich linkers to fuse interacting partners, one of which is unstructured. Initial steps involve isothermal titration calorimetry to identify the minimum binding region of the unstructured protein in its interaction with its stable binding partner. This is followed by computational analysis to identify the approximate site of the interaction and to design an appropriate linker length. Subsequently, fused constructs are generated and characterized using size exclusion chromatography and dynamic light scattering experiments. The structure of the chimeric protein is then solved by crystallization, and validated both in vitro and in vivo by substituting key interacting residues of the full length, unlinked proteins with alanine. This protocol offers the opportunity to study crucial and currently unattainable transient protein interactions involved in various biological processes. PMID:26985443

  15. Connecting two proteins using a fusion alpha helix stabilized by a chemical cross linker

    PubMed Central

    Jeong, Woo Hyeon; Lee, Haerim; Song, Dong Hyun; Eom, Jae-Hoon; Kim, Sun Chang; Lee, Hee-Seung; Lee, Hayyoung; Lee, Jie-Oh

    2016-01-01

    Building a sophisticated protein nano-assembly requires a method for linking protein components in a predictable and stable structure. Most of the cross linkers available have flexible spacers. Because of this, the linked hybrids have significant structural flexibility and the relative structure between their two components is largely unpredictable. Here we describe a method of connecting two proteins via a ‘fusion α helix' formed by joining two pre-existing helices into a single extended helix. Because simple ligation of two helices does not guarantee the formation of a continuous helix, we used EY-CBS, a synthetic cross linker that has been shown to react selectively with cysteines in α-helices, to stabilize the connecting helix. Formation and stabilization of the fusion helix was confirmed by determining the crystal structures of the fusion proteins with and without bound EY-CBS. Our method should be widely applicable for linking protein building blocks to generate predictable structures. PMID:26980593

  16. Linking two DNA duplexes with a rigid linker for DNA nanotechnology

    PubMed Central

    Tashiro, Ryu; Iwamoto, Masahiro; Morinaga, Hironobu; Emura, Tomoko; Hidaka, Kumi; Endo, Masayuki; Sugiyama, Hiroshi

    2015-01-01

    DNA has recently emerged as a promising material for the construction of nanosized architectures. Chemically modified DNA has been suggested to be an important component of such architectural building blocks. We have designed and synthesized a novel H-shaped DNA oligonucleotide dimer that is cross-linked with a structurally rigid linker composed of phenylene and ethynylene groups. A rotatable DNA unit was constructed through the self-assembly of this H-shaped DNA component and two complementary DNA oligonucleotides. In addition to the rotatable unit, a locked DNA unit containing two H-shaped DNA components was also constructed. As an example of an extended locked structure, a hexagonal DNA origami dimer and oligomer were constructed by using H-shaped DNA as linkers. PMID:26130712

  17. Gold Nanoparticle Assemblies on Surfaces: Reactivity Tuning through Capping-Layer and Cross-Linker Design.

    PubMed

    Shankar, Sreejith; Orbach, Meital; Kaminker, Revital; Lahav, Michal; van der Boom, Milko E

    2016-01-26

    The immobilization of metal nanoparticles (NPs) with molecular control over their organization is challenging. Herein, we report the formation of molecularly cross-linked AuNP assemblies using a layer-by-layer approach. We observed four types of assemblies: 1) small aggregates of individual AuNPs, 2) large aggregates of individual AuNPs, 3) networks of fused AuNPs, and 4) gold islands. Interestingly, these assemblies with the different cross-linkers and capping layers represent different stages in the complete fusion of AuNPs to afford islands of continuous gold. We demonstrate that the stability toward fusion of the nanoparticles of the on-surface structures can be controlled by the reactivity of the cross-linkers and the hydrophilicity/hydrophobicity of the nanoparticles. PMID:26743768

  18. Comparison of anti-EGFR-Fab’ conjugated immunoliposomes modified with two different conjugation linkers for siRNa delivery in SMMC-7721 cells

    PubMed Central

    Deng, Li; Zhang, Yingying; Ma, Lulu; Jing, Xiaolong; Ke, Xingfa; Lian, Jianhao; Zhao, Qiang; Yan, Bo; Zhang, Jinfeng; Yao, Jianzhong; Chen, Jianming

    2013-01-01

    Background Targeted liposome-polycation-DNA complex (LPD), mainly conjugated with antibodies using functionalized PEG derivatives, is an effective nanovector for systemic delivery of small interference RNA (siRNA). However, there are few studies reporting the effect of different conjugation linkers on LPD for gene silencing. To clarify the influence of antibody conjugation linkers on LPD, we prepared two different immunoliposomes to deliver siRNA in which DSPE-PEG-COOH and DSPE-PEG-MAL, the commonly used PEG derivative linkers, were used to conjugate anti-EGFR Fab’ with the liposome. Methods First, 600 μg of anti-EGFR Fab’ was conjugated with 28.35 μL of a micelle solution containing DSPE-PEG-MAL or DSPE-PEG-COOH, and then post inserted into the prepared LPD. Various liposome parameters, including particle size, zeta potential, stability, and encapsulation efficiency were evaluated, and the targeting ability and gene silencing activity of TLPD-FPC (DSPE-PEG-COOH conjugated with Fab’) was compared with that of TLPD-FPM (DSPE-PEG-MAL conjugated with Fab’) in SMMC-7721 hepatocellular carcinoma cells. Results There was no significant difference in particle size between the two TLPDs, but the zeta potential was significantly different. Further, although there was no significant difference in siRNA encapsulation efficiency, cell viability, or serum stability between TLPD-FPM and TLPD-FPC, cellular uptake of TLPD-FPM was significantly greater than that of TLPD-FPC in EGFR-overexpressing SMMC-7721 cells. The luciferase gene silencing efficiency of TLPD-FPM was approximately three-fold high than that of TLPD-FPC. Conclusion Different conjugation linkers whereby antibodies are conjugated with LPD can affect the physicochemical properties of LPD and antibody conjugation efficiency, thus directly affecting the gene silencing effect of TLPD. Immunoliposomes prepared by DSPE-PEG-MAL conjugation with anti-EGFR Fab’ are more effective than TLPD containing DSPE

  19. DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequences

    PubMed Central

    Meng, Fanchi; Kurgan, Lukasz

    2016-01-01

    Motivation: Disordered flexible linkers (DFLs) are disordered regions that serve as flexible linkers/spacers in multi-domain proteins or between structured constituents in domains. They are different from flexible linkers/residues because they are disordered and longer. Availability of experimentally annotated DFLs provides an opportunity to build high-throughput computational predictors of these regions from protein sequences. To date, there are no computational methods that directly predict DFLs and they can be found only indirectly by filtering predicted flexible residues with predictions of disorder. Results: We conceptualized, developed and empirically assessed a first-of-its-kind sequence-based predictor of DFLs, DFLpred. This method outputs propensity to form DFLs for each residue in the input sequence. DFLpred uses a small set of empirically selected features that quantify propensities to form certain secondary structures, disordered regions and structured regions, which are processed by a fast linear model. Our high-throughput predictor can be used on the whole-proteome scale; it needs <1 h to predict entire proteome on a single CPU. When assessed on an independent test dataset with low sequence-identity proteins, it secures area under the receiver operating characteristic curve equal 0.715 and outperforms existing alternatives that include methods for the prediction of flexible linkers, flexible residues, intrinsically disordered residues and various combinations of these methods. Prediction on the complete human proteome reveals that about 10% of proteins have a large content of over 30% DFL residues. We also estimate that about 6000 DFL regions are long with ≥30 consecutive residues. Availability and implementation: http://biomine.ece.ualberta.ca/DFLpred/. Contact: lkurgan@vcu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307636

  20. Solid-phase development of a L-hydroxybenzotriazole linker for heterocycle synthesis using analytical constructs.

    PubMed

    Scicinski, J J; Congreve, M S; Jamieson, C; Ley, S V; Newman, E S; Vinader, V M; Carr, R A

    2001-01-01

    The development of a 1-hydroxybenzotriazole linker for the synthesis of heterocyclic derivatives is described, utilizing analytical construct methodology to facilitate the analysis of resin samples. A UV-chromophore-containing analytical construct enabled the accurate determination of resin loading and the automated monitoring of key reactions using only small quantities of resin. The syntheses of an array of isoxazole derivatives are reported. PMID:11442396

  1. Stabilization of a highly porous metal-organic framework utilizing a carborane-based linker.

    PubMed

    Clingerman, Daniel J; Morris, William; Mondloch, Joseph E; Kennedy, Robert D; Sarjeant, Amy A; Stern, Charlotte; Hupp, Joseph T; Farha, Omar K; Mirkin, Chad A

    2015-04-18

    The first tritopic carborane-based linker, H3BCA (C15B24O6H30), based on closo-1,10-C2B8H10, has been synthesized and incorporated into a metal-organic framework (MOF), NU-700 (Cu3(BCA)2). In contrast to the analogous MOF-143, NU-700 can be activated with retention of porosity, yielding a BET surface area of 1870 m(2) g(-1). PMID:25767827

  2. Gold nanoparticles functionalised with fast water exchanging Gd3+ chelates: linker effects on the relaxivity.

    PubMed

    Ferreira, Miguel F; Gonçalves, Janaina; Mousavi, Bibimaryam; Prata, Maria I M; Rodrigues, Sérgio P J; Calle, Daniel; López-Larrubia, Pilar; Cerdan, Sebastian; Rodrigues, Tiago B; Ferreira, Paula M; Helm, Lothar; Martins, José A; Geraldes, Carlos F G C

    2015-03-01

    The relaxivity displayed by Gd(3+) chelates immobilized onto gold nanoparticles is the result of the complex interplay between the nanoparticle size, the water exchange rate and the chelate structure. In this work we study the effect of the length of ω-thioalkyl linkers, anchoring fast water exchanging Gd(3+) chelates onto gold nanoparticles, on the relaxivity of the immobilized chelates. Gold nanoparticles functionalized with Gd(3+) chelates of mercaptoundecanoyl and lipoyl amide conjugates of the DO3A-N-(α-amino)propionate chelator were prepared and studied as potential CA for MRI. High relaxivities per chelate, of the order of magnitude 28-38 mM(-1) s(-1) (30 MHz, 25 °C), were attained thanks to simultaneous optimization of the rotational correlation time and of the water exchange rate. Fast local rotational motions of the immobilized chelates around connecting linkers (internal flexibility) still limit the attainable relaxivity. The degree of internal flexibility of the immobilized chelates seems not to be correlated with the length of the connecting linkers. Biodistribution and MRI studies in mice suggest that the in vivo behavior of the gold nanoparticles was determined mainly by size. Small nanoparticles (HD = 3.9 nm) undergo fast renal clearance and avoidance of the RES organs while larger nanoparticles (HD = 4.8 nm) undergo predominantly hepatobiliary excretion. High relaxivities, allied to chelate and nanoparticle stability and fast renal clearance in vivo suggest that functionalized gold nanoparticles hold great potential for further investigation as MRI contrast agents. This study contributes to a better understanding of the effect of linker length on the relaxivity of gold nanoparticles functionalized with Gd(3+) complexes. It is a relevant contribution towards "design rules" for nanostructures functionalized with Gd(3+) chelates as Contrast Agents for MRI and multimodal imaging. PMID:25611006

  3. Making the Common Good Common

    ERIC Educational Resources Information Center

    Chase, Barbara

    2011-01-01

    How are independent schools to be useful to the wider world? Beyond their common commitment to educate their students for meaningful lives in service of the greater good, can they educate a broader constituency and, thus, share their resources and skills more broadly? Their answers to this question will be shaped by their independence. Any…

  4. Triazole bridges as versatile linkers in electron donor-acceptor conjugates

    PubMed Central

    de Miguel, Gustavo; Wielopolski, Mateusz; Schuster, David I.; Fazio, Michael A; Lee, Olivia P.; Haley, Christopher K.; Ortiz, Angy L.; Echegoyen, Luis; Clark, Timothy; Guldi, Dirk M.

    2011-01-01

    Aromatic triazoles have been frequently used as π-conjugated linkers in intramolecular electron transfer processes. To gain a deeper understanding of the electron mediating function of triazoles, we have synthesized a family of new triazole-based electron donor-acceptor conjugates. We have connected porphyrins and fullerenes through a central triazole moiety – (ZnP-Tri-C60) – each with a single change in their connection through the linker. An extensive photophysical and computational investigation reveals that the electron transfer dynamics – charge separation and charge recombination – in the different ZnP-Tri-C60 conjugates reflect a significant influence of the connectivity at the triazole linker. Except for m4m-ZnP-Tri-C60 17, the conjugates exhibit through-bond electron transfer with varying rate constants. Since the through-bond distance is nearly equal in the ZnP-Tri-C60 conjugates, the variation in charge separation and charge recombination dynamics is mainly associated with the electronic properties of the conjugates, including orbital energies, electron affinity, and the energies of the excited states. The changes of the electronic couplings are, in turn, a consequence of the different connectivity patterns at the triazole moieties. PMID:21702513

  5. Two distinct promoter elements in the human rRNA gene identified by linker scanning mutagenesis.

    PubMed Central

    Haltiner, M M; Smale, S T; Tjian, R

    1986-01-01

    A cell-free RNA polymerase I transcription system was used to evaluate the transcription efficiency of 21 linker scanning mutations that span the human rRNA gene promoter. Our analysis revealed the presence of two major control elements, designated the core and upstream elements, that affect the level of transcription initiation. The core element extends from -45 to +18 relative to the RNA start site, and transcription is severely affected (up to 100-fold) by linker scanning mutations in this region. Linker scanning and deletion mutations in the upstream element, located between nucleotides -156 and -107, cause a three- to fivefold reduction in transcription. Under certain reaction conditions, such as the presence of a high ratio of protein to template or supplementation of the reaction with partially purified protein fractions, sequences upstream of the core element can have an even greater effect (20- to 50-fold) on RNA polymerase I transcription. Primer extension analysis showed that RNA synthesized from all of these mutant templates is initiated at the correct in vivo start site. To examine the functional relationship between the core and the upstream region, mutant promoters were constructed that alter the orientation, distance, or multiplicity of these control elements relative to each other. The upstream control element appears to function in only one orientation, and its position relative to the core is constrained within a fairly narrow region. Moreover, multiple core elements in close proximity to each other have an inhibitory effect on transcription. Images PMID:3785147

  6. An Isotopically Coded CID-cleavable Biotinylated Cross-linker for Structural Proteomics*

    PubMed Central

    Petrotchenko, Evgeniy V.; Serpa, Jason J.; Borchers, Christoph H.

    2011-01-01

    Successful application of cross-linking combined with mass spectrometry for structural proteomics demands specifically designed cross-linking reagents to address challenges in the detection and assignment of cross-links. A combination of affinity enrichment, isotopic coding, and cleavage of the cross-linker is beneficial for detection and identification of the peptide cross-links. Here we describe a novel cross-linker, cyanurbiotindipropionylsuccinimide (CBDPS), that allows affinity enrichment of cross-linker-containing peptides with avidin. Affinity enrichment eliminates interfering non-cross-linked peptides and allows the researcher to focus on the analysis of the cross-linked peptides. CBDPS is also isotopically coded and CID-cleavable. The cleaved fragments still contain a portion of the isotopic label and can therefore be distinguished from unlabeled fragments by their distinct isotopic signatures in the MS/MS spectra. This cleavage information has been incorporated into a program for the automatic analysis of the MS/MS spectra of the cross-links. This allows rapid determination of cross-link type in addition to facilitating identification of the individual peptides constituting the interpeptide cross-links. Thus, affinity enrichment combined with isotopic coding and CID cleavage allows in-depth mass spectrometric analysis of the peptide cross-links. We have characterized the performance of CBDPS on the 120-kDa protein heterodimer of HIV reverse transcriptase. PMID:20622150

  7. Controlling toxicity of Peptide-drug conjugates by different chemical linker structures.

    PubMed

    Böhme, David; Beck-Sickinger, Annette G

    2015-05-01

    The side effects of chemotherapy can be overcome by linking toxic agents to tumor-targeting peptides with cleavable linkers. Herein, this concept is demonstrated by addressing the human Y1 receptor (hY1 R), overexpressed in breast tumors, with analogues of the hY1 R-preferring [F(7) ,P(34) ]NPY. First, carboxytetramethylrhodamine was connected to [F(7) ,P(34) ]NPY by an amide, ester, disulfide, or enzymatic linkage. Live imaging revealed hY1 R-mediated delivery and allowed visualization of time-dependent intracellular release. Next, the fluorophore was replaced by the toxic agent methotrexate (MTX). In addition to linkage through the amide, ester, disulfide bond, or enzymatic cleavage site, a novel disulfide/ester linker was designed and coupled to [F(7) ,P(34) ]NPY by solid-phase peptide synthesis. Internalization studies showed hY1 R subtype selective uptake, and cell viability experiments demonstrated hY1 R-mediated toxicity that was clearly dependent on the linkage type. Fast release profiles for fluorophore-[F(7) ,P(34) ]NPY analogues correlated with high toxicities of MTX conjugates carrying the same linker types and emphasize the relevance of new structures connecting the toxophore and the carrier. PMID:25914147

  8. Independent Biological and Biochemical Functions for Individual Structural Domains of Drosophila Linker Histone H1.

    PubMed

    Kavi, Harsh; Emelyanov, Alexander V; Fyodorov, Dmitry V; Skoultchi, Arthur I

    2016-07-15

    Linker histone H1 is among the most abundant components of chromatin. H1 has profound effects on chromosome architecture. H1 also helps to tether DNA- and histone-modifying enzymes to chromatin. Metazoan linker histones have a conserved tripartite structure comprising N-terminal, globular, and long, unstructured C-terminal domains. Here we utilize truncated Drosophila H1 polypeptides in vitro and H1 mutant transgenes in vivo to interrogate the roles of these domains in multiple biochemical and biological activities of H1. We demonstrate that the globular domain and the proximal part of the C-terminal domain are essential for H1 deposition into chromosomes and for the stability of H1-chromatin binding. The two domains are also essential for fly viability and the establishment of a normal polytene chromosome structure. Additionally, through interaction with the heterochromatin-specific histone H3 Lys-9 methyltransferase Su(var)3-9, the H1 C-terminal domain makes important contributions to formation and H3K9 methylation of heterochromatin as well as silencing of transposons in heterochromatin. Surprisingly, the N-terminal domain does not appear to be required for any of these functions. However, it is involved in the formation of a single chromocenter in polytene chromosomes. In summary, we have discovered that linker histone H1, similar to core histones, exerts its multiple biological functions through independent, biochemically separable activities of its individual structural domains. PMID:27226620

  9. Hydrogen-bonded inclusion compounds with reversed polarity: anionic metal-complexes and cationic organic linkers.

    PubMed

    Prakash, M Jaya; Sevov, Slavi C

    2011-12-19

    Synthesized and structurally characterized is a new series of soft-host frameworks assembled by charge-assisted hydrogen bonds between an anionic metal complex (MC) and cationic organic linkers (OL), specifically [Co(en)(ox)(2)](-) and diprotonated 4,4'-bipyridinium (H(2)bpy) or 1,2-bis(4-pyridinium)ethylene (H(2)bpye). While frameworks built of cationic complexes and anionic organic linkers are already well-known, the seven new compounds described here represent the first series of frameworks with reversed polarity, that is, made of anionic complexes and cationic organic linkers. The compounds have a general formula [OL][MC](2)·n(guest), where the guest molecules 4,4'-biphenol (bp), 4-methoxyphenol (mp), 1,4-dimethoxybenzene (dmb), 1,6-dimethoxynaphtalene (dmn), and 4-nitroanisole (na). Structurally the compounds can be described as pillared-layer frameworks with layers constructed of MC anions and linked together by hydrogen-bonded cationic OL pillars. The guest molecules occupy the galleries between the pillars while their steric, electronic, and π-π and hydrogen-bonding capabilities influence the overall structure of the soft frameworks. PMID:22085246

  10. TGF-β induces fascin expression in gastric cancer via phosphorylation of smad3 linker area

    PubMed Central

    Li, Liling; Cao, Fang; Liu, Baoan; Luo, Xiaojuan; Ma, Xin; Hu, Zhongliang

    2015-01-01

    Background: Fascin is an actin-bundling protein critical for tumor invasion. TGF-β could induce fascin expression in gastric cancer cells. In this study, we attempted to explore the role of p-smad3L in the expression of fascin induced by TGF-β in gastric cancer cells. Methods: Pseudopodia were evaluated by immunofluorescence. Fascin expression was detected by RT-PCR and western blot. Smad3 siRNA was used to repress the endogenous smad3. The phosphorylations of smad3 linker region at sites s204, s208 and s213 were detected by western blot. The fascin promoter reporter activity was measured by dual luciferase assay. Results: TGF-β could increase the formation of pseudopodia and the expression of fascin in gastric cancer cells. Smad3 depletion abrogated the expression of fascin induced by TGF-β. The phosphorylation of smad3 linker region at serine 204, 208 and 213 was enhanced in gastric cancer cells after TGF-β treatment. The fascin promoter reporter activity was significantly enhanced with TGF-β treatment in both wild-type Smad3 group and Smad3EPSM group (P<0.05). Furthermore, the fascin promoter reporter activity in the wild-type Smad3 transfectant cells was significantly higher than that in Smad3EPSM cells (P<0.05). Conclusions: fascin expression induced by TGF-β depends on smad3, at least in part, depends on smad3 linker phosphorylation. PMID:26269751

  11. Lipid membrane editing with peptide cargo linkers in cells and synthetic nanostructures

    PubMed Central

    Pan, Hua; Myerson, Jacob W.; Ivashyna, Olena; Soman, Neelesh R.; Marsh, Jon N.; Hood, Joshua L.; Lanza, Gregory M.; Schlesinger, Paul H.; Wickline, Samuel A.

    2010-01-01

    Current strategies for deploying synthetic nanocarriers involve the creation of agents that incorporate targeting ligands, imaging agents, and/or therapeutic drugs into particles as an integral part of the formulation process. Here we report the development of an amphipathic peptide linker that enables postformulation editing of payloads without the need for reformulation to achieve multiplexing capability for lipidic nanocarriers. To exemplify the flexibility of this peptide linker strategy, 3 applications were demonstrated: converting nontargeted nanoparticles into targeting vehicles; adding cargo to preformulated targeted nanoparticles for in vivo site-specific delivery; and labeling living cells for in vivo tracking. This strategy is expected to enhance the clinical application of molecular imaging and/or targeted therapeutic agents by offering extended flexibility for multiplexing targeting ligands and/or drug payloads that can be selected after base nanocarrier formulation.—Pan, H., Myerson, J. W., Ivashyna, O., Soman, N. R., Marsh, J. N., Hood, J. L., Lanza, G. M., Schlesinger, P. H., Wickline, S. A.. Lipid membrane editing with peptide cargo linkers in cells and synthetic nanostructures. PMID:20335225

  12. Assessment of Local Friction in Protein Folding Dynamics Using a Helix Cross-Linker

    PubMed Central

    Markiewicz, Beatrice N.; Jo, Hyunil; Culik, Robert M.; DeGrado, William F.; Gai, Feng

    2013-01-01

    Internal friction arising from local steric hindrance and/or the excluded volume effect plays an important role in controlling not only the dynamics of protein folding but also conformational transitions occurring within the native state potential well. However, experimental assessment of such local friction is difficult because it does not manifest itself as an independent experimental observable. Herein, we demonstrate, using the miniprotein trp-cage as a testbed, that it is possible to selectively increase the local mass density in a protein and hence the magnitude of local friction, thus making its effect directly measureable via folding kinetic studies. Specifically, we show that when a helix cross-linker, m-xylene, is placed near the most congested region of the trp-cage it leads to a significant decrease in both the folding rate (by a factor of 3.8) and unfolding rate (by a factor of 2.5 at 35 °C), but has little effect on protein stability. Thus, these results, in conjunction with those obtained with another cross-linked trp-cage and two uncross-linked variants, demonstrate the feasibility of using a non-perturbing cross-linker to help quantify the effect of internal friction. In addition, we estimate that an m-xylene cross-linker could lead to an increase in the roughness of the folding energy landscape by as much as 0.4-1.0kBT. PMID:24205975

  13. Tuning of coordination behavior of thiosulfate ion by organic linkers in cadmium thiosulfate compounds

    NASA Astrophysics Data System (ADS)

    Paul, Avijit Kumar

    2016-12-01

    Three new inorganic-organic hybrid molecular cadmium thiosulfate compounds, [Cd(S2O3) (C3H10N2)2], I, [Cd2(C10H8N2)4(S2O3)2](C10H8N2)·2H2O, II and [Cd2(C10H8N2)2(H2O)2(S2O3)2](C10H8N2)·2H2O, III have been synthesized using different organic linkers as co-ligand and characterized them thoroughly. The compounds have connectivity between the Cd-centers, the thiosulfate units and the organic ligands forming molecular (zero-dimensional) structures. The ligating behaviors of thiosulfate unit have been triggered by organic linkers. The coordination number of thiosulfate ion to the metal ion can also be enhanced by varying the aromatic ligands instead of aliphatic ligand. The molecular structures are stabilized and formed three-dimensional packing structures through extensive hydrogen bonds and van der Waals interactions. The free aromatic bipyridine ligands are observed in the crystal structures II and III. The unique type of π⋯π interactions play an important role for the stabilization of these two structures. Theoretical studies also revealed that the value of π⋯π interactions are comparable with the classical hydrogen bond interactions. The present study illustrates the usefulness of the organic linkers for the structural modifications in inorganic-organic hybrid compounds.

  14. Linker proteins enable ultrafast excitation energy transfer in the phycobilisome antenna system of Thermosynechococcus vulcanus.

    PubMed

    Nganou, C; David, L; Adir, N; Mkandawire, M

    2016-01-01

    We applied a femtosecond flash method, using induced transient absorption changes, to obtain a time-resolved view of excitation energy transfer in intact phycobilisomes of Thermosynechococcus vulcanus at room temperature. Our measurement of an excitation energy transfer rate of 888 fs in phycobilisomes shows the existence of ultrafast kinetics along the phycocyanin rod subcomplex to the allophycocyanin core that is faster than expected for previous excitation energy transfer based on Förster theory in phycobilisomes. Allophycocyanin in the core further transfers energy to the terminal emitter(s) in 17 ps. In the phycobilisome, rod doublets composed of hexameric phycocyanin discs and internal linker proteins are arranged in a parallel fashion, facilitating direct rod-rod interactions. Excitonic splitting likely drives rod absorption at 635 nm as a result of strong coupling between β84 chromophores (20 ± 1 Å) in adjacent hexamers. In comparison to the absorbance of the phycobilisome antenna system of the cyanobacterium Acaryochloris marina, which possesses a single rod structure, the linkers in T. vulcanus rods induce a 17 nm red shift in the absorbance spectrum. Furthermore, the kinetics of 888 fs indicates that the presence of the linker protein induces ultrafast excitation energy transfer between phycocyanin and allophycocyanin inside the phycobilisome, which is faster than all previous excitation energy transfer in phycobilisome subunits or sub-complexes reported to date. PMID:26537632

  15. The charged linker of the molecular chaperone Hsp90 modulates domain contacts and biological function

    PubMed Central

    Jahn, Markus; Rehn, Alexandra; Pelz, Benjamin; Hellenkamp, Björn; Richter, Klaus; Rief, Matthias; Buchner, Johannes; Hugel, Thorsten

    2014-01-01

    The heat shock protein 90 (Hsp90) is a dimeric molecular chaperone essential in numerous cellular processes. Its three domains (N, M, and C) are connected via linkers that allow the rearrangement of domains during Hsp90’s chaperone cycle. A unique linker, called charged linker (CL), connects the N- and M-domain of Hsp90. We used an integrated approach, combining single-molecule techniques and biochemical and in vivo methods, to study the unresolved structure and function of this region. Here we show that the CL facilitates intramolecular rearrangements on the milliseconds timescale between a state in which the N-domain is docked to the M-domain and a state in which the N-domain is more flexible. The docked conformation is stabilized by 1.1 kBT (2.7 kJ/mol) through binding of the CL to the N-domain of Hsp90. Docking and undocking of the CL affects the much slower intermolecular domain movement and Hsp90’s chaperone cycle governing client activation, cell viability, and stress tolerance. PMID:25468961

  16. PDP-CON: prediction of domain/linker residues in protein sequences using a consensus approach.

    PubMed

    Chatterjee, Piyali; Basu, Subhadip; Zubek, Julian; Kundu, Mahantapas; Nasipuri, Mita; Plewczynski, Dariusz

    2016-04-01

    The prediction of domain/linker residues in protein sequences is a crucial task in the functional classification of proteins, homology-based protein structure prediction, and high-throughput structural genomics. In this work, a novel consensus-based machine-learning technique was applied for residue-level prediction of the domain/linker annotations in protein sequences using ordered/disordered regions along protein chains and a set of physicochemical properties. Six different classifiers-decision tree, Gaussian naïve Bayes, linear discriminant analysis, support vector machine, random forest, and multilayer perceptron-were exhaustively explored for the residue-level prediction of domain/linker regions. The protein sequences from the curated CATH database were used for training and cross-validation experiments. Test results obtained by applying the developed PDP-CON tool to the mutually exclusive, independent proteins of the CASP-8, CASP-9, and CASP-10 databases are reported. An n-star quality consensus approach was used to combine the results yielded by different classifiers. The average PDP-CON accuracy and F-measure values for the CASP targets were found to be 0.86 and 0.91, respectively. The dataset, source code, and all supplementary materials for this work are available at https://cmaterju.org/cmaterbioinfo/ for noncommercial use. PMID:26969678

  17. Design of CID-Cleavable Protein Cross-linkers: Identical Mass Modifications for Simpler Sequence Analysis

    PubMed Central

    Kandur, Wynne V.; Kao, Athit; Vellucci, Danielle; Huang, Lan; Rychnovsky, Scott D.

    2015-01-01

    The cross-linking Mass Spectrometry (XL-MS) technique has enormous potential for studying the interactions between proteins, and it can provide detailed structural information about the interaction interfaces in large protein complexes. Such information has been difficult to obtain by conventional structural methods. One of the primary impediments to the wider use of the XL-MS technique is the extreme challenge in sequencing cross-linked peptides because of their complex fragmentation patterns in MS. A recent innovation is the development of MS-cleavable cross-linkers, which allows direct sequencing of component peptides for facile identification. Sulfoxides are an intriguing class of thermally-cleavable compounds that have been shown to fragment selectively during low-energy collisional induced dissociation (CID) analysis. Current CID-cleavable cross-linkers create fragmentation patterns in MS2 of multiple peaks for each cross-linked peptide. Reducing the complexity of the fragmentation pattern in MS2 facilitates subsequent MS3 sequencing of the cross-linked peptides. The first authentic identical mass linker (IML) has now been designed, prepared, and evaluated. Multistage tandem mass spectrometry (MSn) analysis has demonstrated that the IML cross-linked peptides indeed yield one peak per peptide constituent in MS2 as predicted, thus allowing effective and sensitive MS3 analysis for unambiguous identification. Selective fragmentation for IML cross-linked peptides from the 19S proteasome complex was observed, providing a proof-of-concept demonstration for XL-MS studies on protein complexes. PMID:26269432

  18. Dishevelled is a NEK2 kinase substrate controlling dynamics of centrosomal linker proteins.

    PubMed

    Cervenka, Igor; Valnohova, Jana; Bernatik, Ondrej; Harnos, Jakub; Radsetoulal, Matej; Sedova, Katerina; Hanakova, Katerina; Potesil, David; Sedlackova, Miroslava; Salasova, Alena; Steinhart, Zachary; Angers, Stephane; Schulte, Gunnar; Hampl, Ales; Zdrahal, Zbynek; Bryja, Vitezslav

    2016-08-16

    Dishevelled (DVL) is a key scaffolding protein and a branching point in Wnt signaling pathways. Here, we present conclusive evidence that DVL regulates the centrosomal cycle. We demonstrate that DVL dishevelled and axin (DIX) domain, but not DIX domain-mediated multimerization, is essential for DVL's centrosomal localization. DVL accumulates during the cell cycle and associates with NIMA-related kinase 2 (NEK2), which is able to phosphorylate DVL at a multitude of residues, as detected by a set of novel phospho-specific antibodies. This creates interfaces for efficient binding to CDK5 regulatory subunit-associated protein 2 (CDK5RAP2) and centrosomal Nek2-associated protein 1 (C-NAP1), two proteins of the centrosomal linker. Displacement of DVL from the centrosome and its release into the cytoplasm on NEK2 phosphorylation is coupled to the removal of linker proteins, an event necessary for centrosomal separation and proper formation of the mitotic spindle. Lack of DVL prevents NEK2-controlled dissolution of loose centrosomal linker and subsequent centrosomal separation. Increased DVL levels, in contrast, sequester centrosomal NEK2 and mimic monopolar spindle defects induced by a dominant negative version of this kinase. Our study thus uncovers molecular crosstalk between centrosome and Wnt signaling. PMID:27486244

  19. Unexpected role of linker position on ammonium gemini surfactant lyotropic gyroid phase stability.

    PubMed

    Sorenson, Gregory P; Mahanthappa, Mahesh K

    2016-02-28

    Arising from the water-driven self-assembly of amphiphiles over generally narrow temperature and composition phase windows, aqueous lyotropic liquid crystal (LLC) network phases are useful in applications as therapeutic delivery vehicles and templates for mesoporous material syntheses. While a clear set of amphiphile design rules that enables access to these intricate three-dimensional structures has yet to emerge, recent work indicates that bis(ammonium), bis(phosphonium), and dicarboxylate gemini ("twin tail") surfactants enable enhanced access to LLC network phases such as the double gyroid (G). In order to better understand the scope of this amphiphile design strategy, we investigated the synthesis and aqueous LLC self-assembly behaviors of a homologous series of quaternary gemini bis(ammonium) dichloride surfactants, in which we varied the position of the hydrophobic linker that connects the constituent single tail surfactants. These experiments demonstrate that the position of the linker directly impacts the maximum counterion-headgroup hydration capacity and the extent of counterion-headgroup association, all of which contribute to the aqueous lyotropic double gyroid network phase stability. Thus, judicious selection of the linker position in ionic gemini surfactants provides a new molecular design tool for manipulating LLC network phase stability. PMID:26806651

  20. Linker Length-Dependent Control of Gemini Surfactant Aqueous Lyotropic Gyroid Phase Stability.

    PubMed

    Perroni, Dominic V; Baez-Cotto, Carlos M; Sorenson, Gregory P; Mahanthappa, Mahesh K

    2015-03-19

    Network-phase lyotropic liquid crystals (LLCs) derived from the water-directed self-assembly of small molecule amphiphiles comprise a useful class of soft nanomaterials, with wide-ranging applications in structural biology and membrane science. However, few known surfactants enable access to these mesophases over wide temperature and amphiphile concentration phase windows. Recent studies have demonstrated that gemini ("twin tail") dicarboxylate surfactants, in which alkyl carboxylates are covalently linked near the headgroups by a hydrophobic bridge, exhibit increased propensities to form double gyroid network phase LLCs. We demonstrate herein that the lyotropic self-assembly behaviors of gemini dicarboxylates sensitively depend on the linker length, whereby odd-carbon linkers stabilize the double gyroid network LLC over unprecedented amphiphile concentration windows up to ∼45 wt % wide between T ≈ 22-80 °C. These self-assembly phenomena, which arise from the linker length-dependent preferred molecular conformations of these amphiphiles, will broaden the technological applications of these nanostructured LLCs. PMID:26262858

  1. Cysteines control the N- and C-linker-dependent gating of KCNH1 potassium channels.

    PubMed

    Sahoo, Nirakar; Schönherr, Roland; Hoshi, Toshinori; Heinemann, Stefan H

    2012-05-01

    KCNH1 (EAG1) is a member of the Kv family of voltage-gated potassium channels. However, KCNH1 channels also show some amino-acid sequence similarity to cyclic-nucleotide-regulated channels: they harbor an N-terminal PAS domain, a C-terminal cyclic nucleotide binding homology domain (cNBHD), and N- and C-terminal binding sites for calmodulin. Another notable feature is the channels' high sensitivity toward oxidative modification. Using human KCNH1 expressed in Xenopus oocytes and HEK 293 cells we investigated how oxidative modification alters channel function. Intracellular application of H(2)O(2) or cysteine-specific modifiers potently inhibited KCNH1 channels in two phases. Our systematic cysteine mutagenesis study showed that the rapid and dominant phase was attributed to a right-shift in the voltage dependence of activation, caused by chemical modification of residues C145 and C214. The slow component depended on the C-terminal residues C532 and C562. The cysteine pairs are situated at structural elements linking the transmembrane S1 segment with the PAS domain (N-linker) and the transmembrane channel gate S6 with the cNBH domain (C-linker), respectively. The functional state of KCNH1 channels is determined by the oxidative status of these linkers that provide an additional dimension of channel regulation. PMID:22310694

  2. A Substructure inside Spiral Arms, and a Mirror Image across the Galactic Meridian

    NASA Astrophysics Data System (ADS)

    Vallée, Jacques P.

    2016-04-01

    Though the galactic density wave theory is over 50 years old and is well known in science, it has been difficult to say whether it fits our own Milky Way disk. Here we show a substructure inside the spiral arms. This substructure is reversing with respect to the Galactic Meridian (longitude zero), and crosscuts of the arms at negative longitudes appear as mirror images of crosscuts of the arms at positive longitudes. Four lanes are delineated: a mid-arm (extended 12CO gas at the mid-arm, H i atoms), an in-between offset by about 100 pc (synchrotron, radio recombination lines), an in-between offset by about 200 pc (masers, colder dust), and an inner edge (hotter dust seen in mid-IR and near-IR).

  3. Serous cutaneous glands in anurans: Fourier transform analysis of the repeating secretory granule substructure

    NASA Astrophysics Data System (ADS)

    Nosi, D.; Delfino, G.; Quercioli, F.

    2013-03-01

    A combined transmission electron microscopy (TEM) and Fourier transform analysis has been performed on the secretory granules storing active peptides/proteins in serous cutaneous glands of n = 12 anuran species. Previous TEM investigation showed that the granules are provided with remarkable repeating substructures based on discrete subunits, arranged into a consistent framework. Furthermore, TEM findings revealed that this recurrent arrangement is acquired during a prolonged post-Golgian (or maturational) processing that affects the secretory product. Maturation leads to a variety of patterns depending on the degree of subunit clustering. This variety of recurrent patterns has been plotted into a range of frequency spectra. Through this quantitative approach, we found that the varying granule substructure can be reduced to a single mechanism of peptide/protein aggregation.

  4. More evidence of substructure in the motions of nearby halo stars

    NASA Astrophysics Data System (ADS)

    Re Fiorentin, P.; Helmi, A.; Lattanzi, M. G.; Spagna, A.

    2004-07-01

    We explore the stellar halo of the Milky Way to search for fossil signatures of past mergers. We use the Beers et al. (2000) catalog of non-kinematically selected metal poor stars in the solar neighborhood to select subsets of halo stars within 1-2 kpc of the Sun. Motivated by the results of high resolution CDM simulations, we look for substructure in the kinematics of the fastest stars. When a two-point velocity correlation function is applied to these subsets, statistical evidence of substructure is found. This appears to be due to a small moving group with dynamical properties similar to the stellar "stream" previously discovered by Helmi et al. (1999).

  5. Visualization of podocyte substructure with structured illumination microscopy (SIM): a new approach to nephrotic disease

    PubMed Central

    Pullman, James M.; Nylk, Jonathan; Campbell, Elaine C.; Gunn-Moore, Frank J.; Prystowsky, Michael B.; Dholakia, Kishan

    2016-01-01

    A detailed microscopic analysis of renal podocyte substructure is essential to understand and diagnose nephrotic kidney disease. Currently only time consuming electron microscopy (EM) can resolve this substructure. We used structured illumination microscopy (SIM) to examine frozen sections of renal biopsies stained with an immunofluorescence marker for podocin, a protein localized to the perimeter of the podocyte foot processes and compared them with EM in both normal and nephrotic disease biopsies. SIM images of normal glomeruli revealed curvilinear patterns of podocin densely covering capillary walls similar to podocyte foot processes seen by EM. Podocin staining of all nephrotic disease biopsies were significantly different than normal, corresponding to and better visualizing effaced foot processes seen by EM. The findings support the first potential use of SIM in the diagnosis of nephrotic disease. PMID:26977341

  6. Characterization Method for 3D Substructure of Nuclear Cell Based on Orthogonal Phase Images

    PubMed Central

    Ji, Ying; Liang, Minjie; Hua, Tingting; Xu, Yuanyuan; Xin, Zhiduo; Wang, Yawei

    2015-01-01

    A set of optical models associated with blood cells are introduced in this paper. All of these models are made up of different parts possessing symmetries. The wrapped phase images as well as the unwrapped ones from two orthogonal directions related to some of these models are obtained by simulation technique. Because the phase mutation occurs on the boundary between nucleus and cytoplasm as well as on the boundary between cytoplasm and environment medium, the equation of inflexion curve is introduced to describe the size, morphology, and substructure of the nuclear cell based on the analysis of the phase features of the model. Furthermore, a mononuclear cell model is discussed as an example to verify this method. The simulation result shows that characterization with inflexion curve based on orthogonal phase images could describe the substructure of the cells availably, which may provide a new way to identify the typical biological cells quickly without scanning. PMID:26355740

  7. Exploring Milky Way Halo Substructures with Large-Area Sky Surveys

    NASA Astrophysics Data System (ADS)

    Li, Ting

    2016-01-01

    Over the last two decades, large-area photometric surveys have provided deep photometric catalogs of stars in the Milky Way. As a result, our understanding of the formation of the Galactic halo has evolved from a simple monolitic collapse model to a much more complex and dynamic structure. The stellar halo is now known to be inhabited by a variety of spatial and kinematic stellar substructures, ranging from stellar clouds and streams to dwarf galaxies, predicted by hierarchical Lambda-CDM models of galaxy formation. In my talk, I will present the latest discoveries of the halo substructures found in the Dark Energy Survey (DES). I will also discuss the spectroscopic follow-up observations of the stellar cloud candidates found in the Two Micron All Sky Survey and the dwarf galaxy candidates found in DES. These newly discovered features can provide a more complete census of our Galaxy's formation history.

  8. The extended stellar substructures of four metal-poor globular clusters in the Galactic bulge

    NASA Astrophysics Data System (ADS)

    Chun, Sang-Hyun; Sohn, Young-Jong

    2016-08-01

    We investigated the stellar density substructures around four metal-poor globular clusters (NGC 6266, NGC 6626, NGC 6642, and NGC 6723) in the Galactic bulge. Wide-field near-infrared (JHK s ) imaging data were obtained from WFCAM of UKIRT telescope. Field stars contamination around the globular clusters was reduced by using a statistical weighted filtering algorithm. Tidal stripping stellar substructures in the form of tidal tail (NGC 6266 and NGC 6626) or small density lobes/chunk (NGC 6642 and NGC 6723) were found around the four globular clusters in the two-dimensional density contour maps. We also find the overdensity features, which deviate from the theoretical models, in the outer region of radial density profiles. The observed results imply that the four globular clusters have experienced a strong tidal force or the bulge/disk shock effect of the Galaxy.

  9. Visualization of podocyte substructure with structured illumination microscopy (SIM): a new approach to nephrotic disease.

    PubMed

    Pullman, James M; Nylk, Jonathan; Campbell, Elaine C; Gunn-Moore, Frank J; Prystowsky, Michael B; Dholakia, Kishan

    2016-02-01

    A detailed microscopic analysis of renal podocyte substructure is essential to understand and diagnose nephrotic kidney disease. Currently only time consuming electron microscopy (EM) can resolve this substructure. We used structured illumination microscopy (SIM) to examine frozen sections of renal biopsies stained with an immunofluorescence marker for podocin, a protein localized to the perimeter of the podocyte foot processes and compared them with EM in both normal and nephrotic disease biopsies. SIM images of normal glomeruli revealed curvilinear patterns of podocin densely covering capillary walls similar to podocyte foot processes seen by EM. Podocin staining of all nephrotic disease biopsies were significantly different than normal, corresponding to and better visualizing effaced foot processes seen by EM. The findings support the first potential use of SIM in the diagnosis of nephrotic disease. PMID:26977341

  10. A Note on Substructuring Preconditioning for Nonconforming Finite Element Approximations of Second Order Elliptic Problems

    NASA Technical Reports Server (NTRS)

    Maliassov, Serguei

    1996-01-01

    In this paper an algebraic substructuring preconditioner is considered for nonconforming finite element approximations of second order elliptic problems in 3D domains with a piecewise constant diffusion coefficient. Using a substructuring idea and a block Gauss elimination, part of the unknowns is eliminated and the Schur complement obtained is preconditioned by a spectrally equivalent very sparse matrix. In the case of quasiuniform tetrahedral mesh an appropriate algebraic multigrid solver can be used to solve the problem with this matrix. Explicit estimates of condition numbers and implementation algorithms are established for the constructed preconditioner. It is shown that the condition number of the preconditioned matrix does not depend on either the mesh step size or the jump of the coefficient. Finally, numerical experiments are presented to illustrate the theory being developed.

  11. Radio lobes and forbidden O III profile substructure in Seyfert galaxies

    SciTech Connect

    Whittle, M.; Pedlar, A.; Unger, S.W.; Axon, D.J.; Meurs, E.J.A.

    1988-03-01

    High spatial and spectral resolution observations are presented for 10 Seyfert galaxies in the H-beta-forbidden O III 5007 A spectral region. In most of the objects, there is evidence for forbidden O III profile substructure, which appears to be most conspicuous close to the location of a radio lobe. The relative intensities of forbidden O III component emission and ambient forbidden O III emission vary greatly from object to object. A control sample shows little evidence for spatially resolved forbidden O III profile substructure. The forbidden O III components usually have high excitation. The component velocities can fall well outside the maximum galactic rotation amplitude and, in some cases, are opposite to the sense of rotation. This strongly suggests that the component gas does not rotate with the rest of the galactic gas but is instead undergoing systematic outflow. 47 references.

  12. Correlation of substructure with time-dependent fatigue properties of aisi304 stainless steel

    NASA Astrophysics Data System (ADS)

    Ermi, A. M.; Moteff, John

    1982-09-01

    Transmission electron microscopy was employed to study the substructure of AISI 304 stainless steel tested at 482, 593, and 650 °C in low-cycle fatigue with various hold times. Total strains investigated ranged from 0.5 to 2.0 pct, strain rates of 4 E-03 and 4 E-05 s-1. The cell size was found to be inversely related to the relaxed tensile saturation stress, but with different constants of proportionality for the two strain rates. At the lower strain rate, substructures tended to resemble those produced by pure creep. A modified work-hardening theory was used to relate the peak saturation stress to both plastic strain and cell size.

  13. Discovering Concept Mappings by Similarity Propagation among Substructures

    NASA Astrophysics Data System (ADS)

    Pan, Qi H.; Hadzic, Fedja; Dillon, Tharam S.

    Concept matching is important when heterogeneous data sources are to be merged for the purpose of knowledge sharing. It has many useful applications in areas such as schema matching, ontology matching, scientific knowledge management, e-commerce, enterprise application integration, etc. With the desire of knowledge sharing and reuse in these fields, merging commonly occurs among different organizations where the knowledge describing the same domain is to be matched. Due to the different naming conventions, granularity and the use of concepts in different contexts, a semantic approach to this problem is preferred in comparison to syntactic approach that performs matches based upon the labels only. We propose a concept matching method that initially does not consider labels when forming candidate matches, but rather utilizes structural information to take the context into account and detect complex matches. Real world knowledge representations (schemas) are used to evaluate the method.

  14. Dislocation substructures developed in martensitic steels under thermal fatigue

    NASA Astrophysics Data System (ADS)

    Alvarez-Armas, I.; Armas, A. F.; Petersen, C.

    1992-09-01

    Thermal fatigue tests were carried out on a martensitic steel, DIN denomination W. Nr. 1.4914, commonly named MANET I. The tests were performed in air by allowing the sample to serve as its own heater and converting any longitudinal thermal deformation of the specimen into elastic or inelastic deformation. The low temperature was held constant and equal to 473 K and variable values, 823, 873, 923, 973 K for the high temperature were selected. The effects of different thermal cycling ranges on the mechanical behavior and the accompanying microstructural changes in the specimen were evaluated. A continous softening preceded by a stability period was observed in all thermal fatigue tests. Higher temperature changes produce an accelerated softening process. The original lath structure evolves to a mixed structure of expanded laths and subgrains or a fully subgrain structure depending on the temperature range.

  15. The substructure and luminescence of low-temperature AlGaAs/GaAs(100) heterostructures

    SciTech Connect

    Seredin, P. V. Glotov, A. V.; Domashevskaya, E. P.; Arsentyev, I. N. Vinokurov, D. A.; Tarasov, I. S.; Zhurbina, I. A.

    2010-02-15

    The substructure and luminescence of low-temperature epitaxial AlGaAs alloys are studied by Raman spectroscopy and photoluminescence spectroscopy. It is shown that the experimental data obtained in the study are consistent with the results of the previous structural and optical study. The assumption that, at high concentrations of carbon acceptors, the acceptor atoms concentrate at lattice defects of the AlGaAs crystal alloys to form carbon nanocrystals is confirmed.

  16. Detection of Lensing Substructure Using ALMA Observations of the Dusty Galaxy SDP.81

    NASA Astrophysics Data System (ADS)

    Hezaveh, Yashar D.; Dalal, Neal; Marrone, Daniel P.; Mao, Yao-Yuan; Morningstar, Warren; Wen, Di; Blandford, Roger D.; Carlstrom, John E.; Fassnacht, Christopher D.; Holder, Gilbert P.; Kemball, Athol; Marshall, Philip J.; Murray, Norman; Perreault Levasseur, Laurence; Vieira, Joaquin D.; Wechsler, Risa H.

    2016-05-01

    We study the abundance of substructure in the matter density near galaxies using ALMA Science Verification observations of the strong lensing system SDP.81. We present a method to measure the abundance of subhalos around galaxies using interferometric observations of gravitational lenses. Using simulated ALMA observations we explore the effects of various systematics, including antenna phase errors and source priors, and show how such errors may be measured or marginalized. We apply our formalism to ALMA observations of SDP.81. We find evidence for the presence of a M = 108.96±0.12 M ⊙ subhalo near one of the images, with a significance of 6.9σ in a joint fit to data from bands 6 and 7; the effect of the subhalo is also detected in both bands individually. We also derive constraints on the abundance of dark matter (DM) subhalos down to M ∼ 2 × 107 M ⊙, pushing down to the mass regime of the smallest detected satellites in the Local Group, where there are significant discrepancies between the observed population of luminous galaxies and predicted DM subhalos. We find hints of additional substructure, warranting further study using the full SDP.81 data set (including, for example, the spectroscopic imaging of the lensed carbon monoxide emission). We compare the results of this search to the predictions of ΛCDM halos, and find that given current uncertainties in the host halo properties of SDP.81, our measurements of substructure are consistent with theoretical expectations. Observations of larger samples of gravitational lenses with ALMA should be able to improve the constraints on the abundance of galactic substructure.

  17. Thinking outside the ROCs: Designing decorrelated taggers (DDT) for jet substructure

    DOE PAGESBeta

    Dolen, James; Harris, Philip; Marzani, Simone; Rappoccio, Salvatore; Tran, Nhan

    2016-05-26

    Here, we explore the scale-dependence and correlations of jet substructure observables to improve upon existing techniques in the identification of highly Lorentz-boosted objects. Modified observables are designed to remove correlations from existing theoretically well-understood observables, providing practical advantages for experimental measurements and searches for new phenomena. We study such observables in W jet tagging and provide recommendations for observables based on considerations beyond signal and background efficiencies.

  18. Thinking outside the ROCs: Designing Decorrelated Taggers (DDT) for jet substructure

    NASA Astrophysics Data System (ADS)

    Dolen, James; Harris, Philip; Marzani, Simone; Rappoccio, Salvatore; Tran, Nhan

    2016-05-01

    We explore the scale-dependence and correlations of jet substructure observables to improve upon existing techniques in the identification of highly Lorentz-boosted objects. Modified observables are designed to remove correlations from existing theoretically well-understood observables, providing practical advantages for experimental measurements and searches for new phenomena. We study such observables in W jet tagging and provide recommendations for observables based on considerations beyond signal and background efficiencies.

  19. Detection of Lensing Substructure Using Alma Observations of the Dusty Galaxy SDP.81

    DOE PAGESBeta

    Hezaveh, Yashar D.; Dalal, Neal; Marrone, Daniel P.; Mao, Yao-Yuan; Morningstar, Warren; Wen, Di; Blandford, Roger D.; Carlstrom, John E.; Fassnacht, Christopher D.; Holder, Gilbert P.; et al

    2016-05-19

    We study the abundance of substructure in the matter density near galaxies using ALMA Science Verification observations of the strong lensing system SDP.81. We present a method to measure the abundance of subhalos around galaxies using interferometric observations of gravitational lenses. Using simulated ALMA observations we explore the effects of various systematics, including antenna phase errors and source priors, and show how such errors may be measured or marginalized. We apply our formalism to ALMA observations of SDP.81. We find evidence for the presence of a M = 108.96±0.12 M⊙ subhalo near one of the images, with a significance ofmore » 6.9σ in a joint fit to data from bands 6 and 7; the effect of the subhalo is also detected in both bands individually. We also derive constraints on the abundance of dark matter (DM) subhalos down to M ~ 2 × 107 M⊙, pushing down to the mass regime of the smallest detected satellites in the Local Group, where there are significant discrepancies between the observed population of luminous galaxies and predicted DM subhalos. We find hints of additional substructure, warranting further study using the full SDP.81 data set (including, for example, the spectroscopic imaging of the lensed carbon monoxide emission). We compare the results of this search to the predictions of ΛCDM halos, and find that given current uncertainties in the host halo properties of SDP.81, our measurements of substructure are consistent with theoretical expectations. Finally, observations of larger samples of gravitational lenses with ALMA should be able to improve the constraints on the abundance of galactic substructure.« less

  20. Calibration of TDR Test Probe for Measuring Moisture in the Body of the Railway Substructure and its Subgrade

    NASA Astrophysics Data System (ADS)

    Dobeš, Peter

    2015-12-01

    In the introduction of the paper there is characterized a way of monitoring the moisture in the railway substructure in the experimental stand, which is a part of the experimental workplace of the Department of Railway Engineering and Track Management. A substantial part of the paper is devoted to the calibration of TDR test probe for selected rock materials as a basic prerequisite for the determination of the actual moisture in the body of the railway substructure and subgrade.

  1. Incorporation of different bridge length linkers in enzyme and its use in the preparation of enzyme conjugates for immunoassay.

    PubMed

    Shrivastav, Tulsidas G

    2004-01-01

    An enzyme horseradish peroxidase (HRP), as a starting material, has been used to introduce different bridge length linkers, and its use in the preparation of enzyme conjugates for immunoassay is described. HRP was conjugated to adipic acid dihydrazide (ADH), gamma amino butyric acid (GABA), followed by ADH and 6-amino caproic acid (6ACA) followed by ADH. The different bridge length linkers-incorporated enzyme was coupled to a carboxylic derivative of cortisol. Four enzyme conjugates with different bridge length were prepared, such as cortisol-21-hemisuccinate-HRP (cortisol-21-HS-HRP), cortisol-21-HS-ADH-HRP, cortisol-21-HS-ADH-GABA-HRP, and cortisol-21-HS-ADH-6ACA-HRP. The influence of linker on sensitivity and specificity of the cortisol assay was studied. The study revealed that incorporation of a linker between hapten and enzyme increases the sensitivity and specificity of the assay. PMID:15461384

  2. CLOSE STELLAR ENCOUNTERS IN YOUNG, SUBSTRUCTURED, DISSOLVING STAR CLUSTERS: STATISTICS AND EFFECTS ON PLANETARY SYSTEMS

    SciTech Connect

    Craig, Jonathan; Krumholz, Mark R.

    2013-06-01

    Both simulations and observations indicate that stars form in filamentary, hierarchically clustered associations, most of which disperse into their galactic field once feedback destroys their parent clouds. However, during their early evolution in these substructured environments, stars can undergo close encounters with one another that might have significant impacts on their protoplanetary disks or young planetary systems. We perform N-body simulations of the early evolution of dissolving, substructured clusters with a wide range of properties, with the aim of quantifying the expected number and orbital element distributions of encounters as a function of cluster properties. We show that the presence of substructure both boosts the encounter rate and modifies the distribution of encounter velocities compared to what would be expected for a dynamically relaxed cluster. However, the boost only lasts for a dynamical time, and as a result the overall number of encounters expected remains low enough that gravitational stripping is unlikely to be a significant effect for the vast majority of star-forming environments in the Galaxy. We briefly discuss the implications of this result for models of the origin of the solar system, and of free-floating planets. We also provide tabulated encounter rates and orbital element distributions suitable for inclusion in population synthesis models of planet formation in a clustered environment.

  3. Constraining dark matter sub-structure with the dynamics of astrophysical systems

    SciTech Connect

    González-Morales, Alma X.; Valenzuela, Octavio; Aguilar, Luis A. E-mail: octavio@astro.unam.mx

    2013-03-01

    The accuracy of the measurements of some astrophysical dynamical systems allows to constrain the existence of incredibly small gravitational perturbations. In particular, the internal Solar System dynamics (planets, Earth-Moon) opens up the possibility, for the first time, to prove the abundance, mass and size, of dark sub-structures at the Earth vicinity. We find that adopting the standard dark matter density, its local distribution can be composed by sub-solar mass halos with no currently measurable dynamical consequences, regardless of the mini-halo fraction. On the other hand, it is possible to exclude the presence of dark streams with linear mass densities higher than λ{sub st} > 10{sup −10}M{sub ☉}/AU (about the Earth mass spread along the diameter of the SS up to the Kuiper belt). In addition, we review the dynamics of wide binaries inside the dwarf spheroidal galaxies in the Milky Way. The dynamics of such kind of binaries seem to be compatible with the presence of a huge fraction of dark sub-structure, thus their existence is not a sharp discriminant of the dark matter hypothesis as been claimed before. However, there are regimes where the constraints from different astrophysical systems may reveal the sub-structure mass function cut-off scale.

  4. A NEW CHANNEL FOR DETECTING DARK MATTER SUBSTRUCTURE IN GALAXIES: GRAVITATIONAL LENS TIME DELAYS

    SciTech Connect

    Keeton, Charles R.; Moustakas, Leonidas A.

    2009-07-10

    We show that dark matter substructure in galaxy-scale halos perturbs the time delays between images in strong gravitational lens systems. The variance of the effect depends on the subhalo mass function, scaling as the product of the substructure mass fraction, and a characteristic mass of subhalos (namely (m {sup 2})/(m)). Time delay perturbations therefore complement gravitational lens flux ratio anomalies and astrometric perturbations by measuring a different moment of the subhalo mass function. Unlike flux ratio anomalies, 'time delay millilensing' is unaffected by dust extinction or stellar microlensing in the lens galaxy. Furthermore, we show that time delay ratios are immune to the radial profile degeneracy that usually plagues lens modeling. We lay out a mathematical theory of time delay perturbations and find it to be tractable and attractive. We predict that in 'cusp' lenses with close triplets of images, substructure may change the arrival-time order of the images (compared with smooth models). We discuss the possibility that this effect has already been observed in RX J1131-1231.

  5. RAG-3D: a search tool for RNA 3D substructures.

    PubMed

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

    2015-10-30

    To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D-a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool-designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding. PMID:26304547

  6. Modeling the Role of Dislocation Substructure During Class M and Exponential Creep. Revised

    NASA Technical Reports Server (NTRS)

    Raj, S. V.; Iskovitz, Ilana Seiden; Freed, A. D.

    1995-01-01

    The different substructures that form in the power-law and exponential creep regimes for single phase crystalline materials under various conditions of stress, temperature and strain are reviewed. The microstructure is correlated both qualitatively and quantitatively with power-law and exponential creep as well as with steady state and non-steady state deformation behavior. These observations suggest that creep is influenced by a complex interaction between several elements of the microstructure, such as dislocations, cells and subgrains. The stability of the creep substructure is examined in both of these creep regimes during stress and temperature change experiments. These observations are rationalized on the basis of a phenomenological model, where normal primary creep is interpreted as a series of constant structure exponential creep rate-stress relationships. The implications of this viewpoint on the magnitude of the stress exponent and steady state behavior are discussed. A theory is developed to predict the macroscopic creep behavior of a single phase material using quantitative microstructural data. In this technique the thermally activated deformation mechanisms proposed by dislocation physics are interlinked with a previously developed multiphase, three-dimensional. dislocation substructure creep model. This procedure leads to several coupled differential equations interrelating macroscopic creep plasticity with microstructural evolution.

  7. Analysis and inverse substructuring computation on dynamic quality of mechanical assembly

    NASA Astrophysics Data System (ADS)

    Lü, Guangqing; Yi, Chuijie; Fang, Ke

    2016-05-01

    Mechanical assembly has its own dynamic quality directly affecting the dynamic quality of whole product and should be considered in quality inspection and estimation of mechanical assembly. Based on functional relations between dynamic characteristics involved in mechanical assembly, the effects of assembling process on dynamic characteristics of substructural components of an assembly system are investigated by substructuring analysis. Assembly-coupling dynamic stiffness is clarified as the dominant factor of the effects and can be used as a quantitative measure of assembly dynamic quality. Two computational schemes using frequency response functions(FRFs) to determine the stiffness are provided and discussed by inverse substructuring analysis, including their applicable conditions and implementation procedure in application. Eigenvalue analysis on matrix-ratios of FRFs before and after assembling is employed and well validates the analytical outcomes and the schemes via both a lumped-parameter model and its analogic experimental counterpart. Applying the two schemes to inspect the dynamic quality provides the message of dynamic performance of the assembly system, and therefore improves conventional quality inspection and estimation of mechanical assembly in completeness.

  8. RAG-3D: A search tool for RNA 3D substructures

    DOE PAGESBeta

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

    2015-08-24

    In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

  9. RAG-3D: A search tool for RNA 3D substructures

    SciTech Connect

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

    2015-08-24

    In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.

  10. DISCOVERY OF SUBSTRUCTURE IN THE SCATTER-BROADENED IMAGE OF SGR A*

    SciTech Connect

    Gwinn, C. R.; Kovalev, Y. Y.; Soglasnov, V. A.

    2014-10-10

    We have detected substructure within the smooth scattering disk of the celebrated Galactic center radio source Sagittarius A* (Sgr A*). We observed this structure at 1.3 cm wavelength with the Very Long Baseline Array together with the Green Bank Telescope, on baselines of up to 3000 km, long enough to completely resolve the average scattering disk. Such structure is predicted theoretically as a consequence of refraction by large-scale plasma fluctuations in the interstellar medium. Along with the much-studied θ{sub d}∝λ{sup 2} scaling of angular broadening θ{sub d} with observing wavelength λ, our observations indicate that the spectrum of interstellar turbulence is shallow with an inner scale larger than 300 km. The substructure is consistent with an intrinsic size of about 1 mas at 1.3 cm wavelength, as inferred from deconvolution of the average scattering. Further observations of the substructure can set stronger constraints on the properties of scattering material and on the intrinsic size of Sgr A*. These constraints will guide our understanding of the effects of scatter broadening and the emission physics near the black hole in images with the Event Horizon Telescope at millimeter wavelengths.

  11. A hybrid system identification methodology for wireless structural health monitoring systems based on dynamic substructuring

    NASA Astrophysics Data System (ADS)

    Dragos, Kosmas; Smarsly, Kay

    2016-04-01

    System identification has been employed in numerous structural health monitoring (SHM) applications. Traditional system identification methods usually rely on centralized processing of structural response data to extract information on structural parameters. However, in wireless SHM systems the centralized processing of structural response data introduces a significant communication bottleneck. Exploiting the merits of decentralization and on-board processing power of wireless SHM systems, many system identification methods have been successfully implemented in wireless sensor networks. While several system identification approaches for wireless SHM systems have been proposed, little attention has been paid to obtaining information on the physical parameters (e.g. stiffness, damping) of the monitored structure. This paper presents a hybrid system identification methodology suitable for wireless sensor networks based on the principles of component mode synthesis (dynamic substructuring). A numerical model of the monitored structure is embedded into the wireless sensor nodes in a distributed manner, i.e. the entire model is segmented into sub-models, each embedded into one sensor node corresponding to the substructure the sensor node is assigned to. The parameters of each sub-model are estimated by extracting local mode shapes and by applying the equations of the Craig-Bampton method on dynamic substructuring. The proposed methodology is validated in a laboratory test conducted on a four-story frame structure to demonstrate the ability of the methodology to yield accurate estimates of stiffness parameters. Finally, the test results are discussed and an outlook on future research directions is provided.

  12. Factorization for groomed jet substructure beyond the next-to-leading logarithm

    NASA Astrophysics Data System (ADS)

    Frye, Christopher; Larkoski, Andrew J.; Schwartz, Matthew D.; Yan, Kai

    2016-07-01

    Jet grooming algorithms are widely used in experimental analyses at hadron colliders to remove contaminating radiation from within jets. While the algorithms perform a great service to the experiments, their intricate algorithmic structure and multiple parameters has frustrated precision theoretic understanding. In this paper, we demonstrate that one particular groomer called soft drop actually makes precision jet substructure easier. In particular, we derive a factorization formula for a large class of soft drop jet substructure observables, including jet mass. The essential observation that allows for this factorization is that, without the soft wide-angle radiation groomed by soft drop, all singular contributions are collinear. The simplicity and universality of the collinear limit in QCD allows us to show that to all orders, the normalized differential cross section has no contributions from non-global logarithms. It is also independent of process, up to the relative fraction of quark and gluon jets. In fact, soft drop allows us to define this fraction precisely. The factorization theorem also explains why soft drop observables are less sensitive to hadronization than their ungroomed counterparts. Using the factorization theorem, we resum the soft drop jet mass to next-to-next-to-leading logarithmic accuracy. This requires calculating some clustering effects that are closely related to corresponding effects found in jet veto calculations. We match our resummed calculation to fixed order results for both e + e - → dijets and pp → Z + j events, producing the first jet substructure predictions (groomed or ungroomed) to this accuracy for the LHC.

  13. Analysis and inverse substructuring computation on dynamic quality of mechanical assembly

    NASA Astrophysics Data System (ADS)

    Lü, Guangqing; Yi, Chuijie; Fang, Ke

    2016-04-01

    Mechanical assembly has its own dynamic quality directly affecting the dynamic quality of whole product and should be considered in quality inspection and estimation of mechanical assembly. Based on functional relations between dynamic characteristics involved in mechanical assembly, the effects of assembling process on dynamic characteristics of substructural components of an assembly system are investigated by substructuring analysis. Assembly-coupling dynamic stiffness is clarified as the dominant factor of the effects and can be used as a quantitative measure of assembly dynamic quality. Two computational schemes using frequency response functions(FRFs) to determine the stiffness are provided and discussed by inverse substructuring analysis, including their applicable conditions and implementation procedure in application. Eigenvalue analysis on matrix-ratios of FRFs before and after assembling is employed and well validates the analytical outcomes and the schemes via both a lumped-parameter model and its analogic experimental counterpart. Applying the two schemes to inspect the dynamic quality provides the message of dynamic performance of the assembly system, and therefore improves conventional quality inspection and estimation of mechanical assembly in completeness.

  14. RAG-3D: a search tool for RNA 3D substructures

    PubMed Central

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

    2015-01-01

    To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding. PMID:26304547

  15. Structural damage identification based on substructure sensitivity and l1 sparse regularization

    NASA Astrophysics Data System (ADS)

    Zhou, Shumei; Bao, Yuequan; Li, Hui

    2013-04-01

    Sparsity constraints are now very popular to regularize inverse problems in the field of applied mathematics. Structural damage identification is a typical inverse problem of structural dynamics and Structural damage is a spatial sparse phenomenon, i.e., structural damage occurs, only part of elements or substructures are damaged. In this paper, a structural damage identification method based on the substructure-based sensitivity analysis and the sparse constraints regularization is proposed. Substructure sensitivity analysis, the establishment of structural damage stiffness parameter variation and change of modal parameters of linear equations between the measured degrees of freedom is limited, the equations for a morbid equation. The introduction of structural damage sparsity conditions, to minimize the l1 norm optimization solution. The numerical example of the 20 bay-truss structure with considering measurement noise, incomplete of measurements and multi-damage cases are carried out. The effects of number sensor and layout to the identification results are also investigated. The results indicated that the damage locations and extents can be effectively identified by the proposed method. Additionally, the sensor location can be random arrangement, which has great significance to the sensor placement of the actual structural health monitoring because robust structural damage identification also can be obtained even a few of sensor are failure.

  16. Discovery of Substructure in the Scatter-broadened Image of Sgr A*

    NASA Astrophysics Data System (ADS)

    Gwinn, C. R.; Kovalev, Y. Y.; Johnson, M. D.; Soglasnov, V. A.

    2014-10-01

    We have detected substructure within the smooth scattering disk of the celebrated Galactic center radio source Sagittarius A* (Sgr A*). We observed this structure at 1.3 cm wavelength with the Very Long Baseline Array together with the Green Bank Telescope, on baselines of up to 3000 km, long enough to completely resolve the average scattering disk. Such structure is predicted theoretically as a consequence of refraction by large-scale plasma fluctuations in the interstellar medium. Along with the much-studied θdvpropλ2 scaling of angular broadening θd with observing wavelength λ, our observations indicate that the spectrum of interstellar turbulence is shallow with an inner scale larger than 300 km. The substructure is consistent with an intrinsic size of about 1 mas at 1.3 cm wavelength, as inferred from deconvolution of the average scattering. Further observations of the substructure can set stronger constraints on the properties of scattering material and on the intrinsic size of Sgr A*. These constraints will guide our understanding of the effects of scatter broadening and the emission physics near the black hole in images with the Event Horizon Telescope at millimeter wavelengths.

  17. Model validation of the Sandia 34-Meter Test Bed Turbine using substructure modal-testing

    SciTech Connect

    Carne, T.G.; Lauffer, J.P.; Gomez, A.J.; Ashwill, T.D.

    1989-01-01

    The Sandia 34-Meter Test Bed Turbine is a vertical-axis wind turbine, thirty-four meters in diameter, designed to provide a test-bed for research in aerodynamics, structures and control. In order to design a large wind turbine, knowledge of the modal frequencies and mode shapes is essential for predicting structural response. During the design, analytical or finite element models are utilized for estimates of these modal parameters. However, when hardware becomes available, modal testing can be used to verify or update the models. The concept of substructure modal testing was developed for the Sandia 34-Meter Test Bed in order to more fully evaluate the accuracy of the finite element model. Instead of performing only one test on the entire turbine, separate tests and analyses were performed on major substructures of the turbine, including three separate blade sections, the tower supported by the guy cables, and the entire turbine. The results were then compared to analytical predictions from the finite element models of the substructures and the entire turbine. 8 refs., 6 figs., 6 tabs.

  18. Dynamic behavior of an intrinsically unstructured linker domain is conserved in the face of negligible amino acid sequence conservation.

    PubMed

    Daughdrill, Gary W; Narayanaswami, Pranesh; Gilmore, Sara H; Belczyk, Agniezka; Brown, Celeste J

    2007-09-01

    Proteins or regions of proteins that do not form compact globular structures are classified as intrinsically unstructured proteins (IUPs). IUPs are common in nature and have essential molecular functions, but even a limited understanding of the evolution of their dynamic behavior is lacking. The primary objective of this work was to test the evolutionary conservation of dynamic behavior for a particular class of IUPs that form intrinsically unstructured linker domains (IULD) that tether flanking folded domains. This objective was accomplished by measuring the backbone flexibility of several IULD homologues using nuclear magnetic resonance (NMR) spectroscopy. The backbone flexibility of five IULDs, representing three kingdoms, was measured and analyzed. Two IULDs from animals, one IULD from fungi, and two IULDs from plants showed similar levels of backbone flexibility that were consistent with the absence of a compact globular structure. In contrast, the amino acid sequences of the IULDs from these three taxa showed no significant similarity. To investigate how the dynamic behavior of the IULDs could be conserved in the absence of detectable sequence conservation, evolutionary rate studies were performed on a set of nine mammalian IULDs. The results of this analysis showed that many sites in the IULD are evolving neutrally, suggesting that dynamic behavior can be maintained in the absence of natural selection. This work represents the first experimental test of the evolutionary conservation of dynamic behavior and demonstrates that amino acid sequence conservation is not required for the conservation of dynamic behavior and presumably molecular function. PMID:17721672

  19. Endothelial dysfunction exacerbates renal interstitial fibrosis through enhancing fibroblast Smad3 linker phosphorylation in the mouse obstructed kidney.

    PubMed

    Sun, Yu Bo Yang; Qu, Xinli; Li, Xueling; Nikolic-Paterson, David J; Li, Jinhua

    2013-01-01

    Endothelial dysfunction and enhanced transforming growth factor-β (TGF-β)/Smad3 signalling are common features of progressive renal fibrosis. This study investigated a potential link between these mechanisms. In unilateral ureteric obstruction (UUO) we observed an acute (6 hr) down-regulation of nitric oxide synthase 3 (NOS3/eNOS) levels and increased phosphorylation of the linker region of Smad3 at T179 and S208 in Smad3/JNK complexes. These events preceded Smad3 C-terminal domain phosphorylation and the induction of myofibroblast proliferation at 48 hrs. Mice deficient in NOS3 showed enhanced myofibroblast proliferation and collagen accumulation compared to wild type mice in a 7 day UUO model. This was associated with enhanced phosphorylation of Smad3 T179 and S208 by 92% and 88%, respectively, whereas Smad3-C-terminal phosphorylation was not affected. Resolvin D1 (RvD1) can suppress renal fibrosis in the UUO model, and further analysis herein showed that RvD1 protected against endothelial dysfunction and suppressed Smad3/JNK complex formation with a consequent reduction in phosphorylation of Smad3 T179 and S208 by 78% and 65%, respectively, while Smad3 C-terminal phosphorylation was unaltered. In vitro, conditioned media from mouse microvascular endothelial cells (MMEC) treated with a general inhibitor of nitric oxide synthase (L-NAME) augmented the proliferation and collagen production of renal fibroblasts (NRK49F cells) compared to control MMEC media and this was associated with increased phosphorylation of JNK and Smad3 T179 and S208, whereas Smad3-C-terminal domain phosphorylation was unaffected. The addition of RvD1 to L-NAME treated MMEC abrogated these effects of the conditioned media on renal fibroblasts. Finally, Smad3 T179/V and S208/A mutations significantly inhibit TGF-β1 induced up-regulation collagen I promoter. In conclusion, these data suggest that endothelial dysfunction can exacerbate renal interstitial fibrosis through increased fibroblast

  20. Absolute proper motions to B approximately 22.5: Evidence for kimematical substructure in halo field stars

    NASA Technical Reports Server (NTRS)

    Majewski, Steven R.; Munn, Jeffrey A.; Hawley, Suzanne L.

    1994-01-01

    Radial velocities have been obtained for six of nine stars identified on the basis of similar distances and common, extreme transverse velocities in the proper motion survey of Majewski (1992) as a candidate halo moving group at the north Galactic pole. These radial velocities correspond to velocities perpendicular to the Galactic plane which span the range -48 +/- 21 to -128 +/- 9 km/sec (but a smaller range, -48 +/- 21 to -86 +/- 19 km/sec, when only our own measurements are considered), significantly different than the expected distribution, with mean 0 km/sec, for a random sample of either halo or thick disk stars. The probability of picking such a set of radial velocities at random is less than 1%. Thus the radial velocity data support the hypothesis that these stars constitute part of a halo moving group or star stream at a distance of approximately 4-5 kpc above the Galactic plane. If real, this moving group is evidence for halo phase space substructure which may be the fossil remains of a destroyed globular cluster, Galactic satellite, or Searle & Zinn (1978) 'fragment.'

  1. Amino acid residues required for fast Na(+)-channel inactivation: charge neutralizations and deletions in the III-IV linker.

    PubMed Central

    Patton, D E; West, J W; Catterall, W A; Goldin, A L

    1992-01-01

    The cytoplasmic linker connecting domains III and IV of the voltage-gated Na+ channel is thought to be involved in fast inactivation. This linker is highly conserved among the various Na+ channels that have been cloned. In the rat brain IIA Na+ channel, it consists of 53 amino acids of which 15 are charged. To investigate the role of this linker in inactivation, we mutated all 15 of the charged residues in various combinations. All but one of these mutants expressed functional channels, and all of these inactivated with kinetics similar to the wild-type channel. We then constructed a series of deletion mutations that span the III-IV linker to determine if any region of the linker is essential for fast inactivation. Deletion of the first 10 amino acids completely eliminated fast inactivation in the channel, whereas deletion of the last 10 amino acids had no substantial effect on inactivation. These results demonstrate that some residues in the amino end of the III-IV linker are critical for fast Na(+)-channel inactivation, but that the highly conserved positively charged and paired negatively charged residues are not essential. PMID:1332059

  2. Measurement of Residual Flexibility for Substructures Having Prominent Flexible Interfaces

    NASA Technical Reports Server (NTRS)

    Tinker, Michael L.; Bookout, Paul S.

    1994-01-01

    Verification of a dynamic model of a constrained structure requires a modal survey test of the physical structure and subsequent modification of the model to obtain the best agreement possible with test data. Constrained-boundary or fixed-base testing has historically been the most common approach for verifying constrained mathematical models, since the boundary conditions of the test article are designed to match the actual constraints in service. However, there are difficulties involved with fixed-base testing, in some cases making the approach impractical. It is not possible to conduct a truly fixed-base test due to coupling between the test article and the fixture. In addition, it is often difficult to accurately simulate the actual boundary constraints, and the cost of designing and constructing the fixture may be prohibitive. For use when fixed-base testing proves impractical or undesirable, alternate free-boundary test methods have been investigated, including the residual flexibility technique. The residual flexibility approach has been treated analytically in considerable detail and has had limited frequency response measurements for the method. This concern is well-justified for a number of reasons. First, residual flexibilities are very small numbers, typically on the order of 1.0E-6 in/lb for translational diagonal terms, and orders of magnitude smaller for off-diagonal values. This poses difficulty in obtaining accurate and noise-free measurements, especially for points removed from the excitation source. A second difficulty encountered in residual measurements lies in obtaining a clean residual function in the process of subtracting synthesized modal data from a measured response function. Inaccuracies occur since modes are not subtracted exactly, but only to the accuracy of the curve fits for each mode; these errors are compounded with increasing distance from the excitation point. In this paper, the residual flexibility method is applied to a simple

  3. Expression and identification of the ADF-linker-3-1E gene of Eimeria acervulina of chicken.

    PubMed

    Yuelan, Zhao; Yiwei, Liu; Liyuan, Liu; Yue, Zhao; Wenbo, Cao; Yongzhan, Bao; Jianhua, Qin

    2016-04-01

    Coccidiosis is a widely distributed disease with higher mortality and morbidity, which is caused by several species of protozoan parasites belonging to the genus Eimeria and recognized as a serious challenge for the poultry industry. This research was conducted to construct the recombinant plasmid pET32a(+)-ADF-linker-3-1E of Eimeria acervulina (E. acervulina) of the chicken and test the bioactivity of the ADF-linker-3-1E protein. The ADF-linker-3-1E gene of E. acervulina of the chicken was cloned by splicing by overlap extension by the polymerase chain reaction (SOE-PCR) and then inserted into the pET32a(+) to construct the recombinant plasmid pET32a(+)-ADF-linker-3-1E. The recombinant plasmid was transformed into Escherichia coli Rosetta (DE3) competent cells and then induced by IPTG (0.6 mmol/L). The expressed product in the culture medium was identified by the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The bioactivity of the ADF-linker-3-1E protein was tested by Western blotting. The result showed that the amplified ADF-linker-3-1E gene was about 1346 bp. The PCR amplification with the recombinant plasmid pET-32a(+)-ADF-linker-3-1E as a template resulted in a special band of 1346 bp. The digested products resulted in two fragments of 1346 bp target fragment and 5.9 kb pET-32a(+)-vector fragment. The results indicated that the ADF-linker3-1E gene was successfully inserted into the pET-32a(+)-vector. The expressed products in the culture medium resulted in a single band of approximately 54.8 kDa by SDS-PAGE. Western blotting analysis indicated that the recombinant protein could be reacted specifically with His-Tag(2A8) Mouse mAb. This study indicated that the ADF-linker-3-1E protein with good bioactivity was successfully obtained, which laid a foundation for the exploitation of the nuclear vaccine by using the ADF-linker-3-1E protein. PMID:26767375

  4. Identification of Sleeping Beauty Transposon Insertions in Solid Tumors using Linker-mediated PCR

    PubMed Central

    Janik, Callie L.; Starr, Timothy K.

    2013-01-01

    Genomic, proteomic, transcriptomic, and epigenomic analyses of human tumors indicate that there are thousands of anomalies within each cancer genome compared to matched normal tissue. Based on these analyses it is evident that there are many undiscovered genetic drivers of cancer1. Unfortunately these drivers are hidden within a much larger number of passenger anomalies in the genome that do not directly contribute to tumor formation. Another aspect of the cancer genome is that there is considerable genetic heterogeneity within similar tumor types. Each tumor can harbor different mutations that provide a selective advantage for tumor formation2. Performing an unbiased forward genetic screen in mice provides the tools to generate tumors and analyze their genetic composition, while reducing the background of passenger mutations. The Sleeping Beauty (SB) transposon system is one such method3. The SB system utilizes mobile vectors (transposons) that can be inserted throughout the genome by the transposase enzyme. Mutations are limited to a specific cell type through the use of a conditional transposase allele that is activated by Cre Recombinase. Many mouse lines exist that express Cre Recombinase in specific tissues. By crossing one of these lines to the conditional transposase allele (e.g. Lox-stop-Lox-SB11), the SB system is activated only in cells that express Cre Recombinase. The Cre Recombinase will excise a stop cassette that blocks expression of the transposase allele, thereby activating transposon mutagenesis within the designated cell type. An SB screen is initiated by breeding three strains of transgenic mice so that the experimental mice carry a conditional transposase allele, a concatamer of transposons, and a tissue-specific Cre Recombinase allele. These mice are allowed to age until tumors form and they become moribund. The mice are then necropsied and genomic DNA is isolated from the tumors. Next, the genomic DNA is subjected to linker-mediated-PCR (LM

  5. Identification of Sleeping Beauty transposon insertions in solid tumors using linker-mediated PCR.

    PubMed

    Janik, Callie L; Starr, Timothy K

    2013-01-01

    Genomic, proteomic, transcriptomic, and epigenomic analyses of human tumors indicate that there are thousands of anomalies within each cancer genome compared to matched normal tissue. Based on these analyses it is evident that there are many undiscovered genetic drivers of cancer(1). Unfortunately these drivers are hidden within a much larger number of passenger anomalies in the genome that do not directly contribute to tumor formation. Another aspect of the cancer genome is that there is considerable genetic heterogeneity within similar tumor types. Each tumor can harbor different mutations that provide a selective advantage for tumor formation(2). Performing an unbiased forward genetic screen in mice provides the tools to generate tumors and analyze their genetic composition, while reducing the background of passenger mutations. The Sleeping Beauty (SB) transposon system is one such method(3). The SB system utilizes mobile vectors (transposons) that can be inserted throughout the genome by the transposase enzyme. Mutations are limited to a specific cell type through the use of a conditional transposase allele that is activated by Cre Recombinase. Many mouse lines exist that express Cre Recombinase in specific tissues. By crossing one of these lines to the conditional transposase allele (e.g. Lox-stop-Lox-SB11), the SB system is activated only in cells that express Cre Recombinase. The Cre Recombinase will excise a stop cassette that blocks expression of the transposase allele, thereby activating transposon mutagenesis within the designated cell type. An SB screen is initiated by breeding three strains of transgenic mice so that the experimental mice carry a conditional transposase allele, a concatamer of transposons, and a tissue-specific Cre Recombinase allele. These mice are allowed to age until tumors form and they become moribund. The mice are then necropsied and genomic DNA is isolated from the tumors. Next, the genomic DNA is subjected to linker

  6. Development of a 3'-amino linker with high conjugation activity and its application to conveniently cross-link blunt ends of a duplex.

    PubMed

    Kowata, Keiko; Kojima, Naoshi; Komatsu, Yasuo

    2016-05-01

    The 2-aminoethyl carbamate linker (ssH linker) exhibits high activity in modifying the 5'-termini of oligonucleotides; however, the ssH linker is not appropriate for 3'-terminal modification because it undergoes intramolecular trans-acylation under heat-aqueous ammonia conditions. We developed an N-(2-aminoethyl)carbamate linker (revH linker), in which the carbamate is oriented in the reverse direction relative to that in 2-aminoethyl carbamate. The revH linker was tolerant to heat-alkaline conditions and retained its high reactivity in conjugation with exogenous molecules. The 3'-revH linker was efficiently linked with the 5'-ssH linker at the termini of complementary double strands with a bifunctional molecule, producing a synthetic loop structure. An anti-microRNA oligonucleotide (AMO) was prepared from the chemical ligation of three-stranded 2'-O-methyl RNAs, and the AMO with two alkyl loops exhibited high inhibition activity toward miRNA function. The revH linker is not only useful for 3'-terminal modification of oligonucleotides but also expands the utility range in combination with the 5'-ssH linker. PMID:27041396

  7. Design of CID-cleavable protein cross-linkers: identical mass modifications for simpler sequence analysis.

    PubMed

    Kandur, Wynne V; Kao, Athit; Vellucci, Danielle; Huang, Lan; Rychnovsky, Scott D

    2015-10-14

    The cross-linking Mass Spectrometry (XL-MS) technique has enormous potential for studying the interactions between proteins, and it can provide detailed structural information about the interaction interfaces in large protein complexes. Such information has been difficult to obtain by conventional structural methods. One of the primary impediments to the wider use of the XL-MS technique is the extreme challenge in sequencing cross-linked peptides because of their complex fragmentation patterns in MS. A recent innovation is the development of MS-cleavable cross-linkers, which allows direct sequencing of component peptides for facile identification. Sulfoxides are an intriguing class of thermally-cleavable compounds that have been shown to fragment selectively during low-energy collisional induced dissociation (CID) analysis. Current CID-cleavable cross-linkers create fragmentation patterns in MS(2) of multiple peaks for each cross-linked peptide. Reducing the complexity of the fragmentation pattern in MS(2) facilitates subsequent MS(3) sequencing of the cross-linked peptides. The first authentic identical mass linker (IML) has now been designed, prepared, and evaluated. Multistage tandem mass spectrometry (MS(n)) analysis has demonstrated that the IML cross-linked peptides indeed yield one peak per peptide constituent in MS(2) as predicted, thus allowing effective and sensitive MS(3) analysis for unambiguous identification. Selective fragmentation for IML cross-linked peptides from the 19S proteasome complex was observed, providing a proof-of-concept demonstration for XL-MS studies on protein complexes. PMID:26269432

  8. Excluded volume effects upon protein stability in covalently crosslinked proteins with variable linker lengths†

    PubMed Central

    Kim, Yun Ho; Stites, Wesley E.

    2008-01-01

    To explore the effects of molecular crowding and excluded volume upon protein stability a series of crosslinking reagents have been used with nine different single cysteine mutants of staphylococcal nuclease to make covalently linked dimers. These crosslinkers ranged in length from 10.5 Å to 21.3 Å, compelling separations which would normally be found only in the most concentrated protein solutions. The stabilities of the dimeric proteins and monomeric controls were determined by guanidine hydrochloride and thermal denaturation. Dimers with short linkers tend to show pronounced three state denaturation behavior, as opposed to the two state behavior of the monomeric controls. Increasing linker length leads to less pronounced three state behavior. The three state behavior is interpreted in a three state model where crosslinked native protein dimer, N-N, interconverts in a two state transition with a dimer where one protein subunit is denatured, N-D. The remaining native protein in turn can denature in another two state transition to a state, D-D, where both tethered proteins are denatured. Three state behavior is best explained by excluded volume effects in the denatured state. For many dimers, linkers longer than 17 Å removed most three state character. This sets a limit on the flexibility and size of the denatured state. Notably, in contradiction to theoretical predictions, these crosslinked dimers were not stabilized. The failure of these predictions is possibly due to neglect of the alteration in hydrophobic exposure that accompanies any significant reduction in the conformational space of the denatured state. PMID:18656955

  9. Dihydroxybenzoquinone as Linker for the Synthesis of Permanently Porous Aluminum Metal-Organic Frameworks.

    PubMed

    Halis, Selda; Inge, A Ken; Dehning, Niklas; Weyrich, Thomas; Reinsch, Helge; Stock, Norbert

    2016-08-01

    Two new dihydroxybenzoquinone-based metal-organic frameworks, ((CH3)2NH2)3[Al4(L1)3(L1(•))3]·3DMF (1, denoted CAU-20) and ((CH3)2NH2)3[Al4(L2)3(L2(•))3]·9DMF (2, denoted CAU-20-Cl2), were synthesized at 120 °C in DMF using 2,5-dihydroxy-p-benzoquinone ((C6H2(OH)2(O)2), H2L1) and 2,5-dichloro-3,6-dihydroxy-p-benzoquinone ((C6Cl2(OH)2(O)2), H2L2), respectively. Compared to other Al-MOFs, which contain carboxylate or phosphonate groups that connect the metal sites, in 1 and 2 the Al(3+) are coordinated by oxido groups. The metal ions are octahedrally surrounded by oxygen atoms of the deprotonated linker molecules to generate honeycomb layers with a metal to linker ratio of Al: L1/L2 = 2:3. The layers contain L1(2-) and L2(2-) ions as well as linker radical ions L1(•3-) and L2(•3-) in a molar ratio of 1 to 1. The presence of radical ions was confirmed by EPR and UV-vis-spectroscopic measurements, and the composition was determined from a combination of PXRD, (1)H NMR, TG, and elemental analyses. Charge balance is accomplished through intercalation of (CH3)2NH2(+) ions which are formed by partial hydrolysis of DMF. In the structures of 1 and 2 the eclipsed layers are AA and ABAB stacked, respectively, and one-dimensional hexagonal channels with diameters of ca. 9 and 6 Å are formed. Both compounds exhibit permanent porosity and have specific surface areas of 1440 and 1430 m(2) g(-1), respectively. PMID:27427885

  10. Preparation and in vivo evaluation of linkers for 211At labeling of humanized anti-Tac.

    PubMed

    Yordanov, A T; Garmestani, K; Zhang, M; Zhang, Z; Yao, Z; Phillips, K E; Herring, B; Horak, E; Beitzel, M P; Schwarz, U P; Gansow, O A; Plascjak, P S; Eckelman, W C; Waldmann, T A; Brechbiel, M W

    2001-10-01

    The syntheses, radiolabeling, antibody conjugation, and in vivo evaluation of new linkers for 211At labeling of humanized anti-Tac (Hu-anti-Tac), an antibody to the alpha-chain of the IL-2 receptor (IL-2Ralpha) shown to be a useful target for radioimmunotherapy are described. Synthesis of the organometallic linker precursors is accomplished by reaction of the corresponding bromo- or iodoaryl esters with bis(tributyltin) in the presence of a palladium catalyst. Subsequent conversion to the corresponding N-succinimidyl ester and labeling with 211At of two new linkers, N-succinimidyl 4-[211At]astato-3-methylbenzoate and N-succinimidyl N-(4-[211At]astatophenethyl)succinamate (SAPS), together with the previously reported N-succinimidyl 4-[211At]astatobenzoate and N-succinimidyl 3-[211At]astato-4-methylbenzoate, are each conjugated to Hu-anti-Tac. The plasma survival times of these conjugates are compared to those of directly iodinated (125I) Hu-anti-Tac. The N-succinimidyl N-(4-[211At]astatophenethyl)succinamate compound (SAPS) emerged from this assay as the most viable candidate for 211At-labeling of Hu-anti-Tac. SAPS, along with the directly analogous radio-iodinated reagent, N-succinimidyl N-(4-[125I]astatophenethyl)succinamate (SIPS), are evaluated in a biodistribution study along with directly iodinated (125I) Hu-anti-Tac. Blood clearance and biological accretion results indicate that SAPS is a viable candidate for further evaluation for radioimmunotherapy of cancer. PMID:11578907

  11. Cross-linker dynamics determine the mechanical properties of actin gels.

    PubMed Central

    Wachsstock, D H; Schwarz, W H; Pollard, T D

    1994-01-01

    To evaluate the contributions of cross-linker dynamics and polymer deformation to the frequency-dependent stiffness of actin filament gels, we compared the rheological properties of actin gels with three types of cross-linkers: a weak one, Acanthamoeba alpha-actinin (dissociation rate constant 5.2 s-1, association rate constant 1.1 x 10(6) M-1 s-1); a strong one, chicken smooth muscle alpha-actinin (dissociation rate constant 0.66 s-1, association rate constant 1.20 x 10(6) M-1 s-1); and an extremely strong one, biotin/avidin (dissociation rate constant approximately zero). The biotin/avidin cross-linked gel, whose behavior is determined by polymer bending alone, behaves like a solid and shows no frequency dependence. The amoeba alpha-actinin cross-linked gel behaves like a viscoelastic fluid, and the frequency dependence of the stiffness can be explained by a mathematical model for dynamically cross-linked gels. The stiffness of the chicken alpha-actinin cross-linked gel is independent of frequency, and has viscoelastic properties intermediate between the two. The two alpha-actinins have similar association rate constants for binding to actin filaments, consistent with a diffusion-limited reaction. Rigid cross-links make the gel stiff, but make it elastic without the ability to deform permanently. Dynamically cross-linked actin filaments should allow the cell to react passively to various outside forces without any sort of signaling. Slower, signal-mediated pathways, such as severing filaments or changing the affinity of cross-linkers, could alter the nature of these passive reactions. PMID:8011912

  12. [Construction of cTnC-linker-TnI (P) Genes, Expression of Fusion Protein and Preparation of Lyophilized Protein].

    PubMed

    Song, Xiaoli; Liu, Xiaoyun; Cai, Lei; Wu, Jianwei; Wang, Jihua

    2015-12-01

    In order to construct and express human cardiac troponin C-linker-troponin I(P) [ cTnC-linker-TnI(P)] fusion protein, detect its activity and prepare lyophilized protein, we searched the CDs of human cTnC and cTnI from GenBank, synthesized cTnC and cTnI(30-110aa) into cloning vector by a short DNA sequence coding for 15 neutral amino acid residues. pCold I-cTnC-linker-TnI(P) was constructed and transformed into E. coli BL21(DE3). Then, cTnC-linker-TnI(P) fusion protein was induced by isopropyl-β-D-thiogalactopyranoside (IPTG). Soluable expression of cTnC-linker-TnI(P) in prokaryotic system was successfully obtained. The fusion protein was purified by Ni²⁺ Sepharose 6 Fast Flow affinity chromatography with over 95% purity and prepared into lyophilized protein. The activity of purified cTnC-linker-TnI(P) and its lyophilized protein were detected by Wondfo Finecare™ cTnI Test. Lyophilized protein of cTnC-linker-TnI(P) was stable for 10 or more days at 37 °C and 4 or more months at 25 °C and 4 °C. The expression system established in this research is feasible and efficient. Lyophilized protein is stable enough to be provided as biological raw materials for further research. PMID:27079099

  13. Small angle x-ray scattering of chromatin. Radius and mass per unit length depend on linker length.

    PubMed Central

    Williams, S P; Langmore, J P

    1991-01-01

    Analyses of low angle x-ray scattering from chromatin, isolated by identical procedures but from different species, indicate that fiber diameter and number of nucleosomes per unit length increase with the amount of nucleosome linker DNA. Experiments were conducted at physiological ionic strength to obtain parameters reflecting the structure most likely present in living cells. Guinier analyses were performed on scattering from solutions of soluble chromatin from Necturus maculosus erythrocytes (linker length 48 bp), chicken erythrocytes (linker length 64 bp), and Thyone briareus sperm (linker length 87 bp). The results were extrapolated to infinite dilution to eliminate interparticle contributions to the scattering. Cross-sectional radii of gyration were found to be 10.9 +/- 0.5, 12.1 +/- 0.4, and 15.9 +/- 0.5 nm for Necturus, chicken, and Thyone chromatin, respectively, which are consistent with fiber diameters of 30.8, 34.2, and 45.0 nm. Mass per unit lengths were found to be 6.9 +/- 0.5, 8.3 +/- 0.6, and 11.8 +/- 1.4 nucleosomes per 10 nm for Necturus, chicken, and Thyone chromatin, respectively. The geometrical consequences of the experimental mass per unit lengths and radii of gyration are consistent with a conserved interaction among nucleosomes. Cross-linking agents were found to have little effect on fiber external geometry, but significant effect on internal structure. The absolute values of fiber diameter and mass per unit length, and their dependencies upon linker length agree with the predictions of the double-helical crossed-linker model. A compilation of all published x-ray scattering data from the last decade indicates that the relationship between chromatin structure and linker length is consistent with data obtained by other investigators. Images FIGURE 1 PMID:2049522

  14. Synthesis and molecular modeling of antimicrobial active fluoroquinolone-pyrazine conjugates with amino acid linkers.

    PubMed

    Panda, Siva S; Detistov, Oleksandr S; Girgis, Adel S; Mohapatra, Prabhu P; Samir, Ahmed; Katritzky, Alan R

    2016-05-01

    Novel fluoroquinolone-pyrazine conjugates 7a-h with amino acid linkers were synthesized in good yields utilizing benzotriazole chemistry. Antimicrobial bioassay showed that the synthesized bis-conjugates have antimicrobial properties comparable to the parent drugs. Compound 7h showed superior antibacterial activity against Staphylococcus aureus and Streptococcus pyogenes (MIC=74.6μM and 149.3μM, respectively). This matched well with the estimated values obtained from 3D-pharmacophore and 2D-QSAR studies (MIC=67μM and 92.9μM, respectively). PMID:27025339

  15. Effects of dark matter substructures on gravitational lensing: results from the Aquarius simulations

    NASA Astrophysics Data System (ADS)

    Xu, D. D.; Mao, Shude; Wang, Jie; Springel, V.; Gao, Liang; White, S. D. M.; Frenk, Carlos S.; Jenkins, Adrian; Li, Guoliang; Navarro, Julio F.

    2009-09-01

    We use the high-resolution Aquarius simulations of the formation of Milky Way-sized haloes in the Λ cold dark matter cosmology to study the effects of dark matter substructures on gravitational lensing. Each halo is resolved with ~108 particles (at a mass resolution mp ~ 103 to 104h-1Msolar) within its virial radius. Subhaloes with masses msub >~ 105h-1Msolar are well resolved, an improvement of at least two orders of magnitude over previous lensing studies. We incorporate a baryonic component modelled as a Hernquist profile and account for the response of the dark matter via adiabatic contraction. We focus on the `anomalous' flux ratio problem, in particular on the violation of the cusp-caustic relation due to substructures. We find that subhaloes with masses less than ~108h-1Msolar play an important role in causing flux anomalies; such low-mass subhaloes have been unresolved in previous studies. There is large scatter in the predicted flux ratios between different haloes and between different projections of the same halo. In some cases, the frequency of predicted anomalous flux ratios is comparable to that observed for the radio lenses, although in most cases it is not. The probability for the simulations to reproduce the observed violations of the cusp lenses is ~10-3. We therefore conclude that the amount of substructure in the central regions of the Aquarius haloes is insufficient to explain the observed frequency of violations of the cusp-caustic relation. These conclusions are based purely on our dark matter simulations which ignore the effect of baryons on subhalo survivability.

  16. The Extraordinary Amount of Substructure in the Hubble Frontier Fields Cluster Abell 2744

    NASA Astrophysics Data System (ADS)

    Jauzac, M.; Eckert, D.; Schwinn, J.; Harvey, D.; Baugh, C. M.; Robertson, A.; Bose, S.; Massey, R.; Owers, M.; Ebeling, H.; Shan, H. Y.; Jullo, E.; Kneib, J.-P.; Richard, J.; Atek, H.; Clément, B.; Egami, E.; Israel, H.; Knowles, K.; Limousin, M.; Natarajan, P.; Rexroth, M.; Taylor, P.; Tchernin, C.

    2016-09-01

    We present a joint optical/X-ray analysis of the massive galaxy cluster Abell 2744 (z=0.308). Our strong- and weak-lensing analysis within the central region of the cluster, i.e., at R < 1 Mpc from the brightest cluster galaxy, reveals eight substructures, including the main core. All of these dark-matter halos are detected with a significance of at least 5σ and feature masses ranging from 0.5 to 1.4× 1014M⊙ within R < 150 kpc. Merten et al. (2011) and Medezinski et al. (2016) substructures are also detected by us. We measure a slightly higher mass for the main core component than reported previously and attribute the discrepancy to the inclusion of our tightly constrained strong-lensing mass model built on Hubble Frontier Fields data. X-ray data obtained by XMM-Newton reveal four remnant cores, one of them a new detection, and three shocks. Unlike Merten et al. (2011), we find all cores to have both dark and luminous counterparts. A comparison with clusters of similar mass in the MXXL simulations yields no objects with as many massive substructures as observed in Abell 2744, confirming that Abell 2744 is an extreme system. We stress that these properties still do not constitute a challenge to ΛCDM, as caveats apply to both the simulation and the observations: for instance, the projected mass measurements from gravitational lensing and the limited resolution of the sub-haloes finders. We discuss implications of Abell 2744 for the plausibility of different dark-matter candidates and, finally, measure a new upper limit on the self-interaction cross-section of dark matter of σDM < 1.28 cm2g-1(68% CL), in good agreement with previous results from Harvey et al. (2015).

  17. Substructuring and model reduction of pipe components interacting with acoustic fluids

    NASA Astrophysics Data System (ADS)

    Maess, Matthias; Gaul, Lothar

    2006-01-01

    This paper presents a model reduction and substructure technique for reduced dynamical models of fluid-filled pipe components. Both linear acoustical domain and structural domain are modelled by finite elements (FE), and they are fully coupled by a fluid-structure interface. The discretised dynamic FE-equations, which use the acoustic pressure as field variable in the fluid, render both non-symmetric mass and stiffness matrices due to the FSI-coupling. Since the partial solutions to the eigenproblem of the coupled system are of special interest, either numerical preconditioning or non-dimensionalisation of the physical quantities is performed to improve the condition and to accelerate the numerical computation. An iterative subspace solver is adopted to generate a sufficient approximate of the low-frequency eigenspace of the constrained problem. Model reduction for component mode synthesis uses constraint modes together with the computed eigenspace. Single-point constraints for the nodal degrees of freedom hold at the interface between substructures. The null space resulting from a QR-decomposition of the single-point constraints at the interface is used as explicit coupling matrix to prevent the deterioration of the conditioning. Partitioning of the reduction space and coupling matrices leads to a structure of the coupled global system matrices, which is similar to the original system structure in physical quantities. Therefore, the iterative subspace eigensolver is used again for numerical modal analysis. Modal analysis is performed for a pipe segment assembled by fully coupled two-field substructures. The results are compared to the results obtained from the full model and to experimentally determined mode shapes.

  18. Dimeric peptides with three different linkers self-assemble with phospholipids to form peptide nanodiscs that stabilize membrane proteins.

    PubMed

    Larsen, Andreas N; Sørensen, Kasper K; Johansen, Nicolai T; Martel, Anne; Kirkensgaard, Jacob J K; Jensen, Knud J; Arleth, Lise; Midtgaard, Søren Roi

    2016-07-01

    Three dimers of the amphipathic α-helical peptide 18A have been synthesized with different interhelical linkers inserted between the two copies of 18A. The dimeric peptides were denoted 'beltides' where Beltide-1 refers to the 18A-dimer without a linker, Beltide-2 is the 18A-dimer with proline (Pro) as a linker and Beltide-3 is the 18A-dimer linked by two glycines (Gly-Gly). The self-assembly of the beltides with the phospholipid DMPC was studied with and without the incorporated membrane protein bacteriorhodopsin (bR) through a combination of coarse-grained MD simulations, size-exclusion chromatography (SEC), circular dichroism (CD) spectroscopy, small-angle scattering (SAS), static light scattering (SLS) and UV-Vis spectroscopy. For all three beltides, MD and combined small-angle X-ray and -neutron scattering were consistent with a disc structure composed by a phospholipid bilayer surrounded by a belt of peptides and with a total disc diameter of approximately 10 nm. CD confirmed that all three beltides were α-helical in the free form and with DMPC. However, as shown by SEC the different interhelical linkers clearly led to different properties of the beltides. Beltide-3, with the Gly-Gly linker, was very adaptable such that peptide nanodiscs could be formed for a broad range of different peptide to lipid stoichiometries and therefore also possible disc-sizes. On the other hand, both Beltide-2 with the Pro linker and Beltide-1 without a linker were less adaptable and would only form discs of certain peptide to lipid stoichiometries. SLS revealed that the structural stability of the formed peptide nanodiscs was also highly affected by the linkers and it was found that Beltide-1 gave more stable discs than the other two beltides. With respect to membrane protein stabilization, each of the three beltides in combination with DMPC stabilizes the seven-helix transmembrane protein bacteriorhodopsin significantly better than the detergent octyl glucoside, but no

  19. Exclusive processes: Tests of coherent QCD phenomena and nucleon substructure at CEBAF

    SciTech Connect

    Brodsky, S.J.

    1994-07-01

    Measurements of exclusive processes such as electroproduction, photoproduction, and Compton scattering are among the most sensitive probes of proton structure and coherent phenomena in quantum chromodynamics. The continuous electron beam at CEBAF, upgraded in laboratory energy to 10--12 GeV, will allow a systematic study of exclusive, semi-inclusive, and inclusive reactions in a kinematic range well-tuned to the study of fundamental nucleon and nuclear substructure. I also discuss the potential at CEBAF for studying novel QCD phenomena at the charm production threshold, including the possible production of nuclear-bound quarkonium.

  20. Predicting target-ligand interactions using protein ligand-binding site and ligand substructures

    PubMed Central

    2015-01-01

    Background Cell proliferation, differentiation, Gene expression, metabolism, immunization and signal transduction require the participation of ligands and targets. It is a great challenge to identify rules governing molecular recognition between chemical topological substructures of ligands and the binding sites of the targets. Methods We suppose that the ligand-target interactions are determined by ligand substructures as well as the physical-chemical properties of the binding sites. Therefore, we propose a fragment interaction model (FIM) to describe the interactions between ligands and targets, with the purpose of facilitating the chemical interpretation of ligand-target binding. First we extract target-ligand complexes from sc-PDB database, based on which, we get the target binding sites and the ligands. Then we represent each binding site as a fragment vector based on a target fragment dictionary that is composed of 199 clusters (denoted as fragements in this work) obtained by clustering 4200 trimers according to their physical-chemical properties. And then, we represent each ligand as a substructure vector based on a dictionary containing 747 substructures. Finally, we build the FIM by generating the interaction matrix M (representing the fragment interaction network), and the FIM can later be used for predicting unknown ligand-target interactions as well as providing the binding details of the interactions. Results The five-fold cross validation results show that the proposed model can get higher AUC score (92%) than three prevalence algorithms CS-PD (80%), BLM-NII (85%) and RF (85%), demonstrating the remarkable predictive ability of FIM. We also show that the ligand binding sites (local information) overweight the sequence similarities (global information) in ligand-target binding, and introducing too much global information would be harmful to the predictive ability. Moreover, The derived fragment interaction network can provide the chemical insights on

  1. Gamma rays from dark matter annihilations strongly constrain the substructure in halos.

    PubMed

    Pinzke, Anders; Pfrommer, Christoph; Bergström, Lars

    2009-10-30

    To fit recent data, e(+/-) from dark matter (DM) needs a boosted annihilation rate. This may imply an observable level of gamma rays from nearby galaxy clusters for the Fermi satellite. Using EGRET data, we limit the minimum mass of DM substructures to be about 5x10(3) times larger than for cold DM, meaning a cutoff similar to, e.g., warm DM. We numerically simulate clusters to reliably model the background. If we assume no anomalous boost factor, we find comparable levels of gamma-ray emission from DM and cosmic ray interactions, giving a chance with future data to characterize the DM. PMID:19905798

  2. The Search for Milky Way Halo Substructure WIMP Annihilations Using the GLAST LAT

    SciTech Connect

    Wai, Larry; /SLAC

    2007-02-05

    The GLAST LAT Collaboration is one among several experimental groups, covering a wide range of approaches, pursuing the search for the nature of dark matter. The GLAST LAT has the unique ability to find new sources of high energy gamma radiation emanating directly from WIMP annihilations in situ in the universe. Using it's wide band spectral and full sky spatial capabilities, the GLAST LAT can form ''images'' in high energy gamma-rays of dark matter substructures in the gamma-ray sky. We describe a preliminary feasibility study for indirect detection of milky way dark matter satellites using the GLAST LAT.

  3. An early neutrino experiment: how we missed quark substructure in 1963

    NASA Astrophysics Data System (ADS)

    Perkins, D. H.

    2013-12-01

    Some 50 years after the event seems to be an appropriate time at which to take a long look back at one of the early neutrino experiments at CERN. This report is principally about a failure in a 1963 bubble chamber experiment to detect substructure in the nucleon, a year before the quark concept was invented by Gell-Mann and Zweig, and some five years before the existence of quarks as real dynamical objects was definitely established in deep inelastic electron scattering experiments at Stanford.

  4. Application of a substructuring technique to the problem of crack extension and closure

    NASA Technical Reports Server (NTRS)

    Armen, H., Jr.

    1974-01-01

    A substructuring technique, originally developed for the efficient reanalysis of structures, is incorporated into the methodology associated with the plastic analysis of structures. An existing finite-element computer program that accounts for elastic-plastic material behavior under cyclic loading was modified to account for changing kinematic constraint conditions - crack growth and intermittent contact of crack surfaces in two dimensional regions. Application of the analysis is presented for a problem of a centercrack panel to demonstrate the efficiency and accuracy of the technique.

  5. Constitutive Smad linker phosphorylation in melanoma: a mechanism of resistance to transforming growth factor-β-mediated growth inhibition.

    PubMed

    Cohen-Solal, Karine A; Merrigan, Kim T; Chan, Joseph L-K; Goydos, James S; Chen, Wenjin; Foran, David J; Liu, Fang; Lasfar, Ahmed; Reiss, Michael

    2011-06-01

    Melanoma cells are resistant to transforming growth factor-β (TGFβ)-induced cell-cycle arrest. In this study, we investigated a mechanism of resistance involving a regulatory domain, called linker region, in Smad2 and Smad3, main downstream effectors of TGFβ. Melanoma cells in culture and tumor samples exhibited constitutive Smad2 and Smad3 linker phosphorylation. Treatment of melanoma cells with the MEK1/2 inhibitor, U0126, or the two pan-CDK and GSK3 inhibitors, Flavopiridol and R547, resulted in decreased linker phosphorylation of Smad2 and Smad3. Overexpression of the linker phosphorylation-resistant Smad3 EPSM mutant in melanoma cells resulted in an increase in expression of p15(INK4B) and p21(WAF1) , as compared with cells transfected with wild-type (WT) Smad3. In addition, the cell numbers of EPSM Smad3-expressing melanoma cells were significantly reduced compared with WT Smad3-expressing cells. These results suggest that the linker phosphorylation of Smad3 contributes to the resistance of melanoma cells to TGFβ-mediated growth inhibition. PMID:21477078

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

    PubMed

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

    2016-07-01

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

  7. Preferential domain orientation of HMGB2 determined by the weak intramolecular interactions mediated by the interdomain linker

    NASA Astrophysics Data System (ADS)

    Uewaki, Jun-ichi; Kamikubo, Hironari; Kurita, Jun-ichi; Hiroguchi, Noriteru; Moriuchi, Hiroshi; Yoshida, Michiteru; Kataoka, Mikio; Utsunomiya-Tate, Naoko; Tate, Shin-ichi

    2013-06-01

    High mobility group box protein 2 (HMGB2) contains homologous tandem HMG box DNA-binding domains, boxes A and B. These two boxes are linked by a short basic linker having a sequence characteristic of an intrinsically disordered element. The combined use of NMR and small angle X-ray scattering (SAXS) showed that the two boxes assume a preferred orientation to make their DNA binding surface in opposite directions, although the linker does not keep any specific conformation. A series of site directed mutations to the residues in the linker showed that a network of CH-π interactions connects the N-terminal part of the linker to box A. The mutants having impaired intramolecular CH-π interactions changed the interdomain dynamics and their dynamic averaged orientation relative to the wild-type. This work demonstrates that the apparently unstructured linker plays a role in defining the preferential domain orientation through the intramolecular CH-π interactions, even though the interactions are weak and transient.

  8. Nanospheres of doxorubicin as cross-linkers for a supramolecular hydrogelation

    PubMed Central

    Xue, Qiang; Ren, He; Xu, Chao; Wang, Gang; Ren, Chunhua; Hao, Jihui; Ding, Dan

    2015-01-01

    In this study, we synthesized a peptide of Nap-GFFYGRGD, which could self-assemble into supramolecular nanofibers. The peptide itself could only form nanofibers but not hydrogels due to the relative weak inter-fiber interactions. The resulting nanofibers were then utilized as the vehicles for anticancer drug doxorubicin. It was found that the nanofibers of Nap-GFFYGRGD could not encapsulate doxorubicin, whereas the drug formed nanospheres, which were located at the surface of the nanofibers. Due to the electrostatic interactions between the negatively charged nanofibers and the positively charged doxorubicin nanospheres, the doxorubicin nanospheres were able to serve as a cross-linker to increase the inter-fiber interactions, leading to the formation of stable three-dimentional fiber networks and hydrogels. The resulting doxorubicin-peptide hydrogels were capable of releasing the drug in a sustained manner, which also showed comparable cytotoxicity as compared to free doxorubicin against a variety of cancer cell lines including HeLa and MCF-7 cancer cells. Therefore, this successful example using drug as the peptide nanofiber cross-linkers provided a new strategy for fabricating supramolecular hydrogelation for controlled delivery of anticancer drugs. PMID:25739554

  9. Developing New Isotope-Coded Mass Spectrometry-Cleavable Cross-Linkers for Elucidating Protein Structures

    PubMed Central

    2015-01-01

    Structural characterization of protein complexes is essential for the understanding of their function and regulation. However, it remains challenging due to limitations in existing tools. With recent technological improvements, cross-linking mass spectrometry (XL-MS) has become a powerful strategy to define protein–protein interactions and elucidate structural topologies of protein complexes. To further advance XL-MS studies, we present here the development of new isotope-coded MS-cleavable homobifunctional cross-linkers: d0- and d10-labeled dimethyl disuccinimidyl sulfoxide (DMDSSO). Detailed characterization of DMDSSO cross-linked peptides further demonstrates that sulfoxide-containing MS-cleavable cross-linkers offer robust and predictable MS2 fragmentation of cross-linked peptides, permitting subsequent MS3 analysis for simplified, unambiguous identification. Concurrent usage of these reagents provides a characteristic doublet pattern of DMDSSO cross-linked peptides, thus aiding in the confidence of cross-link identification by MSn analysis. More importantly, the unique isotopic profile permits quantitative analysis of cross-linked peptides and therefore expands the capability of XL-MS strategies to analyze both static and dynamic protein interactions. Together, our work has established a new XL-MS workflow for future studies toward the understanding of structural dynamics of protein complexes. PMID:24471733

  10. Developing new isotope-coded mass spectrometry-cleavable cross-linkers for elucidating protein structures.

    PubMed

    Yu, Clinton; Kandur, Wynne; Kao, Athit; Rychnovsky, Scott; Huang, Lan

    2014-02-18

    Structural characterization of protein complexes is essential for the understanding of their function and regulation. However, it remains challenging due to limitations in existing tools. With recent technological improvements, cross-linking mass spectrometry (XL-MS) has become a powerful strategy to define protein-protein interactions and elucidate structural topologies of protein complexes. To further advance XL-MS studies, we present here the development of new isotope-coded MS-cleavable homobifunctional cross-linkers: d0- and d10-labeled dimethyl disuccinimidyl sulfoxide (DMDSSO). Detailed characterization of DMDSSO cross-linked peptides further demonstrates that sulfoxide-containing MS-cleavable cross-linkers offer robust and predictable MS2 fragmentation of cross-linked peptides, permitting subsequent MS3 analysis for simplified, unambiguous identification. Concurrent usage of these reagents provides a characteristic doublet pattern of DMDSSO cross-linked peptides, thus aiding in the confidence of cross-link identification by MS(n) analysis. More importantly, the unique isotopic profile permits quantitative analysis of cross-linked peptides and therefore expands the capability of XL-MS strategies to analyze both static and dynamic protein interactions. Together, our work has established a new XL-MS workflow for future studies toward the understanding of structural dynamics of protein complexes. PMID:24471733

  11. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery.

    PubMed

    Papaleo, Elena; Saladino, Giorgio; Lambrughi, Matteo; Lindorff-Larsen, Kresten; Gervasio, Francesco Luigi; Nussinov, Ruth

    2016-06-01

    Proteins are dynamic entities that undergo a plethora of conformational changes that may take place on a wide range of time scales. These changes can be as small as the rotation of one or a few side-chain dihedral angles or involve concerted motions in larger portions of the three-dimensional structure; both kinds of motions can be important for biological function and allostery. It is becoming increasingly evident that "connector regions" are important components of the dynamic personality of protein structures. These regions may be either disordered loops, i.e., poorly structured regions connecting secondary structural elements, or linkers that connect entire protein domains. Experimental and computational studies have, however, revealed that these regions are not mere connectors, and their role in allostery and conformational changes has been emerging in the last few decades. Here we provide a detailed overview of the structural properties and classification of loops and linkers, as well as a discussion of the main computational methods employed to investigate their function and dynamical properties. We also describe their importance for protein dynamics and allostery using as examples key proteins in cellular biology and human diseases such as kinases, ubiquitinating enzymes, and transcription factors. PMID:26889708

  12. Peroxisomes move by hitchhiking on early endosomes using the novel linker protein PxdA.

    PubMed

    Salogiannis, John; Egan, Martin J; Reck-Peterson, Samara L

    2016-02-01

    Eukaryotic cells use microtubule-based intracellular transport for the delivery of many subcellular cargos, including organelles. The canonical view of organelle transport is that organelles directly recruit molecular motors via cargo-specific adaptors. In contrast with this view, we show here that peroxisomes move by hitchhiking on early endosomes, an organelle that directly recruits the transport machinery. Using the filamentous fungus Aspergillus nidulans we found that hitchhiking is mediated by a novel endosome-associated linker protein, PxdA. PxdA is required for normal distribution and long-range movement of peroxisomes, but not early endosomes or nuclei. Using simultaneous time-lapse imaging, we find that early endosome-associated PxdA localizes to the leading edge of moving peroxisomes. We identify a coiled-coil region within PxdA that is necessary and sufficient for early endosome localization and peroxisome distribution and motility. These results present a new mechanism of microtubule-based organelle transport in which peroxisomes hitchhike on early endosomes and identify PxdA as the novel linker protein required for this coupling. PMID:26811422

  13. Allosteric N-WASP activation by an inter-SH3 domain linker in Nck

    PubMed Central

    Okrut, Julia; Prakash, Sumit; Wu, Qiong; Kelly, Mark J. S.; Taunton, Jack

    2015-01-01

    Actin filament networks assemble on cellular membranes in response to signals that locally activate neural Wiskott–Aldrich-syndrome protein (N-WASP) and the Arp2/3 complex. An inactive conformation of N-WASP is stabilized by intramolecular contacts between the GTPase binding domain (GBD) and the C helix of the verprolin-homology, connector-helix, acidic motif (VCA) segment. Multiple SH3 domain-containing adapter proteins can bind and possibly activate N-WASP, but it remains unclear how such binding events relieve autoinhibition to unmask the VCA segment and activate the Arp2/3 complex. Here, we have used purified components to reconstitute a signaling cascade driven by membrane-localized Src homology 3 (SH3) adapters and N-WASP, resulting in the assembly of dynamic actin networks. Among six SH3 adapters tested, Nck was the most potent activator of N-WASP–driven actin assembly. We identify within Nck a previously unrecognized activation motif in a linker between the first two SH3 domains. This linker sequence, reminiscent of bacterial virulence factors, directly engages the N-WASP GBD and competes with VCA binding. Our results suggest that animals, like pathogenic bacteria, have evolved peptide motifs that allosterically activate N-WASP, leading to localized actin nucleation on cellular membranes. PMID:26554011

  14. Molecular genetic analysis of the drought-inducible linker histone variant in Arabidopsis thaliana.

    PubMed

    Ascenzi, R; Gantt, J S

    1999-09-01

    Linker histones are ubiquitous structural components of chromatin that have been shown to influence the expression of a subset of genes in diverse organisms. Plants contain a minor linker histone variant that is expressed in most tissues of all organs, and is induced during drought stress. Based on reporter gene analysis in roots, His1-3 is expressed almost exclusively in emerging secondary roots in unstressed plants, but is primarily expressed in the root meristem and elongation zone of stressed plants. In shoots, expression is higher in younger tissues than older tissues. In order to investigate the function of H1-3, we have generated lines with altered levels of H1-3. Plants expressing an antisense His1-3 transcript exhibit a greatly impaired induction (5% of wild-type RNA levels during stress) of His1-3 transcripts in shoots during drought and contain decreased protein relative to wild-type control plants. In plants overexpressing His1-3, more H1-3 is bound to chromatin than in unstressed wild-type plants. None of the plants containing these transgenes display phenotypic aberrations or differences in water content during drought stress. Additionally, the expression of several drought-responsive genes is not significantly altered in lines misexpressing His1-3. PMID:10579484

  15. SKI promotes Smad3 linker phosphorylations associated with the tumor-promoting trait of TGFbeta.

    PubMed

    Lin, Qiushi; Chen, Dahu; Timchenko, Nikolai A; Medrano, Estela E

    2010-05-01

    The transcriptional co-regulator SKI is a potent inhibitor of TGFbeta-growth inhibitory signals. SKI binds to receptor-activated Smads in the nucleus, forming repressor complexes containing HDACs, mSin3, NCoR, and other protein partners. Alternatively, SKI binds to activated Smads in the cytoplasm, preventing their nuclear translocation. SKI is necessary for anchorage-independent growth of melanoma cells in vitro, and most important, for human melanoma xenograft growth in vivo. We recently identified a novel role of SKI in TGFbeta signaling. SKI promotes the switch of Smad3 from repressor of proliferation to activator of oncogenesis by facilitating phosphorylations in the linker domain. High levels of endogenous SKI are required by the tumor promoting trait of TGFbeta to induce expression of the plasminogen-activator inhibitor-1 (PAI-1), sustained expression of C-Myc and for aborting upregulation of p21(Waf-1). Here we discuss how SKI diversifies and amplifies its functions by associating with multiple protein partners and by promoting Smad3 linker phosphorylation(s) in response to TGFbeta signaling in melanoma cells. PMID:20404506

  16. A structured interdomain linker directs self-polymerization of human uromodulin

    PubMed Central

    Bokhove, Marcel; Nishimura, Kaoru; Brunati, Martina; Han, Ling; de Sanctis, Daniele; Rampoldi, Luca

    2016-01-01

    Uromodulin (UMOD)/Tamm–Horsfall protein, the most abundant human urinary protein, plays a key role in chronic kidney diseases and is a promising therapeutic target for hypertension. Via its bipartite zona pellucida module (ZP-N/ZP-C), UMOD forms extracellular filaments that regulate kidney electrolyte balance and innate immunity, as well as protect against renal stones. Moreover, salt-dependent aggregation of UMOD filaments in the urine generates a soluble molecular net that captures uropathogenic bacteria and facilitates their clearance. Despite the functional importance of its homopolymers, no structural information is available on UMOD and how it self-assembles into filaments. Here, we report the crystal structures of polymerization regions of human UMOD and mouse ZP2, an essential sperm receptor protein that is structurally related to UMOD but forms heteropolymers. The structure of UMOD reveals that an extensive hydrophobic interface mediates ZP-N domain homodimerization. This arrangement is required for filament formation and is directed by an ordered ZP-N/ZP-C linker that is not observed in ZP2 but is conserved in the sequence of deafness/Crohn’s disease-associated homopolymeric glycoproteins α-tectorin (TECTA) and glycoprotein 2 (GP2). Our data provide an example of how interdomain linker plasticity can modulate the function of structurally similar multidomain proteins. Moreover, the architecture of UMOD rationalizes numerous pathogenic mutations in both UMOD and TECTA genes. PMID:26811476

  17. A minimal phycobilisome: fusion and chromophorylation of the truncated core-membrane linker and phycocyanin.

    PubMed

    Tang, Kun; Zeng, Xiao-Li; Yang, Yi; Wang, Zhi-Bin; Wu, Xian-Jun; Zhou, Ming; Noy, Dror; Scheer, Hugo; Zhao, Kai-Hong

    2012-07-01

    Phycobilisomes, the light-harvesting antennas in cyanobacteria and red algae, consist of an allophycocyanin core that is attached to the membrane via a core-membrane linker, and rods comprised of phycocyanin and often also phycoerythrin or phycoerythrocyanin. Phycobiliproteins show excellent energy transfer among the chromophores that renders them biomarkers with large Stokes-shifts absorbing over most of the visible spectrum and into the near infrared. Their application is limited, however, due to covalent binding of the chromophores and by solubility problems. We report construction of a water-soluble minimal chromophore-binding unit of the red-absorbing and fluorescing core-membrane linker. This was fused to minimal chromophore-binding units of phycocyanin. After double chromophorylation with phycocyanobilin, in E. coli, the fused phycobiliproteins absorbed light in the range of 610-660nm, and fluoresced at ~670nm, similar to phycobilisomes devoid of phycoerythr(ocyan)in. The fused phycobiliprotein could also be doubly chromophorylated with phycoerythrobilin, resulting in a chromoprotein absorbing around 540-575nm, and fluorescing at ~585nm. The broad absorptions and the large Stokes shifts render these chromoproteins candidates for imaging; they may also be helpful in studying phycobilisome assembly. PMID:22465853

  18. Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states

    PubMed Central

    Tan, Dan; Li, Qiang; Zhang, Mei-Jun; Liu, Chao; Ma, Chengying; Zhang, Pan; Ding, Yue-He; Fan, Sheng-Bo; Tao, Li; Yang, Bing; Li, Xiangke; Ma, Shoucai; Liu, Junjie; Feng, Boya; Liu, Xiaohui; Wang, Hong-Wei; He, Si-Min; Gao, Ning; Ye, Keqiong; Dong, Meng-Qiu; Lei, Xiaoguang

    2016-01-01

    To improve chemical cross-linking of proteins coupled with mass spectrometry (CXMS), we developed a lysine-targeted enrichable cross-linker containing a biotin tag for affinity purification, a chemical cleavage site to separate cross-linked peptides away from biotin after enrichment, and a spacer arm that can be labeled with stable isotopes for quantitation. By locating the flexible proteins on the surface of 70S ribosome, we show that this trifunctional cross-linker is effective at attaining structural information not easily attainable by crystallography and electron microscopy. From a crude Rrp46 immunoprecipitate, it helped identify two direct binding partners of Rrp46 and 15 protein-protein interactions (PPIs) among the co-immunoprecipitated exosome subunits. Applying it to E. coli and C. elegans lysates, we identified 3130 and 893 inter-linked lysine pairs, representing 677 and 121 PPIs. Using a quantitative CXMS workflow we demonstrate that it can reveal changes in the reactivity of lysine residues due to protein-nucleic acid interaction. DOI: http://dx.doi.org/10.7554/eLife.12509.001 PMID:26952210

  19. Multivalent linkers for improved covalent binding of oligonucleotides to dye-doped silica nanoparticles

    NASA Astrophysics Data System (ADS)

    Kelleher, S. M.; Nooney, R. I.; Flynn, S. P.; Clancy, E.; Burke, M.; Daly, S.; Smith, T. J.; Daniels, S.; McDonagh, C.

    2015-09-01

    This paper describes the fabrication of oligonucleotide-coated Cy5-doped silica nanoparticles using a combination of multivalent linkers and their use in surface-based DNA sandwich hybridization assays. Dipodal silane is introduced as a means to fabricate amine-coated silica nanoparticles and its advantages compared to monopodal silanes are discussed. The use of dipodal silane in conjunction with three different polymer linkers (oxidized dextran, linear and 8-arm polyethylene glycol (PEG)) to immobilize single-stranded DNA to Cy5-doped nanoparticles is investigated and dynamic light scattering measurements and Fourier transform infrared spectroscopy are used to follow the progression of the functionalization of the nanoparticles. We observe a significant improvement in the binding stability of the single-stranded DNA when the dipodal silane and 8-arm PEG are used in combination, when compared to alternative conjugation strategies. Both 8mer and 22mer oligonucleotides are securely conjugated to the high-brightness nanoparticles and their availability to hybridize with a complementary strand is confirmed using solution-based DNA hybridization experiments. In addition, a full surface-based sandwich assay demonstrates the potential these nanoparticles have in the detection of less than 500 femtomolar of a DNA analogue of micro RNA, miR-451.

  20. Evaluation of the antibacterial and antibiofilm activities of novel CRAMP-vancomycin conjugates with diverse linkers.

    PubMed

    Mishra, Nigam M; Briers, Yves; Lamberigts, Chris; Steenackers, Hans; Robijns, Stijn; Landuyt, Bart; Vanderleyden, Jos; Schoofs, Liliane; Lavigne, Rob; Luyten, Walter; Van der Eycken, Erik V

    2015-07-21

    We report the design, synthesis and antibacterial activity analysis of conjugates of vancomycin and cathelicidin-related antimicrobial peptides (CRAMP). Vancomycin inhibits the nascent peptidoglycan synthesis and is highly active against Gram-positive bacteria, whereas Gram-negative bacteria are generally insensitive due to a protective outer membrane. CRAMP is known to translocate across the Gram-negative outer membrane by a self-promoted uptake mechanism. Vancomycin-CRAMP conjugates were synthesized using click chemistry with diverse hydrophilic and hydrophobic linkers, with CRAMP functioning as a carrier peptide for the transfer of vancomycin through the outer membrane. Small hydrophobic linkers with an aromatic group result in the most active conjugates against planktonic Gram-negative bacteria, while maintaining the high activity of vancomycin against Gram-positive bacteria. These conjugates thus show a broad-spectrum activity, which is absent in CRAMP or vancomycin alone, and which is strongly improved compared to an equimolar mixture of CRAMP and vancomycin. In addition, these conjugates also show a strong inhibitory activity against S. Typhimurium biofilm formation. PMID:26068402

  1. Luminescence of Rare-Earth-Doped Nanoparticles with Aromatic Linker Molecules

    NASA Astrophysics Data System (ADS)

    Senty, Tess; Yalamanchi, Mohita; Zhang, Yanwei; Leach, Anya; Seehra, Mohindar; Shi, Xiaodong; Bristow, Alan

    2012-02-01

    Rare-earth-doped vanadate glasses retain their luminescence when formed as shells around magnetic cores [1]. This property has prompted speculation that composite magneto-photoluminescent (CMPL) structures can be used in biological applications. For example, CMPL nanoparticles can be magnetically tuned to separate cells, proteins and nucleic acids [2]. A crucial step in realizing this goal is to attach organic linkers (between the rare-earth-doped shell and bio-probes), which do not affect the luminescence. We demonstrate with IR spectroscopy that Eu:YVO4 nanoparticles treated with benzoic acid, 3-nitro 4-chloro-benzoic acid and 3,4-dimethoxy benzoic acid all result in the modification of the surface states, replacing the native metal-hydroxyl bond with a longer chain aromatic linker, which can be later functionalized. Photoluminescence spectra under UV-excitation show that the dominant ^5D0 -> ^7F2 transition at ˜620 nm is unaffected by the chemical treatment. The result provides a platform to facilitate the attachment of bio-probes to Eu:YVO4 nanoparticles and related CMPL nanostructures with Fe2O4 cores. [1] N. B. McDowell et al, J. Appl. Phys. 107, 09B327 (2010). [2] T. R. Sathe et al, Anal. Chem. 78, 5627 (2006).

  2. Multivalent linkers for improved covalent binding of oligonucleotides to dye-doped silica nanoparticles.

    PubMed

    Kelleher, S M; Nooney, R I; Flynn, S P; Clancy, E; Burke, M; Daly, S; Smith, T J; Daniels, S; McDonagh, C

    2015-09-11

    This paper describes the fabrication of oligonucleotide-coated Cy5-doped silica nanoparticles using a combination of multivalent linkers and their use in surface-based DNA sandwich hybridization assays. Dipodal silane is introduced as a means to fabricate amine-coated silica nanoparticles and its advantages compared to monopodal silanes are discussed. The use of dipodal silane in conjunction with three different polymer linkers (oxidized dextran, linear and 8-arm polyethylene glycol (PEG)) to immobilize single-stranded DNA to Cy5-doped nanoparticles is investigated and dynamic light scattering measurements and Fourier transform infrared spectroscopy are used to follow the progression of the functionalization of the nanoparticles. We observe a significant improvement in the binding stability of the single-stranded DNA when the dipodal silane and 8-arm PEG are used in combination, when compared to alternative conjugation strategies. Both 8mer and 22mer oligonucleotides are securely conjugated to the high-brightness nanoparticles and their availability to hybridize with a complementary strand is confirmed using solution-based DNA hybridization experiments. In addition, a full surface-based sandwich assay demonstrates the potential these nanoparticles have in the detection of less than 500 femtomolar of a DNA analogue of micro RNA, miR-451. PMID:26294441

  3. Fine tuning of spatial arrangement of enzymes in a PCNA-mediated multienzyme complex using a rigid poly-L-proline linker.

    PubMed

    Haga, Tomoaki; Hirakawa, Hidehiko; Nagamune, Teruyuki

    2013-01-01

    Inspired by natural multienzyme complexes, many types of artificial multienzyme complexes have recently been constructed. We previously constructed a self-assembled complex of a bacterial cytochrome P450 and its ferredoxin and ferredoxin reductase partners using heterotrimerization of proliferating cell nuclear antigen (PCNA) from Sulfolobus solfataricus. In this study, we inserted different peptide linkers between ferredoxin and the PCNA subunit, and examined the effect on activity of the self-assembled multienzyme complex. Although the activity was affected by the lengths of both the rigid poly-L-proline-rich linkers and the flexible Gly4-Ser repeating linkers, the poly-L-proline-rich linkers provided the greatest activity enhancement. The optimized poly-L-proline-rich linker enhanced the activity 1.9-fold compared with the GGGGSLVPRGSGGGGS linker used in the previously reported complex, while the Gly4-Ser repeating linkers, (G4S)n (n = 1-6), did not yield higher activity than the maximum activity by the optimized poly-L-proline linker. Both the rigidity/flexibility and length of the peptide linker were found to be important for enhancing the overall activity of the multienzyme complex. PMID:24040392

  4. Characterization of green mutants in Fremyella diplosiphon provides insight into the impact of phycoerythrin deficiency and linker function on complementary chromatic adaptation.

    PubMed

    Whitaker, Melissa J; Pattanaik, Bagmi; Montgomery, Beronda L

    2011-01-01

    Functions of phycobiliprotein (PBP) linkers are less well studied than other PBP polypeptides that are structural components or required for the synthesis of the light-harvesting phycobilisome (PBS) complexes. Linkers serve both structural and functional roles in PBSs. Here, we report the isolation of a phycoerythrin (PE) rod-linker mutant and a novel PE-deficient mutant in Fremyella diplosiphon. We describe their phenotypic characterization, including light-dependent photosynthetic pigment accumulation and photoregulation of cellular morphology. PE-linker protein CpeE and a novel protein impact PE accumulation, and thus PBS function, primarily under green light conditions. PMID:21094137

  5. Rigidifying Fluorescent Linkers by Metal-Organic Framework Formation for Fluorescence Blue Shift and Quantum Yield Enhancement

    SciTech Connect

    Wei, ZW; Gu, ZY; Arvapally, RK; Chen, YP; McDougald, RN; Ivy, JF; Yakovenko, AA; Feng, DW; Omary, MA; Zhou, HC

    2014-06-11

    We demonstrate that rigidifying the structure of fluorescent linkers by structurally constraining them in metal-organic frameworks (MOFs) to control their conformation effectively tunes the fluorescence energy and enhances the quantum yield. Thus, a new tetraphenylethylene-based zirconium MOF exhibits a deep-blue fluorescent emission at 470 nm with a unity quantum yield (99.9 +/- 0.5%) under Ar, representing ca. 3600 cm(-1) blue shift and doubled radiative decay efficiency vs the linker precursor. An anomalous increase in the fluorescence lifetime and relative intensity takes place upon heating the solid MOF from cryogenic to ambient temperatures. The origin of these unusual photoluminescence properties is attributed to twisted linker conformation, intramolecular hindrance, and framework rigidity.

  6. Rigidifying Fluorescent Linkers by Metal–Organic Framework Formation for Fluorescence Blue Shift and Quantum Yield Enhancement

    SciTech Connect

    Wei, Zhangwen; Gu, Zhi-Yuan; Arvapally, Ravi K.; Chen, Ying-Pin; Ivy, Joshua F.; Yakovenko, Andrey A.; Feng, Dawei; Omary, Mohammad A.; Zhou, Hong-Cai

    2014-06-11

    We demonstrate that rigidifying the structure of fluorescent linkers by structurally constraining them in metal–organic frameworks (MOFs) to control their conformation effectively tunes the fluorescence energy and enhances the quantum yield. Thus, a new tetraphenylethylene-based zirconium MOF exhibits a deep-blue fluorescent emission at 470 nm with a unity quantum yield (99.9 ± 0.5%) under Ar, representing ca. 3600 cm⁻¹ blue shift and doubled radiative decay efficiency vs the linker precursor. An anomalous increase in the fluorescence lifetime and relative intensity takes place upon heating the solid MOF from cryogenic to ambient temperatures. The origin of these unusual photoluminescence properties is attributed to twisted linker conformation, intramolecular hindrance, and framework rigidity.

  7. Converting Nonliquid Crystals into Liquid Crystals by N-Methylation in the Central Linker of Triazine-Based Dendrimers.

    PubMed

    Tsai, Meng-Jung; Hsieh, Jei-Way; Lai, Long-Li; Cheng, Kung-Lung; Liu, Shih-Hsien; Lee, Jey-Jau; Hsu, Hsiu-Fu

    2016-06-17

    Two triazine-based dendrimers were successfully prepared in 60-75% yields. These newly prepared dendrimers 2a and 2b containing the -NMe(CH2)2NMe- and the -NMe(CH2)4NMe- linkers between two G3 dendrons, respectively, exhibit columnar phases during the thermal process. However, the corresponding dendrimers 1a and 1b containing the -NH(CH2)2NH- and the -NH(CH2)4NH- linkers between two G3 dendrons, respectively, do not show any LC phases on thermal treatment. Computational investigations on molecular conformations reveal that N-methylation of the dendritic central linker leads dendrimers to possess more isomeric conformations and thus successfully converts non-LC dendrimers (1a and 1b) into LC dendrimers (2a and 2b). PMID:27203100

  8. Cross-linked polyelectrolyte for direct methanol fuel cells applications based on a novel sulfonated cross-linker

    NASA Astrophysics Data System (ADS)

    Li, Mingyu; Zhang, Gang; Xu, Shuai; Zhao, Chengji; Han, Miaomiao; Zhang, Liyuan; Jiang, Hao; Liu, Zhongguo; Na, Hui

    2014-06-01

    A novel type of cross-linked proton exchange membrane of lower methanol permeation and high proton conductivity is prepared, based on a newly synthesized sulfonated cross-linker: carboxyl terminated benzimidazole trimer bearing sulfonic acid groups (s-BI). Compared to membranes cross-linked with non-sulfonated cross-linker (BI), SPEEK/s-BI-n membranes show higher IEC values and proton conductivities. Meanwhile, oxidative stability and mechanical property of SPEEK/s-BI-n membranes are obviously improved. Among SPEEK/s-BI-n membranes, SPEEK/s-BI-2 exhibits high proton conductivity, low swelling ratio (0.122 S cm-1 and 15.2% at 60 °C, respectively) and low methanol permeability coefficient. These results imply that the cross-linked membranes prepared with the newly sulfonated cross-linker are promising for the direct methanol fuel cells (DMFCs) application.

  9. Superposed epoch study of ICME sub-structures near Earth and their effects on Galactic cosmic rays

    NASA Astrophysics Data System (ADS)

    Masías-Meza, J. J.; Dasso, S.; Démoulin, P.; Rodriguez, L.; Janvier, M.

    2016-08-01

    Context. Interplanetary coronal mass ejections (ICMEs) are the interplanetary manifestations of solar eruptions. The overtaken solar wind forms a sheath of compressed plasma at the front of ICMEs. Magnetic clouds (MCs) are a subset of ICMEs with specific properties (e.g. the presence of a flux rope). When ICMEs pass near Earth, ground observations indicate that the flux of Galactic cosmic rays (GCRs) decreases. Aims: The main aims of this paper are to find common plasma and magnetic properties of different ICME sub-structures and which ICME properties affect the flux of GCRs near Earth. Methods: We used a superposed epoch method applied to a large set of ICMEs observed in situ by the spacecraft ACE, between 1998 and 2006. We also applied a superposed epoch analysis on GCRs time series observed with the McMurdo neutron monitors. Results: We find that slow MCs at 1 AU have on average more massive sheaths. We conclude that this is because they are more effectively slowed down by drag during their travel from the Sun. Slow MCs also have a more symmetric magnetic field and sheaths expanding similarly as their following MC, while in contrast, fast MCs have an asymmetric magnetic profile and a sheath in compression. In all types of MCs, we find that the proton density and the temperature and the magnetic fluctuations can diffuse within the front of the MC due to 3D reconnection. Finally, we derive a quantitative model that describes the decrease in cosmic rays as a function of the amount of magnetic fluctuations and field strength. Conclusions: The obtained typical profiles of sheath, MC and GCR properties corresponding to slow, middle, and fast ICMEs, can be used for forecasting or modelling these events, and to better understand the transport of energetic particles in ICMEs. They are also useful for improving future operative space weather activities.

  10. The Substructure of the Solar Corona Observed in the Hi-C Telescope

    NASA Technical Reports Server (NTRS)

    Winebarger, A.; Cirtain, J.; Golub, L.; DeLuca, E.; Savage, S.; Alexander, C.; Schuler, T.

    2014-01-01

    In the summer of 2012, the High-resolution Coronal Imager (Hi-C) flew aboard a NASA sounding rocket and collected the highest spatial resolution images ever obtained of the solar corona. One of the goals of the Hi-C flight was to characterize the substructure of the solar corona. We therefore calculate how the intensity scales from a low-resolution (AIA) pixels to high-resolution (Hi-C) pixels for both the dynamic events and "background" emission (meaning, the steady emission over the 5 minutes of data acquisition time). We find there is no evidence of substructure in the background corona; the intensity scales smoothly from low-resolution to high-resolution Hi-C pixels. In transient events, however, the intensity observed with Hi-C is, on average, 2.6 times larger than observed with AIA. This increase in intensity suggests that AIA is not resolving these events. This result suggests a finely structured dynamic corona embedded in a smoothly varying background.

  11. Band structure and transmission characteristics of complex phononic crystals by multi-level substructure scheme

    NASA Astrophysics Data System (ADS)

    Yin, J.; Zhang, S.; Zhang, H. W.; Chen, B. S.

    2015-10-01

    A fast scheme based on the multi-level substructure technique is proposed for the band structure and transmission characteristics calculation of phononic crystals uniformly. The main idea is that finite element models of phononic crystals are divided into several domains by a special multi-level decomposition. For the band structure calculation, the upscaling calculation is employed to condense the internal stiffness matrix of the unit cell into the Bloch boundary. Due to the internal stiffness matrix does not change along with reduced wave vectors in an iteration process, the scheme can reduce the computational scale and improve the efficiency greatly, meanwhile it does not introduce approximation into the traditional finite element model. For the transmission characteristics calculation, the unit cell of the phononic crystal is periodic which is taken as a substructure with the same coefficient matrix. Moreover, the downscaling calculation of internal displacements can be selected flexibly. Some closely watched examples of the three-dimensional locally resonant, defect state of Lamb wave and Bragg waveguide are analyzed. Numerical results indicate that the proposed scheme is efficient and accurate, which may widely be applicable and suitable for complex phononic crystal problems, and provides a reliable numerical tool to optimize and design crystal devices.

  12. Reheating effects in the matter power spectrum and implications for substructure

    SciTech Connect

    Erickcek, Adrienne L.; Sigurdson, Kris

    2011-10-15

    The thermal and expansion history of the Universe before big bang nucleosynthesis is unknown. We investigate the evolution of cosmological perturbations through the transition from an early matter era to radiation domination. We treat reheating as the perturbative decay of an oscillating scalar field into relativistic plasma and cold dark matter. After reheating, we find that subhorizon perturbations in the decay-produced dark matter density are significantly enhanced, while subhorizon radiation perturbations are instead suppressed. If dark matter originates in the radiation bath after reheating, this suppression may be the primary cutoff in the matter power spectrum. Conversely, for dark matter produced nonthermally from scalar decay, enhanced perturbations can drive structure formation during the cosmic dark ages and dramatically increase the abundance of compact substructures. For low reheat temperatures, we find that as much as 50% of all dark matter is in microhalos with M > or approx. 0.1M{sub +} at z{approx_equal}100, compared to a fraction of {approx}10{sup -10} in the standard case. In this scenario, ultradense substructures may constitute a large fraction of dark matter in galaxies today.

  13. Application of finite element substructuring to composite micromechanics. M.S. Thesis - Akron Univ., May 1984

    NASA Technical Reports Server (NTRS)

    Caruso, J. J.

    1984-01-01

    Finite element substructuring is used to predict unidirectional fiber composite hygral (moisture), thermal, and mechanical properties. COSMIC NASTRAN and MSC/NASTRAN are used to perform the finite element analysis. The results obtained from the finite element model are compared with those obtained from the simplified composite micromechanics equations. A unidirectional composite structure made of boron/HM-epoxy, S-glass/IMHS-epoxy and AS/IMHS-epoxy are studied. The finite element analysis is performed using three dimensional isoparametric brick elements and two distinct models. The first model consists of a single cell (one fiber surrounded by matrix) to form a square. The second model uses the single cell and substructuring to form a nine cell square array. To compare computer time and results with the nine cell superelement model, another nine cell model is constructed using conventional mesh generation techniques. An independent computer program consisting of the simplified micromechanics equation is developed to predict the hygral, thermal, and mechanical properties for this comparison. The results indicate that advanced techniques can be used advantageously for fiber composite micromechanics.

  14. Periodic substructure for multi-frequency energy harvesting with single piezoelectric patch

    NASA Astrophysics Data System (ADS)

    Braghin, F.; Mehdipour, I.; Lecis, N.; Galassi, C.

    2016-04-01

    Simple piezo benders are able to harvest energy almost only at their first natural frequency. Thus, their efficiency is good only in presence of harmonic excitation having frequency equal to their first natural frequency. In case of wide band excitation, instead, more complex solutions have to be sought for. In particular, various forms of nonlinearity have been investigated that allow to "bend" resonance peaks and thus convert kinetic energy into electric energy over a wider frequency band. Also harvester with more benders have been analyzed. In the present paper a novel periodic substructure is proposed that allows to obtain several eigen-frequencies in a given frequency range. Moreover, the position where the piezo bender is placed has the same mode of vibration for all these eigen-frequencies. The bender is therefore able to harvest energy at all these eigen-frequencies thus greatly improving the overall efficiency. The next step will be to introduce nonlinearities in the substructure to even further extend the range of frequencies at which energy is harvested.

  15. CLUMPY: Jeans analysis, γ-ray and ν fluxes from dark matter (sub-)structures

    NASA Astrophysics Data System (ADS)

    Bonnivard, Vincent; Hütten, Moritz; Nezri, Emmanuel; Charbonnier, Aldée; Combet, Céline; Maurin, David

    2016-03-01

    We present an update of the CLUMPY code for the calculation of the astrophysical J-factors (from dark matter annihilation/decay) for any Galactic or extragalactic dark matter halo including substructures: halo-to-halo concentration scatter may now be enabled, boost factors can include several levels of substructures, and triaxiality is a new option for dark matter haloes. This new version takes advantage of the cfitsio and HEALPix libraries to propose fits output maps using the HEALPix pixelisation scheme. Skymaps for γ-ray and ν signals from generic annihilation/decay spectra are now direct outputs of CLUMPY. Making use of HEALPix routines, smoothing by a user-defined instrumental Gaussian beam and computing the angular power spectrum of the maps are now possible. In addition to these improvements, the main novelty is the implementation of a Jeans analysis module, to obtain dark matter density profiles from kinematic data in relaxed spherical systems (e.g., dwarf spheroidal galaxies). The code is also interfaced with the GreAT toolkit designed for Markov Chain Monte Carlo analyses, from which probability density functions and credible intervals can be obtained for velocity dispersions, dark matter profiles, and J-factors.

  16. In silico Prediction of Drug Induced Liver Toxicity Using Substructure Pattern Recognition Method.

    PubMed

    Zhang, Chen; Cheng, Feixiong; Li, Weihua; Liu, Guixia; Lee, Philip W; Tang, Yun

    2016-04-01

    Drug-induced liver injury (DILI) is a leading cause of acute liver failure in the US and less severe liver injury worldwide. It is also one of the major reasons of drug withdrawal from the market. Thus, DILI has become one of the most important concerns of drugs, and should be predicted in very early stage of drug discovery process. In this study, a comprehensive data set containing 1317 diverse compounds was collected from publications. Then, high accuracy classification models were built using five machine learning methods based on MACCS and FP4 fingerprints after evaluating by substructure pattern recognition method. The best model was built using SVM method together with FP4 fingerprint at the IG value threshold of 0.0005. Its overall predictive accuracies were 79.7 % and 64.5 % for the training and test sets, separately, which yielded overall accuracy of 75.0 % for the external validation dataset, consisting of 88 compounds collected from a benchmark DILI database - the Liver Toxicity Knowledge Base. This model could be used for drug-induced liver toxicity prediction. Moreover, some key substructure patterns correlated with drug-induced liver toxicity were also identified as structural alerts. PMID:27491923

  17. The effects of Asian population substructure on Y STR forensic analyses.

    PubMed

    Budowle, Bruce; Ge, Jianye; Low, Joyce; Lai, Crystal; Yee, Wong Hang; Law, Grace; Tan, Wai Fun; Chang, Yuet Meng; Perumal, Revathi; Keat, Phoon Yoong; Mizuno, Natsuko; Kasai, Kentaro; Sekiguchi, Kazumasa; Chakraborty, Ranajit

    2009-03-01

    A total of 3046 males of Chinese, Malay, Thai, Japanese, and Indian population affinity were previously typed for the Y STR loci DYS19, DYS385 (counted as two loci), DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS456, DYS458, DYS635, DYS448, and Y GATA H4 using the AmpFlSTR Yfiler kit. These samples were assessed for population genetic parameters that impact forensic statistical calculations. All population samples were highly polymorphic for the 16 Y STR markers with the marker DYS385 being the most polymorphic, because it is comprised of two loci. Most (2677 out of a total of 2806 distinct haplotypes) of the 16 marker haplotypes observed in the sample populations were represented only once in the data set. Haplotype diversities were greater than 99.57% for the Chinese, Malay, Thai, Japanese, and Indian sample populations. For the Y STR markers, population substructure correction was considered when calculating the rarity of a Y STR profile. An F(ST) value, rather than a R(ST) value, is more appropriate under a forensic model. Because the F(ST) values are very small within the Asian populations, the estimate of the rarity of a haplotype comprised of 10-16 markers does not need substructure correction. However haplotypes with fewer markers may require F(ST) corrections when calculating the rarity of the profile. PMID:19038565

  18. On the Origin of Temperature Substructure within Merging Clusters of Galaxies: Abell 2256

    NASA Astrophysics Data System (ADS)

    Roettiger, Kurt; Burns, Jack O.; Pinkney, Jason

    1995-11-01

    Recent ROSA T PSPC and ASCA observations of several rich clusters of galaxies have revealed complex temperature substructure within the X-ray emitting gas. One of the best and most detailed examples is A2256. Briel & Henry (1994) show four distinct temperature components within the central (<12') of A2256. The purpose of this paper is to suggest a plausible model, within reasonable parameter space, that explains the origin of the hottest (>8 keV) gas near the core of A2256. We find the temperature substructure in A2256 to be consistent with a model in which A2256 is currently in the early stages of a merger. We attempt to quantify this model by comparison with results from our parameter study of merging clusters of galaxies conducted with a numerical Hydro/N-body code. From this, we estimate that A2256 is actually two systems with a 2:1 mass ratio, whose cores are separated by ˜0.5 Mpc with a relative velocity of nearly 3000 km s-1. The proposed merger axis is projected into the plane of the sky by 45°-50° such that the less massive of the two clusters is approaching the observer. Within the frame work of this model, we find the hot gas (>8 keV) to be the result of shock heating during the merger event. We also use this model to explain the discrepancy between X-ray and galaxy-based mass estimates for A2256.

  19. Substructuring FE-XFE approaches applied to three-dimensional crack propagation

    NASA Astrophysics Data System (ADS)

    Wyart, E.; Duflot, M.; Coulon, D.; Martiny, P.; Pardoen, T.; Remacle, J. F.; Lani, F.

    2008-06-01

    Two substructuring methods are investigated in order to allow for the use of the eXtended Finite Element Method (X-FEM) within commercial finite element (FE) codes without need for modifying their kernel. The global FE problem is decomposed into two subdomains, the safe domain and the cracked domain based on the value of the level sets representing the crack. The safe domain is treated by the host FE software while the cracked domain is treated by an independent XFE code. The first substructuring method consists of calculating the Schur matrix of a cracked super-element with the XFE code. The second technique introduces the finite element tearing and interconnecting method (FETI) which ensures the compatibility of the displacements at the interface between the cracked and safe subdomains. The stiffness matrices and nodal forces are provided by the XFE and FE codes for the cracked and safe subdomains, respectively. The solutions obtained with these two techniques are rigorously equivalent to those computed with the stand-alone XFE code. First, the computational efficiency of the two approaches is demonstrated. Second, a validation is proposed towards comparison with reference values of the stress intensity factors in simple 3D cracked geometries. Finally, this contribution presents an application of the FE-XFE-FETI method to the computation of the stress intensity factor induced by a crack inside a hydraulic cylinder under internal pressure.

  20. Local stellar kinematics from large astrometric surveys: mapping the Galactic phase-space substructure

    NASA Astrophysics Data System (ADS)

    Lepine, Sebastien

    2016-05-01

    The potential of future large astrometric catalogs for mapping the velocity-space distribution of local stars in the Galaxy is illustrated with a kinematic study of K and M dwarfs in the SUPERBLINK catalog of 2.5 million stars with large proper motions (mu>40 mas/yr). Low mass K and M dwarfs, found in abundance thanks to the faint magnitude limit of the catalog (V<20) provide the densest possible sampling of the [(X,Y,Z),(U,V,W)] phase-space, making them well-suited to map out substructure (so-called "streams") in the velocity-space distributions, as well as variations in said distribution over >100 parsec scale distances. The SUPERBLINK proper motion catalog thus provides kinematic data for ~1.5 million M dwarfs from the Galactic disk population, located within 200 parsecs of the Sun, and for ~180,000 K and M (sub)dwarfs from the Galactic halo population, all within 500 parsecs of the Sun. While the disk dwarfs show clear signs of velocity-space substructure, the distribution of halo subdwarf does appear to be relatively smooth ("streamless") in contrast. Evidence for spatial variations at the few hundred parsec scale is also discussed. The current and unfortunately "blurry" view of the local velocity-space distribution promises to be set in much sharper focus with the upcoming availability of data from the GAIA mission.

  1. Structural health monitoring system of Ironton-Russell bridge during substructure construction

    NASA Astrophysics Data System (ADS)

    Dalvi, Aditi; Norouzi, Mehdi; Hunt, Victor; Helmicki, Arthur

    2016-04-01

    Monitoring a complex structure has gained popularity worldwide to ensure safety and longevity of the structure. Structural Health Monitoring (SHM) systems have been employed for highway bridges to increase the effectiveness of their in-service inspection, to help measure its degradation or damage, and hence, to ensure it's safe and reliable operation. SHM may also be employed during the construction of a structure in order to ensure the safety and performance of the construction process. Monitoring during construction can also help designers compare the actual behavior of a structure with design models especially because of increasing development of accelerated or otherwise novel construction techniques. Analyzing the behavior of a structure at different stages of construction may also help later define some of the abnormal responses during the lifespan of a bridge. This paper overviews the SHM system of the Ironton-Russell Bridge, Ohio at the construction stage of its substructure. The stages involved in monitoring such as instrumentation of sensors, acquiring data from the sensors, data processing that includes a warning system, static analysis of the data collected and website are detailed in this paper. In addition to this, the effect of construction events as observed by the sensor data for the substructure is analyzed in detail thus validating the capability of the monitoring system.

  2. The extended stellar substructures of four metal-poor globular clusters in the galactic bulge

    NASA Astrophysics Data System (ADS)

    Chun, Sang-Hyun; Sohn, Young-Jong

    2015-08-01

    We investigated stellar spatial density distribution around four metal-poor globular clusters (NGC 6266, NGC 6626, NGC 6642 and NGC 6723) in order to find extended stellar substructures. Wide-field deep J, H, and K imaging data were taken using the WFCAM near-infrared array on United Kingdom Infrared Telescope (UKIRT). The contamination of field stars around clusters was minimised by applying a statistical weighted filtering algorithm for the stars on the color-magnitude diagram. In two-dimensional isodensity contour map, we find that all four of the globular clusters shows tidal stripping stellar features in the form of tidal tails (NGC 6266 and NGC 6723) or small density lobes/chunk (NGC 6642 and NGC 6723). The stellar substructures extend toward the Galactic centre or anticancer, and the proper motion direction of the clusters. The radial density profiles of the clusters also depart from theoretical King and Wilson models and show overdensity feature with a break in a slope of profile at the outer region of clusters. The observed results indicate that four globular clusters in the Galactic bulge have experienced strong tidal force or bulge/disk shock effect of the Galaxy. These observational results provide us further constraints to understand the evolution of clusters in the Galactic bulge region as well as the formation of the Galaxy.

  3. A Synoptic Map of Halo Substructures from the Pan-STARRS1 3π Survey

    NASA Astrophysics Data System (ADS)

    Bernard, Edouard J.; Ferguson, Annette M. N.; Schlafly, Edward F.; Martin, Nicolas F.; Rix, Hans-Walter; Bell, Eric F.; Finkbeiner, Douglas P.; Goldman, Bertrand; Martínez-Delgado, David; Sesar, Branimir; Wyse, Rosemary F. G.; Burgett, William S.; Chambers, Kenneth C.; Draper, Peter W.; Hodapp, Klaus W.; Kaiser, Nicholas; Kudritzki, Rolf-Peter; Magnier, Eugene A.; Metcalfe, Nigel; Wainscoat, Richard J.; Waters, Christopher

    2016-08-01

    We present a panoramic map of the entire Milky Way halo north of δ ˜ -30° (˜ 30,000 deg2), constructed by applying the matched-filter technique to the Pan-STARRS1 3π Survey dataset. Using single-epoch photometry reaching to g ˜22, we are sensitive to stellar substructures with heliocentric distances between 3.5 and ˜35 kpc. We recover almost all previously-reported streams in this volume and demonstrate that several of these are significantly more extended than earlier datasets have indicated. In addition, we also report five new candidate stellar streams. One of these features appears significantly broader and more luminous than the others and is likely the remnant of a dwarf galaxy. The other four streams are consistent with a globular cluster origin, and three of these are rather short in projection (≲ 10°), suggesting that streams like Ophiuchus may not be that rare. Finally, a significant number of more marginal substructures are also revealed by our analysis; many of these features can also be discerned in matched-filter maps produced by other authors from SDSS data, and hence they are very likely to be genuine. However, the extant 3π data is currently too shallow to determine their properties or produce convincing CMDs. The global view of the Milky Way provided by Pan-STARRS1 provides further evidence for the important role of both globular cluster disruption and dwarf galaxy accretion in building the Milky Way's stellar halo.

  4. Detailed Analysis of Japanese Population Substructure with a Focus on the Southwest Islands of Japan

    PubMed Central

    Nishiyama, Takeshi; Kishino, Hirohisa; Suzuki, Sadao; Ando, Ryosuke; Niimura, Hideshi; Uemura, Hirokazu; Horita, Mikako; Ohnaka, Keizo; Kuriyama, Nagato; Mikami, Haruo; Takashima, Naoyuki; Mastuo, Keitaro; Guang, Yin; Wakai, Kenji; Hamajima, Nobuyuki; Tanaka, Hideo

    2012-01-01

    Uncovering population structure is important for properly conducting association studies and for examining the demographic history of a population. Here, we examined the Japanese population substructure using data from the Japan Multi-Institutional Collaborative Cohort (J-MICC), which covers all but the northern region of Japan. Using 222 autosomal loci from 4502 subjects, we investigated population substructure by estimating FST among populations, testing population differentiation, and performing principal component analysis (PCA) and correspondence analysis (CA). All analyses revealed a low but significant differentiation between the Amami Islanders and the mainland Japanese population. Furthermore, we examined the genetic differentiation between the mainland population, Amami Islanders and Okinawa Islanders using six loci included in both the Pan-Asian SNP (PASNP) consortium data and the J-MICC data. This analysis revealed that the Amami and Okinawa Islanders were differentiated from the mainland population. In conclusion, we revealed a low but significant level of genetic differentiation between the mainland population and populations in or to the south of the Amami Islands, although genetic variation between both populations might be clinal. Therefore, the possibility of population stratification must be considered when enrolling the islander population of this area, such as in the J-MICC study. PMID:22509376

  5. Afro-derived Amazonian populations: inferring continental ancestry and population substructure.

    PubMed

    Lopes Maciel, Luana Gomes; Ribeiro Rodrigues, Elzemar Martins; Carneiro Dos Santos, Ney Pereira; Ribeiro Dos Santos, Ândrea; Guerreiro, João Farias; Santos, Sidney

    2011-10-01

    A panel of Ancestry Informative Markers (AIMs) was used to identify population substructure and estimate individual and overall interethnic admixture in 294 individuals from seven African-derived communities of the Brazilian Amazon. A panel of 48 biallelic markers, representing the insertion (IN) or the deletion (DEL) of small DNA fragments, was employed for this purpose. Overall interethnic admixture estimates showed high miscegenation with other ethnic groups in all populations (between 46% and 64%). The proportion of ancestral genes varied significantly among individuals of the sample: the contribution of African genes varied between 12% and 75%; of European genes between 10% and 73%; and of Amerindians genes between 8% and 66%. The obtained data reveal a high contribution of Amerindian genes in these communities, unlike in other African-derived communities of the Northeast and the South of Brazil. In addition, the majority of the Amerindian contribution may result from the preferential inclusion of indigenous women in the African descent groups. High heterogeneity of the proportion of interethnic admixture among analyzed individuals was found when the proportion of ancestral genes of each individual of the sample was estimated. This heterogeneity is reflected in the fact that four populations can be considered as substructured and that the global African descent sample is possibly formed by two subpopulations. PMID:22146065

  6. EBSD and TEM investigation of the hot deformation substructure characteristics of a type 316L austenitic stainless steel.

    PubMed

    Cizek, P; Whiteman, J A; Rainforth, W M; Beynon, J H

    2004-03-01

    The evolution of crystallographic texture and deformation substructure was studied in a type 316L austenitic stainless steel, deformed in rolling at 900 degrees C to true strain levels of about 0.3 and 0.7. Electron backscatter diffraction (EBSD) and transmission electron microscopy (TEM) were used in the investigation and a comparison of the substructural characteristics obtained by these techniques was made. At the lower strain level, the deformation substructure observed by EBSD appeared to be rather poorly developed. There was considerable evidence of a rotation of the pre-existing twin boundaries from their original orientation relationship, as well as the formation of highly distorted grain boundary regions. In TEM, at this strain level, the substructure was more clearly revealed, although it appeared rather inhomogeneously developed from grain to grain. The subgrains were frequently elongated and their boundaries often approximated to traces of [111] slip planes. The corresponding misorientations were small and largely displayed a non-cumulative character. At the larger strain, the substructure within most grains became well developed and the corresponding misorientations increased. This resulted in better detection of sub-boundaries by EBSD, although the percentage of indexing slightly decreased. TEM revealed splitting of some sub-boundaries to form fine microbands, as well as the localized formation of microshear bands. The substructural characteristics observed by EBSD, in particular at the larger strain, generally appeared to compare well with those obtained using TEM. With increased strain level, the mean subgrain size became finer, the corresponding mean misorientation angle increased and both these characteristics became less dependent on a particular grain orientation. The statistically representative data obtained will assist in the development of physically based models of microstructural evolution during thermomechanical processing of austenitic

  7. Developing soil gas and 222Rn entry potentials for substructure surfaces and assessing 222Rn control diagnostic techniques.

    PubMed

    Turk, B H; Harrison, J; Prill, R J; Sextro, R G

    1990-10-01

    Research-based procedures for characterizing the causes of elevated indoor 222Rn levels and guiding the selection of an appropriate control technique were evaluated at seven New Jersey houses. Procedures such as thorough visual inspections, blower door air leakage tests, pressure field mapping, subsurface vacuum extension tests, sampling of 222Rn concentrations throughout the substructure, and measurements of the additional depressurization caused by various appliances all were found to furnish important information to the mitigation contractor or researcher. An analysis of data from these and other diagnostic techniques performed at the seven houses also indicated: (1) regions of very high permeability existed directly adjacent to the exterior of substructure walls and floors; (2) the additional substructure depressurization caused by operation of forced-air furnaces and attic exhaust fans could exceed 1 Pascal; (3) 222Rn concentrations below basement slabs and slabs-on-grade adjoining below grade basement walls were approximately seven times higher than those within block wall cavities; and (4) air leakage areas of crawlspace and basement ceilings were quite large, ranging up to 0.15 m2. The pressure field mapping tests identified the areas surrounding the substructure that were well coupled to the indoors. Using flow, pressure difference, and 222Rn concentration data, indices of soil gas entry potential and 222Rn entry potential were developed to indicate the areas of the substructure that may have high entry rates of soil gas and 222Rn, respectively. These indices could be helpful for quantifying the relative resistance to soil gas movement of substructure surfaces and surrounding soils and for determining the placement of 222Rn control systems. PMID:2398009

  8. Inference of the cold dark matter substructure mass function at z = 0.2 using strong gravitational lenses

    NASA Astrophysics Data System (ADS)

    Vegetti, S.; Koopmans, L. V. E.; Auger, M. W.; Treu, T.; Bolton, A. S.

    2014-08-01

    We present the results of a search for galaxy substructures in a sample of 11 gravitational lens galaxies from the Sloan Lens ACS Survey by Bolton et al. We find no significant detection of mass clumps, except for a luminous satellite in the system SDSS J0956+5110. We use these non-detections, in combination with a previous detection in the system SDSS J0946+1006, to derive constraints on the substructure mass function in massive early-type host galaxies with an average redshift ˜ 0.2 and an average velocity dispersion <σeff> ˜ 270 km s-1. We perform a Bayesian inference on the substructure mass function, within a median region of about 32 kpc2 around the Einstein radius ( ˜ 4.2 kpc). We infer a mean projected substructure mass fraction f = 0.0076_{-0.0052}^{+0.0208} at the 68 per cent confidence level and a substructure mass function slope α < 2.93 at the 95 per cent confidence level for a uniform prior probability density on α. For a Gaussian prior based on cold dark matter (CDM) simulations, we infer f = 0.0064^{+0.0080}_{-0.0042} and a slope of α = 1.90^{+0.098}_{-0.098} at the 68 per cent confidence level. Since only one substructure was detected in the full sample, we have little information on the mass function slope, which is therefore poorly constrained (i.e. the Bayes factor shows no positive preference for any of the two models). The inferred fraction is consistent with the expectations from CDM simulations and with inference from flux ratio anomalies at the 68 per cent confidence level.

  9. Application of a water-soluble pyridyl disulfide amine linker for use in Cu-free click bioconjugation

    PubMed Central

    Thomas, Joshua D.; Burke, Terrence R.

    2011-01-01

    Described herein is the design and synthesis of a discrete heterobifunctional PEG-based pyridyl disulfide/amine-containing linker that can be used in the Cu-free click preparation of bioconjugates. The title PEG-based pyridyl disulfide amine linker is a potentially useful reagent for preparing water-soluble disulfide-linked cargos. It may be particularly valuable in expanding the field of Cu-free click-based bioconjugations to include reductively labile antibody, polymer, or nanoparticle-based drug conjugates. PMID:21826118

  10. Mixed-linker approach in designing porous zirconium-based metal-organic frameworks with high hydrogen storage capacity.

    PubMed

    Naeem, Ayesha; Ting, Valeska P; Hintermair, Ulrich; Tian, Mi; Telford, Richard; Halim, Saaiba; Nowell, Harriott; Hołyńska, Małgorzata; Teat, Simon J; Scowen, Ian J; Nayak, Sanjit

    2016-06-14

    Three highly porous Zr(iv)-based metal-organic frameworks, UBMOF-8, UBMOF-9, and UBMOF-31, were synthesized by using 2,2'-diamino-4,4'-stilbenedicarboxylic acid, 4,4'-stilbenedicarboxylic acid, and combination of both linkers, respectively. The mixed-linker UBMOF-31 showed excellent hydrogen uptake of 4.9 wt% and high selectivity for adsorption of CO2 over N2 with high thermal stability and moderate water stability with permanent porosity and surface area of 2552 m(2) g(-1). PMID:27242066

  11. Covalent attachment of Arc repressor subunits by a peptide linker enhances affinity for operator DNA.

    PubMed

    Robinson, C R; Sauer, R T

    1996-01-01

    By designing a recombinant gene containing tandem copies of the arc coding sequence with intervening DNA encoding the linker sequence GGGSGGGTGGGSGGG, the two subunits of the P22 Are repressor dimer have been covalently linked to form a single-chain protein called Arc-L1-Arc. The 15-residue linker joins the C-terminus of one monomer to the N-terminus of the second, a distance of approximately 45 A in the Arc-operator cocrystal structure. Arc-L1-Arc is expressed at high levels in Escherichia coli, with no evidence of degradation or proteolytic clipping of the linker, and is more active than wild-type Arc in repression assays. The purified Arc-L1-Arc protein has the molecular weight expected for the designed protein and unfolds cooperatively, reversibly, and with no concentration dependence in thermal-denaturation studies. Arc-L1-Arc protects operator DNA in a manner indistinguishable from that of wild-type Arc in DNase I and copper-phenanthroline footprinting studies, but the covalent attachment of the two monomers results in enhanced affinity for operator DNA. Arc-L1-Arc binds operator DNA half-maximally at a concentration of 1.7 pM, compared with the wild-type value of 185 pM, and also binds DNA fragments containing the left or right operator half-sites more tightly than wild type. Because wild-type Arc is monomeric at sub-nanomolar concentrations and must dimerize before binding to the operator, it was anticipated that Arc-L1-Arc would exhibit a lower half-maximal binding concentration. However, even when the change from a monomeric to a dimeric species is taken into account, the affinity of Arc-L1-Arc for operator and half-operator DNA is greater than the wild-type affinity. This tighter binding appears to result from slower dissociation, as Arc-L1-Arc DNA complexes with full or half-site operators dissociate at rates 5-10 times slower than the corresponding Arc--DNA complexes. Hence, the activity of the designed Arc-L1-Arc protein is substantially increased

  12. Developing an Acidic Residue Reactive and Sulfoxide-Containing MS-Cleavable Homobifunctional Cross-Linker for Probing Protein-Protein Interactions.

    PubMed

    Gutierrez, Craig B; Yu, Clinton; Novitsky, Eric J; Huszagh, Alexander S; Rychnovsky, Scott D; Huang, Lan

    2016-08-16

    Cross-linking mass spectrometry (XL-MS) has become a powerful strategy for defining protein-protein interactions and elucidating architectures of large protein complexes. However, one of the inherent challenges in MS analysis of cross-linked peptides is their unambiguous identification. To facilitate this process, we have previously developed a series of amine-reactive sulfoxide-containing MS-cleavable cross-linkers. These MS-cleavable reagents have allowed us to establish a common robust XL-MS workflow that enables fast and accurate identification of cross-linked peptides using multistage tandem mass spectrometry (MS(n)). Although amine-reactive reagents targeting lysine residues have been successful, it remains difficult to characterize protein interaction interfaces with little or no lysine residues. To expand the coverage of protein interaction regions, we present here the development of a new acidic residue-targeting sulfoxide-containing MS-cleavable homobifunctional cross-linker, dihydrazide sulfoxide (DHSO). We demonstrate that DHSO cross-linked peptides display the same predictable and characteristic fragmentation pattern during collision induced dissociation as amine-reactive sulfoxide-containing MS-cleavable cross-linked peptides, thus permitting their simplified analysis and unambiguous identification by MS(n). Additionally, we show that DHSO can provide complementary data to amine-reactive reagents. Collectively, this work not only enlarges the range of the application of XL-MS approaches but also further demonstrates the robustness and applicability of sulfoxide-based MS-cleavability in conjunction with various cross-linking chemistries. PMID:27417384

  13. Developing an Acidic Residue Reactive and Sulfoxide-Containing MS-Cleavable Homobifunctional Cross-Linker for Probing Protein–Protein Interactions

    PubMed Central

    2016-01-01

    Cross-linking mass spectrometry (XL-MS) has become a powerful strategy for defining protein–protein interactions and elucidating architectures of large protein complexes. However, one of the inherent challenges in MS analysis of cross-linked peptides is their unambiguous identification. To facilitate this process, we have previously developed a series of amine-reactive sulfoxide-containing MS-cleavable cross-linkers. These MS-cleavable reagents have allowed us to establish a common robust XL-MS workflow that enables fast and accurate identification of cross-linked peptides using multistage tandem mass spectrometry (MSn). Although amine-reactive reagents targeting lysine residues have been successful, it remains difficult to characterize protein interaction interfaces with little or no lysine residues. To expand the coverage of protein interaction regions, we present here the development of a new acidic residue-targeting sulfoxide-containing MS-cleavable homobifunctional cross-linker, dihydrazide sulfoxide (DHSO). We demonstrate that DHSO cross-linked peptides display the same predictable and characteristic fragmentation pattern during collision induced dissociation as amine-reactive sulfoxide-containing MS-cleavable cross-linked peptides, thus permitting their simplified analysis and unambiguous identification by MSn. Additionally, we show that DHSO can provide complementary data to amine-reactive reagents. Collectively, this work not only enlarges the range of the application of XL-MS approaches but also further demonstrates the robustness and applicability of sulfoxide-based MS-cleavability in conjunction with various cross-linking chemistries. PMID:27417384

  14. Revealing substructures of H4 and H5 hole traps in p-type InP using Laplace deep-level transient spectroscopy

    NASA Astrophysics Data System (ADS)

    Darwich, R.; Mani, A. A.

    2010-08-01

    New substructures of H4 and H5 hole traps have been revealed using Laplace deep-level transient spectroscopy. Our measurements show that the hole traps H4 and H5 can have at least three components for each. Moreover, the activation energies are deduced and the microscopic nature of these substructures is discussed.

  15. Revealing substructures of H4 and H5 hole traps in p-type InP using Laplace deep-level transient spectroscopy

    SciTech Connect

    Darwich, R.; Mani, A. A.

    2010-08-15

    New substructures of H4 and H5 hole traps have been revealed using Laplace deep-level transient spectroscopy. Our measurements show that the hole traps H4 and H5 can have at least three components for each. Moreover, the activation energies are deduced and the microscopic nature of these substructures is discussed.

  16. Boosted objects and jet substructure at the LHC: Report of BOOST2012, held at IFIC Valencia, 23rd-27th of July 2012

    DOE PAGESBeta

    Altheimer, A.

    2014-03-21

    This report of the BOOST2012 workshop presents the results of four working groups that studied key aspects of jet substructure. We discuss the potential of first-principle QCD calculations to yield a precise description of the substructure of jets and study the accuracy of state-of-the-art Monte Carlo tools. Limitations of the experiments’ ability to resolve substructure are evaluated, with a focus on the impact of additional (pile-up) proton proton collisions on jet substructure performance in future LHC operating scenarios. The final section summarizes the lessons learnt from jet substructure analyses in searches for new physics in the production of boosted topmore » quarks.« less

  17. A self-reporting tetrazole-based linker for the biofunctionalization of gold nanorods.

    PubMed

    Stolzer, Lukas; Vigovskaya, Antonina; Barner-Kowollik, Christopher; Fruk, Ljiljana

    2015-10-01

    A photochemical approach based on nitrile imine-mediated tetrazole-ene cycloaddition is introduced to functionalize gold nanorods with biomolecules. For this purpose, a bifunctional, photoreactive linker containing thioctic acid as the Au anchoring group and a tetrazole moiety for the light-induced reaction with maleimide-capped DNA was prepared. The tetrazole-based reaction on the nanoparticles' surface results in a fluorescent pyrazoline product allowing for the spectroscopic monitoring of the reaction. This first example of nitrile imine-mediated tetrazole-ene cycloaddition (NITEC)-mediated biofunctionalization of Au nanorods paves the way for the attachment of sensitive biomolecules, such as antibodies and other proteins, under mild conditions and expands the toolbox for the tailoring of nanomaterials. PMID:26303592

  18. Linker phosphoramidite reagents for the attachment of the first nucleoside to underivatized solid-phase supports

    PubMed Central

    Pon, Richard T.; Yu, Shuyuan

    2004-01-01

    New linker phosphoramidite reagents containing a cleavable 3′-ester linkage are used for attaching the first nucleoside to the surface of a solid- phase support. Inexpensive, underivatized amino supports, such as long chain alkylamine controlled-pore glass, can serve as universal supports. No modifications to phosphoramidite coupling conditions are required and, after synthesis, treatment with NH4OH releases the products with 3′-OH ends. No 3′-dephosphorylation is required. Phosphoramidite reagents containing a succinate and sulfonyl diethanol linkage between the nucleoside and phosphoramidite group are particularly advantageous and can be used to create both 3′-OH and 5′-phosphate ends on oligonucleotides. Reproducibility and quality of oligonucleotide synthesis is demonstrated for either column and 96-well plate formats on low-, medium- or high-loading CPG supports. PMID:14752050

  19. Maleimide-grafted cellulose nanocrystals as cross-linkers for bionanocomposite hydrogels.

    PubMed

    García-Astrain, C; González, K; Gurrea, T; Guaresti, O; Algar, I; Eceiza, A; Gabilondo, N

    2016-09-20

    This article deals with the preparation of bionanocomposite hydrogels from natural polymers and nanoentities, an emerging class of materials for biotechnological and biomedical applications. Herein, the applicability of the Diels-Alder "click" reaction to the design of bionanocomposite hydrogels from furan modified gelatin using maleimide-functionalized cellulose nanocrystals as multifunctional cocross-linkers is demonstrated. The functionalization of cellulose nanocrystals with maleimide moieties was confirmed by XPS. The swelling and rheological properties of the resulting bionanocomposite confirmed the formation of hydrogel networks with covalently embedded nanoentities. The Diels-Alder reaction resulted in the formation of stiffer networks with lower swelling ratios due to the formation of additional cross-linking points. The designed "click" strategy proved to be a promising candidate for the formation of fully renewable bionanocomposite hydrogels. PMID:27261734

  20. Kinesin’s Front Head is Gated by the Backward Orientation of its Neck Linker

    PubMed Central

    Dogan, Merve Yusra; Can, Sinan; Cleary, Frank B.; Purde, Vedud; Yildiz, Ahmet

    2015-01-01

    SUMMARY Kinesin-1 is a two-headed motor that takes processive 8-nm hand-over-hand steps and transports intracellular cargos towards the plus end of microtubules. Processive motility requires a gating mechanism to coordinate the mechanochemical cycles of the two heads. Kinesin gating involves the neck linker (NL), a short peptide that interconnects the heads, but it remains unclear whether gating is facilitated by the NL orientation or tension. Using optical trapping, we measured the force-dependent microtubule release rate of kinesin monomers under different nucleotide conditions and pulling geometries. We find that pulling NL in the backward direction inhibits nucleotide binding and subsequent release from the microtubule. This inhibition is independent from the magnitude of tension (2–8 pN) exerted on NL. Our results provide evidence that the front head of a kinesin dimer is gated by the backward orientation of its NL until the rear head releases from the microtubule. PMID:25818289