WorldWideScience

Sample records for molecular recognition events

  1. Sudden Event Recognition: A Survey

    Directory of Open Access Journals (Sweden)

    Mohd Asyraf Zulkifley

    2013-08-01

    Full Text Available Event recognition is one of the most active research areas in video surveillance fields. Advancement in event recognition systems mainly aims to provide convenience, safety and an efficient lifestyle for humanity. A precise, accurate and robust approach is necessary to enable event recognition systems to respond to sudden changes in various uncontrolled environments, such as the case of an emergency, physical threat and a fire or bomb alert. The performance of sudden event recognition systems depends heavily on the accuracy of low level processing, like detection, recognition, tracking and machine learning algorithms. This survey aims to detect and characterize a sudden event, which is a subset of an abnormal event in several video surveillance applications. This paper discusses the following in detail: (1 the importance of a sudden event over a general anomalous event; (2 frameworks used in sudden event recognition; (3 the requirements and comparative studies of a sudden event recognition system and (4 various decision-making approaches for sudden event recognition. The advantages and drawbacks of using 3D images from multiple cameras for real-time application are also discussed. The paper concludes with suggestions for future research directions in sudden event recognition.

  2. Analogies Between Digital Radio and Chemical Orthogonality as a Method for Enhanced Analysis of Molecular Recognition Events

    Directory of Open Access Journals (Sweden)

    Sang-Hun Lee

    2008-02-01

    Full Text Available Acoustic wave biosensors are a real-time, label-free biosensor technology, which have been exploited for the detection of proteins and cells. One of the conventional biosensor approaches involves the immobilization of a monolayer of antibodies onto the surface of the acoustic wave device for the detection of a specific analyte. The method described within includes at least two immobilizations of two different antibodies onto the surfaces of two separate acoustic wave devices for the detection of several analogous analytes. The chemical specificity of the molecular recognition event is achieved by virtue of the extremely high (nM to pM binding affinity between the antibody and its antigen. In a standard ELISA (Enzyme-Linked ImmunoSorbent Assay test, there are multiple steps and the end result is a measure of what is bound so tightly that it does not wash away easily. The fact that this “gold standard” is very much not real time, masks the dance that is the molecular recognition event. X-Ray Crystallographer, Ian Wilson, demonstrated more than a decade ago that antibodies undergo conformational change during a binding event[1, 2]. Further, it is known in the arena of immunochemistry that some antibodies exhibit significant cross-reactivity and this is widely termed antibody promiscuity. A third piece of the puzzle that we will exploit in our system of acoustic wave biosensors is the notion of chemical orthogonality. These three biochemical constructs, the dance, antibody promiscuity and chemical orthogonality will be combined in this paper with the notions of Int. J. Mol. Sci. 2008, 9 155 in-phase (I and quadrature (Q signals from digital radio to manifest an approach to molecular recognition that allows a level of discrimination and analysis unobtainable without the aggregate. As an example we present experimental data on the detection of TNT, RDX, C4, ammonium nitrate and musk oil from a system of antibody-coated acoustic

  3. Radically enhanced molecular recognition

    KAUST Repository

    Trabolsi, Ali; Khashab, Niveen M.; Fahrenbach, Albert C.; Friedman, Douglas C.; Colvin, Michael T.; Coti, Karla K.; Bení tez, Diego S.; Tkatchouk, Ekaterina; Olsen, John Carl; Belowich, Matthew E.; Carmieli, Raanan; Khatib, Hussam A.; Goddard, William Andrew III; Wasielewski, Michael R.; Stoddart, Fraser Fraser Raser

    2009-01-01

    The tendency for viologen radical cations to dimerize has been harnessed to establish a recognition motif based on their ability to form extremely strong inclusion complexes with cyclobis(paraquat-p-phenylene) in its diradical dicationic redox state. This previously unreported complex involving three bipyridinium cation radicals increases the versatility of host-guest chemistry, extending its practice beyond the traditional reliance on neutral and charged guests and hosts. In particular, transporting the concept of radical dimerization into the field of mechanically interlocked molecules introduces a higher level of control within molecular switches and machines. Herein, we report that bistable and tristable [2]rotaxanes can be switched by altering electrochemical potentials. In a tristable [2]rotaxane composed of a cyclobis(paraquat-p-phenylene) ring and a dumbbell with tetrathiafulvalene, dioxynaphthalene and bipyridinium recognition sites, the position of the ring can be switched. On oxidation, it moves from the tetrathiafulvalene to the dioxynaphthalene, and on reduction, to the bipyridinium radical cation, provided the ring is also reduced simultaneously to the diradical dication. © 2010 Macmillan Publishers Limited. All rights reserved.

  4. Radically enhanced molecular recognition

    KAUST Repository

    Trabolsi, Ali

    2009-12-17

    The tendency for viologen radical cations to dimerize has been harnessed to establish a recognition motif based on their ability to form extremely strong inclusion complexes with cyclobis(paraquat-p-phenylene) in its diradical dicationic redox state. This previously unreported complex involving three bipyridinium cation radicals increases the versatility of host-guest chemistry, extending its practice beyond the traditional reliance on neutral and charged guests and hosts. In particular, transporting the concept of radical dimerization into the field of mechanically interlocked molecules introduces a higher level of control within molecular switches and machines. Herein, we report that bistable and tristable [2]rotaxanes can be switched by altering electrochemical potentials. In a tristable [2]rotaxane composed of a cyclobis(paraquat-p-phenylene) ring and a dumbbell with tetrathiafulvalene, dioxynaphthalene and bipyridinium recognition sites, the position of the ring can be switched. On oxidation, it moves from the tetrathiafulvalene to the dioxynaphthalene, and on reduction, to the bipyridinium radical cation, provided the ring is also reduced simultaneously to the diradical dication. © 2010 Macmillan Publishers Limited. All rights reserved.

  5. Hierarchical Context Modeling for Video Event Recognition.

    Science.gov (United States)

    Wang, Xiaoyang; Ji, Qiang

    2016-10-11

    Current video event recognition research remains largely target-centered. For real-world surveillance videos, targetcentered event recognition faces great challenges due to large intra-class target variation, limited image resolution, and poor detection and tracking results. To mitigate these challenges, we introduced a context-augmented video event recognition approach. Specifically, we explicitly capture different types of contexts from three levels including image level, semantic level, and prior level. At the image level, we introduce two types of contextual features including the appearance context features and interaction context features to capture the appearance of context objects and their interactions with the target objects. At the semantic level, we propose a deep model based on deep Boltzmann machine to learn event object representations and their interactions. At the prior level, we utilize two types of prior-level contexts including scene priming and dynamic cueing. Finally, we introduce a hierarchical context model that systematically integrates the contextual information at different levels. Through the hierarchical context model, contexts at different levels jointly contribute to the event recognition. We evaluate the hierarchical context model for event recognition on benchmark surveillance video datasets. Results show that incorporating contexts in each level can improve event recognition performance, and jointly integrating three levels of contexts through our hierarchical model achieves the best performance.

  6. Synergy of Two Highly Specific Biomolecular Recognition Events

    DEFF Research Database (Denmark)

    Ejlersen, Maria; Christensen, Niels Johan; Sørensen, Kasper K

    2018-01-01

    Two highly specific biomolecular recognition events, nucleic acid duplex hybridization and DNA-peptide recognition in the minor groove, were coalesced in a miniature ensemble for the first time by covalently attaching a natural AT-hook peptide motif to nucleic acid duplexes via a 2'-amino......-LNA scaffold. A combination of molecular dynamics simulations and ultraviolet thermal denaturation studies revealed high sequence-specific affinity of the peptide-oligonucleotide conjugates (POCs) when binding to complementary DNA strands, leveraging the bioinformation encrypted in the minor groove of DNA...

  7. Molecular Recognition in the Colloidal World.

    Science.gov (United States)

    Elacqua, Elizabeth; Zheng, Xiaolong; Shillingford, Cicely; Liu, Mingzhu; Weck, Marcus

    2017-11-21

    Colloidal self-assembly is a bottom-up technique to fabricate functional nanomaterials, with paramount interest stemming from programmable assembly of smaller building blocks into dynamic crystalline domains and photonic materials. Multiple established colloidal platforms feature diverse shapes and bonding interactions, while achieving specific orientations along with short- and long-range order. A major impediment to their universal use as building blocks for predesigned architectures is the inability to precisely dictate and control particle functionalization and concomitant reversible self-assembly. Progress in colloidal self-assembly necessitates the development of strategies that endow bonding specificity and directionality within assemblies. Methodologies that emulate molecular and polymeric three-dimensional (3D) architectures feature elements of covalent bonding, while high-fidelity molecular recognition events have been installed to realize responsive reconfigurable assemblies. The emergence of anisotropic 'colloidal molecules', coupled with the ability to site-specifically decorate particle surfaces with supramolecular recognition motifs, has facilitated the formation of superstructures via directional interactions and shape recognition. In this Account, we describe supramolecular assembly routes to drive colloidal particles into precisely assembled architectures or crystalline lattices via directional noncovalent molecular interactions. The design principles are based upon the fabrication of colloidal particles bearing surface-exposed functional groups that can undergo programmable conjugation to install recognition motifs with high fidelity. Modular and versatile by design, our strategy allows for the introduction and integration of molecular recognition principles into the colloidal world. We define noncovalent molecular interactions as site-specific forces that are predictable (i.e., feature selective and controllable complementary bonding partners

  8. Molecular Mechanisms of Odor Recognition

    National Research Council Canada - National Science Library

    Anholt, Robert

    2000-01-01

    .... We characterized the transduction pathway for the recognition of pheromones in the vomeronasal organ and also characterized subpopulations of olfactory neurons expressing different axonal G proteins...

  9. Molecular recognition by gold, silver and copper nanoparticles

    Science.gov (United States)

    Tauran, Yannick; Brioude, Arnaud; Coleman, Anthony W; Rhimi, Moez; Kim, Beonjoom

    2013-01-01

    The intrinsic physical properties of the noble metal nanoparticles, which are highly sensitive to the nature of their local molecular environment, make such systems ideal for the detection of molecular recognition events. The current review describes the state of the art concerning molecular recognition of Noble metal nanoparticles. In the first part the preparation of such nanoparticles is discussed along with methods of capping and stabilization. A brief discussion of the three common methods of functionalization: Electrostatic adsorption; Chemisorption; Affinity-based coordination is given. In the second section a discussion of the optical and electrical properties of nanoparticles is given to aid the reader in understanding the use of such properties in molecular recognition. In the main section the various types of capping agents for molecular recognition; nucleic acid coatings, protein coatings and molecules from the family of supramolecular chemistry are described along with their numerous applications. Emphasis for the nucleic acids is on complementary oligonucleotide and aptamer recognition. For the proteins the recognition properties of antibodies form the core of the section. With respect to the supramolecular systems the cyclodextrins, calix[n]arenes, dendrimers, crown ethers and the cucurbitales are treated in depth. Finally a short section deals with the possible toxicity of the nanoparticles, a concern in public health. PMID:23977421

  10. Pattern recognition in molecular dynamics. [FORTRAN

    Energy Technology Data Exchange (ETDEWEB)

    Zurek, W H; Schieve, W C [Texas Univ., Austin (USA)

    1977-07-01

    An algorithm for the recognition of the formation of bound molecular states in the computer simulation of a dilute gas is presented. Applications to various related problems in physics and chemistry are pointed out. Data structure and decision processes are described. Performance of the FORTRAN program based on the algorithm in cooperation with the molecular dynamics program is described and the results are presented.

  11. Object and event recognition for stroke rehabilitation

    Science.gov (United States)

    Ghali, Ahmed; Cunningham, Andrew S.; Pridmore, Tony P.

    2003-06-01

    Stroke is a major cause of disability and health care expenditure around the world. Existing stroke rehabilitation methods can be effective but are costly and need to be improved. Even modest improvements in the effectiveness of rehabilitation techniques could produce large benefits in terms of quality of life. The work reported here is part of an ongoing effort to integrate virtual reality and machine vision technologies to produce innovative stroke rehabilitation methods. We describe a combined object recognition and event detection system that provides real time feedback to stroke patients performing everyday kitchen tasks necessary for independent living, e.g. making a cup of coffee. The image plane position of each object, including the patient"s hand, is monitored using histogram-based recognition methods. The relative positions of hand and objects are then reported to a task monitor that compares the patient"s actions against a model of the target task. A prototype system has been constructed and is currently undergoing technical and clinical evaluation.

  12. Soluble Molecularly Imprinted Nanorods for Homogeneous Molecular Recognition

    Directory of Open Access Journals (Sweden)

    Rongning Liang

    2018-03-01

    Full Text Available Nowadays, it is still difficult for molecularly imprinted polymers (MIPs to achieve homogeneous recognition since they cannot be easily dissolved in organic or aqueous phase. To address this issue, soluble molecularly imprinted nanorods have been synthesized by using soluble polyaniline doped with a functionalized organic protonic acid as the polymer matrix. By employing 1-naphthoic acid as a model, the proposed imprinted nanorods exhibit an excellent solubility and good homogeneous recognition ability. The imprinting factor for the soluble imprinted nanoroads is 6.8. The equilibrium dissociation constant and the apparent maximum number of the proposed imprinted nanorods are 248.5 μM and 22.1 μmol/g, respectively. We believe that such imprinted nanorods may provide an appealing substitute for natural receptors in homogeneous recognition related fields.

  13. Soluble Molecularly Imprinted Nanorods for Homogeneous Molecular Recognition

    Science.gov (United States)

    Liang, Rongning; Wang, Tiantian; Zhang, Huan; Yao, Ruiqing; Qin, Wei

    2018-03-01

    Nowadays, it is still difficult for molecularly imprinted polymer (MIPs) to achieve homogeneous recognition since they cannot be easily dissolved in organic or aqueous phase. To address this issue, soluble molecularly imprinted nanorods have been synthesized by using soluble polyaniline doped with a functionalized organic protonic acid as the polymer matrix. By employing 1-naphthoic acid as a model, the proposed imprinted nanorods exhibit an excellent solubility and good homogeneous recognition ability. The imprinting factor for the soluble imprinted nanoroads is 6.8. The equilibrium dissociation constant and the apparent maximum number of the proposed imprinted nanorods are 248.5 μM and 22.1 μmol/g, respectively. We believe that such imprinted nanorods may provide an appealing substitute for natural receptors in homogeneous recognition related fields.

  14. Human-assisted sound event recognition for home service robots.

    Science.gov (United States)

    Do, Ha Manh; Sheng, Weihua; Liu, Meiqin

    This paper proposes and implements an open framework of active auditory learning for a home service robot to serve the elderly living alone at home. The framework was developed to realize the various auditory perception capabilities while enabling a remote human operator to involve in the sound event recognition process for elderly care. The home service robot is able to estimate the sound source position and collaborate with the human operator in sound event recognition while protecting the privacy of the elderly. Our experimental results validated the proposed framework and evaluated auditory perception capabilities and human-robot collaboration in sound event recognition.

  15. Entropy in molecular recognition by proteins.

    Science.gov (United States)

    Caro, José A; Harpole, Kyle W; Kasinath, Vignesh; Lim, Jackwee; Granja, Jeffrey; Valentine, Kathleen G; Sharp, Kim A; Wand, A Joshua

    2017-06-20

    Molecular recognition by proteins is fundamental to molecular biology. Dissection of the thermodynamic energy terms governing protein-ligand interactions has proven difficult, with determination of entropic contributions being particularly elusive. NMR relaxation measurements have suggested that changes in protein conformational entropy can be quantitatively obtained through a dynamical proxy, but the generality of this relationship has not been shown. Twenty-eight protein-ligand complexes are used to show a quantitative relationship between measures of fast side-chain motion and the underlying conformational entropy. We find that the contribution of conformational entropy can range from favorable to unfavorable, which demonstrates the potential of this thermodynamic variable to modulate protein-ligand interactions. For about one-quarter of these complexes, the absence of conformational entropy would render the resulting affinity biologically meaningless. The dynamical proxy for conformational entropy or "entropy meter" also allows for refinement of the contributions of solvent entropy and the loss in rotational-translational entropy accompanying formation of high-affinity complexes. Furthermore, structure-based application of the approach can also provide insight into long-lived specific water-protein interactions that escape the generic treatments of solvent entropy based simply on changes in accessible surface area. These results provide a comprehensive and unified view of the general role of entropy in high-affinity molecular recognition by proteins.

  16. Molecular Recognition Units: Design and diagnostic applications

    International Nuclear Information System (INIS)

    Alvarez, V.L.; Radcliffe, R.D.; Coughlin, D.J.; Lopes, A.D.; Rodwell, J.D.

    1992-01-01

    Molecular Recognition Units (MRUs), small peptides derived from complementarity-determining region (CDR) of IgM antibodies, can mimic the recognition site found in the antibody. One example of an MRU fusion peptide designed to image thrombi was derived from PAC 1.1, an IgM monoclonal antibody specific for the GPIIb/IIa receptor on platelets. The peptide sequence from the third CDR of the heavy chain was engineered for optimal binding activity and synthesized with a metal-binding peptide sequence. After labeling with 99m-Tc, the peptides were injected into either animal models of experimentally induced thrombi in order to determine their effectiveness in imaging model thrombi. Data are presented which demonstrate enhanced binding with open-quotes tandem repeatsclose quotes of the MRU domain and no loss of activity after incorporation of the metal-binding domain. These studies have led to a clinical candidate consisting of 17 amino acids. Extension of this concept to other MRUs and fusion peptides is also discussed

  17. Event Recognition Based on Deep Learning in Chinese Texts.

    Directory of Open Access Journals (Sweden)

    Yajun Zhang

    Full Text Available Event recognition is the most fundamental and critical task in event-based natural language processing systems. Existing event recognition methods based on rules and shallow neural networks have certain limitations. For example, extracting features using methods based on rules is difficult; methods based on shallow neural networks converge too quickly to a local minimum, resulting in low recognition precision. To address these problems, we propose the Chinese emergency event recognition model based on deep learning (CEERM. Firstly, we use a word segmentation system to segment sentences. According to event elements labeled in the CEC 2.0 corpus, we classify words into five categories: trigger words, participants, objects, time and location. Each word is vectorized according to the following six feature layers: part of speech, dependency grammar, length, location, distance between trigger word and core word and trigger word frequency. We obtain deep semantic features of words by training a feature vector set using a deep belief network (DBN, then analyze those features in order to identify trigger words by means of a back propagation neural network. Extensive testing shows that the CEERM achieves excellent recognition performance, with a maximum F-measure value of 85.17%. Moreover, we propose the dynamic-supervised DBN, which adds supervised fine-tuning to a restricted Boltzmann machine layer by monitoring its training performance. Test analysis reveals that the new DBN improves recognition performance and effectively controls the training time. Although the F-measure increases to 88.11%, the training time increases by only 25.35%.

  18. Event Recognition Based on Deep Learning in Chinese Texts.

    Science.gov (United States)

    Zhang, Yajun; Liu, Zongtian; Zhou, Wen

    2016-01-01

    Event recognition is the most fundamental and critical task in event-based natural language processing systems. Existing event recognition methods based on rules and shallow neural networks have certain limitations. For example, extracting features using methods based on rules is difficult; methods based on shallow neural networks converge too quickly to a local minimum, resulting in low recognition precision. To address these problems, we propose the Chinese emergency event recognition model based on deep learning (CEERM). Firstly, we use a word segmentation system to segment sentences. According to event elements labeled in the CEC 2.0 corpus, we classify words into five categories: trigger words, participants, objects, time and location. Each word is vectorized according to the following six feature layers: part of speech, dependency grammar, length, location, distance between trigger word and core word and trigger word frequency. We obtain deep semantic features of words by training a feature vector set using a deep belief network (DBN), then analyze those features in order to identify trigger words by means of a back propagation neural network. Extensive testing shows that the CEERM achieves excellent recognition performance, with a maximum F-measure value of 85.17%. Moreover, we propose the dynamic-supervised DBN, which adds supervised fine-tuning to a restricted Boltzmann machine layer by monitoring its training performance. Test analysis reveals that the new DBN improves recognition performance and effectively controls the training time. Although the F-measure increases to 88.11%, the training time increases by only 25.35%.

  19. Specific Electrostatic Molecular Recognition in Water

    DEFF Research Database (Denmark)

    Li, Ming; Hoeck, Casper; Schoffelen, Sanne

    2016-01-01

    The identification of pairs of small peptides that recognize each other in water exclusively through electrostatic interactions is reported. The target peptide and a structure-biased combinatorial ligand library consisting of ≈78 125 compounds were synthesized on different sized beads. Peptide......-bead binding assay and by 2D NMR spectroscopy. Molecular dynamics (MD) studies revealed a putative mode of interaction for this unusual electrostatic binding event. High binding specificity occurred through a combination of topological matching and electrostatic and hydrogen-bond complementarities. From MD...

  20. Molecular recognition on a cavitand-functionalized silicon surface.

    Science.gov (United States)

    Biavardi, Elisa; Favazza, Maria; Motta, Alessandro; Fragalà, Ignazio L; Massera, Chiara; Prodi, Luca; Montalti, Marco; Melegari, Monica; Condorelli, Guglielmo G; Dalcanale, Enrico

    2009-06-03

    A Si(100) surface featuring molecular recognition properties was obtained by covalent functionalization with a tetraphosphonate cavitand (Tiiii), able to complex positively charged species. Tiiii cavitand was grafted onto the Si by photochemical hydrosilylation together with 1-octene as a spatial spectator. The recognition properties of the Si-Tiiii surface were demonstrated through two independent analytical techniques, namely XPS and fluorescence spectroscopy, during the course of reversible complexation-guest exchange-decomplexation cycles with specifically designed ammonium and pyridinium salts. Control experiments employing a Si(100) surface functionalized with a structurally similar, but complexation inactive, tetrathiophosphonate cavitand (TSiiii) demonstrated no recognition events. This provides evidence for the complexation properties of the Si-Tiiii surface, ruling out the possibility of nonspecific interactions between the substrate and the guests. The residual Si-O(-) terminations on the surface replace the guests' original counterions, thus stabilizing the complex ion pairs. These results represent a further step toward the control of self-assembly of complex supramolecular architectures on surfaces.

  1. DNAzyme Feedback Amplification: Relaying Molecular Recognition to Exponential DNA Amplification.

    Science.gov (United States)

    Liu, Meng; Yin, Qingxin; McConnell, Erin M; Chang, Yangyang; Brennan, John D; Li, Yingfu

    2018-03-26

    Technologies capable of linking DNA amplification to molecular recognition are very desirable for ultrasensitive biosensing applications. We have developed a simple but powerful isothermal DNA amplification method, termed DNAzyme feedback amplification (DFA), that is capable of relaying molecular recognition to exponential DNA amplification. The method incorporates both an RNA-cleaving DNAzyme (RCD) and rolling circle amplification (RCA) carried out by a special DNA polymerase using a circular DNA template. DFA begins with a stimulus-dependent RCA reaction, producing tandemly linked RCDs in long-chain DNA products. These RCDs cleave an RNA-containing DNA sequence to form additional primers that hybridize to the circular DNA molecule, giving rise to DNA assemblies that act as the new inputs for RCA. The RCA reaction and the cleavage event keep on feeding each other autonomously, resulting in exponential growth of repetitive DNA sequences that can be easily detected. This method can be used for the detection of both nucleic acid based targets and non-nucleic acid analytes. In this article, we discuss the conceptual framework of the feedback amplification approach, the essential features of this method as well as remaining challenges and possible solutions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Molecular Recognition: Detection of Colorless Compounds Based on Color Change

    Science.gov (United States)

    Khalafi, Lida; Kashani, Samira; Karimi, Javad

    2016-01-01

    A laboratory experiment is described in which students measure the amount of cetirizine in allergy-treatment tablets based on molecular recognition. The basis of recognition is competition of cetirizine with phenolphthalein to form an inclusion complex with ß-cyclodextrin. Phenolphthalein is pinkish under basic condition, whereas it's complex form…

  3. Signatures of molecular recognition from the topography of ...

    Indian Academy of Sciences (India)

    Administrator

    cules through non-covalent bonding such as hydro- gen bonding ... tion exhibit complementarity of certain properties ... of molecular recognition has been given in terms of .... VA and VB correspond to the monomer MESP in the composite.

  4. Molecular Recognition Involving Anthraquinone Derivatives and Molecular Clips

    Science.gov (United States)

    Alaparthi, Madhubabu

    In the past, we have demonstrated that 1,8-anthraquinone-18-crown-5 (1) and its heterocyclic derivatives act as luminescent hosts for a variety of cations of environmental and clinical concern. We report here a series of heteroatom-substituted macrocycles containing an anthraquinone moiety as a fluorescent signaling unit and a cyclic polyheteroether chain as the receptor. Sulfur, selenium, and tellurium derivatives of 1,8-anthraquinone-18-crown-5 (1) were synthesized by reacting sodium sulfide (Na2S), sodium selenide (Na2Se) and sodium telluride (Na2Te) with 1,8-bis(2-bromoethylethyleneoxy)anthracene - 9,10-dione in a 1:1 ratio (2,3, and 6). These sensors bind metal ions in a 1:1 ratio (7 and 8), and the optical properties of the new complexes were examined and the sulfur and selenium analogues show that selectivity for Pb(II) is markedly improved as compared to the oxygen analogue 1 which was competitive for Ca(II) ion. Selective reduction of 1 yields secondary alcohols where either one or both of the anthraquinone carbonyl groups has been reduced ( 15 and 9). A new mechanism for the fluorescence detection of metal cations in solution is introduced involving a unique keto-enol tautomerization. Reduction of 1 yields the doubly reduced secondary alcohol, 9. 9 acts as a chemodosimeter for Al(III) ion producing a strong blue emission due to the formation of the anthracene fluorophore, 10, via dehydration of the internal secondary alcohol in DMSO/aqueous solution. The enol form is not the most thermodynamically stable form under these conditions however, and slowly converts to the keto form 11.. Currently we are focusing on cucurbituril derivatives, also described as molecular clips due to their folded geometry used as molecular recognition hosts. We first investigated the synthesis and characterization of aromatic methoxy/catechol terminated cucurbituril units that act as hosts for small solvent molecules, such as CH2Cl2, CH3CN, DMF, and MeOH, through dual pi...H-C T

  5. Track-based event recognition in a realistic crowded environment

    Science.gov (United States)

    van Huis, Jasper R.; Bouma, Henri; Baan, Jan; Burghouts, Gertjan J.; Eendebak, Pieter T.; den Hollander, Richard J. M.; Dijk, Judith; van Rest, Jeroen H.

    2014-10-01

    Automatic detection of abnormal behavior in CCTV cameras is important to improve the security in crowded environments, such as shopping malls, airports and railway stations. This behavior can be characterized at different time scales, e.g., by small-scale subtle and obvious actions or by large-scale walking patterns and interactions between people. For example, pickpocketing can be recognized by the actual snatch (small scale), when he follows the victim, or when he interacts with an accomplice before and after the incident (longer time scale). This paper focusses on event recognition by detecting large-scale track-based patterns. Our event recognition method consists of several steps: pedestrian detection, object tracking, track-based feature computation and rule-based event classification. In the experiment, we focused on single track actions (walk, run, loiter, stop, turn) and track interactions (pass, meet, merge, split). The experiment includes a controlled setup, where 10 actors perform these actions. The method is also applied to all tracks that are generated in a crowded shopping mall in a selected time frame. The results show that most of the actions can be detected reliably (on average 90%) at a low false positive rate (1.1%), and that the interactions obtain lower detection rates (70% at 0.3% FP). This method may become one of the components that assists operators to find threatening behavior and enrich the selection of videos that are to be observed.

  6. Spatial pattern recognition of seismic events in South West Colombia

    Science.gov (United States)

    Benítez, Hernán D.; Flórez, Juan F.; Duque, Diana P.; Benavides, Alberto; Lucía Baquero, Olga; Quintero, Jiber

    2013-09-01

    Recognition of seismogenic zones in geographical regions supports seismic hazard studies. This recognition is usually based on visual, qualitative and subjective analysis of data. Spatial pattern recognition provides a well founded means to obtain relevant information from large amounts of data. The purpose of this work is to identify and classify spatial patterns in instrumental data of the South West Colombian seismic database. In this research, clustering tendency analysis validates whether seismic database possesses a clustering structure. A non-supervised fuzzy clustering algorithm creates groups of seismic events. Given the sensitivity of fuzzy clustering algorithms to centroid initial positions, we proposed a methodology to initialize centroids that generates stable partitions with respect to centroid initialization. As a result of this work, a public software tool provides the user with the routines developed for clustering methodology. The analysis of the seismogenic zones obtained reveals meaningful spatial patterns in South-West Colombia. The clustering analysis provides a quantitative location and dispersion of seismogenic zones that facilitates seismological interpretations of seismic activities in South West Colombia.

  7. A computer aided treatment event recognition system in radiation therapy

    International Nuclear Information System (INIS)

    Xia, Junyi; Mart, Christopher; Bayouth, John

    2014-01-01

    Purpose: To develop an automated system to safeguard radiation therapy treatments by analyzing electronic treatment records and reporting treatment events. Methods: CATERS (Computer Aided Treatment Event Recognition System) was developed to detect treatment events by retrieving and analyzing electronic treatment records. CATERS is designed to make the treatment monitoring process more efficient by automating the search of the electronic record for possible deviations from physician's intention, such as logical inconsistencies as well as aberrant treatment parameters (e.g., beam energy, dose, table position, prescription change, treatment overrides, etc). Over a 5 month period (July 2012–November 2012), physicists were assisted by the CATERS software in conducting normal weekly chart checks with the aims of (a) determining the relative frequency of particular events in the authors’ clinic and (b) incorporating these checks into the CATERS. During this study period, 491 patients were treated at the University of Iowa Hospitals and Clinics for a total of 7692 fractions. Results: All treatment records from the 5 month analysis period were evaluated using all the checks incorporated into CATERS after the training period. About 553 events were detected as being exceptions, although none of them had significant dosimetric impact on patient treatments. These events included every known event type that was discovered during the trial period. A frequency analysis of the events showed that the top three types of detected events were couch position override (3.2%), extra cone beam imaging (1.85%), and significant couch position deviation (1.31%). The significant couch deviation is defined as the number of treatments where couch vertical exceeded two times standard deviation of all couch verticals, or couch lateral/longitudinal exceeded three times standard deviation of all couch laterals and longitudinals. On average, the application takes about 1 s per patient when

  8. A computer aided treatment event recognition system in radiation therapy

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Junyi, E-mail: junyi-xia@uiowa.edu; Mart, Christopher [Department of Radiation Oncology, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, Iowa 52242 (United States); Bayouth, John [Department of Radiation Oncology, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, Iowa 52242 and Department of Human Oncology, University of Wisconsin - Madison, 600 Highland Avenue, K4/B55, Madison, Wisconsin 53792-0600 (United States)

    2014-01-15

    Purpose: To develop an automated system to safeguard radiation therapy treatments by analyzing electronic treatment records and reporting treatment events. Methods: CATERS (Computer Aided Treatment Event Recognition System) was developed to detect treatment events by retrieving and analyzing electronic treatment records. CATERS is designed to make the treatment monitoring process more efficient by automating the search of the electronic record for possible deviations from physician's intention, such as logical inconsistencies as well as aberrant treatment parameters (e.g., beam energy, dose, table position, prescription change, treatment overrides, etc). Over a 5 month period (July 2012–November 2012), physicists were assisted by the CATERS software in conducting normal weekly chart checks with the aims of (a) determining the relative frequency of particular events in the authors’ clinic and (b) incorporating these checks into the CATERS. During this study period, 491 patients were treated at the University of Iowa Hospitals and Clinics for a total of 7692 fractions. Results: All treatment records from the 5 month analysis period were evaluated using all the checks incorporated into CATERS after the training period. About 553 events were detected as being exceptions, although none of them had significant dosimetric impact on patient treatments. These events included every known event type that was discovered during the trial period. A frequency analysis of the events showed that the top three types of detected events were couch position override (3.2%), extra cone beam imaging (1.85%), and significant couch position deviation (1.31%). The significant couch deviation is defined as the number of treatments where couch vertical exceeded two times standard deviation of all couch verticals, or couch lateral/longitudinal exceeded three times standard deviation of all couch laterals and longitudinals. On average, the application takes about 1 s per patient when

  9. Creating molecular macrocycles for anion recognition

    Directory of Open Access Journals (Sweden)

    Amar H. Flood

    2016-03-01

    Full Text Available The creation and functionality of new classes of macrocycles that are shape persistent and can bind anions is described. The genesis of triazolophane macrocycles emerges out of activity surrounding 1,2,3-triazoles made using click chemistry; and the same triazoles are responsible for anion capture. Mistakes made and lessons learnt in anion recognition provide deeper understanding that, together with theory, now provides for computer-aided receptor design. The lessons are acted upon in the creation of two new macrocycles. First, cyanostars are larger and like to capture large anions. Second is tricarb, which also favors large anions but shows a propensity to self-assemble in an orderly and stable manner, laying a foundation for future designs of hierarchical nanostructures.

  10. Molecular recognition in protein modification with rhodium metallopeptides

    Science.gov (United States)

    Ball, Zachary T.

    2015-01-01

    Chemical manipulation of natural, unengineered proteins is a daunting challenge which tests the limits of reaction design. By combining transition-metal or other catalysts with molecular recognition ideas, it is possible to achieve site-selective protein reactivity without the need for engineered recognition sequences or reactive sites. Some recent examples in this area have used ruthenium photocatalysis, pyridine organocatalysis, and rhodium(II) metallocarbene catalysis, indicating that the fundamental ideas provide opportunities for using diverse reactivity on complex protein substrates and in complex cell-like environments. PMID:25588960

  11. Control of Target Molecular Recognition in a Small Pore Space with Biomolecule-Recognition Gating Membrane.

    Science.gov (United States)

    Okuyama, Hiroto; Oshiba, Yuhei; Ohashi, Hidenori; Yamaguchi, Takeo

    2018-05-01

    A biomolecule-recognition gating membrane, which introduces thermosensitive graft polymer including molecular recognition receptor into porous membrane substrate, can close its pores by recognizing target biomolecule. The present study reports strategies for improving both versatility and sensitivity of the gating membrane. First, the membrane is fabricated by introducing the receptor via a selectively reactive click reaction improving the versatility. Second, the sensitivity of the membrane is enhanced via an active delivering method of the target molecules into the pores. In the method, the tiny signal of the target biomolecule is amplified as obvious pressure change. Furthermore, this offers 15 times higher sensitivity compared to the previously reported passive delivering method (membrane immersion to sample solution) with significantly shorter recognition time. The improvement will aid in applying the gating membrane to membrane sensors in medical fields. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Programmable molecular recognition based on the geometry of DNA nanostructures.

    Science.gov (United States)

    Woo, Sungwook; Rothemund, Paul W K

    2011-07-10

    From ligand-receptor binding to DNA hybridization, molecular recognition plays a central role in biology. Over the past several decades, chemists have successfully reproduced the exquisite specificity of biomolecular interactions. However, engineering multiple specific interactions in synthetic systems remains difficult. DNA retains its position as the best medium with which to create orthogonal, isoenergetic interactions, based on the complementarity of Watson-Crick binding. Here we show that DNA can be used to create diverse bonds using an entirely different principle: the geometric arrangement of blunt-end stacking interactions. We show that both binary codes and shape complementarity can serve as a basis for such stacking bonds, and explore their specificity, thermodynamics and binding rules. Orthogonal stacking bonds were used to connect five distinct DNA origami. This work, which demonstrates how a single attractive interaction can be developed to create diverse bonds, may guide strategies for molecular recognition in systems beyond DNA nanostructures.

  13. Fluorescent and Colorimetric Molecular Recognition Probe for Hydrogen Bond Acceptors

    OpenAIRE

    Pike, Sarah Jane; Hunter, Christopher Alexander

    2018-01-01

    The association constants for formation of 1 : 1 complexes between a H-bond donor, 1-naphthol, and a diverse range of charged and neutral H-bond acceptors have been measured using UV/vis absorption and fluorescence emission titrations. The performance of 1-naphthol as a dual colorimetric and fluorescent molecular recognition probe for determining the H-bond acceptor (HBA) parameters of charged and neutral solutes has been investigated in three solvents. The data were employed to establish sel...

  14. Preparation and Property Recognition of Nimodipine Molecularly Imprinted Polymer

    Directory of Open Access Journals (Sweden)

    Fei-fei CHEN

    2015-09-01

    Full Text Available Objective: To explore the application of molecular imprinting technique in the separation and detection of nimodipine. Methods: Methacrylic acid as functional monomer, pentaerythritol triacrylate as cross-linking agent were used to prepare molecularly imprinted polymer (MIP with the feature of specific recognition performance on imprinting molecule nimodipine under condition of template molecule nimodipine. The preparation conditions, recognition performance of MIP on nimodipine, different proportions of template molecule and functional monomer, the selectivity to other substrate, and the relationship between adsorption quantity (Q and time were observed. Results: MIP was prepared successfully bynimodipine as template and pentaerythritol triacrylate as cross-linking agent, with the feature of specific recognition performance on nimodipine. The static adsorption distribution coefficient (KD was 0.2264. The equation of Q and the concentration of substrate of template MIP was y = -0.21x+0.2204. Combining capacity of template molecule at the same concentration enhanced with the increasing proportion of functional monomer.Conclusion: Nimodipine MIP based on molecular imprinting technique may become a new approach to chiral separation for nimodipine.

  15. Some algorithms of the events recognition in the Tagged Neutrino Facility

    International Nuclear Information System (INIS)

    Mukhin, S.A.

    1993-01-01

    Some algorithms of the events recognition in Tagged Neutrino Facility are described: the event localization in Bars neutrino detector, the off-line trigger, the reconstruction of events vertex, events reconstruction in Tagging Station. The programming package for realization of clusterization methods that have been used for mentioned algorithms realization is presented. 6 refs., 2 tabs

  16. Molecular imprinting at walls of silica nanotubes for TNT recognition.

    Science.gov (United States)

    Xie, Chenggen; Liu, Bianhua; Wang, Zhenyang; Gao, Daming; Guan, Guijian; Zhang, Zhongping

    2008-01-15

    This paper reports the molecular imprinting at the walls of highly uniform silica nanotubes for the recognition of 2,4,6-trinitrotoluene (TNT). It has been demonstrated that TNT templates were efficiently imprinted into the matrix of silica through the strong acid-base pairing interaction between TNT and 3-aminopropyltriethoxysilane (APTS). TNT-imprinted silica nanotubes were synthesized by the gelation reaction between APTS and tetraethylorthosilicate (TEOS), selectively occurring at the porous walls of APTS-modified alumina membranes. The removal of the original TNT templates leaves the imprinted cavities with covalently anchored amine groups at the cavity walls. A high density of recognition sites with molecular selectivity to the TNT analyte was created at the wall of silica nanotubes. Furthermore, most of these recognition sites are situated at the inside and outside surfaces of tubular walls and in the proximity of the two surfaces due to the ultrathin wall thickness of only 15 nm, providing a better site accessibility and lower mass-transfer resistance. Therefore, greater capacity and faster kinetics of uptaking target species were achieved. The silica nanotube reported herein is an ideal form of material for imprinting various organic or biological molecules toward applications in chemical/biological sensors and bioassay.

  17. Magnetic molecularly imprinted polymer for aspirin recognition and controlled release

    Energy Technology Data Exchange (ETDEWEB)

    Kan Xianwen; Geng Zhirong; Zhao Yao; Wang Zhilin; Zhu Junjie [State Key Laboratory of Coordination Chemistry, MOE Key Lab of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 22 Hankou Road, Nanjing 210093 (China)], E-mail: wangzl@nju.edu.cn, E-mail: jjzhu@nju.edu.cn

    2009-04-22

    Core-shell structural magnetic molecularly imprinted polymers (magnetic MIPs) with combined properties of molecular recognition and controlled release were prepared and characterized. Magnetic MIPs were synthesized by the co-polymerization of methacrylic acid (MAA) and trimethylolpropane trimethacrylate (TRIM) around aspirin (ASP) at the surface of double-bond-functionalized Fe{sub 3}O{sub 4} nanoparticles in chloroform. The obtained spherical magnetic MIPs with diameters of about 500 nm had obvious superparamagnetism and could be separated quickly by an external magnetic field. Binding experiments were carried out to evaluate the properties of magnetic MIPs and magnetic non-molecularly imprinted polymers (magnetic NIPs). The results demonstrated that the magnetic MIPs had high adsorption capacity and selectivity to ASP. Moreover, release profiles and release rate of ASP from the ASP-loaded magnetic MIPs indicated that the magnetic MIPs also had potential applications in drug controlled release.

  18. Magnetic molecularly imprinted polymer for aspirin recognition and controlled release

    International Nuclear Information System (INIS)

    Kan Xianwen; Geng Zhirong; Zhao Yao; Wang Zhilin; Zhu Junjie

    2009-01-01

    Core-shell structural magnetic molecularly imprinted polymers (magnetic MIPs) with combined properties of molecular recognition and controlled release were prepared and characterized. Magnetic MIPs were synthesized by the co-polymerization of methacrylic acid (MAA) and trimethylolpropane trimethacrylate (TRIM) around aspirin (ASP) at the surface of double-bond-functionalized Fe 3 O 4 nanoparticles in chloroform. The obtained spherical magnetic MIPs with diameters of about 500 nm had obvious superparamagnetism and could be separated quickly by an external magnetic field. Binding experiments were carried out to evaluate the properties of magnetic MIPs and magnetic non-molecularly imprinted polymers (magnetic NIPs). The results demonstrated that the magnetic MIPs had high adsorption capacity and selectivity to ASP. Moreover, release profiles and release rate of ASP from the ASP-loaded magnetic MIPs indicated that the magnetic MIPs also had potential applications in drug controlled release.

  19. High-Level Event Recognition in Unconstrained Videos

    Science.gov (United States)

    2013-01-01

    frames per- forms well for urban soundscapes but not for polyphonic music. In place of GMM, Lu et al. [78] adopted spectral clustering to generate...Aucouturier JJ, Defreville B, Pachet F (2007) The bag-of-frames approach to audio pattern recognition: a sufficientmodel for urban soundscapes but not

  20. Fluorescent and colorimetric molecular recognition probe for hydrogen bond acceptors.

    Science.gov (United States)

    Pike, Sarah J; Hunter, Christopher A

    2017-11-22

    The association constants for formation of 1 : 1 complexes between a H-bond donor, 1-naphthol, and a diverse range of charged and neutral H-bond acceptors have been measured using UV/vis absorption and fluorescence emission titrations. The performance of 1-naphthol as a dual colorimetric and fluorescent molecular recognition probe for determining the H-bond acceptor (HBA) parameters of charged and neutral solutes has been investigated in three solvents. The data were employed to establish self-consistent H-bond acceptor parameters (β) for benzoate, azide, chloride, thiocyanate anions, a series of phosphine oxides, phosphate ester, sulfoxide and a tertiary amide. The results demonstrate both the transferability of H-bond parameters between different solvents and the utility of the naphthol-based dual molecular recognition probe to exploit orthogonal spectroscopic techniques to determine the HBA properties of neutral and charged solutes. The benzoate anion is the strongest HBA studied with a β parameter of 15.4, and the neutral tertiary amide is the weakest H-bond acceptor investigated with a β parameter of 8.5. The H-bond acceptor strength of the azide anion is higher than that of chloride (12.8 and 12.2 respectively), and the thiocyanate anion has a β value of 10.8 and thus is a significantly weaker H-bond acceptor than both the azide and chloride anions.

  1. Does Sport Event Involvement Influence Brand Recognition of Official Sponsors and Ambush Marketers?

    Directory of Open Access Journals (Sweden)

    Piątkowska Monika

    2016-12-01

    Full Text Available The main aim of the study is to verify how event involvement in the UEFA Euro 2012 influenced the recognition of both sponsors’ and ambushers’ brands. Computer-Assisted Personal Interviews were conducted on a representative sample of the Polish society (N = 1,000. On the basis of five groups of consumers regarding involvement in the event, authors examined brand recognition, using Top of Mind Awareness (TOMA tests of official sponsors and ambushers.

  2. Molecular recognition in complexes of TRF proteins with telomeric DNA.

    Directory of Open Access Journals (Sweden)

    Miłosz Wieczór

    Full Text Available Telomeres are specialized nucleoprotein assemblies that protect the ends of linear chromosomes. In humans and many other species, telomeres consist of tandem TTAGGG repeats bound by a protein complex known as shelterin that remodels telomeric DNA into a protective loop structure and regulates telomere homeostasis. Shelterin recognizes telomeric repeats through its two major components known as Telomere Repeat-Binding Factors, TRF1 and TRF2. These two homologous proteins are therefore essential for the formation and normal function of telomeres. Indeed, TRF1 and TRF2 are implicated in a plethora of different cellular functions and their depletion leads to telomere dysfunction with chromosomal fusions, followed by apoptotic cell death. More specifically, it was found that TRF1 acts as a negative regulator of telomere length, and TRF2 is involved in stabilizing the loop structure. Consequently, these proteins are of great interest, not only because of their key role in telomere maintenance and stability, but also as potential drug targets. In the current study, we investigated the molecular basis of telomeric sequence recognition by TRF1 and TRF2 and their DNA binding mechanism. We used molecular dynamics (MD to calculate the free energy profiles for binding of TRFs to telomeric DNA. We found that the predicted binding free energies were in good agreement with experimental data. Further, different molecular determinants of binding, such as binding enthalpies and entropies, the hydrogen bonding pattern and changes in surface area, were analyzed to decompose and examine the overall binding free energies at the structural level. With this approach, we were able to draw conclusions regarding the consecutive stages of sequence-specific association, and propose a novel aspartate-dependent mechanism of sequence recognition. Finally, our work demonstrates the applicability of computational MD-based methods to studying protein-DNA interactions.

  3. Quantum origins of molecular recognition and olfaction in Drosophila.

    Science.gov (United States)

    Bittner, Eric R; Madalan, Adrian; Czader, Arkadiusz; Roman, Gregg

    2012-12-14

    The standard model for molecular recognition of an odorant is that receptor sites discriminate by molecular geometry as evidenced that two chiral molecules may smell very differently. However, recent studies of isotopically labeled olfactants indicate that there may be a molecular vibration-sensing component to olfactory reception, specifically in the spectral region around 2300 cm(-1). Here, we present a donor-bridge-acceptor model for olfaction which attempts to explain this effect. Our model, based upon accurate quantum chemical calculations of the olfactant (bridge) in its neutral and ionized states, posits that internal modes of the olfactant are excited impulsively during hole transfer from a donor to acceptor site on the receptor, specifically those modes that are resonant with the tunneling gap. By projecting the impulsive force onto the internal modes, we can determine which modes are excited at a given value of the donor-acceptor tunneling gap. Only those modes resonant with the tunneling gap and are impulsively excited will give a significant contribution to the inelastic transfer rate. Using acetophenone as a test case, our model and experiments on D. melanogaster suggest that isotopomers of a given olfactant give rise to different odorant qualities. These results support the notion that inelastic scattering effects may play a role in discriminating between isotopomers but that this is not a general spectroscopic effect.

  4. Power quality events recognition using a SVM-based method

    Energy Technology Data Exchange (ETDEWEB)

    Cerqueira, Augusto Santiago; Ferreira, Danton Diego; Ribeiro, Moises Vidal; Duque, Carlos Augusto [Department of Electrical Circuits, Federal University of Juiz de Fora, Campus Universitario, 36036 900, Juiz de Fora MG (Brazil)

    2008-09-15

    In this paper, a novel SVM-based method for power quality event classification is proposed. A simple approach for feature extraction is introduced, based on the subtraction of the fundamental component from the acquired voltage signal. The resulting signal is presented to a support vector machine for event classification. Results from simulation are presented and compared with two other methods, the OTFR and the LCEC. The proposed method shown an improved performance followed by a reasonable computational cost. (author)

  5. 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.

  6. Structural insight into RNA recognition motifs: versatile molecular Lego building blocks for biological systems.

    Science.gov (United States)

    Muto, Yutaka; Yokoyama, Shigeyuki

    2012-01-01

    'RNA recognition motifs (RRMs)' are common domain-folds composed of 80-90 amino-acid residues in eukaryotes, and have been identified in many cellular proteins. At first they were known as RNA binding domains. Through discoveries over the past 20 years, however, the RRMs have been shown to exhibit versatile molecular recognition activities and to behave as molecular Lego building blocks to construct biological systems. Novel RNA/protein recognition modes by RRMs are being identified, and more information about the molecular recognition by RRMs is becoming available. These RNA/protein recognition modes are strongly correlated with their biological significance. In this review, we would like to survey the recent progress on these versatile molecular recognition modules. Copyright © 2012 John Wiley & Sons, Ltd.

  7. Molecular events basic to cellular radiation response

    International Nuclear Information System (INIS)

    Kolodny, G.M.

    The initiation and control of the division process in normal cells is studied to gain insight into changes in these regards caused by x-irradiation and neoplasia. The Primer Hypothesis for eukaryotic gene regulation proposes that small molecular weight RNA acts as primer for new RNA synthesis by hybridizing with DNA and there initiating the transcription of a new RNA chain. The experiments reported here indicate that small molecular weight RNA will induce the production of new proteins. These results are consistent with the Primer Hypothesis, and demonstrate that RNA can be taken up from the media by cells in culture and can induce in vitro the production of differentiated cell products

  8. Event recognition using signal spectrograms in long pulse experiments

    International Nuclear Information System (INIS)

    Gonzalez, J.; Ruiz, M.; Barrera, E.; Arcas, G.; Lopez, J. M.; Vega, J.

    2010-01-01

    As discharge duration increases, real-time complex analysis of the signal becomes more important. In this context, data acquisition and processing systems must provide models for designing experiments which use event oriented plasma control. One example of advanced data analysis is signal classification. The off-line statistical analysis of a large number of discharges provides information to develop algorithms for the determination of the plasma parameters from measurements of magnetohydrodinamic waves, for example, to detect density fluctuations induced by the Alfven cascades using morphological patterns. The need to apply different algorithms to the signals and to address different processing algorithms using the previous results necessitates the use of an event-based experiment. The Intelligent Test and Measurement System platform is an example of architecture designed to implement distributed data acquisition and real-time processing systems. The processing algorithm sequence is modeled using an event-based paradigm. The adaptive capacity of this model is based on the logic defined by the use of state machines in SCXML. The Intelligent Test and Measurement System platform mixes a local multiprocessing model with a distributed deployment of services based on Jini.

  9. Application of CA and NN for event recognition in experiments DISTO and STREAMER

    International Nuclear Information System (INIS)

    Bussa, M.P.; Ivanov, V.V.; Kisel, I.V.; Pontecorvo, G.B.

    1997-01-01

    An algorithm for charged particle recognition and event identification applying a cellular automaton (CA) model and a multi-layer neural network (NN) has been developed for the DISTO experiment under way at Saturne (Saclay, France). A further development of the model will be applied for particle recognition in the Dubna Streamer Chamber Spectrometer (DSCS) for studying pion-nucleus absorption (experiments DISTO and STREAMER). (orig.)

  10. Recognition of power quality events by using multiwavelet-based neural networks

    Energy Technology Data Exchange (ETDEWEB)

    Kaewarsa, Suriya; Attakitmongcol, Kitti; Kulworawanichpong, Thanatchai [School of Electrical Engineering, Suranaree University of Technology, 111 University Avenue, Muang District, Nakhon Ratchasima 30000 (Thailand)

    2008-05-15

    Recognition of power quality events by analyzing the voltage and current waveform disturbances is a very important task for the power system monitoring. This paper presents a novel approach for the recognition of power quality disturbances using multiwavelet transform and neural networks. The proposed method employs the multiwavelet transform using multiresolution signal decomposition techniques working together with multiple neural networks using a learning vector quantization network as a powerful classifier. Various transient events are tested, such as voltage sag, swell, interruption, notching, impulsive transient, and harmonic distortion show that the classifier can detect and classify different power quality signal types efficiency. (author)

  11. Automated track recognition and event reconstruction in nuclear emulsion

    International Nuclear Information System (INIS)

    Deines-Jones, P.; Aranas, A.; Cherry, M.L.; Dugas, J.; Kudzia, D.; Nilsen, B.S.; Sengupta, K.; Waddington, C.J.; Wefel, J.P.; Wilczynska, B.; Wilczynski, H.; Wosiek, B.

    1997-01-01

    The major advantages of nuclear emulsion for detecting charged particles are its submicron position resolution and sensitivity to minimum ionizing particles. These must be balanced, however, against the difficult manual microscope measurement by skilled observers required for the analysis. We have developed an automated system to acquire and analyze the microscope images from emulsion chambers. Each emulsion plate is analyzed independently, allowing coincidence techniques to be used in order to reject background and estimate error rates. The system has been used to analyze a sample of high-multiplicity Pb-Pb interactions (charged particle multiplicities ∝ 1100) produced by the 158 GeV/c per nucleon 208 Pb beam at CERN. Automatically measured events agree with our best manual measurements on 97% of all the tracks. We describe the image analysis and track reconstruction techniques, and discuss the measurement and reconstruction uncertainties. (orig.)

  12. Active learning for ontological event extraction incorporating named entity recognition and unknown word handling.

    Science.gov (United States)

    Han, Xu; Kim, Jung-jae; Kwoh, Chee Keong

    2016-01-01

    Biomedical text mining may target various kinds of valuable information embedded in the literature, but a critical obstacle to the extension of the mining targets is the cost of manual construction of labeled data, which are required for state-of-the-art supervised learning systems. Active learning is to choose the most informative documents for the supervised learning in order to reduce the amount of required manual annotations. Previous works of active learning, however, focused on the tasks of entity recognition and protein-protein interactions, but not on event extraction tasks for multiple event types. They also did not consider the evidence of event participants, which might be a clue for the presence of events in unlabeled documents. Moreover, the confidence scores of events produced by event extraction systems are not reliable for ranking documents in terms of informativity for supervised learning. We here propose a novel committee-based active learning method that supports multi-event extraction tasks and employs a new statistical method for informativity estimation instead of using the confidence scores from event extraction systems. Our method is based on a committee of two systems as follows: We first employ an event extraction system to filter potential false negatives among unlabeled documents, from which the system does not extract any event. We then develop a statistical method to rank the potential false negatives of unlabeled documents 1) by using a language model that measures the probabilities of the expression of multiple events in documents and 2) by using a named entity recognition system that locates the named entities that can be event arguments (e.g. proteins). The proposed method further deals with unknown words in test data by using word similarity measures. We also apply our active learning method for the task of named entity recognition. We evaluate the proposed method against the BioNLP Shared Tasks datasets, and show that our method

  13. Recognition of damage-associated, nucleic acid-related molecular patterns during inflammation and vaccination

    Directory of Open Access Journals (Sweden)

    Nao eJounai

    2013-01-01

    Full Text Available All mammalian cells are equipped with large numbers of sensors for protection from various sorts of invaders, who, in turn, are equipped with molecules containing pathogen-associated molecular patterns (PAMPs. Once these sensors recognize non-self antigens containing PAMPs, various physiological responses including inflammation are induced to eliminate the pathogens. However, the host sometimes suffers from chronic infection or continuous injuries, resulting in production of self-molecules containing damage-associated molecular patterns (DAMPs. DAMPs are also responsible for the elimination of pathogens, but promiscuous recognition of DAMPs through sensors against PAMPs has been reported. Accumulation of DAMPs leads to massive inflammation and continuous production of DAMPs; that is, a vicious circle leading to the development of autoimmune disease. From a vaccinological point of view, the accurate recognition of both PAMPs and DAMPs is important for vaccine immunogenicity, because vaccine adjuvants are composed of several PAMPs and/or DAMPs, which are also associated with severe adverse events after vaccination. Here, we review as the roles of PAMPs and DAMPs upon infection with pathogens or inflammation, and the sensors responsible for recognizing them, as well as their relationship with the development of autoimmune disease or the immunogenicity of vaccines.

  14. Molecular tips for scanning tunneling microscopy: intermolecular electron tunneling for single-molecule recognition and electronics.

    Science.gov (United States)

    Nishino, Tomoaki

    2014-01-01

    This paper reviews the development of molecular tips for scanning tunneling microscopy (STM). Molecular tips offer many advantages: first is their ability to perform chemically selective imaging because of chemical interactions between the sample and the molecular tip, thus improving a major drawback of conventional STM. Rational design of the molecular tip allows sophisticated chemical recognition; e.g., chiral recognition and selective visualization of atomic defects in carbon nanotubes. Another advantage is that they provide a unique method to quantify electron transfer between single molecules. Understanding such electron transfer is mandatory for the realization of molecular electronics.

  15. Molecularly Imprinted Polymers: Thermodynamic and Kinetic Considerations on the Specific Sorption and Molecular Recognition

    Directory of Open Access Journals (Sweden)

    Kejun Tong

    2008-04-01

    Full Text Available This article presents a work aiming at thermodynamically and kinetically interpreting the specific sorption and recognition by a molecularly imprinted polymer. Using Boc-L-Phe-OH as a template, the imprinted material was prepared. The result indicates that the prepared polymer can well discriminate the imprint species from its analogue (Boc-D-Phe-OH, so as to adsorb more for the former but less for the latter. Kinetic analysis indicates that this specific sorption, in nature, can be a result of a preferential promotion. The imprint within the polymer causes a larger adsorption rate for the template than for the analogue. Thermodynamic study also implies that the molecular induction from the specific imprint to the template is larger than to the analogue, which thus makes the polymer capable of preferentially alluring the template to bind.

  16. Effect of buffer at nanoscale molecular recognition interfaces - electrostatic binding of biological polyanions.

    Science.gov (United States)

    Rodrigo, Ana C; Laurini, Erik; Vieira, Vânia M P; Pricl, Sabrina; Smith, David K

    2017-10-19

    We investigate the impact of an over-looked component on molecular recognition in water-buffer. The binding of a cationic dye to biological polyanion heparin is shown by isothermal calorimetry to depend on buffer (Tris-HCl > HEPES > PBS). The heparin binding of self-assembled multivalent (SAMul) cationic micelles is even more buffer dependent. Multivalent electrostatic molecular recognition is buffer dependent as a result of competitive interactions between the cationic binding interface and anions present in the buffer.

  17. Event-related theta synchronization predicts deficit in facial affect recognition in schizophrenia.

    Science.gov (United States)

    Csukly, Gábor; Stefanics, Gábor; Komlósi, Sarolta; Czigler, István; Czobor, Pál

    2014-02-01

    Growing evidence suggests that abnormalities in the synchronized oscillatory activity of neurons in schizophrenia may lead to impaired neural activation and temporal coding and thus lead to neurocognitive dysfunctions, such as deficits in facial affect recognition. To gain an insight into the neurobiological processes linked to facial affect recognition, we investigated both induced and evoked oscillatory activity by calculating the Event Related Spectral Perturbation (ERSP) and the Inter Trial Coherence (ITC) during facial affect recognition. Fearful and neutral faces as well as nonface patches were presented to 24 patients with schizophrenia and 24 matched healthy controls while EEG was recorded. The participants' task was to recognize facial expressions. Because previous findings with healthy controls showed that facial feature decoding was associated primarily with oscillatory activity in the theta band, we analyzed ERSP and ITC in this frequency band in the time interval of 140-200 ms, which corresponds to the N170 component. Event-related theta activity and phase-locking to facial expressions, but not to nonface patches, predicted emotion recognition performance in both controls and patients. Event-related changes in theta amplitude and phase-locking were found to be significantly weaker in patients compared with healthy controls, which is in line with previous investigations showing decreased neural synchronization in the low frequency bands in patients with schizophrenia. Neural synchrony is thought to underlie distributed information processing. Our results indicate a less effective functioning in the recognition process of facial features, which may contribute to a less effective social cognition in schizophrenia. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  18. Early molecular events in the development of the diabetic cardiomyopathy.

    NARCIS (Netherlands)

    Monkemann, H.; Vriese, A.S. de; Blom, H.J.; Kluijtmans, L.A.J.; Heil, S.G.; Schild, H.H.; Golubnitschaja, O.

    2002-01-01

    Oxidative damage to DNA has been well documented in cardiac cells isolated from diabetic patients and rats with streptozotocin-induced diabetes mellitus (DM). This study evaluates possible molecular mechanisms for early events in the development of DM-induced cardiomyopathy. Methods: To analyze the

  19. Event-related oscillations (EROs) and event-related potentials (ERPs) comparison in facial expression recognition.

    Science.gov (United States)

    Balconi, Michela; Pozzoli, Uberto

    2007-09-01

    The study aims to explore the significance of event-related potentials (ERPs) and event-related brain oscillations (EROs) (delta, theta, alpha, beta, gamma power) in response to emotional (fear, happiness, sadness) when compared with neutral faces during 180-250 post-stimulus time interval. The ERP results demonstrated that the emotional face elicited a negative peak at approximately 230 ms (N2). Moreover, EEG measures showed that motivational significance of face (emotional vs. neutral) could modulate the amplitude of EROs, but only for some frequency bands (i.e. theta and gamma bands). In a second phase, we considered the resemblance of the two EEG measures by a regression analysis. It revealed that theta and gamma oscillations mainly effect as oscillation activity at the N2 latency. Finally, a posterior increased power of theta was found for emotional faces.

  20. Stress reaction process-based hierarchical recognition algorithm for continuous intrusion events in optical fiber prewarning system

    Science.gov (United States)

    Qu, Hongquan; Yuan, Shijiao; Wang, Yanping; Yang, Dan

    2018-04-01

    To improve the recognition performance of optical fiber prewarning system (OFPS), this study proposed a hierarchical recognition algorithm (HRA). Compared with traditional methods, which employ only a complex algorithm that includes multiple extracted features and complex classifiers to increase the recognition rate with a considerable decrease in recognition speed, HRA takes advantage of the continuity of intrusion events, thereby creating a staged recognition flow inspired by stress reaction. HRA is expected to achieve high-level recognition accuracy with less time consumption. First, this work analyzed the continuity of intrusion events and then presented the algorithm based on the mechanism of stress reaction. Finally, it verified the time consumption through theoretical analysis and experiments, and the recognition accuracy was obtained through experiments. Experiment results show that the processing speed of HRA is 3.3 times faster than that of a traditional complicated algorithm and has a similar recognition rate of 98%. The study is of great significance to fast intrusion event recognition in OFPS.

  1. Molecular basis for convergent evolution of glutamate recognition by pentameric ligand-gated ion channels

    DEFF Research Database (Denmark)

    Lynagh, Timothy; Beech, Robin N.; Lalande, Maryline J.

    2015-01-01

    that glutamate recognition requires an arginine residue in the base of the binding site, which originated at least three distinct times according to phylogenetic analysis. Most remarkably, the arginine emerged on the principal face of the binding site in the Lophotrochozoan lineage, but 65 amino acids upstream......Glutamate is an indispensable neurotransmitter, triggering postsynaptic signals upon recognition by postsynaptic receptors. We questioned the phylogenetic position and the molecular details of when and where glutamate recognition arose in the glutamate-gated chloride channels. Experiments revealed......, on the complementary face, in the Ecdysozoan lineage. This combined experimental and computational approach throws new light on the evolution of synaptic signalling....

  2. Confinement of Aggregation-Induced Emission Molecular Rotors in Ultrathin Two-Dimensional Porous Organic Nanosheets for Enhanced Molecular Recognition.

    Science.gov (United States)

    Dong, Jinqiao; Li, Xu; Zhang, Kang; Di Yuan, Yi; Wang, Yuxiang; Zhai, Linzhi; Liu, Guoliang; Yuan, Daqiang; Jiang, Jianwen; Zhao, Dan

    2018-03-21

    Despite the rapid development of molecular rotors over the past decade, it still remains a huge challenge to understand their confined behavior in ultrathin two-dimensional (2D) nanomaterials for molecular recognition. Here, we report an all-carbon, 2D π-conjugated aromatic polymer, named NUS-25, containing flexible tetraphenylethylene (TPE) units as aggregation-induced emission (AIE) molecular rotors. NUS-25 bulk powder can be easily exfoliated into micrometer-sized lamellar freestanding nanosheets with a thickness of 2-5 nm. The dynamic behavior of the TPE rotors is partially restricted through noncovalent interactions in the ultrathin 2D nanosheets, which is proved by comparative experimental studies including AIE characteristics, size-selective molecular recognition, and theoretical calculations of rotary energy barrier. Because of the partially restricted TPE rotors, NUS-25 nanosheets are highly fluorescent. This property allows NUS-25 nanosheets to be used as a chemical sensor for the specific detection of acenaphthylene among a series of polycyclic aromatic hydrocarbons (PAHs) via fluorescent quenching mechanism. Further investigations show that NUS-25 nanosheets have much higher sensitivity and selectivity than their stacked bulk powder and other similar polymers containing dynamic TPE rotors. The highly efficient molecular recognition can be attributed to the photoinduced electron transfer (PET) from NUS-25 nanosheets to acenaphthylene, which is investigated by time-resolved photoluminescence measurements (TRPL), excitation and emission spectra, and density functional theory (DFT) calculations. Our findings demonstrate that confinement of AIE molecular rotors in 2D nanomaterials can enhance the molecular recognition. We anticipate that the material design strategy demonstrated in this study will inspire the development of other ultrathin 2D nanomaterials equipped with smart molecular machines for various applications.

  3. Molecularly imprinted polymers for the recognition of proteins: the state of the art.

    Science.gov (United States)

    Bossi, A; Bonini, F; Turner, A P F; Piletsky, S A

    2007-01-15

    Molecular imprinting has proved to be an effective technique for the creation of recognition sites on a polymer scaffold. Protein imprinting has been a focus for many chemists working in the area of molecular recognition, since the creation of synthetic polymers that can specifically recognise proteins is a very challenging but potentially extremely rewarding objective. It is expected that molecularly imprinted polymers (MIPs) with specificity for proteins will find application in medicine, diagnostics, proteomics, environmental analysis, sensors and drug delivery. In this review, the authors provide an overview of the progress achieved in the decade between 1994 and 2005, with respect to the challenging area of MIPs for protein recognition. The discussion furnishes a comparative analysis of different approaches developed, underlining their relative advantages and disadvantages and highlighting trends and possible future directions.

  4. Fast recognition of single molecules based on single-event photon statistics

    International Nuclear Information System (INIS)

    Dong Shuangli; Huang Tao; Liu Yuan; Wang Jun; Zhang Guofeng; Xiao Liantuan; Jia Suotang

    2007-01-01

    Mandel's Q parameter, which is determined from single-event photon statistics, provides an alternative way to recognize single molecules with fluorescence detection, other than the second-order correlation function. It is shown that the Q parameter of an assumed ideal double-molecule fluorescence with the same average photon number as that of the sample fluorescence can act as the criterion for single-molecule recognition. The influence of signal-to-background ratio and the error estimates for photon statistics are also presented. We have applied this method to ascertain single Cy5 dye molecules within hundreds of milliseconds

  5. Narrative versus Style: Effect of Genre Typical Events versus Genre Typical Filmic Realizations on Film Viewers' Genre Recognition

    OpenAIRE

    Visch, V.; Tan, E.

    2008-01-01

    This study investigated whether film viewers recognize four basic genres (comic, drama, action and nonfiction) on the basis of genre-typical event cues or of genretypical filmic realization cues of events. Event cues are similar to the narrative content of a film sequence, while filmic realization cues are similar to stylistic surface cues of a film sequence. It was predicted that genre recognition of short film fragments is cued more by filmic realization cues than by event cues. The results...

  6. Recognition Memory in Amnestic-Mild Cognitive Impairment: Insights from Event-Related Potentials

    Directory of Open Access Journals (Sweden)

    David A Wolk

    2013-12-01

    Full Text Available Episodic memory loss is the hallmark cognitive dysfunction associated with Alzheimer’s Disease (AD. Amnestic Mild Cognitive Impairment (a-MCI frequently represents a transitional stage between normal aging and early AD. A better understanding of the qualitative features of memory loss in a-MCI may have important implications for predicting those most likely to harbor AD-related pathology and for disease monitoring. Dual process models of memory argue that recognition memory is subserved by the dissociable processes of recollection and familiarity. Work studying recognition memory in a-MCI from this perspective has been controversial, particularly with regard to the integrity of familiarity. Event-related potentials (ERPs offer an alternative means for assessing these functions without the associated assumptions of behavioral estimation methods. ERPs were recorded while a-MCI patients and cognitively normal (CN age-matched adults performed a recognition memory task. When retrieval success was measured (hits versus correct rejections in which performance was matched by group, a-MCI patients displayed similar neural correlates to that of the CN group, including modulation of the FN400 and the late parietal complex (LPC which are thought to index familiarity and recollection, respectively. Alternatively, when the integrity of these components were measured based on retrieval attempts (studied versus unstudied items, a-MCI patients displayed a reduced FN400 and LPC. Furthermore, modulation of the FN400 correlated with a behavioral estimate of familiarity and the LPC with a behavioral estimates of recollection obtained in a separate experiment in the same individuals, consistent with the proposed mappings of these indices. These results support a global decline of recognition memory in a-MCI, which suggests that the memory loss of prodromal AD may be qualitatively distinct from normal aging.

  7. Recognition of conformational changes in beta-lactoglobulin by molecularly imprinted thin films.

    Science.gov (United States)

    Turner, Nicholas W; Liu, Xiao; Piletsky, Sergey A; Hlady, Vladimir; Britt, David W

    2007-09-01

    Pathogenesis in protein conformational diseases is initiated by changes in protein secondary structure. This molecular restructuring presents an opportunity for novel shape-based detection approaches, as protein molecular weight and chemistry are otherwise unaltered. Here we apply molecular imprinting to discriminate between distinct conformations of the model protein beta-lactoglobulin (BLG). Thermal- and fluoro-alcohol-induced BLG isoforms were imprinted in thin films of 3-aminophenylboronic acid on quartz crystal microbalance chips. Enhanced rebinding of the template isoform was observed in all cases when compared to the binding of nontemplate isoforms over the concentration range of 1-100 microg mL(-1). Furthermore, it was observed that the greater the changes in the secondary structure of the template protein the lower the binding of native BLG challenges to the imprint, suggesting a strong steric influence in the recognition system. This feasibility study is a first demonstration of molecular imprints for recognition of distinct conformations of the same protein.

  8. Orthographic recognition in late adolescents: an assessment through event-related brain potentials.

    Science.gov (United States)

    González-Garrido, Andrés Antonio; Gómez-Velázquez, Fabiola Reveca; Rodríguez-Santillán, Elizabeth

    2014-04-01

    Reading speed and efficiency are achieved through the automatic recognition of written words. Difficulties in learning and recognizing the orthography of words can arise despite reiterative exposure to texts. This study aimed to investigate, in native Spanish-speaking late adolescents, how different levels of orthographic knowledge might result in behavioral and event-related brain potential differences during the recognition of orthographic errors. Forty-five healthy high school students were selected and divided into 3 equal groups (High, Medium, Low) according to their performance on a 5-test battery of orthographic knowledge. All participants performed an orthographic recognition task consisting of the sequential presentation of a picture (object, fruit, or animal) followed by a correctly, or incorrectly, written word (orthographic mismatch) that named the picture just shown. Electroencephalogram (EEG) recording took place simultaneously. Behavioral results showed that the Low group had a significantly lower number of correct responses and increased reaction times while processing orthographical errors. Tests showed significant positive correlations between higher performance on the experimental task and faster and more accurate reading. The P150 and P450 components showed higher voltages in the High group when processing orthographic errors, whereas N170 seemed less lateralized to the left hemisphere in the lower orthographic performers. Also, trials with orthographic errors elicited a frontal P450 component that was only evident in the High group. The present results show that higher levels of orthographic knowledge correlate with high reading performance, likely because of faster and more accurate perceptual processing, better visual orthographic representations, and top-down supervision, as the event-related brain potential findings seem to suggest.

  9. Examining Event-Related Potential (ERP) correlates of decision bias in recognition memory judgments.

    Science.gov (United States)

    Hill, Holger; Windmann, Sabine

    2014-01-01

    Memory judgments can be based on accurate memory information or on decision bias (the tendency to report that an event is part of episodic memory when one is in fact unsure). Event related potentials (ERP) correlates are important research tools for elucidating the dynamics underlying memory judgments but so far have been established only for investigations of accurate old/new discrimination. To identify the ERP correlates of bias, and observe how these interact with ERP correlates of memory, we conducted three experiments that manipulated decision bias within participants via instructions during recognition memory tests while their ERPs were recorded. In Experiment 1, the bias manipulation was performed between blocks of trials (automatized bias) and compared to trial-by-trial shifts of bias in accord with an external cue (flexibly controlled bias). In Experiment 2, the bias manipulation was performed at two different levels of accurate old/new discrimination as the memory strength of old (studied) items was varied. In Experiment 3, the bias manipulation was added to another, bottom-up driven manipulation of bias induced via familiarity. In the first two Experiments, and in the low familiarity condition of Experiment 3, we found evidence of an early frontocentral ERP component at 320 ms poststimulus (the FN320) that was sensitive to the manipulation of bias via instruction, with more negative amplitudes indexing more liberal bias. By contrast, later during the trial (500-700 ms poststimulus), bias effects interacted with old/new effects across all three experiments. Results suggest that the decision criterion is typically activated early during recognition memory trials, and is integrated with retrieved memory signals and task-specific processing demands later during the trial. More generally, the findings demonstrate how ERPs can help to specify the dynamics of recognition memory processes under top-down and bottom-up controlled retrieval conditions.

  10. Examining Event-Related Potential (ERP) Correlates of Decision Bias in Recognition Memory Judgments

    Science.gov (United States)

    Hill, Holger; Windmann, Sabine

    2014-01-01

    Memory judgments can be based on accurate memory information or on decision bias (the tendency to report that an event is part of episodic memory when one is in fact unsure). Event related potentials (ERP) correlates are important research tools for elucidating the dynamics underlying memory judgments but so far have been established only for investigations of accurate old/new discrimination. To identify the ERP correlates of bias, and observe how these interact with ERP correlates of memory, we conducted three experiments that manipulated decision bias within participants via instructions during recognition memory tests while their ERPs were recorded. In Experiment 1, the bias manipulation was performed between blocks of trials (automatized bias) and compared to trial-by-trial shifts of bias in accord with an external cue (flexibly controlled bias). In Experiment 2, the bias manipulation was performed at two different levels of accurate old/new discrimination as the memory strength of old (studied) items was varied. In Experiment 3, the bias manipulation was added to another, bottom-up driven manipulation of bias induced via familiarity. In the first two Experiments, and in the low familiarity condition of Experiment 3, we found evidence of an early frontocentral ERP component at 320 ms poststimulus (the FN320) that was sensitive to the manipulation of bias via instruction, with more negative amplitudes indexing more liberal bias. By contrast, later during the trial (500–700 ms poststimulus), bias effects interacted with old/new effects across all three experiments. Results suggest that the decision criterion is typically activated early during recognition memory trials, and is integrated with retrieved memory signals and task-specific processing demands later during the trial. More generally, the findings demonstrate how ERPs can help to specify the dynamics of recognition memory processes under top-down and bottom-up controlled retrieval conditions. PMID

  11. Examining Event-Related Potential (ERP correlates of decision bias in recognition memory judgments.

    Directory of Open Access Journals (Sweden)

    Holger Hill

    Full Text Available Memory judgments can be based on accurate memory information or on decision bias (the tendency to report that an event is part of episodic memory when one is in fact unsure. Event related potentials (ERP correlates are important research tools for elucidating the dynamics underlying memory judgments but so far have been established only for investigations of accurate old/new discrimination. To identify the ERP correlates of bias, and observe how these interact with ERP correlates of memory, we conducted three experiments that manipulated decision bias within participants via instructions during recognition memory tests while their ERPs were recorded. In Experiment 1, the bias manipulation was performed between blocks of trials (automatized bias and compared to trial-by-trial shifts of bias in accord with an external cue (flexibly controlled bias. In Experiment 2, the bias manipulation was performed at two different levels of accurate old/new discrimination as the memory strength of old (studied items was varied. In Experiment 3, the bias manipulation was added to another, bottom-up driven manipulation of bias induced via familiarity. In the first two Experiments, and in the low familiarity condition of Experiment 3, we found evidence of an early frontocentral ERP component at 320 ms poststimulus (the FN320 that was sensitive to the manipulation of bias via instruction, with more negative amplitudes indexing more liberal bias. By contrast, later during the trial (500-700 ms poststimulus, bias effects interacted with old/new effects across all three experiments. Results suggest that the decision criterion is typically activated early during recognition memory trials, and is integrated with retrieved memory signals and task-specific processing demands later during the trial. More generally, the findings demonstrate how ERPs can help to specify the dynamics of recognition memory processes under top-down and bottom-up controlled retrieval conditions.

  12. Protein recognition by a pattern-generating fluorescent molecular probe

    Science.gov (United States)

    Pode, Zohar; Peri-Naor, Ronny; Georgeson, Joseph M.; Ilani, Tal; Kiss, Vladimir; Unger, Tamar; Markus, Barak; Barr, Haim M.; Motiei, Leila; Margulies, David

    2017-12-01

    Fluorescent molecular probes have become valuable tools in protein research; however, the current methods for using these probes are less suitable for analysing specific populations of proteins in their native environment. In this study, we address this gap by developing a unimolecular fluorescent probe that combines the properties of small-molecule-based probes and cross-reactive sensor arrays (the so-called chemical 'noses/tongues'). On the one hand, the probe can detect different proteins by generating unique identification (ID) patterns, akin to cross-reactive arrays. On the other hand, its unimolecular scaffold and selective binding enable this ID-generating probe to identify combinations of specific protein families within complex mixtures and to discriminate among isoforms in living cells, where macroscopic arrays cannot access. The ability to recycle the molecular device and use it to track several binding interactions simultaneously further demonstrates how this approach could expand the fluorescent toolbox currently used to detect and image proteins.

  13. Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.

    Science.gov (United States)

    Li, Jianwei; Nowak, Piotr; Otto, Sijbren

    2013-06-26

    Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.

  14. All-organic microelectromechanical systems integrating specific molecular recognition--a new generation of chemical sensors.

    Science.gov (United States)

    Ayela, Cédric; Dubourg, Georges; Pellet, Claude; Haupt, Karsten

    2014-09-03

    Cantilever-type all-organic microelectromechanical systems based on molecularly imprinted polymers for specific analyte recognition are used as chemical sensors. They are produced by a simple spray-coating-shadow-masking process. Analyte binding to the cantilever generates a measurable change in its resonance frequency. This allows label-free detection by direct mass sensing of low-molecular-weight analytes at nanomolar concentrations. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Design of supramolecular nanomaterials : from molecular recognition to hierarchical self-assembly

    OpenAIRE

    El Idrissi, Mohamed

    2017-01-01

    In the present thesis, are reported new strategies for the design of nanostructures to partly address environmental issues. The work carried out has been divided into three parts: the design of cyclodextrin (CD)-based polymeric materials, the molecular engineering of a pyrene derivative for the formation of self-assembled nanostructures and the design of smart nanocarriers. Considerable efforts have been devoted to the design of molecular receptors capable of specific recognition of a wid...

  16. Molecular events leading to HPV-induced high grade neoplasia

    Directory of Open Access Journals (Sweden)

    Saskia M. Wilting

    2016-12-01

    Full Text Available Cervical cancer is initiated by high-risk types of the human papillomavirus (hrHPV and develops via precursor stages, called cervical intraepithelial neoplasia (CIN. High-grade CIN lesions are considered true precancerous lesions when the viral oncogenes E6 and E7 are aberrantly expressed in the dividing cells. This results in abolishment of normal cell cycle control via p53 and pRb degradation. However, it has become clear that these viral oncogenes possess additional oncogenic properties, including interference with the DNA methylation machinery and mitotic checkpoints. Identification of the resulting molecular events leading to high-grade neoplasia will 1 increase our understanding of cervical carcinogenesis, 2 yield biomarkers for early diagnosis, and 3 identify therapeutic targets for HPV-induced (pre cancerous lesions.This review will briefly summarise current advances in our understanding of the molecular alterations in the host cell genome that occur during HPV-induced carcinogenesis.

  17. Pathogenesis of pulmonary emphysema – cellular and molecular events

    Directory of Open Access Journals (Sweden)

    Antonio Di Petta

    2010-06-01

    Full Text Available Pulmonary emphysema is a chronic obstructive disease, resulting fromimportant alterations in the whole distal structure of terminal bronchioles, either by enlargement of air spaces or by destruction of the alveolar wall, leading to loss of respiratory surface, decreased elastic recoil and lung hyperinflation. For many years, the hypothesis of protease-antiprotease unbalance prevailed as the central theme in the pathogenesis of pulmonary emphysema. According to this hypothesis, the release of active proteolytic enzymes, produced mainly by neutrophils and macrophages, degrades the extracellular matrix, affecting the integrity of its components, especially collagen and elastic fibers. However, new concepts involving cellular and molecular events were proposed, including oxidative stress, cell apoptosis, cellular senescence and failed lung tissue repair. The aim of this review paper was to evaluate the cellular and molecular mechanisms seen in the pathogenesis of pulmonary emphysema.

  18. Bio-specific recognition and applications: from molecular to colloidal scales

    International Nuclear Information System (INIS)

    Baudry, Jean; Bertrand, Emanuel; Lequeux, Nicolas; Bibette, Jerome

    2004-01-01

    Biomolecules have the well-known ability to build reversible complexes. Indeed, antigens and antibodies or adhesion molecules are able to recognize one another with a strong affinity and a very high specificity. This paper first reviews the various techniques and related results about binding and unbinding, at the scale of a unique ligand/receptor couple. One important biotechnological application arising from these recognition phenomena concerns immuno-diagnosis, which is essentially based on the formation of these specific complexes. We show how the physics of colloids associated with the growing scientific background concerning molecular recognition helps in rationalizing and inventing new diagnostic strategies. Finally the concept of colloidal self-assembling systems as biosensors is presented as directly impacting the most important questions related to molecular recognition and their biotechnological implications. (topical review)

  19. Molecular Events in Primary and Metastatic Colorectal Carcinoma: A Review

    Directory of Open Access Journals (Sweden)

    Rani Kanthan

    2012-01-01

    Full Text Available Colorectal cancer (CRC is a heterogeneous disease, developing through a multipathway sequence of events guided by clonal selections. Pathways included in the development of CRC may be broadly categorized into (a genomic instability, including chromosomal instability (CIN, microsatellite instability (MSI, and CpG island methylator phenotype (CIMP, (b genomic mutations including suppression of tumour suppressor genes and activation of tumour oncogenes, (c microRNA, and (d epigenetic changes. As cancer becomes more advanced, invasion and metastases are facilitated through the epithelial-mesenchymal transition (EMT, with additional genetic alterations. Despite ongoing identification of genetic and epigenetic markers and the understanding of alternative pathways involved in the development and progression of this disease, CRC remains the second highest cause of malignancy-related mortality in Canada. The molecular events that underlie the tumorigenesis of primary and metastatic colorectal carcinoma are detailed in this manuscript.

  20. Tunable Complex Stability in Surface Molecular Recognition Mediated by Self-Complementary Quadruple Hydrogen Bonds

    NARCIS (Netherlands)

    Zou, S(han); Zhang, Zhihong; Forch, Renate; Knoll, Wolfgang; Schönherr, Holger; Vancso, Gyula J.

    2003-01-01

    We show that surfaces modified with asymmetric 2-ureido-4[1H]-pyrimidinone-hydroxyalkane disulfide adsorbates exhibit efficient and controllable self-complementary molecular recognition of the pyrimidinone moieties. Two novel asymmetric 2-ureido-4[1H]-pyrimidinone-hydroxyalkane disulfide adsorbates,

  1. A large-scale dataset of solar event reports from automated feature recognition modules

    Science.gov (United States)

    Schuh, Michael A.; Angryk, Rafal A.; Martens, Petrus C.

    2016-05-01

    The massive repository of images of the Sun captured by the Solar Dynamics Observatory (SDO) mission has ushered in the era of Big Data for Solar Physics. In this work, we investigate the entire public collection of events reported to the Heliophysics Event Knowledgebase (HEK) from automated solar feature recognition modules operated by the SDO Feature Finding Team (FFT). With the SDO mission recently surpassing five years of operations, and over 280,000 event reports for seven types of solar phenomena, we present the broadest and most comprehensive large-scale dataset of the SDO FFT modules to date. We also present numerous statistics on these modules, providing valuable contextual information for better understanding and validating of the individual event reports and the entire dataset as a whole. After extensive data cleaning through exploratory data analysis, we highlight several opportunities for knowledge discovery from data (KDD). Through these important prerequisite analyses presented here, the results of KDD from Solar Big Data will be overall more reliable and better understood. As the SDO mission remains operational over the coming years, these datasets will continue to grow in size and value. Future versions of this dataset will be analyzed in the general framework established in this work and maintained publicly online for easy access by the community.

  2. Molecular Recognition: Preparation and Characterization of Two Tripodal Anion Receptors

    Energy Technology Data Exchange (ETDEWEB)

    Shokri, Alireza; Deng, Shihu; Wang, Xue B.; Kass, Steven R.

    2014-03-01

    Two new tripodal hydroxyl-based anion receptors (1 and 2) are reported and their molecular complexes with Cl–, H2PO4 –, and OAc– along with the (M–1)– ion of 1 were characterized by negative ion photoelectron spectroscopy in the gas phase and by binding constant determinations in four solvents (i.e., CDCl3, CD2Cl2, CD3COCD3, and CD3CN). An intramolecular hydrogen bond network (HBN) in hexaol 1 was found to diminish its binding whereas the triol 2 is the strongest aliphatic hydroxyl-based receptor to date.

  3. Autophagic clearance of bacterial pathogens: molecular recognition of intracellular microorganisms.

    Science.gov (United States)

    Pareja, Maria Eugenia Mansilla; Colombo, Maria I

    2013-01-01

    Autophagy is involved in several physiological and pathological processes. One of the key roles of the autophagic pathway is to participate in the first line of defense against the invasion of pathogens, as part of the innate immune response. Targeting of intracellular bacteria by the autophagic machinery, either in the cytoplasm or within vacuolar compartments, helps to control bacterial proliferation in the host cell, controlling also the spreading of the infection. In this review we will describe the means used by diverse bacterial pathogens to survive intracellularly and how they are recognized by the autophagic molecular machinery, as well as the mechanisms used to avoid autophagic clearance.

  4. Machine learning and pattern recognition from surface molecular architectures.

    Science.gov (United States)

    Maksov, Artem; Ziatdinov, Maxim; Fujii, Shintaro; Sumpter, Bobby; Kalinin, Sergei

    The ability to utilize molecular assemblies as data storage devices requires capability to identify individual molecular states on a scale of thousands of molecules. We present a novel method of applying machine learning techniques for extraction of positional and rotational information from ultra-high vacuum scanning tunneling microscopy (STM) images and apply it to self-assembled monolayer of π-bowl sumanene molecules on gold. From density functional theory (DFT) simulations, we assume existence of distinct polar and multiple azimuthal rotational states. We use DFT-generated templates in conjunction with Markov Chain Monte Carlo (MCMC) sampler and noise modeling to create synthetic images representative of our model. We extract positional information of each molecule and use nearest neighbor criteria to construct a graph input to Markov Random Field (MRF) model to identify polar rotational states. We train a convolutional Neural Network (cNN) on a synthetic dataset and combine it with MRF model to classify molecules based on their azimuthal rotational state. We demonstrate effectiveness of such approach compared to other methods. Finally, we apply our approach to experimental images and achieve complete rotational class information extraction. This research was sponsored by the Division of Materials Sciences and Engineering, Office of Science, Basic Energy Sciences, US DOE.

  5. Conformational Smear Characterization and Binning of Single-Molecule Conductance Measurements for Enhanced Molecular Recognition.

    Science.gov (United States)

    Korshoj, Lee E; Afsari, Sepideh; Chatterjee, Anushree; Nagpal, Prashant

    2017-11-01

    Electronic conduction or charge transport through single molecules depends primarily on molecular structure and anchoring groups and forms the basis for a wide range of studies from molecular electronics to DNA sequencing. Several high-throughput nanoelectronic methods such as mechanical break junctions, nanopores, conductive atomic force microscopy, scanning tunneling break junctions, and static nanoscale electrodes are often used for measuring single-molecule conductance. In these measurements, "smearing" due to conformational changes and other entropic factors leads to large variances in the observed molecular conductance, especially in individual measurements. Here, we show a method for characterizing smear in single-molecule conductance measurements and demonstrate how binning measurements according to smear can significantly enhance the use of individual conductance measurements for molecular recognition. Using quantum point contact measurements on single nucleotides within DNA macromolecules, we demonstrate that the distance over which molecular junctions are maintained is a measure of smear, and the resulting variance in unbiased single measurements depends on this smear parameter. Our ability to identify individual DNA nucleotides at 20× coverage increases from 81.3% accuracy without smear analysis to 93.9% with smear characterization and binning (SCRIB). Furthermore, merely 7 conductance measurements (7× coverage) are needed to achieve 97.8% accuracy for DNA nucleotide recognition when only low molecular smear measurements are used, which represents a significant improvement over contemporary sequencing methods. These results have important implications in a broad range of molecular electronics applications from designing robust molecular switches to nanoelectronic DNA sequencing.

  6. The role of the molecular chaperone heat shock protein A2 (HSPA2 in regulating human sperm-egg recognition

    Directory of Open Access Journals (Sweden)

    Brett Nixon

    2015-01-01

    Full Text Available One of the most common lesions present in the spermatozoa of human infertility patients is an idiopathic failure of sperm-egg recognition. Although this unique cellular interaction can now be readily by-passed by assisted reproductive strategies such as intracytoplasmic sperm injection (ICSI, recent large-scale epidemiological studies have encouraged the cautious use of this technology and highlighted the need for further research into the mechanisms responsible for defective sperm-egg recognition. Previous work in this field has established that the sperm domains responsible for oocyte interaction are formed during spermatogenesis prior to being dynamically modified during epididymal maturation and capacitation in female reproductive tract. While the factors responsible for the regulation of these sequential maturational events are undoubtedly complex, emerging research has identified the molecular chaperone, heat shock protein A2 (HSPA2, as a key regulator of these events in human spermatozoa. HSPA2 is a testis-enriched member of the 70 kDa heat shock protein family that promotes the folding, transport, and assembly of protein complexes and has been positively correlated with in vitro fertilization (IVF success. Furthermore, reduced expression of HSPA2 from the human sperm proteome leads to an impaired capacity for cumulus matrix dispersal, sperm-egg recognition and fertilization following both IVF and ICSI. In this review, we consider the evidence supporting the role of HSPA2 in sperm function and explore the potential mechanisms by which it is depleted in the spermatozoa of infertile patients. Such information offers novel insights into the molecular mechanisms governing sperm function.

  7. Towards structural models of molecular recognition in olfactory receptors.

    Science.gov (United States)

    Afshar, M; Hubbard, R E; Demaille, J

    1998-02-01

    The G protein coupled receptors (GPCR) are an important class of proteins that act as signal transducers through the cytoplasmic membrane. Understanding the structure and activation mechanism of these proteins is crucial for understanding many different aspects of cellular signalling. The olfactory receptors correspond to the largest family of GPCRs. Very little is known about how the structures of the receptors govern the specificity of interaction which enables identification of particular odorant molecules. In this paper, we review recent developments in two areas of molecular modelling: methods for modelling the configuration of trans-membrane helices and methods for automatic docking of ligands into receptor structures. We then show how a subset of these methods can be combined to construct a model of a rat odorant receptor interacting with lyral for which experimental data are available. This modelling can help us make progress towards elucidating the specificity of interactions between receptors and odorant molecules.

  8. Phytosterol Recognition via Rationally Designed Molecularly Imprinted Polymers

    Directory of Open Access Journals (Sweden)

    Lachlan J. Schwarz

    2018-02-01

    Full Text Available Molecularly imprinted polymers (MIPs prepared via a semi-covalent imprinting strategy using stigmasteryl methacrylate as a polymerisable template have been evaluated by static binding methods for their ability to selectively capture other valuable phytosterol targets, including campesterol and brassicasterol. Design criteria based on molecular modelling procedures and interaction energy calculations were employed to aid the selection of the co-monomer type, as well as the choice of co-monomer:template ratios for the formation of the pre-polymerisation complex. These novel hybrid semi-covalently imprinted polymers employed N,N′-dimethylacryl-amide (N,N′-DMAAM as the functional co-monomer and displayed specific binding capacities in the range 5.2–5.9 mg sterol/g MIP resin. Their binding attributes and selectivities towards phytosterol compounds were significantly different to the corresponding MIPs prepared via non-covalent procedures or when compared to non-imprinted polymers. Cross-reactivity studies using stigmasterol, ergosterol, cholesterol, campesterol, and brassicasterol as single analytes revealed the importance of the A-ring C-3-β-hydroxyl group and the orientational preferences of the D-ring alkyl chain structures in their interaction in the templated cavity with the N,N′-dimethylamide functional groups of the MIP. Finally, to obtain useful quantities of both campersterol and brassicasterol for these investigations, improved synthetic routes have been developed to permit the conversion of the more abundant, lower cost stigmasterol via a reactive aldehyde intermediate to these other sterols.

  9. Dielectric and ferroelectric sensing based on molecular recognition in Cu(1,10-phenlothroline)2SeO4.(diol) systems

    Science.gov (United States)

    Ye, Heng-Yun; Liao, Wei-Qiang; Zhou, Qionghua; Zhang, Yi; Wang, Jinlan; You, Yu-Meng; Wang, Jin-Yun; Chen, Zhong-Ning; Li, Peng-Fei; Fu, Da-Wei; Huang, Songping D.; Xiong, Ren-Gen

    2017-02-01

    The process of molecular recognition is the assembly of two or more molecules through weak interactions. Information in the process of molecular recognition can be transmitted to us via physical signals, which may find applications in sensing and switching. The conventional signals are mainly limited to light signal. Here, we describe the recognition of diols with Cu(1,10-phenlothroline)2SeO4 and the transduction of discrete recognition events into dielectric and/or ferroelectric signals. We observe that systems of Cu(1,10-phenlothroline)2SeO4.(diol) exhibit significant dielectric and/or ferroelectric dependence on different diol molecules. The compounds including ethane-1,2-diol or propane-1,2-diol just show small temperature-dependent dielectric anomalies and no reversible polarization, while the compound including ethane-1,3-diol shows giant temperature-dependent dielectric anomalies as well as ferroelectric reversible spontaneous polarization. This finding shows that dielectricity and/or ferroelectricity has the potential to be used for signalling molecular recognition.

  10. Adsorption and recognition characteristics of surface molecularly imprinted polymethacrylic acid/silica toward genistein.

    Science.gov (United States)

    Zhang, Yanyan; Gao, Baojiao; An, Fuqiang; Xu, Zeqing; Zhang, Tingting

    2014-09-12

    In this paper, on the basis of surface-initiated graft polymerization, a new surface molecular imprinting technique is established by molecular design. And molecularly imprinted polymer MIP-PMAA/SiO2 is successfully prepared with genistein as template. The adsorption and recognition characteristics of MIP-PMAA/SiO2 for genistein are studied in depth by using static method, dynamic method and competitive adsorption experiment. The experimental results show that MIP-PMAA/SiO2 possesses very strong adsorption affinity and specific recognition for genistein. The saturated adsorption capacity could reach to 0.36mmolg(-1). The selectivity coefficients relative to quercetin and rutin are 5.4 and 11.8, respectively. Besides, MIP-PMAA/SiO2 is regenerated easily and exhibits excellent reusability. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach.

    Science.gov (United States)

    Guttikonda, Satish K; Marri, Pradeep; Mammadov, Jafar; Ye, Liang; Soe, Khaing; Richey, Kimberly; Cruse, James; Zhuang, Meibao; Gao, Zhifang; Evans, Clive; Rounsley, Steve; Kumpatla, Siva P

    2016-01-01

    Demand for the commercial use of genetically modified (GM) crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS) technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions.

  12. Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach.

    Directory of Open Access Journals (Sweden)

    Satish K Guttikonda

    Full Text Available Demand for the commercial use of genetically modified (GM crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions.

  13. Recognition

    DEFF Research Database (Denmark)

    Gimmler, Antje

    2017-01-01

    In this article, I shall examine the cognitive, heuristic and theoretical functions of the concept of recognition. To evaluate both the explanatory power and the limitations of a sociological concept, the theory construction must be analysed and its actual productivity for sociological theory mus...

  14. Flow detection via sparse frame analysis for suspicious event recognition in infrared imagery

    Science.gov (United States)

    Fernandes, Henrique C.; Batista, Marcos A.; Barcelos, Celia A. Z.; Maldague, Xavier P. V.

    2013-05-01

    It is becoming increasingly evident that intelligent systems are very bene¯cial for society and that the further development of such systems is necessary to continue to improve society's quality of life. One area that has drawn the attention of recent research is the development of automatic surveillance systems. In our work we outline a system capable of monitoring an uncontrolled area (an outside parking lot) using infrared imagery and recognizing suspicious events in this area. The ¯rst step is to identify moving objects and segment them from the scene's background. Our approach is based on a dynamic background-subtraction technique which robustly adapts detection to illumination changes. It is analyzed only regions where movement is occurring, ignoring in°uence of pixels from regions where there is no movement, to segment moving objects. Regions where movement is occurring are identi¯ed using °ow detection via sparse frame analysis. During the tracking process the objects are classi¯ed into two categories: Persons and Vehicles, based on features such as size and velocity. The last step is to recognize suspicious events that may occur in the scene. Since the objects are correctly segmented and classi¯ed it is possible to identify those events using features such as velocity and time spent motionless in one spot. In this paper we recognize the suspicious event suspicion of object(s) theft from inside a parked vehicle at spot X by a person" and results show that the use of °ow detection increases the recognition of this suspicious event from 78:57% to 92:85%.

  15. Event recognition in personal photo collections via multiple instance learning-based classification of multiple images

    Science.gov (United States)

    Ahmad, Kashif; Conci, Nicola; Boato, Giulia; De Natale, Francesco G. B.

    2017-11-01

    Over the last few years, a rapid growth has been witnessed in the number of digital photos produced per year. This rapid process poses challenges in the organization and management of multimedia collections, and one viable solution consists of arranging the media on the basis of the underlying events. However, album-level annotation and the presence of irrelevant pictures in photo collections make event-based organization of personal photo albums a more challenging task. To tackle these challenges, in contrast to conventional approaches relying on supervised learning, we propose a pipeline for event recognition in personal photo collections relying on a multiple instance-learning (MIL) strategy. MIL is a modified form of supervised learning and fits well for such applications with weakly labeled data. The experimental evaluation of the proposed approach is carried out on two large-scale datasets including a self-collected and a benchmark dataset. On both, our approach significantly outperforms the existing state-of-the-art.

  16. Event-related potential evidence of form and meaning coding during online speech recognition.

    Science.gov (United States)

    Friedrich, Claudia K; Kotz, Sonja A

    2007-04-01

    It is still a matter of debate whether initial analysis of speech is independent of contextual influences or whether meaning can modulate word activation directly. Utilizing event-related brain potentials (ERPs), we tested the neural correlates of speech recognition by presenting sentences that ended with incomplete words, such as To light up the dark she needed her can-. Immediately following the incomplete words, subjects saw visual words that (i) matched form and meaning, such as candle; (ii) matched meaning but not form, such as lantern; (iii) matched form but not meaning, such as candy; or (iv) mismatched form and meaning, such as number. We report ERP evidence for two distinct cohorts of lexical tokens: (a) a left-lateralized effect, the P250, differentiates form-matching words (i, iii) and form-mismatching words (ii, iv); (b) a right-lateralized effect, the P220, differentiates words that match in form and/or meaning (i, ii, iii) from mismatching words (iv). Lastly, fully matching words (i) reduce the amplitude of the N400. These results accommodate bottom-up and top-down accounts of human speech recognition. They suggest that neural representations of form and meaning are activated independently early on and are integrated at a later stage during sentence comprehension.

  17. Individual differences in the recognition of facial expressions: an event-related potentials study.

    Directory of Open Access Journals (Sweden)

    Yoshiyuki Tamamiya

    Full Text Available Previous studies have shown that early posterior components of event-related potentials (ERPs are modulated by facial expressions. The goal of the current study was to investigate individual differences in the recognition of facial expressions by examining the relationship between ERP components and the discrimination of facial expressions. Pictures of 3 facial expressions (angry, happy, and neutral were presented to 36 young adults during ERP recording. Participants were asked to respond with a button press as soon as they recognized the expression depicted. A multiple regression analysis, where ERP components were set as predictor variables, assessed hits and reaction times in response to the facial expressions as dependent variables. The N170 amplitudes significantly predicted for accuracy of angry and happy expressions, and the N170 latencies were predictive for accuracy of neutral expressions. The P2 amplitudes significantly predicted reaction time. The P2 latencies significantly predicted reaction times only for neutral faces. These results suggest that individual differences in the recognition of facial expressions emerge from early components in visual processing.

  18. Individual differences in the recognition of facial expressions: an event-related potentials study.

    Science.gov (United States)

    Tamamiya, Yoshiyuki; Hiraki, Kazuo

    2013-01-01

    Previous studies have shown that early posterior components of event-related potentials (ERPs) are modulated by facial expressions. The goal of the current study was to investigate individual differences in the recognition of facial expressions by examining the relationship between ERP components and the discrimination of facial expressions. Pictures of 3 facial expressions (angry, happy, and neutral) were presented to 36 young adults during ERP recording. Participants were asked to respond with a button press as soon as they recognized the expression depicted. A multiple regression analysis, where ERP components were set as predictor variables, assessed hits and reaction times in response to the facial expressions as dependent variables. The N170 amplitudes significantly predicted for accuracy of angry and happy expressions, and the N170 latencies were predictive for accuracy of neutral expressions. The P2 amplitudes significantly predicted reaction time. The P2 latencies significantly predicted reaction times only for neutral faces. These results suggest that individual differences in the recognition of facial expressions emerge from early components in visual processing.

  19. Molecular architecture of protein-RNA recognition sites.

    Science.gov (United States)

    Barik, Amita; C, Nithin; Pilla, Smita P; Bahadur, Ranjit Prasad

    2015-01-01

    The molecular architecture of protein-RNA interfaces are analyzed using a non-redundant dataset of 152 protein-RNA complexes. We find that an average protein-RNA interface is smaller than an average protein-DNA interface but larger than an average protein-protein interface. Among the different classes of protein-RNA complexes, interfaces with tRNA are the largest, while the interfaces with the single-stranded RNA are the smallest. Significantly, RNA contributes more to the interface area than its partner protein. Moreover, unlike protein-protein interfaces where the side chain contributes less to the interface area compared to the main chain, the main chain and side chain contributions flipped in protein-RNA interfaces. We find that the protein surface in contact with the RNA in protein-RNA complexes is better packed than that in contact with the DNA in protein-DNA complexes, but loosely packed than that in contact with the protein in protein-protein complexes. Shape complementarity and electrostatic potential are the two major factors that determine the specificity of the protein-RNA interaction. We find that the H-bond density at the protein-RNA interfaces is similar with that of protein-DNA interfaces but higher than the protein-protein interfaces. Unlike protein-DNA interfaces where the deoxyribose has little role in intermolecular H-bonds, due to the presence of an oxygen atom at the 2' position, the ribose in RNA plays significant role in protein-RNA H-bonds. We find that besides H-bonds, salt bridges and stacking interactions also play significant role in stabilizing protein-nucleic acids interfaces; however, their contribution at the protein-protein interfaces is insignificant.

  20. Molecular events in matrix protein metabolism in the aging kidney

    Science.gov (United States)

    Sataranatarajan, Kavithalakshmi; Feliers, Denis; Mariappan, Meenalakshmi M.; Lee, Hak Joo; Lee, Myung Ja; Day, Robert T.; Yalamanchili, Hima Bindu; Choudhury, Goutam G.; Barnes, Jeffrey L.; Van Remmen, Holly; Richardson, Arlan; Kasinath, Balakuntalam S.

    2018-01-01

    Summary We explored molecular events associated with aging-induced matrix changes in the kidney. C57BL6 mice were studied in youth, middle age, and old age. Albuminuria and serum cystatin C level (an index of glomerular filtration) increased with aging. Renal hypertrophy was evident in middle-aged and old mice and was associated with glomerulomegaly and increase in mesangial fraction occupied by extracellular matrix. Content of collagen types I and III and fibronectin was increased with aging; increment in their mRNA varied with the phase of aging. The content of ZEB1 and ZEB2, collagen type I transcription inhibitors, and their binding to the collagen type Iα2 promoter by ChIP assay also showed age-phase-specific changes. Lack of increase in mRNA and data from polysome assay suggested decreased degradation as a potential mechanism for kidney collagen type I accumulation in the middle-aged mice. These changes occurred with increment in TGFβ mRNA and protein and activation of its SMAD3 pathway; SMAD3 binding to the collagen type Iα2 promoter was also increased. TGFβ-regulated microRNAs (miRs) exhibited selective regulation. The renal cortical content of miR-21 and miR-200c, but not miR-192, miR-200a, or miR-200b, was increased with aging. Increased miR-21 and miR-200c contents were associated with reduced expression of their targets, Sprouty-1 and ZEB2, respectively. These data show that aging is associated with complex molecular events in the kidney that are already evident in the middle age and progress to old age. Agephase-specific regulation of matrix protein synthesis occurs and involves matrix protein-specific transcriptional and post-transcriptional mechanisms. PMID:23020145

  1. Selecting Molecular Recognition. What Can Existing Aptamers Tell Us about Their Inherent Recognition Capabilities and Modes of Interaction?

    Directory of Open Access Journals (Sweden)

    Ralf Landgraf

    2012-05-01

    Full Text Available The use of nucleic acid derived aptamers has rapidly expanded since the introduction of SELEX in 1990. Nucleic acid aptamers have demonstrated their ability to target a broad range of molecules in ways that rival antibodies, but advances have been very uneven for different biochemical classes of targets, and clinical applications have been slow to emerge. What sets different aptamers apart from each other and from rivaling molecular recognition platforms, specifically proteins? What advantages do aptamers as a reagent class offer, and how do the chemical properties and selection procedures of aptamers influence their function? Do the building blocks of nucleic acid aptamers dictate inherent limitations in the nature of molecular targets, and do existing aptamers give us insight in how these challenges might be overcome? This review is written as an introduction for potential endusers of aptamer technology who are evaluating the advantages of aptamers as a versatile, affordable, yet highly expandable platform to target a broad range of biological processes or interactions.

  2. Magnetic deep eutectic solvents molecularly imprinted polymers for the selective recognition and separation of protein

    International Nuclear Information System (INIS)

    Liu, Yanjin; Wang, Yuzhi; Dai, Qingzhou; Zhou, Yigang

    2016-01-01

    A novel and facile magnetic deep eutectic solvents (DES) molecularly imprinted polymers (MIPs) for the selective recognition and separation of Bovine hemoglobin (BHb) was prepared. The new-type DES was adopted as the functional monomer which would bring molecular imprinted technology to a new direction. The amounts of DES were optimized. The obtained magnetic DES-MIPs were characterized with fourier transform infrared spectrometry (FT-IR), thermogravimetric analysis (TGA), field emission scanning electron microscope (FESEM), dynamic light scattering (DLS), elemental analysis and vibrating sample magnetometer (VSM). The results suggested that the imprinted polymers were successfully formed and possessed a charming magnetism. The maximum adsorption capability (Q_m_a_x) and dissociation constant (K_L) were analyzed by Langmuir isotherms (R"2 = 0.9983) and the value were estimated to be 175.44 mg/g and 0.035 mg/mL for the imprinted particles. And the imprinted particles showed a high imprinting factor of 4.77. In addition, the magnetic DES-MIPs presented outstanding recognition specificity and selectivity so that it can be utilized to separate template protein from the mixture of proteins and real samples. Last but not least, the combination of deep eutectic solvents and molecular imprinted technology in this paper provides a new perspective for the recognition and separation of proteins. - Highlights: • Combined green deep eutectic solvents (DES) and molecular imprinted technology in recognition and separation of proteins. • DES was adopted as a new-type functional monomer. • The obtained magnetic DES-MIPs can separate proteins rapidly by an external magnetic field. • Adsorption and selectivity properties were discussed.

  3. Sensors based on carbon nanotube field-effect transistors and molecular recognition approaches

    OpenAIRE

    Cid Salavert, Cristina Carlota

    2009-01-01

    The general objective of this thesis is to develop chemical sensors whose sensing capacities are based on the principle of molecular recognition and where the transduction is carried out by single-walled carbon nanotubes (SWCNT).The sensing device used is the carbon nanotube field-effect transistor (CNTFET). The new structure of the CNTFET allows nanotubes to be integrated at the surface of the devices, thus exploiting SWCNTs' sensitivity to changes in their environment. The functionalization...

  4. Magnetic deep eutectic solvents molecularly imprinted polymers for the selective recognition and separation of protein

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yanjin [State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 (China); Wang, Yuzhi, E-mail: wyzss@hnu.edu.cn [State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 (China); Dai, Qingzhou [State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 (China); Zhou, Yigang [Department of Microbiology, College of Basic Medicine, Central South University, Changsha, 410083 (China)

    2016-09-14

    A novel and facile magnetic deep eutectic solvents (DES) molecularly imprinted polymers (MIPs) for the selective recognition and separation of Bovine hemoglobin (BHb) was prepared. The new-type DES was adopted as the functional monomer which would bring molecular imprinted technology to a new direction. The amounts of DES were optimized. The obtained magnetic DES-MIPs were characterized with fourier transform infrared spectrometry (FT-IR), thermogravimetric analysis (TGA), field emission scanning electron microscope (FESEM), dynamic light scattering (DLS), elemental analysis and vibrating sample magnetometer (VSM). The results suggested that the imprinted polymers were successfully formed and possessed a charming magnetism. The maximum adsorption capability (Q{sub max}) and dissociation constant (K{sub L}) were analyzed by Langmuir isotherms (R{sup 2} = 0.9983) and the value were estimated to be 175.44 mg/g and 0.035 mg/mL for the imprinted particles. And the imprinted particles showed a high imprinting factor of 4.77. In addition, the magnetic DES-MIPs presented outstanding recognition specificity and selectivity so that it can be utilized to separate template protein from the mixture of proteins and real samples. Last but not least, the combination of deep eutectic solvents and molecular imprinted technology in this paper provides a new perspective for the recognition and separation of proteins. - Highlights: • Combined green deep eutectic solvents (DES) and molecular imprinted technology in recognition and separation of proteins. • DES was adopted as a new-type functional monomer. • The obtained magnetic DES-MIPs can separate proteins rapidly by an external magnetic field. • Adsorption and selectivity properties were discussed.

  5. Electrochemical sensor for dopamine based on a novel graphene-molecular imprinted polymers composite recognition element

    DEFF Research Database (Denmark)

    Mao, Yan; Bao, Yu; Gan, Shiyu

    2011-01-01

    A novel composite of graphene sheets/Congo red-molecular imprinted polymers (GSCR-MIPs) was synthesized through free radical polymerization (FRP) and applied as a molecular recognition element to construct dopamine (DA) electrochemical sensor. The template molecules (DA) were firstly absorbed...... at the GSCR surface due to their excellent affinity, and subsequently, selective copolymerization of methacrylic acid (MAA) and ethylene glycol dimethacrylate (EGDMA) was further achieved at the GSCR surface. Potential scanning was presented to extract DA molecules from the imprinted polymers film...

  6. Sparsey^TM: Spatiotemporal Event Recognition via Deep Hierarchical Sparse Distributed Codes

    Directory of Open Access Journals (Sweden)

    Gerard J Rinkus

    2014-12-01

    Full Text Available The visual cortex’s hierarchical, multi-level organization is captured in many biologically inspired computational vision models, the general idea being that progressively larger scale (spatially/temporally and more complex visual features are represented in progressively higher areas. However, most earlier models use localist representations (codes in each representational field (which we equate with the cortical macrocolumn, mac, at each level. In localism, each represented feature/concept/event (hereinafter item is coded by a single unit. The model we describe, Sparsey, is hierarchical as well but crucially, it uses sparse distributed coding (SDC in every mac in all levels. In SDC, each represented item is coded by a small subset of the mac’s units. The SDCs of different items can overlap and the size of overlap between items can be used to represent their similarity. The difference between localism and SDC is crucial because SDC allows the two essential operations of associative memory, storing a new item and retrieving the best-matching stored item, to be done in fixed time for the life of the model. Since the model’s core algorithm, which does both storage and retrieval (inference, makes a single pass over all macs on each time step, the overall model’s storage/retrieval operation is also fixed-time, a criterion we consider essential for scalability to the huge (Big Data problems. A 2010 paper described a non-hierarchical version of this model in the context of purely spatial pattern processing. Here, we elaborate a fully hierarchical model (arbitrary numbers of levels and macs per level, describing novel model principles like progressive critical periods, dynamic modulation of principal cells’ activation functions based on a mac-level familiarity measure, representation of multiple simultaneously active hypotheses, a novel method of time warp invariant recognition, and we report results showing learning/recognition of

  7. Reconstruction efficiency and precision for the events detected by the BIS-2 installation using the Perun pattern recognition program

    International Nuclear Information System (INIS)

    Burilkov, D.T.; Genchev, V.I.; Markov, P.K.; Likhachev, M.F.; Takhtamyshev, G.G.; Todorov, P.T.; Trayanov, P.K.

    1982-01-01

    Results of studying the efficiency and accuracy of the track and event reconstruction with the Perun pattern recognition program used in the experiments carried out at the BIS-2 installation are presented. The Monte Carlo method is used for simulating the processes of neutron interactions with matter. The con-- clusion is made that the Perun program correctly, with good accuracy and high efficiency reconstructs complex multiparticle events [ru

  8. Molecular mechanism for differential recognition of membrane phosphatidylserine by the immune regulatory receptor Tim4.

    Science.gov (United States)

    Tietjen, Gregory T; Gong, Zhiliang; Chen, Chiu-Hao; Vargas, Ernesto; Crooks, James E; Cao, Kathleen D; Heffern, Charles T R; Henderson, J Michael; Meron, Mati; Lin, Binhua; Roux, Benot; Schlossman, Mark L; Steck, Theodore L; Lee, Ka Yee C; Adams, Erin J

    2014-04-15

    Recognition of phosphatidylserine (PS) lipids exposed on the extracellular leaflet of plasma membranes is implicated in both apoptotic cell removal and immune regulation. The PS receptor T cell immunoglobulin and mucin-domain-containing molecule 4 (Tim4) regulates T-cell immunity via phagocytosis of both apoptotic (high PS exposure) and nonapoptotic (intermediate PS exposure) activated T cells. The latter population must be removed at lower efficiency to sensitively control immune tolerance and memory cell population size, but the molecular basis for how Tim4 achieves this sensitivity is unknown. Using a combination of interfacial X-ray scattering, molecular dynamics simulations, and membrane binding assays, we demonstrate how Tim4 recognizes PS in the context of a lipid bilayer. Our data reveal that in addition to the known Ca(2+)-coordinated, single-PS binding pocket, Tim4 has four weaker sites of potential ionic interactions with PS lipids. This organization makes Tim4 sensitive to PS surface concentration in a manner capable of supporting differential recognition on the basis of PS exposure level. The structurally homologous, but functionally distinct, Tim1 and Tim3 are significantly less sensitive to PS surface density, likely reflecting the differences in immunological function between the Tim proteins. These results establish the potential for lipid membrane parameters, such as PS surface density, to play a critical role in facilitating selective recognition of PS-exposing cells. Furthermore, our multidisciplinary approach overcomes the difficulties associated with characterizing dynamic protein/membrane systems to reveal the molecular mechanisms underlying Tim4's recognition properties, and thereby provides an approach capable of providing atomic-level detail to uncover the nuances of protein/membrane interactions.

  9. Recognition of Conformational Changes in β-Lactoglobulin by Molecularly Imprinted Thin Films

    Science.gov (United States)

    Turner, Nicholas W.; Liu, Xiao; Piletsky, Sergey A.; Hlady, Vladimir; Britt, David W.

    2008-01-01

    Pathogenesis in protein conformational diseases is initiated by changes in protein secondary structure. This molecular restructuring presents an opportunity for novel shape-based detection approaches, as protein molecular weight and chemistry are otherwise unaltered. Here we apply molecular imprinting to discriminate between distinct conformations of the model protein β-lactoglobulin (BLG). Thermal- and fluoro-alcohol-induced BLG isoforms were imprinted in thin films of 3-aminophenylboronic acid on quartz crystal microbalance chips. Enhanced rebinding of the template isoform was observed in all cases when compared to the binding of nontemplate isoforms over the concentration range of 1–100 µg mL−1. Furthermore, it was observed that the greater the changes in the secondary structure of the template protein the lower the binding of native BLG challenges to the imprint, suggesting a strong steric influence in the recognition system. This feasibility study is a first demonstration of molecular imprints for recognition of distinct conformations of the same protein. PMID:17665947

  10. Synthesis and Guest Recognition of Switchable Pt-Salphen Based Molecular Tweezers

    Directory of Open Access Journals (Sweden)

    Lorien Benda

    2018-04-01

    Full Text Available Molecular tweezers are artificial receptors that have an open cavity generated by two recognition units pre-organized by a spacer. Switchable molecular tweezers, using a stimuli-responsive spacer, are particularly appealing as prototypes of the molecular machines that combine mechanical motion and allosteric recognition properties. In this present study, the synthesis of switchable molecular tweezers composed of a central terpyridine unit substituted in 4,4″ positions by two Pt(II-salphen complexes is reported. The terpyridine ligand can be reversibly converted upon Zn(II coordination from a free ‘U’-shaped closed form to a coordinated ‘W’ open form. This new substitution pattern enables a reverse control of the mechanical motion compared to the previously reported 6,6″ substituted terpyridine-based tweezers. Guest binding studies with aromatic guests showed an intercalation of coronene in the cavity created by the Pt-salphen moieties in the closed conformation. The formation of 1:1 host-guest complex was investigated by a combination of NMR studies and DFT calculations.

  11. Molecular recognition in myxobacterial outer membrane exchange: functional, social and evolutionary implications.

    Science.gov (United States)

    Wall, Daniel

    2014-01-01

    Through cooperative interactions, bacteria can build multicellular communities. To ensure that productive interactions occur, bacteria must recognize their neighbours and respond accordingly. Molecular recognition between cells is thus a fundamental behaviour, and in bacteria important discoveries have been made. This MicroReview focuses on a recently described recognition system in myxobacteria that is governed by a polymorphic cell surface receptor called TraA. TraA regulates outer membrane exchange (OME), whereby myxobacterial cells transiently fuse their OMs to efficiently transfer proteins and lipids between cells. Unlike other transport systems, OME is rather indiscriminate in what OM goods are transferred. In contrast, the recognition of partnering cells is discriminatory and only occurs between cells that bear identical or closely related TraA proteins. Therefore TraA functions in kin recognition and, in turn, OME helps regulate social interactions between myxobacteria. Here, I discuss and speculate on the social and evolutionary implications of OME and suggest it helps to guide their transition from free-living cells into coherent and functional populations. © 2013 John Wiley & Sons Ltd.

  12. Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches

    KAUST Repository

    Jiang, Hanlun

    2016-12-06

    MicroRNA (miRNA) and Argonaute (AGO) protein together form the RNA-induced silencing complex (RISC) that plays an essential role in the regulation of gene expression. Elucidating the underlying mechanism of AGO-miRNA recognition is thus of great importance not only for the in-depth understanding of miRNA function but also for inspiring new drugs targeting miRNAs. In this chapter we introduce a combined computational approach of molecular dynamics (MD) simulations, Markov state models (MSMs), and protein-RNA docking to investigate AGO-miRNA recognition. Constructed from MD simulations, MSMs can elucidate the conformational dynamics of AGO at biologically relevant timescales. Protein-RNA docking can then efficiently identify the AGO conformations that are geometrically accessible to miRNA. Using our recent work on human AGO2 as an example, we explain the rationale and the workflow of our method in details. This combined approach holds great promise to complement experiments in unraveling the mechanisms of molecular recognition between large, flexible, and complex biomolecules.

  13. Molecularly imprinted titania nanoparticles for selective recognition and assay of uric acid

    Science.gov (United States)

    Mujahid, Adnan; Khan, Aimen Idrees; Afzal, Adeel; Hussain, Tajamal; Raza, Muhammad Hamid; Shah, Asma Tufail; uz Zaman, Waheed

    2015-06-01

    Molecularly imprinted titania nanoparticles are su ccessfully synthesized by sol-gel method for the selective recognition of uric acid. Atomic force microscopy is used to study the morphology of uric acid imprinted titania nanoparticles with diameter in the range of 100-150 nm. Scanning electron microscopy images of thick titania layer indicate the formation of fine network of titania nanoparticles with uniform distribution. Molecular imprinting of uric acid as well as its subsequent washing is confirmed by Fourier transformation infrared spectroscopy measurements. Uric acid rebinding studies reveal the recognition capability of imprinted particles in the range of 0.01-0.095 mmol, which is applicable in monitoring normal to elevated levels of uric acid in human blood. The optical shift (signal) of imprinted particles is six times higher in comparison with non-imprinted particles for the same concentration of uric acid. Imprinted titania particles have shown substantially reduced binding affinity toward interfering and structurally related substances, e.g. ascorbic acid and guanine. These results suggest the possible application of titania nanoparticles in uric acid recognition and quantification in blood serum.

  14. Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches.

    Science.gov (United States)

    Jiang, Hanlun; Zhu, Lizhe; Héliou, Amélie; Gao, Xin; Bernauer, Julie; Huang, Xuhui

    2017-01-01

    MicroRNA (miRNA) and Argonaute (AGO) protein together form the RNA-induced silencing complex (RISC) that plays an essential role in the regulation of gene expression. Elucidating the underlying mechanism of AGO-miRNA recognition is thus of great importance not only for the in-depth understanding of miRNA function but also for inspiring new drugs targeting miRNAs. In this chapter we introduce a combined computational approach of molecular dynamics (MD) simulations, Markov state models (MSMs), and protein-RNA docking to investigate AGO-miRNA recognition. Constructed from MD simulations, MSMs can elucidate the conformational dynamics of AGO at biologically relevant timescales. Protein-RNA docking can then efficiently identify the AGO conformations that are geometrically accessible to miRNA. Using our recent work on human AGO2 as an example, we explain the rationale and the workflow of our method in details. This combined approach holds great promise to complement experiments in unraveling the mechanisms of molecular recognition between large, flexible, and complex biomolecules.

  15. Two dimensional molecular electronics spectroscopy for molecular fingerprinting, DNA sequencing, and cancerous DNA recognition.

    Science.gov (United States)

    Rajan, Arunkumar Chitteth; Rezapour, Mohammad Reza; Yun, Jeonghun; Cho, Yeonchoo; Cho, Woo Jong; Min, Seung Kyu; Lee, Geunsik; Kim, Kwang S

    2014-02-25

    Laser-driven molecular spectroscopy of low spatial resolution is widely used, while electronic current-driven molecular spectroscopy of atomic scale resolution has been limited because currents provide only minimal information. However, electron transmission of a graphene nanoribbon on which a molecule is adsorbed shows molecular fingerprints of Fano resonances, i.e., characteristic features of frontier orbitals and conformations of physisorbed molecules. Utilizing these resonance profiles, here we demonstrate two-dimensional molecular electronics spectroscopy (2D MES). The differential conductance with respect to bias and gate voltages not only distinguishes different types of nucleobases for DNA sequencing but also recognizes methylated nucleobases which could be related to cancerous cell growth. This 2D MES could open an exciting field to recognize single molecule signatures at atomic resolution. The advantages of the 2D MES over the one-dimensional (1D) current analysis can be comparable to those of 2D NMR over 1D NMR analysis.

  16. Selective Nitrate Recognition by a Halogen‐Bonding Four‐Station [3]Rotaxane Molecular Shuttle

    Science.gov (United States)

    Barendt, Timothy A.; Docker, Andrew; Marques, Igor; Félix, Vítor

    2016-01-01

    Abstract The synthesis of the first halogen bonding [3]rotaxane host system containing a bis‐iodo triazolium‐bis‐naphthalene diimide four station axle component is reported. Proton NMR anion binding titration experiments revealed the halogen bonding rotaxane is selective for nitrate over the more basic acetate, hydrogen carbonate and dihydrogen phosphate oxoanions and chloride, and exhibits enhanced recognition of anions relative to a hydrogen bonding analogue. This elaborate interlocked anion receptor functions via a novel dynamic pincer mechanism where upon nitrate anion binding, both macrocycles shuttle from the naphthalene diimide stations at the periphery of the axle to the central halogen bonding iodo‐triazolium station anion recognition sites to form a unique 1:1 stoichiometric nitrate anion–rotaxane sandwich complex. Molecular dynamics simulations carried out on the nitrate and chloride halogen bonding [3]rotaxane complexes corroborate the 1H NMR anion binding results. PMID:27436297

  17. Integrated structural biology to unravel molecular mechanisms of protein-RNA recognition.

    Science.gov (United States)

    Schlundt, Andreas; Tants, Jan-Niklas; Sattler, Michael

    2017-04-15

    Recent advances in RNA sequencing technologies have greatly expanded our knowledge of the RNA landscape in cells, often with spatiotemporal resolution. These techniques identified many new (often non-coding) RNA molecules. Large-scale studies have also discovered novel RNA binding proteins (RBPs), which exhibit single or multiple RNA binding domains (RBDs) for recognition of specific sequence or structured motifs in RNA. Starting from these large-scale approaches it is crucial to unravel the molecular principles of protein-RNA recognition in ribonucleoprotein complexes (RNPs) to understand the underlying mechanisms of gene regulation. Structural biology and biophysical studies at highest possible resolution are key to elucidate molecular mechanisms of RNA recognition by RBPs and how conformational dynamics, weak interactions and cooperative binding contribute to the formation of specific, context-dependent RNPs. While large compact RNPs can be well studied by X-ray crystallography and cryo-EM, analysis of dynamics and weak interaction necessitates the use of solution methods to capture these properties. Here, we illustrate methods to study the structure and conformational dynamics of protein-RNA complexes in solution starting from the identification of interaction partners in a given RNP. Biophysical and biochemical techniques support the characterization of a protein-RNA complex and identify regions relevant in structural analysis. Nuclear magnetic resonance (NMR) is a powerful tool to gain information on folding, stability and dynamics of RNAs and characterize RNPs in solution. It provides crucial information that is complementary to the static pictures derived from other techniques. NMR can be readily combined with other solution techniques, such as small angle X-ray and/or neutron scattering (SAXS/SANS), electron paramagnetic resonance (EPR), and Förster resonance energy transfer (FRET), which provide information about overall shapes, internal domain

  18. Metal oxide nanosensors using polymeric membranes, enzymes and antibody receptors as ion and molecular recognition elements.

    Science.gov (United States)

    Willander, Magnus; Khun, Kimleang; Ibupoto, Zafar Hussain

    2014-05-16

    The concept of recognition and biofunctionality has attracted increasing interest in the fields of chemistry and material sciences. Advances in the field of nanotechnology for the synthesis of desired metal oxide nanostructures have provided a solid platform for the integration of nanoelectronic devices. These nanoelectronics-based devices have the ability to recognize molecular species of living organisms, and they have created the possibility for advanced chemical sensing functionalities with low limits of detection in the nanomolar range. In this review, various metal oxides, such as ZnO-, CuO-, and NiO-based nanosensors, are described using different methods (receptors) of functionalization for molecular and ion recognition. These functionalized metal oxide surfaces with a specific receptor involve either a complex formation between the receptor and the analyte or an electrostatic interaction during the chemical sensing of analytes. Metal oxide nanostructures are considered revolutionary nanomaterials that have a specific surface for the immobilization of biomolecules with much needed orientation, good conformation and enhanced biological activity which further improve the sensing properties of nanosensors. Metal oxide nanostructures are associated with certain unique optical, electrical and molecular characteristics in addition to unique functionalities and surface charge features which shows attractive platforms for interfacing biorecognition elements with effective transducing properties for signal amplification. There is a great opportunity in the near future for metal oxide nanostructure-based miniaturization and the development of engineering sensor devices.

  19. Metal Oxide Nanosensors Using Polymeric Membranes, Enzymes and Antibody Receptors as Ion and Molecular Recognition Elements

    Directory of Open Access Journals (Sweden)

    Magnus Willander

    2014-05-01

    Full Text Available The concept of recognition and biofunctionality has attracted increasing interest in the fields of chemistry and material sciences. Advances in the field of nanotechnology for the synthesis of desired metal oxide nanostructures have provided a solid platform for the integration of nanoelectronic devices. These nanoelectronics-based devices have the ability to recognize molecular species of living organisms, and they have created the possibility for advanced chemical sensing functionalities with low limits of detection in the nanomolar range. In this review, various metal oxides, such as ZnO-, CuO-, and NiO-based nanosensors, are described using different methods (receptors of functionalization for molecular and ion recognition. These functionalized metal oxide surfaces with a specific receptor involve either a complex formation between the receptor and the analyte or an electrostatic interaction during the chemical sensing of analytes. Metal oxide nanostructures are considered revolutionary nanomaterials that have a specific surface for the immobilization of biomolecules with much needed orientation, good conformation and enhanced biological activity which further improve the sensing properties of nanosensors. Metal oxide nanostructures are associated with certain unique optical, electrical and molecular characteristics in addition to unique functionalities and surface charge features which shows attractive platforms for interfacing biorecognition elements with effective transducing properties for signal amplification. There is a great opportunity in the near future for metal oxide nanostructure-based miniaturization and the development of engineering sensor devices.

  20. Event-Related Potential (ERP) Evidence for Fluency-Based Recognition Memory

    Science.gov (United States)

    Leynes, P. Andrew; Zish, Kevin

    2012-01-01

    Two experiments investigated the influence of perceptual fluency on recognition memory. Words were studied using a shallow encoding task to decrease the contribution of recollection on recognition. Fluency was manipulated by blurring half of the test probes. Clarity varied randomly across trials in one experiment and was grouped into two blocks…

  1. Molecular recognition of nucleotides in micelles and the development and expansion of a chemistry outreach program

    Science.gov (United States)

    Schechinger, Linda Sue

    I. To investigate the delivery of nucleotide-based drugs, we are studying molecular recognition of nucleotide derivatives in environments that are similar to cell membranes. The Nowick group previously discovered that membrane-like surfactant micelles tetradecyltrimethylammonium bromide (TTAB) micelle facilitate molecular of adenosine monophosphate (AMP) recognition. The micelles bind nucleotides by means of electrostatic interactions and hydrogen bonding. We observed binding by following 1H NMR chemical shift changes of unique hexylthymine protons upon addition of AMP. Cationic micelles are required for binding. In surfactant-free or sodium dodecylsulfate solutions, no hydrogen bonding is observed. These observations suggest that the cationic surfactant headgroups bind the nucleotide phosphate group, while the intramicellar base binds the nucleotide base. The micellar system was optimized to enhance binding and selectivity for adenosine nucleotides. The selectivity for adenosine and the number of phosphate groups attached to the adenosine were both investigated. Addition of cytidine, guanidine, or uridine monophosphates, results in no significant downfield shifting of the NH resonance. Selectivity for the phosphate is limited, since adenosine mono-, di-, and triphosphates all have similar binding constants. We successfully achieved molecular recognition of adenosine nucleotides in micellar environments. There is significant difference in the binding interactions between the adenosine nucleotides and three other natural nucleotides. II. The UCI Chemistry Outreach Program (UCICOP) addresses the declining interest of the nations youth for science. UCICOP brings fun and exciting chemistry experiments to local high schools, to remind students that science is fun and has many practical uses. Volunteer students and alumni of UCI perform the demonstrations using scripts and material provided by UCICOP. The preparation of scripts and materials is done by two coordinators

  2. Miniature Chemical Sensor Combining Molecular Recognition with Evanescent Wave Cavity Ring-Down Spectroscopy

    International Nuclear Information System (INIS)

    Pipino, Andrew C. R.; Meuse, Curtis W.

    2002-01-01

    To address the chemical sensing needs of DOE, a new class of chemical sensors is being developed that enables qualitative and quantitative, remote, real-time, optical diagnostics of chemical species in hazardous gas, liquid, and semi-solid phases by employing evanescent wave cavity ringdown spectroscopy (EW-CRDS). The sensitivity of EW-CRDS was demonstrated previously under Project No.60231. The objective of this project is to enhance the range of application and selectivity of the technique by combining EW-CRDS with refractive-index-sensitive nanoparticle optics, molecular recognition (MR) chemistry, and by utilizing the polarization-dependence of EW-CRDS. Research Progress and Implications

  3. In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element Specific for Bromacil

    Directory of Open Access Journals (Sweden)

    Ryan M. Williams

    2014-01-01

    Full Text Available Bromacil is a widely used herbicide that is known to contaminate environmental systems. Due to the hazards it presents and inefficient detection methods, it is necessary to create a rapid and efficient sensing device. Towards this end, we have utilized a stringent in vitro selection method to identify single-stranded DNA molecular recognition elements (MRE specific for bromacil. We have identified one MRE with high affinity (Kd=9.6 nM and specificity for bromacil compared to negative targets of selection and other pesticides. The selected ssDNA MRE will be useful as the sensing element in a field-deployable bromacil detection device.

  4. π-Cation Interactions in Molecular Recognition: Perspectives on Pharmaceuticals and Pesticides.

    Science.gov (United States)

    Liang, Zhibin; Li, Qing X

    2018-04-04

    The π-cation interaction that differs from the cation-π interaction is a valuable concept in molecular design of pharmaceuticals and pesticides. In this Perspective we present an up-to-date review (from 1995 to 2017) on bioactive molecules involving π-cation interactions with the recognition site, and categorize into systems of inhibitor-enzyme, ligand-receptor, ligand-transporter, and hapten-antibody. The concept of π-cation interactions offers use of π systems in a small molecule to enhance the binding affinity, specificity, selectivity, lipophilicity, bioavailability, and metabolic stability, which are physiochemical features desired for drugs and pesticides.

  5. Molecular recognition of malachite green by hemoglobin and their specific interactions: insights from in silico docking and molecular spectroscopy.

    Science.gov (United States)

    Peng, Wei; Ding, Fei; Peng, Yu-Kui; Sun, Ying

    2014-01-01

    Malachite green is an organic compound that can be widely used as a dyestuff for various materials; it has also emerged as a controversial agent in aquaculture. Since malachite green is proven to be carcinogenic and mutagenic, it may become a hazard to public health. For this reason, it is urgently required to analyze this controversial dye in more detail. In our current research, the interaction between malachite green and hemoglobin under physiological conditions was investigated by the methods of molecular modeling, fluorescence spectroscopy, circular dichroism (CD) as well as hydrophobic ANS displacement experiments. From the molecular docking, the central cavity of hemoglobin was assigned to possess high-affinity for malachite green, this result was corroborated by time-resolved fluorescence and hydrophobic ANS probe results. The recognition mechanism was found to be of static type, or rather the hemoglobin-malachite green complex formation occurred via noncovalent interactions such as π-π interactions, hydrogen bonds and hydrophobic interactions with an association constant of 10(4) M(-1). Moreover, the results also show that the spatial structure of the biopolymer was changed in the presence of malachite green with a decrease of the α-helix and increase of the β-sheet, turn and random coil suggesting protein damage, as derived from far-UV CD and three-dimensional fluorescence. Results of this work will help to further comprehend the molecular recognition of malachite green by the receptor protein and the possible toxicological profiles of other compounds, which are the metabolites and ramifications of malachite green.

  6. The time course of lexical competition during spoken word recognition in Mandarin Chinese: an event-related potential study.

    Science.gov (United States)

    Huang, Xianjun; Yang, Jin-Chen

    2016-01-20

    The present study investigated the effect of lexical competition on the time course of spoken word recognition in Mandarin Chinese using a unimodal auditory priming paradigm. Two kinds of competitive environments were designed. In one session (session 1), only the unrelated and the identical primes were presented before the target words. In the other session (session 2), besides the two conditions in session 1, the target words were also preceded by the cohort primes that have the same initial syllables as the targets. Behavioral results showed an inhibitory effect of the cohort competitors (primes) on target word recognition. The event-related potential results showed that the spoken word recognition processing in the middle and late latency windows is modulated by whether the phonologically related competitors are presented or not. Specifically, preceding activation of the competitors can induce direct competitions between multiple candidate words and lead to increased processing difficulties, primarily at the word disambiguation and selection stage during Mandarin Chinese spoken word recognition. The current study provided both behavioral and electrophysiological evidences for the lexical competition effect among the candidate words during spoken word recognition.

  7. Molecular imprinting-chemiluminescence determination of trimethoprim using trimethoprim-imprinted polymer as recognition material.

    Science.gov (United States)

    He, Yunhua; Lu, Jiuru; Liu, Mei; Du, Jianxiu

    2005-07-01

    A new molecular imprinting-chemiluminescence method for the determination of trimethoprim was developed, in which trimethoprim-imprinted polymer was used as the molecular recognition material and the CL reaction of trimethoprim with potassium permanganate in acidic medium was used as the detection system. The CL intensity responds linearly to the concentration of trimethoprim within the 5.0 x 10(-8)-5.0 x 10(-6) g mL(-1) range (r= 0.9983) with a detection limit of 2 x 10(-8) g mL(-1). The relative standard deviation for the determination of 1.0 x 10(-7) g mL(-1) trimethoprim solutions is 4.8% (n= 9). The method has been applied to the determination of trimethoprim in pharmaceutical preparations and body fluids, and satisfactory results were obtained.

  8. RECOGNITION DYNAMICS OF ESCHERICHIA COLI THIOREDOXIN PROBED USING MOLECULAR DYNAMICS AND BINDING FREE ENERGY CALCULATIONS

    Directory of Open Access Journals (Sweden)

    M. S. Shahul Hameed

    2016-03-01

    Full Text Available E. coli thioredoxin has been regarded as a hub protein as it interacts with, and regulates, numerous target proteins involved in a wide variety of cellular processes. Thioredoxin can form complexes with a variety of target proteins with a wide range of affinity, using a consensus binding surface. In this study an attempt to deduce the molecular basis for the observed multispecificity of E. coli thioredoxin has been made. In this manuscript it has been shown that structural plasticity, adaptable and exposed hydrophobic binding surface, surface electrostatics, closely clustered multiple hot spot residues and conformational changes brought about by the redox status of the protein have been shown to account for the observed multispecificity and molecular recognition of thioredoxin. Dynamical differences between the two redox forms of the enzyme have also been studied to account for their differing interactions with some target proteins.

  9. Investigating the binding behaviour of two avidin-based testosterone binders using molecular recognition force spectroscopy.

    Science.gov (United States)

    Rangl, Martina; Leitner, Michael; Riihimäki, Tiina; Lehtonen, Soili; Hytönen, Vesa P; Gruber, Hermann J; Kulomaa, Markku; Hinterdorfer, Peter; Ebner, Andreas

    2014-02-01

    Molecular recognition force spectroscopy, a biosensing atomic force microscopy technique allows to characterise the dissociation of ligand-receptor complexes at the molecular level. Here, we used molecular recognition force spectroscopy to study the binding capability of recently developed testosterone binders. The two avidin-based proteins called sbAvd-1 and sbAvd-2 are expected to bind both testosterone and biotin but differ in their binding behaviour towards these ligands. To explore the ligand binding and dissociation energy landscape of these proteins, we tethered biotin or testosterone to the atomic force microscopy probe while the testosterone-binding protein was immobilized on the surface. Repeated formation and rupture of the ligand-receptor complex at different pulling velocities allowed determination of the loading rate dependence of the complex-rupturing force. In this way, we obtained the molecular dissociation rate (k(off)) and energy landscape distances (x(β)) of the four possible complexes: sbAvd-1-biotin, sbAvd-1-testosterone, sbAvd-2-biotin and sbAvd-2-testosterone. It was found that the kinetic off-rates for both proteins and both ligands are similar. In contrast, the x(β) values, as well as the probability of complex formations, varied considerably. In addition, competitive binding experiments with biotin and testosterone in solution differ significantly for the two testosterone-binding proteins, implying a decreased cross-reactivity of sbAvd-2. Unravelling the binding behaviour of the investigated testosterone-binding proteins is expected to improve their usability for possible sensing applications. Copyright © 2014 John Wiley & Sons, Ltd.

  10. Magnetic-graphene based molecularly imprinted polymer nanocomposite for the recognition of bovine hemoglobin.

    Science.gov (United States)

    Guo, Junxia; Wang, Yuzhi; Liu, Yanjin; Zhang, Cenjin; Zhou, Yigang

    2015-11-01

    The protein imprinted technique combining surface imprinting and nanomaterials has been an attractive strategy for recognition and rapid separation of proteins. In this work, magnetic-graphene (MG) was chosen as the supporting substrate for the magnetic nanomaterials, which served to absorb the targeting imprinting molecules, bovine hemoglobin (BHb). Acryl amide (AAm) with a high affinity to BHb and N,N'- methylenebisacrylamide (MBA) were selected as the functional monomer and cross-linking agent, respectively. After in-situ polymerization, the proposed magnetic-graphene based molecularly imprinted polymer (MG-MIP) was obtained with a further extraction step of imprinted BHb. Fourier transform infrared (FT-IR), scanning electron microscopy (SEM), transmission electron microscopy (TEM), raman spectroscopy(RS), X-ray diffraction (XRD) and vibrating sample magnetometer (VSM) were employed to characterize the resulted MG-MIP. The maximum adsorption capability (Qmax) was determined by Langmuir Isotherm Plots and was 186.73 mg/g for imprinted nanomaterials (MIP) with an imprinting factor of 1.96. The selectivity of MG-MIP was investigated by using several proteins that are different in molecular mass and isoelectric points as the reference. The results showed that the shape memory effect of imprinted cavities, the size of proteins and the charge effect of proteins were the major factors for the selective recognition. The proposed method was also employed to specifically capture BHb from a binary protein mixture. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Higher Desolvation Energy Reduces Molecular Recognition in Multi-Drug Resistant HIV-1 Protease

    Directory of Open Access Journals (Sweden)

    Ladislau C. Kovari

    2012-05-01

    Full Text Available Designing HIV-1 protease inhibitors that overcome drug-resistance is still a challenging task. In this study, four clinical isolates of multi-drug resistant HIV-1 proteases that exhibit resistance to all the US FDA-approved HIV-1 protease inhibitors and also reduce the substrate recognition ability were examined. A multi-drug resistant HIV-1 protease isolate, MDR 769, was co-crystallized with the p2/NC substrate and the mutated CA/p2 substrate, CA/p2 P1’F. Both substrates display different levels of molecular recognition by the wild-type and multi-drug resistant HIV-1 protease. From the crystal structures, only limited differences can be identified between the wild-type and multi-drug resistant protease. Therefore, a wild-type HIV-1 protease and four multi-drug resistant HIV-1 proteases in complex with the two peptides were modeled based on the crystal structures and examined during a 10 ns-molecular dynamics simulation. The simulation results reveal that the multi-drug resistant HIV-1 proteases require higher desolvation energy to form complexes with the peptides. This result suggests that the desolvation of the HIV-1 protease active site is an important step of protease-ligand complex formation as well as drug resistance. Therefore, desolvation energy could be considered as a parameter in the evaluation of future HIV-1 protease inhibitor candidates.

  12. Molecularly imprinted poly (methacrylamide-co-methacrylic acid) composite membranes for recognition of curcumin

    International Nuclear Information System (INIS)

    Wang Ping; Hu Wenming; Su Weike

    2008-01-01

    In this study, molecularly imprinted poly (methacrylamide-co-methacrylic acid) composite membranes with different ratio of methacrylamide (MAM) versus methacrylic acid (MAA) were prepared via UV initiated photo-copolymerization on the commercial filter paper. Curcumin was chosen as the template molecule. Infra-red (IR) spectroscopy was used to study the binding mechanism between the imprinted sites and the templates. The morphology of the resultant membranes was visualized by scanning electron microscopy (SEM). Static equilibrium binding and recognition properties of the imprinted composite membranes to curcumin (cur-I) and its analogues demethoxycurcumin (cur-II) or bisdemethoxycurcumin (cur-III) were tested. The results showed that curcumin-imprinted membranes had the best recognition ability to curcumin compared to its analogues. From the results, the biggest selectivity factor of α cur-I/cur-II and α cur-I/cur-III were 1.50 and 5.94, and they were obtained from the composite membranes in which MAM/MAA were 1:4 and 0:1, respectively. The results of this study implied that the molecularly imprinted composite membranes could be used as separation membranes for curcumin enrichment

  13. An Event Related Potentials Study of the Effects of Age, Load and Maintenance Duration on Working Memory Recognition

    Science.gov (United States)

    Pinal, Diego; Zurrón, Montserrat; Díaz, Fernando

    2015-01-01

    Age-related decline in cognitive capacities has been attributed to a generalized slowing of processing speed and a reduction in working memory (WM) capacity. Nevertheless, it is unclear how age affects visuospatial WM recognition and its underlying brain electrical activity. Whether age modulates the effects of memory load or information maintenance duration, which determine the limits of WM, remains also elusive. In this exploratory study, performance in a delayed match to sample task declined with age, particularly in conditions with high memory load. Event related potentials analysis revealed longer N2 and P300 latencies in old than in young adults during WM recognition, which may reflect slowing of stimulus evaluation and classification processes, respectively. Although there were no differences between groups in N2 or P300 amplitudes, the latter was more homogeneously distributed in old than in young adults, which may indicate an age-related increased reliance in frontal vs parietal resources during WM recognition. This was further supported by an age-related reduced posterior cingulate activation and increased superior frontal gyrus activation revealed through standardized low resolution electromagnetic tomography. Memory load and maintenance duration effects on brain activity were similar in both age groups. These behavioral and electrophysiological results add evidence in support of age-related decline in WM recognition theories, with a slowing of processing speed that may be limited to stimulus evaluation and categorization processes -with no effects on perceptual processes- and a posterior to anterior shift in the recruitment of neural resources. PMID:26569113

  14. An Event Related Potentials Study of the Effects of Age, Load and Maintenance Duration on Working Memory Recognition.

    Science.gov (United States)

    Pinal, Diego; Zurrón, Montserrat; Díaz, Fernando

    2015-01-01

    Age-related decline in cognitive capacities has been attributed to a generalized slowing of processing speed and a reduction in working memory (WM) capacity. Nevertheless, it is unclear how age affects visuospatial WM recognition and its underlying brain electrical activity. Whether age modulates the effects of memory load or information maintenance duration, which determine the limits of WM, remains also elusive. In this exploratory study, performance in a delayed match to sample task declined with age, particularly in conditions with high memory load. Event related potentials analysis revealed longer N2 and P300 latencies in old than in young adults during WM recognition, which may reflect slowing of stimulus evaluation and classification processes, respectively. Although there were no differences between groups in N2 or P300 amplitudes, the latter was more homogeneously distributed in old than in young adults, which may indicate an age-related increased reliance in frontal vs parietal resources during WM recognition. This was further supported by an age-related reduced posterior cingulate activation and increased superior frontal gyrus activation revealed through standardized low resolution electromagnetic tomography. Memory load and maintenance duration effects on brain activity were similar in both age groups. These behavioral and electrophysiological results add evidence in support of age-related decline in WM recognition theories, with a slowing of processing speed that may be limited to stimulus evaluation and categorization processes--with no effects on perceptual processes--and a posterior to anterior shift in the recruitment of neural resources.

  15. Word recognition memory in adults with attention-deficit/hyperactivity disorder as reflected by event-related potentials

    Directory of Open Access Journals (Sweden)

    Vanessa Prox-Vagedes

    2011-03-01

    Full Text Available Objective: Attention-deficit/hyperactivity disorder (ADHD is increasingly diagnosed in adults. In this study we address the question whether there are impairments in recognition memory. Methods: In the present study 13 adults diagnosed with ADHD according to DSM-IV and 13 healthy controls were examined with respect to event-related potentials (ERPs in a visual continuous word recognition paradigm to gain information about recognition memory effects in these patients. Results: The amplitude of one attention-related ERP-component, the N1, was significantly increased for the ADHD adults compared with the healthy controls in the occipital electrodes. The ERPs for the second presentation were significantly more positive than the ERPs for the first presentation. This effect did not significantly differ between groups. Conclusion: Neuronal activity related to an early attentional mechanism appears to be enhanced in ADHD patients. Concerning the early or the late part of the old/new effect ADHD patients show no difference which suggests that there are no differences with respect to recollection and familiarity based recognition processes.

  16. Learning and Recognition of a Non-conscious Sequence of Events in Human Primary Visual Cortex.

    Science.gov (United States)

    Rosenthal, Clive R; Andrews, Samantha K; Antoniades, Chrystalina A; Kennard, Christopher; Soto, David

    2016-03-21

    Human primary visual cortex (V1) has long been associated with learning simple low-level visual discriminations [1] and is classically considered outside of neural systems that support high-level cognitive behavior in contexts that differ from the original conditions of learning, such as recognition memory [2, 3]. Here, we used a novel fMRI-based dichoptic masking protocol-designed to induce activity in V1, without modulation from visual awareness-to test whether human V1 is implicated in human observers rapidly learning and then later (15-20 min) recognizing a non-conscious and complex (second-order) visuospatial sequence. Learning was associated with a change in V1 activity, as part of a temporo-occipital and basal ganglia network, which is at variance with the cortico-cerebellar network identified in prior studies of "implicit" sequence learning that involved motor responses and visible stimuli (e.g., [4]). Recognition memory was associated with V1 activity, as part of a temporo-occipital network involving the hippocampus, under conditions that were not imputable to mechanisms associated with conscious retrieval. Notably, the V1 responses during learning and recognition separately predicted non-conscious recognition memory, and functional coupling between V1 and the hippocampus was enhanced for old retrieval cues. The results provide a basis for novel hypotheses about the signals that can drive recognition memory, because these data (1) identify human V1 with a memory network that can code complex associative serial visuospatial information and support later non-conscious recognition memory-guided behavior (cf. [5]) and (2) align with mouse models of experience-dependent V1 plasticity in learning and memory [6]. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Preparation and recognition of surface molecularly imprinted core-shell microbeads for protein in aqueous solutions

    International Nuclear Information System (INIS)

    Lu Yan; Yan Changling; Gao Shuyan

    2009-01-01

    In this paper, a surface molecular imprinting technique was reported for preparing core-shell microbeads of protein imprinting, and bovine hemoglobin or bovine serum albumin were used as model proteins for studying the imprinted core-shell microbeads. 3-Aminophenylboronic acid (APBA) was polymerized onto the surface of polystyrene microbead in the presence of the protein templates to create protein-imprinted core-shell microbeads. The various samples were characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and Brunauer-Emmett-Teller (BET) methods. The effect of pH on rebinding of the template hemoglobin, the specific binding and selective recognition were studied for the imprinted microbeads. The results show that the bovine hemoglobin-imprinted core-shell microbeads were successfully created. The shell was a sort of imprinted thin films with porous structure and larger surface areas. The imprinted microbeads have good selectivity for templates and high stability. Due to the recognition sites locating at or closing to the surface, these imprinted microbeads have good property of mass-transport. Unfortunately, the imprint technology was not successfully applied to imprinting bovine serum albumin (BSA).

  18. Selective Nitrate Recognition by a Halogen-Bonding Four-Station [3]Rotaxane Molecular Shuttle.

    Science.gov (United States)

    Barendt, Timothy A; Docker, Andrew; Marques, Igor; Félix, Vítor; Beer, Paul D

    2016-09-05

    The synthesis of the first halogen bonding [3]rotaxane host system containing a bis-iodo triazolium-bis-naphthalene diimide four station axle component is reported. Proton NMR anion binding titration experiments revealed the halogen bonding rotaxane is selective for nitrate over the more basic acetate, hydrogen carbonate and dihydrogen phosphate oxoanions and chloride, and exhibits enhanced recognition of anions relative to a hydrogen bonding analogue. This elaborate interlocked anion receptor functions via a novel dynamic pincer mechanism where upon nitrate anion binding, both macrocycles shuttle from the naphthalene diimide stations at the periphery of the axle to the central halogen bonding iodo-triazolium station anion recognition sites to form a unique 1:1 stoichiometric nitrate anion-rotaxane sandwich complex. Molecular dynamics simulations carried out on the nitrate and chloride halogen bonding [3]rotaxane complexes corroborate the (1) H NMR anion binding results. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  19. Molecularly imprinted polymer based on chemiluminescence imaging for the chiral recognition of dansyl-phenylalanine.

    Science.gov (United States)

    Wang, Li; Zhang, Zhujun; Huang, Lianggao

    2008-03-01

    A new molecularly imprinted polymer (MIP)-chemiluminescence (CL) imaging detection approach towards chiral recognition of dansyl-phenylalanine (Phe) is presented. The polymer microspheres were synthesized using precipitation polymerization with dansyl-L-Phe as template. Polymer microspheres were immobilized in microtiter plates (96 wells) using poly(vinyl alcohol) (PVA) as glue. The analyte was selectively adsorbed on the MIP microspheres. After washing, the bound fraction was quantified based on peroxyoxalate chemiluminescence (PO-CL) analysis. In the presence of dansyl-Phe, bis(2,4,6-trichlorophenyl)oxalate (TCPO) reacted with hydrogen peroxide (H2O2) to emit chemiluminescence. The signal was detected and quantified with a highly sensitive cooled charge-coupled device (CCD). Influencing factors were investigated and optimized in detail. Control experiments using capillary electrophoresis showed that there was no significant difference between the proposed method and the control method at a confidence level of 95%. The method can perform 96 independent measurements simultaneously in 30 min and the limits of detection (LODs) for dansyl-L-Phe and dansyl-D-Phe were 0.025 micromol L(-1) and 0.075 micromol L(-1) (3sigma), respectively. The relative standard deviation (RSD) for 11 parallel measurements of dansyl-L-Phe (0.78 micromol L(-1)) was 8%. The results show that MIP-based CL imaging can become a useful analytical technology for quick chiral recognition.

  20. Preparation and recognition of surface molecularly imprinted core-shell microbeads for protein in aqueous solutions

    Energy Technology Data Exchange (ETDEWEB)

    Lu Yan, E-mail: yanlu2001@sohu.com [College of Chemistry and Environmental Science, Henan Normal University, 46 Jlanshe Road, Xinxiang 453007 (China); Yan Changling; Gao Shuyan [College of Chemistry and Environmental Science, Henan Normal University, 46 Jlanshe Road, Xinxiang 453007 (China)

    2009-04-01

    In this paper, a surface molecular imprinting technique was reported for preparing core-shell microbeads of protein imprinting, and bovine hemoglobin or bovine serum albumin were used as model proteins for studying the imprinted core-shell microbeads. 3-Aminophenylboronic acid (APBA) was polymerized onto the surface of polystyrene microbead in the presence of the protein templates to create protein-imprinted core-shell microbeads. The various samples were characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and Brunauer-Emmett-Teller (BET) methods. The effect of pH on rebinding of the template hemoglobin, the specific binding and selective recognition were studied for the imprinted microbeads. The results show that the bovine hemoglobin-imprinted core-shell microbeads were successfully created. The shell was a sort of imprinted thin films with porous structure and larger surface areas. The imprinted microbeads have good selectivity for templates and high stability. Due to the recognition sites locating at or closing to the surface, these imprinted microbeads have good property of mass-transport. Unfortunately, the imprint technology was not successfully applied to imprinting bovine serum albumin (BSA).

  1. Electrospun Nanofibers from a Tricyanofuran-Based Molecular Switch for Colorimetric Recognition of Ammonia Gas.

    Science.gov (United States)

    Khattab, Tawfik A; Abdelmoez, Sherif; Klapötke, Thomas M

    2016-03-14

    A chromophore based on tricyanofuran (TCF) with a hydrazone (H) recognition moiety was developed. Its molecular-switching performance is reversible and has differential sensitivity towards aqueous ammonia at comparable concentrations. Nanofibers were fabricated from the TCF-H chromophore by electrospinning. The film fabricated from these nanofibers functions as a solid-state optical chemosensor for probing ammonia vapor. Recognition of ammonia vapor occurs by proton transfer from the hydrazone fragment of the chromophore to the ammonia nitrogen atom and is facilitated by the strongly electron withdrawing TCF fragment. The TCF-H chromophore was added to a solution of poly(acrylic acid), which was electrospun to obtain a nanofibrous sensor device. The morphology of the nanofibrous sensor was determined by SEM, which showed that nanofibers with a diameter range of 200-450 nm formed a nonwoven mat. The resultant nanofibrous sensor showed very good sensitivity in ammonia-vapor detection. Furthermore, very good reversibility and short response time were also observed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Protein-Templated Fragment Ligations-From Molecular Recognition to Drug Discovery.

    Science.gov (United States)

    Jaegle, Mike; Wong, Ee Lin; Tauber, Carolin; Nawrotzky, Eric; Arkona, Christoph; Rademann, Jörg

    2017-06-19

    Protein-templated fragment ligation is a novel concept to support drug discovery and can help to improve the efficacy of protein ligands. Protein-templated fragment ligations are chemical reactions between small molecules ("fragments") utilizing a protein's surface as a reaction vessel to catalyze the formation of a protein ligand with increased binding affinity. The approach exploits the molecular recognition of reactive small-molecule fragments by proteins both for ligand assembly and for the identification of bioactive fragment combinations. In this way, chemical synthesis and bioassay are integrated in one single step. This Review discusses the biophysical basis of reversible and irreversible fragment ligations and gives an overview of the available methods to detect protein-templated ligation products. The chemical scope and recent applications as well as future potential of the concept in drug discovery are reviewed. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Design, preparation, surface recognition properties, and characteristics of icariin molecularly imprinted polymers

    Directory of Open Access Journals (Sweden)

    Xiaohe Jia

    2015-12-01

    Full Text Available Icariin molecularly imprinted polymers (MIPs were prepared by precipitation polymerization. Prior to the polymerization, computer simulation was performed to sketchily choose the suitable functional monomer and the corresponding polymerization solvent. The optimized synthesis parameters, including the functional monomer acrylamide, the mixture of methanol and acetonitrile (V:V = 3:1 as the polymerization solvent, and the reaction molar ratio (1:6:80 of template molecule, functional monomer and cross-linker, were respectively obtained by single factor analysis and orthogonal design methods. The results of the adsorption experiments showed that the resultant MIPs exhibited good adsorption and recognition abilities to icariin. Scatchard analysis illustrated that the homogeneous binding sites only for icariin molecules were formed in the prepared MIPs.

  4. Computational modeling on the recognition of the HRE motif by HIF-1: molecular docking and molecular dynamics studies.

    Science.gov (United States)

    Sokkar, Pandian; Sathis, Vani; Ramachandran, Murugesan

    2012-05-01

    Hypoxia inducible factor-1 (HIF-1) is a bHLH-family transcription factor that controls genes involved in glycolysis, angiogenesis, migration, as well as invasion factors that are important for tumor progression and metastasis. HIF-1, a heterodimer of HIF-1α and HIF-1β, binds to the hypoxia responsive element (HRE) present in the promoter regions of hypoxia responsive genes, such as vascular endothelial growth factor (VEGF). Neither the structure of free HIF-1 nor that of its complex with HRE is available. Computational modeling of the transcription factor-DNA complex has always been challenging due to their inherent flexibility and large conformational space. The present study aims to model the interaction between the DNA-binding domain of HIF-1 and HRE. Experiments showed that rigid macromolecular docking programs (HEX and GRAMM-X) failed to predict the optimal dimerization of individually modeled HIF-1 subunits. Hence, the HIF-1 heterodimer was modeled based on the phosphate system positive regulatory protein (PHO4) homodimer. The duplex VEGF-DNA segment containing HRE with flanking nucleotides was modeled in the B form and equilibrated via molecular dynamics (MD) simulation. A rigid docking approach was used to predict the crude binding mode of HIF-1 dimer with HRE, in which the putative contacts were found to be present. An MD simulation (5 ns) of the HIF-1-HRE complex in explicit water was performed to account for its flexibility and to optimize its interactions. All of the conserved amino acid residues were found to play roles in the recognition of HRE. The present work, which sheds light on the recognition of HRE by HIF-1, could be beneficial in the design of peptide or small molecule therapeutics that can mimic HIF-1 and bind with the HRE sequence.

  5. Preparation of a magnetic molecularly imprinted polymer for selective recognition of rhodamine B

    International Nuclear Information System (INIS)

    Liu, Xiuying; Yu, Dan; Yu, Yingchao; Ji, Shujuan

    2014-01-01

    Graphical abstract: A novel material based on the use of magnetic Fe3O4 nanoparticles coated with MMIP for preconcentration and determination of RhB in real samples prior to fluorospectrophotometry was developed. - Highlights: • A novel rhodamine B magnetic molecularly imprinted polymer by using Fe 3 O 4 magnetite as the magnetically susceptible component was synthesized. • The MMIP had rapid adsorption and high selectivity towards rhodamine B. • Rhodamine B can be extracted selectively by MMIP from real samples. • The method provides the advantages of short analysis time and high sensitivity. - Abstract: A novel magnetic molecularly imprinted polymer (MMIP) was developed as an adsorbent to selectively remove rhodamine B from real samples. The polymer was characterized by scanning electron microscopy, Fourier-transform infrared spectroscopy, and thermo-gravimetric analysis. Static adsorption, kinetic adsorption, and selective recognition experiments were also performed to investigate the specific adsorption equilibrium, kinetics, and selective recognition ability of the MMIP. The MMIPs had outstanding thermal stability, large adsorption capacity, and high competitive selectivity. When they were used as dispersed solid-phase extraction adsorbents in real samples, rhodamine B recovery was 79.97–81.88% and 75.56–79.74% in intra-day and inter-day reproducibility experiments with relative standard deviations lower than 2.62% and 4.28%, respectively. Extraction was optimized for yield and efficiency. Precision, accuracy, and linear working range were determined under optimal experimental conditions. The limits of detection and quantification were 1.05 and 3.49 μg L −1 , respectively. These results suggest MMIPs may be used for determination of rhodamine B in real samples

  6. Engineering responsive polymer building blocks with host-guest molecular recognition for functional applications.

    Science.gov (United States)

    Hu, Jinming; Liu, Shiyong

    2014-07-15

    CONSPECTUS: All living organisms and soft matter are intrinsically responsive and adaptive to external stimuli. Inspired by this fact, tremendous effort aiming to emulate subtle responsive features exhibited by nature has spurred the invention of a diverse range of responsive polymeric materials. Conventional stimuli-responsive polymers are constructed via covalent bonds and can undergo reversible or irreversible changes in chemical structures, physicochemical properties, or both in response to a variety of external stimuli. They have been imparted with a variety of emerging applications including drug and gene delivery, optical sensing and imaging, diagnostics and therapies, smart coatings and textiles, and tissue engineering. On the other hand, in comparison with molecular chemistry held by covalent bonds, supramolecular chemistry built on weak and reversible noncovalent interactions has emerged as a powerful and versatile strategy for materials fabrication due to its facile accessibility, extraordinary reversibility and adaptivity, and potent applications in diverse fields. Typically involving more than one type of noncovalent interactions (e.g., hydrogen bonding, metal coordination, hydrophobic association, electrostatic interactions, van der Waals forces, and π-π stacking), host-guest recognition refers to the formation of supramolecular inclusion complexes between two or more entities connected together in a highly controlled and cooperative manner. The inherently reversible and adaptive nature of host-guest molecular recognition chemistry, stemming from multiple noncovalent interactions, has opened up a new platform to construct novel types of stimuli-responsive materials. The introduction of host-guest chemistry not only enriches the realm of responsive materials but also confers them with promising new applications. Most intriguingly, the integration of responsive polymer building blocks with host-guest recognition motifs will endow the former with

  7. Molecular mechanism of ligand recognition by membrane transport protein, Mhp1

    Science.gov (United States)

    Simmons, Katie J; Jackson, Scott M; Brueckner, Florian; Patching, Simon G; Beckstein, Oliver; Ivanova, Ekaterina; Geng, Tian; Weyand, Simone; Drew, David; Lanigan, Joseph; Sharples, David J; Sansom, Mark SP; Iwata, So; Fishwick, Colin WG; Johnson, A Peter; Cameron, Alexander D; Henderson, Peter JF

    2014-01-01

    The hydantoin transporter Mhp1 is a sodium-coupled secondary active transport protein of the nucleobase-cation-symport family and a member of the widespread 5-helix inverted repeat superfamily of transporters. The structure of Mhp1 was previously solved in three different conformations providing insight into the molecular basis of the alternating access mechanism. Here, we elucidate detailed events of substrate binding, through a combination of crystallography, molecular dynamics, site-directed mutagenesis, biochemical/biophysical assays, and the design and synthesis of novel ligands. We show precisely where 5-substituted hydantoin substrates bind in an extended configuration at the interface of the bundle and hash domains. They are recognised through hydrogen bonds to the hydantoin moiety and the complementarity of the 5-substituent for a hydrophobic pocket in the protein. Furthermore, we describe a novel structure of an intermediate state of the protein with the external thin gate locked open by an inhibitor, 5-(2-naphthylmethyl)-L-hydantoin, which becomes a substrate when leucine 363 is changed to an alanine. We deduce the molecular events that underlie acquisition and transport of a ligand by Mhp1. PMID:24952894

  8. Gelation or molecular recognition; is the bis-(α,β-dihydroxy esters motif an omnigelator?

    Directory of Open Access Journals (Sweden)

    Peter C. Griffiths

    2010-11-01

    Full Text Available Understanding the gelation of liquids by low molecular weight solutes at low concentrations gives an insight into many molecular recognition phenomena and also offers a simple route to modifying the physical properties of the liquid. Bis-(α,β-dihydroxy esters are shown here to gel thermoreversibly a wide range of solvents, raising interesting questions as to the mechanism of gelation. At gelator concentrations of 5–50 mg ml−1, gels were successfully formed in acetone, ethanol/water mixtures, toluene, cyclohexane and chloroform (the latter, albeit at a higher gelator concentration. A range of neutron techniques – in particular small-angle neutron scattering (SANS – have been employed to probe the structure of a selection of these gels. The universality of gelation in a range of solvent types suggests the gelation mechanism is a feature of the bis-(α,β-dihydroxy ester motif, with SANS demonstrating the presence of regular structures in the 30–40 Å range. A correlation between the apparent rodlike character of the structures formed and the polarity of the solvent is evident. Preliminary spin-echo neutron scattering studies (SESANS indicated the absence of any larger scale structures. Inelastic neutron spectroscopy (INS studies demonstrated that the solvent is largely unaffected by gelation, but does reveal insights into the thermal history of the samples. Further neutron studies of this kind (particularly SESANS and INS are warranted, and it is hoped that this work will stimulate others to pursue this line of research.

  9. An Event Related Potentials Study of the Effects of Age, Load and Maintenance Duration on Working Memory Recognition.

    Directory of Open Access Journals (Sweden)

    Diego Pinal

    Full Text Available Age-related decline in cognitive capacities has been attributed to a generalized slowing of processing speed and a reduction in working memory (WM capacity. Nevertheless, it is unclear how age affects visuospatial WM recognition and its underlying brain electrical activity. Whether age modulates the effects of memory load or information maintenance duration, which determine the limits of WM, remains also elusive. In this exploratory study, performance in a delayed match to sample task declined with age, particularly in conditions with high memory load. Event related potentials analysis revealed longer N2 and P300 latencies in old than in young adults during WM recognition, which may reflect slowing of stimulus evaluation and classification processes, respectively. Although there were no differences between groups in N2 or P300 amplitudes, the latter was more homogeneously distributed in old than in young adults, which may indicate an age-related increased reliance in frontal vs parietal resources during WM recognition. This was further supported by an age-related reduced posterior cingulate activation and increased superior frontal gyrus activation revealed through standardized low resolution electromagnetic tomography. Memory load and maintenance duration effects on brain activity were similar in both age groups. These behavioral and electrophysiological results add evidence in support of age-related decline in WM recognition theories, with a slowing of processing speed that may be limited to stimulus evaluation and categorization processes--with no effects on perceptual processes--and a posterior to anterior shift in the recruitment of neural resources.

  10. Metabolic and Molecular Events Occurring during Chromoplast Biogenesis

    Directory of Open Access Journals (Sweden)

    Wanping Bian

    2011-01-01

    Full Text Available Chromoplasts are nonphotosynthetic plastids that accumulate carotenoids. They derive from other plastid forms, mostly chloroplasts. The biochemical events responsible for the interconversion of one plastid form into another are poorly documented. However, thanks to transcriptomics and proteomics approaches, novel information is now available. Data of proteomic and biochemical analysis revealed the importance of lipid metabolism and carotenoids biosynthetic activities. The loss of photosynthetic activity was associated with the absence of the chlorophyll biosynthesis branch and the presence of proteins involved in chlorophyll degradation. Surprisingly, the entire set of Calvin cycle and of the oxidative pentose phosphate pathway persisted after the transition from chloroplast to chromoplast. The role of plastoglobules in the formation and organisation of carotenoid-containing structures and that of the Or gene in the control of chromoplastogenesis are reviewed. Finally, using transcriptomic data, an overview is given the expression pattern of a number of genes encoding plastid-located proteins during tomato fruit ripening.

  11. A microprocessor-based single board computer for high energy physics event pattern recognition

    International Nuclear Information System (INIS)

    Bernstein, H.; Gould, J.J.; Imossi, R.; Kopp, J.K.; Love, W.A.; Ozaki, S.; Platner, E.D.; Kramer, M.A.

    1981-01-01

    A single board MC 68000 based computer has been assembled and bench marked against the CDC 7600 running portions of the pattern recognition code used at the MPS. This computer has a floating coprocessor to achieve throughputs equivalent to several percent that of the 7600. A major part of this work was the construction of a FORTRAN compiler including assembler, linker and library. The intention of this work is to assemble a large number of these single board computers in a parallel FASTBUS environment to act as an on-line and off-line filter for the raw data from MPS II and ISABELLE experiments. (orig.)

  12. Microprocessor-based single board computer for high energy physics event pattern recognition

    International Nuclear Information System (INIS)

    Bernstein, H.; Gould, J.J.; Imossi, R.; Kopp, J.K.; Love, W.A.; Ozaki, S.; Platner, E.D.; Kramer, M.A.

    1981-01-01

    A single board MC 68000 based computer has been assembled and bench marked against the CDC 7600 running portions of the pattern recognition code used at the MPS. This computer has a floating coprocessor to achieve throughputs equivalent to several percent that of the 7600. A major part of this work was the construction of a FORTRAN compiler including assembler, linker and library. The intention of this work is to assemble a large number of these single board computers in a parallel FASTBUS environment to act as an on-line and off-line filter for the raw data from MPS II and ISABELLE experiments

  13. Oxidation-specific epitopes are danger-associated molecular patterns recognized by pattern recognition receptors of innate immunity

    DEFF Research Database (Denmark)

    Miller, Yury I; Choi, Soo-Ho; Wiesner, Philipp

    2011-01-01

    are a major target of innate immunity, recognized by a variety of "pattern recognition receptors" (PRRs). By analogy with microbial "pathogen-associated molecular patterns" (PAMPs), we postulate that host-derived, oxidation-specific epitopes can be considered to represent "danger (or damage......)-associated molecular patterns" (DAMPs). We also argue that oxidation-specific epitopes present on apoptotic cells and their cellular debris provided the primary evolutionary pressure for the selection of such PRRs. Furthermore, because many PAMPs on microbes share molecular identity and/or mimicry with oxidation...

  14. Pattern recognition based on time-frequency analysis and convolutional neural networks for vibrational events in φ-OTDR

    Science.gov (United States)

    Xu, Chengjin; Guan, Junjun; Bao, Ming; Lu, Jiangang; Ye, Wei

    2018-01-01

    Based on vibration signals detected by a phase-sensitive optical time-domain reflectometer distributed optical fiber sensing system, this paper presents an implement of time-frequency analysis and convolutional neural network (CNN), used to classify different types of vibrational events. First, spectral subtraction and the short-time Fourier transform are used to enhance time-frequency features of vibration signals and transform different types of vibration signals into spectrograms, which are input to the CNN for automatic feature extraction and classification. Finally, by replacing the soft-max layer in the CNN with a multiclass support vector machine, the performance of the classifier is enhanced. Experiments show that after using this method to process 4000 vibration signal samples generated by four different vibration events, namely, digging, walking, vehicles passing, and damaging, the recognition rates of vibration events are over 90%. The experimental results prove that this method can automatically make an effective feature selection and greatly improve the classification accuracy of vibrational events in distributed optical fiber sensing systems.

  15. Study on the mechanism of chiral recognition with molecularly imprinted polymers

    International Nuclear Information System (INIS)

    Lu Yan; Li Chenxi; Zhang Hesheng; Liu Xiaohang

    2003-01-01

    This study aimed at elucidating the chiral recognition mechanism with molecularly imprinted polymers (MIPs) in aqueous environment. The system used ethylene glycol dimethacrylate (EGDMA), methacrylic acid (MAA), and 4-L-phenylalanylamino-pyridine (4-L-PheNHPy) as the cross-linking monomer, functional monomer and template, respectively, to assemble the imprinted polymer. A self-assembly mechanism, which includes the pre-organizing functional monomers around template before polymerization process, was proposed. This mechanism was supported by 1 H NMR titration test. Interactions between functional monomer and template were observed using UV-Vis spectroscopy of solutions of these components as well. These studies indicated a 1:2 molecular complex dominantly formed between 4-L-PheNHPy and MAA. Association constant was estimated to be 97,000 M -2 . Based on these results, a model mainly involving two-spot interaction was proposed evolving from our reported concept of exact placement of functional group. Ionic interaction between the primary amino group of 4-L-PheNHPy and carboxylic acid group inside the microcavity on MIPs was believed to play a predominate role in the enantioselectivity as supported by the observation of the relationship between the retention factor of 4-L-PheNHPy and the pH of mobile phase. While thermodynamic study at different pH revealed that, the interaction between the pyridyl group of 4-L-PheNHPy and the carboxylic acid group on the MIPs is also strong, implying that it also plays a profound role in determining the highly chiral selectivity of MIPs

  16. Mapping molecular adhesion sites inside SMIL coated capillaries using atomic force microscopy recognition imaging

    Energy Technology Data Exchange (ETDEWEB)

    Leitner, Michael [Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz (Austria); Stock, Lorenz G. [Division of Chemistry and Bioanalytics, Department of Molecular Biology, University Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg (Austria); Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg (Austria); Traxler, Lukas [Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz (Austria); Leclercq, Laurent [Institut des Biomolécules Max Mousseron (IBMM, UMR 5247, CNRS, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier), Place Eugène Bataillon, CC 1706, 34095 Montpellier (France); Bonazza, Klaus; Friedbacher, Gernot [Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164, 1060 Vienna (Austria); Cottet, Hervé [Institut des Biomolécules Max Mousseron (IBMM, UMR 5247, CNRS, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier), Place Eugène Bataillon, CC 1706, 34095 Montpellier (France); Stutz, Hanno [Division of Chemistry and Bioanalytics, Department of Molecular Biology, University Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg (Austria); Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg (Austria); Ebner, Andreas, E-mail: andreas.ebner@jku.at [Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz (Austria)

    2016-08-03

    Capillary zone electrophoresis (CZE) is a powerful analytical technique for fast and efficient separation of different analytes ranging from small inorganic ions to large proteins. However electrophoretic resolution significantly depends on the coating of the inner capillary surface. High technical efforts like Successive Multiple Ionic Polymer Layer (SMIL) generation have been taken to develop stable coatings with switchable surface charges fulfilling the requirements needed for optimal separation. Although the performance can be easily proven in normalized test runs, characterization of the coating itself remains challenging. Atomic force microscopy (AFM) allows for topographical investigation of biological and analytical relevant surfaces with nanometer resolution and yields information about the surface roughness and homogeneity. Upgrading the scanning tip to a molecular biosensor by adhesive molecules (like partly inverted charged molecules) allows for performing topography and recognition imaging (TREC). As a result, simultaneously acquired sample topography and adhesion maps can be recorded. We optimized this technique for electrophoresis capillaries and investigated the charge distribution of differently composed and treated SMIL coatings. By using the positively charged protein avidin as a single molecule sensor, we compared these SMIL coatings with respect to negative charges, resulting in adhesion maps with nanometer resolution. The capability of TREC as a functional investigation technique at the nanoscale was successfully demonstrated. - Highlights: • SMIL coating allows generation of homogeneous ultra-flat surfaces. • Molecular electrostatic adhesion forces can be determined in the inner wall of CZE capillary with picoNewton accuracy. • Topographical images and simultaneously acquired adhesion maps yield morphological and chemical information at the nanoscale.

  17. Leukemia-Associated Mutations in Nucleophosmin Alter Recognition by CRM1: Molecular Basis of Aberrant Transport.

    Directory of Open Access Journals (Sweden)

    Igor Arregi

    Full Text Available Nucleophosmin (NPM is a nucleocytoplasmic shuttling protein, normally enriched in nucleoli, that performs several activities related to cell growth. NPM mutations are characteristic of a subtype of acute myeloid leukemia (AML, where mutant NPM seems to play an oncogenic role. AML-associated NPM mutants exhibit altered subcellular traffic, being aberrantly located in the cytoplasm of leukoblasts. Exacerbated export of AML variants of NPM is mediated by the nuclear export receptor CRM1, and due, in part, to a mutationally acquired novel nuclear export signal (NES. To gain insight on the molecular basis of NPM transport in physiological and pathological conditions, we have evaluated the export efficiency of NPM in cells, and present new data indicating that, in normal conditions, wild type NPM is weakly exported by CRM1. On the other hand, we have found that AML-associated NPM mutants efficiently form complexes with CRM1HA (a mutant CRM1 with higher affinity for NESs, and we have quantitatively analyzed CRM1HA interaction with the NES motifs of these mutants, using fluorescence anisotropy and isothermal titration calorimetry. We have observed that the affinity of CRM1HA for these NESs is similar, which may help to explain the transport properties of the mutants. We also describe NPM recognition by the import machinery. Our combined cellular and biophysical studies shed further light on the determinants of NPM traffic, and how it is dramatically altered by AML-related mutations.

  18. Helicase Dependent Isothermal Amplification of DNA and RNA using Self-Avoiding Molecular Recognition Systems

    Science.gov (United States)

    Yang, Zunyi; McLendon, Chris; Hutter, Daniel; Bradley, Kevin M.; Hoshika, Shuichi; Frye, Carole; Benner, Steven A.

    2015-01-01

    Assays that target DNA or RNA (xNA) are highly sensitive, as small amounts of xNA can be amplified by PCR. Unfortunately, PCR is inconvenient in low resource environments, requiring equipment and power that may not be available in these environments. However, isothermal procedures that avoid thermal cycling are often confounded by primer dimers, off-target priming, and other artifacts. Here, we show how a “self avoiding molecular recognition system” (SAMRS) eliminates these artifacts to give clean amplicons in a helicase-dependent isothermal amplification (SAMRS-HDA). We also show that incorporating SAMRS into the 3′-ends of primers facilitates the design and screening of primers for HDA assays. Finally, we show that SAMRS-HDA can be twofold multiplexed, something difficult to achieve with HDA using standard primers. This shows that SAMRS-HDA is a more versatile approach than standard HDA with a broader applicability for xNA-targeted diagnostics and research. PMID:25953623

  19. Molecular Recognition of Corticotropin releasing Factor by Its G protein-coupled Receptor CRFR1

    Energy Technology Data Exchange (ETDEWEB)

    Pioszak, Augen A.; Parker, Naomi R.; Suino-Powell, Kelly; Xu, H. Eric (Van Andel)

    2009-01-15

    The bimolecular interaction between corticotropin-releasing factor (CRF), a neuropeptide, and its type 1 receptor (CRFR1), a class B G-protein-coupled receptor (GPCR), is crucial for activation of the hypothalamic-pituitary-adrenal axis in response to stress, and has been a target of intense drug design for the treatment of anxiety, depression, and related disorders. As a class B GPCR, CRFR1 contains an N-terminal extracellular domain (ECD) that provides the primary ligand binding determinants. Here we present three crystal structures of the human CRFR1 ECD, one in a ligand-free form and two in distinct CRF-bound states. The CRFR1 ECD adopts the alpha-beta-betaalpha fold observed for other class B GPCR ECDs, but the N-terminal alpha-helix is significantly shorter and does not contact CRF. CRF adopts a continuous alpha-helix that docks in a hydrophobic surface of the ECD that is distinct from the peptide-binding site of other class B GPCRs, thereby providing a basis for the specificity of ligand recognition between CRFR1 and other class B GPCRs. The binding of CRF is accompanied by clamp-like conformational changes of two loops of the receptor that anchor the CRF C terminus, including the C-terminal amide group. These structural studies provide a molecular framework for understanding peptide binding and specificity by the CRF receptors as well as a template for designing potent and selective CRFR1 antagonists for therapeutic applications.

  20. The Pandora multi-algorithm approach to automated pattern recognition of cosmic-ray muon and neutrino events in the MicroBooNE detector

    Energy Technology Data Exchange (ETDEWEB)

    Acciarri, R.; Bagby, L.; Baller, B.; Carls, B.; Castillo Fernandez, R.; Cavanna, F.; Greenlee, H.; James, C.; Jostlein, H.; Ketchum, W.; Kirby, M.; Kobilarcik, T.; Lockwitz, S.; Lundberg, B.; Marchionni, A.; Moore, C.D.; Palamara, O.; Pavlovic, Z.; Raaf, J.L.; Schukraft, A.; Snider, E.L.; Spentzouris, P.; Strauss, T.; Toups, M.; Wolbers, S.; Yang, T.; Zeller, G.P. [Fermi National Accelerator Laboratory (FNAL), Batavia, IL (United States); Adams, C. [Harvard University, Cambridge, MA (United States); Yale University, New Haven, CT (United States); An, R.; Littlejohn, B.R.; Martinez Caicedo, D.A. [Illinois Institute of Technology (IIT), Chicago, IL (United States); Anthony, J.; Escudero Sanchez, L.; De Vries, J.J.; Marshall, J.; Smith, A.; Thomson, M. [University of Cambridge, Cambridge (United Kingdom); Asaadi, J. [University of Texas, Arlington, TX (United States); Auger, M.; Ereditato, A.; Goeldi, D.; Kreslo, I.; Lorca, D.; Luethi, M.; Rudolf von Rohr, C.; Sinclair, J.; Weber, M. [Universitaet Bern, Bern (Switzerland); Balasubramanian, S.; Fleming, B.T.; Gramellini, E.; Hackenburg, A.; Luo, X.; Russell, B.; Tufanli, S. [Yale University, New Haven, CT (United States); Barnes, C.; Mousseau, J.; Spitz, J. [University of Michigan, Ann Arbor, MI (United States); Barr, G.; Bass, M.; Del Tutto, M.; Laube, A.; Soleti, S.R.; De Pontseele, W.V. [University of Oxford, Oxford (United Kingdom); Bay, F. [TUBITAK Space Technologies Research Institute, Ankara (Turkey); Bishai, M.; Chen, H.; Joshi, J.; Kirby, B.; Li, Y.; Mooney, M.; Qian, X.; Viren, B.; Zhang, C. [Brookhaven National Laboratory (BNL), Upton, NY (United States); Blake, A.; Devitt, D.; Lister, A.; Nowak, J. [Lancaster University, Lancaster (United Kingdom); Bolton, T.; Horton-Smith, G.; Meddage, V.; Rafique, A. [Kansas State University (KSU), Manhattan, KS (United States); Camilleri, L.; Caratelli, D.; Crespo-Anadon, J.I.; Fadeeva, A.A.; Genty, V.; Kaleko, D.; Seligman, W.; Shaevitz, M.H. [Columbia University, New York, NY (United States); Church, E. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Cianci, D.; Karagiorgi, G. [Columbia University, New York, NY (United States); The University of Manchester (United Kingdom); Cohen, E.; Piasetzky, E. [Tel Aviv University, Tel Aviv (Israel); Collin, G.H.; Conrad, J.M.; Hen, O.; Hourlier, A.; Moon, J.; Wongjirad, T.; Yates, L. [Massachusetts Institute of Technology (MIT), Cambridge, MA (United States); Convery, M.; Eberly, B.; Rochester, L.; Tsai, Y.T.; Usher, T. [SLAC National Accelerator Laboratory, Menlo Park, CA (United States); Dytman, S.; Graf, N.; Jiang, L.; Naples, D.; Paolone, V.; Wickremasinghe, D.A. [University of Pittsburgh, Pittsburgh, PA (United States); Esquivel, J.; Hamilton, P.; Pulliam, G.; Soderberg, M. [Syracuse University, Syracuse, NY (United States); Foreman, W.; Ho, J.; Schmitz, D.W.; Zennamo, J. [University of Chicago, IL (United States); Furmanski, A.P.; Garcia-Gamez, D.; Hewes, J.; Hill, C.; Murrells, R.; Porzio, D.; Soeldner-Rembold, S.; Szelc, A.M. [The University of Manchester (United Kingdom); Garvey, G.T.; Huang, E.C.; Louis, W.C.; Mills, G.B.; De Water, R.G.V. [Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Gollapinni, S. [Kansas State University (KSU), Manhattan, KS (United States); University of Tennessee, Knoxville, TN (United States); and others

    2018-01-15

    The development and operation of liquid-argon time-projection chambers for neutrino physics has created a need for new approaches to pattern recognition in order to fully exploit the imaging capabilities offered by this technology. Whereas the human brain can excel at identifying features in the recorded events, it is a significant challenge to develop an automated, algorithmic solution. The Pandora Software Development Kit provides functionality to aid the design and implementation of pattern-recognition algorithms. It promotes the use of a multi-algorithm approach to pattern recognition, in which individual algorithms each address a specific task in a particular topology. Many tens of algorithms then carefully build up a picture of the event and, together, provide a robust automated pattern-recognition solution. This paper describes details of the chain of over one hundred Pandora algorithms and tools used to reconstruct cosmic-ray muon and neutrino events in the MicroBooNE detector. Metrics that assess the current pattern-recognition performance are presented for simulated MicroBooNE events, using a selection of final-state event topologies. (orig.)

  1. The Pandora multi-algorithm approach to automated pattern recognition of cosmic-ray muon and neutrino events in the MicroBooNE detector

    Science.gov (United States)

    Acciarri, R.; Adams, C.; An, R.; Anthony, J.; Asaadi, J.; Auger, M.; Bagby, L.; Balasubramanian, S.; Baller, B.; Barnes, C.; Barr, G.; Bass, M.; Bay, F.; Bishai, M.; Blake, A.; Bolton, T.; Camilleri, L.; Caratelli, D.; Carls, B.; Castillo Fernandez, R.; Cavanna, F.; Chen, H.; Church, E.; Cianci, D.; Cohen, E.; Collin, G. H.; Conrad, J. M.; Convery, M.; Crespo-Anadón, J. I.; Del Tutto, M.; Devitt, D.; Dytman, S.; Eberly, B.; Ereditato, A.; Escudero Sanchez, L.; Esquivel, J.; Fadeeva, A. A.; Fleming, B. T.; Foreman, W.; Furmanski, A. P.; Garcia-Gamez, D.; Garvey, G. T.; Genty, V.; Goeldi, D.; Gollapinni, S.; Graf, N.; Gramellini, E.; Greenlee, H.; Grosso, R.; Guenette, R.; Hackenburg, A.; Hamilton, P.; Hen, O.; Hewes, J.; Hill, C.; Ho, J.; Horton-Smith, G.; Hourlier, A.; Huang, E.-C.; James, C.; Jan de Vries, J.; Jen, C.-M.; Jiang, L.; Johnson, R. A.; Joshi, J.; Jostlein, H.; Kaleko, D.; Karagiorgi, G.; Ketchum, W.; Kirby, B.; Kirby, M.; Kobilarcik, T.; Kreslo, I.; Laube, A.; Li, Y.; Lister, A.; Littlejohn, B. R.; Lockwitz, S.; Lorca, D.; Louis, W. C.; Luethi, M.; Lundberg, B.; Luo, X.; Marchionni, A.; Mariani, C.; Marshall, J.; Martinez Caicedo, D. A.; Meddage, V.; Miceli, T.; Mills, G. B.; Moon, J.; Mooney, M.; Moore, C. D.; Mousseau, J.; Murrells, R.; Naples, D.; Nienaber, P.; Nowak, J.; Palamara, O.; Paolone, V.; Papavassiliou, V.; Pate, S. F.; Pavlovic, Z.; Piasetzky, E.; Porzio, D.; Pulliam, G.; Qian, X.; Raaf, J. L.; Rafique, A.; Rochester, L.; Rudolf von Rohr, C.; Russell, B.; Schmitz, D. W.; Schukraft, A.; Seligman, W.; Shaevitz, M. H.; Sinclair, J.; Smith, A.; Snider, E. L.; Soderberg, M.; Söldner-Rembold, S.; Soleti, S. R.; Spentzouris, P.; Spitz, J.; St. John, J.; Strauss, T.; Szelc, A. M.; Tagg, N.; Terao, K.; Thomson, M.; Toups, M.; Tsai, Y.-T.; Tufanli, S.; Usher, T.; Van De Pontseele, W.; Van de Water, R. G.; Viren, B.; Weber, M.; Wickremasinghe, D. A.; Wolbers, S.; Wongjirad, T.; Woodruff, K.; Yang, T.; Yates, L.; Zeller, G. P.; Zennamo, J.; Zhang, C.

    2018-01-01

    The development and operation of liquid-argon time-projection chambers for neutrino physics has created a need for new approaches to pattern recognition in order to fully exploit the imaging capabilities offered by this technology. Whereas the human brain can excel at identifying features in the recorded events, it is a significant challenge to develop an automated, algorithmic solution. The Pandora Software Development Kit provides functionality to aid the design and implementation of pattern-recognition algorithms. It promotes the use of a multi-algorithm approach to pattern recognition, in which individual algorithms each address a specific task in a particular topology. Many tens of algorithms then carefully build up a picture of the event and, together, provide a robust automated pattern-recognition solution. This paper describes details of the chain of over one hundred Pandora algorithms and tools used to reconstruct cosmic-ray muon and neutrino events in the MicroBooNE detector. Metrics that assess the current pattern-recognition performance are presented for simulated MicroBooNE events, using a selection of final-state event topologies.

  2. RECOGNITION OF DRAINAGE TUNNELS DURING GLACIER LAKE OUTBURST EVENTS FROM TERRESTRIAL IMAGE SEQUENCES

    Directory of Open Access Journals (Sweden)

    E. Schwalbe

    2016-06-01

    Full Text Available In recent years, many glaciers all over the world have been distinctly retreating and thinning. One of the consequences of this is the increase of so called glacier lake outburst flood events (GLOFs. The mechanisms ruling such GLOF events are still not yet fully understood by glaciologists. Thus, there is a demand for data and measurements that can help to understand and model the phenomena. Thereby, a main issue is to obtain information about the location and formation of subglacial channels through which some lakes, dammed by a glacier, start to drain. The paper will show how photogrammetric image sequence analysis can be used to collect such data. For the purpose of detecting a subglacial tunnel, a camera has been installed in a pilot study to observe the area of the Colonia Glacier (Northern Patagonian Ice Field where it dams the Lake Cachet II. To verify the hypothesis, that the course of the subglacial tunnel is indicated by irregular surface motion patterns during its collapse, the camera acquired image sequences of the glacier surface during several GLOF events. Applying tracking techniques to these image sequences, surface feature motion trajectories could be obtained for a dense raster of glacier points. Since only a single camera has been used for image sequence acquisition, depth information is required to scale the trajectories. Thus, for scaling and georeferencing of the measurements a GPS-supported photogrammetric network has been measured. The obtained motion fields of the Colonia Glacier deliver information about the glacier’s behaviour before during and after a GLOF event. If the daily vertical glacier motion of the glacier is integrated over a period of several days and projected into a satellite image, the location and shape of the drainage channel underneath the glacier becomes visible. The high temporal resolution of the motion fields may also allows for an analysis of the tunnels dynamic in comparison to the changing

  3. Event-related potentials and recognition memory for pictures and words: the effects of intentional and incidental learning.

    Science.gov (United States)

    Noldy, N E; Stelmack, R M; Campbell, K B

    1990-07-01

    Event-related potentials were recorded under conditions of intentional or incidental learning of pictures and words, and during the subsequent recognition memory test for these stimuli. Intentionally learned pictures were remembered better than incidentally learned pictures and intentionally learned words, which, in turn, were remembered better than incidentally learned words. In comparison to pictures that were ignored, the pictures that were attended were characterized by greater positive amplitude frontally at 250 ms and centro-parietally at 350 ms and by greater negativity at 450 ms at parietal and occipital sites. There were no effects of attention on the waveforms elicited by words. These results support the view that processing becomes automatic for words, whereas the processing of pictures involves additional effort or allocation of attentional resources. The N450 amplitude was greater for words than for pictures during both acquisition (intentional items) and recognition phases (hit and correct rejection categories for intentional items, hit category for incidental items). Because pictures are better remembered than words, the greater late positive wave (600 ms) elicited by the pictures than the words during the acquisition phase is also consistent with the association between P300 and better memory that has been reported.

  4. VideoStory: A New Multimedia Embedding for Few Example Recognition and Translation of Events

    Science.gov (United States)

    2014-11-07

    series, and movie trailers . We observe these professional videos are typically semantically dissimilar to the event videos which we are interested in...a list of keywords from Wikipedia, which provides an extensive index of celebrity, TV series and movie names1. We exclude the videos whose...Swimming 0.520 0.489 0.691 0.764 Biking 0.324 0.307 0.420 0.561 Graduation 0.083 0.058 0.135 0.121 Birthday 0.149 0.216 0.187 0.257 Wedding reception

  5. Sentinel health events (occupational): a basis for physician recognition and public health surveillance

    International Nuclear Information System (INIS)

    Rutstein, D.D.; Mullan, R.J.; Frazier, T.M.; Halperin, W.E.; Melius, J.M.; Sestito, J.P.

    1984-01-01

    A Sentinel Health Event (SHE) is a preventable disease, disability, or untimely death whose occurrence serves as a warning signal that the quality of preventive and/or therapeutic medical care may need to be improved. A SHE (Occupational) is a disease, disability, or untimely death which is occupationally related and whose occurrence may: (1) provide the impetus for epidemiologic or industrial hygiene studies; or (2) serve as a warning signal that materials substitution, engineering control, personal protection, or medical care may be required. The present SHE(O) list encompasses 50 disease conditions that are linked to the workplace. Only those conditions are included for which objective documentation of an associated agent, industry, and occupation exists in the scientific literature. The list will serve as a framework for developing a national system for occupational health surveillance that may be applied at the state and local level, and as a guide for practicing physicians caring for patients with occupational illnesses. The list will be updated periodically to accommodate new occupational disease events which meet the criteria for inclusion. 190 references, 1 figure, 1 table

  6. Biopolymeric receptor for peptide recognition by molecular imprinting approach—Synthesis, characterization and application

    International Nuclear Information System (INIS)

    Singh, Lav Kumar; Singh, Monika; Singh, Meenakshi

    2014-01-01

    The present work is focused on the development of a biocompatible zwitterionic hydrogel for various applications in analytical chemistry. Biopolymer chitosan was derivatized to obtain a series of zwitterionic hydrogel samples. Free amino groups hanging on the biopolymeric chain were reacted with γ-butyrolactone to quaternize the N-centers of polymeric chain. N,N-methylene-bis-acrylamide acts as a crosslinker via Michael-type addition in the subsequent step and facilitated gelation of betainized chitosan. These biopolymeric hydrogel samples were fully characterized by FTIR, 1 H NMR, 13 C NMR spectra, SEM and XRD. Hydrogels were further characterized for their swelling behavior at varying parameters. The extent of swelling was perceived to be dictated by solvent composition such as pH, ionic strength and temperature. This valuable polymeric format is herein chosen to design an artificial receptor for dipeptide ‘carnosine’, which has adequate societal significance to be analytically determined, by molecular imprinting. Electrostatic interactions along with complementary H-bonding and other hydrophobic interactions inducing additional synergetic effect between the template (carnosine) and the imprinted polymer led to the formation of imprinted sites. The MIP was able to selectively and specifically take up carnosine from aqueous solution quantitatively. Thus prepared MIPs were characterized by FTIR spectroscopy, SEM providing evidence for the quality and quantity of imprinted gels. The binding studies showed that the MIP illustrated good recognition for carnosine as compared to non-imprinted polymers (NIPs). Detection limit was estimated as 3.3 μg mL −1 . Meanwhile, selectivity experiments demonstrated that imprinted gel had a high affinity to carnosine in the presence of close structural analogues (interferrants). - Highlights: • Development of a biocompatible zwitterionic hydrogel • A series of chitosan-derived zwitterionic hydrogel samples • Polymeric

  7. Propagating Molecular Recognition Events through Highly Integrated Sense-Response Chemical Systems

    Science.gov (United States)

    2017-08-01

    Gianneschi: 2015 Outstanding Young Scientist Award, ACS Applied Materials & Interfaces, PAT 2015 2016 Fellow of the Royal Society of Chemistry 2016...Tianfu Distinguished Lecturer in Polymer Science and Engineering , Sichuan University 2017 Blavatnik Young Scientist Award Finalist Protocol Activity...developing the basic polymer chemistry of responsive, biopolymer/polymer hybrid materials. This began with us generating a nobornyl-PNA (peptide

  8. Sex differences in face gender recognition: an event-related potential study.

    Science.gov (United States)

    Sun, Yueting; Gao, Xiaochao; Han, Shihui

    2010-04-23

    Multiple level neurocognitive processes are involved in face processing in humans. The present study examined whether the early face processing such as structural encoding is modulated by task demands that manipulate attention to perceptual or social features of faces and such an effect, if any, is different between men and women. Event-related brain potentials were recorded from male and female adults while they identified a low-level perceptual feature of faces (i.e., face orientation) and a high-level social feature of faces (i.e., gender). We found that task demands that required the processing of face orientations or face gender resulted in modulations of both the early occipital/temporal negativity (N170) and the late central/parietal positivity (P3). The N170 amplitude was smaller in the gender relative to the orientation identification task whereas the P3 amplitude was larger in the gender identification task relative to the orientation identification task. In addition, these effects were much stronger in women than in men. Our findings suggest that attention to social information in faces such as gender modulates both the early encoding of facial structures and late evaluative process of faces to a greater degree in women than in men.

  9. Molecularly imprinted polymer based on MWCNT-QDs as fluorescent biomimetic sensor for specific recognition of target protein

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Zhaoqiang [College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620 (China); Annie Bligh, S.W. [Department of Life Sciences, Faculty of Science and Technology, University of Westminster, 115 New Cavendish Street, London W1W 6UW (United Kingdom); Tao, Lei; Quan, Jing [College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620 (China); Nie, Huali, E-mail: niehuali@dhu.edu.cn [College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620 (China); Zhu, Limin, E-mail: lzhu@dhu.edu.cn [College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620 (China); Gong, Xiao [College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620 (China)

    2015-03-01

    A novel molecularly imprinted optosensing material based on multi-walled carbon nanotube-quantum dots (MWCNT-QDs) has been designed and synthesized for its high selectivity, sensitivity and specificity in the recognition of a target protein bovine serum albumin (BSA). Molecularly imprinted polymer coated MWCNT-QDs using BSA as the template (BMIP-coated MWCNT-QDs) exhibits a fast mass-transfer speed with a response time of 25 min. It is found that the BSA as a target protein can significantly quench the luminescence of BMIP-coated MWCNT-QDs in a concentration-dependent manner that is best described by a Stern–Volmer equation. The K{sub SV} for BSA is much higher than bovine hemoglobin and lysozyme, implying a highly selective recognition of the BMIP-coated MWCNT-QDs to BSA. Under optimal conditions, the relative fluorescence intensity of BMIP-coated MWCNT-QDs decreases linearly with the increasing target protein BSA in the concentration range of 5.0 × 10{sup −7}–35.0 × 10{sup −7} M with a detection limit of 80 nM. - Highlights: • A novel fluorescent biomimetic sensor based on MWCNT-QDs was designed. • The sensor exhibited a fast mass-transfer speed with a response time of 25 min. • The sensor possessed a highly selective recognition to BSA.

  10. Assembling of G-strands into novel tetra-molecular parallel G4-DNA nanostructures using avidin-biotin recognition.

    Science.gov (United States)

    Borovok, Natalia; Iram, Natalie; Zikich, Dragoslav; Ghabboun, Jamal; Livshits, Gideon I; Porath, Danny; Kotlyar, Alexander B

    2008-09-01

    We describe a method for the preparation of novel long (hundreds of nanometers), uniform, inter-molecular G4-DNA molecules composed of four parallel G-strands. The only long continuous G4-DNA reported so far are intra-molecular structures made of a single G-strand. To enable a tetra-molecular assembly of the G-strands we developed a novel approach based on avidin-biotin biological recognition. The steps of the G4-DNA production include: (i) Enzymatic synthesis of long poly(dG)-poly(dC) molecules with biotinylated poly(dG)-strand; (ii) Formation of a complex between avidin-tetramer and four biotinylated poly(dG)-poly(dC) molecules; (iii) Separation of the poly(dC) strands from the poly(dG)-strands, which are connected to the avidin; (iv) Assembly of the four G-strands attached to the avidin into tetra-molecular G4-DNA. The average contour length of the formed structures, as measured by AFM, is equal to that of the initial poly(dG)-poly(dC) molecules, suggesting a tetra-molecular mechanism of the G-strands assembly. The height of tetra-molecular G4-nanostructures is larger than that of mono-molecular G4-DNA molecules having similar contour length. The CD spectra of the tetra- and mono-molecular G4-DNA are markedly different, suggesting different structural organization of these two types of molecules. The tetra-molecular G4-DNA nanostructures showed clear electrical polarizability. This suggests that they may be useful for molecular electronics.

  11. Botryllus schlosseri (Tunicata) whole colony irradiation: Do senescent zooid resorption and immunological resorption involve similar recognition events

    International Nuclear Information System (INIS)

    Rinkevich, B.; Weissman, I.L.

    1990-01-01

    The colonial tunicate Botryllus schlosseri undergoes cyclic blastogenesis where feeding zooids are senescened and resorbed and a new generation of zooids takes over the colony. When non-identical colonies come into direct contact, they either reject each other or fuse. Fusion is usually followed by the resorption of one of the partners in the chimera (immunological resorption). The striking morphological similarities between the two resorption phenomena suggest that both may involve tissue destruction following self-nonself recognition events. Here we attempt to modify these two events by whole colony gamma irradiation assays. Three sets of experiments were performed: (1) different doses of whole colony irradiation for determination of irradiation effects (110 colonies); (2) pairs of irradiated-nonirradiated isografts of clonal replicates for the potential of reconstruction of the irradiated partners (23 pairs); (3) chimeras of irradiated-nonirradiated partners for analysis of resorption hierarchy. Mortality increased with the irradiation dose. All colonies exposed to more than 5,000 rads died within 19 days, while no colony died below 2,000 rads. The average mortality periods, in days, for doses of 6,000-8,000, 5,000, and 2,500-4,000 rads were 14.4 +/- 3.1 (n = 24), 19.8 +/- 6.0 (n = 15), and 19.6 + 5.1 (n = 22), respectively. Younger colonies (3-6 months old) may survive radiation better than older ones (more than 13 months). Many morphological alterations were recorded in irradiated colonies: ampullar contraction and/or dilation, accumulation of pigment cells within ampullae, abnormal bleeding from blood vessels, sluggish blood circulation, necrotic zones, reduction in bud number, and irregularities in zooid and system structures. With doses of 3,000-4,000 rads and above, irradiation arrested the formation of new buds and interrupted normal takeover

  12. Tracking the time course of word-frequency effects in auditory word recognition with event-related potentials.

    Science.gov (United States)

    Dufour, Sophie; Brunellière, Angèle; Frauenfelder, Ulrich H

    2013-04-01

    Although the word-frequency effect is one of the most established findings in spoken-word recognition, the precise processing locus of this effect is still a topic of debate. In this study, we used event-related potentials (ERPs) to track the time course of the word-frequency effect. In addition, the neighborhood density effect, which is known to reflect mechanisms involved in word identification, was also examined. The ERP data showed a clear frequency effect as early as 350 ms from word onset on the P350, followed by a later effect at word offset on the late N400. A neighborhood density effect was also found at an early stage of spoken-word processing on the PMN, and at word offset on the late N400. Overall, our ERP differences for word frequency suggest that frequency affects the core processes of word identification starting from the initial phase of lexical activation and including target word selection. They thus rule out any interpretation of the word frequency effect that is limited to a purely decisional locus after word identification has been completed. Copyright © 2012 Cognitive Science Society, Inc.

  13. Molecular Recognition of PTS-1 Cargo Proteins by Pex5p: Implications for Protein Mistargeting in Primary Hyperoxaluria

    Directory of Open Access Journals (Sweden)

    Noel Mesa-Torres

    2015-02-01

    Full Text Available Peroxisomal biogenesis and function critically depends on the import of cytosolic proteins carrying a PTS1 sequence into this organelle upon interaction with the peroxin Pex5p. Recent structural studies have provided important insights into the molecular recognition of cargo proteins by Pex5p. Peroxisomal import is a key feature in the pathogenesis of primary hyperoxaluria type 1 (PH1, where alanine:glyoxylate aminotransferase (AGT undergoes mitochondrial mistargeting in about a third of patients. Here, we study the molecular recognition of PTS1 cargo proteins by Pex5p using oligopeptides and AGT variants bearing different natural PTS1 sequences, and employing an array of biophysical, computational and cell biology techniques. Changes in affinity for Pex5p (spanning over 3–4 orders of magnitude reflect different thermodynamic signatures, but overall bury similar amounts of molecular surface. Structure/energetic analyses provide information on the contribution of ancillary regions and the conformational changes induced in Pex5p and the PTS1 cargo upon complex formation. Pex5p stability in vitro is enhanced upon cargo binding according to their binding affinities. Moreover, we provide evidence that the rational modulation of the AGT: Pex5p binding affinity might be useful tools to investigate mistargeting and misfolding in PH1 by pulling the folding equilibria towards the native and peroxisomal import competent state.

  14. The Pandora multi-algorithm approach to automated pattern recognition of cosmic-ray muon and neutrino events in the MicroBooNE detector

    CERN Document Server

    Acciarri, R.; An, R.; Anthony, J.; Asaadi, J.; Auger, M.; Bagby, L.; Balasubramanian, S.; Baller, B.; Barnes, C.; Barr, G.; Bass, M.; Bay, F.; Bishai, M.; Blake, A.; Bolton, T.; Camilleri, L.; Caratelli, D.; Carls, B.; Castillo Fernandez, R.; Cavanna, F.; Chen, H.; Church, E.; Cianci, D.; Cohen, E.; Collin, G. H.; Conrad, J. M.; Convery, M.; Crespo-Anadón, J. I.; Del Tutto, M.; Devitt, D.; Dytman, S.; Eberly, B.; Ereditato, A.; Escudero Sanchez, L.; Esquivel, J.; Fadeeva, A. A.; Fleming, B. T.; Foreman, W.; Furmanski, A. P.; Garcia-Gamez, D.; Garvey, G. T.; Genty, V.; Goeldi, D.; Gollapinni, S.; Graf, N.; Gramellini, E.; Greenlee, H.; Grosso, R.; Guenette, R.; Hackenburg, A.; Hamilton, P.; Hen, O.; Hewes, J.; Hill, C.; Ho, J.; Horton-Smith, G.; Hourlier, A.; Huang, E.-C.; James, C.; Jan de Vries, J.; Jen, C.-M.; Jiang, L.; Johnson, R. A.; Joshi, J.; Jostlein, H.; Kaleko, D.; Karagiorgi, G.; Ketchum, W.; Kirby, B.; Kirby, M.; Kobilarcik, T.; Kreslo, I.; Laube, A.; Li, Y.; Lister, A.; Littlejohn, B. R.; Lockwitz, S.; Lorca, D.; Louis, W. C.; Luethi, M.; Lundberg, B.; Luo, X.; Marchionni, A.; Mariani, C.; Marshall, J.; Martinez Caicedo, D. A.; Meddage, V.; Miceli, T.; Mills, G. B.; Moon, J.; Mooney, M.; Moore, C. D.; Mousseau, J.; Murrells, R.; Naples, D.; Nienaber, P.; Nowak, J.; Palamara, O.; Paolone, V.; Papavassiliou, V.; Pate, S. F.; Pavlovic, Z.; Piasetzky, E.; Porzio, D.; Pulliam, G.; Qian, X.; Raaf, J. L.; Rafique, A.; Rochester, L.; Rudolf von Rohr, C.; Russell, B.; Schmitz, D. W.; Schukraft, A.; Seligman, W.; Shaevitz, M. H.; Sinclair, J.; Smith, A.; Snider, E. L.; Soderberg, M.; Söldner-Rembold, S.; Soleti, S. R.; Spentzouris, P.; Spitz, J.; St. John, J.; Strauss, T.; Szelc, A. M.; Tagg, N.; Terao, K.; Thomson, M.; Toups, M.; Tsai, Y.-T.; Tufanli, S.; Usher, T.; Van De Pontseele, W.; Van de Water, R. G.; Viren, B.; Weber, M.; Wickremasinghe, D. A.; Wolbers, S.; Wongjirad, T.; Woodruff, K.; Yang, T.; Yates, L.; Zeller, G. P.; Zennamo, J.; Zhang, C.

    2017-01-01

    The development and operation of Liquid-Argon Time-Projection Chambers for neutrino physics has created a need for new approaches to pattern recognition in order to fully exploit the imaging capabilities offered by this technology. Whereas the human brain can excel at identifying features in the recorded events, it is a significant challenge to develop an automated, algorithmic solution. The Pandora Software Development Kit provides functionality to aid the design and implementation of pattern-recognition algorithms. It promotes the use of a multi-algorithm approach to pattern recognition, in which individual algorithms each address a specific task in a particular topology. Many tens of algorithms then carefully build up a picture of the event and, together, provide a robust automated pattern-recognition solution. This paper describes details of the chain of over one hundred Pandora algorithms and tools used to reconstruct cosmic-ray muon and neutrino events in the MicroBooNE detector. Metrics that assess the...

  15. Action-Derived Molecular Dynamics in the Study of Rare Events

    Energy Technology Data Exchange (ETDEWEB)

    Passerone, Daniele; Parrinello, Michele

    2001-09-03

    We present a practical method to generate classical trajectories with fixed initial and final boundary conditions. Our method is based on the minimization of a suitably defined discretized action. The method finds its most natural application in the study of rare events. Its capabilities are illustrated by nontrivial examples. The algorithm lends itself to straightforward parallelization, and when combined with ab initio molecular dynamics it promises to offer a powerful tool for the study of chemical reactions.

  16. Action-Derived Molecular Dynamics in the Study of Rare Events

    International Nuclear Information System (INIS)

    Passerone, Daniele; Parrinello, Michele

    2001-01-01

    We present a practical method to generate classical trajectories with fixed initial and final boundary conditions. Our method is based on the minimization of a suitably defined discretized action. The method finds its most natural application in the study of rare events. Its capabilities are illustrated by nontrivial examples. The algorithm lends itself to straightforward parallelization, and when combined with ab initio molecular dynamics it promises to offer a powerful tool for the study of chemical reactions

  17. Rapid determination of 239Pu in urine samples using molecular recognition technology product AnaLigRPu-02 gel

    International Nuclear Information System (INIS)

    Silvia Dulanska; Boris Remenec; Jan Bilohuscin; Miroslav Labaska; Bianka Horvathova; Andrej Matel

    2013-01-01

    This paper describes the use of IBC's AnaLig R Pu-02 molecular recognition technology product to effectively and selectively pre-concentrate, separate and recover plutonium from urine samples. This method uses two-stage column separations consisting of two different commercial products, Eichrom's Pre-filter Material and AnaLig R Pu-02 resin from IBC Advanced Technologies. By eliminating the co-precipitation techniques and the ashing steps to remove residual organics, the analysis time was reduced significantly. The method was successfully tested by adding known activities of reference solutions of 242 Pu and 239 Pu to urine samples. (author)

  18. Memory Distortion and Its Avoidance: An Event-Related Potentials Study on False Recognition and Correct Rejection.

    Science.gov (United States)

    Cadavid, Sara; Beato, Maria Soledad

    2016-01-01

    Memory researchers have long been captivated by the nature of memory distortions and have made efforts to identify the neural correlates of true and false memories. However, the underlying mechanisms of avoiding false memories by correctly rejecting related lures remains underexplored. In this study, we employed a variant of the Deese/Roediger-McDermott paradigm to explore neural signatures of committing and avoiding false memories. ERP were obtained for True recognition, False recognition, Correct rejection of new items, and, more importantly, Correct rejection of related lures. With these ERP data, early-frontal, left-parietal, and late right-frontal old/new effects (associated with familiarity, recollection, and monitoring processes, respectively) were analysed. Results indicated that there were similar patterns for True and False recognition in all three old/new effects analysed in our study. Also, False recognition and Correct rejection of related lures activities seemed to share common underlying familiarity-based processes. The ERP similarities between False recognition and Correct rejection of related lures disappeared when recollection processes were examined because only False recognition presented a parietal old/new effect. This finding supported the view that actual false recollections underlie false memories, providing evidence consistent with previous behavioural research and with most ERP and neuroimaging studies. Later, with the onset of monitoring processes, False recognition and Correct rejection of related lures waveforms presented, again, clearly dissociated patterns. Specifically, False recognition and True recognition showed more positive going patterns than Correct rejection of related lures signal and Correct rejection of new items signature. Since False recognition and Correct rejection of related lures triggered familiarity-recognition processes, our results suggest that deciding which items are studied is based more on recollection

  19. Memory Distortion and Its Avoidance: An Event-Related Potentials Study on False Recognition and Correct Rejection.

    Directory of Open Access Journals (Sweden)

    Sara Cadavid

    Full Text Available Memory researchers have long been captivated by the nature of memory distortions and have made efforts to identify the neural correlates of true and false memories. However, the underlying mechanisms of avoiding false memories by correctly rejecting related lures remains underexplored. In this study, we employed a variant of the Deese/Roediger-McDermott paradigm to explore neural signatures of committing and avoiding false memories. ERP were obtained for True recognition, False recognition, Correct rejection of new items, and, more importantly, Correct rejection of related lures. With these ERP data, early-frontal, left-parietal, and late right-frontal old/new effects (associated with familiarity, recollection, and monitoring processes, respectively were analysed. Results indicated that there were similar patterns for True and False recognition in all three old/new effects analysed in our study. Also, False recognition and Correct rejection of related lures activities seemed to share common underlying familiarity-based processes. The ERP similarities between False recognition and Correct rejection of related lures disappeared when recollection processes were examined because only False recognition presented a parietal old/new effect. This finding supported the view that actual false recollections underlie false memories, providing evidence consistent with previous behavioural research and with most ERP and neuroimaging studies. Later, with the onset of monitoring processes, False recognition and Correct rejection of related lures waveforms presented, again, clearly dissociated patterns. Specifically, False recognition and True recognition showed more positive going patterns than Correct rejection of related lures signal and Correct rejection of new items signature. Since False recognition and Correct rejection of related lures triggered familiarity-recognition processes, our results suggest that deciding which items are studied is based more on

  20. Molecular Recognition in the Oxidation of Catechols by Dicobalt-BISDIEN Dioxygen Complexes

    Science.gov (United States)

    1992-01-30

    Recognition in the Oxidation of Catechols by Dicobalt-RISDIEN Dioxygen Complexes Lizete F S Cezar and Bruno Szpoganicz Departamento de Quimica ...bridged bi- nuclear Co(II)-BISDIEN dioxygen complexes; Co20 2 LCat2 + is the bivalent form, and Co20 2 (OH)LCat + and Co 20 2 (OH)2 Cat° are hydroxo

  1. Molecular recognition of halogen-tagged aromatic VOCs at the air-silicon interface.

    Science.gov (United States)

    Condorelli, Guglielmo G; Motta, Alessandro; Favazza, Maria; Gurrieri, Ettore; Betti, Paolo; Dalcanale, Enrico

    2010-01-14

    Selective and reversible complexation of halogen-tagged aromatic VOCs by a quinoxaline cavitand-decorated Si surface is demonstrated. The specific host-guest interactions of the Si-bonded receptors are proved to be responsible of the surface recognition properties, while extracavity non specific adsorptions are totally suppressed compared to the bulk material.

  2. Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)-adenine derivatives.

    Science.gov (United States)

    Stojković, Marijana Radić; Skugor, Marko; Dudek, Lukasz; Grolik, Jarosław; Eilmes, Julita; Piantanida, Ivo

    2014-01-01

    An investigation of the interactions of two novel and several known DBTAA-adenine conjugates with double-stranded DNA and RNA has revealed the DNA/RNA groove as the dominant binding site, which is in contrast to the majority of previously studied DBTAA analogues (DNA/RNA intercalators). Only DBTAA-propyladenine conjugates revealed the molecular recognition of AT-DNA by an ICD band pattern > 300 nm, whereas significant ICD bands did not appear for other ds-DNA/RNA. A structure-activity relation for the studied series of compounds showed that the essential structural features for the ICD recognition are a) the presence of DNA-binding appendages (adenine side chain and positively charged side chain) on both DBTAA side chains, and b) the presence of a short propyl linker, which does not support intramolecular aromatic stacking between DBTAA and adenine. The observed AT-DNA-ICD pattern differs from previously reported ss-DNA (poly dT) ICD recognition by a strong negative ICD band at 350 nm, which allows for the dynamic differentiation between ss-DNA (poly dT) and coupled ds-AT-DNA.

  3. Molecularly Imprinted Sol-Gel-Based QCM Sensor Arrays for the Detection and Recognition of Volatile Aldehydes

    Directory of Open Access Journals (Sweden)

    Chuanjun Liu

    2017-02-01

    Full Text Available The detection and recognition of metabolically derived aldehydes, which have been identified as important products of oxidative stress and biomarkers of cancers; are considered as an effective approach for early cancer detection as well as health status monitoring. Quartz crystal microbalance (QCM sensor arrays based on molecularly imprinted sol-gel (MISG materials were developed in this work for highly sensitive detection and highly selective recognition of typical aldehyde vapors including hexanal (HAL; nonanal (NAL and bezaldehyde (BAL. The MISGs were prepared by a sol-gel procedure using two matrix precursors: tetraethyl orthosilicate (TEOS and tetrabutoxytitanium (TBOT. Aminopropyltriethoxysilane (APT; diethylaminopropyltrimethoxysilane (EAP and trimethoxy-phenylsilane (TMP were added as functional monomers to adjust the imprinting effect of the matrix. Hexanoic acid (HA; nonanoic acid (NA and benzoic acid (BA were used as psuedotemplates in view of their analogous structure to the target molecules as well as the strong hydrogen-bonding interaction with the matrix. Totally 13 types of MISGs with different components were prepared and coated on QCM electrodes by spin coating. Their sensing characters towards the three aldehyde vapors with different concentrations were investigated qualitatively. The results demonstrated that the response of individual sensors to each target strongly depended on the matrix precursors; functional monomers and template molecules. An optimization of the 13 MISG materials was carried out based on statistical analysis such as principle component analysis (PCA; multivariate analysis of covariance (MANCOVA and hierarchical cluster analysis (HCA. The optimized sensor array consisting of five channels showed a high discrimination ability on the aldehyde vapors; which was confirmed by quantitative comparison with a randomly selected array. It was suggested that both the molecularly imprinting (MIP effect and the matrix

  4. Facilitating adverse drug event detection in pharmacovigilance databases using molecular structure similarity: application to rhabdomyolysis

    Science.gov (United States)

    Vilar, Santiago; Harpaz, Rave; Chase, Herbert S; Costanzi, Stefano; Rabadan, Raul

    2011-01-01

    Background Adverse drug events (ADE) cause considerable harm to patients, and consequently their detection is critical for patient safety. The US Food and Drug Administration maintains an adverse event reporting system (AERS) to facilitate the detection of ADE in drugs. Various data mining approaches have been developed that use AERS to detect signals identifying associations between drugs and ADE. The signals must then be monitored further by domain experts, which is a time-consuming task. Objective To develop a new methodology that combines existing data mining algorithms with chemical information by analysis of molecular fingerprints to enhance initial ADE signals generated from AERS, and to provide a decision support mechanism to facilitate the identification of novel adverse events. Results The method achieved a significant improvement in precision in identifying known ADE, and a more than twofold signal enhancement when applied to the ADE rhabdomyolysis. The simplicity of the method assists in highlighting the etiology of the ADE by identifying structurally similar drugs. A set of drugs with strong evidence from both AERS and molecular fingerprint-based modeling is constructed for further analysis. Conclusion The results demonstrate that the proposed methodology could be used as a pharmacovigilance decision support tool to facilitate ADE detection. PMID:21946238

  5. Molecular recognition of H3/H4 histone tails by the tudor domains of JMJD2A: a comparative molecular dynamics simulations study.

    Directory of Open Access Journals (Sweden)

    Musa Ozboyaci

    Full Text Available BACKGROUND: Histone demethylase, JMJD2A, specifically recognizes and binds to methylated lysine residues at histone H3 and H4 tails (especially trimethylated H3K4 (H3K4me3, trimethylated H3K9 (H3K9me3 and di,trimethylated H4K20 (H4K20me2, H4K20me3 via its tandem tudor domains. Crystal structures of JMJD2A-tudor binding to H3K4me3 and H4K20me3 peptides are available whereas the others are not. Complete picture of the recognition of the four histone peptides by the tandem tudor domains yet remains to be clarified. METHODOLOGY/PRINCIPAL FINDINGS: We report a detailed molecular dynamics simulation and binding energy analysis of the recognition of JMJD2A-tudor with four different histone tails. 25 ns fully unrestrained molecular dynamics simulations are carried out for each of the bound and free structures. We investigate the important hydrogen bonds and electrostatic interactions between the tudor domains and the peptide molecules and identify the critical residues that stabilize the complexes. Our binding free energy calculations show that H4K20me2 and H3K9me3 peptides have the highest and lowest affinity to JMJD2A-tudor, respectively. We also show that H4K20me2 peptide adopts the same binding mode with H4K20me3 peptide, and H3K9me3 peptide adopts the same binding mode with H3K4me3 peptide. Decomposition of the enthalpic and the entropic contributions to the binding free energies indicate that the recognition of the histone peptides is mainly driven by favourable van der Waals interactions. Residue decomposition of the binding free energies with backbone and side chain contributions as well as their energetic constituents identify the hotspots in the binding interface of the structures. CONCLUSION: Energetic investigations of the four complexes suggest that many of the residues involved in the interactions are common. However, we found two receptor residues that were related to selective binding of the H3 and H4 ligands. Modifications or mutations

  6. Iterative Calibration: A Novel Approach for Calibrating the Molecular Clock Using Complex Geological Events.

    Science.gov (United States)

    Loeza-Quintana, Tzitziki; Adamowicz, Sarah J

    2018-02-01

    During the past 50 years, the molecular clock has become one of the main tools for providing a time scale for the history of life. In the era of robust molecular evolutionary analysis, clock calibration is still one of the most basic steps needing attention. When fossil records are limited, well-dated geological events are the main resource for calibration. However, biogeographic calibrations have often been used in a simplistic manner, for example assuming simultaneous vicariant divergence of multiple sister lineages. Here, we propose a novel iterative calibration approach to define the most appropriate calibration date by seeking congruence between the dates assigned to multiple allopatric divergences and the geological history. Exploring patterns of molecular divergence in 16 trans-Bering sister clades of echinoderms, we demonstrate that the iterative calibration is predominantly advantageous when using complex geological or climatological events-such as the opening/reclosure of the Bering Strait-providing a powerful tool for clock dating that can be applied to other biogeographic calibration systems and further taxa. Using Bayesian analysis, we observed that evolutionary rate variability in the COI-5P gene is generally distributed in a clock-like fashion for Northern echinoderms. The results reveal a large range of genetic divergences, consistent with multiple pulses of trans-Bering migrations. A resulting rate of 2.8% pairwise Kimura-2-parameter sequence divergence per million years is suggested for the COI-5P gene in Northern echinoderms. Given that molecular rates may vary across latitudes and taxa, this study provides a new context for dating the evolutionary history of Arctic marine life.

  7. Fabrication of micromagnetic beads with molecular recognition/electron-transfer peptides for the sensing of ovalbumin

    Energy Technology Data Exchange (ETDEWEB)

    Sugawara, Kazuharu, E-mail: kzsuga@maebashi-it.ac.jp [Maebashi Institute of Technology, Gunma, 371-0816 (Japan); Kuramitz, Hideki [Department of Environmental Biology and Chemistry, Graduate School of Science and Engineering for Research, University of Toyama, Toyama, 930-8555 (Japan); Shinohara, Hiroki [Maebashi Institute of Technology, Gunma, 371-0816 (Japan)

    2017-03-15

    Electrochemical sensing of ovalbumin (OVA) was performed using magnetic beads with OVA recognition (RNRCKGTDVQAW)/electron-transfer (YYYYC) peptides. The focus of this study was to construct a highly sensitive and regenerative tool for OVA detection based on the interaction between a protein and peptide-1(RNRCKGTDVQAWYYYYC). The peptide-1 was introduced to the bead through four types of cross-linking reagents. Magnetic beads of different sizes with N-(6-maleimidocaproyloxy)sulfosuccinimide (Sulfo-EMCS) were also prepared. An oxidation peak due to tyrosine residues at 0.65 V depended on the distance of the electron-transfer peptide from the bead surface and on the surface area of the magnetic beads that contacted the electrode surface. The response of the electro-transfer peptide moiety was decreased because the protein was accumulated via the recognition peptide on the beads. When using Sulfo-EMCS and beads that were 6.0–6.9 μm in diameter, the calibration curve of OVA was linear and ranged from 8.0 × 10{sup −13} to 2.0 × 10{sup −11} M. To regenerate the magnetic beads, the measurements were achieved after removal of the OVA using a denaturing reagent. When OVA was added to fetal bovine serum containing a complex matrix, OVA was recovered at a rate of 98–100%. Consequently, these magnetic beads could be a powerful tool for the sensing of OVA in real samples. - Highlights: • Ovalbumin recognition/electron-transfer peptides were immobilized on magnetic beads. • The accumulation of the protein through the peptides on the beads caused the change of electrode response. • The magnetic beads could be reused for sensing of ovalbumin.

  8. Novel molecular events associated with altered steroidogenesis induced by exposure to atrazine in the intact and castrate male rat

    Science.gov (United States)

    Toxicology is increasingly focused on molecular events comprising adverse outcome pathways. Atrazine activates the hypothalamic-pituitary adrenal axis, but relationships to gonadal alterations are unknown. We characterized hormone profiles and adrenal (intact and castrate) and te...

  9. Aptamer-Based Molecular Recognition of Lysergamine, Metergoline and Small Ergot Alkaloids

    Directory of Open Access Journals (Sweden)

    Johan Robbens

    2012-12-01

    Full Text Available Ergot alkaloids are mycotoxins produced by fungi of the genus Claviceps, which infect cereal crops and grasses. The uptake of ergot alkaloid contaminated cereal products can be lethal to humans and animals. For food safety assessment, analytical techniques are currently used to determine the presence of ergot alkaloids in food and feed samples. However, the number of samples which can be analyzed is limited, due to the cost of the equipment and the need for skilled personnel. In order to compensate for the lack of rapid tests for the detection of ergot alkaloids, the aim of this study was to develop a specific recognition element for ergot alkaloids, which could be further applied to produce a colorimetric reaction in the presence of these toxins. As recognition elements, single-stranded DNA ligands were selected by using an iterative selection procedure named SELEX, i.e., Systematic Evolution of Ligands by EXponential enrichment. After several selection cycles, the resulting aptamers were cloned and sequenced. A surface plasmon resonance analysis enabled determination of the dissociation constants of the complexes of aptamers and lysergamine. Dissociation constants in the nanomolar range were obtained with three selected aptamers. One of the selected aptamers, having a dissociation constant of 44 nM, was linked to gold nanoparticles and it was possible to produce a colorimetric reaction in the presence of lysergamine. This system could also be applied to small ergot alkaloids in an ergot contaminated flour sample.

  10. Molecular cloning and characterization of a short peptidoglycan recognition protein from silkworm Bombyx mori.

    Science.gov (United States)

    Yang, P-J; Zhan, M-Y; Ye, C; Yu, X-Q; Rao, X-J

    2017-12-01

    Peptidoglycan is the major bacterial component recognized by the insect immune system. Peptidoglycan recognition proteins (PGRPs) are a family of pattern-recognition receptors that recognize peptidoglycans and modulate innate immune responses. Some PGRPs retain N-acetylmuramoyl-L-alanine amidase (Enzyme Commission number: 3.5.1.28) activity to hydrolyse bacterial peptidoglycans. Others have lost the enzymatic activity and work only as immune receptors. They are all important modulators for innate immunity. Here, we report the cloning and functional analysis of PGRP-S4, a short-form PGRP from the domesticated silkworm, Bombyx mori. The PGRP-S4 gene encodes a protein of 199 amino acids with a signal peptide and a PGRP domain. PGRP-S4 was expressed in the fat body, haemocytes and midgut. Its expression level was significantly induced by bacterial challenges in the midgut. The recombinant PGRP-S4 bound bacteria and different peptidoglycans. In addition, it inhibited bacterial growth and hydrolysed an Escherichia coli peptidoglycan in the presence of Zn 2+ . Scanning electron microscopy showed that PGRP-S4 disrupted the bacterial cell surface. PGRP-S4 further increased prophenoloxidase activation caused by peptidoglycans. Taken together, our data suggest that B. mori PGRP-S4 has multiple functions in immunity. © 2017 The Royal Entomological Society.

  11. Molecular Pathways for Immune Recognition of Preproinsulin Signal Peptide in Type 1 Diabetes.

    Science.gov (United States)

    Kronenberg-Versteeg, Deborah; Eichmann, Martin; Russell, Mark A; de Ru, Arnoud; Hehn, Beate; Yusuf, Norkhairin; van Veelen, Peter A; Richardson, Sarah J; Morgan, Noel G; Lemberg, Marius K; Peakman, Mark

    2018-04-01

    The signal peptide region of preproinsulin (PPI) contains epitopes targeted by HLA-A-restricted (HLA-A0201, A2402) cytotoxic T cells as part of the pathogenesis of β-cell destruction in type 1 diabetes. We extended the discovery of the PPI epitope to disease-associated HLA-B*1801 and HLA-B*3906 (risk) and HLA-A*1101 and HLA-B*3801 (protective) alleles, revealing that four of six alleles present epitopes derived from the signal peptide region. During cotranslational translocation of PPI, its signal peptide is cleaved and retained within the endoplasmic reticulum (ER) membrane, implying it is processed for immune recognition outside of the canonical proteasome-directed pathway. Using in vitro translocation assays with specific inhibitors and gene knockout in PPI-expressing target cells, we show that PPI signal peptide antigen processing requires signal peptide peptidase (SPP). The intramembrane protease SPP generates cytoplasm-proximal epitopes, which are transporter associated with antigen processing (TAP), ER-luminal epitopes, which are TAP independent, each presented by different HLA class I molecules and N-terminal trimmed by ER aminopeptidase 1 for optimal presentation. In vivo, TAP expression is significantly upregulated and correlated with HLA class I hyperexpression in insulin-containing islets of patients with type 1 diabetes. Thus, PPI signal peptide epitopes are processed by SPP and loaded for HLA-guided immune recognition via pathways that are enhanced during disease pathogenesis. © 2018 by the American Diabetes Association.

  12. Investigations into the origin of the molecular recognition of several adenosine deaminase inhibitors.

    Science.gov (United States)

    Gillerman, Irina; Fischer, Bilha

    2011-01-13

    Inhibitors of adenosine deaminase (ADA, EC 3.5.4.4) are potential therapeutic agents for the treatment of various health disorders. Several highly potent inhibitors were previously identified, yet they exhibit unacceptable toxicities. We performed a SAR study involving a series of C2 or C8 substituted purine-riboside analogues with a view to discover less potent inhibitors with a lesser toxicity. We found that any substitution at C8 position of nebularine resulted in total loss of activity toward calf intestinal ADA. However, several 2-substituted-adenosine, 8-aza-adenosine, and nebularine analogues exhibited inhibitory activity. Specifically, 2-Cl-purine riboside, 8-aza-2-thiohexyl adenosine, 2-thiohexyl adenosine, and 2-MeS-purine riboside were found to be competitive inhibitors of ADA with K(i) values of 25, 22, 6, and 3 μM, respectively. We concluded that electronic parameters are not major recognition determinants of ADA but rather steric parameters. A C2 substituent which fits ADA hydrophobic pocket and improves H-bonding with the enzyme makes a good inhibitor. In addition, a gg rotamer about C4'-C5' bond is apparently an important recognition determinant.

  13. Energetic atomic and molecular ions of ionospheric origin observed in distant magnetotail flow-reversal events

    Science.gov (United States)

    Christon, S. P.; Gloeckler, G.; Williams, D. J.; Mukai, T.; Mcentire, R. W.; Jacquey, C.; Angelopoulos, V.; Lui, A. T. Y.; Kokubun, S.; Fairfield, D. H.

    1994-01-01

    Energetic atomic (O(+1) and N(+1)) and molecular (O2(+1), NO(+1), and N2(+1)) ions of ionospheric origin were observed in Earth's magnetotail at X approximately -146 R(sub E) during two plasma sheet sunward/tailward flow-reversal events measured by instruments on the GEOTAIL spacecraft. These events were associated with concurrent ground-measured geomagnetic disturbance intensification at auroral-and mid-latitudes (Kp = 7(-)). Energetic ions in the sunward-component and tailward flows were from both the solar wind and ionosphere. Plasma and energetic ions participated in the flows. During tailward flow, ionospheric origin ion abundance ratios at approximately 200-900 km/s in the rest frame were N(+1)/O(+1) = approximately 25-30% and ((O2(+1), NO(+1), and N2(+1))/O(+1) = approximately 1-2%. We argue that tailward flow most likely initiated approximately 80-100 R(sub E) tailward of Earth and molecular ions were in the plasma sheet prior to geomagnetic intensification onset.

  14. Insights into the Molecular Events That Regulate Heat-Induced Chilling Tolerance in Citrus Fruits.

    Science.gov (United States)

    Lafuente, María T; Establés-Ortíz, Beatriz; González-Candelas, Luis

    2017-01-01

    Low non-freezing temperature may cause chilling injury (CI), which is responsible for external quality deterioration in many chilling-sensitive horticultural crops. Exposure of chilling-sensitive citrus cultivars to non-lethal high-temperature conditioning may increase their chilling tolerance. Very little information is available about the molecular events involved in such tolerance. In this work, the molecular events associated with the low temperature tolerance induced by heating Fortune mandarin, which is very sensitive to chilling, for 3 days at 37°C prior to cold storage is presented. A transcriptomic analysis reveals that heat-conditioning has an important impact favoring the repression of genes in cold-stored fruit, and that long-term heat-induced chilling tolerance is an active process that requires activation of transcription factors involved in transcription initiation and of the WRKY family. The analysis also shows that chilling favors degradation processes, which affect lipids and proteins, and that the protective effect of the heat-conditioning treatment is more likely to be related to the repression of the genes involved in lipid degradation than to the modification of fatty acids unsaturation, which affects membrane permeability. Another major factor associated with the beneficial effect of the heat treatment on reducing CI is the regulation of stress-related proteins. Many of the genes that encoded such proteins are involved in secondary metabolism and in oxidative stress-related processes.

  15. Insights into the Molecular Events That Regulate Heat-Induced Chilling Tolerance in Citrus Fruits

    Directory of Open Access Journals (Sweden)

    María T. Lafuente

    2017-06-01

    Full Text Available Low non-freezing temperature may cause chilling injury (CI, which is responsible for external quality deterioration in many chilling-sensitive horticultural crops. Exposure of chilling-sensitive citrus cultivars to non-lethal high-temperature conditioning may increase their chilling tolerance. Very little information is available about the molecular events involved in such tolerance. In this work, the molecular events associated with the low temperature tolerance induced by heating Fortune mandarin, which is very sensitive to chilling, for 3 days at 37°C prior to cold storage is presented. A transcriptomic analysis reveals that heat-conditioning has an important impact favoring the repression of genes in cold-stored fruit, and that long-term heat-induced chilling tolerance is an active process that requires activation of transcription factors involved in transcription initiation and of the WRKY family. The analysis also shows that chilling favors degradation processes, which affect lipids and proteins, and that the protective effect of the heat-conditioning treatment is more likely to be related to the repression of the genes involved in lipid degradation than to the modification of fatty acids unsaturation, which affects membrane permeability. Another major factor associated with the beneficial effect of the heat treatment on reducing CI is the regulation of stress-related proteins. Many of the genes that encoded such proteins are involved in secondary metabolism and in oxidative stress-related processes.

  16. Effective Use of Molecular Recognition in Gas Sensing: Results from Acoustic Wave and In-Situ FTIR Measurements

    Energy Technology Data Exchange (ETDEWEB)

    Bodenhofer, K,; Gopel, W.; Hierlemann, A.; Ricco, A.J.

    1998-12-09

    To probe directly the analyte/film interactions that characterize molecular recognition in gas sensors, we recorded changes to the in-situ surface vibrational spectra of specifically fictionalized surface acoustic wave (SAW) devices concurrently with analyte exposure and SAW measurement of the extent of sorption. Fourier-lmnsform infrared external- reflectance spectra (FTIR-ERS) were collected from operating 97-MH2 SAW delay lines during exposure to a range of analytes as they interacted with thin-film coatings previously shown to be selective: cyclodextrins for chiral recognition, Ni-camphorates for Lewis bases such as pyridine and organophosphonates, and phthalocyanines for aromatic compounds. In most cases where specific chemical interactions-metal coordination, "cage" compound inclusion, or z stacking-were expected, analyte dosing caused distinctive changes in the IR spectr~ together with anomalously large SAW sensor responses. In contrast, control experiments involving the physisorption of the same analytes by conventional organic polymers did not cause similar changes in the IR spectra, and the SAW responses were smaller. For a given conventional polymer, the partition coefficients (or SAW sensor signals) roughly followed the analyte fraction of saturation vapor pressure. These SAW/FTIR results support earlier conclusions derived from thickness-shear mode resonator data.

  17. Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition.

    Science.gov (United States)

    Duss, Olivier; Michel, Erich; Diarra dit Konté, Nana; Schubert, Mario; Allain, Frédéric H-T

    2014-04-01

    The carbon storage regulator/regulator of secondary metabolism (Csr/Rsm) type of small non-coding RNAs (sRNAs) is widespread throughout bacteria and acts by sequestering the global translation repressor protein CsrA/RsmE from the ribosome binding site of a subset of mRNAs. Although we have previously described the molecular basis of a high affinity RNA target bound to RsmE, it remains unknown how other lower affinity targets are recognized by the same protein. Here, we have determined the nuclear magnetic resonance solution structures of five separate GGA binding motifs of the sRNA RsmZ of Pseudomonas fluorescens in complex with RsmE. The structures explain how the variation of sequence and structural context of the GGA binding motifs modulate the binding affinity for RsmE by five orders of magnitude (∼10 nM to ∼3 mM, Kd). Furthermore, we see that conformational adaptation of protein side-chains and RNA enable recognition of different RNA sequences by the same protein contributing to binding affinity without conferring specificity. Overall, our findings illustrate how the variability in the Csr/Rsm protein-RNA recognition allows a fine-tuning of the competition between mRNAs and sRNAs for the CsrA/RsmE protein.

  18. Tragacanth gum-based nanogel as a superparamagnetic molecularly imprinted polymer for quercetin recognition and controlled release.

    Science.gov (United States)

    Hemmati, Khadijeh; Masoumi, Arameh; Ghaemy, Mousa

    2016-01-20

    A highly selective magnetic molecularly imprinted polymer (MMIP) with core-shell structure has been synthesized by a sol-gel process composed of Tragacanth Gum (TG) crosslinker, Fe3O4/SiO2 nanoparticles, and N-vinyl imidazole(VI) functional monomer in the presence of template Quercetin (QC). Different techniques including scanning electron microscopy (SEM), SEM-energy dispersive spectroscopy (SEM-EDS), vibrating sample magnetometer (VSM), and transmission electron microscopy (TEM) were used to verify the successful synthesis of MIP on the surface of Fe3O4/SiO2 nanoparticles. The swelling behavior of MMIP, its recognition and selectivity for QC and structural analog, Catechin (CT), were tested and compared with magnetic non imprinted polymer (MNIP). MMIP adsorbs the template drug quickly and equilibrium could be reached in 2h. The mechanism for adsorption was found to follow the Langmuir model with the maximum capacity of 175.43 mg g(-1). The MMIP indicated excellent recognition and binding affinity toward QC, selectivity factor (ɛ) relative to CT was 2.16. Finally, the MMIP was evaluated as a drug delivery device by performing in vitro release studies in PBS. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Electrochemical impedimetric sensor based on molecularly imprinted polymers/sol-gel chemistry for methidathion organophosphorous insecticide recognition.

    Science.gov (United States)

    Bakas, Idriss; Hayat, Akhtar; Piletsky, Sergey; Piletska, Elena; Chehimi, Mohamed M; Noguer, Thierry; Rouillon, Régis

    2014-12-01

    We report here a novel method to detect methidathion organophosphorous insecticides. The sensing platform was architected by the combination of molecularly imprinted polymers and sol-gel technique on inexpensive, portable and disposable screen printed carbon electrodes. Electrochemical impedimetric detection technique was employed to perform the label free detection of the target analyte on the designed MIP/sol-gel integrated platform. The selection of the target specific monomer by electrochemical impedimetric methods was consistent with the results obtained by the computational modelling method. The prepared electrochemical MIP/sol-gel based sensor exhibited a high recognition capability toward methidathion, as well as a broad linear range and a low detection limit under the optimized conditions. Satisfactory results were also obtained for the methidathion determination in waste water samples. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Molecular imprinting polymer electrosensor based on gold nanoparticles for theophylline recognition and determination

    International Nuclear Information System (INIS)

    Kan, X.; Liu, T.; Zhou, H.; Li, C.; Fang, B.

    2010-01-01

    An electrochemical sensor for theophylline (ThPh) was prepared by electropolymerizing o-phenylenediamine on a glassy carbon electrode in the presence of ThPh via cyclic voltammetry, followed by deposition of gold nanoparticles using a potentiostatic method. The effects of pH, ratio between template molecule and monomer, number of cycles for electropolymerization, and of the solution for extraction were optimized. The current of the electro-active model system hexacyanoferrate(III) and hexacyanoferrate(IV) decreased linearly with successive addition of ThPh in the concentration range between 4. 0 x 10 -7 ∼ 1. 5 x 10 -5 mol.L -1 and 2. 4 x 10 -4 ∼ 3. 4 x 10 -3 mol.L -1 , with a detection limit of 1. 0 x 10 -7 mol.L -1 . The sensor has an excellent recognition capability for ThPh compared to structurally related molecules, can be regenerated and is stable. (author)

  1. Application of Machine Learning tools to recognition of molecular patterns in STM images

    Science.gov (United States)

    Maksov, Artem; Ziatdinov, Maxim; Fujii, Shintaro; Kiguchi, Manabu; Higashibayashi, Shuhei; Sakurai, Hidehiro; Kalinin, Sergei; Sumpter, Bobby

    The ability to utilize individual molecules and molecular assemblies as data storage elements has motivated scientist for years, concurrent with the continuous effort to shrink a size of data storage devices in microelectronics industry. One of the critical issues in this effort lies in being able to identify individual molecular assembly units (patterns), on a large scale in an automated fashion of complete information extraction. Here we present a novel method of applying machine learning techniques for extraction of positional and rotational information from scanning tunneling microscopy (STM) images of π-bowl sumanene molecules on gold. We use Markov Random Field (MRF) model to decode the polar rotational states for each molecule in a large scale STM image of molecular film. We further develop an algorithm that uses a convolutional Neural Network combined with MRF and input from density functional theory to classify molecules into different azimuthal rotational classes. Our results demonstrate that a molecular film is partitioned into distinctive azimuthal rotational domains consisting typically of 20-30 molecules. In each domain, the ``bowl-down'' molecules are generally surrounded by six nearest neighbor molecules in ``bowl-up'' configuration, and the resultant overall structure form a periodic lattice of rotational and polar states within each domain. Research was supported by the US Department of Energy.

  2. Structural analysis and unique molecular recognition properties of a Bauhinia forficata lectin that inhibits cancer cell growth.

    Science.gov (United States)

    Lubkowski, Jacek; Durbin, Sarah V; Silva, Mariana C C; Farnsworth, David; Gildersleeve, Jeffrey C; Oliva, Maria Luiza V; Wlodawer, Alexander

    2017-02-01

    Lectins have been used at length for basic research and clinical applications. New insights into the molecular recognition properties enhance our basic understanding of carbohydrate-protein interactions and aid in the design/development of new lectins. In this study, we used a combination of cell-based assays, glycan microarrays, and X-ray crystallography to evaluate the structure and function of the recombinant Bauhinia forficata lectin (BfL). The lectin was shown to be cytostatic for several cancer cell lines included in the NCI-60 panel; in particular, it inhibited growth of melanoma cancer cells (LOX IMVI) by over 95%. BfL is dimeric in solution and highly specific for binding of oligosaccharides and glycopeptides with terminal N-acetylgalactosamine (GalNAc). BfL was found to have especially strong binding (apparent K d  = 0.5-1.0 nm) to the tumor-associated Tn antigen. High-resolution crystal structures were determined for the ligand-free lectin, as well as for its complexes with three Tn glycopeptides, globotetraose, and the blood group A antigen. Extensive analysis of the eight crystal structures and comparison to structures of related lectins revealed several unique features of GalNAc recognition. Of special note, the carboxylate group of Glu126, lining the glycan-binding pocket, forms H-bonds with both the N-acetyl of GalNAc and the peptide amido group of Tn antigens. Stabilization provided by Glu126 is described here for the first time for any GalNAc-specific lectin. Taken together, the results provide new insights into the molecular recognition of carbohydrates and provide a structural understanding that will enable rational engineering of BfL for a variety of applications. Structural data are available in the PDB under the accession numbers 5T50, 5T52, 5T55, 5T54, 5T5L, 5T5J, 5T5P, and 5T5O. © 2016 Federation of European Biochemical Societies.

  3. Narrative versus Style : Effect of Genre Typical Events versus Genre Typical Filmic Realizations on Film Viewers' Genre Recognition

    NARCIS (Netherlands)

    Visch, V.; Tan, E.

    2008-01-01

    This study investigated whether film viewers recognize four basic genres (comic, drama, action and nonfiction) on the basis of genre-typical event cues or of genretypical filmic realization cues of events. Event cues are similar to the narrative content of a film sequence, while filmic realization

  4. Narrative versus style: Effect of genre-typical events versus genre-typical filmic realizations on film viewers’ genre recognition

    NARCIS (Netherlands)

    Visch, V.; Tan, E.

    2008-01-01

    This study investigated whether film viewers recognize four basic genres (comic, drama, action and nonfiction) on the basis of genre-typical event cues or of genre-typical filmic realization cues of events. Event cues are similar to the narrative content of a film sequence, while filmic realization

  5. Two Processes for Recognition Memory in Children of Early School Age: An Event-Related Potential Study

    Science.gov (United States)

    Mecklinger, Axel; Brunnemann, Nicole; Kipp, Kerstin

    2011-01-01

    We examined the ERP correlates of familiarity and recollection and their development in 8- to 10-year-old children and a control group of young adults. Capitalizing on the different temporal dynamics of familiarity and recollection, we tested recognition memory in both groups with a speeded and nonspeeded response condition. Consistent with the…

  6. The Effects of Early Experience on Face Recognition: An Event-Related Potential Study of Institutionalized Children in Romania

    Science.gov (United States)

    Moulson, Margaret C.; Westerlund, Alissa; Fox, Nathan A.; Zeanah, Charles H.; Nelson, Charles A.

    2009-01-01

    Data are reported from 3 groups of children residing in Bucharest, Romania. Face recognition in currently institutionalized, previously institutionalized, and never-institutionalized children was assessed at 3 time points: preintervention (n = 121), 30 months of age (n = 99), and 42 months of age (n = 77). Children watched photographs of caregiver…

  7. Synthesis and Characterization of Magnetic-Graphene Molecularly Imprinted Polymers for Selective Recognition of Ltryptophan

    Directory of Open Access Journals (Sweden)

    Zhang Yi

    2017-01-01

    Full Text Available In this paper, a novel molecular imprinted polymer using L-tryptophan(L-Trp as the template, dopamine(DA as both functional monomer and cross linking agent, magnetic graphene as the supporting matrix was synthesized. The prepared magnetic-graphene molecularly imprinted polymers(Fe3O4@GO-MIPs were characterized by Fourier transform infrared spectrometer(FT-IR, transmission electron microscopy (TEM, vibrating sample magnetometer (VSM, respectively. The results showed that when the molar ratio of L- tryptophan and dopamine was 1:4 and the reaction temperature was 60 °C, Fe3O4@GO-MIPs had the best adsorption quantity of 31.9 mg/g. The rebinding experiments indicated that Fe3O4@GO-MIPs not only have outstanding affinity and selectivity towards L-Trp over structurally related compounds but also easily reach the magnetic separation under an external magnetic field.

  8. Synthesis and Theoretical Study of Molecularly Imprinted Nanospheres for Recognition of Tocopherols

    Directory of Open Access Journals (Sweden)

    Chartchalerm Isarankura-Na-Ayudhya

    2009-08-01

    Full Text Available Molecular imprinting is a technology that facilitates the production of artificial receptors toward compounds of interest. The molecularly imprinted polymers act as artificial antibodies, artificial receptors, or artificial enzymes with the added benefit over their biological counterparts of being highly durable. In this study, we prepared molecularly imprinted polymers for the purpose of binding specifically to tocopherol (vitamin E and its derivative, tocopherol acetate. Binding of the imprinted polymers to the template was found to be two times greater than that of the control, non-imprinted polymers, when using only 10 mg of polymers. Optimization of the rebinding solvent indicated that ethanol-water at a molar ratio of 6:4 (v/v was the best solvent system as it enhanced the rebinding performance of the imprinted polymers toward both tocopherol and tocopherol acetate with a binding capacity of approximately 2 mg/g of polymer. Furthermore, imprinted nanospheres against tocopherol was successfully prepared by precipitation polymerization with ethanol-water at a molar ratio of 8:2 (v/v as the optimal rebinding solvent. Computer simulation was also performed to provide mechanistic insights on the binding mode of template-monomer complexes. Such polymers show high potential for industrial and medical applications, particularly for selective separation of tocopherol and derivatives.

  9. Preparation of a molecularly imprinted sensor based on quartz crystal microbalance for specific recognition of sialic acid in human urine.

    Science.gov (United States)

    Qiu, Xiuzhen; Xu, Xian-Yan; Chen, Xuncai; Wu, Yiyong; Guo, Huishi

    2018-05-08

    A novel molecularly imprinted quartz crystal microbalance (QCM) sensor was successfully prepared for selective determination of sialic acid (SA) in human urine samples. To obtain the QCM sensor, we first modified the gold surface of the QCM chip by self-assembling of allylmercaptane to introduce polymerizable double bonds on the chip surface. Then, SA molecularly imprinted polymer (MIP) nanofilm was attached to the modified QCM chip surface. For comparison, we have also characterized the nonmodified and improved surfaces of the QCM sensor by using atomic force microscopy (AFM) and Fourier transform infrared (FTIR) spectroscopy. We then tested the selectivity and detection limit of the imprinted QCM sensor via a series of adsorption experiments. The results show a linear response in the range of 0.025-0.50 μmol L -1 for sialic acid. Moreover, the limit of detection (LOD) of the prepared imprinted QCM sensor was found to be 1.0 nmol L -1 for sialic acid, and high recovery values range from 87.6 to 108.5% with RSD sensor was developed and used to detect sialic acid in human urine samples. Graphical abstract Specific recognition of sialic acid by the MIP-QCM sensor system.

  10. Molecular recognition of the environment and mechanisms of the origin of species in quantum-like modeling of evolution.

    Science.gov (United States)

    Melkikh, Alexey V; Khrennikov, Andrei

    2017-11-01

    A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown that these mechanisms, at the molecular level, cannot work steadily in terms of classical mechanics. Quantum mechanisms of changes in the genome, based on the long-range interaction potential between biologically important molecules, are proposed as one of possible explanation. Different variants of interactions of the organism and environment based on molecular recognition and leading to new species origins are considered. Experiments to verify the model are proposed. This bio-physical study is completed by the general operational model of based on quantum information theory. The latter is applied to model of epigenetic evolution. We briefly present the basics of the quantum-like approach to modeling of bio-informational processes. This approach is illustrated by the quantum-like model of epigenetic evolution. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Characterization of the molecular basis of group II intron RNA recognition by CRS1-CRM domains.

    Science.gov (United States)

    Keren, Ido; Klipcan, Liron; Bezawork-Geleta, Ayenachew; Kolton, Max; Shaya, Felix; Ostersetzer-Biran, Oren

    2008-08-22

    CRM (chloroplast RNA splicing and ribosome maturation) is a recently recognized RNA-binding domain of ancient origin that has been retained in eukaryotic genomes only within the plant lineage. Whereas in bacteria CRM domains exist as single domain proteins involved in ribosome maturation, in plants they are found in a family of proteins that contain between one and four repeats. Several members of this family with multiple CRM domains have been shown to be required for the splicing of specific plastidic group II introns. Detailed biochemical analysis of one of these factors in maize, CRS1, demonstrated its high affinity and specific binding to the single group II intron whose splicing it facilitates, the plastid-encoded atpF intron RNA. Through its association with two intronic regions, CRS1 guides the folding of atpF intron RNA into its predicted "catalytically active" form. To understand how multiple CRM domains cooperate to achieve high affinity sequence-specific binding to RNA, we analyzed the RNA binding affinity and specificity associated with each individual CRM domain in CRS1; whereas CRM3 bound tightly to the RNA, CRM1 associated specifically with a unique region found within atpF intron domain I. CRM2, which demonstrated only low binding affinity, also seems to form specific interactions with regions localized to domains I, III, and IV. We further show that CRM domains share structural similarities and RNA binding characteristics with the well known RNA recognition motif domain.

  12. Dissecting molecular interactions involved in recognition of target disulfides by the barley thioredoxin system

    DEFF Research Database (Denmark)

    Björnberg, Olof; Maeda, Kenji; Svensson, Birte

    2012-01-01

    Thioredoxin reduces disulfide bonds, thus regulating activities of target proteins in various biological systems, e.g., inactivation of inhibitors of starch hydrolases and proteases in germinating plant seeds. In the three-dimensional structure of a complex with barley α-amylase/subtilisin inhibi......Thioredoxin reduces disulfide bonds, thus regulating activities of target proteins in various biological systems, e.g., inactivation of inhibitors of starch hydrolases and proteases in germinating plant seeds. In the three-dimensional structure of a complex with barley α...... thioredoxin reductase. HvTrxh2 M88G and M88A adjacent to the invariant cis-proline lost efficiency in both BASI disulfide reduction and recycling by thioredoxin reductase. These effects were further pronounced in M88P lacking a backbone NH group. Remarkably, HvTrxh2 E86R in the same loop displayed overall...... retained catalytic properties, with the exception of a 3-fold increased activity toward BASI. From the 104VGA106 loop, a backbone hydrogen bond donated by A106 appears to be important for target disulfide recognition as A106P lost 90% activity toward BASI but was efficiently recycled by thioredoxin...

  13. Comparison of extraction chromatography and a procedure based on the molecular recognition method as separation methods in the determination of neptunium and plutonium radionuclides

    International Nuclear Information System (INIS)

    Strisovska, Jana; Galanda, Dusan; Drabova, Veronika; Kuruc, Jozef

    2012-01-01

    The potential of various types of sorbents for separation of radionuclides of plutonium and neptunium were examined. Extraction chromatography and a procedure based on the molecular recognition method were used for the separation. The suitability of the various sorbent types and brands for this purpose was determined. (orig.)

  14. iBodies: modular synthetic antibody mimetics based on hydrophilic polymers decorated with functional moieties as tools for molecular recognition, imaging and specific drug delivery

    Czech Academy of Sciences Publication Activity Database

    Šácha, Pavel; Dvořáková, Petra; Knedlík, Tomáš; Schimer, Jiří; Šubr, Vladimír; Ulbrich, Karel; Bušek, P.; Navrátil, Václav; Sedlák, František; Majer, Pavel; Šedo, A.; Konvalinka, Jan

    2017-01-01

    Roč. 284, Suppl 1 (2017), s. 340 ISSN 1742-464X. [FEBS Congress /42./ From Molecules to Cells and Back. 10.09.2017-14.09.2017, Jerusalem] Institutional support: RVO:61388963 ; RVO:61389013 Keywords : antibody mimetics * molecular recognition * polymer conjugates Subject RIV: CE - Biochemistry

  15. Conductometric Sensor for PAH Detection with Molecularly Imprinted Polymer as Recognition Layer

    Directory of Open Access Journals (Sweden)

    Usman Latif

    2018-03-01

    Full Text Available A conductometric sensor based on screen-printed interdigital gold electrodes on glass substrate coated with molecularly imprinted polyurethane layers was fabricated to detect polycyclic aromatic hydrocarbons (PAHs in water. The results prove that screen-printed interdigital electrodes are very suitable transducers to fabricate low-cost sensor systems for measuring change in resistance of PAH-imprinted layers while exposing to different PAHs. The sensor showed good selectivity to its templated molecules and high sensitivity with a detection limit of 1.3 nmol/L e.g., for anthracene in water which is lower than WHO’s permissible limit.

  16. Application of TensorFlow to recognition of visualized results of fragment molecular orbital (FMO) calculations

    OpenAIRE

    Saitou, Sona; Iijima, Jun; Fujimoto, Mayu; Mochizuki, Yuji; Okuwaki, Koji; Doi, Hideo; Komeiji, Yuto

    2018-01-01

    We have applied Google's TensorFlow deep learning toolkit to recognize the visualized results of the fragment molecular orbital (FMO) calculations. Typical protein structures of alpha-helix and beta-sheet provide some characteristic patterns in the two-dimensional map of inter-fragment interaction energy termed as IFIE-map (Kurisaki et al., Biophys. Chem. 130 (2007) 1). A thousand of IFIE-map images with labels depending on the existences of alpha-helix and beta-sheet were prepared by employi...

  17. Events

    Directory of Open Access Journals (Sweden)

    Igor V. Karyakin

    2016-02-01

    Full Text Available The 9th ARRCN Symposium 2015 was held during 21st–25th October 2015 at the Novotel Hotel, Chumphon, Thailand, one of the most favored travel destinations in Asia. The 10th ARRCN Symposium 2017 will be held during October 2017 in the Davao, Philippines. International Symposium on the Montagu's Harrier (Circus pygargus «The Montagu's Harrier in Europe. Status. Threats. Protection», organized by the environmental organization «Landesbund für Vogelschutz in Bayern e.V.» (LBV was held on November 20-22, 2015 in Germany. The location of this event was the city of Wurzburg in Bavaria.

  18. Early use of orthographic information in spoken word recognition: Event-related potential evidence from the Korean language.

    Science.gov (United States)

    Kwon, Youan; Choi, Sungmook; Lee, Yoonhyoung

    2016-04-01

    This study examines whether orthographic information is used during prelexical processes in spoken word recognition by investigating ERPs during spoken word processing for Korean words. Differential effects due to orthographic syllable neighborhood size and sound-to-spelling consistency on P200 and N320 were evaluated by recording ERPs from 42 participants during a lexical decision task. The results indicate that P200 was smaller for words whose orthographic syllable neighbors are large in number rather than those that are small. In addition, a word with a large orthographic syllable neighborhood elicited a smaller N320 effect than a word with a small orthographic syllable neighborhood only when the word had inconsistent sound-to-spelling mapping. The results provide support for the assumption that orthographic information is used early during the prelexical spoken word recognition process. © 2015 Society for Psychophysiological Research.

  19. Molecular recognition of live methicillin-resistant staphylococcus aureus cells using DNA aptamers.

    Science.gov (United States)

    Turek, Diane; Van Simaeys, Dimitri; Johnson, Judith; Ocsoy, Ismail; Tan, Weihong

    2013-01-01

    To generate DNA-aptamers binding to Methicillin-resistant Staphylococcus aureus (MRSA) . The Cell-Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology was used to run the selection against MRSA bacteria and develop target-specific aptamers. MRSA bacteria were targeted while Enterococcus faecalis bacteria were used for counter selection during that process. Binding assays to determine the right aptamer candidates as well as binding assays on clinical samples were performed through flow cytometry and analyzed using the FlowJo software. The characterization of the aptamers was done by determination of their K d values and determined by analysis of flow data at different aptamer concentration using SigmaPlot. Finally, the recognition of the complex Gold-nanoparticle-aptamer to the bacteria cells was observed using transmission electron microscopy (TEM). During the cell-SELEX selection process, 17 rounds were necessary to generate enrichment of the pool. While the selection was run using fixed cells, it was shown that the binding of the pools with live cells was giving similar results. After sequencing and analysis of the two last pools, four sequences were identified to be aptamer candidates. The characterization of those aptamers showed that based on their K d values, DTMRSA4 presented the best binding with a K d value of 94.61 ± 18.82 nmol/L. A total of ten clinical samples of MRSA , S. aureus and Enterococcus faecalis were obtained to test those aptamers and determine their binding on a panel of samples. DTMRSA1 and DTMRSA3 showed the best results regarding their specificity to MRSA , DTMRSA1 being the most specific of all. Finally, those aptamers were coupled with gold-nanoparticle and their binding to MRSA cells was visualized through TEM showing that adduction of nanoparticles on the aptamers did not change their binding property. A total of four aptamers that bind to MRSA were obtained with K d values ranking from 94 to 200 nmol/L.

  20. Molecular recognition of ketamine by a subset of olfactory G protein–coupled receptors

    Science.gov (United States)

    Saven, Jeffery G.; Matsunami, Hiroaki; Eckenhoff, Roderic G.

    2015-01-01

    Ketamine elicits various neuropharmacological effects, including sedation, analgesia, general anesthesia, and antidepressant activity. Through an in vitro screen, we identified four mouse olfactory receptors (ORs) that responded to ketamine. In addition to their presence in the olfactory epithelium, these G protein (heterotrimeric guanine nucleotide–binding protein)–coupled receptors (GPCRs) are distributed throughout the central nervous system. To better understand the molecular basis of the interactions between ketamine and ORs, we used sequence comparison and molecular modeling to design mutations that (i) increased, reduced, or abolished ketamine responsiveness in responding receptors, and (ii) rendered non-responding receptors responsive to ketamine. We showed that olfactory sensory neurons (OSNs) that expressed distinct ORs responded to ketamine in vivo, suggesting that ORs may serve as functional targets for ketamine. The ability to both abolish and introduce responsiveness to ketamine in GPCRs enabled us to identify and confirm distinct interaction loci in the binding site, which suggested a signature ketamine-binding pocket that may guide exploration of additional receptors for this general anesthetic drug. PMID:25829447

  1. Sequence analysis of serum albumins reveals the molecular evolution of ligand recognition properties.

    Science.gov (United States)

    Fanali, Gabriella; Ascenzi, Paolo; Bernardi, Giorgio; Fasano, Mauro

    2012-01-01

    Serum albumin (SA) is a circulating protein providing a depot and carrier for many endogenous and exogenous compounds. At least seven major binding sites have been identified by structural and functional investigations mainly in human SA. SA is conserved in vertebrates, with at least 49 entries in protein sequence databases. The multiple sequence analysis of this set of entries leads to the definition of a cladistic tree for the molecular evolution of SA orthologs in vertebrates, thus showing the clustering of the considered species, with lamprey SAs (Lethenteron japonicum and Petromyzon marinus) in a separate outgroup. Sequence analysis aimed at searching conserved domains revealed that most SA sequences are made up by three repeated domains (about 600 residues), as extensively characterized for human SA. On the contrary, lamprey SAs are giant proteins (about 1400 residues) comprising seven repeated domains. The phylogenetic analysis of the SA family reveals a stringent correlation with the taxonomic classification of the species available in sequence databases. A focused inspection of the sequences of ligand binding sites in SA revealed that in all sites most residues involved in ligand binding are conserved, although the versatility towards different ligands could be peculiar of higher organisms. Moreover, the analysis of molecular links between the different sites suggests that allosteric modulation mechanisms could be restricted to higher vertebrates.

  2. Face learning and the emergence of view-independent face recognition: an event-related brain potential study.

    Science.gov (United States)

    Zimmermann, Friederike G S; Eimer, Martin

    2013-06-01

    Recognizing unfamiliar faces is more difficult than familiar face recognition, and this has been attributed to qualitative differences in the processing of familiar and unfamiliar faces. Familiar faces are assumed to be represented by view-independent codes, whereas unfamiliar face recognition depends mainly on view-dependent low-level pictorial representations. We employed an electrophysiological marker of visual face recognition processes in order to track the emergence of view-independence during the learning of previously unfamiliar faces. Two face images showing either the same or two different individuals in the same or two different views were presented in rapid succession, and participants had to perform an identity-matching task. On trials where both faces showed the same view, repeating the face of the same individual triggered an N250r component at occipito-temporal electrodes, reflecting the rapid activation of visual face memory. A reliable N250r component was also observed on view-change trials. Crucially, this view-independence emerged as a result of face learning. In the first half of the experiment, N250r components were present only on view-repetition trials but were absent on view-change trials, demonstrating that matching unfamiliar faces was initially based on strictly view-dependent codes. In the second half, the N250r was triggered not only on view-repetition trials but also on view-change trials, indicating that face recognition had now become more view-independent. This transition may be due to the acquisition of abstract structural codes of individual faces during face learning, but could also reflect the formation of associative links between sets of view-specific pictorial representations of individual faces. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. Ab initio molecular dynamics simulations of low energy recoil events in MgO

    International Nuclear Information System (INIS)

    Petersen, B. A.; Liu, B.; Weber, W. J.; Oak Ridge National Laboratory; Zhang, Y.; Oak Ridge National Laboratory

    2017-01-01

    In this paper, low-energy recoil events in MgO are studied using ab initio molecular dynamics simulations to reveal the dynamic displacement processes and final defect configurations. Threshold displacement energies, E_d, are obtained for Mg and O along three low-index crystallographic directions, [100], [110], and [111]. The minimum values for E_d are found along the [110] direction consisting of the same element, either Mg or O atoms. Minimum threshold values of 29.5 eV for Mg and 25.5 eV for O, respectively, are suggested from the calculations. For other directions, the threshold energies are considerably higher, 65.5 and 150.0 eV for O along [111] and [100], and 122.5 eV for Mg along both [111] and [100] directions, respectively. These results show that the recoil events in MgO are partial-charge transfer assisted processes where the charge transfer plays an important role. Finally, there is a similar trend found in other oxide materials, where the threshold displacement energy correlates linearly with the peak partial-charge transfer, suggesting this behavior might be universal in ceramic oxides.

  4. Defining molecular initiating events in the adverse outcome pathway framework for risk assessment.

    Science.gov (United States)

    Allen, Timothy E H; Goodman, Jonathan M; Gutsell, Steve; Russell, Paul J

    2014-12-15

    Consumer and environmental safety decisions are based on exposure and hazard data, interpreted using risk assessment approaches. The adverse outcome pathway (AOP) conceptual framework has been presented as a logical sequence of events or processes within biological systems which can be used to understand adverse effects and refine current risk assessment practices in ecotoxicology. This framework can also be applied to human toxicology and is explored on the basis of investigating the molecular initiating events (MIEs) of compounds. The precise definition of the MIE has yet to reach general acceptance. In this work we present a unified MIE definition: an MIE is the initial interaction between a molecule and a biomolecule or biosystem that can be causally linked to an outcome via a pathway. Case studies are presented, and issues with current definitions are addressed. With the development of a unified MIE definition, the field can look toward defining, classifying, and characterizing more MIEs and using knowledge of the chemistry of these processes to aid AOP research and toxicity risk assessment. We also present the role of MIE research in the development of in vitro and in silico toxicology and suggest how, by using a combination of biological and chemical approaches, MIEs can be identified and characterized despite a lack of detailed reports, even for some of the most studied molecules in toxicology.

  5. Cellular and molecular events leading to the development of skin cancer

    International Nuclear Information System (INIS)

    Melnikova, Vladislava O.; Ananthaswamy, Honnavara N.

    2005-01-01

    The transition from a normal cell to a neoplastic cell is a complex process and involves both genetic and epigenetic changes. The process of carcinogenesis begins when the DNA is damaged, which then leads to a cascade of events leading to the development of a tumor. Ultraviolet (UV) radiation causes DNA damage, inflammation, erythema, sunburn, immunosuppression, photoaging, gene mutations, and skin cancer. Upon DNA damage, the p53 tumor suppressor protein undergoes phosphorylation and translocation to the nucleus and aids in DNA repair or causes apoptosis. Excessive UV exposure overwhelms DNA repair mechanisms leading to induction of p53 mutations and loss of Fas-FasL interaction. Keratinocytes carrying p53 mutations acquire a growth advantage by virtue of their increased resistance to apoptosis. Thus, resistance to cell death is a key event in photocarcinogenesis and conversely, elimination of cells containing excessive UV-induced DNA damage is a key step in protecting against skin cancer development. Apoptosis-resistant keratinocytes undergo clonal expansion that eventually leads to formation of actinic keratoses and squamous cell carcinomas. In this article, we will review some of the cellular and molecular mechanisms involved in initiation and progression of UV-induced skin cancer

  6. Cellular and molecular events leading to the development of skin cancer

    Energy Technology Data Exchange (ETDEWEB)

    Melnikova, Vladislava O. [Department of Immunology, University of Texas M.D. Anderson Cancer Center, P.O. Box 301402, Unit 902, Houston, TX 77030 (United States); Ananthaswamy, Honnavara N. [Department of Immunology, University of Texas M.D. Anderson Cancer Center, P.O. Box 301402, Unit 902, Houston, TX 77030 (United States)]. E-mail: hanantha@mdanderson.org

    2005-04-01

    The transition from a normal cell to a neoplastic cell is a complex process and involves both genetic and epigenetic changes. The process of carcinogenesis begins when the DNA is damaged, which then leads to a cascade of events leading to the development of a tumor. Ultraviolet (UV) radiation causes DNA damage, inflammation, erythema, sunburn, immunosuppression, photoaging, gene mutations, and skin cancer. Upon DNA damage, the p53 tumor suppressor protein undergoes phosphorylation and translocation to the nucleus and aids in DNA repair or causes apoptosis. Excessive UV exposure overwhelms DNA repair mechanisms leading to induction of p53 mutations and loss of Fas-FasL interaction. Keratinocytes carrying p53 mutations acquire a growth advantage by virtue of their increased resistance to apoptosis. Thus, resistance to cell death is a key event in photocarcinogenesis and conversely, elimination of cells containing excessive UV-induced DNA damage is a key step in protecting against skin cancer development. Apoptosis-resistant keratinocytes undergo clonal expansion that eventually leads to formation of actinic keratoses and squamous cell carcinomas. In this article, we will review some of the cellular and molecular mechanisms involved in initiation and progression of UV-induced skin cancer.

  7. An Event-Driven Hybrid Molecular Dynamics and Direct Simulation Monte Carlo Algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Donev, A; Garcia, A L; Alder, B J

    2007-07-30

    A novel algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with the solvent particles with hard core potentials. The algorithm uses event-driven molecular dynamics (MD) for the simulation of the polymer chain and the interactions between the chain beads and the surrounding solvent particles. The interactions between the solvent particles themselves are not treated deterministically as in event-driven algorithms, rather, the momentum and energy exchange in the solvent is determined stochastically using the Direct Simulation Monte Carlo (DSMC) method. The coupling between the solvent and the solute is consistently represented at the particle level, however, unlike full MD simulations of both the solvent and the solute, the spatial structure of the solvent is ignored. The algorithm is described in detail and applied to the study of the dynamics of a polymer chain tethered to a hard wall subjected to uniform shear. The algorithm closely reproduces full MD simulations with two orders of magnitude greater efficiency. Results do not confirm the existence of periodic (cycling) motion of the polymer chain.

  8. Nanosilica-based molecularly imprinted polymer nanoshell for specific recognition and determination of rhodamine B in red wine and beverages.

    Science.gov (United States)

    Long, Zerong; Xu, Weiwei; Lu, Yi; Qiu, Hongdeng

    2016-09-01

    A new and facile rhodamine B (RhB)-imprinted polymer nanoshell coating for SiO2 nanoparticles was readily prepared by a combination of silica gel modification and molecular surface imprinting. The RhB-imprinted polymers (RhB-MIPs) were characterized by Fourier transform infrared spectroscopy, scanning electron microscopy, and UV-vis spectroscopy; the binding properties and selectivity of these MIPs were investigated in detail. The uniformly imprinted nanoparticles displayed a rather thin shell thickness (23nm) with highly effective recognition sites, showing homogenous distribution and monolayer adsorption. The maximum MIP adsorption capacity (Qm) was as high as 45.2mgg(-1), with an adsorption equilibrium time of about 15min at ambient temperature. Dynamic rebinding experiments showed that chemical adsorption is crucial for RhB binding to RhB-MIPs. The adsorption isotherm for RhB-MIPs binding could also be described by the Langmuir equation at different temperatures and pH values. Increasing temperature led to an enhanced Qm, a decreased dissociation constant (K'd), and a more negative free energy (ΔG), indicating that adsorption is favored at higher temperatures. Moreover, the adsorption capacity of RhB was remarkably affected by pH. At pH>7, the adsorption of RhB was driven by hydrogen bonding interactions, while at pH<7 electrostatic forces were dominant. Additionally, the MIPs also showed specific recognition of RhB from the standard mixture solution containing five structurally analogs. This method was also successfully employed to determine RhB content in red wine and beverages using three levels of spiking, with recoveries in the range of 91.6-93.1% and relative standard deviations lower than 4.1%. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. A structural and mutagenic blueprint for molecular recognition of strychnine and d-tubocurarine by different cys-loop receptors.

    Directory of Open Access Journals (Sweden)

    Marijke Brams

    2011-03-01

    Full Text Available Cys-loop receptors (CLR are pentameric ligand-gated ion channels that mediate fast excitatory or inhibitory transmission in the nervous system. Strychnine and d-tubocurarine (d-TC are neurotoxins that have been highly instrumental in decades of research on glycine receptors (GlyR and nicotinic acetylcholine receptors (nAChR, respectively. In this study we addressed the question how the molecular recognition of strychnine and d-TC occurs with high affinity and yet low specificity towards diverse CLR family members. X-ray crystal structures of the complexes with AChBP, a well-described structural homolog of the extracellular domain of the nAChRs, revealed that strychnine and d-TC adopt multiple occupancies and different ligand orientations, stabilizing the homopentameric protein in an asymmetric state. This introduces a new level of structural diversity in CLRs. Unlike protein and peptide neurotoxins, strychnine and d-TC form a limited number of contacts in the binding pocket of AChBP, offering an explanation for their low selectivity. Based on the ligand interactions observed in strychnine- and d-TC-AChBP complexes we performed alanine-scanning mutagenesis in the binding pocket of the human α1 GlyR and α7 nAChR and showed the functional relevance of these residues in conferring high potency of strychnine and d-TC, respectively. Our results demonstrate that a limited number of ligand interactions in the binding pocket together with an energetic stabilization of the extracellular domain are key to the poor selective recognition of strychnine and d-TC by CLRs as diverse as the GlyR, nAChR, and 5-HT(3R.

  10. Diagnostic and molecular evaluation of three iridovirus-associated salamander mortality events

    Science.gov (United States)

    Docherty, D.E.; Meteyer, C.U.; Wang, Jingyuan; Mao, J.; Case, S.T.; Chinchar, V.G.

    2003-01-01

    In 1998 viruses were isolated from tiger salamander larvae (Ambystoma tigrinum diaboli and A. tigrinum melanostictum) involved in North Dakota and Utah (USA) mortality events and spotted salamander (A. maculatum) larvae in a third event in Maine (USA). Although sympatric caudates and anurans were present at all three sites only ambystomid larvae appeared to be affected. Mortality at the North Dakota site was in the thousands while at the Utah and Maine sites mortality was in the hundreds. Sick larvae were lethargic and slow moving. They swam in circles with obvious buoyancy problems and were unable to remain upright. On the ventral surface, near the gills and hind limbs, red spots or swollen areas were noted. Necropsy findings included: hemorrhages and ulceration of the skin, subcutaneous and intramuscular edema, swollen and pale livers with multifocal hemorrhage, and distended fluid-filled intestines with areas of hemorrhage. Light microscopy revealed intracytoplasmic inclusions, suggestive of a viral infection, in a variety of organs. Electron microscopy of ultra thin sections of the same tissues revealed iridovirus-like particles within the inclusions. These viruses were isolated from a variety of organs, indicating a systemic infection. Representative viral isolates from the three mortality events were characterized using molecular assays. Characterization confirmed that the viral isolates were iridoviruses and that the two tiger salamander isolates were similar and could be distinguished from the spotted salamander isolate. The spotted salamander isolate was similar to frog virus 3, the type species of the genus Ranavirus, while the tiger salamander isolates were not. These data indicate that different species of salamanders can become infected and die in association with different iridoviruses. Challenge assays are required to determine the fish and amphibian host range of these isolates and to assess the susceptibility of tiger and spotted salamanders to

  11. Fuzzy method of recognition of high molecular substances in evidence-based biology

    Science.gov (United States)

    Olevskyi, V. I.; Smetanin, V. T.; Olevska, Yu. B.

    2017-10-01

    Nowadays modern requirements to achieving reliable results along with high quality of researches put mathematical analysis methods of results at the forefront. Because of this, evidence-based methods of processing experimental data have become increasingly popular in the biological sciences and medicine. Their basis is meta-analysis, a method of quantitative generalization of a large number of randomized trails contributing to a same special problem, which are often contradictory and performed by different authors. It allows identifying the most important trends and quantitative indicators of the data, verification of advanced hypotheses and discovering new effects in the population genotype. The existing methods of recognizing high molecular substances by gel electrophoresis of proteins under denaturing conditions are based on approximate methods for comparing the contrast of electrophoregrams with a standard solution of known substances. We propose a fuzzy method for modeling experimental data to increase the accuracy and validity of the findings of the detection of new proteins.

  12. Transfer of molecular recognition information from DNA nanostructures to gold nanoparticles

    Science.gov (United States)

    Edwardson, Thomas G. W.; Lau, Kai Lin; Bousmail, Danny; Serpell, Christopher J.; Sleiman, Hanadi F.

    2016-02-01

    DNA nanotechnology offers unparalleled precision and programmability for the bottom-up organization of materials. This approach relies on pre-assembling a DNA scaffold, typically containing hundreds of different strands, and using it to position functional components. A particularly attractive strategy is to employ DNA nanostructures not as permanent scaffolds, but as transient, reusable templates to transfer essential information to other materials. To our knowledge, this approach, akin to top-down lithography, has not been examined. Here we report a molecular printing strategy that chemically transfers a discrete pattern of DNA strands from a three-dimensional DNA structure to a gold nanoparticle. We show that the particles inherit the DNA sequence configuration encoded in the parent template with high fidelity. This provides control over the number of DNA strands and their relative placement, directionality and sequence asymmetry. Importantly, the nanoparticles produced exhibit the site-specific addressability of DNA nanostructures, and are promising components for energy, information and biomedical applications.

  13. Molecular recognition applied to gas detection: the contribution of Langmuir-Blodgett films

    International Nuclear Information System (INIS)

    Clemendot, Sylvain

    1992-01-01

    In the first part of this research thesis, the author presents the Langmuir-Blodgett technique and outlines how it can face the challenge of molecular electronics. Then, he proposes an overview of the state-of-the-art of chemical sensors based on LB films, and an assessment of the state of the art of conductive LB films based on TCNQ (tetracyanoquinodimethane) and on tetrathiafulvalene for which the author proposes a modelling. He describes how phosphine sensors with varying conductivity based on TCNQ-based conductive LB films have been developed and reports the study of electric performance of these sensors. He describes and compares mechanisms of interaction of phosphine with conductive LB films for films based on TCNQ and those based on tetrathiafulvalene [fr

  14. PASBio: predicate-argument structures for event extraction in molecular biology

    Science.gov (United States)

    Wattarujeekrit, Tuangthong; Shah, Parantu K; Collier, Nigel

    2004-01-01

    Background The exploitation of information extraction (IE), a technology aiming to provide instances of structured representations from free-form text, has been rapidly growing within the molecular biology (MB) research community to keep track of the latest results reported in literature. IE systems have traditionally used shallow syntactic patterns for matching facts in sentences but such approaches appear inadequate to achieve high accuracy in MB event extraction due to complex sentence structure. A consensus in the IE community is emerging on the necessity for exploiting deeper knowledge structures such as through the relations between a verb and its arguments shown by predicate-argument structure (PAS). PAS is of interest as structures typically correspond to events of interest and their participating entities. For this to be realized within IE a key knowledge component is the definition of PAS frames. PAS frames for non-technical domains such as newswire are already being constructed in several projects such as PropBank, VerbNet, and FrameNet. Knowledge from PAS should enable more accurate applications in several areas where sentence understanding is required like machine translation and text summarization. In this article, we explore the need to adapt PAS for the MB domain and specify PAS frames to support IE, as well as outlining the major issues that require consideration in their construction. Results We introduce PASBio by extending a model based on PropBank to the MB domain. The hypothesis we explore is that PAS holds the key for understanding relationships describing the roles of genes and gene products in mediating their biological functions. We chose predicates describing gene expression, molecular interactions and signal transduction events with the aim of covering a number of research areas in MB. Analysis was performed on sentences containing a set of verbal predicates from MEDLINE and full text journals. Results confirm the necessity to analyze

  15. Multiple ways to the prior occurrence of an event: an electrophysiological dissociation of experimental and conceptually driven familiarity in recognition memory.

    Science.gov (United States)

    Wiegand, Iris; Bader, Regine; Mecklinger, Axel

    2010-11-11

    Recent research has shown that familiarity contributes to associative memory when the to-be-associated stimuli are unitized during encoding. However, the specific processes underlying familiarity-based recognition of unitized representations are still indefinite. In this study, we present electrophysiologically dissociable early old/new effects, presumably related to two different kinds of familiarity inherent in associative recognition tasks. In a study-test associative recognition memory paradigm, we employed encoding conditions that established unitized representations of two pre-experimentally unrelated words, e.g. vegetable-bible. We compared event-related potentials (ERP) during the retrieval of these unitized word pairs using different retrieval cues. Word pairs presented in the same order as during unitization at encoding elicited a parietally distributed early old/new effect which we interpret as reflecting conceptually driven familiarity for newly formed concepts. Conversely, word pairs presented in reversed order only elicited a topographically dissociable early effect, i.e. the mid-frontal old/new effect, the putative correlate of experimental familiarity. The late parietal old/new effect, the putative ERP correlate of recollection, was obtained irrespective of word order, though it was larger for words presented in same order. These results indicate that familiarity may not be a unitary process and that different task demands can promote the assessment of conceptually driven familiarity for novel unitized concepts or experimentally-induced increments of experimental familiarity, respectively. Copyright © 2010 Elsevier B.V. All rights reserved.

  16. A Targeted "Capture" and "Removal" Scavenger toward Multiple Pollutants for Water Remediation based on Molecular Recognition.

    Science.gov (United States)

    Wang, Jie; Shen, Haijing; Hu, Xiaoxia; Li, Yan; Li, Zhihao; Xu, Jinfan; Song, Xiufeng; Zeng, Haibo; Yuan, Quan

    2016-03-01

    For the water remediation techniques based on adsorption, the long-standing contradictories between selectivity and multiple adsorbability, as well as between affinity and recyclability, have put it on weak defense amid more and more severe environment crisis. Here, a pollutant-targeting hydrogel scavenger is reported for water remediation with both high selectivity and multiple adsorbability for several pollutants, and with strong affinity and good recyclability through rationally integrating the advantages of multiple functional materials. In the scavenger, aptamers fold into binding pockets to accommodate the molecular structure of pollutants to afford perfect selectivity, and Janus nanoparticles with antibacterial function as well as anisotropic surfaces to immobilize multiple aptamers allow for simultaneously handling different kinds of pollutants. The scavenger exhibits high efficiencies in removing pollutants from water and it can be easily recycled for many times without significant loss of loading capacities. Moreover, the residual concentrations of each contaminant are well below the drinking water standards. Thermodynamic behavior of the adsorption process is investigated and the rate-controlling process is determined. Furthermore, a point of use device is constructed and it displays high efficiency in removing pollutants from environmental water. The scavenger exhibits great promise to be applied in the next generation of water purification systems.

  17. Molecular imprinting polymer with polyoxometalate/carbon nitride nanotubes for electrochemical recognition of bilirubin

    International Nuclear Information System (INIS)

    Yola, Mehmet Lütfi; Göde, Ceren; Atar, Necip

    2017-01-01

    Highlights: •Bilirubin-imprinted sensor is developed for the sensitive detection of bilirubin •The prepared based on nanocomposite were characterized by several methods. •Bilirubin-imprinted sensor offers the important advantages •Bilirubin-imprinted sensor is preferred to the other methods for analysis -- Abstract: In this work, a new molecular imprinted sensor based on polyoxometalate (H 3 PW 12 O 40 , POM) functionalized carbon nitride nanotubes (C 3 N 4 NTs) nanocomposite was prepared for bilirubin (BR) analysis. The structures of prepared surfaces based on the nanocomposite were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), x-ray photoelectron spectroscopy (XPS) and energy dispersive x-ray analysis (EDX). After that, BR imprinted electrode on H 3 PW 12 O 40 /C 3 N 4 NTs nanocomposite was developed by cyclic voltammetry (CV) in 100 mM pyrrole containing 25 mM BR. The linearity range and the detection limit of the developed method were calculated as 1.0 × 10 −12 –1.0 × 10 −10 M and 3.0 × 10 −13 M, respectively. In addition, the imprinted sensor was applied to human plasma samples with high recovery and selectivity.

  18. Recognition of dual targets by a molecular beacon-based sensor: subtyping of influenza A virus.

    Science.gov (United States)

    Lee, Chun-Ching; Liao, Yu-Chieh; Lai, Yu-Hsuan; Lee, Chang-Chun David; Chuang, Min-Chieh

    2015-01-01

    A molecular beacon (MB)-based sensor to offer a decisive answer in combination with information originated from dual-target inputs is designed. The system harnesses an assistant strand and thermodynamically favored designation of unpaired nucleotides (UNs) to process the binary targets in "AND-gate" format and report fluorescence in "off-on" mechanism via a formation of a DNA four-way junction (4WJ). By manipulating composition of the UNs, the dynamic fluorescence difference between the binary targets-coexisting circumstance and any other scenario was maximized. Characteristic equilibrium constant (K), change of entropy (ΔS), and association rate constant (k) between the association ("on") and dissociation ("off") states of the 4WJ were evaluated to understand unfolding behavior of MB in connection to its sensing capability. Favorable MB and UNs were furthermore designed toward analysis of genuine genetic sequences of hemagglutinin (HA) and neuraminidase (NA) in an influenza A H5N2 isolate. The MB-based sensor was demonstrated to yield a linear calibration range from 1.2 to 240 nM and detection limit of 120 pM. Furthermore, high-fidelity subtyping of influenza virus was implemented in a sample of unpurified amplicons. The strategy opens an alternative avenue of MB-based sensors for dual targets toward applications in clinical diagnosis.

  19. Preparation and evaluation of molecularly imprinted polymer for selective recognition and adsorption of gossypol.

    Science.gov (United States)

    Zhi, Keke; Wang, Lulu; Zhang, Yagang; Zhang, Xuemin; Zhang, Letao; Liu, Li; Yao, Jun; Xiang, Wei

    2018-03-01

    Molecularly imprinted polymers (MIPs) were designed and prepared via bulk thermal polymerization with gossypol as the template molecule and dimethylaminoethyl methacrylate as the functional monomer. The morphology and microstructures of MIPs were characterized by scanning electron microscope and Brunauer-Emmett-Teller surface areas. Static adsorption tests were performed to evaluate adsorption behavior of gossypol by the MIPs. It was found that adsorption kinetics and adsorption isotherms data of MIPs for gossypol were fit well with the pseudo-second-order model and Freundlich model, respectively. Scatchard analysis showed that heterogeneous binding sites were formed in the MIPs, including lower-affinity binding sites with the maximum adsorption of 252 mg/g and higher-affinity binding sites with the maximum adsorption of 632 mg/g. Binding studies also revealed that MIPs had favorable selectivity towards gossypol compared with non-imprinted polymers. Furthermore, adsorption capacity of MIPs maintained above 90% after 5 regeneration cycles, indicating MIPs were recyclable and could be used multiple times. These results demonstrated that prepared MIPs could be a promising functional material for selective adsorption of gossypol. Copyright © 2017 John Wiley & Sons, Ltd.

  20. Detection of magnetic-labeled antibody specific recognition events by combined atomic force and magnetic force microscopy

    International Nuclear Information System (INIS)

    Hong Xia; Liu Yanmei; Li Jun; Guo Wei; Bai Yubai

    2009-01-01

    Atomic force (AFM) and magnetic force microscopy (MFM) were developed to detect biomolecular specific interaction. Goat anti-mouse immunoglobulin (anti-IgG) was covalently attached onto gold substrate modified by a self-assembly monolayer of thioctic acid via 1-ethyl-3-[3-(dimethylamino) propyl] carbodiimide (EDC) activation. Magnetic-labeled IgG then specifically adsorbed onto anti-IgG surface. The morphological variation was identified by AFM. MFM was proved to be a fine assistant tool to distinguish the immunorecognized nanocomposites from the impurities by detection of the magnetic signal from magnetic-labeled IgG. It would enhance the understanding of biomolecular recognition process.

  1. Detection of magnetic-labeled antibody specific recognition events by combined atomic force and magnetic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Hong Xia [Center for Advanced Optoelectronic Functional Materials Research, Key Laboratory of UV Light-Emitting Materials and Technology, Ministry of Education, Northeast Normal University, Changchun 130024 (China); College of Chemistry, Jilin University, Changchun 130023 (China)], E-mail: xiahong@nenu.edu.cn; Liu Yanmei; Li Jun; Guo Wei; Bai Yubai [College of Chemistry, Jilin University, Changchun 130023 (China)

    2009-09-15

    Atomic force (AFM) and magnetic force microscopy (MFM) were developed to detect biomolecular specific interaction. Goat anti-mouse immunoglobulin (anti-IgG) was covalently attached onto gold substrate modified by a self-assembly monolayer of thioctic acid via 1-ethyl-3-[3-(dimethylamino) propyl] carbodiimide (EDC) activation. Magnetic-labeled IgG then specifically adsorbed onto anti-IgG surface. The morphological variation was identified by AFM. MFM was proved to be a fine assistant tool to distinguish the immunorecognized nanocomposites from the impurities by detection of the magnetic signal from magnetic-labeled IgG. It would enhance the understanding of biomolecular recognition process.

  2. Electrochemical sensor for catechol and dopamine based on a catalytic molecularly imprinted polymer-conducting polymer hybrid recognition element.

    Science.gov (United States)

    Lakshmi, Dhana; Bossi, Alessandra; Whitcombe, Michael J; Chianella, Iva; Fowler, Steven A; Subrahmanyam, Sreenath; Piletska, Elena V; Piletsky, Sergey A

    2009-05-01

    One of the difficulties with using molecularly imprinted polymers (MIPs) and other electrically insulating materials as the recognition element in electrochemical sensors is the lack of a direct path for the conduction of electrons from the active sites to the electrode. We have sought to address this problem through the preparation and characterization of novel hybrid materials combining a catalytic MIP, capable of oxidizing the template, catechol, with an electrically conducting polymer. In this way a network of "molecular wires" assists in the conduction of electrons from the active sites within the MIP to the electrode surface. This was made possible by the design of a new monomer that combines orthogonal polymerizable functionality; comprising an aniline group and a methacrylamide. Conducting films were prepared on the surface of electrodes (Au on glass) by electropolymerization of the aniline moiety. A layer of MIP was photochemically grafted over the polyaniline, via N,N'-diethyldithiocarbamic acid benzyl ester (iniferter) activation of the methacrylamide groups. Detection of catechol by the hybrid-MIP sensor was found to be specific, and catechol oxidation was detected by cyclic voltammetry at the optimized operating conditions: potential range -0.6 V to +0.8 V (vs Ag/AgCl), scan rate 50 mV/s, PBS pH 7.4. The calibration curve for catechol was found to be linear to 144 microM, with a limit of detection of 228 nM. Catechol and dopamine were detected by the sensor, whereas analogues and potentially interfering compounds, including phenol, resorcinol, hydroquinone, serotonin, and ascorbic acid, had minimal effect (< or = 3%) on the detection of either analyte. Non-imprinted hybrid electrodes and bare gold electrodes failed to give any response to catechol at concentrations below 0.5 mM. Finally, the catalytic properties of the sensor were characterized by chronoamperometry and were found to be consistent with Michaelis-Menten kinetics.

  3. Molecular recognition of floral volatile with two olfactory related proteins in the Eastern honeybee (Apis cerana).

    Science.gov (United States)

    Li, Hongliang; Zhang, Linya; Ni, Cuixia; Shang, Hanwu; Zhuang, Shulin; Li, Jianke

    2013-05-01

    The honeybee relies on its sensitive olfaction to perform the foraging activities in the field. In the antennal chemoreception system of honeybee, odorant-binding proteins (OBPs) and chemosensory protein (CSPs) are major two protein families capable of binding with some plant volatiles and chemical ligands. However, the chemical binding interaction of plant odors with OBPs and CSPs in the honeybee olfactory system is still not clear yet. Hence, complex fluorescent spectra, ultraviolet absorption spectra, circular dichroism spectra and molecular docking were used to investigate the binding property of AcerASP2 (an OBP of Apis cerana) and AcerASP3 (a CSP of Apis cerana) with β-ionone, one of ordinary floral volatiles in botanical flower. As a result, β-ionone had a strong capability to quench the fluorescence that the two proteins produced, and their interaction was a dynamic process that was mainly driven by a hydrophobic force. AcerASP2 had a larger hydrophobic cavity than that of AcerASP3 and the conformation of AcerASP2 was changed less than AcerASP3 when binding with β-ionone. Our data suggests that OBPs like AcerASP2 might make a large contribution toward assisting the honeybee in sensing and foraging flowers, and A. cerana has evolved a good circadian rhythm to perceive a flower's odor following the fluctuation of temperature in the olfactory system. This significantly extends our knowledge on how to strengthen the honeybees' pollination service via manipulation of target proteins in the olfactory system. Copyright © 2013 Elsevier B.V. All rights reserved.

  4. The molecular bases of δ/αβ T cell-mediated antigen recognition.

    Science.gov (United States)

    Pellicci, Daniel G; Uldrich, Adam P; Le Nours, Jérôme; Ross, Fiona; Chabrol, Eric; Eckle, Sidonia B G; de Boer, Renate; Lim, Ricky T; McPherson, Kirsty; Besra, Gurdyal; Howell, Amy R; Moretta, Lorenzo; McCluskey, James; Heemskerk, Mirjam H M; Gras, Stephanie; Rossjohn, Jamie; Godfrey, Dale I

    2014-12-15

    αβ and γδ T cells are disparate T cell lineages that can respond to distinct antigens (Ags) via the use of the αβ and γδ T cell Ag receptors (TCRs), respectively. Here we characterize a population of human T cells, which we term δ/αβ T cells, expressing TCRs comprised of a TCR-δ variable gene (Vδ1) fused to joining α and constant α domains, paired with an array of TCR-β chains. We demonstrate that these cells, which represent ∼50% of all Vδ1(+) human T cells, can recognize peptide- and lipid-based Ags presented by human leukocyte antigen (HLA) and CD1d, respectively. Similar to type I natural killer T (NKT) cells, CD1d-lipid Ag-reactive δ/αβ T cells recognized α-galactosylceramide (α-GalCer); however, their fine specificity for other lipid Ags presented by CD1d, such as α-glucosylceramide, was distinct from type I NKT cells. Thus, δ/αβTCRs contribute new patterns of Ag specificity to the human immune system. Furthermore, we provide the molecular bases of how δ/αβTCRs bind to their targets, with the Vδ1-encoded region providing a major contribution to δ/αβTCR binding. Our findings highlight how components from αβ and γδTCR gene loci can recombine to confer Ag specificity, thus expanding our understanding of T cell biology and TCR diversity. © 2014 Pellicci et al.

  5. The molecular bases of δ/αβ T cell–mediated antigen recognition

    Science.gov (United States)

    Pellicci, Daniel G.; Uldrich, Adam P.; Le Nours, Jérôme; Ross, Fiona; Chabrol, Eric; Eckle, Sidonia B.G.; de Boer, Renate; Lim, Ricky T.; McPherson, Kirsty; Besra, Gurdyal; Howell, Amy R.; Moretta, Lorenzo; McCluskey, James; Heemskerk, Mirjam H.M.; Gras, Stephanie

    2014-01-01

    αβ and γδ T cells are disparate T cell lineages that can respond to distinct antigens (Ags) via the use of the αβ and γδ T cell Ag receptors (TCRs), respectively. Here we characterize a population of human T cells, which we term δ/αβ T cells, expressing TCRs comprised of a TCR-δ variable gene (Vδ1) fused to joining α and constant α domains, paired with an array of TCR-β chains. We demonstrate that these cells, which represent ∼50% of all Vδ1+ human T cells, can recognize peptide- and lipid-based Ags presented by human leukocyte antigen (HLA) and CD1d, respectively. Similar to type I natural killer T (NKT) cells, CD1d-lipid Ag-reactive δ/αβ T cells recognized α-galactosylceramide (α-GalCer); however, their fine specificity for other lipid Ags presented by CD1d, such as α-glucosylceramide, was distinct from type I NKT cells. Thus, δ/αβTCRs contribute new patterns of Ag specificity to the human immune system. Furthermore, we provide the molecular bases of how δ/αβTCRs bind to their targets, with the Vδ1-encoded region providing a major contribution to δ/αβTCR binding. Our findings highlight how components from αβ and γδTCR gene loci can recombine to confer Ag specificity, thus expanding our understanding of T cell biology and TCR diversity. PMID:25452463

  6. Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1

    Science.gov (United States)

    Musselman, Catherine A.; Avvakumov, Nikita; Watanabe, Reiko; Abraham, Christopher G.; Lalonde, Marie-Eve; Hong, Zehui; Allen, Christopher; Roy, Siddhartha; Nuñez, James K.; Nickoloff, Jac; Kulesza, Caroline A.; Yasui, Akira; Côté, Jacques; Kutateladze, Tatiana G.

    2013-01-01

    The PHD finger protein 1 (PHF1) is essential in epigenetic regulation and genome maintenance. Here, we demonstrate that the Tudor domain of human PHF1 binds to histone H3 trimethylated at Lys36 (H3K36me3). We report a 1.9 Å resolution crystal structure of the Tudor domain in complex with H3K36me3 and describe the molecular mechanism of H3K36me3 recognition using NMR analysis. Binding of PHF1 to H3K36me3 inhibits the ability of the Polycomb PRC2 complex to methylate H3K27 in vitro and in vivo. Laser micro-irradiation data reveal that PHF1 is transiently recruited to DNA double-strand breaks (DSBs), and PHF1 mutants impaired in the H3K36me3 interaction exhibit reduced retention at DSB sites. Together, our findings suggest that PHF1 can mediate deposition of the repressive H3K27me3 mark and acts as an early DNA damage response cofactor. PMID:23142980

  7. Structural, mutational and biophysical studies reveal a canonical mode of molecular recognition between immune receptor TIGIT and nectin-2

    Energy Technology Data Exchange (ETDEWEB)

    Samanta, Dibyendu; Guo, Haisu; Rubinstein, Rotem; Ramagopal, Udupi A.; Almo, Steven C.

    2017-01-01

    In addition to antigen-specific stimulation of T cell receptor (TCR) by a peptide-MHC complex, the functional outcome of TCR engagement is regulated by antigen-independent costimulatory signals. Costimulatory signals are provided by an array of interactions involving activating and inhibitory receptors expressed on T cells and their cognate ligands on antigen presenting cells. T cell immunoglobulin and ITIM domain (TIGIT), a recently identified immune receptor expressed on T and NK cells, upon interaction with either of its two ligands, nectin-2 or poliovirus receptor (PVR), inhibits activation of T and NK cells. Here we report the crystal structure of the human TIGIT ectodomain, which exhibits the classic two-layer β-sandwich topology observed in other immunoglobulin super family (IgSF) members. Biophysical studies indicate that TIGIT is monomeric in solution but can form a dimer at high concentrations, consistent with the observation of a canonical immunoglobulin-like dimer interface in the crystalline state. Based on existing structural data, we present a model of the TIGIT:nectin-2 complex and utilized complementary biochemical studies to map the nectin-binding interface on TIGIT. Our data provide important structural and biochemical determinants responsible for the recognition of nectin-2 by TIGIT. Defining the TIGIT:nectin-2 binding interface provides the basis for rational manipulation of this molecular interaction for the development of immunotherapeutic reagents in autoimmunity and cancer.

  8. [Preparation of molecularly imprinted polypyrrole/Fe3O4 composite material and its application in recognition of tryptophan enantiomers].

    Science.gov (United States)

    Chen, Zhidong; Shan, Xueling; Kong, Yong

    2012-04-01

    Ferrosoferric oxide (Fe(3)O(4)) magnetic material was first synthesized, and then the in-situ chemical polymerization of pyrrole was carried out on the surface of Fe(3)O(4) by using pyrole and L-tryptophan (L-Trp) as the functional monomer and templates, respectively. As a result, molecularly imprinted polypyrrole/Fe(3)O(4) composite material was obtained. This composite material was separated from the solution because of its magnetic property. Polypyrrole in the composite was overoxidized in 1 mol/L NaOH solution by applying a potential of 1.0 V, and thus L-Trp templates were de-deoped from the composite. Scanning electron microscopy (SEM), X-ray diffraction (XRD) and electrochemical methods were employed to characterize the composite. The solution containing L- or D-Trp was pumped through a porous ceramic tube packed with the composite, separately. High performance liquid chromatography (HPLC) was adopted for the detection of L- or D-Trp in the eluate, and the results indicated that the enrichment ability of the composite for L-Trp was almost 2 times that of D-Trp. Therefore, the electro-magnetic composite material has potential applications as chromatographic stationary phase for chiral recognition.

  9. Helicase-Dependent Isothermal Amplification of DNA and RNA by Using Self-Avoiding Molecular Recognition Systems.

    Science.gov (United States)

    Yang, Zunyi; McLendon, Chris; Hutter, Daniel; Bradley, Kevin M; Hoshika, Shuichi; Frye, Carole B; Benner, Steven A

    2015-06-15

    Assays that detect DNA or RNA (xNA) are highly sensitive, as small amounts of xNA can be amplified by PCR. Unfortunately, PCR is inconvenient in low-resource environments, and requires equipment and power that might not be available in these environments. Isothermal procedures, which avoid thermal cycling, are often confounded by primer dimers, off-target priming, and other artifacts. Here, we show how a "self avoiding molecular recognition system" (SAMRS) eliminates these artifacts and gives clean amplicons in a helicase-dependent isothermal amplification (SAMRS-HDA). We also show that incorporating SAMRS into the 3'-ends of primers facilitates the design and screening of primers for HDA assays. Finally, we show that SAMRS-HDA can be twofold multiplexed, difficult to achieve with HDA using standard primers. Thus, SAMRS-HDA is a more versatile approach than standard HDA, with a broader applicability for xNA-targeted diagnostics and research. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. The influence of constitutional isomerism and change on molecular recognition processes.

    Science.gov (United States)

    Williams, Avril R; Northrop, Brian H; Houk, Kendall N; Stoddart, J Fraser; Williams, David J

    2004-10-25

    Three constitutionally isomeric bis(naphthylmethyl)ammonium ions, in which the two naphthyl groups are substituted 1) both at their 1-positions, 2) one at its 1-position and the other at its 2-position, and 3) both at their 2-positions, have been investigated separately in solution for their propensities to undergo spontaneous self-assembly with three different [24]crown-8 derivatives, namely, pyrido[24]crown-8 (P24C8), dipyrido[24]crown-8 (DP24C8) and dibenzo[24]crown-8 (DB24C8), in turn to form [2]pseudorotaxanes. The strengths of the 1:1 complexes depend on the composition of the secondary dialkylammonium ions and on the nature of the crown ether hosts; generally, as far as the guest cation is concerned, the 1/1- and 2/2-isomers form stronger complexes, as indicated by stability constant measurements, than the 1/2-isomer and, as far as the crown ethers are concerned, the more flexible P24C8 is a much more efficient host than either DP24C8 or DB24C8. The rates of formation of the [2]pseudorotaxanes are fast (i.e., taking no more than a few minutes) in solution with the exception of one case, that is, in which the crown ether host is DB24C8 and the guest cation is the 1/1-isomer, when it can take upwards of one month for the complexation-decomplexation equilibrium to be established at room temperature. In all cases, the equilibrium between complexed and uncomplexed species is slow on the NMR timescale, allowing the determination of stability constants to be made readily using the single-point method. X-ray crystallography and molecular modeling have been used to gain insight into ground and transition state interactions, respectively, in some of the [2]pseudorotaxanes. The relative stabilities of the three [2]pseudorotaxanes formed by each guest cation in the presence of the three crown ether hosts were also evaluated in solution by competition experiments that were monitored by (1)H NMR spectroscopy. By and large the results of the competition experiments could

  11. Molecular recognition of naphthalene diimide ligands by telomeric quadruplex-DNA: the importance of the protonation state and mediated hydrogen bonds.

    Science.gov (United States)

    Spinello, A; Barone, G; Grunenberg, J

    2016-01-28

    In depth Monte Carlo conformational scans in combination with molecular dynamics (MD) simulations and electronic structure calculations were applied in order to study the molecular recognition process between tetrasubstituted naphthalene diimide (ND) guests and G-quadruplex (G4) DNA receptors. ND guests are a promising class of telomere stabilizers due to which they are used in novel anticancer therapeutics. Though several ND guests have been studied experimentally in the past, the protonation state under physiological conditions is still unclear. Based on chemical intuition, in the case of N-methyl-piperazine substitution, different protonation states are possible and might play a crucial role in the molecular recognition process by G4-DNA. Depending on the proton concentration, different nitrogen atoms of the N-methyl-piperazine might (or might not) be protonated. This fact was considered in our simulation in terms of a case by case analysis, since the process of molecular recognition is determined by possible donor or acceptor positions. The results of our simulations show that the electrostatic interactions between the ND ligands and the G4 receptor are maximized in the case of the protonation of the terminal nitrogen atoms, forming compact ND G4 complexes inside the grooves. The influence of different protonation states in terms of the ability to form hydrogen bonds with the sugar-phosphate backbone, as well as the importance of mediated vs. direct hydrogen bonding, was analyzed in detail by MD and relaxed force constant (compliance constant) simulations.

  12. The menagerie of human lipocalins: a natural protein scaffold for molecular recognition of physiological compounds.

    Science.gov (United States)

    Schiefner, André; Skerra, Arne

    2015-04-21

    While immunoglobulins are well-known for their characteristic ability to bind macromolecular antigens (i.e., as antibodies during an immune response), the lipocalins constitute a family of proteins whose role is the complexation of small molecules for various physiological processes. In fact, a number of low-molecular-weight substances in multicellular organisms show poor solubility, are prone to chemical decomposition, or play a pathophysiological role and thus require specific binding proteins for transport through body fluids, storage, or sequestration. In many cases, lipocalins are involved in such tasks. Lipocalins are small, usually monomeric proteins with 150-180 residues and diameters of approximately 40 Å, adopting a compact fold that is dominated by a central eight-stranded up-and-down β-barrel. At the amino-terminal end, this core is flanked by a coiled polypeptide segment, while its carboxy-terminal end is followed by an α-helix that leans against the β-barrel as well as an amino acid stretch in a more-or-less extended conformation, which finally is fixed by a disulfide bond. Within the β-barrel, the antiparallel strands (designated A to H) are arranged in a (+1)7 topology and wind around a central axis in a right-handed manner such that part of strand A is hydrogen-bonded to strand H again. Whereas the lower region of the β-barrel is closed by short loops and densely packed hydrophobic side chains, including many aromatic residues, the upper end is usually open to solvent. There, four long loops, each connecting one pair of β-strands, together form the entrance to a cup-shaped cavity. Depending on the individual structure of a lipocalin, and especially on the lengths and amino acid sequences of its four loops, this pocket can accommodate chemical ligands of various sizes and shapes, including lipids, steroids, and other chemical hormones as well as secondary metabolites such as vitamins, cofactors, or odorants. While lipocalins are ubiquitous in

  13. Event recognition by detrended fluctuation analysis: An application to Teide-Pico Viejo volcanic complex, Tenerife, Spain

    International Nuclear Information System (INIS)

    Del Pin, Enrico; Carniel, Roberto; Tarraga, Marta

    2008-01-01

    In this work we investigate the application of the detrended fluctuation analysis (DFA) to seismic data recorded in the island of Tenerife (Canary Islands, Spain) during the month of July 2004, in a phase of possible unrest of the Teide-Pico Viejo volcanic complex. Tectonic events recorded in the area are recognized and located by the Spanish national agency Instituto Geografico Nacional (IGN) and their catalogue is the only currently available dataset, whose completeness unfortunately suffers from the strong presence of anthropogenic noise. In this paper we propose the use of DFA to help to automatically identify events. The evaluation of this case study proves DFA to be a promising tool to be used for rapidly screening large seismic datasets and highlighting time windows with the potential presence of discrete events

  14. Collapse of proteostasis represents an early molecular event in Caenorhabditis elegans aging.

    Science.gov (United States)

    Ben-Zvi, Anat; Miller, Elizabeth A; Morimoto, Richard I

    2009-09-01

    Protein damage contributes prominently to cellular aging. To address whether this occurs at a specific period during aging or accumulates gradually, we monitored the biochemical, cellular, and physiological properties of folding sensors expressed in different tissues of C. elegans. We observed the age-dependent misfolding and loss of function of diverse proteins harboring temperature-sensitive missense mutations in all somatic tissues at the permissive condition. This widespread failure in proteostasis occurs rapidly at an early stage of adulthood, and coincides with a severely reduced activation of the cytoprotective heat shock response and the unfolded protein response. Enhancing stress responsive factors HSF-1 or DAF-16 suppresses misfolding of these metastable folding sensors and restores the ability of the cell to maintain a functional proteome. This suggests that a compromise in the regulation of proteostatic stress responses occurs early in adulthood and tips the balance between the load of damaged proteins and the proteostasis machinery. We propose that the collapse of proteostasis represents an early molecular event of aging that amplifies protein damage in age-associated diseases of protein conformation.

  15. Molecular insights on the recognition of a Lactococcus lactis cell wall pellicle by the phage 1358 receptor binding protein.

    Science.gov (United States)

    Farenc, Carine; Spinelli, Silvia; Vinogradov, Evgeny; Tremblay, Denise; Blangy, Stéphanie; Sadovskaya, Irina; Moineau, Sylvain; Cambillau, Christian

    2014-06-01

    The Gram-positive bacterium Lactococcus lactis is used for the production of cheeses and other fermented dairy products. Accidental infection of L. lactis cells by virulent lactococcal tailed phages is one of the major risks of fermentation failures in industrial dairy factories. Lactococcal phage 1358 possesses a host range limited to a few L. lactis strains and strong genomic similarities to Listeria phages. We report here the X-ray structures of phage 1358 receptor binding protein (RBP) in complex with monosaccharides. Each monomer of its trimeric RBP is formed of two domains: a "shoulder" domain linking the RBP to the rest of the phage and a jelly roll fold "head/host recognition" domain. This domain harbors a saccharide binding crevice located in the middle of a monomer. Crystal structures identified two sites at the RBP surface, ∼8 Å from each other, one accommodating a GlcNAc monosaccharide and the other accommodating a GlcNAc or a glucose 1-phosphate (Glc1P) monosaccharide. GlcNAc and GlcNAc1P are components of the polysaccharide pellicle that we identified at the cell surface of L. lactis SMQ-388, the host of phage 1358. We therefore modeled a galactofuranose (Galf) sugar bridging the two GlcNAc saccharides, suggesting that the trisaccharidic motif GlcNAc-Galf-GlcNAc (or Glc1P) might be common to receptors of genetically distinct lactococcal phages p2, TP091-1, and 1358. Strain specificity might therefore be elicited by steric clashes induced by the remaining components of the pellicle hexasaccharide. Taken together, these results provide a first insight into the molecular mechanism of host receptor recognition by lactococcal phages. Siphophages infecting the Gram-positive bacterium Lactococcus lactis are sources of milk fermentation failures in the dairy industry. We report here the structure of the pellicle polysaccharide from L. lactis SMQ-388, the specific host strain of phage 1358. We determined the X-ray structures of the lytic lactococcal phage

  16. Parahippocampal activation during successful recognition of words: a self-paced event-related fMRI study

    NARCIS (Netherlands)

    Daselaar, S. M.; Rombouts, S. A.; Veltman, D. J.; Raaijmakers, J. G.; Lazeron, R. H.; Jonker, C.

    2001-01-01

    In this study, we investigated retrieval from verbal episodic memory using a self-paced event-related fMRI paradigm, similar to the designs typically used in behavioral studies of memory function. We tested the hypothesis that the medial temporal lobe (MTL) is involved in the actual recovery of

  17. Synergetic dual recognition and separation of the fungicide carbendazim by using magnetic nanoparticles carrying a molecularly imprinted polymer and immobilized β-cyclodextrin

    International Nuclear Information System (INIS)

    Li, Shuhuai; Wu, Xuejin; Zhang, Qun; Li, Pingping

    2016-01-01

    The authors describe a nanomaterial for solid-phase extraction of carbendazim. Magnetic molecularly imprinted polymer nanoparticles (mag-MIP-NPs) were obtained by immobilizing the MIP and a thiolated β-cyclodextrin on the surface of magnetite (Fe_3O_4) nanoparticles coated with gold nanoparticles. Both the recognition sites of the MIP and the hydrophobic cavities in the β-cyclodextrin contribute to the specific molecular recognition and extraction of carbendazim. The mag-MIP-NPs have an apparent adsorption capacity of 190 mg⋅g"-"1. Spiked vegetables were analyzed by using this material for extraction of carbendazim prior to its determination by ultra performance liquid chromatography (UHPLC). Recoveries range from 90.5 % to 109 %, and the detection limit is 3.0 pg⋅mL"-"1. (author)

  18. Engineering of an Extremely Thermostable Alpha/Beta Barrel Scaffold to Serve as a High Affinity Molecular Recognition Element for Use in Sensor Applications

    Science.gov (United States)

    2015-12-23

    Molecular Recognition Element For Use in Sensor Applications Report Title The overall goal of the project was to evolve a highly thermostable enzyme ( alcohol ...SECURITY CLASSIFICATION OF: The overall goal of the project was to evolve a highly thermostable enzyme ( alcohol dehydrogenase D (AdhD) from Pyrococcus...furiosus) to bind an explosive molecule, RDX. The enzyme naturally catalyzes the nicotinamide cofactor-dependent oxidation or reduction of alcohols

  19. Molecularly imprinted nanoparticles with recognition properties towards a laminin H-Tyr-Ile-Gly-Ser-Arg-OH sequence for tissue engineering applications

    International Nuclear Information System (INIS)

    Rosellini, Elisabetta; Barbani, Niccoletta; Giusti, Paolo; Ciardelli, Gianluca; Cristallini, Caterina

    2010-01-01

    Nanotechnology is an emerging field that promises to revolutionize medicine and is increasingly used in tissue engineering applications. Our research group proposed for the first time molecular imprinting as a new nanotechnology for the creation of advanced synthetic support structures for cell adhesion and proliferation. The aim of this work was the synthesis and characterization of molecularly imprinted polymers with recognition properties towards a laminin peptide sequence and their application as functionalization structures in the development of bioactive materials. Nanoparticles with an average diameter of 200 nm were synthesized by precipitation polymerization of methacrylic acid in the presence of the template molecule and trimethylpropane trimethacrylate as the cross-linking agent. The imprinted nanoparticles showed good performance in terms of recognition capacity and selectivity. The cytotoxicity tests showed normal vitality of C2C12 myoblasts cultured in the medium that was put in contact with the imprinted polymers. After the deposition on the polymeric film surface, the imprinted particles maintained their specific recognition and rebinding behaviour, showing an even higher quantitative binding than free nanoparticles. Preliminary in vitro cell culture tests demonstrated the ability of functionalized materials to promote cell adhesion, proliferation and differentiation, suggesting that molecular imprinting can be used as an innovative functionalization technique.

  20. Exploring the molecular basis of dsRNA recognition by NS1 protein of influenza A virus using molecular dynamics simulation and free energy calculation.

    Science.gov (United States)

    Pan, Dabo; Sun, Huijun; Shen, Yulin; Liu, Huanxiang; Yao, Xiaojun

    2011-12-01

    The frequent outbreak of influenza pandemic and the limited available anti-influenza drugs highlight the urgent need for the development of new antiviral drugs. The dsRNA-binding surface of nonstructural protein 1 of influenza A virus (NS1A) is a promising target. The detailed understanding of NS1A-dsRNA interaction will be valuable for structure-based anti-influenza drug discovery. To characterize and explore the key interaction features between dsRNA and NS1A, molecular dynamics simulation combined with MM-GBSA calculations were performed. Based on the MM-GBSA calculations, we find that the intermolecular van der Waals interaction and the nonpolar solvation term provide the main driving force for the binding process. Meanwhile, 17 key residues from NS1A were identified to be responsible for the dsRNA binding. Compared with the wild type NS1A, all the studied mutants S42A, T49A, R38A, R35AR46A have obvious reduced binding free energies with dsRNA reflecting in the reduction of the polar and/or nonpolar interactions. In addition, the structural and energy analysis indicate the mutations have a small effect to the backbone structures but the loss of side chain interactions is responsible for the decrease of the binding affinity. The uncovering of NS1A-dsRNA recognition mechanism will provide some useful insights and new chances for the development of anti-influenza drugs. Copyright © 2011 Elsevier B.V. All rights reserved.

  1. Microwave-assisted RAFT polymerization of well-constructed magnetic surface molecularly imprinted polymers for specific recognition of benzimidazole residues

    Science.gov (United States)

    Chen, Fangfang; Wang, Jiayu; Chen, Huiru; Lu, Ruicong; Xie, Xiaoyu

    2018-03-01

    Magnetic nanoparticles have been widely used as support core for fast separation, which could be directly separated from complicated matrices using an external magnet in few minutes. Surface imprinting based on magnetic core has shown favorable adsorption and separation performance, including good adsorption capacity, fast adsorption kinetics and special selectivity adsorption. Reversible addition-fragmentation chain transfer (RAFT) is an ideal choice for producing well-defined complex architecture with mild reaction conditions. We herein describe the preparation of well-constructed magnetic molecularly imprinted polymers (MMIPs) for the recognition of benzimidazole (BMZ) residues via the microwave-assisted RAFT polymerization. The merits of RAFT polymerization assisting with microwave heating allowed successful and more efficient preparation of well-constructed imprinted coats. Moreover, the polymerization time dramatically shortened and was just 1/24th of the time taken by conventional heating. The results indicated that a uniform nanoscale imprinted layer was formed on the Fe3O4 core successfully, and enough saturation magnetization of MMIPs (16.53 emu g-1) was got for magnetic separation. The desirable adsorption capacity (30.18 μmol g-1) and high selectivity toward template molecule with a selectivity coefficient (k) of 13.85 of MMIPs were exhibited by the adsorption isothermal assay and competitive binding assay, respectively. A solid phase extraction enrichment approach was successfully established for the determination of four BMZ residues from apple samples using MMIPs coupled to HPLC. Overall, this study provides a versatile approach for highly efficient fabrication of well-constructed MMIPs for enrichment and determination of target molecules from complicated samples.

  2. Molecular Modeling Study of Chiral Separation and Recognition Mechanism of β-Adrenergic Antagonists by Capillary Electrophoresis

    Directory of Open Access Journals (Sweden)

    Yifeng Chai

    2012-01-01

    Full Text Available Chiral separations of five β-adrenergic antagonists (propranolol, esmolol, atenolol, metoprolol, and bisoprolol were studied by capillary electrophoresis using six cyclodextrins (CDs as the chiral selectors. Carboxymethylated-β-cyclodextrin (CM-β-CD exhibited a higher enantioselectivity power compared to the other tested CDs. The influences of the concentration of CM-β-CD, buffer pH, buffer concentration, temperature, and applied voltage were investigated. The good chiral separation of five β-adrenergic antagonists was achieved using 50 mM Tris buffer at pH 4.0 containing 8 mM CM-β-CD with an applied voltage of 24 kV at 20 °C. In order to understand possible chiral recognition mechanisms of these racemates with CM-β-CD, host-guest binding procedures of CM-β-CD and these racemates were studied using the molecular docking software Autodock. The binding free energy was calculated using the Autodock semi-empirical binding free energy function. The results showed that the phenyl or naphthyl ring inserted in the hydrophobic cavity of CM-β-CD and the side chain was found to point out of the cyclodextrin rim. Hydrogen bonding between CM-β-CD and these racemates played an important role in the process of enantionseparation and a model of the hydrogen bonding interaction positions was constructed. The difference in hydrogen bonding formed with the –OH next to the chiral center of the analytes may help to increase chiral discrimination and gave rise to a bigger separation factor. In addition, the longer side chain in the hydrophobic phenyl ring of the enantiomer was not beneficial for enantioseparation and the chiral selectivity factor was found to correspond to the difference in binding free energy.

  3. Rapid Colorimetric Detection of Cartap Residues by AgNP Sensor with Magnetic Molecularly Imprinted Microspheres as Recognition Elements

    Directory of Open Access Journals (Sweden)

    Mao Wu

    2018-06-01

    Full Text Available The overuse of cartap in tea tree leads to hazardous residues threatening human health. A colorimetric determination was established to detect cartap residues in tea beverages by silver nanoparticles (AgNP sensor with magnetic molecularly imprinted polymeric microspheres (Fe3O4@mSiO2@MIPs as recognition elements. Using Fe3O4 as supporting core, mesoporous SiO2 as intermediate shell, methylacrylic acid as functional monomer, and cartap as template, Fe3O4@mSiO2@MIPs were prepared to selectively and magnetically separate cartap from tea solution before colorimetric determination by AgNP sensors. The core-shell Fe3O4@mSiO2@MIPs were also characterized by FT-IR, TEM, VSM, and experimental adsorption. The Fe3O4@mSiO2@MIPs could be rapidly separated by an external magnet in 10 s with good reusability (maintained 95.2% through 10 cycles. The adsorption process of cartap on Fe3O4@mSiO2@MIPs conformed to Langmuir adsorption isotherm with maximum adsorption capacity at 0.257 mmol/g and short equilibrium time of 30 min at 298 K. The AgNP colorimetric method semi-quantified cartap ≥5 mg/L by naked eye and quantified cartap 0.1–5 mg/L with LOD 0.01 mg/L by UV-vis spectroscopy. The AgNP colorimetric detection after pretreatment with Fe3O4@mSiO2@MIPs could be successfully utilized to recognize and detect cartap residues in tea beverages.

  4. Event-related potentials in auditory backward recognition masking: a new way to study the neurophysiological basis of sensory memory in humans.

    Science.gov (United States)

    Winkler, I; Näätänen, R

    1992-06-22

    Task-irrelevant pairs of short tones were presented to healthy human subjects while electric potentials were recorded from their scalp ('event-related brain potential', ERP). Infrequent increments in the frequency of the first tone of the repetitive tone-pair elicited an extra ERP component termed 'mismatch negativity' (MMN) when the silent interval between the first and second tone of the pair ('inter-tone interval') was long (150, 300, or 400 ms) but not when this interval was short (20 or 50 ms). This effect did not depend on whether the two tones of the tone-pair were presented to the same or to different ears. The present inter-tone interval effect is consistent with the effects of backward-masking on recognition performance in audition, suggesting that the MMN reflects the neurophysiological basis of echoic memory.

  5. Signal transduction by FcεRI: Analysis of the early molecular events

    Directory of Open Access Journals (Sweden)

    Henry Metzger

    1999-01-01

    Full Text Available We are analysing the initial molecular events stimulated by the high-affinity receptor for IgE, FcεRI. Earlier studies have shown that the first response when the receptor-bound IgE interacts with a multivalent antigen is a transphosphorylation of receptor tyrosines, induced by the approximation of two or more receptors by a constitutively associated src-family kinase (Lyn. The amount of weakly associated kinase regulates the intensity of the response. Several aspects are being analyzed: (i the sites on Lyn and the receptor that account for the constitutive interaction; (ii how the intrinsic affinity of a ligand for the receptor-bound IgE influences the responses; and (iii the mechanism(s by which low-affinity ligands can act as antagonists. In the latter studies, mast cell responses were followed by monitoring the phosphorylation of tyrosines on several proteins and secretion. At equivalent levels of receptor phosphorylation, a ligand with high affinity stimulated vigorous phosphorylation of downstream components, whereas a low-affinity ligand was unable to stimulate phosphorylation of the same components effectively. Cells stimulated with a mixture of high- and low-affinity ligands, under a protocol where simple displacement of one by the other was prevented, remarkably showed that excess low-affinity ligand inhibited the phosphorylation as well as degranulation by the high-affinity ligand. This antagonism results from a competition for the limiting amount of the constitutive initiating kinase. Related receptors that depend on recruitment of initiating kinases may be subject to similar regulatory mechanisms.

  6. Molecular confirmation of Bacillus Calmette Guerin vaccine related adverse events among Saudi Arabian children.

    Directory of Open Access Journals (Sweden)

    Sahal Al-Hajoj

    Full Text Available Bacillus Calmette Guerin (BCG is the only available vaccine for tuberculosis (TB. Low grade complications in healthy recipients and disseminated vaccine associated complications among immuno-suppressed individuals were noticed globally after administration. Recently a series of clinically suspected BCG associated suppurative and non-suppurative lymphadenitis cases were reported from different regions of Saudi Arabia. However a molecular confirmative analysis was lacking to prove these claims.During 2009-2010, 42 Mycobacterium bovis BCG suspected clinical isolates from children diagnosed with suppurative lymphadenitis from different provinces of the country were collected and subjected to 24 loci based MIRU-VNTR typing, spoligotyping and first line anti-TB drugs susceptibility testing.Of the total 42 cases, 41 (97.6% were Saudi nationals and particularly male (64.3%. Majority of the cases were aged below 6 months (83.3% with a median of age 4 months. All the enrolled subjects showed left axillary mass which suppurated in a median of 4 months after vaccination. Among the study subjects, 1 (2.4% case was reactive to HIV antigen and 2 (4.8% case had severe combined immunodeficiency. Genotyping results showed that, 41 (97.6% isolates were identical to the vaccine strain Danish 1331 and one to Tokyo 172-1. Phylogenetic analysis revealed all the Danish 1331 isolates in a single cluster.Elevated proportion of suppurative lymphadenitis caused by M. bovis BCG reported in the country recently is majorly related to the vaccine strain Danish 1331. However lack of nationwide data on real magnitude of BCG related adverse events warrants population centric, long term future studies.

  7. Initial Chemical Events in CL-20 Under Extreme Conditions: An Ab Initio Molecular Dynamics Study

    National Research Council Canada - National Science Library

    Isaev, Olexandr; Kholod, Yana; Gorb, Leonid; Qasim, Mohammad; Fredrickson, Herb; Leszczynski, Jerzy

    2006-01-01

    .... In the present study molecular structure, electrostatic potential, vibrational spectrum and dynamics of thermal decomposition of CL-20 have been investigated by static and dynamic methods of ab...

  8. Preparation of molecularly imprinted nanoparticles with superparamagnetic susceptibility through atom transfer radical emulsion polymerization for the selective recognition of tetracycline from aqueous medium

    International Nuclear Information System (INIS)

    Dai, Jiangdong; Pan, Jianming; Xu, Longcheng; Li, Xiuxiu; Zhou, Zhiping; Zhang, Rongxian; Yan, Yongsheng

    2012-01-01

    Highlights: ► Atom transfer radical emulsion polymerization is a “living” and green technique. ► Nanoparticles can overcome mass transfer limitations and improve accessibility. ► Molecular imprinted nanoparticles with magnetic property for fast separation. ► The performance of imprinted nanoparticles was investigated in detail. ► Nanoparticles were used to selective recognize Tetracycline from water medium. - Abstract: In the work, we reported an effective method for the preparation of molecularly imprinted nanoparticles with superparamagnetic susceptibility through atom transfer radical emulsion polymerization (ATREP), and then as-prepared magnetic molecularly imprinted nanoparticles (MMINs) were evaluated as adsorbents for selective recognition of tetracycline (TC) molecules from aqueous medium. The resulting nanoparticles were characterized by FT-IR, TGA, VSM, SEM and TEM. The results demonstrated MMINs with a narrow diameter distribution were cross-linked with modified Fe 3 O 4 particles, composed of imprinted layer and exhibited good magnetic sensitivity, magnetic and thermal stability. Batch rebinding studies were carried out to determine the specific adsorption equilibrium, kinetics, and selective recognition. The estimated adsorption capacity of MMINs towards TC by the Langmuir isotherm model was 12.10 mg g −1 at 298 K, which was 6.33 times higher than that of magnetic non-molecularly imprinted nanoparticles (MNINs). The kinetic property of MMINs was well-described by the pseudo-second-order rate equation. The results of selective recognition experiments demonstrated outstanding affinity and selectivity towards TC over competitive antibiotics. The reusability of MMINs showed no obviously deterioration at least five repeated cycles in performance. In addition, the MMINs prepared were successfully applied to the extraction of TC from the spiked pork sample.

  9. Preparation of molecularly imprinted nanoparticles with superparamagnetic susceptibility through atom transfer radical emulsion polymerization for the selective recognition of tetracycline from aqueous medium

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Jiangdong; Pan, Jianming; Xu, Longcheng; Li, Xiuxiu [School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013 (China); Zhou, Zhiping [School of Material Science and Engineering, Jiangsu University, Zhenjiang 212013 (China); Zhang, Rongxian [School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013 (China); Yan, Yongsheng, E-mail: djdxxx123@163.com [School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013 (China); State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100191 (China)

    2012-02-29

    Highlights: Black-Right-Pointing-Pointer Atom transfer radical emulsion polymerization is a 'living' and green technique. Black-Right-Pointing-Pointer Nanoparticles can overcome mass transfer limitations and improve accessibility. Black-Right-Pointing-Pointer Molecular imprinted nanoparticles with magnetic property for fast separation. Black-Right-Pointing-Pointer The performance of imprinted nanoparticles was investigated in detail. Black-Right-Pointing-Pointer Nanoparticles were used to selective recognize Tetracycline from water medium. - Abstract: In the work, we reported an effective method for the preparation of molecularly imprinted nanoparticles with superparamagnetic susceptibility through atom transfer radical emulsion polymerization (ATREP), and then as-prepared magnetic molecularly imprinted nanoparticles (MMINs) were evaluated as adsorbents for selective recognition of tetracycline (TC) molecules from aqueous medium. The resulting nanoparticles were characterized by FT-IR, TGA, VSM, SEM and TEM. The results demonstrated MMINs with a narrow diameter distribution were cross-linked with modified Fe{sub 3}O{sub 4} particles, composed of imprinted layer and exhibited good magnetic sensitivity, magnetic and thermal stability. Batch rebinding studies were carried out to determine the specific adsorption equilibrium, kinetics, and selective recognition. The estimated adsorption capacity of MMINs towards TC by the Langmuir isotherm model was 12.10 mg g{sup -1} at 298 K, which was 6.33 times higher than that of magnetic non-molecularly imprinted nanoparticles (MNINs). The kinetic property of MMINs was well-described by the pseudo-second-order rate equation. The results of selective recognition experiments demonstrated outstanding affinity and selectivity towards TC over competitive antibiotics. The reusability of MMINs showed no obviously deterioration at least five repeated cycles in performance. In addition, the MMINs prepared were successfully

  10. Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations.

    Science.gov (United States)

    Wang, Bo; Li, Liwei; Hurley, Thomas D; Meroueh, Samy O

    2013-10-28

    End-point free energy calculations using MM-GBSA and MM-PBSA provide a detailed understanding of molecular recognition in protein-ligand interactions. The binding free energy can be used to rank-order protein-ligand structures in virtual screening for compound or target identification. Here, we carry out free energy calculations for a diverse set of 11 proteins bound to 14 small molecules using extensive explicit-solvent MD simulations. The structure of these complexes was previously solved by crystallography and their binding studied with isothermal titration calorimetry (ITC) data enabling direct comparison to the MM-GBSA and MM-PBSA calculations. Four MM-GBSA and three MM-PBSA calculations reproduced the ITC free energy within 1 kcal·mol(-1) highlighting the challenges in reproducing the absolute free energy from end-point free energy calculations. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). An increase in ε resulted in significantly better rank-ordering for MM-PBSA (ρ = 0.91 for ε = 10), but larger ε significantly reduced the contributions of electrostatics, suggesting that the improvement is due to the nonpolar and entropy components, rather than a better representation of the electrostatics. The SVRKB scoring function applied to MD snapshots resulted in excellent rank-ordering (ρ = 0.81). Calculations of the configurational entropy using normal-mode analysis led to free energies that correlated significantly better to the ITC free energy than the MD-based quasi-harmonic approach, but the computed entropies showed no correlation with the ITC entropy. When the adaptation energy is taken into consideration by running separate simulations for complex, apo, and ligand (MM-PBSAADAPT), there is less agreement with the ITC data for the individual free energies, but remarkably good rank-ordering is observed (ρ = 0.89). Interestingly, filtering MD snapshots by prescoring

  11. Feature-Specific Event-Related Potential Effects to Action- and Sound-Related Verbs during Visual Word Recognition.

    Science.gov (United States)

    Popp, Margot; Trumpp, Natalie M; Kiefer, Markus

    2016-01-01

    Grounded cognition theories suggest that conceptual representations essentially depend on modality-specific sensory and motor systems. Feature-specific brain activation across different feature types such as action or audition has been intensively investigated in nouns, while feature-specific conceptual category differences in verbs mainly focused on body part specific effects. The present work aimed at assessing whether feature-specific event-related potential (ERP) differences between action and sound concepts, as previously observed in nouns, can also be found within the word class of verbs. In Experiment 1, participants were visually presented with carefully matched sound and action verbs within a lexical decision task, which provides implicit access to word meaning and minimizes strategic access to semantic word features. Experiment 2 tested whether pre-activating the verb concept in a context phase, in which the verb is presented with a related context noun, modulates subsequent feature-specific action vs. sound verb processing within the lexical decision task. In Experiment 1, ERP analyses revealed a differential ERP polarity pattern for action and sound verbs at parietal and central electrodes similar to previous results in nouns. Pre-activation of the meaning of verbs in the preceding context phase in Experiment 2 resulted in a polarity-reversal of feature-specific ERP effects in the lexical decision task compared with Experiment 1. This parallels analogous earlier findings for primed action and sound related nouns. In line with grounded cognitions theories, our ERP study provides evidence for a differential processing of action and sound verbs similar to earlier observation for concrete nouns. Although the localizational value of ERPs must be viewed with caution, our results indicate that the meaning of verbs is linked to different neural circuits depending on conceptual feature relevance.

  12. Chiral Recognition in Molecular and Macromolecular Pairs of(S)- and (R)- 1-Cyano-2-Methylpropyl 4’((4-(8-Vinyloxyoctyloxy)Benzoyl) Biphenyl-4-Carboxylate Enantiomers

    Science.gov (United States)

    1994-06-30

    above please provide a graphical abstract of the paper ar, return it to the Editorial Office as soon as possible. 4oeg0 o F-99S or TS A& I DTI•’ I J. u1...TCLSICAON 2.LIMITATION OF ABSTRAC •F oFPORT OF THIS PAGE OF ABSTRACT . unclass ified Graphical Abstracts for Perkin Txans. 1 Example TITLE GRAPHICAL ... ABSTRACT AUTHORS’ N AMES Template (S)-II Chiral recognition in molecular and . -- macromolecular pairs of (S)- and -- (R)-i-cyano-2-methyipropyl 4’-{[4

  13. Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)–adenine derivatives

    OpenAIRE

    Stojković, Marijana Radić; Škugor, Marko; Dudek, Łukasz; Grolik, Jarosław; Eilmes, Julita; Piantanida, Ivo

    2014-01-01

    Summary An investigation of the interactions of two novel and several known DBTAA–adenine conjugates with double-stranded DNA and RNA has revealed the DNA/RNA groove as the dominant binding site, which is in contrast to the majority of previously studied DBTAA analogues (DNA/RNA intercalators). Only DBTAA–propyladenine conjugates revealed the molecular recognition of AT-DNA by an ICD band pattern > 300 nm, whereas significant ICD bands did not appear for other ds-DNA/RNA. A structure–activity...

  14. Células madre: generalidades, eventos biológicos y moleculares Stem cells: general aspects, biological and molecular events

    Directory of Open Access Journals (Sweden)

    Mónica María Cortés Márquez

    2008-09-01

    Full Text Available Las autorrenovación y la diferenciación son características de las células madre que varían entre los diferentes tipos celulares según el tejido en el que se encuentren y el microambiente que las rodee. En ambos procesos intervienen inhibidores del ciclo celular, genes implicados en rearreglos cromosómicos, proteínas del desarrollo esencial y vías de señalización específicas. La autorrenovación está regulada por diversos mecanismos, entre los cuales se destacan las vías Wnt, Notch y Hedgehog, y los factores BMI-1, p16Ink4a, ARF, NANOG, OCT3/4, SOX2, HOXB4 y sus páralogos. Los adelantos en el conocimiento de la biología de las células madre y de los mecanismos moleculares que regulan la autorrenovación y la diferenciación han convertido a estas células en una importante promesa para la investigación básica y aplicada. Self-renewal capacity and differentiation are features of stem cells that vary among the different cellular types according to the tissue in which they reside and the surrounding microenvironment. Cellular cycle inhibitors, genes implied in chromosomal rearrangements, essential development proteins and specific signaling pathways intervene in these processes. Self-renewal is regulated by different mechanisms, the most important of which are the Wnt, Notch and Hedgehog pathways, and the factors BMI-1, p16Ink4a, ARF, NANOG, OCT3/4, SOX2, HOXB4 and their paralogs. Advances in the knowledge of stem cells biology and of the molecular mechanisms that influence their selfrenewal and differentiation have made these cells an important promise for both basic and appliedresearch.

  15. HLA DNA sequence variation among human populations: molecular signatures of demographic and selective events.

    Directory of Open Access Journals (Sweden)

    Stéphane Buhler

    2011-02-01

    Full Text Available Molecular differences between HLA alleles vary up to 57 nucleotides within the peptide binding coding region of human Major Histocompatibility Complex (MHC genes, but it is still unclear whether this variation results from a stochastic process or from selective constraints related to functional differences among HLA molecules. Although HLA alleles are generally treated as equidistant molecular units in population genetic studies, DNA sequence diversity among populations is also crucial to interpret the observed HLA polymorphism. In this study, we used a large dataset of 2,062 DNA sequences defined for the different HLA alleles to analyze nucleotide diversity of seven HLA genes in 23,500 individuals of about 200 populations spread worldwide. We first analyzed the HLA molecular structure and diversity of these populations in relation to geographic variation and we further investigated possible departures from selective neutrality through Tajima's tests and mismatch distributions. All results were compared to those obtained by classical approaches applied to HLA allele frequencies.Our study shows that the global patterns of HLA nucleotide diversity among populations are significantly correlated to geography, although in some specific cases the molecular information reveals unexpected genetic relationships. At all loci except HLA-DPB1, populations have accumulated a high proportion of very divergent alleles, suggesting an advantage of heterozygotes expressing molecularly distant HLA molecules (asymmetric overdominant selection model. However, both different intensities of selection and unequal levels of gene conversion may explain the heterogeneous mismatch distributions observed among the loci. Also, distinctive patterns of sequence divergence observed at the HLA-DPB1 locus suggest current neutrality but old selective pressures on this gene. We conclude that HLA DNA sequences advantageously complement HLA allele frequencies as a source of data used

  16. Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)–adenine derivatives

    Science.gov (United States)

    Stojković, Marijana Radić; Škugor, Marko; Dudek, Łukasz; Grolik, Jarosław; Eilmes, Julita

    2014-01-01

    Summary An investigation of the interactions of two novel and several known DBTAA–adenine conjugates with double-stranded DNA and RNA has revealed the DNA/RNA groove as the dominant binding site, which is in contrast to the majority of previously studied DBTAA analogues (DNA/RNA intercalators). Only DBTAA–propyladenine conjugates revealed the molecular recognition of AT-DNA by an ICD band pattern > 300 nm, whereas significant ICD bands did not appear for other ds-DNA/RNA. A structure–activity relation for the studied series of compounds showed that the essential structural features for the ICD recognition are a) the presence of DNA-binding appendages (adenine side chain and positively charged side chain) on both DBTAA side chains, and b) the presence of a short propyl linker, which does not support intramolecular aromatic stacking between DBTAA and adenine. The observed AT-DNA-ICD pattern differs from previously reported ss-DNA (poly dT) ICD recognition by a strong negative ICD band at 350 nm, which allows for the dynamic differentiation between ss-DNA (poly dT) and coupled ds-AT-DNA. PMID:25246976

  17. Fast transient current response to switching events in short chains of molecular islands

    Czech Academy of Sciences Publication Activity Database

    Kalvová, Anděla; Špička, Václav; Velický, B.

    2013-01-01

    Roč. 26, č. 4 (2013), s. 773-777 ISSN 1557-1939 R&D Projects: GA ČR GAP204/12/0897 Institutional support: RVO:68378271 Keywords : nonequilibrium * molecular islands * initial correlations * transient currents Subject RIV: BE - Theoretical Physics Impact factor: 0.930, year: 2013

  18. Fluorescence and room temperature phosphorescence of 6-bromo-2-naphthol in {beta}-cyclodextrin solution and its selective molecular recognition for cyclohexane

    Energy Technology Data Exchange (ETDEWEB)

    Zhai Yanqiang; Zhang Shuzhen; Xie Jianwei; Liu Changsong

    2003-10-08

    The room temperature phosphorescence (RTP) and fluorescence behavior of 6-bromo-2-naphthol (BN) in water and {beta}-cyclodextrin ({beta}-CD) aerated aqueous solution was investigated. The study of fluorescence behavior at different pH values indicated that three kinds of species of BN (protonated, uncharged and anionic species) formed 1:1 inclusion complexes with {beta}-CD, and RTP and fluorescence emission depended on the pH of the solution. The inclusion complex constants were 430{+-}25 l mol{sup -1} (pH 1.80), 840{+-}25 l mol{sup -1} (pH 5.80), 1850{+-}75 l mol{sup -1} (pH 11.50), respectively. Experimental results elucidated that RTP of the BN/{beta}-CD/cyclohexane solution came from the protonated and uncharged species of BN, but not from the anionic species, though the inclusion constant of the anionic species of BN with {beta}-CD was larger than that of the other two species of BN Selective molecular recognition of BN/{beta}-CD as an RTP sensor for 28 small organic molecules was studied, it was shown that BN/{beta}-CD could be develop as a new RTP sensor with high selectivity molecular recognition ability for cyclohexane.

  19. Fluorescence and room temperature phosphorescence of 6-bromo-2-naphthol in β-cyclodextrin solution and its selective molecular recognition for cyclohexane

    International Nuclear Information System (INIS)

    Zhai Yanqiang; Zhang Shuzhen; Xie Jianwei; Liu Changsong

    2003-01-01

    The room temperature phosphorescence (RTP) and fluorescence behavior of 6-bromo-2-naphthol (BN) in water and β-cyclodextrin (β-CD) aerated aqueous solution was investigated. The study of fluorescence behavior at different pH values indicated that three kinds of species of BN (protonated, uncharged and anionic species) formed 1:1 inclusion complexes with β-CD, and RTP and fluorescence emission depended on the pH of the solution. The inclusion complex constants were 430±25 l mol -1 (pH 1.80), 840±25 l mol -1 (pH 5.80), 1850±75 l mol -1 (pH 11.50), respectively. Experimental results elucidated that RTP of the BN/β-CD/cyclohexane solution came from the protonated and uncharged species of BN, but not from the anionic species, though the inclusion constant of the anionic species of BN with β-CD was larger than that of the other two species of BN Selective molecular recognition of BN/β-CD as an RTP sensor for 28 small organic molecules was studied, it was shown that BN/β-CD could be develop as a new RTP sensor with high selectivity molecular recognition ability for cyclohexane

  20. Interconnectivity of macroporous molecularly imprinted polymers fabricated by hydroxyapatite-stabilized Pickering high internal phase emulsions-hydrogels for the selective recognition of protein.

    Science.gov (United States)

    Sun, Yanhua; Li, Yuqing; Xu, Jiangfeng; Huang, Ling; Qiu, Tianyun; Zhong, Shian

    2017-07-01

    Hydroxyapatite hybridized molecularly imprinted polydopamine polymers with selective recognition of bovine hemoglobin (BHb) were successfully prepared via Pickering oil-in-water high internal phase emulsions-hydrogels and molecularly imprinting technique. The emulsions were stabilized by hydroxyapatite of which the wettability was modified by 3-methacryloxypropyltrimethoxysilane. The materials were characterized by SEM, IR and TGA. The results showed that the BHb imprinted polymers based on Pickering hydrogels (Hydro-MIPs) possess macropores ranging from 20μm to 50μm, and their large numbers of amino groups and hydroxyl groups result in a favorable adsorption capacity for BHb. The maximum adsorption capacity of Hydro-MIPs for BHb was 438mg/g, 3.27 times more than that of the non-imprinted polymers (Hydro-NIPs). The results indicated that Hydro-MIPs possessing well-defined hierarchical porous structures exhibited outstanding recognition behavior towards the target protein molecules. This work provided a promising alternative method for the fabrication of polymer materials with tunable and interconnected pores structures for the separation and purification of protein in vitro. Copyright © 2017. Published by Elsevier B.V.

  1. Molecular Evolution of the CYP2D Subfamily in Primates: Purifying Selection on Substrate Recognition Sites without the Frequent or Long-Tract Gene Conversion

    Science.gov (United States)

    Yasukochi, Yoshiki; Satta, Yoko

    2015-01-01

    The human cytochrome P450 (CYP) 2D6 gene is a member of the CYP2D gene subfamily, along with the CYP2D7P and CYP2D8P pseudogenes. Although the CYP2D6 enzyme has been studied extensively because of its clinical importance, the evolution of the CYP2D subfamily has not yet been fully understood. Therefore, the goal of this study was to reveal the evolutionary process of the human drug metabolic system. Here, we investigate molecular evolution of the CYP2D subfamily in primates by comparing 14 CYP2D sequences from humans to New World monkey genomes. Window analysis and statistical tests revealed that entire genomic sequences of paralogous genes were extensively homogenized by gene conversion during molecular evolution of CYP2D genes in primates. A neighbor-joining tree based on genomic sequences at the nonsubstrate recognition sites showed that CYP2D6 and CYP2D8 genes were clustered together due to gene conversion. In contrast, a phylogenetic tree using amino acid sequences at substrate recognition sites did not cluster the CYP2D6 and CYP2D8 genes, suggesting that the functional constraint on substrate specificity is one of the causes for purifying selection at the substrate recognition sites. Our results suggest that the CYP2D gene subfamily in primates has evolved to maintain the regioselectivity for a substrate hydroxylation activity between individual enzymes, even though extensive gene conversion has occurred across CYP2D coding sequences. PMID:25808902

  2. Genetic plasticity of the Shigella virulence plasmid is mediated by intra- and inter-molecular events between insertion sequences.

    Science.gov (United States)

    Pilla, Giulia; McVicker, Gareth; Tang, Christoph M

    2017-09-01

    Acquisition of a single copy, large virulence plasmid, pINV, led to the emergence of Shigella spp. from Escherichia coli. The plasmid encodes a Type III secretion system (T3SS) on a 30 kb pathogenicity island (PAI), and is maintained in a bacterial population through a series of toxin:antitoxin (TA) systems which mediate post-segregational killing (PSK). The T3SS imposes a significant cost on the bacterium, and strains which have lost the plasmid and/or genes encoding the T3SS grow faster than wild-type strains in the laboratory, and fail to bind the indicator dye Congo Red (CR). Our aim was to define the molecular events in Shigella flexneri that cause loss of Type III secretion (T3S), and to examine whether TA systems exert positional effects on pINV. During growth at 37°C, we found that deletions of regions of the plasmid including the PAI lead to the emergence of CR-negative colonies; deletions occur through intra-molecular recombination events between insertion sequences (ISs) flanking the PAI. Furthermore, by repositioning MvpAT (which belongs to the VapBC family of TA systems) near the PAI, we demonstrate that the location of this TA system alters the rearrangements that lead to loss of T3S, indicating that MvpAT acts both globally (by reducing loss of pINV through PSK) as well as locally (by preventing loss of adjacent sequences). During growth at environmental temperatures, we show for the first time that pINV spontaneously integrates into different sites in the chromosome, and this is mediated by inter-molecular events involving IS1294. Integration leads to reduced PAI gene expression and impaired secretion through the T3SS, while excision of pINV from the chromosome restores T3SS function. Therefore, pINV integration provides a reversible mechanism for Shigella to circumvent the metabolic burden imposed by pINV. Intra- and inter-molecular events between ISs, which are abundant in Shigella spp., mediate plasticity of S. flexneri pINV.

  3. A Network of AOPs for reduced thyroid hormone synthesis derived from inhibition of Thyroperoxidase - A common Molecular Initiating Event Leading to Species-Specific Indices of Adversity.

    Science.gov (United States)

    This collection of 3 AOPs describe varying outcomes of adversity dependent upon species in response to inhibition of thyroperoxidase (TPO) during development. Chemical inhibition of TPO, the molecular-initiating event (MIE), results in decreased thyroid hormone (TH) synthesis, a...

  4. Selective separation of hydroxy polychlorinated biphenyls (HO-PCBs) by the structural recognition on the molecularly imprinted polymers: Direct separation of the thyroid hormone active analogues from mixtures

    International Nuclear Information System (INIS)

    Kubo, Takuya; Matsumoto, Hideyuki; Shiraishi, Fujio; Nomachi, Makoto; Nemoto, Koji; Hosoya, Ken; Kaya, Kunimitsu

    2007-01-01

    We developed novel separation media for hydroxy polychlorinated biphenyls (HO-PCBs) using the molecular imprinting techniques. The results of evaluation for the molecularly imprinted polymers (MIPs) by the liquid chromatography (LC) suggested that MIPs had selective separation ability for certain HO-PCB analogues. The results of the LC evaluations and molecular modeling indicated that the molecular volumes and pK a values of template molecules were related with the retention factor of HO-PCBs. Additionally, according to the detail evaluation toward the selective separation behaviors of MIPs, these HO-PCB analogues have low pK a values dependent on their chemical structures. In other words, the prepared MIPs had selective recognition ability against the analogues, which have an OH group on a phenyl carbon and two chlorine atoms on the both neighboring carbons of the carbon attached with the OH group. Moreover, these analogues may have a potential for thyroid hormone activities so that we attempted to separate these analogues directly from mixtures of HO-PCBs using a prepared MIP

  5. The role of stable α-synuclein oligomers in the molecular events underlying amyloid formation

    DEFF Research Database (Denmark)

    Lorenzen, Nikolai; Nielsen, Søren Bang; Buell, Alexander K.

    2014-01-01

    α-synuclein (αSN), whose aggregation is strongly implicated in the development of Parkinson’s disease (PD). The two types of oligomers are both formed under conditions where amyloid fibril formation is observed but differ in molecular weight by an order of magnitude. Both possess a degree of β......, either as precursors of fibrils or as species involved in the fibril elongation process or instead if they are associated with an aggregation process that is distinct from that generating mature fibrils. Here we describe and characterize in detail two well-defined oligomeric species formed by the protein...

  6. Quantification of pancreatic cancer proteome and phosphorylome: indicates molecular events likely contributing to cancer and activity of drug targets.

    Directory of Open Access Journals (Sweden)

    David Britton

    Full Text Available LC-MS/MS phospho-proteomics is an essential technology to help unravel the complex molecular events that lead to and propagate cancer. We have developed a global phospho-proteomic workflow to determine activity of signaling pathways and drug targets in pancreatic cancer tissue for clinical application.Peptides resulting from tryptic digestion of proteins extracted from frozen tissue of pancreatic ductal adenocarcinoma and background pancreas (n = 12, were labelled with tandem mass tags (TMT 8-plex, separated by strong cation exchange chromatography, then were analysed by LC-MS/MS directly or first enriched for phosphopeptides using IMAC and TiO2, prior to analysis. In-house, commercial and freeware bioinformatic platforms were used to identify relevant biological events from the complex dataset.Of 2,101 proteins identified, 152 demonstrated significant difference in abundance between tumor and non-tumor tissue. They included proteins that are known to be up-regulated in pancreatic cancer (e.g. Mucin-1, but the majority were new candidate markers such as HIPK1 & MLCK. Of the 6,543 unique phosphopeptides identified (6,284 unique phosphorylation sites, 635 showed significant regulation, particularly those from proteins involved in cell migration (Rho guanine nucleotide exchange factors & MRCKα and formation of focal adhesions. Activator phosphorylation sites on FYN, AKT1, ERK2, HDAC1 and other drug targets were found to be highly modulated (≥2 fold in different cases highlighting their predictive power.Here we provided critical information enabling us to identify the common and unique molecular events likely contributing to cancer in each case. Such information may be used to help predict more bespoke therapy suitable for an individual case.

  7. Quantification of pancreatic cancer proteome and phosphorylome: indicates molecular events likely contributing to cancer and activity of drug targets.

    Science.gov (United States)

    Britton, David; Zen, Yoh; Quaglia, Alberto; Selzer, Stefan; Mitra, Vikram; Löβner, Christopher; Jung, Stephan; Böhm, Gitte; Schmid, Peter; Prefot, Petra; Hoehle, Claudia; Koncarevic, Sasa; Gee, Julia; Nicholson, Robert; Ward, Malcolm; Castellano, Leandro; Stebbing, Justin; Zucht, Hans Dieter; Sarker, Debashis; Heaton, Nigel; Pike, Ian

    2014-01-01

    LC-MS/MS phospho-proteomics is an essential technology to help unravel the complex molecular events that lead to and propagate cancer. We have developed a global phospho-proteomic workflow to determine activity of signaling pathways and drug targets in pancreatic cancer tissue for clinical application. Peptides resulting from tryptic digestion of proteins extracted from frozen tissue of pancreatic ductal adenocarcinoma and background pancreas (n = 12), were labelled with tandem mass tags (TMT 8-plex), separated by strong cation exchange chromatography, then were analysed by LC-MS/MS directly or first enriched for phosphopeptides using IMAC and TiO2, prior to analysis. In-house, commercial and freeware bioinformatic platforms were used to identify relevant biological events from the complex dataset. Of 2,101 proteins identified, 152 demonstrated significant difference in abundance between tumor and non-tumor tissue. They included proteins that are known to be up-regulated in pancreatic cancer (e.g. Mucin-1), but the majority were new candidate markers such as HIPK1 & MLCK. Of the 6,543 unique phosphopeptides identified (6,284 unique phosphorylation sites), 635 showed significant regulation, particularly those from proteins involved in cell migration (Rho guanine nucleotide exchange factors & MRCKα) and formation of focal adhesions. Activator phosphorylation sites on FYN, AKT1, ERK2, HDAC1 and other drug targets were found to be highly modulated (≥2 fold) in different cases highlighting their predictive power. Here we provided critical information enabling us to identify the common and unique molecular events likely contributing to cancer in each case. Such information may be used to help predict more bespoke therapy suitable for an individual case.

  8. Phylogenetic and molecular epidemiological studies reveal evidence of multiple past recombination events between infectious laryngotracheitis viruses.

    Directory of Open Access Journals (Sweden)

    Sang-Won Lee

    Full Text Available In contrast to the RNA viruses, the genome of large DNA viruses such as herpesviruses have been considered to be relatively stable. Intra-specific recombination has been proposed as an important, but underestimated, driving force in herpesvirus evolution. Recently, two distinct field strains of infectious laryngotracheitis virus (ILTV have been shown to have arisen from independent recombination events between different commercial ILTV vaccines. In this study we sequenced the genomes of additional ILTV strains and also utilized other recently updated complete genome sequences of ILTV to confirm the existence of a number of ILTV recombinants in nature. Multiple recombination events were detected in the unique long and repeat regions of the genome, but not in the unique short region. Most recombinants contained a pair of crossover points between two distinct lineages of ILTV, corresponding to the European origin and the Australian origin vaccine strains of ILTV. These results suggest that there are two distinct genotypic lineages of ILTV and that these commonly recombine in the field.

  9. Evidence for nucleosynthetic enrichment of the protosolar molecular cloud core by multiple supernova events

    DEFF Research Database (Denmark)

    Schiller, Martin; Paton, Chad; Bizzarro, Martin

    2015-01-01

    The presence of isotope heterogeneity of nucleosynthetic origin amongst meteorites and their components provides a record of the diverse stars that contributed matter to the protosolar molecular cloud core. Understanding how and when the solar system's nucleosynthetic heterogeneity was established...... and preserved within the solar protoplanetary disk is critical for unraveling the earliest formative stages of the solar system. Here, we report calcium and magnesium isotope measurements of primitive and differentiated meteorites as well as various types of refractory inclusions, including refractory...... and differentiated meteorites along with canonical and FUN-CAIs define correlated, mass-independent variations in 43Ca, 46Ca and 48Ca. Moreover, sequential dissolution experiments of the Ivuna carbonaceous chondrite aimed at identifying the nature and number of presolar carriers of isotope anomalies within primitive...

  10. Molecular events by which dendritic cells promote Th2 immune protection in helmith infection.

    Science.gov (United States)

    Méndez-Samperio, Patricia

    2016-10-01

    Helminth parasites are a major cause of global infectious diseases, affecting nearly one quarter of the world's population. The common feature of helminth infections is to skew the immune system towards a T-helper 2 (Th2) response that helps to control disease. Dendritic cells (DCs), which are professional antigen-presenting cells, play a critical role for Th2 skewing against helminth parasites. However, the molecular mechanisms by which helminth antigens activate DCs for Th2 polarization have not yet been clearly defined. This review provides a focused update on the major role of DCs for inducing and/or enhancing Th2 immune responses in helminthic infection and will discuss the main signalling-dependent and independent mechanisms by which helminth antigens activate DCs for Th2 skewing.

  11. Molecular cloning and functional characterization of peptidoglycan recognition protein OmPGRP-L2 from the rainbow trout, Oncorhynchus mykiss.

    Science.gov (United States)

    Jang, Ju Hye; Kim, Hyun; Cho, Ju Hyun

    2017-10-01

    Peptidoglycan recognition proteins (PGRPs), a group of pattern recognition receptors (PRRs), are innate immune molecules that are structurally conserved through evolution in both invertebrate and vertebrate animals. In teleost fish, several PGRPs have been characterized recently. They have both amidase activity and bactericidal activity and are involved in indirectly killing bacteria and regulating multiple signaling pathways. However, the knowledge of functional similarity and divergence between PGRP paralogs for their role as an immune modulator in teleost fish is still limited. In this study, we identified a novel PGRP paralog, termed OmPGRP-L2 from the rainbow trout (Oncorhynchus mykiss). OmPGRP-L2 contains the conserved PGRP domain and the four Zn 2+ -binding amino acid residues required for amidase activity. Quantitative RT-PCR analysis indicated that OmPGRP-L2 is highly expressed in liver. Overexpression of OmPGRP-L2 in a rainbow trout hepatocyte cell line RTH-149 challenged with Edwardsiella tarda resulted in down-regulation of IL-1β and TNF-α expression. When overexpressed in RTH-149 cells, OmPGRP-L2 inhibited NF-κB activity with or without bacterial stimulation. Collectively, these findings suggest that OmPGRP-L2 has an immunomodulatory function, via NF-κB inhibition in liver. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Molecular insights into the specific recognition between the RNA binding domain qRRM2 of hnRNP F and G-tract RNA: A molecular dynamics study.

    Science.gov (United States)

    Wang, Lingyun; Yan, Feng

    2017-12-09

    Heterogeneous nuclear ribonucleoprotein F (hnRNP F) controls the expression of various genes through regulating the alternative splicing of pre-mRNAs in the nucleus. It uses three quasi-RNA recognition motifs (qRRMs) to recognize G-tract RNA which contains at least three consecutive guanines. The structures containing qRRMs of hnRNP F in complex with G-tract RNA have been determined by nuclear magnetic resonance (NMR) spectroscopy, shedding light on the recognition mechanism of qRRMs with G-tract RNA. However, knowledge of the recognition details is still lacking. To investigate how qRRMs specifically bind with G-tract RNA and how the mutations of any guanine to an adenine in the G-tract affect the binding, molecular dynamics simulations with binding free energy analysis were performed based on the NMR structure of qRRM2 in complex with G-tract RNA. Simulation results demonstrate that qRRM2 binds strongly with G-tract RNA, but any mutation of the G-tract leads to a drastic reduction of the binding free energy. Further comparisons of the energetic components reveal that van der Waals and non-polar interactions play essential roles in the binding between qRRM2 and G-tract RNA, but the interactions are weakened by the effect of RNA mutations. Structural and dynamical analyses indicate that when qRRM2 binds with G-tract RNA, both qRRM2 and G-tract maintain stabilized structures and dynamics; however, the stability is disrupted by the mutations of the G-tract. These results provide novel insights into the recognition mechanism of qRRM2 with G-tract RNA that are not elucidated by the NMR technique. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Zipper-like magnetic molecularly imprinted microspheres for on/off-switchable recognition and extraction of 17β-estradiol from food samples.

    Science.gov (United States)

    Zhu, Wenting; Peng, Hailong; Luo, Mei; Yu, Ningxiang; Xiong, Hua; Wang, Ronghui; Li, Yanbin

    2018-09-30

    Zipper-like on/off-switchable and magnetic molecularly imprinted microspheres (SM-MIMs) were constructed using acrylamide (AAm) and 2-acrylamide-2-methyl propanesulfonic acid (AMPS) as functional monomers for 17β-estradiol (17β-E 2 ) recognition and extraction. The imprinted polymer interactions between poly(AAm) (PAAm) and poly(AMPS) (PAMPS) with on/off-switchable property to temperature, exhibited dissociation at relatively higher temperatures (such as 30 °C) and helped 17β-E 2 enter into imprinted sites, leading to higher binding capability. Conversely, the interpolymer complexes between PAAm and PAMPS formed and blocked 17β-E 2 access to imprinted sites at lower temperature (such as 20 °C). SM-MIMs were used as dispersive solid phase extraction (SPE) adsorbent with HPLC for 17β-E 2 pretreatment and detection in food samples, and low limit detection (2.52 µg L -1 ) and quantification (10.76 µg L -1 ) with higher recovery were obtained. Therefore, SM-MIMs may be a promising adsorbent for 17β-E 2 pretreatment in food samples owing to its advantages of on/off-switchable recognition, eco-friendly elution, and efficient separation. Copyright © 2018. Published by Elsevier Ltd.

  14. Molecularly imprinted polymer beads for nicotine recognition prepared by RAFT precipitation polymerization: a step forward towards multifunctionalities

    DEFF Research Database (Denmark)

    Zhou, Tongchang; Jørgensen, Lars; Mattebjerg, Maria Ahlm

    2014-01-01

    A nicotine imprinted polymer was synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization using methacrylic acid (MAA) as a functional monomer. The resulting molecularly imprinted polymers were monodispersed beads with an average diameter of 1.55 mm. The molecular...... selectivity of the imprinted polymer beads was evaluated by studying the uptake of nicotine and its structural analogs by the polymer beads. Equilibrium binding results indicate that the amount of nicotine bound to the imprinted polymer beads is significantly higher than that bound to the nonimprinted polymer...

  15. Molecular events basic to cellular radiation response. Progress report, October 1, 1978-September 30, 1979

    International Nuclear Information System (INIS)

    Kolodny, G.M.

    1980-01-01

    Research during the past year has been directed at induction of specific protein synthesis in differentiated mammalian cells. The Primer Hypothesis for the regulation of eukaryotic gene expression suggests that RNA transcription is primed by small molecular weight RNA. It predicts that albumin mRNA transcription in a 3T3 fibroblast, which ordinarily does not produce albumin, can be initiated by RNA primer present in liver cells. In experiments this past year, mouse fibroblasts were incubated with mouse liver RNA. These cells did indeed produce albumin which was detected by counterimmunoelectrophoresis. Confluent 3T3 cell cultures were incubated with mouse liver RNA and polylysine in serum free media. Counterimmunoelectrophoresis (CIEP) of the dialyzed and lyophilized media against mouse albumin antisera gave a single precipitin line indicating albumin snthesis by the fibroblasts. The synthesis of this protein immunologicaly similar to albumin required new albumin mRNA transcription since it was not synthesized in the presence of actinomycin, could be found in media which had been incubated with RNA significantly smaller in size than albumin mRNA, and was synthesized in the absence of added poly A containing RNA. These results represent the first reported demonstration that RNA can be taken up from the media by cells in culture, and can induce in those cells the production of a differentiated cell product not ordinarily synthesized by those cells, i.e, a change in the normal transcription pattern in those cells

  16. ACUTE CEREBROVASCULAR EVENTS IN PATIENTS WITH ARTERIAL HYPERTENSION: MOLECULAR GENETIC ASPECTS

    Directory of Open Access Journals (Sweden)

    M. A. Karpenko

    2008-01-01

    Full Text Available Aim. To study association between stroke and gene polymorphism of angeotensin converting enzyme (ACE, angeotensin II type 1 receptor (ATR1, apolipoprotein СIII (APO CIII, apoproteine Е (APO E, methylentetrahydrofolate reductase (MTHFR, fibrinogen (Fb, endothelial NO-synthase (NOS3 in arterial hypertension (HT.Material and methods. Molecular genetic analysis by polymerase chain reaction was done in 41 patients with HT, who experienced first episode of acute disturbances of cerebral blood circulation (ADCBC.Results. Stroke rate in patients with HT is associated with A1166C of ATR1 gene polymorphism, G-455A of Fb gene polymorphism and C677T of MTHFR gene polymorphism. The high risk markers are C-allele of ATR1 gene, -455А allele and AA genotype of Fb gene, 677T allele of MTHFR. The A-allele and genotype AA of ATR1 gene, G-445 allele of Fb gene, С677-allele and CC genotype of MTHFR gene play protective role against ADCBC in HT.Conclusion. It is established an association between gene polymorphism of some molecules and ADCBC in HT.

  17. Origin of microbial life: Nano- and molecular events, thermodynamics/entropy, quantum mechanisms and genetic instructions.

    Science.gov (United States)

    Trevors, J T

    2011-03-01

    Currently, there are no agreed upon mechanisms and supporting evidence for the origin of the first microbial cells on the Earth. However, some hypotheses have been proposed with minimal supporting evidence and experimentation/observations. The approach taken in this article is that life originated at the nano- and molecular levels of biological organization, using quantum mechanic principles that became manifested as classical microbial cell(s), allowing the origin of microbial life on the Earth with a core or minimal, organic, genetic code containing the correct instructions for cell(s) for growth and division, in a micron dimension environment, with a local entropy range conducive to life (present about 4 billion years ago), and obeying the laws of thermodynamics. An integrated approach that explores all encompassing factors necessary for the origin of life, may bring forth plausible hypotheses (and mechanisms) with much needed supporting experimentation and observations for an origin of life theory. Copyright © 2010 Elsevier B.V. All rights reserved.

  18. Charge pattern matching as a ‘fuzzy’ mode of molecular recognition for the functional phase separations of intrinsically disordered proteins

    Science.gov (United States)

    Lin, Yi-Hsuan; Brady, Jacob P.; Forman-Kay, Julie D.; Chan, Hue Sun

    2017-11-01

    Biologically functional liquid-liquid phase separation of intrinsically disordered proteins (IDPs) is driven by interactions encoded by their amino acid sequences. Little is currently known about the molecular recognition mechanisms for distributing different IDP sequences into various cellular membraneless compartments. Pertinent physics was addressed recently by applying random-phase-approximation (RPA) polymer theory to electrostatics, which is a major energetic component governing IDP phase properties. RPA accounts for charge patterns and thus has advantages over Flory-Huggins (FH) and Overbeek-Voorn mean-field theories. To make progress toward deciphering the phase behaviors of multiple IDP sequences, the RPA formulation for one IDP species plus solvent is hereby extended to treat polyampholyte solutions containing two IDP species plus solvent. The new formulation generally allows for binary coexistence of two phases, each containing a different set of volume fractions ({φ }1,{φ }2) for the two different IDP sequences. The asymmetry between the two predicted coexisting phases with regard to their {φ }1/{φ }2 ratios for the two sequences increases with increasing mismatch between their charge patterns. This finding points to a multivalent, stochastic, ‘fuzzy’ mode of molecular recognition that helps populate various IDP sequences differentially into separate phase compartments. An intuitive illustration of this trend is provided by FH models, whereby a hypothetical case of ternary coexistence is also explored. Augmentations of the present RPA theory with a relative permittivity {ɛ }{{r}}(φ ) that depends on IDP volume fraction φ ={φ }1+{φ }2 lead to higher propensities to phase separate, in line with the case with one IDP species we studied previously. Notably, the cooperative, phase-separation-enhancing effects predicted by the prescriptions for {ɛ }{{r}}(φ ) we deem physically plausible are much more prominent than that entailed by common

  19. Molecular recognition at methyl methacrylate/n-butyl acrylate (MMA/nBA) monomer unit boundaries of phospholipids at p-MMA/nBA copolymer surfaces.

    Science.gov (United States)

    Yu, Min; Urban, Marek W; Sheng, Yinghong; Leszczynski, Jerzy

    2008-09-16

    Lipid structural features and their interactions with proteins provide a useful vehicle for further advances in membrane proteins research. To mimic one of potential lipid-protein interactions we synthesized poly(methyl methacrylate/ n-butyl acrylate) (p-MMA/nBA) colloidal particles that were stabilized by phospholipid (PLs). Upon the particle coalescence, PL stratification resulted in the formation of surface localized ionic clusters (SLICs). These entities are capable of recognizing MMA/nBA monomer interfaces along the p-MMA/nBA copolymer backbone and form crystalline SLICs at the monomer interface. By utilizing attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy and selected area electron diffraction (SAD) combined with ab initio calculations, studies were conducted that identified the origin of SLICs as well as their structural features formed on the surface of p-MMA/nBA copolymer films stabilized by 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) PL. Specific entities responsible for SLIC formation are selective noncovalent bonds of anionic phosphate and cationic quaternary ammonium segments of DLPC that interact with two neighboring carbonyl groups of nBA and MMA monomers of the p-MMA/nBA polymer backbone. To the best of our knowledge this is the first example of molecular recognition facilitated by coalescence of copolymer colloidal particles and the ability of PLs to form SLICs at the boundaries of the neighboring MMA and nBA monomer units of the p-MMA/nBA chain. The dominating noncovalent bonds responsible for the molecular recognition is a combination of H-bonding and electrostatic interactions.

  20. Use of UV-vis-NIR spectroscopy to monitor label-free interaction between molecular recognition elements and erythropoietin on a gold-coated polycarbonate platform.

    Science.gov (United States)

    Citartan, Marimuthu; Gopinath, Subash C B; Tominaga, Junji; Chen, Yeng; Tang, Thean-Hock

    2014-08-01

    Label-free-based detection is pivotal for real-time monitoring of biomolecular interactions and to eliminate the need for labeling with tags that can occupy important binding sites of biomolecules. One simplest form of label-free-based detection is ultraviolet-visible-near-infrared (UV-vis-NIR) spectroscopy, which measure changes in reflectivity as a means to monitor immobilization and interaction of biomolecules with their corresponding partners. In biosensor development, the platform used for the biomolecular interaction should be suitable for different molecular recognition elements. In this study, gold (Au)-coated polycarbonate was used as a platform and as a proof-of-concept, erythropoietin (EPO), a doping substance widely abused by the athletes was used as the target. The interaction of EPO with its corresponding molecular recognition elements (anti-EPO monoclonal antibody and anti-EPO DNA aptamer) is monitored by UV-vis-NIR spectroscopy. Prior to this, to show that UV-vis-NIR spectroscopy is a suitable method for measuring biomolecular interaction, the interaction between biotin and streptavidin was demonstrated via this strategy and reflectivity of this interaction decreased by 25%. Subsequent to this, interaction of the EPO with anti-EPO monoclonal antibody and anti-EPO DNA aptamer resulted in the decrease of reflectivity by 5% and 10%, respectively. The results indicated that Au-coated polycarbonate could be an ideal biosensor platform for monitoring biomolecular interactions using UV-vis-NIR spectroscopy. A smaller version of the Au-coated polycarbonate substrates can be derived from the recent set-up, to be applied towards detecting EPO abuse among atheletes. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. A malonitrile-functionalized metal-organic framework for hydrogen sulfide detection and selective amino acid molecular recognition

    Science.gov (United States)

    Li, Haiwei; Feng, Xiao; Guo, Yuexin; Chen, Didi; Li, Rui; Ren, Xiaoqian; Jiang, Xin; Dong, Yuping; Wang, Bo

    2014-03-01

    A novel porous polymeric fluorescence probe, MN-ZIF-90, has been designed and synthesized for quantitative hydrogen sulfide (H2S) fluorescent detection and highly selective amino acid recognition. This distinct crystalline structure, derived from rational design and malonitrile functionalization, can trigger significant enhancement of its fluorescent intensity when exposed to H2S or cysteine molecules. Indeed this new metal-organic framework (MOF) structure shows high selectivity of biothiols over other amino acids and exhibits favorable stability. Moreover, in vitro viability assays on HeLa cells show low cytotoxicity of MN-ZIF-90 and its imaging contrast efficiency is further demonstrated by fluorescence microscopy studies. This facile yet powerful strategy also offers great potential of using open-framework materials (i.e. MOFs) as the novel platform for sensing and other biological applications.

  2. Visualization of early events in acetic acid denaturation of HIV-1 protease: a molecular dynamics study.

    Directory of Open Access Journals (Sweden)

    Aditi Narendra Borkar

    Full Text Available Protein denaturation plays a crucial role in cellular processes. In this study, denaturation of HIV-1 Protease (PR was investigated by all-atom MD simulations in explicit solvent. The PR dimer and monomer were simulated separately in 9 M acetic acid (9 M AcOH solution and water to study the denaturation process of PR in acetic acid environment. Direct visualization of the denaturation dynamics that is readily available from such simulations has been presented. Our simulations in 9 M AcOH reveal that the PR denaturation begins by separation of dimer into intact monomers and it is only after this separation that the monomer units start denaturing. The denaturation of the monomers is flagged off by the loss of crucial interactions between the α-helix at C-terminal and surrounding β-strands. This causes the structure to transit from the equilibrium dynamics to random non-equilibrating dynamics. Residence time calculations indicate that denaturation occurs via direct interaction of the acetic acid molecules with certain regions of the protein in 9 M AcOH. All these observations have helped to decipher a picture of the early events in acetic acid denaturation of PR and have illustrated that the α-helix and the β-sheet at the C-terminus of a native and functional PR dimer should maintain both the stability and the function of the enzyme and thus present newer targets for blocking PR function.

  3. Syntheses, structures, molecular and cationic recognitions and catalytic properties of two lanthanide coordination polymers based on a flexible tricarboxylate

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Yu; Wang, Yan-Mei; Xu, Ji; Liu, Pan; Weththasinha, H.A.B.M.D.; Wu, Yun-Long; Lu, Xiao-Qing; Xie, Ji-Min, E-mail: xiejm391@sohu.com

    2014-11-15

    Two lanthanide coordination polymers, namely, ([La(TTTA)(H{sub 2}O){sub 2}]·2H{sub 2}O){sub n} (La-TTTA) and [Nd(TTTA)(H{sub 2}O){sub 2}]·2H{sub 2}O){sub n} (Nd-TTTA) have been hydrothermally synthesized through the reaction of lanthanide ions (La{sup 3+} and Nd{sup 3+}) with the flexible tripodal ligand 2,2′,2″-[1,3,5-triazine-2,4,6-triyltris(thio)]tris-acetic acid (H{sub 3}TTTA). La-TTTA and Nd-TTTA are isostructural and both show three dimensional structures. La-TTTA and Nd-TTTA show good recognition of amine molecules via quenching the luminescent intensities in amines emulsions. They can also recognize Fe{sup 3+}, Cu{sup 2+}, Mg{sup 2+}, Cr{sup 3+} and Co{sup 2+} ions with the quenching the peak around 361 nm when the compounds immersed in ionic solutions. The two compounds act as efficient Lewis acid catalysts for the cyanosilylation of benzaldehyde and derivatives in high yields shortly due to the strong Lewis acidity and the possible open sites of the lanthanide ions. - Graphical abstract: We have synthesized two isostructural 3D compounds based on H{sub 3}TTTA. They are chemical sensor of amine solvents and cations. They have higher yields and TOFs to catalyze cyanosilylation reactions. - Highlights: • The compounds show recognition of amine molecules via quenching luminescent intensities. • The compounds recognize Fe{sup 3+}, Cu{sup 2+}, Mg{sup 2+}, Cr{sup 3+} and Co{sup 2+} ions via quenching the peak around 361 nm. • They act as efficient Lewis acid catalysts for the cyanosilylation reactions in high yields.

  4. Combining an Elastic Network With a Coarse-Grained Molecular Force Field : Structure, Dynamics, and Intermolecular Recognition

    NARCIS (Netherlands)

    Periole, Xavier; Cavalli, Marco; Marrink, Siewert-Jan; Ceruso, Marco A.

    Structure-based and physics-based coarse-grained molecular force fields have become attractive approaches to gain mechanistic insight into the function of large biomolecular assemblies. Here, we study how both approaches can be combined into a single representation, that we term ELNEDIN. In this

  5. Assessment of molecular events during in vitro re-epithelialization under honey-alginate matrix ambience

    International Nuclear Information System (INIS)

    Barui, Ananya; Mandal, Naresh; Majumder, Subhadipa; Das, Raunak Kumar; Sengupta, Sanghamitra; Banerjee, Provas; Ray, Ajoy Kumar; RoyChaudhuri, Chirosree; Chatterjee, Jyotirmoy

    2013-01-01

    Re-epithelialization is one of the most important stages of cutaneous regeneration and its success requires supportive micro-ambience which may be provided with suitable bio-matrix. Biocompatibility and efficacy of such bio-matrix in re-epithelialization could be explored by multimodal analysis of structural and functional attributes of in vitro wound healing model including evaluation of prime molecular expressions of the epithelial cells during repair. Present study examines the influence of honey-alginate and alginate matrices on re-epithelialization in keratinocyte (HaCaT) population in a 2-D wound model. Cellular viability, proliferation and cell–cell adhesion status were assessed during wound closure using live/dead cell assay and by evaluating expressions of Ki67, p63 and E-cadherin along-with % change in cellular electrical impedance. Efficacy of honey-alginate matrix in comparison to only alginate one was demonstrated by a quicker reduction in wound gap, improved cellular viability, enhanced expressions of Ki67, p63 and its isoforms (TAp63, ΔNp63) as well as E-cadherin. Faster restoration of electrical attribute (% of impedance change) after wounding also indicated better impact of honey-alginate matrix in re-epithelialization. - Highlights: • Role of honey based matrix is evaluated in wound re-epithelialization. • Healing impact of matrix studied in 2D in vitro keratinocyte (HaCaT) wound model. • Faster impedance restoration indicated rapid healing rate of HaCaT under honey. • PCR observations showed faster initiation of cell proliferation under honey. • ICC study indicated better up-regulation of healing markers under honey matrix

  6. Assessment of molecular events during in vitro re-epithelialization under honey-alginate matrix ambience

    Energy Technology Data Exchange (ETDEWEB)

    Barui, Ananya [Centre for Healthcare Science and Technology, BESU, Shibpur, Howrah 711103, West Bengal (India); Mandal, Naresh [Dept. of Electronics and Telecommunication Engg., BESU, Shibpur, Howrah 711103, West Bengal (India); Majumder, Subhadipa [Department of Biochemistry, University of Calcutta Ballygunge, Circular Road, Kolkata 700 019, West Bengal (India); Das, Raunak Kumar [School of Medical Science and Technology, IIT, Kharagpur 721 302, West Bengal (India); Sengupta, Sanghamitra [Department of Biochemistry, University of Calcutta Ballygunge, Circular Road, Kolkata 700 019, West Bengal (India); Banerjee, Provas [School of Medical Science and Technology, IIT, Kharagpur 721 302, West Bengal (India); Ray, Ajoy Kumar; RoyChaudhuri, Chirosree [Dept. of Electronics and Telecommunication Engg., BESU, Shibpur, Howrah 711103, West Bengal (India); Chatterjee, Jyotirmoy, E-mail: jchatterjee@smst.iitkgp.ernet.in [School of Medical Science and Technology, IIT, Kharagpur 721 302, West Bengal (India)

    2013-08-01

    Re-epithelialization is one of the most important stages of cutaneous regeneration and its success requires supportive micro-ambience which may be provided with suitable bio-matrix. Biocompatibility and efficacy of such bio-matrix in re-epithelialization could be explored by multimodal analysis of structural and functional attributes of in vitro wound healing model including evaluation of prime molecular expressions of the epithelial cells during repair. Present study examines the influence of honey-alginate and alginate matrices on re-epithelialization in keratinocyte (HaCaT) population in a 2-D wound model. Cellular viability, proliferation and cell–cell adhesion status were assessed during wound closure using live/dead cell assay and by evaluating expressions of Ki67, p63 and E-cadherin along-with % change in cellular electrical impedance. Efficacy of honey-alginate matrix in comparison to only alginate one was demonstrated by a quicker reduction in wound gap, improved cellular viability, enhanced expressions of Ki67, p63 and its isoforms (TAp63, ΔNp63) as well as E-cadherin. Faster restoration of electrical attribute (% of impedance change) after wounding also indicated better impact of honey-alginate matrix in re-epithelialization. - Highlights: • Role of honey based matrix is evaluated in wound re-epithelialization. • Healing impact of matrix studied in 2D in vitro keratinocyte (HaCaT) wound model. • Faster impedance restoration indicated rapid healing rate of HaCaT under honey. • PCR observations showed faster initiation of cell proliferation under honey. • ICC study indicated better up-regulation of healing markers under honey matrix.

  7. An effective HIV-1 integrase inhibitor screening platform: Rationality validation of drug screening, conformational mobility and molecular recognition analysis for PFV integrase complex with viral DNA.

    Science.gov (United States)

    Du, Wenyi; Zuo, Ke; Sun, Xin; Liu, Wei; Yan, Xiao; Liang, Li; Wan, Hua; Chen, Fengzheng; Hu, Jianping

    2017-11-01

    As an important target for the development of novel anti-AIDS drugs, HIV-1 integrase (IN) has been widely concerned. However, the lack of a complete accurate crystal structure of HIV-1 IN greatly blocks the discovery of novel inhibitors. In this work, an effective HIV-1 IN inhibitor screening platform, namely PFV IN, was filtered from all species of INs. Next, the 40.8% similarity with HIV-1 IN, as well as the high efficiency of virtual screening and the good agreement between calculated binding free energies and experimental ones all proved PFV IN is a promising screening platform for HIV-1 IN inhibitors. Then, the molecular recognition mechanism of PFV IN by its substrate viral DNA and six naphthyridine derivatives (NRDs) inhibitors was investigated through molecular docking, molecular dynamics simulations and water-mediated interactions analyses. The functional partition of NRDs IN inhibitors could be divided into hydrophobic and hydrophilic ones, and the Mg 2+ ions, water molecules and conserved DDE motif residues all interacted with the hydrophilic partition, while the bases in viral DNA and residues like Tyr212, Pro214 interacted with the hydrophobic one. Finally, the free energy landscape (FEL) and cluster analyses were performed to explore the molecular motion of PFV IN-DNA system. It is found that the association with NRDs inhibitors would obviously decrease the motion amplitude of PFV IN-DNA, which may be one of the most potential mechanisms of IN inhibitors. This work will provide a theoretical basis for the inhibitor design based on the structure of HIV-1 IN. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Molecular events in the induction of murine tumors by ionizing radiation

    International Nuclear Information System (INIS)

    Andrews, K.L.

    1993-01-01

    A new method is presented to identify and clone novel transforming genes from radiation-induced tumors. It involves the creation of a cDNA expression library from radiation-induced tumors. The library is transfected into non-transformed cells, and the nude mouse tumorigenicity assay functionally defines the acquisition of a transformed phenotype. cDNA clones responsible for transformation are rescued by PCR amplification. This method is applicable to a variety of mammalian systems. The only requirement is a functional assay with which to measure the acquisition of an altered phenotype following transfection of a cDNA library. This method has identified a cDNA for the 16 kD subunit of v-H + -ATPase, which has been associated with cellular transformation. Two protocols were used to generate radiation-induced tumors. One experiment utilizing fractionated doses of ionizing radiation had a much greater tumor yield than the second protocol using a single dose of 11.25 Gy. To determine if the mechanism of gene activation is different in radiation- and chemically-induced tumors, the expression pattern of five tumor-associated genes was analyzed. The expression patterns of mals 1-4 were not significantly different. However, transin, a secreted protease, was overexpressed in radiation-induced papillomas and undetectable in chemically-induced papillomas. Transin degrades basement membrane proteins and may be involved in the progression of benign, encapsulated tumors to malignant, invasive squamous cell carcinomas. Isolation and characterization of genes with dominant transforming activity from radiation-induced tumors will provide information to bridge the gap between the initial ionizing radiation event and the subsequent development of malignant tumors. The function of these genes may also provide information about the development of human malignancies. An understanding the natural biology of cells will help elucidate the pathogenesis cancer and other diseases

  9. Early molecular events involved in Pinus pinaster Ait. somatic embryo development under reduced water availability: transcriptomic and proteomic analyses.

    Science.gov (United States)

    Morel, Alexandre; Teyssier, Caroline; Trontin, Jean-François; Eliášová, Kateřina; Pešek, Bedřich; Beaufour, Martine; Morabito, Domenico; Boizot, Nathalie; Le Metté, Claire; Belal-Bessai, Leila; Reymond, Isabelle; Harvengt, Luc; Cadene, Martine; Corbineau, Françoise; Vágner, Martin; Label, Philippe; Lelu-Walter, Marie-Anne

    2014-09-01

    Maritime pine somatic embryos (SEs) require a reduction in water availability (high gellan gum concentration in the maturation medium) to reach the cotyledonary stage. This key switch, reported specifically for pine species, is not yet well understood. To facilitate the use of somatic embryogenesis for mass propagation of conifers, we need a better understanding of embryo development. Comparison of both transcriptome (Illumina RNA sequencing) and proteome [two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis with mass spectrometry (MS) identification] of immature SEs, cultured on either high (9G) or low (4G) gellan gum concentration, was performed, together with analysis of water content, fresh and dry mass, endogenous abscisic acid (ABA; gas chromatography-MS), soluble sugars (high-pressure liquid chromatography), starch and confocal laser microscope observations. This multiscale, integrated analysis was used to unravel early molecular and physiological events involved in SE development. Under unfavorable conditions (4G), the glycolytic pathway was enhanced, possibly in relation to cell proliferation that may be antagonistic to SE development. Under favorable conditions (9G), SEs adapted to culture constraint by activating specific protective pathways, and ABA-mediated molecular and physiological responses promoting embryo development. Our results suggest that on 9G, germin-like protein and ubiquitin-protein ligase could be used as predictive markers of SE development, whereas protein phosphatase 2C could be a biomarker for culture adaptive responses. This is the first characterization of early molecular mechanisms involved in the development of pine SEs following an increase in gellan gum concentration in the maturation medium, and it is also the first report on somatic embryogenesis in conifers combining transcriptomic and proteomic datasets. © 2014 Scandinavian Plant Physiology Society.

  10. Recognition, signaling, and repair of DNA double-strand breaks produced by ionizing radiation in mammalian cells: the molecular choreography.

    Science.gov (United States)

    Thompson, Larry H

    2012-01-01

    The faithful maintenance of chromosome continuity in human cells during DNA replication and repair is critical for preventing the conversion of normal diploid cells to an oncogenic state. The evolution of higher eukaryotic cells endowed them with a large genetic investment in the molecular machinery that ensures chromosome stability. In mammalian and other vertebrate cells, the elimination of double-strand breaks with minimal nucleotide sequence change involves the spatiotemporal orchestration of a seemingly endless number of proteins ranging in their action from the nucleotide level to nucleosome organization and chromosome architecture. DNA DSBs trigger a myriad of post-translational modifications that alter catalytic activities and the specificity of protein interactions: phosphorylation, acetylation, methylation, ubiquitylation, and SUMOylation, followed by the reversal of these changes as repair is completed. "Superfluous" protein recruitment to damage sites, functional redundancy, and alternative pathways ensure that DSB repair is extremely efficient, both quantitatively and qualitatively. This review strives to integrate the information about the molecular mechanisms of DSB repair that has emerged over the last two decades with a focus on DSBs produced by the prototype agent ionizing radiation (IR). The exponential growth of molecular studies, heavily driven by RNA knockdown technology, now reveals an outline of how many key protein players in genome stability and cancer biology perform their interwoven tasks, e.g. ATM, ATR, DNA-PK, Chk1, Chk2, PARP1/2/3, 53BP1, BRCA1, BRCA2, BLM, RAD51, and the MRE11-RAD50-NBS1 complex. Thus, the nature of the intricate coordination of repair processes with cell cycle progression is becoming apparent. This review also links molecular abnormalities to cellular pathology as much a possible and provides a framework of temporal relationships. Copyright © 2012 Elsevier B.V. All rights reserved.

  11. Towards a molecular interpretation of astringency: synthesis, 3D structure, colloidal state, and human saliva protein recognition of procyanidins.

    Science.gov (United States)

    Cala, Olivier; Fabre, Sandy; Pinaud, Noël; Dufourc, Erick J; Fouquet, Eric; Laguerre, Michel; Pianet, Isabelle

    2011-07-01

    Astringency is a sensation in the mouth used in judging the quality of red wine. The rough, dry, and puckering sensation called astringency is the result of an interaction between tannins and saliva proteins, mainly proline-rich proteins (PRP), which leads to the formation and precipitation of a complex. A dry and rough sensation is then perceived in the mouth. To get an insight into astringency at the molecular level we investigated: (i) An efficient and iterative method for 4-8 procyanidin synthesis, which gives rise to all possible 4-8 procyanidins up to the tetramer with total control of degree of oligomerization and stereochemistry. (ii) The 3D-structural preferences, which take into account their internal movements, using 2D NMR and molecular modeling. (iii) The self-association process in water or hydroalcoholic solutions using diffusion NMR spectroscopy that gives the active proportion of tannins able to fix proteins. (iv) A comprehensive description of the PRP-procyanidin complex formation to get information about stoichiometry, binding site localization, and affinity constants for different procyanidins. The data collected suggest that the interactions are controlled by both procyanidin conformational and colloidal state preferences. All these results provide new insights into the molecular interpretation of tannin astringency. © Georg Thieme Verlag KG Stuttgart · New York.

  12. Molecularly imprinted electrochemical sensing interface based on in-situ-polymerization of amino-functionalized ionic liquid for specific recognition of bovine serum albumin.

    Science.gov (United States)

    Wang, Yanying; Han, Miao; Liu, Guishen; Hou, Xiaodong; Huang, Yina; Wu, Kangbing; Li, Chunya

    2015-12-15

    A molecularly imprinted polymer film was in situ polymerized on a carboxyl functionalized multi-walled carbon nanotubes modified glassy carbon electrode surface under room temperature. This technique provides a promising imprinting approach for protein in an aqueous solution using 3-(3-aminopropyl)-1-vinylimidazolium tetrafluoroborate ionic liquid as functional monomer, N, N'-methylenebisacrylamide as crossing linker, ammonium persulfate and N,N,N',N'-tetramethylethylenediamine as initiator, and bovine serum albumin (BSA) as template. The molecularly imprinted polymerized ionic liquid film shows enhanced accessibility, high specificity and sensitivity towards BSA. Electrochemical sensing performance of the imprinted sensor was thoroughly investigated using K3Fe[CN]6/K4Fe[CN]6 as electroactive probes. Under optimal conditions, the current difference before and after specific recognition of BSA was found linearly related to its concentration in the range from 1.50×10(-9) to 1.50×10(-6) mol L(-1). The detection limit was calculated to be 3.91×10(-10) mol L(-1) (S/N=3). The practical application of the imprinted sensor was demonstrated by determining BSA in liquid milk samples. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. CARMA2sh and ULK2 control pathogen-associated molecular patterns recognition in human keratinocytes: psoriasis-linked CARMA2sh mutants escape ULK2 censorship.

    Science.gov (United States)

    Scudiero, Ivan; Mazzone, Pellegrino; D'Andrea, Luca E; Ferravante, Angela; Zotti, Tiziana; Telesio, Gianluca; De Rubis, Gabriele; Reale, Carla; Pizzulo, Maddalena; Muralitharan, Shanmugakonar; Vito, Pasquale; Stilo, Romania

    2017-02-23

    The molecular complexes formed by specific members of the family of CARMA proteins, the CARD domain-containing adapter molecule BCL10 and MALT1 (CBM complex) represent a central hub in regulating activation of the pleiotropic transcription factor NF-κB. Recently, missense mutations in CARMA2sh have been shown to cause psoriasis in a dominant manner and with high penetrancy. Here, we demonstrate that in human keratinocytes CARMA2sh plays an essential role in the signal transduction pathway that connects pathogen-associated molecular patterns recognition to NF-κB activation. We also find that the serine/threonine kinase ULK2 binds to and phosphorylates CARMA2sh, thereby inhibiting its capacity to activate NF-κB by promoting lysosomal degradation of BCL10, which is essential for CARMA2sh-mediated NF-κB signaling. Remarkably, CARMA2sh mutants associated with psoriasis escape ULK2 inhibition. Finally, we show that a peptide blocking CARD-mediated BCL10 interactions reduces the capacity of psoriasis-linked CARMA2sh mutants to activate NF-κB. Our work elucidates a fundamental signaling mechanism operating in human keratinocytes and opens to novel potential tools for the therapeutical treatment of human skin disorders.

  14. DNA aptamer functionalized gold nanostructures for molecular recognition and photothermal inactivation of methicillin-Resistant Staphylococcus aureus.

    Science.gov (United States)

    Ocsoy, Ismail; Yusufbeyoglu, Sadi; Yılmaz, Vedat; McLamore, Eric S; Ildız, Nilay; Ülgen, Ahmet

    2017-11-01

    In this work, we report the development of DNA aptamer-functionalized gold nanoparticles (Apt@Au NPs) and gold nanorods (Apt@Au NRs) for inactivation of Methicillin-resistant Staphylococcus aureus (MRSA) with targeted photothermal therapy (PTT). Although both Apt@Au NPs and Apt@Au NRs specifically bind to MRSA cells, Apt@Au NPs and Apt@Au NRs inactivated ∼5% and over 95% of the cells,respectively through PTT. This difference in inactivation was based on the relatively high longitudinal absorption of near-infrared (NIR) radiation and strong photothermal conversion capability for the Apt@Au NRs compared to the Apt@Au NPs. The Au NRs served as a nanoplatform for the loading of thiolated aptamer and also provided multivalent effects for increasing binding strength and affinity to MRSA. Our results indicate that the type of aptamer and the degree of multivalent effect(s) are important factors for MRSA inactivation efficiency in PTT. We show that the Apt@Au NRs are a very effective and promising nanosystem for specific cell recognition and in vitro PTT. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Recognition of RNA by amide modified backbone nucleic acids: molecular dynamics simulations of DNA-RNA hybrids in aqueous solution.

    Science.gov (United States)

    Nina, Mafalda; Fonné-Pfister, Raymonde; Beaudegnies, Renaud; Chekatt, Habiba; Jung, Pierre M J; Murphy-Kessabi, Fiona; De Mesmaeker, Alain; Wendeborn, Sebastian

    2005-04-27

    Thermodynamic and structural properties of a chemically modified DNA-RNA hybrid in which a phosphodiester linkage is replaced by a neutral amide-3 linkage (3'-CH(2)-CONH-5') were investigated using UV melting experiments, molecular dynamics simulations in explicit water, and continuum solvent models. van't Hoff analysis of the experimental UV melting curves suggests that the significant increase of the thermodynamic stability of a 15-mer DNA-RNA with seven alternated amide-3 modifications (+11 degrees C) is mainly due to an increased binding enthalpy. To further evaluate the origin in the observed affinities differences, the electrostatic contribution to the binding free energy was calculated by solving the Poisson-Boltzmann equation numerically. The nonelectrostatic contribution was estimated as the product of a hydrophobic surface tension coefficient and the surface area that is buried upon double strand formation. Structures were taken from 10 ns molecular dynamics simulations computed in a consistent fashion using explicit solvent, counterions, and the particle-mesh Ewald procedure. The present preliminary thermodynamic study suggests that the favorable binding free energy of the amide-3 DNA single strand to the complementary RNA is equally driven by electrostatic and nonpolar contributions to the binding compared to their natural analogues. In addition, molecular dynamics simulations in explicit water were performed on an amide-3 DNA single strand and the corresponding natural DNA. Results from the conformations cluster analysis of the simulated amide-3 DNA single strand ensembles suggest that the 25% of the population sampled within 10 ns has a pre-organized conformation where the sugar C3' endo pucker is favored at the 3'-flanking nucleotides. These structural and thermodynamic features contribute to the understanding of the observed increased affinities of the amide-3 DNA-RNA hybrids at the microscopic level.

  16. Triple-negative breast cancer: the importance of molecular and histologic subtyping, and recognition of low-grade variants.

    Science.gov (United States)

    Pareja, Fresia; Geyer, Felipe C; Marchiò, Caterina; Burke, Kathleen A; Weigelt, Britta; Reis-Filho, Jorge S

    2016-01-01

    Triple-negative breast cancers (TNBCs), defined by lack of expression of estrogen receptor, progesterone receptor and HER2, account for 12-17% of breast cancers and are clinically perceived as a discrete breast cancer subgroup. Nonetheless, TNBC has been shown to constitute a vastly heterogeneous disease encompassing a wide spectrum of entities with marked genetic, transcriptional, histological and clinical differences. Although most TNBCs are high-grade tumors, there are well-characterized low-grade TNBCs that have an indolent clinical course, whose natural history, molecular features and optimal therapy vastly differ from those of high-grade TNBCs. Secretory and adenoid cystic carcinomas are two histologic types of TNBCs underpinned by specific fusion genes; these tumors have an indolent clinical behavior and lack all of the cardinal molecular features of high-grade triple-negative disease. Recent studies of rare entities, including lesions once believed to constitute mere benign breast disease (e.g., microglandular adenosis), have resulted in the identification of potential precursors of TNBC and suggested the existence of a family of low-grade triple-negative lesions that, despite having low-grade morphology and indolent clinical behavior, have been shown to harbor the complex genomic landscape of common forms of TNBC, and may progress to high-grade disease. In this review, we describe the heterogeneity of TNBC and focus on the histologic and molecular features of low-grade forms of TNBC. Germane to addressing the challenges posed by the so-called triple-negative disease is the realization that TNBC is merely a descriptive term, and that low-grade types of TNBC may be driven by distinct sets of genetic alterations.

  17. Recognition/removal of phloretic acid on molecularly imprinted poly(n-vinyl imidazole) based polymers grafted onto nonwoven fabrics

    International Nuclear Information System (INIS)

    Ranada, Ma. Llorina; Abad, Lucille; Akbulut, Meshude; Guven, Olgun

    2013-01-01

    Molecular imprinting is the process of developing polymeric matrices for recognizing a target molecule in the presence of chemically similar structures. These matrices can be tailored using one or more functional monomers with a cross linker in the presence of a molecule behaving as the template. Phloretic acid is one of the members of dietary phenolic group which may have physiological antioxidant properties, potentially modifying pathological mechanisms relevant to some health problems such as cardiovascular diseases and cancer. The content of these compounds is generally very low in plants to be detected by traditional instruments. Thus, the development of an easy, cheap and reliable method is an important issue. In this study, a solution of n-vinyl imidazole was grafted onto polypropylene/polyethylene (PP/PE) films through gamma irradiation to create a film-based polymer matrix for phloretic acid. These films are assessed in terms of structural and binding capacity. The maximum free-volume ratio was obtained at 5 kGy using positron annihilation lifetime spectroscopy (PALS). The imprinting capacity of the matrix system is 2.41 between the molecularly-imprinted and the non-imprinted films. Scanning electron microscopy and Fourier-Transform Infrared Spectroscopy complemented the PALS data in elucidating the structure of the grafted films. (author)

  18. Molecularly imprinted macroporous monoliths for solid-phase extraction: Effect of pore size and column length on recognition properties.

    Science.gov (United States)

    Vlakh, E G; Stepanova, M A; Korneeva, Yu M; Tennikova, T B

    2016-09-01

    The series of macroporous monolithic molecularly imprinted monoliths differed by pore size, column length (volume) and amount of template used for imprinting was synthesized using methacrylic acid and glycerol dimethacrylate as co-monomers and antibiotic ciprofloxacin as a template. The prepared monoliths were characterized regarding to their permeability, pore size, porosity, and resistance to the flow of a mobile phase. The surface morphology was also analyzed. The slight dependence of imprinting factor on flow rate, as well as its independence on pore size of macroporous molecularly imprinted monolithic media was observed. The column obtained at different conditions exhibited different affinity of ciprofloxacin to the imprinted sites that was characterized with Kdiss values in the range of 10(-5)-10(-4)M. The solid-phase extraction of ciprofloxacin from such biological liquids as human blood serum, human urine and cow milk serum was performed using the developed monolithic columns. In all cases, the extraction was found to be 95.0-98.6%. Additionally, the comparison of extraction of three fluoroqinolone analogues, e.g. ciprofloxacin, levofloxacin and moxifloxacin, from human blood plasma was carried out. Contrary to ciprofloxacin extracted with more than 95%, this parameter did not exceed 40% for its analogues. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Galatheoidea are not monophyletic - molecular and morphological phylogeny of the squat lobsters (Decapoda: Anomura) with recognition of a new superfamily.

    Science.gov (United States)

    Schnabel, K E; Ahyong, S T; Maas, E W

    2011-02-01

    The monophyletic status of the squat lobster superfamily Galatheoidea has come under increasing doubt by studies using evidence as diverse as larval and adult somatic morphology, sperm ultrastructure, and molecular data. Here we synthesize phylogenetic data from these diverse strands, with the addition of new molecular and morphological data to examine the phylogeny of the squat lobsters and assess the status of the Galatheoidea. A total of 64 species from 16 of the 17 currently recognised anomuran families are included. Results support previous work pointing towards polyphyly in the superfamily Galatheoidea and Paguroidea, specifically, suggesting independent origins of the Galatheidae+Porcellanidae and the Chirostylidae+Kiwaidae. Morphological characters are selected that support clades resolved in the combined analysis and the taxonomic status of Galatheoidea sensu lato is revised. Results indicate that Chirostylidae are more closely related to an assemblage including Aegloidea, Lomisoidea and Paguroidea than to the remaining Galatheoidea and are referred to the superfamily Chirostyloidea to include the Chirostylidae and Kiwaidae. A considerable amount of research highlighting morphological differences supporting this split is discussed. The Galatheoidea sensu stricto is restricted to the families Galatheidae and Porcellanidae, and diagnoses for both Chirostyloidea and Galatheoidea are provided. Present results highlight the need for a detailed revision of a number of taxa, challenge some currently used morphological synapomorphies, and emphasise the need for integrated studies with wide taxon sampling and multiple data sources to resolve complex phylogenetic questions. Copyright © 2010 Elsevier Inc. All rights reserved.

  20. Molecularly Imprinted Polymer Enables High-Efficiency Recognition and Trapping Lithium Polysulfides for Stable Lithium Sulfur Battery.

    Science.gov (United States)

    Liu, Jie; Qian, Tao; Wang, Mengfan; Liu, Xuejun; Xu, Na; You, Yizhou; Yan, Chenglin

    2017-08-09

    Using molecularly imprinted polymer to recognize various target molecules emerges as a fascinating research field. Herein, we applied this strategy for the first time to efficiently recognize and trap long-chain polysulfides (Li 2 S x , x = 6-8) in lithium sulfur battery to minimize the polysulfide shuttling between anode and cathode, which enables us to achieve remarkable electrochemical performance including a high specific capacity of 1262 mAh g -1 at 0.2 C and superior capacity retention of over 82.5% after 400 cycles at 1 C. The outstanding performance is attributed to the significantly reduced concentration of long-chain polysulfides in electrolyte as evidenced by in situ UV/vis spectroscopy and Li 2 S nucleation tests, which were further confirmed by density functional theory calculations. The molecular imprinting is demonstrated as a promising approach to effectively prevent the free diffusion of long-chain polysulfides, providing a new avenue to efficiently recognize and trap lithium polysulfides for high-performance lithium sulfur battery with greatly suppressed shuttle effect.

  1. Insight into the intermolecular recognition mechanism between Keap1 and IKKβ combining homology modelling, protein-protein docking, molecular dynamics simulations and virtual alanine mutation.

    Directory of Open Access Journals (Sweden)

    Zheng-Yu Jiang

    Full Text Available Degradation of certain proteins through the ubiquitin-proteasome pathway is a common strategy taken by the key modulators responsible for stress responses. Kelch-like ECH-associated protein-1(Keap1, a substrate adaptor component of the Cullin3 (Cul3-based ubiquitin E3 ligase complex, mediates the ubiquitination of two key modulators, NF-E2-related factor 2 (Nrf2 and IκB kinase β (IKKβ, which are involved in the redox control of gene transcription. However, compared to the Keap1-Nrf2 protein-protein interaction (PPI, the intermolecular recognition mechanism of Keap1 and IKKβ has been poorly investigated. In order to explore the binding pattern between Keap1 and IKKβ, the PPI model of Keap1 and IKKβ was investigated. The structure of human IKKβ was constructed by means of the homology modeling method and using reported crystal structure of Xenopus laevis IKKβ as the template. A protein-protein docking method was applied to develop the Keap1-IKKβ complex model. After the refinement and visual analysis of docked proteins, the chosen pose was further optimized through molecular dynamics simulations. The resulting structure was utilized to conduct the virtual alanine mutation for the exploration of hot-spots significant for the intermolecular interaction. Overall, our results provided structural insights into the PPI model of Keap1-IKKβ and suggest that the substrate specificity of Keap1 depend on the interaction with the key tyrosines, namely Tyr525, Tyr574 and Tyr334. The study presented in the current project may be useful to design molecules that selectively modulate Keap1. The selective recognition mechanism of Keap1 with IKKβ or Nrf2 will be helpful to further know the crosstalk between NF-κB and Nrf2 signaling.

  2. Pattern recognition

    CERN Document Server

    Theodoridis, Sergios

    2003-01-01

    Pattern recognition is a scientific discipline that is becoming increasingly important in the age of automation and information handling and retrieval. Patter Recognition, 2e covers the entire spectrum of pattern recognition applications, from image analysis to speech recognition and communications. This book presents cutting-edge material on neural networks, - a set of linked microprocessors that can form associations and uses pattern recognition to ""learn"" -and enhances student motivation by approaching pattern recognition from the designer's point of view. A direct result of more than 10

  3. Equilibrium shift in solution: molecular shape recognition and precipitation of a synthetic double helix using helicene-grafted silica nanoparticles.

    Science.gov (United States)

    Miyagawa, Masamichi; Ichinose, Wataru; Yamaguchi, Masahiko

    2014-01-27

    Chiral silica nanoparticles (70 nm) grafted with (P)-helicene recognized the molecular shape of double helix and random coil (P)-ethynylhelicene oligomers in solution. A mixture of the (P)-nanoparticles and double helix precipitated much faster than a mixture of the (P)-nanoparticles and random coil, and the precipitate contained only the double helix. The mixture of the (P)-nanoparticles and (P)-ethynylhelicene pentamer reversibly dispersed in trifluoromethylbenzene upon heating at 70 °C and precipitated upon cooling at 25 °C. When a 10:90 equilibrium mixture of the double helix and random coil in solution was treated with the (P)-nanoparticles, the double helix was precipitated in 53% yield and was accompanied by equilibrium shift. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Radiation synthesis of carboxymethyl cellulose hydrogel imprinted with β-estradiol for molecular recognition of endocrine disruptive chemicals

    International Nuclear Information System (INIS)

    Dela Cruz, Rafael Miguel M.; Estorque, Kit Joshua J.

    2015-03-01

    This study demonstrates the possibility of synthesizing molecularly imprinted polymers (MIP) using carboxymethyl cellulose in low concentration and pH, and intiated by γ-irradiation. The capability of the synthesized MIPs to absorb specific molecules was demonstrated using an NIP which adsorbing capability was successfully done. The selectivity of molecules is beyond the scope of this study. Right amount of monomer and solvents affects the capability of the imprinted polymer to be formed. It was also found out that it is important to acidify the CMC mixture to enable the cross-linking of CMC chains without using a cross-linker. It was confirmed that β-estradiol is soluble in acentonitrile by subjecting the mixture to UV-Vis spectrophotometry. The Incorporation of β-estradiol to CMC after γ-irradiation was also confirmed using FTIR-ATR. (author)

  5. Evidence of molecular evolution driven by recombination events influencing tropism in a novel human adenovirus that causes epidemic keratoconjunctivitis.

    Directory of Open Access Journals (Sweden)

    Michael P Walsh

    2009-06-01

    the first genomic, bioinformatic, and biological descriptions of the molecular evolution events engendering an emerging pathogenic adenovirus.

  6. High-capacity hollow porous dummy molecular imprinted polymers using ionic liquid as functional monomer for selective recognition of salicylic acid.

    Science.gov (United States)

    Xiang, Haiyan; Peng, Mijun; Li, Hui; Peng, Sheng; Shi, Shuyun

    2017-01-30

    The existence of strong intramolecular hydrogen bond in salicylic acid (SA) weakens its intermolecular hydrogen bonding with functional monomer, then it is a challenge work to fabricate molecularly imprinted polymers (MIPs) for SA recognition with high capacity and good selectivity. Here, hollow porous dummy MIPs (HPDMIPs) were prepared using benzoic acid (BA) as dummy template, ionic liquid (i.e. 1-vinyl-3-methylimidazolium chloride) as functional monomer, and MCM-48 as sacrificial support. Factors that affected adsorption, such as type of template and porogen, mole ratio of template-functional monomer-cross-linker and type of binding solvent, were optimized in detail. Multiple strong interactions between SA and ionic liquid in HPDMIPs deduced higher binding capacity (29.75mg/g), imprinting factor (5.61) and selectivity than any previously reported MIPs by traditional or surface imprinting technology. The large surface area (543.9m 2 /g) with hollow porous structure resulted in faster kinetic binding (25min). The equilibrium data fitted well to Freundlich equation and the adsorption process could be described by pseudo-second order model. Finally, HPDMIPs were successfully applied to selectively extract and enrich SA from Actinidia chinensis with a relatively high recovery (84.6-94.5%). Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Role of DNA conformation & energetic insights in Msx-1-DNA recognition as revealed by molecular dynamics studies on specific and nonspecific complexes.

    Science.gov (United States)

    Kachhap, Sangita; Singh, Balvinder

    2015-01-01

    In most of homeodomain-DNA complexes, glutamine or lysine is present at 50th position and interacts with 5th and 6th nucleotide of core recognition region. Molecular dynamics simulations of Msx-1-DNA complex (Q50-TG) and its variant complexes, that is specific (Q50K-CC), nonspecific (Q50-CC) having mutation in DNA and (Q50K-TG) in protein, have been carried out. Analysis of protein-DNA interactions and structure of DNA in specific and nonspecific complexes show that amino acid residues use sequence-dependent shape of DNA to interact. The binding free energies of all four complexes were analysed to define role of amino acid residue at 50th position in terms of binding strength considering the variation in DNA on stability of protein-DNA complexes. The order of stability of protein-DNA complexes shows that specific complexes are more stable than nonspecific ones. Decomposition analysis shows that N-terminal amino acid residues have been found to contribute maximally in binding free energy of protein-DNA complexes. Among specific protein-DNA complexes, K50 contributes more as compared to Q50 towards binding free energy in respective complexes. The sequence dependence of local conformation of DNA enables Q50/Q50K to make hydrogen bond with nucleotide(s) of DNA. The changes in amino acid sequence of protein are accommodated and stabilized around TAAT core region of DNA having variation in nucleotides.

  8. Recognition and determination of bovine hemoglobin using a gold electrode modified with gold nanoparticles and molecularly imprinted self-polymerized dopamine

    International Nuclear Information System (INIS)

    Li, Lu; Fan, Limei; Dai, Yunlong; Kan, Xianwen

    2015-01-01

    A molecularly imprinted polymer (MIP) was prepared by self-polymerization of dopamine in the presence of bovine hemoglobin (BHb) and then deposited on the surface of an electrode modified with gold nanoparticles (AuNPs). Scanning electron microscopy, cyclic voltammetry, and differential pulse voltammetry were employed to characterize the modified electrode using the hexacyanoferrate redox system as an electroactive probe. The effects of BHb concentration, dopamine concentration, and polymerization time were optimized. Under optimized conditions, the modified electrode selectively recognizes BHb even in the presence of other proteins. The peak current for hexacyanoferrate, typically measured at + 0.17 V (vs. SCE), depends on the concentration of BHb in the 1.0 × 10 −11 to 1.0 × 10 −2 mg mL −1 range. Due to the ease of preparation and tight adherence of polydopamine to various support materials, the present strategy conceivably also provides a platform for the recognition and detection of other proteins. (author)

  9. In Vitro Selection of Single-Stranded DNA Molecular Recognition Elements against S. aureus Alpha Toxin and Sensitive Detection in Human Serum

    Directory of Open Access Journals (Sweden)

    Ka L. Hong

    2015-01-01

    Full Text Available Alpha toxin is one of the major virulence factors secreted by Staphylococcus aureus, a bacterium that is responsible for a wide variety of infections in both community and hospital settings. Due to the prevalence of S. aureus related infections and the emergence of methicillin-resistant S. aureus, rapid and accurate diagnosis of S. aureus infections is crucial in benefiting patient health outcomes. In this study, a rigorous Systematic Evolution of Ligands by Exponential Enrichment (SELEX variant previously developed by our laboratory was utilized to select a single-stranded DNA molecular recognition element (MRE targeting alpha toxin with high affinity and specificity. At the end of the 12-round selection, the selected MRE had an equilibrium dissociation constant (Kd of 93.7 ± 7.0 nM. Additionally, a modified sandwich enzyme-linked immunosorbent assay (ELISA was developed by using the selected ssDNA MRE as the toxin-capturing element and a sensitive detection of 200 nM alpha toxin in undiluted human serum samples was achieved.

  10. Molecular basis of IgE-recognition of Lol p 5, a major allergen of rye-grass pollen.

    Science.gov (United States)

    Suphioglu, C; Blaher, B; Rolland, J M; McCluskey, J; Schäppi, G; Kenrick, J; Singh, M B; Knox, R B

    1998-04-01

    Grass pollen, especially of rye-grass (Lolium perenne). represents an important cause of type I allergy. Identification of IgE-binding (allergenic) epitopes of major grass pollen allergens is essential for understanding the molecular basis of interaction between allergens and human IgE antibodies and therefore facilitates the devising of safer and more effective diagnostic and immunotherapy reagents. The aim of this study was to identify the allergenic epitopes of Lol p 5, a major allergen of rye-grass pollen, immunodissect these epitopes further so that the amino acid residues critical for antibody binding can be determined and investigate the conservation and nature of these epitopes within the context of the natural grass pollen allergens. Peptides, 12-13 amino acid residues long and overlapping each other by 4 amino acid residues, based on the entire deduced amino acid sequence of the coding region of Lol p 5, were synthesised and assayed for IgE-binding. Two strong IgE-binding epitopes (Lol p 5 (49-60) and (265-276), referred to as peptides 7 and 34, respectively) were identified. These epitopes were further resolved by truncated peptides and amino acid replacement studies and the amino acid residues critical for IgE-binding determined (Lol p 5 (49-60) residue Lys57 and (265-276) residue Lys275). Sequences of these epitopes were conserved in related allergens and may form the conserved allergenic domains responsible for the cross-reactivity observed between pollen allergens of taxonomically related grasses. Furthermore, due to its strong IgE-reactivity, synthetic peptide Lol p 5 (265-276) was used to affinity-purify specific IgE antibodies which recognised proteins of other clinically important grass pollens. further indicating presence of allergenic cross-reactivity at the level of allergenic epitope. Moreover, Lol p 5 (265 276) demonstrated a strong capacity to inhibit IgE-binding to natural rye-grass pollen proteins highlighting the antibody accessibility

  11. Adsorption characteristics, recognition properties, and preliminary application of nordihydroguaiaretic acid molecularly imprinted polymers prepared by sol–gel surface imprinting technology

    Energy Technology Data Exchange (ETDEWEB)

    Liao, Sen; Zhang, Wen; Long, Wei; Hou, Dan; Yang, Xuechun; Tan, Ni, E-mail: tannii@21cn.com

    2016-02-28

    Graphical abstract: - Highlights: • Nordihydroguaiaretic acid imprinted polymer with imprinting factor 2.12 was prepared for the first time through hydrogen bonding and hydrophobic interaction between the template molecules and the bifunctional monomers. • The obtained surface molecularly imprinting polymers exhibited high affinity and selectivity to the template molecules. • The prepared surface molecularly imprinted polymers were used in separation the natural active component nordihydroguaiaretic acid from medicinal plants. - Abstract: In this paper, a new core-shell composite of nordihydroguaiaretic acid (NDGA) molecularly imprinted polymers layer-coated silica gel (MIP@SiO{sub 2}) was prepared through sol–gel technique and applied as a material for extraction of NDGA from Ephedra. It was synthesized using NDGA as the template molecule, γ-aminopropyltriethoxysilane (APTS) and methyltriethoxysilane (MTEOS) as the functional monomers, tetraethyl orthosilicate (TEOS) as the cross-linker and ethanol as the porogenic solvent in the surface of silica. The non-imprinted polymers layer-coated silica gel (NIP@SiO{sub 2}) were prepared with the same procedure, but with the absence of template molecule. In addition, the optimum adsorption affinity occurred when the molar ratio of NDGA:APTS:MTEOS:TEOS was 1:6:2:80. The prepared MIP@SiO{sub 2} and NIP@SiO{sub 2} were analyzed by scanning electron microscopy (SEM), thermogravimetric analysis (TGA), and Fourier transform-infrared spectroscopy (FT-IR). Their affinity properties to NDGA were evaluated through dynamic adsorption, static adsorption, and selective recognition experiments, and the results showed the saturated adsorption capacity of MIP@SiO{sub 2} could reach to 5.90 mg g{sup −1}, which was two times more than that of NIP@SiO{sub 2}. High performance liquid chromatography (HPLC) was used to evaluate the extraction of NDGA from the medicinal plant ephedra by the above prepared materials, and the results

  12. Adsorption characteristics, recognition properties, and preliminary application of nordihydroguaiaretic acid molecularly imprinted polymers prepared by sol–gel surface imprinting technology

    International Nuclear Information System (INIS)

    Liao, Sen; Zhang, Wen; Long, Wei; Hou, Dan; Yang, Xuechun; Tan, Ni

    2016-01-01

    Graphical abstract: - Highlights: • Nordihydroguaiaretic acid imprinted polymer with imprinting factor 2.12 was prepared for the first time through hydrogen bonding and hydrophobic interaction between the template molecules and the bifunctional monomers. • The obtained surface molecularly imprinting polymers exhibited high affinity and selectivity to the template molecules. • The prepared surface molecularly imprinted polymers were used in separation the natural active component nordihydroguaiaretic acid from medicinal plants. - Abstract: In this paper, a new core-shell composite of nordihydroguaiaretic acid (NDGA) molecularly imprinted polymers layer-coated silica gel (MIP@SiO_2) was prepared through sol–gel technique and applied as a material for extraction of NDGA from Ephedra. It was synthesized using NDGA as the template molecule, γ-aminopropyltriethoxysilane (APTS) and methyltriethoxysilane (MTEOS) as the functional monomers, tetraethyl orthosilicate (TEOS) as the cross-linker and ethanol as the porogenic solvent in the surface of silica. The non-imprinted polymers layer-coated silica gel (NIP@SiO_2) were prepared with the same procedure, but with the absence of template molecule. In addition, the optimum adsorption affinity occurred when the molar ratio of NDGA:APTS:MTEOS:TEOS was 1:6:2:80. The prepared MIP@SiO_2 and NIP@SiO_2 were analyzed by scanning electron microscopy (SEM), thermogravimetric analysis (TGA), and Fourier transform-infrared spectroscopy (FT-IR). Their affinity properties to NDGA were evaluated through dynamic adsorption, static adsorption, and selective recognition experiments, and the results showed the saturated adsorption capacity of MIP@SiO_2 could reach to 5.90 mg g"−"1, which was two times more than that of NIP@SiO_2. High performance liquid chromatography (HPLC) was used to evaluate the extraction of NDGA from the medicinal plant ephedra by the above prepared materials, and the results indicated that the MIP@SiO_2 had

  13. Emotional arousal and recognition memory are differentially reflected in pupil diameter responses during emotional memory for negative events in younger and older adults.

    Science.gov (United States)

    Hämmerer, Dorothea; Hopkins, Alexandra; Betts, Matthew J; Maaß, Anne; Dolan, Ray J; Düzel, Emrah

    2017-10-01

    A better memory for negative emotional events is often attributed to a conjoint impact of increased arousal and noradrenergic modulation (NA). A decline in NA during aging is well documented but its impact on memory function during aging is unclear. Using pupil diameter (PD) as a proxy for NA, we examined age differences in memory for negative events in younger (18-30 years) and older (62-83 years) adults based on a segregation of early arousal to negative events, and later retrieval-related PD responses. In keeping with the hypothesis of reduced age-related NA influences, older adults showed attenuated induced PD responses to negative emotional events. The findings highlight a likely contribution of NA to negative emotional memory, mediated via arousal that may be compromised with aging. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Role of protein structure and the role of individual fingers in zinc finger protein-DNA recognition: a molecular dynamics simulation study and free energy calculations

    Science.gov (United States)

    Hamed, Mazen Y.

    2018-05-01

    Molecular dynamics and MM_GBSA energy calculations on various zinc finger proteins containing three and four fingers bound to their target DNA gave insights into the role of each finger in the DNA binding process as part of the protein structure. The wild type Zif 268 (PDB code: 1AAY) gave a ΔG value of - 76.1 (14) kcal/mol. Zinc fingers ZF1, ZF2 and ZF3 were mutated in one experiment and in another experiment one finger was cut and the rest of the protein was studied for binding. The ΔΔG values for the Zinc Finger protein with both ZF1 and ZF2 mutated was + 80 kcal/mol, while mutating only ZF1 the ΔΔG value was + 52 kcal/mol (relative to the wild type). Cutting ZF3 and studying the protein consisting only of ZF1 linked to ZF2 gave a ΔΔG value of + 68 kcal/mol. Upon cutting ZF1, the resulting ZF2 linked to ZF3 protein gave a ΔΔG value of + 41 kcal/mol. The above results shed light on the importance of each finger in the binding process, especially the role of ZF1 as the anchoring finger followed in importance by ZF2 and ZF3. The energy difference between the binding of the wild type protein Zif268 (1AAY) and that for individual finger binding to DNA according to the formula: ΔΔGlinkers, otherstructuralfactors = ΔGzif268 - (ΔGF1+F2+F3) gave a value = - 44.5 kcal/mol. This stabilization can be attributed to the contribution of linkers and other structural factors in the intact protein in the DNA binding process. DNA binding energies of variant proteins of the wild type Zif268 which differ in their ZF1 amino acid sequence gave evidence of a good relationship between binding energy and recognition and specificity, this finding confirms the reported vital role of ZF1 in the ZF protein scanning and anchoring to the target DNA sequence. The role of hydrogen bonds in both specific and nonspecific amino acid-DNA contacts is discussed in relation to mutations. The binding energies of variant Zinc Finger proteins confirmed the role of ZF1 in the recognition

  15. Speech Recognition

    Directory of Open Access Journals (Sweden)

    Adrian Morariu

    2009-01-01

    Full Text Available This paper presents a method of speech recognition by pattern recognition techniques. Learning consists in determining the unique characteristics of a word (cepstral coefficients by eliminating those characteristics that are different from one word to another. For learning and recognition, the system will build a dictionary of words by determining the characteristics of each word to be used in the recognition. Determining the characteristics of an audio signal consists in the following steps: noise removal, sampling it, applying Hamming window, switching to frequency domain through Fourier transform, calculating the magnitude spectrum, filtering data, determining cepstral coefficients.

  16. Adsorption characteristics, recognition properties, and preliminary application of nordihydroguaiaretic acid molecularly imprinted polymers prepared by sol-gel surface imprinting technology

    Science.gov (United States)

    Liao, Sen; Zhang, Wen; Long, Wei; Hou, Dan; Yang, Xuechun; Tan, Ni

    2016-02-01

    In this paper, a new core-shell composite of nordihydroguaiaretic acid (NDGA) molecularly imprinted polymers layer-coated silica gel (MIP@SiO2) was prepared through sol-gel technique and applied as a material for extraction of NDGA from Ephedra. It was synthesized using NDGA as the template molecule, γ-aminopropyltriethoxysilane (APTS) and methyltriethoxysilane (MTEOS) as the functional monomers, tetraethyl orthosilicate (TEOS) as the cross-linker and ethanol as the porogenic solvent in the surface of silica. The non-imprinted polymers layer-coated silica gel (NIP@SiO2) were prepared with the same procedure, but with the absence of template molecule. In addition, the optimum adsorption affinity occurred when the molar ratio of NDGA:APTS:MTEOS:TEOS was 1:6:2:80. The prepared MIP@SiO2 and NIP@SiO2 were analyzed by scanning electron microscopy (SEM), thermogravimetric analysis (TGA), and Fourier transform-infrared spectroscopy (FT-IR). Their affinity properties to NDGA were evaluated through dynamic adsorption, static adsorption, and selective recognition experiments, and the results showed the saturated adsorption capacity of MIP@SiO2 could reach to 5.90 mg g-1, which was two times more than that of NIP@SiO2. High performance liquid chromatography (HPLC) was used to evaluate the extraction of NDGA from the medicinal plant ephedra by the above prepared materials, and the results indicated that the MIP@SiO2 had potential application in separation of the natural active component NDGA from medicinal plants.

  17. The past and the future of Alzheimer’s disease CSF biomarkers – a journey towards validated biochemical tests covering the whole spectra of molecular events

    Directory of Open Access Journals (Sweden)

    Kaj eBlennow

    2015-09-01

    Full Text Available This paper gives a short review on cerebrospinal fluid (CSF biomarkers for Alzheimer’s disease (AD, from early developments to high-precision validated assays on fully automated lab analyzers. We also discuss developments on novel biomarkers, such as synaptic proteins and Aβ oligomers. Our vision for the future is that assaying a set of biomarkers in a single CSF tube can monitor the whole spectra of AD molecular pathogenic events. CSF biomarkers will have a central position not only for clinical diagnosis, but also for the understanding of the sequence of molecular events in the pathogenic process underlying AD and as tools to monitor the effects of novel drug candidates targeting these different mechanisms.

  18. Inherent dynamics of head domain correlates with ATP-recognition of P2X4 receptors: insights gained from molecular simulations.

    Directory of Open Access Journals (Sweden)

    Li-Dong Huang

    Full Text Available P2X receptors are ATP-gated ion channels involved in many physiological functions, and determination of ATP-recognition (AR of P2X receptors will promote the development of new therapeutic agents for pain, inflammation, bladder dysfunction and osteoporosis. Recent crystal structures of the zebrafish P2X4 (zfP2X4 receptor reveal a large ATP-binding pocket (ABP located at the subunit interface of zfP2X4 receptors, which is occupied by a conspicuous cluster of basic residues to recognize triphosphate moiety of ATP. Using the engineered affinity labeling and molecular modeling, at least three sites (S1, S2 and S3 within ABP have been identified that are able to recognize the adenine ring of ATP, implying the existence of at least three distinct AR modes in ABP. The open crystal structure of zfP2X4 confirms one of three AR modes (named AR1, in which the adenine ring of ATP is buried into site S1 while the triphosphate moiety interacts with clustered basic residues. Why architecture of ABP favors AR1 not the other two AR modes still remains unexplored. Here, we examine the potential role of inherent dynamics of head domain, a domain involved in ABP formation, in AR determinant of P2X4 receptors. In silico docking and binding free energy calculation revealed comparable characters of three distinct AR modes. Inherent dynamics of head domain, especially the downward motion favors the preference of ABP for AR1 rather than AR2 and AR3. Along with the downward motion of head domain, the closing movement of loop139-146 and loop169-183, and structural rearrangements of K70, K72, R298 and R143 enabled ABP to discriminate AR1 from other AR modes. Our observations suggest the essential role of head domain dynamics in determining AR of P2X4 receptors, allowing evaluation of new strategies aimed at developing specific blockers/allosteric modulators by preventing the dynamics of head domain associated with both AR and channel activation of P2X4 receptors.

  19. Corporate Policy Conferences and Events

    International Development Research Centre (IDRC) Digital Library (Canada)

    André Lavoie

    2015-10-15

    Oct 15, 2015 ... Hospitality as defined in the Corporate Hospitality Policy; ... awards and recognition ceremonies; social events and any other ... The Convenor is the person who initiates an event and takes responsibility for its conduct.

  20. FY1995 four-terminal-device intelligent LSI system for real-time event recognition; 1995 nendo shunji ninshiki kino wo motta 4 tanshi device chino LSI no kenkyu

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-03-01

    Development of an intelligent LSI system having real-time response capability for real-word events. This is accomplished by enhancing the functionality of an elemental device, employing ultra-fine-grain parallelism and merging software directly in the LSI hardware. Intelligent functions are created directly on the LSI hardware, thus enabling real-time recognition by electronic systems. The origin of human intelligence lies in the huge memory data base acquired through one's life and the very fast search mechanism to recall the 'most similar' event to the current input. Based on this principle components of intelligent LSI systems have been developed. An analog EEPROM technology capable of storing 256 levels of data per cell without time-consuming write/verify operations has been developed. In situ monitoring of memory content during writing has allowed us high-accuracy data writing. A high-speed parallel-search engine for the minimum distance vector (an associator) has been developed using neuron MOS technology. The associator has been applied to the motion vector detector as an example, which has shown a very fast detection with an extremely simple hardware configuration. The association architecture has been applied to a real-time motion picture compression system, demonstrating three orders of magnitude higher performance than typical CISC processors (Pentium 166MHz). (NEDO)

  1. FY1995 four-terminal-device intelligent LSI system for real-time event recognition; 1995 nendo shunji ninshiki kino wo motta 4 tanshi device chino LSI no kenkyu

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-03-01

    Development of an intelligent LSI system having real-time response capability for real-word events. This is accomplished by enhancing the functionality of an elemental device, employing ultra-fine-grain parallelism and merging software directly in the LSI hardware. Intelligent functions are created directly on the LSI hardware, thus enabling real-time recognition by electronic systems. The origin of human intelligence lies in the huge memory data base acquired through one's life and the very fast search mechanism to recall the 'most similar' event to the current input. Based on this principle components of intelligent LSI systems have been developed. An analog EEPROM technology capable of storing 256 levels of data per cell without time-consuming write/verify operations has been developed. In situ monitoring of memory content during writing has allowed us high-accuracy data writing. A high-speed parallel-search engine for the minimum distance vector (an associator) has been developed using neuron MOS technology. The associator has been applied to the motion vector detector as an example, which has shown a very fast detection with an extremely simple hardware configuration. The association architecture has been applied to a real-time motion picture compression system, demonstrating three orders of magnitude higher performance than typical CISC processors (Pentium 166MHz). (NEDO)

  2. Molecular Events Accompanying Rous Sarcoma Virus Rescue from Rodent Cells and the Role of Viral Gene Complementation

    Czech Academy of Sciences Publication Activity Database

    Lounková, Anna; Dráberová, Eduarda; Šenigl, Filip; Trejbalová, Kateřina; Geryk, Josef; Hejnar, Jiří; Svoboda, Jan

    2014-01-01

    Roč. 88, č. 6 (2014), s. 3505-3515 ISSN 0022-538X R&D Projects: GA ČR GAP502/11/2207; GA ČR GAP302/12/1673 Institutional support: RVO:68378050 Keywords : Rous sarcoma virus * heterotransmission * cell non-permissiveness Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.439, year: 2014

  3. Molecular events associated with increased regenerative capacity of the goldfish retinal ganglion cells following X-irradiation: decreased level of axonal growth inhibitors

    International Nuclear Information System (INIS)

    Rachailovich, I.; Schwartz, M.

    1984-01-01

    In our previous work we established conditions to study the contribution of non-neuronal cells to the process of goldfish optic nerve regeneration. This issue has been studied successfully by adapting the use of X-irradiation to manipulate division of non-neuronal cells associated with the injured nerve. The regenerative capacity of the goldfish retinal ganglion cells was determined subsequent to the X-ray treatment. The authors present an analysis of the molecular events associated with regeneration and enhanced regenerative capacity which follows X-irradiation. (Auth.)

  4. Molecular events associated with increased regenerative capacity of the goldfish retinal ganglion cells following X-irradiation: decreased level of axonal growth inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Rachailovich, I.; Schwartz, M. (Weizmann Inst. of Science, Rehovot (Israel). Dept. of Neurobiology)

    1984-07-23

    In our previous work we established conditions to study the contribution of non-neuronal cells to the process of goldfish optic nerve regeneration. This issue has been studied successfully by adapting the use of X-irradiation to manipulate division of non-neuronal cells associated with the injured nerve. The regenerative capacity of the goldfish retinal ganglion cells was determined subsequent to the X-ray treatment. The authors present an analysis of the molecular events associated with regeneration and enhanced regenerative capacity which follows X-irradiation.

  5. Speaker Recognition

    DEFF Research Database (Denmark)

    Mølgaard, Lasse Lohilahti; Jørgensen, Kasper Winther

    2005-01-01

    Speaker recognition is basically divided into speaker identification and speaker verification. Verification is the task of automatically determining if a person really is the person he or she claims to be. This technology can be used as a biometric feature for verifying the identity of a person...

  6. Evolution of Soybean mosaic virus-G7 molecularly cloned genome in Rsv1-genotype soybean results in emergence of a mutant capable of evading Rsv1-mediated recognition

    International Nuclear Information System (INIS)

    Hajimorad, M.R.; Eggenberger, A.L.; Hill, J.H.

    2003-01-01

    Plant resistance (R) genes direct recognition of pathogens harboring matching avirluent signals leading to activation of defense responses. It has long been hypothesized that under selection pressure the infidelity of RNA virus replication together with large population size and short generation times results in emergence of mutants capable of evading R-mediated recognition. In this study, the Rsv1/Soybean mosaic virus (SMV) pathosystem was used to investigate this hypothesis. In soybean line PI 96983 (Rsv1), the progeny of molecularly cloned SMV strain G7 (pSMV-G7) provokes a lethal systemic hypersensitive response (LSHR) with up regulation of a defense-associated gene transcript (PR-1). Serial passages of a large population of the progeny in PI 96983 resulted in emergence of a mutant population (vSMV-G7d), incapable of provoking either Rsv1-mediated LSHR or PR-1 protein gene transcript up regulation. An infectious clone of the mutant (pSMV-G7d) was synthesized whose sequences were very similar but not identical to the vSMV-G7d population; however, it displayed a similar phenotype. The genome of pSMV-G7d differs from parental pSMV-G7 by 17 substitutions, of which 10 are translationally silent. The seven amino acid substitutions in deduced sequences of pSMV-G7d differ from that of pSMV-G7 by one each in P1 proteinase, helper component-proteinase, and coat protein, respectively, and by four in P3. To the best of our knowledge, this is the first demonstration in which experimental evolution of a molecularly cloned plant RNA virus resulted in emergence of a mutant capable of evading an R-mediated recognition

  7. Study on pivot-point vibration of molecular bond-rupture events by quartz crystal microbalance for biomedical diagnostics.

    Science.gov (United States)

    Yuan, Yong J; Jia, Renjie

    2012-01-01

    Bond-rupture scanning for biomedical diagnostics is examined using quartz crystal microbalance (QCM) experiments and microparticle mechanics modeling calculations. Specific and nonspecific interactions between a microparticle and its binding QCM surface can be distinguished by gradually increasing the amplitude of driving voltage applied to QCM and monitoring its frequency changes. This research proposes a mechanical model of interactions between biological molecules and a QCM substrate surface. The mechanical force required to break a biotin-streptavidin bond was calculated through a one-pivot-point bottom-up vibration model. The bond-rupture force increases with an increase of the microparticle radius, the QCM resonant frequency, and the amplitude of driving voltage applied to the QCM. The significance of the research on biological molecular bond rupture is extremely important in characterizing microbial (such as cells and virus) specificity, due to the force magnitude needed to break bonds using a transducer.

  8. Molecular detection of a putatively novel cyprinid herpesvirus in sichel (Pelecus cultratus) during a mass mortality event in Hungary.

    Science.gov (United States)

    Doszpoly, Andor; Papp, Melitta; Deákné, Petra P; Glávits, Róbert; Ursu, Krisztina; Dán, Ádám

    2015-05-01

    In the early summer of 2014, mass mortality of sichel (Pelecus cultratus) was observed in Lake Balaton, Hungary. Histological examination revealed degenerative changes within the tubular epithelium, mainly in the distal tubules and collecting ducts in the kidneys and multifocal vacuolisation in the brain stem and cerebellum. Routine molecular investigations showed the presence of the DNA of an unknown alloherpesvirus in some specimens. Subsequently, three genes of the putative herpesviral genome (DNA polymerase, terminase, and helicase) were amplified and partially sequenced. A phylogenetic tree reconstruction based on the concatenated sequence of these three conserved genes implied that the virus belongs to the genus Cyprinivirus within the family Alloherpesviridae. The sequences of the sichel herpesvirus differ markedly from those of the cypriniviruses CyHV-1, CyHV-2 and CyHV-3, putatively representing a fifth species in the genus.

  9. A two-step recognition of signal sequences determines the translocation efficiency of proteins.

    OpenAIRE

    Belin, D; Bost, S; Vassalli, J D; Strub, K

    1996-01-01

    The cytosolic and secreted, N-glycosylated, forms of plasminogen activator inhibitor-2 (PAI-2) are generated by facultative translocation. To study the molecular events that result in the bi-topological distribution of proteins, we determined in vitro the capacities of several signal sequences to bind the signal recognition particle (SRP) during targeting, and to promote vectorial transport of murine PAI-2 (mPAI-2). Interestingly, the six signal sequences we compared (mPAI-2 and three mutated...

  10. Recommendations for Recognizing Video Events by Concept Vocabularies

    NARCIS (Netherlands)

    Habibian, A.; Snoek, C.G.M.

    2014-01-01

    Representing videos using vocabularies composed of concept detectors appears promising for generic event recognition. While many have recently shown the benefits of concept vocabularies for recognition, studying the characteristics of a universal concept vocabulary suited for representing events is

  11. Molecular composition of rainwater and aerosol during rain events in León, Spain, using high resolution mass spectrometry.

    Science.gov (United States)

    Fee, Anna

    2017-04-01

    Anna Fee (1), Markus Kalberer (1), Roberto Fraile (2), Amaya Castro (2), Ana. I. Calvo (2), Carlos Blanco-Alegre (2), Fernanda Oduber (2) and Mário Cerqueira (3). 1 Department of Chemistry, University of Cambridge, UK. 2 Department of Applied Chemistry and Physics, IMARENAB, University of León, Spain. 3 Department of Environmental Planning, University of Aveiro, Portugal. A wide range of atmospheric compounds which are present in rainwater are often also present in aerosol. They can be taken up during cloud droplet formation (in-cloud scavenging) or washed out during precipitation (below-cloud scavenging). Such compounds including aromatic hydrocarbons and organic nitrogen containing compounds are hazardous to health. In this study, the organic chemical composition of rainwater and aerosol from rain events in León, Spain, is being analysed using high resolution mass spectrometry. Collected rainwater along with high volume and low volume filters from rain events which occurred during spring, summer and winter of 2016 have been selected for analysis. Rainwater samples were prepared using Polymeric Reversed Phase Solid Phase Extraction (SPE) and filters have been extracted in water with and without SPE. Three different SPE polymer based sorbents were tested; one for extracting neutral compounds and two which are more suitable for extracting organic compounds containing sulphate and other polar functional groups. The sorbent for extracting neutral compounds was found to yield a higher number of compounds from the sample extraction than the other two varieties. Kendrick masses, Van Krevelen plots and carbon oxidation states have been investigated to identify compounds and patterns. Preliminary results show a predominance in peaks with O/C ratios between 0.2 and 0.7 and H/C ratios between 1 and 2 in both rain and aerosol samples which indicates substituted aromatic compounds. Cellulose material and fatty acids may also be present. The rain samples also have a

  12. Study on pivot-point vibration of molecular bond-rupture events by quartz crystal microbalance for biomedical diagnostics

    Directory of Open Access Journals (Sweden)

    Yuan YJ

    2012-01-01

    Full Text Available Yong J Yuan, Renjie JiaLaboratory of Biosensing and MicroMechatronics, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, People's Republic of ChinaAbstract: Bond-rupture scanning for biomedical diagnostics is examined using quartz crystal microbalance (QCM experiments and microparticle mechanics modeling calculations. Specific and nonspecific interactions between a microparticle and its binding QCM surface can be distinguished by gradually increasing the amplitude of driving voltage applied to QCM and monitoring its frequency changes. This research proposes a mechanical model of interactions between biological molecules and a QCM substrate surface. The mechanical force required to break a biotin–streptavidin bond was calculated through a one-pivot-point bottom-up vibration model. The bond-rupture force increases with an increase of the microparticle radius, the QCM resonant frequency, and the amplitude of driving voltage applied to the QCM. The significance of the research on biological molecular bond rupture is extremely important in characterizing microbial (such as cells and virus specificity, due to the force magnitude needed to break bonds using a transducer.Keywords: bond rupture, mechanical force, biomolecular binding energy spectra, quartz crystal microbalance (QCM

  13. Meta-analysis of cancer transcriptomes: A new approach to uncover molecular pathological events in different cancer tissues

    Directory of Open Access Journals (Sweden)

    Sundus Iqbal

    2014-03-01

    Full Text Available To explore secrets of metastatic cancers, individual expression of true sets of respective genes must spread across the tissue. In this study, meta-analysis for transcriptional profiles of oncogenes was carried out to hunt critical genes or networks helping in metastasizing cancers. For this, transcriptomic analysis of different cancerous tissues causing leukemia, lung, liver, spleen, colorectal, colon, breast, bladder, and kidney cancers was performed by extracting microarray expression data from online resource; Gene Expression Omnibus. A newly developed bioinformatics technique; Dynamic Impact Approach (DIA was applied for enrichment analysis of transcriptional profiles using Database for Annotation Visualization and Integrated Discovery (DAVID. Furthermore, oPOSSUM (v. 2.0 and Cytoscape (v. 2.8.2 were used for in-depth analysis of transcription factors and regulatory gene networks respectively. DAVID analysis uncovered the most significantly enriched pathways in molecular functions that were 'Ubiquitin thiolesterase activity' up regulated in blood, breast, bladder, colorectal, lung, spleen, prostrate cancer. 'Transforming growth factor beta receptor activity' was inhibited in all cancers except leukemia, colon and liver cancer. oPOSSUM further revealed highly over-represented Transcription Factors (TFs; Broad-complex_3, Broad-complex_4, and Foxd3 except for leukemia and bladder cancer. From these findings, it is possible to target genes and networks, play a crucial role in the development of cancer. In the future, these transcription factors can serve as potential candidates for the therapeutic drug targets which can impede the deadly spread.

  14. Interrogating the Molecular Basis for Substrate Recognition in Serotonin and Dopamine Transporters with High-Affinity Substrate-Based Bivalent Ligands

    DEFF Research Database (Denmark)

    Andersen, Jacob; Ladefoged, Lucy Kate; Kristensen, Trine N. Bjerre

    2016-01-01

    insight into substrate recognition in SERT and DAT. An optimized bivalent ligand comprising two serotonin moieties binds SERT with 3,800-fold increased affinity compared to that of serotonin, suggesting that the human transporters have two distinct substrate binding sites. We show that the bivalent...... ligands are inhibitors of SERT and an experimentally validated docking model suggests that the bivalent compounds bind with one substrate moiety in the central binding site (the S1 site), whereas the other substrate moiety binds in a distinct binding site (the S2 site). A systematic study of nonconserved...

  15. Molecular evolution of glutamine synthetase II: Phylogenetic evidence of a non-endosymbiotic gene transfer event early in plant evolution

    Directory of Open Access Journals (Sweden)

    Tartar Aurélien

    2010-06-01

    Full Text Available Abstract Background Glutamine synthetase (GS is essential for ammonium assimilation and the biosynthesis of glutamine. The three GS gene families (GSI, GSII, and GSIII are represented in both prokaryotic and eukaryotic organisms. In this study, we examined the evolutionary relationship of GSII from eubacterial and eukaryotic lineages and present robust phylogenetic evidence that GSII was transferred from γ-Proteobacteria (Eubacteria to the Chloroplastida. Results GSII sequences were isolated from four species of green algae (Trebouxiophyceae, and additional green algal (Chlorophyceae and Prasinophytae and streptophyte (Charales, Desmidiales, Bryophyta, Marchantiophyta, Lycopodiophyta and Tracheophyta sequences were obtained from public databases. In Bayesian and maximum likelihood analyses, eubacterial (GSIIB and eukaryotic (GSIIE GSII sequences formed distinct clades. Both GSIIB and GSIIE were found in chlorophytes and early-diverging streptophytes. The GSIIB enzymes from these groups formed a well-supported sister clade with the γ-Proteobacteria, providing evidence that GSIIB in the Chloroplastida arose by horizontal gene transfer (HGT. Bayesian relaxed molecular clock analyses suggest that GSIIB and GSIIE coexisted for an extended period of time but it is unclear whether the proposed HGT happened prior to or after the divergence of the primary endosymbiotic lineages (the Archaeplastida. However, GSIIB genes have not been identified in glaucophytes or red algae, favoring the hypothesis that GSIIB was gained after the divergence of the primary endosymbiotic lineages. Duplicate copies of the GSIIB gene were present in Chlamydomonas reinhardtii, Volvox carteri f. nagariensis, and Physcomitrella patens. Both GSIIB proteins in C. reinhardtii and V. carteri f. nagariensis had N-terminal transit sequences, indicating they are targeted to the chloroplast or mitochondrion. In contrast, GSIIB proteins of P. patens lacked transit sequences, suggesting

  16. Sleep Enhances Explicit Recollection in Recognition Memory

    Science.gov (United States)

    Drosopoulos, Spyridon; Wagner, Ullrich; Born, Jan

    2005-01-01

    Recognition memory is considered to be supported by two different memory processes, i.e., the explicit recollection of information about a previous event and an implicit process of recognition based on a contextual sense of familiarity. Both types of memory supposedly rely on distinct memory systems. Sleep is known to enhance the consolidation of…

  17. Output Interference in Recognition Memory

    Science.gov (United States)

    Criss, Amy H.; Malmberg, Kenneth J.; Shiffrin, Richard M.

    2011-01-01

    Dennis and Humphreys (2001) proposed that interference in recognition memory arises solely from the prior contexts of the test word: Interference does not arise from memory traces of other words (from events prior to the study list or on the study list, and regardless of similarity to the test item). We evaluate this model using output…

  18. Surface molecular imprinting onto fluorescein-coated magnetic nanoparticlesvia reversible addition fragmentation chain transfer polymerization: A facile three-in-one system for recognition and separation of endocrine disrupting chemicals

    Science.gov (United States)

    Li, Ying; Dong, Cunku; Chu, Jia; Qi, Jingyao; Li, Xin

    2011-01-01

    In this study, we present a general protocol for the making of surface-imprinted magnetic fluorescence beads viareversible addition-fragmentation chain transfer polymerization. The resulting composites were characterized by X-ray diffraction analysis, transmission electron microscopy, scanning electron microscopy, fluorescence spectroscopy, Fourier transform infrared spectroscopy, and energy dispersive spectroscopy. The as-synthesized beads exhibited homogeneous polymer films (thickness of about 5.7 nm), spherical shape, high fluorescence intensity and magnetic property (Magnetization (Ms) = 3.67 emu g-1). The hybrids bind the original template 17β-estradiol with an appreciable selectivity over structurally related compounds. In addition, the resulting hybrids performed without obvious deterioration after five repeated cycles. This study therefore demonstrates the potential of molecularly imprinted polymers for the recognition and separation of endocrine disrupting chemicals.In this study, we present a general protocol for the making of surface-imprinted magnetic fluorescence beads viareversible addition-fragmentation chain transfer polymerization. The resulting composites were characterized by X-ray diffraction analysis, transmission electron microscopy, scanning electron microscopy, fluorescence spectroscopy, Fourier transform infrared spectroscopy, and energy dispersive spectroscopy. The as-synthesized beads exhibited homogeneous polymer films (thickness of about 5.7 nm), spherical shape, high fluorescence intensity and magnetic property (Magnetization (Ms) = 3.67 emu g-1). The hybrids bind the original template 17β-estradiol with an appreciable selectivity over structurally related compounds. In addition, the resulting hybrids performed without obvious deterioration after five repeated cycles. This study therefore demonstrates the potential of molecularly imprinted polymers for the recognition and separation of endocrine disrupting chemicals. Electronic

  19. Molecular initiating events of the intersex phenotype: Low-dose exposure to 17α-ethinylestradiol rapidly regulates molecular networks associated with gonad differentiation in the adult fathead minnow testis

    International Nuclear Information System (INIS)

    Feswick, April; Loughery, Jennifer R.; Isaacs, Meghan A.; Munkittrick, Kelly R.; Martyniuk, Christopher J.

    2016-01-01

    Highlights: • Male fathead minnow were exposed to 17alpha ethinylestradiol (EE2). • Both 11-ketotestosterone and testosterone production was decreased relative to controls. • A gene network associated with doublesex and mab-3 related transcription factor 1 were suppressed. • Genes involved in granulosa cell development were increased and sensitive to EE2 exposure. • Molecular initiating events that may be related to the intersex condition were identified. - Abstract: Intersex, or the presence of oocytes in the testes, has been documented in fish following exposure to wastewater effluent and estrogenic compounds. However, the molecular networks underlying the intersex condition are not completely known. To address this, we exposed male fathead minnows to a low, environmentally-relevant concentration of 17alpha-ethinylestradiol (EE2) (15 ng/L) and measured the transcriptome response in the testis after 96 h to identify early molecular initiating events that may proceed the intersex condition. The short-term exposure to EE2 did not affect gonadosomatic index and proportion of gametes within the testes. However, the production of 11-ketotestosterone and testosterone from the testis in vitro was decreased relative to controls. Expression profiling using a 8 × 60 K fathead minnow microarray identified 10 transcripts that were differentially expressed in the testes, the most dramatic change being that of coagulation factor XIII A chain (20-fold increase). Transcripts that included guanine nucleotide binding protein (Beta Polypeptide 2), peroxisome proliferator-activated receptor delta, and WNK lysine deficient protein kinase 1a, were down-regulated by EE2. Subnetwork enrichment analysis revealed that EE2 suppressed transcriptional networks associated with steroid metabolism, hormone biosynthesis, and sperm mobility. Most interesting was that gene networks associated with doublesex and mab-3 related transcription factor 1 (dmrt1) were suppressed in the adult

  20. Molecular initiating events of the intersex phenotype: Low-dose exposure to 17α-ethinylestradiol rapidly regulates molecular networks associated with gonad differentiation in the adult fathead minnow testis

    Energy Technology Data Exchange (ETDEWEB)

    Feswick, April; Loughery, Jennifer R.; Isaacs, Meghan A.; Munkittrick, Kelly R.; Martyniuk, Christopher J., E-mail: cmartyni@yahoo.ca

    2016-12-15

    Highlights: • Male fathead minnow were exposed to 17alpha ethinylestradiol (EE2). • Both 11-ketotestosterone and testosterone production was decreased relative to controls. • A gene network associated with doublesex and mab-3 related transcription factor 1 were suppressed. • Genes involved in granulosa cell development were increased and sensitive to EE2 exposure. • Molecular initiating events that may be related to the intersex condition were identified. - Abstract: Intersex, or the presence of oocytes in the testes, has been documented in fish following exposure to wastewater effluent and estrogenic compounds. However, the molecular networks underlying the intersex condition are not completely known. To address this, we exposed male fathead minnows to a low, environmentally-relevant concentration of 17alpha-ethinylestradiol (EE2) (15 ng/L) and measured the transcriptome response in the testis after 96 h to identify early molecular initiating events that may proceed the intersex condition. The short-term exposure to EE2 did not affect gonadosomatic index and proportion of gametes within the testes. However, the production of 11-ketotestosterone and testosterone from the testis in vitro was decreased relative to controls. Expression profiling using a 8 × 60 K fathead minnow microarray identified 10 transcripts that were differentially expressed in the testes, the most dramatic change being that of coagulation factor XIII A chain (20-fold increase). Transcripts that included guanine nucleotide binding protein (Beta Polypeptide 2), peroxisome proliferator-activated receptor delta, and WNK lysine deficient protein kinase 1a, were down-regulated by EE2. Subnetwork enrichment analysis revealed that EE2 suppressed transcriptional networks associated with steroid metabolism, hormone biosynthesis, and sperm mobility. Most interesting was that gene networks associated with doublesex and mab-3 related transcription factor 1 (dmrt1) were suppressed in the adult

  1. A 9-vinyladenine-based molecularly imprinted polymeric membrane for the efficient recognition of plant hormone 1H-indole-3-acetic acid

    International Nuclear Information System (INIS)

    Chen Changbao; Chen Yanjun; Zhou Jie; Wu Chunhui

    2006-01-01

    9-Vinyladenine was synthesized as a novel functional monomer for molecular imprinting techniques and its structure was established with elemental analysis and 1 H NMR spectroscopy. The binding mechanism between this functional monomer 9-vinyladenine and the plant hormone 1 H-indole-3-acetic acid in acetonitrile was studied with UV-vis spectrophotometry. Based on this study, using 1 H-indole-3-acetic acid as a template molecule, a specific 9-vinyladenine-based molecularly imprinted polymeric membrane was prepared. Then, the resultant polymeric membrane morphologies were visualized with scanning electron microscopy, and the membrane permselectivity for 1 H-indole-3-acetic acid, 1 H-indole-3-butyric acid and kinetin was tested with separate experiments and competitive diffusion experiments. These results showed that the imprinted polymeric membrane prepared with 9-vinyladenine exhibited higher transport selectivity for the template molecule 1 H-indole-3-acetic acid than 1 H-indole-3-butyric acid or kinetin. The membrane prepared with 9-vinyladenine also took on higher permselectivity for 1 H-indole-3-acetic acid in comparison with the imprinted membrane made with methacrylic acid. It is predicted that the 9-vinyladenine-based molecularly imprinted membrane may be applicable to the assay of 1 H-indole-3-acetic acid or for the preparation of a molecularly imprinted polymer sensor for the analysis of 1 H-indole-3-acetic acid in plant samples

  2. Recognition tunneling

    Czech Academy of Sciences Publication Activity Database

    Lindsay, S.; He, J.; Sankey, O.; Hapala, Prokop; Jelínek, Pavel; Zhang, P.; Chang, S.; Huang, S.

    2010-01-01

    Roč. 21, č. 26 (2010), 262001/1-262001/12 ISSN 0957-4484 R&D Projects: GA ČR GA202/09/0545 Institutional research plan: CEZ:AV0Z10100521 Keywords : STM * tunneling current * molecular electronics * DFT calculations Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.644, year: 2010

  3. Voice congruency facilitates word recognition.

    Directory of Open Access Journals (Sweden)

    Sandra Campeanu

    Full Text Available Behavioral studies of spoken word memory have shown that context congruency facilitates both word and source recognition, though the level at which context exerts its influence remains equivocal. We measured event-related potentials (ERPs while participants performed both types of recognition task with words spoken in four voices. Two voice parameters (i.e., gender and accent varied between speakers, with the possibility that none, one or two of these parameters was congruent between study and test. Results indicated that reinstating the study voice at test facilitated both word and source recognition, compared to similar or no context congruency at test. Behavioral effects were paralleled by two ERP modulations. First, in the word recognition test, the left parietal old/new effect showed a positive deflection reflective of context congruency between study and test words. Namely, the same speaker condition provided the most positive deflection of all correctly identified old words. In the source recognition test, a right frontal positivity was found for the same speaker condition compared to the different speaker conditions, regardless of response success. Taken together, the results of this study suggest that the benefit of context congruency is reflected behaviorally and in ERP modulations traditionally associated with recognition memory.

  4. Voice congruency facilitates word recognition.

    Science.gov (United States)

    Campeanu, Sandra; Craik, Fergus I M; Alain, Claude

    2013-01-01

    Behavioral studies of spoken word memory have shown that context congruency facilitates both word and source recognition, though the level at which context exerts its influence remains equivocal. We measured event-related potentials (ERPs) while participants performed both types of recognition task with words spoken in four voices. Two voice parameters (i.e., gender and accent) varied between speakers, with the possibility that none, one or two of these parameters was congruent between study and test. Results indicated that reinstating the study voice at test facilitated both word and source recognition, compared to similar or no context congruency at test. Behavioral effects were paralleled by two ERP modulations. First, in the word recognition test, the left parietal old/new effect showed a positive deflection reflective of context congruency between study and test words. Namely, the same speaker condition provided the most positive deflection of all correctly identified old words. In the source recognition test, a right frontal positivity was found for the same speaker condition compared to the different speaker conditions, regardless of response success. Taken together, the results of this study suggest that the benefit of context congruency is reflected behaviorally and in ERP modulations traditionally associated with recognition memory.

  5. Molecular Recognition of Human Papilloma Virus (HPV Using Proprietary PCR Method Based on L1 Gene and the Evaluation of its Frequency in Tissue Samples from Patients with Cervical Cancer

    Directory of Open Access Journals (Sweden)

    Roohollah Dorostkar

    2015-06-01

    Full Text Available Abstract Background: In 1970, human papillomavirus (HPV was introduced as the main etiologic factor of cervical carcinoma. Since there is no possibility of detecting the virus and its subtypes using serological methods and cell culture, the molecular methods such as PCR have particular importance in accurate, early and definite diagnosis of the virus. So, in this research, our goal is to use a proprietary PCR assay based on L1 gene of human papillomavirus for molecular recognition of HPV and to evaluate its prevalence in patient samples. Materials and Methods: In this experimental study, after collecting of samples from malignant cervical lesions, the viral DNA was extracted from paraffin blocks of 50 clinical samples and PCR was done by specific primers for L1 gene of human papillomavirus in all samples. After the analysis of PCR products by 2% agarose gel electrophoresis, sensitivity and specificity of the test were also evaluated. Results: Among 50 patient samples, 33 cases were confirmed to be positive for HPV infection and 17 cases were negative, showing high frequency of HPV in this patient population (about 66%. The results of specificity assay were positive for papilloma samples and sensitivity of the assay was 20 copies of recombinant construct containing L1 per reaction. Conclusion: This study showed that PCR by specific primers for L1 gene of human papilloma virus is a proper and accurate method for detection of this virus and the results confirm the previous reports of correlation between HPV and cervical carcinoma.

  6. An overview of techniques for linking high-dimensional molecular data to time-to-event endpoints by risk prediction models.

    Science.gov (United States)

    Binder, Harald; Porzelius, Christine; Schumacher, Martin

    2011-03-01

    Analysis of molecular data promises identification of biomarkers for improving prognostic models, thus potentially enabling better patient management. For identifying such biomarkers, risk prediction models can be employed that link high-dimensional molecular covariate data to a clinical endpoint. In low-dimensional settings, a multitude of statistical techniques already exists for building such models, e.g. allowing for variable selection or for quantifying the added value of a new biomarker. We provide an overview of techniques for regularized estimation that transfer this toward high-dimensional settings, with a focus on models for time-to-event endpoints. Techniques for incorporating specific covariate structure are discussed, as well as techniques for dealing with more complex endpoints. Employing gene expression data from patients with diffuse large B-cell lymphoma, some typical modeling issues from low-dimensional settings are illustrated in a high-dimensional application. First, the performance of classical stepwise regression is compared to stage-wise regression, as implemented by a component-wise likelihood-based boosting approach. A second issues arises, when artificially transforming the response into a binary variable. The effects of the resulting loss of efficiency and potential bias in a high-dimensional setting are illustrated, and a link to competing risks models is provided. Finally, we discuss conditions for adequately quantifying the added value of high-dimensional gene expression measurements, both at the stage of model fitting and when performing evaluation. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Comparative mRNA and microRNA expression profiling of three genitourinary cancers reveals common hallmarks and cancer-specific molecular events.

    Directory of Open Access Journals (Sweden)

    Xianxin Li

    Full Text Available Genome-wide gene expression profile using deep sequencing technologies can drive the discovery of cancer biomarkers and therapeutic targets. Such efforts are often limited to profiling the expression signature of either mRNA or microRNA (miRNA in a single type of cancer.Here we provided an integrated analysis of the genome-wide mRNA and miRNA expression profiles of three different genitourinary cancers: carcinomas of the bladder, kidney and testis.Our results highlight the general or cancer-specific roles of several genes and miRNAs that may serve as candidate oncogenes or suppressors of tumor development. Further comparative analyses at the systems level revealed that significant aberrations of the cell adhesion process, p53 signaling, calcium signaling, the ECM-receptor and cell cycle pathways, the DNA repair and replication processes and the immune and inflammatory response processes were the common hallmarks of human cancers. Gene sets showing testicular cancer-specific deregulation patterns were mainly implicated in processes related to male reproductive function, and general disruptions of multiple metabolic pathways and processes related to cell migration were the characteristic molecular events for renal and bladder cancer, respectively. Furthermore, we also demonstrated that tumors with the same histological origins and genes with similar functions tended to group together in a clustering analysis. By assessing the correlation between the expression of each miRNA and its targets, we determined that deregulation of 'key' miRNAs may result in the global aberration of one or more pathways or processes as a whole.This systematic analysis deciphered the molecular phenotypes of three genitourinary cancers and investigated their variations at the miRNA level simultaneously. Our results provided a valuable source for future studies and highlighted some promising genes, miRNAs, pathways and processes that may be useful for diagnostic or

  8. Chiral recognition of proteins having L-histidine residues on the surface with lanthanide ion complex incorporated-molecularly imprinted fluorescent nanoparticles

    International Nuclear Information System (INIS)

    Uzun, Lokman; Uzek, Recep; Şenel, Serap; Say, Ridvan; Denizli, Adil

    2013-01-01

    In this study, lanthanide ion complex incorporated molecularly imprinted fluorescent nanoparticles were synthesized. A combination of three novel approaches was applied for the purpose. First, lanthanide ions [Terbium(III)] were complexed with N-methacryloyl-L-histidine (MAH), polymerizable derivative of L-histidine amino acid, in order to incorporate the complex directly into the polymeric backbone. At the second stage, L-histidine molecules imprinted nanoparticles were utilized instead of whole protein imprinting in order to avoid whole drawbacks such as fragility, complexity, denaturation tendency, and conformation dependency. At the third stage following the first two steps mentioned above, imprinted L-histidine was coordinated with cupric ions [Cu(II)] to conduct the study under mild conditions. Then, molecularly imprinted fluorescent nanoparticles synthesized were used for L-histidine adsorption from aqueous solution to optimize conditions for adsorption and fluorimetric detection. Finally, usability of nanoparticles was investigated for chiral biorecognition using stereoisomer, D-histidine, racemic mixture, D,L-histidine, proteins with surface L-histidine residue, lysozyme, cytochrome C, or without ribonuclease A. The results revealed that the proposed polymerization strategy could make significant contribution to the solution of chronic problems of fluorescent component introduction into polymers. Additionally, the fluorescent nanoparticles reported here could be used for selective separation and fluorescent monitoring purposes. Highlights: • Lanthanide ion complex incorporated molecularly imprinted fluorescent nanoparticles • Direct incorporation of the fluorescent complex into polymeric backbone. • Imprinting by assistance of cupric ion coordination into nanoparticles • Evaluation of the chiral biorecognition ability of nanoparticles • Simultaneous selective separation and fluorescent monitoring

  9. Chiral recognition of proteins having L-histidine residues on the surface with lanthanide ion complex incorporated-molecularly imprinted fluorescent nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Uzun, Lokman, E-mail: lokman@hacettepe.edu.tr [Hacettepe University, Department of Chemistry, 06381, Ankara (Turkey); Uzek, Recep; Şenel, Serap [Hacettepe University, Department of Chemistry, 06381, Ankara (Turkey); Say, Ridvan [Anadolu University, Department of Chemistry, 26470, Eskisehir (Turkey); Denizli, Adil [Hacettepe University, Department of Chemistry, 06381, Ankara (Turkey)

    2013-08-01

    In this study, lanthanide ion complex incorporated molecularly imprinted fluorescent nanoparticles were synthesized. A combination of three novel approaches was applied for the purpose. First, lanthanide ions [Terbium(III)] were complexed with N-methacryloyl-L-histidine (MAH), polymerizable derivative of L-histidine amino acid, in order to incorporate the complex directly into the polymeric backbone. At the second stage, L-histidine molecules imprinted nanoparticles were utilized instead of whole protein imprinting in order to avoid whole drawbacks such as fragility, complexity, denaturation tendency, and conformation dependency. At the third stage following the first two steps mentioned above, imprinted L-histidine was coordinated with cupric ions [Cu(II)] to conduct the study under mild conditions. Then, molecularly imprinted fluorescent nanoparticles synthesized were used for L-histidine adsorption from aqueous solution to optimize conditions for adsorption and fluorimetric detection. Finally, usability of nanoparticles was investigated for chiral biorecognition using stereoisomer, D-histidine, racemic mixture, D,L-histidine, proteins with surface L-histidine residue, lysozyme, cytochrome C, or without ribonuclease A. The results revealed that the proposed polymerization strategy could make significant contribution to the solution of chronic problems of fluorescent component introduction into polymers. Additionally, the fluorescent nanoparticles reported here could be used for selective separation and fluorescent monitoring purposes. Highlights: • Lanthanide ion complex incorporated molecularly imprinted fluorescent nanoparticles • Direct incorporation of the fluorescent complex into polymeric backbone. • Imprinting by assistance of cupric ion coordination into nanoparticles • Evaluation of the chiral biorecognition ability of nanoparticles • Simultaneous selective separation and fluorescent monitoring.

  10. Madagascar sheds new light on the molecular systematics and biogeography of grammitid ferns: New unexpected lineages and numerous long-distance dispersal events.

    Science.gov (United States)

    Bauret, Lucie; Gaudeul, Myriam; Sundue, Michael A; Parris, Barbara S; Ranker, Tom A; Rakotondrainibe, France; Hennequin, Sabine; Ranaivo, Jaona; Selosse, Marc-André; Rouhan, Germinal

    2017-06-01

    Based on a worldwide phylogenetic framework filling the taxonomic gap of Madagascar and surrounding islands of the Western Indian Ocean (WIO), we revisited the systematics of grammitid fern species (Polypodiaceae). We also investigated the biogeographic origin of the extant diversity in Madagascar and estimated the relative influence of vicariance, long-distance dispersals (LDD) and in situ diversification. Phylogenetic inferences were based on five plastid DNA regions (atpB, rbcL, rps4-trnS, trnG-trnR, trnL-trnF) and the most comprehensive taxonomic sampling ever assembled (224 species belonging to 31 out of 33 recognized grammitids genera). 31 species from Madagascar were included representing 87% of the described diversity and 77% of the endemics. Our results confirmed a Paleotropical clade nested within an amphi-Atlantic grade. In addition, we identified three new major clades involving species currently belonging to Grammitis s.l., Ctenopterella and Enterosora. We resolved for the first time Grammitis s.s. as monophyletic, and Ctenopterella (newly tested here) and Enterosora as polyphyletic. The Neotropical genus Moranopteris was shown to also occur in Madagascar through a newly discovered species. Most importantly, we suggest a >30% inflation of the species number in the WIO due to the hidden diversity in >10 cryptic lineages, best explained by high morphological homoplasy. Molecular dating and ancestral areas reconstruction allowed identifying the Neotropics as the predominant source of LDD to the African-WIO region, with at least 12 colonization events within the last 20Ma. Repeated eastward migrations may be explained by transoceanic westerly winds transporting the dust-like spores. Tropical Asia s.l. would also have played a (minor) role through one dispersal event to Madagascar at the end of the Oligocene. Last, within the complex Malagasy region made of a mosaic of continental and oceanic islands located close to the African continent, we showed that

  11. Pattern Recognition

    Directory of Open Access Journals (Sweden)

    Aleš Procházka

    2018-05-01

    Full Text Available Multimodal signal analysis based on sophisticated sensors, efficient communicationsystems and fast parallel processing methods has a rapidly increasing range of multidisciplinaryapplications. The present paper is devoted to pattern recognition, machine learning, and the analysisof sleep stages in the detection of sleep disorders using polysomnography (PSG data, includingelectroencephalography (EEG, breathing (Flow, and electro-oculogram (EOG signals. The proposedmethod is based on the classification of selected features by a neural network system with sigmoidaland softmax transfer functions using Bayesian methods for the evaluation of the probabilities of theseparate classes. The application is devoted to the analysis of the sleep stages of 184 individualswith different diagnoses, using EEG and further PSG signals. Data analysis points to an averageincrease of the length of the Wake stage by 2.7% per 10 years and a decrease of the length of theRapid Eye Movement (REM stages by 0.8% per 10 years. The mean classification accuracy for givensets of records and single EEG and multimodal features is 88.7% ( standard deviation, STD: 2.1 and89.6% (STD:1.9, respectively. The proposed methods enable the use of adaptive learning processesfor the detection and classification of health disorders based on prior specialist experience andman–machine interaction.

  12. Synthesis of molecularly imprinted silica nanospheres embedded mercaptosuccinic acid-coated CdTe quantum dots for selective recognition of λ-cyhalothrin

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Xiao [School of Material Science and Engineering, Jiangsu University, Zhenjiang 212013 (China); School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013 (China); Meng, Minjia; Song, Zhilong; Gao, Lin; Li, Hongji [School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013 (China); Dai, Jiangdong; Zhou, Zhiping [School of Material Science and Engineering, Jiangsu University, Zhenjiang 212013 (China); Li, Chunxiang, E-mail: weixiaokeyan@163.com [School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013 (China); Pan, Jianming; Yu, Ping; Yan, Yongsheng [School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013 (China)

    2014-09-15

    In this study, a simple procedure for the determination of λ-cyhalothrin was reported. CdTe quantum dots (QDs) capped by molecularly imprinted polymers (MIPs) were prepared and characterized by spectrofluorometer, Fourier transform infrared spectroscopy (FTIR), transmission electron microscope (TEM) and scanning electron microscope (SEM). Mercaptosuccinic acid (MSA) was chosen as a stabilizer for CdTe QDs synthesis. The MSA stabilizer which comprises both thioglycolic acid (TGA)-like and 3-mercaptopropionic acid (MPA)-like moieties could accelerate the whole growth process of CdTe QDs comparing with TGA-like or MPA-like stabilizer. Meanwhile, the spectrofluorometer was used to evaluate the optical stability, effect of pH, and selective and sensitive determination of λ-cyhalothrin (LC). Moreover, LC could quench the fluorescence of the molecularly imprinted silica nanospheres (CdTe@SiO{sub 2}@MIPs) in a concentration-dependent manner, which was best described by a Stern–Volmer-type equation. - Highlights: • We choose Mercaptosuccinic acid (MSA) as the stabilizer for CdTe QDs synthesis. • The composite materials were prepared by the reverse microemulsion method. • The composite materials can be used for the direct analysis of relevant real samples.

  13. Factors affecting nucleolytic efficiency of some ternary metal complexes with DNA binding and recognition domains. Crystal and molecular structure of Zn(phen)(edda).

    Science.gov (United States)

    Seng, Hoi-Ling; Ong, Han-Kiat Alan; Rahman, Raja Noor Zaliha Raja Abd; Yamin, Bohari M; Tiekink, Edward R T; Tan, Kong Wai; Maah, Mohd Jamil; Caracelli, Ignez; Ng, Chew Hee

    2008-11-01

    The binding selectivity of the M(phen)(edda) (M=Cu, Co, Ni, Zn; phen=1,10-phenanthroline, edda=ethylenediaminediacetic acid) complexes towards ds(CG)(6), ds(AT)(6) and ds(CGCGAATTCGCG) B-form oligonucleotide duplexes were studied by CD spectroscopy and molecular modeling. The binding mode is intercalation and there is selectivity towards AT-sequence and stacking preference for A/A parallel or diagonal adjacent base steps in their intercalation. The nucleolytic properties of these complexes were investigated and the factors affecting the extent of cleavage were determined to be: concentration of complex, the nature of metal(II) ion, type of buffer, pH of buffer, incubation time, incubation temperature, and the presence of hydrogen peroxide or ascorbic acid as exogenous reagents. The fluorescence property of these complexes and its origin were also investigated. The crystal structure of the Zn(phen)(edda) complex is reported in which the zinc atom displays a distorted trans-N(4)O(2) octahedral geometry; the crystal packing features double layers of complex molecules held together by extensive hydrogen bonding that inter-digitate with adjacent double layers via pi...pi interactions between 1,10-phenanthroline residues. The structure is compared with that of the recently described copper(II) analogue and, with the latter, included in molecular modeling.

  14. Chiral recognition of proteins having L-histidine residues on the surface with lanthanide ion complex incorporated-molecularly imprinted fluorescent nanoparticles.

    Science.gov (United States)

    Uzun, Lokman; Uzek, Recep; Senel, Serap; Say, Ridvan; Denizli, Adil

    2013-08-01

    In this study, lanthanide ion complex incorporated molecularly imprinted fluorescent nanoparticles were synthesized. A combination of three novel approaches was applied for the purpose. First, lanthanide ions [Terbium(III)] were complexed with N-methacryloyl-L-histidine (MAH), polymerizable derivative of L-histidine amino acid, in order to incorporate the complex directly into the polymeric backbone. At the second stage, L-histidine molecules imprinted nanoparticles were utilized instead of whole protein imprinting in order to avoid whole drawbacks such as fragility, complexity, denaturation tendency, and conformation dependency. At the third stage following the first two steps mentioned above, imprinted L-histidine was coordinated with cupric ions [Cu(II)] to conduct the study under mild conditions. Then, molecularly imprinted fluorescent nanoparticles synthesized were used for L-histidine adsorption from aqueous solution to optimize conditions for adsorption and fluorimetric detection. Finally, usability of nanoparticles was investigated for chiral biorecognition using stereoisomer, D-histidine, racemic mixture, D,L-histidine, proteins with surface L-histidine residue, lysozyme, cytochrome C, or without ribonuclease A. The results revealed that the proposed polymerization strategy could make significant contribution to the solution of chronic problems of fluorescent component introduction into polymers. Additionally, the fluorescent nanoparticles reported here could be used for selective separation and fluorescent monitoring purposes. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. Molecular and Functional Characterization of GR2-R1 Event Based Backcross Derived Lines of Golden Rice in the Genetic Background of a Mega Rice Variety Swarna.

    Directory of Open Access Journals (Sweden)

    Haritha Bollinedi

    Full Text Available Homozygous Golden Rice lines developed in the background of Swarna through marker assisted backcross breeding (MABB using transgenic GR2-R1 event as a donor for the provitamin A trait have high levels of provitamin A (up to 20 ppm but are dwarf with pale green leaves and drastically reduced panicle size, grain number and yield as compared to the recurrent parent, Swarna. In this study, we carried out detailed morphological, biochemical and molecular characterization of these lines in a quest to identify the probable reasons for their abnormal phenotype. Nucleotide blast analysis with the primer sequences used to amplify the transgene revealed that the integration of transgene disrupted the native OsAux1 gene, which codes for an auxin transmembrane transporter protein. Real time expression analysis of the transgenes (ZmPsy and CrtI driven by endosperm-specific promoter revealed the leaky expression of the transgene in the vegetative tissues. We propose that the disruption of OsAux1 disturbed the fine balance of plant growth regulators viz., auxins, gibberellic acid and abscisic acid, leading to the abnormalities in the growth and development of the lines homozygous for the transgene. The study demonstrates the conserved roles of OsAux1 gene in rice and Arabidopsis.

  16. Synthesis, recognition and evaluation of molecularly imprinted polymer nanoparticle using miniemulsion polymerization for controlled release and analysis of risperidone in human plasma samples

    International Nuclear Information System (INIS)

    Asadi, Ebadullah; Azodi-Deilami, Saman; Abdouss, Majid; Kordestani, Davood; Rahimi, Alireza; Asadi, Somayeh

    2014-01-01

    We prepared high selective imprinted nanoparticle polymers by a miniemulsion polymerization technique, using risperidone as the template, MAA as the functional monomers, and TRIM as the cross-linker in acetonitrile as solvent. The morphology of the nanoparticles determined by scanning electron microscopy (SEM) images and drug release, binding properties and dynamic light scattering (DLS) of molecularly imprinted polymers (MIPs) were studied. Controlled release of risperidone from nanoparticles was investigated through in 1% wt sodium dodecyl sulfate aqueous solution and by measuring the absorbance by HPLC-UV. The results showed that the imprinted nanoparticles exhibited a higher binding level and slower release rate than non-imprinted nanoparticles, which contributed to interaction of risperidone with imprinted cavities within nanoparticles. Furthermore, the results from HPLC showed good precision (5% for 50.0 µg L -1 ) and recoveries (between 86-91) using MIP from human plasma samples

  17. The use of coenzyme Q0 as a template in the development of a molecularly imprinted polymer for the selective recognition of coenzyme Q10.

    Science.gov (United States)

    Contin, Mario; Flor, Sabrina; Martinefski, Manuela; Lucangioli, Silvia; Tripodi, Valeria

    2014-01-07

    In this work, a novel molecularly imprinted polymer (MIP) for use as a solid phase extraction sorbent was developed for the determination of coenzyme Q10 (CoQ10) in liver extract. CoQ10 is an essential cofactor in mitochondrial oxidative phosphorylation and a powerful antioxidant agent found in low concentrations in biological samples. This fact and its high hydrophobicity make the analysis of CoQ10 technically challenging. Accordingly, a MIP was synthesised using coenzyme Q0 as the template, methacrylic acid as the functional monomer, acetonitrile as the porogen, ethylene glycol dimethacrylate as the crosslinker and benzoyl peroxide as the initiator. Various parameters affecting the polymer preparation and extraction efficiency were evaluated. Morphological characterisation of the MIP and its proper comparison with C18 as a sorbent in solid phase extraction were performed. The optimal conditions for the molecularly imprinted solid phase extraction (MISPE) consisted of 400 μL of sample mixed with 30 mg of MIP and 600 μL of water to reach the optimum solution loading. The loading was followed by a washing step consisting of 1 mL of a 1-propanol solution (1-propanol:water, 30:70,v/v) and elution with 1 mL of 1-propanol. After clean-up, the CoQ10 in the samples was analysed by high performance liquid chromatography. The extraction recoveries were higher than 73.7% with good precision (3.6-8.3%). The limits of detection and quantification were 2.4 and 7.5 μg g(-1), respectively, and a linear range between 7.5 and 150 μg g(-1) of tissue was achieved. The new MISPE procedure provided a successful clean-up for the determination of CoQ10 in a complex matrix. Copyright © 2013 Elsevier B.V. All rights reserved.

  18. Structural and molecular dynamics studies of a C1-oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Bing [Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala Sweden; Kognole, Abhishek A. [Department of Chemical and Materials Engineering, University of Kentucky, Lexington KY USA; Wu, Miao [Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala Sweden; Westereng, Bjørge [Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås Norway; Crowley, Michael F. [Biosciences Center, National Renewable Energy Laboratory, Golden CO USA; Kim, Seonah [Biosciences Center, National Renewable Energy Laboratory, Golden CO USA; Dimarogona, Maria [Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala Sweden; Department of Chemical Engineering, University of Patras, Greece; Payne, Christina M. [Department of Chemical and Materials Engineering, University of Kentucky, Lexington KY USA; Directorate of Engineering, Division of Chemical, Bioengineering, Environmental, and Transport Systems, National Science Foundation, Alexandria VA USA; Sandgren, Mats [Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala Sweden

    2018-04-24

    Lytic polysaccharide monooxygenases (LPMOs) are a group of recently discovered enzymes that play important roles in the decomposition of recalcitrant polysaccharides. Here, we report the biochemical, structural, and computational characterization of an LPMO from the white-rot fungus Heterobasidion irregulare (HiLPMO9B). This enzyme oxidizes cellulose at the C1 carbon of glycosidic linkages. The crystal structure of HiLPMO9B was determined at 2.1 A resolution using X-ray crystallography. Unlike the majority of the currently available C1-specific LPMO structures, the HiLPMO9B structure contains an extended L2 loop, connecting ..beta..-strands ..beta..2 and ..beta..3 of the ..beta..-sandwich structure. Molecular dynamics (MD) simulations suggest roles for both aromatic and acidic residues in the substrate binding of HiLPMO9B, with the main contribution from the residues located on the extended region of the L2 loop (Tyr20) and the LC loop (Asp205, Tyr207, and Glu210). Asp205 and Glu210 were found to be involved in the hydrogen bonding with the hydroxyl group of the C6 carbon of glucose moieties directly or via a water molecule. Two different binding orientations were observed over the course of the MD simulations. In each orientation, the active-site copper of this LPMO preferentially skewed toward the pyranose C1 of the glycosidic linkage over the targeted glycosidic bond. This study provides additional insight into cellulose binding by C1-specific LPMOs, giving a molecular-level picture of active site substrate interactions.

  19. Molecular characterization of HIV-1 CRF01_AE in Mekong Delta, Vietnam, and impact of T-cell epitope mutations on HLA recognition (ANRS 12159.

    Directory of Open Access Journals (Sweden)

    Estibaliz Lazaro

    Full Text Available BACKGROUND: To date, 11 HIV-1 subtypes and 48 circulating recombinant forms have been described worldwide. The underlying reason why their distribution is so heterogeneous is not clear. Host genetic factors could partly explain this distribution. The aim of this study was to describe HIV-1 strains circulating in an unexplored area of Mekong Delta, Vietnam, and to assess the impact of optimal epitope mutations on HLA binding. METHODS: We recruited 125 chronically antiretroviral-naive HIV-1-infected subjects from five cities in the Mekong Delta. We performed high-resolution DNA typing of HLA class I alleles, sequencing of Gag and RT-Prot genes and phylogenetic analysis of the strains. Epitope mutations were analyzed in patients bearing the HLA allele restricting the studied epitope. Optimal wild-type epitopes from the Los Alamos database were used as reference. T-cell epitope recognition was predicted using the immune epitope database tool according to three different scores involved in antigen processing (TAP and proteasome scores and HLA binding (MHC score. RESULTS: All sequences clustered with CRF01_AE. HLA class I genotyping showed the predominance of Asian alleles as A*11:01 and B*46:01 with a Vietnamese specificity held by two different haplotypes. The percentage of homology between Mekong and B consensus HIV-1 sequences was above 85%. Divergent epitopes had TAP and proteasome scores comparable with wild-type epitopes. MHC scores were significantly lower in divergent epitopes with a mean of 2.4 (±0.9 versus 2 (±0.7 in non-divergent ones (p<0.0001. CONCLUSIONS: Our study confirms the wide predominance of CRF01_AE in the Mekong Delta where patients harbor a specific HLA pattern. Moreover, it demonstrates the lower MHC binding affinity among divergent epitopes. This weak immune pressure combined with a narrow genetic diversity favors immune escape and could explain why CRF01_AE is still predominant in Vietnam, particularly in the Mekong area.

  20. Molecular dynamics simulations shed light on the enthalpic and entropic driving forces that govern the sequence specific recognition between netropsin and DNA.

    Science.gov (United States)

    Dolenc, Jozica; Gerster, Sarah; van Gunsteren, Wilfred F

    2010-09-02

    With the aim to gain a better understanding of the various driving forces that govern sequence specific DNA minor groove binding, we performed a thermodynamic analysis of netropsin binding to an AT-containing and to a set of six mixed AT/GC-containing binding sequences in the DNA minor groove. The relative binding free energies obtained using molecular dynamics simulations and free energy calculations show significant variations with the binding sequence. While the introduction of a GC base pair in the middle or close to the middle of the binding site is unfavorable for netropsin binding, a GC base pair at the end of the binding site appears to have no negative influence on the binding. The results of the structural and energetic analyses of the netropsin-DNA complexes reveal that the differences in the calculated binding affinities cannot be explained solely in terms of netropsin-DNA hydrogen-bonding or interaction energies. In addition, solvation effects and entropic contributions to the relative binding free energy provide a more complete picture of the various factors determining binding. Analysis of the relative binding entropy indicates that its magnitude is highly sequence-dependent, with the ratio |TDeltaDeltaS|/|DeltaDeltaH| ranging from 0.07 for the AAAGA to 1.7 for the AAGAG binding sequence, respectively.

  1. Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Yi; Han, Gye Won; Abagyan, Ruben; Wu, Beili; Stevens, Raymond C.; Cherezov, Vadim; Kufareva, Irina; Handel, Tracy M. (USC); (Chinese Aca. Sci.); (UCSD)

    2017-06-01

    CCR5 is the primary chemokine receptor utilized by HIV to infect leukocytes, whereas CCR5 ligands inhibit infection by blocking CCR5 engagement with HIV gp120. To guide the design of improved therapeutics, we solved the structure of CCR5 in complex with chemokine antagonist [5P7]CCL5. Several structural features appeared to contribute to the anti-HIV potency of [5P7]CCL5, including the distinct chemokine orientation relative to the receptor, the near-complete occupancy of the receptor binding pocket, the dense network of intermolecular hydrogen bonds, and the similarity of binding determinants with the FDA-approved HIV inhibitor Maraviroc. Molecular modeling indicated that HIV gp120 mimicked the chemokine interaction with CCR5, providing an explanation for the ability of CCR5 to recognize diverse ligands and gp120 variants. Our findings reveal that structural plasticity facilitates receptor-chemokine specificity and enables exploitation by HIV, and provide insight into the design of small molecule and protein inhibitors for HIV and other CCR5-mediated diseases.

  2. The development of a new optical sensor based on the Mn doped ZnS quantum dots modified with the molecularly imprinted polymers for sensitive recognition of florfenicol

    Science.gov (United States)

    Sadeghi, Susan; Jahani, Moslem; Belador, Foroogh

    2016-04-01

    The Mn doped ZnS quantum dots (Mn:ZnS QDs) capped with the florfenicol molecularly imprinted polymer (Mn:ZnS QDs@MIP) were prepared via the sol-gel surface imprinting approach using 3-aminopropyltriethoxysilane (APTES) as the functional monomer and tetraethoxysilane (TEOS) as the cross-linker for the optosensing of the florfenicol. Transmission electron microscopy (TEM), X-ray diffractometer, IR spectroscopy, UV-Vis absorption spectrophotometry, and spectrofluorometry were used to elucidate the formation, morphology, and identification of the products. To illustrate the usefulness of the new imprinted material, the non-imprinted coated Mn:ZnS QDs (Mn:ZnS QDs@NIP) were synthesized without the presence of the florfenicol. It was revealed that the fluorescence (FL) intensity of the Mn:ZnS QDs@MIP increased with increasing the FF concentration. Under the optimal conditions, changes in the FL intensity in the presence of the target molecule showed a linear response in the concentration range of 30-700 μmol L- 1 with a detection limit of 24 μmol L- 1. The developed method was finally applied successfully to the determination of FF in different meat samples with satisfactory recoveries.

  3. The development of a new optical sensor based on the Mn doped ZnS quantum dots modified with the molecularly imprinted polymers for sensitive recognition of florfenicol.

    Science.gov (United States)

    Sadeghi, Susan; Jahani, Moslem; Belador, Foroogh

    2016-04-15

    The Mn doped ZnS quantum dots (Mn:ZnS QDs) capped with the florfenicol molecularly imprinted polymer (Mn:ZnS QDs@MIP) were prepared via the sol-gel surface imprinting approach using 3-aminopropyltriethoxysilane (APTES) as the functional monomer and tetraethoxysilane (TEOS) as the cross-linker for the optosensing of the florfenicol. Transmission electron microscopy (TEM), X-ray diffractometer, IR spectroscopy, UV-Vis absorption spectrophotometry, and spectrofluorometry were used to elucidate the formation, morphology, and identification of the products. To illustrate the usefulness of the new imprinted material, the non-imprinted coated Mn:ZnS QDs (Mn:ZnS QDs@NIP) were synthesized without the presence of the florfenicol. It was revealed that the fluorescence (FL) intensity of the Mn:ZnS QDs@MIP increased with increasing the FF concentration. Under the optimal conditions, changes in the FL intensity in the presence of the target molecule showed a linear response in the concentration range of 30-700 μmol L(-1) with a detection limit of 24 μmol L(-1). The developed method was finally applied successfully to the determination of FF in different meat samples with satisfactory recoveries. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Halide anion solvation and recognition by a macro tri-cyclic tetra-ammonium host in an ionic liquid: a molecular dynamics stud

    International Nuclear Information System (INIS)

    Chaumont, A.; Wipff, G.

    2006-01-01

    We report a molecular dynamics study of halide anions X - and their inclusion complexes X - - L 4+ with a macro-tri-cyclic tetrahedral host L 4+ built from four quaternary ammonium sites, in an ionic liquid (IL) based on the 1-butyl-3-methyl-imidazolium (BMI + ) cation and the PF 6 - anion. The 'dry' and 'humid' forms of the [BMI][PF 6 ] IL are compared, showing the importance of IL ions in the 'dry' IL and, in some cases, of water molecules in the 'humid' IL. In the 'dry' IL the F - , Cl - , Br - and I - un-complexed halides are surrounded by 4-5 BMI + cations whose binding mode evolves from hydrogen bonding to facial coordination along this series. Solvent humidity has the largest impact on the solvation of F - whose first shell BMI + cations are all displaced by H 2 O molecules, while the first solvation shell of Cl - , Br - and I - comprises 3-4 BMI + cations plus ca. 4 H 2 O molecules. The solvation of the L 4+ host and of its X - - L 4+ complex mainly involves PF 6 - anions in the 'dry' IL, and additional H 2 O molecules in the 'humid' IL. The question of anion binding selectivity is addressed by free energy perturbation calculations which predict that, in the 'dry' liquid, F - is preferred over Cl - , Br - and I - , which contrasts with the aqueous solution where L 4+ is selective for Cl - . In the 'humid' liquid however, there is no F - /Cl - discrimination, showing the importance of small amounts of water on the complexation selectivity. (authors)

  5. Familiar Person Recognition: Is Autonoetic Consciousness More Likely to Accompany Face Recognition Than Voice Recognition?

    Science.gov (United States)

    Barsics, Catherine; Brédart, Serge

    2010-11-01

    Autonoetic consciousness is a fundamental property of human memory, enabling us to experience mental time travel, to recollect past events with a feeling of self-involvement, and to project ourselves in the future. Autonoetic consciousness is a characteristic of episodic memory. By contrast, awareness of the past associated with a mere feeling of familiarity or knowing relies on noetic consciousness, depending on semantic memory integrity. Present research was aimed at evaluating whether conscious recollection of episodic memories is more likely to occur following the recognition of a familiar face than following the recognition of a familiar voice. Recall of semantic information (biographical information) was also assessed. Previous studies that investigated the recall of biographical information following person recognition used faces and voices of famous people as stimuli. In this study, the participants were presented with personally familiar people's voices and faces, thus avoiding the presence of identity cues in the spoken extracts and allowing a stricter control of frequency exposure with both types of stimuli (voices and faces). In the present study, the rate of retrieved episodic memories, associated with autonoetic awareness, was significantly higher from familiar faces than familiar voices even though the level of overall recognition was similar for both these stimuli domains. The same pattern was observed regarding semantic information retrieval. These results and their implications for current Interactive Activation and Competition person recognition models are discussed.

  6. Idiosyncratic recognition of UUG/UUA codons by modified nucleoside 5-taurinomethyluridine, τm5U present at 'wobble' position in anticodon loop of tRNALeu: A molecular modeling approach.

    Directory of Open Access Journals (Sweden)

    Asmita S Kamble

    Full Text Available Lack of naturally occurring modified nucleoside 5-taurinomethyluridine (τm5U at the 'wobble' 34th position in tRNALeu causes mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS. The τm5U34 specifically recognizes UUG and UUA codons. Structural consequences of τm5U34 to read cognate codons have not been studied so far in detail at the atomic level. Hence, 50ns multiple molecular dynamics (MD simulations of various anticodon stem loop (ASL models of tRNALeu in presence and absence of τm5U34 along with UUG and UUA codons were performed to explore the dynamic behaviour of τm5U34 during codon recognition process. The MD simulation results revealed that τm5U34 recognizes G/A ending codons by 'wobble' as well as a novel 'single' hydrogen bonding interactions. RMSD and RMSF values indicate the comparative stability of the ASL models containing τm5U34 modification over the other models, lacking τm5U34. Another MD simulation study of 55S mammalian mitochondrial rRNA with tRNALeu showed crucial interactions between the A-site residues, A918, A919, G256 and codon-anticodon bases. Thus, these results could improve our understanding about the decoding efficiency of human mt tRNALeu with τm5U34 to recognize UUG and UUA codons.

  7. PKC-epsilon activation is required for recognition memory in the rat.

    Science.gov (United States)

    Zisopoulou, Styliani; Asimaki, Olga; Leondaritis, George; Vasilaki, Anna; Sakellaridis, Nikos; Pitsikas, Nikolaos; Mangoura, Dimitra

    2013-09-15

    Activation of PKCɛ, an abundant and developmentally regulated PKC isoform in the brain, has been implicated in memory throughout life and across species. Yet, direct evidence for a mechanistic role for PKCɛ in memory is still lacking. Hence, we sought to evaluate this in rats, using short-term treatments with two PKCɛ-selective peptides, the inhibitory ɛV1-2 and the activating ψɛRACK, and the novel object recognition task (NORT). Our results show that the PKCɛ-selective activator ψɛRACK, did not have a significant effect on recognition memory. In the short time frames used, however, inhibition of PKCɛ activation with the peptide inhibitor ɛV1-2 significantly impaired recognition memory. Moreover, when we addressed at the molecular level the immediate proximal signalling events of PKCɛ activation in acutely dissected rat hippocampi, we found that ψɛRACK increased in a time-dependent manner phosphorylation of MARCKS and activation of Src, Raf, and finally ERK1/2, whereas ɛV1-2 inhibited all basal activity of this pathway. Taken together, these findings present the first direct evidence that PKCɛ activation is an essential molecular component of recognition memory and point toward the use of systemically administered PKCɛ-regulating peptides as memory study tools and putative therapeutic agents. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Molecular characterization of UGT94F2 and UGT86C4, two glycosyltransferases from Picrorhiza kurrooa: comparative structural insight and evaluation of substrate recognition.

    Directory of Open Access Journals (Sweden)

    Wajid Waheed Bhat

    Full Text Available Uridine diphosphate glycosyltransferases (UGTs are pivotal in the process of glycosylation for decorating natural products with sugars. It is one of the versatile mechanisms in determining chemical complexity and diversity for the production of suite of pharmacologically active plant natural products. Picrorhiza kurrooa is a highly reputed medicinal herb known for its hepato-protective properties which are attributed to a novel group of iridoid glycosides known as picrosides. Although the plant is well studied in terms of its pharmacological properties, very little is known about the biosynthesis of these important secondary metabolites. In this study, we identified two family-1 glucosyltransferases from P. kurrooa. The full length cDNAs of UGT94F4 and UGT86C4 contained open reading frames of 1455 and 1422 nucleotides, encoding polypeptides of 484 and 473 amino acids respectively. UGT94F2 and UGT86C4 showed differential expression pattern in leaves, rhizomes and inflorescence. To elucidate whether the differential expression pattern of the two Picrorhiza UGTs correlate with transcriptional regulation via their promoters and to identify elements that could be recognized by known iridoid-specific transcription factors, upstream regions of each gene were isolated and scanned for putative cis-regulatory elements. Interestingly, the presence of cis-regulatory elements within the promoter regions of each gene correlated positively with their expression profiles in response to different phytohormones. HPLC analysis of picrosides extracted from different tissues and elicitor-treated samples showed a significant increase in picroside levels, corroborating well with the expression profile of UGT94F2 possibly indicating its implication in picroside biosynthesis. Using homology modeling and molecular docking studies, we provide an insight into the donor and acceptor specificities of both UGTs identified in this study. UGT94F2 was predicted to be an iridoid

  9. Activity recognition from minimal distinguishing subsequence mining

    Science.gov (United States)

    Iqbal, Mohammad; Pao, Hsing-Kuo

    2017-08-01

    Human activity recognition is one of the most important research topics in the era of Internet of Things. To separate different activities given sensory data, we utilize a Minimal Distinguishing Subsequence (MDS) mining approach to efficiently find distinguishing patterns among different activities. We first transform the sensory data into a series of sensor triggering events and operate the MDS mining procedure afterwards. The gap constraints are also considered in the MDS mining. Given the multi-class nature of most activity recognition tasks, we modify the MDS mining approach from a binary case to a multi-class one to fit the need for multiple activity recognition. We also study how to select the best parameter set including the minimal and the maximal support thresholds in finding the MDSs for effective activity recognition. Overall, the prediction accuracy is 86.59% on the van Kasteren dataset which consists of four different activities for recognition.

  10. Face Detection and Recognition

    National Research Council Canada - National Science Library

    Jain, Anil K

    2004-01-01

    This report describes research efforts towards developing algorithms for a robust face recognition system to overcome many of the limitations found in existing two-dimensional facial recognition systems...

  11. Graphical symbol recognition

    OpenAIRE

    K.C. , Santosh; Wendling , Laurent

    2015-01-01

    International audience; The chapter focuses on one of the key issues in document image processing i.e., graphical symbol recognition. Graphical symbol recognition is a sub-field of a larger research domain: pattern recognition. The chapter covers several approaches (i.e., statistical, structural and syntactic) and specially designed symbol recognition techniques inspired by real-world industrial problems. It, in general, contains research problems, state-of-the-art methods that convey basic s...

  12. Designer molecule for molecular recognition and photoinduced ...

    Indian Academy of Sciences (India)

    amitava

    Signaling unit: Transform the cation-receptor interaction into output signal. 1H NMR ..... solution of Hg2+ (10 μM) and then to a water/ethanol (7/3 v/v) solution of solution of Hg2+ (10 μM) and .... System extended in the [010] direction. 2.5 fs.

  13. Molecular Recognition Studies on Naphthyridine Derivatives

    Directory of Open Access Journals (Sweden)

    José Carlos Iglesias-Sánchez

    2010-03-01

    Full Text Available The association constants Kb of three hosts I–III designed to have both enhanced hydrogen bonding donor strength and conformational preorganization with biotin analogues 1–5 are reported. 1H-NMR titrations under two different concentration conditions have been employed to determine the association constants Kb. A statistical analysis using a presence absence matrix has been applied to calculate the different contributions. Hydrogen bond interactions make naphthyridine derivatives II and III potent binders and effective receptors for (+-biotin methyl ester (1, due to the complex stabilization by additional hydrogen bonds.

  14. Recognition and Toleration

    DEFF Research Database (Denmark)

    Lægaard, Sune

    2010-01-01

    Recognition and toleration are ways of relating to the diversity characteristic of multicultural societies. The article concerns the possible meanings of toleration and recognition, and the conflict that is often claimed to exist between these two approaches to diversity. Different forms...... or interpretations of recognition and toleration are considered, confusing and problematic uses of the terms are noted, and the compatibility of toleration and recognition is discussed. The article argues that there is a range of legitimate and importantly different conceptions of both toleration and recognition...

  15. Accessing Specific Peptide Recognition by Combinatorial Chemistry

    DEFF Research Database (Denmark)

    Li, Ming

    Molecular recognition is at the basis of all processes for life, and plays a central role in many biological processes, such as protein folding, the structural organization of cells and organelles, signal transduction, and the immune response. Hence, my PhD project is entitled “Accessing Specific...... Peptide Recognition by Combinatorial Chemistry”. Molecular recognition is a specific interaction between two or more molecules through noncovalent bonding, such as hydrogen bonding, metal coordination, van der Waals forces, π−π, hydrophobic, or electrostatic interactions. The association involves kinetic....... Combinatorial chemistry was invented in 1980s based on observation of functional aspects of the adaptive immune system. It was employed for drug development and optimization in conjunction with high-throughput synthesis and screening. (chapter 2) Combinatorial chemistry is able to rapidly produce many thousands...

  16. 8 CFR 1292.2 - Organizations qualified for recognition; requests for recognition; withdrawal of recognition...

    Science.gov (United States)

    2010-01-01

    ...; requests for recognition; withdrawal of recognition; accreditation of representatives; roster. 1292.2...; requests for recognition; withdrawal of recognition; accreditation of representatives; roster. (a) Qualifications of organizations. A non-profit religious, charitable, social service, or similar organization...

  17. Improved hemicryptophane hosts for the stereoselective recognition of glucopyranosides

    Czech Academy of Sciences Publication Activity Database

    Schmitt, A.; Perraud, O.; Payet, E.; Chatelet, B.; Bousquet, B.; Valls, M.; Padula, Daniele; Di Bari, L.; Dutasta, J. P.; Martinez, A.

    2014-01-01

    Roč. 12, č. 24 (2014), s. 4211-4217 ISSN 1477-0520 Institutional support: RVO:61388963 Keywords : hydrogen-bonding receptors * molecular recognition * artificial receptors Subject RIV: CC - Organic Chemistry Impact factor: 3.562, year: 2014

  18. Optical Pattern Recognition

    Science.gov (United States)

    Yu, Francis T. S.; Jutamulia, Suganda

    2008-10-01

    Contributors; Preface; 1. Pattern recognition with optics Francis T. S. Yu and Don A. Gregory; 2. Hybrid neural networks for nonlinear pattern recognition Taiwei Lu; 3. Wavelets, optics, and pattern recognition Yao Li and Yunglong Sheng; 4. Applications of the fractional Fourier transform to optical pattern recognition David Mendlovic, Zeev Zalesky and Haldum M. Oxaktas; 5. Optical implementation of mathematical morphology Tien-Hsin Chao; 6. Nonlinear optical correlators with improved discrimination capability for object location and recognition Leonid P. Yaroslavsky; 7. Distortion-invariant quadratic filters Gregory Gheen; 8. Composite filter synthesis as applied to pattern recognition Shizhou Yin and Guowen Lu; 9. Iterative procedures in electro-optical pattern recognition Joseph Shamir; 10. Optoelectronic hybrid system for three-dimensional object pattern recognition Guoguang Mu, Mingzhe Lu and Ying Sun; 11. Applications of photrefractive devices in optical pattern recognition Ziangyang Yang; 12. Optical pattern recognition with microlasers Eung-Gi Paek; 13. Optical properties and applications of bacteriorhodopsin Q. Wang Song and Yu-He Zhang; 14. Liquid-crystal spatial light modulators Aris Tanone and Suganda Jutamulia; 15. Representations of fully complex functions on real-time spatial light modulators Robert W. Cohn and Laurence G. Hassbrook; Index.

  19. Psychophysiological indices of recognition memory

    OpenAIRE

    Heaver, Becky

    2012-01-01

    It has recently been found that during recognition memory tests participants’ pupils dilate more when they view old items compared to novel items. This thesis sought to replicate this novel ‘‘Pupil Old/New Effect’’ (PONE) and to determine its relationship to implicit and explicit mnemonic processes, the veracity of participants’ responses, and the analogous Event-Related Potential (ERP) old/new effect. Across 9 experiments, pupil-size was measured with a video-based eye-tracker during a varie...

  20. The Neural Correlates of Everyday Recognition Memory

    Science.gov (United States)

    Milton, F.; Muhlert, N.; Butler, C. R.; Benattayallah, A.; Zeman, A. Z.

    2011-01-01

    We used a novel automatic camera, SenseCam, to create a recognition memory test for real-life events. Adapting a "Remember/Know" paradigm, we asked healthy undergraduates, who wore SenseCam for 2 days, in their everyday environments, to classify images as strongly or weakly remembered, strongly or weakly familiar or novel, while brain activation…

  1. DNA recognition by synthetic constructs.

    Science.gov (United States)

    Pazos, Elena; Mosquera, Jesús; Vázquez, M Eugenio; Mascareñas, José L

    2011-09-05

    The interaction of transcription factors with specific DNA sites is key for the regulation of gene expression. Despite the availability of a large body of structural data on protein-DNA complexes, we are still far from fully understanding the molecular and biophysical bases underlying such interactions. Therefore, the development of non-natural agents that can reproduce the DNA-recognition properties of natural transcription factors remains a major and challenging goal in chemical biology. In this review we summarize the basics of double-stranded DNA recognition by transcription factors, and describe recent developments in the design and preparation of synthetic DNA binders. We mainly focus on synthetic peptides that have been designed by following the DNA interaction of natural proteins, and we discuss how the tools of organic synthesis can be used to make artificial constructs equipped with functionalities that introduce additional properties to the recognition process, such as sensing and controllability. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. A centennial record of anthropogenic impacts and extreme weather events in southwestern Taiwan: Evidence from sedimentary molecular markers in coastal margin

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Li-Jung; Lee, Chon-Lin; Louchouarn, Patrick; Huh, Chih-An; Liu, James T.; Chen, Jian-Cheng; Lee, Kun-Je

    2014-09-15

    A 100-year history of human and natural disturbances in southwestern Taiwan was reconstructed using a suite of molecular markers in four dated sediment cores from the upper slope region off the Gaoping River mouth. Trends in polycyclic aromatic hydrocarbons (PAHs) tracked Taiwan's industrialization/urbanization starting in the 1970s, and the enactment of environmental regulatory policies thereafter.

  3. Transient downregulation of Sema3A mRNA in a rat model for temporal lobe epilepsy. A novel molecular event potentially contributing to mossy fiber sprouting

    NARCIS (Netherlands)

    Holtmaat, Anthony J D G; Gorter, Jan A; de Wit, Joris; Tolner, Else A; Spijker, Sabine; Giger, Roman J; Lopes da Silva, Fernando H; Verhaagen, J.

    Mossy fiber sprouting (MFS) in the hippocampal dentate gyrus is thought to play a critical role in the hyperexcitability of the hippocampus in temporal lobe epilepsy patients. The composition of molecular signals that is needed to direct this sprouting response has not yet been elucidated to a great

  4. Neuronal Functions Associated with Endo- and Exocytotic Events-cum-Molecular Trafficking May Be Cell Maturation-Dependent: Lessons Learned from Studies on Botulism

    Science.gov (United States)

    2011-01-01

    Clostridium botulinum type A progenitor toxins . Infect Immun 64:1589–1594 Li L, Singh BR (1999) Structure -function relationship of clostridial...experimental design and demonstration of the validity of the targeted neurologic therapeutic delivery approach based on recombinant botulinum toxin ...Endocytosis Exocytosis Molecular trafficking Cell maturation Botulism Targeted therapeutic Background Botulinum neurotoxins (BoNTs) are produced by

  5. Deciphering the molecular events necessary for synergistic tumor cell apoptosis mediated by the histone deacetylase inhibitor vorinostat and the BH3 mimetic ABT-737

    NARCIS (Netherlands)

    Wiegmans, Adrian P.; Alsop, Amber E.; Bots, Michael; Cluse, Leonie A.; Williams, Steven P.; Banks, Kellie-Marie; Ralli, Rachael; Scott, Clare L.; Frenzel, Anna; Villunger, Andreas; Johnstone, Ricky W.

    2011-01-01

    The concept of personalized anticancer therapy is based on the use of targeted therapeutics through in-depth knowledge of the molecular mechanisms of action of these agents when used alone and in combination. We have identified the apoptotic proteins and pathways necessary for synergistic tumor cell

  6. Pattern recognition & machine learning

    CERN Document Server

    Anzai, Y

    1992-01-01

    This is the first text to provide a unified and self-contained introduction to visual pattern recognition and machine learning. It is useful as a general introduction to artifical intelligence and knowledge engineering, and no previous knowledge of pattern recognition or machine learning is necessary. Basic for various pattern recognition and machine learning methods. Translated from Japanese, the book also features chapter exercises, keywords, and summaries.

  7. A two-step recognition of signal sequences determines the translocation efficiency of proteins.

    Science.gov (United States)

    Belin, D; Bost, S; Vassalli, J D; Strub, K

    1996-02-01

    The cytosolic and secreted, N-glycosylated, forms of plasminogen activator inhibitor-2 (PAI-2) are generated by facultative translocation. To study the molecular events that result in the bi-topological distribution of proteins, we determined in vitro the capacities of several signal sequences to bind the signal recognition particle (SRP) during targeting, and to promote vectorial transport of murine PAI-2 (mPAI-2). Interestingly, the six signal sequences we compared (mPAI-2 and three mutated derivatives thereof, ovalbumin and preprolactin) were found to have the differential activities in the two events. For example, the mPAI-2 signal sequence first binds SRP with moderate efficiency and secondly promotes the vectorial transport of only a fraction of the SRP-bound nascent chains. Our results provide evidence that the translocation efficiency of proteins can be controlled by the recognition of their signal sequences at two steps: during SRP-mediated targeting and during formation of a committed translocation complex. This second recognition may occur at several time points during the insertion/translocation step. In conclusion, signal sequences have a more complex structure than previously anticipated, allowing for multiple and independent interactions with the translocation machinery.

  8. Construction and updating of event models in auditory event processing.

    Science.gov (United States)

    Huff, Markus; Maurer, Annika E; Brich, Irina; Pagenkopf, Anne; Wickelmaier, Florian; Papenmeier, Frank

    2018-02-01

    Humans segment the continuous stream of sensory information into distinct events at points of change. Between 2 events, humans perceive an event boundary. Present theories propose changes in the sensory information to trigger updating processes of the present event model. Increased encoding effort finally leads to a memory benefit at event boundaries. Evidence from reading time studies (increased reading times with increasing amount of change) suggest that updating of event models is incremental. We present results from 5 experiments that studied event processing (including memory formation processes and reading times) using an audio drama as well as a transcript thereof as stimulus material. Experiments 1a and 1b replicated the event boundary advantage effect for memory. In contrast to recent evidence from studies using visual stimulus material, Experiments 2a and 2b found no support for incremental updating with normally sighted and blind participants for recognition memory. In Experiment 3, we replicated Experiment 2a using a written transcript of the audio drama as stimulus material, allowing us to disentangle encoding and retrieval processes. Our results indicate incremental updating processes at encoding (as measured with reading times). At the same time, we again found recognition performance to be unaffected by the amount of change. We discuss these findings in light of current event cognition theories. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  9. Statistical Pattern Recognition

    CERN Document Server

    Webb, Andrew R

    2011-01-01

    Statistical pattern recognition relates to the use of statistical techniques for analysing data measurements in order to extract information and make justified decisions.  It is a very active area of study and research, which has seen many advances in recent years. Applications such as data mining, web searching, multimedia data retrieval, face recognition, and cursive handwriting recognition, all require robust and efficient pattern recognition techniques. This third edition provides an introduction to statistical pattern theory and techniques, with material drawn from a wide range of fields,

  10. Pattern recognition of state variables by neural networks

    International Nuclear Information System (INIS)

    Faria, Eduardo Fernandes; Pereira, Claubia

    1996-01-01

    An artificial intelligence system based on artificial neural networks can be used to classify predefined events and emergency procedures. These systems are being used in different areas. In the nuclear reactors safety, the goal is the classification of events whose data can be processed and recognized by neural networks. In this works we present a preliminary simple system, using neural networks in the recognition of patterns the recognition of variables which define a situation. (author)

  11. Molecular threading and tunable molecular recognition on DNA origami nanostructures.

    Science.gov (United States)

    Wu, Na; Czajkowsky, Daniel M; Zhang, Jinjin; Qu, Jianxun; Ye, Ming; Zeng, Dongdong; Zhou, Xingfei; Hu, Jun; Shao, Zhifeng; Li, Bin; Fan, Chunhai

    2013-08-21

    The DNA origami technology holds great promise for the assembly of nanoscopic technological devices and studies of biochemical reactions at the single-molecule level. For these, it is essential to establish well controlled attachment of functional materials to predefined sites on the DNA origami nanostructures for reliable measurements and versatile applications. However, the two-sided nature of the origami scaffold has shown limitations in this regard. We hypothesized that holes of the commonly used two-dimensional DNA origami designs are large enough for the passage of single-stranded (ss)-DNA. Sufficiently long ssDNA initially located on one side of the origami should thus be able to "thread" to the other side through the holes in the origami sheet. By using an origami sheet attached with patterned biotinylated ssDNA spacers and monitoring streptavidin binding with atomic force microscopic (AFM) imaging, we provide unambiguous evidence that the biotin ligands positioned on one side have indeed threaded through to the other side. Our finding reveals a previously overlooked critical design feature that should provide new interpretations to previous experiments and new opportunities for the construction of origami structures with new functional capabilities.

  12. Social appraisal influences recognition of emotions.

    Science.gov (United States)

    Mumenthaler, Christian; Sander, David

    2012-06-01

    The notion of social appraisal emphasizes the importance of a social dimension in appraisal theories of emotion by proposing that the way an individual appraises an event is influenced by the way other individuals appraise and feel about the same event. This study directly tested this proposal by asking participants to recognize dynamic facial expressions of emotion (fear, happiness, or anger in Experiment 1; fear, happiness, anger, or neutral in Experiment 2) in a target face presented at the center of a screen while a contextual face, which appeared simultaneously in the periphery of the screen, expressed an emotion (fear, happiness, anger) or not (neutral) and either looked at the target face or not. We manipulated gaze direction to be able to distinguish between a mere contextual effect (gaze away from both the target face and the participant) and a specific social appraisal effect (gaze toward the target face). Results of both experiments provided evidence for a social appraisal effect in emotion recognition, which differed from the mere effect of contextual information: Whereas facial expressions were identical in both conditions, the direction of the gaze of the contextual face influenced emotion recognition. Social appraisal facilitated the recognition of anger, happiness, and fear when the contextual face expressed the same emotion. This facilitation was stronger than the mere contextual effect. Social appraisal also allowed better recognition of fear when the contextual face expressed anger and better recognition of anger when the contextual face expressed fear. 2012 APA, all rights reserved

  13. An initial event in the insect innate immune response: structural and biological studies of interactions between β-1,3-glucan and the N-terminal domain of β-1,3-glucan recognition protein.

    Science.gov (United States)

    Dai, Huaien; Hiromasa, Yasuaki; Takahashi, Daisuke; VanderVelde, David; Fabrick, Jeffrey A; Kanost, Michael R; Krishnamoorthi, Ramaswamy

    2013-01-08

    In response to invading microorganisms, insect β-1,3-glucan recognition protein (βGRP), a soluble receptor in the hemolymph, binds to the surfaces of bacteria and fungi and activates serine protease cascades that promote destruction of pathogens by means of melanization or expression of antimicrobial peptides. Here we report on the nuclear magnetic resonance (NMR) solution structure of the N-terminal domain of βGRP (N-βGRP) from Indian meal moth (Plodia interpunctella), which is sufficient to activate the prophenoloxidase (proPO) pathway resulting in melanin formation. NMR and isothermal calorimetric titrations of N-βGRP with laminarihexaose, a glucose hexamer containing β-1,3 links, suggest a weak binding of the ligand. However, addition of laminarin, a glucose polysaccharide (~6 kDa) containing β-1,3 and β-1,6 links that activates the proPO pathway, to N-βGRP results in the loss of NMR cross-peaks from the backbone (15)N-(1)H groups of the protein, suggesting the formation of a large complex. Analytical ultracentrifugation (AUC) studies of formation of the N-βGRP-laminarin complex show that ligand binding induces self-association of the protein-carbohydrate complex into a macro structure, likely containing six protein and three laminarin molecules (~102 kDa). The macro complex is quite stable, as it does not undergo dissociation upon dilution to submicromolar concentrations. The structural model thus derived from this study for the N-βGRP-laminarin complex in solution differs from the one in which a single N-βGRP molecule has been proposed to bind to a triple-helical form of laminarin on the basis of an X-ray crystallographic structure of the N-βGRP-laminarihexaose complex [Kanagawa, M., Satoh, T., Ikeda, A., Adachi, Y., Ohno, N., and Yamaguchi, Y. (2011) J. Biol. Chem. 286, 29158-29165]. AUC studies and phenoloxidase activation measurements conducted with the designed mutants of N-βGRP indicate that electrostatic interactions involving Asp45, Arg54

  14. Paradigms in object recognition

    International Nuclear Information System (INIS)

    Mutihac, R.; Mutihac, R.C.

    1999-09-01

    A broad range of approaches has been proposed and applied for the complex and rather difficult task of object recognition that involves the determination of object characteristics and object classification into one of many a priori object types. Our paper revises briefly the three main different paradigms in pattern recognition, namely Bayesian statistics, neural networks, and expert systems. (author)

  15. Infant Visual Recognition Memory

    Science.gov (United States)

    Rose, Susan A.; Feldman, Judith F.; Jankowski, Jeffery J.

    2004-01-01

    Visual recognition memory is a robust form of memory that is evident from early infancy, shows pronounced developmental change, and is influenced by many of the same factors that affect adult memory; it is surprisingly resistant to decay and interference. Infant visual recognition memory shows (a) modest reliability, (b) good discriminant…

  16. Recognition and Toleration

    DEFF Research Database (Denmark)

    Lægaard, Sune

    2010-01-01

    Recognition and toleration are ways of relating to the diversity characteristic of multicultural societies. The article concerns the possible meanings of toleration and recognition, and the conflict that is often claimed to exist between these two approaches to diversity. Different forms or inter...

  17. Challenging ocular image recognition

    Science.gov (United States)

    Pauca, V. Paúl; Forkin, Michael; Xu, Xiao; Plemmons, Robert; Ross, Arun A.

    2011-06-01

    Ocular recognition is a new area of biometric investigation targeted at overcoming the limitations of iris recognition performance in the presence of non-ideal data. There are several advantages for increasing the area beyond the iris, yet there are also key issues that must be addressed such as size of the ocular region, factors affecting performance, and appropriate corpora to study these factors in isolation. In this paper, we explore and identify some of these issues with the goal of better defining parameters for ocular recognition. An empirical study is performed where iris recognition methods are contrasted with texture and point operators on existing iris and face datasets. The experimental results show a dramatic recognition performance gain when additional features are considered in the presence of poor quality iris data, offering strong evidence for extending interest beyond the iris. The experiments also highlight the need for the direct collection of additional ocular imagery.

  18. Event Investigation

    International Nuclear Information System (INIS)

    Korosec, D.

    2000-01-01

    The events in the nuclear industry are investigated from the license point of view and from the regulatory side too. It is well known the importance of the event investigation. One of the main goals of such investigation is to prevent the circumstances leading to the event and the consequences of the event. The protection of the nuclear workers against nuclear hazard, and the protection of general public against dangerous effects of an event could be achieved by systematic approach to the event investigation. Both, the nuclear safety regulatory body and the licensee shall ensure that operational significant events are investigated in a systematic and technically sound manner to gather information pertaining to the probable causes of the event. One of the results should be appropriate feedback regarding the lessons of the experience to the regulatory body, nuclear industry and general public. In the present paper a general description of systematic approach to the event investigation is presented. The systematic approach to the event investigation works best where cooperation is present among the different divisions of the nuclear facility or regulatory body. By involving management and supervisors the safety office can usually improve their efforts in the whole process. The end result shall be a program which serves to prevent events and reduce the time and efforts solving the root cause which initiated each event. Selection of the proper method for the investigation and an adequate review of the findings and conclusions lead to the higher level of the overall nuclear safety. (author)

  19. A multiple translocation event in a patient with hexadactyly, facial dysmorphism, mental retardation and behaviour disorder characterised comprehensively by molecular cytogenetics. Case report and review of the literature.

    Science.gov (United States)

    Seidel, Jörg; Heller, Anita; Senger, Gabriele; Starke, Heike; Chudoba, Ilse; Kelbova, Christina; Tönnies, Holger; Neitzel, Heidemarie; Haase, Claudia; Beensen, Volkmar; Zintl, Felix; Claussen, Uwe; Liehr, Thomas

    2003-09-01

    We report a 13-year-old female patient with multiple congenital abnormalities (microcephaly, facial dysmorphism, anteverted dysplastic ears and postaxial hexadactyly), mental retardation, and adipose-gigantism. Ultrasonography revealed no signs of a heart defect or renal abnormalities. She showed no speech development and suffered from a behavioural disorder. CNS abnormalities were excluded by cerebral MRI. Initial cytogenetic studies by Giemsa banding revealed an aberrant karyotype involving three chromosomes, t(2;4;11). By high resolution banding and multicolour fluoresence in-situ hybridisation (M-FISH, MCB), chromosome 1 was also found to be involved in the complex chromosomal aberrations, confirming the karyotype 46,XX,t(2;11;4).ish t(1;4;2;11)(q43;q21.1;p12-p13.1;p14.1). To the best of our knowledge no patient has been previously described with such a complex translocation involving 4 chromosomes. This case demonstrates that conventional chromosome banding techniques such as Giemsa banding are not always sufficient to characterise complex chromosomal abnormalities. Only by the additional utilisation of molecular cytogenetic techniques could the complexity of the present chromosomal rearrangements and the origin of the involved chromosomal material be detected. Further molecular genetic studies will be performed to clarify the chromosomal breakpoints potentially responsible for the observed clinical symptoms. This report demonstrates that multicolour-fluorescence in-situ hybridisation studies should be performed in patients with congenital abnormalities and suspected aberrant karyotypes in addition to conventional Giemsa banding.

  20. [Face recognition in patients with autism spectrum disorders].

    Science.gov (United States)

    Kita, Yosuke; Inagaki, Masumi

    2012-07-01

    The present study aimed to review previous research conducted on face recognition in patients with autism spectrum disorders (ASD). Face recognition is a key question in the ASD research field because it can provide clues for elucidating the neural substrates responsible for the social impairment of these patients. Historically, behavioral studies have reported low performance and/or unique strategies of face recognition among ASD patients. However, the performance and strategy of ASD patients is comparable to those of the control group, depending on the experimental situation or developmental stage, suggesting that face recognition of ASD patients is not entirely impaired. Recent brain function studies, including event-related potential and functional magnetic resonance imaging studies, have investigated the cognitive process of face recognition in ASD patients, and revealed impaired function in the brain's neural network comprising the fusiform gyrus and amygdala. This impaired function is potentially involved in the diminished preference for faces, and in the atypical development of face recognition, eliciting symptoms of unstable behavioral characteristics in these patients. Additionally, face recognition in ASD patients is examined from a different perspective, namely self-face recognition, and facial emotion recognition. While the former topic is intimately linked to basic social abilities such as self-other discrimination, the latter is closely associated with mentalizing. Further research on face recognition in ASD patients should investigate the connection between behavioral and neurological specifics in these patients, by considering developmental changes and the spectrum clinical condition of ASD.

  1. 8 CFR 292.2 - Organizations qualified for recognition; requests for recognition; withdrawal of recognition...

    Science.gov (United States)

    2010-01-01

    ...; requests for recognition; withdrawal of recognition; accreditation of representatives; roster. 292.2...; withdrawal of recognition; accreditation of representatives; roster. (a) Qualifications of organizations. A non-profit religious, charitable, social service, or similar organization established in the United...

  2. A dynamic approach to recognition memory.

    Science.gov (United States)

    Cox, Gregory E; Shiffrin, Richard M

    2017-11-01

    We present a dynamic model of memory that integrates the processes of perception, retrieval from knowledge, retrieval of events, and decision making as these evolve from 1 moment to the next. The core of the model is that recognition depends on tracking changes in familiarity over time from an initial baseline generally determined by context, with these changes depending on the availability of different kinds of information at different times. A mathematical implementation of this model leads to precise, accurate predictions of accuracy, response time, and speed-accuracy trade-off in episodic recognition at the levels of both groups and individuals across a variety of paradigms. Our approach leads to novel insights regarding word frequency, speeded responding, context reinstatement, short-term priming, similarity, source memory, and associative recognition, revealing how the same set of core dynamic principles can help unify otherwise disparate phenomena in the study of memory. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  3. SENTINEL EVENTS

    Directory of Open Access Journals (Sweden)

    Andrej Robida

    2004-09-01

    Full Text Available Background. The Objective of the article is a two year statistics on sentinel events in hospitals. Results of a survey on sentinel events and the attitude of hospital leaders and staff are also included. Some recommendations regarding patient safety and the handling of sentinel events are given.Methods. In March 2002 the Ministry of Health introduce a voluntary reporting system on sentinel events in Slovenian hospitals. Sentinel events were analyzed according to the place the event, its content, and root causes. To show results of the first year, a conference for hospital directors and medical directors was organized. A survey was conducted among the participants with the purpose of gathering information about their view on sentinel events. One hundred questionnaires were distributed.Results. Sentinel events. There were 14 reports of sentinel events in the first year and 7 in the second. In 4 cases reports were received only after written reminders were sent to the responsible persons, in one case no reports were obtained. There were 14 deaths, 5 of these were in-hospital suicides, 6 were due to an adverse event, 3 were unexplained. Events not leading to death were a suicide attempt, a wrong side surgery, a paraplegia after spinal anaesthesia, a fall with a femoral neck fracture, a damage of the spleen in the event of pleural space drainage, inadvertent embolization with absolute alcohol into a femoral artery and a physical attack on a physician by a patient. Analysis of root causes of sentinel events showed that in most cases processes were inadequate.Survey. One quarter of those surveyed did not know about the sentinel events reporting system. 16% were having actual problems when reporting events and 47% beleived that there was an attempt to blame individuals. Obstacles in reporting events openly were fear of consequences, moral shame, fear of public disclosure of names of participants in the event and exposure in mass media. The majority of

  4. Harmonization versus Mutual Recognition

    DEFF Research Database (Denmark)

    Jørgensen, Jan Guldager; Schröder, Philipp

    The present paper examines trade liberalization driven by the coordination of product standards. For oligopolistic firms situated in separate markets that are initially sheltered by national standards, mutual recognition of standards implies entry and reduced profits at home paired with the oppor......The present paper examines trade liberalization driven by the coordination of product standards. For oligopolistic firms situated in separate markets that are initially sheltered by national standards, mutual recognition of standards implies entry and reduced profits at home paired...... countries and three firms, where firms first lobby for the policy coordination regime (harmonization versus mutual recognition), and subsequently, in case of harmonization, the global standard is auctioned among the firms. We discuss welfare effects and conclude with policy implications. In particular......, harmonized standards may fail to harvest the full pro-competitive effects from trade liberalization compared to mutual recognition; moreover, the issue is most pronounced in markets featuring price competition....

  5. CASE Recognition Awards.

    Science.gov (United States)

    Currents, 1985

    1985-01-01

    A total of 294 schools, colleges, and universities received prizes in this year's CASE Recognition program. Awards were given in: public relations programs, student recruitment, marketing, program pulications, news writing, fund raising, radio programming, school periodicals, etc. (MLW)

  6. Forensic speaker recognition

    NARCIS (Netherlands)

    Meuwly, Didier

    2013-01-01

    The aim of forensic speaker recognition is to establish links between individuals and criminal activities, through audio speech recordings. This field is multidisciplinary, combining predominantly phonetics, linguistics, speech signal processing, and forensic statistics. On these bases, expert-based

  7. The Recognition Of Fatigue

    DEFF Research Database (Denmark)

    Elsass, Peter; Jensen, Bodil; Mørup, Rikke

    2007-01-01

    Elsass P., Jensen B., Morup R., Thogersen M.H. (2007). The Recognition Of Fatigue: A qualitative study of life-stories from rehabilitation clients. International Journal of Psychosocial Rehabilitation. 11 (2), 75-87......Elsass P., Jensen B., Morup R., Thogersen M.H. (2007). The Recognition Of Fatigue: A qualitative study of life-stories from rehabilitation clients. International Journal of Psychosocial Rehabilitation. 11 (2), 75-87...

  8. Evaluating music emotion recognition

    DEFF Research Database (Denmark)

    Sturm, Bob L.

    2013-01-01

    A fundamental problem with nearly all work in music genre recognition (MGR)is that evaluation lacks validity with respect to the principal goals of MGR. This problem also occurs in the evaluation of music emotion recognition (MER). Standard approaches to evaluation, though easy to implement, do...... not reliably differentiate between recognizing genre or emotion from music, or by virtue of confounding factors in signals (e.g., equalization). We demonstrate such problems for evaluating an MER system, and conclude with recommendations....

  9. Why recognition is rational

    Directory of Open Access Journals (Sweden)

    Clintin P. Davis-Stober

    2010-07-01

    Full Text Available The Recognition Heuristic (Gigerenzer and Goldstein, 1996; Goldstein and Gigerenzer, 2002 makes the counter-intuitive prediction that a decision maker utilizing less information may do as well as, or outperform, an idealized decision maker utilizing more information. We lay a theoretical foundation for the use of single-variable heuristics such as the Recognition Heuristic as an optimal decision strategy within a linear modeling framework. We identify conditions under which over-weighting a single predictor is a mini-max strategy among a class of a priori chosen weights based on decision heuristics with respect to a measure of statistical lack of fit we call ``risk''. These strategies, in turn, outperform standard multiple regression as long as the amount of data available is limited. We also show that, under related conditions, weighting only one variable and ignoring all others produces the same risk as ignoring the single variable and weighting all others. This approach has the advantage of generalizing beyond the original environment of the Recognition Heuristic to situations with more than two choice options, binary or continuous representations of recognition, and to other single variable heuristics. We analyze the structure of data used in some prior recognition tasks and find that it matches the sufficient conditions for optimality in our results. Rather than being a poor or adequate substitute for a compensatory model, the Recognition Heuristic closely approximates an optimal strategy when a decision maker has finite data about the world.

  10. A centennial record of anthropogenic impacts and extreme weather events in southwestern Taiwan: Evidence from sedimentary molecular markers in coastal margin

    International Nuclear Information System (INIS)

    Kuo, Li-Jung; Lee, Chon-Lin; Louchouarn, Patrick; Huh, Chih-An; Liu, James T.; Chen, Jian-Cheng; Lee, Kun-Je

    2014-01-01

    Highlights: • Historical reconstruction of human and natural disturbances in SW Taiwan. • Comparative analysis of PAHs and lignin to evaluate sources/processes. • Distinct timing of PAH maxima between western Pacific, Europe and North America. • Consistently low (Ad/Al) v suggests quick transport of TOM by mountainous rivers. • Both PAHs and lignin point to turbidite flows driven by typhoon floods. - Abstract: A 100-year history of human and natural disturbances in southwestern Taiwan was reconstructed using a suite of molecular markers in four dated sediment cores from the upper slope region off the Gaoping River mouth. Trends in polycyclic aromatic hydrocarbons (PAHs) tracked Taiwan’s industrialization/urbanization starting in the 1970s, and the enactment of environmental regulatory policies thereafter. The predominant pyrogenic sources include vehicular, smelter, and coal combustion but spatial differences are observed among sub-regions of the shelf. Profiles of lignin oxidation products (LOPs) point to a significant increase in terrestrial organic matter inputs driven by land development after the 1970s. Low lignin diagenetic signature ratios [(Ad/Al) v ] in all sediments suggest quick transport of fresh plant material from land to sea via mountainous rivers. Shifts in PAHs, LOPs, and radionuclides in recent sediments reveal the deposition of turbidites resulting from typhoon-induced floods. Multiproxy analysis illustrates the interplay between anthropogenic activities and natural processes

  11. A centennial record of anthropogenic impacts and extreme weather events in southwestern Taiwan: evidence from sedimentary molecular markers in coastal margin.

    Science.gov (United States)

    Kuo, Li-Jung; Lee, Chon-Lin; Louchouarn, Patrick; Huh, Chih-An; Liu, James T; Chen, Jian-Cheng; Lee, Kun-Je

    2014-09-15

    A 100-year history of human and natural disturbances in southwestern Taiwan was reconstructed using a suite of molecular markers in four dated sediment cores from the upper slope region off the Gaoping River mouth. Trends in polycyclic aromatic hydrocarbons (PAHs) tracked Taiwan's industrialization/urbanization starting in the 1970s, and the enactment of environmental regulatory policies thereafter. The predominant pyrogenic sources include vehicular, smelter, and coal combustion but spatial differences are observed among sub-regions of the shelf. Profiles of lignin oxidation products (LOPs) point to a significant increase in terrestrial organic matter inputs driven by land development after the 1970s. Low lignin diagenetic signature ratios [(Ad/Al)v] in all sediments suggest quick transport of fresh plant material from land to sea via mountainous rivers. Shifts in PAHs, LOPs, and radionuclides in recent sediments reveal the deposition of turbidites resulting from typhoon-induced floods. Multiproxy analysis illustrates the interplay between anthropogenic activities and natural processes. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Acquired copy-neutral loss of heterozygosity of chromosome 1p as a molecular event associated with marrow fibrosis in MPL-mutated myeloproliferative neoplasms.

    Science.gov (United States)

    Rumi, Elisa; Pietra, Daniela; Guglielmelli, Paola; Bordoni, Roberta; Casetti, Ilaria; Milanesi, Chiara; Sant'Antonio, Emanuela; Ferretti, Virginia; Pancrazzi, Alessandro; Rotunno, Giada; Severgnini, Marco; Pietrelli, Alessandro; Astori, Cesare; Fugazza, Elena; Pascutto, Cristiana; Boveri, Emanuela; Passamonti, Francesco; De Bellis, Gianluca; Vannucchi, Alessandro; Cazzola, Mario

    2013-05-23

    We studied mutations of MPL exon 10 in patients with essential thrombocythemia (ET) or primary myelofibrosis (PMF), first investigating a cohort of 892 consecutive patients. MPL mutation scanning was performed on granulocyte genomic DNA by using a high-resolution melt assay, and the mutant allele burden was evaluated by using deep sequencing. Somatic mutations of MPL, all but one involving codon W515, were detected in 26/661 (4%) patients with ET, 10/187 (5%) with PMF, and 7/44 (16%) patients with post-ET myelofibrosis. Comparison of JAK2 (V617F)-mutated and MPL-mutated patients showed only minor phenotypic differences. In an extended group of 62 MPL-mutated patients, the granulocyte mutant allele burden ranged from 1% to 95% and was significantly higher in patients with PMF or post-ET myelofibrosis compared with those with ET. Patients with higher mutation burdens had evidence of acquired copy-neutral loss of heterozygosity (CN-LOH) of chromosome 1p in granulocytes, consistent with a transition from heterozygosity to homozygosity for the MPL mutation in clonal cells. A significant association was found between MPL-mutant allele burden greater than 50% and marrow fibrosis. These observations suggest that acquired CN-LOH of chromosome 1p involving the MPL location may represent a molecular mechanism of fibrotic transformation in MPL-mutated myeloproliferative neoplasms.

  13. Event Modeling

    DEFF Research Database (Denmark)

    Bækgaard, Lars

    2001-01-01

    The purpose of this chapter is to discuss conceptual event modeling within a context of information modeling. Traditionally, information modeling has been concerned with the modeling of a universe of discourse in terms of information structures. However, most interesting universes of discourse...... are dynamic and we present a modeling approach that can be used to model such dynamics.We characterize events as both information objects and change agents (Bækgaard 1997). When viewed as information objects events are phenomena that can be observed and described. For example, borrow events in a library can...

  14. Pattern recognition in high energy physics

    International Nuclear Information System (INIS)

    Tenner, A.G.

    1980-01-01

    In high energy physics experiments tracks of elementary particles are recorded by different types of equipment. Coordinates of points of these tracks have to be measured for the geometrical reconstruction and the further analysis of the observed events. Pattern recognition methods may facilitate the detection of tracks or whole events and the separation of relevant from non-relevant information. They may also serve for the automation of measurement. Generally, all work is done by digital computation. In a bubble chamber tracks appear as strings of vapour bubbles that can be recorded photographically. Two methods of pattern recognition are discussed. The flying spot digitizer encodes the pattern on the photograph into point coordinates in the memory of a computer. The computer carries out the pattern recognition procedure entirely on the basis of the stored information. Cathode ray instruments scan the photograph by means of a computer steered optical device. Data acquisition from the film is performed in a feedback loop of the computation. In electronic experimental equipment tracks are defined by the spacial distribution of hits of counters (wire counters, scintillation counters, spark chambers). Pattern recognition is generally performed in various stages both by on-line and off-line equipment. Problems in the data handling arise both from the great abundance of data and from the time limits imposed on the on-line computation by high measuring rates. The on-line computation is carried out by hardwired logic, small computers, and to an increasing extent by microprocessors. (Auth.)

  15. Stigma-pollen recognition: a new look

    Directory of Open Access Journals (Sweden)

    C. Dumas

    2014-01-01

    Full Text Available During the last two decades, there have been several conceptual developments in our understanding of pollen-stigma recognition and molecular mechanisms involved. The main models proposed are compared. Based on additional data a hypothesis to complete these models especially for pollen hydration and adhesion is proposed. After attachment of the pollen to the stigma surface a close interaction exists involving lipoproteic membrane-like compounds (pollenkitt and stigma pellicle and pollen agglutinating ability.

  16. Changing predictions, stable recognition: Children's representations of downward incline motion.

    Science.gov (United States)

    Hast, Michael; Howe, Christine

    2017-11-01

    Various studies to-date have demonstrated children hold ill-conceived expressed beliefs about the physical world such as that one ball will fall faster than another because it is heavier. At the same time, they also demonstrate accurate recognition of dynamic events. How these representations relate is still unresolved. This study examined 5- to 11-year-olds' (N = 130) predictions and recognition of motion down inclines. Predictions were typically in error, matching previous work, but children largely recognized correct events as correct and rejected incorrect ones. The results also demonstrate while predictions change with increasing age, recognition shows signs of stability. The findings provide further support for a hybrid model of object representations and argue in favour of stable core cognition existing alongside developmental changes. Statement of contribution What is already known on this subject? Children's predictions of physical events show limitations in accuracy Their recognition of such events suggests children may use different knowledge sources in their reasoning What the present study adds? Predictions fluctuate more strongly than recognition, suggesting stable core cognition But recognition also shows some fluctuation, arguing for a hybrid model of knowledge representation. © 2017 The British Psychological Society.

  17. Early energy metabolism-related molecular events in skeletal muscle of diabetic rats: The effects of l-arginine and SOD mimic.

    Science.gov (United States)

    Stancic, Ana; Filipovic, Milos; Ivanovic-Burmazovic, Ivana; Masovic, Sava; Jankovic, Aleksandra; Otasevic, Vesna; Korac, Aleksandra; Buzadzic, Biljana; Korac, Bato

    2017-06-25

    Considering the vital role of skeletal muscle in control of whole-body metabolism and the severity of long-term diabetic complications, we aimed to reveal the molecular pattern of early diabetes-related skeletal muscle phenotype in terms of energy metabolism, focusing on regulatory mechanisms, and the possibility to improve it using two redox modulators, l-arginine and superoxide dismutase (SOD) mimic. Alloxan-induced diabetic rats (120 mg/kg) were treated with l-arginine or the highly specific SOD mimic, M40403, for 7 days. As appropriate controls, non-diabetic rats received the same treatments. We found that l-arginine and M40403 restored diabetes-induced impairment of phospho-5'-AMP-activated protein kinase α (AMPKα) signaling by upregulating AMPKα protein itself and its downstream effectors, peroxisome proliferator-activated receptor-γ coactivator-1α and nuclear respiratory factor 1. Also, there was a restitution of the protein levels of oxidative phosphorylation components (complex I, complex II and complex IV) and mitofusin 2. Furthermore, l-arginine and M40403 induced translocation of glucose transporter 4 to the membrane and upregulation of protein of phosphofructokinase and acyl coenzyme A dehydrogenase, diminishing negative diabetic effects on limiting factors of glucose and lipid metabolism. Both treatments abolished diabetes-induced downregulation of sarcoplasmic reticulum calcium-ATPase proteins (SERCA 1 and 2). Similar effects of l-arginine and SOD mimic treatments suggest that disturbances in the superoxide/nitric oxide ratio may be responsible for skeletal muscle mitochondrial and metabolic impairment in early diabetes. Our results provide evidence that l-arginine and SOD mimics have potential in preventing and treating metabolic disturbances accompanying this widespread metabolic disease. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Object recognition memory: neurobiological mechanisms of encoding, consolidation and retrieval.

    Science.gov (United States)

    Winters, Boyer D; Saksida, Lisa M; Bussey, Timothy J

    2008-07-01

    Tests of object recognition memory, or the judgment of the prior occurrence of an object, have made substantial contributions to our understanding of the nature and neurobiological underpinnings of mammalian memory. Only in recent years, however, have researchers begun to elucidate the specific brain areas and neural processes involved in object recognition memory. The present review considers some of this recent research, with an emphasis on studies addressing the neural bases of perirhinal cortex-dependent object recognition memory processes. We first briefly discuss operational definitions of object recognition and the common behavioural tests used to measure it in non-human primates and rodents. We then consider research from the non-human primate and rat literature examining the anatomical basis of object recognition memory in the delayed nonmatching-to-sample (DNMS) and spontaneous object recognition (SOR) tasks, respectively. The results of these studies overwhelmingly favor the view that perirhinal cortex (PRh) is a critical region for object recognition memory. We then discuss the involvement of PRh in the different stages--encoding, consolidation, and retrieval--of object recognition memory. Specifically, recent work in rats has indicated that neural activity in PRh contributes to object memory encoding, consolidation, and retrieval processes. Finally, we consider the pharmacological, cellular, and molecular factors that might play a part in PRh-mediated object recognition memory. Recent studies in rodents have begun to indicate the remarkable complexity of the neural substrates underlying this seemingly simple aspect of declarative memory.

  19. Ring recognition in the CBM RICH detector

    International Nuclear Information System (INIS)

    Lebedev, S.; Ososkov, G.; Hoehne, C.

    2007-01-01

    Two algorithms of ring recognition, a standalone ring finder (using only RICH information) and an algorithm based on the information from vertex tracks are described. The fake ring problem and its solution using a set of two-dimensional cuts or an artificial neural network are discussed. Results of a comparative study are given. All developed algorithms were tested on large statistics of simulated events and were then included into the CBM framework for common use

  20. Page Recognition: Quantum Leap In Recognition Technology

    Science.gov (United States)

    Miller, Larry

    1989-07-01

    No milestone has proven as elusive as the always-approaching "year of the LAN," but the "year of the scanner" might claim the silver medal. Desktop scanners have been around almost as long as personal computers. And everyone thinks they are used for obvious desktop-publishing and business tasks like scanning business documents, magazine articles and other pages, and translating those words into files your computer understands. But, until now, the reality fell far short of the promise. Because it's true that scanners deliver an accurate image of the page to your computer, but the software to recognize this text has been woefully disappointing. Old optical-character recognition (OCR) software recognized such a limited range of pages as to be virtually useless to real users. (For example, one OCR vendor specified 12-point Courier font from an IBM Selectric typewriter: the same font in 10-point, or from a Diablo printer, was unrecognizable!) Computer dealers have told me the chasm between OCR expectations and reality is so broad and deep that nine out of ten prospects leave their stores in disgust when they learn the limitations. And this is a very important, very unfortunate gap. Because the promise of recognition -- what people want it to do -- carries with it tremendous improvements in our productivity and ability to get tons of written documents into our computers where we can do real work with it. The good news is that a revolutionary new development effort has led to the new technology of "page recognition," which actually does deliver the promise we've always wanted from OCR. I'm sure every reader appreciates the breakthrough represented by the laser printer and page-makeup software, a combination so powerful it created new reasons for buying a computer. A similar breakthrough is happening right now in page recognition: the Macintosh (and, I must admit, other personal computers) equipped with a moderately priced scanner and OmniPage software (from Caere

  1. Examining ERP correlates of recognition memory: Evidence of accurate source recognition without recollection

    Science.gov (United States)

    Addante, Richard, J.; Ranganath, Charan; Yonelinas, Andrew, P.

    2012-01-01

    Recollection is typically associated with high recognition confidence and accurate source memory. However, subjects sometimes make accurate source memory judgments even for items that are not confidently recognized, and it is not known whether these responses are based on recollection or some other memory process. In the current study, we measured event related potentials (ERPs) while subjects made item and source memory confidence judgments in order to determine whether recollection supported accurate source recognition responses for items that were not confidently recognized. In line with previous studies, we found that recognition memory was associated with two ERP effects: an early on-setting FN400 effect, and a later parietal old-new effect [Late Positive Component (LPC)], which have been associated with familiarity and recollection, respectively. The FN400 increased gradually with item recognition confidence, whereas the LPC was only observed for highly confident recognition responses. The LPC was also related to source accuracy, but only for items that had received a high confidence item recognition response; accurate source judgments to items that were less confidently recognized did not exhibit the typical ERP correlate of recollection or familiarity, but rather showed a late, broadly distributed negative ERP difference. The results indicate that accurate source judgments of episodic context can occur even when recollection fails. PMID:22548808

  2. Application of biomolecular recognition via magnetic nanoparticle in nanobiotechnology

    Science.gov (United States)

    Shen, Wei-Zheng; Cetinel, Sibel; Montemagno, Carlo

    2018-05-01

    The marriage of biomolecular recognition and magnetic nanoparticle creates tremendous opportunities in the development of advanced technology both in academic research and in industrial sectors. In this paper, we review current progress on the magnetic nanoparticle-biomolecule hybrid systems, particularly employing the recognition pairs of DNA-DNA, DNA-protein, protein-protein, and protein-inorganics in several nanobiotechnology application areas, including molecular biology, diagnostics, medical treatment, industrial biocatalysts, and environmental separations.

  3. MOLECULARLY IMPRINTED POLYMER TECHNOLOGY: A ...

    African Journals Online (AJOL)

    dell

    Cross-linking ensures polymer rigidity that “freezes” the 3-D molecular architecture of the binding cavity when the ... molecular technology applications whose potential is still .... recognition element is responsible for the selective ... organic treatments, making them superior ... efficiency with which such materials may be.

  4. The Pandora software development kit for pattern recognition

    Energy Technology Data Exchange (ETDEWEB)

    Marshall, J.S.; Thomson, M.A. [University of Cambridge, Cavendish Laboratory, Cambridge (United Kingdom)

    2015-09-15

    The development of automated solutions to pattern recognition problems is important in many areas of scientific research and human endeavour. This paper describes the implementation of the Pandora software development kit, which aids the process of designing, implementing and running pattern recognition algorithms. The Pandora Application Programming Interfaces ensure simple specification of the building-blocks defining a pattern recognition problem. The logic required to solve the problem is implemented in algorithms. The algorithms request operations to create or modify data structures and the operations are performed by the Pandora framework. This design promotes an approach using many decoupled algorithms, each addressing specific topologies. Details of algorithms addressing two pattern recognition problems in High Energy Physics are presented: reconstruction of events at a high-energy e{sup +}e{sup -} linear collider and reconstruction of cosmic ray or neutrino events in a liquid argon time projection chamber. (orig.)

  5. Probabilistic Open Set Recognition

    Science.gov (United States)

    Jain, Lalit Prithviraj

    Real-world tasks in computer vision, pattern recognition and machine learning often touch upon the open set recognition problem: multi-class recognition with incomplete knowledge of the world and many unknown inputs. An obvious way to approach such problems is to develop a recognition system that thresholds probabilities to reject unknown classes. Traditional rejection techniques are not about the unknown; they are about the uncertain boundary and rejection around that boundary. Thus traditional techniques only represent the "known unknowns". However, a proper open set recognition algorithm is needed to reduce the risk from the "unknown unknowns". This dissertation examines this concept and finds existing probabilistic multi-class recognition approaches are ineffective for true open set recognition. We hypothesize the cause is due to weak adhoc assumptions combined with closed-world assumptions made by existing calibration techniques. Intuitively, if we could accurately model just the positive data for any known class without overfitting, we could reject the large set of unknown classes even under this assumption of incomplete class knowledge. For this, we formulate the problem as one of modeling positive training data by invoking statistical extreme value theory (EVT) near the decision boundary of positive data with respect to negative data. We provide a new algorithm called the PI-SVM for estimating the unnormalized posterior probability of class inclusion. This dissertation also introduces a new open set recognition model called Compact Abating Probability (CAP), where the probability of class membership decreases in value (abates) as points move from known data toward open space. We show that CAP models improve open set recognition for multiple algorithms. Leveraging the CAP formulation, we go on to describe the novel Weibull-calibrated SVM (W-SVM) algorithm, which combines the useful properties of statistical EVT for score calibration with one-class and binary

  6. Touchless palmprint recognition systems

    CERN Document Server

    Genovese, Angelo; Scotti, Fabio

    2014-01-01

    This book examines the context, motivation and current status of biometric systems based on the palmprint, with a specific focus on touchless and less-constrained systems. It covers new technologies in this rapidly evolving field and is one of the first comprehensive books on palmprint recognition systems.It discusses the research literature and the most relevant industrial applications of palmprint biometrics, including the low-cost solutions based on webcams. The steps of biometric recognition are described in detail, including acquisition setups, algorithms, and evaluation procedures. Const

  7. [Prosopagnosia and facial expression recognition].

    Science.gov (United States)

    Koyama, Shinichi

    2014-04-01

    This paper reviews clinical neuropsychological studies that have indicated that the recognition of a person's identity and the recognition of facial expressions are processed by different cortical and subcortical areas of the brain. The fusiform gyrus, especially the right fusiform gyrus, plays an important role in the recognition of identity. The superior temporal sulcus, amygdala, and medial frontal cortex play important roles in facial-expression recognition. Both facial recognition and facial-expression recognition are highly intellectual processes that involve several regions of the brain.

  8. Molecularly Imprinted Membranes

    Science.gov (United States)

    Trotta, Francesco; Biasizzo, Miriam; Caldera, Fabrizio

    2012-01-01

    Although the roots of molecularly imprinted polymers lie in the beginning of 1930s in the past century, they have had an exponential growth only 40–50 years later by the works of Wulff and especially by Mosbach. More recently, it was also proved that molecular imprinted membranes (i.e., polymer thin films) that show recognition properties at molecular level of the template molecule are used in their formation. Different procedures and potential application in separation processes and catalysis are reported. The influences of different parameters on the discrimination abilities are also discussed. PMID:24958291

  9. Optical Character Recognition.

    Science.gov (United States)

    Converso, L.; Hocek, S.

    1990-01-01

    This paper describes computer-based optical character recognition (OCR) systems, focusing on their components (the computer, the scanner, the OCR, and the output device); how the systems work; and features to consider in selecting a system. A list of 26 questions to ask to evaluate systems for potential purchase is included. (JDD)

  10. Recognition of fractal graphs

    NARCIS (Netherlands)

    Perepelitsa, VA; Sergienko, [No Value; Kochkarov, AM

    1999-01-01

    Definitions of prefractal and fractal graphs are introduced, and they are used to formulate mathematical models in different fields of knowledge. The topicality of fractal-graph recognition from the point of view, of fundamental improvement in the efficiency of the solution of algorithmic problems

  11. Facial Expression Recognition

    NARCIS (Netherlands)

    Pantic, Maja; Li, S.; Jain, A.

    2009-01-01

    Facial expression recognition is a process performed by humans or computers, which consists of: 1. Locating faces in the scene (e.g., in an image; this step is also referred to as face detection), 2. Extracting facial features from the detected face region (e.g., detecting the shape of facial

  12. Track-based event recognition in a realistic crowded environment

    NARCIS (Netherlands)

    Huis, J.R. van; Bouma, H.; Baan, J.; Burghouts, G.J.; Eendebak, P.T.; Hollander, R.J.M.; Dijk, J.; Rest, J.H.C. van

    2014-01-01

    Automatic detection of abnormal behavior in CCTV cameras is important to improve the security in crowded environments, such as shopping malls, airports and railway stations. This behavior can be characterized at different time scales, e.g., by small-scale subtle and obvious actions or by large-scale

  13. Fusion events

    International Nuclear Information System (INIS)

    Aboufirassi, M; Angelique, J.C.; Bizard, G.; Bougault, R.; Brou, R.; Buta, A.; Colin, J.; Cussol, D.; Durand, D.; Genoux-Lubain, A.; Horn, D.; Kerambrun, A.; Laville, J.L.; Le Brun, C.; Lecolley, J.F.; Lefebvres, F.; Lopez, O.; Louvel, M.; Meslin, C.; Metivier, V.; Nakagawa, T.; Peter, J.; Popescu, R.; Regimbart, R.; Steckmeyer, J.C.; Tamain, B.; Vient, E.; Wieloch, A.; Yuasa-Nakagawa, K.

    1998-01-01

    The fusion reactions between low energy heavy ions have a very high cross section. First measurements at energies around 30-40 MeV/nucleon indicated no residue of either complete or incomplete fusion, thus demonstrating the disappearance of this process. This is explained as being due to the high amount o energies transferred to the nucleus, what leads to its total dislocation in light fragments and particles. Exclusive analyses have permitted to mark clearly the presence of fusion processes in heavy systems at energies above 30-40 MeV/nucleon. Among the complete events of the Kr + Au reaction at 60 MeV/nucleon the majority correspond to binary collisions. Nevertheless, for the most considerable energy losses, a class of events do occur for which the detected fragments appears to be emitted from a unique source. These events correspond to an incomplete projectile-target fusion followed by a multifragmentation. Such events were singled out also in the reaction Xe + Sn at 50 MeV/nucleon. For the events in which the energy dissipation was maximal it was possible to isolate an isotropic group of events showing all the characteristics of fusion nuclei. The fusion is said to be incomplete as pre-equilibrium Z = 1 and Z = 2 particles are emitted. The cross section is of the order of 25 mb. Similar conclusions were drown for the systems 36 Ar + 27 Al and 64 Zn + nat Ti. A cross section value of ∼ 20 mb was determined at 55 MeV/nucleon in the first case, while the measurement of evaporation light residues in the last system gave an upper limit of 20-30 mb for the cross section at 50 MeV/nucleon

  14. Galeotti on recognition as inclusion

    DEFF Research Database (Denmark)

    Lægaard, Sune

    2008-01-01

    Anna Elisabetta Galeotti's theory of 'toleration as recognition' has been criticised by Peter Jones for being conceptually incoherent, since liberal toleration presupposes a negative attitude to differences, whereas multicultural recognition requires positive affirmation hereof. The paper spells ...

  15. School IPM Recognition and Certification

    Science.gov (United States)

    Schools and school districts can get support and recognition for implementation of school IPM. EPA is developing a program to provide recognition for school districts that are working towards or have achieved a level of success with school IPM programs.

  16. Stereotype Associations and Emotion Recognition

    NARCIS (Netherlands)

    Bijlstra, Gijsbert; Holland, Rob W.; Dotsch, Ron; Hugenberg, Kurt; Wigboldus, Daniel H. J.

    We investigated whether stereotype associations between specific emotional expressions and social categories underlie stereotypic emotion recognition biases. Across two studies, we replicated previously documented stereotype biases in emotion recognition using both dynamic (Study 1) and static

  17. A REVIEW: OPTICAL CHARACTER RECOGNITION

    OpenAIRE

    Swati Tomar*1 & Amit Kishore2

    2018-01-01

    This paper presents detailed review in the field of Optical Character Recognition. Various techniques are determine that have been proposed to realize the center of character recognition in an optical character recognition system. Even though, sufficient studies and papers are describes the techniques for converting textual content from a paper document into machine readable form. Optical character recognition is a process where the computer understands automatically the image of handwritten ...

  18. Molecular profiling of childhood cancer: Biomarkers and novel therapies

    Directory of Open Access Journals (Sweden)

    Federica Saletta

    2014-06-01

    General significance: The increasing recognition of the heterogeneity of molecular causes of cancer favors the continued development of molecularly targeted agents, and their transfer to pediatric and adolescent populations.

  19. Superficial Priming in Episodic Recognition

    Science.gov (United States)

    Dopkins, Stephen; Sargent, Jesse; Ngo, Catherine T.

    2010-01-01

    We explored the effect of superficial priming in episodic recognition and found it to be different from the effect of semantic priming in episodic recognition. Participants made recognition judgments to pairs of items, with each pair consisting of a prime item and a test item. Correct positive responses to the test item were impeded if the prime…

  20. Word Recognition in Auditory Cortex

    Science.gov (United States)

    DeWitt, Iain D. J.

    2013-01-01

    Although spoken word recognition is more fundamental to human communication than text recognition, knowledge of word-processing in auditory cortex is comparatively impoverished. This dissertation synthesizes current models of auditory cortex, models of cortical pattern recognition, models of single-word reading, results in phonetics and results in…

  1. Visual Recognition Memory across Contexts

    Science.gov (United States)

    Jones, Emily J. H.; Pascalis, Olivier; Eacott, Madeline J.; Herbert, Jane S.

    2011-01-01

    In two experiments, we investigated the development of representational flexibility in visual recognition memory during infancy using the Visual Paired Comparison (VPC) task. In Experiment 1, 6- and 9-month-old infants exhibited recognition when familiarization and test occurred in the same room, but showed no evidence of recognition when…

  2. Forensic Face Recognition: A Survey

    NARCIS (Netherlands)

    Ali, Tauseef; Spreeuwers, Lieuwe Jan; Veldhuis, Raymond N.J.; Quaglia, Adamo; Epifano, Calogera M.

    2012-01-01

    The improvements of automatic face recognition during the last 2 decades have disclosed new applications like border control and camera surveillance. A new application field is forensic face recognition. Traditionally, face recognition by human experts has been used in forensics, but now there is a

  3. Three duplication events and variable molecular evolution ...

    Indian Academy of Sciences (India)

    2Staff Development Institute of CNTC, Zhengzhou, Henan 450008, People's Republic of China .... more strict selective constraint than others and none of high ω value ... (2007) description, M1a versus M2a is less power than M7 ... We failed to.

  4. Three duplication events and variable molecular evolution ...

    Indian Academy of Sciences (India)

    Some large insertion fragments of NbeGGPS1 and NbeGGPS3 were deleted for more visibility. Three conserved motifs were located in the middle region of proteins and were conservative in all 25 sequences. Four positive selection sites were detected in N-terminal region of proteins that are labelled as red arrows.

  5. Electrophysiological distinctions between recognition memory with and without awareness

    Science.gov (United States)

    Ko, Philip C.; Duda, Bryant; Hussey, Erin P.; Ally, Brandon A.

    2013-01-01

    The influence of implicit memory representations on explicit recognition may help to explain cases of accurate recognition decisions made with high uncertainty. During a recognition task, implicit memory may enhance the fluency of a test item, biasing decision processes to endorse it as “old”. This model may help explain recognition-without-identification, a remarkable phenomenon in which participants make highly accurate recognition decisions despite the inability to identify the test item. The current study investigated whether recognition-without-identification for pictures elicits a similar pattern of neural activity as other types of accurate recognition decisions made with uncertainty. Further, this study also examined whether recognition-without-identification for pictures could be attained by the use of perceptual and conceptual information from memory. To accomplish this, participants studied pictures and then performed a recognition task under difficult viewing conditions while event-related potentials (ERPs) were recorded. Behavioral results showed that recognition was highly accurate even when test items could not be identified, demonstrating recognition-without identification. The behavioral performance also indicated that recognition-without-identification was mediated by both perceptual and conceptual information, independently of one another. The ERP results showed dramatically different memory related activity during the early 300 to 500 ms epoch for identified items that were studied compared to unidentified items that were studied. Similar to previous work highlighting accurate recognition without retrieval awareness, test items that were not identified, but correctly endorsed as “old,” elicited a negative posterior old/new effect (i.e., N300). In contrast, test items that were identified and correctly endorsed as “old,” elicited the classic positive frontal old/new effect (i.e., FN400). Importantly, both of these effects were

  6. Seeing iconic gestures while encoding events facilitates children's memory of these events

    OpenAIRE

    Aussems, Suzanne; Kita, Sotaro

    2017-01-01

    An experiment with 72 three-year-olds investigated whether encoding events while seeing iconic gestures boosts children's memory representation of these events. The events, shown in videos of actors moving in an unusual manner, were presented with either iconic gestures depicting how the actors performed these actions, interactive gestures, or no gesture. In a recognition memory task, children in the iconic gesture condition remembered actors and actions better than children in the control co...

  7. Semantic Activity Recognition

    OpenAIRE

    Thonnat , Monique

    2008-01-01

    International audience; Extracting automatically the semantics from visual data is a real challenge. We describe in this paper how recent work in cognitive vision leads to significative results in activity recognition for visualsurveillance and video monitoring. In particular we present work performed in the domain of video understanding in our PULSAR team at INRIA in Sophia Antipolis. Our main objective is to analyse in real-time video streams captured by static video cameras and to recogniz...

  8. Pattern Recognition Control Design

    Science.gov (United States)

    Gambone, Elisabeth A.

    2018-01-01

    Spacecraft control algorithms must know the expected vehicle response to any command to the available control effectors, such as reaction thrusters or torque devices. Spacecraft control system design approaches have traditionally relied on the estimated vehicle mass properties to determine the desired force and moment, as well as knowledge of the effector performance to efficiently control the spacecraft. A pattern recognition approach was used to investigate the relationship between the control effector commands and spacecraft responses. Instead of supplying the approximated vehicle properties and the thruster performance characteristics, a database of information relating the thruster ring commands and the desired vehicle response was used for closed-loop control. A Monte Carlo simulation data set of the spacecraft dynamic response to effector commands was analyzed to establish the influence a command has on the behavior of the spacecraft. A tool developed at NASA Johnson Space Center to analyze flight dynamics Monte Carlo data sets through pattern recognition methods was used to perform this analysis. Once a comprehensive data set relating spacecraft responses with commands was established, it was used in place of traditional control methods and gains set. This pattern recognition approach was compared with traditional control algorithms to determine the potential benefits and uses.

  9. Molecular immune recognition of botulinum neurotoxin B. The light chain regions that bind human blocking antibodies from toxin-treated cervical dystonia patients. Antigenic structure of the entire BoNT/B molecule.

    Science.gov (United States)

    Atassi, M Zouhair; Jankovic, Joseph; Steward, Lance E; Aoki, K Roger; Dolimbek, Behzod Z

    2012-01-01

    We recently mapped the regions on the heavy (H) chain of botulinum neurotoxin, type B (BoNT/B) recognized by blocking antibodies (Abs) from cervical dystonia (CD) patients who develop immunoresistance during toxin treatment. Since blocking could also be effected by Abs directed against regions on the light (L) chain, we have mapped here the L chain, using the same 30 CD antisera. We synthesized, purified and characterized 32 19-residue L chain peptides that overlapped successively by 5 residues (peptide L32 overlapped with peptide N1 of the H chain by 12 residues). In a given patient, Abs against the L chain seemed less intense than those against H chain. Most sera recognized a limited set of L chain peptides. The levels of Abs against a given region varied with the patient, consistent with immune responses to each epitope being under separate MHC control. The peptides most frequently recognized were: L13, by 30 of 30 antisera (100%); L22, by 23 of 30 (76.67%); L19, by 15 of 30 (50.00%); L26, by 11 of 30 (36.70%); and L14, by 12 of 30 (40.00%). The activity of L14 probably derives from its overlap with L13. The levels of Ab binding decreased in the following order: L13 (residues 169-187), L22 (295-313), L19 (253-271), and L26 (351-369). Peptides L12 (155-173), L18 (239-257), L15 (197-215), L1 (1-19) and L23 (309-327) exhibited very low Ab binding. The remaining peptides had little or no Ab-binding activity. The antigenic regions are analyzed in terms of their three-dimensional locations and the enzyme active site. With the previous localization of the antigenic regions on the BoNT/B H chain, the human Ab recognition of the entire BoNT/B molecule is presented and compared to the recognition of BoNT/A by human blocking Abs. Copyright © 2011. Published by Elsevier GmbH.

  10. A pattern recognition account of decision making.

    Science.gov (United States)

    Massaro, D W

    1994-09-01

    In the domain of pattern recognition, experiments have shown that perceivers integrate multiple sources of information in an optimal manner. In contrast, other research has been interpreted to mean that decision making is nonoptimal. As an example, Tversky and Kahneman (1983) have shown that subjects commit a conjunction fallacy because they judge it more likely that a fictitious person named Linda is a bank teller and a feminist than just a bank teller. This judgment supposedly violates probability theory, because the probability of two events can never be greater than the probability of either event alone. The present research tests the hypothesis that subjects interpret this judgment task as a pattern recognition task. If this hypothesis is correct, subjects' judgments should be described accurately by the fuzzy logical model of perception (FLMP)--a successful model of pattern recognition. In the first experiment, the Linda task was extended to an expanded factorial design with five vocations and five avocations. The probability ratings were described well by the FLMP and described poorly by a simple probability model. The second experiment included (1) two fictitious people, Linda and Joan, as response alternatives and (2) both ratings and categorization judgments. Although the ratings were accurately described by both the FLMP and an averaging of the sources of information, the categorization judgments were described better by the FLMP. These results reveal important similarities in recognizing patterns and in decision making. Given that the FLMP is an optimal method for combining multiple sources of information, the probability judgments appear to be optimal in the same manner as pattern-recognition judgments.

  11. Molecularly Imprinted Polymer Technology: A Powerful, Generic ...

    African Journals Online (AJOL)

    Molecularly Imprinted Polymer Technology: A Powerful, Generic, Facile and Cost Effective Alternative for Enantio-recognition and Separation: A Glance at Advances and Applications. ... Tanzania Journal of Science. Journal Home · ABOUT ...

  12. Threshold models of recognition and the recognition heuristic

    Directory of Open Access Journals (Sweden)

    Edgar Erdfelder

    2011-02-01

    Full Text Available According to the recognition heuristic (RH theory, decisions follow the recognition principle: Given a high validity of the recognition cue, people should prefer recognized choice options compared to unrecognized ones. Assuming that the memory strength of choice options is strongly correlated with both the choice criterion and recognition judgments, the RH is a reasonable strategy that approximates optimal decisions with a minimum of cognitive effort (Davis-Stober, Dana, and Budescu, 2010. However, theories of recognition memory are not generally compatible with this assumption. For example, some threshold models of recognition presume that recognition judgments can arise from two types of cognitive states: (1 certainty states in which judgments are almost perfectly correlated with memory strength and (2 uncertainty states in which recognition judgments reflect guessing rather than differences in memory strength. We report an experiment designed to test the prediction that the RH applies to certainty states only. Our results show that memory states rather than recognition judgments affect use of recognition information in binary decisions.

  13. Structural insights into the recognition of phosphopeptide by the FHA domain of kanadaptin

    DEFF Research Database (Denmark)

    Xu, Qingping; Deller, Marc C; Nielsen, Tine K

    2014-01-01

    with a phosphopeptide mimic derived from a peptide segment from the N-terminus of a symmetry-related molecule as well as a sulfate bound to the structurally conserved phosphothreonine recognition cleft. This structure provides insights into the molecular recognition features utilized by this family of proteins...

  14. Ficolins and FIBCD1: Soluble and membrane bound pattern recognition molecules with acetyl group selectivity

    DEFF Research Database (Denmark)

    Thomsen, Theresa; Schlosser, Anders; Holmskov, Uffe

    2011-01-01

    as pattern recognition molecules. Ficolins are soluble oligomeric proteins composed of trimeric collagen-like regions linked to fibrinogen-related domains (FReDs) that have the ability to sense molecular patterns on both pathogens and apoptotic cell surfaces and activate the complement system. The ficolins......D-containing molecules, and discusses structural resemblance but also diversity in recognition of acetylated ligands....

  15. The NA50 segmented target and vertex recognition system

    International Nuclear Information System (INIS)

    Bellaiche, F.; Cheynis, B.; Contardo, D.; Drapier, O.; Grossiord, J.Y.; Guichard, A.; Haroutunian, R.; Jacquin, M.; Ohlsson-Malek, F.; Pizzi, J.R.

    1997-01-01

    The NA50 segmented target and vertex recognition system is described. The segmented target consists of 7 sub-targets of 1-2 mm thickness. The vertex recognition system used to determine the sub-target where an interaction has occured is based upon quartz elements which produce Cerenkov light when traversed by charged particles from the interaction. The geometrical arrangement of the quartz elements has been optimized for vertex recognition in 208 Pb-Pb collisions at 158 GeV/nucleon. A simple algorithm provides a vertex recognition efficiency of better than 85% for dimuon trigger events collected with a 1 mm sub-target set-up. A method for recognizing interactions of projectile fragments (nuclei and/or groups of nucleons) is presented. The segmented target allows a large target thickness which together with a high beam intensity (∼10 7 ions/s) enables high statistics measurements. (orig.)

  16. A bacterial tyrosine phosphatase inhibits plant pattern recognition receptor activation

    Science.gov (United States)

    Perception of pathogen-associated molecular patterns (PAMPs) by surface-localised pattern-recognition receptors (PRRs) is a key component of plant innate immunity. Most known plant PRRs are receptor kinases and initiation of PAMP-triggered immunity (PTI) signalling requires phosphorylation of the PR...

  17. Electrochromic Molecular Imprinting Sensor for Visual and Smartphone-Based Detections.

    Science.gov (United States)

    Capoferri, Denise; Álvarez-Diduk, Ruslan; Del Carlo, Michele; Compagnone, Dario; Merkoçi, Arben

    2018-05-01

    Electrochromic effect and molecularly imprinted technology have been used to develop a sensitive and selective electrochromic sensor. The polymeric matrices obtained using the imprinting technology are robust molecular recognition elements and have the potential to mimic natural recognition entities with very high selectivity. The electrochromic behavior of iridium oxide nanoparticles (IrOx NPs) as physicochemical transducer together with a molecularly imprinted polymer (MIP) as recognition layer resulted in a fast and efficient translation of the detection event. The sensor was fabricated using screen-printing technology with indium tin oxide as a transparent working electrode; IrOx NPs where electrodeposited onto the electrode followed by thermal polymerization of polypyrrole in the presence of the analyte (chlorpyrifos). Two different approaches were used to detect and quantify the pesticide: direct visual detection and smartphone imaging. Application of different oxidation potentials for 10 s resulted in color changes directly related to the concentration of the analyte. For smartphone imaging, at fixed potential, the concentration of the analyte was dependent on the color intensity of the electrode. The electrochromic sensor detects a highly toxic compound (chlorpyrifos) with a 100 fM and 1 mM dynamic range. So far, to the best of our knowledge, this is the first work where an electrochromic MIP sensor uses the electrochromic properties of IrOx to detect a certain analyte with high selectivity and sensitivity.

  18. Pedestrian Movement Direction Recognition Using Convolutional Neural Networks

    OpenAIRE

    Dominguez-Sanchez, Alex; Cazorla, Miguel; Orts-Escolano, Sergio

    2017-01-01

    Pedestrian movement direction recognition is an important factor in autonomous driver assistance and security surveillance systems. Pedestrians are the most crucial and fragile moving objects in streets, roads, and events, where thousands of people may gather on a regular basis. People flow analysis on zebra crossings and in shopping centers or events such as demonstrations are a key element to improve safety and to enable autonomous cars to drive in real life environments. This paper focuses...

  19. Re-thinking employee recognition: understanding employee experiences of recognition

    OpenAIRE

    Smith, Charlotte

    2013-01-01

    Despite widespread acceptance of the importance of employee recognition for both individuals and organisations and evidence of its increasing use in organisations, employee recognition has received relatively little focused attention from academic researchers. Particularly lacking is research exploring the lived experience of employee recognition and the interpretations and meanings which individuals give to these experiences. Drawing on qualitative interviews conducted as part of my PhD rese...

  20. The Coding of Biological Information: From Nucleotide Sequence to Protein Recognition

    Science.gov (United States)

    Štambuk, Nikola

    The paper reviews the classic results of Swanson, Dayhoff, Grantham, Blalock and Root-Bernstein, which link genetic code nucleotide patterns to the protein structure, evolution and molecular recognition. Symbolic representation of the binary addresses defining particular nucleotide and amino acid properties is discussed, with consideration of: structure and metric of the code, direct correspondence between amino acid and nucleotide information, and molecular recognition of the interacting protein motifs coded by the complementary DNA and RNA strands.

  1. Event Index - a LHCb Event Search System

    CERN Document Server

    INSPIRE-00392208; Kazeev, Nikita; Redkin, Artem

    2015-12-23

    LHC experiments generate up to $10^{12}$ events per year. This paper describes Event Index - an event search system. Event Index's primary function is quickly selecting subsets of events from a combination of conditions, such as the estimated decay channel or stripping lines output. Event Index is essentially Apache Lucene optimized for read-only indexes distributed over independent shards on independent nodes.

  2. An ERP Study on Self-Relevant Object Recognition

    Science.gov (United States)

    Miyakoshi, Makoto; Nomura, Michio; Ohira, Hideki

    2007-01-01

    We performed an event-related potential study to investigate the self-relevance effect in object recognition. Three stimulus categories were prepared: SELF (participant's own objects), FAMILIAR (disposable and public objects, defined as objects with less-self-relevant familiarity), and UNFAMILIAR (others' objects). The participants' task was to…

  3. Neural network application to the neutral meson recognition

    International Nuclear Information System (INIS)

    Lefevre, F.; Delagrange, H.; Merrouch, R.; Ostendorf, R.; Schutz, Y.; Matulewicz, T.

    1991-01-01

    The combinatorial background produced by high photon multiplicities expected in TAPS experiments causes problems in precise meson recognition. We use neural networks to reduce this background. First we give a description of this technique, hereafter the first results obtained by applying this method to simulated events and future perspective will be discussed [fr

  4. Activity Recognition and Localization on a Truck Parking Lot

    NARCIS (Netherlands)

    Andersson, M.; Patino, L.; Burghouts, G.J.; Flizikowski, A.; Evans, M.; Gustafsson, D.; Petersson, H.; Schutte, K.; Ferryman, J.

    2013-01-01

    In this paper we present a set of activity recognition and localization algorithms that together assemble a large amount of information about activities on a parking lot. The aim is to detect and recognize events that may pose a threat to truck drivers and trucks. The algorithms perform zone-based

  5. An open-label randomized controlled trial of low molecular weight heparin compared to heparin and coumadin for the treatment of venous thromboembolic events in children: the REVIVE trial.

    Science.gov (United States)

    Massicotte, Patricia; Julian, Jim A; Gent, Michael; Shields, Karen; Marzinotto, Velma; Szechtman, Barbara; Andrew, Maureen

    2003-01-25

    Venous thromboembolic events (VTE) are serious complications in children and for which the standard of care, unfractionated heparin followed by oral anticoagulation (UFH/OA), is problematic. The objective of REVIVE was to compare the efficacy and safety of a low molecular weight heparin (reviparin-sodium) to UFH/OA for the treatment of VTE in children. This multicenter, open-label study, with blinded central outcome adjudication, randomized patients with objectively confirmed VTE to receive either reviparin-sodium or UFH/OA. Dose adjustments were made using nomograms. The efficacy outcome was based on recurrent VTE and death due to VTE during the 3-month treatment period. The safety outcomes were major bleeding, minor bleeding and death. Due to slow patient accrual, REVIVE was closed prematurely. At 3 months, with reviparin-sodium, 2/36 patients (5.6%) had recurrent VTE or death compared to 4/40 patients (10.0%) receiving UFH/OA (odds ratio=0.53; 95% CI=(0.05, 4.00); Fisher's exact test: 2P=0.677). There were 7 major bleeds, 2/36 (5.6%) in the reviparin-sodium group and 5/40 (12.5%) in UFH/OA group (odds ratio=0.41; 95% confidence interval 0.04, 2.76); Fisher's exact test: P=0.435). There were 5 deaths during the study period, 1 (2.8%) in the reviparin-sodium group and 4 (10.0%) in the UFH/OA group. All five deaths were unrelated to VTE but one was due to an intracranial hemorrhage in the UFH/OA group. Although limited by small sample size, REVIVE provides valuable information on the incidence of recurrent VTE, major bleeding and problematic issues associated with therapy of VTE in children.

  6. Human activity recognition and prediction

    CERN Document Server

    2016-01-01

    This book provides a unique view of human activity recognition, especially fine-grained human activity structure learning, human-interaction recognition, RGB-D data based action recognition, temporal decomposition, and causality learning in unconstrained human activity videos. The techniques discussed give readers tools that provide a significant improvement over existing methodologies of video content understanding by taking advantage of activity recognition. It links multiple popular research fields in computer vision, machine learning, human-centered computing, human-computer interaction, image classification, and pattern recognition. In addition, the book includes several key chapters covering multiple emerging topics in the field. Contributed by top experts and practitioners, the chapters present key topics from different angles and blend both methodology and application, composing a solid overview of the human activity recognition techniques. .

  7. [Comparative studies of face recognition].

    Science.gov (United States)

    Kawai, Nobuyuki

    2012-07-01

    Every human being is proficient in face recognition. However, the reason for and the manner in which humans have attained such an ability remain unknown. These questions can be best answered-through comparative studies of face recognition in non-human animals. Studies in both primates and non-primates show that not only primates, but also non-primates possess the ability to extract information from their conspecifics and from human experimenters. Neural specialization for face recognition is shared with mammals in distant taxa, suggesting that face recognition evolved earlier than the emergence of mammals. A recent study indicated that a social insect, the golden paper wasp, can distinguish their conspecific faces, whereas a closely related species, which has a less complex social lifestyle with just one queen ruling a nest of underlings, did not show strong face recognition for their conspecifics. Social complexity and the need to differentiate between one another likely led humans to evolve their face recognition abilities.

  8. Genetic specificity of face recognition.

    Science.gov (United States)

    Shakeshaft, Nicholas G; Plomin, Robert

    2015-10-13

    Specific cognitive abilities in diverse domains are typically found to be highly heritable and substantially correlated with general cognitive ability (g), both phenotypically and genetically. Recent twin studies have found the ability to memorize and recognize faces to be an exception, being similarly heritable but phenotypically substantially uncorrelated both with g and with general object recognition. However, the genetic relationships between face recognition and other abilities (the extent to which they share a common genetic etiology) cannot be determined from phenotypic associations. In this, to our knowledge, first study of the genetic associations between face recognition and other domains, 2,000 18- and 19-year-old United Kingdom twins completed tests assessing their face recognition, object recognition, and general cognitive abilities. Results confirmed the substantial heritability of face recognition (61%), and multivariate genetic analyses found that most of this genetic influence is unique and not shared with other cognitive abilities.

  9. Control of DNA hybridization by photoswitchable molecular glue.

    Science.gov (United States)

    Dohno, Chikara; Nakatani, Kazuhiko

    2011-12-01

    Hybridization of DNA is one of the most intriguing events in molecular recognition and is essential for living matter to inherit life beyond generations. In addition to the function of DNA as genetic material, DNA hybridization is a key to control the function of DNA-based materials in nanoscience. Since the hybridization of two single stranded DNAs is a thermodynamically favorable process, dissociation of the once formed DNA duplex is normally unattainable under isothermal conditions. As the progress of DNA-based nanoscience, methodology to control the DNA hybridization process has become increasingly important. Besides many reports using the chemically modified DNA for the regulation of hybridization, we focused our attention on the use of a small ligand as the molecular glue for the DNA. In 2001, we reported the first designed molecule that strongly and specifically bound to the mismatched base pairs in double stranded DNA. Further studies on the mismatch binding molecules provided us a key discovery of a novel mode of the binding of a mismatch binding ligand that induced the base flipping. With these findings we proposed the concept of molecular glue for DNA for the unidirectional control of DNA hybridization and, eventually photoswitchable molecular glue for DNA, which enabled the bidirectional control of hybridization under photoirradiation. In this tutorial review, we describe in detail how we integrated the mismatch binding ligand into photoswitchable molecular glue for DNA, and the application and perspective in DNA-based nanoscience.

  10. Simulating events

    Energy Technology Data Exchange (ETDEWEB)

    Ferretti, C; Bruzzone, L [Techint Italimpianti, Milan (Italy)

    2000-06-01

    The Petacalco Marine terminal on the Pacific coast in the harbour of Lazaro Carclenas (Michoacan) in Mexico, provides coal to the thermoelectric power plant at Pdte Plutarco Elias Calles in the port area. The plant is being converted from oil to burn coal to generate 2100 MW of power. The article describes the layout of the terminal and equipment employed in the unloading, coal stacking, coal handling areas and the receiving area at the power plant. The contractor Techint Italimpianti has developed a software system, MHATIS, for marine terminal management which is nearly complete. The discrete event simulator with its graphic interface provides a real-type decision support system for simulating changes to the terminal operations and evaluating impacts. The article describes how MHATIS is used. 7 figs.

  11. Event generators

    International Nuclear Information System (INIS)

    Durand, D.; Gulminelli, F.; Lopez, O.; Vient, E.

    1998-01-01

    The results concerning the heavy ion collision simulations at Fermi energies by means of phenomenological models obtained in the last two years ar presented. The event generators are essentially following the phase of elaboration of analysis methods of data obtained by INDRA or NAUTILUS 4 π multidetectors. To identify and correctly quantify a phenomenon or a physical quantity it is necessary to verify by simulation the feasibility and validity of the analysis and also to estimate the bias introduced by the experimental filter. Many studies have shown this, for instance: the determination of the collision reaction plan for flow studies, determination of kinematical characteristics of the quasi-projectiles, and the excitation energy measurement stored in the hot nuclei. To Eugene, the currently utilised generator, several improvements were added: introduction of space-time correlations between the different products emitted in the decay of excited nuclei by calculating the trajectories of the particles in the final phase of the reaction; taking into account in the decay cascade of the discrete levels of the lighter fragments; the possibility of the schematically description of the explosion of the nucleus by simultaneous emission of multi-fragments. Thus, by comparing the calculations with the data relative to heavy systems studied with the NAUTILUS assembly it was possible to extract the time scales in the nuclear fragmentation. The utilisation of these event generators was extended to the analysis of INDRA data concerning the determination of the vaporization threshold in the collisions Ar + Ni and also the research of the expansion effects in the collisions Xe + Sn at 50 MeV/u

  12. Pattern recognition methods for acoustic emission analysis

    International Nuclear Information System (INIS)

    Doctor, P.G.; Harrington, T.P.; Hutton, P.H.

    1979-07-01

    Models have been developed that relate the rate of acoustic emissions to structural integrity. The implementation of these techniques in the field has been hindered by the noisy environment in which the data must be taken. Acoustic emissions from noncritical sources are recorded in addition to those produced by critical sources, such as flaws. A technique is discussed for prescreening acoustic events and filtering out those that are produced by noncritical sources. The methodology that was investigated is pattern recognition. Three different pattern recognition techniques were applied to a data set that consisted of acoustic emissions caused by crack growth and acoustic signals caused by extraneous noise sources. Examination of the acoustic emission data presented has uncovered several features of the data that can provide a reasonable filter. Two of the most valuable features are the frequency of maximum response and the autocorrelation coefficient at Lag 13. When these two features and several others were combined with a least squares decision algorithm, 90% of the acoustic emissions in the data set were correctly classified. It appears possible to design filters that eliminate extraneous noise sources from flaw-growth acoustic emissions using pattern recognition techniques

  13. Speech Recognition on Mobile Devices

    DEFF Research Database (Denmark)

    Tan, Zheng-Hua; Lindberg, Børge

    2010-01-01

    in the mobile context covering motivations, challenges, fundamental techniques and applications. Three ASR architectures are introduced: embedded speech recognition, distributed speech recognition and network speech recognition. Their pros and cons and implementation issues are discussed. Applications within......The enthusiasm of deploying automatic speech recognition (ASR) on mobile devices is driven both by remarkable advances in ASR technology and by the demand for efficient user interfaces on such devices as mobile phones and personal digital assistants (PDAs). This chapter presents an overview of ASR...

  14. Markov Models for Handwriting Recognition

    CERN Document Server

    Plotz, Thomas

    2011-01-01

    Since their first inception, automatic reading systems have evolved substantially, yet the recognition of handwriting remains an open research problem due to its substantial variation in appearance. With the introduction of Markovian models to the field, a promising modeling and recognition paradigm was established for automatic handwriting recognition. However, no standard procedures for building Markov model-based recognizers have yet been established. This text provides a comprehensive overview of the application of Markov models in the field of handwriting recognition, covering both hidden

  15. Allergen recognition by innate immune cells: critical role of dendritic and epithelial cells

    Directory of Open Access Journals (Sweden)

    Fabian eSalazar

    2013-11-01

    Full Text Available Allergy is an exacerbated response of the immune system against non-self-proteins called allergens and is typically characterized by biased type-2 T helper cell and deleterious IgE mediated immune responses. The allergic cascade starts with the recognition of allergens by antigen presenting cells, mainly dendritic cells, culminating in mast cell sensitization and triggering. Dendritic cells have been demonstrated to play a crucial role in orchestrating allergic diseases. Using different C-type lectin receptors dendritic cells are able to recognize and internalize a number of allergens from diverse sources leading to sensitization. Furthermore, there is increasing evidence highlighting the role of epithelial cells in triggering and modulating immune responses to allergens. As well as providing a physical barrier, epithelial cells can interact with allergens and influence dendritic cells behaviour through the release of a number of Th2 promoting cytokines. In this review we will summarise current understanding of how allergens are recognised by dendritic cells and epithelial cells and what are the consequences of such interaction in the context of allergic sensitisation and downstream events leading to allergic inflammation. Better understanding of the molecular mechanisms of allergen recognition and associated signalling pathways could enable developing more effective therapeutic strategies that target the initial steps of allergic sensitisation hence hindering development or progression of allergic diseases.

  16. Piezoelectric sensors based on molecular imprinted polymers for detection of low molecular mass analytes.

    Science.gov (United States)

    Uludağ, Yildiz; Piletsky, Sergey A; Turner, Anthony P F; Cooper, Matthew A

    2007-11-01

    Biomimetic recognition elements employed for the detection of analytes are commonly based on proteinaceous affibodies, immunoglobulins, single-chain and single-domain antibody fragments or aptamers. The alternative supra-molecular approach using a molecularly imprinted polymer now has proven utility in numerous applications ranging from liquid chromatography to bioassays. Despite inherent advantages compared with biochemical/biological recognition (which include robustness, storage endurance and lower costs) there are few contributions that describe quantitative analytical applications of molecularly imprinted polymers for relevant small molecular mass compounds in real-world samples. There is, however, significant literature describing the use of low-power, portable piezoelectric transducers to detect analytes in environmental monitoring and other application areas. Here we review the combination of molecularly imprinted polymers as recognition elements with piezoelectric biosensors for quantitative detection of small molecules. Analytes are classified by type and sample matrix presentation and various molecularly imprinted polymer synthetic fabrication strategies are also reviewed.

  17. Track recognition with an associative pattern memory

    International Nuclear Information System (INIS)

    Bok, H.W. den; Visschers, J.L.; Borgers, A.J.; Lourens, W.

    1991-01-01

    Using Programmable Gate Arrays (PGAs), a prototype for a fast Associative Pattern Memory module has been realized. The associative memory performs the recognition of tracks within the hadron detector data acquisition system at NIKHEF-K. The memory matches the detector state with a set of 24 predefined tracks to identify the particle tracks that occur during an event. This information enables the trigger hardware to classify and select or discriminate the event. Mounted on a standard size (6U) VME board, several PGAs together form an associative memory. The internal logic architecture of the Gate Array is used in such a way as to minimize signal propagation delay. The memory cells, containing a binary representation of the particle tracks, are dynamically loadable through a VME bus interface, providing a high level of flexibility. The hadron detector and its readout system are briefly described and our track representation method is presented. Results from measurements under experimental conditions are discussed. (orig.)

  18. Events diary

    Science.gov (United States)

    2000-01-01

    as Imperial College, the Royal Albert Hall, the Royal College of Art, the Natural History and Science Museums and the Royal Geographical Society. Under the heading `Shaping the future together' BA2000 will explore science, engineering and technology in their wider cultural context. Further information about this event on 6 - 12 September may be obtained from Sandra Koura, BA2000 Festival Manager, British Association for the Advancement of Science, 23 Savile Row, London W1X 2NB (tel: 0171 973 3075, e-mail: sandra.koura@britassoc.org.uk ). Details of the creating SPARKS events may be obtained from creating.sparks@britassoc.org.uk or from the website www.britassoc.org.uk . Other events 3 - 7 July, Porto Alegre, Brazil VII Interamerican conference on physics education: The preparation of physicists and physics teachers in contemporary society. Info: IACPE7@if.ufrgs.br or cabbat1.cnea.gov.ar/iacpe/iacpei.htm 27 August - 1 September, Barcelona, Spain GIREP conference: Physics teacher education beyond 2000. Info: www.blues.uab.es/phyteb/index.html

  19. Geophysical events

    Science.gov (United States)

    This is a summary of SEAN Bulletin, 13(3), March 31, 1988, a publication of the Smithsonian Institution's Scientific Event Alert Network. The complete bulletin is available in the microfiche edition of Eos as a microfiche supplement or as a paper reprint. For the microfiche, order document E88-002 at $2.50 (U.S.) by writing to AGU Orders, 2000 Florida Avenue, N.W., Washington, DC 20009 or by calling toll free on 800-424-2488. For the paper reprint, order SEAN Bulletin (giving volume and issue numbers and issue date) through the same address; the price is $3.50 for one copy of each issue number for those who do not have a deposit account, $2 for those who do; additional copies of each issue number are $1. Subscriptions to SEAN Bulletin are also available from AGU-Orders; the price is $18 for 12 monthly issues mailed to a U.S. address, $28 if mailed elsewhere, and must be prepaid.

  20. SAR: Stroke Authorship Recognition

    KAUST Repository

    Shaheen, Sara; Rockwood, Alyn; Ghanem, Bernard

    2015-01-01

    Are simple strokes unique to the artist or designer who renders them? If so, can this idea be used to identify authorship or to classify artistic drawings? Also, could training methods be devised to develop particular styles? To answer these questions, we propose the Stroke Authorship Recognition (SAR) approach, a novel method that distinguishes the authorship of 2D digitized drawings. SAR converts a drawing into a histogram of stroke attributes that is discriminative of authorship. We provide extensive classification experiments on a large variety of data sets, which validate SAR's ability to distinguish unique authorship of artists and designers. We also demonstrate the usefulness of SAR in several applications including the detection of fraudulent sketches, the training and monitoring of artists in learning a particular new style and the first quantitative way to measure the quality of automatic sketch synthesis tools. © 2015 The Eurographics Association and John Wiley & Sons Ltd.