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Sample records for scanning reveals ligand

  1. Heterobifunctional crosslinkers for tethering single ligand molecules to scanning probes

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    Riener, Christian K.; Kienberger, Ferry; Hahn, Christoph D.; Buchinger, Gerhard M.; Egwim, Innocent O.C.; Haselgruebler, Thomas; Ebner, Andreas; Romanin, Christoph; Klampfl, Christian; Lackner, Bernd; Prinz, Heino; Blaas, Dieter; Hinterdorfer, Peter; Gruber, Hermann J

    2003-11-14

    Single molecule recognition force microscopy (SMRFM) is a versatile atomic force microscopy (AFM) method to probe specific interactions of cognitive molecules on the single molecule level. It allows insights to be gained into interaction potentials and kinetic barriers and is capable of mapping interaction sites with nm positional accuracy. These applications require a ligand to be attached to the AFM tip, preferably by a distensible poly(ethylene glycol) (PEG) chain between the measuring tip and the ligand molecule. The PEG chain greatly facilitates specific binding of the ligand to immobile receptor sites on the sample surface. The present study contributes to tip-PEG-ligand tethering in three ways: (i) a convenient synthetic route was found to prepare NH{sub 2}-PEG-COOH which is the key intermediate for long heterobifunctional crosslinkers; (ii) a variety of heterobifunctional PEG derivatives for tip-PEG-ligand linking were prepared from NH{sub 2}-PEG-COOH; (iii) in particular, a new PEG crosslinker with one thiol-reactive end and one terminal nitrilotriacetic acid (NTA) group was synthesized and successfully used to tether His{sub 6}-tagged protein molecules to AFM tips via noncovalent NTA-Ni{sup 2+}-His{sub 6} bridges. The new crosslinker was applied to link a recombinant His{sub 6}-tagged fragment of the very-low density lipoprotein receptor to the AFM tip whereupon specific docking to the capsid of human rhinovirus particles was observed by force microscopy. In a parallel study, the specific interaction of the small GTPase Ran with the nuclear import receptor importin {beta}1 was studied in detail by SMRFM, using the new crosslinker to link His{sub 6}-tagged Ran to the measuring tip [Nat. Struct. Biol. (2003), 10, 553-557].

  2. HDX reveals unique fragment ligands for the vitamin D receptor.

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    Carson, Matthew W; Zhang, Jun; Chalmers, Michael J; Bocchinfuso, Wayne P; Holifield, Karol D; Masquelin, Thierry; Stites, Ryan E; Stayrook, Keith R; Griffin, Patrick R; Dodge, Jeffery A

    2014-08-01

    Modulation of the vitamin D receptor (VDR) with a ligand has the potential to be useful for the oral treatment of osteoporosis. One component of our lead generation strategy to identify synthetic ligands for VDR included a fragment based drug design approach. Screening of ligands in a VDR fluorescence polarization assay and a RXR/VDR conformation sensing assay resulted in the identification of multiple fragment hits (lean >0.30). These fragment scaffolds were subsequently evaluated for interaction with the VDR ligand binding domain using hydrogen-deuterium exchange (HDX) mass spectrometry. Significant protection of H/D exchange was observed for some fragments in helixes 3, 7, and 8 of the ligand binding domain, regions which are similar to those seen for the natural hormone VD3. The fragments appear to mimic the A-ring of VD3 thereby providing viable starting points for synthetic expansion. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Revealing sources and chemical identity of iron ligands across the California Current System

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    Boiteau, R.; Repeta, D.; Fitzsimmons, J. N.; Parker, C.; Twining, B. S.; Baines, S.

    2016-02-01

    The California Current System is one of the most productive regions of the ocean, fueled by the upwelling of nutrient rich water. Differences in the supply of micronutrient iron to surface waters along the coast lead to a mosaic of iron-replete and iron-limited conditions across the region, affecting primary production and community composition. Most of the iron in this region is supplied by upwelling of iron from the benthic boundary layer that is complexed by strong organic ligands. However, the source, identity, and bioavailability of these ligands are unknown. Here, we used novel hyphenated chromatography mass spectrometry approaches to structurally characterize organic ligands across the region. With these methods, iron ligands are detected with liquid chromatography coupled to inductively coupled plasma mass spectrometry (LC-ICPMS), and then their mass and fragmentation spectra are determined by high resolution electrospray ionization mass spectrometry (LC-ESIMS). Iron isotopic exchange was used to compare the relative binding strengths of different ligands. Our survey revealed a broad range of ligands from multiple sources. Benthic boundary layers and anoxic sediments were sources of structurally amorphous weak ligands, likely organic degradation products, as well as siderophores, strong iron binding molecules that facilitate iron acquisition. In the euphotic zone, marine microbes and zooplankton grazing produced a wide distribution of other compounds that included known and novel siderophores. This work demonstrates that the chemical nature of ligands from different sources varies substantially and has important implications for iron biogeochemical cycling and availability to members of the microbial community.

  4. Revealing a steroid receptor ligand as a unique PPAR[gamma] agonist

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    Lin, Shengchen; Han, Ying; Shi, Yuzhe; Rong, Hui; Zheng, Songyang; Jin, Shikan; Lin, Shu-Yong; Lin, Sheng-Cai; Li, Yong (Pitt); (Xiamen)

    2012-06-28

    Peroxisome proliferator-activated receptor gamma (PPAR{gamma}) regulates metabolic homeostasis and is a molecular target for anti-diabetic drugs. We report here the identification of a steroid receptor ligand, RU-486, as an unexpected PPAR{gamma} agonist, thereby uncovering a novel signaling route for this steroid drug. Similar to rosiglitazone, RU-486 modulates the expression of key PPAR{gamma} target genes and promotes adipocyte differentiation, but with a lower adipogenic activity. Structural and functional studies of receptor-ligand interactions reveal the molecular basis for a unique binding mode for RU-486 in the PPAR{gamma} ligand-binding pocket with distinctive properties and epitopes, providing the molecular mechanisms for the discrimination of RU-486 from thiazolidinediones (TZDs) drugs. Our findings together indicate that steroid compounds may represent an alternative approach for designing non-TZD PPAR{gamma} ligands in the treatment of insulin resistance.

  5. Scanning electron microscopy of Dermatobia hominis reveals cutaneous anchoring features.

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    Möhrenschlager, Matthias; Mempel, Martin; Weichenmeier, Ingrid; Engst, Reinhard; Ring, Johannnes; Behrendt, Heidrun

    2007-10-01

    We report the case of a 45-year-old Caucasian woman suffering from cutaneous myiasis. With the use of scanning electron microscopy, we placed special focus on the mechanisms by which Dermatobia hominis can fasten securely within the human skin.

  6. Ligand induced conformational changes of the human serotonin transporter revealed by molecular dynamics simulations.

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    Heidi Koldsø

    Full Text Available The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design.

  7. Ligand induced structural isomerism in phosphine coordinated gold clusters revealed by ion mobility mass spectrometry

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    Ligare, Marshall R.; Baker, Erin S.; Laskin, Julia; Johnson, Grant E.

    2017-01-01

    Structural isomerism in ligated gold clusters is revealed using electrospray ionization ion mobility spectrometry mass spectrometry. Phosphine ligated Au8 clusters are shown to adopt more “extended” type structures with increasing exchange of methyldiphenylphosphine (MePPh2) for triphenylphosphine (PPh3). These ligand-dependant structure-property relationships are critical to applications of clusters in catalysis.

  8. Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery.

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    Robert Kalescky

    2016-04-01

    Full Text Available Intra-protein information is transmitted over distances via allosteric processes. This ubiquitous protein process allows for protein function changes due to ligand binding events. Understanding protein allostery is essential to understanding protein functions. In this study, allostery in the second PDZ domain (PDZ2 in the human PTP1E protein is examined as model system to advance a recently developed rigid residue scan method combining with configurational entropy calculation and principal component analysis. The contributions from individual residues to whole-protein dynamics and allostery were systematically assessed via rigid body simulations of both unbound and ligand-bound states of the protein. The entropic contributions of individual residues to whole-protein dynamics were evaluated based on covariance-based correlation analysis of all simulations. The changes of overall protein entropy when individual residues being held rigid support that the rigidity/flexibility equilibrium in protein structure is governed by the La Châtelier's principle of chemical equilibrium. Key residues of PDZ2 allostery were identified with good agreement with NMR studies of the same protein bound to the same peptide. On the other hand, the change of entropic contribution from each residue upon perturbation revealed intrinsic differences among all the residues. The quasi-harmonic and principal component analyses of simulations without rigid residue perturbation showed a coherent allosteric mode from unbound and bound states, respectively. The projection of simulations with rigid residue perturbation onto coherent allosteric modes demonstrated the intrinsic shifting of ensemble distributions supporting the population-shift theory of protein allostery. Overall, the study presented here provides a robust and systematic approach to estimate the contribution of individual residue internal motion to overall protein dynamics and allostery.

  9. Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome

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    Yang, Xiaojing; Ren, Zhong; Kuk, Jane; Moffat, Keith (UC)

    2012-03-27

    Light is a fundamental signal that regulates important physiological processes such as development and circadian rhythm in living organisms. Phytochromes form a major family of photoreceptors responsible for red light perception in plants, fungi and bacteria. They undergo reversible photoconversion between red-absorbing (Pr) and far-red-absorbing (Pfr) states, thereby ultimately converting a light signal into a distinct biological signal that mediates subsequent cellular responses. Several structures of microbial phytochromes have been determined in their dark-adapted Pr or Pfr states. However, the structural nature of initial photochemical events has not been characterized by crystallography. Here we report the crystal structures of three intermediates in the photoreaction of Pseudomonas aeruginosa bacteriophytochrome (PaBphP). We used cryotrapping crystallography to capture intermediates, and followed structural changes by scanning the temperature at which the photoreaction proceeded. Light-induced conformational changes in PaBphP originate in ring D of the biliverdin (BV) chromophore, and E-to-Z isomerization about the C{sub 15} = C{sub 16} double bond between rings C and D is the initial photochemical event. As the chromophore relaxes, the twist of the C{sub 15} methine bridge about its two dihedral angles is reversed. Structural changes extend further to rings B and A, and to the surrounding protein regions. These data indicate that absorption of a photon by the Pfr state of PaBphP converts a light signal into a structural signal via twisting and untwisting of the methine bridges in the linear tetrapyrrole within the confined protein cavity.

  10. Candida albicans morphologies revealed by scanning electron microscopy analysis

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    M. Staniszewska

    2013-09-01

    Full Text Available Scanning electron microscope (SEM observations were used to analyze particular morphologies of Candida albicans clinical isolate (strain 82 and mutants defective in hyphae-promoting genes EFG1 (strain HLC52 and/ or CPH1 (strains HLC54 and Can16. Transcription factors Efg1 and Cph1 play role in regulating filamentation and adhesion of C. albicans' morphologies. Comparative analysis of such mutants and clinical isolate showed that Efg1 is required for human serum-induced cell growth and morphological switching. In the study, distinct differences between ultrastructural patterns of clinical strain's and null mutants' morphologies were observed (spherical vs tube-like blastoconidia, or solid and fragile constricted septa vs only the latter observed in strains with EFG1 deleted. In addition, wild type strain displayed smooth colonies of cells in comparison to mutants which exhibited wrinkled phenotype. It was observed that blastoconidia of clinical strain exhibited either polarly or randomly located budding. Contrariwise, morphotypes of mutants showed either multiple polar budding or a centrally located single bud scar (mother-daughter cell junction distinguishing tube-like yeast/ pseudohyphal growth (the length-to-width ratios larger than 1.5. In their planktonic form of growth, blastoconidia of clinical bloodstream isolate formed constitutively true hyphae under undiluted human serum inducing conditions. It was found that true hyphae are essential elements for developing structural integrity of conglomerate, as mutants displaying defects in their flocculation and conglomerate-forming abilities in serum. While filamentation is an important virulence trait in C. albicans the true hyphae are the morphologies which may be expected to play a role in bloodstream infections.

  11. Observed bromodomain flexibility reveals histone peptide- and small molecule ligand-compatible forms of ATAD2.

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    Poncet-Montange, Guillaume; Zhan, Yanai; Bardenhagen, Jennifer P; Petrocchi, Alessia; Leo, Elisabetta; Shi, Xi; Lee, Gilbert R; Leonard, Paul G; Geck Do, Mary K; Cardozo, Mario G; Andersen, Jannik N; Palmer, Wylie S; Jones, Philip; Ladbury, John E

    2015-03-01

    Preventing histone recognition by bromodomains emerges as an attractive therapeutic approach in cancer. Overexpression of ATAD2 (ATPase family AAA domain-containing 2 isoform A) in cancer cells is associated with poor prognosis making the bromodomain of ATAD2 a promising epigenetic therapeutic target. In the development of an in vitro assay and identification of small molecule ligands, we conducted structure-guided studies which revealed a conformationally flexible ATAD2 bromodomain. Structural studies on apo-, peptide-and small molecule-ATAD2 complexes (by co-crystallization) revealed that the bromodomain adopts a 'closed', histone-compatible conformation and a more 'open' ligand-compatible conformation of the binding site respectively. An unexpected conformational change of the conserved asparagine residue plays an important role in driving the peptide-binding conformation remodelling. We also identified dimethylisoxazole-containing ligands as ATAD2 binders which aided in the validation of the in vitro screen and in the analysis of these conformational studies.

  12. Crystal structures reveal the multi-ligand binding mechanism of Staphylococcus aureus ClfB.

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    Hua Xiang

    Full Text Available Staphylococcus aureus (S. aureus pathogenesis is a complex process involving a diverse array of extracellular and cell wall components. ClfB, an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules family surface protein, described as a fibrinogen-binding clumping factor, is a key determinant of S. aureus nasal colonization, but the molecular basis for ClfB-ligand recognition remains unknown. In this study, we solved the crystal structures of apo-ClfB and its complexes with fibrinogen α (Fg α and cytokeratin 10 (CK10 peptides. Structural comparison revealed a conserved glycine-serine-rich (GSR ClfB binding motif (GSSGXGXXG within the ligands, which was also found in other human proteins such as Engrailed protein, TCF20 and Dermokine proteins. Interaction between Dermokine and ClfB was confirmed by subsequent binding assays. The crystal structure of ClfB complexed with a 15-residue peptide derived from Dermokine revealed the same peptide binding mode of ClfB as identified in the crystal structures of ClfB-Fg α and ClfB-CK10. The results presented here highlight the multi-ligand binding property of ClfB, which is very distinct from other characterized MSCRAMMs to-date. The adherence of multiple peptides carrying the GSR motif into the same pocket in ClfB is reminiscent of MHC molecules. Our results provide a template for the identification of other molecules targeted by S. aureus during its colonization and infection. We propose that other MSCRAMMs like ClfA and SdrG also possess multi-ligand binding properties.

  13. Ligand-induced dynamical change of G-protein-coupled receptor revealed by neutron scattering

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    Shrestha, Utsab R.; Bhowmik, Debsindhu; Mamontov, Eugene; Chu, Xiang-Qiang

    Light activation of the visual G-protein-coupled receptor rhodopsin leads to the significant change in protein conformation and structural fluctuations, which further activates the cognate G-protein (transducin) and initiates the biological signaling. In this work, we studied the rhodopsin activation dynamics using state-of-the-art neutron scattering technique. Our quasi-elastic neutron scattering (QENS) results revealed a broadly distributed relaxation rate of the hydrogen atom in rhodopsin on the picosecond to nanosecond timescale (beta-relaxation region), which is crucial for the protein function. Furthermore, the application of mode-coupling theory to the QENS analysis uncovers the subtle changes in rhodopsin dynamics due to the retinal cofactor. Comparing the dynamics of the ligand-free apoprotein, opsin versus the dark-state rhodopsin, removal of the retinal cofactor increases the relaxation time in the beta-relaxation region, which is due to the possible open conformation. Moreover, we utilized the concept of free-energy landscape to explain our results for the dark-state rhodopsin and opsin dynamics, which can be further applied to other GPCR systems to interpret various dynamic behaviors in ligand-bound and ligand-free protein.

  14. The Fragment Molecular Orbital Method Reveals New Insight into the Chemical Nature of GPCR-Ligand Interactions.

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    Heifetz, Alexander; Chudyk, Ewa I; Gleave, Laura; Aldeghi, Matteo; Cherezov, Vadim; Fedorov, Dmitri G; Biggin, Philip C; Bodkin, Mike J

    2016-01-25

    Our interpretation of ligand-protein interactions is often informed by high-resolution structures, which represent the cornerstone of structure-based drug design. However, visual inspection and molecular mechanics approaches cannot explain the full complexity of molecular interactions. Quantum Mechanics approaches are often too computationally expensive, but one method, Fragment Molecular Orbital (FMO), offers an excellent compromise and has the potential to reveal key interactions that would otherwise be hard to detect. To illustrate this, we have applied the FMO method to 18 Class A GPCR-ligand crystal structures, representing different branches of the GPCR genome. Our work reveals key interactions that are often omitted from structure-based descriptions, including hydrophobic interactions, nonclassical hydrogen bonds, and the involvement of backbone atoms. This approach provides a more comprehensive picture of receptor-ligand interactions than is currently used and should prove useful for evaluation of the chemical nature of ligand binding and to support structure-based drug design.

  15. Structure of the Membrane-tethering GRASP Domain Reveals a Unique PDZ Ligand Interaction That Mediates Golgi Biogenesis

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    Truschel, S.T.; Heroux, A.; Sengupta, D.; Foote, A.; Macbeth, M. R.; Linstedt, A. D.

    2011-06-10

    Biogenesis of the ribbon-like membrane network of the mammalian Golgi requires membrane tethering by the conserved GRASP domain in GRASP65 and GRASP55, yet the tethering mechanism is not fully understood. Here, we report the crystal structure of the GRASP55 GRASP domain, which revealed an unusual arrangement of two tandem PDZ folds that more closely resemble prokaryotic PDZ domains. Biochemical and functional data indicated that the interaction between the ligand-binding pocket of PDZ1 and an internal ligand on PDZ2 mediates the GRASP self-interaction, and structural analyses suggest that this occurs via a unique mode of internal PDZ ligand recognition. Our data uncover the structural basis for ligand specificity and provide insight into the mechanism of GRASP-dependent membrane tethering of analogous Golgi cisternae.

  16. Structure of the Membrane-tethering GRASP Domain Reveals a Unique PDZ Ligand Interaction That Mediates Golgi Biogenesis

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    S Truschel; D Sengupta; A Foote; A Heroux; M Macbeth; A Linstedt

    2011-12-31

    Biogenesis of the ribbon-like membrane network of the mammalian Golgi requires membrane tethering by the conserved GRASP domain in GRASP65 and GRASP55, yet the tethering mechanism is not fully understood. Here, we report the crystal structure of the GRASP55 GRASP domain, which revealed an unusual arrangement of two tandem PDZ folds that more closely resemble prokaryotic PDZ domains. Biochemical and functional data indicated that the interaction between the ligand-binding pocket of PDZ1 and an internal ligand on PDZ2 mediates the GRASP self-interaction, and structural analyses suggest that this occurs via a unique mode of internal PDZ ligand recognition. Our data uncover the structural basis for ligand specificity and provide insight into the mechanism of GRASP-dependent membrane tethering of analogous Golgi cisternae.

  17. REDOR NMR Reveals Multiple Conformers for a Protein Kinase C Ligand in a Membrane Environment

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    Hao Yang

    2018-01-01

    Full Text Available Bryostatin 1 (henceforth bryostatin is in clinical trials for the treatment of Alzheimer’s disease and for HIV/AIDS eradication. It is also a preclinical lead for cancer immunotherapy and other therapeutic indications. Yet nothing is known about the conformation of bryostatin bound to its protein kinase C (PKC target in a membrane microenvironment. As a result, efforts to design more efficacious, better tolerated, or more synthetically accessible ligands have been limited to structures that do not include PKC or membrane effects known to influence PKC–ligand binding. This problem extends more generally to many membrane-associated proteins in the human proteome. Here, we use rotational-echo double-resonance (REDOR solid-state NMR to determine the conformations of PKC modulators bound to the PKCδ-C1b domain in the presence of phospholipid vesicles. The conformationally limited PKC modulator phorbol diacetate (PDAc is used as an initial test substrate. While unanticipated partitioning of PDAc between an immobilized protein-bound state and a mobile state in the phospholipid assembly was observed, a single conformation in the bound state was identified. In striking contrast, a bryostatin analogue (bryolog was found to exist exclusively in a protein-bound state, but adopts a distribution of conformations as defined by three independent distance measurements. The detection of multiple PKCδ-C1b-bound bryolog conformers in a functionally relevant phospholipid complex reveals the inherent dynamic nature of cellular systems that is not captured with single-conformation static structures. These results indicate that binding, selectivity, and function of PKC modulators, as well as the design of new modulators, are best addressed using a dynamic multistate model, an analysis potentially applicable to other membrane-associated proteins.

  18. Cone and Rod Loss in Stargardt Disease Revealed by Adaptive Optics Scanning Light Ophthalmoscopy

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    Song, Hongxin; Rossi, Ethan A.; Latchney, Lisa; Bessette, Angela; Stone, Edwin; Hunter, Jennifer J.; Williams, David R.; Chung, Mina

    2015-01-01

    Importance Stargardt disease (STGD1) is characterized by macular atrophy and flecks in the retinal pigment epithelium. The causative ABCA4 gene encodes a protein localizing to photoreceptor outer segments. The pathologic steps by which ABCA4 mutations lead to clinically detectable retinal pigment epithelium changes remain unclear. We investigated early STGD1 using adaptive optics scanning light ophthalmoscopy. Observations Adaptive optics scanning light ophthalmoscopy imaging of 2 brothers with early STGD1 and their unaffected parents was compared with conventional imaging. Cone and rod spacing were increased in both patients (P optics scanning light ophthalmoscopy reveals increased cone and rod spacing in areas that appear normal in conventional images, suggesting that photoreceptor loss precedes clinically detectable retinal pigment epithelial disease in STGD1. PMID:26247787

  19. Dissociable Modulation of Overt Visual Attention in Valence and Arousal Revealed by Topology of Scan Path

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    Ni, Jianguang; Jiang, Huihui; Jin, Yixiang; Chen, Nanhui; Wang, Jianhong; Wang, Zhengbo; Luo, Yuejia; Ma, Yuanye; Hu, Xintian

    2011-01-01

    Emotional stimuli have evolutionary significance for the survival of organisms; therefore, they are attention-grabbing and are processed preferentially. The neural underpinnings of two principle emotional dimensions in affective space, valence (degree of pleasantness) and arousal (intensity of evoked emotion), have been shown to be dissociable in the olfactory, gustatory and memory systems. However, the separable roles of valence and arousal in scene perception are poorly understood. In this study, we asked how these two emotional dimensions modulate overt visual attention. Twenty-two healthy volunteers freely viewed images from the International Affective Picture System (IAPS) that were graded for affective levels of valence and arousal (high, medium, and low). Subjects' heads were immobilized and eye movements were recorded by camera to track overt shifts of visual attention. Algebraic graph-based approaches were introduced to model scan paths as weighted undirected path graphs, generating global topology metrics that characterize the algebraic connectivity of scan paths. Our data suggest that human subjects show different scanning patterns to stimuli with different affective ratings. Valence salient stimuli (with neutral arousal) elicited faster and larger shifts of attention, while arousal salient stimuli (with neutral valence) elicited local scanning, dense attention allocation and deep processing. Furthermore, our model revealed that the modulatory effect of valence was linearly related to the valence level, whereas the relation between the modulatory effect and the level of arousal was nonlinear. Hence, visual attention seems to be modulated by mechanisms that are separate for valence and arousal. PMID:21494331

  20. Dissociable modulation of overt visual attention in valence and arousal revealed by topology of scan path.

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    Jianguang Ni

    Full Text Available Emotional stimuli have evolutionary significance for the survival of organisms; therefore, they are attention-grabbing and are processed preferentially. The neural underpinnings of two principle emotional dimensions in affective space, valence (degree of pleasantness and arousal (intensity of evoked emotion, have been shown to be dissociable in the olfactory, gustatory and memory systems. However, the separable roles of valence and arousal in scene perception are poorly understood. In this study, we asked how these two emotional dimensions modulate overt visual attention. Twenty-two healthy volunteers freely viewed images from the International Affective Picture System (IAPS that were graded for affective levels of valence and arousal (high, medium, and low. Subjects' heads were immobilized and eye movements were recorded by camera to track overt shifts of visual attention. Algebraic graph-based approaches were introduced to model scan paths as weighted undirected path graphs, generating global topology metrics that characterize the algebraic connectivity of scan paths. Our data suggest that human subjects show different scanning patterns to stimuli with different affective ratings. Valence salient stimuli (with neutral arousal elicited faster and larger shifts of attention, while arousal salient stimuli (with neutral valence elicited local scanning, dense attention allocation and deep processing. Furthermore, our model revealed that the modulatory effect of valence was linearly related to the valence level, whereas the relation between the modulatory effect and the level of arousal was nonlinear. Hence, visual attention seems to be modulated by mechanisms that are separate for valence and arousal.

  1. Structural basis for PPAR partial or full activation revealed by a novel ligand binding mode

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    Capelli, Davide; Cerchia, Carmen; Montanari, Roberta; Loiodice, Fulvio; Tortorella, Paolo; Laghezza, Antonio; Cervoni, Laura; Pochetti, Giorgio; Lavecchia, Antonio

    2016-10-01

    The peroxisome proliferator-activated receptors (PPARs) are nuclear receptors involved in the regulation of the metabolic homeostasis and therefore represent valuable therapeutic targets for the treatment of metabolic diseases. The development of more balanced drugs interacting with PPARs, devoid of the side-effects showed by the currently marketed PPARγ full agonists, is considered the major challenge for the pharmaceutical companies. Here we present a structure-based virtual screening approach that let us identify a novel PPAR pan-agonist with a very attractive activity profile and its crystal structure in the complex with PPARα and PPARγ, respectively. In PPARα this ligand occupies a new pocket whose filling is allowed by the ligand-induced switching of the F273 side chain from a closed to an open conformation. The comparison between this pocket and the corresponding cavity in PPARγ provides a rationale for the different activation of the ligand towards PPARα and PPARγ, suggesting a novel basis for ligand design.

  2. Ligand- and drug-binding studies of membrane proteins revealed through circular dichroism spectroscopy.

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    Siligardi, Giuliano; Hussain, Rohanah; Patching, Simon G; Phillips-Jones, Mary K

    2014-01-01

    A great number of membrane proteins have proven difficult to crystallise for use in X-ray crystallographic structural determination or too complex for NMR structural studies. Circular dichroism (CD) is a fast and relatively easy spectroscopic technique to study protein conformational behaviour. In this review examples of the applications of CD and synchrotron radiation CD (SRCD) to membrane protein ligand binding interaction studies are discussed. The availability of SRCD has been an important advancement in recent progress, most particularly because it can be used to extend the spectral region in the far-UV region (important for increasing the accuracy of secondary structure estimations) and for working with membrane proteins available in only small quantities for which SRCD has facilitated molecular recognition studies. Such studies have been accomplished by probing in the near-UV region the local tertiary structure of aromatic amino acid residues upon addition of chiral or non-chiral ligands using long pathlength cells of small volume capacity. In particular, this review describes the most recent use of the technique in the following areas: to obtain quantitative data on ligand binding (exemplified by the FsrC membrane sensor kinase receptor); to distinguish between functionally similar drugs that exhibit different mechanisms of action towards membrane proteins (exemplified by secretory phospholipase A2); and to identify suitable detergent conditions to observe membrane protein-ligand interactions using stabilised proteins (exemplified by the antiseptic transporter SugE). Finally, the importance of characterising in solution the conformational behaviour and ligand binding properties of proteins in both far- and near-UV regions is discussed. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding. © 2013.

  3. X-ray CT Scanning Reveals Long-Term Copper Pollution Effects on Functional Soil Structure

    DEFF Research Database (Denmark)

    Naveed, Muhammad; Møldrup, Per; Homstrup, Martin

    factors such as soil type, land use, and soil contamination. In this study, we quantified the soil structure using X-ray CT scanning and revealed the effect of a long history of Copper (Cu) pollution on it. A fallow field at Hygum Denmark provides this opportunity as it had a long history of Copper...... sulphate contamination in a gradient with Cu content varies from 21 mg kg-1 to 3837 mg kg-1. Total 20 intact soil columns (diameter of 10 cm and height of 8 cm) were sampled at five locations along the Cu-gradient from a depth of 5 to 15 cm below surface level. The soil columns were scanned at a voxel...... resolution of 0.21 mm x 0.21 mm x 0.21 mm. Images were analyzed using the Image-J software. Three-dimensional visualization of macropores showed that biopores (pores formed by organisms and plant roots) are present in abundance in this field at a Cu level of 21 mg kg-1 and decreased as the Cu content...

  4. Proteomic analysis reveals novel ligands and substrates for LNX1 E3 ubiquitin ligase.

    Directory of Open Access Journals (Sweden)

    Joan A Lenihan

    Full Text Available Ligand of Numb protein X1 (LNX1 is an E3 ubiquitin ligase that contains a catalytic RING (Really Interesting New Gene domain and four PDZ (PSD-95, DlgA, ZO-1 domains. LNX1 can ubiquitinate Numb, as well as a number of other ligands. However, the physiological relevance of these interactions in vivo remain unclear. To gain functional insights into the LNX family, we have characterised the LNX1 interactome using affinity purification and mass spectrometry. This approach identified a large number of novel LNX1-interacting proteins, as well as confirming known interactions with NUMB and ERC2. Many of the novel interactions mapped to the LNX PDZ domains, particularly PDZ2, and many showed specificity for LNX1 over the closely related LNX2. We show that PPFIA1 (liprin-α1, KLHL11, KIF7 and ERC2 are substrates for ubiquitination by LNX1. LNX1 ubiquitination of liprin-α1 is dependent on a PDZ binding motif containing a carboxyl terminal cysteine that binds LNX1 PDZ2. Surprisingly, the neuronally-expressed LNX1p70 isoform, that lacks the RING domain, was found to promote ubiquitination of PPFIA1 and KLHL11, albeit to a lesser extent than the longer RING-containing LNX1p80 isoform. Of several E3-ligases identified in the LNX1 interactome we confirm interactions of LNX1 with MID2/TRIM1 and TRIM27. On this basis we propose a model whereby LNX1p70, despite lacking a catalytic RING domain, may function as a scaffold to promote ubiquitination of its ligands through recruitment of other E3-ligases. These findings provide functional insights into the LNX protein family, particularly the neuronal LNX1p70 isoform.

  5. Multilayered proteomics reveals molecular switches dictating ligand-dependent EGFR trafficking

    DEFF Research Database (Denmark)

    Francavilla, Chiara; Papetti, Moreno; Rigbolt, Kristoffer T G

    2016-01-01

    , we devised an integrated multilayered proteomics approach (IMPA). We analyzed dynamic changes in the receptor interactome, ubiquitinome, phosphoproteome, and late proteome in response to both ligands in human cells by quantitative MS and identified 67 proteins regulated at multiple levels. We...... identified RAB7 phosphorylation and RCP recruitment to EGFR as switches for EGF and TGF-α outputs, controlling receptor trafficking, signaling duration, proliferation, and migration. By manipulating RCP levels or phosphorylation of RAB7 in EGFR-positive cancer cells, we were able to switch a TGF......-α-mediated response to an EGF-like response or vice versa as EGFR trafficking was rerouted. We propose IMPA as an approach to uncover fine-tuned regulatory mechanisms in cell signaling....

  6. High resolution crystal structures of unliganded and liganded human liver ACBP reveal a new mode of binding for the acyl-CoA ligand

    DEFF Research Database (Denmark)

    Taskinen, Jukka P; van Aalten, Daan M; Knudsen, Jens

    2007-01-01

    The acyl-CoA binding protein (ACBP) is essential for the fatty acid metabolism, membrane structure, membrane fusion, and ceramide synthesis. Here high resolution crystal structures of human cytosolic liver ACBP, unliganded and liganded with a physiological ligand, myristoyl-CoA are described...

  7. A Protein Data Bank survey reveals shortening of intermolecular hydrogen bonds in ligand-protein complexes when a halogenated ligand is an H-bond donor.

    Directory of Open Access Journals (Sweden)

    Jarosław Poznański

    Full Text Available Halogen bonding in ligand-protein complexes is currently widely exploited, e.g. in drug design or supramolecular chemistry. But little attention has been directed to other effects that may result from replacement of a hydrogen by a strongly electronegative halogen. Analysis of almost 30000 hydrogen bonds between protein and ligand demonstrates that the length of a hydrogen bond depends on the type of donor-acceptor pair. Interestingly, lengths of hydrogen bonds between a protein and a halogenated ligand are visibly shorter than those estimated for the same family of proteins in complexes with non-halogenated ligands. Taking into account the effect of halogenation on hydrogen bonding is thus important when evaluating structural and/or energetic parameters of ligand-protein complexes. All these observations are consistent with the concept that halogenation increases the acidity of the proximal amino/imino/hydroxyl groups and thus makes them better, i.e. stronger, H-bond donors.

  8. A Protein Data Bank Survey Reveals Shortening of Intermolecular Hydrogen Bonds in Ligand-Protein Complexes When a Halogenated Ligand Is an H-Bond Donor

    Science.gov (United States)

    Poznański, Jarosław; Poznańska, Anna; Shugar, David

    2014-01-01

    Halogen bonding in ligand-protein complexes is currently widely exploited, e.g. in drug design or supramolecular chemistry. But little attention has been directed to other effects that may result from replacement of a hydrogen by a strongly electronegative halogen. Analysis of almost 30000 hydrogen bonds between protein and ligand demonstrates that the length of a hydrogen bond depends on the type of donor-acceptor pair. Interestingly, lengths of hydrogen bonds between a protein and a halogenated ligand are visibly shorter than those estimated for the same family of proteins in complexes with non-halogenated ligands. Taking into account the effect of halogenation on hydrogen bonding is thus important when evaluating structural and/or energetic parameters of ligand-protein complexes. All these observations are consistent with the concept that halogenation increases the acidity of the proximal amino/imino/hydroxyl groups and thus makes them better, i.e. stronger, H-bond donors. PMID:24933273

  9. Immunogold labeling of amelogenin in developing porcine enamel revealed by field emission scanning electron microscopy.

    Science.gov (United States)

    Du, Chang; Fan, Daming; Sun, Zhi; Fan, Yuwei; Lakshminarayanan, Rajamani; Moradian-Oldak, Janet

    2009-01-01

    The present study describes a method using immunohistochemical labeling in combination with high-resolution imaging (field emission scanning electron microscopy) to investigate the spatial localization of amelogenins on apatite crystallites in developing porcine enamel. Cross-sections of developing enamel tissue from freeze-fractured pig third molar were treated with antiserum against recombinant mouse amelogenin and immunoreactivity confirmed by Western blot analysis. The samples were then treated with the goat anti-rabbit IgG conjugated with 10-nm gold particles. The control samples were treated with the secondary antibody only. The in-lens secondary electrons detector and quadrant back-scattering detector were employed to reveal the high-resolution morphology of enamel structures and gold particle distribution. The immunolabeling showed a preference of the gold particle localization along the side faces of the ribbon-like apatite crystals. The preferential localization of amelogenin in vivo on enamel crystals strongly supports its direct function in controlling crystal morphology. Copyright 2008 S. Karger AG, Basel.

  10. Synchrotron scanning reveals the palaeoneurology of the head-butting Moschops capensis (Therapsida, Dinocephalia

    Directory of Open Access Journals (Sweden)

    Julien Benoit

    2017-08-01

    Full Text Available Dinocephalian therapsids are renowned for their massive, pachyostotic and ornamented skulls adapted for head-to-head fighting during intraspecific combat. Synchrotron scanning of the tapinocephalid Moschops capensis reveals, for the first time, numerous anatomical adaptations of the central nervous system related to this combative behaviour. Many neural structures (such as the brain, inner ear and ophthalmic branch of the trigeminal nerve were completely enclosed and protected by bones, which is unusual for non-mammaliaform therapsids. The nearly complete ossification of the braincase enables precise determination of the brain cavity volume and encephalization quotient, which appears greater than expected for such a large and early herbivore. The practice of head butting is often associated with complex social behaviours and gregariousness in extant species, which are known to influence brain size evolution. Additionally, the plane of the lateral (horizontal semicircular canal of the bony labyrinth is oriented nearly vertically if the skull is held horizontally, which suggests that the natural position of the head was inclined about 60–65°to the horizontal. This is consistent with the fighting position inferred from osteology, as well as ground-level browsing. Finally, the unusually large parietal tube may have been filled with thick conjunctive tissue to protect the delicate pineal eye from injury sustained during head butting.

  11. Chromosome 21 Scan in Down Syndrome Reveals DSCAM as a Predisposing Locus in Hirschsprung Disease

    Science.gov (United States)

    Jannot, Anne-Sophie; Chaoui, Asma; Masse-Morel, Marine; Arnold, Stacey; Sanlaville, Damien; Ceccherini, Isabella; Borrego, Salud; Hofstra, Robert M. W.; Munnich, Arnold; Bondurand, Nadège; Chakravarti, Aravinda; Clerget-Darpoux, Françoise; Amiel, Jeanne; Lyonnet, Stanislas

    2013-01-01

    Hirschsprung disease (HSCR) genetics is a paradigm for the study and understanding of multigenic disorders. Association between Down syndrome and HSCR suggests that genetic factors that predispose to HSCR map to chromosome 21. To identify these additional factors, we performed a dose-dependent association study on chromosome 21 in Down syndrome patients with HSCR. Assessing 10,895 SNPs in 26 Caucasian cases and their parents led to identify two associated SNPs (rs2837770 and rs8134673) at chromosome-wide level. Those SNPs, which were located in intron 3 of the DSCAM gene within a 19 kb-linkage disequilibrium block region were in complete association and are consistent with DSCAM expression during enteric nervous system development. We replicated the association of HSCR with this region in an independent sample of 220 non-syndromic HSCR Caucasian patients and their parents. At last, we provide the functional rationale to the involvement of DSCAM by network analysis and assessment of SOX10 regulation. Our results reveal the involvement of DSCAM as a HSCR susceptibility locus, both in Down syndrome and HSCR isolated cases. This study further ascertains the chromosome-scan dose-dependent methodology used herein as a mean to map the genetic bases of other sub-phenotypes both in Down syndrome and other aneuploidies. PMID:23671607

  12. Murine whole-organ immune cell populations revealed by multi-epitope-ligand cartography.

    Science.gov (United States)

    Eckhardt, Jenny; Ostalecki, Christian; Kuczera, Katarzyna; Schuler, Gerold; Pommer, Ansgar J; Lechmann, Matthias

    2013-02-01

    Multi-epitope-ligand cartography (MELC) is an innovative high-throughput fluorescence microscopy-based method. A tissue section is analyzed through a repeated cycling of (1) incubation with a fluorophore-labeled antibody, (2) fluorescence imaging, and (3) soft bleaching. This method allows staining of the same tissue section with up to 100 fluorescent markers and to analyze their toponomic expression using further image processing and pixel-precise overlay of the corresponding images. In this study, we adapted this method to identify a large panel of murine leukocyte subpopulations in a whole frozen section of a peripheral lymph node. Using the resulting antibody library, we examined non-inflamed versus inflamed tissues of brain and spinal cord in the experimental autoimmune encephalomyelitis (EAE) model. The presence and activity of specific leukocyte subpopulations (different T cell subpopulations, dendritic cells, macrophages, etc.) could be assessed and the cellular localizations and the corresponding activation status in situ were investigated. The results were then correlated with quantitative RT-PCR.

  13. Photoreceptor perturbation around subretinal drusenoid deposits as revealed by adaptive optics scanning laser ophthalmoscopy.

    Science.gov (United States)

    Zhang, Yuhua; Wang, Xiaolin; Rivero, Ernesto Blanco; Clark, Mark E; Witherspoon, Clark Douglas; Spaide, Richard F; Girkin, Christopher A; Owsley, Cynthia; Curcio, Christine A

    2014-09-01

    To describe the microscopic structure of photoreceptors impacted by subretinal drusenoid deposits, also called pseudodrusen, an extracellular lesion associated with age-related macular degeneration (AMD), using adaptive optics scanning laser ophthalmoscopy (AOSLO). Observational case series. We recruited 53 patients with AMD and 10 age-similar subjects who had normal retinal health. All subjects underwent color fundus photography, infrared reflectance, red-free reflectance, autofluorescence, and spectral-domain optical coherence tomography (OCT). Subretinal drusenoid deposits were classified by a 3-stage OCT-based grading system. Lesions and surrounding photoreceptors were examined by AOSLO. Subretinal drusenoid deposits were found in 26 eyes of 13 patients with AMD and imaged by AOSLO and spectral-domain OCT in 18 eyes (n = 342 lesions). Spectral-domain OCT showed subretinal drusenoid deposits as highly reflective material accumulated internal to the retinal pigment epithelium. AOSLO revealed that photoreceptor reflectivity was qualitatively reduced by stage 1 subretinal drusenoid deposits and was greatly reduced by stage 2. AOSLO presented a distinct structure in stage 3, a hyporeflective annulus consisting of deflected, degenerated or absent photoreceptors. A central core with a reflectivity superficially resembling photoreceptors is formed by the lesion material itself. A hyporeflective gap in the photoreceptor ellipsoid zone on either side of this core shown in spectral-domain OCT corresponded to the hyporeflective annulus seen by AOSLO. AOSLO and multimodal imaging of subretinal drusenoid deposits indicate solid, space-filling lesions in the subretinal space. Associated retinal reflectivity changes are related to lesion stages and are consistent with perturbations to photoreceptors, as suggested by histology. Copyright © 2014 Elsevier Inc. All rights reserved.

  14. Comparative Multi-Epitope-Ligand-Cartography reveals essential immunological alterations in Barrett's metaplasia and esophageal adenocarcinoma.

    Science.gov (United States)

    Berndt, Uta; Philipsen, Lars; Bartsch, Sebastian; Hu, Yuqin; Röcken, Christoph; Bertram, Wiedenmann; Hämmerle, Marcus; Rösch, Thomas; Sturm, Andreas

    2010-07-06

    Barrett's esophagus (BE) is caused by gastroesophageal reflux with consecutive mucosal inflammation, predisposing patients to the development of esophageal adenocarcinoma (EAC). We investigated changes in T cell-related mucosal combinatorial molecular protein patterns in both diseases using the novel Multi-Epitope-Ligand-Cartography, a unique robotic whole-cell imaging technology that simultaneously visualizes dozens of proteins in structurally intact tissues and correlates cellular localization of proteins with function. Biopsies were taken during endoscopy from BE, EAC, and normal control tissue, and proteomic microscopy was performed on 32 different epitopes. When the significance level was set to p < 0.0005 and the search depth to five antibody combinations, controls and BE can be differentiated by 63, controls and EAC by 3222, and BE from EAC by 1521 distinct protein combinations.For example, the number of activated apoptotic naïve and memory T cells was significantly increased only in BE, whereas the number of activated apoptotic helper and regulatory T cells was significantly elevated in BE and EAC. In contrast, the number of activated apoptotic cytotoxic T cells was significantly elevated only in EAC. Confirming different pathways in BE and EAC, the number of T lymphocytes with p53 expression and downregulation of bcl2 expression (CD3+p53+Bcl2-NfkB-) was significantly increased in EAC compared to BE and controls. Interestingly, the number of precursor T cells (CD7+) was significantly elevated only in EAC. These cells lack Bax and caspase-8, suggesting impaired apoptosis in the early stages of T cell differentiation. Proteomic analysis showed for the first time that proteins, which are critically involved in the mucosal immune system of the esophagus, are distinctly expressed in BE and EAC, whereas others are comparably altered in both diseases, suggesting that many pathogenic events might be shared by both diseases. Topological proteomic analysis

  15. Comparative thermodynamic studies on substrate and product binding of O-Acetylserine Sulfhydrylase reveals two different ligand recognition modes†

    Directory of Open Access Journals (Sweden)

    Kumaran Sangaralingam

    2011-06-01

    Full Text Available Abstract Background The importance of understanding the detailed mechanism of cysteine biosynthesis in bacteria is underscored by the fact that cysteine is the only sulfur donor for all cellular components containing reduced sulfur. O-acetylserine sulfhydrylase (OASS catalyzes this crucial last step in the cysteine biosynthesis and has been recognized as an important gene for the survival and virulence of pathogenic bacteria. Structural and kinetic studies have contributed to the understanding of mechanistic aspects of OASS, but details of ligand recognition features of OASS are not available. In the absence of any detailed study on the energetics of ligand binding, we have studied the thermodynamics of OASS from Salmonella typhimurium (StOASS, Haemophilus influenzae (HiOASS, and Mycobacterium tuberculosis (MtOASS binding to their substrate O-acetylserine (OAS, substrate analogue (methionine, and product (cysteine. Results Ligand binding properties of three OASS enzymes are studied under defined solution conditions. Both substrate and product binding is an exothermic reaction, but their thermodynamic signatures are very different. Cysteine binding to OASS shows that both enthalpy and entropy contribute significantly to the binding free energy at all temperatures (10-30°C examined. The analyses of interaction between OASS with OAS (substrate or methionine (substrate analogue revealed a completely different mode of binding. Binding of both OAS and methionine to OASS is dominated by a favorable entropy change, with minor contribution from enthalpy change (ΔHSt-Met = -1.5 ± 0.1 kJ/mol; TΔSSt-Met = 8.2 kJ/mol at 20°C. Our salt dependent ligand binding studies indicate that methionine binding affinity is more sensitive to [NaCl] as compared to cysteine affinity. Conclusions We show that OASS from three different pathogenic bacteria bind substrate and product through two different mechanisms. Results indicate that predominantly entropy driven

  16. Atomic force microscopy measurements reveal multiple bonds between Helicobacter pylori blood group antigen binding adhesin and Lewis b ligand.

    Science.gov (United States)

    Parreira, P; Shi, Q; Magalhaes, A; Reis, C A; Bugaytsova, J; Borén, T; Leckband, D; Martins, M C L

    2014-12-06

    The strength of binding between the Helicobacter pylori blood group antigen-binding adhesin (BabA) and its cognate glycan receptor, the Lewis b blood group antigen (Le(b)), was measured by means of atomic force microscopy. High-resolution measurements of rupture forces between single receptor-ligand pairs were performed between the purified BabA and immobilized Le(b) structures on self-assembled monolayers. Dynamic force spectroscopy revealed two similar but statistically different bond populations. These findings suggest that the BabA may form different adhesive attachments to the gastric mucosa in ways that enhance the efficiency and stability of bacterial adhesion. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  17. Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

    Science.gov (United States)

    Kohlhoff, Kai J.; Shukla, Diwakar; Lawrenz, Morgan; Bowman, Gregory R.; Konerding, David E.; Belov, Dan; Altman, Russ B.; Pande, Vijay S.

    2014-01-01

    Simulations can provide tremendous insight into the atomistic details of biological mechanisms, but micro- to millisecond timescales are historically only accessible on dedicated supercomputers. We demonstrate that cloud computing is a viable alternative that brings long-timescale processes within reach of a broader community. We used Google's Exacycle cloud-computing platform to simulate two milliseconds of dynamics of a major drug target, the G-protein-coupled receptor β2AR. Markov state models aggregate independent simulations into a single statistical model that is validated by previous computational and experimental results. Moreover, our models provide an atomistic description of the activation of a G-protein-coupled receptor and reveal multiple activation pathways. Agonists and inverse agonists interact differentially with these pathways, with profound implications for drug design.

  18. Timelapse scanning reveals spatial variation in tomato (Solanum lycopersicum L.) root elongation rates during partial waterlogging

    DEFF Research Database (Denmark)

    Dresbøll, Dorte; Thorup-Kristensen, Kristian; Mckenzie, Blair M.

    2013-01-01

    by increasing elongation rates. Methods Tomato plants (Solanum lycopersicum L.) were grown in peat in root chambers (300×215× 6 mm) with a transparent front. Root chambers were maintained in flatbed scanners tilted at 30° to vertical and scanned every 3 h before, during and after waterlogging the lower layer...

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

    Energy Technology Data Exchange (ETDEWEB)

    Breustedt, Daniel A.; Chatwell, Lorenz; Skerra, Arne, E-mail: skerra@wzw.tum.de [Munich Center for Integrated Protein Science, CIPS-M, and Lehrstuhl für Biologische Chemie, Technische Universität München, 85350 Freising-Weihenstephan (Germany)

    2009-10-01

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

  20. Revealing the 1 nm/s Extensibility of Nanoscale Amorphous Carbon in a Scanning Electron Microscope

    DEFF Research Database (Denmark)

    Zhang, Wei

    2013-01-01

    In an ultra-high vacuum scanning electron microscope, the edged branches of amorphous carbon film (∼10 nm thickness) can be continuously extended with an eye-identifying speed (on the order of ∼1 nm/s) under electron beam. Such unusual mobility of amorphous carbon may be associated with deformati...... positive implications to explore some amorphous carbon as electron field emission device. SCANNING 35: 261-264, 2013. © 2012 Wiley Periodicals, Inc.......In an ultra-high vacuum scanning electron microscope, the edged branches of amorphous carbon film (∼10 nm thickness) can be continuously extended with an eye-identifying speed (on the order of ∼1 nm/s) under electron beam. Such unusual mobility of amorphous carbon may be associated with deformation...... promoted by the electric field, which resulted from an inner secondary electron potential difference from the main trunk of carbon film to the tip end of branches under electron beam. This result demonstrates importance of applying electrical effects to modify properties of carbon materials. It may have...

  1. Atomic-scale structure of dislocations revealed by scanning tunneling microscopy and molecular dynamics

    DEFF Research Database (Denmark)

    Christiansen, Jesper; Morgenstern, K.; Schiøtz, Jakob

    2002-01-01

    The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations......, the simulations can be used to determine dislocation structure and orientation in the near-surface region. In a similar way, the subsurface structure of other extended defects can be studied. The simulations show dislocations to reorient the partials in the surface region leading to an increased splitting width...

  2. Crystal structure of the ligand-binding domain of the promiscuous EphA4 receptor reveals two distinct conformations

    Energy Technology Data Exchange (ETDEWEB)

    Singla, Nikhil; Goldgur, Yehuda; Xu, Kai; Paavilainen, Sari; Nikolov, Dimitar B.; Himanen, Juha P. (MSKCC); (Turku)

    2010-09-08

    Eph receptors and their ephrin ligands are important mediators of cell-cell communication. They are divided in two subclasses based on their affinities for each other and on sequence conservation. Receptor-ligand binding within each subclass is fairly promiscuous, while binding cross the subclasses happens rarely. EphA4 is an exception to this general rule, since it has long been known to bind both A- and B-class ephrin ligands but the reason for this exceptional behavior has not been worked out at molecular level. Recent structural and biochemical studies on EphA4 ligand-binding domain alone and in complex with its ligands have addressed this question. However, the published structures of EphA4/ephrin complexes differ considerably from each other and strikingly different explanations for the exceptional promiscuity of EphA4 were proposed. To address these contradictory findings, we have determined a crystal structure of the EphA4 ligand-binding domain at 2.3 {angstrom} resolution and show that the receptor has an unprecedented ability to exist in two very different, well-ordered conformations even in the unbound state. Our results suggest that the ligand promiscuity of the Ephs is directly correlated with the structural flexibility of the ligand-binding surface of the receptor.

  3. High-Resolution Laser Scanning Reveals Plant Architectures that Reflect Universal Network Design Principles.

    Science.gov (United States)

    Conn, Adam; Pedmale, Ullas V; Chory, Joanne; Navlakha, Saket

    2017-07-26

    Transport networks serve critical functions in biological and engineered systems, and yet their design requires trade-offs between competing objectives. Due to their sessile lifestyle, plants need to optimize their architecture to efficiently acquire and distribute resources while also minimizing costs in building infrastructure. To understand how plants resolve this design trade-off, we used high-precision three-dimensional laser scanning to map the architectures of tomato, tobacco, or sorghum plants grown in several environmental conditions and through multiple developmental time points, scanning in total 505 architectures from 37 plants. Using a graph-theoretic algorithm that we developed to evaluate design strategies, we find that plant architectures lie along the Pareto front between two simple length-based objectives-minimizing total branch length and minimizing nutrient transport distance-thereby conferring a selective fitness advantage for plant transport processes. The location along the Pareto front can distinguish among species and conditions, suggesting that during evolution, natural selection may employ common network design principles despite different optimization trade-offs. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. External morphogenesis of the tardigrade Hypsibius dujardini as revealed by scanning electron microscopy.

    Science.gov (United States)

    Gross, Vladimir; Minich, Irene; Mayer, Georg

    2017-04-01

    Tardigrada, commonly called water bears, is a taxon of microscopic panarthropods with five-segmented bodies and four pairs of walking legs. Although tardigrades have been known to science for several centuries, questions remain regarding many aspects of their biology, such as embryogenesis. Herein, we used scanning electron microscopy to document the external changes that occur during embryonic development in the tardigrade Hypsibius dujardini (Eutardigrada, Parachela, Hypsibiidae). Our results show an accelerated development of external features, with approximately 30 hrs separating the point at which external structures first become recognizable and a fully formed embryo. All segments appear to arise simultaneously between ∼20 and 25 hrs of development, and no differences in the degree of development could be detected between the limb buds at any stage. Claws emerge shortly after the limb buds and are morphologically similar to those of adults. The origin of the claws is concurrent with that of the sclerotized parts of the mouth, suggesting that all cuticular structures arise simultaneously at ∼30 hrs. The mouth arises as an invagination in the terminal region of the head at ∼25 hrs, closes later in development, and opens again shortly before hatching. The anlagen of the peribuccal lobes arise as one dorsal and one ventral row, each consisting of three lobes, and later form a ring in the late embryo, whereas there is no indication of a labrum anlage at any point during development. Furthermore, we describe limited postembryonic development in the form of cuticular pores that are absent in juveniles but present in adults. This study represents the first scanning electron micrographs of tardigrade embryos, demonstrating the utility of this technique for studying embryogenesis in tardigrades. This work further adds an external morphological perspective to the developmental data already available for H. dujardini, facilitating future comparisons to related

  5. Super-resolution scanning patch clamp reveals clustering of functional ion channels in adult ventricular myocyte.

    Science.gov (United States)

    Bhargava, Anamika; Lin, Xianming; Novak, Pavel; Mehta, Kinneri; Korchev, Yuri; Delmar, Mario; Gorelik, Julia

    2013-04-12

    Compartmentation of ion channels on the cardiomyocyte surface is important for electric propagation and electromechanical coupling. The specialized T-tubule and costameric structures facilitate spatial coupling of various ion channels and receptors. Existing methods such as immunofluorescence and patch clamp techniques are limited in their ability to localize functional ion channels. As such, a correlation between channel protein location and channel function remains incomplete. To validate a method that permits routine imaging of the topography of a live cardiomyocyte and study clustering of functional ion channels from a specific microdomain. We used scanning ion conductance microscopy and conventional cell-attached patch clamp with a software modification that allows controlled increase of pipette tip diameter. The sharp nanopipette used for topography scan was modified into a larger patch pipette that could be positioned with nanoscale precision to a specific site of interest (crest, groove, or T-tubules of cardiomyocytes) and sealed to the membrane for cell-attached recording of ion channels. Using this method, we significantly increased the probability of detecting activity of L-type calcium channels in the T-tubules of ventricular cardiomyocytes. We also demonstrated that active sodium channels do not distribute homogenously on the sarcolemma instead, they segregate into clusters of various densities, most crowded in the crest region, that are surrounded by areas virtually free of functional sodium channels. Our new method substantially increases the throughput of recording location-specific functional ion channels on the cardiomyocyte sarcolemma, thereby allowing characterization of ion channels in relation to the microdomain where they reside.

  6. Ion milling coupled field emission scanning electron microscopy reveals current misunderstanding of morphology of polymeric nanoparticles.

    Science.gov (United States)

    Francis, Donny; Mouftah, Samiha; Steffen, Robert; Beduneau, Arnaud; Pellequer, Yann; Lamprecht, Alf

    2015-01-01

    Nanoparticles (NPs) are currently used as drug delivery systems for numerous therapeutic macromolecules, e.g. proteins or DNA. Based on the preparation by double emulsion solvent evaporation a sponge-like structure was postulated entrapping hydrophilic drugs inside an internal aqueous phase. However, a direct proof of this hypothesized structure is still missing today. NPs were prepared from different polymers using a double-emulsion method and characterized for their physicochemical properties. Combining ion milling with field emission scanning electron microscopy allowed to cross section single NP and to visualize their internal morphology. The imaging procedure permitted cross-sectioning of NPs and visualization of the internal structure as well as localizing drugs associated with NPs. It was observed that none of the model actives was encapsulated inside the polymeric matrix when particle diameters were below around 470 nm but predominantly adsorbed to the particle surface. Even at larger diameters only a minority of particles of a diameter below 1 μm contained an internal phase. The properties of such drug loaded NPs, i.e. drug release or the observations in cellular uptake or even drug targeting needs to be interpreted carefully since in most cases NP surface properties are potentially dominated by the 'encapsulated' drug characteristics. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Revealing phenotype-associated functional differences by genome-wide scan of ancient haplotype blocks.

    Directory of Open Access Journals (Sweden)

    Ritsuko Onuki

    Full Text Available Genome-wide scans for positive selection have become important for genomic medicine, and many studies aim to find genomic regions affected by positive selection that are associated with risk allele variations among populations. Most such studies are designed to detect recent positive selection. However, we hypothesize that ancient positive selection is also important for adaptation to pathogens, and has affected current immune-mediated common diseases. Based on this hypothesis, we developed a novel linkage disequilibrium-based pipeline, which aims to detect regions associated with ancient positive selection across populations from single nucleotide polymorphism (SNP data. By applying this pipeline to the genotypes in the International HapMap project database, we show that genes in the detected regions are enriched in pathways related to the immune system and infectious diseases. The detected regions also contain SNPs reported to be associated with cancers and metabolic diseases, obesity-related traits, type 2 diabetes, and allergic sensitization. These SNPs were further mapped to biological pathways to determine the associations between phenotypes and molecular functions. Assessments of candidate regions to identify functions associated with variations in incidence rates of these diseases are needed in the future.

  8. REVEALING THE SECRETS OF STONEHENGE THROUGH THE APPLICATION OF LASER SCANNING, PHOTOGRAMMETRY AND VISUALISATION TECHNIQUES

    Directory of Open Access Journals (Sweden)

    P. G. Bryan

    2013-07-01

    Full Text Available Stonehenge is perhaps the most famous prehistoric monument in the world. Begun as a simple earthwork enclosure, it was built in several stages with the unique lintelled stone circle being erected in the Neolithic period in around 2,500 BC. Today Stonehenge, together with Avebury and other associated sites, form the heart of a World Heritage Site (WHS with a unique and dense concentration of outstanding prehistoric monuments. In 2011 English Heritage (EH embarked on a new survey of the monument. Undertaken by the Greenhatch Group, a commercial survey company based near Derby, a combination of laser scanning and photogrammetric approaches were used to generate the required scale and detailed level of output required by English Heritage. This paper will describe the background to this project and its context within previous survey activities at this World Heritage Site. It will explain the data acquisition technology and processes undertaken on site, the datasets derived from post-processing and their filtering and analysis within both subsequent research projects. Alongside a description of how the data is currently being exploited and proposed future applications within the conservation and management of the site, it will finish by considering the impact of developing geospatial imaging technologies.

  9. Revealing the Secrets of Stonehenge Through the Application of Laser Scanning, Photogrammetry and Visualisation Techniques

    Science.gov (United States)

    Bryan, P. G.; Abbott, M.; Dodson, A. J.

    2013-07-01

    Stonehenge is perhaps the most famous prehistoric monument in the world. Begun as a simple earthwork enclosure, it was built in several stages with the unique lintelled stone circle being erected in the Neolithic period in around 2,500 BC. Today Stonehenge, together with Avebury and other associated sites, form the heart of a World Heritage Site (WHS) with a unique and dense concentration of outstanding prehistoric monuments. In 2011 English Heritage (EH) embarked on a new survey of the monument. Undertaken by the Greenhatch Group, a commercial survey company based near Derby, a combination of laser scanning and photogrammetric approaches were used to generate the required scale and detailed level of output required by English Heritage. This paper will describe the background to this project and its context within previous survey activities at this World Heritage Site. It will explain the data acquisition technology and processes undertaken on site, the datasets derived from post-processing and their filtering and analysis within both subsequent research projects. Alongside a description of how the data is currently being exploited and proposed future applications within the conservation and management of the site, it will finish by considering the impact of developing geospatial imaging technologies.

  10. Immunogold scanning electron microscopy can reveal the polysaccharide architecture of xylem cell walls.

    Science.gov (United States)

    Sun, Qiang; Sun, Yuliang; Juzenas, Kevin

    2017-04-01

    Immunofluorescence microscopy (IFM) and immunogold transmission electron microscopy (TEM) are the two main techniques commonly used to detect polysaccharides in plant cell walls. Both are important in localizing cell wall polysaccharides, but both have major limitations, such as low resolution in IFM and restricted sample size for immunogold TEM. In this study, we have developed a robust technique that combines immunocytochemistry with scanning electron microscopy (SEM) to study cell wall polysaccharide architecture in xylem cells at high resolution over large areas of sample. Using multiple cell wall monoclonal antibodies (mAbs), this immunogold SEM technique reliably localized groups of hemicellulosic and pectic polysaccharides in the cell walls of five different xylem structures (vessel elements, fibers, axial and ray parenchyma cells, and tyloses). This demonstrates its important advantages over the other two methods for studying cell wall polysaccharide composition and distribution in these structures. In addition, it can show the three-dimensional distribution of a polysaccharide group in the vessel lateral wall and the polysaccharide components in the cell wall of developing tyloses. This technique, therefore, should be valuable for understanding the cell wall polysaccharide composition, architecture and functions of diverse cell types. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  11. Scanning a microhabitat: plant-microbe interactions revealed by confocal laser microscopy.

    Science.gov (United States)

    Cardinale, Massimiliano

    2014-01-01

    No plant or cryptogam exists in nature without microorganisms associated with its tissues. Plants as microbial hosts are puzzles of different microhabitats, each of them colonized by specifically adapted microbiomes. The interactions with such microorganisms have drastic effects on the host fitness. Since the last 20 years, the combination of microscopic tools and molecular approaches contributed to new insights into microbe-host interactions. Particularly, confocal laser scanning microscopy (CLSM) facilitated the exploration of microbial habitats and allowed the observation of host-associated microorganisms in situ with an unprecedented accuracy. Here I present an overview of the progresses made in the study of the interactions between microorganisms and plants or plant-like organisms, focusing on the role of CLSM for the understanding of their significance. I critically discuss risks of misinterpretation when procedures of CLSM are not properly optimized. I also review approaches for quantitative and statistical analyses of CLSM images, the combination with other molecular and microscopic methods, and suggest the re-evaluation of natural autofluorescence. In this review, technical aspects were coupled with scientific outcomes, to facilitate the readers in identifying possible CLSM applications in their research or to expand their existing potential. The scope of this review is to highlight the importance of confocal microscopy in the study of plant-microbe interactions and also to be an inspiration for integrating microscopy with molecular techniques in future researches of microbial ecology.

  12. Scanning a microhabitat: plant-microbe interactions revealed by confocal laser microscopy

    Directory of Open Access Journals (Sweden)

    Massimiliano eCardinale

    2014-03-01

    Full Text Available No plant or cryptogam exists in nature without microorganisms associated with its tissues. Plants as microbial hosts are puzzles of different microhabitats, each of them colonized by specifically adapted microbiomes. The interactions with such microorganisms have drastic effects on the host fitness. Since the last 20 years, the combination of microscopic tools and molecular approaches contributed to new insights into microbe-host interactions. Particularly, confocal laser scanning microscopy (CLSM facilitated the exploration of microbial habitats and allowed the observation of host-associated microorganisms in situ with an unprecedented accuracy. Here I present an overview of the progresses made in the study of the interactions between microorganisms and plants or plant-like organisms, focusing on the role of CLSM for the understanding of their significance. I critically discuss risks of misinterpretation when procedures of CLSM are not properly optimized. I also review approaches for quantitative and statistical analyses of CLSM images, the combination with other molecular and microscopic methods, and suggest the re-evaluation of natural autofluorescence. In this review, technical aspects were coupled with scientific outcomes, to facilitate the readers in identifying possible CLSM applications in their research or to expand their existing potential. The scope of this review is to highlight the importance of confocal microscopy in the study of plant-microbe interactions and also to be an inspiration for integrating microscopy with molecular techniques in future researches of microbial ecology.

  13. Clinical study on eating disorders. Brain atrophy revealed by cranial computed tomography scans

    Energy Technology Data Exchange (ETDEWEB)

    Nishiwaki, Shinichi

    1988-06-01

    Cranial computed tomography (CT) scans were reviewed in 34 patients with anorexia nervosa (Group I) and 22 with bulimia (Group II) to elucidate the cause and pathological significance of morphological brain alterations. The findings were compared with those from 47 normal women. The incidence of brain atrophy was significantly higher in Group I (17/34, 50%) and Group II (11/22, 50%) than the control group (3/47, 6%). In Group I, there was a significant increase in the left septum-caudate distance, the maximum width of interhemispheric fissure, the width of the both-side Sylvian fissures adjacent to the skull, and the maximum width of the third ventricle. A significant increase in the maximum width of interhemispheric fissure and the width of the left-side Sylvian fissure adjacent to the skull were noted as well in Group II. Ventricular brain ratios were significantly higher in Groups I and II than the control group (6.76 and 7.29 vs 4.55). Brain atrophy did not correlate with age, body weight, malnutrition, eating behavior, depression, thyroid function, EEG findings, or intelligence scale. In Group I, serum cortisol levels after the administration of dexamethasone were correlated with ventricular brain ratio. (Namekawa, K) 51 refs.

  14. Genomic scan reveals loci under altitude adaptation in Tibetan and Dahe pigs.

    Directory of Open Access Journals (Sweden)

    Kunzhe Dong

    Full Text Available High altitude environments are of particular interest in the studies of local adaptation as well as their implications in physiology and clinical medicine in human. Some Chinese pig breeds, such as Tibetan pig (TBP that is well adapted to the high altitude and Dahe pig (DHP that dwells at the moderate altitude, provide ideal materials to study local adaptation to altitudes. Yet, it is still short of in-depth analysis and understanding of the genetic adaptation to high altitude in the two pig populations. In this study we conducted a genomic scan for selective sweeps using FST to identify genes showing evidence of local adaptations in TBP and DHP, with Wuzhishan pig (WZSP as the low-altitude reference. Totally, we identified 12 specific selective genes (CCBE1, F2RL1, AGGF1, ZFPM2, IL2, FGF5, PLA2G4A, ADAMTS9, NRBF2, JMJD1C, VEGFC and ADAM19 for TBP and six (OGG1, FOXM, FLT3, RTEL1, CRELD1 and RHOG for DHP. In addition, six selective genes (VPS13A, GNA14, GDAP1, PARP8, FGF10 and ADAMTS16 were shared by the two pig breeds. Among these selective genes, three (VEGFC, FGF10 and ADAMTS9 were previously reported to be linked to the local adaptation to high altitudes in pigs, while many others were newly identified by this study. Further bioinformatics analysis demonstrated that majority of these selective signatures have some biological functions relevant to the altitude adaptation, for examples, response to hypoxia, development of blood vessels, DNA repair and several hematological involvements. These results suggest that the local adaptation to high altitude environments is sophisticated, involving numerous genes and multiple biological processes, and the shared selective signatures by the two pig breeds may provide an effective avenue to identify the common adaptive mechanisms to different altitudes.

  15. Properties of the Mechanosensitive Channel MscS Pore Revealed by Tryptophan Scanning Mutagenesis.

    Science.gov (United States)

    Rasmussen, Tim; Rasmussen, Akiko; Singh, Shivani; Galbiati, Heloisa; Edwards, Michelle D; Miller, Samantha; Booth, Ian R

    2015-07-28

    Bacterial mechanosensitive channels gate when the transmembrane turgor rises to levels that compromise the structural integrity of the cell wall. Gating creates a transient large diameter pore that allows hydrated solutes to pass from the cytoplasm at rates close to those of diffusion. In the closed conformation, the channel limits transmembrane solute movement, even that of protons. In the MscS crystal structure (Protein Data Bank entry 2oau ), a narrow, hydrophobic opening is visible in the crystal structure, and it has been proposed that a vapor lock created by the hydrophobic seals, L105 and L109, is the barrier to water and ions. Tryptophan scanning mutagenesis has proven to be a highly valuable tool for the analysis of channel structure. Here Trp residues were introduced along the pore-forming TM3a helix and in selected other parts of the protein. Mutants were investigated for their expression, stability, and activity and as fluorescent probes of the physical properties along the length of the pore. Most Trp mutants were expressed at levels similar to that of the parent (MscS YFF) and were stable as heptamers in detergent in the presence and absence of urea. Fluorescence data suggest a long hydrophobic region with low accessibility to aqueous solvents, extending from L105/L109 to G90. Steady-state fluorescence anisotropy data are consistent with significant homo-Förster resonance energy transfer between tryptophan residues from different subunits within the narrow pore. The data provide new insights into MscS structure and gating.

  16. Myelin Organization in the Nodal, Paranodal, and Juxtaparanodal Regions Revealed by Scanning X-Ray Microdiffraction

    Science.gov (United States)

    Makowski, Lee; Palmisano, Marilena; Burghammer, Manfred; Riekel, Christian; Kirschner, Daniel A.

    2014-01-01

    X-ray diffraction has provided extensive information about the arrangement of lipids and proteins in multilamellar myelin. This information has been limited to the abundant inter-nodal regions of the sheath because these regions dominate the scattering when x-ray beams of 100 µm diameter or more are used. Here, we used a 1 µm beam, raster-scanned across a single nerve fiber, to obtain detailed information about the molecular architecture in the nodal, paranodal, and juxtaparanodal regions. Orientation of the lamellar membrane stacks and membrane periodicity varied spatially. In the juxtaparanode-internode, 198–202 Å-period membrane arrays oriented normal to the nerve fiber axis predominated, whereas in the paranode-node, 205–208 Å-period arrays oriented along the fiber direction predominated. In parts of the sheath distal to the node, multiple sets of lamellar reflections were observed at angles to one another, suggesting that the myelin multilayers are deformed at the Schmidt-Lanterman incisures. The calculated electron density of myelin in the different regions exhibited membrane bilayer profiles with varied electron densities at the polar head groups, likely due to different amounts of major myelin proteins (P0 glycoprotein and myelin basic protein). Scattering from the center of the nerve fibers, where the x-rays are incident en face (perpendicular) to the membrane planes, provided information about the lateral distribution of protein. By underscoring the heterogeneity of membrane packing, microdiffraction analysis suggests a powerful new strategy for understanding the underlying molecular foundation of a broad spectrum of myelinopathies dependent on local specializations of myelin structure in both the PNS and CNS. PMID:24984037

  17. Respiratory concerts revealed by scanning microrespirography in a termite Prorhinotermes simplex (Isoptera: Rhinotermitidae).

    Science.gov (United States)

    Sláma, K; Sobotník, J; Hanus, R

    2007-04-01

    Respiratory metabolism of different developmental stages (larvae, pseudergates, nymphs, soldiers, neotenic reproductives; 0.6-4.5 mg body mass) of Prorhinotermes simplex was individually monitored by scanning respirographic method sensitive to subnanoliter amounts of O(2) consumption or CO(2) output per minute. Specimens exposed to dry air after removal from the colony performed enormously large, discontinuous bursts of CO(2) lasting usually 2 min. The volume of CO(2) produced during the burst often surpassed the volume of the whole body and it was 10- to 20-fold in excess of the air-filled endogenous tracheal volume. The initial velocity of CO(2) production during the burst was more than 90-fold faster in comparison to O(2) consumption. In the presence of enough moisture within the respiratory vessel, the termites breathed continuously without any larger outburst of CO(2). This fact fully corroborates validity of the so-called water retention theory in discontinuous CO(2) release. The highest rates of O(2) consumption were found in the second instar larvae (0.9 mg, 1000-2000 microl O(2)/g/h), the soldier caste was intermediate (700 microl O(2)/g/h) while pseudergates and neotenic reproductives consumed between 300 and 600 microl O(2)/g/h, at 25 degrees C. All developmental stages feeding on a cellulose diet had CO(2)/O(2) values (RQ) over 1 (1.2-1.4, i.e. carbohydrate metabolism), pigmented soldiers fed by the workers had RQ around 0.75 (predominating lipid or protein metabolism). The unusually large, sudden eruptions of CO(2) in specimens exposed to dry air allow us to make the following conclusions: (1) the bursts were due to special chemical processes, such as by enzymatic hydration of carbonic acid by carbonic anhydrase and; (2) the bulk of chemically evolved gaseous CO(2) escaped from the body by a mass flow supported by active ventilation, not by a passive diffusion. These results demonstrated that the periodic emissions of CO(2) and the associated

  18. Accurate 3d Scanning of Damaged Ancient Greek Inscriptions for Revealing Weathered Letters

    Science.gov (United States)

    Papadaki, A. I.; Agrafiotis, P.; Georgopoulos, A.; Prignitz, S.

    2015-02-01

    In this paper two non-invasive non-destructive alternative techniques to the traditional and invasive technique of squeezes are presented alongside with specialized developed processing methods, aiming to help the epigraphists to reveal and analyse weathered letters in ancient Greek inscriptions carved in masonry or marble. The resulting 3D model would serve as a detailed basis for the epigraphists to try to decipher the inscription. The data were collected by using a Structured Light scanner. The creation of the final accurate three dimensional model is a complicated procedure requiring large computation cost and human effort. It includes the collection of geometric data in limited space and time, the creation of the surface, the noise filtering and the merging of individual surfaces. The use of structured light scanners is time consuming and requires costly hardware and software. Therefore an alternative methodology for collecting 3D data of the inscriptions was also implemented for reasons of comparison. Hence, image sequences from varying distances were collected using a calibrated DSLR camera aiming to reconstruct the 3D scene through SfM techniques in order to evaluate the efficiency and the level of precision and detail of the obtained reconstructed inscriptions. Problems in the acquisition processes as well as difficulties in the alignment step and mesh optimization are also encountered. A meta-processing framework is proposed and analysed. Finally, the results of processing and analysis and the different 3D models are critically inspected and then evaluated by a specialist in terms of accuracy, quality and detail of the model and the capability of revealing damaged and "hidden" letters.

  19. ACCURATE 3D SCANNING OF DAMAGED ANCIENT GREEK INSCRIPTIONS FOR REVEALING WEATHERED LETTERS

    Directory of Open Access Journals (Sweden)

    A. I. Papadaki

    2015-02-01

    Full Text Available In this paper two non-invasive non-destructive alternative techniques to the traditional and invasive technique of squeezes are presented alongside with specialized developed processing methods, aiming to help the epigraphists to reveal and analyse weathered letters in ancient Greek inscriptions carved in masonry or marble. The resulting 3D model would serve as a detailed basis for the epigraphists to try to decipher the inscription. The data were collected by using a Structured Light scanner. The creation of the final accurate three dimensional model is a complicated procedure requiring large computation cost and human effort. It includes the collection of geometric data in limited space and time, the creation of the surface, the noise filtering and the merging of individual surfaces. The use of structured light scanners is time consuming and requires costly hardware and software. Therefore an alternative methodology for collecting 3D data of the inscriptions was also implemented for reasons of comparison. Hence, image sequences from varying distances were collected using a calibrated DSLR camera aiming to reconstruct the 3D scene through SfM techniques in order to evaluate the efficiency and the level of precision and detail of the obtained reconstructed inscriptions. Problems in the acquisition processes as well as difficulties in the alignment step and mesh optimization are also encountered. A meta-processing framework is proposed and analysed. Finally, the results of processing and analysis and the different 3D models are critically inspected and then evaluated by a specialist in terms of accuracy, quality and detail of the model and the capability of revealing damaged and ”hidden” letters.

  20. Synchrotron scanning reveals amphibious ecomorphology in a new clade of bird-like dinosaurs

    Science.gov (United States)

    Cau, Andrea; Beyrand, Vincent; Voeten, Dennis F. A. E.; Fernandez, Vincent; Tafforeau, Paul; Stein, Koen; Barsbold, Rinchen; Tsogtbaatar, Khishigjav; Currie, Philip J.; Godefroit, Pascal

    2017-12-01

    Maniraptora includes birds and their closest relatives among theropod dinosaurs. During the Cretaceous period, several maniraptoran lineages diverged from the ancestral coelurosaurian bauplan and evolved novel ecomorphologies, including active flight, gigantism, cursoriality and herbivory. Propagation X-ray phase-contrast synchrotron microtomography of a well-preserved maniraptoran from Mongolia, still partially embedded in the rock matrix, revealed a mosaic of features, most of them absent among non-avian maniraptorans but shared by reptilian and avian groups with aquatic or semiaquatic ecologies. This new theropod, Halszkaraptor escuilliei gen. et sp. nov., is related to other enigmatic Late Cretaceous maniraptorans from Mongolia in a novel clade at the root of Dromaeosauridae. This lineage adds an amphibious ecomorphology to those evolved by maniraptorans: it acquired a predatory mode that relied mainly on neck hyperelongation for food procurement, it coupled the obligatory bipedalism of theropods with forelimb proportions that may support a swimming function, and it developed postural adaptations convergent with short-tailed birds.

  1. High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model.

    Directory of Open Access Journals (Sweden)

    Chiao-Ling Lo

    2016-08-01

    Full Text Available Investigations on the influence of nature vs. nurture on Alcoholism (Alcohol Use Disorder in human have yet to provide a clear view on potential genomic etiologies. To address this issue, we sequenced a replicated animal model system bidirectionally-selected for alcohol preference (AP. This model is uniquely suited to map genetic effects with high reproducibility, and resolution. The origin of the rat lines (an 8-way cross resulted in small haplotype blocks (HB with a corresponding high level of resolution. We sequenced DNAs from 40 samples (10 per line of each replicate to determine allele frequencies and HB. We achieved ~46X coverage per line and replicate. Excessive differentiation in the genomic architecture between lines, across replicates, termed signatures of selection (SS, were classified according to gene and region. We identified SS in 930 genes associated with AP. The majority (50% of the SS were confined to single gene regions, the greatest numbers of which were in promoters (284 and intronic regions (169 with the least in exon's (4, suggesting that differences in AP were primarily due to alterations in regulatory regions. We confirmed previously identified genes and found many new genes associated with AP. Of those newly identified genes, several demonstrated neuronal function involved in synaptic memory and reward behavior, e.g. ion channels (Kcnf1, Kcnn3, Scn5a, excitatory receptors (Grin2a, Gria3, Grip1, neurotransmitters (Pomc, and synapses (Snap29. This study not only reveals the polygenic architecture of AP, but also emphasizes the importance of regulatory elements, consistent with other complex traits.

  2. High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model.

    Science.gov (United States)

    Lo, Chiao-Ling; Lossie, Amy C; Liang, Tiebing; Liu, Yunlong; Xuei, Xiaoling; Lumeng, Lawrence; Zhou, Feng C; Muir, William M

    2016-08-01

    Investigations on the influence of nature vs. nurture on Alcoholism (Alcohol Use Disorder) in human have yet to provide a clear view on potential genomic etiologies. To address this issue, we sequenced a replicated animal model system bidirectionally-selected for alcohol preference (AP). This model is uniquely suited to map genetic effects with high reproducibility, and resolution. The origin of the rat lines (an 8-way cross) resulted in small haplotype blocks (HB) with a corresponding high level of resolution. We sequenced DNAs from 40 samples (10 per line of each replicate) to determine allele frequencies and HB. We achieved ~46X coverage per line and replicate. Excessive differentiation in the genomic architecture between lines, across replicates, termed signatures of selection (SS), were classified according to gene and region. We identified SS in 930 genes associated with AP. The majority (50%) of the SS were confined to single gene regions, the greatest numbers of which were in promoters (284) and intronic regions (169) with the least in exon's (4), suggesting that differences in AP were primarily due to alterations in regulatory regions. We confirmed previously identified genes and found many new genes associated with AP. Of those newly identified genes, several demonstrated neuronal function involved in synaptic memory and reward behavior, e.g. ion channels (Kcnf1, Kcnn3, Scn5a), excitatory receptors (Grin2a, Gria3, Grip1), neurotransmitters (Pomc), and synapses (Snap29). This study not only reveals the polygenic architecture of AP, but also emphasizes the importance of regulatory elements, consistent with other complex traits.

  3. Metasomatic Diamond Formation revealed by X-Ray CT Scanning of Diamondiferous Eclogites from Southern Africa

    Science.gov (United States)

    Richardson, S. H.; Kahle, R. L.; Shaw-Kahle, B.; Gurney, J. J.; du Plessis, A.

    2014-12-01

    In this study, a private collection of diamondiferous eclogite xenoliths has been made available for non-destructive investigation. All samples have at least one diamond visible. The samples are predominantly sourced from the Excelsior and Newlands mines (South Africa), with additional samples from Roberts Victor mine (South Africa) and Orapa (Botswana). 3D volume models of the samples were created using X-ray tomography. The 3D images reveal abundant secondary veining that is clearly younger than the eclogite. Diamonds are located in fluid pathways and occur in both altered garnet and altered clinopyroxene. Most of the veining is unrelated to the spatial positioning of diamond in the samples. In some instances, early veining has annealed or partially annealed, suggesting a range in timing of at least some of the several metasomatic events that have affected the rock. Importantly, in the most graphic examples, a clear distinction can be seen between diamond-bearing and non-diamond-bearing veins, even where sulphide is present in abundance in the non-diamond-bearing veins. The amount of diamond detected in the xenoliths varies from a single crystal to well over 50 diamonds forming more than 9% of the rock. This extreme value contrasts with the diamond recovery from currently viable diamond mines of less than 2ppm or 0.0002%. The morphology of the diamonds includes step-faced flat-faced octahedra, single crystals and aggregates. This is particularly a feature of diamonds in the Excelsior specimens. In the samples from Newlands and Orapa, in contrast, diamond surfaces reflect resorption processes such as rounding and corrosion of the diamonds. The following conclusions can be drawn from this study: Diamonds in this collection, sourced from within the Kalahari craton, appear to have formed by a metasomatic process during which fluids infiltrated pre-existing mantle-derived eclogite; Several metasomatic events have occurred during the residence of the eclogite in the

  4. Revealing the sequence and resulting cellular morphology of receptor-ligand interactions during Plasmodium falciparum invasion of erythrocytes.

    Directory of Open Access Journals (Sweden)

    Greta E Weiss

    2015-02-01

    Full Text Available During blood stage Plasmodium falciparum infection, merozoites invade uninfected erythrocytes via a complex, multistep process involving a series of distinct receptor-ligand binding events. Understanding each element in this process increases the potential to block the parasite's life cycle via drugs or vaccines. To investigate specific receptor-ligand interactions, they were systematically blocked using a combination of genetic deletion, enzymatic receptor cleavage and inhibition of binding via antibodies, peptides and small molecules, and the resulting temporal changes in invasion and morphological effects on erythrocytes were filmed using live cell imaging. Analysis of the videos have shown receptor-ligand interactions occur in the following sequence with the following cellular morphologies; 1 an early heparin-blockable interaction which weakly deforms the erythrocyte, 2 EBA and PfRh ligands which strongly deform the erythrocyte, a process dependant on the merozoite's actin-myosin motor, 3 a PfRh5-basigin binding step which results in a pore or opening between parasite and host through which it appears small molecules and possibly invasion components can flow and 4 an AMA1-RON2 interaction that mediates tight junction formation, which acts as an anchor point for internalization. In addition to enhancing general knowledge of apicomplexan biology, this work provides a rational basis to combine sequentially acting merozoite vaccine candidates in a single multi-receptor-blocking vaccine.

  5. Conformational changes and ligand recognition of Escherichia coli D-xylose binding protein revealed

    DEFF Research Database (Denmark)

    Sooriyaarachchi, Sanjeewani; Ubhayasekera, Wimal; Park, Chankyu

    2010-01-01

    . The open liganded structure shows that xylose binds first to the C-terminal domain, with only very small conformational changes resulting. After a 34° closing motion, additional interactions are formed with the N-terminal domain; changes in this domain are larger and serve to make the structure more...

  6. Mechanism of selective VEGF-A binding by neuropilin-1 reveals a basis for specific ligand inhibition.

    Directory of Open Access Journals (Sweden)

    Matthew W Parker

    Full Text Available Neuropilin (Nrp receptors function as essential cell surface receptors for the Vascular Endothelial Growth Factor (VEGF family of proangiogenic cytokines and the semaphorin 3 (Sema3 family of axon guidance molecules. There are two Nrp homologues, Nrp1 and Nrp2, which bind to both overlapping and distinct members of the VEGF and Sema3 family of molecules. Nrp1 specifically binds the VEGF-A(164/5 isoform, which is essential for developmental angiogenesis. We demonstrate that VEGF-A specific binding is governed by Nrp1 residues in the b1 coagulation factor domain surrounding the invariant Nrp C-terminal arginine binding pocket. Further, we show that Sema3F does not display the Nrp-specific binding to the b1 domain seen with VEGF-A. Engineered soluble Nrp receptor fragments that selectively sequester ligands from the active signaling complex are an attractive modality for selectively blocking the angiogenic and chemorepulsive functions of Nrp ligands. Utilizing the information on Nrp ligand binding specificity, we demonstrate Nrp constructs that specifically sequester Sema3 in the presence of VEGF-A. This establishes that unique mechanisms are used by Nrp receptors to mediate specific ligand binding and that these differences can be exploited to engineer soluble Nrp receptors with specificity for Sema3.

  7. Crystal structure of an ACh-binding protein reveals the ligand-binding domain of nicotinic receptors

    NARCIS (Netherlands)

    Brejc, K.; Dijk, van W.J.; Klaassen, R.V.; Schuurmans, M.; Oost, van der J.; Smit, A.B.; Sixma, T.K.

    2001-01-01

    Pentameric ligand gated ion-channels, or Cys-loop receptors, mediate rapid chemical transmission of signals. This superfamily of allosteric transmembrane proteins includes the nicotinic acetylcholine (nAChR), serotonin 5-HT3, -aminobutyric-acid (GABAA and GABAC) and glycine receptors. Biochemical

  8. Revealing the Sequence and Resulting Cellular Morphology of Receptor-Ligand Interactions during Plasmodium falciparum Invasion of Erythrocytes

    Science.gov (United States)

    Weiss, Greta E.; Gilson, Paul R.; Taechalertpaisarn, Tana; Tham, Wai-Hong; de Jong, Nienke W. M.; Harvey, Katherine L.; Fowkes, Freya J. I.; Barlow, Paul N.; Rayner, Julian C.; Wright, Gavin J.; Cowman, Alan F.; Crabb, Brendan S.

    2015-01-01

    During blood stage Plasmodium falciparum infection, merozoites invade uninfected erythrocytes via a complex, multistep process involving a series of distinct receptor-ligand binding events. Understanding each element in this process increases the potential to block the parasite’s life cycle via drugs or vaccines. To investigate specific receptor-ligand interactions, they were systematically blocked using a combination of genetic deletion, enzymatic receptor cleavage and inhibition of binding via antibodies, peptides and small molecules, and the resulting temporal changes in invasion and morphological effects on erythrocytes were filmed using live cell imaging. Analysis of the videos have shown receptor-ligand interactions occur in the following sequence with the following cellular morphologies; 1) an early heparin-blockable interaction which weakly deforms the erythrocyte, 2) EBA and PfRh ligands which strongly deform the erythrocyte, a process dependant on the merozoite’s actin-myosin motor, 3) a PfRh5-basigin binding step which results in a pore or opening between parasite and host through which it appears small molecules and possibly invasion components can flow and 4) an AMA1–RON2 interaction that mediates tight junction formation, which acts as an anchor point for internalization. In addition to enhancing general knowledge of apicomplexan biology, this work provides a rational basis to combine sequentially acting merozoite vaccine candidates in a single multi-receptor-blocking vaccine. PMID:25723550

  9. Crystal structures of manganese- and cobalt-substituted myoglobin in complex with NO and nitrite reveal unusual ligand conformations.

    Science.gov (United States)

    Zahran, Zaki N; Chooback, Lilian; Copeland, Daniel M; West, Ann H; Richter-Addo, George B

    2008-02-01

    Nitrite is now recognized as a storage pool of bioactive nitric oxide (NO). Hemoglobin (Hb) and myoglobin (Mb) convert, under certain conditions, nitrite to NO. This newly discovered nitrite reductase activity of Hb and Mb provides an attractive alternative to mammalian NO synthesis from the NO synthase pathway that requires dioxygen. We recently reported the X-ray crystal structure of the nitrite adduct of ferric horse heart Mb, and showed that the nitrite ligand binds in an unprecedented O-binding (nitrito) mode to the d(5) ferric center in Mb(III)(ONO) [D.M. Copeland, A. Soares, A.H. West, G.B. Richter-Addo, J. Inorg. Biochem. 100 (2006) 1413-1425]. We also showed that the distal pocket in Mb allows for different conformations of the NO ligand (120 degrees and 144 degrees ) in Mb(II)NO depending on the mode of preparation of the compound. In this article, we report the crystal structures of the nitrite and NO adducts of manganese-substituted hh Mb (a d(4) system) and of the nitrite adduct of cobalt-substituted hh Mb (a d(6) system). We show that the distal His64 residue directs the nitrite ligand towards the rare nitrito O-binding mode in Mn(III)Mb and Co(III)Mb. We also report that the distal pocket residues allow a stabilization of an unprecendented bent MnNO moiety in Mn(II)MbNO. These crystal structural data, when combined with the data for the aquo, methanol, and azide MnMb derivatives, provide information on the role of distal pocket residues in the observed binding modes of nitrite and NO ligands to wild-type and metal-substituted Mb.

  10. Ligand-Directed Functional Selectivity at the Mu Opioid Receptor Revealed by Label-Free Integrative Pharmacology On-Target

    Science.gov (United States)

    Morse, Megan; Tran, Elizabeth; Sun, Haiyan; Levenson, Robert; Fang, Ye

    2011-01-01

    Development of new opioid drugs that provide analgesia without producing dependence is important for pain treatment. Opioid agonist drugs exert their analgesia effects primarily by acting at the mu opioid receptor (MOR) sites. High-resolution differentiation of opioid ligands is crucial for the development of new lead drug candidates with better tolerance profiles. Here, we use a label-free integrative pharmacology on-target (iPOT) approach to characterize the functional selectivity of a library of known opioid ligands for the MOR. This approach is based on the ability to detect dynamic mass redistribution (DMR) arising from the activation of the MOR in living cells. DMR assays were performed in HEK-MOR cells with and without preconditioning with probe molecules using label-free resonant waveguide grating biosensors, wherein the probe molecules were used to modify the activity of specific signaling proteins downstream the MOR. DMR signals obtained were then translated into high resolution heat maps using similarity analysis based on a numerical matrix of DMR parameters. Our data indicate that the iPOT approach clearly differentiates functional selectivity for distinct MOR signaling pathways among different opioid ligands, thus opening new avenues to discover and quantify the functional selectivity of currently used and novel opioid receptor drugs. PMID:22003401

  11. Thermal stability and molecular microstructure of heat-induced cereal grains, revealed with Raman molecular microspectroscopy and differential scanning calorimetry.

    Science.gov (United States)

    Khan, Md Majibur Rahman; Yu, Peiqiang

    2013-07-03

    The objectives of the present study were to use Raman molecular microspectroscopy and differential scanning calorimetry (DSC) to reveal molecular thermal stability and thermal degradation behavior of heat-induced cereal grains and reveal the molecular chemistry of the protein structures of cereal grain tissues affected by heat processing and to quantify the protein secondary structures using multicomponent peak modeling Gaussian and Lorentzian methods. Hierarchical cluster analysis (CLA) and principal components analysis (PCA) were also conducted to identify molecular differences in the Raman spectra. Three cereal grain seeds, wheat, triticale, and corn, were used as the model for feed protein in the experiment. The specimens were autoclaved (moist heating) and dry-heated (roasted) at 121 °C for 80 min, respectively. Raman spectroscopy results revealed that there are marked differences in the secondary structures of the proteins subjected to various heating treatments of different cereals. The sensitivity of cereals to moist heating was much higher than the sensitivity to dry heating. The multivariate analyses (CLA and PCA) showed that heat treatment was significantly isolated between the different Raman raw spectra. The DSC study revealed that the thermal degradation behavior of cereals was significantly changed after moist- and dry-heat treatments. The position of the major endothermic peak of dry-heated cereals shifted toward a higher temperature, from 131.7 to 134.0 °C, suggesting the high thermal stability of dry-heated cereals. In contrast, the endothermic peak position was slightly decreased to 132.1 °C in the case of moist autoclaved heating. The digestive behavior and nutritive value of rumen-undegradable protein in animals may be related to the changes of the protein secondary molecular structure and thermal stability of the cereal grain materials, which is attributed by Raman microspectroscopy and DSC endotherm profiles.

  12. Structures of SdrD from Staphylococcus aureus reveal the molecular mechanism of how the cell surface receptors recognize their ligands.

    Science.gov (United States)

    Wang, Xiao; Ge, Jingpeng; Liu, Bao; Hu, Yulin; Yang, Maojun

    2013-04-01

    Staphylococcus aureus is the most important Gram-positive colonizer of human skin and nasal passage, causing high morbidity and mortality. SD-repeat containing protein D (SdrD), an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules) family surface protein, plays an important role in S. aureus adhesion and pathogenesis, while its binding target and molecular mechanism remain largely unknown. Here we solved the crystal structures of SdrD N2-N3 domain and N2-N3-B1 domain. Through structural analysis and comparisons, we characterized the ligand binding site of SdrD, and proposed a featured sequence motif of its potential ligands. In addition, the structures revealed for the first time the interactions between B1 domain and N2-N3 domain among B domain-containing MSCRAMMs. Our results may help in understanding the roles SdrD plays in S. aureus adhesion and shed light on the development of novel antibiotics.

  13. Retinal damage in chloroquine maculopathy, revealed by high resolution imaging: a case report utilizing adaptive optics scanning laser ophthalmoscopy.

    Science.gov (United States)

    Bae, Eun Jin; Kim, Kyoung Rae; Tsang, Stephen H; Park, Sung Pyo; Chang, Stanley

    2014-02-01

    A 53-year-old Asian woman was treated with hydroxychloroquine and chloroquine for lupus erythematosus. Within a few years, she noticed circle-shaped shadows in her central vision. Upon examination, the patient's visual acuity was 20 / 25 in both eyes. Humphrey visual field (HVF) testing revealed a central visual defect, and fundoscopy showed a ring-shaped area of parafoveal retinal pigment epithelium depigmentation. Fundus autofluorescence imaging showed a hypofluorescent lesion consistent with bull's eye retinopathy. Adaptive optics scanning laser ophthalmoscope (AO-SLO) revealed patch cone mosaic lesions, in which cones were missing or lost. In addition, the remaining cones consisted of asymmetrical shapes and sizes that varied in brightness. Unlike previous studies employing deformable mirrors for wavefront aberration correction, our AO-SLO approach utilized dual liquid crystal on silicon spatial light modulators. Thus, by using AO-SLO, we were able to create a photographic montage consisting of high quality images. Disrupted cone AO-SLO images were matched with visual field test results and functional deficits were associated with a precise location on the montage, which allowed correlation of histological findings with functional changes determined by HVF. We also investigated whether adaptive optics imaging was more sensitive to anatomical changes compared with spectral-domain optical coherence tomography.

  14. Two crystal structures of dihydrofolate reductase-thymidylate synthase from Cryptosporidium hominis reveal protein–ligand interactions including a structural basis for observed antifolate resistance

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Amy C., E-mail: aca@dartmouth.edu [Dartmouth College, Department of Chemistry, Burke Laboratories, Hanover, NH 03755 (United States)

    2005-03-01

    An analysis of the protein–ligand interactions in two crystal structures of DHFR-TS from C. hominis reveals a possible structural basis for observed antifolate resistance in C. hominis DHFR. A comparison with the structure of human DHFR reveals residue substitutions that may be exploited for the design of species-selective inhibitors. Cryptosporidium hominis is a protozoan parasite that causes acute gastrointestinal illness. There are no effective therapies for cryptosporidiosis, highlighting the need for new drug-lead discovery. An analysis of the protein–ligand interactions in two crystal structures of dihydrofolate reductase-thymidylate synthase (DHFR-TS) from C. hominis, determined at 2.8 and 2.87 Å resolution, reveals that the interactions of residues Ile29, Thr58 and Cys113 in the active site of C. hominis DHFR provide a possible structural basis for the observed antifolate resistance. A comparison with the structure of human DHFR reveals active-site differences that may be exploited for the design of species-selective inhibitors.

  15. Biochemical and pharmacological characterization of three opioid-nociceptin hybrid peptide ligands reveals substantially differing modes of their actions.

    Science.gov (United States)

    Erdei, Anna I; Borbély, Adina; Magyar, Anna; Taricska, Nóra; Perczel, András; Zsíros, Ottó; Garab, Győző; Szűcs, Edina; Ötvös, Ferenc; Zádor, Ferenc; Balogh, Mihály; Al-Khrasani, Mahmoud; Benyhe, Sándor

    2018-01-01

    In an attempt to design opioid-nociceptin hybrid peptides, three novel bivalent ligands, H-YGGFGGGRYYRIK-NH 2 , H-YGGFRYYRIK-NH 2 and Ac-RYYRIKGGGYGGFL-OH were synthesized and studied by biochemical, pharmacological, biophysical and molecular modelling tools. These chimeric molecules consist of YGGF sequence, a crucial motif in the N-terminus of natural opioid peptides, and Ac-RYYRIK-NH 2, which was isolated from a combinatorial peptide library as an antagonist or partial agonist that inhibits the biological activity of the endogenously occurring heptadecapeptide nociceptin. Solution structures for the peptides were studied by analysing their circular dichroism spectra. Receptor binding affinities were measured by equilibrium competition experiments using four highly selective radioligands. G-protein activating properties of the multitarget peptides were estimated in [ 35 S]GTPγS binding tests. The three compounds were also measured in electrically stimulated mouse vas deferens (MVD) bioassay. H-YGGFGGGRYYRIK-NH 2 (BA55), carrying N-terminal opioid and C-terminal nociceptin-like sequences interconnected with GGG tripeptide spacer displayed a tendency of having either unordered or β-sheet structures, was moderately potent in MVD and possessed a NOP/KOP receptor preference. A similar peptide without spacer H-YGGFRYYRIK-NH 2 (BA62) exhibited the weakest effect in MVD, more α-helical periodicity was present in its structure and it exhibited the most efficacious agonist actions in the G-protein stimulation assays. The third hybrid peptide Ac-RYYRIKGGGYGGFL-OH (BA61) unexpectedly displayed opioid receptor affinities, because the opioid message motif is hidden within the C-terminus. The designed chimeric peptide ligands presented in this study accommodate well into a group of multitarget opioid compounds that include opioid-non-opioid peptide dimer analogues, dual non-peptide dimers and mixed peptide- non-peptide bifunctional ligands. Copyright © 2017 Elsevier Inc

  16. Clonal analysis of kit ligand a functional expression reveals lineage-specific competence to promote melanocyte rescue in the mutant regenerating caudal fin.

    Directory of Open Access Journals (Sweden)

    Robert C Tryon

    Full Text Available The study of regeneration in an in vivo vertebrate system has the potential to reveal targetable genes and pathways that could improve our ability to heal and repair damaged tissue. We have developed a system for clonal labeling of discrete cell lineages and independently inducing gene expression under control of the heat shock promoter in the zebrafish caudal fin. Consequently we are able to test the affects of overexpressing a single gene in the context of regeneration within each of the nine different cell lineage classes that comprise the caudal fin. This can test which lineage is necessary or sufficient to provide gene function. As a first example to demonstrate this approach, we explored which lineages were competent to functionally express the kit ligand a protein as assessed by the local complementation of the mutation in the sparse-like (kitlgatc244b background. We show that dermal fibroblast expression of kit ligand a robustly supports the rescue of melanocytes in the regenerating caudal fin. kit ligand a expression from skin and osteoblasts results in more modest and variable rescue of melanocytes, while lateral line expression was unable to complement the mutation.

  17. Micro-CT scan reveals an unexpected high-volume and interconnected pore network in a Cretaceous Sanagasta dinosaur eggshell.

    Science.gov (United States)

    Hechenleitner, E Martín; Grellet-Tinner, Gerald; Foley, Matthew; Fiorelli, Lucas E; Thompson, Michael B

    2016-03-01

    The Cretaceous Sanagasta neosauropod nesting site (La Rioja, Argentina) was the first confirmed instance of extinct dinosaurs using geothermal-generated heat to incubate their eggs. The nesting strategy and hydrothermal activities at this site led to the conclusion that the surprisingly 7 mm thick-shelled eggs were adapted to harsh hydrothermal microenvironments. We used micro-CT scans in this study to obtain the first three-dimensional microcharacterization of these eggshells. Micro-CT-based analyses provide a robust assessment of gas conductance in fossil dinosaur eggshells with complex pore canal systems, allowing calculation, for the first time, of the shell conductance through its thickness. This novel approach suggests that the shell conductance could have risen during incubation to seven times more than previously estimated as the eggshell erodes. In addition, micro-CT observations reveal that the constant widening and branching of pore canals form a complex funnel-like pore canal system. Furthermore, the high density of pore canals and the presence of a lateral canal network in the shell reduce the risks of pore obstruction during the extended incubation of these eggs in a relatively highly humid and muddy nesting environment. © 2016 The Author(s).

  18. Micro-CT scan reveals an unexpected high-volume and interconnected pore network in a Cretaceous Sanagasta dinosaur eggshell

    Science.gov (United States)

    Grellet-Tinner, Gerald; Foley, Matthew; Thompson, Michael B.

    2016-01-01

    The Cretaceous Sanagasta neosauropod nesting site (La Rioja, Argentina) was the first confirmed instance of extinct dinosaurs using geothermal-generated heat to incubate their eggs. The nesting strategy and hydrothermal activities at this site led to the conclusion that the surprisingly 7 mm thick-shelled eggs were adapted to harsh hydrothermal microenvironments. We used micro-CT scans in this study to obtain the first three-dimensional microcharacterization of these eggshells. Micro-CT-based analyses provide a robust assessment of gas conductance in fossil dinosaur eggshells with complex pore canal systems, allowing calculation, for the first time, of the shell conductance through its thickness. This novel approach suggests that the shell conductance could have risen during incubation to seven times more than previously estimated as the eggshell erodes. In addition, micro-CT observations reveal that the constant widening and branching of pore canals form a complex funnel-like pore canal system. Furthermore, the high density of pore canals and the presence of a lateral canal network in the shell reduce the risks of pore obstruction during the extended incubation of these eggs in a relatively highly humid and muddy nesting environment. PMID:27009182

  19. Tryptophan Scanning Reveals Dense Packing of Connexin Transmembrane Domains in Gap Junction Channels Composed of Connexin32*

    Science.gov (United States)

    Brennan, Matthew J.; Karcz, Jennifer; Vaughn, Nicholas R.; Woolwine-Cunningham, Yvonne; DePriest, Adam D.; Escalona, Yerko; Perez-Acle, Tomas; Skerrett, I. Martha

    2015-01-01

    Tryptophan was substituted for residues in all four transmembrane domains of connexin32. Function was assayed using dual cell two-electrode voltage clamp after expression in Xenopus oocytes. Tryptophan substitution was poorly tolerated in all domains, with the greatest impact in TM1 and TM4. For instance, in TM1, 15 substitutions were made, six abolished coupling and five others significantly reduced function. Only TM2 and TM3 included a distinct helical face that lacked sensitivity to tryptophan substitution. Results were visualized on a comparative model of Cx32 hemichannel. In this model, a region midway through the membrane appears highly sensitive to tryptophan substitution and includes residues Arg-32, Ile-33, Met-34, and Val-35. In the modeled channel, pore-facing regions of TM1 and TM2 were highly sensitive to tryptophan substitution, whereas the lipid-facing regions of TM3 and TM4 were variably tolerant. Residues facing a putative intracellular water pocket (the IC pocket) were also highly sensitive to tryptophan substitution. Although future studies will be required to separate trafficking-defective mutants from those that alter channel function, a subset of interactions important for voltage gating was identified. Interactions important for voltage gating occurred mainly in the mid-region of the channel and focused on TM1. To determine whether results could be extrapolated to other connexins, TM1 of Cx43 was scanned revealing similar but not identical sensitivity to TM1 of Cx32. PMID:25969535

  20. The identification of the endogenous ligands of natural killer T cells reveals the presence of mammalian α-linked glycosylceramides.

    Science.gov (United States)

    Kain, Lisa; Webb, Bill; Anderson, Brian L; Deng, Shenglou; Holt, Marie; Costanzo, Anne; Constanzo, Anne; Zhao, Meng; Self, Kevin; Teyton, Anais; Everett, Chris; Kronenberg, Mitchell; Zajonc, Dirk M; Bendelac, Albert; Savage, Paul B; Teyton, Luc

    2014-10-16

    Glycosylceramides in mammalian species are thought to be present in the form of β-anomers. This conclusion was reinforced by the identification of only one glucosylceramide and one galactosylceramide synthase, both β-transferases, in mammalian genomes. Thus, the possibility that small amounts of α-anomers could be produced by an alternative enzymatic pathway, by an unfaithful enzyme, or spontaneously in unusual cellular compartments has not been examined in detail. We approached the question by taking advantage of the exquisite specificity of T and B lymphocytes and combined it with the specificity of catabolic enzymes of the sphingolipid pathway. Here, we demonstrate that mammalian immune cells produce constitutively very small quantities of α-glycosylceramides, which are the major endogenous ligands of natural killer T cells. Catabolic enzymes of the ceramide and glycolipid pathway tightly control the amount of these α-glycosylceramides. The exploitation of this pathway to manipulate the immune response will create new therapeutic opportunities.

  1. Anti-analgesic effect of the mu/delta opioid receptor heteromer revealed by ligand-biased antagonism.

    Directory of Open Access Journals (Sweden)

    Laura Milan-Lobo

    Full Text Available Delta (DOR and mu opioid receptors (MOR can complex as heteromers, conferring functional properties in agonist binding, signaling and trafficking that can differ markedly from their homomeric counterparts. Because of these differences, DOR/MOR heteromers may be a novel therapeutic target in the treatment of pain. However, there are currently no ligands selective for DOR/MOR heteromers, and, consequently, their role in nociception remains unknown. In this study, we used a pharmacological opioid cocktail that selectively activates and stabilizes the DOR/MOR heteromer at the cell surface by blocking its endocytosis to assess its role in antinociception. We found that mice treated chronically with this drug cocktail showed a significant right shift in the ED50 for opioid-mediated analgesia, while mice treated with a drug that promotes degradation of the heteromer did not. Furthermore, promoting degradation of the DOR/MOR heteromer after the right shift in the ED50 had occurred, or blocking signal transduction from the stabilized DOR/MOR heteromer, shifted the ED50 for analgesia back to the left. Taken together, these data suggest an anti-analgesic role for the DOR/MOR heteromer in pain. In conclusion, antagonists selective for DOR/MOR heteromer could provide an avenue for alleviating reduced analgesic response during chronic pain treatment.

  2. Structure analysis of the IL-5 ligand-receptor complex reveals a wrench-like architecture for IL-5Rα.

    Science.gov (United States)

    Patino, Edwin; Kotzsch, Alexander; Saremba, Stefan; Nickel, Joachim; Schmitz, Werner; Sebald, Walter; Mueller, Thomas D

    2011-12-07

    Interleukin-5 (IL-5) is the key mediator for the function of eosinophil granulocytes, whose deregulation is characteristic of hypereosinophilic diseases and presumably contributes to allergic asthma. IL-5 signaling involves two transmembrane receptors, IL-5Rα and the common β chain, which upon formation of the ternary complex activate the JAK/STAT signaling cascade. To investigate the mechanism underlying ligand-receptor recognition, we determined the structure of IL-5 bound to the extracellular domain of IL-5Rα. IL-5 makes contact with all three fibronectin III-like domains of IL-5Rα, with the receptor architecture resembling a wrench. Mutagenesis data provide evidence that this wrench-like architecture is likely preformed. The structure demonstrates that for steric reasons, homodimeric IL-5 can bind only one receptor molecule, even though two equivalent receptor-binding sites exist. In regard to strong efforts being made to develop IL-5 antagonists for treating asthma and hypereosinophilic diseases, the advances in molecular understanding provided by this structure are of greatest value. Copyright © 2011 Elsevier Ltd. All rights reserved.

  3. A disulfide-stabilized conformer of methionine synthase reveals an unexpected role for the histidine ligand of the cobalamin cofactor

    Energy Technology Data Exchange (ETDEWEB)

    Datta, Supratim; Koutmos, Markos; Pattridge, Katherine A.; Ludwig, Martha L.; Matthews, Rowena G. (Michigan)

    2008-07-08

    B{sub 12}-dependent methionine synthase (MetH) from Escherichia coli is a large modular protein that is alternately methylated by methyltetrahydrofolate to form methylcobalamin and demethylated by homocysteine to form cob(I)alamin. Major domain rearrangements are required to allow cobalamin to react with three different substrates: homocysteine, methyltetrahydrofolate, and S-adenosyl-l-methionine (AdoMet). These same rearrangements appear to preclude crystallization of the wild-type enzyme. Disulfide cross-linking was used to lock a C-terminal fragment of the enzyme into a unique conformation. Cysteine point mutations were introduced at Ile-690 and Gly-743. These cysteine residues span the cap and the cobalamin-binding module and form a cross-link that reduces the conformational space accessed by the enzyme, facilitating protein crystallization. Here, we describe an x-ray structure of the mutant fragment in the reactivation conformation; this conformation enables the transfer of a methyl group from AdoMet to the cobalamin cofactor. In the structure, the axial ligand to the cobalamin, His-759, dissociates from the cobalamin and forms intermodular contacts with residues in the AdoMet-binding module. This unanticipated intermodular interaction is expected to play a major role in controlling the distribution of conformers required for the catalytic and the reactivation cycles of the enzyme.

  4. Ligand orientation in a membrane-embedded receptor site revealed by solid-state NMR with paramagnetic relaxation enhancement.

    Science.gov (United States)

    Whittaker, Christopher A P; Patching, Simon G; Esmann, Mikael; Middleton, David A

    2015-03-07

    NMR relaxation enhancement by paramagnetic metals provides powerful restraints on the three-dimensional structures of proteins in solution, and this approach has recently been utilized in several NMR structural investigations of proteins in the solid-state. Here we utilize paramagnetic relaxation enhancement (PRE) by Mn(2+) with cross-polarization magic-angle spinning (CP-MAS) solid-state NMR to investigate the interaction of a membrane-embedded protein the Na,K-ATPase (NKA) with a cardiotonic steroid inhibitor. The inhibitor, a diacetonide derivate of the cardiac glycoside ouabain, with (13)C labelled acetonide groups in the rhamnose sugar and steroid moieties ([(13)C2]ODA), is 1000-fold less potent than the parent compound. It is shown that the (13)C CP-MAS solid-state NMR spectra of the NKA-[(13)C2]ODA complex exhibit distinct signals for the two (13)C labels of the inhibitor when bound to the ouabain site of membrane-embedded NKA. Recent crystal structures of NKA indicate that the catalytic α-subunit binds a single Mn(2+) in a transmembrane site close to the high-affinity ouabain site. Here, complexation of NKA with Mn(2+) broadens the resonance line from the rhamnose group substantially more than the steroid peak, indicating that the rhamnose group is closer to the Mn(2+) site than is the steroid group. These observations agree with computational molecular docking simulations and are consistent with ODA adopting an inverted orientation compared to ouabain in the cardiac glycoside site, with the modified rhamnose group drawn toward the transmembrane centre of the protein. This work demonstrates that PRE can provide unique information on the positions and orientations of ligands within their binding pockets of transmembrane proteins.

  5. Selective engineering of oxygen-containing functional groups using the alkyl ligand oleylamine for revealing the luminescence mechanism of graphene oxide quantum dots.

    Science.gov (United States)

    Jang, Min-Ho; Yang, Hyunseung; Chang, Yun Hee; Park, Hyun-Chul; Park, Hyeonjung; Cho, Han Hee; Kim, Bumjoon J; Kim, Yong-Hyun; Cho, Yong-Hoon

    2017-10-13

    Oxygen-containing functional groups such as epoxy, hydroxyl, carboxylic, and carboxyl groups have a great influence on the luminescence properties of graphene oxide quantum dots (GOQDs). Understanding their roles is essential for the design and optimization of GOQD performance. Herein, we investigate the effect of epoxide functional groups in GOQDs on the luminescence mechanism through passivation of the epoxide functional groups using the alkyl ligand oleylamine. Luminescence in the as-synthesized GOQDs has two separate origins: intrinsic states derived from localized sp(2) carbon subdomains and extrinsic states formed by oxygen-functional groups. When the oleylamine ligand is conjugated on the GOQDs, intrinsic PL emission from the localized sp(2) carbon subdomains decreases. This is discussed in detail, based on optical characterization and first-principles density functional theory calculations, which reveal that the role of the epoxide functional groups is to form localized sp(2) carbon subdomains emitting intrinsic PL. To the best of our knowledge, this is the first investigation of the role of epoxide functional groups on the luminescence mechanism in GOQDs.

  6. Structural basis for functional selectivity and ligand recognition revealed by crystal structures of human secreted phospholipase A2 group IIE.

    Science.gov (United States)

    Hou, Shulin; Xu, Tingting; Xu, Jinxin; Qu, Linbing; Xu, Yong; Chen, Ling; Liu, Jinsong

    2017-09-07

    Secreted phospholipases A2s (sPLA2s) are involved in various pathological conditions such as rheumatoid arthritis and cardiovascular disease. Many inhibitors were developed and studied in clinical trials, but none have reached the market yet. This failure may be attributed to the lack of subtype selectivity for these inhibitors. Therefore, more structural information for subtype sPLA2 is needed to guide the selective inhibitor development. In this study, the crystal structure of human sPLA2 Group IIE (hGIIE), coupled with mutagenesis experiments, proved that the flexible second calcium binding site and residue Asn21 in hGIIE are essential to its enzymatic activity. Five inhibitor bound hGIIE complex structures revealed the key residues (Asn21 and Gly6) of hGIIE that are responsible for interacting with inhibitors, and illustrated the difference in the inhibitor binding pocket with other sPLA2s. This will facilitate the structure-based design of sPLA2's selective inhibitors.

  7. Structures of Rhodopsin Kinase in Different Ligand States Reveal Key Elements Involved in G Protein-coupled Receptor Kinase Activation

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Puja; Wang, Benlian; Maeda, Tadao; Palczewski, Krzysztof; Tesmer, John J.G. (Case Western); (Michigan)

    2008-10-08

    G protein-coupled receptor (GPCR) kinases (GRKs) phosphorylate activated heptahelical receptors, leading to their uncoupling from G proteins. Here we report six crystal structures of rhodopsin kinase (GRK1), revealing not only three distinct nucleotide-binding states of a GRK but also two key structural elements believed to be involved in the recognition of activated GPCRs. The first is the C-terminal extension of the kinase domain, which was observed in all nucleotide-bound GRK1 structures. The second is residues 5-30 of the N terminus, observed in one of the GRK1{center_dot}(Mg{sup 2+}){sub 2} {center_dot}ATP structures. The N terminus was also clearly phosphorylated, leading to the identification of two novel phosphorylation sites by mass spectral analysis. Co-localization of the N terminus and the C-terminal extension near the hinge of the kinase domain suggests that activated GPCRs stimulate kinase activity by binding to this region to facilitate full closure of the kinase domain.

  8. Standing-wave-excited multiplanar fluorescence in a laser scanning microscope reveals 3D information on red blood cells

    CERN Document Server

    Amor, Rumelo; Amos, William Bradshaw; McConnell, Gail

    2014-01-01

    Standing-wave excitation of fluorescence is highly desirable in optical microscopy because it improves the axial resolution. We demonstrate here that multiplanar excitation of fluorescence by a standing wave can be produced in a single-spot laser scanning microscope by placing a plane reflector close to the specimen. We report that the relative intensities in each plane of excitation depend on the Stokes shift of the fluorochrome. We show by the use of dyes specific for the cell membrane how standing-wave excitation can be exploited to generate precise contour maps of the surface membrane of red blood cells, with an axial resolution of ~90 nm. The method, which requires only the addition of a plane mirror to an existing confocal laser scanning microscope, may well prove useful in studying diseases which involve the red cell membrane, such as malaria.

  9. Helium ion microscopy and ultra-high-resolution scanning electron microscopy analysis of membrane-extracted cells reveals novel characteristics of the cytoskeleton of Giardia intestinalis.

    Science.gov (United States)

    Gadelha, Ana Paula Rocha; Benchimol, Marlene; de Souza, Wanderley

    2015-06-01

    Giardia intestinalis presents a complex microtubular cytoskeleton formed by specialized structures, such as the adhesive disk, four pairs of flagella, the funis and the median body. The ultrastructural organization of the Giardia cytoskeleton has been analyzed using different microscopic techniques, including high-resolution scanning electron microscopy. Recent advances in scanning microscopy technology have opened a new venue for the characterization of cellular structures and include scanning probe microscopy techniques such as ultra-high-resolution scanning electron microscopy (UHRSEM) and helium ion microscopy (HIM). Here, we studied the organization of the cytoskeleton of G. intestinalis trophozoites using UHRSEM and HIM in membrane-extracted cells. The results revealed a number of new cytoskeletal elements associated with the lateral crest and the dorsal surface of the parasite. The fine structure of the banded collar was also observed. The marginal plates were seen linked to a network of filaments, which were continuous with filaments parallel to the main cell axis. Cytoplasmic filaments that supported the internal structures were seen by the first time. Using anti-actin antibody, we observed a labeling in these filamentous structures. Taken together, these data revealed new surface characteristics of the cytoskeleton of G. intestinalis and may contribute to an improved understanding of the structural organization of trophozoites. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. AFLP genome scanning reveals divergent selection in natural populations of Liriodendron chinense (Magnoliaceae along a latitudinal transect

    Directory of Open Access Journals (Sweden)

    Aihong eYang

    2016-05-01

    Full Text Available Understanding adaptive genetic variation and its relation to environmental factors are important for understanding how plants adapt to climate change and for managing genetic resources. Genome scans for the loci exhibiting either notably high or low levels of population differentiation (outlier loci provide one means of identifying genomic regions possibly associated with convergent or divergent selection. In this study, we combined AFLP genome scan and environmental association analysis to test for signals of natural selection in natural populations of Liriodendron chinense (Chinese Tulip Tree; Magnoliaceae along a latitudinal transect. We genotyped 276 individuals from 11 populations of L. chinense using 987 AFLP markers. Two complementary methods (Dfdist and BayeScan and association analysis between AFLP loci and climate factors were applied to detect outlier loci. Our analyses recovered both neutral and potentially adaptive genetic differentiation among populations of L. chinense. We found moderate genetic diversity within populations and high genetic differentiation among populations with reduced genetic diversity towards the periphery of the species ranges. Nine AFLP marker loci showed evidence of being outliers for population differentiation for both detection methods. Of these, six were strongly associated with at least one climate factor. Temperature, precipitation and radiation were found to be three important factors influencing local adaptation of L. chinense. The outlier AFLP loci are likely not the target of natural selection, but the neighboring genes of these loci might be involved in local adaptation. Hence, these candidates should be validated by further studies.

  11. Genome-wide scans reveal variants at EDAR predominantly affecting hair straightness in Han Chinese and Uyghur populations.

    Science.gov (United States)

    Wu, Sijie; Tan, Jingze; Yang, Yajun; Peng, Qianqian; Zhang, Manfei; Li, Jinxi; Lu, Dongsheng; Liu, Yu; Lou, Haiyi; Feng, Qidi; Lu, Yan; Guan, Yaqun; Zhang, Zhaoxia; Jiao, Yi; Sabeti, Pardis; Krutmann, Jean; Tang, Kun; Jin, Li; Xu, Shuhua; Wang, Sijia

    2016-11-01

    Hair straightness/curliness is one of the most conspicuous features of human variation and is particularly diverse among populations. A recent genome-wide scan found common variants in the Trichohyalin (TCHH) gene that are associated with hair straightness in Europeans, but different genes might affect this phenotype in other populations. By sampling 2899 Han Chinese, we performed the first genome-wide scan of hair straightness in East Asians, and found EDAR (rs3827760) as the predominant gene (P = 4.67 × 10-16), accounting for 3.66 % of the total variance. The candidate gene approach did not find further significant associations, suggesting that hair straightness may be affected by a large number of genes with subtle effects. Notably, genetic variants associated with hair straightness in Europeans are generally low in frequency in Han Chinese, and vice versa. To evaluate the relative contribution of these variants, we performed a second genome-wide scan in 709 samples from the Uyghur, an admixed population with both eastern and western Eurasian ancestries. In Uyghurs, both EDAR (rs3827760: P = 1.92 × 10-12) and TCHH (rs11803731: P = 1.46 × 10-3) are associated with hair straightness, but EDAR (OR 0.415) has a greater effect than TCHH (OR 0.575). We found no significant interaction between EDAR and TCHH (P = 0.645), suggesting that these two genes affect hair straightness through different mechanisms. Furthermore, haplotype analysis indicates that TCHH is not subject to selection. While EDAR is under strong selection in East Asia, it does not appear to be subject to selection after the admixture in Uyghurs. These suggest that hair straightness is unlikely a trait under selection.

  12. Lighting up G protein-coupled purinergic receptors with engineered fluorescent ligands

    Science.gov (United States)

    Ciruela, Francisco; Fernández-Dueñas, Víctor; Jacobson, Kenneth A.

    2015-01-01

    The use of G protein-coupled receptors fluorescent ligands is undergoing continuous expansion. In line with this, fluorescent agonists and antagonists of high affinity for G protein-coupled adenosine and P2Y receptors have been shown to be useful pharmacological probe compounds. Fluorescent ligands for A1R, A2AR, and A3R (adenosine receptors) and P2Y2R, P2Y4R, P2Y6R, and P2Y14R (nucleotide receptors) have been reported. Such ligands have been successfully applied to drug discovery and to GPCR characterization by flow cytometry, fluorescence correlation spectroscopy, fluorescence microscopy, fluorescence polarization, fluorescence resonance energy transfer and scanning confocal microscopy. Here we summarize recently reported and readily available representative fluorescent ligands of purinergic receptors. In addition, we pay special attention on the use of this family of fluorescent ligands revealing two main aspects of purinergic receptor biology, namely ligand binding and receptor oligomerization. PMID:25890205

  13. Crystal structure of the PEG-bound SH3 domain of myosin IB from Entamoeba histolytica reveals its mode of ligand recognition.

    Science.gov (United States)

    Gautam, Gunjan; Rehman, Syed Arif Abdul; Pandey, Preeti; Gourinath, Samudrala

    2017-08-01

    The versatility in the recognition of various interacting proteins by the SH3 domain drives a variety of cellular functions. Here, the crystal structure of the C-terminal SH3 domain of myosin IB from Entamoeba histolytica (EhMySH3) is reported at a resolution of 1.7 Å in native and PEG-bound states. Comparisons with other structures indicated that the PEG molecules occupy protein-protein interaction pockets similar to those occupied by the peptides in other peptide-bound SH3-domain structures. Also, analysis of the PEG-bound EhMySH3 structure led to the recognition of two additional pockets, apart from the conventional polyproline and specificity pockets, that are important for ligand interaction. Molecular-docking studies combined with various comparisons revealed structural similarity between EhMySH3 and the SH3 domain of β-Pix, and this similarity led to the prediction that EhMySH3 preferentially binds targets containing type II-like PXXP motifs. These studies expand the understanding of the EhMySH3 domain and provide extensive structural knowledge, which is expected to help in predicting the interacting partners which function together with myosin IB during phagocytosis in E. histolytica infections.

  14. Scanning photocurrent microscopy reveals electron-hole asymmetry in ionic liquid-gated WS{sub 2} transistors

    Energy Technology Data Exchange (ETDEWEB)

    Ubrig, Nicolas, E-mail: nicolas.ubrig@unige.ch; Kuzmenko, Alexey B., E-mail: Alexey.Kuzmenko@unige.ch [DPMC, Université de Genève, 24 quai Ernest Ansermet, CH-1211 Geneva (Switzerland); Jo, Sanghyun; Morpurgo, Alberto F. [DPMC, Université de Genève, 24 quai Ernest Ansermet, CH-1211 Geneva (Switzerland); GAP, Université de Genève, 24 quai Ernest Ansermet, CH-1211 Geneva (Switzerland); Berger, Helmuth [Institut de Physique de la Matière Condendée, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne (Switzerland)

    2014-04-28

    We perform scanning photocurrent microscopy on WS{sub 2} ionic liquid-gated field effect transistors exhibiting high-quality ambipolar transport. By properly biasing the gate electrode, we can invert the sign of the photocurrent showing that the minority photocarriers are either electrons or holes. Both in the electron- and hole-doping regimes the photocurrent decays exponentially as a function of the distance between the illumination spot and the nearest contact, in agreement with a two-terminal Schottky-barrier device model. This allows us to compare the value and the doping dependence of the diffusion length of the minority electrons and holes on a same sample. Interestingly, the diffusion length of the minority carriers is several times larger in the hole accumulation regime than in the electron accumulation regime, pointing out an electron-hole asymmetry in WS{sub 2}.

  15. Scanning electron microscopy of stellate cells of mammalian adrenal cortex as revealed by NaOH maceration.

    Science.gov (United States)

    Martinotti, A; Macchiarelli, G; Finn, D W; Correr, S; Motta, P M

    1991-01-01

    After removal of connective tissues by the NaOH maceration method, adrenal gland stellate cells of monkeys, rats and rabbits were studied by scanning electron microscopy. The stellate cells were situated in the perivascular and interstitial spaces and showed an ovoid cell body with numerous round or flat processes. Through these processes they were in contact with other adjacent stellate cells and thus formed a continuous cellular net around capillaries and parenchymal cells. This net, which probably provides a cellular scaffolding for the gland, may also play additional roles such as capillary contraction and nutrition for adjacent parenchymal cells. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 Fig. 7 PMID:1817138

  16. Binding site and interlobe interactions of the ionotropic glutamate receptor GluK3 ligand binding domain revealed by high resolution crystal structure in complex with (S)-glutamate

    DEFF Research Database (Denmark)

    Venskutonyte, Raminta; Frydenvang, Karla; Gajhede, Michael

    2011-01-01

    present the first X-ray crystal structure of the ligand binding domain of GluK3 in complex with glutamate, determined to 1.6Å resolution. The structure reveals a conserved glutamate binding mode, characteristic for iGluRs, and a water molecule network in the glutamate binding site similar to that seen...

  17. A chimeric prokaryotic-eukaryotic pentameric ligand gated ion channel reveals interactions between the extracellular and transmembrane domains shape neurosteroid modulation.

    Science.gov (United States)

    Ghosh, Borna; Tsao, Tzu-Wei; Czajkowski, Cynthia

    2017-10-01

    Pentameric ligand-gated ion channels (pLGICs) are the targets of several clinical and endogenous allosteric modulators including anesthetics and neurosteroids. Molecular mechanisms underlying allosteric drug modulation are poorly understood. Here, we constructed a chimeric pLGIC by fusing the extracellular domain (ECD) of the proton-activated, cation-selective bacterial channel GLIC to the transmembrane domain (TMD) of the human ρ1 chloride-selective GABAAR, and tested the hypothesis that drug actions are regulated locally in the domain that houses its binding site. The chimeric channels were proton-gated and chloride-selective demonstrating the GLIC ECD was functionally coupled to the GABAρ TMD. Channels were blocked by picrotoxin and inhibited by pentobarbital, etomidate and propofol. The point mutation, ρ TMD W328M, conferred positive modulation and direct gating by pentobarbital. The data suggest that the structural machinery mediating general anesthetic modulation resides in the TMD. Proton-activation and neurosteroid modulation of the GLIC-ρ chimeric channels, however, did not simply mimic their respective actions on GLIC and GABAρ revealing that across domain interactions between the ECD and TMD play important roles in determining their actions. Proton-induced current responses were biphasic suggesting that the chimeric channels contain an additional proton sensor. Neurosteroid modulation of the GLIC-ρ chimeric channels by the stereoisomers, 5α-THDOC and 5β-THDOC, were swapped compared to their actions on GABAρ indicating that positive versus negative neurosteroid modulation is not encoded solely in the TMD nor by neurosteroid isomer structure but is dependent on specific interdomain connections between the ECD and TMD. Our data reveal a new mechanism for shaping neurosteroid modulation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Human formyl peptide receptor ligand binding domain(s). Studies using an improved mutagenesis/expression vector reveal a novel mechanism for the regulation of receptor occupancy.

    Science.gov (United States)

    Perez, H D; Vilander, L; Andrews, W H; Holmes, R

    1994-09-09

    Recently, we reported the domain requirements for the binding of formyl peptide to its specific receptor. Based on experiments using receptor chimeras, we also postulated an importance for the amino-terminal domain of the receptor in ligand binding (Perez, H. D., Holmes, R., Vilander, L., Adams, R., Manzana, W., Jolley, D., and Andrews, W. H. (1993) J. Biol. Chem. 268, 2292-2295). We have begun to perform a detailed analysis of the regions within the formyl peptide receptor involved in ligand binding. To address the importance of the receptor amino-terminal domain, we substituted (or inserted) hydrophilic sequences within the amino-terminal domain, expressed the receptors, and determined their ability to bind ligand. A stretch of nine amino acids next to the initial methionine was identified as crucial for receptor occupancy. A peptide containing such a sequence specifically completed binding of the ligand to the receptor. Alanine screen mutagenesis of the second extracellular domain also identified amino acids involved in ligand binding as well as a disulfide bond (Cys98 to Cys176) crucial for maintaining the binding pocket. These studies provide evidence for a novel mechanism involved in regulation of receptor occupancy. Binding of the ligand induces conformational changes in the receptor that result in the apposition of the amino-terminal domain over the ligand, providing a lid to the binding pocket.

  19. Musculature of Notholca acuminata (Rotifera: Ploima: Brachionidae) revealed by confocal scanning laser microscopy

    DEFF Research Database (Denmark)

    Sørensen, M.V.; Funch, P.; Hooge, M.

    2003-01-01

    , stomach, gut, and cloaca, including thin longitudinal gut fibers and viscero-cloacal fibers, never before reported in other species of rotifers. The dorsal, lateral, and ventral retractor muscles and the incomplete circular muscles associated with the body wall appear to be apomorphies for the Rotifera....... Muscle-revealing staining shows promise for providing additional information on previously unrecognized complexity in rotifer musculature that will be useful in functional morphology and phylogenetic analyses...

  20. Musculature of Notholca acuminata (Rotifera : Ploima : Brachionidae) revealed by confocal scanning laser microscopy

    DEFF Research Database (Denmark)

    Sørensen, M.V.; Funch, P.; Hooge, M.

    2003-01-01

    , stomach, gut, and cloaca, including thin longitudinal gut fibers and viscero-cloacal fibers, never before reported in other species of rotifers. The dorsal, lateral, and ventral retractor muscles and the incomplete circular muscles associated with the body wall appear to be apomorphies for the Rotifera....... Muscle-revealing staining shows promise for providing additional information on previously unrecognized complexity in rotifer musculature that will be useful in functional morphology and phylogenetic analyses...

  1. Surface and flagella morphology of the motile form of Chromera velia revealed by field-emission scanning electron microscopy.

    Science.gov (United States)

    Weatherby, Kate; Murray, Shauna; Carter, Dee; Slapeta, Jan

    2011-01-01

    Chromera velia(Chromerida; Alveolata) is an autotrophic protist isolated from stony corals.Ch. veliapossesses a chloroplast thought to be most closely related to the apicoplasts of non-photosynthetic apicomplexa. Phylogenetic analyses placeCh. veliaas a close relative of parasitic apicomplexa and predatory colpodellids. We have used field-emission scanning electron microscopy of cells sputter-coated with gold or chromium and non-coated cells to characterise the surface ultrastructure of the motile form ofCh. velia. In overall morphology the biflagellatedCh. veliacells resemble the colpodellidColpodella edax, but with some notable differences. The ventral side of the flagellatedCh. veliacell has two grooves extending from the anterior flagella insertion point with a ridge rising towards the anterior apex of the cell. The anterior flagellum is shorter than the posterior flagellum and possesses a distinct, small curved appendage. The insertion point of the anterior flagellum is partly enclosed by a flap extending from the cell. The posterior flagellum is approximately four times the length of the cell and possesses mastigonemes. The combination of coating techniques proved superior to the commonly used gold coating to determine fine surface ultrastructure. This new ultrastructural information forCh. veliaallowed us to emend its diagnosis. 2010 Elsevier GmbH. All rights reserved.

  2. Inter- and intraspecific structural variations among intervascular pit membranes, as revealed by field-emission scanning electron microscopy.

    Science.gov (United States)

    Sano, Yuzou

    2005-07-01

    The structure of the intervascular pit membranes of four dicotyledonous species (Salix sachalinensis, Betula platyphylla var. japonica, Acer mono, and Fraxinus mandshurica var. japonica) was examined by field-emission scanning electron microscopy. The intervascular pit membranes of F. mandshurica var. japonica had thin surface layers and a dense middle layer, while no similar middle layer was detectable in the other three species. In F. mandshurica var. japonica, the entire area of each pit membrane was densely covered with microfibrils. In the other three species, by contrast, openings were found in the pit membranes. In some of the intervascular pit membranes of S. sachalinensis, B. platyphylla var. japonica, and A. mono, microfibrils were sparsely interwoven in small areas of the pit membranes and openings of up to several hundred nanometers in diameter were present in such regions. These porous regions tended to be located in peripheral areas of pit membranes. In S. sachalinensis and B. platyphylla var. japonica, ethanol-soluble extracts, whose chemical nature and function remain unknown, were heavily distributed over the intervascular pit membranes. Our observations suggest that the structure of intervascular pit membranes is more complicated than has previously been acknowledged.

  3. Species-scanning mutagenesis of the serotonin transporter reveals residues essential in selective, high-affinity recognition of antidepressants

    DEFF Research Database (Denmark)

    Mortensen, O V; Kristensen, A S; Wiborg, O

    2001-01-01

    of the antidepressants citalopram, fluoxetine, paroxetine and imipramine were several-fold higher at hSERT compared with bSERT. No species selectivity was observed for the antidepressants fluvoxamine, and sertraline or for the psychostimulants cocaine, the cocaine analogue beta-carbomethoxy-3beta-(4-iodophenyl......, and phenylalanine-513 and to reveal molecular interactions with individual functional groups of citalopram. We suggest that methionine-180 interacts with the heterocyclic nucleus of citalopram or stabilizes the binding pocket and phenylalanine-513 to be a steric blocker of antidepressant recognition....

  4. Revealing the Cell-Material Interface with Nanometer Resolution by Focused Ion Beam/Scanning Electron Microscopy.

    Science.gov (United States)

    Santoro, Francesca; Zhao, Wenting; Joubert, Lydia-Marie; Duan, Liting; Schnitker, Jan; van de Burgt, Yoeri; Lou, Hsin-Ya; Liu, Bofei; Salleo, Alberto; Cui, Lifeng; Cui, Yi; Cui, Bianxiao

    2017-08-22

    The interface between cells and nonbiological surfaces regulates cell attachment, chronic tissue responses, and ultimately the success of medical implants or biosensors. Clinical and laboratory studies show that topological features of the surface profoundly influence cellular responses; for example, titanium surfaces with nano- and microtopographical structures enhance osteoblast attachment and host-implant integration as compared to a smooth surface. To understand how cells and tissues respond to different topographical features, it is of critical importance to directly visualize the cell-material interface at the relevant nanometer length scale. Here, we present a method for in situ examination of the cell-to-material interface at any desired location, based on focused ion beam milling and scanning electron microscopy imaging to resolve the cell membrane-to-material interface with 10 nm resolution. By examining how cell membranes interact with topographical features such as nanoscale protrusions or invaginations, we discovered that the cell membrane readily deforms inward and wraps around protruding structures, but hardly deforms outward to contour invaginating structures. This asymmetric membrane response (inward vs outward deformation) causes the cleft width between the cell membrane and the nanostructure surface to vary by more than an order of magnitude. Our results suggest that surface topology is a crucial consideration for the development of medical implants or biosensors whose performances are strongly influenced by the cell-to-material interface. We anticipate that the method can be used to explore the direct interaction of cells/tissue with medical devices such as metal implants in the future.

  5. Revealing the selection history of adaptive loci using genome-wide scans for selection: an example from domestic sheep.

    Science.gov (United States)

    Rochus, Christina Marie; Tortereau, Flavie; Plisson-Petit, Florence; Restoux, Gwendal; Moreno-Romieux, Carole; Tosser-Klopp, Gwenola; Servin, Bertrand

    2018-01-23

    One of the approaches to detect genetics variants affecting fitness traits is to identify their surrounding genomic signatures of past selection. With established methods for detecting selection signatures and the current and future availability of large datasets, such studies should have the power to not only detect these signatures but also to infer their selective histories. Domesticated animals offer a powerful model for these approaches as they adapted rapidly to environmental and human-mediated constraints in a relatively short time. We investigated this question by studying a large dataset of 542 individuals from 27 domestic sheep populations raised in France, genotyped for more than 500,000 SNPs. Population structure analysis revealed that this set of populations harbour a large part of European sheep diversity in a small geographical area, offering a powerful model for the study of adaptation. Identification of extreme SNP and haplotype frequency differences between populations listed 126 genomic regions likely affected by selection. These signatures revealed selection at loci commonly identified as selection targets in many species ("selection hotspots") including ABCG2, LCORL/NCAPG, MSTN, and coat colour genes such as ASIP, MC1R, MITF, and TYRP1. For one of these regions (ABCG2, LCORL/NCAPG), we could propose a historical scenario leading to the introgression of an adaptive allele into a new genetic background. Among selection signatures, we found clear evidence for parallel selection events in different genetic backgrounds, most likely for different mutations. We confirmed this allelic heterogeneity in one case by resequencing the MC1R gene in three black-faced breeds. Our study illustrates how dense genetic data in multiple populations allows the deciphering of evolutionary history of populations and of their adaptive mutations.

  6. Revealing the consequences and errors of substance arising from the inverse confusion between the crystal (ligand) field quantities and the zero-field splitting ones

    Energy Technology Data Exchange (ETDEWEB)

    Rudowicz, Czesław, E-mail: crudowicz@zut.edu.pl [Institute of Physics, West Pomeranian University of Technology, Al. Piastów 17, 70-310 Szczecin (Poland); Karbowiak, Mirosław [Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław (Poland)

    2015-01-01

    Survey of recent literature has revealed a doubly-worrying tendency concerning the treatment of the two distinct types of Hamiltonians, namely, the physical crystal field (CF), or equivalently ligand field (LF), Hamiltonians and the zero-field splitting (ZFS) Hamiltonians, which appear in the effective spin Hamiltonians (SH). The nature and properties of the CF (LF) Hamiltonians have been mixed up in various ways with those of the ZFS Hamiltonians. Such cases have been identified in a rapidly growing number of studies of the transition-ion based systems using electron magnetic resonance (EMR), optical spectroscopy, and magnetic measurements. These findings have far ranging implications since these Hamiltonians are cornerstones for interpretation of magnetic and spectroscopic properties of the single transition ions in various crystals or molecules as well as the exchange coupled systems (ECS) of transition ions, e.g. single molecule magnets (SMM) or single ion magnets (SIM). The seriousness of the consequences of such conceptual problems and related terminological confusions has reached a level that goes far beyond simple semantic issues or misleading keyword classifications of papers in journals and scientific databases. The prevailing confusion, denoted as the CF=ZFS confusion, pertains to the cases of labeling the true ZFS quantities as purportedly the CF (LF) quantities. Here we consider the inverse confusion between the CF (LF) quantities and the SH (ZFS) ones, denoted the ZFS=CF confusion, which consists in referring to the parameters (or Hamiltonians), which are the true CF (LF) quantities, as purportedly the ZFS (or SH) quantities. Specific cases of the ZFS=CF confusion identified in recent textbooks, reviews and papers, especially SMM- and SIM-related ones, are surveyed and the pertinent misconceptions are clarified. The serious consequences of the terminological confusions include misinterpretation of data from a wide range of experimental techniques and

  7. Tryptophan scanning mutagenesis reveals distortions in the helical structure of the δM4 transmembrane domain of the Torpedo californica nicotinic acetylcholine receptor.

    Science.gov (United States)

    Caballero-Rivera, Daniel; Cruz-Nieves, Omar A; Oyola-Cintrón, Jessica; Torres-Nunez, David A; Otero-Cruz, Jose D; Lasalde-Dominicci, José A

    2012-01-01

    The lipid-protein interface is an important domain of the nicotinic acetylcholine receptor (nAChR) that has recently garnered increased relevance. Several studies have made significant advances toward determining the structure and dynamics of the lipid-exposed domains of the nAChR. However, there is still a need to gain insight into the mechanism by which lipid-protein interactions regulate the function and conformational transitions of the nAChR. In this study, we extended the tryptophan scanning mutagenesis (TrpScanM) approach to dissect secondary structure and monitor the conformational changes experienced by the δM4 transmembrane domain (TMD) of the Torpedo californica nAChR, and to identify which positions on this domain are potentially linked to the regulation of ion channel kinetics. The difference in oscillation patterns between the closed- and open-channel states suggests a substantial conformational change along this domain as a consequence of channel activation. Furthermore, TrpScanM revealed distortions along the helical structure of this TMD that are not present on current models of the nAChR. Our results show that a Thr-Pro motif at positions 462-463 markedly bends the helical structure of the TMD, consistent with the recent crystallographic structure of the GluCl Cys-loop receptor which reveals a highly bent TMD4 in each subunit. This Thr-Pro motif acts as a molecular hinge that delineates two gating blocks in the δM4 TMD. These results suggest a model in which a hinge-bending motion that tilts the helical structure is combined with a spring-like motion during transition between the closed- and open-channel states of the δM4 TMD.

  8. X-ray structures of progesterone receptor ligand binding domain in its agonist state reveal differing mechanisms for mixed profiles of 11beta-substituted steroids.

    NARCIS (Netherlands)

    Lusher, S.J.; Raaijmakers, H.C.A.; Vu-Pham, D.; Kazemier, B.; Bosch, R.; McGuire, R.; Azevedo, R.; Hamersma, H.; Dechering, K.; Oubrie, A.; Duin, M. van; Vlieg, J. de

    2012-01-01

    We present here the x-ray structures of the progesterone receptor (PR) in complex with two mixed profile PR modulators whose functional activity results from two differing molecular mechanisms. The structure of Asoprisnil bound to the agonist state of PR demonstrates the contribution of the ligand

  9. Negative Ion Photoelectron Spectroscopy Reveals Remarkable Noninnocence of Ligands in Nickel Bis(dithiolene) Complexes [Ni(dddt)2](-) and [Ni(edo)2](-).

    Science.gov (United States)

    Liu, Xing; Hou, Gao-Lei; Wang, Xuefeng; Wang, Xue-Bin

    2016-05-12

    [Ni(dddt)2](-) (dddt = 5,6-dihydro-1,4-dithiine-2,3-dithiolate) and [Ni(edo)2](-) (edo = 5,6-dihydro-1,4-dioxine-2,3-dithiolate) are two donor-type nickel bis(dithiolene) complexes, with the tendency of donating low binding energy electrons. These two structurally similar complexes differ only with respect to the outer atoms in the ligand framework where the former has four S atoms while the latter has four O atoms. Herein, we report a negative ion photoelectron spectroscopy (NIPES) study on these two complexes to probe the electronic structures of the anions and their corresponding neutrals. The NIPE spectra exhibit the adiabatic electron detachment energy (ADE) or, equivalently, the electron affinity (EA) of the neutral [Ni(L)2](0) to be relatively low for this type of complexes, 2.780 and 2.375 eV for L = dddt and edo, respectively. The 0.4 eV difference in ADEs shows a significant substitution effect for sulfur in dddt by oxygen in edo, i.e., noninnocence of the ligands, which has decreased the electronic stability of [Ni(edo)2](-) by lowering its electron binding energy by ∼0.4 eV. The observed substitution effect on gas-phase EA values correlates well with the measured redox potentials for [Ni(dddt)2](-/0) and [Ni(edo)2](-/0) in solutions. The singlet-triplet splitting (ΔEST) of [Ni(dddt)2](0) and [Ni(edo)2](0) is also determined from the spectra to be 0.57 and 0.53 eV, respectively. Accompanying DFT calculations and molecular orbital (MO) composition analyses show significant ligand contributions to the redox MOs and allow the components of the orbitals involved in each electronic transition and spectral assignments to be identified.

  10. Scanning mutagenesis reveals roles for helix n of the bacteriophage T7 RNA polymerase thumb subdomain in transcription complex stability, pausing, and termination.

    Science.gov (United States)

    Brieba, L G; Gopal, V; Sousa, R

    2001-03-30

    Deletions within the thumb subdomain (residues 335-408) of T7 RNA polymerase decrease elongation complex stability and processivity, but the structure of a T7RNAP initial transcription complex containing a 3-nucleotide RNA reveals no interactions between the thumb and the RNA or DNA. Modeling of a longer RNA in this structure, using a T7DNAP-primer-template structure as a guide, suggests that the phosphate ribose backbone of the RNA contacts a stretch of mostly positively charged side chains between residues 385 and 395 of helix N of the thumb. Scanning mutagenesis of this region reveals that alanine substitutions of Arg(391), Ser(393), and Arg(394) destabilize elongation complexes and that substitutions at 393 and 394 increase termination of transcripts 5 or more bases in length. The alpha-carbons of all 3 of these residues lie on the side of helix N, which faces into the template-binding cleft of the RNA polymerase, and modeling suggests that they can contact the RNA 4-5 bases away from the 3'-end. Alanine substitutions of other residues within 385-395 do not have marked effects on transcription complex stability, but alanine substitutions of Asp(388) and Tyr(385) reduce pausing and termination at the T7 concatemer junction. Both of these side chains lie on the outer side of helix N, pointing away from the template binding cleft. The thumb subdomain of T7RNAP therefore has roles both in transcription complex stabilization and in pausing and termination at the T7 concatemer junction.

  11. Genome-wide SNP scan of pooled DNA reveals nonsense mutation in FGF20 in the scaleless line of featherless chickens.

    Science.gov (United States)

    Wells, Kirsty L; Hadad, Yair; Ben-Avraham, Danny; Hillel, Jossi; Cahaner, Avigdor; Headon, Denis J

    2012-06-19

    Scaleless (sc/sc) chickens carry a single recessive mutation that causes a lack of almost all body feathers, as well as foot scales and spurs, due to a failure of skin patterning during embryogenesis. This spontaneous mutant line, first described in the 1950s, has been used extensively to explore the tissue interactions involved in ectodermal appendage formation in embryonic skin. Moreover, the trait is potentially useful in tropical agriculture due to the ability of featherless chickens to tolerate heat, which is at present a major constraint to efficient poultry meat production in hot climates. In the interests of enhancing our understanding of feather placode development, and to provide the poultry industry with a strategy to breed heat-tolerant meat-type chickens (broilers), we mapped and identified the sc mutation. Through a cost-effective and labour-efficient SNP array mapping approach using DNA from sc/sc and sc/+ blood sample pools, we map the sc trait to chromosome 4 and show that a nonsense mutation in FGF20 is completely associated with the sc/sc phenotype. This mutation, common to all sc/sc individuals and absent from wild type, is predicted to lead to loss of a highly conserved region of the FGF20 protein important for FGF signalling. In situ hybridisation and quantitative RT-PCR studies reveal that FGF20 is epidermally expressed during the early stages of feather placode patterning. In addition, we describe a dCAPS genotyping assay based on the mutation, developed to facilitate discrimination between wild type and sc alleles. This work represents the first loss of function genetic evidence supporting a role for FGF ligand signalling in feather development, and suggests FGF20 as a novel central player in the development of vertebrate skin appendages, including hair follicles and exocrine glands. In addition, this is to our knowledge the first report describing the use of the chicken SNP array to map genes based on genotyping of DNA samples from pooled

  12. Genome-wide SNP scan of pooled DNA reveals nonsense mutation in FGF20 in the scaleless line of featherless chickens

    Directory of Open Access Journals (Sweden)

    Wells Kirsty L

    2012-06-01

    Full Text Available Abstract Background Scaleless (sc/sc chickens carry a single recessive mutation that causes a lack of almost all body feathers, as well as foot scales and spurs, due to a failure of skin patterning during embryogenesis. This spontaneous mutant line, first described in the 1950s, has been used extensively to explore the tissue interactions involved in ectodermal appendage formation in embryonic skin. Moreover, the trait is potentially useful in tropical agriculture due to the ability of featherless chickens to tolerate heat, which is at present a major constraint to efficient poultry meat production in hot climates. In the interests of enhancing our understanding of feather placode development, and to provide the poultry industry with a strategy to breed heat-tolerant meat-type chickens (broilers, we mapped and identified the sc mutation. Results Through a cost-effective and labour-efficient SNP array mapping approach using DNA from sc/sc and sc/+ blood sample pools, we map the sc trait to chromosome 4 and show that a nonsense mutation in FGF20 is completely associated with the sc/sc phenotype. This mutation, common to all sc/sc individuals and absent from wild type, is predicted to lead to loss of a highly conserved region of the FGF20 protein important for FGF signalling. In situ hybridisation and quantitative RT-PCR studies reveal that FGF20 is epidermally expressed during the early stages of feather placode patterning. In addition, we describe a dCAPS genotyping assay based on the mutation, developed to facilitate discrimination between wild type and sc alleles. Conclusions This work represents the first loss of function genetic evidence supporting a role for FGF ligand signalling in feather development, and suggests FGF20 as a novel central player in the development of vertebrate skin appendages, including hair follicles and exocrine glands. In addition, this is to our knowledge the first report describing the use of the chicken SNP array to

  13. Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity.

    Science.gov (United States)

    Chapman, Carol; Henry, Matthew; Bishop-Lilly, Kimberly A; Awosika, Joy; Briska, Adam; Ptashkin, Ryan N; Wagner, Trevor; Rajanna, Chythanya; Tsang, Hsinyi; Johnson, Shannon L; Mokashi, Vishwesh P; Chain, Patrick S G; Sozhamannan, Shanmuga

    2015-01-01

    Historically, cholera outbreaks have been linked to V. cholerae O1 serogroup strains or its derivatives of the O37 and O139 serogroups. A genomic study on the 2010 Haiti cholera outbreak strains highlighted the putative role of non O1/non-O139 V. cholerae in causing cholera and the lack of genomic sequences of such strains from around the world. Here we address these gaps by scanning a global collection of V. cholerae strains as a first step towards understanding the population genetic diversity and epidemic potential of non O1/non-O139 strains. Whole Genome Mapping (Optical Mapping) based bar coding produces a high resolution, ordered restriction map, depicting a complete view of the unique chromosomal architecture of an organism. To assess the genomic diversity of non-O1/non-O139 V. cholerae, we applied a Whole Genome Mapping strategy on a well-defined and geographically and temporally diverse strain collection, the Sakazaki serogroup type strains. Whole Genome Map data on 91 of the 206 serogroup type strains support the hypothesis that V. cholerae has an unprecedented genetic and genomic structural diversity. Interestingly, we discovered chromosomal fusions in two unusual strains that possess a single chromosome instead of the two chromosomes usually found in V. cholerae. We also found pervasive chromosomal rearrangements such as duplications and indels in many strains. The majority of Vibrio genome sequences currently in public databases are unfinished draft sequences. The Whole Genome Mapping approach presented here enables rapid screening of large strain collections to capture genomic complexities that would not have been otherwise revealed by unfinished draft genome sequencing and thus aids in assembling and finishing draft sequences of complex genomes. Furthermore, Whole Genome Mapping allows for prediction of novel V. cholerae non-O1/non-O139 strains that may have the potential to cause future cholera outbreaks.

  14. Whole genome PCR scanning reveals the syntenic genome structure of toxigenic Vibrio cholerae strains in the O1/O139 population.

    Directory of Open Access Journals (Sweden)

    Bo Pang

    Full Text Available Vibrio cholerae is commonly found in estuarine water systems. Toxigenic O1 and O139 V. cholerae strains have caused cholera epidemics and pandemics, whereas the nontoxigenic strains within these serogroups only occasionally lead to disease. To understand the differences in the genome and clonality between the toxigenic and nontoxigenic strains of V. cholerae serogroups O1 and O139, we employed a whole genome PCR scanning (WGPScanning method, an rrn operon-mediated fragment rearrangement analysis and comparative genomic hybridization (CGH to analyze the genome structure of different strains. WGPScanning in conjunction with CGH revealed that the genomic contents of the toxigenic strains were conservative, except for a few indels located mainly in mobile elements. Minor nucleotide variation in orthologous genes appeared to be the major difference between the toxigenic strains. rrn operon-mediated rearrangements were infrequent in El Tor toxigenic strains tested using I-CeuI digested pulsed-field gel electrophoresis (PFGE analysis and PCR analysis based on flanking sequence of rrn operons. Using these methods, we found that the genomic structures of toxigenic El Tor and O139 strains were syntenic. The nontoxigenic strains exhibited more extensive sequence variations, but toxin coregulated pilus positive (TCP+ strains had a similar structure. TCP+ nontoxigenic strains could be subdivided into multiple lineages according to the TCP type, suggesting the existence of complex intermediates in the evolution of toxigenic strains. The data indicate that toxigenic O1 El Tor and O139 strains were derived from a single lineage of intermediates from complex clones in the environment. The nontoxigenic strains with non-El Tor type TCP may yet evolve into new epidemic clones after attaining toxigenic attributes.

  15. Nuclear Scans

    Science.gov (United States)

    Nuclear scans use radioactive substances to see structures and functions inside your body. They use a special ... images. Most scans take 20 to 45 minutes. Nuclear scans can help doctors diagnose many conditions, including ...

  16. Identification of estrogen receptor dimer selective ligands reveals growth-inhibitory effects on cells that co-express ERα and ERβ.

    Directory of Open Access Journals (Sweden)

    Emily Powell

    Full Text Available Estrogens play essential roles in the progression of mammary and prostatic diseases. The transcriptional effects of estrogens are transduced by two estrogen receptors, ERα and ERβ, which elicit opposing roles in regulating proliferation: ERα is proliferative while ERβ is anti-proliferative. Exogenous expression of ERβ in ERα-positive cancer cell lines inhibits cell proliferation in response to estrogen and reduces xenografted tumor growth in vivo, suggesting that ERβ might oppose ERα's proliferative effects via formation of ERα/β heterodimers. Despite biochemical and cellular evidence of ERα/β heterodimer formation in cells co-expressing both receptors, the biological roles of the ERα/β heterodimer remain to be elucidated. Here we report the identification of two phytoestrogens that selectively activate ERα/β heterodimers at specific concentrations using a cell-based, two-step high throughput small molecule screen for ER transcriptional activity and ER dimer selectivity. Using ERα/β heterodimer-selective ligands at defined concentrations, we demonstrate that ERα/β heterodimers are growth inhibitory in breast and prostate cells which co-express the two ER isoforms. Furthermore, using Automated Quantitative Analysis (AQUA to examine nuclear expression of ERα and ERβ in human breast tissue microarrays, we demonstrate that ERα and ERβ are co-expressed in the same cells in breast tumors. The co-expression of ERα and ERβ in the same cells supports the possibility of ERα/β heterodimer formation at physio- and pathological conditions, further suggesting that targeting ERα/β heterodimers might be a novel therapeutic approach to the treatment of cancers which co-express ERα and ERβ.

  17. Mutational analysis of the multiple-antibiotic resistance regulator MarR reveals a ligand binding pocket at the interface between the dimerization and DNA binding domains.

    Science.gov (United States)

    Duval, Valérie; McMurry, Laura M; Foster, Kimberly; Head, James F; Levy, Stuart B

    2013-08-01

    The Escherichia coli regulator MarR represses the multiple-antibiotic resistance operon marRAB and responds to phenolic compounds, including sodium salicylate, which inhibit its activity. Crystals obtained in the presence of a high concentration of salicylate indicated two possible salicylate sites, SAL-A and SAL-B. However, it was unclear whether these sites were physiologically significant or were simply a result of the crystallization conditions. A study carried out on MarR homologue MTH313 suggested the presence of a salicylate binding site buried at the interface between the dimerization and the DNA-binding domains. Interestingly, the authors of the study indicated a similar pocket conserved in the MarR structure. Since no mutagenesis analysis had been performed to test which amino acids were essential in salicylate binding, we examined the role of residues that could potentially interact with salicylate. We demonstrated that mutations in residues shown as interacting with salicylate at SAL-A and SAL-B in the MarR-salicylate structure had no effect on salicylate binding, indicating that these sites were not the physiological regulatory sites. However, some of these residues (P57, R86, M74, and R77) were important for DNA binding. Furthermore, mutations in residues R16, D26, and K44 significantly reduced binding to both salicylate and 2,4-dinitrophenol, while a mutation in residue H19 impaired the binding to 2,4-dinitrophenol only. These findings indicate, as for MTH313, the presence of a ligand binding pocket located between the dimerization and DNA binding domains.

  18. Ligand-induced movements of inner transmembrane helices of Glut1 revealed by chemical cross-linking of di-cysteine mutants.

    Directory of Open Access Journals (Sweden)

    Mike Mueckler

    Full Text Available The relative orientation and proximity of the pseudo-symmetrical inner transmembrane helical pairs 5/8 and 2/11 of Glut1 were analyzed by chemical cross-linking of di-cysteine mutants. Thirteen functional di-cysteine mutants were created from a C-less Glut1 reporter construct containing cysteine substitutions in helices 5 and 8 or helices 2 and 11. The mutants were expressed in Xenopus oocytes and the sensitivity of each mutant to intramolecular cross-linking by two homobifunctional thiol-specific reagents was ascertained by protease cleavage followed by immunoblot analysis. Five of 9 mutants with cysteine residues predicted to lie in close proximity to each other were susceptible to cross-linking by one or both reagents. None of 4 mutants with cysteine substitutions predicted to lie on opposite faces of their respective helices was susceptible to cross-linking. Additionally, the cross-linking of a di-cysteine pair (A70C/M420C, helices 2/11 predicted to lie near the exoplasmic face of the membrane was stimulated by ethylidene glucose, a non-transported glucose analog that preferentially binds to the exofacial substrate-binding site, suggesting that the binding of this ligand stimulates the closure of helices at the exoplasmic face of the membrane. In contrast, the cross-linking of a second di-cysteine pair (T158C/L325, helices 5/8, predicted to lie near the cytoplasmic face of the membrane, was stimulated by cytochalasin B, a glucose transport inhibitor that competitively inhibits substrate efflux, suggesting that this compound recruits the transporter to a conformational state in which closure of inner helices occurs at the cytoplasmic face of the membrane. This observation provides a structural explanation for the competitive inhibition of substrate efflux by cytochalasin B. These data indicate that the binding of competitive inhibitors of glucose efflux or influx induce occluded states in the transporter in which substrate is excluded from

  19. Purified monomeric ligand.MD-2 complexes reveal molecular and structural requirements for activation and antagonism of TLR4 by Gram-negative bacterial endotoxins.

    Science.gov (United States)

    Gioannini, Theresa L; Teghanemt, Athmane; Zhang, DeSheng; Esparza, Gregory; Yu, Liping; Weiss, Jerrold

    2014-08-01

    A major focus of work in our laboratory concerns the molecular mechanisms and structural bases of Gram-negative bacterial endotoxin recognition by host (e.g., human) endotoxin-recognition proteins that mediate and/or regulate activation of Toll-like receptor (TLR) 4. Here, we review studies of wild-type and variant monomeric endotoxin.MD-2 complexes first produced and characterized in our laboratories. These purified complexes have provided unique experimental reagents, revealing both quantitative and qualitative determinants of TLR4 activation and antagonism. This review is dedicated to the memory of Dr. Theresa L. Gioannini (1949-2014) who played a central role in many of the studies and discoveries that are reviewed.

  20. Renal scan

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/003790.htm Renal scan To use the sharing features on this ... anaphylaxis . Alternative Names Renogram; Kidney scan Images Kidney anatomy Kidney - blood and urine flow References Chernecky CC, ...

  1. Real time analysis of β2-adrenoceptor-mediated signaling kinetics in Human Primary Airway Smooth Muscle Cells reveals both ligand and dose dependent differences

    Directory of Open Access Journals (Sweden)

    Hall Ian P

    2011-07-01

    Full Text Available Abstract Background β2-adrenoceptor agonists elicit bronchodilator responses by binding to β2-adrenoceptors on airway smooth muscle (ASM. In vivo, the time between drug administration and clinically relevant bronchodilation varies significantly depending on the agonist used. Our aim was to utilise a fluorescent cyclic AMP reporter probe to study the temporal profile of β2-adrenoceptor-mediated signaling induced by isoproterenol and a range of clinically relevant agonists in human primary ASM (hASM cells by using a modified Epac protein fused to CFP and a variant of YFP. Methods Cells were imaged in real time using a spinning disk confocal system which allowed rapid and direct quantification of emission ratio imaging following direct addition of β2-adrenoceptor agonists (isoproterenol, salbutamol, salmeterol, indacaterol and formoterol into the extracellular buffer. For pharmacological comparison a radiolabeling assay for whole cell cyclic AMP formation was used. Results Temporal analysis revealed that in hASM cells the β2-adrenoceptor agonists studied did not vary significantly in the onset of initiation. However, once a response was initiated, significant differences were observed in the rate of this response with indacaterol and isoproterenol inducing a significantly faster response than salmeterol. Contrary to expectation, reducing the concentration of isoproterenol resulted in a significantly faster initiation of response. Conclusions We conclude that confocal imaging of the Epac-based probe is a powerful tool to explore β2-adrenoceptor signaling in primary cells. The ability to analyse the kinetics of clinically used β2-adrenoceptor agonists in real time and at a single cell level gives an insight into their possible kinetics once they have reached ASM cells in vivo.

  2. An eye tracking system for monitoring face scanning patterns reveals the enhancing effect of oxytocin on eye contact in common marmosets.

    Science.gov (United States)

    Kotani, Manato; Shimono, Kohei; Yoneyama, Toshihiro; Nakako, Tomokazu; Matsumoto, Kenji; Ogi, Yuji; Konoike, Naho; Nakamura, Katsuki; Ikeda, Kazuhito

    2017-09-01

    Eye tracking systems are used to investigate eyes position and gaze patterns presumed as eye contact in humans. Eye contact is a useful biomarker of social communication and known to be deficient in patients with autism spectrum disorders (ASDs). Interestingly, the same eye tracking systems have been used to directly compare face scanning patterns in some non-human primates to those in human. Thus, eye tracking is expected to be a useful translational technique for investigating not only social attention and visual interest, but also the effects of psychiatric drugs, such as oxytocin, a neuropeptide that regulates social behavior. In this study, we report on a newly established method for eye tracking in common marmosets as unique New World primates that, like humans, use eye contact as a mean of communication. Our investigation was aimed at characterizing these primates face scanning patterns and evaluating the effects of oxytocin on their eye contact behavior. We found that normal common marmosets spend more time viewing the eyes region in common marmoset's picture than the mouth region or a scrambled picture. In oxytocin experiment, the change in eyes/face ratio was significantly greater in the oxytocin group than in the vehicle group. Moreover, oxytocin-induced increase in the change in eyes/face ratio was completely blocked by the oxytocin receptor antagonist L-368,899. These results indicate that eye tracking in common marmosets may be useful for evaluating drug candidates targeting psychiatric conditions, especially ASDs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Mineralogical composition and phase-to-phase relationships in natural hydraulic lime and/or natural cement - raw materials and burnt products revealed by scanning electron microscopy

    Science.gov (United States)

    Kozlovcev, Petr; Přikryl, Richard; Racek, Martin; Přikrylová, Jiřina

    2016-04-01

    In contrast to modern process of production of cement clinker, traditional burning of natural hydraulic lime below sintering temperature relied on the formation of new phases from ion migration between neighbouring mineral grains composing raw material. The importance of the mineralogical composition and spatial distribution of rock-forming minerals in impure limestones used as a raw material for natural hydraulic lime presents not well explored issue in the scientific literature. To fill this gap, the recent study focuses in detailed analysis of experimentally burnt impure limestones (mostly from Barrandian area, Bohemian Massif). The phase changes were documented by optical microscopy, X-ray diffraction, and scanning electron microscopy with an energy dispersive spectrometer (SEM-EDS) coupled with x-ray elemental mapping. The latest allowed for visualization of distribution of elements within raw materials and burnt products. SEM/EDS study brought valuable data on the presence of transitional and/or minor phases, which were poorly detectable by other methods.

  4. Relationships of Trichomonas gallinae to the palatal-esophageal junction of ring doves (Streptopelia risoria) as revealed by scanning electron microscopy.

    Science.gov (United States)

    Kietzmann, G E

    1993-06-01

    Ring doves (Streptopelia risoria) were experimentally infected with pathogenic (virulent) Trichomonas gallinae so that trichomonad activities in the upper alimentary tract, prior to canker formation, could be examined with scanning electron microscopy. Between 6 and 15 hr postinoculation low numbers of ameboid T. gallinae were attached to apical microfolds and cell borders of the palatal-esophageal junction squamous epithelium. Initial parasite activities at tightly attached cell borders and apical microfolds suggest that some parasite-secreted factor or factors initiated squamous cell damage, separation, and removal. As squamous cell borders separated, trichomonads invaded areas beneath them and ultimately aided in their complete removal. Accelerated parasite-mediated desquamation, the invasion of increased mucosal surface area by trichomonads, and the eruption and expansion of cankers were the primary changes to the palatal-esophageal junction and other upper alimentary tract tissues that occurred between 19 and 240 hr postinoculation.

  5. Laser-scanning astrocyte mapping reveals increased glutamate-responsive domain size and disrupted maturation of glutamate uptake following neonatal cortical freeze-lesion

    Directory of Open Access Journals (Sweden)

    Mortiz eArmbruster

    2014-09-01

    Full Text Available Astrocytic uptake of glutamate shapes extracellular neurotransmitter dynamics, receptor activation, and synaptogenesis. During development, glutamate transport becomes more robust. How neonatal brain insult affects the functional maturation of glutamate transport remains unanswered. Neonatal brain insult can lead to developmental delays, cognitive losses, and epilepsy; the disruption of glutamate transport is known to cause changes in synaptogenesis, receptor activation, and seizure. Using the neonatal freeze-lesion (FL model, we have investigated how insult affects the maturation of astrocytic glutamate transport. As lesioning occurs on the day of birth, a time when astrocytes are still functionally immature, this model is ideal for identifying changes in astrocyte maturation following insult. Reactive astrocytosis, astrocyte proliferation, and in vitro hyperexcitability are known to occur in this model. To probe astrocyte glutamate transport with better spatial precision we have developed a novel technique, Laser Scanning Astrocyte Mapping (LSAM, which combines glutamate transport current (TC recording from astrocytes with laser scanning glutamate photolysis. LSAM allows us to identify the area from which a single astrocyte can transport glutamate and to quantify spatial heterogeneity in the rate of glutamate clearance kinetics within that domain. Using LSAM, we report that cortical astrocytes have an increased glutamate-responsive area following FL and that TCs have faster decay times in distal, as compared to proximal processes. Furthermore, the developmental shift from GLAST- to GLT-1-dominated clearance is disrupted following FL. These findings introduce a novel method to probe astrocyte glutamate uptake and show that neonatal cortical FL disrupts the functional maturation of cortical astrocytes.

  6. Revealing the synergetic effects in Ni nanoparticle-carbon nanotube hybrids by scanning transmission X-ray microscopy and their application in the hydrolysis of ammonia borane

    Science.gov (United States)

    Zhao, Guanqi; Zhong, Jun; Wang, Jian; Sham, Tsun-Kong; Sun, Xuhui; Lee, Shuit-Tong

    2015-05-01

    The hybrids of carbon nanotubes (CNTs) and the supported Ni nanoparticles (NPs) have been studied by scanning transmission X-ray microscopy (STXM) and tested by the hydrolysis reaction of ammonia borane (AB, NH3BH3). Data clearly showed the existence of a strong interaction between Ni NPs and thin CNTs (C-O-Ni bonds), which favored the tunable (buffer) electronic structure of Ni NPs facilitating the catalytic process. The hydrolysis process of AB confirmed the hypothesis that the hybrids with a strong interfacial interaction would show superior catalytic performance, while the hybrids with a weak interfacial interaction show poor performance. Our results provide a wealth of detailed information regarding the electronic structure of the NP-CNT hybrids and provide guidance towards the rational design of high-performance catalysts for energy applications.The hybrids of carbon nanotubes (CNTs) and the supported Ni nanoparticles (NPs) have been studied by scanning transmission X-ray microscopy (STXM) and tested by the hydrolysis reaction of ammonia borane (AB, NH3BH3). Data clearly showed the existence of a strong interaction between Ni NPs and thin CNTs (C-O-Ni bonds), which favored the tunable (buffer) electronic structure of Ni NPs facilitating the catalytic process. The hydrolysis process of AB confirmed the hypothesis that the hybrids with a strong interfacial interaction would show superior catalytic performance, while the hybrids with a weak interfacial interaction show poor performance. Our results provide a wealth of detailed information regarding the electronic structure of the NP-CNT hybrids and provide guidance towards the rational design of high-performance catalysts for energy applications. Electronic supplementary information (ESI) available: Magnified TEM images, high resolution TEM images and the particle size distributions of the samples, the STXM results of a thick tube at different positions, XPS results, stability test. See DOI: 10.1039/c5nr01168j

  7. Highly dynamic biological seabed alterations revealed by side scan sonar tracking of Lanice conchilega beds offshore the island of Sylt (German Bight)

    Science.gov (United States)

    Heinrich, C.; Feldens, P.; Schwarzer, K.

    2017-06-01

    Hydroacoustic surveys are common tools for habitat investigation and monitoring that aid in the realisation of the aims of the EU Marine Directives. However, the creation of habitat maps is difficult, especially when benthic organisms densely populate the seafloor. This study assesses the sensitivity of entropy and homogeneity image texture parameters derived from backscatter strength data to benthic habitats dominated by the tubeworm Lanice conchilega. Side scan sonar backscatter surveys were carried out in 2010 and 2011 in the German Bight (southern North Sea) at two sites approx. 20 km offshore of the island of Sylt. Abiotic and biotic seabed facies, such as sorted bedforms, areas of fine to medium sand and L. conchilega beds with different tube densities, were identified and characterised based on manual expert analysis and image texture analysis. Ground truthing was performed by grab sampling and underwater video observations. Compared to the manual expert analysis, the k- means classification of image textures proves to be a semi-automated method to investigate small-scale differences in a biologically altered seabed from backscatter data. The texture parameters entropy and homogeneity appear linearly interrelated with tube density, the former positively and the latter negatively. Reinvestigation of one site after 1 year showed an extensive change in the distribution of the L. conchilega-altered seabed. Such marked annual fluctuations in L. conchilega tube cover demonstrate the need for dense time series and high spatial coverage to meaningfully monitor ecological patterns on the seafloor with acoustic backscatter methods in the study region and similar settings worldwide, particularly because the sand mason plays a pivotal role in promoting biodiversity. In this context, image texture analysis provides a cost-effective and reproducible method to track biologically altered seabeds from side scan sonar backscatter signatures.

  8. Bitopic Ligands and Metastable Binding Sites

    DEFF Research Database (Denmark)

    Fronik, Philipp; Gaiser, Birgit I; Sejer Pedersen, Daniel

    2017-01-01

    G protein-coupled receptors (GPCRs) belong to a large superfamily of membrane receptors mediating a variety of physiological functions. As such they are attractive targets for drug therapy. However, it remains a challenge to develop subtype selective GPCR ligands due to the high conservation...... sites. Computational studies on ligand binding to GPCRs have revealed transient, low-affinity binding sites, termed metastable binding sites. Metastable binding sites may provide a new source of allosteric binding sites that could be exploited in the design of bitopic ligands. Unlike the bitopic ligands...

  9. Synthesis, crystal structure, fluorescence and electrochemical studies of a new tridentate Schiff base ligand and its nickel(II) and palladium(II) complexes.

    Science.gov (United States)

    Shafaatian, Bita; Soleymanpour, Ahmad; Kholghi Oskouei, Nasim; Notash, Behrouz; Rezvani, Seyyed Ahmad

    2014-07-15

    A new unsymmetrical tridentate Schiff base ligand was derived from the 1:1M condensation of ortho-vanillin with 2-mercaptoethylamine. Nickel and palladium complexes were obtained by the reaction of the tridentate Schiff base ligand with nickel(II) acetate tetrahydrate and palladium(II) acetate in 2:1M ratio. In nickel and palladium complexes the ligand was coordinated to metals via the imine N and enolic O atoms. The S groups of Schiff bases were not coordinated to the metals and S-S coupling was occured. The complexes have been found to possess 1:2 Metal:Ligand stoichiometry and the molar conductance data revealed that the metal complexes were non-electrolytes. The complexes exhibited octahedral coordination geometry. The emission spectra of the ligand and its complexes were studied in methanol. Electrochemical properties of the ligand and its metal complexes were investigated in the CH3CN solvent at the 100 mV s(-1) scan rate. The ligand and metal complexes showed both reversible and quasi-reversible processes at this scan rate. The Schiff base and its complexes have been characterized by IR, (1)H NMR, UV/Vis, elemental analyses and conductometry. The crystal structure of nickel complex has been determined by single crystal X-ray diffraction. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Cooperative scans

    NARCIS (Netherlands)

    M. Zukowski (Marcin); P.A. Boncz (Peter); M.L. Kersten (Martin)

    2004-01-01

    textabstractData mining, information retrieval and other application areas exhibit a query load with multiple concurrent queries touching a large fraction of a relation. This leads to individual query plans based on a table scan or large index scan. The implementation of this access path in most

  11. Cardiac Myocyte Diversity and a Fibroblast Network in the Junctional Region of the Zebrafish Heart Revealed by Transmission and Serial Block-Face Scanning Electron Microscopy

    KAUST Repository

    Lafontant, Pascal J.

    2013-08-23

    The zebrafish has emerged as an important model of heart development and regeneration. While the structural characteristics of the developing and adult zebrafish ventricle have been previously studied, little attention has been paid to the nature of the interface between the compact and spongy myocardium. Here we describe how these two distinct layers are structurally and functionally integrated. We demonstrate by transmission electron microscopy that this interface is complex and composed primarily of a junctional region occupied by collagen, as well as a population of fibroblasts that form a highly complex network. We also describe a continuum of uniquely flattened transitional cardiac myocytes that form a circumferential plate upon which the radially-oriented luminal trabeculae are anchored. In addition, we have uncovered within the transitional ring a subpopulation of markedly electron dense cardiac myocytes. At discrete intervals the transitional cardiac myocytes form contact bridges across the junctional space that are stabilized through localized desmosomes and fascia adherentes junctions with adjacent compact cardiac myocytes. Finally using serial block-face scanning electron microscopy, segmentation and volume reconstruction, we confirm the three-dimensional nature of the junctional region as well as the presence of the sheet-like fibroblast network. These ultrastructural studies demonstrate the previously unrecognized complexity with which the compact and spongy layers are structurally integrated, and provide a new basis for understanding development and regeneration in the zebrafish heart. © 2013 Lafontant et al.

  12. ASYMMETRY OF EYESPOT AND MATING STRUCTURE POSITIONS IN ULVA COMPRESSA (ULVALES, CHLOROPHYTA) REVEALED BY A NEW FIELD EMISSION SCANNING ELECTRON MICROSCOPY METHOD(1).

    Science.gov (United States)

    Mogi, Yuko; Kagami, Yayoi; Kuwano, Kazuyoshi; Miyamura, Shinichi; Nagumo, Tamotsu; Kawano, Shigeyuki

    2008-10-01

    Gametes of the marine green alga Ulva compressa L. are biflagellate and pear shaped, with one eyespot at the posterior end of the cell. The species is at an early evolutionary stage between isogamy and anisogamy. In the past, zygote formation of green algae was categorized solely by the relative sizes of gametes produced by two mating types (+ and -). Recently, however, locations of cell fusion sites and/or mating structures of gametes have been observed to differ between mating types in several green algae (asymmetry of cell fusion site and/or mating structure positions). To use this asymmetry for determining gamete mating type, we explored a new method, field emission scanning electron microscopy (FE-SEM), for visualizing the mating structure of U. compressa. When gametes were subjected to drying stress in the process of a conventional critical-point-drying method, a round structure was observed on the cell surfaces. In the mating type MGEC-1 (mt(+) ), this structure was located on the same side of the cell as the eyespot, whereas it was on the side opposite the eyespot in the mating type MGEC-2 (mt(-) ). The gametes fuse at the round structures. TEM showed an alignment of vesicles inside the cytoplasm directly below the round structures, which are indeed the mating structures. Serial sectioning and three-dimensional construction of TEM micrographs confirmed the association of the mating structure with flagellar roots. The mating structure was associated with 1d root in the MGEC-1 gamete but with 2d root in the MGEC-2 gamete. © 2008 Phycological Society of America.

  13. Evidence for Time-Reversal Symmetry Breaking of the Superconducting State near Twin-Boundary Interfaces in FeSe Revealed by Scanning Tunneling Spectroscopy

    Directory of Open Access Journals (Sweden)

    T. Watashige

    2015-08-01

    Full Text Available Junctions and interfaces consisting of unconventional superconductors provide an excellent experimental playground to study exotic phenomena related to the phase of the order parameter. Not only does the complex structure of unconventional order parameters have an impact on the Josephson effects, but it also may profoundly alter the quasiparticle excitation spectrum near a junction. Here, by using spectroscopic-imaging scanning tunneling microscopy, we visualize the spatial evolution of the LDOS near twin boundaries (TBs of the nodal superconductor FeSe. The π/2 rotation of the crystallographic orientation across the TB twists the structure of the unconventional order parameter, which may, in principle, bring about a zero-energy LDOS peak at the TB. The LDOS at the TB observed in our study, in contrast, does not exhibit any signature of a zero-energy peak, and an apparent gap amplitude remains finite all the way across the TB. The low-energy quasiparticle excitations associated with the gap nodes are affected by the TB over a distance more than an order of magnitude larger than the coherence length ξ_{ab}. The modification of the low-energy states is even more prominent in the region between two neighboring TBs separated by a distance ≈7ξ_{ab}. In this region, the spectral weight near the Fermi level (≈±0.2  meV due to the nodal quasiparticle spectrum is almost completely removed. These behaviors suggest that the TB induces a fully gapped state, invoking a possible twist of the order parameter structure, which breaks time-reversal symmetry.

  14. Physical properties of archaeal tetraether lipid membranes as revealed by differential scanning and pressure perturbation calorimetry, molecular acoustics, and neutron reflectometry: effects of pressure and cell growth temperature.

    Science.gov (United States)

    Zhai, Yong; Chong, Parkson Lee-Gau; Taylor, Leeandrew Jacques-Asa; Erlkamp, Mirko; Grobelny, Sebastian; Czeslik, Claus; Watkins, Erik; Winter, Roland

    2012-03-20

    The polar lipid fraction E (PLFE) is a major tetraether lipid component in the thermoacidophilic archaeon Sulfolobus acidocaldarius. Using differential scanning and pressure perturbation calorimetry as well as ultrasound velocity and density measurements, we have determined the compressibilities and volume fluctuations of PLFE liposomes derived from different cell growth temperatures (T(g) = 68, 76, and 81 °C). The compressibility and volume fluctuation values of PLFE liposomes, which are substantially less than those detected from diester lipid membranes (e.g., DPPC), exhibit small but significant differences with T(g). Among the three T(g)s employed, 76 °C leads to the least compressible and most tightly packed PLFE membranes. This temperature is within the range for optimal cell growth (75-80 °C). It is known that a decrease in T(g) decreases the number of cyclopentane rings in archael tetraether lipids. Thus, our data enable us to present the new view that membrane packing in PLFE liposomes varies with the number of cyclopentane rings in a nonlinear manner, reaching maximal tightness when the tetraether lipids are derived from cells grown at optimal T(g)s. In addition, we have studied the effects of pressure on total layer thickness, d, and neutron scattering length density, ρ(n), of a silicon-D(2)O interface that is covered with a PLFE membrane using neutron reflectometry (NR). At 55 °C, d and ρ(n) are found to be rather insensitive to pressure up to 1800 bar, suggesting minor changes of the thickness of the membrane's hydrophobic core and headgroup orientation upon compression only.

  15. Noncytopathic hepatitis A virus induces surface alterations in LLC-MK2 cells revealed by thin sections, negative staining, and scanning electron microscopy

    Directory of Open Access Journals (Sweden)

    Francisco Hernández-Chavarría

    2002-06-01

    Full Text Available Previous electron microscope studies of ultrastructural events during hepatitis A virus replication in experimentally infected cells have used only ultrathin section techniques. Nevertheless, no important differences were observed between infected and uninfected cells. This study was carried out using scanning electron microscopy and negative staining of whole LLC-MK2 cells grown directly on grids covered with support membranes, and then infected with an hepatitis A virus strain. Thin sections of infected and unifected controls were also analyzed. An intricate web of projections forming a net between cell interfaces was observed only in infected cells. Some of these projections were more than 700 nm long and had ballooning tips. Nevertheless, HAV particles were not visualized in the infected cellsLos estudios previos sobre los eventos ultraestructurales en la replicación del virus de la hepatitis Aen cultivos de células infectadas experimentalmente, se han realizado exclusivamente mediante cortes ultrafinos. No obstante, no se han observado diferencias importantes entre células infectadas y no infectadas. Este estudio fue realizado empleando microscopia electrónica de rastreo, tinción negativa de células (LLC-MK2 cultivadas directamente sobre rejillas para microscopia electrónica de transmisión e infectadas con el virus de la hepatitis A. Adicionalmente se analizaron cortes ultrafinos de células infectadas y no infectadas. Se observó una intrincada red de proyecciones entre las superficies de las células, que apareció solo en las células infectadas. Algunas de esas proyecciones medían más de 700 nm de largo y terminaban en extremos abultados. Sin embargo, no se observaron viriones en las células infectadas

  16. A genome-wide association scan on the levels of markers of inflammation in Sardinians reveals associations that underpin its complex regulation.

    Directory of Open Access Journals (Sweden)

    Silvia Naitza

    2012-01-01

    Full Text Available Identifying the genes that influence levels of pro-inflammatory molecules can help to elucidate the mechanisms underlying this process. We first conducted a two-stage genome-wide association scan (GWAS for the key inflammatory biomarkers Interleukin-6 (IL-6, the general measure of inflammation erythrocyte sedimentation rate (ESR, monocyte chemotactic protein-1 (MCP-1, and high-sensitivity C-reactive protein (hsCRP in a large cohort of individuals from the founder population of Sardinia. By analysing 731,213 autosomal or X chromosome SNPs and an additional ∼1.9 million imputed variants in 4,694 individuals, we identified several SNPs associated with the selected quantitative trait loci (QTLs and replicated all the top signals in an independent sample of 1,392 individuals from the same population. Next, to increase power to detect and resolve associations, we further genotyped the whole cohort (6,145 individuals for 293,875 variants included on the ImmunoChip and MetaboChip custom arrays. Overall, our combined approach led to the identification of 9 genome-wide significant novel independent signals-5 of which were identified only with the custom arrays-and provided confirmatory evidence for an additional 7. Novel signals include: for IL-6, in the ABO gene (rs657152, p = 2.13×10(-29; for ESR, at the HBB (rs4910472, p = 2.31×10(-11 and UCN119B/SPPL3 (rs11829037, p = 8.91×10(-10 loci; for MCP-1, near its receptor CCR2 (rs17141006, p = 7.53×10(-13 and in CADM3 (rs3026968, p = 7.63×10(-13; for hsCRP, within the CRP gene (rs3093077, p = 5.73×10(-21, near DARC (rs3845624, p = 1.43×10(-10, UNC119B/SPPL3 (rs11829037, p = 1.50×10(-14, and ICOSLG/AIRE (rs113459440, p = 1.54×10(-08 loci. Confirmatory evidence was found for IL-6 in the IL-6R gene (rs4129267; for ESR at CR1 (rs12567990 and TMEM57 (rs10903129; for MCP-1 at DARC (rs12075; and for hsCRP at CRP (rs1205, HNF1A (rs225918, and APOC-I (rs4420638. Our

  17. MRI Scans

    Science.gov (United States)

    Magnetic resonance imaging (MRI) uses a large magnet and radio waves to look at organs and structures inside your body. Health care professionals use MRI scans to diagnose a variety of conditions, from ...

  18. Bone Scan

    Science.gov (United States)

    ... posts Join Mayo Clinic Connect Bone scan About Advertisement Mayo Clinic does not endorse companies or products. ... a Job Site Map About This Site Twitter Facebook Google YouTube Pinterest Mayo Clinic is a not- ...

  19. Comprehensive SNP scan of DNA repair and DNA damage response genes reveal multiple susceptibility loci conferring risk to tobacco associated leukoplakia and oral cancer.

    Science.gov (United States)

    Mondal, Pinaki; Datta, Sayantan; Maiti, Guru Prasad; Baral, Aradhita; Jha, Ganga Nath; Panda, Chinmay Kumar; Chowdhury, Shantanu; Ghosh, Saurabh; Roy, Bidyut; Roychoudhury, Susanta

    2013-01-01

    Polymorphic variants of DNA repair and damage response genes play major role in carcinogenesis. These variants are suspected as predisposition factors to Oral Squamous Cell Carcinoma (OSCC). For identification of susceptible variants affecting OSCC development in Indian population, the "maximally informative" method of SNP selection from HapMap data to non-HapMap populations was applied. Three hundred twenty-five SNPs from 11 key genes involved in double strand break repair, mismatch repair and DNA damage response pathways were genotyped on a total of 373 OSCC, 253 leukoplakia and 535 unrelated control individuals. The significantly associated SNPs were validated in an additional cohort of 144 OSCC patients and 160 controls. The rs12515548 of MSH3 showed significant association with OSCC both in the discovery and validation phases (discovery P-value: 1.43E-05, replication P-value: 4.84E-03). Two SNPs (rs12360870 of MRE11A, P-value: 2.37E-07 and rs7003908 of PRKDC, P-value: 7.99E-05) were found to be significantly associated only with leukoplakia. Stratification of subjects based on amount of tobacco consumption identified SNPs that were associated with either high or low tobacco exposed group. The study reveals a synergism between associated SNPs and lifestyle factors in predisposition to OSCC and leukoplakia.

  20. Structure of the unique SEFIR domain from human interleukin 17 receptor A reveals a composite ligand-binding site containing a conserved α-helix for Act1 binding and IL-17 signaling.

    Science.gov (United States)

    Zhang, Bing; Liu, Caini; Qian, Wen; Han, Yue; Li, Xiaoxia; Deng, Junpeng

    2014-05-01

    Interleukin 17 (IL-17) cytokines play a crucial role in mediating inflammatory and autoimmune diseases. A unique intracellular signaling domain termed SEFIR is found within all IL-17 receptors (IL-17Rs) as well as the key adaptor protein Act1. SEFIR-mediated protein-protein interaction is a crucial step in IL-17 cytokine signaling. Here, the 2.3 Å resolution crystal structure of the SEFIR domain of IL-17RA, the most commonly shared receptor for IL-17 cytokine signaling, is reported. The structure includes the complete SEFIR domain and an additional α-helical C-terminal extension, which pack tightly together to form a compact unit. Structural comparison between the SEFIR domains of IL-17RA and IL-17RB reveals substantial differences in protein topology and folding. The uniquely long insertion between strand βC and helix αC in IL-17RA SEFIR is mostly well ordered, displaying a helix (αCC'ins) and a flexible loop (CC'). The DD' loop in the IL-17RA SEFIR structure is much shorter; it rotates nearly 90° with respect to the counterpart in the IL-17RB SEFIR structure and shifts about 12 Å to accommodate the αCC'ins helix without forming any knots. Helix αC was identified as critical for its interaction with Act1 and IL-17-stimulated gene expression. The data suggest that the heterotypic SEFIR-SEFIR association via helix αC is a conserved and signature mechanism specific for IL-17 signaling. The structure also suggests that the downstream motif of IL-17RA SEFIR together with helix αC could provide a composite ligand-binding surface for recruiting Act1 during IL-17 signaling.

  1. Structure of the unique SEFIR domain from human interleukin 17 receptor A reveals a composite ligand-binding site containing a conserved α-helix for Act1 binding and IL-17 signaling

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Bing [Oklahoma State University, Stillwater, OK 74078 (United States); Liu, Caini; Qian, Wen [Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195 (United States); Han, Yue [Oklahoma State University, Stillwater, OK 74078 (United States); Li, Xiaoxia, E-mail: lix@ccf.org [Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195 (United States); Deng, Junpeng, E-mail: lix@ccf.org [Oklahoma State University, Stillwater, OK 74078 (United States)

    2014-05-01

    Crystal structure of the SEFIR domain from human IL-17 receptor A provides new insights into IL-17 signaling. Interleukin 17 (IL-17) cytokines play a crucial role in mediating inflammatory and autoimmune diseases. A unique intracellular signaling domain termed SEFIR is found within all IL-17 receptors (IL-17Rs) as well as the key adaptor protein Act1. SEFIR-mediated protein–protein interaction is a crucial step in IL-17 cytokine signaling. Here, the 2.3 Å resolution crystal structure of the SEFIR domain of IL-17RA, the most commonly shared receptor for IL-17 cytokine signaling, is reported. The structure includes the complete SEFIR domain and an additional α-helical C-terminal extension, which pack tightly together to form a compact unit. Structural comparison between the SEFIR domains of IL-17RA and IL-17RB reveals substantial differences in protein topology and folding. The uniquely long insertion between strand βC and helix αC in IL-17RA SEFIR is mostly well ordered, displaying a helix (αCC′{sub ins}) and a flexible loop (CC′). The DD′ loop in the IL-17RA SEFIR structure is much shorter; it rotates nearly 90° with respect to the counterpart in the IL-17RB SEFIR structure and shifts about 12 Å to accommodate the αCC′{sub ins} helix without forming any knots. Helix αC was identified as critical for its interaction with Act1 and IL-17-stimulated gene expression. The data suggest that the heterotypic SEFIR–SEFIR association via helix αC is a conserved and signature mechanism specific for IL-17 signaling. The structure also suggests that the downstream motif of IL-17RA SEFIR together with helix αC could provide a composite ligand-binding surface for recruiting Act1 during IL-17 signaling.

  2. Synthesis, characterization, single crystal X-ray determination, fluorescence and electrochemical studies of new dinuclear nickel(II) and oxovanadium(IV) complexes containing double Schiff base ligands.

    Science.gov (United States)

    Shafaatian, Bita; Ozbakzaei, Zahra; Notash, Behrouz; Rezvani, S Ahmad

    2015-04-05

    A series of new bimetallic complexes of nickel(II) and vanadium(IV) have been synthesized by the reaction of the new double bidentate Schiff base ligands with nickel acetate and vanadyl acetylacetonate in 1:1 M ratio. In nickel and also vanadyl complexes the ligands were coordinated to the metals via the imine N and enolic O atoms. The complexes have been found to possess 1:1 metals to ligands stoichiometry and the molar conductance data revealed that the metal complexes were non-electrolytes. The nickel and vanadyl complexes exhibited distorted square planar and square pyramidal coordination geometries, respectively. The emission spectra of the ligands and their complexes were studied in methanol. Electrochemical properties of the ligands and their metal complexes were also investigated in DMSO solvent at 150 mV s(-1) scan rate. The ligands and metal complexes showed both quasi-reversible and irreversible processes at this scan rate. The Schiff bases and their complexes have been characterized by FT-IR, 1H NMR, UV/Vis spectroscopies, elemental analysis and conductometry. The crystal structure of the nickel complex has been determined by single crystal X-ray diffraction. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Scanning table

    CERN Multimedia

    1960-01-01

    Before the invention of wire chambers, particles tracks were analysed on scanning tables like this one. Today, the process is electronic and much faster. Bubble chamber film - currently available - (links can be found below) was used for this analysis of the particle tracks.

  4. Scan Statistics

    CERN Document Server

    Glaz, Joseph

    2009-01-01

    Suitable for graduate students and researchers in applied probability and statistics, as well as for scientists in biology, computer science, pharmaceutical science and medicine, this title brings together a collection of chapters illustrating the depth and diversity of theory, methods and applications in the area of scan statistics.

  5. Characterization of B7H6, an endogenous ligand for the NK cell activating receptor NKp30, reveals the identity of two different soluble isoforms during normal human pregnancy.

    Science.gov (United States)

    Gutierrez-Franco, Jorge; Hernandez-Gutierrez, Rodolfo; Bueno-Topete, Miriam Ruth; Haramati, Jesse; Navarro-Hernandez, Rosa Elena; Escarra-Senmarti, Marta; Vega-Magaña, Natali; Del Toro-Arreola, Alicia; Pereira-Suarez, Ana Laura; Del Toro-Arreola, Susana

    2018-01-01

    B7H6, an endogenous ligand expressed on tumor cell surfaces, triggers NKp30-mediated activation of human NK cells. In contrast, the release of soluble B7H6 has been proposed as a novel mechanism by which tumors might evade NK cell-mediated recognition. Since NK cells are critical for the maintenance of early pregnancy, it is not illogical that soluble B7H6 might also be an important factor in directing NK cell activity during normal pregnancy. Thus, this study was focused on the characterization of soluble B7H6 during the development of normal pregnancy. Serum samples were obtained from healthy pregnant women who were experiencing their second pregnancies (n=36). Additionally, 17 of these pregnant participants were longitudinally studied for the presence of B7H6 during their second and third trimesters. Age-matched healthy non-pregnant women served as controls (n=30). The presence of soluble B7H6 was revealed by Western blotting. A further characterization was performed using an immunoproteomic approach based on 2DE-Western blotting combined with MALDI-MS. The results show that sera from all pregnant women were characterized by the presence of two novel isoforms of B7H6, both with lower MW than the reported of 51kDa. These isoforms were either a heavy (∼37kDa) or a light isoform (∼30kDa) and were mutually exclusive. N-glycosylation did not completely explain the different molecular weights exhibited by the two isoforms, as was demonstrated by enzymatic deglycosylation with PNGase F. The confirmation of the identity and molecular mass of each isoform indicates that B7H6, while maintaining the C- and N-termini, is most likely released during pregnancy by a mechanism distinct from proteolytic cleavage. We found that both isoforms, but mainly the heavier B7H6, were released via exosomes; and that the lighter isoform was also released in an exosome-free manner that was not observed in the heavy isoform samples. In conclusion, we find that soluble B7H6 is

  6. Crystal structure of thioflavin T bound to the peripheral site of Torpedo californica acetylcholinesterase reveals how thioflavin T acts as a sensitive fluorescent reporter of ligand binding to the acylation site.

    Science.gov (United States)

    Harel, Michal; Sonoda, Leilani K; Silman, Israel; Sussman, Joel L; Rosenberry, Terrone L

    2008-06-25

    Acetylcholinesterase plays a key role in cholinergic synaptic transmission by hydrolyzing the neurotransmitter acetylcholine with one of the highest known catalytic rate constants. Hydrolysis occurs in a narrow and deep gorge that contains two sites of ligand binding: A peripheral site, or P-site, near the gorge entrance that contributes to catalytic efficiency both by transiently trapping substrate molecules as they enter the gorge and by allosterically accelerating the transfer of the substrate acyl group to a serine hydroxyl in an acylation site or A-site at the base of the gorge. Thioflavin T is a useful reporter of ligand interactions with the A-site. It binds specifically to the P-site with fluorescence that is enhanced approximately 1000-fold over that of unbound thioflavin T, and the enhanced fluorescence is quenched 1.5- to 4-fold when another ligand binds to the A-site in a ternary complex. To clarify the structural basis of this advantageous signal change, we here report the X-ray structure of the complex of thioflavin T with Torpedo californica acetylcholinesterase. The two aromatic rings in thioflavin T are coplanar and are packed snugly parallel to the aromatic side chains of Trp279, Tyr334, and Phe330. Overlays of this structure with the crystal structures of Torpedo californica acetylcholinesterase complexes with either edrophonium or m-( N, N, N-trimethylammonio)-2,2,2-trifluoroacetophenone, two small aromatic ligands that bind specifically to the A-site, indicate that the phenyl side chain of Phe330 must rotate to sterically accommodate both thioflavin T and the A-site ligand in the ternary complex. This rotation may allow some relaxation of the strict coplanarity of the aromatic rings in the bound thioflavin T and result in partial quenching of its fluorescence.

  7. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... News Physician Resources Professions Site Index A-Z Thyroid Scan and Uptake Thyroid scan and uptake uses ... the Thyroid Scan and Uptake? What is a Thyroid Scan and Uptake? A thyroid scan is a ...

  8. Thyroid Scan and Uptake

    Science.gov (United States)

    ... News Physician Resources Professions Site Index A-Z Thyroid Scan and Uptake Thyroid scan and uptake uses ... the Thyroid Scan and Uptake? What is a Thyroid Scan and Uptake? A thyroid scan is a ...

  9. Ligand modeling and design

    Energy Technology Data Exchange (ETDEWEB)

    Hay, B.P. [Pacific Northwest National Lab., Richland, WA (United States)

    1997-10-01

    The purpose of this work is to develop and implement a molecular design basis for selecting organic ligands that would be used in the cost-effective removal of specific radionuclides from nuclear waste streams. Organic ligands with metal ion specificity are critical components in the development of solvent extraction and ion exchange processes that are highly selective for targeted radionuclides. The traditional approach to the development of such ligands involves lengthy programs of organic synthesis and testing, which in the absence of reliable methods for screening compounds before synthesis, results in wasted research effort. The author`s approach breaks down and simplifies this costly process with the aid of computer-based molecular modeling techniques. Commercial software for organic molecular modeling is being configured to examine the interactions between organic ligands and metal ions, yielding an inexpensive, commercially or readily available computational tool that can be used to predict the structures and energies of ligand-metal complexes. Users will be able to correlate the large body of existing experimental data on structure, solution binding affinity, and metal ion selectivity to develop structural design criteria. These criteria will provide a basis for selecting ligands that can be implemented in separations technologies through collaboration with other DOE national laboratories and private industry. The initial focus will be to select ether-based ligands that can be applied to the recovery and concentration of the alkali and alkaline earth metal ions including cesium, strontium, and radium.

  10. A screening cascade to identify ERβ ligands.

    Science.gov (United States)

    Filgueira, Carly S; Benod, Cindy; Lou, Xiaohua; Gunamalai, Prem S; Villagomez, Rosa A; Strom, Anders; Gustafsson, Jan-Åke; Berkenstam, Anders L; Webb, Paul

    2014-01-01

    The establishment of effective high throughput screening cascades to identify nuclear receptor (NR) ligands that will trigger defined, therapeutically useful sets of NR activities is of considerable importance. Repositioning of existing approved drugs with known side effect profiles can provide advantages because de novo drug design suffers from high developmental failure rates and undesirable side effects which have dramatically increased costs. Ligands that target estrogen receptor β (ERβ) could be useful in a variety of diseases ranging from cancer to neurological to cardiovascular disorders. In this context, it is important to minimize cross-reactivity with ERα, which has been shown to trigger increased rates of several types of cancer. Because of high sequence similarities between the ligand binding domains of ERα and ERβ, preferentially targeting one subtype can prove challenging. Here, we describe a sequential ligand screening approach comprised of complementary in-house assays to identify small molecules that are selective for ERβ. Methods include differential scanning fluorimetry, fluorescence polarization and a GAL4 transactivation assay. We used this strategy to screen several commercially-available chemical libraries, identifying thirty ERβ binders that were examined for their selectivity for ERβ versus ERα, and tested the effects of selected ligands in a prostate cancer cell proliferation assay. We suggest that this approach could be used to rapidly identify candidates for drug repurposing.

  11. Hydroxide ion versus chloride and methoxide as an exogenous ligand reveals the influence of hydrogen bonding with second-sphere coordination water molecules in the electron transfer kinetics of Mn complexes.

    Science.gov (United States)

    El Ghachtouli, Sanae; Guillot, Régis; Aukauloo, Ally; Dorlet, Pierre; Anxolabéhère-Mallart, Elodie; Costentin, Cyrille

    2012-03-19

    We recently reported on the synthesis of a new pentadentate N(4)O ligand, tBuL(-), together with the X-ray diffraction structure of the corresponding mononuclear manganese(III)-hydroxo complex namely [(tBuL)Mn(III)OH](ClO(4)), (1 (ClO(4))). [El Ghachtouli et al. Energy Environ. Sci. 2011, 4, 2041.] In the present work, we evidence through electrochemical analysis that complex 1(+), in the presence of water, shows a peculiar behavior toward electron-transfer kinetics. The synthesis, single-crystal X-ray diffraction, and EPR spectroscopic characterization of two other mononuclear manganese(III)-chlorido and methoxo complexes-namely, [(tBuL)Mn(III)Cl](PF(6)), (2(PF(6))) and [(tBuL)Mn(III)OMe](ClO(4)), (3(ClO(4)))-are also reported. 2(PF(6)) and 3(ClO(4)) compounds will serve as reference complexes for the electron-transfer kinetics investigation. The peculiar behavior of 1(ClO(4)) is attributed to the specificity of hydroxide anion as ligand presumably allowing intermolecular hydrogen-bonding interactions and thus affecting electron-transfer properties. © 2012 American Chemical Society

  12. Ligand modeling and design

    Energy Technology Data Exchange (ETDEWEB)

    Hay, B. [Pacific Northwest Lab., Richland, WA (United States)

    1996-10-01

    The purpose of this work is to develop and implement a molecular design basis for selecting organic ligands that would be used tin applications for the cost-effective removal of specific radionuclides from nuclear waste streams.

  13. Negative Ion Photoelectron Spectroscopy Reveals Remarkable Noninnocence of Ligands in Nickel Bis(dithiolene) Complexes [Ni(dddt) 2 ] - and [Ni(edo) 2 ] -

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Xing; Hou, Gao-Lei; Wang, Xue B.; Wang, Xuefeng

    2016-04-21

    [Ni(dddt)2] (dddt = 5,6-dihydro-1,4-dithiine-2,3-dithiolate) and [Ni(edo)2] (edo = 5,6-dihydro-1,4-dioxine-2,3-dithiolate) are two donor-type nickel bis(dithiolene) complexes, with the tendency of donating low binding energy electrons. These two structurally similar complexes differ only with respect to the outer atoms in the ligand framework where the former has four S atoms while the latter has four O atoms. Herein, we report a negative ion photoelectron spectroscopy (NIPES) study on these two complexes to probe electronic structures of the anions and their corresponding neutrals. The NIPE spectra exhibit the adiabatic electron detachment energy (ADE) or, equivalently, the electron affinity (EA) of the neutral [Ni(L)2]0 to be relatively low for this type complexes, 2.780 and 2.375 eV for L = dddt and edo, respectively. The 0.4 eV difference in ADEs shows significant substitution effect for sulfur in dddt by oxygen in edo, i.e., noninnocence of the ligands, which has decreased the electronic stability of [Ni(edo)2] by lowering its electron binding energy by ~0.4 eV. The observed substitution effect on gas-phase EA values correlates well with the measured redox potentials for [Ni(dddt)2]–/0 and [Ni(edo)2]–/0 in solutions. The singlet-triplet splitting (ΔEST) of [Ni(dddt)2]0 and [Ni(edo)2]0 is also determined from the spectra to be 0.57 and 0.53 eV, respectively. Accompanying DFT calculations and molecular orbital (MO) composition analyses show significant ligand contributions to the redox MOs and allow the components of the orbitals involved in each electronic transition and spectral assignments to be identified.

  14. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... limitations of the Thyroid Scan and Uptake? What is a Thyroid Scan and Uptake? A thyroid scan is ... top of page What are some common uses of the procedure? The thyroid scan is used to ...

  15. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... of the Thyroid Scan and Uptake? What is a Thyroid Scan and Uptake? A thyroid scan is ... of page What are some common uses of the procedure? The thyroid scan is used to determine ...

  16. Lumbar spine CT scan

    Science.gov (United States)

    CAT scan - lumbar spine; Computed axial tomography scan - lumbar spine; Computed tomography scan - lumbar spine; CT - lower ... The lumbar CT scan is good for evaluating large herniated disks, ... smaller ones. This test can be combined with a myelogram to get ...

  17. Arm CT scan

    Science.gov (United States)

    CAT scan - arm; Computed axial tomography scan - arm; Computed tomography scan - arm; CT scan - arm ... stopping.) A computer creates separate images of the arm area, called slices. These images can be stored, ...

  18. Thoracic spine CT scan

    Science.gov (United States)

    CAT scan - thoracic spine; Computed axial tomography scan - thoracic spine; Computed tomography scan - thoracic spine; CT scan - ... Philadelphia, PA: Elsevier Mosby; 2013:chap 44. US Food and Drug Administration. Computed tomography (CT). Updated August ...

  19. Transcriptome Analysis of the Central and Peripheral Nervous Systems of the Spider Cupiennius salei Reveals Multiple Putative Cys-Loop Ligand Gated Ion Channel Subunits and an Acetylcholine Binding Protein.

    Directory of Open Access Journals (Sweden)

    Päivi H Torkkeli

    Full Text Available Invertebrates possess a diverse collection of pentameric Cys-loop ligand gated ion channel (LGIC receptors whose molecular structures, evolution and relationships to mammalian counterparts have been intensely investigated in several clinically and agriculturally important species. These receptors are targets for a variety of control agents that may also harm beneficial species. However, little is known about Cys-loop receptors in spiders, which are important natural predators of insects. We assembled de novo transcriptomes from the central and peripheral nervous systems of the Central American wandering spider Cupiennius salei, a model species for neurophysiological, behavioral and developmental studies. We found 15 Cys-loop receptor subunits that are expected to form anion or cation permeable channels, plus a putative acetylcholine binding protein (AChBP that has only previously been reported in molluscs and one annelid. We used phylogenetic and sequence analysis to compare the spider subunits to homologous receptors in other species and predicted the 3D structures of each protein using the I-Tasser server. The quality of homology models improved with increasing sequence identity to the available high-resolution templates. We found that C. salei has orthologous γ-aminobutyric acid (GABA, GluCl, pHCl, HisCl and nAChα LGIC subunits to other arthropods, but some subgroups are specific to arachnids, or only to spiders. C. salei sequences were phylogenetically closest to gene fragments from the social spider, Stegodyphus mimosarum, indicating high conservation within the Araneomorphae suborder of spiders. C. salei sequences had similar ligand binding and transmembrane regions to other invertebrate and vertebrate LGICs. They also had motifs associated with high sensitivity to insecticides and antiparasitic agents such as fipronil, dieldrin and ivermectin. Development of truly selective control agents for pest species will require information about

  20. Characterizing common substructures of ligands for GPCR protein subfamilies.

    Science.gov (United States)

    Erguner, Bekir; Hattori, Masahiro; Goto, Susumu; Kanehisa, Minoru

    2010-01-01

    The G-protein coupled receptor (GPCR) superfamily is the largest class of proteins with therapeutic value. More than 40% of present prescription drugs are GPCR ligands. The high therapeutic value of GPCR proteins and recent advancements in virtual screening methods gave rise to many virtual screening studies for GPCR ligands. However, in spite of vast amounts of research studying their functions and characteristics, 3D structures of most GPCRs are still unknown. This makes target-based virtual screenings of GPCR ligands extremely difficult, and successful virtual screening techniques rely heavily on ligand information. These virtual screening methods focus on specific features of ligands on GPCR protein level, and common features of ligands on higher levels of GPCR classification are yet to be studied. Here we extracted common substructures of GPCR ligands of GPCR protein subfamilies. We used the SIMCOMP, a graph-based chemical structure comparison program, and hierarchical clustering to reveal common substructures. We applied our method to 850 GPCR ligands and we found 53 common substructures covering 439 ligands. These substructures contribute to deeper understanding of structural features of GPCR ligands which can be used in new drug discovery methods.

  1. Brain PET scan

    Science.gov (United States)

    ... have false results on a PET scan. Blood sugar or insulin levels may affect the test results in people with diabetes . PET scans may be done along with a CT scan. This combination scan is called a PET/CT. Alternative Names Brain positron emission tomography; PET scan - brain References Chernecky ...

  2. Coronary Calcium Scan

    Science.gov (United States)

    ... Back To Health Topics / Coronary Calcium Scan Coronary Calcium Scan Also known as Calcium Scan Test A coronary calcium scan is a CT scan of your heart that detects and measures the amount of calcium in the walls of your coronary arteries. Overview ...

  3. Sterically demanding iminopyridine ligands

    NARCIS (Netherlands)

    Irrgang, Torsten; Keller, Sandra; Maisel, Heidi; Kretschmer, Winfried; Kempe, Rhett

    Two sterically demanding iminopyridine ligands, (2,6-diisopropylphenyl)[6-(2,4,6-triisopropylphenyl)pyridin-2-ylmeth- ylene]amine and (2,6-diisopropylphenyl)]6-(2,6-dimethylphenyl)pyridin-2-ylmethylene]amine, were prepared by a two-step process: first, condensation of 6-bromopyridine-2-carbaldehyde

  4. Incorporation of ionic ligands accelerates drug release from LDI-glycerol polyurethanes.

    Science.gov (United States)

    Sivak, Wesley N; Zhang, Jianying; Petoud, Stephane; Beckman, Eric J

    2010-01-01

    This study seeks to determine the effect of ionic ligands on the drug delivery characteristics of biodegradable polyurethane materials synthesized from lysine diisocyanate (LDI) and glycerol. Two naturally occurring, structurally related ionic species, choline chloride (CC) and isethionic acid (ISE), along with 3,3-dimethyl-butanol (DMB), their neutral carbon analog, were covalently incorporated into LDI-glycerol polyurethane materials. Selected organometallic and tertiary amine catalysts were used to fashion films and foams, respectively. The potent anticancer compound DB-67, a fluorescent camptothecin derivative, was also covalently linked to the polyurethane constructs. It was first determined that the sulfonate functional group on ISE does not react to a significant degree with isocyanate. The morphological characteristics of the polyurethane films and foams were assessed via scanning electron microscopy, showing significant differences related to the ionic ligands. The ionic materials displayed increased swelling in aqueous media over the neutral control materials. Differences in the distribution of DB-67 throughout the films and foams were then detected by fluorescence microscopy. The drug delivery characteristics of the materials were then evaluated in vitro, revealing accelerated release from ionic materials. The results of this study demonstrate the unique effects that incorporation of ionic ligands into LDI-glycerol polyurethanes have on the morphology and drug distribution of the materials. These differences have a significant impact on the drug delivery characteristics of the materials, and this information should prove useful in the design and synthesis of biodegradable controlled release systems.

  5. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... of the Thyroid Scan and Uptake? What is a Thyroid Scan and Uptake? A thyroid scan is ... code: Phone no: Thank you! Do you have a personal story about radiology? Share your patient story ...

  6. Heart PET scan

    Science.gov (United States)

    ... nuclear medicine scan; Heart positron emission tomography; Myocardial PET scan ... A PET scan requires a small amount of radioactive material (tracer). This tracer is given through a vein (IV), ...

  7. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... of the Thyroid Scan and Uptake? What is a Thyroid Scan and Uptake? A thyroid scan is ... taking our brief survey: Survey Do you have a personal story about radiology? Share your patient story ...

  8. Metal-ligand cooperation at tethered pi-ligands

    NARCIS (Netherlands)

    Verhoeven, Dide G. A.; Moret, Marc-Etienne

    2016-01-01

    Metal–ligand cooperativity in homogeneous catalysis is emerging as a powerful tool for the design of efficient transition-metal catalysts. This perspective highlights recent advances in the use of neutral π-coordinating ligands, tethered to a transition-metal center by other donor ligands, as

  9. Ligand binding and thermostability of different allosteric states of the insulin zinc-hexamer

    DEFF Research Database (Denmark)

    Huus, Kasper; Havelund, Svend; Olsen, Helle B

    2006-01-01

    The influence of ligand binding and conformation state on the thermostability of hexameric zinc-insulin was studied by differential scanning calorimetry (DSC). The insulin hexamer exists in equilibrium between the forms T6, T3R3, and R6. Phenolic ligands induce and stabilize the T3R3- and R6-stat...

  10. MIBG scans in patients with stage 4 neuroblastoma reveal two metastatic patterns, one is associated with MYCN amplification and in MYCN-amplified tumours correlates with a better prognosis

    NARCIS (Netherlands)

    G. Bleeker (Gitta); B.L.F. van Eck-Smit (Berthe); K. Zwinderman (Koos); R. Versteeg (Rogier); M.M. van Noesel (Max); B.L. Kam (Boen); G.J. Kaspers (Gertjan J.); A. van Schie (Annelies); S.G. Kreissman (Susan G.); G. Yanik (Gregory); B. Hero (Barbara); M. Schmidt (Matthias); G. Laureys (Geneviève); B. Lambert (Bieke); I. Øra (Ingrid); J.H. Schulte (Johannes); H.N. Caron (Huib); G.A.M. Tytgat (Godelieve )

    2014-01-01

    textabstractMethods: Diagnostic 123I-MIBG scans from 249 patients (123 from a European and 126 from the COG cohort) were assessed for metastatic spread in 14 body segments and the form of the lesions: “focal” (clear margins distinguishable from adjacent background) or “diffuse”

  11. MIBG scans in patients with stage 4 neuroblastoma reveal two metastatic patterns, one is associated with MYCN amplification and in MYCN-amplified tumours correlates with a better prognosis

    NARCIS (Netherlands)

    Bleeker, Gitta; van Eck-Smit, Berthe L.; Zwinderman, Koos H.; Versteeg, Rogier; van Noesel, Max M.; Kam, Boen L.; Kaspers, Gertjan J.; van Schie, Annelies; Kreissman, Susan G.; Yanik, Gregory; Hero, Barbara; Schmidt, Matthias; Laureys, Geneviève; Lambert, Bieke; Øra, Ingrid; Schulte, Johannes H.; Caron, Huib N.; Tytgat, Godelieve A.

    2015-01-01

    Purpose The aim of this study was to find clinically relevant MIBG-avid metastatic patterns in patients with newly diagnosed stage 4 neuroblastoma. Methods Diagnostic I-123-MIBG scans from 249 patients (123 from a European and 126 from the COG cohort) were assessed for metastatic spread in 14 body

  12. Models of protein-ligand crystal structures: trust, but verify

    Science.gov (United States)

    Deller, Marc C.; Rupp, Bernhard

    2015-09-01

    X-ray crystallography provides the most accurate models of protein-ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein-ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein-ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein-ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein-ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein-ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein-ligand models for their computational and biological studies, and we provide an overview of how this can be achieved.

  13. Competitive antagonism of AMPA receptors by ligands of different classes

    DEFF Research Database (Denmark)

    Hogner, Anders; Greenwood, Jeremy R; Liljefors, Tommy

    2003-01-01

    Ionotropic glutamate receptors (iGluRs) constitute a family of ligand-gated ion channels that are essential for mediating fast synaptic transmission in the central nervous system. This study presents a high-resolution X-ray structure of the competitive antagonist (S)-2-amino-3-[5-tert-butyl-3......-(phosphonomethoxy)-4-isoxazolyl]propionic acid (ATPO) in complex with the ligand-binding core of the receptor. Comparison with the only previous structure of the ligand-binding core in complex with an antagonist, 6,7-dinitro-2,3-quinoxalinedione (DNQX) (Armstrong, N.; Gouaux, E. Neuron 2000, 28, 165-181), reveals...

  14. Glutamate receptor ligands

    DEFF Research Database (Denmark)

    Guldbrandt, Mette; Johansen, Tommy N; Frydenvang, Karla Andrea

    2002-01-01

    Homologation and substitution on the carbon backbone of (S)-glutamic acid [(S)-Glu, 1], as well as absolute stereochemistry, are structural parameters of key importance for the pharmacological profile of (S)-Glu receptor ligands. We describe a series of methyl-substituted 2-aminoadipic acid (AA.......g., IC(50) = 300 microM for (2R,4S)-4-methyl-AA (5d)]. The two unsaturated analogs (S)- (7a) and (R)-(E)-Delta(4)-5-methyl-AA (7b) turned out to be a weak AMPA receptor agonist and a weak mixed NMDA/AMPA receptor antagonist, respectively....

  15. AMPA receptor ligands

    DEFF Research Database (Denmark)

    Strømgaard, Kristian; Mellor, Ian

    2004-01-01

    Alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptors (AMPAR), subtype of the ionotropic glutamate receptors (IGRs), mediate fast synaptic transmission in the central nervous system (CNS), and are involved in many neurological disorders, as well as being a key player...... polyamines are known to modulate the function of these receptors in vivo. In this study, recent developments in the medicinal chemistry of polyamine-based ligands are given, particularly focusing on the use of solid-phase synthesis (SPS) as a tool for the facile generation of libraries of polyamine toxin...

  16. Amino acid ionic liquids as chiral ligands in ligand-exchange chiral separations.

    Science.gov (United States)

    Liu, Qian; Wu, Kangkang; Tang, Fei; Yao, Lihua; Yang, Fei; Nie, Zhou; Yao, Shouzhuo

    2009-09-28

    Recently, amino acid ionic liquids (AAILs) have attracted much research interest. In this paper, we present the first application of AAILs in chiral separation based on the chiral ligand exchange principle. By using 1-alkyl-3-methylimidazolium L-proline (L-Pro) as a chiral ligand coordinated with copper(II), four pairs of underivatized amino acid enantiomers-dl-phenylalanine (dl-Phe), dl-histidine (dl-His), dl-tryptophane (dl-Trp), and dl-tyrosine (dl-Tyr)-were successfully separated in two major chiral separation techniques, HPLC and capillary electrophoresis (CE), with higher enantioselectivity than conventionally used amino acid ligands (resolution (R(s))=3.26-10.81 for HPLC; R(s)=1.34-4.27 for CE). Interestingly, increasing the alkyl chain length of the AAIL cation remarkably enhanced the enantioselectivity. It was inferred that the alkylmethylimidazolium cations and L-Pro form ion pairs on the surface of the stationary phase or on the inner surface of the capillary. The ternary copper complexes with L-Pro are consequently attached to the support surface, thus inducing an ion-exchange type of retention for the dl-enantiomers. Therefore, the AAIL cation plays an essential role in the separation. This work demonstrates that AAILs are good alternatives to conventional amino acid ligands for ligand-exchange-based chiral separation. It also reveals the tremendous application potential of this new type of task-specific ILs.

  17. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... concern for you. If you had an intravenous line inserted for the procedure, it will usually be ... procedure that same day that requires an intravenous line. Actual scanning time for a thyroid scan is ...

  18. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... the limitations of the Thyroid Scan and Uptake? What is a Thyroid Scan and Uptake? A thyroid ... body converts food to energy. top of page What are some common uses of the procedure? The ...

  19. RBC nuclear scan

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003835.htm RBC nuclear scan To use the sharing features on this page, please enable JavaScript. An RBC nuclear scan uses small amounts of radioactive material to ...

  20. Conformational diversity and ligand tunnels of mammalian cytochrome P450s.

    Science.gov (United States)

    Yu, Xiaofeng; Cojocaru, Vlad; Wade, Rebecca C

    2013-01-01

    The mammalian cytochrome P450 (CYP) enzymes play important roles in drug metabolism, steroid biosynthesis, and xenobiotic degradation. The active site of CYPs is buried in the protein and thus the ligands have to enter and exit the active site via ligand tunnels. Conformational changes of flexible parts of the protein usually accompany the entrance and exit of ligands. Comparison of the crystal structures of mammalian CYPs in closed, open, and partially open states reveals that the greatest conformational diversity associated with ligand tunnel opening is in the regions of the B-C and F-G loops. Some CYPs have been observed to adopt different open and closed conformations when bound to different ligands, suggesting that the ligand entrance and exit routes might differ according to the ligand properties. Mammalian CYPs are mostly membrane-bound enzymes, making them difficult to characterize structurally and dynamically. A range of molecular dynamics simulation techniques has been applied to investigate the dynamics and the ligand tunnels of these proteins both in the aqueous environment, and more recently, in lipid bilayers. These simulations not only reveal multiple tunnels through which ligands can pass but also show that different tunnels are preferred by different ligands and that the lipid bilayer can influence the protein dynamics and tunnel opening. The results indicate that not only the active site but also the ligand tunnels can contribute to the different substrate specificity profiles of the mammalian CYPs. © 2013 International Union of Biochemistry and Molecular Biology, Inc.

  1. Metal-ligand cooperation at tethered π-ligands.

    Science.gov (United States)

    Verhoeven, Dide G A; Moret, Marc-Etienne

    2016-10-12

    Metal-ligand cooperativity in homogeneous catalysis is emerging as a powerful tool for the design of efficient transition-metal catalysts. This perspective highlights recent advances in the use of neutral π-coordinating ligands, tethered to a transition-metal center by other donor ligands, as cooperative reaction centers. The state-of-the-art organometallic complexes, including π-coordinating ligands originating from C[double bond, length as m-dash]C, C[double bond, length as m-dash]E (E = O, N) and boron containing moieties, are described here, with special attention on their specific reactivity. Geometric and electronic aspects of ligand design and their influence on the coordination mode and reactivity of the π-system are discussed.

  2. Macrocyclic G-quadruplex ligands

    DEFF Research Database (Denmark)

    Nielsen, M C; Ulven, Trond

    2010-01-01

    are macrocyclic structures which have been modeled after the natural product telomestatin or from porphyrin-based ligands discovered in the late 1990s. These two structural classes of G-quadruplex ligands are reviewed here with special attention to selectivity and structure-activity relationships, and with focus...

  3. Coordination polymers from the self-assembly of silver(I) salts and two nonlinear aliphatic dinitrile ligands, cis-1,3-cyclopentanedicarbonitrile and cis-1,3-bis(cyanomethyl)cyclopentane: synthesis, structures, and photoluminescent properties.

    Science.gov (United States)

    Genuis, Emerson D; Kelly, Joel A; Patel, Malay; McDonald, Robert; Ferguson, Michael J; Greidanus-Strom, Grace

    2008-07-21

    Six coordination polymers with aliphatic dinitrile ligands, {[Ag(cpdcn)2]ClO4}n (6a), {[Ag(cpdcn)2]PF6}n (6b), {[Ag(cpdcn)2]SbF6}n (6c, cpdcn = cis-1,3-cyclopentanedicarbonitrile), {[Ag(bcmcp)2] ClO4}n (7a), {[Ag(bcmcp)2]PF6}n (7b), {[Ag(bcmcp)2]SbF6}n, (7c, bcmcp = cis-1,3-bis(cyanomethyl)cyclopentane) have been synthesized and structurally characterized by IR spectroscopy, differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and X-ray crystallography. Both ligands used in this study are meso-compounds; while the ligand cpdcn is structurally rigid, the ligand bcmcp has greater conformational flexibility. X-ray crystallography has revealed that structures 6a-c consist of chiral 1D-polymers. The structure of complexes 7a and 7b are best described as a 2D chiral (4,4) square mesh with 3-fold parallel interpenetration. Surprisingly, complex 7c was characterized to be an achiral 1D coordination polymer. The synthesis of the ligands, IR spectra of the free and coordinated CN groups, DSC and TGA, and the photoluminescent properties of complexes 6a-c and 7a-c are also discussed.

  4. MIBG scans in patients with stage 4 neuroblastoma reveal two metastatic patterns, one is associated with MYCN amplification and in MYCN-amplified tumours correlates with a better prognosis

    Energy Technology Data Exchange (ETDEWEB)

    Bleeker, Gitta [Academic Medical Centre/Emma Children' s Hospital, Department of Paediatric Oncology, Amsterdam (Netherlands); Academic Medical Centre, Department of Oncogenomics, Amsterdam (Netherlands); Eck-Smit, Berthe L. van [Academic Medical Centre, Department of Nuclear Medicine, Amsterdam (Netherlands); Zwinderman, Koos H. [Academic Medical Centre, Department of Biostatistics, Amsterdam (Netherlands); Versteeg, Rogier [Academic Medical Centre, Department of Oncogenomics, Amsterdam (Netherlands); Noesel, Max M. van [Erasmus Medical Centre/Sophia Children' s Hospital, Department of Paediatric Oncology/Haematology, Rotterdam (Netherlands); Kam, Boen L. [Erasmus Medical Centre, Department of Nuclear Medicine, Rotterdam (Netherlands); Kaspers, Gertjan J. [VU University Medical Centre, Department of Paediatric Oncology, Amsterdam (Netherlands); Schie, Annelies van [VU University Medical Centre, Department of Nuclear Medicine, Amsterdam (Netherlands); Kreissman, Susan G. [Duke University Medical Centre, Durham, NC (United States); University of Florida, Children' s Oncology Group (COG), Gainesville, FL (United States); Yanik, Gregory [University of Florida, Children' s Oncology Group (COG), Gainesville, FL (United States); University of Michigan, Department of Paediatrics, Division of Haematology and Oncology, Ann Arbor, MI (United States); Hero, Barbara [University Hospital of Cologne, Children' s Hospital, Cologne (Germany); Schmidt, Matthias [University Hospital of Cologne, Department of Nuclear Medicine, Cologne (Germany); Laureys, Genevieve [Ghent University Hospital, Department of Paediatric Haematology and Oncology, Ghent (Belgium); Lambert, Bieke [Ghent University Hospital, Department of Nuclear Medicine, Ghent (Belgium); Oera, Ingrid [Academic Medical Centre, Department of Oncogenomics, Amsterdam (Netherlands); Lund University Hospital, Department of Paediatric Oncology, Lund (Sweden); Schulte, Johannes H. [University Children' s Hospital Essen, Essen (Germany); Caron, Huib N.; Tytgat, Godelieve A. [Academic Medical Centre/Emma Children' s Hospital, Department of Paediatric Oncology, Amsterdam (Netherlands); Dutch Childhood Oncology Group (DCOG), The Hague (Netherlands)

    2014-09-30

    The aim of this study was to find clinically relevant MIBG-avid metastatic patterns in patients with newly diagnosed stage 4 neuroblastoma. Diagnostic {sup 123}I-MIBG scans from 249 patients (123 from a European and 126 from the COG cohort) were assessed for metastatic spread in 14 body segments and the form of the lesions: ''focal'' (clear margins distinguishable from adjacent background) or ''diffuse'' (indistinct margins, dispersed throughout the body segment). The total numbers of diffuse and focal lesions were recorded. Patients were then categorized as having lesions exclusively focal, lesions more focal than diffuse, lesions more diffuse than focal, or lesions exclusively diffuse. Diffuse lesions affected a median of seven body segments and focal lesions a median of two body segments (P < 0.001, both cohorts). Patients with a focal pattern had a median of 2 affected body segments and those with a diffuse pattern a median of 11 affected body segments (P < 0.001, both cohorts). Thus, two MIBG-avid metastatic patterns emerged: ''limited-focal'' and ''extensive-diffuse''. The median numbers of affected body segments in MYCN-amplified (MNA) tumours were 5 (European cohort) and 4 (COG cohort) compared to 9 and 11, respectively, in single-copy MYCN (MYCNsc) tumours (P < 0.001). Patients with exclusively focal metastases were more likely to have a MNA tumour (60 % and 70 %, respectively) than patients with the other types of metastases (23 % and 28 %, respectively; P < 0.001). In a multivariate Cox regression analysis, focal metastases were associated with a better event-free and overall survival than the other types of metastases in patients with MNA tumours in the COG cohort (P < 0.01). Two metastatic patterns were found: a ''limited and focal'' pattern found mainly in patients with MNA neuroblastoma that correlated with prognosis, and an ''extensive and

  5. Two novel mixed-ligand complexes containing organosulfonate ligands.

    Science.gov (United States)

    Li, Mingtian; Huang, Jun; Zhou, Xuan; Fang, Hua; Ding, Liyun

    2008-07-01

    The structures reported herein, viz. bis(4-aminonaphthalene-1-sulfonato-kappaO)bis(4,5-diazafluoren-9-one-kappa(2)N,N')copper(II), [Cu(C(10)H(8)NO(3)S)(2)(C(11)H(6)N(2)O)(2)], (I), and poly[[[diaquacadmium(II)]-bis(mu-4-aminonaphthalene-1-sulfonato)-kappa(2)O:N;kappa(2)N:O] dihydrate], {[Cd(C(10)H(8)NO(3)S)(2)(H(2)O)(2)].2H(2)O}(n), (II), are rare examples of sulfonate-containing complexes where the anion does not fulfill a passive charge-balancing role, but takes an active part in coordination as a monodentate and/or bridging ligand. Monomeric complex (I) possesses a crystallographic inversion center at the Cu(II) atom, and the asymmetric unit contains one-half of a Cu atom, one complete 4-aminonaphthalene-1-sulfonate (ans) ligand and one 4,5-diazafluoren-9-one (DAFO) ligand. The Cu(II) atom has an elongated distorted octahedral coordination geometry formed by two O atoms from two monodentate ans ligands and by four N atoms from two DAFO molecules. Complex (II) is polymeric and its crystal structure is built up by one-dimensional chains and solvent water molecules. Here also the cation (a Cd(II) atom) lies on a crystallographic inversion center and adopts a slightly distorted octahedral geometry. Each ans anion serves as a bridging ligand linking two Cd(II) atoms into one-dimensional infinite chains along the [010] direction, with each Cd(II) center coordinated by four ans ligands via O and N atoms and by two aqua ligands. In both structures, there are significant pi-pi stacking interactions between adjacent ligands and hydrogen bonds contribute to the formation of two- and three-dimensional networks.

  6. Scanning laser Doppler vibrometry

    DEFF Research Database (Denmark)

    Brøns, Marie; Thomsen, Jon Juel

    With a Scanning Laser Doppler Vibrometer (SLDV) a vibrating surface is automatically scanned over predefined grid points, and data processed for displaying vibration properties like mode shapes, natural frequencies, damping ratios, and operational deflection shapes. Our SLDV – a PSV-500H from...

  7. Frequency scanning microstrip antennas

    DEFF Research Database (Denmark)

    Danielsen, Magnus; Jørgensen, Rolf

    1979-01-01

    The principles of using radiating microstrip resonators as elements in a frequency scanning antenna array are described. The resonators are cascade-coupled. This gives a scan of the main lobe due to the phase-shift in the resonator in addition to that created by the transmission line phase...

  8. Correcting ligands, metabolites, and pathways

    NARCIS (Netherlands)

    Ott, M.A.; Vriend, G.

    2006-01-01

    BACKGROUND: A wide range of research areas in bioinformatics, molecular biology and medicinal chemistry require precise chemical structure information about molecules and reactions, e.g. drug design, ligand docking, metabolic network reconstruction, and systems biology. Most available databases,

  9. FAS Ligand Triggers Pulmonary Silicosis

    Science.gov (United States)

    Borges, Valéria M.; Falcão, Haroldo; Leite-Júnior, José H.; Alvim, Luciana; Teixeira, Gerlinde P.; Russo, Momtchilo; Nóbrega, Alberto F.; Lopes, Marcela F.; Rocco, Patricia M.; Davidson, Wendy F.; Linden, Rafael; Yagita, Hideo; Zin, Walter A.; DosReis, George A.

    2001-01-01

    We investigated the role of Fas ligand in murine silicosis. Wild-type mice instilled with silica developed severe pulmonary inflammation, with local production of tumor necrosis factor (TNF)-α, and interstitial neutrophil and macrophage infiltration in the lungs. Strikingly, Fas ligand–deficient generalized lymphoproliferative disease mutant (gld) mice did not develop silicosis. The gld mice had markedly reduced neutrophil extravasation into bronchoalveolar space, and did not show increased TNF-α production, nor pulmonary inflammation. Bone marrow chimeras and local adoptive transfer demonstrated that wild-type, but not Fas ligand–deficient lung macrophages recruit neutrophils and initiate silicosis. Silica induced Fas ligand expression in lung macrophages in vitro and in vivo, and promoted Fas ligand–dependent macrophage apoptosis. Administration of neutralizing anti-Fas ligand antibody in vivo blocked induction of silicosis. Thus, Fas ligand plays a central role in induction of pulmonary silicosis. PMID:11457890

  10. Crystal structure of nonadentate tricompartmental ligand derived from pyridine-2,6-dicarboxylic acid: Spectroscopic, electrochemical and thermal investigations of its transition metal(II) complexes

    Science.gov (United States)

    Vadavi, Ramesh S.; Shenoy, Rashmi V.; Badiger, Dayananda S.; Gudasi, Kalagouda B.; Devi, L. Gomathi; Nethaji, Munirathinam

    2011-07-01

    The coordinating behavior of a new dihydrazone ligand, 2,6-bis[(3-methoxysalicylidene)hydrazinocarbonyl]pyridine towards manganese(II), cobalt(II), nickel(II), copper(II), zinc(II) and cadmium(II) has been described. The metal complexes were characterized by magnetic moments, conductivity measurements, spectral (IR, NMR, UV-Vis, FAB-Mass and EPR) and thermal studies. The ligand crystallizes in triclinic system, space group P-1, with α = 98.491(10)°, β = 110.820(10)° and γ = 92.228(10)°. The cell dimensions are a = 10.196(7) Å, b = 10.814(7) Å, c = 10.017(7) Å, Z = 2 and V = 1117.4(12). IR spectral studies reveal the nonadentate behavior of the ligand. All the complexes are neutral in nature and possess six-coordinate geometry around each metal center. The X-band EPR spectra of copper(II) complex at both room temperature and liquid nitrogen temperature showed unresolved broad signals with giso = 2.106. Cyclic voltametric studies of copper(II) complex at different scan rates reveal that all the reaction occurring are irreversible.

  11. A General Strategy for Ligand Exchange on Upconversion Nanoparticles.

    Science.gov (United States)

    Kong, Wei; Sun, Tianying; Chen, Bing; Chen, Xian; Ai, Fujin; Zhu, Xiaoyue; Li, Mingyu; Zhang, Wenjun; Zhu, Guangyu; Wang, Feng

    2017-01-17

    Lanthanide-doped upconversion nanoparticles with a suitable surface coating are appealing for biomedical applications. Because high-quality upconversion nanoparticles are typically prepared in an organic solvent and passivated by hydrophobic oleate ligands, a convenient and reliable method for the surface modification of upconversion nanoparticles is thus highly desired to satisfy downstream biological investigations. In this work, we describe a facile and versatile strategy for displacing native oleate ligands on upconversion nanoparticles with a diversity of hydrophilic molecules. The ligand-exchange procedure involves the removal of original oleate ligands followed by the attachment of new ligands in a separate step. The successful coating of relevant ligands was confirmed by Fourier transform infrared spectroscopy, thermogravimetry analysis, and ζ-potential measurement. The surface-modified nanoparticles display high stability and good biocompatibility, as revealed by electron microscopy, photoluminescence spectroscopy, and cytotoxicity assessment. Our study demonstrates that functional biomolecules such as biotin can be directly immobilized on the nanoparticle surface using this approach for the quick and effective detection of streptavidin.

  12. Laser Scanning in Forests

    Directory of Open Access Journals (Sweden)

    Håkan Olsson

    2012-09-01

    Full Text Available The introduction of Airborne Laser Scanning (ALS to forests has been revolutionary during the last decade. This development was facilitated by combining earlier ranging lidar discoveries [1–5], with experience obtained from full-waveform ranging radar [6,7] to new airborne laser scanning systems which had components such as a GNSS receiver (Global Navigation Satellite System, IMU (Inertial Measurement Unit and a scanning mechanism. Since the first commercial ALS in 1994, new ALS-based forest inventory approaches have been reported feasible for operational activities [8–12]. ALS is currently operationally applied for stand level forest inventories, for example, in Nordic countries. In Finland alone, the adoption of ALS for forest data collection has led to an annual savings of around 20 M€/year, and the work is mainly done by companies instead of governmental organizations. In spite of the long implementation times and there being a limited tradition of making changes in the forest sector, laser scanning was commercially and operationally applied after about only one decade of research. When analyzing high-ranked journal papers from ISI Web of Science, the topic of laser scanning of forests has been the driving force for the whole laser scanning research society over the last decade. Thus, the topic “laser scanning in forests” has provided a significant industrial, societal and scientific impact. [...

  13. Tris(pyrazolyl)phosphine oxide and Tris(triazolyl)phosphine oxide scorpion ligands

    NARCIS (Netherlands)

    Tazelaar, Cornelis G J; Lyaskovskyy, Volodymyr; Van Doorn, Ilana M.; Schaapkens, Xander; Lutz, Martin; Ehlers, Andreas W.; Slootweg, Jack; Lammertsma, Koop

    2014-01-01

    DFT calculations were performed on copper(I) complexes of neutral scorpion ligands based on either pyrazolyl (Pz) or triazolyl (Tz) rings with both methane and phosphine oxide apexes, that is, HC(Pz)3, OP(Pz)3, HC(Tz)3, and OP(Tz)3. The analyses reveal that all four ligands have similar donor

  14. The effect of axial ligand on the oxidation of syringyl alcohol by Co(salen) adducts

    Science.gov (United States)

    Thomas Elder; Joseph Bozell; Diana Cedeno

    2013-01-01

    Experimental work on the oxidation of the lignin model, syringyl alcohol, using oxygen and a Co(salen) catalyst has revealed variations in yield with different imidazole-based axial ligands. A reasonable linear relationship was found between product yield and pKa of the axial ligand. The current work, using density functional calculations, examined geometric,...

  15. Langmuir-Blodgett monolayers of InP quantum dots with short chain ligands.

    Science.gov (United States)

    Lambert, K; Wittebrood, L; Moreels, I; Deresmes, D; Grandidier, B; Hens, Z

    2006-08-15

    We demonstrate the organization of nearly monodisperse colloidal InP quantum dots at the air/water interface in Langmuir monolayers. The organization of the particles is monitored in situ by surface pressure-surface area measurements and ex situ by AFM measurements on films transferred to mica by Langmuir-Blodgett deposition. The influence of different ligands on the quality of the monolayer formed has been studied. We show that densely packed monolayers with little holes can be formed using short chain ligands like pyridine and pentamethylene sulfide. The advantage of using short chain ligands for electron tunneling to or from the quantum dots is demonstrated using scanning tunneling spectroscopy.

  16. Iron-binding ligands in the southern California Current System: mechanistic studies

    Directory of Open Access Journals (Sweden)

    Randelle M Bundy

    2016-03-01

    Full Text Available The distributions of dissolved iron and organic iron-binding ligands were examined in water column profiles and deckboard incubation experiments in the southern California Current System (sCCS along a transition from coastal to semi-oligotrophic waters. Analysis of the iron-binding ligand pool by competitive ligand exchange-adsorptive cathodic stripping voltammetry (CLE-ACSV using multiple analytical windows (MAWs revealed three classes of iron-binding ligands present throughout the water column (L1-L3, whose distributions closely matched those of dissolved iron and nitrate. Despite significant biogeochemical gradients, ligand profiles were similar between stations, with surface minima in strong ligands (L1 and L2, and relatively constant concentrations of weaker ligands (L3 down to 500 m. A phytoplankton grow-out incubation, initiated from an iron-limited water mass, showed dynamic temporal cycling of iron-binding ligands. A biological iron model was able to capture the patterns of the strong ligands in the grow-out incubation relatively well with only the microbial community as a biological source. An experiment focused on remineralization of particulate organic matter showed production of both strong and weak iron-binding ligands by the heterotrophic community, supporting a mechanism for in-situ production of both strong and weak iron-binding ligands in the subsurface water column. Photochemical experiments showed a variable influence of sunlight on the degradation of natural iron-binding ligands, providing some evidence to explain differences in surface ligand concentrations between stations. Patterns in ligand distributions between profiles and in the incubation experiments were primarily related to macronutrient concentrations, suggesting microbial remineralization processes might dominate on longer time-scales over short-term changes associated with photochemistry or phytoplankton growth.

  17. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... energy. top of page What are some common uses of the procedure? The thyroid scan is used ... gland evaluate changes in the gland following medication use, surgery, radiotherapy or chemotherapy top of page How ...

  18. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... nuclear medicine procedures are able to pinpoint molecular activity within the body, they offer the potential to ... tells you otherwise, you may resume your normal activities after your nuclear medicine scan. If any special ...

  19. Body CT (CAT Scan)

    Science.gov (United States)

    ... Professions Site Index A-Z Computed Tomography (CT) - Body Computed tomography (CT) of the body uses special ... the Body? What is CT Scanning of the Body? Computed tomography, more commonly known as a CT ...

  20. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... scan and uptake uses small amounts of radioactive materials called radiotracers, a special camera and a computer ... last two months that used iodine-based contrast material. Your doctor will instruct you on how to ...

  1. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... evaluate changes in the gland following medication use, surgery, radiotherapy or chemotherapy top of page How should ... such as an x-ray or CT scan, surgeries or treatments using iodinated contrast material within the ...

  2. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... imaging procedures. For many diseases, nuclear medicine scans yield the most useful information needed to make a ... any. Nuclear medicine is less expensive and may yield more precise information than exploratory surgery. Risks Because ...

  3. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... Actual scanning time for each thyroid uptake is five minutes or less. top of page What will ... diagnostic procedures have been used for more than five decades, and there are no known long-term ...

  4. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... A thyroid scan is a type of nuclear medicine imaging. The radioactive iodine uptake test (RAIU) is ... thyroid function, but does not involve imaging. Nuclear medicine is a branch of medical imaging that uses ...

  5. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... several hours before your exam because eating can affect the accuracy of the uptake measurement. Jewelry and ... often unattainable using other imaging procedures. For many diseases, nuclear medicine scans yield the most useful information ...

  6. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... iodine, medications and anesthetics. are breastfeeding. In the days prior to your examination, blood tests may be ... are scheduled for an additional procedure that same day that requires an intravenous line. Actual scanning time ...

  7. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... gland in the neck that controls metabolism , a chemical process that regulates the rate at which the body converts food to energy. top of page What are some common uses of the procedure? The thyroid scan is ...

  8. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... liquid or capsule form, it is typically swallowed up to 24 hours before the scan. The radiotracer given by intravenous injection is usually given up to 30 minutes prior to the test. When ...

  9. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... regulates the rate at which the body converts food to energy. top of page What are some ... often unattainable using other imaging procedures. For many diseases, nuclear medicine scans yield the most useful information ...

  10. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... Because nuclear medicine procedures are able to pinpoint molecular activity within the body, they offer the potential ... or imaging device that produces pictures and provides molecular information. The thyroid scan and thyroid uptake provide ...

  11. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... body. top of page How does the procedure work? With ordinary x-ray examinations, an image is ... with other imaging techniques, such as CT or MRI. However, nuclear medicine scans are more sensitive than ...

  12. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... a special camera or imaging device that produces pictures and provides molecular information. The thyroid scan and ... and with the help of a computer, create pictures offering details on both the structure and function ...

  13. Pediatric CT Scans

    Science.gov (United States)

    The Radiation Epidemiology Branch and collaborators have initiated a retrospective cohort study to evaluate the relationship between radiation exposure from CT scans conducted during childhood and adolescence and the subsequent development of cancer.

  14. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... abnormal was found, and should not be a cause of concern for you. If you had an ... abnormal was found, and should not be a cause of concern for you. Actual scanning time for ...

  15. Scanning Auger Electron Microscope

    Data.gov (United States)

    Federal Laboratory Consortium — A JEOL model 7830F field emission source, scanning Auger microscope.Specifications / Capabilities:Ultra-high vacuum (UHV), electron gun range from 0.1 kV to 25 kV,...

  16. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... scan and thyroid uptake provide information about the structure and function of the thyroid. The thyroid is ... computer, create pictures offering details on both the structure and function of organs and tissues in your ...

  17. The Scanning Optical Microscope.

    Science.gov (United States)

    Sheppard, C. J. R.

    1978-01-01

    Describes the principle of the scanning optical microscope and explains its advantages over the conventional microscope in the improvement of resolution and contrast, as well as the possibility of producing a picture from optical harmonies generated within the specimen.

  18. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... scan you are undergoing. top of page What does the equipment look like? The special camera and ... area of your body. top of page How does the procedure work? With ordinary x-ray examinations, ...

  19. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... eat for several hours before your exam because eating can affect the accuracy of the uptake measurement. ... often unattainable using other imaging procedures. For many diseases, nuclear medicine scans yield the most useful information ...

  20. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... found, and should not be a cause of concern for you. If you had an intravenous line ... found, and should not be a cause of concern for you. Actual scanning time for each thyroid ...

  1. Slow Scan Telemedicine

    Science.gov (United States)

    1984-01-01

    Originally developed under contract for NASA by Ball Bros. Research Corporation for acquiring visual information from lunar and planetary spacecraft, system uses standard closed circuit camera connected to a device called a scan converter, which slows the stream of images to match an audio circuit, such as a telephone line. Transmitted to its destination, the image is reconverted by another scan converter and displayed on a monitor. In addition to assist scans, technique allows transmission of x-rays, nuclear scans, ultrasonic imagery, thermograms, electrocardiograms or live views of patient. Also allows conferencing and consultation among medical centers, general practitioners, specialists and disease control centers. Commercialized by Colorado Video, Inc., major employment is in business and industry for teleconferencing, cable TV news, transmission of scientific/engineering data, security, information retrieval, insurance claim adjustment, instructional programs, and remote viewing of advertising layouts, real estate, construction sites or products.

  2. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... of page What are some common uses of the procedure? The thyroid scan is used to determine ... you are undergoing. top of page What does the equipment look like? The special camera and imaging ...

  3. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... to identify disease in its earliest stages as well as a patient’s immediate response to therapeutic interventions. ... but is often performed on hospitalized patients as well. Thyroid Scan You will be positioned on an ...

  4. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... Uptake? A thyroid scan is a type of nuclear medicine imaging. The radioactive iodine uptake test (RAIU) ... of thyroid function, but does not involve imaging. Nuclear medicine is a branch of medical imaging that ...

  5. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... medical tests that help physicians diagnose and evaluate medical conditions. These imaging scans use radioactive materials called radiopharmaceuticals or radiotracers . Depending on the type of nuclear medicine exam, the radiotracer is either injected into the body, ...

  6. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... many types of cancers, heart disease, gastrointestinal, endocrine, neurological disorders and other abnormalities within the body. Because ... with other imaging techniques, such as CT or MRI. However, nuclear medicine scans are more sensitive than ...

  7. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... are noninvasive and, with the exception of intravenous injections, are usually painless medical tests that help physicians ... before the scan. The radiotracer given by intravenous injection is usually given up to 30 minutes prior ...

  8. Scan path entropy and Arrow plots: Capturing scanning behavior of multiple observers

    Directory of Open Access Journals (Sweden)

    Ignace T C Hooge

    2013-12-01

    Full Text Available Designers of visual communication material want their material to attract and retain attention. In marketing research, heat maps, dwell time, and time to AOI first hit are often used as evaluation parameters. Here we present two additional measures 1 scan path entropy to quantify gaze guidance and 2 the arrow plot to visualize the average scan path. Both are based on string representations of scan paths. The latter also incorporates transition matrices and time required for 50% of the observers to first hit AOIs (T50. The new measures were tested in an eye tracking study (48 observers, 39 advertisements. Scan path entropy is a sensible measure for gaze guidance and the new visualization method reveals aspects of the average scan path and gives a better indication in what order global scanning takes place.

  9. Scanning ultrafast electron microscopy

    OpenAIRE

    Yang, Ding-Shyue; Mohammed, Omar F.; Zewail, Ahmed H.

    2010-01-01

    Progress has been made in the development of four-dimensional ultrafast electron microscopy, which enables space-time imaging of structural dynamics in the condensed phase. In ultrafast electron microscopy, the electrons are accelerated, typically to 200 keV, and the microscope operates in the transmission mode. Here, we report the development of scanning ultrafast electron microscopy using a field-emission-source configuration. Scanning of pulses is made in the single-electron mode, for whic...

  10. Improving diagnosis of appendicitis. Early autologous leukocyte scanning.

    Science.gov (United States)

    DeLaney, A R; Raviola, C A; Weber, P N; McDonald, P T; Navarro, D A; Jasko, I

    1989-10-01

    A prospective nonrandomized study investigating the accuracy and utility of autologous leukocyte scanning in the diagnosis of apendicitis was performed. One hundred patients in whom the clinical diagnosis of appendicitis was uncertain underwent indium 111 oxyquinoline labelling of autologous leukocytes and underwent scanning 2 hours following reinjection. Of 32 patients with proved appendicitis, three scans revealed normal results (false-negative rate, 0.09). Of 68 patients without appendicitis, three scans had positive results (false-positive rate, 0.03; sensitivity, 0.91; specificity, 0.97; predictive value of positive scan, 0.94; predictive value of negative scan, 0.96; and overall accuracy, 0.95). Scan results altered clinical decisions in 19 patients. In 13 cases, the scan produced images consistent with diagnoses other than appendicitis, expediting appropriate management. Early-imaging111 In oxyquinoline autologous leukocyte scanning is a practical and highly accurate adjunct for diagnosing appendicitis.

  11. Ligand-induced protein mobility in complexes of carbonic anhydrase II and benzenesulfonamides with oligoglycine chains.

    Directory of Open Access Journals (Sweden)

    Vijay M Krishnamurthy

    Full Text Available This paper describes a biophysical investigation of residual mobility in complexes of bovine carbonic anhydrase II (BCA and para-substituted benzenesulfonamide ligands with chains of 1-5 glycine subunits, and explains the previously observed increase in entropy of binding with chain length. The reported results represent the first experimental demonstration that BCA is not the rigid, static globulin that has been typically assumed, but experiences structural fluctuations upon binding ligands. NMR studies with (15N-labeled ligands demonstrated that the first glycine subunit of the chain binds without stabilization or destabilization by the more distal subunits, and suggested that the other glycine subunits of the chain behave similarly. These data suggest that a model based on ligand mobility in the complex cannot explain the thermodynamic data. Hydrogen/deuterium exchange studies provided a global estimate of protein mobility and revealed that the number of exchanged hydrogens of BCA was higher when the protein was bound to a ligand with five glycine subunits than when bound to a ligand with only one subunit, and suggested a trend of increasing number of exchanged hydrogens with increasing chain length of the BCA-bound ligand, across the series. These data support the idea that the glycine chain destabilizes the structure of BCA in a length-dependent manner, causing an increase in BCA mobility. This study highlights the need to consider ligand-induced mobility of even "static" proteins in studies of protein-ligand binding, including rational ligand design approaches.

  12. AlaScan: A Graphical User Interface for Alanine Scanning Free-Energy Calculations.

    Science.gov (United States)

    Ramadoss, Vijayaraj; Dehez, François; Chipot, Christophe

    2016-06-27

    Computation of the free-energy changes that underlie molecular recognition and association has gained significant importance due to its considerable potential in drug discovery. The massive increase of computational power in recent years substantiates the application of more accurate theoretical methods for the calculation of binding free energies. The impact of such advances is the application of parent approaches, like computational alanine scanning, to investigate in silico the effect of amino-acid replacement in protein-ligand and protein-protein complexes, or probe the thermostability of individual proteins. Because human effort represents a significant cost that precludes the routine use of this form of free-energy calculations, minimizing manual intervention constitutes a stringent prerequisite for any such systematic computation. With this objective in mind, we propose a new plug-in, referred to as AlaScan, developed within the popular visualization program VMD to automate the major steps in alanine-scanning calculations, employing free-energy perturbation as implemented in the widely used molecular dynamics code NAMD. The AlaScan plug-in can be utilized upstream, to prepare input files for selected alanine mutations. It can also be utilized downstream to perform the analysis of different alanine-scanning calculations and to report the free-energy estimates in a user-friendly graphical user interface, allowing favorable mutations to be identified at a glance. The plug-in also assists the end-user in assessing the reliability of the calculation through rapid visual inspection.

  13. Structural characterization, luminescence and electrochemical properties of the Schiff base ligands

    Energy Technology Data Exchange (ETDEWEB)

    Ceyhan, Goekhan [Chemistry Department, K. Maras Suetcue Imam University, 46100 K. Maras (Turkey); Tuemer, Mehmet, E-mail: mtumer@ksu.edu.tr [Chemistry Department, K. Maras Suetcue Imam University, 46100 K. Maras (Turkey); Koese, Muhammet; McKee, Vickie [Chemistry Department, Loughborough University, LE11 3TU Leics (United Kingdom); Akar, Seyhan [Chemistry Department, K. Maras Suetcue Imam University, 46100 K. Maras (Turkey)

    2012-11-15

    In this study, we prepared two Schiff base ligands N-(4-hydroxy phenyl)-2,4-di-methoxy benzaldimine (TS{sup 1}) and N-(4-hydroxy phenyl)-2,5-di-methoxybenzaldimine (TS{sup 2}) which were characterized by structural, spectroscopic and analytical methods. The ligands TS{sup 1} and TS{sup 2} were obtained as single crystals from ethanol solution. X-ray diffraction data for two compounds showed that the bond lengths are within the normal ranges. The electrochemical properties of the Schiff base ligands were studied in different solvents and at various scan rates. The luminescence properties of the ligands TS{sup 1} and TS{sup 2} in different solvents and at different pH values have been investigated. The results show that the ligands exhibit more efficient luminescence properties in CH{sub 3}CN and n-butanol. - Highlights: Black-Right-Pointing-Pointer Schiff base ligands were prepared and fully characterized. Black-Right-Pointing-Pointer X-ray crystal structures of Schiff base ligands were reported. Black-Right-Pointing-Pointer Electrochemical properties of Schiff base ligands were investigated. Black-Right-Pointing-Pointer Absorption and photoluminescence properties of the Schiff bases were examined.

  14. Why mercury prefers soft ligands

    Energy Technology Data Exchange (ETDEWEB)

    Riccardi, Demian M [ORNL; Guo, Hao-Bo [ORNL; Gu, Baohua [ORNL; Parks, Jerry M [ORNL; Summers, Anne [University of Georgia, Athens, GA; Miller, S [University of California, San Francisco; Liang, Liyuan [ORNL; Smith, Jeremy C [ORNL

    2013-01-01

    Mercury (Hg) is a major global pollutant arising from both natural and anthropogenic sources. Defining the factors that determine the relative affinities of different ligands for the mercuric ion, Hg2+, is critical to understanding its speciation, transformation, and bioaccumulation in the environment. Here, we use quantum chemistry to dissect the relative binding free energies for a series of inorganic anion complexes of Hg2+. Comparison of Hg2+ ligand interactions in the gaseous and aqueous phases shows that differences in interactions with a few, local water molecules led to a clear periodic trend within the chalcogenide and halide groups and resulted in the well-known experimentally observed preference of Hg2+ for soft ligands such as thiols. Our approach establishes a basis for understanding Hg speciation in the biosphere.

  15. Polysulfide ligand exchange on zinc sulfide nanocrystal surfaces for improved film formation

    Energy Technology Data Exchange (ETDEWEB)

    Herron, Steven M. [Department of Chemistry, Stanford University, Stanford, CA 94305 (United States); Lawal, Qudus O. [Department of Chemical Engineering, Stanford University, Stanford, CA 94305 (United States); Bent, Stacey F., E-mail: sbent@stanford.edu [Department of Chemical Engineering, Stanford University, Stanford, CA 94305 (United States)

    2015-12-30

    Graphical abstract: - Highlights: • Ammonium polysulfides are prepared in aprotic solvents. • Native ligands on surfaces of colloidal ZnS nanocrystals are efficiently exchanged with polysulfides. • Ligand exchange improves crystallinity and composition in annealed ZnS thin films. • Polysulfide nanocrystal inks increase mass retention from 62% to 88%. - Abstract: The physical and chemical properties of nanocrystals can be modified by changing the ligands attached at their surfaces. A ligand exchange procedure with ammonium polysulfides has been developed to replace the native ligands on cubic zinc sulfide nanocrystals. Several mixtures of polysulfides in formamide and other solvents were prepared with different average chain lengths and used to achieve high yield ligand exchange, as confirmed by UV–vis spectroscopy, infrared spectroscopy and X-ray photoelectron spectroscopy. The results show that polysulfide content can be increased with longer surface ligands and that the exchange process yields compositionally pure surfaces before and after high temperature anneals. X-ray diffraction and scanning electron microscopy show that, when annealed in nitrogen at 525 °C, polysulfide ligands lead to average crystal sizes 2–3 times larger than in the un-exchanged control sample. The ligand exchange procedure itself does not alter nanocrystal size. Nanocrystal inks prepared from the exchanged samples form thin films that exhibit superior grain growth, morphology, mass retention, and composition compared to the un-exchanged material. Overall, polysulfide species are demonstrated as alternative ligands for the surfaces of metal chalcogenide nanocrystals which, when incorporated in an efficient ligand-exchange procedure, can improve the quality of ZnS nanocrystal inks.

  16. Laser Scanning Fluorescence Microscope

    Science.gov (United States)

    Hansen, Eric W.; Zelten, J. Peter; Wiseman, Benjamin A.

    1988-06-01

    We report on the development of a laser scanning fluorescence microscope possessing several features which facilitate its application to biological and biophysical analyses in living cells. It is built around a standard inverted microscope stand, enabling the use of standard optics, micromanipulation apparatus, and conventional (including video) microscopy in conjunction with laser scanning. The beam is scanned across the specimen by a pair of galvanometer-mounted mirrors, driven by a programmable controller which can operate in three modes: full raster scan, region of interest, and random-access. A full 512x512 pixel image can be acquired in one second. In region of interest mode, several subareas of the field can be selected for more rapid or detailed analysis. For those cases where the time scale of the observed phenomenon precludes full-field imaging, or where a full-field image is unnecessary, the random access mode enables an arbitrary pattern of isolated points to be selected and rapidly sequenced through. Via a graphical user interface implemented on the system's host computer, a user will be able to take a scout image either with video or a full-field laser scan, select regions or points on the scout image with a mouse, and set up experimental parameters such as detector integration times with a window-style menu. The instrument is designed to be a flexible testbed for investigating new techniques, without compromising its utility as a tool for biological research.

  17. Ligand-based virtual screening under partial shape constraints

    Science.gov (United States)

    von Behren, Mathias M.; Rarey, Matthias

    2017-04-01

    Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure. The new method is integrated into the LBVS tool mRAISE providing multiple options for such constraints. The applied constraints can either be derived automatically from a protein-ligand complex structure or by manual selection of ligand atoms. In this way, the descriptor directly encodes the fit of a ligand into the binding site. Furthermore, the conservation of close contacts between the binding site surface and the query ligand can be enforced. We validated our new method on the DUD and DUD-E datasets. Although the statistical performance remains on the same level, detailed analysis reveal that for certain and especially very flexible targets a significant improvement can be achieved. This is further highlighted looking at the quality of calculated molecular alignments using the recently introduced mRAISE dataset. The new partial shape constraints improved the overall quality of molecular alignments especially for difficult targets with highly flexible or different sized molecules. The software tool mRAISE is freely available on Linux operating systems for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise).

  18. Ligand-based virtual screening under partial shape constraints.

    Science.gov (United States)

    von Behren, Mathias M; Rarey, Matthias

    2017-04-01

    Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure. The new method is integrated into the LBVS tool mRAISE providing multiple options for such constraints. The applied constraints can either be derived automatically from a protein-ligand complex structure or by manual selection of ligand atoms. In this way, the descriptor directly encodes the fit of a ligand into the binding site. Furthermore, the conservation of close contacts between the binding site surface and the query ligand can be enforced. We validated our new method on the DUD and DUD-E datasets. Although the statistical performance remains on the same level, detailed analysis reveal that for certain and especially very flexible targets a significant improvement can be achieved. This is further highlighted looking at the quality of calculated molecular alignments using the recently introduced mRAISE dataset. The new partial shape constraints improved the overall quality of molecular alignments especially for difficult targets with highly flexible or different sized molecules. The software tool mRAISE is freely available on Linux operating systems for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise ).

  19. Scanning laser video camera/ microscope

    Science.gov (United States)

    Wang, C. P.; Bow, R. T.

    1984-10-01

    A laser scanning system capable of scanning at standard video rate has been developed. The scanning mirrors, circuit design and system performance, as well as its applications to video cameras and ultra-violet microscopes, are discussed.

  20. Conformer selection and differential restriction of ligand mobility by a plant lectin--conformational behaviour of Galbeta1-3GlcNAcbeta1-R, Galbeta1-3GalNAcbeta1-R and Galbeta1-2Galbeta1-R' in the free state and complexed with galactoside-specific mistletoe lectin as revealed by random-walk and conformational-clustering molecular-mechanics.

    Science.gov (United States)

    Gilleron, M; Siebert, H C; Kaltner, H; von der Lieth, C W; Kozár, T; Halkes, K M; Korchagina, E Y; Bovin, N V; Gabius, H J; Vliegenthart, J F

    1998-03-15

    To study conformational parameters of ligands before and after complex formation with the galactoside-binding agglutinin of Viscum album L. (VAA) in solution, combined computer-assisted random walk molecular mechanics (RAMM) calculations extended by conformational clustering analysis (CCA), molecular dynamics (MD) simulations as well as two-dimensional rotating-frame nuclear Overhauser effect (ROE) and two-dimensional nuclear Overhauser effect (NOE) spectroscopy NMR experiments were employed. Derivatives of the naturally occurring disaccharides Galbeta1-3GlcNAcbeta1-R and Galbeta1-3GalNAcbeta1-R as well as of a synthetic high-affinity binding partner, i.e. the disaccharide Galbeta1-2Galbeta1-R', were chosen as ligands in this study. The disaccharides displayed inherent flexibility in the valley of the global minimum between phi/psi combinations of (40 degrees/60 degrees) and (40 degrees/-60 degrees). Calculations of the de-N-acetylated sugars revealed that presence of this group did not markedly influence the distribution of low-energy conformers in the phi, psi, epsilon plot. Occupation of side minima at phi/psi (180 degrees/0 degrees) or (0 degrees/180 degrees) is either unlikely or low according to the results of MD simulations and RAMM calculations extended by CCA. Notably, these side minima define conformations which are not stable during a MD simulation. Transitions to other minima occur already a few picoseconds after the start of the simulation. NMR experiments of the free-state ligand confirmed the validity of the data sets obtained by the calculations. Following the description of the conformational space in the free-state NMR experiments were performed for these disaccharides complexed with VAA. They yielded two interresidual contacts for Galbeta1-3GlcNAcbeta1-R and Galbeta1-2Galbeta1-R'. The ligand conformations in the complex did not deviate markedly from those of a minimum conformation in the free state. One- and two-dimensional transferred nuclear

  1. Calibration of scanning Lidar

    DEFF Research Database (Denmark)

    Gómez Arranz, Paula; Courtney, Michael

    This report describes the tests carried out on a scanning lidar at the DTU Test Station for large wind turbines, Høvsøre. The tests were divided in two parts. In the first part, the purpose was to obtain wind speed calibrations at two heights against two cup anemometers mounted on a mast. Additio......This report describes the tests carried out on a scanning lidar at the DTU Test Station for large wind turbines, Høvsøre. The tests were divided in two parts. In the first part, the purpose was to obtain wind speed calibrations at two heights against two cup anemometers mounted on a mast...

  2. Tomographic scanning imager.

    Science.gov (United States)

    Hovland, Harald

    2009-07-06

    In tomographic scanning (TOSCA) imaging, light from a scene is focused onto a reticle mask using conical scan optics, and collected on a single element detector. Alternatively, one or several detectors replace the reticle. Tomographic processing techniques are then applied to the one-dimensional signal to reproduce a two-dimensional image. The TOSCA technique is presented in detail, including its mathematical foundations and some of its limitations. It is shown how TOSCA imaging can be used in a multispectral configuration, and compares well with more conventional alternatives both in simplicity and performance. Examples of image reconstruction using TOSCA techniques are shown.

  3. Scanning the phenomenological MSSM

    CERN Document Server

    Wuerzinger, Jonas

    2017-01-01

    A framework to perform scans in the 19-dimensional phenomenological MSSM is developed and used to re-evaluate the ATLAS experiments' sensitivity to R-parity-conserving supersymmetry with LHC Run 2 data ($\\sqrt{s}=13$ TeV), using results from 14 separate ATLAS searches. We perform a $\\tilde{t}_1$ dedicated scan, only considering models with $m_{\\tilde{t}_1}<1$ TeV, while allowing both a neutralino ($\\tilde{\\chi}_1^0$) and a sneutrino ($\\tilde{\

  4. Multicolor Scanning Laser Imaging in Diabetic Retinopathy.

    Science.gov (United States)

    Ahmad, Mohammad S Z; Carrim, Zia Iqbal

    2017-11-01

    Diabetic retinopathy is a common cause of blindness in individuals younger than 60 years. Screening for retinopathy is undertaken using conventional color fundus photography and relies on the identification of hemorrhages, vascular abnormalities, exudates, and cotton-wool spots. These can sometimes be difficult to identify. Multicolor scanning laser imaging, a new imaging modality, may have a role in improving screening outcomes, as well as facilitating treatment decisions. Observational case series comprising two patients with known diabetes who were referred for further examination after color fundus photography revealed abnormal findings. Multicolor scanning laser imaging was undertaken. Features of retinal disease from each modality were compared. Multicolor scanning laser imaging provides superior visualization of retinal anatomy and pathology, thereby facilitating risk stratification and treatment decisions. Multicolor scanning laser imaging is a novel imaging technique offering the potential for improving the reliability of screening for diabetic retinopathy. Validation studies are warranted.

  5. Rosetta Ligand docking with flexible XML protocols.

    Science.gov (United States)

    Lemmon, Gordon; Meiler, Jens

    2012-01-01

    RosettaLigand is premiere software for predicting how a protein and a small molecule interact. Benchmark studies demonstrate that 70% of the top scoring RosettaLigand predicted interfaces are within 2Å RMSD from the crystal structure [1]. The latest release of Rosetta ligand software includes many new features, such as (1) docking of multiple ligands simultaneously, (2) representing ligands as fragments for greater flexibility, (3) redesign of the interface during docking, and (4) an XML script based interface that gives the user full control of the ligand docking protocol.

  6. THERMODYNAMIC ASSESSMENT OF ANIONIC LIGANDS ...

    African Journals Online (AJOL)

    DJFLEX

    2010-06-30

    Jun 30, 2010 ... ion. This brings about repulsion between the adsorbent and positively charged ion and consequently a reduction in the amount of heavy metal adsorbed at lower pH. (Lee, 1999). The effectiveness of the anionic ligands in the removal of heavy metal ions from aqueous solution seems to be low for the EDTA.

  7. Scanning transmission electron microscope

    NARCIS (Netherlands)

    Kruit, P.

    2006-01-01

    The invention relates to a scanning transmission electron microscope comprising an electron source, an electron accelerator and deflection means for directing electrons emitted by the electron source at an object to be examined, and in addition a detector for detecting electrons coming from the

  8. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... you: have had any tests, such as an x-ray or CT scan, surgeries or treatments using iodinated ... page How does the procedure work? With ordinary x-ray examinations, an image is made by passing x- ...

  9. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... may be performed to measure the level of thyroid hormones in your blood. You may be told not to eat for several hours before your exam because eating can affect the ... as well. Thyroid Scan You will be positioned on an examination ...

  10. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... or less. top of page What will I experience during and after the procedure? Most thyroid scan ... areas. Outside links: For the convenience of our users, RadiologyInfo .org provides links to relevant websites. RadiologyInfo. ...

  11. Scanning bubble chamber pictures

    CERN Multimedia

    1974-01-01

    These were taken at the 2 m hydrogen bubble chamber. The photo shows an early Shiva system where the pre-measurements needed to qualify the event were done manually (cf photo 7408136X). The scanning tables were located in bld. 12. Gilberte Saulmier sits on foreground, Inge Arents at centre.

  12. Cervical MRI scan

    Science.gov (United States)

    ... cancer in the spine Arthritis in the spine MRI works better than CT scan in diagnosing these problems ... test. The strong magnetic fields created during an MRI can cause heart pacemakers and other implants to not work as well. It can also cause a piece ...

  13. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... of page Additional Information and Resources RTAnswers.org Radiation Therapy for Head and Neck Cancer top of page ... and Neck Cancer Treatment Radioactive Iodine (I-131) Therapy Head and Neck Cancer X-ray, Interventional Radiology and Nuclear ... to Thyroid Scan and Uptake ...

  14. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available ... A thyroid scan is a type of nuclear medicine imaging. The radioactive iodine uptake test (RAIU) is also known as a thyroid uptake. ... a patient’s immediate response to therapeutic interventions. Nuclear ... medical tests that help physicians diagnose and evaluate medical conditions. ...

  15. Thyroid Scan and Uptake

    Medline Plus

    Full Text Available Toggle navigation Test/Treatment Patient Type Screening/Wellness Disease/Condition Safety En Español More Info Images/Videos About Us News Physician Resources Professions Site Index A-Z Thyroid Scan and Uptake ...

  16. Terahertz scanning probe microscope

    NARCIS (Netherlands)

    Klapwijk, T.M.

    2014-01-01

    The invention provides aterahertz scanning probe microscope setup comprising (i) a terahertz radiation source configured to generate terahertz radiation; (ii) a terahertz lens configured to receive at least part of the terahertz radiation from the terahertz radiation source; (iii) a cantilever unit

  17. SPM: Scanning positron microscope

    Directory of Open Access Journals (Sweden)

    Marcel Dickmann

    2015-08-01

    Full Text Available The Munich scanning positron microscope, operated by the Universität der Bundeswehr München and the Technische Universität München, located at NEPOMUC, permits positron lifetime measurements with a lateral resolution in the µm range and within an energy range of 1 – 20 keV.

  18. Laser Beam Scanning Device.

    Science.gov (United States)

    metal mirror. Multiple thermocouple wires attached to the rear of the mirror provide temperature (and hence beam power) information at various points...on the mirror. Scanning is achieved by means of a selector switch which sequentially samples the thermocouple outputs. The thermocouple output voltages are measured and recorded as a function of laser beam power.

  19. Control of Energy Flow Dynamics between Tetracene Ligands and PbS Quantum Dots by Size Tuning and Ligand Coverage

    Energy Technology Data Exchange (ETDEWEB)

    Kroupa, Daniel M. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Arias, Dylan H. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Blackburn, Jeffrey L. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Carroll, Gerard M. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Granger, Devin B. [Department; Anthony, John E. [Department; Beard, Matthew C. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States; Johnson, Justin C. [National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States

    2018-01-08

    We have prepared a series of samples with the ligand 6,13-bistri(iso-propyl)silylethynyl tetracene 2-carboxylic acid (TIPS-Tc-COOH) attached to PbS quantum dot (QD) samples of three different sizes in order to monitor and control the extent and time scales of energy flow after photoexcitation. Fast energy transfer (~1 ps) to the PbS QD occurs upon direct excitation of the ligand for all samples. The largest size QD maintains the microsecond exciton lifetime characteristic of the as-prepared oleate terminated PbS QDs. However, two smaller QD sizes with lowest exciton energies similar to or larger than the TIPS-Tc-COO- triplet energy undergo energy transfer between QD core and ligand triplet on nanosecond to microsecond timescales. For the intermediate size QDs in particular, energy can be recycled many times between ligand and core, but the triplet remains the dominant excited species at long times, living for ~3 us for fully exchanged QDs and up to 30 us for partial ligand exchange, which is revealed as a method for controlling the triplet lifetime. A unique upconverted luminescence spectrum is observed that results from annihilation of triplets after exclusive excitation of the QD core.

  20. Ligand-specific homology modeling of human cannabinoid (CB1) receptor.

    Science.gov (United States)

    Ai, Rizi; Chang, Chia-en A

    2012-09-01

    Cannabinoid (CB1) receptor is a therapeutic drug target, and its structure and conformational changes after ligand binding are of great interest. To study the protein conformations in ligand bound state and assist in drug discovery, CB1 receptor homology models are needed for computer-based ligand screening. The known CB1 ligands are highly diverse structurally, so CB1 receptor may undergo considerable conformational changes to accept different ligands, which is challenging for molecular docking methods. To account for the flexibility of CB1 receptor, we constructed four CB1 receptor models based on four structurally distinct ligands, HU-210, ACEA, WIN55212-2 and SR141716A, using the newest X-ray crystal structures of human β₂ adrenergic receptor and adenosine A(2A) receptor as templates. The conformations of these four CB1-ligand complexes were optimized by molecular dynamics (MD) simulations. The models revealed interactions between CB1 receptor and known binders suggested by experiments and could successfully discriminate known ligands and non-binders in our docking assays. MD simulations were used to study the most flexible ligand, ACEA, in its free and bound states to investigate structural mobility achieved by the rearrangement of the fatty acid chain. Our models may capture important conformational changes of CB1 receptor to help improve accuracy in future CB1 drug screening. Copyright © 2012 Elsevier Inc. All rights reserved.

  1. Remote Control of Multimodal Nanoscale Ligand Oscillations Regulates Stem Cell Adhesion and Differentiation.

    Science.gov (United States)

    Kang, Heemin; Wong, Dexter Siu Hong; Yan, Xiaohui; Jung, Hee Joon; Kim, Sungkyu; Lin, Sien; Wei, Kongchang; Li, Gang; Dravid, Vinayak P; Bian, Liming

    2017-10-24

    Cellular adhesion is regulated by the dynamic ligation process of surface receptors, such as integrin, to adhesive motifs, such as Arg-Gly-Asp (RGD). Remote control of adhesive ligand presentation using external stimuli is an appealing strategy for the temporal regulation of cell-implant interactions in vivo and was recently demonstrated using photochemical reaction. However, the limited tissue penetration of light potentially hampers the widespread applications of this method in vivo. Here, we present a strategy for modulating the nanoscale oscillations of an integrin ligand simply and solely by adjusting the frequency of an oscillating magnetic field to regulate the adhesion and differentiation of stem cells. A superparamagnetic iron oxide nanoparticle (SPION) was conjugated with the RGD ligand and anchored to a glass substrate by a long flexible poly(ethylene glycol) linker to allow the oscillatory motion of the ligand to be magnetically tuned. In situ magnetic scanning transmission electron microscopy and atomic force microscopy imaging confirmed the nanoscale motion of the substrate-tethered RGD-grafted SPION. Our findings show that ligand oscillations under a low oscillation frequency (0.1 Hz) of the magnetic field promoted integrin-ligand binding and the formation and maturation of focal adhesions and therefore the substrate adhesion of stem cells, while ligands oscillating under high frequency (2 Hz) inhibited integrin ligation and stem cell adhesion, both in vitro and in vivo. Temporal switching of the multimodal ligand oscillations between low- and high-frequency modes reversibly regulated stem cell adhesion. The ligand oscillations further induced the stem cell differentiation and mechanosensing in the same frequency-dependent manner. Our study demonstrates a noninvasive, penetrative, and tunable approach to regulate cellular responses to biomaterials in vivo. Our work not only provides additional insight into the design considerations of biomaterials to

  2. -Pincer Ligand Family through Ligand Post-Modification

    KAUST Repository

    Huang, Mei-Hui

    2017-10-02

    A series of air-stable nickel complexes containing triazine-based PN3P-pincer ligands were synthesized and fully characterized. Complex 3 contains a de-aromatized central triazine ring from the deprotonation of one of the N–H arms. With a post-modification strategy, the Me-PN3P*NiCl complex (3) could be converted into a new class of diimine–traizine PN3P-pincer nickel complexes.

  3. Effects of successive additions of two capping ligands on the structural properties of PbO nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Bangi, Uzma K. H.; Han, Wooje [Yonsei University, Department of Materials Science and Engineering (Korea, Republic of); Yoo, Byungwook [Korea Electronics Technology Institute, Flexible Display Research Center (Korea, Republic of); Park, Hyung-Ho, E-mail: hhpark@yonsei.ac.kr [Yonsei University, Department of Materials Science and Engineering (Korea, Republic of)

    2013-11-15

    A cost-effective approach to the synthesis of lead oxide (PbO) nanoparticles by successive additions of two capping ligands using a simple method of precipitation is reported herein. The successive additions of polyvinyl pyrrolidone (PVP) and cetyltrimethyl ammonium bromide (CTAB) cap the Pb(OH){sub 2} with a primary layer of PVP and a secondary layer of CTAB, forming a bilayer system around Pb(OH){sub 2}. PVP controls the PbO particle size, while CTAB enhances the particle size of the PVP-treated PbO by seeding growth process. The effects of the successive additions of these two capping ligands were studied by varying the relative percentages of PVP and CTAB from 0 to 100 %. From transmission electron microscopy and X-ray diffraction results, it was confirmed that the size of the PbO nanoparticles decreased with a relative increase in the percentage of PVP (and corresponding decrease in the percentage of CTAB). Furthermore, X-ray diffraction results demonstrated the formation of a pure α-PbO phase. Field emission scanning electron microscopy images showed the increase in grain size with the decrease in the percentage of PVP. Infrared spectroscopy depicted the formation of PbO along with the presence of PVP and CTAB covering the particle surface. Thermogravimetric analysis and differential thermal analysis revealed the decomposition of lead oxalate to α-PbO at around 370 °C.

  4. Mammographic scanning equalization radiography.

    Science.gov (United States)

    Sabol, J M; Soutar, I C; Plewes, D B

    1993-01-01

    It is well recognized that variations in breast thickness and parenchymal composition can produce a range of exposure which exceeds the latitude of high contrast mammographic film/screen combinations. Optimal imaging of the dense breast is desired since 30%-60% of women present with dense breasts, and they are believed to be at the highest relative risk of developing breast cancer. The application of scanning equalization radiography to mammography has been investigated through the construction and characterization of a prototype mammographic scanning equalization radiography (MSER) system, designed to image mammographic phantoms. The MSER system exposes a Min-R/MRH cassette by raster scanning a 2.0 x 1.6 cm beam of pulsed x-rays across the cassette. A scanning detector behind the cassette measures the local x-ray transmission of the breast. Feedback of the transmission information is used to modulate the duration of each x-ray pulse, to equalize the film exposure. The effective dynamic range of the MSER system is 25 times greater than that of conventional mammography. Artifact-free images of mammographic phantoms show that MSER effectively overcomes the latitude limitations of film/screen mammography, enabling high contrast imaging over a wide range of object x-ray transmission. Anthropomorphic phantom images show that MSER offers up to a sixfold increase in film contrast in the normally underexposed regions of conventional mammograms. Characterization of the entrance exposure shows that there is not a significant difference in exposure between MSER and conventional mammographic techniques, suggesting that both would pose comparable risk to the patient. Calculations show that the construction of a clinical multiple beam MSER system is feasible with minor changes to existing technology.

  5. Scanning transmission electron microscope

    OpenAIRE

    Kruit, P.

    2006-01-01

    The invention relates to a scanning transmission electron microscope comprising an electron source, an electron accelerator and deflection means for directing electrons emitted by the electron source at an object to be examined, and in addition a detector for detecting electrons coming from the object and, connected to the detector, a device for processing the detected electrons so as to form an object image, wherein a beam splitter is provided for dividing the electron beam from the electron...

  6. Scanning micro-sclerometer

    Science.gov (United States)

    Oliver, Warren C.; Blau, Peter J.

    1994-01-01

    A scanning micro-sclerometer measures changes in contact stiffness and correlates these changes to characteristics of a scratch. A known force is applied to a contact junction between two bodies and a technique employing an oscillating force is used to generate the contact stiffness between the two bodies. As the two bodies slide relative to each other, the contact stiffness changes. The change is measured to characterize the scratch.

  7. Scanning drop sensor

    Science.gov (United States)

    Jin, Jian; Xiang, Chengxiang; Gregoire, John M.; Shinde, Aniketa A.; Guevarra, Dan W.; Jones, Ryan J.; Marcin, Martin R.; Mitrovic, Slobodan

    2017-05-09

    Electrochemical or electrochemical and photochemical experiments are performed on a collection of samples by suspending a drop of electrolyte solution between an electrochemical experiment probe and one of the samples that serves as a test sample. During the electrochemical experiment, the electrolyte solution is added to the drop and an output solution is removed from the drop. The probe and collection of samples can be moved relative to one another so the probe can be scanned across the samples.

  8. Scanning ultrafast electron microscopy.

    Science.gov (United States)

    Yang, Ding-Shyue; Mohammed, Omar F; Zewail, Ahmed H

    2010-08-24

    Progress has been made in the development of four-dimensional ultrafast electron microscopy, which enables space-time imaging of structural dynamics in the condensed phase. In ultrafast electron microscopy, the electrons are accelerated, typically to 200 keV, and the microscope operates in the transmission mode. Here, we report the development of scanning ultrafast electron microscopy using a field-emission-source configuration. Scanning of pulses is made in the single-electron mode, for which the pulse contains at most one or a few electrons, thus achieving imaging without the space-charge effect between electrons, and still in ten(s) of seconds. For imaging, the secondary electrons from surface structures are detected, as demonstrated here for material surfaces and biological specimens. By recording backscattered electrons, diffraction patterns from single crystals were also obtained. Scanning pulsed-electron microscopy with the acquired spatiotemporal resolutions, and its efficient heat-dissipation feature, is now poised to provide in situ 4D imaging and with environmental capability.

  9. A selection fit mechanism in BMP receptor IA as a possible source for BMP ligand-receptor promiscuity.

    Directory of Open Access Journals (Sweden)

    Stefan Harth

    Full Text Available BACKGROUND: Members of the TGF-β superfamily are characterized by a highly promiscuous ligand-receptor interaction as is readily apparent from the numeral discrepancy of only seven type I and five type II receptors available for more than 40 ligands. Structural and functional studies have been used to address the question of how specific signals can be deduced from a limited number of receptor combinations and to unravel the molecular mechanisms underlying the protein-protein recognition that allow such limited specificity. PRINCIPAL FINDINGS: In this study we have investigated how an antigen binding antibody fragment (Fab raised against the extracellular domain of the BMP receptor type IA (BMPR-IA recognizes the receptor's BMP-2 binding epitope and thereby neutralizes BMP-2 receptor activation. The crystal structure of the complex of the BMPR-IA ectodomain bound to the Fab AbD1556 revealed that the contact surface of BMPR-IA overlaps extensively with the contact surface for BMP-2 interaction. Although the structural epitopes of BMPR-IA to both binding partners coincides, the structures of BMPR-IA in the two complexes differ significantly. In contrast to the structural differences, alanine-scanning mutagenesis of BMPR-IA showed that the functional determinants for binding to the antibody and BMP-2 are almost identical. CONCLUSIONS: Comparing the structures of BMPR-IA bound to BMP-2 or bound to the Fab AbD1556 with the structure of unbound BMPR-IA shows that binding of BMPR-IA to its interaction partners follows a selection fit mechanism, possibly indicating that the ligand promiscuity of BMPR-IA is inherently encoded by structural adaptability. The functional and structural analysis of the BMPR-IA binding antibody AbD1556 mimicking the BMP-2 binding epitope may thus pave the way for the design of low-molecular weight synthetic receptor binders/inhibitors.

  10. Tumor targeting via integrin ligands

    Directory of Open Access Journals (Sweden)

    Udaya Kiran eMarelli

    2013-08-01

    Full Text Available Selective and targeted delivery of drugs to tumors is a major challenge for an effective cancer therapy and also to overcome the side effects associated with current treatments. Overexpression of various receptors on tumor cells is a characteristic structural and biochemical aspect of tumors and distinguishes them from physiologically normal cells. This abnormal feature is therefore suitable for selectively directing anticancer molecules to tumors by using ligands that can preferentially recognize such receptors. Several subtypes of integrin receptors that are crucial for cell adhesion, cell signaling, cell viability and motility have been shown to have an upregulated expression on cancer cells. Thus, ligands that recognize specific integrin subtypes represent excellent candidates to be conjugated to drugs or drug carrier systems and be targeted to tumors. In this regard, integrins recognizing the RGD cell adhesive sequence have been extensively targeted for tumor specific drug delivery. Here we review key recent examples on the presentation of RGD-based integrin ligands by means of distinct drug delivery systems, and discuss the prospects of such therapies to specifically target tumor cells.

  11. Chitosan and carboxymethyl-chitosan capping ligands: Effects on the nucleation and growth of hydroxyapatite nanoparticles for producing biocomposite membranes.

    Science.gov (United States)

    Dumont, Vitor C; Mansur, Alexandra A P; Carvalho, Sandhra M; Medeiros Borsagli, Fernanda G L; Pereira, Marivalda M; Mansur, Herman S

    2016-02-01

    Synthetic biomaterials based on calcium phosphates (CaP) have been widely studied for bone tissue reconstruction therapies, but no definitive solution that fulfills all of the required properties has been identified. Thus, this study reports the synthesis of composite membranes based on nanohydroxyapatite particles (nHA) embedded in chitosan (CHI) and O-carboxymethyl chitosan (CMC) matrices produced using a one-step co-precipitation method in water media. Biopolymers were used as capping ligands for simultaneously controlling the nucleation and growth of the nHA particles during the precipitation process and also to form the polymeric network of the biocomposites. The bionanocomposites were extensively characterized using light microscopy (LM), scanning and transmission electron microscopy (SEM/TEM), energy-dispersive X-ray spectroscopy (EDX), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), atomic force microscopy (AFM), X-ray micro-CT analysis (μCT), andMTT (3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazoliumbromide) cell proliferation assays for cell cytotoxicity. The results demonstrated that the ligands used during the synthesis highly affected the composites produced, primarily due the changes in the mechanisms and kinetics of nucleation and growth of the HA particles at the nanoscale level. The SEMimages revealed that the use of carboxyl-functionalized chitosan (CMC) ligands significantly reduced the average size of theHA nanoparticles and caused the formation of a narrower size distribution (90±20nm) compared to theHAnanoparticles producedwith chitosan ligands (220±50nm). The same trend was verified by the AFM analysis,where the nHA particles were formed evenly dispersed in the polymer matrix. However, the CMC-based composites were more homogeneously distributed, which was endorsed by the images collected via X-ray micro-CT. The FTIR spectra and the XRD analysis indicated that nanosized hydroxyapatite was the predominant calcium

  12. Metabolic Value Chemoattractants Are Preferentially Recognized at Broad Ligand Range Chemoreceptor of Pseudomonas putida KT2440

    Directory of Open Access Journals (Sweden)

    Matilde Fernández

    2017-05-01

    Full Text Available Bacteria have evolved a wide range of chemoreceptors with different ligand specificities. Typically, chemoreceptors bind ligands with elevated specificity and ligands serve as growth substrates. However, there is a chemoreceptor family that has a broad ligand specificity including many compounds that are not of metabolic value. To advance the understanding of this family, we have used the PcaY_PP (PP2643 chemoreceptor of Pseudomonas putida KT2440 as a model. Using Isothermal Titration Calorimetry we showed here that the recombinant ligand binding domain (LBD of PcaY_PP recognizes 17 different C6-ring containing carboxylic acids with KD values between 3.7 and 138 μM and chemoeffector affinity correlated with the magnitude of the chemotactic response. Mutation of the pcaY_PP gene abolished chemotaxis to these compounds; phenotype that was restored following gene complementation. Growth experiments using PcaY_PP ligands as sole C-sources revealed functional relationships between their metabolic potential and affinity for the chemoreceptor. Thus, only 7 PcaY_PP ligands supported growth and their KD values correlated with the length of the bacterial lag phase. Furthermore, PcaY_PP ligands that did not support growth had significantly higher KD values than those that did. The receptor has thus binds preferentially compounds that serve as C-sources and amongst them those that rapidly promote growth. Tightest binding compounds were quinate, shikimate, 3-dehydroshikimate and protocatechuate, which are at the interception of the biosynthetic shikimate and catabolic quinate pathways. Analytical ultracentrifugation studies showed that ligand free PcaY_PP-LBD is present in a monomer-dimer equilibrium (KD = 57.5 μM. Ligand binding caused a complete shift to the dimeric state, which appears to be a general feature of four-helix bundle LBDs. This study indicates that the metabolic potential of compounds is an important parameter in the molecular recognition

  13. Scanning radiographic apparatus

    Energy Technology Data Exchange (ETDEWEB)

    Albert, R.D.

    1980-04-01

    Visual display of dental, medical or other radiographic images is realized with an x-ray tube in which an electron beam is scanned through an x-y raster pattern on a broad anode plate, the scanning being synchronized with the x-y sweep signals of a cathode ray tube display and the intensity signal for the display being derived from a small x-ray detector which receives x-rays that have passed through the subject to be imaged. Positioning and support of the detector are provided for by disposing the detector in a probe which may be attached to the x-ray tube at any of a plurality of different locations and by providing a plurality of such probes of different configuration in order to change focal length, to accommodate to different detector placements relative to the subject, to enhance patient comfort and to enable production of both periapical images and wider angle pantomographic images. High image definition with reduced radiation dosage is provided for by a lead glass collimator situated between the x-ray tube and subject and having a large number of spaced-apart minute radiation transmissive passages convergent on the position of the detector. Releasable mounting means enable changes of collimator in conjunction with changes of the probe to change focal length. A control circuit modifies the x-y sweep signals applied to the x-ray tube and modulates electron beam energy and current in order to correct for image distortions and other undesirable effects which can otherwise be present in a scanning x-ray system.

  14. Horizon Scanning for Pharmaceuticals

    DEFF Research Database (Denmark)

    Lepage-Nefkens, Isabelle; Douw, Karla; Mantjes, GertJan

    In 2016, the Belgian, Dutch, Luxembourg and Austrian governments declared their intention to collaborate on pharmaceutical policy (BeNeLuxA Collaboration). KCE was asked to lead a task force responsible for developing a Horizon Scanning methodology for pharmaceuticals and a possible model...... and filtration of new and emerging pharmaceutical products. It will maintain and update the HS database, organise company pipeline meetings, and disseminate the HSS’s outputs.  The HS unit works closely together with the designated national HS experts in each collaborating country. The national HS experts...

  15. Surface micromachined scanning mirrors

    DEFF Research Database (Denmark)

    Mattsson, Kent Erik

    1992-01-01

    Both aluminum cantilever and torsional scanning mirrors have been fabricated and their static and dynamic properties are studied experimentally and theoretically. The experiments showed resonance frequencies in the range of 163 k-Hz - 632 kHz for cantilever beams with Q values between 5 and 11....... Torsional mirrors showed resonance frequencies in the range of 410 kHz - 667 kHz with Q values of 10 - 17. All measurements performed at atmospheric pressure. Both types of mechanical structures were deflected electrostatically at large angles (± 5°) more than 1011 times without breaking and without any...

  16. The Liver X Receptor Ligand T0901317 Down-regulates APOA5 GeneExpression through Activation of SREBP-1c

    Energy Technology Data Exchange (ETDEWEB)

    Jakel, Heidelinde; Nowak, Maxime; Moitrot, Emanuelle; Dehondt, Helene; Hum, Dean W.; Pennacchio, Len A.; Fruchart-Najib, Jamila; Fruchart,Jean-Charles

    2004-07-23

    Alterations in the expression of the recently discovered apolipoprotein A5 gene strongly affect plasma triglyceride levels. In this study, we investigated the contribution of APOA5 to the liver X-receptor (LXR) ligand mediated effect on plasma triglyceride levels.Following treatment with the LXR ligand T0901317, we found that APOA5mRNA levels were decreased in hepatoma cell lines. The observation that no down-regulation of APOA5 promoter activity was obtained by LXR-retinoid X receptor (RXR) co-transfection prompted us to explore the possible involvement of the known LXR target gene SREBP-1c (sterol regulatory element-binding protein 1c). In fact, we found that co-transfection with the active form of SREBP-1c down-regulated APOA5promoter activity in a dose-dependent manner. We then scanned the human APOA5 promoter sequence and identified two putative E-box elements that were able to bind specifically SREBP-1c in gel-shift assays and were shown to be functional by mutation analysis. Subsequent suppression of SREBP-1 mRNA through small interfering RNA interference abolished the decrease of APOA5 mRNA in response to T0901317. Finally, administration of T0901317 to hAPOA5 transgenic mice revealed a significant decrease OF APOA5 mRNA in liver tissue and circulating apolipoprotein AV protein in plasma, confirming that the described down-regulation also occurs in vivo. Taken together, our results demonstrate that APOA5 gene expression is regulated by the LXR ligand T0901317 in a negative manner through SREBP-1c. These findings may provide a new mechanism responsible for the elevation of plasma triglyceride levels by LXR ligands and support the development of selective LXR agonists, not affecting SREBP-1c, as beneficial modulators of lipid metabolism.

  17. Ligand-Mediated Folding of the OmpA Periplasmic Domain from Acinetobacter baumannii.

    Science.gov (United States)

    Mushtaq, Ameeq Ul; Park, Jeong Soon; Bae, Sung-Hun; Kim, Hye-Yeon; Yeo, Kwon Joo; Hwang, Eunha; Lee, Ki Yong; Jee, Jun-Goo; Cheong, Hae-Kap; Jeon, Young Ho

    2017-05-23

    The periplasmic domain of OmpA from Acinetobacter baumannii (AbOmpA-PD) binds to diaminopimelate and anchors the outer membrane to the peptidoglycan layer in the cell wall. Although the crystal structure of AbOmpA-PD with its ligands has been reported, the mechanism of ligand-mediated folding of AbOmpA remains elusive. Here, we report that in vitro refolded apo-AbOmpA-PD in the absence of ligand exists as a mixture of two partially folded forms in solution: mostly unfolded (apo-state I) and hololike (apo-state II) states. Binding of the diaminopimelate or glycine ligand induced complete folding of AbOmpA-PD. The apo-state I was highly flexible and contained some secondary structural elements, whereas the apo-state II closely resembled the holo-state in terms of both structure and backbone dynamics, except for the ligand-binding region. (15)N-relaxation-dispersion analyses for apo-state II revealed substantial motion on a millisecond timescale of residues in the H3 helix near the ligand-binding site, with this motion disappearing upon ligand binding. These results provide an insight into the ligand-mediated folding mechanism of AbOmpA-PD in solution. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  18. Confocal scanning Mueller polarimeter

    Science.gov (United States)

    Lompado, Arthur

    2009-08-01

    We describe the design, construction, calibration and testing of a confocal scanning Mueller polarimeter. A polarization state generator and polarization state analyzer have been inserted into the optical path of a conventional confocal scanning imager to collect the reflectance Muller matrix of samples measuring up to 6.26 mm on a side. Four sources are available for sample interrogation using diode lasers centered at 532 nm, 635 nm, 670 nm, and 785 nm. The device captures all required imagery to calculate the Mueller matrix of each image pixel in approximately 90 s. These matrices are then reduced into polarization imagery such as the diattenuation, retardance and depolarization index. Oftentimes this polarization imagery is quite different and potentially more informative than a conventional intensity image. There are a number of fields that can benefit from alternative/enhanced imagery, most notably in the biomedical, discrimination, and target recognition communities. The sensor has been designed for biomedical applications aimed at improving the technique of noninvasive detection of melanoma lesions.

  19. The selenium metabolite methylselenol regulates the expression of ligands that trigger immune activation through the lymphocyte receptor NKG2D

    DEFF Research Database (Denmark)

    Hagemann-Jensen, Michael Henrik; Uhlenbrock, Franziska Katharina; Kehlet, Stephanie

    2014-01-01

    : Increased formation of reactive oxygen species (ROS), induction of DNA damage, triggering of apoptosis and the inhibition of angiogenesis. Here, we revealed that CH3SeH modulates cell surface expression of NKG2D ligands. The expression of NKG2D ligands is induced by stress-associated pathways, which occur...... ligands. A balanced cell-surface expression of NKG2D ligands is considered as an innate barrier against tumor development. Our work therefore indicates that the application of selenium compounds, which are metabolized to CH3SeH, could improve NKG2D-based immune therapy....

  20. Metal ligand aromatic cation-pi interactions in metalloproteins: ligands coordinated to metal interact with aromatic residues.

    Science.gov (United States)

    Zarić, S D; Popović, D M; Knapp, E W

    2000-11-03

    Cation-pi interactions between aromatic residues and cationic amino groups in side chains and have been recognized as noncovalent bonding interactions relevant for molecular recognition and for stabilization and definition of the native structure of proteins. We propose a novel type of cation-pi interaction in metalloproteins; namely interaction between ligands coordinated to a metal cation--which gain positive charge from the metal--and aromatic groups in amino acid side chains. Investigation of crystal structures of metalloproteins in the Protein Data Bank (PDB) has revealed that there exist quite a number of metalloproteins in which aromatic rings of phenylalanine, tyrosine, and tryptophan are situated close to a metal center interacting with coordinated ligands. Among these ligands are amino acids such as asparagine, aspartate, glutamate, histidine, and threonine, but also water and substrates like ethanol. These interactions play a role in the stability and conformation of metalloproteins, and in some cases may also be directly involved in the mechanism of enzymatic reactions, which occur at the metal center. For the enzyme superoxide dismutase, we used quantum chemical computation to calculate that Trp163 has an interaction energy of 10.09 kcal mol(-1) with the ligands coordinated to iron.

  1. Scanning quantum decoherence microscopy.

    Science.gov (United States)

    Cole, Jared H; Hollenberg, Lloyd C L

    2009-12-09

    The use of qubits as sensitive nanoscale magnetometers has been studied theoretically and recently demonstrated experimentally. In this paper we propose a new concept, in which a scanning two-state quantum system is used to probe a sample through the subtle effects of decoherence. Mapping both the Hamiltonian and decoherence properties of a qubit simultaneously provides a unique image of the magnetic (or electric) field properties at the nanoscale. The resulting images are sensitive to the temporal as well as spatial variation in the fields created by the sample. As examples we theoretically study two applications; one from condensed matter physics, the other biophysics. The individual components required to realize the simplest version of this device (characterization and measurement of qubits, nanoscale positioning) have already been demonstrated experimentally.

  2. Automatic Ultrasound Scanning

    DEFF Research Database (Denmark)

    Moshavegh, Ramin

    Medical ultrasound has been a widely used imaging modality in healthcare platforms for examination, diagnostic purposes, and for real-time guidance during surgery. However, despite the recent advances, medical ultrasound remains the most operator-dependent imaging modality, as it heavily relies...... on the user adjustments on the scanner interface to optimize the scan settings. This explains the huge interest in the subject of this PhD project entitled “AUTOMATIC ULTRASOUND SCANNING”. The key goals of the project have been to develop automated techniques to minimize the unnecessary settings...... on the scanners, and to improve the computer-aided diagnosis (CAD) in ultrasound by introducing new quantitative measures. Thus, four major issues concerning automation of the medical ultrasound are addressed in this PhD project. They touch upon gain adjustments in ultrasound, automatic synthetic aperture image...

  3. Scanning Tunneling Spectroscopy of Graphene on Graphite

    OpenAIRE

    Li, Guohong; Luican, Adina; Andrei, Eva Y.

    2008-01-01

    We report low temperature high magnetic field scanning tunneling microscopy and spectroscopy of graphene flakes on graphite that exhibit the structural and electronic properties of graphene decoupled from the substrate. Pronounced peaks in the tunneling spectra develop with field revealing a Landau level sequence that provides a direct way to identify graphene and to determine the degree of its coupling to the substrate. The Fermi velocity and quasiparticle lifetime, obtained from the positio...

  4. Zinc complexes of Ttz(R,Me) with O and S donors reveal differences between Tp and Ttz ligands: acid stability and binding to H or an additional metal (Ttz(R,Me) = tris(3-R-5-methyl-1,2,4-triazolyl)borate; R = Ph, tBu).

    Science.gov (United States)

    Kumar, Mukesh; Papish, Elizabeth T; Zeller, Matthias; Hunter, Allen D

    2011-08-07

    Alkylzinc complexes, (Ttz(R,Me))ZnR' (R = tBu, Ph; R' = Me, Et), show interesting reactivity with acids, bases and water. With acids (e.g. fluorinated alcohols, phenols, thiophenol, acetylacetone, acetic acid, HCl and triflic acid) zinc complexes of the conjugate base (CB), (Ttz(R,Me))ZnCB, are generated. Thus the B-N bonds in Ttz ligands are acid stable. (Ttz(R,Me))ZnCB complexes were characterized by (1)H, (13)C-NMR, IR, MS, elemental analysis, and, in most cases, single crystal X-ray diffraction. The four coordinate crystal structures included (Ttz(R,Me))Zn(CB) [where R = Ph, CB (conjugate base) = OCH(2)CF(3) (2), OPh (6), SPh (8), p-OC(6)H(4)(NO(2)) (10); R = tBu, CB = OCH(CF(3))(2) (3), OPh (5), SPh (7)*, p-OC(6)H(4)(NO(2)) (9) (* indicates a rearranged Ttz ligand)]. The use of bidentate ligands resulted in structures [(Ttz(Ph,Me))Zn(CB) (CB = acac (12), OAc (14))] in which the coordination geometries are five, and intermediate between four and five, respectively. Interestingly, three forms of (Ttz(Ph,Me))Zn(p-OC(6)H(4)(NO(2))) (10) were analyzed crystallographically including a Zn coordinated water molecule in 10(H(2)O), a coordination polymer in 10(CP), and a p-nitrophenol molecule hydrogen bonded to a triazole ring in 10(Nit). Ttz ligands are flexible since they are capable of providing κ(3) or κ(2) metal binding and intermolecular interactions with either a metal center or H through the four position nitrogen (e.g. in 10(CP) and HTtz(tBu,Me)·H(2)O, respectively). Preliminary kinetic studies on the protonolysis of LZnEt (L = Ttz(tBu,Me), Tp(tBu,Me)) with p-nitrophenol in toluene at 95 °C show that these reactions are zero order in acid and first order in the LZnEt.

  5. Ligand photo-isomerization triggers conformational changes in iGluR2 ligand binding domain.

    Directory of Open Access Journals (Sweden)

    Tino Wolter

    Full Text Available Neurological glutamate receptors bind a variety of artificial ligands, both agonistic and antagonistic, in addition to glutamate. Studying their small molecule binding properties increases our understanding of the central nervous system and a variety of associated pathologies. The large, oligomeric multidomain membrane protein contains a large and flexible ligand binding domains which undergoes large conformational changes upon binding different ligands. A recent application of glutamate receptors is their activation or inhibition via photo-switchable ligands, making them key systems in the emerging field of optochemical genetics. In this work, we present a theoretical study on the binding mode and complex stability of a novel photo-switchable ligand, ATA-3, which reversibly binds to glutamate receptors ligand binding domains (LBDs. We propose two possible binding modes for this ligand based on flexible ligand docking calculations and show one of them to be analogues to the binding mode of a similar ligand, 2-BnTetAMPA. In long MD simulations, it was observed that transitions between both binding poses involve breaking and reforming the T686-E402 protein hydrogen bond. Simulating the ligand photo-isomerization process shows that the two possible configurations of the ligand azo-group have markedly different complex stabilities and equilibrium binding modes. A strong but slow protein response is observed after ligand configuration changes. This provides a microscopic foundation for the observed difference in ligand activity upon light-switching.

  6. Amine ligand-based hydrothermal synthesis of Co3O4 nanoparticles, characterization and magnetic study

    Science.gov (United States)

    Mansournia, Mohammadreza; Rakhshan, Narges

    2016-12-01

    Cobalt(II,III) oxid (Co3O4) nanostructures have been successfully synthesized using [Co(NH3)6]Cl3 and [Co(en)3]Cl3 (en: ethylenediamine) as the single precursors via hydrothermal method, and CoCl2·6H2O through a facile ammonia-assisted approach. Indeed, ammine and en ligands, as well as ammonia vapor, act as the sources of hydroxide ion in the preparation of Co3O4 nanoparticles. The structure of products was confirmed by X-ray diffraction (XRD) technique and Fourier-transform infrared (FT-IR) spectroscopy and their morphologies were examined by scanning electron microscopy (SEM). The optical study of the as-prepared Co3O4 nanostructures using UV-Vis diffused reflectance spectroscopy (DRS) exhibited their semiconducting property by revealing one optical band gap in 3.3 eV. Moreover, the vibrating sample magnetometry (VSM) measurements showed a weak ferromagnetic behavior that could be attributed to uncompensated surface spins and/or finite-size effects. Further, the effects of the nature of the precursor, its concentration, temperature and reaction time on the size and morphology of the samples were studied in detail.

  7. Clinical Use of PPARγ Ligands in Cancer

    Directory of Open Access Journals (Sweden)

    Jennifer L. Hatton

    2008-01-01

    Full Text Available The role of PPARγ in adipocyte differentiation has fueled intense interest in the function of this steroid nuclear receptor for regulation of malignant cell growth and differentiation. Given the antiproliferative and differentiating effects of PPARγ ligands on liposarcoma cells, investigation of PPARγ expression and ligand activation in other solid tumors such as breast, colon, and prostate cancers ensued. The anticancer effects of PPARγ ligands in cell culture and rodent models of a multitude of tumor types suggest broad applicability of these agents to cancer therapy. This review focuses on the clinical use of PPARγ ligands, specifically the thiazolidinediones, for the treatment and prevention of cancer.

  8. Structural and Electrochemical Consequences of [Cp*] Ligand Protonation.

    Science.gov (United States)

    Peng, Yun; Ramos-Garcés, Mario V; Lionetti, Davide; Blakemore, James D

    2017-09-05

    There are few examples of the isolation of analogous metal complexes bearing [η5-Cp*] and [η4-Cp*H] (Cp* = pentamethylcyclopentadienyl) complexes within the same metal/ligand framework, despite the relevance of such structures to catalytic applications. Recently, protonation of Cp*Rh(bpy) (bpy = 2,2'-bipyridyl) has been shown to yield a complex bearing the uncommon [η4-Cp*H] ligand, rather than generating a [RhIII-H] complex. We now report the purification and isolation of this protonated species, as well as characterization of analogous complexes of 1,10-phenanthroline (phen). Specifically, reaction of Cp*Rh(bpy) or Cp*Rh(phen) with 1 equiv of Et3NH+Br- affords rhodium compounds bearing endo-η4-pentamethylcyclopentadiene (η4-Cp*H) as a ligand. NMR spectroscopy and single-crystal X-ray diffraction studies confirm protonation of the Cp* ligand, rather than formation of metal hydride complexes. Analysis of new structural data and electronic spectra suggests that phen is significantly reduced in Cp*Rh(phen), similar to the case of Cp*Rh(bpy). Backbonding interactions with olefinic motifs are activated by formation of [η4-Cp*H]; protonation of [Cp*] stabilizes the low-valent metal center and results in loss of reduced character on the diimine ligands. In accord with these changes in electronic structure, electrochemical studies reveal a distinct manifold of redox processes that are accessible in the [Cp*H] complexes in comparison with their [Cp*] analogues; these processes suggest new applications in catalysis for the complexes bearing endo-η4-Cp*H.

  9. Scandium SALEN complexes bearing chloro, aryloxo, and hydroxo ligands.

    Science.gov (United States)

    Meermann, Christian; Törnroos, Karl W; Anwander, Reiner

    2009-03-16

    Heteroleptic amide complexes (SALEN)Sc[N(SiHMe(2))(2)] (SALEN = Salen(tBu,tBu), Salcyc(tBu,tBu), or Salpren(tBu,tBu) if not stated differently) were examined as synthesis precursors according to silylamine elimination reactions. Treatment of (SALEN)Sc[N(SiHMe(2))(2)] with H(2)O or phenols (HOAr(R,R); R = tBu, iPr) afforded complexes [(SALEN)Sc(mu-OH)](2) and (SALEN)Sc(OAr(R,R)), while chloro exchange products were formed from the respective reactions with NH(4)Cl or AlMe(2)Cl. Such complexes [(SALEN)Sc(mu-Cl)](2) and (SALEN)ScCl(thf) were also obtained by utilizing alternative synthesis protocols, allowing for controlled donor absence and presence. Heteroleptic amide precursors [Sc(NiPr(2))(2)(mu-Cl)(thf)](2) and [Sc[N(SiHMe(2))(2)](2)(mu-Cl)(thf)](2) readily undergo amine elimination reactions with H(2)SALEN derivatives to form the corresponding chloride complexes. Spectroscopic and X-ray structural data of the heteroleptic scandium complexes revealed an exclusive intramolecular tetradentate coordination mode of the SALEN ligands independent of the SALEN ligand bite angle and the nature of the "second" ligand (chloro, amido, aryloxo, hydroxo). The coordination of the SALEN ligands is rationalized on the basis of (a) the displacement d of the metal center from the [N(2)O(2)] least-squares plane, (b) the dihedral angle alpha between the phenyl rings of the salicylidene moieties, and (c) the angle beta = Ct-Ln-Ct (Ct = centroid of the phenyl rings) in the case of strongly twisted ligands.

  10. Ligand regulation of a constitutively dimeric EGF receptor

    Science.gov (United States)

    Freed, Daniel M.; Alvarado, Diego; Lemmon, Mark A.

    2015-06-01

    Ligand-induced receptor dimerization has traditionally been viewed as the key event in transmembrane signalling by epidermal growth factor receptors (EGFRs). Here we show that the Caenorhabditis elegans EGFR orthologue LET-23 is constitutively dimeric, yet responds to its ligand LIN-3 without changing oligomerization state. SAXS and mutational analyses further reveal that the preformed dimer of the LET-23 extracellular region is mediated by its domain II dimerization arm and resembles other EGFR extracellular dimers seen in structural studies. Binding of LIN-3 induces only minor structural rearrangements in the LET-23 dimer to promote signalling. Our results therefore argue that EGFR can be regulated by allosteric changes within an existing receptor dimer--resembling signalling by insulin receptor family members, which share similar extracellular domain compositions but form covalent dimers.

  11. LANL Robotic Vessel Scanning

    Energy Technology Data Exchange (ETDEWEB)

    Webber, Nels W. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-11-25

    Los Alamos National Laboratory in J-1 DARHT Operations Group uses 6ft spherical vessels to contain hazardous materials produced in a hydrodynamic experiment. These contaminated vessels must be analyzed by means of a worker entering the vessel to locate, measure, and document every penetration mark on the vessel. If the worker can be replaced by a highly automated robotic system with a high precision scanner, it will eliminate the risks to the worker and provide management with an accurate 3D model of the vessel presenting the existing damage with the flexibility to manipulate the model for better and more in-depth assessment.The project was successful in meeting the primary goal of installing an automated system which scanned a 6ft vessel with an elapsed time of 45 minutes. This robotic system reduces the total time for the original scope of work by 75 minutes and results in excellent data accumulation and transmission to the 3D model imaging program.

  12. GPR scan assessment

    Directory of Open Access Journals (Sweden)

    Abbas M. Abbas

    2015-06-01

    Full Text Available Mekaad Radwan monument is situated in the neighborhood of Bab Zuweila in the historical Cairo, Egypt. It was constructed at the middle XVII century (1635 AD. The building has a rectangle shape plan (13 × 6 m with the longitudinal sides approximately WNW-ESE. It comprises three storages namely; the ground floor; the opened floor (RADWAN Bench and the living floor with a total elevation of 15 m above the street level. The building suffers from severe deterioration phenomena with patterns of damage which have occurred over time. These deterioration and damages could be attributed to foundation problems, subsoil water and also to the earthquake that affected the entire Greater Cairo area in October 1992. Ground Penetrating Radar (GPR scan was accomplished against the walls of the opened floor (RADWAN Bench to evaluate the hazard impact on the walls textures and integrity. The results showed an anomalous feature through the southern wall of RADWAN Bench. A mathematical model has been simulated to confirm the obtained anomaly and the model response exhibited a good matching with the outlined anomaly.

  13. Macrocyclic ligands for uranium complexation

    Energy Technology Data Exchange (ETDEWEB)

    Potts, K.T.

    1991-04-01

    A highly preorganized 24-macrocycle containing biuret, thiobiuret and pyridine subunits has been prepared by high dilution ring-closure procedures. Intermediate products to this macrocycle have been utilized to extend this synthetic route to include further representatives where solubility and stability will be influenced by substituent variation. A 1:1 complex has been formed from uranyl acetate and a quinquepyridine derivative, this representing a new type of ligand for the uranyl ion. A very convenient synthetic procedure that will allow the incorporation of these macrocycles into polymeric systems has been developed for the introduction of a vinyl substituent into the 4-position of the pyridine ring. Using triflate, vinyltributyltin and Pd{sup 0} chemistry, this procedure should make a variety of substituted 4-vinylpyridines available for the first time. 3 refs.

  14. Rigid-body ligand recognition drives cytotoxic T-lymphocyte antigen 4 (CTLA-4) receptor triggering.

    Science.gov (United States)

    Yu, Chao; Sonnen, Andreas F-P; George, Roger; Dessailly, Benoit H; Stagg, Loren J; Evans, Edward J; Orengo, Christine A; Stuart, David I; Ladbury, John E; Ikemizu, Shinji; Gilbert, Robert J C; Davis, Simon J

    2011-02-25

    The inhibitory T-cell surface-expressed receptor, cytotoxic T lymphocyte-associated antigen-4 (CTLA-4), which belongs to the class of cell surface proteins phosphorylated by extrinsic tyrosine kinases that also includes antigen receptors, binds the related ligands, B7-1 and B7-2, expressed on antigen-presenting cells. Conformational changes are commonly invoked to explain ligand-induced "triggering" of this class of receptors. Crystal structures of ligand-bound CTLA-4 have been reported, but not the apo form, precluding analysis of the structural changes accompanying ligand binding. The 1.8-Å resolution structure of an apo human CTLA-4 homodimer emphasizes the shared evolutionary history of the CTLA-4/CD28 subgroup of the immunoglobulin superfamily and the antigen receptors. The ligand-bound and unbound forms of both CTLA-4 and B7-1 are remarkably similar, in marked contrast to B7-2, whose binding to CTLA-4 has elements of induced fit. Isothermal titration calorimetry reveals that ligand binding by CTLA-4 is enthalpically driven and accompanied by unfavorable entropic changes. The similarity of the thermodynamic parameters determined for the interactions of CTLA-4 with B7-1 and B7-2 suggests that the binding is not highly specific, but the conformational changes observed for B7-2 binding suggest some level of selectivity. The new structure establishes that rigid-body ligand interactions are capable of triggering CTLA-4 phosphorylation by extrinsic kinase(s).

  15. Synthesis, characterization and antimicrobial activities of mixed ligand transition metal complexes with isatin monohydrazone Schiff base ligands and heterocyclic nitrogen base

    Science.gov (United States)

    Devi, Jai; Batra, Nisha

    2015-01-01

    Mixed ligand complexes of Co(II), Ni(II), Cu(II) and Zn(II) with various uninegative tridentate ligands derived from isatin monohydrazone with 2-hydroxynapthaldehyde/substituted salicylaldehyde and heterocyclic nitrogen base 8-hydroxyquinoline have been synthesized and characterized by elemental analysis, conductometric studies, magnetic susceptibility and spectroscopic techniques (IR, UV-VIS, NMR, mass and ESR). On the basis of these characterizations, it was revealed that Schiff base ligands existed as monobasic tridentate ONO bonded to metal ion through oxygen of carbonyl group, azomethine nitrogen and deprotonated hydroxyl oxygen and heterocyclic nitrogen base 8-hydroxyquinoline existed as monobasic bidentate ON bonded through oxygen of hydroxyl group and nitrogen of quinoline ring with octahedral or distorted octahedral geometry around metal ion. All the compounds have been tested in vitro against various pathogenic Gram positive bacteria, Gram negative bacteria and fungi using different concentrations (25, 50, 100, 200 μg/mL) of ligands and their complexes. Comparative study of antimicrobial activity of ligands, and their mixed complexes indicated that complexes exhibit enhanced activity as compared to free ligands and copper(II) Cu(LIV)(Q)ṡH2O complex was found to be most potent antimicrobial agent.

  16. One ligand capable of in situ reaction in a mixed-ligand system with two new different frameworks

    KAUST Repository

    Wang, Xiaofang

    2017-12-24

    The in situ ligand 2,3-pyrazinedicarboxylic acid (2,3-H2pzdc) mixed with 1,1′-(1,4-butanediyl)bis(benzimidazole) (bbbi) is used to form two coordination polymers ([Cd(2,3-pzdc)(bbbi)] (1) and [Cd2Cl3(2-pzc)(bbbi)2] (2)) under hydrothermal conditions. Complex 1 was obtained in the absence of in situ reaction and 2 was synthesized with 2,3-H2pzdc in situ generating 2-pyrazinecarboxylate (2-pzc−). The structural details reveal that 1 has a 3D framework with dia topology, and 2 is a 2D layer structure and develops a 3D supramolecular structure via strong π⋯π stacking interactions. The ligand effects were compared for the two frameworks. In addition, fluorescence properties and thermal stabilities of 1 and 2 in the solid were studied.

  17. Cellular trafficking of quantum dot-ligand bioconjugates and their induction of changes in normal routing of unconjugated ligands

    DEFF Research Database (Denmark)

    Tekle, Christina; van Deurs, Bo; Sandvig, Kirsten

    2008-01-01

    Can quantum dots (Qdots) act as relevant intracellular probes to investigate routing of ligands in live cells? The intracellular trafficking of Qdots that were coupled to the plant toxin ricin, Shiga toxin, or the ligand transferrin (Tf) was studied by confocal fluorescence microscopy. The Tf......:Qdots were internalized by clathrin-dependent endocytosis as fast as Tf, but their recycling was blocked. Unlike Shiga toxin, the Shiga:Qdot bioconjugate was not routed to the Golgi apparatus. The internalized ricin:Qdot bioconjugates localized to the same endosomes as ricin itself but could...... not be visualized in the Golgi apparatus. Importantly, we find that the endosomal accumulation of ricin:Qdots affects endosome-to-Golgi transport of both ricin and Shiga toxin: Transport of ricin was reduced whereas transport of Shiga toxin was increased. In conclusion, the data reveal that, although coupling...

  18. Scanning Tunneling Microscopy

    Science.gov (United States)

    1992-03-17

    the study of surfact strain. A variety of studies were conducted on Au(in air) CdTe (in air), Hg1-xMnxTe (under glycerin), and Hg 1-xCdx Te (in air...HgCdTe and CdMnTe. (7) Scribing of adjacent parallel lines on the HgCdTe and CdMnTe surfaces. (8) Identification of a new c(4x6) reconstruction on some...tihodoluminescence spectroscopy, coupled with pulsed laser annealing-to reveal systematics between interface chemical and electronic structure. The

  19. Hyperchromatic laser scanning cytometry

    Science.gov (United States)

    Tárnok, Attila; Mittag, Anja

    2007-02-01

    In the emerging fields of high-content and high-throughput single cell analysis for Systems Biology and Cytomics multi- and polychromatic analysis of biological specimens has become increasingly important. Combining different technologies and staining methods polychromatic analysis (i.e. using 8 or more fluorescent colors at a time) can be pushed forward to measure anything stainable in a cell, an approach termed hyperchromatic cytometry. For cytometric cell analysis microscope based Slide Based Cytometry (SBC) technologies are ideal as, unlike flow cytometry, they are non-consumptive, i.e. the analyzed sample is fixed on the slide. Based on the feature of relocation identical cells can be subsequently reanalyzed. In this manner data on the single cell level after manipulation steps can be collected. In this overview various components for hyperchromatic cytometry are demonstrated for a SBC instrument, the Laser Scanning Cytometer (Compucyte Corp., Cambridge, MA): 1) polychromatic cytometry, 2) iterative restaining (using the same fluorochrome for restaining and subsequent reanalysis), 3) differential photobleaching (differentiating fluorochromes by their different photostability), 4) photoactivation (activating fluorescent nanoparticles or photocaged dyes), and 5) photodestruction (destruction of FRET dyes). With the intelligent combination of several of these techniques hyperchromatic cytometry allows to quantify and analyze virtually all components of relevance on the identical cell. The combination of high-throughput and high-content SBC analysis with high-resolution confocal imaging allows clear verification of phenotypically distinct subpopulations of cells with structural information. The information gained per specimen is only limited by the number of available antibodies and by sterical hindrance.

  20. Ligand-binding kinetics on histamine receptors

    NARCIS (Netherlands)

    Bosma, Reggie; Mocking, T.A.M.; Leurs, R.; Vischer, H.F.

    2017-01-01

    Equilibrium-binding affinities of ligands for a drug target do not always accurately reflect the success of drug candidates in the clinic. Affinity-based predictions concerning competitive antagonism on the target will only be accurate if equilibrium binding of both ligands is allowed. Unless

  1. Ligand based pharmacophore modelling of anticancer histone ...

    African Journals Online (AJOL)

    USER

    2010-06-21

    Jun 21, 2010 ... deacetylases (HDAC) have emerged as an important class of anticancer agents. Various side effects like myocardium damage and ... calculated through the software Jmol. The proposed model has been .... The study was carried out using the software Ligand Scout (version. 2.03[i2_001]). Ligand Scout is a ...

  2. Simple tertiary phosphines to hexaphosphane ligands: Syntheses ...

    Indian Academy of Sciences (India)

    Abstract. Designing efficient phosphorus-based ligands to make catalysts for homogeneous catalysis has been a great challenge for chemists. Despite a plethora of phosphorus ligands ranging from simple tertiary phosphines to polyphosphines are known, the enthusiasm to generate new ones is mainly due to the demand.

  3. Organotellurium ligands – designing and complexation reactions

    Indian Academy of Sciences (India)

    Unknown

    Abstract. A variety of tellurium ligands has been designed and studied for their complexation reactions in the last decade. Of these hybrid telluroethers, halotellurium ligands and polytellurides are the most notable ones. RTe–and polytelluride ions have also been used to design clusters. Ligation of ditelluroethers and ...

  4. CXCR4 Ligands : The Next Big Hit?

    NARCIS (Netherlands)

    Walenkamp, Annemiek M. E.; Lapa, Constantin; Herrmann, Ken; Wester, Hans-Juergen

    2017-01-01

    The G protein-coupled protein receptor C-X-C chemokine receptor 4 (CXCR4) is an attractive target for cancer diagnosis and treatment, as it is overexpressed in many solid and hematologic cancers. Binding of its ligand, C-X-C chemokine ligand 12 (CXCL12), results in receptor internalization and

  5. Novel chalcone-based fluorescent human histamine H3 receptor ligands as pharmacological tools

    Directory of Open Access Journals (Sweden)

    Holger eStark

    2012-03-01

    Full Text Available Novel fluorescent chalcone-based ligands at human histamine H3 receptors (hH3R have been designed, synthesized and characterized. Compounds described are non-imidazole analogues of ciproxifan with a tetralone motif. Tetralones as chemical precursors and related fluorescent chalcones exhibit affinities at hH3R in the same concentration range like that of the reference antagonist ciproxifan (hH3R pKi value of 7.2. Fluorescence characterization of our novel ligands shows emission maxima about 570 nm for yellow fluorescent chalcones and ≥600 nm for the red fluorescent derivatives. Interferences to cellular autofluorescence could be excluded. All synthesized chalcone compounds could be taken to visualize hH3R proteins in stably transfected HEK-293 cells using confocal laser scanning fluorescence microscopy. These novel fluorescent ligands possess high potential to be used as pharmacological tools for hH3R visualization in different tissues.

  6. Synergistic Regulation of Coregulator/Nuclear Receptor Interaction by Ligand and DNA.

    Science.gov (United States)

    de Vera, Ian Mitchelle S; Zheng, Jie; Novick, Scott; Shang, Jinsai; Hughes, Travis S; Brust, Richard; Munoz-Tello, Paola; Gardner, William J; Marciano, David P; Kong, Xiangming; Griffin, Patrick R; Kojetin, Douglas J

    2017-10-03

    Nuclear receptor (NR) transcription factors bind various coreceptors, small-molecule ligands, DNA response element sequences, and transcriptional coregulator proteins to affect gene transcription. Small-molecule ligands and DNA are known to influence receptor structure, coregulator protein interaction, and function; however, little is known on the mechanism of synergy between ligand and DNA. Using quantitative biochemical, biophysical, and solution structural methods, including 13C-detected nuclear magnetic resonance and hydrogen/deuterium exchange (HDX) mass spectrometry, we show that ligand and DNA cooperatively recruit the intrinsically disordered steroid receptor coactivator-2 (SRC-2/TIF2/GRIP1/NCoA-2) receptor interaction domain to peroxisome proliferator-activated receptor gamma-retinoid X receptor alpha (PPARγ-RXRα) heterodimer and reveal the binding determinants of the complex. Our data reveal a thermodynamic mechanism by which DNA binding propagates a conformational change in PPARγ-RXRα, stabilizes the receptor ligand binding domain dimer interface, and impacts ligand potency and cooperativity in NR coactivator recruitment. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Flexible ligand docking using a genetic algorithm

    Science.gov (United States)

    Oshiro, C. M.; Kuntz, I. D.; Dixon, J. Scott

    1995-04-01

    Two computational techniques have been developed to explore the orientational and conformational space of a flexible ligand within an enzyme. Both methods use the Genetic Algorithm (GA) to generate conformationally flexible ligands in conjunction with algorithms from the DOCK suite of programs to characterize the receptor site. The methods are applied to three enzyme-ligand complexes: dihydrofolate reductase-methotrexate, thymidylate synthase-phenolpthalein and HIV protease-thioketal haloperidol. Conformations and orientations close to the crystallographically determined structures are obtained, as well as alternative structures with low energy. The potential for the GA method to screen a database of compounds is also examined. A collection of ligands is evaluated simultaneously, rather than docking the ligands individually into the enzyme.

  8. Scanning Ion Conductance Microscopy of Live Keratinocytes

    Science.gov (United States)

    Hegde, V.; Mason, A.; Saliev, T.; Smith, F. J. D.; McLean, W. H. I.; Campbell, P. A.

    2012-07-01

    Scanning ion conductance microscopy (SICM) is perhaps the least well known technique from the scanning probe microscopy (SPM) family of instruments. As with its more familiar counterpart, atomic force microscopy (AFM), the technique provides high-resolution topographic imaging, with the caveat that target structures must be immersed in a conducting solution so that a controllable ion current may be utilised as the basis for feedback. In operation, this non-contact characteristic of SICM makes it ideal for the study of delicate structures, such as live cells. Moreover, the intrinsic architecture of the instrument, incorporating as it does, a scanned micropipette, lends itself to combination approaches with complementary techniques such as patch-clamp electrophysiology: SICM therefore boasts the capability for both structural and functional imaging. For the present observations, an ICnano S system (Ionscope Ltd., Melbourn, UK) operating in 'hopping mode' was used, with the objective of assessing the instrument's utility for imaging live keratinocytes under physiological buffers. In scans employing cultured HaCaT cells (spontaneously immortalised, human keratinocytes), we compared the qualitative differences of live cells imaged with SICM and AFM, and also with their respective counterparts after chemical fixation in 4% paraformaldehyde. Characteristic surface microvilli were particularly prominent in live cell imaging by SICM. Moreover, time lapse SICM imaging on live cells revealed that changes in the pattern of microvilli could be tracked over time. By comparison, AFM imaging on live cells, even at very low contact forces (monitoring the most delicate living structures with attendant high spatial resolutions.

  9. Conjugated metallorganic macrocycles: opportunities for coordination-driven planarization of bidentate, pyridine-based ligands.

    Science.gov (United States)

    Hamm, Danielle C; Braun, Lindsey A; Burazin, Alex N; Gauthier, Amanda M; Ness, Kendra O; Biebel, Casey E; Sauer, Jon S; Tanke, Robin; Noll, Bruce C; Bosch, Eric; Bowling, Nathan P

    2013-01-28

    Two conjugated systems that can be constrained to planarity via metal coordination have been generated and their metal complexes studied. The potential for these architectures to be incorporated into metal-sensing arylene ethynylene/vinylene oligomers and polymers was probed by verifying that these ligands (1) bind strongly to Ag(I) and Pd(II) cations, and (2) that this event leads to complexes that are planar. Single crystal structures confirm that introduction of Ag(I) or Pd(II) cations enforces planarity in the newly formed macrocycles. Likewise, (1)H-NMR titration studies reveal stoichiometric binding of Pd(II) and strong binding of Ag(I) (K(a (Ligand 1)) = 1.3 × 10(2) M(-1); K(a (Ligand 2)) = 5.4 × 10(2) M(-1)) for each conjugated ligand.

  10. Scanning tunneling microscopy II further applications and related scanning techniques

    CERN Document Server

    Güntherodt, Hans-Joachim

    1995-01-01

    Scanning Tunneling Microscopy II, like its predecessor, presents detailed and comprehensive accounts of the basic principles and broad range of applications of STM and related scanning probe techniques. The applications discussed in this volume come predominantly from the fields of electrochemistry and biology. In contrast to those described in STM I, these studies may be performed in air and in liquids. The extensions of the basic technique to map other interactions are described in chapters on scanning force microscopy, magnetic force microscopy, and scanning near-field optical microscopy, together with a survey of other related techniques. Also described here is the use of a scanning proximal probe for surface modification. Together, the two volumes give a comprehensive account of experimental aspects of STM. They provide essential reading and reference material for all students and researchers involved in this field. In this second edition the text has been updated and new methods are discussed.

  11. Scanning tunneling microscopy II further applications and related scanning techniques

    CERN Document Server

    Güntherodt, Hans-Joachim

    1992-01-01

    Scanning Tunneling Microscopy II, like its predecessor, presents detailed and comprehensive accounts of the basic principles and broad range of applications of STM and related scanning probe techniques. The applications discussed in this volume come predominantly from the fields of electrochemistry and biology. In contrast to those described in Vol. I, these sudies may be performed in air and in liquids. The extensions of the basic technique to map other interactions are described inchapters on scanning force microscopy, magnetic force microscopy, scanning near-field optical microscopy, together with a survey of other related techniques. Also described here is the use of a scanning proximal probe for surface modification. Togehter, the two volumes give a comprehensive account of experimental aspcets of STM. They provide essentialreading and reference material for all students and researchers involvedin this field.

  12. Gallium-67 citrate scan in extrapulmonary tuberculosis

    Energy Technology Data Exchange (ETDEWEB)

    Lin Wanyu [Taichung Veterans General Hospital (Taiwan). Dept. of Nuclear Medicine; Hsieh Jihfang [Chi-Mei Foundation Hospital, Tainan (Taiwan)

    1999-07-01

    Aim: Whole-body gallium scan was performed to evaluate the usefulness of gallium scan for detecting extrapulmonary tuberculosis (TB) lesions. Methods: Thirty-seven patients with extrapulmonary TB were included in this study. Four patients were found to have two lesions. Totally, 41 lesions were identified, including 19 TB arthritis, 8 spinal TB, 5 TB meningitis, 3 TB lymphadenopathy, 2 TB pericarditis, 1 TB peritonitis, 1 intestinal TB, 1 skin TB and 1 renal TB. Results: Of the 41 extrapulmonary TB lesions, gallium scan detected 32 lesions with a sensitivity of 78%. All the patients with TB meningitis showed negative gallium scan. When the five cases of TB meningitis were excluded, the detection sensitivity of gallium scan increased to 88.9% (32/36). Conclusion: Our data revealed that gallium scan is a convenient and useful method for evaluating extrapulmonary TB lesions other than TB-meningitis. We suggest that gallium scan be included in the clinical routine for patients with suspected extrapulmonary TB. (orig.) [German] Ziel: Es wurden Ganzkoerper-Gallium-Szintigramme angefertigt, um den Nutzen der Gallium-Szintigraphie zur Erfassung von extrapulmonalen Tuberkuloseherden (TB) zu erfassen. Methoden: 37 Patienten mit extrapulmonaler TB wurden eingeschlossen. 4 Patienten hatten 2 Laesionen. Insgesamt wurden 41 Laesionen identifiziert, hierunter 19 TB-Arthritis, 8 spinale TB, 5 TB-Meningitis, 3 TB-Lymphadenopathie, 2 TB-Perikarditis, 1 TB-Peritonitis, 1 intestinale TB, 1 Haut-TB und eine Nieren-TB. Ergebnisse: Von den 41 extrapulmonalen TB-Herden erfasste die Gallium-Szintigraphie 32 Herde mit einer Sensitivitaet von 78%. Alle Patienten mit TB-Meningitis zeigten einen negativen Gallium-Scan. Wenn die 5 Faelle mit TB-Meningitis ausgeschlossen wurden, stieg die Sensitivititaet der Gallium-Szintigraphie auf 88,9% (32/36). Schlussfolgerung: Die Daten zeigen, dass die Gallium-Szintigraphie eine einfache und nuetzliche Methode zur Erfassung extrapulmonaler TB-Herde ist

  13. First examples of hybrids based on polyoxometalates, metal halide clusters and organic ligands

    Energy Technology Data Exchange (ETDEWEB)

    Wang Lamei; Fan Yong; Wang Yan; Xiao Lina; Hu Yangyang; Peng Yu; Wang Tiegang; Gao Zhongmin; Zheng Dafang [College of Chemistry and State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Department of Chemistry, Jilin University, Changchun 130023 (China); Cui Xiaobing, E-mail: cuixb@mail.jlu.edu.cn [College of Chemistry and State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Department of Chemistry, Jilin University, Changchun 130023 (China); Xu Jiqing, E-mail: xjq@mail.jlu.edu.cn [College of Chemistry and State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Department of Chemistry, Jilin University, Changchun 130023 (China)

    2012-07-15

    Two new organic-inorganic compounds based on polyoxometalates, metal halide clusters and organic ligands: [BW{sub 12}O{sub 40}]{sub 2}[Cu{sub 2}(Phen){sub 4}Cl](H{sub 2}4, 4 Prime -bpy){sub 4}{center_dot}H{sub 3}O{center_dot}5H{sub 2}O (1) and [HPW{sub 12}O{sub 40}][Cd{sub 2}(Phen){sub 4}Cl{sub 2}](4, 4 Prime -bpy) (2) (Phen=1, 10-phenanthroline, bpy=bipyridine), have been prepared and characterized by IR, UV-vis, XPS, XRD and single crystal X-ray diffraction analyses. Crystal structure analyses reveal that compound 1 is constructed from [BW{sub 12}O{sub 40}]{sup 5-}, metal halide clusters [Cu{sub 2}(Phen){sub 4}Cl]{sup +}and 4, 4 Prime -bpy ligands, while compound 2 is constructed from [PW{sub 12}O{sub 40}]{sup 3-}, metal halide cluster [Cd{sub 2}(Phen){sub 4}Cl{sub 2}]{sup 2+} and 4, 4 Prime -bpy ligands. Compound 1 and compound 2 are not common hybrids based on polyoxometalates and metal halide clusters, they also contain dissociated organic ligands, therefore, compound 1 and 2 are the first examples of hybrids based on polyoxometalates, metal halide clusters and organic ligands. - Graphical Abstract: Two new compounds have been synthesized and characterized. Structure analyses revealed that the two compounds are the first examples of hybrids based on polyoxometalates, metal halide clusters and organic ligands. Highlights: Black-Right-Pointing-Pointer First examples of hybrids based on polyoxometalates, metal halide clusters and organic ligands. Black-Right-Pointing-Pointer Two different kinds of metal halide clusters. Black-Right-Pointing-Pointer Supramolecular structures based on polyoxometalates, metal halide clusters and organic ligands. Black-Right-Pointing-Pointer Hybridization of three different of building blocks.

  14. A ligand field series for the 4f-block from experimental and DFT computed Ce(IV/III) electrochemical potentials.

    Science.gov (United States)

    Bogart, Justin A; Lewis, Andrew J; Boreen, Michael A; Lee, Heui Beom; Medling, Scott A; Carroll, Patrick J; Booth, Corwin H; Schelter, Eric J

    2015-03-16

    Understanding of the sensitivity of the reduction potential of cerium(IV) cations to ligand field strength has yet to benefit from systematic variation of the ligand environment. Detailed analyses for a series of seven cerium(IV) tetrakis(pyridyl-nitroxide) compounds and their cerium(III) analogues in varying ligand field strengths are presented. Electrochemical, spectroscopic, and computational results reveal a close correlation of electronic properties with ligand substituents. Together with electrochemical data for reported eight-coordinate compounds, DFT calculations reveal a broad range of the cerium(IV/III) redox potentials correlated to ligand field strengths, establishing a semiempirical, predictive model for the modulation of cerium redox thermodynamics and ligand field strengths. Applications over a variety of scientific disciplines make use of the fundamental redox thermodynamics of cerium. Such applications will benefit from a combined experimental and theoretical approach for assessing redox cycling of cerium compounds.

  15. Review of MEMS differential scanning calorimetry for biomolecular study

    Science.gov (United States)

    Yu, Shifeng; Wang, Shuyu; Lu, Ming; Zuo, Lei

    2017-12-01

    Differential scanning calorimetry (DSC) is one of the few techniques that allow direct determination of enthalpy values for binding reactions and conformational transitions in biomolecules. It provides the thermodynamics information of the biomolecules which consists of Gibbs free energy, enthalpy and entropy in a straightforward manner that enables deep understanding of the structure function relationship in biomolecules such as the folding/unfolding of protein and DNA, and ligand bindings. This review provides an up to date overview of the applications of DSC in biomolecular study such as the bovine serum albumin denaturation study, the relationship between the melting point of lysozyme and the scanning rate. We also introduce the recent advances of the development of micro-electro-mechanic-system (MEMS) based DSCs.

  16. Review of MEMS differential scanning calorimetry for biomolecular study

    Science.gov (United States)

    Yu, Shifeng; Wang, Shuyu; Lu, Ming; Zuo, Lei

    2017-07-01

    Differential scanning calorimetry (DSC) is one of the few techniques that allow direct determination of enthalpy values for binding reactions and conformational transitions in biomolecules. It provides the thermodynamics information of the biomolecules which consists of Gibbs free energy, enthalpy and entropy in a straightforward manner that enables deep understanding of the structure function relationship in biomolecules such as the folding/unfolding of protein and DNA, and ligand bindings. This review provides an up to date overview of the applications of DSC in biomolecular study such as the bovine serum albumin denaturation study, the relationship between the melting point of lysozyme and the scanning rate. We also introduce the recent advances of the development of micro-electro-mechanic-system (MEMS) based DSCs.

  17. Scanning Productivity in Interlibrary Loan

    Science.gov (United States)

    Pedersen, Wayne A.; Runestad, Anders

    2009-01-01

    The authors report findings of a research study conducted at the Iowa State University Library. Data was gathered on the scanning of library materials by students working in the Interlibrary Loan (ILL) unit. The goals of the study were fourfold: (1) Develop measures of scanning productivity in ILL, (2) Determine if it is more productive to scan…

  18. Scan converting video tape recorder

    Science.gov (United States)

    Holt, N. I. (Inventor)

    1971-01-01

    A video tape recorder is disclosed of sufficient bandwidth to record monochrome television signals or standard NTSC field sequential color at current European and American standards. The system includes scan conversion means for instantaneous playback at scanning standards different from those at which the recording is being made.

  19. Detectors for scanning video imagers

    Science.gov (United States)

    Webb, Robert H.; Hughes, George W.

    1993-11-01

    In scanning video imagers, a single detector sees each pixel for only 100 ns, so the bandwidth of the detector needs to be about 10 MHz. How this fact influences the choice of detectors for scanning systems is described here. Some important parametric quantities obtained from manufacturer specifications are related and it is shown how to compare detectors when specified quantities differ.

  20. Correcting ligands, metabolites, and pathways

    Directory of Open Access Journals (Sweden)

    Vriend Gert

    2006-11-01

    Full Text Available Abstract Background A wide range of research areas in bioinformatics, molecular biology and medicinal chemistry require precise chemical structure information about molecules and reactions, e.g. drug design, ligand docking, metabolic network reconstruction, and systems biology. Most available databases, however, treat chemical structures more as illustrations than as a datafield in its own right. Lack of chemical accuracy impedes progress in the areas mentioned above. We present a database of metabolites called BioMeta that augments the existing pathway databases by explicitly assessing the validity, correctness, and completeness of chemical structure and reaction information. Description The main bulk of the data in BioMeta were obtained from the KEGG Ligand database. We developed a tool for chemical structure validation which assesses the chemical validity and stereochemical completeness of a molecule description. The validation tool was used to examine the compounds in BioMeta, showing that a relatively small number of compounds had an incorrect constitution (connectivity only, not considering stereochemistry and that a considerable number (about one third had incomplete or even incorrect stereochemistry. We made a large effort to correct the errors and to complete the structural descriptions. A total of 1468 structures were corrected and/or completed. We also established the reaction balance of the reactions in BioMeta and corrected 55% of the unbalanced (stoichiometrically incorrect reactions in an automatic procedure. The BioMeta database was implemented in PostgreSQL and provided with a web-based interface. Conclusion We demonstrate that the validation of metabolite structures and reactions is a feasible and worthwhile undertaking, and that the validation results can be used to trigger corrections and improvements to BioMeta, our metabolite database. BioMeta provides some tools for rational drug design, reaction searches, and

  1. Subcellular localization of L-selectin ligand in the endometrium implies a novel function for pinopodes in endometrial receptivity

    Directory of Open Access Journals (Sweden)

    Nejatbakhsh Reza

    2012-06-01

    Full Text Available Abstract Background Apical surfaces of human endometrial epithelium and endothelium are key elements for the initiation of molecular interactions to capture the blastocyst or leukocyte, respectively. The L-selectin adhesion system has been strongly proposed to play an important role in the initial steps of trophoblast adhesion and promotion of integrin-dependent processes, ultimately culminating in the establishment of the embryo-maternal interface. On the basis of these facts, we hypothesized a novel role for pinopodes as the first embryo-fetal contact sites to contain the highest subcellular expression of L-selectin ligand suggesting its role in early adhesion as predicted. Thus, the objective of this study was therefore to determine the subcellular pattern of distribution of the L-selectin ligand (MECA-79 in human endometrial apical membrane region during the window of implantation. Methods Endometrial biopsies of secretory phases from fertile females ranging in age between 25 and 42years were studied using several approaches, including scanning electron microscopy (SEM, immunostaining for light microscopy and transmission electron microscopy (TEM, and immunoblotting as well as statistical analysis of the area-related numerical densities of immunoreactive MECA-79-bound nanogolds to detect the expression pattern and the subcellular distribution pattern of L-selectin ligand (MECA-79 in human endometrium during the window of implantation. Results The endometrial biopsies were scored according the dating criteria of Noyes et al. by an experienced histologist. The SEM images of the midluteal phase specimens revealed that fully developed pinopodes were abundant in our samples. HRP-immunostaining and immunofluorescent staining as well as immunoblotting revealed that MECA-79 was expressed in the midluteal phase specimens. The results of immunogold TEM illustrated the expression of MECA-79 in human pinopodes in the midluteal phase and a higher area

  2. Synthesis, spectroscopic, thermogravimetric and antimicrobial studies of mixed ligands complexes

    Science.gov (United States)

    Mahmoud, Walaa H.; Mahmoud, Nessma F.; Mohamed, Gehad G.; El-Sonbati, Adel Z.; El-Bindary, Ashraf A.

    2015-09-01

    An interesting series of mixed ligand complexes have been synthesized by the reaction of metal chloride with guaifenesin (GFS) in the presence of 2-aminoacetic acid (HGly) (1:1:1 molar ratio). The elemental analysis, magnetic moments, molar conductance, spectral (UV-Vis, IR, 1H NMR and ESR) and thermal studies were used to characterize the isolated complexes. The molecular structure of GFS is optimized theoretically and the quantum chemical parameters are calculated. The IR showed that the ligand (GFS) acts as monobasic tridentate through the hydroxyl, phenoxy etheric and methoxy oxygen atoms and co-ligand (HGly) as monobasic bidentate through the deprotonated carboxylate oxygen atom and nitrogen atom of amino group. The molar conductivities showed that all the complexes are non-electrolytes except Cr(III) complex is electrolyte. Electronic and magnetic data proposed the octahedral structure for all complexes under investigation. ESR spectrum for Cu(II) revealed data which confirm the proposed structure. Antibacterial screening of the compounds were carried out in vitro on gram positive (Bacillus subtilis and Staphylococcus aureus), gram negative (Escherichia coli and Neisseria gonorrhoeae) bacteria and for in vitro antifungal activity against Candida albicans organism. However, some complexes showed more chemotherapeutic efficiency than the parent GFS drug. The complexes were also screened for their in vitro anticancer activity against the breast cell line (MFC7) and the results obtained showed that they exhibit a considerable anticancer activity.

  3. Using inositol as a biocompatible ligand for efficient transgene expression

    Science.gov (United States)

    Zhang, Lei; Bellis, Susan L; Fan, Yiwen; Wu, Yunkun

    2015-01-01

    Transgene transfection techniques using cationic polymers such as polyethylenimines (PEIs) and PEI derivatives as gene vectors have shown efficacy, although they also have shortcomings. PEIs have decent DNA-binding capability and good cell internalization performance, but they cannot deliver gene payloads very efficiently to cell nuclei. In this study, three hyperbranched polyglycerol-polyethylenimine (PG6-PEI) polymers conjugated with myo-inositol (INO) molecules were developed. The three resulting PG6-PEI-INO polymers have an increased number of INO ligands per molecule. PG6-PEI-INO 1 had only 14 carboxymethyl INO (CMINO) units per molecule. PG6-PEI-INO 2 had approximately 130 CMINO units per molecule. PG6-PEI-INO 3 had as high as 415 CMINO units approximately. Mixing PG6-PEI-INO polymers with DNA produced compact nanocomposites. We then performed localization studies using fluorescent microscopy. As the number of conjugated inositol ligands increased in PG6-PEI-INO polymers, there was a corresponding increase in accumulation of the polymers within 293T cell nuclei. Transfection performed with spherical 293T cells yielded 82% of EGFP-positive cells when using PG6-PEI-INO 3 as the vehicle. Studies further revealed that extracellular adenosine triphosphate (eATP) can inhibit the transgene efficiency of PG6-PEI-INO polymers, as compared with PEI and PG6-PEI that were not conjugated with inositol. Our work unveiled the possibility of using inositol as an effective ligand for transgene expression. PMID:25926732

  4. Nanopore force spectroscopy of aptamer-ligand complexes.

    Science.gov (United States)

    Arnaut, Vera; Langecker, Martin; Simmel, Friedrich C

    2013-09-03

    The stability of aptamer-ligand complexes is probed in nanopore-based dynamic force spectroscopy experiments. Specifically, the ATP-binding aptamer is investigated using a backward translocation technique, in which the molecules are initially pulled through an α-hemolysin nanopore from the cis to the trans side of a lipid bilayer membrane, allowed to refold and interact with their target, and then translocated back in the trans-cis direction. From these experiments, the distribution of bound and unbound complexes is determined, which in turn allows determination of the dissociation constant Kd ≈ 0.1 mM of the aptamer and of voltage-dependent unfolding rates. The experiments also reveal differences in binding of the aptamer to AMP, ADP, or ATP ligands. Investigation of an aptamer variant with a stabilized ATP-binding site indicates fast conformational switching of the original aptamer before ATP binding. Nanopore force spectroscopy is also used to study binding of the thrombin-binding aptamer to its target. To detect aptamer-target interactions in this case, the stability of the ligand-free aptamer-containing G-quadruplexes-is tuned via the potassium content of the buffer. Although the presence of thrombin was detected, limitations of the method for aptamers with strong secondary structures and complexes with nanomolar Kd were identified. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  5. Nanopore Force Spectroscopy of Aptamer–Ligand Complexes

    Science.gov (United States)

    Arnaut, Vera; Langecker, Martin; Simmel, Friedrich C.

    2013-01-01

    The stability of aptamer–ligand complexes is probed in nanopore-based dynamic force spectroscopy experiments. Specifically, the ATP-binding aptamer is investigated using a backward translocation technique, in which the molecules are initially pulled through an α-hemolysin nanopore from the cis to the trans side of a lipid bilayer membrane, allowed to refold and interact with their target, and then translocated back in the trans–cis direction. From these experiments, the distribution of bound and unbound complexes is determined, which in turn allows determination of the dissociation constant Kd ≈ 0.1 mM of the aptamer and of voltage-dependent unfolding rates. The experiments also reveal differences in binding of the aptamer to AMP, ADP, or ATP ligands. Investigation of an aptamer variant with a stabilized ATP-binding site indicates fast conformational switching of the original aptamer before ATP binding. Nanopore force spectroscopy is also used to study binding of the thrombin-binding aptamer to its target. To detect aptamer–target interactions in this case, the stability of the ligand-free aptamer—containing G-quadruplexes—is tuned via the potassium content of the buffer. Although the presence of thrombin was detected, limitations of the method for aptamers with strong secondary structures and complexes with nanomolar Kd were identified. PMID:24010663

  6. Chemistry of marine ligands and siderophores.

    Science.gov (United States)

    Vraspir, Julia M; Butler, Alison

    2009-01-01

    Marine microorganisms are presented with unique challenges to obtain essential metal ions required to survive and thrive in the ocean. The production of organic ligands to complex transition metal ions is one strategy to both facilitate uptake of specific metals, such as iron, and to mitigate the potential toxic effects of other metal ions, such as copper. A number of important trace metal ions are complexed by organic ligands in seawater, including iron, cobalt, nickel, copper, zinc, and cadmium, thus defining the speciation of these metal ions in the ocean. In the case of iron, siderophores have been identified and structurally characterized. Siderophores are low molecular weight iron-binding ligands produced by marine bacteria. Although progress has been made toward the identity of in situ iron-binding ligands, few compounds have been identified that coordinate the other trace metals. Deciphering the chemical structures and production stimuli of naturally produced organic ligands and the organisms they come from is fundamental to understanding metal speciation and bioavailability. The current evidence for marine ligands, with an emphasis on siderophores, and discussion of the importance and implications of metal-binding ligands in controlling metal speciation and cycling within the world's oceans are presented.

  7. Coordinate unsaturation with fluorinated ligands

    Energy Technology Data Exchange (ETDEWEB)

    Rack, J.L.; Hurlburt, P.K.; Anderson, O.P.; Strauss, S.H. [Colorado State Univ., Ft. Collins, CO (United States)

    1993-12-31

    The preparation and characterization of Zn(OTeF{sub 5}){sub 2} has resulted in a model compound with which to explore the concept of coordinative unsaturation. The coordination of solvents of varying donicity and dielectric constant to the Zn(II) ions in Zn(OTeF{sub 5}){sub 2} was studied by vapor phase monometry, NMR and IR spectroscopy, conductimetry, and X-Ray crystallography. The structures of [Zn(C{sub 6}H{sub 5}NO{sub 2}){sub 2}(OTeF{sub 5})2]2 and Zn(C{sub 6}H{sub 5}NO{sub 2}){sub 3}(OTEF{sub 5}){sub 2} demonstrate the electronic flexibility of some weakly coordinating solvents in that nitrobenzene can function as either an {eta}{sup 1}O or {eta}{sup 2}O,O`-ligand. The dependence of the number of bound solvent molecules and the degree of OTeF{sub 5}{minus} dissociation on solvent donor number and dielectric constant will be presented.

  8. Site specific polarization transfer from a hyperpolarized ligand of dihydrofolate reductase

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yunyi [Texas A& M University, Chemistry Department (United States); Ragavan, Mukundan [University of Florida, Department of Biochemistry and Molecular Biology, College of Medicine (United States); Hilty, Christian, E-mail: chilty@tamu.edu [Texas A& M University, Chemistry Department (United States)

    2016-05-15

    Protein–ligand interaction is often characterized using polarization transfer by the intermolecular nuclear Overhauser effect (NOE). For such NOE experiments, hyperpolarization of nuclear spins presents the opportunity to increase the spin magnetization, which is transferred, by several orders of magnitude. Here, folic acid, a ligand of dihydrofolate reductase (DHFR), was hyperpolarized on {sup 1}H spins using dissolution dynamic nuclear polarization (D-DNP). Mixing hyperpolarized ligand with protein resulted in observable increases in protein {sup 1}H signal predominantly in the methyl group region of the spectra. Using {sup 13}C single quantum selection in a series of one-dimensional spectra, the carbon chemical shift ranges of the corresponding methyl groups can be elucidated. Signals observed in these hyperpolarized spectra could be confirmed using 3D isotope filtered NOESY spectra, although the hyperpolarized spectra were obtained in single scans. By further correlating the signal intensities observed in the D-DNP experiments with the occurrence of short distances in the crystal structure of the protein–ligand complex, the observed methyl proton signals could be matched to the chemical shifts of six amino acids in the active site of DHFR-folic acid binary complex. These data demonstrate that {sup 13}C chemical shift selection of protein resonances, combined with the intrinsic selectivity towards magnetization originating from the initially hyperpolarized spins, can be used for site specific characterization of protein–ligand interactions.

  9. Ionic strength-dependent changes in tentacular ion exchangers with variable ligand density. I. Structural properties.

    Science.gov (United States)

    Bhambure, Rahul; Gillespie, Christopher M; Phillips, Michael; Graalfs, Heiner; Lenhoff, Abraham M

    2016-09-09

    The ligand density critically affects the performance of ion-exchange resins in such measures as the adsorption capacity and transport characteristics. However, for tentacular and other polymer-modified exchangers, the mechanistic basis of the effect of ligand density on performance is not yet fully understood. In this study we map the ionic strength-dependent structural changes in tentacular cation exchangers with variable ligand densities as the basis for subsequent investigation of effects on functional properties. Inverse size-exclusion chromatography (ISEC), scanning electron microscopy (SEM) and small-angle x-ray scattering (SAXS) were used to assess the effect of ionic strength on the pore size and intraparticle architecture of resin variants with different ligand densities. Comparison of ISEC and cryo-SEM results shows a considerable reduction in average pore size with increasing ligand density; these methods also confirm an increase of average pore size at higher ionic strengths. SAXS analysis of ionic strength-dependent conformational changes in the grafted polyelectrolyte layer shows a characteristic ionomer peak at values of the scattering vector q (0.1-0.2Å(-1)) that depend on the ligand density and the ionic strength of the solution. This peak attribution reflects nanoscale changes in the structure of the grafted polyelectrolyte chains that can in turn be responsible for observed pore-size changes in the resins. Finally, salt breakthrough experiments confirm a stronger Donnan exclusion effect on pore accessibility for small ions in the high ligand density variant. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Binding-Induced Fluorescence of Serotonin Transporter Ligands

    DEFF Research Database (Denmark)

    Wilson, James; Ladefoged, Lucy Kate; Babinchak, Michael

    2014-01-01

    The binding-induced fluorescence of 4-(4-(dimethylamino)-phenyl)-1-methylpyridinium (APP(+)) and two new serotonin transporter (SERT)-binding fluorescent analogues, 1-butyl-4-[4-(1-dimethylamino)phenyl]-pyridinium bromide (BPP(+)) and 1-methyl-4-[4-(1-piperidinyl)phenyl]-pyridinium (PPP(+)), has...... calculations reveal that the probes are able to access the nonpolar and conformationally restrictive binding pocket of SERT. As a result, the probes exhibit previously not identified binding-induced turn-on emission that is spectroscopically distinct from dyes that have accumulated intracellularly. Thus......, binding and transport dynamics of SERT ligands can be resolved both spatially and spectroscopically....

  11. Sampling and energy evaluation challenges in ligand binding protein design

    Science.gov (United States)

    Dou, Jiayi; Doyle, Lindsey; Jr. Greisen, Per; Schena, Alberto; Park, Hahnbeom; Johnsson, Kai; Stoddard, Barry L.

    2017-01-01

    Abstract The steroid hormone 17α‐hydroxylprogesterone (17‐OHP) is a biomarker for congenital adrenal hyperplasia and hence there is considerable interest in development of sensors for this compound. We used computational protein design to generate protein models with binding sites for 17‐OHP containing an extended, nonpolar, shape‐complementary binding pocket for the four‐ring core of the compound, and hydrogen bonding residues at the base of the pocket to interact with carbonyl and hydroxyl groups at the more polar end of the ligand. Eight of 16 designed proteins experimentally tested bind 17‐OHP with micromolar affinity. A co‐crystal structure of one of the designs revealed that 17‐OHP is rotated 180° around a pseudo‐two‐fold axis in the compound and displays multiple binding modes within the pocket, while still interacting with all of the designed residues in the engineered site. Subsequent rounds of mutagenesis and binding selection improved the ligand affinity to nanomolar range, while appearing to constrain the ligand to a single bound conformation that maintains the same “flipped” orientation relative to the original design. We trace the discrepancy in the design calculations to two sources: first, a failure to model subtle backbone changes which alter the distribution of sidechain rotameric states and second, an underestimation of the energetic cost of desolvating the carbonyl and hydroxyl groups of the ligand. The difference between design model and crystal structure thus arises from both sampling limitations and energy function inaccuracies that are exacerbated by the near two‐fold symmetry of the molecule. PMID:28980354

  12. Sampling and energy evaluation challenges in ligand binding protein design.

    Science.gov (United States)

    Dou, Jiayi; Doyle, Lindsey; Jr Greisen, Per; Schena, Alberto; Park, Hahnbeom; Johnsson, Kai; Stoddard, Barry L; Baker, David

    2017-12-01

    The steroid hormone 17α-hydroxylprogesterone (17-OHP) is a biomarker for congenital adrenal hyperplasia and hence there is considerable interest in development of sensors for this compound. We used computational protein design to generate protein models with binding sites for 17-OHP containing an extended, nonpolar, shape-complementary binding pocket for the four-ring core of the compound, and hydrogen bonding residues at the base of the pocket to interact with carbonyl and hydroxyl groups at the more polar end of the ligand. Eight of 16 designed proteins experimentally tested bind 17-OHP with micromolar affinity. A co-crystal structure of one of the designs revealed that 17-OHP is rotated 180° around a pseudo-two-fold axis in the compound and displays multiple binding modes within the pocket, while still interacting with all of the designed residues in the engineered site. Subsequent rounds of mutagenesis and binding selection improved the ligand affinity to nanomolar range, while appearing to constrain the ligand to a single bound conformation that maintains the same "flipped" orientation relative to the original design. We trace the discrepancy in the design calculations to two sources: first, a failure to model subtle backbone changes which alter the distribution of sidechain rotameric states and second, an underestimation of the energetic cost of desolvating the carbonyl and hydroxyl groups of the ligand. The difference between design model and crystal structure thus arises from both sampling limitations and energy function inaccuracies that are exacerbated by the near two-fold symmetry of the molecule. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  13. Extraosseous radiotracer uptake on bone scan in beta-thalassemia: report of one case; Fixation extraosseuse du radiotraceur lors de la realisation d'une scintigraphie du squelette chez un patient atteint de beta-thalassemie: a propos d'un cas

    Energy Technology Data Exchange (ETDEWEB)

    Guezguez, M.; Nouira, M.; Sfar, R.; Chatti, K.; Ben Fradj, M.; Ben Ali, K.; Ajmi, S.; Essabbah, H. [CHU Sahloul, Service de Medecine Nucleaire, Sousse (Tunisia); Zrour, S. [EPS F. Bourguiba, Service de Rhumatologie, Monastir (Tunisia)

    2009-10-15

    Red blood cell transfusion, main therapeutic modality of beta-thalassemia, leads to iron overload which may perturb several metabolic ways. The aim of this paper is to illustrate the uptake abnormalities observed on bone scan of thalassaemic patients and to discuss mechanisms of extraosseous accumulation of the radiopharmaceutical in this pathology. We report a 16-year-old child suffering from beta-thalassemia major undergoing transfusion therapy. A bone scan was indicated to look for osseous infection. This study revealed a little skeletal uptake and abnormal liver, splenic and renal accumulation. A repeat bone scan, performed three weeks later showed a better skeletal uptake which enabled the discovery of focal abnormalities and made the diagnostic easier. The effect of iron overload on radiopharmaceuticals uptake in bone scan is known since 1975. Dissociation of {sup 99m}Tc from the carrier ligand due to the presence of iron excess seems the most plausible hypothesis. Free {sup 99m}Tc can be bound to other tissular substrates which can explain extraosseous uptake. The normally available pool for bone is reduced and then the skeletal uptake decreased. This report limits considerably the sensitivity of the bone scan. A well-led iron chelation and eventually the use of diuretic drug may guarantee a better quality of bone scan images. (authors)

  14. Computational Elucidation of Structural Basis for Ligand Binding with Leishmania donovani Adenosine Kinase

    Directory of Open Access Journals (Sweden)

    Rajiv K. Kar

    2013-01-01

    Full Text Available Enzyme adenosine kinase is responsible for phosphorylation of adenosine to AMP and is crucial for parasites which are purine auxotrophs. The present study describes development of robust homology model of Leishmania donovani adenosine kinase to forecast interaction phenomenon with inhibitory molecules using structure-based drug designing strategy. Docking calculation using reported organic small molecules and natural products revealed key active site residues such as Arg131 and Asp16 for ligand binding, which is consistent with previous studies. Molecular dynamics simulation of ligand protein complex revealed the importance of hydrogen bonding with active site residues and solvent molecules, which may be crucial for successful development of drug candidates. Precise role of Phe168 residue in the active site was elucidated in this report that provided stability to ligand-protein complex via aromatic-π contacts. Overall, the present study is believed to provide valuable information to design a new compound with improved activity for antileishmanial therapeutics development.

  15. Scanning tunneling spectroscopy of graphene on graphite.

    Science.gov (United States)

    Li, Guohong; Luican, Adina; Andrei, Eva Y

    2009-05-01

    We report low temperature high magnetic field scanning tunneling microscopy and spectroscopy of graphene flakes on graphite that exhibit the structural and electronic properties of graphene decoupled from the substrate. Pronounced peaks in the tunneling spectra develop with increasing field revealing a Landau level sequence that provides a direct way to identify graphene and to determine the degree of its coupling to the substrate. The Fermi velocity and quasiparticle lifetime, obtained from the positions and width of the peaks, provide access to the electron-phonon and electron-electron interactions.

  16. Chitosan and carboxymethyl-chitosan capping ligands: Effects on the nucleation and growth of hydroxyapatite nanoparticles for producing biocomposite membranes

    Energy Technology Data Exchange (ETDEWEB)

    Dumont, Vitor C.; Mansur, Alexandra A.P.; Carvalho, Sandhra M.; Medeiros Borsagli, Fernanda G.L.; Pereira, Marivalda M.; Mansur, Herman S., E-mail: hmansur@demet.ufmg.br

    2016-02-01

    Synthetic biomaterials based on calcium phosphates (CaP) have been widely studied for bone tissue reconstruction therapies, but no definitive solution that fulfills all of the required properties has been identified. Thus, this study reports the synthesis of composite membranes based on nanohydroxyapatite particles (nHA) embedded in chitosan (CHI) and O-carboxymethyl chitosan (CMC) matrices produced using a one-step co-precipitation method in water media. Biopolymers were used as capping ligands for simultaneously controlling the nucleation and growth of the nHA particles during the precipitation process and also to form the polymeric network of the biocomposites. The bionanocomposites were extensively characterized using light microscopy (LM), scanning and transmission electron microscopy (SEM/TEM), energy-dispersive X-ray spectroscopy (EDX), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), atomic force microscopy (AFM), X-ray micro-CT analysis (μCT), and MTT (3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide) cell proliferation assays for cell cytotoxicity. The results demonstrated that the ligands used during the synthesis highly affected the composites produced, primarily due the changes in the mechanisms and kinetics of nucleation and growth of the HA particles at the nanoscale level. The SEM images revealed that the use of carboxyl-functionalized chitosan (CMC) ligands significantly reduced the average size of the HA nanoparticles and caused the formation of a narrower size distribution (90 ± 20 nm) compared to the HA nanoparticles produced with chitosan ligands (220 ± 50 nm). The same trend was verified by the AFM analysis, where the nHA particles were formed evenly dispersed in the polymer matrix. However, the CMC-based composites were more homogeneously distributed, which was endorsed by the images collected via X-ray micro-CT. The FTIR spectra and the XRD analysis indicated that nanosized hydroxyapatite was the

  17. Ligand based pharmacophore modelling of anticancer histone ...

    African Journals Online (AJOL)

    USER

    2010-06-21

    Jun 21, 2010 ... for designing the pharmacophore onto the set of 70 compounds of three different classes and two subclasses. ... More effective anticancer drug production with novel modes of action .... with Ligand Scout using default settings.

  18. Controlling Signal Transduction with Synthetic Ligands

    Science.gov (United States)

    Spencer, David M.; Wandless, Thomas J.; Schreiber, Stuart L.; Crabtree, Gerald R.

    1993-11-01

    Dimerization and oligomerization are general biological control mechanisms contributing to the activation of cell membrane receptors, transcription factors, vesicle fusion proteins, and other classes of intra- and extracellular proteins. Cell permeable, synthetic ligands were devised that can be used to control the intracellular oligomerization of specific proteins. To demonstrate their utility, these ligands were used to reduce intracellular oligomerization of cell surface receptors that lacked their transmembrane and extracellular regions but contained intracellular signaling domains. Addition of these ligands to cells in culture resulted in signal transmission and specific target gene activation. Monomeric forms of the ligands blocked the pathway. This method of ligandregulated activation and termination of signaling pathways has the potential to be applied wherever precise control of a signal transduction pathway is desired.

  19. Organometallic chemistry of chiral diphosphazane ligands ...

    Indian Academy of Sciences (India)

    Unknown

    Organometallic chemistry of chiral diphosphazane ligands: Synthesis and structural characterisation. KANNAN RAGHURAMAN, SWADHIN K MANDAL,. T S VENKATAKRISHNAN, SETHARAMPATTU S. KRISHNAMURTHY* and MUNIRATHINAM NETHAJI. Department of Inorganic and Physical Chemistry, Indian Institute of ...

  20. EGFR Activation by Spatially Restricted Ligands

    National Research Council Canada - National Science Library

    Goodrich, Jennifer S

    2005-01-01

    ...) activity has been associated with an increased prognosis of breast cancer. During oogenesis in Drosophila melanogaster, local EGFR activation by the spatially restricted TGF alpha-like ligand, Gurken (Grk...

  1. Asymmetric hydrogenation using monodentate phosphoramidite ligands

    NARCIS (Netherlands)

    Minnaard, Adriaan J.; Feringa, Ben L.; Lefort, Laurent; De Vries, Johannes G.

    2007-01-01

    Monodentate phosphoramidites are excellent ligands for Rh-catalyzed asymmetric hydrogenations of substituted olefins. Enantioselectivities between 95 and 99% were obtained in the asymmetric hydrogenation of protected alpha- and beta-dehydroamino acids and esters, itaconic acid and esters, aromatic

  2. Bystander protein protects potential vaccine-targeting ligands against intestinal proteolysis.

    Science.gov (United States)

    Reuter, Fabian; Bade, Steffen; Hirst, Timothy R; Frey, Andreas

    2009-07-20

    Endowing mucosal vaccines with ligands that target antigen to mucosal lymphoid tissues may improve immunization efficacy provided that the ligands withstand the proteolytic environment of the gastro-intestinal tract until they reach their destination. Our aim was to investigate whether and how three renowned ligands - Ulex europaeus agglutinin I and the B subunits of cholera toxin and E. coli heat-labile enterotoxin - master this challenge. We assessed the digestive power of natural murine intestinal fluid (natIF) using assays for trypsin, chymotrypsin and pancreatic elastase along with a test for nonspecific proteolysis. The natIF was compared with simulated murine intestinal fluid (simIF) that resembled the trypsin, chymotrypsin and elastase activities of its natural counterpart but lacked or contained albumins as additional protease substrates. The ligands were exposed to the digestive fluids and degradation was determined. The studies revealed that (i) the three pancreatic endoproteases constitute only one third of the total protease activity of natIF and (ii) the ligands resist proteolysis in natIF and protein-enriched simIF over 3 h but (iii) are partially destroyed in simIF that lacks additional protease substrate. We assume that the proteins of natIF are preferred substrates for the intestinal proteases and thus can protect vaccine-targeting ligands from destruction.

  3. Investigations of Takeout proteins' ligand binding and release mechanism using molecular dynamics simulation.

    Science.gov (United States)

    Zhang, Huijing; Yu, Hui; Zhao, Xi; Liu, Xiaoguang; Feng, Xianli; Huang, Xuri

    2017-05-01

    Takeout (To) proteins exist in a diverse range of insect species. They are involved in many important processes of insect physiology and behaviors. As the ligand carriers, To proteins can transport the small molecule to the target tissues. However, ligand release mechanism of To proteins is unclear so far. In this contribution, the process and pathway of the ligand binding and release are revealed by conventional molecular dynamics simulation, steered molecular dynamics simulation and umbrella sampling methods. Our results show that the α4-side of the protein is the unique gate for the ligand binding and release. The structural analysis confirms that the internal cavity of the protein has high rigidity, which is in accordance with the recent experimental results. By using the potential of mean force calculations in combination with residue cross correlation calculation, we concluded that the binding between the ligand and To proteins is a process of conformational selection. Furthermore, the conformational changes of To proteins and the hydrophobic interactions both are the key factors for ligand binding and release.

  4. Bone Densitometry (Bone Density Scan)

    Science.gov (United States)

    ... back pain. if a DEXA scan gives borderline readings. top of page How should I prepare? On the day ... radiology protection organizations continually review and update the technique ... that those parts of a patient's body not being imaged receive minimal ...

  5. Ligand Interface Chemistry of Lead Chalcogenide Nanocrystals

    Science.gov (United States)

    Liu, Kun; Bealing, Clive; Hennig, Richard; Hennig Group Team

    2013-03-01

    Lead chalcogenides nanocrystals (NCs) have shown promise in photovoltaic applications. Surface chemistry is one of the most important, yet least understood aspects of NC synthesis and functionalization controlling their properties. For example, an incomplete surface passivation could create trap states that enhance undesired exciton recombination. Clever choices of ligands ensure that neighboring NCs are electronically coupled while maintaining their quantum size effects. These two barriers limiting performance of NC solar cells illustrate the importance of fundamental studies for the interaction between ligands and NC surfaces. We use density functional theory to determine the binding sites and energies of ligands commonly used in NC synthesis and functionalization. Specifically we study amine-, carboxyl-, and thiol-ligands on different PbSe and PbS surfaces. For methylamine ligands we find a similar binding energy on the (100) and (111) facet while carboxylic acid ligands strongly prefer the (111) facet leading to different effective NC shapes. This work was supported in part by Award No. KUS-C1-018-02, made by King Abdullah University of Science and Technology (KAUST) and by the Energy Materials Center at Cornell (EMC2) funded by the U.S. Department of Energy under Award Number DE-SC0001086

  6. Designer TGFβ superfamily ligands with diversified functionality.

    Directory of Open Access Journals (Sweden)

    George P Allendorph

    Full Text Available Transforming Growth Factor--beta (TGFβ superfamily ligands, including Activins, Growth and Differentiation Factors (GDFs, and Bone Morphogenetic Proteins (BMPs, are excellent targets for protein-based therapeutics because of their pervasiveness in numerous developmental and cellular processes. We developed a strategy termed RASCH (Random Assembly of Segmental Chimera and Heteromer, to engineer chemically-refoldable TGFβ superfamily ligands with unique signaling properties. One of these engineered ligands, AB208, created from Activin-βA and BMP-2 sequences, exhibits the refolding characteristics of BMP-2 while possessing Activin-like signaling attributes. Further, we find several additional ligands, AB204, AB211, and AB215, which initiate the intracellular Smad1-mediated signaling pathways more strongly than BMP-2 but show no sensitivity to the natural BMP antagonist Noggin unlike natural BMP-2. In another design, incorporation of a short N-terminal segment from BMP-2 was sufficient to enable chemical refolding of BMP-9, without which was never produced nor refolded. Our studies show that the RASCH strategy enables us to expand the functional repertoire of TGFβ superfamily ligands through development of novel chimeric TGFβ ligands with diverse biological and clinical values.

  7. Construction of dinuclear complexes using multidentate ligands

    Energy Technology Data Exchange (ETDEWEB)

    Sampson, C.L

    2000-04-01

    This work details the synthesis of novel copper(I), copper(II), nickel(II) and zinc(II) dinuclear complexes. Attempts have been made to control the co-ordination architectures of the metal centres by using bis-bidentate and tridentate chelating N,S- and N-donor ligands to generate dinuclear systems. The ligands were both symmetrically and asymmetrically disubstituted pyridazine-based and pyridine-based ligands consisting of a mixture of N-only and mixed N,S-donors. The study using the pyridazine-based ligands continues previous research in our group using 3,6-bis disubstituted pyridazine-based ligands to form complexes with copper(l) and copper(II). The pyridazine-based ligands have been seen to be bis-bidentate upon co-ordination of copper. The pyridazine-based ligands could be envisaged to generate dinuclear complexes by directly bridging between two metal ions. This study involved the formation of copper(l), nickel(II) and zinc(II) complexes with these ligands. The structural properties of two particular complexes have been explored using X-ray crystallography and spectroscopic techniques. Pyridine-based ligands have also been used previously in our group as tridentate chelating ligands. They have been seen to form dinuclear complexes with copper(I) and copper(II) when reacted with an additional bridging ligand e.g. 4,4'-bipyridine. This provides an alternative method for generating dinuclear complexes. Chapter 1 presents an introduction to the area of supramolecular chemistry from which we can learn the principles of polymer formation and them 'in reverse' to generate discrete dinuclear systems. Chapter 2 details the synthesis of the pyridazine and pyridine-based ligands including a detailed nmr study of the ligands. Since the ligands were synthesised using cyclic thioamides as terminal groups it has been found that thiol-thione tautomerisation occurred during synthesis giving rise to two possible ligand conformations. The nmr study has been used

  8. Semiconductor Quantum Dots with Photoresponsive Ligands.

    Science.gov (United States)

    Sansalone, Lorenzo; Tang, Sicheng; Zhang, Yang; Thapaliya, Ek Raj; Raymo, Françisco M; Garcia-Amorós, Jaume

    2016-10-01

    Photochromic or photocaged ligands can be anchored to the outer shell of semiconductor quantum dots in order to control the photophysical properties of these inorganic nanocrystals with optical stimulations. One of the two interconvertible states of the photoresponsive ligands can be designed to accept either an electron or energy from the excited quantum dots and quench their luminescence. Under these conditions, the reversible transformations of photochromic ligands or the irreversible cleavage of photocaged counterparts translates into the possibility to switch luminescence with external control. As an alternative to regulating the photophysics of a quantum dot via the photochemistry of its ligands, the photochemistry of the latter can be controlled by relying on the photophysics of the former. The transfer of excitation energy from a quantum dot to a photocaged ligand populates the excited state of the species adsorbed on the nanocrystal to induce a photochemical reaction. This mechanism, in conjunction with the large two-photon absorption cross section of quantum dots, can be exploited to release nitric oxide or to generate singlet oxygen under near-infrared irradiation. Thus, the combination of semiconductor quantum dots and photoresponsive ligands offers the opportunity to assemble nanostructured constructs with specific functions on the basis of electron or energy transfer processes. The photoswitchable luminescence and ability to photoinduce the release of reactive chemicals, associated with the resulting systems, can be particularly valuable in biomedical research and can, ultimately, lead to the realization of imaging probes for diagnostic applications as well as to therapeutic agents for the treatment of cancer.

  9. LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone

    KAUST Repository

    Chen, Peng

    2014-12-03

    Background Protein-ligand binding is important for some proteins to perform their functions. Protein-ligand binding sites are the residues of proteins that physically bind to ligands. Despite of the recent advances in computational prediction for protein-ligand binding sites, the state-of-the-art methods search for similar, known structures of the query and predict the binding sites based on the solved structures. However, such structural information is not commonly available. Results In this paper, we propose a sequence-based approach to identify protein-ligand binding residues. We propose a combination technique to reduce the effects of different sliding residue windows in the process of encoding input feature vectors. Moreover, due to the highly imbalanced samples between the ligand-binding sites and non ligand-binding sites, we construct several balanced data sets, for each of which a random forest (RF)-based classifier is trained. The ensemble of these RF classifiers forms a sequence-based protein-ligand binding site predictor. Conclusions Experimental results on CASP9 and CASP8 data sets demonstrate that our method compares favorably with the state-of-the-art protein-ligand binding site prediction methods.

  10. Characterization of quinoxolinol salen ligands as selective ligands for chemosensors for uranium

    Energy Technology Data Exchange (ETDEWEB)

    DeVore, Michael A. II; Kerns, Spencer A.; Gorden, Anne E.V. [Department of Chemistry and Biochemistry, Auburn University, Auburn, AL (United States)

    2015-12-15

    Quinoxalinol salen ligands have been characterized as selective ligands for the rapid identification of uranyl. The absorption maximum of ligand 1 presented a hypsochromic (blue) shift with the addition of UO{sub 2}{sup 2+} (as the acetate salt), and a bathochromic (red) shift in the presence of Cu{sup 2+} or Co{sup 2+} acetate salts, resulting in distinct, visible color changes for all three metal ions. The absorption maximum of ligand 2 was not observed to change with the addition of UO{sub 2}{sup 2+}; however, it does present a bathochromic shift with the addition of Cu{sup 2+}, and a hypsochromic shift with Co{sup 2+} added. Using TDDFT calculations, it was demonstrated that the hypsochromic shift for UO{sub 2}{sup 2+} ion complexation with ligand 1 is caused by a ligand-to-metal charge transfer, while the bathochromic shift observed with Cu{sup 2+} ion addition was caused by a metal-to-ligand charge transfer. Finally, it was found that the addition of Cu{sup 2+} (as metal salts) to either ligand resulted in rapid, complete quenching of the ligand fluorescence. (Copyright copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  11. Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand.

    Directory of Open Access Journals (Sweden)

    Samuel DeLuca

    Full Text Available RosettaLigand has been successfully used to predict binding poses in protein-small molecule complexes. However, the RosettaLigand docking protocol is comparatively slow in identifying an initial starting pose for the small molecule (ligand making it unfeasible for use in virtual High Throughput Screening (vHTS. To overcome this limitation, we developed a new sampling approach for placing the ligand in the protein binding site during the initial 'low-resolution' docking step. It combines the translational and rotational adjustments to the ligand pose in a single transformation step. The new algorithm is both more accurate and more time-efficient. The docking success rate is improved by 10-15% in a benchmark set of 43 protein/ligand complexes, reducing the number of models that typically need to be generated from 1000 to 150. The average time to generate a model is reduced from 50 seconds to 10 seconds. As a result we observe an effective 30-fold speed increase, making RosettaLigand appropriate for docking medium sized ligand libraries. We demonstrate that this improved initial placement of the ligand is critical for successful prediction of an accurate binding position in the 'high-resolution' full atom refinement step.

  12. Mixed ligand ruthenium(III) complexes of benzaldehyde 4-methyl-3-thiosemicarbazones with triphenylphosphine/triphenylarsine co-ligands: Synthesis, DNA binding, DNA cleavage, antioxidative and cytotoxic activity

    Science.gov (United States)

    Sampath, K.; Sathiyaraj, S.; Raja, G.; Jayabalakrishnan, C.

    2013-08-01

    The new ruthenium(III) complexes with 4-methyl-3-thiosemicarbazone ligands, (E)-2-(2-chlorobenzylidene)-N-methylhydrazinecarbothioamide (HL1) and (E)-2-(2-nitrobenzylidene)-N-methylhydrazinecarbothioamide (HL2), were prepared and characterized by various physico-chemical and spectroscopic methods. The title compounds act as bidentate, monobasic chelating ligands with S and N as the donor sites and are preferably found in the thiol form in all the complexes studied. The molecular structure of HL1 and HL2 were determined by single crystal X-ray diffraction method. DNA binding of the ligands and complexes were investigated by absorption spectroscopy and IR spectroscopy. It reveals that the compounds bind to nitrogenous bases of DNA via intercalation. The oxidative cleavage of the complexes with CT-DNA inferred that the effects of cleavage are dose dependent. Antioxidant study of the ligands and complexes showed the significant antioxidant activity against DPPH radical. In addition, the in vitro cytotoxicity of the ligands and complexes against MCF-7 cell line was assayed which showed higher cytotoxic activity with the lower IC50 values indicating their efficiency in killing the cancer cells even at low concentrations.

  13. Heteroleptic copper(I) complexes prepared from phenanthroline and bis-phosphine ligands.

    Science.gov (United States)

    Kaeser, Adrien; Mohankumar, Meera; Mohanraj, John; Monti, Filippo; Holler, Michel; Cid, Juan-José; Moudam, Omar; Nierengarten, Iwona; Karmazin-Brelot, Lydia; Duhayon, Carine; Delavaux-Nicot, Béatrice; Armaroli, Nicola; Nierengarten, Jean-François

    2013-10-21

    Preparation of [Cu(NN)(PP)](+) derivatives has been systematically investigated starting from two libraries of phenanthroline (NN) derivatives and bis-phosphine (PP) ligands, namely, (A) 1,10-phenanthroline (phen), neocuproine (2,9-dimethyl-1,10-phenanthroline, dmp), bathophenanthroline (4,7-diphenyl-1,10-phenanthroline, Bphen), 2,9-diphenethyl-1,10-phenanthroline (dpep), and 2,9-diphenyl-1,10-phenanthroline (dpp); (B) bis(diphenylphosphino)methane (dppm), 1,2-bis(diphenylphosphino)ethane (dppe), 1,3-bis(diphenylphosphino)propane (dppp), 1,2-bis(diphenylphosphino)benzene (dppb), 1,1'-bis(diphenylphosphino)ferrocene (dppFc), and bis[(2-diphenylphosphino)phenyl] ether (POP). Whatever the bis-phosphine ligand, stable heteroleptic [Cu(NN)(PP)](+) complexes are obtained from the 2,9-unsubstituted-1,10-phenanthroline ligands (phen and Bphen). By contrast, heteroleptic complexes obtained from dmp and dpep are stable in the solid state, but a dynamic ligand exchange reaction is systematically observed in solution, and the homoleptic/heteroleptic ratio is highly dependent on the bis-phosphine ligand. Detailed analysis revealed that the dynamic equilibrium resulting from ligand exchange reactions is mainly influenced by the relative thermodynamic stability of the different possible complexes. Finally, in the case of dpp, only homoleptic complexes were obtained whatever the bis-phosphine ligand. Obviously, steric effects resulting from the presence of the bulky phenyl rings on the dpp ligand destabilize the heteroleptic [Cu(NN)(PP)](+) complexes. In addition to the remarkable thermodynamic stability of [Cu(dpp)2]BF4, this negative steric effect drives the dynamic complexation scenario toward almost exclusive formation of homoleptic [Cu(NN)2](+) and [Cu(PP)2](+) complexes. This work provides the definitive rationalization of the stability of [Cu(NN)(PP)](+) complexes, marking the way for future developments in this field.

  14. Molecular mechanisms of ligand-mediated attenuation of DNA binding by MarR family transcriptional regulators.

    Science.gov (United States)

    Perera, Inoka C; Grove, Anne

    2010-10-01

    Bacteria and archaea encode members of the large multiple antibiotic resistance regulator (MarR) family of transcriptional regulators. Generally, MarR homologs regulate activity of genes involved in antibiotic resistance, stress responses, virulence or catabolism of aromatic compounds. They constitute a diverse group of transcriptional regulators that includes both repressors and activators, and the conventional mode of regulation entails a genetic locus in which the MarR homolog and a gene under its regulation are encoded divergently; binding of the MarR homolog to the intergenic region typically represses transcription of both genes, while binding of a specific ligand to the transcription factor results in attenuated DNA binding and hence activated gene expression. For many homologs, the natural ligand is unknown. Crystal structures reveal a common architecture with a characteristic winged helix domain for DNA binding, and recent structural information of homologs solved both in the absence and presence of their respective ligands, as well as biochemical data, is finally converging to illuminate the mechanisms by which ligand-binding causes attenuated DNA binding. As MarR homologs regulate pathways that are critical to bacterial physiology, including virulence, a molecular understanding of mechanisms by which ligands affect a regulation of gene activity is essential. Specifying the position of ligand-binding pockets further has the potential to aid in identifying the ligands for MarR homologs for which the ligand remains unknown.

  15. Synthesis and characterization of mixed ligand chiral nanoclusters

    KAUST Repository

    Guven, Zekiye P.

    2016-06-22

    Chiral mixed ligand silver nanoclusters were synthesized in the presence of a chiral and an achiral ligand. While the chiral ligand led mostly to the formation of nanoparticles, the presence of the achiral ligand drastically increased the yield of nanoclusters with enhanced chiral properties. © 2016 The Royal Society of Chemistry.

  16. Lidar arc scan uncertainty reduction through scanning geometry optimization

    Science.gov (United States)

    Wang, Hui; Barthelmie, Rebecca J.; Pryor, Sara C.; Brown, Gareth.

    2016-04-01

    Doppler lidars are frequently operated in a mode referred to as arc scans, wherein the lidar beam scans across a sector with a fixed elevation angle and the resulting measurements are used to derive an estimate of the n minute horizontal mean wind velocity (speed and direction). Previous studies have shown that the uncertainty in the measured wind speed originates from turbulent wind fluctuations and depends on the scan geometry (the arc span and the arc orientation). This paper is designed to provide guidance on optimal scan geometries for two key applications in the wind energy industry: wind turbine power performance analysis and annual energy production prediction. We present a quantitative analysis of the retrieved wind speed uncertainty derived using a theoretical model with the assumption of isotropic and frozen turbulence, and observations from three sites that are onshore with flat terrain, onshore with complex terrain and offshore, respectively. The results from both the theoretical model and observations show that the uncertainty is scaled with the turbulence intensity such that the relative standard error on the 10 min mean wind speed is about 30 % of the turbulence intensity. The uncertainty in both retrieved wind speeds and derived wind energy production estimates can be reduced by aligning lidar beams with the dominant wind direction, increasing the arc span and lowering the number of beams per arc scan. Large arc spans should be used at sites with high turbulence intensity and/or large wind direction variation.

  17. Plutonium(IV) complexation by diglycolamide ligands - coordination chemistry insight into TODGA-based actinide separations

    NARCIS (Netherlands)

    Reilly, S.D.; Gaunt, A.J.; Scott, B.L.; Modolo, G.; Iqbal, M.; Verboom, Willem; Sarsfield, M.J.

    2012-01-01

    Complexation of Pu(IV) with TMDGA, TEDGA, and TODGA diglycolamide ligands was followed by vis-NIR spectroscopy. A crystal structure determination reveals that TMDGA forms a 1:3 homoleptic Pu(IV) complex with the nitrate anions forced into the outer coordination sphere

  18. Obstacles to Industrial Implementation of Scanning Systems

    Science.gov (United States)

    Anders Astrom; Olog Broman; John Graffman; Anders Gronlund; Armas Jappinene; Jari Luostarinen; Jan Nystrom; Daniel L. Schmoldt

    1998-01-01

    Initially the group discussed what is meant by scanning systems. An operational definition was adopted to consider scanning system in the current context to be nontraditional scanning. Where, traditional scanning is defined as scanning that has been industrially operational and relatively common for several years-a mature technology. For example,...

  19. Remotely scanned multiphoton temporal focusing by axial grism scanning.

    Science.gov (United States)

    Dana, Hod; Shoham, Shy

    2012-07-15

    A simple technique for remote scanning of the focal plane in temporal focusing multiphoton microscopy is demonstrated both theoretically and experimentally. A new on-axis light propagation optical setup design enables this scanning, which was considered not feasible in previous studies. The focal plane is axially displaced by the movement of a remote optical device, consisting of a double prism grating, and optionally a cylindrical lens. The displacement is linear, and its slope is inversely proportional to the square of the optical system's magnification.

  20. Scanning probe and micropatterning approaches for biomolecular screening applications

    CERN Document Server

    Wilde, L M

    2002-01-01

    Force mapping using atomic force microscopy (AFM) allows for the simultaneous acquisition of topography and probe-sample interaction data. For example, AFM probes functionalised with an antigen can be employed to map the spatial distribution of recognition events on a substrate functionalised with the complementary specific antibody. However, this technique is currently limited to the detection of a single receptor-ligand species. Were the detection of multiple receptor-ligand interactions possible, AFM force mapping would offer greater scope as a sensitive tool for bioassay and screening applications. This thesis outlines developments in probe and substrate immobilisation methods to facilitate this process. We have developed an immobilisation strategy, which allows two antigen species, human serum albumin (HSA) and the beta subunit of human chorionic gonadotropin (beta hCG) to be simultaneously present on an AFM probe. Single point force spectroscopy results have revealed the ability of such probes to discri...

  1. The boundary-scan handbook

    CERN Document Server

    Parker, Kenneth P

    2016-01-01

    Aimed at electronics industry professionals, this 4th edition of the Boundary Scan Handbook describes recent changes to the IEEE1149.1 Standard Test Access Port and Boundary-Scan Architecture. This updated edition features new chapters on the possible effects of the changes on the work of the practicing test engineers and the new 1149.8.1 standard. Anyone needing to understand the basics of boundary scan and its practical industrial implementation will need this book. Provides an overview of the recent changes to the 1149.1 standard and the effect of the changes on the work of test engineers;   Explains the new IEEE 1149.8.1 subsidiary standard and applications;   Describes the latest updates on the supplementary IEEE testing standards. In particular, addresses: IEEE Std 1149.1                      Digital Boundary-Scan IEEE Std 1149.4                      Analog Boundary-Scan IEEE Std 1149.6                      Advanced I/O Testing IEEE Std 1149.8.1           �...

  2. Immobilisation of ligands by radio-derivatized polymers; Immobilisering av ligander med radioderiverte polymerer

    Energy Technology Data Exchange (ETDEWEB)

    Varga, J.M.; Fritsch, P.

    1995-01-30

    The invention relates to radio-derivatized polymers and a method of producing them by contacting non-polymerizable conjugands with radiolysable polymers in the presence of irradiation. The resulting radio-derivatized polymers can be further linked with ligand of organic or inorganic nature to immobilize such ligands. 2 figs., 5 tabs.

  3. Influence of Capping Ligand and Synthesis Method on Structure and Morphology of Aqueous Phase Synthesized CuInSe2 Nanoparticles

    Science.gov (United States)

    Ram Kumar, J.; Ananthakumar, S.; Moorthy Babu, S.

    2017-01-01

    A facile route to synthesize copper indium diselenide (CuInSe2) nanoparticles in aqueous medium was developed using mercaptoacetic acid (MAA) as capping agent. Two different mole ratios (5 and 10) of MAA were used to synthesize CuInSe2 nanoparticles at room temperature, as well as hydrothermal (high temperature) method. Powder x-ray diffraction analysis reveals that the nanoparticles exhibit chalcopyrite phase and the crystallinity increases with increasing the capping ratio. Raman analysis shows a strong band at 233 cm-1 due to the combination of B2 (E) modes. Broad absorption spectra were observed for the synthesized CuInSe2 nanoparticles. The effective surface capping by MAA on the nanoparticles surface was confirmed through attenuated total reflection-Fourier transform infrared spectral analysis. The thermal stability of the synthesized samples was analyzed through thermogravimetric analysis-differential scanning calorimetry. The change in morphology of the synthesized samples was analyzed through scanning electron microscope and it shows that the samples prepared at room temperature are spherical in shape, whereas hydrothermally synthesized samples were found to have nanorod- and nanoflake-like structures. Transmission electron microscope analysis further indicates larger grains for the hydrothermally prepared samples with 10 mol ratio of MAA. Comparative analyses were made for synthesizing CuInSe2 nanoparticles by two different methods to explore the role of ligand and influence of temperature.

  4. A new class of PN3-pincer ligands for metal–ligand cooperative catalysis

    KAUST Repository

    Li, Huaifeng

    2014-12-01

    Work on a new class of PN3-pincer ligands for metal-ligand cooperative catalysis is reviewed. While the field of the pyridine-based PN3-transition metal pincer complexes is still relatively young, many important applications of these complexes have already emerged. In several cases, the PN3-pincer complexes for metal-ligand cooperative catalysis result in significantly improved or unprecedented activities. The synthesis and coordination chemistry of PN3-pincer ligands are briefly summarized first to cover the synthetic routes for their preparation, followed by a focus review on their applications in catalysis. A specific emphasis is placed on the later section about the role of PN3-pincer ligands\\' dearomatization-rearomatization steps during the catalytic cycles. The mechanistic insights from density functional theory (DFT) calculations are also discussed.

  5. PPARα Ligands as Antitumorigenic and Antiangiogenic Agents

    Directory of Open Access Journals (Sweden)

    Ambra Pozzi

    2008-01-01

    Full Text Available Peroxisome proliferator-activated receptors (PPARs belong to the nuclear receptor family of ligand-activated transcription factors. This subfamily is composed of three members—PPARα, PPARδ, and PPARγ—that differ in their cell and tissue distribution as well as in their target genes. PPARα is abundantly expressed in liver, brown adipose tissue, kidney, intestine, heart, and skeletal muscle; and its ligands have been used to treat diseases such as obesity and diabetes. The recent finding that members of the PPAR family, including the PPARα, are expressed by tumor and endothelial cells together with the observation that PPAR ligands regulate cell growth, survival, migration, and invasion, suggested that PPARs also play a role in cancer. In this review, we focus on the contribution of PPARα to tumor and endothelial cell functions and provide compelling evidence that PPARα can be viewed as a new class of ligand activated tumor “suppressor” gene with antiangiogenic and antitumorigenic activities. Given that PPAR ligands are currently used in medicine as hypolipidemic drugs with excellent tolerance and limited toxicity, PPARα activation might offer a novel and potentially low-toxic approach for the treatment of tumor-associated angiogenesis and cancer.

  6. Nanobits: customizable scanning probe tips

    DEFF Research Database (Denmark)

    Kumar, Rajendra; Shaik, Hassan Uddin; Sardan Sukas, Özlem

    2009-01-01

    We present here a proof-of-principle study of scanning probe tips defined by planar nanolithography and integrated with AFM probes using nanomanipulation. The so-called 'nanobits' are 2-4 mu m long and 120-150 nm thin flakes of Si3N4 or SiO2, fabricated by electron beam lithography and standard...... silicon processing. Using a microgripper they were detached from an array and fixed to a standard pyramidal AFM probe or alternatively inserted into a tipless cantilever equipped with a narrow slit. The nanobit-enhanced probes were used for imaging of deep trenches, without visible deformation, wear...... or dislocation of the tips of the nanobit after several scans. This approach allows an unprecedented freedom in adapting the shape and size of scanning probe tips to the surface topology or to the specific application....

  7. Footwear scanning systems and methods

    Energy Technology Data Exchange (ETDEWEB)

    Fernandes, Justin L.; McMakin, Douglas L.; Sheen, David M.; Tedeschi, Jonathan R.

    2017-07-25

    Methods and apparatus for scanning articles, such as footwear, to provide information regarding the contents of the articles are described. According to one aspect, a footwear scanning system includes a platform configured to contact footwear to be scanned, an antenna array configured to transmit electromagnetic waves through the platform into the footwear and to receive electromagnetic waves from the footwear and the platform, a transceiver coupled with antennas of the antenna array and configured to apply electrical signals to at least one of the antennas to generate the transmitted electromagnetic waves and to receive electrical signals from at least another of the antennas corresponding to the electromagnetic waves received by the others of the antennas, and processing circuitry configured to process the received electrical signals from the transceiver to provide information regarding contents within the footwear.

  8. Cooperative equilibrium curves generated by ordered ligand binding to multi-site molecules.

    Science.gov (United States)

    Michel, Denis

    2007-09-01

    The sigmoid shape of equilibrium curves in normal axes and Hill coefficients higher than unity, are indexes of cooperativity or homotropic allostery where the affinity for the ligand increases as saturation progresses. The mathematical transformation of the Adair scheme of equilibria in the Hill plot, reveals that sigmoid binding curves can also be generated by ordered ligand binding to a receptor with multiple binding sites of identical microscopic association constants. This mechanism only based on the law of mass action, could participate to some extent to certain cooperative effects observed in non-biological systems and perhaps in the physiological binding of oxygen to heme proteins.

  9. Design and Synthesis of a Novel Ganglioside Ligand for Influenza A Viruses

    Directory of Open Access Journals (Sweden)

    Tomohiro Nohara

    2012-08-01

    Full Text Available A novel ganglioside bearing Neua2-3Gal and Neua2-6Gal structures as distal sequences was designed as a ligand for influenza A viruses. The efficient synthesis of the designed ganglioside was accomplished by employing the cassette coupling approach as a key reaction, which was executed between the non-reducing end of the oligosaccharide and the cyclic glucosylceramide moiety. Examination of its binding activity to influenza A viruses revealed that the new ligand is recognized by Neua2-3 and 2-6 type viruses.

  10. Conformational restrictions in ligand binding to the human intestinal di-/tripeptide transporter

    DEFF Research Database (Denmark)

    Våbenø, Jon; Nielsen, Carsten Uhd; Steffansen, Bente

    2005-01-01

    by conformational analysis and 2D dihedral driving analysis of 15 hPEPT1 substrates, which suggested that psi(1) approximately 165 degrees , omega(1) approximately 180 degrees , and phi(2) approximately 280 degrees were descriptive of the bioactive conformation. Subsequently, the conformational energy required...... between DeltaE(bbone) and log1/K(i), showing that DeltaE(bbone) contributes significantly to the experimentally observed affinity for hPEPT1 ligands. Qualitatively, the results revealed that compounds classified as high affinity ligands (K(i)...

  11. RPC High Voltage Scan 2015

    CERN Document Server

    CMS Collaboration

    2016-01-01

    During the LS1 the CMS RPC system has been upgraded with 144 new chambers installed on the forth endcap stations. An annual HV (RPC efficiency vs HV) scan for the entire RPC system has been performed during the Run2 data taking period in 2015. The obtained results have been compared to the HV scans performed in 2011 and 2012. No significant differences are observed in the compared results. The optimal HV working points for the newly installed chambers have been evaluated for the first time with collision data.

  12. Pyrophosphate heart scan in cardiomyopathies

    Energy Technology Data Exchange (ETDEWEB)

    Duska, F.; Novak, J.; Kubicek, J.; Vizda, J.; Kafka, P.; Blaha, V.; Nesvadba, Z.; Zdansky, P. (Karlova Univ., Hradec Kralove (Czechoslovakia). Lekarska Fakulta)

    1982-01-01

    Scintigraphic examination of the heart with pyrophosphate labelled sup(99m)Tc was made in 26 patients with cardiomyopathies of different etiology. From a total of 11 children with secondary affections of the myocardium in myodystrophia musculorum progressiva a positive scintigraphic finding was only obtained in two cases. 12 patients with primary non-obstructive cardiomyopathies the scan was positive in nine cases. One positive scintigraphic finding was shown in examinating three patients with obstructive cardiomyopathies (subvalvular aortic stenosis). The positive scan suggests acute progress of the pathological process in the heart.

  13. Integrated micromachined scanning display systems

    Science.gov (United States)

    Hagelin, Paul M.; Krishnamoorthy, Uma; Conant, Robert A.; Muller, Richard S.; Lau, Kam Y.; Solgaard, Olav

    1999-07-01

    We describe a raster-scanning display system comprised of two tilt-up micromachined polysilicon mirrors that rotate about orthogonal axes. We have demonstrated a resolution of 102 X 119 pixels. The optical efficiency of our two- mirror micro-optical raster-scanning system is comparable to that of micromachined display systems developed by Texas Instruments and Silicon Light Machines. Ease of integration with on-chip light sources and lenses has the potential to reduce packaging size, complexity and cost of the display system and makes it well suited for head-mounted display applications.

  14. Insights into the evolution of the ErbB receptor family and their ligands from sequence analysis

    Directory of Open Access Journals (Sweden)

    Staros James V

    2006-10-01

    Full Text Available Abstract Background In the time since we presented the first molecular evolutionary study of the ErbB family of receptors and the EGF family of ligands, there has been a dramatic increase in genomic sequences available. We have utilized this greatly expanded data set in this study of the ErbB family of receptors and their ligands. Results In our previous analysis we postulated that EGF family ligands could be characterized by the presence of a splice site in the coding region between the fourth and fifth cysteines of the EGF module and the placement of that module near the transmembrane domain. The recent identification of several new ligands for the ErbB receptors supports this characterization of an ErbB ligand; further, applying this characterization to available sequences suggests additional potential ligands for these receptors, the EGF modules from previously identified proteins: interphotoreceptor matrix proteoglycan-2, the alpha and beta subunit of meprin A, and mucins 3, 4, 12, and 17. The newly available sequences have caused some reorganizations of relationships among the ErbB ligand family, but they add support to the previous conclusion that three gene duplication events gave rise to the present family of four ErbB receptors among the tetrapods. Conclusion This study provides strong support for the hypothesis that the presence of an easily identifiable sequence motif can distinguish EGF family ligands from other EGF-like modules and reveals several potential new EGF family ligands. It also raises interesting questions about the evolution of ErbB2 and ErbB3: Does ErbB2 in teleosts function differently from ErbB2 in tetrapods in terms of ligand binding and intramolecular tethering? When did ErbB3 lose kinase activity, and what is the functional significance of the divergence of its kinase domain among teleosts?

  15. Another brick in the wall. Validation of the σ1 receptor 3D model by computer-assisted design, synthesis, and activity of new σ1 ligands.

    Science.gov (United States)

    Laurini, Erik; Marson, Domenico; Dal Col, Valentina; Fermeglia, Maurizio; Mamolo, Maria Grazia; Zampieri, Daniele; Vio, Luciano; Pricl, Sabrina

    2012-11-05

    Originally considered an enigmatic polypeptide, the σ(1) receptor has recently been identified as a unique ligand-regulated protein. Many studies have shown the potential of σ(1) receptor ligands for the treatment of various diseases of the central nervous system (CNS); nevertheless, almost no information about the 3D structure of the receptor and/or the possible modes of interaction of the σ(1) protein with its ligands have been unveiled so far. With the present work we validated our σ(1) 3D homology model and assessed its reliability as a platform for σ(1) ligand structure-based drug design. To this purpose, the 3D σ(1) model was exploited in the design of 33 new σ(1) ligands and in their ranking for receptor affinity by extensive molecular dynamics simulation-based free energy calculations. Also, the main interactions involved in receptor/ligand binding were analyzed by applying a per residue free energy deconvolution and in silico alanine scanning mutagenesis calculations. Subsequently, all compounds were synthesized in our laboratory and tested for σ(1) binding activity in vitro. The agreement between in silico and in vitro results confirms the reliability of the proposed σ(1) 3D model in the a priori prediction of the affinity of new σ(1) ligands. Moreover, it also supports and corroborates the currently available biochemical data concerning the σ(1) protein residues considered essential for σ(1) ligand binding and activity.

  16. Revealing Non-Covalent Interactions

    Science.gov (United States)

    Johnson, Erin R.; Keinan, Shahar; Mori-Sánchez, Paula; Contreras-García, Julia; Cohen, Aron J.; Yang, Weitao

    2010-01-01

    Molecular structure does not easily identify the intricate non-covalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect non-covalent interactions in real space, based on the electron density and its derivatives. Our approach reveals underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of non-bonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands. PMID:20394428

  17. Effects of PPARγ Ligands on Leukemia

    Directory of Open Access Journals (Sweden)

    Yoko Tabe

    2012-01-01

    Full Text Available Peroxisome proliferator-activated receptors (PPARs and retinoic acid receptors (RARs, members of the nuclear receptor superfamily, are transcription factors that regulate a variety of important cellular functions. PPARs form heterodimers retinoid X receptor (RXR, an obligate heterodimeric partner for other nuclear receptors. Several novel links between retinoid metabolism and PPAR responses have been identified, and activation of PPAR/RXR expression has been shown to increase response to retinoids. PPARγ has emerged as a key regulator of cell growth and survival, whose activity is modulated by a number of synthetic and natural ligands. While clinical trials in cancer patients with thiazolidinediones (TZD have been disappointing, novel structurally different PPARγ ligands, including triterpenoids, have entered clinical arena as therapeutic agents for epithelial and hematopoietic malignancies. Here we shall review the antitumor advances of PPARγ, alone and in combination with RARα ligands in control of cell proliferation, differentiation, and apoptosis and their potential therapeutic applications in hematological malignancies.

  18. Flexible Ligand Docking Using Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Thomsen, Rene

    2003-01-01

    The docking of ligands to proteins can be formulated as a computational problem where the task is to find the most favorable energetic conformation among the large space of possible protein–ligand complexes. Stochastic search methods such as evolutionary algorithms (EAs) can be used to sample large...... search spaces effectively and is one of the commonly used methods for flexible ligand docking. During the last decade, several EAs using different variation operators have been introduced, such as the ones provided with the AutoDock program. In this paper we evaluate the performance of different EA...... settings such as choice of variation operators, population size, and usage of local search. The comparison is performed on a suite of six docking problems previously used to evaluate the performance of search algorithms provided with the AutoDock program package. The results from our investigation confirm...

  19. Hydrothermal reactions: From the synthesis of ligand to new lanthanide 3D-coordination polymers

    Science.gov (United States)

    da Silva, Fausthon Fred; de Oliveira, Carlos Alberto Fernandes; Falcão, Eduardo Henrique Lago; Gatto, Claudia Cristina; da Costa, Nivan Bezerra; Freire, Ricardo Oliveira; Chojnacki, Jarosław; Alves Júnior, Severino

    2013-11-01

    The organic ligand 2,5-piperazinedione-1,4-diacetic acid (H2PDA) was synthesized under hydrothermal conditions starting from the iminodiacetic acid and catalyzed by oxalic acid. The X-ray powder diffraction data indicates that the compound crystallizes in the P21/c monoclinic system as reported in the literature. The ligand was also characterized by elemental analysis, magnetic nuclear resonance, infrared spectroscopy and thermogravimetric analysis. Two new coordination networks based on lanthanide ions were obtained with this ligand using hydrothermal reaction. In addition to single-crystal X-ray diffraction, the compounds were characterized by infrared spectroscopy, thermogravimetric analysis, scanning electron microscopy and elemental analysis. Single-crystal XRD showed that the compounds are isostructural, crystallizing in P21/n monoclinic system with chemical formula [Ln(PDA)1.5(H2O)](H2O)3 (Ln=Gd3+(1) and Eu3+(2)).The luminescence properties of both compounds were studied. In the compound (1), a broad emission band was observed at 479 nm, redshifted by 70 nm in comparison of the free ligand. In (2), the typical f-f transition was observed with a maximum peak at 618 nm, related with the red emission of the europium ions. Computational methods were performed to simulate the crystal structure of (2). The theoretical calculations of the intensity parameters are in good agreement with the experimental values.

  20. Distinctive responses of brain tumor cells to TLR2 ligands.

    Science.gov (United States)

    Yoon, Hee Jung; Jeon, Sae-Bom; Koh, Han Seok; Song, Jae-Young; Kim, Sang Soo; Kim, In-Hoo; Park, Eun Jung

    2015-05-01

    Malignant brain tumor mass contains significant numbers of infiltrating glial cells that may intimately interact with tumor cells and influence cancer treatments. Understanding of characteristic discrepancies between normal GLIA and tumor cells would, therefore, be valuable for improving anticancer therapeutics. Here, we report distinct differences in toll-like receptors (TLR)-2-mediated responses between normal glia and primary brain tumor cell lines. We found that tyrosine phosphorylation of STAT1 by TLR2 ligands and its downstream events did not occur in mouse, rat, or human brain tumor cell lines, but were markedly induced in normal primary microglia and astrocytes. Using TLR2-deficient, interferon (IFN)-γ-deficient, and IFNγ-receptor-1-deficient mice, we revealed that the impaired phosphorylation of STAT1 might be linked with defective TLR2 system in tumor cells, and that a TLR2-dependent pathway, not IFNγ-receptor machinery, might be critical for tyrosine STAT1 phosphorylation by TLR2 ligands. We also found that TLR2 and its heterodimeric partners, TLR1 and 6, on brain tumor cells failed to properly respond to TLR2 ligands, and representative TLR2-dependent cellular events, such as inflammatory responses and cell death, were not detected in brain tumor cells. Similar results were obtained in in vitro and in vivo experiments using orthotopic mouse and rat brain tumor models. Collectively, these results suggest that primary brain tumor cells may exhibit a distinctive dysfunction of TLR2-associated responses, resulting in abnormal signaling and cellular events. Careful targeting of this distinctive property could serve as the basis for effective therapeutic approaches against primary brain tumors. © 2015 Wiley Periodicals, Inc.

  1. Infrared Scanning For Electrical Maintenance

    Science.gov (United States)

    Eisenbath, Steven E.

    1983-03-01

    Given the technological age that we have now entered, the purpose of this paper is to relate how infrared scanning can be used for an electrical preventative maintenance program. An infrared scanner is able to produce an image because objects give off infrared radiation in relationship to their temperature. Most electrical problems will show up as an increase in temperature, thereby making the infrared scanner a useful preventative maintenance tool. Because of the sensitivity of most of the scanners, .1 to .2 of a degree, virtually all electrical problems can be pinpointed long before they become a costly failure. One of the early uses of infrared scanning was to check the power company's electrical distribution system. Most of this was performed via aircraft or truck mounted scanning devices which necessitated its semi-permanent mounting. With the advent of small hand held infrared imagers, along with more portability of the larger systems, infrared scanning has gained more popularity in checking electrical distribution systems. But the distribution systems are now a scaled down model, mainly the in-plant electrical systems. By in-plant, I mean any distribution of electricity; once it leaves the power company's grid. This can be in a hospital, retail outlet, warehouse or manufacturing facility.

  2. Vacuum scanning capillary photoemission microscopy

    DEFF Research Database (Denmark)

    Aseyev, S.A.; Cherkun, A P; Mironov, B N

    2017-01-01

    We demonstrate the use of a conical capillary in a scanning probe microscopy for surface analysis. The probe can measure photoemission from a substrate by transmitting photoelectrons along the capillary as a function of probe position. The technique is demonstrated on a model substrate consisting...

  3. High Resolution Scanning Ion Microscopy

    NARCIS (Netherlands)

    Castaldo, V.

    2011-01-01

    The structure of the thesis is the following. The first chapter is an introduction to scanning microscopy, where the path that led to the Focused Ion Beam (FIB) is described and the main differences between electrons and ion beams are highlighted. Chapter 2 is what is normally referred to (which I

  4. Phase sensitive scanning optical microscope

    Energy Technology Data Exchange (ETDEWEB)

    Jungerman, R.L.; Hobbs, P.C.D.; Kino, G.S.

    1984-10-15

    An electronically scanned optical microscope which quantitatively measures amplitude and phase is described. The system is insenstive to mechanical vibrations. The phase infromation makes it possible to measure surface height variations with an accuracy of better than 100 A and can also be used to improve the lateral resolution.

  5. Electronically-Scanned Pressure Sensors

    Science.gov (United States)

    Coe, C. F.; Parra, G. T.; Kauffman, R. C.

    1984-01-01

    Sensors not pneumatically switched. Electronic pressure-transducer scanning system constructed in modular form. Pressure transducer modules and analog to digital converter module small enough to fit within cavities of average-sized wind-tunnel models. All switching done electronically. Temperature controlled environment maintained within sensor modules so accuracy maintained while ambient temperature varies.

  6. Introduction to scanning tunneling microscopy

    CERN Document Server

    Chen, C Julian

    2008-01-01

    The scanning tunneling and the atomic force microscope, both capable of imaging individual atoms, were crowned with the Physics Nobel Prize in 1986, and are the cornerstones of nanotechnology today. This is a thoroughly updated version of this 'bible' in the field.

  7. Gigantiform cementoma showing apparent activity on a bone scan.

    Science.gov (United States)

    Millet, D T

    1990-08-01

    A bone scan in a Negroid female suspected of myeloma showed no uptake other than in the jaws. A panoramic radiograph revealed multiple mixed-density lesions, in particular in the mandible, suggestive of gigantiform cementoma. The significance of this association is discussed.

  8. Imidazole-based Potential Bi- and Tridentate Nitrogen Ligands: Synthesis, Characterization and Application in Asymmetric Catalysis

    Directory of Open Access Journals (Sweden)

    Jiří Kulhánek

    2008-09-01

    Full Text Available Twelve new imidazole-based potential bi- and tridentate ligands were synthesized and characterized. Whereas in the first series the α-amino acid and imidazole moieties were linked by an amino bond, in the second series the tridentate ligands, containing two imidazole groups, were separated by an amide bond. The first series was obtained by the reductive amination of 2-phenylimidazole-4-carboxaldehyde with α-amino acid esters. The tridentate ligands were prepared from 2-phenylimidazole-4-carboxylic acid and chiral amines. In the Henry reaction, the amines were revealed as a more reactive species than the less nucleophilic amides, however the enantiomeric excesses were generally poor.

  9. Selective ligand recognition by a diversity-generating retroelement variable protein.

    Directory of Open Access Journals (Sweden)

    Jason L Miller

    2008-06-01

    Full Text Available Diversity-generating retroelements (DGRs recognize novel ligands through massive protein sequence variation, a property shared uniquely with the adaptive immune response. Little is known about how recognition is achieved by DGR variable proteins. Here, we present the structure of the Bordetella bacteriophage DGR variable protein major tropism determinant (Mtd bound to the receptor pertactin, revealing remarkable adaptability in the static binding sites of Mtd. Despite large dissimilarities in ligand binding mode, principles underlying selective recognition were strikingly conserved between Mtd and immunoreceptors. Central to this was the differential amplification of binding strengths by avidity (i.e., multivalency, which not only relaxed the demand for optimal complementarity between Mtd and pertactin but also enhanced distinctions among binding events to provide selectivity. A quantitatively similar balance between complementarity and avidity was observed for Bordetella bacteriophage DGR as occurs in the immune system, suggesting that variable repertoires operate under a narrow set of conditions to recognize novel ligands.

  10. Molecular Recognition and Immobilization of Ligand-Conjugated Redox-Responsive Polymer Nanocontainers.

    Science.gov (United States)

    de Vries, Wilke C; Tesch, Matthias; Studer, Armido; Ravoo, Bart Jan

    2017-12-06

    We present the preparation of ligand-conjugated redox-responsive polymer nanocontainers by the supramolecular decoration of cyclodextrin vesicles with a thin redox-cleavable polymer shell that displays molecular recognition units on its surface. Two widely different recognition motifs (mannose-Concanavalin A and biotin-streptavidin) are compared and the impact of ligand density on the nanocontainer surface as well as an additional functionalization with nonadhesive poly(ethylene glycol) is studied. Aggregation assays, dynamic light scattering, and a fluorometric quantification reveal that the molecular recognition of ligand-conjugated polymer nanocontainers by receptor proteins is strongly affected by the multivalency of interactions and the association strength of the recognition motif. Finally, microcontact printing is used to prepare streptavidin-patterned surfaces, and the specific immobilization of biotin-conjugated nanocontainers is demonstrated. As a prototype of a nanosensor, these tethered nanocontainers can sense a reductive environment and react by releasing a payload.

  11. Improving the binding capacities of protein A chromatographic materials by means of ligand polymerization.

    Science.gov (United States)

    Freiherr von Roman, Matthias; Berensmeier, Sonja

    2014-06-20

    Protein A chromatography is one of the most important techniques used in the purification of monoclonal antibodies. Due to the low dynamic binding capacity of protein A chromatographic materials compared to other stationary phases, protein A chromatography is often discussed to be the bottleneck among current purification processes. Several approaches were tested within this study in order to maximize IgG binding capacities of current acrylamido-based based resins. Genetic engineering techniques were used in order to polymerize one of the IgG binding domains (B-domain) of protein A from Staphylococcus aureus (SpA) to achieve ligands with an increased length. The solution-binding ratio and the total size of ligand-antibody complexes were used to characterize the interaction potential of novel ligands, revealing a relatively linear dependency between the number of binding domains upon the amount of bound antibody molecules. This relationship was also valid up to a ligand which was comprised of 8 B-domains after attaching them onto acrylamido-based based stationary phases using epoxy coupling techniques. Equilibrium binding capacities of more than 80mghIgGmL(-1) were achieved using the B8 ligand. Furthermore, static binding capacities, especially for smaller ligands comprised of fewer B-domains, were improved up to 87mghIgGmL(-1) using site-specific coupling chemistry, which is an improvement of more than 20% compared to commercially available materials. In order to evaluate pore exclusion effects due to the use of prolonged affinity ligands, prepared materials were characterized regarding their effective intraparticle porosity and breakthrough capacity. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Scanning Quantum Cryogenic Atom Microscope

    Science.gov (United States)

    Yang, Fan; Kollár, Alicia J.; Taylor, Stephen F.; Turner, Richard W.; Lev, Benjamin L.

    2017-03-01

    Microscopic imaging of local magnetic fields provides a window into the organizing principles of complex and technologically relevant condensed-matter materials. However, a wide variety of intriguing strongly correlated and topologically nontrivial materials exhibit poorly understood phenomena outside the detection capability of state-of-the-art high-sensitivity high-resolution scanning probe magnetometers. We introduce a quantum-noise-limited scanning probe magnetometer that can operate from room-to-cryogenic temperatures with unprecedented dc-field sensitivity and micron-scale resolution. The Scanning Quantum Cryogenic Atom Microscope (SQCRAMscope) employs a magnetically levitated atomic Bose-Einstein condensate (BEC), thereby providing immunity to conductive and blackbody radiative heating. The SQCRAMscope has a field sensitivity of 1.4 nT per resolution-limited point (approximately 2 μ m ) or 6 nT /√{Hz } per point at its duty cycle. Compared to point-by-point sensors, the long length of the BEC provides a naturally parallel measurement, allowing one to measure nearly 100 points with an effective field sensitivity of 600 pT /√{Hz } for each point during the same time as a point-by-point scanner measures these points sequentially. Moreover, it has a noise floor of 300 pT and provides nearly 2 orders of magnitude improvement in magnetic flux sensitivity (down to 10-6 Φ0/√{Hz } ) over previous atomic probe magnetometers capable of scanning near samples. These capabilities are carefully benchmarked by imaging magnetic fields arising from microfabricated wire patterns in a system where samples may be scanned, cryogenically cooled, and easily exchanged. We anticipate the SQCRAMscope will provide charge-transport images at temperatures from room temperature to 4 K in unconventional superconductors and topologically nontrivial materials.

  13. Isotherm of ligand adsorption on DNA at multiplicative noise.

    Science.gov (United States)

    Arakelyan, Valeri; Harutyunyan, Sos; Andriasyan, Vardan; Arakelyan, Hakob

    2012-01-01

    Fluctuations of the number of ligands adsorbed on macromolecules are considered in the case when the number of ligands in the solution fluctuates under the action of fluctuations of the external medium (external noise). For the case of small filling, the multiplicative type of stochastic differential equation is obtained, describing the time variation of the number of ligands adsorbed on macromolecules. The isotherm of adsorption of ligands on DNA is obtained. It is shown that at small ligand concentrations, for some relations between adsorption parameters and the intensity of the external noise, no macromolecule adsorption of ligands takes place.

  14. Direct observation of ligand dynamics in cytochrome c.

    Science.gov (United States)

    Thielges, Megan C; Zimmermann, Jörg; Romesberg, Floyd E

    2009-05-06

    Horse heart cytochrome c (cyt c) has emerged as a paradigm for the study of protein folding, in large part because the covalently bound heme facilitates its characterization. The folding of reduced cyt c induced by photodissociation of CO from the CO-bound unfolded protein has been extensively studied. Following a nanosecond light pulse, four transitions with time constants of approximately 1-5, 50-100, 200-500, and 1000-10000 micros have been resolved. While originally thought to be associated with CO rebinding to two different partially folded states of cyt c, the two slower processes are now understood to reflect the bimolecular reassociation of CO followed by religation of His18, which by the base elimination mechanism is induced to dissociate after CO photolysis. Thus, it turns out that the two longer time constants do not report on protein folding but instead reflect the complexity of heme ligation. The two shorter time constants have been attributed to ligation at the heme center by Met65 or Met80 and His33 or His26 and have been used to estimate interchain diffusion rates of the protein. Here, to unambiguously determine the post-photodissociation steps involving CO, we have monitored the CO vibration following photodissociation with step-scan FT-IR spectroscopy. We have found that like the longer time scale processes, the 50-100 mus time scale process is associated not with protein dynamics but with CO ligand dynamics. The data clearly demonstrate that whatever the origins of the spectral changes, they clearly involve CO rebinding or changes in the environment of an already bound CO ligand. We speculate that the observed changes reflect His18 religation after fast geminate recombination of the CO. The data suggest that the associated time constant should not be used as a measure of interchain diffusion, and the results emphasize the importance of studying protein folding with probes that have inherently high structural resolution.

  15. Thermodynamic properties of mixed-ligand rare earth pivalates

    Energy Technology Data Exchange (ETDEWEB)

    Dobrokhotova, Zh.V., E-mail: Zhdobro@yandex.ru [Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, 31 Leninsky Prosp., 119991 Moscow (Russian Federation); Tyurin, A.V., E-mail: tac@igic.ras.ru [Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, 31 Leninsky Prosp., 119991 Moscow (Russian Federation); Fomina, I.G., E-mail: fomina@igic.ras.ru [Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, 31 Leninsky Prosp., 119991 Moscow (Russian Federation); Gavrichev, K.S., E-mail: gavrich@igic.ras.ru [Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, 31 Leninsky Prosp., 119991 Moscow (Russian Federation); Ryumin, M.A., E-mail: Ryumin80@mail.ru [Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, 31 Leninsky Prosp., 119991 Moscow (Russian Federation); Bykov, M.A., E-mail: mich@td.chem.msu.ru [Department of Chemistry, Lomonosov Moscow State University, 1 Leninskie Gory, 119889 Moscow (Russian Federation); Emelina, A.L., E-mail: emelina@td.chem.msu.ru [Department of Chemistry, Lomonosov Moscow State University, 1 Leninskie Gory, 119889 Moscow (Russian Federation); Novotortsev, V.M., E-mail: vmnov@igic.ras.ru [Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, 31 Leninsky Prosp., 119991 Moscow (Russian Federation); Eremenko, I.L., E-mail: ilerem@igic.ras.ru [Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, 31 Leninsky Prosp., 119991 Moscow (Russian Federation)

    2013-03-20

    Highlights: ► 12 rare earth pivalate complexes were measured by adiabatic calorimetry and DSC. ► Thermodynamic functions in the studied temperature range were calculated. ► No phase transitions for the (phen){sub 2}Ln{sub 2}(piv){sub 6} were found from 5 K to temperature of ligand removal. - Abstract: For structurally characterized dinuclear rare earth pivalate complexes, Ln{sub 2}(piv){sub 6}(Hpiv){sub 6}·Hpiv (Hpiv is pivalic acid, Ln = La (1), Sm (2), Eu (3), and Gd (4)), Tb{sub 2}(piv){sub 6}(Hpiv){sub 6} (5), (bpy){sub 2}Ln{sub 2}(piv){sub 6}, (bpy = 2,2′-bipyridine, Ln = Sm (6), Eu (7), Gd (8), and Er (9)), and (phen){sub 2}Ln{sub 2}(piv){sub 6} (phen = 1,10-phenanthroline, Ln = Sm (10), Eu (11), and Tb (12)), the temperature dependences of the heat capacities were measured by adiabatic and differential scanning calorimetry, and the thermodynamic functions C{sub p}{sup 0}(T), S{sup 0}(T), φ{sup 0}(T), and H{sup 0}(T) − H{sup 0}(0) were calculated. The C{sub p}{sup 0}(T) curves for the complexes with pivalic acid and 2,2′-bipyridine show anomalies, whereas no structural changes are observed for the complexes with 1,10-phenanthroline between the temperature range from 5 K to the temperature of the ligand removal.

  16. Predicting Allosteric Effects from Orthosteric Binding in Hsp90-Ligand Interactions: Implications for Fragment-Based Drug Design.

    Directory of Open Access Journals (Sweden)

    Arun Chandramohan

    2016-06-01

    Full Text Available A key question in mapping dynamics of protein-ligand interactions is to distinguish changes at binding sites from those associated with long range conformational changes upon binding at distal sites. This assumes a greater challenge when considering the interactions of low affinity ligands (dissociation constants, KD, in the μM range or lower. Amide hydrogen deuterium Exchange mass spectrometry (HDXMS is a robust method that can provide both structural insights and dynamics information on both high affinity and transient protein-ligand interactions. In this study, an application of HDXMS for probing the dynamics of low affinity ligands to proteins is described using the N-terminal ATPase domain of Hsp90. Comparison of Hsp90 dynamics between high affinity natural inhibitors (KD ~ nM and fragment compounds reveal that HDXMS is highly sensitive in mapping the interactions of both high and low affinity ligands. HDXMS reports on changes that reflect both orthosteric effects and allosteric changes accompanying binding. Orthosteric sites can be identified by overlaying HDXMS onto structural information of protein-ligand complexes. Regions distal to orthosteric sites indicate long range conformational changes with implications for allostery. HDXMS, thus finds powerful utility as a high throughput method for compound library screening to identify binding sites and describe allostery with important implications for fragment-based ligand discovery (FBLD.

  17. Ligand binding reduces SUMOylation of the peroxisome proliferator-activated receptor γ (PPARγ activation function 1 (AF1 domain.

    Directory of Open Access Journals (Sweden)

    Rolf Diezko

    Full Text Available Peroxisome proliferator-activated receptor gamma (PPARγ is a ligand-activated nuclear receptor regulating adipogenesis, glucose homeostasis and inflammatory responses. The activity of PPARγ is controlled by post-translational modifications including SUMOylation and phosphorylation that affects its biological and molecular functions. Several important aspects of PPARγ SUMOylation including SUMO isoform-specificity and the impact of ligand binding on SUMOylation remain unresolved or contradictory. Here, we present a comprehensive study of PPARγ1 SUMOylation. We show that PPARγ1 can be modified by SUMO1 and SUMO2. Mutational analyses revealed that SUMOylation occurs exclusively within the N-terminal activation function 1 (AF1 domain predominantly at lysines 33 and 77. Ligand binding to the C-terminal ligand-binding domain (LBD of PPARγ1 reduces SUMOylation of lysine 33 but not of lysine 77. SUMOylation of lysine 33 and lysine 77 represses basal and ligand-induced activation by PPARγ1. We further show that lysine 365 within the LBD is not a target for SUMOylation as suggested in a previous report, but it is essential for full LBD activity. Our results suggest that PPARγ ligands negatively affect SUMOylation by interdomain communication between the C-terminal LBD and the N-terminal AF1 domain. The ability of the LBD to regulate the AF1 domain may have important implications for the evaluation and mechanism of action of therapeutic ligands that bind PPARγ.

  18. Supramolecular spectral studies on metal-ligand bonding of novel quinoline azodyes

    Science.gov (United States)

    Diab, M. A.; El-Sonbati, A. Z.; El-Bindary, A. A.; Barakat, A. M.

    2013-12-01

    A series of novel bidentate azodye quinoline ligands were synthesized with various p-aromatic amines like p-(OCH3, CH3, H, Cl and NO2). All ligands and their complexes have been characterized on the basis of elemental analysis, IR, 1H and 13C NMR data and spectroscopic studies. IR and 1H NMR studies reveal that the ligands (HLn) exists in the tautomeric azo/hydrazo form in both states with intramolecular hydrogen bonding. The ligands obtained contain Ndbnd N and phenolic functional groups in different positions with respect to the quinoline group. IR spectra show that the azo compounds (HLn) act as monobasic bidentate ligand by coordinating via the azodye (sbnd Ndbnd Nsbnd ) and oxygen atom of the phenolic group. The ESR (g|| and g⊥) and bonding α2 parameters of the copper ion were greatly affected by substituting several groups position of ring of quinoline and p-aromatic ring. The ESR spectra of copper complexes in powder form show a broad signal with values in order g|| > g⊥ > ge > 2.0023. The value of covalency factor β and orbital reduction factor K accounts for the covalent nature of the complexes. All complexes possessed an octahedral and square planar geometry. The thermal properties of the complexes were investigated using TGA and DSC. It is found that the change of substituent affects the thermal properties of complexes.

  19. Including surface ligand effects in continuum elastic models of nanocrystal vibrations

    Science.gov (United States)

    Lee, Elizabeth M. Y.; Mork, A. Jolene; Willard, Adam P.; Tisdale, William A.

    2017-07-01

    The measured low frequency vibrational energies of some quantum dots (QDs) deviate from the predictions of traditional elastic continuum models. Recent experiments have revealed that these deviations can be tuned by changing the ligands that passivate the QD surface. This observation has led to speculation that these deviations are due to a mass-loading effect of the surface ligands. In this article, we address this speculation by formulating a continuum elastic theory that includes the dynamical loading by elastic surface ligands. We demonstrate that this model is capable of accurately reproducing the l = 0 phonon energy across a variety of different QD samples, including cores with different ligand identities and epitaxially grown CdSe/CdS core/shell heterostructures. We highlight that our model performs well even in the small QD regime, where traditional elastic continuum models are especially prone to failure. Furthermore, we show that our model combined with Raman measurements can be used to infer the elastic properties of surface bound ligands, such as sound velocities and elastic moduli, that are otherwise challenging to measure.

  20. Changing Mechanical Strength in Cr(III)- Metallosupramolecular Polymers with Ligand Groups and Light Irradiation.

    Science.gov (United States)

    Razgoniaev, Anton O; Butaeva, Evgeniia V; Iretskii, Alexei V; Ostrowski, Alexis D

    2016-06-06

    We have demonstrated the ability to control the mechanical properties of metallosupramolecular materials via choice of ligand binding group, as well as with external light irradiation. These photoresponsive Cr(III)-based materials were prepared from a series of modified hydrogenated poly(ethylene-co-butylene) polymers linked through metal-ligand interactions between a Cr(III) metal center and pyridyl ligand termini of the polymers. The introduction of these Cr(III)-pyridine bonds gave rise to new mechanical and optical properties of the polymer materials. Depending on the type of pyridyl ligand, density functional theory calculations revealed changes in coordination to the Cr(III), which ultimately led to materials with significantly different mechanical properties. Electronic excitation of the Cr(III) materials with 450 and 655 nm CW lasers (800 mW/cm(2)) resulted in generation of excited state photophysical processes which led to temporary softening of the materials up to 143 kPa (41.5%) in storage modulus (G') magnitude. The initial mechanical strength of the materials was recovered when the light stimulus was removed, and no change in mechanical properties was observed with light irradiation where there was no absorbance by the Cr(III) moiety. These materials demonstrate that introduction of metal-ligand bonding interactions into polymers enables the design and synthesis of photoresponsive materials with tunable optical-mechanical properties not seen in traditional polymeric materials.

  1. Genetic deletion of the EGFR ligand epigen does not affect mouse embryonic development and tissue homeostasis.

    Science.gov (United States)

    Dahlhoff, Maik; Schäfer, Matthias; Wolf, Eckhard; Schneider, Marlon R

    2013-02-15

    The epidermal growth factor receptor (EGFR) is a tyrosine kinase receptor with manifold functions during development, tissue homeostasis and disease. EGFR activation, the formation of homodimers or heterodimers (with the related ERBB2-4 receptors) and downstream signaling is initiated by the binding of a family of structurally related growth factors, the EGFR ligands. Genetic deletion experiments clarified the biological function of all family members except for the last characterized ligand, epigen. We employed gene targeting in mouse embryonic stem cells to generate mice lacking epigen expression. Loss of epigen did not affect mouse development, fertility, or organ physiology. Quantitative RT-PCR analysis revealed increased expression of betacellulin and EGF in a few organs of epigen-deficient mice, suggesting a functional compensation by these ligands. In conclusion, we completed the genetic analysis of EGFR ligands and show that epigen has non-essential functions or functions that can be compensated by other EGFR ligands during growth and tissue homeostasis. Copyright © 2012 Elsevier Inc. All rights reserved.

  2. A ligand-reversible dimerization system for controlling protein-protein interactions.

    Science.gov (United States)

    Rollins, C T; Rivera, V M; Woolfson, D N; Keenan, T; Hatada, M; Adams, S E; Andrade, L J; Yaeger, D; van Schravendijk, M R; Holt, D A; Gilman, M; Clackson, T

    2000-06-20

    Chemically induced dimerization provides a general way to gain control over intracellular processes. Typically, FK506-binding protein (FKBP) domains are fused to a signaling domain of interest, allowing crosslinking to be initiated by addition of a bivalent FKBP ligand. In the course of protein engineering studies on human FKBP, we discovered that a single point mutation in the ligand-binding site (Phe-36 --> Met) converts the normally monomeric protein into a ligand-reversible dimer. Two-hybrid, gel filtration, analytical ultracentrifugation, and x-ray crystallographic studies show that the mutant (F(M)) forms discrete homodimers with micromolar affinity that can be completely dissociated within minutes by addition of monomeric synthetic ligands. These unexpected properties form the basis for a "reverse dimerization" regulatory system involving F(M) fusion proteins, in which association is the ground state and addition of ligand abolishes interactions. We have used this strategy to rapidly and reversibly aggregate fusion proteins in different cellular compartments, and to provide an off switch for transcription. Reiterated F(M) domains should be generally useful as conditional aggregation domains (CADs) to control intracellular events where rapid, reversible dissolution of interactions is required. Our results also suggest that dimerization is a latent property of the FKBP fold: the crystal structure reveals a remarkably complementary interaction between the monomer binding sites, with only subtle changes in side-chain disposition accounting for the dramatic change in quaternary structure.

  3. Structural linkage between ligand discrimination and receptor activation by type I interferons.

    Science.gov (United States)

    Thomas, Christoph; Moraga, Ignacio; Levin, Doron; Krutzik, Peter O; Podoplelova, Yulia; Trejo, Angelica; Lee, Choongho; Yarden, Ganit; Vleck, Susan E; Glenn, Jeffrey S; Nolan, Garry P; Piehler, Jacob; Schreiber, Gideon; Garcia, K Christopher

    2011-08-19

    Type I Interferons (IFNs) are important cytokines for innate immunity against viruses and cancer. Sixteen human type I IFN variants signal through the same cell-surface receptors, IFNAR1 and IFNAR2, yet they can evoke markedly different physiological effects. The crystal structures of two human type I IFN ternary signaling complexes containing IFNα2 and IFNω reveal recognition modes and heterotrimeric architectures that are unique among the cytokine receptor superfamily but conserved between different type I IFNs. Receptor-ligand cross-reactivity is enabled by conserved receptor-ligand "anchor points" interspersed among ligand-specific interactions that "tune" the relative IFN-binding affinities, in an apparent extracellular "ligand proofreading" mechanism that modulates biological activity. Functional differences between IFNs are linked to their respective receptor recognition chemistries, in concert with a ligand-induced conformational change in IFNAR1, that collectively control signal initiation and complex stability, ultimately regulating differential STAT phosphorylation profiles, receptor internalization rates, and downstream gene expression patterns. Copyright © 2011 Elsevier Inc. All rights reserved.

  4. Enthalpy-Based Screening of Focused Combinatorial Libraries for the Identification of Potent and Selective Ligands.

    Science.gov (United States)

    Baggio, Carlo; Udompholkul, Parima; Barile, Elisa; Pellecchia, Maurizio

    2017-12-15

    In modern drug discovery, the ability of biophysical methods, including nuclear magnetic resonance spectroscopy or surface plasmon resonance, to detect and characterize ligand-protein interactions accurately and unambiguously makes these approaches preferred versus conventional biochemical high-throughput screening of large collections of compounds. Nonetheless, ligand screening strategies that address simultaneously potency and selectivity have not yet been fully developed. In this work, we propose a novel method for screening large collections of combinatorial libraries using enthalpy measurements as a primary screening technique. We demonstrate that selecting binders that are driven by enthalpy (ΔH) results in agents that are not only potent but also more selective for a given target. This general and novel approach, we termed ΔH screening of fPOS (enthalpy screening of focused positional scanning library), combines the principles of focused combinatorial chemistry with rapid calorimetry measurements to efficiently identify potent and selective inhibitors.

  5. Effect of urea on protein-ligand association.

    Science.gov (United States)

    Stepanian, Lora; Son, Ikbae; Chalikian, Tigran V

    2017-12-01

    We combine experimental and theoretical approaches to investigate the influence of a cosolvent on a ligand-protein association event. We apply fluorescence measurements to determining the affinity of the inhibitor tri-N-acetylglucosamine [(GlcNAc)3] for lysozyme at urea concentrations ranging from 0 to 8M. Notwithstanding that, at room temperature and neutral pH, lysozyme retains its native conformation up to the solubility limit of urea, the affinity of (GlcNAc)3 for the protein steadily decreases as the concentration of urea increases. We analyze the urea dependence of the binding free energy within the framework of a simplified statistical thermodynamics-based model that accounts for the excluded volume effect and direct solute-solvent interactions. The analysis reveals that the detrimental action of urea on the inhibitor-lysozyme binding originates from competition between the free energy contributions of the excluded volume effect and direct solute-solvent interactions. The free energy contribution of direct urea-solute interactions narrowly overcomes the excluded volume contribution thereby resulting in urea weakening the protein-ligand association. More broadly, the successful application of the simple model employed in this work points to the possibility of its use in quantifying the stabilizing/destabilizing action of individual cosolvents on biochemical folding and binding reactions. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Ligand Exchange Kinetics of Environmentally Relevant Metals

    Energy Technology Data Exchange (ETDEWEB)

    Panasci, Adele Frances [Univ. of California, Davis, CA (United States)

    2014-07-15

    The interactions of ground water with minerals and contaminants are of broad interest for geochemists but are not well understood. Experiments on the molecular scale can determine reaction parameters (i.e. rates of ligand exchange, activation entropy, activation entropy, and activation volume) that can be used in computations to gain insight into reactions that occur in natural groundwaters. Experiments to determine the rate of isotopic ligand exchange for three environmentally relevant metals, rhodium (Rh), iron (Fe), and neptunium (Np), are described. Many environmental transformations of metals (e.g. reduction) in soil occur at trivalent centers, Fe(III) in particular. Contaminant ions absorb to mineral surfaces via ligand exchange, and the reversal of this reaction can be dangerous, releasing contaminants into the environment. Ferric iron is difficult to study spectroscopically because most of its complexes are paramagnetic and are generally reactive toward ligand exchange; therefore, Rh(III), which is diamagnetic and less reactive, was used to study substitution reactions that are analogous to those that occur on mineral oxide surfaces. Studies on both Np(V) and Np(VI) are important in their own right, as 237Np is a radioactive transuranic element with a half-life of 2 million years.

  7. Supramolecular architectures constructed using angular bipyridyl ligands

    CERN Document Server

    Barnett, S A

    2003-01-01

    This work details the synthesis and characterization of a series of coordination frameworks that are formed using bidentate angular N-donor ligands. Pyrimidine was reacted with metal(ll) nitrate salts. Reactions using Cd(NO sub 3) sub 2 receive particular focus and the analogous reactions using the linear ligand, pyrazine, were studied for comparison. In all cases, two-dimensional coordination networks were prepared. Structural diversity is observed for the Cd(ll) centres including metal-nitrate bridging. In contrast, first row transition metal nitrates form isostructural one-dimensional chains with only the bridging N-donor ligands generating polymeric propagation. The angular ligand, 2,4-bis(4-pyridyl)-1,3,5-triazine (dpt), was reacted with Cd(NO sub 3) sub 2 and Zn(NO sub 3) sub 2. Whereas Zn(NO sub 3) sub 2 compounds exhibit solvent mediated polymorphism, a range of structures were obtained for the reactions with Cd(NO sub 3) sub 2 , including the first example of a doubly parallel interpenetrated 4.8 sup...

  8. Flexible Ligand Docking Using Differential Evolution

    DEFF Research Database (Denmark)

    Thomsen, René

    2003-01-01

    Molecular docking of biomolecules is becoming an increasingly important part in the process of developing new drugs, as well as searching compound databases for promising drug candidates. The docking of ligands to proteins can be formulated as an optimization problem where the task is to find...

  9. A versatile dinucleating ligand containing sulfonamide groups

    DEFF Research Database (Denmark)

    Sundberg, Jonas; Witt, Hannes; Cameron, Lisa

    2014-01-01

    Copper, iron, and gallium coordination chemistries of the new pentadentate bis-sulfonamide ligand 2,6-bis(N-2-pyridylmethylsulfonamido)-4-methylphenol (psmpH3) were investigated. PsmpH3 is capable of varying degrees of deprotonation, and notably, complexes containing the fully trideprotonated...

  10. Noncalcemic actions of vitamin D receptor ligands.

    Science.gov (United States)

    Nagpal, Sunil; Na, Songqing; Rathnachalam, Radhakrishnan

    2005-08-01

    1alpha,25-Dihydroxyvitamin D(3) [1,25-(OH)(2)D(3)], the active metabolite of vitamin D(3), is known for the maintenance of mineral homeostasis and normal skeletal architecture. However, apart from these traditional calcium-related actions, 1,25-(OH)(2)D(3) and its synthetic analogs are being increasingly recognized for their potent antiproliferative, prodifferentiative, and immunomodulatory activities. These actions of 1,25-(OH)(2)D(3) are mediated through vitamin D receptor (VDR), which belongs to the superfamily of steroid/thyroid hormone nuclear receptors. Physiological and pharmacological actions of 1,25-(OH)(2)D(3) in various systems, along with the detection of VDR in target cells, have indicated potential therapeutic applications of VDR ligands in inflammation (rheumatoid arthritis, psoriatic arthritis), dermatological indications (psoriasis, actinic keratosis, seborrheic dermatitis, photoaging), osteoporosis (postmenopausal and steroid-induced osteoporosis), cancers (prostate, colon, breast, myelodysplasia, leukemia, head and neck squamous cell carcinoma, and basal cell carcinoma), secondary hyperparathyroidism, and autoimmune diseases (systemic lupus erythematosus, type I diabetes, multiple sclerosis, and organ transplantation). As a result, VDR ligands have been developed for the treatment of psoriasis, osteoporosis, and secondary hyperparathyroidism. Furthermore, encouraging results have been obtained with VDR ligands in clinical trials of prostate cancer and hepatocellular carcinoma. This review deals with the molecular aspects of noncalcemic actions of vitamin D analogs that account for the efficacy of VDR ligands in the above-mentioned indications.

  11. CHELATING LIGANDS: ENHANCERS OF QUALITY AND PURITY ...

    African Journals Online (AJOL)

    Nwokem et al.

    ABSTRACT. The quality of biogas depends largely on the percentage of methane and hydrogen sulphide gas present. High concentration of hydrogen sulphide results in low quality biogas. This work employed the use of chelating ligands in scrubbing hydrogen sulphide gas while improving the yield of methane gas.

  12. Ligand sphere conversions in terminal carbide complexes

    DEFF Research Database (Denmark)

    Morsing, Thorbjørn Juul; Reinholdt, Anders; Sauer, Stephan P. A.

    2016-01-01

    Metathesis is introduced as a preparative route to terminal carbide complexes. The chloride ligands of the terminal carbide complex [RuC(Cl)2(PCy3)2] (RuC) can be exchanged, paving the way for a systematic variation of the ligand sphere. A series of substituted complexes, including the first...... demonstrates that details of the coordination geometry affect the carbide chemical shift equally as much as variations in the nature of the auxiliary ligands. Furthermore, the kinetics of formation of the sqaure pyramidal dicyano complex, trans-[RuC(CN)2(PCy3)2], from RuC has been examined and the reaction...... found to be quite sluggish and of first order in both RuC and cyanide with a rate constant of k = 0.0104(6) M–1 s–1. Further reaction with cyanide leads to loss of the carbide ligand and formation of trans-[Ru(CN)4(PCy3)2]2–, which was isolated and structurally characterized as its PPh4+ salt....

  13. Simple tertiary phosphines to hexaphosphane ligands: Syntheses ...

    Indian Academy of Sciences (India)

    In this context, we have developed new synthetic methodologies for making unusual inorganic ring systems containing trivalent phosphorus centres, novel phosphorus-based multidentate and hybrid ligands and explored their rich transition metal chemistry and catalytic applications. We have also fine tuned a few existing ...

  14. Integrated Confocal and Scanning Probe Microscopy for Biomedical Research

    Directory of Open Access Journals (Sweden)

    B.J. Haupt

    2006-01-01

    Full Text Available Atomic force microscopy (AFM continues to be developed, not only in design, but also in application. The new focus of using AFM is changing from pure material to biomedical studies. More frequently, it is being used in combination with other optical imaging methods, such as confocal laser scanning microscopy (CLSM and fluorescent imaging, to provide a more comprehensive understanding of biological systems. To date, AFM has been used increasingly as a precise micromanipulator, probing and altering the mechanobiological characteristics of living cells and tissues, in order to examine specific, receptor-ligand interactions, material properties, and cell behavior. In this review, we discuss the development of this new hybrid AFM, current research, and potential applications in diagnosis and the detection of disease.

  15. Crystallographic Identification and Functional Characterization of Phospholipids as Ligands for the Orphan Nuclear Receptor Steroidogenic Factor-1

    Energy Technology Data Exchange (ETDEWEB)

    Li, Yong; Choi, Mihwa; Cavey, Greg; Daugherty, Jennifer; Suino, Kelly; Kovach, Amanda; Bingham, Nathan C.; Kliewer, Steven A.; Xu, H.Eric (Van Andel); (U. of Texas-SMED)

    2010-11-10

    The orphan nuclear receptor steroidogenic factor 1 (SF-1) regulates the differentiation and function of endocrine glands. Although SF-1 is constitutively active in cell-based assays, it is not known whether this transcriptional activity is modulated by ligands. Here, we describe the 1.5 {angstrom} crystal structure of the SF-1 ligand binding domain in complex with an LXXLL motif from a coregulator protein. The structure reveals the presence of a phospholipid ligand in a surprisingly large pocket ({approx}1600 {angstrom}{sup 3}), with the receptor adopting the canonical active conformation. The bound phospholipid is readily exchanged and modulates SF-1 interactions with coactivators. Mutations designed to reduce the size of the SF-1 pocket or to disrupt hydrogen bonds with the phospholipid abolish SF-1/coactivator interactions and significantly reduce SF-1 transcriptional activity. These findings provide evidence that SF-1 is regulated by endogenous ligands and suggest an unexpected relationship between phospholipids and endocrine development and function.

  16. Seismic scanning tunneling macroscope - Theory

    KAUST Repository

    Schuster, Gerard T.

    2012-09-01

    We propose a seismic scanning tunneling macroscope (SSTM) that can detect the presence of sub-wavelength scatterers in the near-field of either the source or the receivers. Analytic formulas for the time reverse mirror (TRM) profile associated with a single scatterer model show that the spatial resolution limit to be, unlike the Abbe limit of λ/2, independent of wavelength and linearly proportional to the source-scatterer separation as long as the point scatterer is in the near-field region; if the sub-wavelength scatterer is a spherical impedance discontinuity then the resolution will also be limited by the radius of the sphere. Therefore, superresolution imaging can be achieved as the scatterer approaches the source. This is analogous to an optical scanning tunneling microscope that has sub-wavelength resolution. Scaled to seismic frequencies, it is theoretically possible to extract 100 Hz information from 20 Hz data by imaging of near-field seismic energy.

  17. Scanning of Markov Random Processes

    Directory of Open Access Journals (Sweden)

    Gustav Cepciansky

    2003-01-01

    Full Text Available Function of most electronic devices is based on the microprocessor control. A microprocessor must scan and evaluate function of many controlled equipment that can be transformed into 2 statuses - "free" or "busy". Microprocessors in a digital exchange are the typical example of that. It can be said the microprocessors are in a discrete dialogue with the controlled parts. They ascertain in regular time intervals whether the status of the controlled equipment has changed. 1 or more "busy" statuses may exist in the same time. As the changes from "free" to "busy" and from "busy" to "free" occur randomly, the state of i busy statuses lasts for a random period too. If the changes have pro-perties of Markov process, the probability which each change will be detected with and hence the scanning rate needed can be derived.

  18. Ammonia formation by metal-ligand cooperative hydrogenolysis of a nitrido ligand

    Science.gov (United States)

    Askevold, Bjorn; Nieto, Jorge Torres; Tussupbayev, Samat; Diefenbach, Martin; Herdtweck, Eberhardt; Holthausen, Max C.; Schneider, Sven

    2011-07-01

    Bioinspired hydrogenation of N2 to ammonia at ambient conditions by stepwise nitrogen protonation/reduction with metal complexes in solution has experienced remarkable progress. In contrast, the highly desirable direct hydrogenation with H2 remains difficult. In analogy to the heterogeneously catalysed Haber-Bosch process, such a reaction is conceivable via metal-centred N2 splitting and unprecedented hydrogenolysis of the nitrido ligands to ammonia. We report the synthesis of a ruthenium(IV) nitrido complex. The high nucleophilicity of the nitrido ligand is demonstrated by unusual N-C coupling with π-acidic CO. Furthermore, the terminal nitrido ligand undergoes facile hydrogenolysis with H2 at ambient conditions to produce ammonia in high yield. Kinetic and quantum chemical examinations of this reaction suggest cooperative behaviour of a phosphorus-nitrogen-phosphorus pincer ligand in rate-determining heterolytic hydrogen splitting.

  19. ceramics by differential scanning calorimetry

    Indian Academy of Sciences (India)

    Administrator

    YbxGd2–xZr2O7 (x = 0, 1, 2) ceramics were pressureless-sintered using ceramic powders acquired by chemical-coprecipitation and calcination methods. Heat capacities of YbxGd2–xZr2O7 were measured with a heat flux-type differential scanning calorimetry in the temperature range of 298–1200 K. At 298 K, the heat.

  20. A fluorescence scanning electron microscope

    OpenAIRE

    Kanemaru, Takaaki; Hirata, Kazuho; Takasu, Shin-ichi; Isobe, Shin-Ichiro; Mizuki, Keiji; Mataka, Shuntaro; Nakamura, Kei-ichiro

    2010-01-01

    Fluorescence techniques are widely used in biological research to examine molecular localization, while electron microscopy can provide unique ultrastructural information. To date, correlative images from both fluorescence and electron microscopy have been obtained separately using two different instruments, i.e. a fluorescence microscope (FM) and an electron microscope (EM). In the current study, a scanning electron microscope (SEM) (JEOL JXA8600 M) was combined with a fluorescence digital c...

  1. New Snail Mail Scanning Service

    CERN Multimedia

    2012-01-01

    Modernisation does not stop at the CERN postal service (GS/PS). “With more and more digitisation and the prevalence of e-mail throughout the site, we were hoping to provide more timely delivery of letters and make further saving in resources”, said Tueri Datta, head of GS/PS.   Instead of the standard delivery to your P.O. box, the CERN postal service will digitally scan all letters and books up to 100 pages on reception. These scans will subsequently be sent via e-mail to the corresponding recipient as PDF (Portable Data Format - you will need to install “Acrobat Reader” on your PC). Express mail will be handled with priority. Users without a valid CERN mailbox can register at mail.scan.service@cern.ch in order to have their letters read to them via the phone line (we are currently investigating whether we can use the voices of the last five DGs).   This service will start on 1st April 2012 on the Meyrin site and will gradually replace th...

  2. Quantum.Ligand.Dock: protein-ligand docking with quantum entanglement refinement on a GPU system.

    Science.gov (United States)

    Kantardjiev, Alexander A

    2012-07-01

    Quantum.Ligand.Dock (protein-ligand docking with graphic processing unit (GPU) quantum entanglement refinement on a GPU system) is an original modern method for in silico prediction of protein-ligand interactions via high-performance docking code. The main flavour of our approach is a combination of fast search with a special account for overlooked physical interactions. On the one hand, we take care of self-consistency and proton equilibria mutual effects of docking partners. On the other hand, Quantum.Ligand.Dock is the the only docking server offering such a subtle supplement to protein docking algorithms as quantum entanglement contributions. The motivation for development and proposition of the method to the community hinges upon two arguments-the fundamental importance of quantum entanglement contribution in molecular interaction and the realistic possibility to implement it by the availability of supercomputing power. The implementation of sophisticated quantum methods is made possible by parallelization at several bottlenecks on a GPU supercomputer. The high-performance implementation will be of use for large-scale virtual screening projects, structural bioinformatics, systems biology and fundamental research in understanding protein-ligand recognition. The design of the interface is focused on feasibility and ease of use. Protein and ligand molecule structures are supposed to be submitted as atomic coordinate files in PDB format. A customization section is offered for addition of user-specified charges, extra ionogenic groups with intrinsic pK(a) values or fixed ions. Final predicted complexes are ranked according to obtained scores and provided in PDB format as well as interactive visualization in a molecular viewer. Quantum.Ligand.Dock server can be accessed at http://87.116.85.141/LigandDock.html.

  3. Role of Lanthanide-Ligand bonding in the magnetization relaxation ...

    Indian Academy of Sciences (India)

    Ligand bonding. Our calculations transpire comparatively improved Single-Ion Magnet (SIM) behaviour for carbene analogues due to the more axially compressed trigonal prismatic ligand environment. Furthermore, our detailed Mulliken charge, ...

  4. Fluorescent GPCR ligands as new tools in pharmacology.

    Science.gov (United States)

    Kuder, Kamil; Kieć-Kononowicz, Katarzyna

    2008-01-01

    The expansion of fluorescent techniques for studying the ligand-receptor interaction resulted in a burst of the novel fluorescent ligands development. The discovery of the ligand, that is of high affinity to the receptor and whose localization could be easily visualized, even on the single cell level, gave the researchers a strong impulse to investigate that field of GPCR ligands. Moreover, paying attention to the "non pharmacological" advantages of these ligands, as well as the techniques to be used, fluorescent ligands are becoming treated more seriously, as the ligands themselves, and as novel, useful tools for studying GPCRs. Herein, we review results described in the literature, starting from the year 2000, in the field of the fluorescent GPCR small, non-peptide ligands according to the affinity to the selected receptors (histamine, adenosine, adrenergic, cannabinoid, muscarinie, neuropeptide Y and serotonine) as well as the fluorophores that have been used to tag the molecules.

  5. Ligand-Mediated Coating of Liposomes with Human Serum Albumin.

    Science.gov (United States)

    Sato, Hikari; Nakhaei, Elnaz; Kawano, Takahito; Murata, Masaharu; Kishimura, Akihiro; Mori, Takeshi; Katayama, Yoshiki

    2018-02-13

    Coating liposome surfaces with human serum albumin (HSA) can improve the colloidal stability and prevent opsonization. HSA coating via specific binding with alkyl ligands is promising because although the ligand-mediated coating is relatively stable it can spontaneously exchange with fresh HSA. However, to achieve surface coating with HSA, multiple hydrophobic ligands must be exposed to an aqueous medium prior to binding with HSA. This presents a challenge, as hydrophobic ligands tend to be buried in the liposomal membrane. Here we present the first HSA modification of liposome surfaces via alkyl ligands. We found that a relatively short alkyl ligand, or a long alkyl ligand with a terminal carboxylate, could be exposed on the liposome surface without causing aggregation of the liposomes and these ligands could subsequently bind HSA. The resulting HSA-coated liposomes were as inert as conventional PEGylated liposomes in terms of macrophage recognition.

  6. Demand of Innovative Services on a Computed Tomography Scan

    Directory of Open Access Journals (Sweden)

    Na Ayudhya Chamaiporn Sudasna

    2016-01-01

    Full Text Available This paper seeks to investigate the needs of service, innovative Mobile Computed Tomography (CT Scan service, from the leading level of Neurosurgeon in Bangkok, Thailand. The research is proposed investigating Neurosurgeon’s expectations for Mobile CT Scan and current problems of CT scan operating. This is a survey research approach, performing in-depth interview which collected data from 21 Neurosurgeons, 12 hospitals in Bangkok and surrounding areas. Due to the number of samples limited, the descriptive statistics were used to analyze the data. The research address two research questions: According to the first research question, the authors’ findings that most of Neurosurgeon need to use Mobile CT Scan at Operation Room (OR, Intensive Care Unit (ICU, and Emergency Room (ER, respectively. Regarding the second research question, the authors’ analysis reveals purposes and found the current problems that when Neurosurgeon use CT Scan they faced low resolution and slice, moving unstable patients, wriggle patients, and Claustrophobia patients. Therefore, what are the findings of the survey are very useful in the design of new services for Mobile CT Scan to work in the next step.

  7. Synthesis of Janus-like gold nanoparticles with hydrophilic/hydrophobic faces by surface ligand exchange and their self-assemblies in water.

    Science.gov (United States)

    Iida, Ryo; Kawamura, Hitoshi; Niikura, Kenichi; Kimura, Takashi; Sekiguchi, Shota; Joti, Yasumasa; Bessho, Yoshitaka; Mitomo, Hideyuki; Nishino, Yoshinori; Ijiro, Kuniharu

    2015-04-14

    This study aims at the synthesis of Janus gold nanoparticles (Janus GNPs) with hydrophilic/hydrophobic faces by a simple ligand exchange reaction in an homogeneous system and at the elucidation of the self-assembled structures of the Janus GNPs in water. As hydrophilic surface ligands, we synthesized hexaethylene glycol (E6)-terminated thiolate ligands with C3, C7, or C11 alkyl chains, referred to as E6C3, E6C7, and E6C11, respectively. As a hydrophobic ligand, a butyl-headed thiolate ligand C4-E6C11, in which a C4 alkyl was introduced on the E6C11 terminus, was synthesized. The degree of segregation between the two ligands on the GNPs (5 nm in diameter) was examined by matrix-assisted laser desorption/ionization time-of fright mass spectrometry (MALDI-TOF MS) analysis. We found that the choice of immobilization methods, one-step or two-step addition of the two ligands to the GNP solution, crucially affects the degree of segregation. The two-step addition of a hydrophilic ligand (E6C3) followed by a hydrophobic ligand (C4-E6C11) produced a large degree of segregation on the GNPs, providing Janus-like GNPs. When dispersed in water, these Janus-like GNPs formed assemblies of ∼160 nm in diameter, whereas Domain GNPs, in which the two ligands formed partial domains on the surface, were precipitated even when the molar ratio of the hydrophilic ligand and the hydrophobic ligand on the surface of the NPs was almost 1:1. The assembled structure of the Janus-like GNPs in water was directly observed by pulsed coherent X-ray solution scattering using an X-ray free-electron laser, revealing irregular spherical structures with uneven surfaces.

  8. Identification of novel peptide ligands for the cancer-specific receptor mutation EFGRvIII using a mixture-based synthetic combinatorial library

    DEFF Research Database (Denmark)

    Denholt, Charlotte Lund; Hansen, Paul Robert; Pedersen, Nina

    2009-01-01

    We report here, the design and synthesis of a positional scanning synthetic combinatorial library for the identification of novel peptide ligands targeted against the cancer-specific epidermal growth factor tyrosine kinase receptor mutation variant III (EGFRvIII). This receptor is expressed in se...

  9. Consequences of Morphology on Molecularly Imprinted Polymer-Ligand Recognition

    Directory of Open Access Journals (Sweden)

    Annika M. Rosengren

    2013-01-01

    Full Text Available The relationship between molecularly imprinted polymer (MIP morphology and template-rebinding over a series of warfarin-imprinted methacrylic acid co(ethylene dimethacrylate polymers has been explored. Detailed investigations of the nature of template recognition revealed that an optimal template binding was obtained with polymers possessing a narrow population of pores (~3–4 nm in the mesopore size range. Importantly, the warfarin-polymer rebinding analyses suggest strategies for regulating ligand binding capacity and specificity through variation of the degree of cross-linking, where polymers prepared with a lower degree of cross-linking afford higher capacity though non-specific in character. In contrast, the co-existence of specific and non-specific binding was found in conjunction with higher degrees of cross-linking and resultant meso- and macropore size distributions.

  10. Consequences of Morphology on Molecularly Imprinted Polymer-Ligand Recognition

    Science.gov (United States)

    Rosengren, Annika M.; Karlsson, Björn C. G.; Nicholls, Ian A.

    2013-01-01

    The relationship between molecularly imprinted polymer (MIP) morphology and template-rebinding over a series of warfarin-imprinted methacrylic acid co(ethylene dimethacrylate) polymers has been explored. Detailed investigations of the nature of template recognition revealed that an optimal template binding was obtained with polymers possessing a narrow population of pores (~3–4 nm) in the mesopore size range. Importantly, the warfarin-polymer rebinding analyses suggest strategies for regulating ligand binding capacity and specificity through variation of the degree of cross-linking, where polymers prepared with a lower degree of cross-linking afford higher capacity though non-specific in character. In contrast, the co-existence of specific and non-specific binding was found in conjunction with higher degrees of cross-linking and resultant mesoand macropore size distributions. PMID:23303280

  11. GLIDA: GPCR-ligand database for chemical genomic drug discovery

    OpenAIRE

    Okuno, Yasushi; Yang, Jiyoon; Taneishi, Kei; Yabuuchi, Hiroaki; Tsujimoto, Gozoh

    2005-01-01

    G-protein coupled receptors (GPCRs) represent one of the most important families of drug targets in pharmaceutical development. GPCR-LIgand DAtabase (GLIDA) is a novel public GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands, as well as access information to the various web databases regarding GPCRs. Thes...

  12. CT-scanning of ancient Greenlandic Inuit temporal bones

    DEFF Research Database (Denmark)

    Homøe, P; Lynnerup, N; Videbaek, H

    1992-01-01

    Additional morphological evidence of former infectious middle ear disease (IMED) was found by CT-scanning in 5 of 6 Greenlandic Inuit crania strongly suspected for former IMED due to earlier examination revealing either bilateral hypocellularity or asymmetry of the pneumatized area of the temporal...... as a congenital malformation or an infection in infanthood. CT-scan confirms and even adds to the results of conventional X-ray of temporal bones making hypotheses of paleopathology more reliable. The findings also support the environmental theory of pneumatization of the air cell system in the temporal bones....

  13. AutoSite: an automated approach for pseudo-ligands prediction—from ligand-binding sites identification to predicting key ligand atoms

    Science.gov (United States)

    Ravindranath, Pradeep Anand; Sanner, Michel F.

    2016-01-01

    Motivation: The identification of ligand-binding sites from a protein structure facilitates computational drug design and optimization, and protein function assignment. We introduce AutoSite: an efficient software tool for identifying ligand-binding sites and predicting pseudo ligand corresponding to each binding site identified. Binding sites are reported as clusters of 3D points called fills in which every point is labelled as hydrophobic or as hydrogen bond donor or acceptor. From these fills AutoSite derives feature points: a set of putative positions of hydrophobic-, and hydrogen-bond forming ligand atoms. Results: We show that AutoSite identifies ligand-binding sites with higher accuracy than other leading methods, and produces fills that better matches the ligand shape and properties, than the fills obtained with a software program with similar capabilities, AutoLigand. In addition, we demonstrate that for the Astex Diverse Set, the feature points identify 79% of hydrophobic ligand atoms, and 81% and 62% of the hydrogen acceptor and donor hydrogen ligand atoms interacting with the receptor, and predict 81.2% of water molecules mediating interactions between ligand and receptor. Finally, we illustrate potential uses of the predicted feature points in the context of lead optimization in drug discovery projects. Availability and Implementation: http://adfr.scripps.edu/AutoDockFR/autosite.html Contact: sanner@scripps.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27354702

  14. Integrating structural and mutagenesis data to elucidate GPCR ligand binding

    DEFF Research Database (Denmark)

    Munk, Christian; Harpsøe, Kasper; Hauser, Alexander S

    2016-01-01

    G protein-coupled receptors (GPCRs) represent the largest family of human membrane proteins, as well as drug targets. A recent boom in GPCR structural biology has provided detailed images of receptor ligand binding sites and interactions on the molecular level. An ever-increasing number of ligands...... elucidate new GPCR ligand binding sites, and ultimately design drugs with tailored pharmacological activity....

  15. New mixed ligand complexes of ruthenium (II) that incorporate a ...

    Indian Academy of Sciences (India)

    New mixed ligand complexes of ruthenium(II) that incorporate a modified phenanthroline ligand: Synthesis, spectral characterization and DNA binding. S Murali C V ... Fulltext. Click here to view fulltext PDF ... Ruthenium(II) complexes; modified phenanthroline ligand; spectroscopy; DNA binding; fluorescence enhancement.

  16. Novel peptide ligand with high binding capacity for antibody purification

    DEFF Research Database (Denmark)

    Lund, L. N.; Gustavsson, P. E.; Michael, R.

    2012-01-01

    ligands have an advantage over biological ligands; they are cheaper to produce, ligand leakage by enzymatic degradation is either eliminated or significantly reduced, and they can in general better withstand cleaning in place (CIP) conditions such as 0.1 M NaOH. Here, we present a novel synthetic peptide...

  17. Page 1 ASSESSMENT OF BINDING ENERGIES AND LIGAND ...

    African Journals Online (AJOL)

    The successive binding energies of up to six water ligands to ferric ion and the reduction in the gross binding energies by ligand-ligand repulsion are determined by electrostatic interaction. The gross binding energy is found to be both geometry and coordination nuitber dependent: whereas it increases with number of ...

  18. Extracellular Loop 2 of the Adenosine A1 Receptor Has a Key Role in Orthosteric Ligand Affinity and Agonist Efficacy.

    Science.gov (United States)

    Nguyen, Anh T N; Baltos, Jo-Anne; Thomas, Trayder; Nguyen, Toan D; Muñoz, Laura López; Gregory, Karen J; White, Paul J; Sexton, Patrick M; Christopoulos, Arthur; May, Lauren T

    2016-12-01

    The adenosine A 1 G protein-coupled receptor (A 1 AR) is an important therapeutic target implicated in a wide range of cardiovascular and neuronal disorders. Although it is well established that the A 1 AR orthosteric site is located within the receptor's transmembrane (TM) bundle, prior studies have implicated extracellular loop 2 (ECL2) as having a significant role in contributing to orthosteric ligand affinity and signaling for various G protein-coupled receptors (GPCRs). We thus performed extensive alanine scanning mutagenesis of A 1 AR-ECL2 to explore the role of this domain on A 1 AR orthosteric ligand pharmacology. Using quantitative analytical approaches and molecular modeling, we identified ECL2 residues that interact either directly or indirectly with orthosteric agonists and antagonists. Discrete mutations proximal to a conserved ECL2-TM3 disulfide bond selectively affected orthosteric ligand affinity, whereas a cluster of five residues near the TM4-ECL2 juncture influenced orthosteric agonist efficacy. A combination of ligand docking, molecular dynamics simulations, and mutagenesis results suggested that the orthosteric agonist 5'-N-ethylcarboxamidoadenosine binds transiently to an extracellular vestibule formed by ECL2 and the top of TM5 and TM7, prior to entry into the canonical TM bundle orthosteric site. Collectively, this study highlights a key role for ECL2 in A 1 AR orthosteric ligand binding and receptor activation. Copyright © 2016 by The American Society for Pharmacology and Experimental Therapeutics.

  19. Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers.

    Science.gov (United States)

    Jarillo, Javier; Morín, José A; Beltrán-Heredia, Elena; Villaluenga, Juan P G; Ibarra, Borja; Cao, Francisco J

    2017-01-01

    Ligands binding to polymers regulate polymer functions by changing their physical and chemical properties. This ligand regulation plays a key role in many biological processes. We propose here a model to explain the mechanical, thermodynamic, and kinetic properties of the process of binding of small ligands to long biopolymers. These properties can now be measured at the single molecule level using force spectroscopy techniques. Our model performs an effective decomposition of the ligand-polymer system on its covered and uncovered regions, showing that the elastic properties of the ligand-polymer depend explicitly on the ligand coverage of the polymer (i.e., the fraction of the polymer covered by the ligand). The equilibrium coverage that minimizes the free energy of the ligand-polymer system is computed as a function of the applied force. We show how ligands tune the mechanical properties of a polymer, in particular its length and stiffness, in a force dependent manner. In addition, it is shown how ligand binding can be regulated applying mechanical tension on the polymer. Moreover, the binding kinetics study shows that, in the case where the ligand binds and organizes the polymer in different modes, the binding process can present transient shortening or lengthening of the polymer, caused by changes in the relative coverage by the different ligand modes. Our model will be useful to understand ligand-binding regulation of biological processes, such as the metabolism of nucleic acid. In particular, this model allows estimating the coverage fraction and the ligand mode characteristics from the force extension curves of a ligand-polymer system.

  20. Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers.

    Directory of Open Access Journals (Sweden)

    Javier Jarillo

    Full Text Available Ligands binding to polymers regulate polymer functions by changing their physical and chemical properties. This ligand regulation plays a key role in many biological processes. We propose here a model to explain the mechanical, thermodynamic, and kinetic properties of the process of binding of small ligands to long biopolymers. These properties can now be measured at the single molecule level using force spectroscopy techniques. Our model performs an effective decomposition of the ligand-polymer system on its covered and uncovered regions, showing that the elastic properties of the ligand-polymer depend explicitly on the ligand coverage of the polymer (i.e., the fraction of the polymer covered by the ligand. The equilibrium coverage that minimizes the free energy of the ligand-polymer system is computed as a function of the applied force. We show how ligands tune the mechanical properties of a polymer, in particular its length and stiffness, in a force dependent manner. In addition, it is shown how ligand binding can be regulated applying mechanical tension on the polymer. Moreover, the binding kinetics study shows that, in the case where the ligand binds and organizes the polymer in different modes, the binding process can present transient shortening or lengthening of the polymer, caused by changes in the relative coverage by the different ligand modes. Our model will be useful to understand ligand-binding regulation of biological processes, such as the metabolism of nucleic acid. In particular, this model allows estimating the coverage fraction and the ligand mode characteristics from the force extension curves of a ligand-polymer system.

  1. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  2. Scanning mirror for infrared sensors

    Science.gov (United States)

    Anderson, R. H.; Bernstein, S. B.

    1972-01-01

    A high resolution, long life angle-encoded scanning mirror, built for application in an infrared attitude sensor, is described. The mirror uses a Moire' fringe type optical encoder and unique torsion bar suspension together with a magnetic drive to meet stringent operational and environmental requirements at a minimum weight and with minimum power consumption. Details of the specifications, design, and construction are presented with an analysis of the mirror suspension that allows accurate prediction of performance. The emphasis is on mechanical design considerations, and brief discussions are included on the encoder and magnetic drive to provide a complete view of the mirror system and its capabilities.

  3. Membrane partitioning of anionic, ligand-coated nanoparticles is accompanied by ligand snorkeling, local disordering, and cholesterol depletion.

    Directory of Open Access Journals (Sweden)

    Paraskevi Gkeka

    2014-12-01

    Full Text Available Intracellular uptake of nanoparticles (NPs may induce phase transitions, restructuring, stretching, or even complete disruption of the cell membrane. Therefore, NP cytotoxicity assessment requires a thorough understanding of the mechanisms by which these engineered nanostructures interact with the cell membrane. In this study, extensive Coarse-Grained Molecular Dynamics (MD simulations are performed to investigate the partitioning of an anionic, ligand-decorated NP in model membranes containing dipalmitoylphosphatidylcholine (DPPC phospholipids and different concentrations of cholesterol. Spontaneous fusion and translocation of the anionic NP is not observed in any of the 10-µs unbiased MD simulations, indicating that longer timescales may be required for such phenomena to occur. This picture is supported by the free energy analysis, revealing a considerable free energy barrier for NP translocation across the lipid bilayer. 5-µs unbiased MD simulations with the NP inserted in the bilayer core reveal that the hydrophobic and hydrophilic ligands of the NP surface rearrange to form optimal contacts with the lipid bilayer, leading to the so-called snorkeling effect. Inside cholesterol-containing bilayers, the NP induces rearrangement of the structure of the lipid bilayer in its vicinity from the liquid-ordered to the liquid phase spanning a distance almost twice its core radius (8-10 nm. Based on the physical insights obtained in this study, we propose a mechanism of cellular anionic NP partitioning, which requires structural rearrangements of both the NP and the bilayer, and conclude that the translocation of anionic NPs through cholesterol-rich membranes must be accompanied by formation of cholesterol-lean regions in the proximity of NPs.

  4. A ligand's view of target similarity

    DEFF Research Database (Denmark)

    Garland, Stephen L; Gloriam, David E

    2011-01-01

    shows with several examples how focusing on the binding site(s) has a clear advantage when it comes to establishing sequence-correlated pharmacological profiles. By organizing and comparing sequence and structural data it is possible to "borrow" SAR from similar targets to increase the speed of lead......-finding and, potentially, to produce ligands for previously intractable receptors. Sequence motifs correlated with ligands can be applied in the design of target-specific focused libraries that are both efficient and cost-effective and should provide increased hit-rates over diversity screening. Furthermore......, in the optimization phase, the binding motif approach offers the possibility to identify quickly the most likely off-target candidates to be chosen for selectivity screening, as well as potentially characterizing those pockets which may best be exploited for improved selectivity....

  5. Sigma-2 receptor ligands QSAR model dataset

    Directory of Open Access Journals (Sweden)

    Antonio Rescifina

    2017-08-01

    Full Text Available The data have been obtained from the Sigma-2 Receptor Selective Ligands Database (S2RSLDB and refined according to the QSAR requirements. These data provide information about a set of 548 Sigma-2 (σ2 receptor ligands selective over Sigma-1 (σ1 receptor. The development of the QSAR model has been undertaken with the use of CORAL software using SMILES, molecular graphs and hybrid descriptors (SMILES and graph together. Data here reported include the regression for σ2 receptor pKi QSAR models. The QSAR model was also employed to predict the σ2 receptor pKi values of the FDA approved drugs that are herewith included.

  6. Hydrothermal reactions: From the synthesis of ligand to new lanthanide 3D-coordination polymers

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Fausthon Fred da; Fernandes de Oliveira, Carlos Alberto; Lago Falcão, Eduardo Henrique [Laboratório de Terras Raras, Departamento de Química Fundamental, Universidade Federal de Pernambuco (DQF-UFPE), 50590-470 Recife, PE (Brazil); Gatto, Claudia Cristina [Laboratório de Síntese Inorgânica e Cristalografia, Instituto de Química, Universidade de Brasília (IQ-UnB), 70904-970 Brasilia, DF (Brazil); Bezerra da Costa, Nivan; Oliveira Freire, Ricardo [Pople Computational Chemistry Laboratory, Departamento de Química, Universidade Federal de Sergipe, São Cristóvão-SE 49100-000 (Brazil); Chojnacki, Jarosław [Department of Inorganic Chemistry, Gdansk University of Technology, 80-233 Gdansk (Poland); Alves Júnior, Severino, E-mail: salvesjr@ufpe.br [Laboratório de Terras Raras, Departamento de Química Fundamental, Universidade Federal de Pernambuco (DQF-UFPE), 50590-470 Recife, PE (Brazil)

    2013-11-15

    The organic ligand 2,5-piperazinedione-1,4-diacetic acid (H{sub 2}PDA) was synthesized under hydrothermal conditions starting from the iminodiacetic acid and catalyzed by oxalic acid. The X-ray powder diffraction data indicates that the compound crystallizes in the P2{sub 1}/c monoclinic system as reported in the literature. The ligand was also characterized by elemental analysis, magnetic nuclear resonance, infrared spectroscopy and thermogravimetric analysis. Two new coordination networks based on lanthanide ions were obtained with this ligand using hydrothermal reaction. In addition to single-crystal X-ray diffraction, the compounds were characterized by infrared spectroscopy, thermogravimetric analysis, scanning electron microscopy and elemental analysis. Single-crystal XRD showed that the compounds are isostructural, crystallizing in P2{sub 1}/n monoclinic system with chemical formula [Ln(PDA){sub 1.5}(H{sub 2}O)](H{sub 2}O){sub 3} (Ln=Gd{sup 3+}(1) and Eu{sup 3+}(2)).The luminescence properties of both compounds were studied. In the compound (1), a broad emission band was observed at 479 nm, redshifted by 70 nm in comparison of the free ligand. In (2), the typical f–f transition was observed with a maximum peak at 618 nm, related with the red emission of the europium ions. Computational methods were performed to simulate the crystal structure of (2). The theoretical calculations of the intensity parameters are in good agreement with the experimental values. - Graphical abstract: Scheme of obtaining the ligand 2,5-piperazinedione-1,4-diacetic acid (H{sub 2}PDA) and two new isostructural 3D-coordination polymers [Ln(PDA){sub 1.5}(H{sub 2}O)](H{sub 2}O){sub 3} (Ln=Gd{sup 3+} and Eu{sup 3+}) by hydrothermal synthesis. Display Omitted - Highlights: • The ligand 2,5-piperazinedione-1,4-diacetic acid was synthetized using the hydrothermic method and characterized. • Two new 3D-coordination polymers with this ligand containing Gd{sup 3+} and Eu{sup 3+} ions

  7. Structural characterization of natural nickel and copper binding ligands along the US GEOTRACES Eastern Pacific Zonal transect

    Directory of Open Access Journals (Sweden)

    Rene M Boiteau

    2016-11-01

    Full Text Available Organic ligands form strong complexes with many trace elements in seawater. Various metals can compete for the same ligand chelation sites, and the final speciation of bound metals is determined by relative binding affinities, concentrations of binding sites, uncomplexed metal concentrations, and association/dissociation kinetics. Different ligands have a wide range of metal affinities and specificities. However, the chemical composition of these ligands in the marine environment remains poorly constrained, which has hindered progress in modeling marine metal speciation. In this study, we detected and characterized natural ligands that bind copper (Cu and nickel (Ni in the eastern South Pacific Ocean with liquid chromatography tandem inductively coupled plasma mass spectrometry (LC-ICPMS, and high resolution electrospray ionization mass spectrometry (ESIMS. Dissolved Cu, Ni, and ligand concentrations were highest near the coast. Chromatographically unresolved polar compounds dominated ligands isolated near the coast by solid phase extraction. Offshore, metal and ligand concentrations decreased, but several new ligands appeared. One major ligand was detected that bound both Cu2+ and Ni2+. Based on accurate mass and fragmentation measurements, this compound has a molecular formula of C20H21N4O8S2 + M+ (M = metal isotope and contains several azole-like metal binding groups. Additional lipophilic Ni complexes were also present only in oligotrophic waters, with masses of 649, 698, and 712 m/z (corresponding to the 58Ni metal complex. Molecular formulae of C32H54N3O6S2Ni+ and C33H56N3O6S2Ni+ were determined for two of these compounds. Addition of Cu and Ni to the samples also revealed the presence of additional compounds that can bind both Ni and Cu. Although these specific compounds represent a small fraction of the total dissolved Cu and Ni pool, they highlight the compositional diversity and spatial heterogeneity of marine Ni and Cu ligands, as

  8. The electronic structure of LaO: Ligand field versus ab initio calculations

    Science.gov (United States)

    Schamps, Joël; Bencheikh, Mohammed; Barthelat, Jean-Claude; Field, Robert W.

    1995-11-01

    The potentially pathological example of LaO has been chosen to test the application of ligand field theory (LFT) to metal monoxides. The test consists of a comparison of closed-shell ligand LFT (CSLLFT) results (in which a 2+/2- ionic M2+O2- model is a priori postulated with a point-charge ligand) against ab initio multiconfiguration self-consistent-field-multireference configuration interaction (MCSCF-MRCI) results (in which no ionicity is assumed a priori and an internal structure is allowed for the ligand). Special care has been devoted to the determination of a La3+ pseudopotential and its associated atomic basis set in order to keep the ab initio model close to the LFT one, yet at the same time capable of clearly exhibiting the consequences and the importance of the restrictions imposed in the CSLLFT model. The ab initio calculations reveal that the effective (Mulliken) ionicity in LaO is not La2+O2- but quite close to La+O-. Despite this, the (2+/2-) ionic CSLLFT model leads to the correct orbital occupations in the ground state but this model cannot account for the significant covalency contribution via the nominal 2pσ and 2pπ oxygen orbitals. The CSLLFT calculations correctly reproduce the excitation energies of the four lowest-lying observed states of LaO: these states are calculated to within 2000 cm-1 and globally better than via ab initio calculations. However, the (2+/2-) ionic CSLLFT model is shown to ignore the existence of a manifold of low-lying quartet (and doublet) states of (1+/1-) ionicity that might be relevant for interpreting features of the spectrum. This result exemplifies the need for developing, beyond the first attempts made in this direction, a computationally manageable open-shell ligand theory for the frequently encountered case of predominantly ionic structures with an open-shell ligand.

  9. Doubling the Size of the Glucocorticoid Receptor Ligand Binding Pocket by Deacylcortivazol

    Energy Technology Data Exchange (ETDEWEB)

    Suino-Powell, Kelly; Xu, Yong; Zhang, Chenghai; Tao, Yong-guang; Tolbert, W. David; Simons, Jr., S. Stoney; Xu, H. Eric (NIH)

    2010-03-08

    A common feature of nuclear receptor ligand binding domains (LBD) is a helical sandwich fold that nests a ligand binding pocket within the bottom half of the domain. Here we report that the ligand pocket of glucocorticoid receptor (GR) can be continuously extended into the top half of the LBD by binding to deacylcortivazol (DAC), an extremely potent glucocorticoid. It has been puzzling for decades why DAC, which contains a phenylpyrazole replacement at the conserved 3-ketone of steroid hormones that are normally required for activation of their cognate receptors, is a potent GR activator. The crystal structure of the GR LBD bound to DAC and the fourth LXXLL motif of steroid receptor coactivator 1 reveals that the GR ligand binding pocket is expanded to a size of 1,070 {angstrom}{sup 3}, effectively doubling the size of the GR dexamethasone-binding pocket of 540 {angstrom}{sup 3} and yet leaving the structure of the coactivator binding site intact. DAC occupies only {approx}50% of the space of the pocket but makes intricate interactions with the receptor around the phenylpyrazole group that accounts for the high-affinity binding of DAC. The dramatic expansion of the DAC-binding pocket thus highlights the conformational adaptability of GR to ligand binding. The new structure also allows docking of various nonsteroidal ligands that cannot be fitted into the previous structures, thus providing a new rational template for drug discovery of steroidal and nonsteroidal glucocorticoids that can be specifically designed to reach the unoccupied space of the expanded pocket.

  10. Toward improving selectivity in affinity chromatography with PEGylated affinity ligands: the performance of PEGylated protein A.

    Science.gov (United States)

    González-Valdez, José; Yoshikawa, Alex; Weinberg, Justin; Benavides, Jorge; Rito-Palomares, Marco; Przybycien, Todd M

    2014-01-01

    Chemical modification of macromolecular affinity chromatography ligands with polyethylene glycol chains or "PEGylation" can potentially improve selectivity by sterically suppressing non-specific binding interactions without sacrificing binding capacity. For a commercial protein A affinity media and with yeast extract (YE) and fetal bovine serum (FBS) serving as mock contaminants, we found that the ligand accounted for more than 90% of the media-associated non-specific binding, demonstrating an opportunity for improvement. The IgG static binding affinity of protein A mono-PEGylated with 5.0 and 20.7 kDa poly(ethylene glycol) chains was found to be preserved using a biomolecular interaction screening platform. Similar in situ PEGylations of the commercial protein A media were conducted and the modified media was functionally characterized with IgG solutions spiked with YE and FBS. Ligand PEGylation reduced the mass of media-associated contaminants by a factor of two to three or more. Curiously, we also found an increase of up to 15% in the average recovery of IgG on elution after PEGylation. Combined, these effects produced an order of magnitude increase in the IgG selectivity on average when spiked with YE and a two- to three-fold increase when spiked with FBS relative to the commercial media. Dynamic binding capacity and mass-transfer resistance measurements revealed a reduction in dynamic capacity attributed to a decrease in IgG effective pore diffusivity and possibly slower IgG association kinetics for the PEGylated protein A ligands. Ligand PEGylation is a viable approach to improving selectivity in affinity chromatography with macromolecular ligands. © 2014 American Institute of Chemical Engineers.

  11. Comparing laser printing and barcode scanning designs

    Science.gov (United States)

    MacArthur, Thomas D.

    1991-02-01

    A comparison of requirements and designs for barcode and non-impact printer scanners reveals similarities and differences that may be useful in leading to new solutions for barcode scanner problems. The non-impact printer scanner has been in volume production for over 10 years successfully achieving low cost high performance and high quality targets. Where requirements are found to overlap solutions already implemented and proven for printer applications may fmd further application in bar code scanners. Typical technologies used for printing include flying spot scanners liquid crystal shutters scophony scanners and LED arrays. Of primary concern in measuring figure of merit are such critical parameters as cost lifetime reliability conformance to regulatory standards environmental ruggedness power consumption compactness insensitivity to orientation acoustic noise produced modularity spot size depth of field exposure level and uniformity data rate scan length and uniformity and many more. A comparison of printing technologies their capabilities and their limitations with those used in barcode scanners may reveal common problems where we can take advantage of work already completed in similar application where requirements are found to overlap.

  12. Thermodynamics and solvent linkage of macromolecule-ligand interactions

    Science.gov (United States)

    Duff, Michael R.; Howell, Elizabeth E.

    2014-01-01

    Binding involves two steps, desolvation and association. While water is ubiquitous and occurs at high concentration, it is typically ignored. In vitro experiments typically use infinite dilution conditions, while in vivo, the concentration of water is decreased due to the presence of high concentrations of molecules in the cellular milieu. This review discusses isothermal titration calorimetry approaches that address the role of water in binding. For example, use of D2O allows the contribution of solvent reorganization to the enthalpy component to be assessed. Further, the addition of osmolytes will decrease the water activity of a solution and allow effects on Ka to be determined. In most cases, binding becomes tighter in the presence of osmolytes as the desolvation penalty associated with binding is minimized. In other cases, the osmolytes prefer to interact with the ligand or protein, and if their removal is more difficult than shedding water, then binding can be weakened. These complicating layers can be discerned by different slopes in ln(Ka) vs osmolality plots and by differential scanning calorimetry in the presence of the osmolyte. PMID:25462561

  13. Cadmium Removal Performances of Different Dye Ligands Attached Cryogel Disks

    Directory of Open Access Journals (Sweden)

    Burak Keleş

    2015-07-01

    Full Text Available Poly(HEMA cryogel disks were synthesized by free radical polymerization of 2-hydroxy-ethylmethacrylate (HEMA, and then Cibacron Blue F3GA (CB, Reactive Green 19 (RG and Congo Red (CR were immobilized as dye ligands. Disks were characterized by Fourier transform infrared spectroscopy (FTIR, scanning electron microscope (SEM and swelling degree, porosity calculations. Cd2+ adsorption experiments were performed for 60 min. Maximum adsorption capacities were determined as 25.5 mg/g; 48.0 mg/g and 28.5 mg/g at pH = 7.0 for poly(HEMA-CB; poly(HEMA-RG and poly(HEMA-CR, respectively. Langmuir isotherm fitted best with the adsorption data and adsorption thermodynamics showed that Cd2+ adsorption is thermodynamically favorable and a physisorption process. A great majority of adsorbed Cd2+ desorbed with 1 M NaCl and cryogel disks can be re-used in adsorption experiments. Cd2+ removal efficiencies of disks from human plasma are approximately 45 %. Dye-attached cryogel disks synthesized in this study have potential in use for environmental and therapeutic applications.

  14. Hydrogen bonding penalty upon ligand binding.

    Directory of Open Access Journals (Sweden)

    Hongtao Zhao

    Full Text Available Ligand binding involves breakage of hydrogen bonds with water molecules and formation of new hydrogen bonds between protein and ligand. In this work, the change of hydrogen bonding energy in the binding process, namely hydrogen bonding penalty, is evaluated with a new method. The hydrogen bonding penalty can not only be used to filter unrealistic poses in docking, but also improve the accuracy of binding energy calculation. A new model integrated with hydrogen bonding penalty for free energy calculation gives a root mean square error of 0.7 kcal/mol on 74 inhibitors in the training set and of 1.1 kcal/mol on 64 inhibitors in the test set. Moreover, an application of hydrogen bonding penalty into a high throughput docking campaign for EphB4 inhibitors is presented, and remarkably, three novel scaffolds are discovered out of seven tested. The binding affinity and ligand efficiency of the most potent compound is about 300 nM and 0.35 kcal/mol per non-hydrogen atom, respectively.

  15. The effect of ligand-ligand interactions on the formation of photoluminescent gold nanoclusters embedded in Au(i)-thiolate supramolecules.

    Science.gov (United States)

    Chang, Hsiang-Yu; Tseng, Yu-Ting; Yuan, Zhiqin; Chou, Hung-Lung; Chen, Ching-Hsiang; Hwang, Bing-Joe; Tsai, Meng-Che; Chang, Huan-Tsung; Huang, Chih-Ching

    2017-05-17

    In this study, we prepared photoluminescent l-cysteine (Cys)-capped gold nanoclusters (Cys-Au NCs) via NaBH4-mediated reduction of aggregated coordination polymers (supramolecules) of -[Cys-Au(i)]n-. The -[Cys-Au(i)]n- supramolecules with interesting chiral properties were formed through simple reactions of chloroauric acid (HAuCl4) with Cys at certain pH values (pH 3-7). The -[Cys-Au(i)]n- polymers could self-assemble into -[Cys-Au(i)]n- supramolecules with irregular morphologies and diameters larger than 500 nm through stacked hydrogen bonding and zwitterionic interactions between Cys ligands and through Au(i)Au(i) aurophilic interactions in solutions with pH values ≤7. The photoluminescent Au NCs (quantum yield = 11.6%) dominated by a Au13 core were embedded in -[Cys-Au(i)]n- supramolecules after NaBH4-mediated reduction. The optical and structural properties of Cys-Au NCs/-[Cys-Au(i)]n- nanocomposites were investigated, revealing that the interaction between Cys ligands plays a critical role in the self-assembly of -[Cys-Au(i)]n- supramolecules and in the formation of photoluminescent Cys-Au NCs embedded in the supramolecules. To further demonstrate that the photoluminescence properties and structures of the nanocomposites are mediated by the intermolecular forces of thiol ligands, other thiol ligands (l-penicillamine, l-homocysteine, 3-mercaptopropionic acid, and l-glutathione) and a ligand-crosslinking agent [bis(sulfosuccinimidyl) suberate; BS3] were used. We concluded that the electrostatic interactions, hydrogen bonding and steric effects dominate the polymer self-assembly into thiol-ligand-Au(i) supramolecules and thus the formation of Au NCs. Our study provides insights into the bottom-up synthesis of photoluminescent Au NCs from thiol-ligand-Au(i) complexes, polymers, and supramolecules. The hybrid Au NCs/-[Cys-Au(i)]n- nanocomposites can potentially be employed as drug carriers and bioimaging agents.

  16. Electromechanical performance of piezoelectric scanning mirrors for medical endoscopy.

    Science.gov (United States)

    Gilchrist, Kristin H; Dausch, David E; Grego, Sonia

    2012-05-01

    The electromechanical performance of piezoelectric scanning mirrors for endoscopy imaging is presented. The devices are supported by a single actuating cantilever to achieve a high fill factor, the ratio of mirror area to the combined mirror and actuator area. The largest fill factor devices (74%) achieved 10° mechanical scan range at +/-10V with a 300 μm long cantilever. The largest angular displacement of 30° mechanical scan range was obtained with a 500 μm long cantilever device with a 63% fill factor driven at 40 Vpp. A systematic investigation of device performance (displacement and speed) as a function of fabrication and operational parameters including the stress balance in the cantilever revealed unexpectedly large displacements with lack of inversion at the coercive field. An interpretation of the results is presented based on piezoelectric film domain orientation and clamping with supporting piezoelectric film characterization measurements.

  17. CT-scanning of ancient Greenlandic Inuit temporal bones

    Energy Technology Data Exchange (ETDEWEB)

    Homoe, P. (Copenhagen Univ. (Denmark). Lab. of Biological Anthropology and Dept. of Otolaryngology, Head and Neck Surgery); Lynnerup, N. (Copenhagen Univ., Lab. of Biological Anthropology and Univ. Inst. of Ferensic Medicine, Copenhagen (Denmark)); Videbaek, H. (Hvidovre Univ. Hospital, Copenhagen (Denmark). Dept. of Radiology)

    1992-01-01

    Additional morphological evidence of former infectious middle ear disease (IMED) was found by CT-scanning in 5 of 6 Greenlandic Inuit crania strongly suspected for former IMED due to earlier examination revealing either bilateral hypocellularity or asymmetry of the pneumatized area of the temporal bones. The CT-scans showed sclerosing and obliteration of the air cells and even destruction of the cellular septae, and a high degree of irregularity of the cells. Sclerosing of the surrounding bone tissue was also found. The findings in one cranium were dubious and could both be regarded as a congenital malformation or an infection in infanthood. CT-scan confirms and even adds to the results of conventional X-ray of temporal bones making hypotheses of paleopathology more reliable. The findings also support the environmental theory of pneumatization of the air cell system in the temporal bones. (13 refs., 10 figs.).

  18. Effectiveness and usability of Scanning Wizard software: a tool for enhancing switch scanning.

    Science.gov (United States)

    Koester, Heidi Horstmann; Simpson, Richard C

    2017-11-24

    Scanning Wizard software helps scanning users improve the setup of their switch and scanning system. This study evaluated Scanning Wizard's effectiveness and usability. Ten people who use switch scanning and ten practitioners used Scanning Wizard in the initial session. Usability was high, based on survey responses averaging over 4.5 out of 5, and qualitative feedback was very positive. Five switch users were able to complete the multi-week protocol, using settings on their own scanning system that were recommended from the Scanning Wizard session. Using these revised settings, text entry rates improved by an average of 71%, ranging from 29% to 172% improvement. Results suggest that Scanning Wizard is a useful tool for improving the configuration of scanning systems for people who use switch scanning to communicate. Implications for Rehabilitation Some individuals with severe physical impairments use switch scanning for spoken and written communication. Scanning Wizard software helps scanning users improve the setup of their switch and scanning system. This study demonstrated high usability of Scanning Wizard (with 10 switch userpractitioner teams) and increased text entry rate by an average of 71% (for five switch users). Results suggest that Scanning Wizard is a useful tool for improving the configuration of scanning systems for people who use switch scanning to communicate.

  19. Design of HIV-1 protease inhibitors with pyrrolidinones and oxazolidinones as novel P1'-ligands to enhance backbone-binding interactions with protease: synthesis, biological evaluation, and protein-ligand X-ray studies

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Arun K.; Leshchenko-Yashchuk, Sofiya; Anderson, David D.; Baldridge, Abigail; Noetzel, Marcus; Miller, Heather B.; Tie, Yunfeng; Wang, Yuan-Fang; Koh, Yasuhiro; Weber, Irene T.; Mitsuya, Hiroaki; (GSU); (Purdue); (NCI); (Kumamoto University School of Medicine)

    2009-09-02

    Structure-based design, synthesis, and biological evaluation of a series of novel HIV-1 protease inhibitors are described. In an effort to enhance interactions with protease backbone atoms, we have incorporated stereochemically defined methyl-2-pyrrolidinone and methyl oxazolidinone as the P1{prime}-ligands. These ligands are designed to interact with Gly-27{prime} carbonyl and Arg-8 side chain in the S1{prime}-subsite of the HIV protease. We have investigated the potential of these ligands in combination with our previously developed bis-tetrahydrofuran (bis-THF) and cyclopentanyltetrahydrofuran (Cp-THF) as the P2-ligands. Inhibitor 19b with a (R)-aminomethyl-2-pyrrolidinone and a Cp-THF was shown to be the most potent compound. This inhibitor maintained near full potency against multi-PI-resistant clinical HIV-1 variants. A high resolution protein-ligand X-ray crystal structure of 19b-bound HIV-1 protease revealed that the P1{prime}-pyrrolidinone heterocycle and the P2-Cp-ligand are involved in several critical interactions with the backbone atoms in the S1{prime} and S2 subsites of HIV-1 protease.

  20. Multifunctional scanning ion conductance microscopy.

    Science.gov (United States)

    Page, Ashley; Perry, David; Unwin, Patrick R

    2017-04-01

    Scanning ion conductance microscopy (SICM) is a nanopipette-based technique that has traditionally been used to image topography or to deliver species to an interface, particularly in a biological setting. This article highlights the recent blossoming of SICM into a technique with a much greater diversity of applications and capability that can be used either standalone, with advanced control (potential-time) functions, or in tandem with other methods. SICM can be used to elucidate functional information about interfaces, such as surface charge density or electrochemical activity (ion fluxes). Using a multi-barrel probe format, SICM-related techniques can be employed to deposit nanoscale three-dimensional structures and further functionality is realized when SICM is combined with scanning electrochemical microscopy (SECM), with simultaneous measurements from a single probe opening up considerable prospects for multifunctional imaging. SICM studies are greatly enhanced by finite-element method modelling for quantitative treatment of issues such as resolution, surface charge and (tip) geometry effects. SICM is particularly applicable to the study of living systems, notably single cells, although applications extend to materials characterization and to new methods of printing and nanofabrication. A more thorough understanding of the electrochemical principles and properties of SICM provides a foundation for significant applications of SICM in electrochemistry and interfacial science.

  1. Schistosomiasis collection at NHM (SCAN

    Directory of Open Access Journals (Sweden)

    Emery Aidan M

    2012-09-01

    Full Text Available Abstract Background The Natural History Museum (NHM is developing a repository for schistosomiasis-related material, the Schistosomiasis Collection at NHM (SCAN as part of its existing Wolfson Wellcome Biomedical Laboratory (WWBL. This is timely because a major research and evaluation effort to understand control and move towards elimination of schistosomiasis in Africa has been initiated by the Schistosomiasis Consortium for Operational Research and Evaluation (SCORE, resulting in the collection of many important biological samples, including larval schistosomes and snails. SCAN will collaborate with a number of research groups and control teams and the repository will acquire samples relevant to both immediate and future research interest. The samples collected through ongoing research and field activities, WWBL’s existing collections, and other acquisitions will be maintained over the long term and made available to the global research community for approved research purposes. Goals include: · Consolidation of the existing NHM schistosome and snail collections and transfer of specimens into suitable long-term storage systems for DNA retrieval, · Long-term and stable storage of specimens collected as part of on going field programmes initially in Africa especially relating to the SCORE research programmes, · Provision of access to snail and schistosome collections for approved research activities.

  2. α-Alkylation of ketones with primary alcohols catalyzed by a Cp*Ir complex bearing a functional bipyridonate ligand.

    Science.gov (United States)

    Li, Feng; Ma, Juan; Wang, Nana

    2014-11-07

    A Cp*Ir complex bearing a functional bipyridonate ligand was found to be a highly effective and versatile catalyst for the α-alkylation of ketones with primary alcohols under extremely environmentally benign and mild conditions (0.1 equiv of Cs2CO3 per substrate, reflux in tert-amyl alcohol under an air atmosphere for 6 h). Furthermore, this complex also exhibited a high level of catalytic activity for the α-methylation of ketones with methanol. The mechanistic investigation revealed that the carbonyl group on the ligand is of critical importance for catalytic hydrogen transfer. Notably, the results of this study revealed the unique potential of Cp*Ir complexes bearing a functional bipyridonate ligand for the development of C-C bond-forming reactions with the activation of primary alcohols as electrophiles.

  3. Ligand mediated evolution of size dependent magnetism in cobalt nanoclusters.

    Science.gov (United States)

    Hartmann, Michael J; Millstone, Jill E; Häkkinen, Hannu

    2018-02-07

    We use density functional theory to model the impact of a ligand shell on the magnetic properties of CoN (15 ≤ N ≤ 55) nanoclusters. We study three different ligand shells on each nanocluster core size, each known to have different electronic interactions with the surface: pure Cl ligand shells (X-type), pure PH3 ligand shells (L-type), and two component ligand shells with mixtures of Cl and PH3 ligands. The simulations show that the identity, arrangement, and total coverage of the ligand shell controls the distribution of local magnetic moments across the CoN core. On the surface of an unpassivated CoN nanocluster, the Co-Co coordination number (CN) is known to determine the local magnetic moments. Upon the introduction of a ligand, the Co-Co CN remains important, however the nature of the metal-ligand bond changes the extent to which increasing Co-Co CN quenches magnetism. Further, we identify an additional and significant long-range impact on local magnetic moments (LMM) from the PH3 ligand shells. Thus, we establish important design principles of magnetic nanoclusters, where ligand shell chemistry mediates the distribution of LMMs across a CoNLM nanocluster, allowing a route to rational design of specific magnetic properties.

  4. Design and fabrication of a differential scanning nanocalorimeter

    Science.gov (United States)

    Zuo, Lei; Chen, Xiaoming; Yu, Shifeng; Lu, Ming

    2017-02-01

    This paper describes the design, fabrication, and characterization of a differential scanning nanocalorimeter that significantly reduces the sample volume to microliters and can potentially improve the temperature sensitivity to 10 µK. The nanocalorimeter consists of a polymeric freestanding membrane, four high-sensitive low-noise thermistors based on silicon carbide (SiC), and a platinum heater and temperature sensor. With the integrated heater and sensors, temperature scanning and power compensation can be achieved for calorimetric measurement. Temperature sensing SiC film was prepared by using sintered SiC target and DC magnetron sputtering under different gas pressures and sputtering power. The SiC sensing material is characterized through the measurement of current-voltage curves and noise levels. The thermal performance of a fabricated nanocalorimeter is studied in simulation and experiment. The experiment results show the device has excellent thermal isolation to hold thermal energy. The noise test together with the simulation show the device is promising for micro 10 µK temperature sensitivity and nanowatt resolution which will lead to low-volume ultra-sensitive nanocalorimetry for biological processes, such as protein folding and ligand binding.

  5. Separation of tryptophan enantiomers by ligand-exchange chromatography with novel chiral ionic liquids ligand.

    Science.gov (United States)

    Qing, Haiqun; Jiang, Xinyu; Yu, Jingang

    2014-03-01

    Chiral ionic liquids (CILs) with amino acids as cations have been applied as novel chiral ligands coordinated with Cu(2+) to separate tryptophan enantiomers in ligand exchange chromatography. Four kinds of amino acid ionic liquids, including [L-Pro][CF3COO], [L-Pro][NO3], [L-Pro]2[SO4], and [L-Phe][CF3COO] were successfully synthesized and used for separation of tryptophan enantiomers. To optimize the separation conditions, [L-Pro][CF3COO] was selected as the model ligand. Some factors influencing the efficiency of chiral separation, such as copper ion concentration, CILs concentration, methanol ratio (methanol/H2O, v/v), and pH, were investigated. The obtained optimal separation conditions were as follows: 8.0 mmol/L Cu(OAc)2, 4.0 mmol/L [L-Pro][CF3COO], and 20% (v/v) methanol at pH 3.6. Under the optimum conditions, acceptable enantioseparation of tryptophan enantiomers could be observed with a resolution of 1.89. The results demonstrate the good applicability of CILs with amino acids as cations for chiral separation. Furthermore, a comparative study was also conducted for exploring the mechanism of the CILs as new ligands in ligand exchange chromatography. © 2014 Wiley Periodicals, Inc.

  6. 3D Scanning technology for offshore purposes

    DEFF Research Database (Denmark)

    Christoffersen, Morten Thoft

    2005-01-01

    New scanning technology makes for construction of precision 3D models of production plants and offshore production facilities......New scanning technology makes for construction of precision 3D models of production plants and offshore production facilities...

  7. CDMP Scan Task Production Flow Sheets

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Climate Database Modernization Program contractor documentation of batches scanned. Details include the name of the operator, time/date of scans, duplicates,...

  8. A latent ruthenium based olefin metathesis catalyst with a sterically demanding NHC ligand

    KAUST Repository

    Leitgeb, Anita

    2012-01-01

    An olefin metathesis catalyst featuring a SIPr NHC and an ester chelating carbene ligand is introduced. In contrast to its previously published SIMes analogue, only the trans dichloro configurated isomer was obtained. The two counterparts are tested in various olefin metathesis reactions, revealing a striking superiority of the new complex in the cross metathesis of olefins with methyl vinyl ketone allowing for full conversion with only 500 ppm catalyst loading. © 2012 The Royal Society of Chemistry.

  9. Identifying Carbohydrate Ligands of a Norovirus P Particle using a Catch and Release Electrospray Ionization Mass Spectrometry Assay

    Science.gov (United States)

    Han, Ling; Kitova, Elena N.; Tan, Ming; Jiang, Xi; Klassen, John S.

    2014-01-01

    Noroviruses (NoVs), the major cause of epidemic acute gastroenteritis, recognize human histo-blood group antigens (HBGAs), which are present as free oligosaccharides in bodily fluid or glycolipids and glycoproteins on the surfaces of cells. The subviral P particle formed by the protruding (P) domain of the NoV capsid protein serves as a useful model for the study NoV-HBGA interactions. Here, we demonstrate the application of a catch-and-release electrospray ionization mass spectrometry (CaR-ESI-MS) assay for screening carbohydrate libraries against the P particle to rapidly identify NoV ligands and potential inhibitors. Carbohydrate libraries of 50 and 146 compounds, which included 18 and 24 analogs of HBGA receptors, respectively, were screened against the P particle of VA387, a member of the predominant GII.4 NoVs. Deprotonated ions corresponding to the P particle bound to carbohydrates were isolated and subjected to collision-induced dissociation to release the ligands in their deprotonated forms. The released ligands were identified by ion mobility separation followed by mass analysis. All 13 and 16 HBGA ligands with intrinsic affinities >500 M-1 were identified in the 50 and the 146 compound libraries, respectively. Furthermore, screening revealed interactions with a series of oligosaccharides with structures found in the cell wall of mycobacteria and human milk. The affinities of these newly discovered ligands are comparable to those of the HBGA receptors, as estimated from the relative abundance of released ligand ions.

  10. Ligand binding induces a conformational change in ifnar1 that is propagated to its membrane-proximal domain.

    Science.gov (United States)

    Strunk, Jennifer Julia; Gregor, Ingo; Becker, Yvonne; Li, Zongli; Gavutis, Martynas; Jaks, Eva; Lamken, Peter; Walz, Thomas; Enderlein, Jörg; Piehler, Jacob

    2008-03-28

    The type I interferon (IFN) receptor plays a key role in innate immunity against viral and bacterial infections. Here, we show by intramolecular Förster resonance energy transfer spectroscopy that ligand binding induces substantial conformational changes in the ectodomain of ifnar1 (ifnar1-EC). Binding of IFN alpha 2 and IFN beta induce very similar conformations of ifnar1, which were confirmed by single-particle electron microscopy analysis of the ternary complexes formed by IFN alpha 2 or IFN beta with the two receptor subunits ifnar1-EC and ifnar2-EC. Photo-induced electron-transfer-based fluorescence quenching and single-molecule fluorescence lifetime measurements revealed that the ligand-induced conformational change in the membrane-distal domains of ifnar1-EC is propagated to its membrane-proximal domain, which is not involved in ligand recognition but is essential for signal activation. Temperature-dependent ligand binding studies as well as stopped-flow fluorescence experiments corroborated a multistep conformational change in ifnar1 upon ligand binding. Our results thus suggest that the relatively intricate architecture of the type I IFN receptor complex is designed to propagate the ligand binding event to and possibly even across the membrane by conformational changes.

  11. Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser

    Directory of Open Access Journals (Sweden)

    Maike Bublitz

    2015-07-01

    Full Text Available Membrane proteins are key players in biological systems, mediating signalling events and the specific transport of e.g. ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX for the structure determination of membrane protein–ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data reveal the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.

  12. Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser

    Energy Technology Data Exchange (ETDEWEB)

    Bublitz, Maike; Nass, Karol; Drachmann, Nikolaj D.; Markvardsen, Anders J.; Gutmann, Matthias J.; Barends, Thomas R. M.; Mattle, Daniel; Shoeman, Robert L.; Doak, R. Bruce; Boutet, Sébastien; Messerschmidt, Marc; Seibert, Marvin M.; Williams, Garth J.; Foucar, Lutz; Reinhard, Linda; Sitsel, Oleg; Gregersen, Jonas L.; Clausen, Johannes D.; Boesen, Thomas; Gotfryd, Kamil; Wang, Kai-Tuo; Olesen, Claus; Møller, Jesper V.; Nissen, Poul; Schlichting, Ilme

    2015-06-11

    Membrane proteins are key players in biological systems, mediating signalling events and the specific transport ofe.g.ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX) for the structure determination of membrane protein–ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data reveal the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.

  13. Mixed-ligand copper(ii) Schiff base complexes: the role of the co-ligand in DNA binding, DNA cleavage, protein binding and cytotoxicity.

    Science.gov (United States)

    Lian, Wen-Jing; Wang, Xin-Tian; Xie, Cheng-Zhi; Tian, He; Song, Xue-Qing; Pan, He-Ting; Qiao, Xin; Xu, Jing-Yuan

    2016-05-31

    Four novel mononuclear Schiff base copper(ii) complexes, namely, [Cu(L)(OAc)]·H2O (), [Cu(HL)(C2O4)(EtOH)]·EtOH (), [Cu(L)(Bza)] () and [Cu(L)(Sal)] () (HL = 1-(((2-((2-hydroxypropyl)amino)ethyl)imino)methyl)naphthalene-2-ol), Bza = benzoic acid, Sal = salicylic acid), were synthesized and characterized by X-ray crystallography, elemental analysis and infrared spectroscopy. Single-crystal diffraction analysis revealed that all the complexes were mononuclear molecules, in which the Schiff base ligand exhibited different coordination modes and conformations. The N-HO and O-HO inter- and intramolecular hydrogen bonding interactions linked these molecules into multidimensional networks. Their interactions with calf thymus DNA (CT-DNA) were investigated by UV-visible and fluorescence spectrometry, as well as by viscosity measurements. The magnitude of the Kapp values of the four complexes was 10(5), indicating a moderate intercalative binding mode between the complexes and DNA. Electrophoresis results showed that all these complexes induced double strand breaks of pUC19 plasmid DNA in the presence of H2O2 through an oxidative pathway. In addition, the fluorescence spectrum of human serum albumin (HSA) with the complexes suggested that the quenching mechanism of HSA by the complexes was a static process. Moreover, the antiproliferative activity of the four complexes against HeLa (human cervical carcinoma) and HepG-2 (human liver hepatocellular carcinoma) cells evaluated by colorimetric cell proliferation assay and clonogenic assay revealed that all four complexes had improved cytotoxicity against cancer cells. Inspiringly, complex , with salicylic acid as the auxiliary ligand, displayed a stronger anticancer activity, suggesting that a synergistic effect of the Schiff base complex and the nonsteroidal anti-inflammatory drug may be involved in the cell killing process. The biological features of mixed-ligand copper(ii) Schiff base complexes and how acetic auxiliary

  14. Knowledge Discovery of Port Scans from Darknet

    OpenAIRE

    Lagraa, Sofiane; Francois, Jerome

    2017-01-01

    International audience; Port scanning is widely used in Internet prior for attacks in order to identify accessible and potentially vulnerable hosts. In this work, we propose an approach that allows to discover port scanning behavior patterns and group properties of port scans. This approach is based on graph modelling and graph mining. It provides to security analysts relevant information of what services are jointly targeted, and the relationship of the scanned ports. This is helpful to asse...

  15. Serial CT scans and Menkes' kinky hair disease

    Energy Technology Data Exchange (ETDEWEB)

    Nakada, Eizo; Kameyama, Junji; Yoshimitsu, Hajime; Mori, Mikio; Tanaka, Mutsuo; Yoshimitsu, Kazunori.

    1988-02-01

    Menkes' kinky hair disease is a sex-linked recessive disorder of copper metabolism, characterized by progressive psychomotor deterioration, seizures, and peculiar hair structure. We examined serial CT scans of patients with this disease. A 2,210-g male infant was delivered after an uneventful gestation of 36 weeks. His one-minute Apgar score was 9. His uncle had died at 1 year of age. His first cousin was also diagnosed as having Menkes' kinky hair disease when our patient was 2 years old. Shortly after birth he had mild respiratory distress. At 5 days of age, he developed setting-sun signs. The first CT scan, at 10 days of age, revealed mild posterior fossa hemorrhages. At 3 months of age, myoclonic seizures began, and the CT scan revealed subdural effusion and mild brain atrophy. The seizures were controllable by using phenobarbital, valproic acid, and nitrazepam. He did not follow light or a fixate, but the fundi were normal. He was diffusely hypotonic. At 9 months of age, the seizures became uncontrollable. The CT scans at 15 and 31 months of age showed subdural hemorrhage and/or brain atrophy. At 15 months of age, the serum copper level was 42 ..mu.. g/dl, while the serum ceruloplasmin level was 3.2 mg/dl. He exhibited severe developmental failure. At 4 years of age, he died.

  16. Acute hematogenous osteomyelitis: has the bone scan betrayed us. [/sup 99m/Tc-phosphate compounds; /sup 67/Ga-citrate

    Energy Technology Data Exchange (ETDEWEB)

    Handmaker, H.

    1980-06-01

    Technetium-99m bone scanning reveals a spectrum of findings in the diagnosis of acute hematogenous osteomyelitis. Both cold and hot abnormalities are found. Gallium-67 citrate imaging is recommended when /sup 99m/Tc phosphate scans are inconclusive.

  17. Parallel line scanning ophthalmoscope for retinal imaging

    NARCIS (Netherlands)

    Vienola, Kari V.; Damodaran, Mathi; Braaf, Boy; Vermeer, Koenraad A.; de Boer, Johannes F.

    2016-01-01

    Purpose: To visualize retinal structures using a newly developed parallel line scanning ophthalmoscope (PLSO). Methods: A PLSO was built using a digital micromirror device (DMD) instead of traditional scanning mirrors to scan lines over the field of view (FOV). The DMD consists of 912 × 1140

  18. Suspension system for gimbal supported scanning payloads

    Science.gov (United States)

    Polites, Michael E.

    1995-03-01

    Gimballed scanning devices or instruments are the subject of this invention. Scanning is an important aspect of space science. To achieve a scan pattern some means must be provided which impart to the payload an oscillatory motion. Various forms of machines have been employed for controllably conferring on scanning instruments predetermined scan patterns. They include control moment gyroscopes, reaction wheels, torque motors, reaction control systems, and the like. But rotating unbalanced mass (RUM) devices are a new and efficient way to generate scans in gimballed payloads. RUM devices are superior to previous scanning apparatus, but they require power consuming and frequently complex auxiliary control systems to position and reposition the particular scan pattern relative to a target or a number of targets. Herein the control system is simplified. The most frequently employed method for achieving the various scan patterns is to gimbal the scanning device. Gimbals are suspended in such a way that they can be activated to generate the scan pattern. The suspension means described is for payloads supported in gimbals wherein the payload rotation is restricted by a flex pivot so that the payload oscillates, thereby moving in a scan pattern.

  19. Getting a CAT Scan (For Kids)

    Science.gov (United States)

    ... Too Tall or Too Short Getting a CAT Scan (Video) KidsHealth > For Kids > Getting a CAT Scan (Video) Print A A A en español Obtención de una tomografía computada (video) CAT stands for ... what's going on inside your body. The scan itself is painless. All you'll need to ...

  20. Getting a CAT Scan (For Kids)

    Medline Plus

    Full Text Available ... Too Tall or Too Short Getting a CAT Scan (Video) KidsHealth > For Kids > Getting a CAT Scan (Video) Print A A A en español Obtención de una tomografía computada (video) CAT stands for ... what's going on inside your body. The scan itself is painless. All you'll need to ...

  1. Probing protein flexibility reveals a mechanism for selective promiscuity.

    Science.gov (United States)

    Pabon, Nicolas A; Camacho, Carlos J

    2017-04-22

    Many eukaryotic regulatory proteins adopt distinct bound and unbound conformations, and use this structural flexibility to bind specifically to multiple partners. However, we lack an understanding of how an interface can select some ligands, but not others. Here, we present a molecular dynamics approach to identify and quantitatively evaluate the interactions responsible for this selective promiscuity. We apply this approach to the anticancer target PD-1 and its ligands PD-L1 and PD-L2. We discover that while unbound PD-1 exhibits a hard-to-drug hydrophilic interface, conserved specific triggers encoded in the cognate ligands activate a promiscuous binding pathway that reveals a flexible hydrophobic binding cavity. Specificity is then established by additional contacts that stabilize the PD-1 cavity into distinct bound-like modes. Collectively, our studies provide insight into the structural basis and evolution of multiple binding partners, and also suggest a biophysical approach to exploit innate binding pathways to drug seemingly undruggable targets.

  2. Relationship Between Plasma Levels of Soluble CD40 Ligand and the Presence and Severity of Isolated Coronary Artery Ectasia.

    Science.gov (United States)

    Ozde, Cem; Korkmaz, Ahmet; Kundi, Harun; Oflar, Ersan; Ungan, Ismail; Xankisi, Vusal; Nurlu, Nilhan

    2016-01-01

    We aimed to investigate whether soluble CD40 ligand (CD40L) levels are higher in patients with isolated coronary artery ectasia (CAE) compared to patients with angiographically normal coronary arteries and those with stable coronary artery disease (CAD). In all, 55 patients with isolated CAE without stenosis, 55 with stable CAD, and 55 control participants with angiographically normal coronary arteries were included. The CAE severity was determined according to the Markis classification. Plasma levels of soluble CD40 ligand were measured by enzyme-linked immunosorbent assay. The baseline characteristics of the 3 groups were similar. Plasma levels of soluble CD40 ligand were significantly higher in patients with CAE and CAD than in controls (2.6 ± 3.1 ng/mL and 2.0 ± 3.1 ng/mL vs 1.8 ± 2.1 ng/mL, P = .004). No difference was found between the CAE and CAD groups. Soluble CD40 ligand level was significantly higher in the type 1 Markis subgroup than that in the type 3 or type 4 subgroups ( P = .01). A receiver operating characteristic curve analysis revealed that soluble CD40 ligand level >1.2 ng/mL identified patients with isolated CAE. Significantly higher levels of soluble CD40 ligand were detected in patients with CAE than that in control participants with normal coronary arteries, suggesting that soluble CD40 ligand may be involved in the pathogenesis of CAE. The CD40-CD40 ligand system likely plays a role in the pathogenesis of CAE.

  3. ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites.

    Science.gov (United States)

    Konc, Janez; Janežič, Dušanka

    2014-07-01

    The ProBiS-ligands web server predicts binding of ligands to a protein structure. Starting with a protein structure or binding site, ProBiS-ligands first identifies template proteins in the Protein Data Bank that share similar binding sites. Based on the superimpositions of the query protein and the similar binding sites found, the server then transposes the ligand structures from those sites to the query protein. Such ligand prediction supports many activities, e.g. drug repurposing. The ProBiS-ligands web server, an extension of the ProBiS web server, is open and free to all users at http://probis.cmm.ki.si/ligands. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. QUANTITATIVE CONFOCAL LASER SCANNING MICROSCOPY

    Directory of Open Access Journals (Sweden)

    Merete Krog Raarup

    2011-05-01

    Full Text Available This paper discusses recent advances in confocal laser scanning microscopy (CLSM for imaging of 3D structure as well as quantitative characterization of biomolecular interactions and diffusion behaviour by means of one- and two-photon excitation. The use of CLSM for improved stereological length estimation in thick (up to 0.5 mm tissue is proposed. The techniques of FRET (Fluorescence Resonance Energy Transfer, FLIM (Fluorescence Lifetime Imaging Microscopy, FCS (Fluorescence Correlation Spectroscopy and FRAP (Fluorescence Recovery After Photobleaching are introduced and their applicability for quantitative imaging of biomolecular (co-localization and trafficking in live cells described. The advantage of two-photon versus one-photon excitation in relation to these techniques is discussed.

  5. Scanning strategies for imaging arrays

    Science.gov (United States)

    Kovács, Attila

    2008-07-01

    Large-format (sub)millimeter wavelength imaging arrays are best operated in scanning observing modes rather than traditional position-switched (chopped) modes. The choice of observing mode is critical for isolating source signals from various types of noise interference, especially for ground-based instrumentation operating under a bright atmosphere. Ideal observing strategies can combat 1/f noise, resist instrumental defects, sensitively recover emission on large scales, and provide an even field coverage - all under feasible requirements of telescope movement. This work aims to guide the design of observing patterns that maximize scientific returns. It also compares some of the popular choices of observing modes for (sub)millimeter imaging, such as random, Lissajous, billiard, spiral, On-The-Fly (OTF), DREAM, chopped and stare patterns. Many of the conclusions are also applicable other imaging applications and imaging in one dimension (e.g. spectroscopic observations).

  6. Scanning laser polarimetry in glaucoma.

    Science.gov (United States)

    Dada, Tanuj; Sharma, Reetika; Angmo, Dewang; Sinha, Gautam; Bhartiya, Shibal; Mishra, Sanjay K; Panda, Anita; Sihota, Ramanjit

    2014-11-01

    Glaucoma is an acquired progressive optic neuropathy which is characterized by changes in the optic nerve head and retinal nerve fiber layer (RNFL). White-on-white perimetry is the gold standard for the diagnosis of glaucoma. However, it can detect defects in the visual field only after the loss of as many as 40% of the ganglion cells. Hence, the measurement of RNFL thickness has come up. Optical coherence tomography and scanning laser polarimetry (SLP) are the techniques that utilize the evaluation of RNFL for the evaluation of glaucoma. SLP provides RNFL thickness measurements based upon the birefringence of the retinal ganglion cell axons. We have reviewed the published literature on the use of SLP in glaucoma. This review elucidates the technological principles, recent developments and the role of SLP in the diagnosis and monitoring of glaucomatous optic neuropathy, in the light of scientific evidence so far.

  7. UAVSAR Active Electronically Scanned Array

    Science.gov (United States)

    Sadowy, Gregory, A.; Chamberlain, Neil F.; Zawadzki, Mark S.; Brown, Kyle M.; Fisher, Charles D.; Figueroa, Harry S.; Hamilton, Gary A.; Jones, Cathleen E.; Vorperian, Vatche; Grando, Maurio B.

    2011-01-01

    The Uninhabited Airborne Vehicle Synthetic Aperture Radar (UAVSAR) is a pod-based, L-band (1.26 GHz), repeatpass, interferometric, synthetic aperture radar (InSAR) used for Earth science applications. Repeat-pass interferometric radar measurements from an airborne platform require an antenna that can be steered to maintain the same angle with respect to the flight track over a wide range of aircraft yaw angles. In order to be able to collect repeat-pass InSAR data over a wide range of wind conditions, UAVSAR employs an active electronically scanned array (AESA). During data collection, the UAVSAR flight software continuously reads the aircraft attitude state measured by the Embedded GPS/INS system (EGI) and electronically steers the beam so that it remains perpendicular to the flight track throughout the data collection

  8. Scanning ARM Cloud Radar Handbook

    Energy Technology Data Exchange (ETDEWEB)

    Widener, K; Bharadwaj, N; Johnson, K

    2012-06-18

    The scanning ARM cloud radar (SACR) is a polarimetric Doppler radar consisting of three different radar designs based on operating frequency. These are designated as follows: (1) X-band SACR (X-SACR); (2) Ka-band SACR (Ka-SACR); and (3) W-band SACR (W-SACR). There are two SACRs on a single pedestal at each site where SACRs are deployed. The selection of the operating frequencies at each deployed site is predominantly determined by atmospheric attenuation at the site. Because RF attenuation increases with atmospheric water vapor content, ARM's Tropical Western Pacific (TWP) sites use the X-/Ka-band frequency pair. The Southern Great Plains (SGP) and North Slope of Alaska (NSA) sites field the Ka-/W-band frequency pair. One ARM Mobile Facility (AMF1) has a Ka/W-SACR and the other (AMF2) has a X/Ka-SACR.

  9. Scanning Electrochemical Microscopy in Neuroscience

    Science.gov (United States)

    Schulte, Albert; Nebel, Michaela; Schuhmann, Wolfgang

    2010-07-01

    This article reviews recent work involving the application of scanning electrochemical microscopy (SECM) to the study of individual cultured living cells, with an emphasis on topographical and functional imaging of neuronal and secretory cells of the nervous and endocrine system. The basic principles of biological SECM and associated negative amperometric-feedback and generator/collector-mode SECM imaging are discussed, and successful use of the methodology for screening soft and fragile membranous objects is outlined. The drawbacks of the constant-height mode of probe movement and the benefits of the constant-distance mode of SECM operation are described. Finally, representative examples of constant-height and constant-distance mode SECM on a variety of live cells are highlighted to demonstrate the current status of single-cell SECM in general and of SECM in neuroscience in particular.

  10. Transmittance measurement using scanning LED

    Science.gov (United States)

    Ping, Yao; Mohan, Rosmin Elsa; Lau, Gih-Keong; Asundi, Anand Krishna

    2017-06-01

    In order to measure the transmittance for a large field of view (FOV), a system based on scanning LED is developed. The system mainly consists of tunable LEDs, a glass diffuser and a camera. The LED panel would display different colors in the CIE color space. An algorithm of converting the light wavelength to the RGB values is adopted. The images are captured using a monochrome camera. Depending on the number of colors displayed, the transmittance map for the entire spread of visible colors can be determined. Results are compared with those measured through a spectrometer. The spectral transmittance for the two methods exhibit good similarity. The system provides a means of measuring transmittance with no moving parts and can be extended to other hyperspectral imaging applications.

  11. Scanning laser polarimetry in glaucoma

    Directory of Open Access Journals (Sweden)

    Tanuj Dada

    2014-01-01

    Full Text Available Glaucoma is an acquired progressive optic neuropathy which is characterized by changes in the optic nerve head and retinal nerve fiber layer (RNFL. White-on-white perimetry is the gold standard for the diagnosis of glaucoma. However, it can detect defects in the visual field only after the loss of as many as 40% of the ganglion cells. Hence, the measurement of RNFL thickness has come up. Optical coherence tomography and scanning laser polarimetry (SLP are the techniques that utilize the evaluation of RNFL for the evaluation of glaucoma. SLP provides RNFL thickness measurements based upon the birefringence of the retinal ganglion cell axons. We have reviewed the published literature on the use of SLP in glaucoma. This review elucidates the technological principles, recent developments and the role of SLP in the diagnosis and monitoring of glaucomatous optic neuropathy, in the light of scientific evidence so far.

  12. Scanning Probe Microscopy of Graphene

    Science.gov (United States)

    Tautz, Pamela

    2011-10-01

    Scanning tunneling microscopy has been used to study the unusual electronic properties of graphene. In an effort to support the graphene with minimal interaction with the substrate, we used a hexagonal boron nitride (hBN) substrate. To minimize contaminants between the CVD graphene and boron nitride, the graphene samples were cleaned with distilled water and isopropanol prior to transfer to hBN substrate. We have also examined the growth of graphene flakes by chemical vapor deposition. In particular, we examined the relationship between the orientations of the first and second layer of CVD grown graphene. We found the growth mechanism preferentially resulted in rotations of 9^o or less indicating flakes with first and second layers aligned.

  13. Virtual substitution scan via single-step free energy perturbation.

    Science.gov (United States)

    Chiang, Ying-Chih; Wang, Yi

    2016-02-05

    With the rapid expansion of our computing power, molecular dynamics (MD) simulations ranging from hundreds of nanoseconds to microseconds or even milliseconds have become increasingly common. The majority of these long trajectories are obtained from plain (vanilla) MD simulations, where no enhanced sampling or free energy calculation method is employed. To promote the 'recycling' of these trajectories, we developed the Virtual Substitution Scan (VSS) toolkit as a plugin of the open-source visualization and analysis software VMD. Based on the single-step free energy perturbation (sFEP) method, VSS enables the user to post-process a vanilla MD trajectory for a fast free energy scan of substituting aryl hydrogens by small functional groups. Dihedrals of the functional groups are sampled explicitly in VSS, which improves the performance of the calculation and is found particularly important for certain groups. As a proof-of-concept demonstration, we employ VSS to compute the solvation free energy change upon substituting the hydrogen of a benzene molecule by 12 small functional groups frequently considered in lead optimization. Additionally, VSS is used to compute the relative binding free energy of four selected ligands of the T4 lysozyme. Overall, the computational cost of VSS is only a fraction of the corresponding multi-step FEP (mFEP) calculation, while its results agree reasonably well with those of mFEP, indicating that VSS offers a promising tool for rapid free energy scan of small functional group substitutions. This article is protected by copyright. All rights reserved. © 2016 Wiley Periodicals, Inc.

  14. Ligand Binding and Substrate Discrimination by UDP-Galactopyranose Mutase

    Energy Technology Data Exchange (ETDEWEB)

    Gruber, Todd D.; Borrok, M. Jack; Westler, William M.; Forest, Katrina T.; Kiessling, Laura L.; (UW)

    2009-07-31

    Galactofuranose (Galf) residues are present in cell wall glycoconjugates of numerous pathogenic microbes. Uridine 5{prime}-diphosphate (UDP) Galf, the biosynthetic precursor of Galf-containing glycoconjugates, is produced from UDP-galactopyranose (UDP-Galp) by the flavoenzyme UDP-galactopyranose mutase (UGM). The gene encoding UGM (glf) is essential for the viability of pathogens, including Mycobacterium tuberculosis, and this finding underscores the need to understand how UGM functions. Considerable effort has been devoted to elucidating the catalytic mechanism of UGM, but progress has been hindered by a lack of structural data for an enzyme-substrate complex. Such data could reveal not only substrate binding interactions but how UGM can act preferentially on two very different substrates, UDP-Galp and UDP-Galf, yet avoid other structurally related UDP sugars present in the cell. Herein, we describe the first structure of a UGM-ligand complex, which provides insight into the catalytic mechanism and molecular basis for substrate selectivity. The structure of UGM from Klebsiella pneumoniae bound to the substrate analog UDP-glucose (UDP-Glc) was solved by X-ray crystallographic methods and refined to 2.5 {angstrom} resolution. The ligand is proximal to the cofactor, a finding that is consistent with a proposed mechanism in which the reduced flavin engages in covalent catalysis. Despite this proximity, the glucose ring of the substrate analog is positioned such that it disfavors covalent catalysis. This orientation is consistent with data indicating that UDP-Glc is not a substrate for UGM. The relative binding orientations of UDP-Galp and UDP-Glc were compared using saturation transfer difference NMR. The results indicate that the uridine moiety occupies a similar location in both ligand complexes, and this relevant binding mode is defined by our structural data. In contrast, the orientations of the glucose and galactose sugar moieties differ. To understand the

  15. The utility of bone scans in rheumatology

    Energy Technology Data Exchange (ETDEWEB)

    Duncan, I.; Dorai-Raj, A.; Khoo, K.; Tymans, K.; Brook, A. [The Canberra Hospital, Canberra, ACT, (Australia)

    1997-09-01

    Full text: Introduction: Bone scans are the commonest diagnostic imaging services requested by Australian rheumatologists. Medicare figures suggest that an average rheumatologist orders about $50 000 (AUS) of bone scans annually. Aims: To ascertain the reasons why rheumatologists request bone scans and how it affects their patient management. Methods: A two-part prospective survey was administered before and after every bone scan ordered by four rheumatologists over a six-month period in 1996. Results: A total of 136 bone scans were requested (66.2% whole body; 33.8% regional; 6% SPECT). The primary indications for scanning were (1) to confirm a clinical diagnosis (38%); (2) to exclude a diagnosis (34%); (3) to localize site of pain (17%); and (4) to assist in management (6%). The common diseases that rheumatologists were attempting to confirm/exclude with bone scanning were inflammatory arthritis, malignancy, and fracture. However, the commonest provisional and final diagnosis was soft tissue rheumatism (18%) followed by inflammatory arthritis (15%) and osteoarthritis (11%). In 24% of patients with a provisional diagnosis of soft tissue rheumatism the diagnosis was changed by the bone scan. The scan was successful in excluding a diagnosis in 88 per cent where this was the primary indication for the test. It was successful in confirming a diagnosis in 79 per cent where this was the primary indication. In 32 per cent the bone scan altered the clinical diagnosis and in 43 per cent it altered management. The bone scan result prevented further investigations in 60 per cent. Conclusions: The commonest pre-scan and post-scan diagnosis is soft tissue rheumatism. Rheumatologists predominantly request bone scanning to confirm or exclude their clinical suspicion of inflammatory arthritis, malignancy, and fracture. Bone scans were successful in achieving these objectives in at least 79 per cent of cases.

  16. Direct synthesis of aqueous quantum dots through 4,4'-bipyridine-based twin ligand strategy.

    Science.gov (United States)

    Kalita, Mausam; Cingarapu, Sreeram; Roy, Santanu; Park, Seok Chan; Higgins, Daniel; Jankowiak, Ryszard; Chikan, Viktor; Klabunde, Kenneth J; Bossmann, Stefan H

    2012-04-16

    We report a new class of derivatized 4,4'-bipyridinium ligands for use in synthesizing highly fluorescent, extremely stable, water-soluble CdSe and CdTe quantum dots (QDs) for bioconjugation. We employed an evaporation-condensation technique, also known as solvated metal atom dispersion (SMAD), followed by a digestive ripening procedure. This method has been used to synthesize both metal nanoparticles and semiconductors in the gram scale with several stabilizing ligands in various solvents. The SMAD technique comprised evaporation condensation and stabilization of CdSe or CdTe in tetrahydrofuran. The as-prepared product was then digestively ripened in both water and dimethyl formamide, leading to narrowing of the particle size distributions. The ligands were synthesized by nucleophilic substitution (S(N)2) reactions using 4,4'-bipyridine as a nucleophile. Confocal microscopy images revealed the orange color of the nanocrystalline QDs with diameters of ~5 nm. The size has been confirmed by using transmission electron microscopy. As a part of our strategy, 85% of the 4,4'-bipyridinium salt was synthesized as propionic acid derivative and used to both stabilize the QDs in water and label basic amino acids and different biomarkers utilizing the carboxylic acid functional group. Fifteen percent of the 4,4'-bipyridinium salt was synthesized as N-propyl maleimide and used as a second ligand to label any protein containing the amino acid cysteine by means of a 1,4-Michael addition. © 2012 American Chemical Society

  17. A disymmetric terpyridine based ligand for the formation of luminescent di-aquo lanthanide complexes.

    Science.gov (United States)

    Charbonnière, Loïc J; Mameri, Samir; Flot, David; Waltz, Fanny; Zandanel, Christelle; Ziessel, Raymond F

    2007-06-14

    The synthesis of ligand H3 based on a disymmetrically substituted terpyridine core functionalised by a carboxylic acid in the 6-position and a bis(carboxymethyl)aminomethyl function in the 6''-position is described. The coordination behaviour of this heptadentate (4N/3O) ligand with lanthanide cations (Ln=Eu, Gd and Tb) was studied in solution showing the formation of complexes with [Ln] stoichiometry. Complexes with general formula [Ln(H2O)2] were isolated from neutral water solutions containing equimolar amounts of cations and ligands, and the complexes were characterized in the solid state (elemental analysis, IR) and in solution (mass spectrometry). The photo-physical properties of the luminescent complexes of Eu and Tb were studied in water solution by means of absorption, steady state and time-resolved emission spectroscopies. Evolution of the luminescence lifetimes of the Eu and Tb complexes in H2O and D2O reveals the presence of two water molecules coordinated in the first coordination sphere of the cations. Despite this important hydration number, the overall luminescence quantum yields of the complexes remained elevated, especially in the case of Tb (Phi=22.0 and 6.5% respectively for Tb and Eu). Upon crystallisation the Gd complex formed dimeric species in which two gadolinium atoms are each heptacoordinated by one ligand, the coordination sphere being completed by a single water molecule and a bridging carboxylate function, pointing to different behaviours in the solid and liquid states.

  18. A new target ligand Ser-Glu for PEPT1-overexpressing cancer imaging.

    Science.gov (United States)

    Dai, Tongcheng; Li, Na; Zhang, Lingzhi; Zhang, Yuanxing; Liu, Qin

    2016-01-01

    Nanoparticles functionalized with active target ligands have been widely used for tumor-specific diagnosis and therapy. The target ligands include antibodies, peptides, proteins, small molecules, and nucleic acid aptamers. Here, we utilize dipeptide Ser-Glu (DIP) as a new ligand to functionalize polymer-based fluorescent nanoparticles (NPs) for pancreatic cancer target imaging. We demonstrate that in the first step, Ser-Glu-conjugated NPs (NPs-DIP) efficiently bind to AsPC-1 and in the following NPs-DIP are internalized into AsPC-1 in vitro. The peptide transporter 1 inhibition experiment reveals that the targeting effects mainly depend on the specific binding of DIP to peptide transporter 1, which is remarkably upregulated in pancreatic cancer cells compared with varied normal cells. Furthermore, NPs-DIP specifically accumulate in the site of pancreatic tumor xenograft and are further internalized into the tumor cells in vivo after intravenous administration, indicating that DIP successfully enhanced nanoparticles internalization efficacy into tumor cells in vivo. This work establishes Ser-Glu to be a new tumor-targeting ligand and provides a promising tool for future tumor diagnostic or therapeutic applications.

  19. Synthesis, crystal structure and photoluminescence property of Eu/Tb MOFs with mixed polycarboxylate ligands

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Lu; Zhang, Sheng; Qu, Xiaoni; Yang, Qi [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127 (China); Liu, Xiangyu [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127 (China); School of Chemistry and Chemical Engineering, Ningxia University, Yinchuan 750021 (China); Wei, Qing; Xie, Gang [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127 (China); Chen, Sanping, E-mail: sanpingchen@126.com [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127 (China)

    2015-11-15

    Lanthanide MOFs, [Eu(TCA)(NDC)·H{sub 2}O]{sub n} (1) and [Tb(TCA)(NDC)·H{sub 2}O]{sub n} (2), have been prepared with the mixed aromatic carboxylate ligands, namely, 4,4′,4″-tricarboxytriphenylamine (H{sub 3}TCA) and 1,4-naphthalenedicarboxylate (H{sub 2}NDC). Single-crystal X-ray diffraction analysis reveals that isomorphic 1 and 2 present pillar-layered 3D framework that Eu/Tb(III) bond with carboxylate in various coordination fashions. Optical investigation indicates that the as-prepared compounds feature characteristic luminescence emission bands of Eu/Tb ions in the visible regions at room temperature. Moreover, compound 2 shows a relatively longer luminescence lifetime (τ=0.342 ms) and significantly enhanced quantum yield (Φ{sub overall}=11%) comparing with those of 1 (τ=0.335 ms, Φ{sub overall}=0.06%). - Graphical abstract: Synoptic: Two Ln-MOFs (Ln=Eu{sup III}, Tb{sup III}) with mixed polycarboxylate ligands present different luminescent properties. - Highlights: • Two Eu/Tb-MOFs with H{sub 3}TCA and H{sub 2}NDC ligands have been obtained. • The ancillary ligand is employed to decrease water molecule coordinate numbers. • 2displays superior quantum yield and lifetime than those of 1.

  20. Divergent Label-free Cell Phenotypic Pharmacology of Ligands at the Overexpressed β2-Adrenergic Receptors

    Science.gov (United States)

    Ferrie, Ann M.; Sun, Haiyan; Zaytseva, Natalya; Fang, Ye

    2014-01-01

    We present subclone sensitive cell phenotypic pharmacology of ligands at the β2-adrenergic receptor (β2-AR) stably expressed in HEK-293 cells. The parental cell line was transfected with green fluorescent protein (GFP)-tagged β2-AR. Four stable subclones were established and used to profile a library of sixty-nine AR ligands. Dynamic mass redistribution (DMR) profiling resulted in a pharmacological activity map suggesting that HEK293 endogenously expresses functional Gi-coupled α2-AR and Gs-coupled β2-AR, and the label-free cell phenotypic activity of AR ligands are subclone dependent. Pathway deconvolution revealed that the DMR of epinephrine is originated mostly from the remodeling of actin microfilaments and adhesion complexes, to less extent from the microtubule networks and receptor trafficking, and certain agonists displayed different efficacy towards the cAMP-Epac pathway. We demonstrate that receptor signaling and ligand pharmacology is sensitive to the receptor expression level, and the organization of the receptor and its signaling circuitry.