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Sample records for biomolecular structures functional

  1. Multiscale Persistent Functions for Biomolecular Structure Characterization

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Kelin [Nanyang Technological University (Singapore). Division of Mathematical Sciences, School of Physical, Mathematical Sciences and School of Biological Sciences; Li, Zhiming [Central China Normal University, Wuhan (China). Key Laboratory of Quark and Lepton Physics (MOE) and Institute of Particle Physics; Mu, Lin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computer Science and Mathematics Division

    2017-11-02

    Here in this paper, we introduce multiscale persistent functions for biomolecular structure characterization. The essential idea is to combine our multiscale rigidity functions (MRFs) with persistent homology analysis, so as to construct a series of multiscale persistent functions, particularly multiscale persistent entropies, for structure characterization. To clarify the fundamental idea of our method, the multiscale persistent entropy (MPE) model is discussed in great detail. Mathematically, unlike the previous persistent entropy (Chintakunta et al. in Pattern Recognit 48(2):391–401, 2015; Merelli et al. in Entropy 17(10):6872–6892, 2015; Rucco et al. in: Proceedings of ECCS 2014, Springer, pp 117–128, 2016), a special resolution parameter is incorporated into our model. Various scales can be achieved by tuning its value. Physically, our MPE can be used in conformational entropy evaluation. More specifically, it is found that our method incorporates in it a natural classification scheme. This is achieved through a density filtration of an MRF built from angular distributions. To further validate our model, a systematical comparison with the traditional entropy evaluation model is done. Additionally, it is found that our model is able to preserve the intrinsic topological features of biomolecular data much better than traditional approaches, particularly for resolutions in the intermediate range. Moreover, by comparing with traditional entropies from various grid sizes, bond angle-based methods and a persistent homology-based support vector machine method (Cang et al. in Mol Based Math Biol 3:140–162, 2015), we find that our MPE method gives the best results in terms of average true positive rate in a classic protein structure classification test. More interestingly, all-alpha and all-beta protein classes can be clearly separated from each other with zero error only in our model. Finally, a special protein structure index (PSI) is proposed, for the first

  2. From dynamics to structure and function of model biomolecular systems

    NARCIS (Netherlands)

    Fontaine-Vive-Curtaz, F.

    2007-01-01

    The purpose of this thesis was to extend recent works on structure and dynamics of hydrogen bonded crystals to model biomolecular systems and biological processes. The tools that we have used are neutron scattering (NS) and density functional theory (DFT) and force field (FF) based simulation

  3. A unified framework for unraveling the functional interaction structure of a biomolecular network based on stimulus-response experimental data.

    Science.gov (United States)

    Cho, Kwang-Hyun; Choo, Sang-Mok; Wellstead, Peter; Wolkenhauer, Olaf

    2005-08-15

    We propose a unified framework for the identification of functional interaction structures of biomolecular networks in a way that leads to a new experimental design procedure. In developing our approach, we have built upon previous work. Thus we begin by pointing out some of the restrictions associated with existing structure identification methods and point out how these restrictions may be eased. In particular, existing methods use specific forms of experimental algebraic equations with which to identify the functional interaction structure of a biomolecular network. In our work, we employ an extended form of these experimental algebraic equations which, while retaining their merits, also overcome some of their disadvantages. Experimental data are required in order to estimate the coefficients of the experimental algebraic equation set associated with the structure identification task. However, experimentalists are rarely provided with guidance on which parameters to perturb, and to what extent, to perturb them. When a model of network dynamics is required then there is also the vexed question of sample rate and sample time selection to be resolved. Supplying some answers to these questions is the main motivation of this paper. The approach is based on stationary and/or temporal data obtained from parameter perturbations, and unifies the previous approaches of Kholodenko et al. (PNAS 99 (2002) 12841-12846) and Sontag et al. (Bioinformatics 20 (2004) 1877-1886). By way of demonstration, we apply our unified approach to a network model which cannot be properly identified by existing methods. Finally, we propose an experiment design methodology, which is not limited by the amount of parameter perturbations, and illustrate its use with an in numero example.

  4. Biomolecular structure refinement using the GROMOS simulation software

    International Nuclear Information System (INIS)

    Schmid, Nathan; Allison, Jane R.; Dolenc, Jožica; Eichenberger, Andreas P.; Kunz, Anna-Pitschna E.; Gunsteren, Wilfred F. van

    2011-01-01

    For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, 3 J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure refinement combining different types of experimental data with different types of restraining functions, while using a variety of methods to enhance conformational searching and sampling and the thermodynamically calibrated GROMOS force field for biomolecular simulation.

  5. Biomolecular structure refinement using the GROMOS simulation software

    Energy Technology Data Exchange (ETDEWEB)

    Schmid, Nathan; Allison, Jane R.; Dolenc, Jozica; Eichenberger, Andreas P.; Kunz, Anna-Pitschna E.; Gunsteren, Wilfred F. van, E-mail: wfvgn@igc.phys.chem.ethz.ch [Swiss Federal Institute of Technology ETH, Laboratory of Physical Chemistry (Switzerland)

    2011-11-15

    For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, {sup 3}J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure refinement combining different types of experimental data with different types of restraining functions, while using a variety of methods to enhance conformational searching and sampling and the thermodynamically calibrated GROMOS force field for biomolecular simulation.

  6. hPDB – Haskell library for processing atomic biomolecular structures in protein data bank format

    OpenAIRE

    Gajda, Michał Jan

    2013-01-01

    Background Protein DataBank file format is used for the majority of biomolecular data available today. Haskell is a lazy functional language that enjoys a high-level class-based type system, a growing collection of useful libraries and a reputation for efficiency. Findings I present a fast library for processing biomolecular data in the Protein Data Bank format. I present benchmarks indicating that this library is faster than other frequently used Protein Data Bank parsing programs. The propo...

  7. Computer Programming and Biomolecular Structure Studies: A Step beyond Internet Bioinformatics

    Science.gov (United States)

    Likic, Vladimir A.

    2006-01-01

    This article describes the experience of teaching structural bioinformatics to third year undergraduate students in a subject titled "Biomolecular Structure and Bioinformatics." Students were introduced to computer programming and used this knowledge in a practical application as an alternative to the well established Internet bioinformatics…

  8. Prediction of Biomolecular Complexes

    KAUST Repository

    Vangone, Anna

    2017-04-12

    Almost all processes in living organisms occur through specific interactions between biomolecules. Any dysfunction of those interactions can lead to pathological events. Understanding such interactions is therefore a crucial step in the investigation of biological systems and a starting point for drug design. In recent years, experimental studies have been devoted to unravel the principles of biomolecular interactions; however, due to experimental difficulties in solving the three-dimensional (3D) structure of biomolecular complexes, the number of available, high-resolution experimental 3D structures does not fulfill the current needs. Therefore, complementary computational approaches to model such interactions are necessary to assist experimentalists since a full understanding of how biomolecules interact (and consequently how they perform their function) only comes from 3D structures which provide crucial atomic details about binding and recognition processes. In this chapter we review approaches to predict biomolecular complexesBiomolecular complexes, introducing the concept of molecular dockingDocking, a technique which uses a combination of geometric, steric and energetics considerations to predict the 3D structure of a biological complex starting from the individual structures of its constituent parts. We provide a mini-guide about docking concepts, its potential and challenges, along with post-docking analysis and a list of related software.

  9. Prediction of Biomolecular Complexes

    KAUST Repository

    Vangone, Anna; Oliva, Romina; Cavallo, Luigi; Bonvin, Alexandre M. J. J.

    2017-01-01

    Almost all processes in living organisms occur through specific interactions between biomolecules. Any dysfunction of those interactions can lead to pathological events. Understanding such interactions is therefore a crucial step in the investigation of biological systems and a starting point for drug design. In recent years, experimental studies have been devoted to unravel the principles of biomolecular interactions; however, due to experimental difficulties in solving the three-dimensional (3D) structure of biomolecular complexes, the number of available, high-resolution experimental 3D structures does not fulfill the current needs. Therefore, complementary computational approaches to model such interactions are necessary to assist experimentalists since a full understanding of how biomolecules interact (and consequently how they perform their function) only comes from 3D structures which provide crucial atomic details about binding and recognition processes. In this chapter we review approaches to predict biomolecular complexesBiomolecular complexes, introducing the concept of molecular dockingDocking, a technique which uses a combination of geometric, steric and energetics considerations to predict the 3D structure of a biological complex starting from the individual structures of its constituent parts. We provide a mini-guide about docking concepts, its potential and challenges, along with post-docking analysis and a list of related software.

  10. Minimal metabolic pathway structure is consistent with associated biomolecular interactions

    DEFF Research Database (Denmark)

    Bordbar, Aarash; Nagarajan, Harish; Lewis, Nathan E.

    2014-01-01

    Pathways are a universal paradigm for functionally describing cellular processes. Even though advances in high-throughput data generation have transformed biology, the core of our biological understanding, and hence data interpretation, is still predicated on human-defined pathways. Here, we......, effectively doubling the known regulatory roles for Nac and MntR. This study suggests an underlying and fundamental principle in the evolutionary selection of pathway structures; namely, that pathways may be minimal, independent, and segregated....

  11. Charge patterns as templates for the assembly of layered biomolecular structures.

    Science.gov (United States)

    Naujoks, Nicola; Stemmer, Andreas

    2006-08-01

    Electric fields are used to guide the assembly of biomolecules in predefined geometric patterns on solid substrates. Local surface charges serve as templates to selectively position proteins on thin-film polymeric electret layers, thereby creating a basis for site-directed layered assembly of biomolecular structures. Charge patterns are created using the lithographic capabilities of an atomic force microscope, namely by applying voltage pulses between a conductive tip and the sample. Samples consist of a poly(methyl methacrylate) layer on a p-doped silicon support. Subsequently, the sample is developed in a water-in-oil emulsion, consisting of a dispersed aqueous phase containing biotin-modified immunoglobulinG molecules, and a continuous nonpolar, insulating oil phase. The electrostatic fields cause a net force of (di)electrophoretic nature on the droplet, thereby guiding the proteins to the predefined locations. Due to the functionalization of the immunoglobulinG molecules with biotin-groups, these patterns can now be used to initiate the localized layer-by-layer assembly of biomolecules based on the avidin-biotin mechanism. By binding 40 nm sized biotin-labelled beads to the predefined locations via a streptavidin linker, we verify the functionality of the previously deposited immunoglobulinG-biotin. All assembly steps following the initial deposition of the immunoglobulinG from emulsion can conveniently be conducted in aqueous solutions. Results show that pattern definition is maintained after immersion into aqueous solution.

  12. HPDB-Haskell library for processing atomic biomolecular structures in Protein Data Bank format.

    Science.gov (United States)

    Gajda, Michał Jan

    2013-11-23

    Protein DataBank file format is used for the majority of biomolecular data available today. Haskell is a lazy functional language that enjoys a high-level class-based type system, a growing collection of useful libraries and a reputation for efficiency. I present a fast library for processing biomolecular data in the Protein Data Bank format. I present benchmarks indicating that this library is faster than other frequently used Protein Data Bank parsing programs. The proposed library also features a convenient iterator mechanism, and a simple API modeled after BioPython. I set a new standard for convenience and efficiency of Protein Data Bank processing in a Haskell library, and release it to open source.

  13. The structural bioinformatics library: modeling in biomolecular science and beyond.

    Science.gov (United States)

    Cazals, Frédéric; Dreyfus, Tom

    2017-04-01

    Software in structural bioinformatics has mainly been application driven. To favor practitioners seeking off-the-shelf applications, but also developers seeking advanced building blocks to develop novel applications, we undertook the design of the Structural Bioinformatics Library ( SBL , http://sbl.inria.fr ), a generic C ++/python cross-platform software library targeting complex problems in structural bioinformatics. Its tenet is based on a modular design offering a rich and versatile framework allowing the development of novel applications requiring well specified complex operations, without compromising robustness and performances. The SBL involves four software components (1-4 thereafter). For end-users, the SBL provides ready to use, state-of-the-art (1) applications to handle molecular models defined by unions of balls, to deal with molecular flexibility, to model macro-molecular assemblies. These applications can also be combined to tackle integrated analysis problems. For developers, the SBL provides a broad C ++ toolbox with modular design, involving core (2) algorithms , (3) biophysical models and (4) modules , the latter being especially suited to develop novel applications. The SBL comes with a thorough documentation consisting of user and reference manuals, and a bugzilla platform to handle community feedback. The SBL is available from http://sbl.inria.fr. Frederic.Cazals@inria.fr. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  14. Contemporary Use of Anomalous Diffraction in Biomolecular Structure Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Liu Q.; Hendrickson, W.

    2017-01-01

    The normal elastic X-ray scattering that depends only on electron density can be modulated by an ?anomalous? component due to resonance between X-rays and electronic orbitals. Anomalous scattering thereby precisely identifies atomic species, since orbitals distinguish atomic elements, which enables the multi- and single-wavelength anomalous diffraction (MAD and SAD) methods. SAD now predominates in de novo structure determination of biological macromolecules, and we focus here on the prevailing SAD method. We describe the anomalous phasing theory and the periodic table of phasing elements that are available for SAD experiments, differentiating between those readily accessible for at-resonance experiments and those that can be effective away from an edge. We describe procedures for present-day SAD phasing experiments and we discuss optimization of anomalous signals for challenging applications. We also describe methods for using anomalous signals as molecular markers for tracing and element identification. Emerging developments and perspectives are discussed in brief.

  15. Stable isotope applications in biomolecular structure and mechanisms. A meeting to bring together producers and users of stable-isotope-labeled compounds to assess current and future needs

    International Nuclear Information System (INIS)

    Trewhella, J.; Cross, T.A.; Unkefer, C.J.

    1994-12-01

    Knowledge of biomolecular structure is a prerequisite for understanding biomolecular function, and stable isotopes play an increasingly important role in structure determination of biological molecules. The first Conference on Stable Isotope Applications in Biomolecular Structure and Mechanisms was held in Santa Fe, New Mexico, March 27--31, 1994. More than 120 participants from 8 countries and 44 institutions reviewed significant developments, discussed the most promising applications for stable isotopes, and addressed future needs and challenges. Participants focused on applications of stable isotopes for studies of the structure and function of proteins, peptides, RNA, and DNA. Recent advances in NMR techniques neutron scattering, EPR, and vibrational spectroscopy were highlighted in addition to the production and synthesis of labeled compounds. This volume includes invited speaker and poster presentations as well as a set of reports from discussion panels that focused on the needs of the scientific community and the potential roles of private industry, the National Stable Isotope Resource, and the National High Magnetic Field Laboratory in serving those needs. This is the leading abstract. Individual papers are processed separately for the database

  16. Stable isotope applications in biomolecular structure and mechanisms. A meeting to bring together producers and users of stable-isotope-labeled compounds to assess current and future needs

    Energy Technology Data Exchange (ETDEWEB)

    Trewhella, J.; Cross, T.A.; Unkefer, C.J. [eds.

    1994-12-01

    Knowledge of biomolecular structure is a prerequisite for understanding biomolecular function, and stable isotopes play an increasingly important role in structure determination of biological molecules. The first Conference on Stable Isotope Applications in Biomolecular Structure and Mechanisms was held in Santa Fe, New Mexico, March 27--31, 1994. More than 120 participants from 8 countries and 44 institutions reviewed significant developments, discussed the most promising applications for stable isotopes, and addressed future needs and challenges. Participants focused on applications of stable isotopes for studies of the structure and function of proteins, peptides, RNA, and DNA. Recent advances in NMR techniques neutron scattering, EPR, and vibrational spectroscopy were highlighted in addition to the production and synthesis of labeled compounds. This volume includes invited speaker and poster presentations as well as a set of reports from discussion panels that focused on the needs of the scientific community and the potential roles of private industry, the National Stable Isotope Resource, and the National High Magnetic Field Laboratory in serving those needs. This is the leading abstract. Individual papers are processed separately for the database.

  17. Biomolecular Structure Information from High-Speed Quantum Mechanical Electronic Spectra Calculation.

    Science.gov (United States)

    Seibert, Jakob; Bannwarth, Christoph; Grimme, Stefan

    2017-08-30

    A fully quantum mechanical (QM) treatment to calculate electronic absorption (UV-vis) and circular dichroism (CD) spectra of typical biomolecules with thousands of atoms is presented. With our highly efficient sTDA-xTB method, spectra averaged along structures from molecular dynamics (MD) simulations can be computed in a reasonable time frame on standard desktop computers. This way, nonequilibrium structure and conformational, as well as purely quantum mechanical effects like charge-transfer or exciton-coupling, are included. Different from other contemporary approaches, the entire system is treated quantum mechanically and neither fragmentation nor system-specific adjustment is necessary. Among the systems considered are a large DNA fragment, oligopeptides, and even entire proteins in an implicit solvent. We propose the method in tandem with experimental spectroscopy or X-ray studies for the elucidation of complex (bio)molecular structures including metallo-proteins like myoglobin.

  18. A biomolecular recognition approach for the functionalization of cellulose with gold nanoparticles.

    Science.gov (United States)

    Almeida, A; Rosa, A M M; Azevedo, A M; Prazeres, D M F

    2017-09-01

    Materials with new and improved functionalities can be obtained by modifying cellulose with gold nanoparticles (AuNPs) via the in situ reduction of a gold precursor or the deposition or covalent immobilization of pre-synthesized AuNPs. Here, we present an alternative biomolecular recognition approach to functionalize cellulose with biotin-AuNPs that relies on a complex of 2 recognition elements: a ZZ-CBM3 fusion that combines a carbohydrate-binding module (CBM) with the ZZ fragment of the staphylococcal protein A and an anti-biotin antibody. Paper and cellulose microparticles with AuNPs immobilized via the ZZ-CBM3:anti-biotin IgG supramolecular complex displayed an intense red color, whereas essentially no color was detected when AuNPs were deposited over the unmodified materials. Scanning electron microscopy analysis revealed a homogeneous distribution of AuNPs when immobilized via ZZ-CBM3:anti-biotin IgG complexes and aggregation of AuNPs when deposited over paper, suggesting that color differences are due to interparticle plasmon coupling effects. The approach could be used to functionalize paper substrates and cellulose nanocrystals with AuNPs. More important, however, is the fact that the occurrence of a biomolecular recognition event between the CBM-immobilized antibody and its specific, AuNP-conjugated antigen is signaled by red color. This opens up the way for the development of simple and straightforward paper/cellulose-based tests where detection of a target analyte can be made by direct use of color signaling. Copyright © 2017 John Wiley & Sons, Ltd.

  19. Combining vibrational biomolecular spectroscopy with chemometric techniques for the study of response and sensitivity of molecular structures/functional groups mainly related to lipid biopolymer to various processing applications.

    Science.gov (United States)

    Yu, Gloria Qingyu; Yu, Peiqiang

    2015-09-01

    The objectives of this project were to (1) combine vibrational spectroscopy with chemometric multivariate techniques to determine the effect of processing applications on molecular structural changes of lipid biopolymer that mainly related to functional groups in green- and yellow-type Crop Development Centre (CDC) pea varieties [CDC strike (green-type) vs. CDC meadow (yellow-type)] that occurred during various processing applications; (2) relatively quantify the effect of processing applications on the antisymmetric CH3 ("CH3as") and CH2 ("CH2as") (ca. 2960 and 2923 cm(-1), respectively), symmetric CH3 ("CH3s") and CH2 ("CH2s") (ca. 2873 and 2954 cm(-1), respectively) functional groups and carbonyl C=O ester (ca. 1745 cm(-1)) spectral intensities as well as their ratios of antisymmetric CH3 to antisymmetric CH2 (ratio of CH3as to CH2as), ratios of symmetric CH3 to symmetric CH2 (ratio of CH3s to CH2s), and ratios of carbonyl C=O ester peak area to total CH peak area (ratio of C=O ester to CH); and (3) illustrate non-invasive techniques to detect the sensitivity of individual molecular functional group to the various processing applications in the recently developed different types of pea varieties. The hypothesis of this research was that processing applications modified the molecular structure profiles in the processed products as opposed to original unprocessed pea seeds. The results showed that the different processing methods had different impacts on lipid molecular functional groups. Different lipid functional groups had different sensitivity to various heat processing applications. These changes were detected by advanced molecular spectroscopy with chemometric techniques which may be highly related to lipid utilization and availability. The multivariate molecular spectral analyses, cluster analysis, and principal component analysis of original spectra (without spectral parameterization) are unable to fully distinguish the structural differences in the

  20. Biomolecular condensates: organizers of cellular biochemistry.

    Science.gov (United States)

    Banani, Salman F; Lee, Hyun O; Hyman, Anthony A; Rosen, Michael K

    2017-05-01

    Biomolecular condensates are micron-scale compartments in eukaryotic cells that lack surrounding membranes but function to concentrate proteins and nucleic acids. These condensates are involved in diverse processes, including RNA metabolism, ribosome biogenesis, the DNA damage response and signal transduction. Recent studies have shown that liquid-liquid phase separation driven by multivalent macromolecular interactions is an important organizing principle for biomolecular condensates. With this physical framework, it is now possible to explain how the assembly, composition, physical properties and biochemical and cellular functions of these important structures are regulated.

  1. Biomolecular EPR spectroscopy

    CERN Document Server

    Hagen, Wilfred Raymond

    2008-01-01

    Comprehensive, Up-to-Date Coverage of Spectroscopy Theory and its Applications to Biological SystemsAlthough a multitude of books have been published about spectroscopy, most of them only occasionally refer to biological systems and the specific problems of biomolecular EPR (bioEPR). Biomolecular EPR Spectroscopy provides a practical introduction to bioEPR and demonstrates how this remarkable tool allows researchers to delve into the structural, functional, and analytical analysis of paramagnetic molecules found in the biochemistry of all species on the planet. A Must-Have Reference in an Intrinsically Multidisciplinary FieldThis authoritative reference seamlessly covers all important bioEPR applications, including low-spin and high-spin metalloproteins, spin traps and spin lables, interaction between active sites, and redox systems. It is loaded with practical tricks as well as do's and don'ts that are based on the author's 30 years of experience in the field. The book also comes with an unprecedented set of...

  2. A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design.

    Science.gov (United States)

    Alford, Rebecca F; Leaver-Fay, Andrew; Gonzales, Lynda; Dolan, Erin L; Gray, Jeffrey J

    2017-12-01

    Computational biology is an interdisciplinary field, and many computational biology research projects involve distributed teams of scientists. To accomplish their work, these teams must overcome both disciplinary and geographic barriers. Introducing new training paradigms is one way to facilitate research progress in computational biology. Here, we describe a new undergraduate program in biomolecular structure prediction and design in which students conduct research at labs located at geographically-distributed institutions while remaining connected through an online community. This 10-week summer program begins with one week of training on computational biology methods development, transitions to eight weeks of research, and culminates in one week at the Rosetta annual conference. To date, two cohorts of students have participated, tackling research topics including vaccine design, enzyme design, protein-based materials, glycoprotein modeling, crowd-sourced science, RNA processing, hydrogen bond networks, and amyloid formation. Students in the program report outcomes comparable to students who participate in similar in-person programs. These outcomes include the development of a sense of community and increases in their scientific self-efficacy, scientific identity, and science values, all predictors of continuing in a science research career. Furthermore, the program attracted students from diverse backgrounds, which demonstrates the potential of this approach to broaden the participation of young scientists from backgrounds traditionally underrepresented in computational biology.

  3. A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design.

    Directory of Open Access Journals (Sweden)

    Rebecca F Alford

    2017-12-01

    Full Text Available Computational biology is an interdisciplinary field, and many computational biology research projects involve distributed teams of scientists. To accomplish their work, these teams must overcome both disciplinary and geographic barriers. Introducing new training paradigms is one way to facilitate research progress in computational biology. Here, we describe a new undergraduate program in biomolecular structure prediction and design in which students conduct research at labs located at geographically-distributed institutions while remaining connected through an online community. This 10-week summer program begins with one week of training on computational biology methods development, transitions to eight weeks of research, and culminates in one week at the Rosetta annual conference. To date, two cohorts of students have participated, tackling research topics including vaccine design, enzyme design, protein-based materials, glycoprotein modeling, crowd-sourced science, RNA processing, hydrogen bond networks, and amyloid formation. Students in the program report outcomes comparable to students who participate in similar in-person programs. These outcomes include the development of a sense of community and increases in their scientific self-efficacy, scientific identity, and science values, all predictors of continuing in a science research career. Furthermore, the program attracted students from diverse backgrounds, which demonstrates the potential of this approach to broaden the participation of young scientists from backgrounds traditionally underrepresented in computational biology.

  4. Biomolecular engineering for nanobio/bionanotechnology

    Science.gov (United States)

    Nagamune, Teruyuki

    2017-04-01

    Biomolecular engineering can be used to purposefully manipulate biomolecules, such as peptides, proteins, nucleic acids and lipids, within the framework of the relations among their structures, functions and properties, as well as their applicability to such areas as developing novel biomaterials, biosensing, bioimaging, and clinical diagnostics and therapeutics. Nanotechnology can also be used to design and tune the sizes, shapes, properties and functionality of nanomaterials. As such, there are considerable overlaps between nanotechnology and biomolecular engineering, in that both are concerned with the structure and behavior of materials on the nanometer scale or smaller. Therefore, in combination with nanotechnology, biomolecular engineering is expected to open up new fields of nanobio/bionanotechnology and to contribute to the development of novel nanobiomaterials, nanobiodevices and nanobiosystems. This review highlights recent studies using engineered biological molecules (e.g., oligonucleotides, peptides, proteins, enzymes, polysaccharides, lipids, biological cofactors and ligands) combined with functional nanomaterials in nanobio/bionanotechnology applications, including therapeutics, diagnostics, biosensing, bioanalysis and biocatalysts. Furthermore, this review focuses on five areas of recent advances in biomolecular engineering: (a) nucleic acid engineering, (b) gene engineering, (c) protein engineering, (d) chemical and enzymatic conjugation technologies, and (e) linker engineering. Precisely engineered nanobiomaterials, nanobiodevices and nanobiosystems are anticipated to emerge as next-generation platforms for bioelectronics, biosensors, biocatalysts, molecular imaging modalities, biological actuators, and biomedical applications.

  5. Scanning number and brightness yields absolute protein concentrations in live cells: a crucial parameter controlling functional bio-molecular interaction networks.

    Science.gov (United States)

    Papini, Christina; Royer, Catherine A

    2018-02-01

    Biological function results from properly timed bio-molecular interactions that transduce external or internal signals, resulting in any number of cellular fates, including triggering of cell-state transitions (division, differentiation, transformation, apoptosis), metabolic homeostasis and adjustment to changing physical or nutritional environments, amongst many more. These bio-molecular interactions can be modulated by chemical modifications of proteins, nucleic acids, lipids and other small molecules. They can result in bio-molecular transport from one cellular compartment to the other and often trigger specific enzyme activities involved in bio-molecular synthesis, modification or degradation. Clearly, a mechanistic understanding of any given high level biological function requires a quantitative characterization of the principal bio-molecular interactions involved and how these may change dynamically. Such information can be obtained using fluctation analysis, in particular scanning number and brightness, and used to build and test mechanistic models of the functional network to define which characteristics are the most important for its regulation.

  6. Programming in biomolecular computation

    DEFF Research Database (Denmark)

    Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue

    2011-01-01

    Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We identify a number of common features in programming that seem...... conspicuously absent from the literature on biomolecular computing; to partially redress this absence, we introduce a model of computation that is evidently programmable, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined...... by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only executable, but are also compilable and interpretable. It is universal: all computable functions can be computed (in natural ways...

  7. Computational methods to study the structure and dynamics of biomolecules and biomolecular processes from bioinformatics to molecular quantum mechanics

    CERN Document Server

    2014-01-01

    Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over t...

  8. Aligning Biomolecular Networks Using Modular Graph Kernels

    Science.gov (United States)

    Towfic, Fadi; Greenlee, M. Heather West; Honavar, Vasant

    Comparative analysis of biomolecular networks constructed using measurements from different conditions, tissues, and organisms offer a powerful approach to understanding the structure, function, dynamics, and evolution of complex biological systems. We explore a class of algorithms for aligning large biomolecular networks by breaking down such networks into subgraphs and computing the alignment of the networks based on the alignment of their subgraphs. The resulting subnetworks are compared using graph kernels as scoring functions. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit. Our experiments using Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository of protein-protein interaction data demonstrate that the performance of the proposed algorithms (as measured by % GO term enrichment of subnetworks identified by the alignment) is competitive with some of the state-of-the-art algorithms for pair-wise alignment of large protein-protein interaction networks. Our results also show that the inter-species similarity scores computed based on graph kernels can be used to cluster the species into a species tree that is consistent with the known phylogenetic relationships among the species.

  9. Integrative NMR for biomolecular research

    International Nuclear Information System (INIS)

    Lee, Woonghee; Cornilescu, Gabriel; Dashti, Hesam; Eghbalnia, Hamid R.; Tonelli, Marco; Westler, William M.; Butcher, Samuel E.; Henzler-Wildman, Katherine A.; Markley, John L.

    2016-01-01

    NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page ( http://pine.nmrfam.wisc.edu/download-packages.html http://pine.nmrfam.wisc.edu/download_packages.html ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( http://pine.nmrfam.wisc.edu/integrative.html http://pine.nmrfam.wisc.edu/integrative.html ).

  10. Integrative NMR for biomolecular research

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu; Cornilescu, Gabriel; Dashti, Hesam; Eghbalnia, Hamid R.; Tonelli, Marco; Westler, William M.; Butcher, Samuel E.; Henzler-Wildman, Katherine A.; Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States)

    2016-04-15

    NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page ( http://pine.nmrfam.wisc.edu/download-packages.html http://pine.nmrfam.wisc.edu/download{sub p}ackages.html ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( http://pine.nmrfam.wisc.edu/integrative.html http://pine.nmrfam.wisc.edu/integrative.html ).

  11. Biomolecular modelling and simulations

    CERN Document Server

    Karabencheva-Christova, Tatyana

    2014-01-01

    Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology series is the essential resource for protein chemists. Each volume brings forth new information about protocols and analysis of proteins. Each thematically organized volume is guest edited by leading experts in a broad range of protein-related topics. Describes advances in biomolecular modelling and simulations Chapters are written by authorities in their field Targeted to a wide audience of researchers, specialists, and students The information provided in the volume is well supported by a number of high quality illustrations, figures, and tables.

  12. Synthesis and biosynthesis of 13C, 15N labeled deoxynucleosides useful for biomolecular structural determinations

    International Nuclear Information System (INIS)

    Ashburn, D.A.; Garcia, K.; Hanners, J.L.; Silks, L.A. III; Unkefer, C.J.

    1994-01-01

    Currently, there is a great emphasis on elucidating the structure, function, and dynamics of DNA. Much of the research involved in this study utilizes nuclear magnetic resonance (NMR) spectroscopy. Effective use of NMR spectroscopy (more than 10,000 mw) in this arena requires stable isotope enrichment. Herein, the authors present strategies for the site-specific isotopic labeling of the purine bases adenosine and guanosine and the biosynthesis of [U- 13 C, 15 N] DNA from methylotrophic bacteria. With commercially available 6-chloropurine, an effective 2-step route leads to [6- 15 N]-2'-deoxadenosine (dA). The resulting [6- 15 N]-dA is used in a series of reactions to synthesize [2- 13 C, 1,2'- 15 N 2 ]-2'-deoxyguanosine or any combination thereof. An improved biosynthesis of labeled DNA has been accomplished using Methylobacterium extorquens AS1. Each liter of growth medium contains 4g of methanol to yield 1 gram of lyophilized cells. As much as 200 mg of RNA per liter of culture has been obtained. The authors are currently developing large scale isolation protocols. General synthetic pathways to oligomeric DNA are presented

  13. Synthesis and biosynthesis of 13C-, 15N-labeled deoxynucleosides useful for biomolecular structural determinations

    International Nuclear Information System (INIS)

    Ashburn, D.A.; Garcia, K.; Hanners, J.L.; Silks, L.A. III; Unkefer, C.J.

    1994-01-01

    Currently, there is a great emphasis on elucidating the structure, function, and dynamics of DNA. Much of the research involved in this study uses nuclear magnetic resonance (NMR) spectroscopy. Effective use of NMR spectroscopy for DNA molecules with mw > 10,000 requires stable isotope enrichment. We present strategies for site-specific isotopic labeling of the purine bases adenosine and guanosine and the biosynthesis of (U- 13 C, 15 N) DNA from methylotropic bacteria. With commercially available 6-chloropurine, an effective two-step route leads to 2'-deoxy-(amino- 15 N)adenosine (dA). The resulting d(amino- 15 N)A is used in a series of reactions to synthesize 2'-deoxy-(2- 13 C,1,amino- 15 N 2 )guanosine or any combination thereof. An improved biosynthesis of labeled DNA has been accomplished using Methylobacterium extorquens AS1. Each liter of growth medium contains 4 g of methanol to yield 1 g of lyophilized cells. As much as 200 mg of RNA per liter of culture has been obtained. We are currently developing large-scale isolation protocols. General synthetic pathways to oligomeric DNA will be presented

  14. Traditional biomolecular structure determination by NMR spectroscopy allows for major errors

    NARCIS (Netherlands)

    Nabuurs, S.B.; Spronk, C.A.E.M.; Vuister, G.W.; Vriend, G.

    2006-01-01

    One of the major goals of structural genomics projects is to determine the three-dimensional structure of representative members of as many different fold families as possible. Comparative modeling is expected to fill the remaining gaps by providing structural models of homologs of the

  15. Imaging and chemical surface analysis of biomolecular functionalization of monolithically integrated on silicon Mach-Zehnder interferometric immunosensors

    International Nuclear Information System (INIS)

    Gajos, Katarzyna; Angelopoulou, Michailia; Petrou, Panagiota; Awsiuk, Kamil; Kakabakos, Sotirios; Haasnoot, Willem; Bernasik, Andrzej; Rysz, Jakub; Marzec, Mateusz M.; Misiakos, Konstantinos; Raptis, Ioannis; Budkowski, Andrzej

    2016-01-01

    Highlights: • Optimization of probe immobilization with robotic spotter printing overlapping spots. • In-situ inspection of microstructured surfaces of biosensors integrated on silicon. • Imaging and chemical analysis of immobilization, surface blocking and immunoreaction. • Insight with molecular discrimination into step-by-step sensor surface modifications. • Optimized biofunctionalization improves sensor sensitivity and response repeatability. - Abstract: Time-of-flight secondary ion mass spectrometry (imaging, micro-analysis) has been employed to evaluate biofunctionalization of the sensing arm areas of Mach-Zehnder interferometers monolithically integrated on silicon chips for the immunochemical (competitive) detection of bovine κ-casein in goat milk. Biosensor surfaces are examined after: modification with (3-aminopropyl)triethoxysilane, application of multiple overlapping spots of κ-casein solutions, blocking with 100-times diluted goat milk, and reaction with monoclonal mouse anti-κ-casein antibodies in blocking solution. The areas spotted with κ-casein solutions of different concentrations are examined and optimum concentration providing homogeneous coverage is determined. Coverage of biosensor surfaces with biomolecules after each of the sequential steps employed in immunodetection is also evaluated with TOF-SIMS, supplemented by Atomic force microscopy and X-ray photoelectron spectroscopy. Uniform molecular distributions are observed on the sensing arm areas after spotting with optimum κ-casein concentration, blocking and immunoreaction. The corresponding biomolecular compositions are determined with a Principal Component Analysis that distinguished between protein amino acids and milk glycerides, as well as between amino acids characteristic for Mabs and κ-casein, respectively. Use of the optimum conditions (κ-casein concentration) for functionalization of chips with arrays of ten Mach-Zehnder interferometers provided on-chips assays

  16. Imaging and chemical surface analysis of biomolecular functionalization of monolithically integrated on silicon Mach-Zehnder interferometric immunosensors

    Energy Technology Data Exchange (ETDEWEB)

    Gajos, Katarzyna, E-mail: kasia.fornal@uj.edu.pl [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland); Angelopoulou, Michailia; Petrou, Panagiota [Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR Demokritos, P. Grigoriou & Neapoleos St, Aghia Paraksevi 15310, Athens (Greece); Awsiuk, Kamil [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland); Kakabakos, Sotirios [Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR Demokritos, P. Grigoriou & Neapoleos St, Aghia Paraksevi 15310, Athens (Greece); Haasnoot, Willem [RIKILT Wageningen UR, Akkermaalsbos 2, 6708 WB Wageningen (Netherlands); Bernasik, Andrzej [Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Mickiewicza 30, 30-059 Kraków (Poland); Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, Mickiewicza 30, 30-059 Kraków (Poland); Rysz, Jakub [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland); Marzec, Mateusz M. [Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, Mickiewicza 30, 30-059 Kraków (Poland); Misiakos, Konstantinos; Raptis, Ioannis [Department of Microelectronics, Institute of Nanoscience and Nanotechnology, NCSR Demokritos, P. Grigoriou & Neapoleos St, Aghia Paraksevi 15310, Athens (Greece); Budkowski, Andrzej [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland)

    2016-11-01

    Highlights: • Optimization of probe immobilization with robotic spotter printing overlapping spots. • In-situ inspection of microstructured surfaces of biosensors integrated on silicon. • Imaging and chemical analysis of immobilization, surface blocking and immunoreaction. • Insight with molecular discrimination into step-by-step sensor surface modifications. • Optimized biofunctionalization improves sensor sensitivity and response repeatability. - Abstract: Time-of-flight secondary ion mass spectrometry (imaging, micro-analysis) has been employed to evaluate biofunctionalization of the sensing arm areas of Mach-Zehnder interferometers monolithically integrated on silicon chips for the immunochemical (competitive) detection of bovine κ-casein in goat milk. Biosensor surfaces are examined after: modification with (3-aminopropyl)triethoxysilane, application of multiple overlapping spots of κ-casein solutions, blocking with 100-times diluted goat milk, and reaction with monoclonal mouse anti-κ-casein antibodies in blocking solution. The areas spotted with κ-casein solutions of different concentrations are examined and optimum concentration providing homogeneous coverage is determined. Coverage of biosensor surfaces with biomolecules after each of the sequential steps employed in immunodetection is also evaluated with TOF-SIMS, supplemented by Atomic force microscopy and X-ray photoelectron spectroscopy. Uniform molecular distributions are observed on the sensing arm areas after spotting with optimum κ-casein concentration, blocking and immunoreaction. The corresponding biomolecular compositions are determined with a Principal Component Analysis that distinguished between protein amino acids and milk glycerides, as well as between amino acids characteristic for Mabs and κ-casein, respectively. Use of the optimum conditions (κ-casein concentration) for functionalization of chips with arrays of ten Mach-Zehnder interferometers provided on-chips assays

  17. Density-functional, density-functional tight-binding, and wave-function calculations on biomolecular systems

    Czech Academy of Sciences Publication Activity Database

    Kubař, Tomáš; Jurečka, Petr; Černý, Jiří; Řezáč, Jan; Otyepka, M.; Valdes, Haydee; Hobza, Pavel

    2007-01-01

    Roč. 111, č. 26 (2007), s. 5642-5647 ISSN 1089-5639 R&D Projects: GA MŠk LC512; GA AV ČR IAA400550510; GA ČR(CZ) GD203/05/H001; GA ČR GA203/05/0009 Institutional research plan: CEZ:AV0Z40550506 Keywords : density functional theory * empirical dispersion-energy term * non-covalent interactions Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.918, year: 2007

  18. A guide to the visual analysis and communication of biomolecular structural data.

    Science.gov (United States)

    Johnson, Graham T; Hertig, Samuel

    2014-10-01

    Biologists regularly face an increasingly difficult task - to effectively communicate bigger and more complex structural data using an ever-expanding suite of visualization tools. Whether presenting results to peers or educating an outreach audience, a scientist can achieve maximal impact with minimal production time by systematically identifying an audience's needs, planning solutions from a variety of visual communication techniques and then applying the most appropriate software tools. A guide to available resources that range from software tools to professional illustrators can help researchers to generate better figures and presentations tailored to any audience's needs, and enable artistically inclined scientists to create captivating outreach imagery.

  19. H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.

    Science.gov (United States)

    Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V

    2012-07-01

    The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.

  20. Structure, dynamics, and function of biomolecules

    International Nuclear Information System (INIS)

    Frauenfelder, H.; Berendzen, J.R.; Garcia, A.; Gupta, G.; Olah, G.A.; Terwilliger, T.C.; Trewhella, J.; Wood, C.C.; Woodruff, W.H.

    1998-01-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The authors enhanced Los Alamos' core competency in Bioscience and Biotechnology by building on present strengths in experimental techniques, theory, high-performance computing, modeling, and simulation applied to biomolecular structure, dynamics, and function. Specifically, the authors strengthened their capabilities in neutron/x-ray scattering, x-ray crystallography, NMR, laser, and optical spectroscopies. Initially they focused on supporting the Los alamos Neutron Science Center (LANSCE) in the design and implementation of new neutron scattering instrumentation, they developed new methods for analysis of scattering data, and they developed new projects to study the structures of biomolecular complexes. The authors have also worked to strengthen interactions between theory and experiment, and between the biological and physical sciences. They sponsored regular meetings of members from all interested LANL technical divisions, and supported two lecture series: ''Biology for Physicists'' and ''Issues in Modern Biology''. They also supported the formation of interdisciplinary/inter-divisional teams to develop projects in science-based bioremediation and an integrated structural biology resource. Finally, they successfully worked with a multidisciplinary team to put forward the Laboratory's Genome and Beyond tactical goal

  1. Biomolecular Science (Fact Sheet)

    Energy Technology Data Exchange (ETDEWEB)

    2012-04-01

    A brief fact sheet about NREL Photobiology and Biomolecular Science. The research goal of NREL's Biomolecular Science is to enable cost-competitive advanced lignocellulosic biofuels production by understanding the science critical for overcoming biomass recalcitrance and developing new product and product intermediate pathways. NREL's Photobiology focuses on understanding the capture of solar energy in photosynthetic systems and its use in converting carbon dioxide and water directly into hydrogen and advanced biofuels.

  2. Photon structure function - theory

    International Nuclear Information System (INIS)

    Bardeen, W.A.

    1984-12-01

    The theoretical status of the photon structure function is reviewed. Particular attention is paid to the hadronic mixing problem and the ability of perturbative QCD to make definitive predictions for the photon structure function. 11 references

  3. High spin structure functions

    International Nuclear Information System (INIS)

    Khan, H.

    1990-01-01

    This thesis explores deep inelastic scattering of a lepton beam from a polarized nuclear target with spin J=1. After reviewing the formation for spin-1/2, the structure functions for a spin-1 target are defined in terms of the helicity amplitudes for forward compton scattering. A version of the convolution model, which incorporates relativistic and binding energy corrections is used to calculate the structure functions of a neutron target. A simple parameterization of these structure functions is given in terms of a few neutron wave function parameters and the free nucleon structure functions. This allows for an easy comparison of structure functions calculated using different neutron models. (author)

  4. Biomolecular Sciences: uniting Biology and Chemistry

    NARCIS (Netherlands)

    Vrieling, Engel

    2017-01-01

    Biomolecular Sciences: uniting Biology and Chemistry www.rug.nl/research/gbb The scientific discoveries in biomolecular sciences have benefitted enormously from technological innovations. At the Groningen Biomolecular Science and Biotechnology Institute (GBB) we now sequence a genome in days,

  5. Hadron structure functions

    International Nuclear Information System (INIS)

    Martin, F.

    1981-03-01

    The x dependence of hadron structure functions is investigated. If quarks can exist in very low mass states (10 MeV for d and u quarks) the pion structure function is predicted to behave like (1-x) and not (1-x) 2 in a x-region around 1. Relativistic and non-relativistic quark bound state pictures of hadrons are considered together with their relation with the Q 2 evolution of structure functions. Good agreement with data is in general obtained

  6. Photon structure function

    International Nuclear Information System (INIS)

    Bardeen, W.A.

    1980-11-01

    Theoretical understanding of the photon structure function is reviewed. As an illustration of the pointlike component, the parton model is briefly discussed. However, the systematic study of the photon structure function is presented through the framework of the operator product expansion. Perturbative QCD is used as the theoretical basis for the calculation of leading contributions to the operator product expansion. The influence of higher order QCD effects on these results is discussed. Recent results for the polarized structure functions are discussed

  7. Synthesis and biosynthesis of {sup 13}C-, {sup 15}N-labeled deoxynucleosides useful for biomolecular structural determinations

    Energy Technology Data Exchange (ETDEWEB)

    Ashburn, D.A.; Garcia, K.; Hanners, J.L.; Silks, L.A. III; Unkefer, C.J. [Los Alamos National Laboratory, NM (United States)

    1994-12-01

    Currently, there is a great emphasis on elucidating the structure, function, and dynamics of DNA. Much of the research involved in this study uses nuclear magnetic resonance (NMR) spectroscopy. Effective use of NMR spectroscopy for DNA molecules with mw > 10,000 requires stable isotope enrichment. We present strategies for site-specific isotopic labeling of the purine bases adenosine and guanosine and the biosynthesis of (U-{sup 13}C, {sup 15}N) DNA from methylotropic bacteria. With commercially available 6-chloropurine, an effective two-step route leads to 2{prime}-deoxy-(amino-{sup 15}N)adenosine (dA). The resulting d(amino-{sup 15}N)A is used in a series of reactions to synthesize 2{prime}-deoxy-(2-{sup 13}C,1,amino-{sup 15}N{sub 2})guanosine or any combination thereof. An improved biosynthesis of labeled DNA has been accomplished using Methylobacterium extorquens AS1. Each liter of growth medium contains 4 g of methanol to yield 1 g of lyophilized cells. As much as 200 mg of RNA per liter of culture has been obtained. We are currently developing large-scale isolation protocols. General synthetic pathways to oligomeric DNA will be presented.

  8. Membrane-based biomolecular smart materials

    International Nuclear Information System (INIS)

    Sarles, Stephen A; Leo, Donald J

    2011-01-01

    Membrane-based biomolecular materials are a new class of smart material that feature networks of artificial lipid bilayers contained within durable synthetic substrates. Bilayers contained within this modular material platform provide an environment that can be tailored to host an enormous diversity of functional biomolecules, where the functionality of the global material system depends on the type(s) and organization(s) of the biomolecules that are chosen. In this paper, we review a series of biomolecular material platforms developed recently within the Leo Group at Virginia Tech and we discuss several novel coupling mechanisms provided by these hybrid material systems. The platforms developed demonstrate that the functions of biomolecules and the properties of synthetic materials can be combined to operate in concert, and the examples provided demonstrate how the formation and properties of a lipid bilayer can respond to a variety of stimuli including mechanical forces and electric fields

  9. Hydrogen exchange mass spectrometry of bacteriorhodopsin reveals light-induced changes in the structural dynamics of a biomolecular machine.

    Science.gov (United States)

    Pan, Yan; Brown, Leonid; Konermann, Lars

    2011-12-21

    Many proteins act as molecular machines that are fuelled by a nonthermal energy source. Examples include transmembrane pumps and stator-rotor complexes. These systems undergo cyclic motions (CMs) that are being driven along a well-defined conformational trajectory. Superimposed on these CMs are thermal fluctuations (TFs) that are coupled to stochastic motions of the solvent. Here we explore whether the TFs of a molecular machine are affected by the occurrence of CMs. Bacteriorhodopsin (BR) is a light-driven proton pump that serves as a model system in this study. The function of BR is based on a photocycle that involves trans/cis isomerization of a retinal chromophore, as well as motions of transmembrane helices. Hydrogen/deuterium exchange (HDX) mass spectrometry was used to monitor the TFs of BR, focusing on the monomeric form of the protein. Comparative HDX studies were conducted under illumination and in the dark. The HDX kinetics of BR are dramatically accelerated in the presence of light. The isotope exchange rates and the number of backbone amides involved in EX2 opening transitions increase roughly 2-fold upon illumination. In contrast, light/dark control experiments on retinal-free protein produced no discernible differences. It can be concluded that the extent of TFs in BR strongly depends on photon-driven CMs. The light-induced differences in HDX behavior are ascribed to protein destabilization. Specifically, the thermodynamic stability of the dark-adapted protein is estimated to be 5.5 kJ mol(-1) under the conditions of our work. This value represents the free energy difference between the folded state F and a significantly unfolded conformer U. Illumination reduces the stability of F by 2.2 kJ mol(-1). Mechanical agitation caused by isomerization of the chromophore is transferred to the surrounding protein scaffold, and subsequently, the energy dissipates into the solvent. Light-induced retinal motions therefore act analogously to an internal heat

  10. Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition

    Science.gov (United States)

    Chu, Xiakun; Gan, Linfeng; Wang, Erkang; Wang, Jin

    2013-01-01

    Biomolecular functions are determined by their interactions with other molecules. Biomolecular recognition is often flexible and associated with large conformational changes involving both binding and folding. However, the global and physical understanding for the process is still challenging. Here, we quantified the intrinsic energy landscapes of flexible biomolecular recognition in terms of binding–folding dynamics for 15 homodimers by exploring the underlying density of states, using a structure-based model both with and without considering energetic roughness. By quantifying three individual effective intrinsic energy landscapes (one for interfacial binding, two for monomeric folding), the association mechanisms for flexible recognition of 15 homodimers can be classified into two-state cooperative “coupled binding–folding” and three-state noncooperative “folding prior to binding” scenarios. We found that the association mechanism of flexible biomolecular recognition relies on the interplay between the underlying effective intrinsic binding and folding energy landscapes. By quantifying the whole global intrinsic binding–folding energy landscapes, we found strong correlations between the landscape topography measure Λ (dimensionless ratio of energy gap versus roughness modulated by the configurational entropy) and the ratio of the thermodynamic stable temperature versus trapping temperature, as well as between Λ and binding kinetics. Therefore, the global energy landscape topography determines the binding–folding thermodynamics and kinetics, crucial for the feasibility and efficiency of realizing biomolecular function. We also found “U-shape” temperature-dependent kinetic behavior and a dynamical cross-over temperature for dividing exponential and nonexponential kinetics for two-state homodimers. Our study provides a unique way to bridge the gap between theory and experiments. PMID:23754431

  11. Unpolarized Structure Functions

    International Nuclear Information System (INIS)

    Christy, M.E.; Melnitchouk, W.

    2011-01-01

    Over the past decade measurements of unpolarized structure functions with unprecedented precision have significantly advanced our knowledge of nucleon structure. These have for the first time allowed quantitative tests of the phenomenon of quark-hadron duality, and provided a deeper understanding of the transition from hadron to quark degrees of freedom in inclusive scattering. Dedicated Rosenbluth-separation experiments have yielded high-precision transverse and longitudinal structure functions in regions previously unexplored, and new techniques have enabled the first glimpses of the structure of the free neutron, without contamination from nuclear effects.

  12. Biomolecular and structural analyses of cauliflower-like DNAs by ultraviolet, circular dichroism, and fluorescence spectroscopies in comparison with natural DNA.

    Science.gov (United States)

    Gill, Pooria; Ranjbar, Bijan; Saber, Reza; Khajeh, Khosro; Mohammadian, Mehdi

    2011-07-01

    Cauliflower-like DNAs are stem-loop DNAs that are fabricated periodically in inverted repetitions from deoxyribonucleic acid phosphates (dNTPs) by loop-mediated isothermal amplification (LAMP). Cauliflower-like DNAs have ladder-shape behaviors on gel electrophoresis, and increasing the time of LAMP leads to multiplying the repetitions, stem-loops, and electrophoretic bands. Cauliflower-like DNAs were fabricated via LAMP using two loop primers, two bumper primers, dNTPs, a λ-phage DNA template, and a Bst DNA polymerase in 75- and 90-min periods. These times led to manufacturing two types of cauliflower-like DNAs with different contents of inverted repetitions and stem-loops, which were clearly indicated by two comparable electrophoresis patterns in agarose gel. LAMP-fabricated DNAs and natural dsB-DNA (salmon genomic DNA) were dialyzed in Gomori phosphate buffer (10 mM, pH 7.4) to be isolated from salts, nucleotides, and primers. Dialyzed DNAs were studied using UV spectroscopy, circular dichroism spectropolarimetry, and fluorescence spectrophotometry. Structural analyses indicated reduction of the molecular ellipticity and extinction coefficients in comparison with B-DNA. Also, cauliflower-like DNAs demonstrated less intrinsic and more extrinsic fluorescence in comparison with natural DNA. The overwinding and lengthening of the cauliflower-like configurations of LAMP DNAs led to changes in physical parameters of this type of DNA in comparison with natural DNA. The results obtained introduced new biomolecular characteristics of DNA macromolecules fabricated within a LAMP process and show the effects of more inverted repeats and stem-loops, which are manufactured by lengthening the process.

  13. Biomolecular ions in superfluid helium nanodroplets

    International Nuclear Information System (INIS)

    Gonzalez Florez, Ana Isabel

    2016-01-01

    The function of a biological molecule is closely related to its structure. As a result, understanding and predicting biomolecular structure has become the focus of an extensive field of research. However, the investigation of molecular structure can be hampered by two main difficulties: the inherent complications that may arise from studying biological molecules in their native environment, and the potential congestion of the experimental results as a consequence of the large number of degrees of freedom present in these molecules. In this work, a new experimental setup has been developed and established in order to overcome the afore mentioned limitations combining structure-sensitive gas-phase methods with superfluid helium droplets. First, biological molecules are ionised and brought into the gas phase, often referred to as a clean-room environment, where the species of interest are isolated from their surroundings and, thus, intermolecular interactions are absent. The mass-to-charge selected biomolecules are then embedded inside clusters of superfluid helium with an equilibrium temperature of ∝0.37 K. As a result, the internal energy of the molecules is lowered, thereby reducing the number of populated quantum states. Finally, the local hydrogen bonding patterns of the molecules are investigated by probing specific vibrational modes using the Fritz Haber Institute's free electron laser as a source of infrared radiation. Although the structure of a wide variety of molecules has been studied making use of the sub-Kelvin environment provided by superfluid helium droplets, the suitability of this method for the investigation of biological molecular ions was still unclear. However, the experimental results presented in this thesis demonstrate the applicability of this experimental approach in order to study the structure of intact, large biomolecular ions and the first vibrational spectrum of the protonated pentapeptide leu-enkephalin embedded in helium

  14. Biomolecular ions in superfluid helium nanodroplets

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez Florez, Ana Isabel

    2016-07-01

    The function of a biological molecule is closely related to its structure. As a result, understanding and predicting biomolecular structure has become the focus of an extensive field of research. However, the investigation of molecular structure can be hampered by two main difficulties: the inherent complications that may arise from studying biological molecules in their native environment, and the potential congestion of the experimental results as a consequence of the large number of degrees of freedom present in these molecules. In this work, a new experimental setup has been developed and established in order to overcome the afore mentioned limitations combining structure-sensitive gas-phase methods with superfluid helium droplets. First, biological molecules are ionised and brought into the gas phase, often referred to as a clean-room environment, where the species of interest are isolated from their surroundings and, thus, intermolecular interactions are absent. The mass-to-charge selected biomolecules are then embedded inside clusters of superfluid helium with an equilibrium temperature of ∝0.37 K. As a result, the internal energy of the molecules is lowered, thereby reducing the number of populated quantum states. Finally, the local hydrogen bonding patterns of the molecules are investigated by probing specific vibrational modes using the Fritz Haber Institute's free electron laser as a source of infrared radiation. Although the structure of a wide variety of molecules has been studied making use of the sub-Kelvin environment provided by superfluid helium droplets, the suitability of this method for the investigation of biological molecular ions was still unclear. However, the experimental results presented in this thesis demonstrate the applicability of this experimental approach in order to study the structure of intact, large biomolecular ions and the first vibrational spectrum of the protonated pentapeptide leu-enkephalin embedded in helium

  15. Introduction to structure functions

    International Nuclear Information System (INIS)

    Kwiecinski, J.

    1996-07-01

    The theory of deep inelastic scattering structure functions is reviewed with an emphasis put on the QCD expectations of their behaviour in the region of small values of Bjorken parameter x. (author). 56 refs

  16. Structure function monitor

    Science.gov (United States)

    McGraw, John T [Placitas, NM; Zimmer, Peter C [Albuquerque, NM; Ackermann, Mark R [Albuquerque, NM

    2012-01-24

    Methods and apparatus for a structure function monitor provide for generation of parameters characterizing a refractive medium. In an embodiment, a structure function monitor acquires images of a pupil plane and an image plane and, from these images, retrieves the phase over an aperture, unwraps the retrieved phase, and analyzes the unwrapped retrieved phase. In an embodiment, analysis yields atmospheric parameters measured at spatial scales from zero to the diameter of a telescope used to collect light from a source.

  17. Purely Functional Structured Programming

    OpenAIRE

    Obua, Steven

    2010-01-01

    The idea of functional programming has played a big role in shaping today's landscape of mainstream programming languages. Another concept that dominates the current programming style is Dijkstra's structured programming. Both concepts have been successfully married, for example in the programming language Scala. This paper proposes how the same can be achieved for structured programming and PURELY functional programming via the notion of LINEAR SCOPE. One advantage of this proposal is that m...

  18. Synthetic Approach to biomolecular science by cyborg supramolecular chemistry.

    Science.gov (United States)

    Kurihara, Kensuke; Matsuo, Muneyuki; Yamaguchi, Takumi; Sato, Sota

    2018-02-01

    To imitate the essence of living systems via synthetic chemistry approaches has been attempted. With the progress in supramolecular chemistry, it has become possible to synthesize molecules of a size and complexity close to those of biomacromolecules. Recently, the combination of precisely designed supramolecules with biomolecules has generated structural platforms for designing and creating unique molecular systems. Bridging between synthetic chemistry and biomolecular science is also developing methodologies for the creation of artificial cellular systems. This paper provides an overview of the recently expanding interdisciplinary research to fuse artificial molecules with biomolecules, that can deepen our understanding of the dynamical ordering of biomolecules. Using bottom-up approaches based on the precise chemical design, synthesis and hybridization of artificial molecules with biological materials have been realizing the construction of sophisticated platforms having the fundamental functions of living systems. The effective hybrid, molecular cyborg, approaches enable not only the establishment of dynamic systems mimicking nature and thus well-defined models for biophysical understanding, but also the creation of those with highly advanced, integrated functions. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Application of Nanodiamonds in Biomolecular Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Ping Cheng

    2010-03-01

    Full Text Available The combination of nanodiamond (ND with biomolecular mass spectrometry (MS makes rapid, sensitive detection of biopolymers from complex biosamples feasible. Due to its chemical inertness, optical transparency and biocompatibility, the advantage of NDs in MS study is unique. Furthermore, functionalization on the surfaces of NDs expands their application in the fields of proteomics and genomics for specific requirements greatly. This review presents methods of MS analysis based on solid phase extraction and elution on NDs and different application examples including peptide, protein, DNA, glycan and others. Owing to the quick development of nanotechnology, surface chemistry, new MS methods and the intense interest in proteomics and genomics, a huge increase of their applications in biomolecular MS analysis in the near future can be predicted.

  20. Biomolecular electrostatics and solvation: a computational perspective.

    Science.gov (United States)

    Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G; Schnieders, Michael J; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A

    2012-11-01

    An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

  1. Chromatin Structure and Function

    CERN Document Server

    Wolffe, Alan P

    1999-01-01

    The Third Edition of Chromatin: Structure and Function brings the reader up-to-date with the remarkable progress in chromatin research over the past three years. It has been extensively rewritten to cover new material on chromatin remodeling, histone modification, nuclear compartmentalization, DNA methylation, and transcriptional co-activators and co-repressors. The book is written in a clear and concise fashion, with 60 new illustrations. Chromatin: Structure and Function provides the reader with a concise and coherent account of the nature, structure, and assembly of chromatin and its active

  2. NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers.

    Science.gov (United States)

    Sekhar, Ashok; Kay, Lewis E

    2013-08-06

    The importance of dynamics to biomolecular function is becoming increasingly clear. A description of the structure-function relationship must, therefore, include the role of motion, requiring a shift in paradigm from focus on a single static 3D picture to one where a given biomolecule is considered in terms of an ensemble of interconverting conformers, each with potentially diverse activities. In this Perspective, we describe how recent developments in solution NMR spectroscopy facilitate atomic resolution studies of sparsely populated, transiently formed biomolecular conformations that exchange with the native state. Examples of how this methodology is applied to protein folding and misfolding, ligand binding, and molecular recognition are provided as a means of illustrating both the power of the new techniques and the significant roles that conformationally excited protein states play in biology.

  3. Nucleon structure functions

    International Nuclear Information System (INIS)

    Virchaux, M.

    1992-11-01

    The present status of experimental measurements of the nucleon structure functions is reviewed. The results from nearly all deep inelastic experiments are in good mutual agreement. Principles of the analysis of these structure function data in the framework of QCD are described. The specific features of the perturbative QCD predictions are observed in the data. This provides quantitative tests of the validity of QCD as well as determinations of the various parton distributions in the nucleon and some of the most precise measurements of the strong coupling constant αs. The future of this field of experimental physics is sketched

  4. Selected topics in solution-phase biomolecular NMR spectroscopy

    Science.gov (United States)

    Kay, Lewis E.; Frydman, Lucio

    2017-05-01

    Solution bio-NMR spectroscopy continues to enjoy a preeminent role as an important tool in elucidating the structure and dynamics of a range of important biomolecules and in relating these to function. Equally impressive is how NMR continues to 'reinvent' itself through the efforts of many brilliant practitioners who ask increasingly demanding and increasingly biologically relevant questions. The ability to manipulate spin Hamiltonians - almost at will - to dissect the information of interest contributes to the success of the endeavor and ensures that the NMR technology will be well poised to contribute to as yet unknown frontiers in the future. As a tribute to the versatility of solution NMR in biomolecular studies and to the continued rapid advances in the field we present a Virtual Special Issue (VSI) that includes over 40 articles on various aspects of solution-state biomolecular NMR that have been published in the Journal of Magnetic Resonance in the past 7 years. These, in total, help celebrate the achievements of this vibrant field.

  5. DNA: Structure and function

    DEFF Research Database (Denmark)

    Sinden, Richard R.; E. Pearson, Christopher; N. Potaman, Vladimir

    1998-01-01

    This chapter discusses the structure and function of DNA. DNA occupies a critical role in cells, because it is the source of all intrinsic genetic information. Chemically, DNA is a very stable molecule, a characteristic important for a macromolecule that may have to persist in an intact form...

  6. THz time domain spectroscopy of biomolecular conformational modes

    International Nuclear Information System (INIS)

    Markelz, Andrea; Whitmire, Scott; Hillebrecht, Jay; Birge, Robert

    2002-01-01

    We discuss the use of terahertz time domain spectroscopy for studies of conformational flexibility and conformational change in biomolecules. Protein structural dynamics are vital to biological function with protein flexibility affecting enzymatic reaction rates and sensory transduction cycling times. Conformational mode dynamics occur on the picosecond timescale and with the collective vibrational modes associated with these large scale structural motions in the 1-100 cm -1 range. We have performed THz time domain spectroscopy (TTDS) of several biomolecular systems to explore the sensitivity of TTDS to distinguish different molecular species, different mutations within a single species and different conformations of a given biomolecule. We compare the measured absorbances to normal mode calculations and find that the TTDS absorbance reflects the density of normal modes determined by molecular mechanics calculations, and is sensitive to both conformation and mutation. These early studies demonstrate some of the advantages and limitations of using TTDS for the study of biomolecules

  7. Laser photodissociation and spectroscopy of mass-separated biomolecular ions

    CERN Document Server

    Polfer, Nicolas C

    2014-01-01

    This lecture notes book presents how enhanced structural information of biomolecular ions can be obtained from interaction with photons of specific frequency - laser light. The methods described in the book ""Laser photodissociation and spectroscopy of mass-separated biomolecular ions"" make use of the fact that the discrete energy and fast time scale of photoexcitation can provide more control in ion activation. This activation is the crucial process producing structure-informative product ions that cannot be generated with more conventional heating methods, such as collisional activation. Th

  8. The HADDOCK web server for data-driven biomolecular docking

    NARCIS (Netherlands)

    de Vries, S.J.|info:eu-repo/dai/nl/304837717; van Dijk, M.|info:eu-repo/dai/nl/325811113; Bonvin, A.M.J.J.|info:eu-repo/dai/nl/113691238

    2010-01-01

    Computational docking is the prediction or modeling of the three-dimensional structure of a biomolecular complex, starting from the structures of the individual molecules in their free, unbound form. HADDOC K is a popular docking program that takes a datadriven approach to docking, with support for

  9. Review of MEMS differential scanning calorimetry for biomolecular study

    Science.gov (United States)

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

    2017-12-01

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

  10. Design rules for biomolecular adhesion: lessons from force measurements.

    Science.gov (United States)

    Leckband, Deborah

    2010-01-01

    Cell adhesion to matrix, other cells, or pathogens plays a pivotal role in many processes in biomolecular engineering. Early macroscopic methods of quantifying adhesion led to the development of quantitative models of cell adhesion and migration. The more recent use of sensitive probes to quantify the forces that alter or manipulate adhesion proteins has revealed much greater functional diversity than was apparent from population average measurements of cell adhesion. This review highlights theoretical and experimental methods that identified force-dependent molecular properties that are central to the biological activity of adhesion proteins. Experimental and theoretical methods emphasized in this review include the surface force apparatus, atomic force microscopy, and vesicle-based probes. Specific examples given illustrate how these tools have revealed unique properties of adhesion proteins and their structural origins.

  11. Micro and Nanotechnologies Enhanced Biomolecular Sensing

    Directory of Open Access Journals (Sweden)

    Tza-Huei Wang

    2013-07-01

    Full Text Available This editorial summarizes some of the recent advances of micro and nanotechnology-based tools and devices for biomolecular detection. These include the incorporation of nanomaterials into a sensor surface or directly interfacing with molecular probes to enhance target detection via more rapid and sensitive responses, and the use of self-assembled organic/inorganic nanocomposites that inhibit exceptional spectroscopic properties to enable facile homogenous assays with efficient binding kinetics. Discussions also include some insight into microfluidic principles behind the development of an integrated sample preparation and biosensor platform toward a miniaturized and fully functional system for point of care applications.

  12. Plasmodesmata: Structure and Function

    Directory of Open Access Journals (Sweden)

    Thomas David Geydan

    2006-07-01

    Full Text Available Plasmodesmata are channels that transverse the cell wall and membrane. These specialized and non passive channels act like gates that facilitate and regulate both communication and transportation of molecules such as water, nutrients, metabolites and macromolecules between plant cells. In the last decade a new point of view of plasmodesmata has emerged, and studies have  demonstrated that these channels are more complex. In this brief note, we pretend to expose the actual knowledge of plasmodesmata, focusing on their structure and function.

  13. A Project-Based Biochemistry Laboratory Promoting the Understanding and Uses of Fluorescence Spectroscopy in the Study of Biomolecular Structures and Interactions

    Science.gov (United States)

    Briese, Nicholas; Jakubowsk, Henry V.

    2007-01-01

    A laboratory project for a first semester biochemistry course is described, which integrates the traditional classroom study of the structure and function of biomolecules with the laboratory study of these molecules using fluorescence spectroscopy. Students are assigned a specific question addressing the stability/function of lipids, proteins, or…

  14. Multi-functional composite structures

    Science.gov (United States)

    Mulligan, Anthony C.; Halloran, John; Popovich, Dragan; Rigali, Mark J.; Sutaria, Manish P.; Vaidyanathan, K. Ranji; Fulcher, Michael L.; Knittel, Kenneth L.

    2004-10-19

    Fibrous monolith processing techniques to fabricate multifunctional structures capable of performing more than one discrete function such as structures capable of bearing structural loads and mechanical stresses in service and also capable of performing at least one additional non-structural function.

  15. Smartphones for cell and biomolecular detection.

    Science.gov (United States)

    Liu, Xiyuan; Lin, Tung-Yi; Lillehoj, Peter B

    2014-11-01

    Recent advances in biomedical science and technology have played a significant role in the development of new sensors and assays for cell and biomolecular detection. Generally, these efforts are aimed at reducing the complexity and costs associated with diagnostic testing so that it can be performed outside of a laboratory or hospital setting, requiring minimal equipment and user involvement. In particular, point-of-care (POC) testing offers immense potential for many important applications including medical diagnosis, environmental monitoring, food safety, and biosecurity. When coupled with smartphones, POC systems can offer portability, ease of use and enhanced functionality while maintaining performance. This review article focuses on recent advancements and developments in smartphone-based POC systems within the last 6 years with an emphasis on cell and biomolecular detection. These devices typically comprise multiple components, such as detectors, sample processors, disposable chips, batteries, and software, which are integrated with a commercial smartphone. One of the most important aspects of developing these systems is the integration of these components onto a compact and lightweight platform that requires minimal power. Researchers have demonstrated several promising approaches employing various detection schemes and device configurations, and it is expected that further developments in biosensors, battery technology and miniaturized electronics will enable smartphone-based POC technologies to become more mainstream tools in the scientific and biomedical communities.

  16. Programming in biomolecular computation

    DEFF Research Database (Denmark)

    Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue

    2010-01-01

    in a strong sense: a universal algorithm exists, that is able to execute any program, and is not asymptotically inefficient. A prototype model has been implemented (for now in silico on a conventional computer). This work opens new perspectives on just how computation may be specified at the biological level......., by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only...... executable, but are also compilable and interpretable. It is universal: all computable functions can be computed (in natural ways and without arcane encodings of data and algorithm); it is also uniform: new “hardware” is not needed to solve new problems; and (last but not least) it is Turing complete...

  17. Biomolecular detection device

    Science.gov (United States)

    Huo, Qisheng [Albuquerque, NM; Liu, Jun [Albuquerque, NM

    2008-10-21

    A device for detecting and measuring the concentration of biomolecules in solution, utilizing a conducting electrode in contact with a solution containing target biomolecules, with a film with controllable pore size distribution characteristics applied to at least one surface of the conducting electrode. The film is functionalized with probe molecules that chemically interact with the target biomolecules at the film surface, blocking indicator molecules present in solution from diffusing from the solution to the electrode, thereby changing the electrochemical response of the electrode.

  18. Nuclear correlations and structure functions

    International Nuclear Information System (INIS)

    Hu Guoju; Irvine, J.M.

    1989-01-01

    It is argued that the search for a mass number dependence of the nuclear structure function per nucleon is profitably directed to the region of Bjorken scaling variable x > 1. We show that in the convolution model of the nuclear structure function the nuclear momentum distribution and energy spectrum generated by cluster expansion techniques, here realised in the correlated basis function method, invoking tensor correlations and short-range density-dependent repulsions adequately describes the structure function for 12 C in the region x > 1. The results of structure functions for a number of light-, medium- and heavy-mass nuclei are presented. (author)

  19. Calculations of nucleon structure functions

    International Nuclear Information System (INIS)

    Signal, A.I.

    1990-01-01

    We present a method of calculating deep inelastic nucleon structure functions using bag model wavefunctions. Our method uses the Peierls - Yoccoz projection to form translation invariant bag states. We obtain the correct support for the structure functions and satisfy the positivity requirements for quark and anti-quark distribution functions. (orig.)

  20. Insights Into the Bifunctional Aphidicolan-16-ß-ol Synthase Through Rapid Biomolecular Modeling Approaches.

    Science.gov (United States)

    Hirte, Max; Meese, Nicolas; Mertz, Michael; Fuchs, Monika; Brück, Thomas B

    2018-01-01

    Diterpene synthases catalyze complex, multi-step C-C coupling reactions thereby converting the universal, aliphatic precursor geranylgeranyl diphosphate into diverse olefinic macrocylces that form the basis for the structural diversity of the diterpene natural product family. Since catalytically relevant crystal structures of diterpene synthases are scarce, homology based biomolecular modeling techniques offer an alternative route to study the enzyme's reaction mechanism. However, precise identification of catalytically relevant amino acids is challenging since these models require careful preparation and refinement techniques prior to substrate docking studies. Targeted amino acid substitutions in this protein class can initiate premature quenching of the carbocation centered reaction cascade. The structural characterization of those alternative cyclization products allows for elucidation of the cyclization reaction cascade and provides a new source for complex macrocyclic synthons. In this study, new insights into structure and function of the fungal, bifunctional Aphidicolan-16-ß-ol synthase were achieved using a simplified biomolecular modeling strategy. The applied refinement methodologies could rapidly generate a reliable protein-ligand complex, which provides for an accurate in silico identification of catalytically relevant amino acids. Guided by our modeling data, ACS mutations lead to the identification of the catalytically relevant ACS amino acid network I626, T657, Y658, A786, F789, and Y923. Moreover, the ACS amino acid substitutions Y658L and D661A resulted in a premature termination of the cyclization reaction cascade en-route from syn-copalyl diphosphate to Aphidicolan-16-ß-ol. Both ACS mutants generated the diterpene macrocycle syn-copalol and a minor, non-hydroxylated labdane related diterpene, respectively. Our biomolecular modeling and mutational studies suggest that the ACS substrate cyclization occurs in a spatially restricted location of

  1. Insights Into the Bifunctional Aphidicolan-16-ß-ol Synthase Through Rapid Biomolecular Modeling Approaches

    Directory of Open Access Journals (Sweden)

    Max Hirte

    2018-04-01

    Full Text Available Diterpene synthases catalyze complex, multi-step C-C coupling reactions thereby converting the universal, aliphatic precursor geranylgeranyl diphosphate into diverse olefinic macrocylces that form the basis for the structural diversity of the diterpene natural product family. Since catalytically relevant crystal structures of diterpene synthases are scarce, homology based biomolecular modeling techniques offer an alternative route to study the enzyme's reaction mechanism. However, precise identification of catalytically relevant amino acids is challenging since these models require careful preparation and refinement techniques prior to substrate docking studies. Targeted amino acid substitutions in this protein class can initiate premature quenching of the carbocation centered reaction cascade. The structural characterization of those alternative cyclization products allows for elucidation of the cyclization reaction cascade and provides a new source for complex macrocyclic synthons. In this study, new insights into structure and function of the fungal, bifunctional Aphidicolan-16-ß-ol synthase were achieved using a simplified biomolecular modeling strategy. The applied refinement methodologies could rapidly generate a reliable protein-ligand complex, which provides for an accurate in silico identification of catalytically relevant amino acids. Guided by our modeling data, ACS mutations lead to the identification of the catalytically relevant ACS amino acid network I626, T657, Y658, A786, F789, and Y923. Moreover, the ACS amino acid substitutions Y658L and D661A resulted in a premature termination of the cyclization reaction cascade en-route from syn-copalyl diphosphate to Aphidicolan-16-ß-ol. Both ACS mutants generated the diterpene macrocycle syn-copalol and a minor, non-hydroxylated labdane related diterpene, respectively. Our biomolecular modeling and mutational studies suggest that the ACS substrate cyclization occurs in a spatially

  2. Insights into the bifunctional Aphidicolan-16-ß-ol synthase through rapid biomolecular modelling approaches

    Science.gov (United States)

    Hirte, Max; Meese, Nicolas; Mertz, Michael; Fuchs, Monika; Brück, Thomas B.

    2018-04-01

    Diterpene synthases catalyze complex, multi-step C-C coupling reactions thereby converting the universal, aliphatic precursor geranylgeranyl diphosphate into diverse olefinic macrocylces that form the basis for the structural diversity of the diterpene natural product family. Since catalytically relevant crystal structures of diterpene synthases are scarce, homology based biomolecular modelling techniques offer an alternative route to study the enzyme’s reaction mechanism. However, precise identification of catalytically relevant amino acids is challenging since these models require careful preparation and refinement techniques prior to substrate docking studies. Targeted amino acid substitutions in this protein class can initiate premature quenching of the carbocation centered reaction cascade. The structural characterization of those alternative cyclization products allows for elucidation of the cyclization reaction cascade and provides a new source for complex macrocyclic synthons. In this study, new insights into structure and function of the fungal, bifunctional Aphidicolan-16-ß-ol synthase were achieved using a simplified biomolecular modelling strategy. The applied refinement methodologies could rapidly generate a reliable protein-ligand complex, which provides for an accurate in silico identification of catalytically relevant amino acids. Guided by our modelling data, ACS mutations lead to the identification of the catalytically relevant ACS amino acid network I626, T657, Y658, A786, F789 and Y923. Moreover, the ACS amino acid substitutions Y658L and D661A resulted in a premature termination of the cyclization reaction cascade en-route from syn-copalyl diphosphate to Aphidicolan-16-ß-ol. Both ACS mutants generated the diterpene macrocycle syn-copalol and a minor, non-hydroxylated labdane related diterpene, respectively. Our biomolecular modelling and mutational studies suggest that the ACS substrate cyclization occurs in a spatially restricted location

  3. Spin dependent photon structure functions

    International Nuclear Information System (INIS)

    Manohar, A.V.; Massachusetts Inst. of Tech., Cambridge

    1989-01-01

    Spin dependent structure functions of the photon are studied using the operator product expansion. There are new twist-two photon and gluon operators which contribute. The structure functions g 1 and F 3 are calculable in QCD, but differ from their free quark values. The corrections to F 3 are suppressed by 1/log Q 2 . The calculation is an extension of the analysis of Witten for the spin averaged structure functions F 1 and F 2 . (orig.)

  4. Biomolecular simulations on petascale: promises and challenges

    International Nuclear Information System (INIS)

    Agarwal, Pratul K; Alam, Sadaf R

    2006-01-01

    Proteins work as highly efficient machines at the molecular level and are responsible for a variety of processes in all living cells. There is wide interest in understanding these machines for implications in biochemical/biotechnology industries as well as in health related fields. Over the last century, investigations of proteins based on a variety of experimental techniques have provided a wealth of information. More recently, theoretical and computational modeling using large scale simulations is providing novel insights into the functioning of these machines. The next generation supercomputers with petascale computing power, hold great promises as well as challenges for the biomolecular simulation scientists. We briefly discuss the progress being made in this area

  5. Micro- and nanodevices integrated with biomolecular probes.

    Science.gov (United States)

    Alapan, Yunus; Icoz, Kutay; Gurkan, Umut A

    2015-12-01

    Understanding how biomolecules, proteins and cells interact with their surroundings and other biological entities has become the fundamental design criterion for most biomedical micro- and nanodevices. Advances in biology, medicine, and nanofabrication technologies complement each other and allow us to engineer new tools based on biomolecules utilized as probes. Engineered micro/nanosystems and biomolecules in nature have remarkably robust compatibility in terms of function, size, and physical properties. This article presents the state of the art in micro- and nanoscale devices designed and fabricated with biomolecular probes as their vital constituents. General design and fabrication concepts are presented and three major platform technologies are highlighted: microcantilevers, micro/nanopillars, and microfluidics. Overview of each technology, typical fabrication details, and application areas are presented by emphasizing significant achievements, current challenges, and future opportunities. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Study of quark structure functions

    International Nuclear Information System (INIS)

    Dao, F.T.; Flaminio, E.; Lai, K.; Metcalf, M.; Wang, L.

    1977-01-01

    The quark structure functions of the proton are determined through a combined analysis of the reactions pN → ll-barX and eN → eX. The valence-quark structure function of the pion is also given by analyzing the πN → μμ-barX data measured by the Branson et al

  7. The Beamline X28C of the Center for Synchrotron Biosciences: a National Resource for Biomolecular Structure and Dynamics Experiments Using Synchrotron Footprinting

    International Nuclear Information System (INIS)

    Gupta, S.; Sullivan, M.; Toomey, J.; Kiselar, J.; Chance, M.

    2007-01-01

    Structural mapping of proteins and nucleic acids with high resolution in solution is of critical importance for understanding their biological function. A wide range of footprinting technologies have been developed over the last ten years to address this need. Beamline X28C, a white-beam X-ray source at the National Synchrotron Light Source of Brookhaven National Laboratory, functions as a platform for synchrotron footprinting research and further technology development in this growing field. An expanding set of user groups utilize this national resource funded by the National Institute of Biomedical Imaging and Bioengineering of the National Institutes of Health. The facility is operated by the Center for Synchrotron Biosciences and the Center for Proteomics of Case Western Reserve University. The facility includes instrumentation suitable for conducting both steady-state and millisecond time-resolved footprinting experiments based on the production of hydroxyl radicals by X-rays. Footprinting studies of nucleic acids are routinely conducted with X-ray exposures of tens of milliseconds, which include studies of nucleic acid folding and their interactions with proteins. This technology can also be used to study protein structure and dynamics in solution as well as protein-protein interactions in large macromolecular complexes. This article provides an overview of the X28C beamline technology and defines protocols for its adoption at other synchrotron facilities. Lastly, several examples of published results provide illustrations of the kinds of experiments likely to be successful using these approaches

  8. Interacting with the biomolecular solvent accessible surface via a haptic feedback device

    Directory of Open Access Journals (Sweden)

    Hayward Steven

    2009-10-01

    Full Text Available Abstract Background From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation. Results A haptic rendering application for biomolecular visualisation has been developed that allows the user to gain three-dimensional awareness of the shape of a biomolecule. By using a water molecule as the probe, modelled as an oxygen atom having hard-sphere interactions with the biomolecule, the process of exploration has the further benefit of being able to determine regions on the molecular surface that are accessible to the solvent. This gives insight into how awkward it is for a water molecule to gain access to or escape from channels and cavities, indicating possible entropic bottlenecks. In the case of liver alcohol dehydrogenase bound to the inhibitor SAD, it was found that there is a channel just wide enough for a single water molecule to pass through. Placing the probe coincident with crystallographic water molecules suggests that they are sometimes located within small pockets that provide a sterically stable environment irrespective of hydrogen bonding considerations. Conclusion By using the software, named HaptiMol ISAS (available from http://www.haptimol.co.uk, one can explore the accessible surface of biomolecules using a three-dimensional input device to gain insights into the shape and water

  9. The photon structure function

    International Nuclear Information System (INIS)

    Berger, C.

    1984-01-01

    In principle we have to distinguish between three cases: In no-tag experiments, none of the outgoing leptons e + e - is detected. The photon flux is completely dominated by transversely polarized photons, which are practically on-mass-shell. In single-tag experiments, either the outgoing e - or e + is detected in a forward spectrometer. Sometimes the tagging information is only used for separating a multihadronic twophoton final state from e + e - annihilation states. On the other hand, the information from the forward detectors can be used to investigate the Q 2 behaviour of the cross-section. A combination of tagging on one side with antitagging on the other allows an easy interpretation of the results in terms of electron scattering off a real photon target. In double-tag experiments, both outgoing leptons are measured. In principle, the full kinematical structure of the process can be studied, but we are still a long way from starting to tackle this difficult task

  10. Biomolecular strategies for cell surface engineering

    Science.gov (United States)

    Wilson, John Tanner

    Islet transplantation has emerged as a promising cell-based therapy for the treatment of diabetes, but its clinical efficacy remains limited by deleterious host responses that underlie islet destruction. In this dissertation, we describe the assembly of ultrathin conformal coatings that confer molecular-level control over the composition and biophysicochemical properties of the islet surface with implications for improving islet engraftment. Significantly, this work provides novel biomolecular strategies for cell surface engineering with broad biomedical and biotechnological applications in cell-based therapeutics and beyond. Encapsulation of cells and tissue offers a rational approach for attenuating deleterious host responses towards transplanted cells, but a need exists to develop cell encapsulation strategies that minimize transplant volume. Towards this end, we endeavored to generate nanothin films of diverse architecture with tunable properties on the extracellular surface of individual pancreatic islets through a process of layer-by-layer (LbL) self assembly. We first describe the formation of poly(ethylene glycol) (PEG)-rich conformal coatings on islets via LbL self assembly of poly(L-lysine)-g-PEG(biotin) and streptavidin. Multilayer thin films conformed to the geometrically and chemically heterogeneous islet surface, and could be assembled without loss of islet viability or function. Significantly, coated islets performed comparably to untreated controls in a murine model of allogenic intraportal islet transplantation, and, to our knowledge, this is the first study to report in vivo survival and function of nanoencapsulated cells or cell aggregates. Based on these findings, we next postulated that structurally similar PLL-g-PEG copolymers comprised of shorter PEG grafts might be used to initiate and propagate the assembly of polyelectrolyte multilayer (PEM) films on pancreatic islets, while simultaneously preserving islet viability. Through control of PLL

  11. Mind, brain, structure and function

    Energy Technology Data Exchange (ETDEWEB)

    Aleksander, I

    1982-01-01

    The author discusses the type of problem one encounters when trying to formalise the nature of a state structure associated with the brain and the origins of this state structure. The paper first defines in broad terms the nature of the structure function problem, and then goes on to separate out those parts of a structure that lead to the variational and adaptive nature of the state structure. It is argued that the relationship between the structure that leads to adaptation and its embedding in an external environment are crucial areas for further study. 4 references.

  12. Diquarks and nucleon structure functions

    International Nuclear Information System (INIS)

    Linkevich, A.D.; Savrin, V.I.; Skachkov, N.B.

    1982-01-01

    Formulae for structure functions of the deep-inelastic lepton-nucleon scattering are obtained through relativistic wave functions of systems composed of particles with spins 0, 1/2 and 1, 1/2. These wave functions are solutions of covariant two-particle single-time equations describing the nucleon as a system formed out of a quark and a diquark. Diquark is considered as a boson with the spin 0 and 1. The expressions for the nucleon structure functions are obtained by using the matrix elements of the current operator corresponding to the elastic scattering of the photon on a quark and on a diquark [ru

  13. Proton and neutron structure functions

    International Nuclear Information System (INIS)

    Rock, S.

    1991-01-01

    New result on charged lepton scattering from hydrogen and deuterium targets by the BCDMS, NMC and SLAC collaborations have greatly increased our knowledge of the structure functions of protons and neutrons. The disagreement between the high energy muon scattering cross sections obtained by the EMC and BCDMS collaborations have been almost completely resolved by comparison with a global analysis of old and new SLAC data and a reanalysis of EMC data. We now have a consistent set of structure functions which covers an approximate range 1 ≤ Q 2 ≤ 200 (GeV/c) 2 and 0.07 ≤ x ≤ 0.7. The ratio of neutron to proton structure functions decreases with increasing Q 2 for values of x ≥ 0.1. The difference between proton and neutron structure functions approaches zero as x decreases, consistent with the expected √x behavior. (orig.)

  14. Stochastic Simulation of Biomolecular Reaction Networks Using the Biomolecular Network Simulator Software

    National Research Council Canada - National Science Library

    Frazier, John; Chusak, Yaroslav; Foy, Brent

    2008-01-01

    .... The software uses either exact or approximate stochastic simulation algorithms for generating Monte Carlo trajectories that describe the time evolution of the behavior of biomolecular reaction networks...

  15. Physics at the biomolecular interface fundamentals for molecular targeted therapy

    CERN Document Server

    Fernández, Ariel

    2016-01-01

    This book focuses primarily on the role of interfacial forces in understanding biological phenomena at the molecular scale. By providing a suitable statistical mechanical apparatus to handle the biomolecular interface, the book becomes uniquely positioned to address core problems in molecular biophysics. It highlights the importance of interfacial tension in delineating a solution to the protein folding problem, in unravelling the physico-chemical basis of enzyme catalysis and protein associations, and in rationally designing molecular targeted therapies. Thus grounded in fundamental science, the book develops a powerful technological platform for drug discovery, while it is set to inspire scientists at any level in their careers determined to address the major challenges in molecular biophysics. The acknowledgment of how exquisitely the structure and dynamics of proteins and their aqueous environment are related attests to the overdue recognition that biomolecular phenomena cannot be effectively understood w...

  16. Conducting polymer based biomolecular electronic devices

    Indian Academy of Sciences (India)

    Conducting polymers; LB films; biosensor microactuators; monolayers. ... have been projected for applications for a wide range of biomolecular electronic devices such as optical, electronic, drug-delivery, memory and biosensing devices.

  17. Functional Insights from Structural Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Forouhar,F.; Kuzin, A.; Seetharaman, J.; Lee, I.; Zhou, W.; Abashidze, M.; Chen, Y.; Montelione, G.; Tong, L.; et al

    2007-01-01

    Structural genomics efforts have produced structural information, either directly or by modeling, for thousands of proteins over the past few years. While many of these proteins have known functions, a large percentage of them have not been characterized at the functional level. The structural information has provided valuable functional insights on some of these proteins, through careful structural analyses, serendipity, and structure-guided functional screening. Some of the success stories based on structures solved at the Northeast Structural Genomics Consortium (NESG) are reported here. These include a novel methyl salicylate esterase with important role in plant innate immunity, a novel RNA methyltransferase (H. influenzae yggJ (HI0303)), a novel spermidine/spermine N-acetyltransferase (B. subtilis PaiA), a novel methyltransferase or AdoMet binding protein (A. fulgidus AF{_}0241), an ATP:cob(I)alamin adenosyltransferase (B. subtilis YvqK), a novel carboxysome pore (E. coli EutN), a proline racemase homolog with a disrupted active site (B. melitensis BME11586), an FMN-dependent enzyme (S. pneumoniae SP{_}1951), and a 12-stranded {beta}-barrel with a novel fold (V. parahaemolyticus VPA1032).

  18. Functional Generalized Structured Component Analysis.

    Science.gov (United States)

    Suk, Hye Won; Hwang, Heungsun

    2016-12-01

    An extension of Generalized Structured Component Analysis (GSCA), called Functional GSCA, is proposed to analyze functional data that are considered to arise from an underlying smooth curve varying over time or other continua. GSCA has been geared for the analysis of multivariate data. Accordingly, it cannot deal with functional data that often involve different measurement occasions across participants and a large number of measurement occasions that exceed the number of participants. Functional GSCA addresses these issues by integrating GSCA with spline basis function expansions that represent infinite-dimensional curves onto a finite-dimensional space. For parameter estimation, functional GSCA minimizes a penalized least squares criterion by using an alternating penalized least squares estimation algorithm. The usefulness of functional GSCA is illustrated with gait data.

  19. Structure functions and parton distributions

    International Nuclear Information System (INIS)

    Martin, A.D.; Stirling, W.J.; Roberts, R.G.

    1995-01-01

    The MRS parton distribution analysis is described. The latest sets are shown to give an excellent description of a wide range of deep-inelastic and other hard scattering data. Two important theoretical issues-the behavior of the distributions at small x and the flavor structure of the quark sea-are discussed in detail. A comparison with the new structure function data from HERA is made, and the outlook for the future is discussed

  20. Collagens - structure, function and biosynthesis.

    OpenAIRE

    Gelse, K; Poschl, E; Aigner, T

    2003-01-01

    The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified so far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. This review focuses on the dis...

  1. Structure functions and parton distributions

    International Nuclear Information System (INIS)

    Olness, F.; Tung, Wu-Ki

    1991-04-01

    Activities of the structure functions and parton distributions group is summarized. The impact of scheme-dependence of parton distributions (especially sea-quarks and gluons) on the quantitative formulation of the QCD parton model is highlighted. Recent progress on the global analysis of parton distributions is summarized. Issues on the proper use of the next-to-leading parton distributions are stressed

  2. Rise in proton structure function

    International Nuclear Information System (INIS)

    Fazal-e-Aleem; Rashid, H.; Ali, S.

    1996-08-01

    By the choice of a new scale factor we obtain a good qualitative fit to the HERA data for the proton structure function in the small x region which exhibits double asymptotic scaling. Any scaling violations in the future measurements when made in smaller bins will be of immense value. (author). 19 refs, 6 figs

  3. Structure functions at low x

    International Nuclear Information System (INIS)

    Roeck, A.De.

    2000-01-01

    Deep recent data and phenomenology on low-x structure functions are discussed inelastic scattering. We will be interested primordially in the regions Q 2 → 0 i.e. the transition from γp to, and x → 10 -4 - 10 -6 i.e. the region of high parton densities

  4. The notochord: structure and functions.

    Science.gov (United States)

    Corallo, Diana; Trapani, Valeria; Bonaldo, Paolo

    2015-08-01

    The notochord is an embryonic midline structure common to all members of the phylum Chordata, providing both mechanical and signaling cues to the developing embryo. In vertebrates, the notochord arises from the dorsal organizer and it is critical for proper vertebrate development. This evolutionary conserved structure located at the developing midline defines the primitive axis of embryos and represents the structural element essential for locomotion. Besides its primary structural function, the notochord is also a source of developmental signals that patterns surrounding tissues. Among the signals secreted by the notochord, Hedgehog proteins play key roles during embryogenesis. The Hedgehog signaling pathway is a central regulator of embryonic development, controlling the patterning and proliferation of a wide variety of organs. In this review, we summarize the current knowledge on notochord structure and functions, with a particular emphasis on the key developmental events that take place in vertebrates. Moreover, we discuss some genetic studies highlighting the phenotypic consequences of impaired notochord development, which enabled to understand the molecular basis of different human congenital defects and diseases.

  5. Structure and function of wood

    Science.gov (United States)

    Alex Wiedenhoeft

    2010-01-01

    Wood is a complex biological structure, a composite of many chemistries and cell types acting together to serve the needs of a living plant. Attempting to understand wood in the context of wood technology, we have often overlooked the key and basic fact that wood evolved over the course of millions of years to serve three main functions in plants― conduction of water...

  6. Biomolecular simulation: historical picture and future perspectives.

    Science.gov (United States)

    van Gunsteren, Wilfred F; Dolenc, Jozica

    2008-02-01

    Over the last 30 years, computation based on molecular models is playing an increasingly important role in biology, biological chemistry and biophysics. Since only a very limited number of properties of biomolecular systems are actually accessible to measurement by experimental means, computer simulation complements experiments by providing not only averages, but also distributions and time series of any definable, observable or non-observable, quantity. Biomolecular simulation may be used (i) to interpret experimental data, (ii) to provoke new experiments, (iii) to replace experiments and (iv) to protect intellectual property. Progress over the last 30 years is sketched and perspectives are outlined for the future.

  7. Computational Methods for Biomolecular Electrostatics

    Science.gov (United States)

    Dong, Feng; Olsen, Brett; Baker, Nathan A.

    2008-01-01

    An understanding of intermolecular interactions is essential for insight into how cells develop, operate, communicate and control their activities. Such interactions include several components: contributions from linear, angular, and torsional forces in covalent bonds, van der Waals forces, as well as electrostatics. Among the various components of molecular interactions, electrostatics are of special importance because of their long range and their influence on polar or charged molecules, including water, aqueous ions, and amino or nucleic acids, which are some of the primary components of living systems. Electrostatics, therefore, play important roles in determining the structure, motion and function of a wide range of biological molecules. This chapter presents a brief overview of electrostatic interactions in cellular systems with a particular focus on how computational tools can be used to investigate these types of interactions. PMID:17964951

  8. CYCLOPHILIN A: STRUCTURE AND FUNCTIONS

    Directory of Open Access Journals (Sweden)

    A. A. Kalinina

    2017-01-01

    Full Text Available Cyclophilins belong to a large family of ancient conservative proteins with peptidyl-prolyl-cis-trans isomerase activity. The main member of this family – cyclophilin A – was discovered as an intracellular ligand for cyclosporine A. Further investigations revealed a wide range of functions of cyclophilin A. Cyclophilin A is involved in T-cell signaling, it takes part in folding, assembly and intracellular transport of proteins, as well as acts as an antioxidant. Different cell types secrete cyclophilin A under infection or oxidative stress. Cyclophilin A is one of the main factors involved in inflammation and pathogenesis of autoimmune, cardiovascular and other diseases. This protein is thought to take part in tumor progression. In this review we describe the structure of cyclophilin A and its main known functions in health and disease.

  9. Supramolecular Structure and Function 9

    CERN Document Server

    Pifat-Mrzljak, Greta

    2007-01-01

    The book is based on International Summer Schools on Biophysics held in Croatia which, contrary to other workshops centered mainly on one topic or technique, has very broad scope providing advanced training in areas related to biophysics. This volume is presenting papers in the field of biophysics for studying biological phenomena by using physical methods (NMR, EPR, FTIR, Mass Spectrometry, etc.) and/or concepts (predictions of protein-protein interactions, virtual ligand screening etc.). The interrelationship of supramolecular structures and there functions is enlightened by applications of principals of these physical methods in the biophysical and molecular biology context.

  10. Functional nanometer-scale structures

    Science.gov (United States)

    Chan, Tsz On Mario

    Nanometer-scale structures have properties that are fundamentally different from their bulk counterparts. Much research effort has been devoted in the past decades to explore new fabrication techniques, model the physical properties of these structures, and construct functional devices. The ability to manipulate and control the structure of matter at the nanoscale has made many new classes of materials available for the study of fundamental physical processes and potential applications. The interplay between fabrication techniques and physical understanding of the nanostructures and processes has revolutionized the physical and material sciences, providing far superior properties in materials for novel applications that benefit society. This thesis consists of two major aspects of my graduate research in nano-scale materials. In the first part (Chapters 3--6), a comprehensive study on the nanostructures based on electrospinning and thermal treatment is presented. Electrospinning is a well-established method for producing high-aspect-ratio fibrous structures, with fiber diameter ranging from 1 nm--1 microm. A polymeric solution is typically used as a precursor in electrospinning. In our study, the functionality of the nanostructure relies on both the nanostructure and material constituents. Metallic ions containing precursors were added to the polymeric precursor following a sol-gel process to prepare the solution suitable for electrospinning. A typical electrospinning process produces as-spun fibers containing both polymer and metallic salt precursors. Subsequent thermal treatments of the as-spun fibers were carried out in various conditions to produce desired structures. In most cases, polymer in the solution and the as-spun fibers acted as a backbone for the structure formation during the subsequent heat treatment, and were thermally removed in the final stage. Polymers were also designed to react with the metallic ion precursors during heat treatment in some

  11. Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology.

    Science.gov (United States)

    Thibault, J C; Roe, D R; Eilbeck, K; Cheatham, T E; Facelli, J C

    2015-01-01

    Biomolecular simulations aim to simulate structure, dynamics, interactions, and energetics of complex biomolecular systems. With the recent advances in hardware, it is now possible to use more complex and accurate models, but also reach time scales that are biologically significant. Molecular simulations have become a standard tool for toxicology and pharmacology research, but organizing and sharing data - both within the same organization and among different ones - remains a substantial challenge. In this paper we review our recent work leading to the development of a comprehensive informatics infrastructure to facilitate the organization and exchange of biomolecular simulations data. Our efforts include the design of data models and dictionary tools that allow the standardization of the metadata used to describe the biomedical simulations, the development of a thesaurus and ontology for computational reasoning when searching for biomolecular simulations in distributed environments, and the development of systems based on these models to manage and share the data at a large scale (iBIOMES), and within smaller groups of researchers at laboratory scale (iBIOMES Lite), that take advantage of the standardization of the meta data used to describe biomolecular simulations.

  12. Thermodynamic properties of water solvating biomolecular surfaces

    Science.gov (United States)

    Heyden, Matthias

    Changes in the potential energy and entropy of water molecules hydrating biomolecular interfaces play a significant role for biomolecular solubility and association. Free energy perturbation and thermodynamic integration methods allow calculations of free energy differences between two states from simulations. However, these methods are computationally demanding and do not provide insights into individual thermodynamic contributions, i.e. changes in the solvent energy or entropy. Here, we employ methods to spatially resolve distributions of hydration water thermodynamic properties in the vicinity of biomolecular surfaces. This allows direct insights into thermodynamic signatures of the hydration of hydrophobic and hydrophilic solvent accessible sites of proteins and small molecules and comparisons to ideal model surfaces. We correlate dynamic properties of hydration water molecules, i.e. translational and rotational mobility, to their thermodynamics. The latter can be used as a guide to extract thermodynamic information from experimental measurements of site-resolved water dynamics. Further, we study energy-entropy compensations of water at different hydration sites of biomolecular surfaces. This work is supported by the Cluster of Excellence RESOLV (EXC 1069) funded by the Deutsche Forschungsgemeinschaft.

  13. Microfluidic Devices for Studying Biomolecular Interactions

    Science.gov (United States)

    Wilson, Wilbur W.; Garcia, Carlos d.; Henry, Charles S.

    2006-01-01

    Microfluidic devices for monitoring biomolecular interactions have been invented. These devices are basically highly miniaturized liquid-chromatography columns. They are intended to be prototypes of miniature analytical devices of the laboratory on a chip type that could be fabricated rapidly and inexpensively and that, because of their small sizes, would yield analytical results from very small amounts of expensive analytes (typically, proteins). Other advantages to be gained by this scaling down of liquid-chromatography columns may include increases in resolution and speed, decreases in the consumption of reagents, and the possibility of performing multiple simultaneous and highly integrated analyses by use of multiple devices of this type, each possibly containing multiple parallel analytical microchannels. The principle of operation is the same as that of a macroscopic liquid-chromatography column: The column is a channel packed with particles, upon which are immobilized molecules of the protein of interest (or one of the proteins of interest if there are more than one). Starting at a known time, a solution or suspension containing molecules of the protein or other substance of interest is pumped into the channel at its inlet. The liquid emerging from the outlet of the channel is monitored to detect the molecules of the dissolved or suspended substance(s). The time that it takes these molecules to flow from the inlet to the outlet is a measure of the degree of interaction between the immobilized and the dissolved or suspended molecules. Depending on the precise natures of the molecules, this measure can be used for diverse purposes: examples include screening for solution conditions that favor crystallization of proteins, screening for interactions between drugs and proteins, and determining the functions of biomolecules.

  14. Novel search algorithms for biomolecular structure refinement

    NARCIS (Netherlands)

    Schaik, Catharinus van

    1994-01-01

    Biomacromoleculen zoals eiwitten en nucleïnezuren karakteriseren de eigenschappen van levende organismes. Nucleïnezuren (DNA, RNA) dragen de erfelijke eigenschappen en eiwitten verrichten een aantal zeer uiteenlopende functies. Zo zijn er o.a. eiwitten met een transportfunctie (b.v. hemoglobine),

  15. Converting biomolecular modelling data based on an XML representation.

    Science.gov (United States)

    Sun, Yudong; McKeever, Steve

    2008-08-25

    Biomolecular modelling has provided computational simulation based methods for investigating biological processes from quantum chemical to cellular levels. Modelling such microscopic processes requires atomic description of a biological system and conducts in fine timesteps. Consequently the simulations are extremely computationally demanding. To tackle this limitation, different biomolecular models have to be integrated in order to achieve high-performance simulations. The integration of diverse biomolecular models needs to convert molecular data between different data representations of different models. This data conversion is often non-trivial, requires extensive human input and is inevitably error prone. In this paper we present an automated data conversion method for biomolecular simulations between molecular dynamics and quantum mechanics/molecular mechanics models. Our approach is developed around an XML data representation called BioSimML (Biomolecular Simulation Markup Language). BioSimML provides a domain specific data representation for biomolecular modelling which can effciently support data interoperability between different biomolecular simulation models and data formats.

  16. Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Jeffrey K Noel

    2016-01-01

    Full Text Available Experimentally derived structural constraints have been crucial to the implementation of computational models of biomolecular dynamics. For example, not only does crystallography provide essential starting points for molecular simulations but also high-resolution structures permit for parameterization of simplified models. Since the energy landscapes for proteins and other biomolecules have been shown to be minimally frustrated and therefore funneled, these structure-based models have played a major role in understanding the mechanisms governing folding and many functions of these systems. Structural information, however, may be limited in many interesting cases. Recently, the statistical analysis of residue co-evolution in families of protein sequences has provided a complementary method of discovering residue-residue contact interactions involved in functional configurations. These functional configurations are often transient and difficult to capture experimentally. Thus, co-evolutionary information can be merged with that available for experimentally characterized low free-energy structures, in order to more fully capture the true underlying biomolecular energy landscape.

  17. Ion induced fragmentation of biomolecular systems at low collision energies

    International Nuclear Information System (INIS)

    Bernigaud, V; Adoui, L; Chesnel, J Y; Rangama, J; Huber, B A; Manil, B; Alvarado, F; Bari, S; Hoekstra, R; Postma, J; Schlathoelter, T

    2009-01-01

    In this paper, we present results of different collision experiments between multiply charged ions at low collision energies (in the keV-region) and biomolecular systems. This kind of interaction allows to remove electrons form the biomolecule without transferring a large amount of vibrational excitation energy. Nevertheless, following the ionization of the target, fragmentation of biomolecular species may occur. It is the main objective of this work to study the physical processes involved in the dissociation of highly electronically excited systems. In order to elucidate the intrinsic properties of certain biomolecules (porphyrins and amino acids) we have performed experiments in the gas phase with isolated systems. The obtained results demonstrate the high stability of porphyrins after electron removal. Furthermore, a dependence of the fragmentation pattern produced by multiply charged ions on the isomeric structure of the alanine molecule has been shown. By considering the presence of other surrounding biomolecules (clusters of nucleobases), a strong influence of the environment of the biomolecule on the fragmentation channels and their modification, has been clearly proven. This result is explained, in the thymine and uracil case, by the formation of hydrogen bonds between O and H atoms, which is known to favor planar cluster geometries.

  18. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations.

    Science.gov (United States)

    Vergara-Perez, Sandra; Marucho, Marcelo

    2016-01-01

    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post- analysis of structural and electrical properties of biomolecules.

  19. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

    Science.gov (United States)

    Vergara-Perez, Sandra; Marucho, Marcelo

    2016-01-01

    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson-Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post-analysis of structural and electrical properties of biomolecules.

  20. An Overview of Biomolecular Event Extraction from Scientific Documents.

    Science.gov (United States)

    Vanegas, Jorge A; Matos, Sérgio; González, Fabio; Oliveira, José L

    2015-01-01

    This paper presents a review of state-of-the-art approaches to automatic extraction of biomolecular events from scientific texts. Events involving biomolecules such as genes, transcription factors, or enzymes, for example, have a central role in biological processes and functions and provide valuable information for describing physiological and pathogenesis mechanisms. Event extraction from biomedical literature has a broad range of applications, including support for information retrieval, knowledge summarization, and information extraction and discovery. However, automatic event extraction is a challenging task due to the ambiguity and diversity of natural language and higher-level linguistic phenomena, such as speculations and negations, which occur in biological texts and can lead to misunderstanding or incorrect interpretation. Many strategies have been proposed in the last decade, originating from different research areas such as natural language processing, machine learning, and statistics. This review summarizes the most representative approaches in biomolecular event extraction and presents an analysis of the current state of the art and of commonly used methods, features, and tools. Finally, current research trends and future perspectives are also discussed.

  1. An Overview of Biomolecular Event Extraction from Scientific Documents

    Directory of Open Access Journals (Sweden)

    Jorge A. Vanegas

    2015-01-01

    Full Text Available This paper presents a review of state-of-the-art approaches to automatic extraction of biomolecular events from scientific texts. Events involving biomolecules such as genes, transcription factors, or enzymes, for example, have a central role in biological processes and functions and provide valuable information for describing physiological and pathogenesis mechanisms. Event extraction from biomedical literature has a broad range of applications, including support for information retrieval, knowledge summarization, and information extraction and discovery. However, automatic event extraction is a challenging task due to the ambiguity and diversity of natural language and higher-level linguistic phenomena, such as speculations and negations, which occur in biological texts and can lead to misunderstanding or incorrect interpretation. Many strategies have been proposed in the last decade, originating from different research areas such as natural language processing, machine learning, and statistics. This review summarizes the most representative approaches in biomolecular event extraction and presents an analysis of the current state of the art and of commonly used methods, features, and tools. Finally, current research trends and future perspectives are also discussed.

  2. NMRbox: A Resource for Biomolecular NMR Computation.

    Science.gov (United States)

    Maciejewski, Mark W; Schuyler, Adam D; Gryk, Michael R; Moraru, Ion I; Romero, Pedro R; Ulrich, Eldon L; Eghbalnia, Hamid R; Livny, Miron; Delaglio, Frank; Hoch, Jeffrey C

    2017-04-25

    Advances in computation have been enabling many recent advances in biomolecular applications of NMR. Due to the wide diversity of applications of NMR, the number and variety of software packages for processing and analyzing NMR data is quite large, with labs relying on dozens, if not hundreds of software packages. Discovery, acquisition, installation, and maintenance of all these packages is a burdensome task. Because the majority of software packages originate in academic labs, persistence of the software is compromised when developers graduate, funding ceases, or investigators turn to other projects. To simplify access to and use of biomolecular NMR software, foster persistence, and enhance reproducibility of computational workflows, we have developed NMRbox, a shared resource for NMR software and computation. NMRbox employs virtualization to provide a comprehensive software environment preconfigured with hundreds of software packages, available as a downloadable virtual machine or as a Platform-as-a-Service supported by a dedicated compute cloud. Ongoing development includes a metadata harvester to regularize, annotate, and preserve workflows and facilitate and enhance data depositions to BioMagResBank, and tools for Bayesian inference to enhance the robustness and extensibility of computational analyses. In addition to facilitating use and preservation of the rich and dynamic software environment for biomolecular NMR, NMRbox fosters the development and deployment of a new class of metasoftware packages. NMRbox is freely available to not-for-profit users. Copyright © 2017 Biophysical Society. All rights reserved.

  3. A statistical nanomechanism of biomolecular patterning actuated by surface potential

    Science.gov (United States)

    Lin, Chih-Ting; Lin, Chih-Hao

    2011-02-01

    Biomolecular patterning on a nanoscale/microscale on chip surfaces is one of the most important techniques used in vitro biochip technologies. Here, we report upon a stochastic mechanics model we have developed for biomolecular patterning controlled by surface potential. The probabilistic biomolecular surface adsorption behavior can be modeled by considering the potential difference between the binding and nonbinding states. To verify our model, we experimentally implemented a method of electroactivated biomolecular patterning technology and the resulting fluorescence intensity matched the prediction of the developed model quite well. Based on this result, we also experimentally demonstrated the creation of a bovine serum albumin pattern with a width of 200 nm in 5 min operations. This submicron noncovalent-binding biomolecular pattern can be maintained for hours after removing the applied electrical voltage. These stochastic understandings and experimental results not only prove the feasibility of submicron biomolecular patterns on chips but also pave the way for nanoscale interfacial-bioelectrical engineering.

  4. PREFACE: Radiation Damage in Biomolecular Systems (RADAM07)

    Science.gov (United States)

    McGuigan, Kevin G.

    2008-03-01

    The annual meeting of the COST P9 Action `Radiation damage in biomolecular systems' took place from 19-22 June 2007 in the Royal College of Surgeons in Ireland, in Dublin. The conference was structured into 5 Working Group sessions: Electrons and biomolecular interactions Ions and biomolecular interactions Radiation in physiological environments Theoretical developments for radiation damage Track structure in cells Each of the five working groups presented two sessions of invited talks. Professor Ron Chesser of Texas Tech University, USA gave a riveting plenary talk on `Mechanisms of Adaptive Radiation Responses in Mammals at Chernobyl' and the implications his work has on the Linear-No Threshold model of radiation damage. In addition, this was the first RADAM meeting to take place after the Alexander Litvenenko affair and we were fortunate to have one of the leading scientists involved in the European response Professor Herwig Paretzke of GSF-Institut für Strahlenschutz, Neuherberg, Germany, available to speak. The remaining contributions were presented in the poster session. A total of 72 scientific contributions (32 oral, 40 poster), presented by 97 participants from 22 different countries, gave an overview on the current progress in the 5 different subfields. A 1-day pre-conference `Early Researcher Tutorial Workshop' on the same topic kicked off on 19 June attended by more than 40 postgrads, postdocs and senior researchers. Twenty papers, based on these reports, are included in this volume of Journal of Physics: Conference Series. All the contributions in this volume were fully refereed, and they represent a sample of the courses, invited talks and contributed talks presented during RADAM07. The interdisciplinary RADAM07 conference brought together researchers from a variety of different fields with a common interest in biomolecular radiation damage. This is reflected by the disparate backgrounds of the authors of the papers presented in these proceedings

  5. Disgust: Evolved function and structure

    NARCIS (Netherlands)

    Tybur, J.M.; Lieberman, D.; Kurzban, R.; DeScioli, P.

    2013-01-01

    Interest in and research on disgust has surged over the past few decades. The field, however, still lacks a coherent theoretical framework for understanding the evolved function or functions of disgust. Here we present such a framework, emphasizing 2 levels of analysis: that of evolved function and

  6. Biomolecular Chemistry of Isopropyl Fibrates

    Science.gov (United States)

    Rath, Niharika; Kotheimer, Amenda; Miller, Chad; Zeller, Matthias; Rath, Nigam P.

    2012-01-01

    Isopropyl 2-[4-(4-chlorobenzoyl)-phenoxy]-2-methylpropanoic acid and isopropyl 2-(4-chlorophenoxy)-2-methylpropanoate, also known as fenofibrate and isopropyl clofibrate, are hypolipidemic agents of the fibrate family. In a previously reported triclinic structure of fenofibrate (polymorph I) the methyl groups of the isopropyl moiety (iPr) are located symmetrically about the carboxylate group. We report a new monoclinic form (polymorph II) of fenofibrate and a first structural description of isopropyl clofibrate, and in these the methyl groups are placed asymmetrically about the carboxylate group. In particular the dihedral (torsion) angle between the hydrogen atom on the secondary C and the C atom of the carboxyl group makes a 2.74° angle about the ester O-C bond in the symmetric fenofibrate structure of polymorph I, whereas the same dihedral angle is 45.94° in polymorph II and -30.9° in the crystal structure of isopropyl clofibrate. Gas phase DFT geometry minimizations of fenofibrate and isopropyl clofibrate result in lowest energy conformations for both molecules with a value of about ± 30° for this same angle between the O=C-O-C plane and the C-H bond of the iPr group. A survey of crystal structures containing an iPr ester group reveals that the asymmetric conformation is predominant. Although the hydrogen atom on the secondary C atom of the isopropyl group is located at a comparable distance from the carbonyl oxygen in the symmetric and asymmetric fenofibrate (2.52 and 2.28 Å) and the isopropyl clofibrate (2.36 Å) structures, this hydrogen atom participates in a puckered five membered ring arrangement in the latter two that is unlike the planar arrangement found in symmetric fenofibrate (polymorph I). Polar molecular surface area (PSA) values indicate fenofibrate and isopropyl clofibrate are less able to act as acceptors of hydrogen bonds than their corresponding acid derivatives. Surface area calculations show dynamic polar molecular surface area (PSAd

  7. ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations.

    Science.gov (United States)

    Parvatikar, Akash; Vacaliuc, Gabriel S; Ramanathan, Arvind; Chennubhotla, S Chakra

    2018-05-08

    Anharmonicity in time-dependent conformational fluctuations is noted to be a key feature of functional dynamics of biomolecules. Although anharmonic events are rare, long-timescale (μs-ms and beyond) simulations facilitate probing of such events. We have previously developed quasi-anharmonic analysis to resolve higher-order spatial correlations and characterize anharmonicity in biomolecular simulations. In this article, we have extended this toolbox to resolve higher-order temporal correlations and built a scalable Python package called anharmonic conformational analysis (ANCA). ANCA has modules to: 1) measure anharmonicity in the form of higher-order statistics and its variation as a function of time, 2) output a storyboard representation of the simulations to identify key anharmonic conformational events, and 3) identify putative anharmonic conformational substates and visualization of transitions between these substates. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  8. Positrons in biomolecular systems. II

    International Nuclear Information System (INIS)

    Glass, J.C.; Graf, G.; Costabal, H.; Ewert, D.H.; English, L.

    1982-01-01

    Pickoff-annihilation parameters, as related to the free volume model, are shown to be indicators of structural fluctuations in membranes and membrane bound proteins. Nitrous oxide anesthetic induces lateral rigidity in a membrane, and an anesthetic mechanism is suggested. Conformational changes of (Na + ,K + )ATPase in natural membrane are observed with ATP and Mg-ion binding. New positron applications to active transport and photosynthetic systems are suggested. (Auth.)

  9. Polarized DIS Structure Functions from Neural Networks

    International Nuclear Information System (INIS)

    Del Debbio, L.; Guffanti, A.; Piccione, A.

    2007-01-01

    We present a parametrization of polarized Deep-Inelastic-Scattering (DIS) structure functions based on Neural Networks. The parametrization provides a bias-free determination of the probability measure in the space of structure functions, which retains information on experimental errors and correlations. As an example we discuss the application of this method to the study of the structure function g 1 p (x,Q 2 )

  10. The structural science of functional materials.

    Science.gov (United States)

    Catlow, C Richard A

    2018-01-01

    The growing complexity of functional materials and the major challenges this poses to structural science are discussed. The diversity of structural materials science and the contributions that computation is making to the field are highlighted.

  11. Structure and Function of Your Skin

    Science.gov (United States)

    ... Name: Category: Share: Yes No, Keep Private Structure & Function of Your Skin Share | What It Looks Like . . . ... in the dermis. What It Does . . . The major function of skin is to provide a barrier between ...

  12. Structure functions from chiral soliton models

    International Nuclear Information System (INIS)

    Weigel, H.; Reinhardt, H.; Gamberg, L.

    1997-01-01

    We study nucleon structure functions within the bosonized Nambu-Jona-Lasinio (NJL) model where the nucleon emerges as a chiral soliton. We discuss the model predictions on the Gottfried sum rule for electron-nucleon scattering. A comparison with a low-scale parametrization shows that the model reproduces the gross features of the empirical structure functions. We also compute the leading twist contributions of the polarized structure functions g 1 and g 2 in this model. We compare the model predictions on these structure functions with data from the E143 experiment by GLAP evolving them from the scale characteristic for the NJL-model to the scale of the data

  13. Scalable Molecular Dynamics for Large Biomolecular Systems

    Directory of Open Access Journals (Sweden)

    Robert K. Brunner

    2000-01-01

    Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

  14. Orientation of biomolecular assemblies in a microfluidic jet

    International Nuclear Information System (INIS)

    Priebe, M; Kalbfleisch, S; Tolkiehn, M; Salditt, T; Koester, S; Abel, B; Davies, R J

    2010-01-01

    We have investigated multilamellar lipid assemblies in a microfluidic jet, operating at high shear rates of the order of 10 7 s -1 . Compared to classical Couette cells or rheometers, the shear rate was increased by at least 2-3 orders of magnitude, and the sample volume was scaled down correspondingly. At the same time, the jet is characterized by high extensional stress due to elongational flow. A focused synchrotron x-ray beam was used to measure the structure and orientation of the lipid assemblies in the jet. The diffraction patterns indicate conventional multilamellar phases, aligned with the membrane normals oriented along the velocity gradient of the jet. The results indicate that the setup may be well suited for coherent diffractive imaging of oriented biomolecular assemblies and macromolecules at the future x-ray free electron laser (XFEL) sources.

  15. Hybrid organic semiconductor lasers for bio-molecular sensing.

    Science.gov (United States)

    Haughey, Anne-Marie; Foucher, Caroline; Guilhabert, Benoit; Kanibolotsky, Alexander L; Skabara, Peter J; Burley, Glenn; Dawson, Martin D; Laurand, Nicolas

    2014-01-01

    Bio-functionalised luminescent organic semiconductors are attractive for biophotonics because they can act as efficient laser materials while simultaneously interacting with molecules. In this paper, we present and discuss a laser biosensor platform that utilises a gain layer made of such an organic semiconductor material. The simple structure of the sensor and its operation principle are described. Nanolayer detection is shown experimentally and analysed theoretically in order to assess the potential and the limits of the biosensor. The advantage conferred by the organic semiconductor is explained, and comparisons to laser sensors using alternative dye-doped materials are made. Specific biomolecular sensing is demonstrated, and routes to functionalisation with nucleic acid probes, and future developments opened up by this achievement, are highlighted. Finally, attractive formats for sensing applications are mentioned, as well as colloidal quantum dots, which in the future could be used in conjunction with organic semiconductors.

  16. DNA-assisted swarm control in a biomolecular motor system.

    Science.gov (United States)

    Keya, Jakia Jannat; Suzuki, Ryuhei; Kabir, Arif Md Rashedul; Inoue, Daisuke; Asanuma, Hiroyuki; Sada, Kazuki; Hess, Henry; Kuzuya, Akinori; Kakugo, Akira

    2018-01-31

    In nature, swarming behavior has evolved repeatedly among motile organisms because it confers a variety of beneficial emergent properties. These include improved information gathering, protection from predators, and resource utilization. Some organisms, e.g., locusts, switch between solitary and swarm behavior in response to external stimuli. Aspects of swarming behavior have been demonstrated for motile supramolecular systems composed of biomolecular motors and cytoskeletal filaments, where cross-linkers induce large scale organization. The capabilities of such supramolecular systems may be further extended if the swarming behavior can be programmed and controlled. Here, we demonstrate that the swarming of DNA-functionalized microtubules (MTs) propelled by surface-adhered kinesin motors can be programmed and reversibly regulated by DNA signals. Emergent swarm behavior, such as translational and circular motion, can be selected by tuning the MT stiffness. Photoresponsive DNA containing azobenzene groups enables switching between solitary and swarm behavior in response to stimulation with visible or ultraviolet light.

  17. Structural symmetry and protein function.

    Science.gov (United States)

    Goodsell, D S; Olson, A J

    2000-01-01

    The majority of soluble and membrane-bound proteins in modern cells are symmetrical oligomeric complexes with two or more subunits. The evolutionary selection of symmetrical oligomeric complexes is driven by functional, genetic, and physicochemical needs. Large proteins are selected for specific morphological functions, such as formation of rings, containers, and filaments, and for cooperative functions, such as allosteric regulation and multivalent binding. Large proteins are also more stable against denaturation and have a reduced surface area exposed to solvent when compared with many individual, smaller proteins. Large proteins are constructed as oligomers for reasons of error control in synthesis, coding efficiency, and regulation of assembly. Symmetrical oligomers are favored because of stability and finite control of assembly. Several functions limit symmetry, such as interaction with DNA or membranes, and directional motion. Symmetry is broken or modified in many forms: quasisymmetry, in which identical subunits adopt similar but different conformations; pleomorphism, in which identical subunits form different complexes; pseudosymmetry, in which different molecules form approximately symmetrical complexes; and symmetry mismatch, in which oligomers of different symmetries interact along their respective symmetry axes. Asymmetry is also observed at several levels. Nearly all complexes show local asymmetry at the level of side chain conformation. Several complexes have reciprocating mechanisms in which the complex is asymmetric, but, over time, all subunits cycle through the same set of conformations. Global asymmetry is only rarely observed. Evolution of oligomeric complexes may favor the formation of dimers over complexes with higher cyclic symmetry, through a mechanism of prepositioned pairs of interacting residues. However, examples have been found for all of the crystallographic point groups, demonstrating that functional need can drive the evolution of

  18. Structure and Function of Lipase

    DEFF Research Database (Denmark)

    Skjold-Jørgensen, Jakob

    .e. the waterlipidinterface. For Thermomyces lanuginosus lipase (TlL) and related lipases, activation of the enzymeinvolves a rearrangement of a structural domain, called the “lid”, which covers the active site inhomogenous aqueous solution. At the water-lipid interface, the lid is displaced from the active site andmoves...... the water-lipid interface, structural movements occurring during activation have been difficult to probeexperimentally. In this work, novel variants of TlL were constructed based on rational design with amutated lid-region in order to elucidate the impact of the lid-residue composition and characteristics...... onthe activation mechanism. From characterization studies of these variants we have shown (Paper I) thatthe lid-region plays a crucial role in governing interfacial activation and enzymatic activity. Specifically,using a combination of spectroscopic and enzymatic activity-based methods we have...

  19. Structure and function in biology

    International Nuclear Information System (INIS)

    Hirs, C.H.W.

    1976-01-01

    A summary is given of the history of the developments of structural chemistry in biology beginning with the work of the bacteriologist Ehrlich leading to a comprehensive examination of the influence of size and configuration on the interaction between specific antibodies and side-chain determinants. Recent developments include the recognition of a higher order of specificity in the interaction of proteins with one another

  20. Structure functions and correlations in nuclei

    International Nuclear Information System (INIS)

    Fantoni, S.

    1988-01-01

    In this paper the results obtained for the static structure function S(k) and the longitudinal structure function S L (k) of 3 H, 3 He and 4 He nuclei and nuclear matter are presented and discussed. The calculations have been performed using realistic wave functions obtained from Faddeev and variational theories. The Monte Carlo method has been used to calculate the structure functions of finite systems, and the FHNC/SOC method for nuclear matter. The results for the 3 He nucleus are in agreement with the recent Saclay data. The results for nuclear matter are compared with the experimental data relative to heavier nuclei, like e.g. 40 Ca

  1. Interferons: between structure and function

    Directory of Open Access Journals (Sweden)

    Katarzyna Bandurska

    2014-05-01

    Full Text Available Interferons are a family of proteins that are released by a variety of cells in response to infections caused by viruses. Currently, we distinguish three types of interferons. They are classified based on the nucleotide sequence, interaction with specific receptors, chromosomal location, structure and physicochemical properties. The following interferons are classified as type I: α, β, ω, κ, ε, ζ, τ, δ, ν. They are recognized and bound by a receptor formed by two peptides, IFN-αR1 and IFN-αR2. Representative of type II interferons is interferon-γ. It binds to a receptor composed of chains IFNGR-1 and IFNGR-2. The recently classified type III interferons comprise IFN-λ1, IFN-λ2, and IFN-λ3. They act on receptors formed by λR1 IFN-and IL-10R2 subunits. A high level of antiviral protection is achieved by IFN-α, IFN-β and IFN-λ. Antiviral activity of interferons is based on the induction and regulation of innate and acquired immune mechanisms. By binding to transmembrane receptors, IFN interacts with target cells mainly by activating the JAK/STAT, but also other signaling pathways. This leads to induction and activation of many antiviral agents, such as protein kinase RNA-activated (PKR, ribonuclease 2-5A pathway, and Mx proteins, as well as numerous apoptotic pathways. As a result of the protective effect of interferons, the virus binding to cells and viral particles penetration into cells is stopped, and the release of the nucleocapsid from an envelope is suppressed. Disruption of transcription and translation processes of the structural proteins prevents the formation of virions or budding of viruses, and as a result degradation of the viral mRNA; the started processes inhibit the chain synthesis of viral proteins and therefore further stimulate the immune system cells.

  2. Integration of biomolecular logic gates with field-effect transducers

    Energy Technology Data Exchange (ETDEWEB)

    Poghossian, A., E-mail: a.poghossian@fz-juelich.de [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Institute of Bio- and Nanosystems, Research Centre Juelich GmbH, D-52425 Juelich (Germany); Malzahn, K. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Abouzar, M.H. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Institute of Bio- and Nanosystems, Research Centre Juelich GmbH, D-52425 Juelich (Germany); Mehndiratta, P. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Katz, E. [Department of Chemistry and Biomolecular Science, NanoBio Laboratory (NABLAB), Clarkson University, Potsdam, NY 13699-5810 (United States); Schoening, M.J. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Institute of Bio- and Nanosystems, Research Centre Juelich GmbH, D-52425 Juelich (Germany)

    2011-11-01

    Highlights: > Enzyme-based AND/OR logic gates are integrated with a capacitive field-effect sensor. > The AND/OR logic gates compose of multi-enzyme system immobilised on sensor surface. > Logic gates were activated by different combinations of chemical inputs (analytes). > The logic output (pH change) produced by the enzymes was read out by the sensor. - Abstract: The integration of biomolecular logic gates with field-effect devices - the basic element of conventional electronic logic gates and computing - is one of the most attractive and promising approaches for the transformation of biomolecular logic principles into macroscopically useable electrical output signals. In this work, capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensors based on a p-Si-SiO{sub 2}-Ta{sub 2}O{sub 5} structure modified with a multi-enzyme membrane have been used for electronic transduction of biochemical signals processed by enzyme-based OR and AND logic gates. The realised OR logic gate composes of two enzymes (glucose oxidase and esterase) and was activated by ethyl butyrate or/and glucose. The AND logic gate composes of three enzymes (invertase, mutarotase and glucose oxidase) and was activated by two chemical input signals: sucrose and dissolved oxygen. The developed integrated enzyme logic gates produce local pH changes at the EIS sensor surface as a result of biochemical reactions activated by different combinations of chemical input signals, while the pH value of the bulk solution remains unchanged. The pH-induced charge changes at the gate-insulator (Ta{sub 2}O{sub 5}) surface of the EIS transducer result in an electronic signal corresponding to the logic output produced by the immobilised enzymes. The logic output signals have been read out by means of a constant-capacitance method.

  3. Integration of biomolecular logic gates with field-effect transducers

    International Nuclear Information System (INIS)

    Poghossian, A.; Malzahn, K.; Abouzar, M.H.; Mehndiratta, P.; Katz, E.; Schoening, M.J.

    2011-01-01

    Highlights: → Enzyme-based AND/OR logic gates are integrated with a capacitive field-effect sensor. → The AND/OR logic gates compose of multi-enzyme system immobilised on sensor surface. → Logic gates were activated by different combinations of chemical inputs (analytes). → The logic output (pH change) produced by the enzymes was read out by the sensor. - Abstract: The integration of biomolecular logic gates with field-effect devices - the basic element of conventional electronic logic gates and computing - is one of the most attractive and promising approaches for the transformation of biomolecular logic principles into macroscopically useable electrical output signals. In this work, capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensors based on a p-Si-SiO 2 -Ta 2 O 5 structure modified with a multi-enzyme membrane have been used for electronic transduction of biochemical signals processed by enzyme-based OR and AND logic gates. The realised OR logic gate composes of two enzymes (glucose oxidase and esterase) and was activated by ethyl butyrate or/and glucose. The AND logic gate composes of three enzymes (invertase, mutarotase and glucose oxidase) and was activated by two chemical input signals: sucrose and dissolved oxygen. The developed integrated enzyme logic gates produce local pH changes at the EIS sensor surface as a result of biochemical reactions activated by different combinations of chemical input signals, while the pH value of the bulk solution remains unchanged. The pH-induced charge changes at the gate-insulator (Ta 2 O 5 ) surface of the EIS transducer result in an electronic signal corresponding to the logic output produced by the immobilised enzymes. The logic output signals have been read out by means of a constant-capacitance method.

  4. High-speed AFM for Studying Dynamic Biomolecular Processes

    Science.gov (United States)

    Ando, Toshio

    2008-03-01

    Biological molecules show their vital activities only in aqueous solutions. It had been one of dreams in biological sciences to directly observe biological macromolecules (protein, DNA) at work under a physiological condition because such observation is straightforward to understanding their dynamic behaviors and functional mechanisms. Optical microscopy has no sufficient spatial resolution and electron microscopy is not applicable to in-liquid samples. Atomic force microscopy (AFM) can visualize molecules in liquids at high resolution but its imaging rate was too low to capture dynamic biological processes. This slow imaging rate is because AFM employs mechanical probes (cantilevers) and mechanical scanners to detect the sample height at each pixel. It is quite difficult to quickly move a mechanical device of macroscopic size with sub-nanometer accuracy without producing unwanted vibrations. It is also difficult to maintain the delicate contact between a probe tip and fragile samples. Two key techniques are required to realize high-speed AFM for biological research; fast feedback control to maintain a weak tip-sample interaction force and a technique to suppress mechanical vibrations of the scanner. Various efforts have been carried out in the past decade to materialize high-speed AFM. The current high-speed AFM can capture images on video at 30-60 frames/s for a scan range of 250nm and 100 scan lines, without significantly disturbing week biomolecular interaction. Our recent studies demonstrated that this new microscope can reveal biomolecular processes such as myosin V walking along actin tracks and association/dissociation dynamics of chaperonin GroEL-GroES that occurs in a negatively cooperative manner. The capacity of nanometer-scale visualization of dynamic processes in liquids will innovate on biological research. In addition, it will open a new way to study dynamic chemical/physical processes of various phenomena that occur at the liquid-solid interfaces.

  5. Functional materials discovery using energy-structure-function maps.

    Science.gov (United States)

    Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz; Holden, Daniel; Little, Marc A; Chong, Samantha Y; Slater, Benjamin J; McMahon, David P; Bonillo, Baltasar; Stackhouse, Chloe J; Stephenson, Andrew; Kane, Christopher M; Clowes, Rob; Hasell, Tom; Cooper, Andrew I; Day, Graeme M

    2017-03-30

    Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

  6. Phenomenology of the electron structure function

    International Nuclear Information System (INIS)

    Slominski, W.; Szwed, J.

    2001-01-01

    The advantages of introducing the electron structure function (ESF) in electron induced processes are demonstrated. Contrary to the photon structure function it is directly measured in such processes. At present energies, a simultaneous analysis of both the electron and the photon structure functions gives an important test of the experimentally applied methods. Estimates of the ESF at LEP momenta are given. At very high momenta contributions from W and Z bosons together with γ-Z interference can be observed. Predictions for the next generation of experiments are given. (orig.)

  7. Biochemical Stability Analysis of Nano Scaled Contrast Agents Used in Biomolecular Imaging Detection of Tumor Cells

    Science.gov (United States)

    Kim, Jennifer; Kyung, Richard

    Imaging contrast agents are materials used to improve the visibility of internal body structures in the imaging process. Many agents that are used for contrast enhancement are now studied empirically and computationally by researchers. Among various imaging techniques, magnetic resonance imaging (MRI) has become a major diagnostic tool in many clinical specialties due to its non-invasive characteristic and its safeness in regards to ionizing radiation exposure. Recently, researchers have prepared aqueous fullerene nanoparticles using electrochemical methods. In this paper, computational simulations of thermodynamic stabilities of nano scaled contrast agents that can be used in biomolecular imaging detection of tumor cells are presented using nanomaterials such as fluorescent functionalized fullerenes. In addition, the stability and safety of different types of contrast agents composed of metal oxide a, b, and c are tested in the imaging process. Through analysis of the computational simulations, the stabilities of the contrast agents, determined by optimized energies of the conformations, are presented. The resulting numerical data are compared. In addition, Density Functional Theory (DFT) is used in order to model the electron properties of the compound.

  8. Converting Biomolecular Modelling Data Based on an XML Representation

    Directory of Open Access Journals (Sweden)

    Sun Yudong

    2008-06-01

    Full Text Available Biomolecular modelling has provided computational simulation based methods for investigating biological processes from quantum chemical to cellular levels. Modelling such microscopic processes requires atomic description of a biological system and conducts in fine timesteps. Consequently the simulations are extremely computationally demanding. To tackle this limitation, different biomolecular models have to be integrated in order to achieve high-performance simulations. The integration of diverse biomolecular models needs to convert molecular data between different data representations of different models. This data conversion is often non-trivial, requires extensive human input and is inevitably error prone. In this paper we present an automated data conversion method for biomolecular simulations between molecular dynamics and quantum mechanics/molecular mechanics models. Our approach is developed around an XML data representation called BioSimML (Biomolecular Simulation Markup Language. BioSimML provides a domain specific data representation for biomolecular modelling which can effciently support data interoperability between different biomolecular simulation models and data formats.

  9. Four RNA families with functional transient structures.

    Science.gov (United States)

    Zhu, Jing Yun A; Meyer, Irmtraud M

    2015-01-01

    Protein-coding and non-coding RNA transcripts perform a wide variety of cellular functions in diverse organisms. Several of their functional roles are expressed and modulated via RNA structure. A given transcript, however, can have more than a single functional RNA structure throughout its life, a fact which has been previously overlooked. Transient RNA structures, for example, are only present during specific time intervals and cellular conditions. We here introduce four RNA families with transient RNA structures that play distinct and diverse functional roles. Moreover, we show that these transient RNA structures are structurally well-defined and evolutionarily conserved. Since Rfam annotates one structure for each family, there is either no annotation for these transient structures or no such family. Thus, our alignments either significantly update and extend the existing Rfam families or introduce a new RNA family to Rfam. For each of the four RNA families, we compile a multiple-sequence alignment based on experimentally verified transient and dominant (dominant in terms of either the thermodynamic stability and/or attention received so far) RNA secondary structures using a combination of automated search via covariance model and manual curation. The first alignment is the Trp operon leader which regulates the operon transcription in response to tryptophan abundance through alternative structures. The second alignment is the HDV ribozyme which we extend to the 5' flanking sequence. This flanking sequence is involved in the regulation of the transcript's self-cleavage activity. The third alignment is the 5' UTR of the maturation protein from Levivirus which contains a transient structure that temporarily postpones the formation of the final inhibitory structure to allow translation of maturation protein. The fourth and last alignment is the SAM riboswitch which regulates the downstream gene expression by assuming alternative structures upon binding of SAM. All

  10. Network structure shapes spontaneous functional connectivity dynamics.

    Science.gov (United States)

    Shen, Kelly; Hutchison, R Matthew; Bezgin, Gleb; Everling, Stefan; McIntosh, Anthony R

    2015-04-08

    The structural organization of the brain constrains the range of interactions between different regions and shapes ongoing information processing. Therefore, it is expected that large-scale dynamic functional connectivity (FC) patterns, a surrogate measure of coordination between brain regions, will be closely tied to the fiber pathways that form the underlying structural network. Here, we empirically examined the influence of network structure on FC dynamics by comparing resting-state FC (rsFC) obtained using BOLD-fMRI in macaques (Macaca fascicularis) to structural connectivity derived from macaque axonal tract tracing studies. Consistent with predictions from simulation studies, the correspondence between rsFC and structural connectivity increased as the sample duration increased. Regions with reciprocal structural connections showed the most stable rsFC across time. The data suggest that the transient nature of FC is in part dependent on direct underlying structural connections, but also that dynamic coordination can occur via polysynaptic pathways. Temporal stability was found to be dependent on structural topology, with functional connections within the rich-club core exhibiting the greatest stability over time. We discuss these findings in light of highly variable functional hubs. The results further elucidate how large-scale dynamic functional coordination exists within a fixed structural architecture. Copyright © 2015 the authors 0270-6474/15/355579-10$15.00/0.

  11. Dipole rescattering and the nuclear structure function

    Energy Technology Data Exchange (ETDEWEB)

    Carvalho, F. [Depto de Ciencias Exatas e da Terra, Universidade Federal de Sao Paulo, SP (Brazil); Goncalves, V. P. [Instituto de Fisica e Matematica, Universidade Federal de Pelotas, Caixa Postal 354, CEP 96010-900, Pelotas, RS (Brazil); Navarra, F. S.; Oliveira, E. G. [Instituto de Fisica, Universidade de Sao Paulo Rua do Matao, Travessa R, 187, 05508-090 Sao Paulo, SP (Brazil)

    2013-03-25

    In the framework of the dipole model, we study the effects of the dipole multiple scatterings in a nuclear target and compute the nuclear structure function. We compare different unitarization schemes and confront our results with the E665 data.

  12. Introduction to a Protein Interaction System Used for Quantitative Evaluation of Biomolecular Interactions

    OpenAIRE

    Yamniuk, Aaron

    2013-01-01

    A central goal of molecular biology is the determination of biomolecular function. This comes largely from a knowledge of the non-covalent interactions that biological small and macro-molecules experience. The fundamental mission of the Molecular Interactions Research Group (MIRG) of the ABRF is to show how solution biophysical tools are used to quantitatively characterize molecular interactions, and to educate the ABRF members and scientific community on the utility and limitations of core t...

  13. Biomolecular Markers in Cancer of the Tongue

    Directory of Open Access Journals (Sweden)

    Daris Ferrari

    2009-01-01

    Full Text Available The incidence of tongue cancer is increasing worldwide, and its aggressiveness remains high regardless of treatment. Genetic changes and the expression of abnormal proteins have been frequently reported in the case of head and neck cancers, but the little information that has been published concerning tongue tumours is often contradictory. This review will concentrate on the immunohistochemical expression of biomolecular markers and their relationships with clinical behaviour and prognosis. Most of these proteins are associated with nodal stage, tumour progression and metastases, but there is still controversy concerning their impact on disease-free and overall survival, and treatment response. More extensive clinical studies are needed to identify the patterns of molecular alterations and the most reliable predictors in order to develop tailored anti-tumour strategies based on the targeting of hypoxia markers, vascular and lymphangiogenic factors, epidermal growth factor receptors, intracytoplasmatic signalling and apoptosis.

  14. Structure and Structure-activity Relationship of Functional Organic Molecules

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    @@ Research theme The group is made up of junior scientists from the State Key Laboratory of Elemento-organic Chemistry, Nankai University.The scientists focus their studis on the structure and structure-activity relationship of functional organic molecules not only because it has been the basis of their research, but also because the functional study of organic compounds is now a major scientific issue for organic chemists around the world.

  15. Structure functions of electroweak boson and leptons

    International Nuclear Information System (INIS)

    Slominski, W.; Szwed, J.

    1996-01-01

    The QCD structure of the electroweak bosons is reviewed and the lepton structure function is defined and calculated. The leading order splitting functions of electron into quarks are extracted, showing an important contribution from γ-Z interference. Leading logarithmic QCD evolution equations are constructed and solved in the asymptotic region where log 2 behavior of the Parton densities is observed. Possible applications with clear manifestation of ''resolved'' photon and weak bosons are discussed. 8 refs., 3 figs

  16. Proton structure functions at small x

    International Nuclear Information System (INIS)

    Hentschinski, Martin

    2015-01-01

    Proton structure functions are measured in electron-proton collision through inelastic scattering of virtual photons with virtuality Q on protons; x denotes the momentum fraction carried by the struck parton. Proton structure functions are currently described with excellent accuracy in terms of scale dependent parton distribution functions, defined in terms of collinear factorization and DGLAP evolution in Q. With decreasing x however, parton densities increase and are ultimately expected to saturate. In this regime DGLAP evolution will finally break down and non-linear evolution equations w.r.t x are expected to take over. In the first part of the talk we present recent result on an implementation of physical DGLAP evolution. Unlike the conventional description in terms of parton distribution functions, the former describes directly the Q dependence of the measured structure functions. It is therefore physical insensitive to factorization scheme and scale ambiguities. It therefore provides a more stringent test of DGLAP evolution and eases the manifestation of (non-linear) small x effects. It however requires a precise measurement of both structure functions F 2 and F L , which will be only possible at future facilities, such as an Electron Ion Collider. In the second part we present a recent analysis of the small x region of the combined HERA data on the structure function F 2 . We demonstrate that (linear) next-to-leading order BFKL evolution describes the effective Pomeron intercept, determined from the combined HERA data, once a resummation of collinear enhanced terms is included and the renormalization scale is fixed using the BLM optimal scale setting procedure. We also provide a detailed description of the Q and x dependence of the full structure functions F 2 in the small x region, as measured at HERA. Predictions for the structure function F L are found to be in agreement with the existing HERA data. (paper)

  17. AGE STRUCTURE OR FUNCTIONAL RESPONSE? RECONCILING ...

    African Journals Online (AJOL)

    ... surplus production that differ from traditional single-species management models. ... Specifically, while the ECOSIM “Arena” functional response and the von ... as a proxy for age structure rather than as a function of predator/prey behaviour, ...

  18. 2004 Structural, Function and Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Douglas L. Brutlag Nancy Ryan Gray

    2005-03-23

    This Gordon conference will cover the areas of structural, functional and evolutionary genomics. It will take a systematic approach to genomics, examining the evolution of proteins, protein functional sites, protein-protein interactions, regulatory networks, and metabolic networks. Emphasis will be placed on what we can learn from comparative genomics and entire genomes and proteomes.

  19. Structure functions in the chiral bag model

    International Nuclear Information System (INIS)

    Sanjose, V.; Vento, V.; Centro Mixto CSIC/Valencia Univ., Valencia

    1989-01-01

    We calculate the structure functions of an isoscalar nuclear target for the deep inelastic scattering by leptons in an extended version of the chiral bag model which incorporates the qanti q structure of the pions in the cloud. Bjorken scaling and Regge behavior are satisfied. The model calculation reproduces the low-x behavior of the data but fails to explain the medium- to large-x behavior. Evolution of the quark structure functions seem inevitable to attempt a connection between the low-energy models and the high-energy behavior of quantum chromodynamics. (orig.)

  20. Structure functions in the chiral bag model

    Energy Technology Data Exchange (ETDEWEB)

    Sanjose, V.; Vento, V.

    1989-07-13

    We calculate the structure functions of an isoscalar nuclear target for the deep inelastic scattering by leptons in an extended version of the chiral bag model which incorporates the qanti q structure of the pions in the cloud. Bjorken scaling and Regge behavior are satisfied. The model calculation reproduces the low-x behavior of the data but fails to explain the medium- to large-x behavior. Evolution of the quark structure functions seem inevitable to attempt a connection between the low-energy models and the high-energy behavior of quantum chromodynamics. (orig.).

  1. Structure functions and correlations in nuclei

    International Nuclear Information System (INIS)

    Schiavilla, R.; Lewart, D.S.; Pandharipande, V.R.

    1987-01-01

    The static longitudinal structure function S l (k) and the static structure function S(k) of 3 H, 3 He and 4 He nuclei and nuclear matter are calculated using realistic wave functions obtained from Faddeev and variational calculations. In order to study the variation of the structure function with the number of particles in the system we also calculate S(k) of atomic helium liquid drops containing 4, 8, 20, 40, 70, 168 and 240 atoms. Monte Carlo integration is used to calculate the structure functions of finite systems, while those of nuclear matter are calculated with chain summation methods. The behaivior of S(k) and S l (k) at small values of k is discussed. We find that the recent Saclay data on S l (k) of the 3 He nucleus are in agreement with theory. Though the data indicate the the existence of correlations between the two protons in the 3 He nucleus, they are not accurate enough to draw interesting conclusions about the repulsive core in the nucleon-nucleon interaction. The structure functions of atomic helium liquid drops indicate a smooth variation of S(k) with the number of atoms in the drop. The S L (k) of the 4 He nucleus and nuclear matter are very similar for k > 1.5 fm -1 , and it appears plausible that S L (k) of nuclei having A > 3 may not depend significantly on A when k > 1.5 fm -1 . (orig.)

  2. Effective constraint algebras with structure functions

    International Nuclear Information System (INIS)

    Bojowald, Martin; Brahma, Suddhasattwa

    2016-01-01

    This article presents the result that fluctuations and higher moments of a state, by themselves, do not imply quantum corrections in structure functions of constrained systems. Moment corrections are isolated from other types of quantum effects, such as factor-ordering choices and regularization, by introducing a new condition with two parts: (i) having a direct (or faithful) quantization of the classical structure functions, (ii) free of factor-ordering ambiguities. In particular, it is assumed that the classical constraints can be quantized in an anomaly free way, so that properties of the resulting constraint algebras can be derived. If the two-part condition is not satisfied, effective constraints can still be evaluated, but quantum effects may be stronger. Consequences for canonical quantum gravity, whose structure functions encode space–time structure, are discussed. In particular, deformed algebras found in models of loop quantum gravity provide reliable information even in the Planck regime. (paper)

  3. Magnetism and Structure in Functional Materials

    CERN Document Server

    Planes, Antoni; Saxena, Avadh

    2005-01-01

    Magnetism and Structure in Functional Materials addresses three distinct but related topics: (i) magnetoelastic materials such as magnetic martensites and magnetic shape memory alloys, (ii) the magnetocaloric effect related to magnetostructural transitions, and (iii) colossal magnetoresistance (CMR) and related magnanites. The goal is to identify common underlying principles in these classes of materials that are relevant for optimizing various functionalities. The emergence of apparently different magnetic/structural phenomena in disparate classes of materials clearly points to a need for common concepts in order to achieve a broader understanding of the interplay between magnetism and structure in this general class of new functional materials exhibiting ever more complex microstructure and function. The topic is interdisciplinary in nature and the contributors correspondingly include physicists, materials scientists and engineers. Likewise the book will appeal to scientists from all these areas.

  4. Structure functions are not parton probabilities

    International Nuclear Information System (INIS)

    Brodsky, Stanley J.; Hoyer, Paul; Sannino, Francesco; Marchal, Nils; Peigne, Stephane

    2002-01-01

    The common view that structure functions measured in deep inelastic lepton scattering are determined by the probability of finding quarks and gluons in the target is not correct in gauge theory. We show that gluon exchange between the fast, outgoing partons and target spectators, which is usually assumed to be an irrelevant gauge artifact, affects the leading twist structure functions in a profound way. This observation removes the apparent contradiction between the projectile (eikonal) and target (parton model) views of diffractive and small x B phenomena. The diffractive scattering of the fast outgoing quarks on spectators in the target causes shadowing in the DIS cross section. Thus the depletion of the nuclear structure functions is not intrinsic to the wave function of the nucleus, but is a coherent effect arising from the destructive interference of diffractive channels induced by final state interactions. This is consistent with the Glauber-Gribov interpretation of shadowing as a rescattering effect

  5. Rapid prototyping of nanofluidic systems using size-reduced electrospun nanofibers for biomolecular analysis.

    Science.gov (United States)

    Park, Seung-Min; Huh, Yun Suk; Szeto, Kylan; Joe, Daniel J; Kameoka, Jun; Coates, Geoffrey W; Edel, Joshua B; Erickson, David; Craighead, Harold G

    2010-11-05

    Biomolecular transport in nanofluidic confinement offers various means to investigate the behavior of biomolecules in their native aqueous environments, and to develop tools for diverse single-molecule manipulations. Recently, a number of simple nanofluidic fabrication techniques has been demonstrated that utilize electrospun nanofibers as a backbone structure. These techniques are limited by the arbitrary dimension of the resulting nanochannels due to the random nature of electrospinning. Here, a new method for fabricating nanofluidic systems from size-reduced electrospun nanofibers is reported and demonstrated. As it is demonstrated, this method uses the scanned electrospinning technique for generation of oriented sacrificial nanofibers and exposes these nanofibers to harsh, but isotropic etching/heating environments to reduce their cross-sectional dimension. The creation of various nanofluidic systems as small as 20 nm is demonstrated, and practical examples of single biomolecular handling, such as DNA elongation in nanochannels and fluorescence correlation spectroscopic analysis of biomolecules passing through nanochannels, are provided.

  6. Investigation of the Human Disease Osteogenesis Imperfecta: A Research-Based Introduction to Concepts and Skills in Biomolecular Analysis

    Science.gov (United States)

    Mate, Karen; Sim, Alistair; Weidenhofer, Judith; Milward, Liz; Scott, Judith

    2013-01-01

    A blended approach encompassing problem-based learning (PBL) and structured inquiry was used in this laboratory exercise based on the congenital disease Osteogenesis imperfecta (OI), to introduce commonly used techniques in biomolecular analysis within a clinical context. During a series of PBL sessions students were presented with several…

  7. Structure and Functions of Linker Histones.

    Science.gov (United States)

    Lyubitelev, A V; Nikitin, D V; Shaytan, A K; Studitsky, V M; Kirpichnikov, M P

    2016-03-01

    Linker histones such as variants H1, H5, and other similar proteins play an important role in regulation of chromatin structure and dynamics. However, interactions of linker histones with DNA and proteins, as well as specific functions of their different variants, are poorly studied. This is because they acquire tertiary structure only when interacting with a nucleosome, and because of limitations of currently available methods. However, deeper investigation of linker histones and their interactions with other proteins will address a number of important questions - from structure of compacted chromatin to regulation of early embryogenesis. In this review, structures of histone H1 variants and its interaction with chromatin DNA are considered. A possible functional significance of different H1 variants, a role of these proteins in maintaining interphase chromatin structure, and interactions of linker histones with other cellular proteins are also discussed.

  8. DNA algorithms of implementing biomolecular databases on a biological computer.

    Science.gov (United States)

    Chang, Weng-Long; Vasilakos, Athanasios V

    2015-01-01

    In this paper, DNA algorithms are proposed to perform eight operations of relational algebra (calculus), which include Cartesian product, union, set difference, selection, projection, intersection, join, and division, on biomolecular relational databases.

  9. Modeling, Analysis, Simulation, and Synthesis of Biomolecular Networks

    National Research Council Canada - National Science Library

    Ruben, Harvey; Kumar, Vijay; Sokolsky, Oleg

    2006-01-01

    ...) a first example of reachability analysis applied to a biomolecular system (lactose induction), 4) a model of tetracycline resistance that discriminates between two possible mechanisms for tetracycline diffusion through the cell membrane, and 5...

  10. Changes in biomolecular profile in a single nucleolus during cell fixation.

    Science.gov (United States)

    Kuzmin, Andrey N; Pliss, Artem; Prasad, Paras N

    2014-11-04

    Fixation of biological sample is an essential technique applied in order to "freeze" in time the intracellular molecular content. However, fixation induces changes of the cellular molecular structure, which mask physiological distribution of biomolecules and bias interpretation of results. Accurate, sensitive, and comprehensive characterization of changes in biomolecular composition, occurring during fixation, is crucial for proper analysis of experimental data. Here we apply biomolecular component analysis for Raman spectra measured in the same nucleoli of HeLa cells before and after fixation by either formaldehyde solution or by chilled ethanol. It is found that fixation in formaldehyde does not strongly affect the Raman spectra of nucleolar biomolecular components, but may significantly decrease the nucleolar RNA concentration. At the same time, ethanol fixation leads to a proportional increase (up to 40%) in concentrations of nucleolar proteins and RNA, most likely due to cell shrinkage occurring in the presence of coagulant fixative. Ethanol fixation also triggers changes in composition of nucleolar proteome, as indicated by an overall reduction of the α-helical structure of proteins and increase in the concentration of proteins containing the β-sheet conformation. We conclude that cross-linking fixation is a more appropriate protocol for mapping of proteins in situ. At the same time, ethanol fixation is preferential for studies of RNA-containing macromolecules. We supplemented our quantitative Raman spectroscopic measurements with mapping of the protein and lipid macromolecular groups in live and fixed cells using coherent anti-Stokes Raman scattering nonlinear optical imaging.

  11. Nanogap biosensors for electrical and label-free detection of biomolecular interactions

    International Nuclear Information System (INIS)

    Kyu Kim, Sang; Cho, Hyunmin; Park, Hye-Jung; Kwon, Dohyoung; Min Lee, Jeong; Hyun Chung, Bong

    2009-01-01

    We demonstrate nanogap biosensors for electrical and label-free detection of biomolecular interactions. Parallel fabrication of nanometer distance gaps has been achieved using a silicon anisotropic wet etching technique on a silicon-on-insulator (SOI) wafer with a finely controllable silicon device layer. Since silicon anisotropic wet etching resulted in a trapezoid-shaped structure whose end became narrower during the etching, the nanogap structure was simply fabricated on the device layer of a SOI wafer. The nanogap devices were individually addressable and a gap size of less than 60 nm was obtained. We demonstrate that the nanogap biosensors can electrically detect biomolecular interactions such as biotin/streptavidin and antigen/antibody pairs. The nanogap devices show a current increase when the proteins are bound to the surface. The current increases proportionally depending upon the concentrations of the molecules in the range of 100 fg ml -1 -100 ng ml -1 at 1 V bias. It is expected that the nanogap developed here could be a highly sensitive biosensor platform for label-free detection of biomolecular interactions.

  12. AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems.

    Science.gov (United States)

    LeVine, Michael V; Weinstein, Harel

    2015-05-01

    In performing their biological functions, molecular machines must process and transmit information with high fidelity. Information transmission requires dynamic coupling between the conformations of discrete structural components within the protein positioned far from one another on the molecular scale. This type of biomolecular "action at a distance" is termed allostery . Although allostery is ubiquitous in biological regulation and signal transduction, its treatment in theoretical models has mostly eschewed quantitative descriptions involving the system's underlying structural components and their interactions. Here, we show how Ising models can be used to formulate an approach to allostery in a structural context of interactions between the constitutive components by building simple allosteric constructs we termed Allosteric Ising Models (AIMs). We introduce the use of AIMs in analytical and numerical calculations that relate thermodynamic descriptions of allostery to the structural context, and then show that many fundamental properties of allostery, such as the multiplicative property of parallel allosteric channels, are revealed from the analysis of such models. The power of exploring mechanistic structural models of allosteric function in more complex systems by using AIMs is demonstrated by building a model of allosteric signaling for an experimentally well-characterized asymmetric homodimer of the dopamine D2 receptor.

  13. Cancer genetics meets biomolecular mechanism-bridging an age-old gulf.

    Science.gov (United States)

    González-Sánchez, Juan Carlos; Raimondi, Francesco; Russell, Robert B

    2018-02-01

    Increasingly available genomic sequencing data are exploited to identify genes and variants contributing to diseases, particularly cancer. Traditionally, methods to find such variants have relied heavily on allele frequency and/or familial history, often neglecting to consider any mechanistic understanding of their functional consequences. Thus, while the set of known cancer-related genes has increased, for many, their mechanistic role in the disease is not completely understood. This issue highlights a wide gap between the disciplines of genetics, which largely aims to correlate genetic events with phenotype, and molecular biology, which ultimately aims at a mechanistic understanding of biological processes. Fortunately, new methods and several systematic studies have proved illuminating for many disease genes and variants by integrating sequencing with mechanistic data, including biomolecular structures and interactions. These have provided new interpretations for known mutations and suggested new disease-relevant variants and genes. Here, we review these approaches and discuss particular examples where these have had a profound impact on the understanding of human cancers. © 2018 Federation of European Biochemical Societies.

  14. A Starting Point for Fluorescence-Based Single-Molecule Measurements in Biomolecular Research

    Directory of Open Access Journals (Sweden)

    Alexander Gust

    2014-09-01

    Full Text Available Single-molecule fluorescence techniques are ideally suited to provide information about the structure-function-dynamics relationship of a biomolecule as static and dynamic heterogeneity can be easily detected. However, what type of single-molecule fluorescence technique is suited for which kind of biological question and what are the obstacles on the way to a successful single-molecule microscopy experiment? In this review, we provide practical insights into fluorescence-based single-molecule experiments aiming for scientists who wish to take their experiments to the single-molecule level. We especially focus on fluorescence resonance energy transfer (FRET experiments as these are a widely employed tool for the investigation of biomolecular mechanisms. We will guide the reader through the most critical steps that determine the success and quality of diffusion-based confocal and immobilization-based total internal reflection fluorescence microscopy. We discuss the specific chemical and photophysical requirements that make fluorescent dyes suitable for single-molecule fluorescence experiments. Most importantly, we review recently emerged photoprotection systems as well as passivation and immobilization strategies that enable the observation of fluorescently labeled molecules under biocompatible conditions. Moreover, we discuss how the optical single-molecule toolkit has been extended in recent years to capture the physiological complexity of a cell making it even more relevant for biological research.

  15. New Distributed Multipole Methods for Accurate Electrostatics for Large-Scale Biomolecular Simultations

    Science.gov (United States)

    Sagui, Celeste

    2006-03-01

    An accurate and numerically efficient treatment of electrostatics is essential for biomolecular simulations, as this stabilizes much of the delicate 3-d structure associated with biomolecules. Currently, force fields such as AMBER and CHARMM assign ``partial charges'' to every atom in a simulation in order to model the interatomic electrostatic forces, so that the calculation of the electrostatics rapidly becomes the computational bottleneck in large-scale simulations. There are two main issues associated with the current treatment of classical electrostatics: (i) how does one eliminate the artifacts associated with the point-charges (e.g., the underdetermined nature of the current RESP fitting procedure for large, flexible molecules) used in the force fields in a physically meaningful way? (ii) how does one efficiently simulate the very costly long-range electrostatic interactions? Recently, we have dealt with both of these challenges as follows. In order to improve the description of the molecular electrostatic potentials (MEPs), a new distributed multipole analysis based on localized functions -- Wannier, Boys, and Edminston-Ruedenberg -- was introduced, which allows for a first principles calculation of the partial charges and multipoles. Through a suitable generalization of the particle mesh Ewald (PME) and multigrid method, one can treat electrostatic multipoles all the way to hexadecapoles all without prohibitive extra costs. The importance of these methods for large-scale simulations will be discussed, and examplified by simulations from polarizable DNA models.

  16. Resonance contribution to electromagnetic structure functions

    International Nuclear Information System (INIS)

    Bowling, A.L. Jr.

    1974-01-01

    The part of the pion and proton electromagnetic structure functions due to direct channel resonances in the virtual Compton amplitude is discussed. After a phenomenological discussion, based on the work of Bloom and Gilman, of resonance production in inelastic electroproduction, the single resonance contribution to the pion and proton structure functions is expressed in terms of transition form factors. Froissart-Gribov representations of the Compton amplitude partial waves are presented and are used to specify the spin dependence of the transition form factors. The dependence of the form factors on momentum transfer and resonance mass is assumed on the basis of the behavior of exclusive resonance electroproduction. The single resonance contributions are summed in the Bjorken limit, and the result exhibits Bjorken scaling. Transverse photons are found to dominate in the Bjorken limit, and the threshold behavior of the resonant part of the structure functions is related to the asymptotic behavior of exclusive form factors at large momentum transfer. The resonant parts of the annihilation structure functions are not in general given by simple analytic continuation in the scaling vari []ble ω' of the electroproduction structure functions. (Diss. Abstr. Int., B)

  17. The Structure-Function Linkage Database.

    Science.gov (United States)

    Akiva, Eyal; Brown, Shoshana; Almonacid, Daniel E; Barber, Alan E; Custer, Ashley F; Hicks, Michael A; Huang, Conrad C; Lauck, Florian; Mashiyama, Susan T; Meng, Elaine C; Mischel, David; Morris, John H; Ojha, Sunil; Schnoes, Alexandra M; Stryke, Doug; Yunes, Jeffrey M; Ferrin, Thomas E; Holliday, Gemma L; Babbitt, Patricia C

    2014-01-01

    The Structure-Function Linkage Database (SFLD, http://sfld.rbvi.ucsf.edu/) is a manually curated classification resource describing structure-function relationships for functionally diverse enzyme superfamilies. Members of such superfamilies are diverse in their overall reactions yet share a common ancestor and some conserved active site features associated with conserved functional attributes such as a partial reaction. Thus, despite their different functions, members of these superfamilies 'look alike', making them easy to misannotate. To address this complexity and enable rational transfer of functional features to unknowns only for those members for which we have sufficient functional information, we subdivide superfamily members into subgroups using sequence information, and lastly into families, sets of enzymes known to catalyze the same reaction using the same mechanistic strategy. Browsing and searching options in the SFLD provide access to all of these levels. The SFLD offers manually curated as well as automatically classified superfamily sets, both accompanied by search and download options for all hierarchical levels. Additional information includes multiple sequence alignments, tab-separated files of functional and other attributes, and sequence similarity networks. The latter provide a new and intuitively powerful way to visualize functional trends mapped to the context of sequence similarity.

  18. Boson structure functions from inelastic electron scattering

    International Nuclear Information System (INIS)

    De Jager, C.W.

    1986-01-01

    The even /sup 104-110/Pd isotopes and /sup 196/Pt have been investigated at NIKHEF-K by high-resolution inelastic electron scattering. A new IBA-2 calculation has been performed for the Pd isotopes, in which the ratio of the proton and neutron coupling constants is taken from pion scattering. One set of boson structure functions sufficed for the description of the first and second E2-excitations in all Pd isotopes. The data showed no sensitivity for different structure functions for proton and neutron bosons. A preliminary analysis of a number of negative parity states (3/sup -/,5/sup -/ and 7/sup -/), observed in /sup 196/Pt, was performed through the introduction of an f-boson. The first E4-excitation in the palladium isotopes can be reasonably described with a β-structure function, but all other E4-excitations require the introduction of g-boson admixtures

  19. Biomolecular surface construction by PDE transform.

    Science.gov (United States)

    Zheng, Qiong; Yang, Siyang; Wei, Guo-Wei

    2012-03-01

    This work proposes a new framework for the surface generation based on the partial differential equation (PDE) transform. The PDE transform has recently been introduced as a general approach for the mode decomposition of images, signals, and data. It relies on the use of arbitrarily high-order PDEs to achieve the time-frequency localization, control the spectral distribution, and regulate the spatial resolution. The present work provides a new variational derivation of high-order PDE transforms. The fast Fourier transform is utilized to accomplish the PDE transform so as to avoid stringent stability constraints in solving high-order PDEs. As a consequence, the time integration of high-order PDEs can be done efficiently with the fast Fourier transform. The present approach is validated with a variety of test examples in two-dimensional and three-dimensional settings. We explore the impact of the PDE transform parameters, such as the PDE order and propagation time, on the quality of resulting surfaces. Additionally, we utilize a set of 10 proteins to compare the computational efficiency of the present surface generation method and a standard approach in Cartesian meshes. Moreover, we analyze the present method by examining some benchmark indicators of biomolecular surface, that is, surface area, surface-enclosed volume, solvation free energy, and surface electrostatic potential. A test set of 13 protein molecules is used in the present investigation. The electrostatic analysis is carried out via the Poisson-Boltzmann equation model. To further demonstrate the utility of the present PDE transform-based surface method, we solve the Poisson-Nernst-Planck equations with a PDE transform surface of a protein. Second-order convergence is observed for the electrostatic potential and concentrations. Finally, to test the capability and efficiency of the present PDE transform-based surface generation method, we apply it to the construction of an excessively large biomolecule, a

  20. Vortex structure and characterization of quasiperiodic functions

    International Nuclear Information System (INIS)

    Dana, Itzhack; Chernov, Vladislav E

    2002-01-01

    Quasiperiodic functions (QPFs) are characterized by their full vortex structure in one unit cell. This characterization is much finer and more sensitive than the topological one given by the total vorticity per unit cell (the 'Chern index'). It is shown that QPFs with an arbitrarily prescribed vortex structure exist by constructing explicitly such a 'standard' QPF. Two QPFs with the same vortex structure are equivalent, in the sense that their ratio is a function which is strictly periodic, nonvanishing and at least continuous. A general QPF can then be approximately reconstructed from its vortex structure on the basis of the standard QPF and the equivalence concept. As another application of this concept, a simple method is proposed for calculating the quasiperiodic eigenvectors of periodic matrices. Possible applications to the quantum-chaos problem on a phase-space torus are briefly discussed

  1. Unique temporal and spatial biomolecular emission profile on individual zinc oxide nanorods

    Science.gov (United States)

    Singh, Manpreet; Song, Sheng; Hahm, Jong-In

    2013-12-01

    Zinc oxide nanorods (ZnO NRs) have emerged in recent years as extremely useful, optical signal-enhancing platforms in DNA and protein detection. Although the use of ZnO NRs in biodetection has been demonstrated so far in systems involving many ZnO NRs per detection element, their future applications will likely take place in a miniaturized setting while exploiting single ZnO NRs in a low-volume, high-throughput bioanalysis. In this paper, we investigate temporal and spatial characteristics of the biomolecular fluorescence on individual ZnO NR systems. Quantitative and qualitative examinations of the biomolecular intensity and photostability are carried out as a function of two important criteria, the time and position along the long axis (length) of NRs. Photostability profiles are also measured with respect to the position on NRs and compared to those characteristics of biomolecules on polymeric control platforms. Unlike the uniformly distributed signal observed on the control platforms, both the fluorescence intensity and photostability are position-dependent on individual ZnO NRs. We have identified a unique phenomenon of highly localized, fluorescence intensification on the nanorod ends (FINE) of well-characterized, individual ZnO nanostructures. When compared to the polymeric controls, the biomolecular fluorescence intensity and photostability are determined to be higher on individual ZnO NRs regardless of the position on NRs. We have also carried out finite-difference time-domain simulations the results of which are in good agreement with the observed FINE. The outcomes of our investigation will offer a much needed basis for signal interpretation for biodetection devices and platforms consisting of single ZnO NRs and, at the same time, contribute significantly to provide insight in understanding the biomolecular fluorescence observed from ZnO NR ensemble-based systems.Zinc oxide nanorods (ZnO NRs) have emerged in recent years as extremely useful, optical

  2. Transparent wood for functional and structural applications

    Science.gov (United States)

    Li, Yuanyuan; Fu, Qiliang; Yang, Xuan; Berglund, Lars

    2017-12-01

    Optically transparent wood combines mechanical performance with optical functionalities is an emerging candidate for applications in smart buildings and structural optics and photonics. The present review summarizes transparent wood preparation methods, optical and mechanical performance, and functionalization routes, and discusses potential applications. The various challenges are discussed for the purpose of improved performance, scaled-up production and realization of advanced applications. This article is part of a discussion meeting issue `New horizons for cellulose nanotechnology'.

  3. Biomolecular transport and separation in nanotubular networks.

    Energy Technology Data Exchange (ETDEWEB)

    Stachowiak, Jeanne C.; Stevens, Mark Jackson (Sandia National Laboratories, Albuquerque, NM); Robinson, David B.; Branda, Steven S.; Zendejas, Frank; Meagher, Robert J.; Sasaki, Darryl Yoshio; Bachand, George David (Sandia National Laboratories, Albuquerque, NM); Hayden, Carl C.; Sinha, Anupama; Abate, Elisa; Wang, Julia; Carroll-Portillo, Amanda (Sandia National Laboratories, Albuquerque, NM); Liu, Haiqing (Sandia National Laboratories, Albuquerque, NM)

    2010-09-01

    Cell membranes are dynamic substrates that achieve a diverse array of functions through multi-scale reconfigurations. We explore the morphological changes that occur upon protein interaction to model membrane systems that induce deformation of their planar structure to yield nanotube assemblies. In the two examples shown in this report we will describe the use of membrane adhesion and particle trajectory to form lipid nanotubes via mechanical stretching, and protein adsorption onto domains and the induction of membrane curvature through steric pressure. Through this work the relationship between membrane bending rigidity, protein affinity, and line tension of phase separated structures were examined and their relationship in biological membranes explored.

  4. Clustering aspects in nuclear structure functions

    International Nuclear Information System (INIS)

    Hirai, M.; Saito, K.; Watanabe, T.; Kumano, S.

    2011-01-01

    For understanding an anomalous nuclear effect experimentally observed for the beryllium-9 nucleus at the Thomas Jefferson National Accelerator Facility, clustering aspects are studied in structure functions of deep inelastic lepton-nucleus scattering by using momentum distributions calculated in antisymmetrized (or fermionic) molecular dynamics (AMD) and also in a simple shell model for comparison. According to AMD, the 9 Be nucleus consists of two α-like clusters with a surrounding neutron. The clustering produces high-momentum components in nuclear wave functions, which affects nuclear modifications of the structure functions. We investigated whether clustering features could appear in the structure function F 2 of 9 Be along with studies for other light nuclei. We found that nuclear modifications of F 2 are similar in both AMD and shell models within our simple convolution description although there are slight differences in 9 Be. It indicates that the anomalous 9 Be result should be explained by a different mechanism from the nuclear binding and Fermi motion. If nuclear-modification slopes d(F 2 A /F 2 D )/dx are shown by the maximum local densities, the 9 Be anomaly can be explained by the AMD picture, namely by the clustering structure, whereas it certainly cannot be described in the simple shell model. This fact suggests that the large nuclear modification in 9 Be should be explained by large densities in the clusters. For example, internal nucleon structure could be modified in the high-density clusters. The clustering aspect of nuclear structure functions is an unexplored topic which is interesting for future investigations.

  5. Integrated Spintronic Platforms for Biomolecular Recognition Detection

    Science.gov (United States)

    Martins, V. C.; Cardoso, F. A.; Loureiro, J.; Mercier, M.; Germano, J.; Cardoso, S.; Ferreira, R.; Fonseca, L. P.; Sousa, L.; Piedade, M. S.; Freitas, P. P.

    2008-06-01

    This paper covers recent developments in magnetoresistive based biochip platforms fabricated at INESC-MN, and their application to the detection and quantification of pathogenic waterborn microorganisms in water samples for human consumption. Such platforms are intended to give response to the increasing concern related to microbial contaminated water sources. The presented results concern the development of biological active DNA chips and protein chips and the demonstration of the detection capability of the present platforms. Two platforms are described, one including spintronic sensors only (spin-valve based or magnetic tunnel junction based), and the other, a fully scalable platform where each probe site consists of a MTJ in series with a thin film diode (TFD). Two microfluidic systems are described, for cell separation and concentration, and finally, the read out and control integrated electronics are described, allowing the realization of bioassays with a portable point of care unit. The present platforms already allow the detection of complementary biomolecular target recognition with 1 pM concentration.

  6. A multiscale modeling approach for biomolecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Bowling, Alan, E-mail: bowling@uta.edu; Haghshenas-Jaryani, Mahdi, E-mail: mahdi.haghshenasjaryani@mavs.uta.edu [The University of Texas at Arlington, Department of Mechanical and Aerospace Engineering (United States)

    2015-04-15

    This paper presents a new multiscale molecular dynamic model for investigating the effects of external interactions, such as contact and impact, during stepping and docking of motor proteins and other biomolecular systems. The model retains the mass properties ensuring that the result satisfies Newton’s second law. This idea is presented using a simple particle model to facilitate discussion of the rigid body model; however, the particle model does provide insights into particle dynamics at the nanoscale. The resulting three-dimensional model predicts a significant decrease in the effect of the random forces associated with Brownian motion. This conclusion runs contrary to the widely accepted notion that the motor protein’s movements are primarily the result of thermal effects. This work focuses on the mechanical aspects of protein locomotion; the effect ATP hydrolysis is estimated as internal forces acting on the mechanical model. In addition, the proposed model can be numerically integrated in a reasonable amount of time. Herein, the differences between the motion predicted by the old and new modeling approaches are compared using a simplified model of myosin V.

  7. Human Skin Barrier Structure and Function Analyzed by Cryo-EM and Molecular Dynamics Simulation.

    Science.gov (United States)

    Lundborg, Magnus; Narangifard, Ali; Wennberg, Christian L; Lindahl, Erik; Daneholt, Bertil; Norlén, Lars

    2018-04-24

    In the present study we have analyzed the molecular structure and function of the human skin's permeability barrier using molecular dynamics simulation validated against cryo-electron microscopy data from near native skin. The skin's barrier capacity is located to an intercellular lipid structure embedding the cells of the superficial most layer of skin - the stratum corneum. According to the splayed bilayer model (Iwai et al., 2012) the lipid structure is organized as stacked bilayers of ceramides in a splayed chain conformation with cholesterol associated with the ceramide sphingoid moiety and free fatty acids associated with the ceramide fatty acid moiety. However, knowledge about the lipid structure's detailed molecular organization, and the roles of its different lipid constituents, remains circumstantial. Starting from a molecular dynamics model based on the splayed bilayer model, we have, by stepwise structural and compositional modifications, arrived at a thermodynamically stable molecular dynamics model expressing simulated electron microscopy patterns matching original cryo-electron microscopy patterns from skin extremely closely. Strikingly, the closer the individual molecular dynamics models' lipid composition was to that reported in human stratum corneum, the better was the match between the models' simulated electron microscopy patterns and the original cryo-electron microscopy patterns. Moreover, the closest-matching model's calculated water permeability and thermotropic behaviour were found compatible with that of human skin. The new model may facilitate more advanced physics-based skin permeability predictions of drugs and toxicants. The proposed procedure for molecular dynamics based analysis of cellular cryo-electron microscopy data might be applied to other biomolecular systems. Copyright © 2018. Published by Elsevier Inc.

  8. Progress on nuclear modifications of structure functions

    Directory of Open Access Journals (Sweden)

    Kumano S.

    2016-01-01

    Full Text Available We report progress on nuclear structure functions, especially on their nuclear modifications and a new tensor structure function for the deuteron. To understand nuclear structure functions is an important step toward describing nuclei and QCD matters from low to high densities and from low to high energies in terms of fundamental quark and gluon degrees of freedom beyond conventional hadron and nuclear physics. It is also practically important for understanding new phenomena in high-energy heavy-ion collisions at RHIC and LHC. Furthermore, since systematic errors of current neutrinooscillation experiments are dominated by uncertainties of neutrino-nucleus interactions, such studies are valuable for finding new physics beyond current framework. Next, a new tensor-polarized structure function b1 is discussed for the deuteron. There was a measurement by HERMES; however, its data are inconsistent with the conventional convolution estimate based on the standard deuteron model with D-state admixture. This fact suggests that a new hadronic phenomenon should exist in the tensor-polarized deuteron at high energies, and it will be experimentally investigated at JLab from the end of 2010’s.

  9. Structure and function of mammalian cilia

    DEFF Research Database (Denmark)

    Satir, Peter; Christensen, Søren T

    2008-01-01

    In the past half century, beginning with electron microscopic studies of 9 + 2 motile and 9 + 0 primary cilia, novel insights have been obtained regarding the structure and function of mammalian cilia. All cilia can now be viewed as sensory cellular antennae that coordinate a large number...

  10. Collagens--structure, function, and biosynthesis.

    Science.gov (United States)

    Gelse, K; Pöschl, E; Aigner, T

    2003-11-28

    The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified so far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. This review focuses on the distribution and function of various collagen types in different tissues. It introduces their basic structural subunits and points out major steps in the biosynthesis and supramolecular processing of fibrillar collagens as prototypical members of this protein family. A final outlook indicates the importance of different collagen types not only for the understanding of collagen-related diseases, but also as a basis for the therapeutical use of members of this protein family discussed in other chapters of this issue.

  11. MRI in Optic Neuritis: Structure, Function, Interactions

    DEFF Research Database (Denmark)

    Fuglø, Dan

    2011-01-01

    resonance imaging (MRI), and the visual evoked potential (VEP) continues to show a delayed P100 indicating persistent demyelination. The explanation for this apparent discrepancy between structure and function could be due to either a redundancy in the visual pathways so that some degree of signal loss...... will have very few or no clinical symptoms, or it could be due to compensatory mechanisms in the visual pathway or the visual cortex. In order to understand the pathophysiology and recovery processes in ON it is essential to have sensitive methods to asses both structure and function. These methods...... are low. Functional MRI (fMRI) is a non-invasive technique that can measure brain activity with a high spatial resolution. Recently, technical and methodological advancements have made it feasible to record VEPs and fMRI simultaneously and the relationship between averaged VEPs and averaged fMRI signals...

  12. Generalized functions, convergence structures, and their applications

    CERN Document Server

    Pap, Endre; Pilipović, Stevan; Vladimirov, Vasilij; International Conference "Generalized functions, convergence structures and their applications" (GFCA-87)

    1988-01-01

    This Proceedings consists of a collection of papers presented at the International Conference "Generalized functions, convergence structures and their applications" held from June 23-27, 1987 in Dubrovnik, Yugoslavia (GFCA-87): 71 participants from 21 countr~es from allover the world took part in the Conference. Proceedings reflects the work of the Conference. Plenary lectures of J. Burzyk, J. F. Colombeau, W. Gahler, H. Keiter, H. Komatsu, B. Stankovic, H. G. Tillman, V. S. Vladimirov provide an up-to-date account of the cur­ rent state of the subject. All these lectures, except H. G. Tillman's, are published in this volume. The published communications give the contemporary problems and achievements in the theory of generalized functions, in the theory of convergence structures and in their applications, specially in the theory of partial differential equations and in the mathematical physics. New approaches to the theory of generalized functions are presented, moti­ vated by concrete problems of applicat...

  13. Recognition of functional sites in protein structures.

    Science.gov (United States)

    Shulman-Peleg, Alexandra; Nussinov, Ruth; Wolfson, Haim J

    2004-06-04

    Recognition of regions on the surface of one protein, that are similar to a binding site of another is crucial for the prediction of molecular interactions and for functional classifications. We first describe a novel method, SiteEngine, that assumes no sequence or fold similarities and is able to recognize proteins that have similar binding sites and may perform similar functions. We achieve high efficiency and speed by introducing a low-resolution surface representation via chemically important surface points, by hashing triangles of physico-chemical properties and by application of hierarchical scoring schemes for a thorough exploration of global and local similarities. We proceed to rigorously apply this method to functional site recognition in three possible ways: first, we search a given functional site on a large set of complete protein structures. Second, a potential functional site on a protein of interest is compared with known binding sites, to recognize similar features. Third, a complete protein structure is searched for the presence of an a priori unknown functional site, similar to known sites. Our method is robust and efficient enough to allow computationally demanding applications such as the first and the third. From the biological standpoint, the first application may identify secondary binding sites of drugs that may lead to side-effects. The third application finds new potential sites on the protein that may provide targets for drug design. Each of the three applications may aid in assigning a function and in classification of binding patterns. We highlight the advantages and disadvantages of each type of search, provide examples of large-scale searches of the entire Protein Data Base and make functional predictions.

  14. Oblique photon expansion of QED structure functions

    International Nuclear Information System (INIS)

    Chahine, C.

    1986-01-01

    In the oblique photon expansion, the collinear part of photon emission is summed up to all orders in perturbation theory. The number of oblique or non-collinear photons is the expansion order. Unlike in perturbation theory, every term of the expansion is both infrared finite and gauge invariant. The zero oblique photon contribution to the electromagnetic structure tensor in QED is computed in detail. The behaviors of the structure functions F1 and F2 are discussed in the soft and ultra-soft limits

  15. Structure of β-decay strength functions

    International Nuclear Information System (INIS)

    Naumov, Y.V.; Bykov, A.A.; Izosimov, I.N.

    1983-01-01

    The experimental and theoretical studies on the structure of the Gamow--Teller β-decay strength functions are reviewed. Also considered are processes such as M1 γ decay of analog states, the emission of delayed protons, neutrons, and α particles, delayed fission, and the (p, n) reaction at proton energies 100--200 MeV. The results of measurements of the strength functions by γ-ray total absorption are analyzed. It is shown that the β + decay of nuclei far from the stability band exhibits a new type of collective charge-exchange excitation: Gamow--Teller resonance with μ/sub tau/ = +1

  16. Structure of BRS-invariant local functionals

    International Nuclear Information System (INIS)

    Brandt, F.

    1993-01-01

    For a large class of gauge theories a nilpotent BRS-operator s is constructed and its cohomology in the space of local functionals of the off-shell fields is shown to be isomorphic to the cohomology of s=s+d on functions f(C,T) of tensor fields T and of variables C which are constructed of the ghosts and the connection forms. The result allows general statements about the structure of invariant classical actions and anomaly cadidates whose BRS-variation vanishes off-shell. The assumptions under which the result holds are thoroughly discussed. (orig.)

  17. NAC transcription factors: structurally distinct, functionally diverse

    DEFF Research Database (Denmark)

    Olsen, Addie Nina; Ernst, Heidi A; Leggio, Leila Lo

    2005-01-01

    level and localization, and to the first indications of NAC participation in transcription factor networks. The recent determination of the DNA and protein binding NAC domain structure offers insight into the molecular functions of the protein family. Research into NAC transcription factors has......NAC proteins constitute one of the largest families of plant-specific transcription factors, and the family is present in a wide range of land plants. Here, we summarize the biological and molecular functions of the NAC family, paying particular attention to the intricate regulation of NAC protein...

  18. Proteins with Novel Structure, Function and Dynamics

    Science.gov (United States)

    Pohorille, Andrew

    2014-01-01

    Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

  19. Functional and structural responses to marine urbanisation

    Science.gov (United States)

    Mayer-Pinto, M.; Cole, V. J.; Johnston, E. L.; Bugnot, A.; Hurst, H.; Airoldi, L.; Glasby, T. M.; Dafforn, K. A.

    2018-01-01

    Urban areas have broad ecological footprints with complex impacts on natural systems. In coastal areas, growing populations are advancing their urban footprint into the ocean through the construction of seawalls and other built infrastructure. While we have some understanding of how urbanisation might drive functional change in terrestrial ecosystems, coastal systems have been largely overlooked. This study is one of the first to directly assess how changes in diversity relate to changes in ecosystem properties and functions (e.g. productivity, filtration rates) of artificial and natural habitats in one of the largest urbanised estuaries in the world, Sydney Harbour. We complemented our surveys with an extensive literature search. We found large and important differences in the community structure and function between artificial and natural coastal habitats. However, differences in diversity and abundance of organisms do not necessarily match observed functional changes. The abundance and composition of important functional groups differed among habitats with rocky shores having 40% and 70% more grazers than seawalls or pilings, respectively. In contrast, scavengers were approximately 8 times more abundant on seawalls than on pilings or rocky shores and algae were more diverse on natural rocky shores and seawalls than on pilings. Our results confirm previous findings in the literature. Oysters were more abundant on pilings than on rocky shores, but were also smaller. Interestingly, these differences in oyster populations did not affect in situ filtration rates between habitats. Seawalls were the most invaded habitats while pilings supported greater secondary productivity than other habitats. This study highlights the complexity of the diversity-function relationship and responses to ocean sprawl in coastal systems. Importantly, we showed that functional properties should be considered independently from structural change if we are to design and manage artificial

  20. Geometrical scaling in charm structure function ratios

    International Nuclear Information System (INIS)

    Boroun, G.R.; Rezaei, B.

    2014-01-01

    By using a Laplace-transform technique, we solve the next-to-leading-order master equation for charm production and derive a compact formula for the ratio R c =F L cc ¯ /F 2 cc ¯ , which is useful for extracting the charm structure function from the reduced charm cross section, in particular, at DESY HERA, at small x. Our results show that this ratio is independent of x at small x. In this method of determining the ratios, we apply geometrical scaling in charm production in deep inelastic scattering (DIS). Our analysis shows that the renormalization scales have a sizable impact on the ratio R c at high Q 2 . Our results for the ratio of the charm structure functions are in a good agreement with some phenomenological models

  1. Phosphatidylinositol 4-kinases: Function, structure, and inhibition

    International Nuclear Information System (INIS)

    Boura, Evzen; Nencka, Radim

    2015-01-01

    The phosphatidylinositol 4-kinases (PI4Ks) synthesize phosphatidylinositol 4-phosphate (PI4P), a key member of the phosphoinositide family. PI4P defines the membranes of Golgi and trans-Golgi network (TGN) and regulates trafficking to and from the Golgi. Humans have two type II PI4Ks (α and β) and two type III enzymes (α and β). Recently, the crystal structures were solved for both type II and type III kinase revealing atomic details of their function. Importantly, the type III PI4Ks are hijacked by +RNA viruses to create so-called membranous web, an extensively phosphorylated and modified membrane system dedicated to their replication. Therefore, selective and potent inhibitors of PI4Ks have been developed as potential antiviral agents. Here we focus on the structure and function of PI4Ks and their potential in human medicine

  2. Phosphatidylinositol 4-kinases: Function, structure, and inhibition

    Energy Technology Data Exchange (ETDEWEB)

    Boura, Evzen, E-mail: boura@uochb.cas.cz; Nencka, Radim, E-mail: nencka@uochb.cas.cz

    2015-10-01

    The phosphatidylinositol 4-kinases (PI4Ks) synthesize phosphatidylinositol 4-phosphate (PI4P), a key member of the phosphoinositide family. PI4P defines the membranes of Golgi and trans-Golgi network (TGN) and regulates trafficking to and from the Golgi. Humans have two type II PI4Ks (α and β) and two type III enzymes (α and β). Recently, the crystal structures were solved for both type II and type III kinase revealing atomic details of their function. Importantly, the type III PI4Ks are hijacked by +RNA viruses to create so-called membranous web, an extensively phosphorylated and modified membrane system dedicated to their replication. Therefore, selective and potent inhibitors of PI4Ks have been developed as potential antiviral agents. Here we focus on the structure and function of PI4Ks and their potential in human medicine.

  3. Theoretical analysis of polarized structure functions

    International Nuclear Information System (INIS)

    Altarelli, G.; ); Ball, R.D.; Forte, S.; Ridolfi, G.

    1998-01-01

    We review the analysis of polarized structure function data using perturbative QCD and NLO We use the most recent experimental data to obtain updated results for polarized parton distributions, first moments and the strong coupling. We also discuss several theoretical issues involving in this analysis and in the interpretation of its results. Finally, we compare our results with other similar analyses in the recent literature. (author)

  4. Theoretical Analysis of Polarized Structure Functions

    CERN Document Server

    Altarelli, Guido; Forte, Stefano; Ridolfi, G

    1998-01-01

    We review the analysis of polarized structure function data using perturbative QCD at next-to-leading order. We use the most recent experimental data to obtain updated results for polarized parton distributions, first moments and the strong coupling. We also discuss several theoretical issues involved in this analysis and in the interpretation of its results. Finally, we compare our results with other similar analyses in the recent literature.

  5. Ecosocial System: Structure, Development Laws and Functioning

    Directory of Open Access Journals (Sweden)

    E. I. Alekseev

    2004-01-01

    Full Text Available The paper substantiates necessity to develop a unified system of socio-ecological knowledge. Ecosophy being a forming component of dialectic-materialistic philosophy has been proposed as such system. Structure, development laws and functioning of eco-social system are considered as a part of ecosophy theory. Standard laws and ecological principles being widely recognized by ecologically orientated theorists are stated in the paper.

  6. Neuropsychological functioning and brain structure in schizophrenia.

    Science.gov (United States)

    Crespo-Facorro, Benedicto; Barbadillo, Laura; Pelayo-Terán, José Maria; Rodríguez-Sánchez, José Manuel

    2007-08-01

    Cognitive deficits are core features of schizophrenia that are already evident at early phases of the illness. The study of specific relationships between cognition and brain structure might provide valuable clues about neural basis of schizophrenia and its phenomenology. The aim of this article was to review the most consistent findings of the studies exploring the relationships between cognitive deficits and brain anomalies in schizophrenia. Besides several important methodological shortcomings to bear in mind before drawing any consistent conclusion from the revised literature, we have attempted to systematically summarize these findings. Thus, this review has revealed that whole brain volume tends to positively correlate with a range of cognitive domains in healthy volunteers and female patients. An association between prefrontal morphological characteristics and general inability to control behaviour seems to be present in schizophrenia patients. Parahippocampal volume is related to semantic cognitive functions. Thalamic anomalies have been associated with executive deficits specifically in patients. Available evidence on the relationship between cognitive functions and cerebellar structure is still contradictory. Nonetheless, a larger cerebellum appears to be associated with higher IQ in controls and in female patients. Enlarged ventricles, including lateral and third ventricles, are associated with deficits in attention, executive and premorbid cognitive functioning in patients. Several of these reported findings seem to be counterintuitive according to neural basis of cognitive functioning drawn from animal, lesion, and functional imaging investigations. Therefore, there is still a great need for more methodologically stringent investigations that would help in the advance of our understanding of the cognition/brain structure relationships in schizophrenia.

  7. Industrial entrepreneurial network: Structural and functional analysis

    Science.gov (United States)

    Medvedeva, M. A.; Davletbaev, R. H.; Berg, D. B.; Nazarova, J. J.; Parusheva, S. S.

    2016-12-01

    Structure and functioning of two model industrial entrepreneurial networks are investigated in the present paper. One of these networks is forming when implementing an integrated project and consists of eight agents, which interact with each other and external environment. The other one is obtained from the municipal economy and is based on the set of the 12 real business entities. Analysis of the networks is carried out on the basis of the matrix of mutual payments aggregated over the certain time period. The matrix is created by the methods of experimental economics. Social Network Analysis (SNA) methods and instruments were used in the present research. The set of basic structural characteristics was investigated: set of quantitative parameters such as density, diameter, clustering coefficient, different kinds of centrality, and etc. They were compared with the random Bernoulli graphs of the corresponding size and density. Discovered variations of random and entrepreneurial networks structure are explained by the peculiarities of agents functioning in production network. Separately, were identified the closed exchange circuits (cyclically closed contours of graph) forming an autopoietic (self-replicating) network pattern. The purpose of the functional analysis was to identify the contribution of the autopoietic network pattern in its gross product. It was found that the magnitude of this contribution is more than 20%. Such value allows using of the complementary currency in order to stimulate economic activity of network agents.

  8. EFFECTIVE HYPERFINE-STRUCTURE FUNCTIONS OF AMMONIA

    Energy Technology Data Exchange (ETDEWEB)

    Augustovičová, L.; Soldán, P.; Špirko, V., E-mail: spirko@marge.uochb.cas.cz [Charles University in Prague, Faculty of Mathematics and Physics, Department of Chemical Physics and Optics, Ke Karlovu 3, CZ-12116 Prague 2 (Czech Republic)

    2016-06-20

    The hyperfine structure of the rotation-inversion ( v {sub 2} = 0{sup +}, 0{sup −}, 1{sup +}, 1{sup −}) states of the {sup 14}NH{sub 3} and {sup 15}NH{sub 3} ammonia isotopomers is rationalized in terms of effective (ro-inversional) hyperfine-structure (hfs) functions. These are determined by fitting to available experimental data using the Hougen’s effective hyperfine-structure Hamiltonian within the framework of the non-rigid inverter theory. Involving only a moderate number of mass independent fitting parameters, the fitted hfs functions provide a fairly close reproduction of a large majority of available experimental data, thus evidencing adequacy of these functions for reliable prediction. In future experiments, this may help us derive spectroscopic constants of observed inversion and rotation-inversion transitions deperturbed from hyperfine effects. The deperturbed band centers of ammonia come to the forefront of fundamental physics especially as the probes of a variable proton-to-electron mass ratio.

  9. Structure functions of nucleons and nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Bentz, Wolfgang; Ito, Takuya [Department of Physics, Tokai University, Kanagawa (Japan); Cloet, Ian [Department of Physics, University of Washington, Seattle (United States); Thomas, Anthony [Jefferson Lab., Newport News, VA (United States); Yazaki, Koichi [RIKEN, Wako-shi, Saitama (Japan)

    2009-07-01

    We use an effective chiral quark theory to calculate the quark distributions and structure functions of nucleons and nuclei. The description of the single nucleon is based on the Faddeev framework, and nuclear systems are described in the mean field approximation. Particular amphasis is put on the prediction of the polarized EMC effect in nuclei, and on applications to deep inelastic neutrino-nucleus scattering. Concerning the polarized EMC effect, we discuss the quenching of the quark spin sum in nuclei and its implications for the spin dependent nuclear structure functions, and present results for several nuclei where an experimental observation is feasible. Concerning the case of deep inelastic neutrino-nucleus scattering, we estimate the effect of medium modifications of the quark distribution functions on the measured cross sections, and discuss an interesting resolution of the so called NuTeV anomaly. Finally, we discuss extensions of our model to describe fragmentation functions for semi-inclusive processes. The connection between our effective quark model description and the jet model of Field and Feynman is discussed.

  10. Threshold resummation of the structure function FL

    International Nuclear Information System (INIS)

    Moch, S.; Vogt, A.

    2009-02-01

    The behaviour of the quark coefficient function for the longitudinal structure function F L in deepinelastic scattering is investigated for large values of the Bjorken variable x. We combine a highly plausible conjecture on the large-x limit of the physical evolution kernel for this quantity with our explicit three-loop results to derive the coefficients of the three leading large-x logarithms, α s n ln 2n-1-k (1-x), k=1,2,3, to all orders in the strong coupling constant α s . Corresponding results are derived for the non-C F part of the gluon coefficient function suppressed by a factor 1-x, and for the analogous subleading (1-x)ln k (1-x) contributions in the quark case. Our results appear to indicate an obstacle for an exponentiation with a higher logarithmic accuracy. (orig.)

  11. Structural and regulatory functions of keratins

    International Nuclear Information System (INIS)

    Magin, Thomas M.; Vijayaraj, Preethi; Leube, Rudolf E.

    2007-01-01

    The diversity of epithelial functions is reflected by the expression of distinct keratin pairs that are responsible to protect epithelial cells against mechanical stress and to act as signaling platforms. The keratin cytoskeleton integrates these functions by forming a supracellular scaffold that connects at desmosomal cell-cell adhesions. Multiple human diseases and murine knockouts in which the integrity of this system is destroyed testify to its importance as a mechanical stabilizer in certain epithelia. Yet, surprisingly little is known about the precise mechanisms responsible for assembly and disease pathology. In addition to these structural aspects of keratin function, experimental evidence accumulating in recent years has led to a much more complex view of the keratin cytoskeleton. Distinct keratins emerge as highly dynamic scaffolds in different settings and contribute to cell size determination, translation control, proliferation, cell type-specific organelle transport, malignant transformation and various stress responses. All of these properties are controlled by highly complex patterns of phosphorylation and molecular associations

  12. Exploring Protein Structure and Dynamics through a Project-Oriented Biochemistry Laboratory Module

    Science.gov (United States)

    Lipchock, James M.; Ginther, Patrick S.; Douglas, Bonnie B.; Bird, Kelly E.; Loria, J. Patrick

    2017-01-01

    Here, we present a 10-week project-oriented laboratory module designed to provide a course-based undergraduate research experience in biochemistry that emphasizes the importance of biomolecular structure and dynamics in enzyme function. This module explores the impact of mutagenesis on an important active site loop for a biomedically-relevant…

  13. Challenges for Super-Resolution Localization Microscopy and Biomolecular Fluorescent Nano-Probing in Cancer Research

    Science.gov (United States)

    Ilić, Nataša; Pilarczyk, Götz; Lee, Jin-Ho; Logeswaran, Abiramy; Borroni, Aurora Paola; Krufczik, Matthias; Theda, Franziska; Waltrich, Nadine; Bestvater, Felix; Hildenbrand, Georg; Cremer, Christoph; Blank, Michael

    2017-01-01

    Understanding molecular interactions and regulatory mechanisms in tumor initiation, progression, and treatment response are key requirements towards advanced cancer diagnosis and novel treatment procedures in personalized medicine. Beyond decoding the gene expression, malfunctioning and cancer-related epigenetic pathways, investigations of the spatial receptor arrangements in membranes and genome organization in cell nuclei, on the nano-scale, contribute to elucidating complex molecular mechanisms in cells and tissues. By these means, the correlation between cell function and spatial organization of molecules or molecular complexes can be studied, with respect to carcinogenesis, tumor sensitivity or tumor resistance to anticancer therapies, like radiation or antibody treatment. Here, we present several new applications for bio-molecular nano-probes and super-resolution, laser fluorescence localization microscopy and their potential in life sciences, especially in biomedical and cancer research. By means of a tool-box of fluorescent antibodies, green fluorescent protein (GFP) tagging, or specific oligonucleotides, we present tumor relevant re-arrangements of Erb-receptors in membranes, spatial organization of Smad specific ubiquitin protein ligase 2 (Smurf2) in the cytosol, tumor cell characteristic heterochromatin organization, and molecular re-arrangements induced by radiation or antibody treatment. The main purpose of this article is to demonstrate how nano-scaled distance measurements between bio-molecules, tagged by appropriate nano-probes, can be applied to elucidate structures and conformations of molecular complexes which are characteristic of tumorigenesis and treatment responses. These applications open new avenues towards a better interpretation of the spatial organization and treatment responses of functionally relevant molecules, at the single cell level, in normal and cancer cells, offering new potentials for individualized medicine. PMID:28956810

  14. Challenges for Super-Resolution Localization Microscopy and Biomolecular Fluorescent Nano-Probing in Cancer Research

    Directory of Open Access Journals (Sweden)

    Michael Hausmann

    2017-09-01

    Full Text Available Understanding molecular interactions and regulatory mechanisms in tumor initiation, progression, and treatment response are key requirements towards advanced cancer diagnosis and novel treatment procedures in personalized medicine. Beyond decoding the gene expression, malfunctioning and cancer-related epigenetic pathways, investigations of the spatial receptor arrangements in membranes and genome organization in cell nuclei, on the nano-scale, contribute to elucidating complex molecular mechanisms in cells and tissues. By these means, the correlation between cell function and spatial organization of molecules or molecular complexes can be studied, with respect to carcinogenesis, tumor sensitivity or tumor resistance to anticancer therapies, like radiation or antibody treatment. Here, we present several new applications for bio-molecular nano-probes and super-resolution, laser fluorescence localization microscopy and their potential in life sciences, especially in biomedical and cancer research. By means of a tool-box of fluorescent antibodies, green fluorescent protein (GFP tagging, or specific oligonucleotides, we present tumor relevant re-arrangements of Erb-receptors in membranes, spatial organization of Smad specific ubiquitin protein ligase 2 (Smurf2 in the cytosol, tumor cell characteristic heterochromatin organization, and molecular re-arrangements induced by radiation or antibody treatment. The main purpose of this article is to demonstrate how nano-scaled distance measurements between bio-molecules, tagged by appropriate nano-probes, can be applied to elucidate structures and conformations of molecular complexes which are characteristic of tumorigenesis and treatment responses. These applications open new avenues towards a better interpretation of the spatial organization and treatment responses of functionally relevant molecules, at the single cell level, in normal and cancer cells, offering new potentials for individualized medicine.

  15. CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function.

    Science.gov (United States)

    Krüger, Dennis M; Rathi, Prakash Chandra; Pfleger, Christopher; Gohlke, Holger

    2013-07-01

    The Constraint Network Analysis (CNA) web server provides a user-friendly interface to the CNA approach developed in our laboratory for linking results from rigidity analyses to biologically relevant characteristics of a biomolecular structure. The CNA web server provides a refined modeling of thermal unfolding simulations that considers the temperature dependence of hydrophobic tethers and computes a set of global and local indices for quantifying biomacromolecular stability. From the global indices, phase transition points are identified where the structure switches from a rigid to a floppy state; these phase transition points can be related to a protein's (thermo-)stability. Structural weak spots (unfolding nuclei) are automatically identified, too; this knowledge can be exploited in data-driven protein engineering. The local indices are useful in linking flexibility and function and to understand the impact of ligand binding on protein flexibility. The CNA web server robustly handles small-molecule ligands in general. To overcome issues of sensitivity with respect to the input structure, the CNA web server allows performing two ensemble-based variants of thermal unfolding simulations. The web server output is provided as raw data, plots and/or Jmol representations. The CNA web server, accessible at http://cpclab.uni-duesseldorf.de/cna or http://www.cnanalysis.de, is free and open to all users with no login requirement.

  16. Psychedelics Promote Structural and Functional Neural Plasticity

    Directory of Open Access Journals (Sweden)

    Calvin Ly

    2018-06-01

    Full Text Available Summary: Atrophy of neurons in the prefrontal cortex (PFC plays a key role in the pathophysiology of depression and related disorders. The ability to promote both structural and functional plasticity in the PFC has been hypothesized to underlie the fast-acting antidepressant properties of the dissociative anesthetic ketamine. Here, we report that, like ketamine, serotonergic psychedelics are capable of robustly increasing neuritogenesis and/or spinogenesis both in vitro and in vivo. These changes in neuronal structure are accompanied by increased synapse number and function, as measured by fluorescence microscopy and electrophysiology. The structural changes induced by psychedelics appear to result from stimulation of the TrkB, mTOR, and 5-HT2A signaling pathways and could possibly explain the clinical effectiveness of these compounds. Our results underscore the therapeutic potential of psychedelics and, importantly, identify several lead scaffolds for medicinal chemistry efforts focused on developing plasticity-promoting compounds as safe, effective, and fast-acting treatments for depression and related disorders. : Ly et al. demonstrate that psychedelic compounds such as LSD, DMT, and DOI increase dendritic arbor complexity, promote dendritic spine growth, and stimulate synapse formation. These cellular effects are similar to those produced by the fast-acting antidepressant ketamine and highlight the potential of psychedelics for treating depression and related disorders. Keywords: neural plasticity, psychedelic, spinogenesis, synaptogenesis, depression, LSD, DMT, ketamine, noribogaine, MDMA

  17. Psychedelics Promote Structural and Functional Neural Plasticity.

    Science.gov (United States)

    Ly, Calvin; Greb, Alexandra C; Cameron, Lindsay P; Wong, Jonathan M; Barragan, Eden V; Wilson, Paige C; Burbach, Kyle F; Soltanzadeh Zarandi, Sina; Sood, Alexander; Paddy, Michael R; Duim, Whitney C; Dennis, Megan Y; McAllister, A Kimberley; Ori-McKenney, Kassandra M; Gray, John A; Olson, David E

    2018-06-12

    Atrophy of neurons in the prefrontal cortex (PFC) plays a key role in the pathophysiology of depression and related disorders. The ability to promote both structural and functional plasticity in the PFC has been hypothesized to underlie the fast-acting antidepressant properties of the dissociative anesthetic ketamine. Here, we report that, like ketamine, serotonergic psychedelics are capable of robustly increasing neuritogenesis and/or spinogenesis both in vitro and in vivo. These changes in neuronal structure are accompanied by increased synapse number and function, as measured by fluorescence microscopy and electrophysiology. The structural changes induced by psychedelics appear to result from stimulation of the TrkB, mTOR, and 5-HT2A signaling pathways and could possibly explain the clinical effectiveness of these compounds. Our results underscore the therapeutic potential of psychedelics and, importantly, identify several lead scaffolds for medicinal chemistry efforts focused on developing plasticity-promoting compounds as safe, effective, and fast-acting treatments for depression and related disorders. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  18. The structure and function of presynaptic endosomes

    Energy Technology Data Exchange (ETDEWEB)

    Jähne, Sebastian, E-mail: sebastian.jaehne1@stud.uni-goettingen.de [Department of Neuro- and Sensory Physiology, University of Göttingen Medical Center, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, Humboldtallee 23, 37073 Göttingen (Germany); International Max Planck Research School for Neurosciences, 37077 Göttingen (Germany); Rizzoli, Silvio O. [Department of Neuro- and Sensory Physiology, University of Göttingen Medical Center, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, Humboldtallee 23, 37073 Göttingen (Germany); Helm, Martin S., E-mail: martin.helm@med.uni-goettingen.de [Department of Neuro- and Sensory Physiology, University of Göttingen Medical Center, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, Humboldtallee 23, 37073 Göttingen (Germany); International Max Planck Research School for Molecular Biology, 37077 Göttingen (Germany)

    2015-07-15

    The function of endosomes and of endosome-like structures in the presynaptic compartment is still controversial. This is in part due to the absence of a consensus on definitions and markers for these compartments. Synaptic endosomes are sometimes seen as stable organelles, permanently present in the synapse. Alternatively, they are seen as short-lived intermediates in synaptic vesicle recycling, arising from the endocytosis of large vesicles from the plasma membrane, or from homotypic fusion of small vesicles. In addition, the potential function of the endosome is largely unknown in the synapse. Some groups have proposed that the endosome is involved in the sorting of synaptic vesicle proteins, albeit others have produced data that deny this possibility. In this review, we present the existing evidence for synaptic endosomes, we discuss their potential functions, and we highlight frequent technical pitfalls in the analysis of this elusive compartment. We also sketch a roadmap to definitely determine the role of synaptic endosomes for the synaptic vesicle cycle. Finally, we propose a common definition of synaptic endosome-like structures.

  19. The structure and function of presynaptic endosomes

    International Nuclear Information System (INIS)

    Jähne, Sebastian; Rizzoli, Silvio O.; Helm, Martin S.

    2015-01-01

    The function of endosomes and of endosome-like structures in the presynaptic compartment is still controversial. This is in part due to the absence of a consensus on definitions and markers for these compartments. Synaptic endosomes are sometimes seen as stable organelles, permanently present in the synapse. Alternatively, they are seen as short-lived intermediates in synaptic vesicle recycling, arising from the endocytosis of large vesicles from the plasma membrane, or from homotypic fusion of small vesicles. In addition, the potential function of the endosome is largely unknown in the synapse. Some groups have proposed that the endosome is involved in the sorting of synaptic vesicle proteins, albeit others have produced data that deny this possibility. In this review, we present the existing evidence for synaptic endosomes, we discuss their potential functions, and we highlight frequent technical pitfalls in the analysis of this elusive compartment. We also sketch a roadmap to definitely determine the role of synaptic endosomes for the synaptic vesicle cycle. Finally, we propose a common definition of synaptic endosome-like structures

  20. Catchment Classification: Connecting Climate, Structure and Function

    Science.gov (United States)

    Sawicz, K. A.; Wagener, T.; Sivapalan, M.; Troch, P. A.; Carrillo, G. A.

    2010-12-01

    Hydrology does not yet possess a generally accepted catchment classification framework. Such a classification framework needs to: [1] give names to things, i.e. the main classification step, [2] permit transfer of information, i.e. regionalization of information, [3] permit development of generalizations, i.e. to develop new theory, and [4] provide a first order environmental change impact assessment, i.e., the hydrologic implications of climate, land use and land cover change. One strategy is to create a catchment classification framework based on the notion of catchment functions (partitioning, storage, and release). Results of an empirical study presented here connects climate and structure to catchment function (in the form of select hydrologic signatures), based on analyzing over 300 US catchments. Initial results indicate a wide assortment of signature relationships with properties of climate, geology, and vegetation. The uncertainty in the different regionalized signatures varies widely, and therefore there is variability in the robustness of classifying ungauged basins. This research provides insight into the controls of hydrologic behavior of a catchment, and enables a classification framework applicable to gauged and ungauged across the study domain. This study sheds light on what we can expect to achieve in mapping climate, structure and function in a top-down manner. Results of this study complement work done using a bottom-up physically-based modeling framework to generalize this approach (Carrillo et al., this session).

  1. FACTOR STRUCTURE OF FUNCTIONAL CAPABILITIES OF BODYBUILDERS

    Directory of Open Access Journals (Sweden)

    Predrag Milenović

    2007-05-01

    Full Text Available It is evident that researches in the fi eld of kineziology and sports sciences on the topic of body-building here are very rare mainly and probably because of its place in the system of hyerarchy of sports. Lack of interest in body-building and its insuffi cient popularization springs probably, among other things, from its different interpretation and, according to some people, from its ultimate goals which are not justifi ed by many. Others, experts from the fi eld of body-building, starting from the basic principles of its exercising point out its numerous positive characteristics and sides. Undoubtedly, characteristics of functional capabilities of sportspeople are specifi c for each sport or discipline. In body-building the functional sphere is bordered and defi ned by the nature of the sport’s activity itself, as well as by genetics and internal and external factors in a very complex training process of a bodu-builder. The goal of this research was determining the structure of the functional sphere of a body-builder. It was performed on the sample of 30 selected sportsmen, body-builders, of chronological age between 17 and 19 ( 6 months, members of the Sports' Club Strength ''Leskovac'', the Weight Lifters' Club '' Dubočica'' and the Body-building Club '' Dubočica'' from Leskovac. All the examiees have been submitted to training processes during a period longer than a year. For the purpose of determining the structure of the morphological sphere the Factor Analysis has been applied. Based on the data from the matrix of the Factor Structure the isolated factors can be interpreted in the following manner: The fi rst isolated factor in the sphere of applied functional variables is best defi ned by the variable of pulse under stress (FPUOP and the variable of maximum Oxygen consumption in liters per minute (FOLM. This isolated factor can be defi ned as a dimension of the transportation system of Oxygen. The second isolated factor in the

  2. Biomolecular detection using a metal semiconductor field effect transistor

    Science.gov (United States)

    Estephan, Elias; Saab, Marie-Belle; Buzatu, Petre; Aulombard, Roger; Cuisinier, Frédéric J. G.; Gergely, Csilla; Cloitre, Thierry

    2010-04-01

    In this work, our attention was drawn towards developing affinity-based electrical biosensors, using a MESFET (Metal Semiconductor Field Effect Transistor). Semiconductor (SC) surfaces must be prepared before the incubations with biomolecules. The peptides route was adapted to exceed and bypass the limits revealed by other types of surface modification due to the unwanted unspecific interactions. As these peptides reveal specific recognition of materials, then controlled functionalization can be achieved. Peptides were produced by phage display technology using a library of M13 bacteriophage. After several rounds of bio-panning, the phages presenting affinities for GaAs SC were isolated; the DNA of these specific phages were sequenced, and the peptide with the highest affinity was synthesized and biotinylated. To explore the possibility of electrical detection, the MESFET fabricated with the GaAs SC were used to detect the streptavidin via the biotinylated peptide in the presence of the bovine Serum Albumin. After each surface modification step, the IDS (current between the drain and the source) of the transistor was measured and a decrease in the intensity was detected. Furthermore, fluorescent microscopy was used in order to prove the specificity of this peptide and the specific localisation of biomolecules. In conclusion, the feasibility of producing an electrical biosensor using a MESFET has been demonstrated. Controlled placement, specific localization and detection of biomolecules on a MESFET transistor were achieved without covering the drain and the source. This method of functionalization and detection can be of great utility for biosensing application opening a new way for developing bioFETs (Biomolecular Field-Effect Transistor).

  3. Summary of the Photon Structure Functions - Measurements at LEP

    International Nuclear Information System (INIS)

    Przybycien, M.

    2002-01-01

    The present status of the photon structure functions measurements at LEP is discussed. The short introduction to the kinematics and theoretical framework of the structure functions measurements at LEP is given first. Then follow presentations of the most important measurements, ranging from the QED photon structure function, through the hadronic structure functions of real and virtual photons, and at the end the first measurement of the electron structure function is shown. (author)

  4. Conformation of bovine submaxillary mucin layers on hydrophobic surface as studied by biomolecular probes

    DEFF Research Database (Denmark)

    Pakkanen, Kirsi I.; Madsen, Jan Busk; Lee, Seunghwan

    2015-01-01

    In the present study, the conformational changes of bovine submaxillary mucin (BSM) adsorbed on a hydrophobic surface (polystyrene (PS)) as a function of concentration in bulk solution (up to 2mg/mL) have been investigated with biomolecular probe-based approaches, including bicinchoninic acid (BCA),enzyme-linkedimmunosorbentassay(EIA...... solution. Adsorbed masses of BSM onto hydrophobic surface, as probe by BCA, showed a continuously increasing trend up to 2mg/mL. But, the signals from EIA and ELLA, which probe the concentration of available unglycosylatedC-terminals and the central glycosylated regions, respectively, showed complicated...

  5. FY 2000 report on the results of the R and D of the fusion domain. Volume 3. Biomolecular mechanism and design; 2000 nendo yugo ryoiki kenkyu kaihatsu. 3. Biomolecular mechanism and design

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-03-01

    For the purpose of creating cells/tissue assemblies and the molecular machine that substitute for self-organizing and self-repairing functions of a living body outside the body, the basic technology research was conducted, and the FY 2000 results were reported. In the study of 3D cell and tissue module engineering, the following were conducted: study of the surface modification and functional expression of biomaterials, study of the mechanical stress to cartilaginous cells and the response, development of the production method of biodegradable synthetic polymer porous materials, study of organism hard tissue materials/bone remodeling and cultured bone transportation, development of zinc-releasing calcium phosphate ceramics. In the study of biomolecular mechanism and design, 1D unidirectional movement of microtubules by applying microlithography technology, structural study of kinesin-family molecular motor by low temperature microscope, ribozyme and the application to leukemia, basic study on assessment of chemical substances by human cultured cells, study of a low molecule detection system using nucleic acid and peptide. (NEDO)

  6. Measurement of the nucleon structure functions

    International Nuclear Information System (INIS)

    Gordon, B.A.; Loomis, W.A.; Pipkin, F.M.; Pordes, S.H.; Sessoms, A.L.; Shambroom, W.D.; Tao, C.; Verhey, L.J.; Wilson, R.; Anderson, H.L.; Fine, R.M.; Heisterberg, R.H.; Kinnison, W.W.; Matis, H.S.; Mo, L.W.; Myrianthopoulos, L.C.; Wright, S.C.; Francis, W.R.; Hicks, R.G.; Kirk, T.B.W.; Quirk, T.W.; Bharadwaj, V.K.; Booth, N.E.; Kirkbride, G.I.; Proudfoot, J.; Skuja, A.; Staton, M.A.; Williams, W.S.C.

    1979-01-01

    Measurements have been made of the inclusive scattering of 96, 147, and 219 GeV muons from hydrogen, and of 147 GeV muons from deuterium. Results are presented for the nucleon structure function F 2 (x,Q 2 ) [equivalentνW 2 (x,Q 2 )] for 10 2 2 . The value of F 2 rises with Q 2 at small x, and falls with Q 2 at large x, in agreement with the ideas of quantum chromodynamics. An average value of the ratio sigma/sub L//sigma/sub T/ equivalent R = 0.52 +- 0.35 has been obtained for the region 0.003 2 2 . The values of F 2 from this experiment have been combined with those from other charged-lepton scattering experiments to determine moments of the structure functions. The variation with Q 2 of these moments is used to derive values for Λ, taking into account corrections up to second order in α/sub s/. The fit to the data is very good

  7. Structural and functional intermetallics - an overview

    International Nuclear Information System (INIS)

    Varin, R.A.

    2000-01-01

    This overview presents the current status of the research and development of both structural and functional intermetallics. On the one hand, the discussion is focused on commercialization and existing industrial applications of intermetallics. Within this frame the applications of titanium aluminides (TiAl) for turbocharger rotors and exhaust valves in automotive industry are being discussed. Advances in the applications of TiAl alloys for the next generation of turbine blades in aerospace/aircraft segment are also presented. The entire spectrum of nickel and iron aluminide alloys developed commercially by the Oak Ridge national Laboratory (USA) and the examples of their application in various segments of industry are thoroughly discussed. Some inroads made in the application of directionally solidified (DS) multiphase niobium silicides (Nb 3 Si+Nb 5 Si 3 ) in situ intermetallic composites with the goal of pushing the service temperature envelope of turbine blades to ∼ 1200-1300 o C are also discussed. On the other hand, various topics in basic or curiosity driven research of titanium aluminides and trialuminides, iron aluminides and high temperature structural silicides are discussed. Some very recent findings on the improvements in fracture toughness and strength of titanium trialuminides and magnetic behaviour of unconventionally cold - worked iron aluminides are highlighted. The topic of functional intermetallics is limited to the systems must suitable for hydrogen storage applications. A perspective on the directions of future research and development of intermetallics is also provided. (author)

  8. The universal statistical distributions of the affinity, equilibrium constants, kinetics and specificity in biomolecular recognition.

    Directory of Open Access Journals (Sweden)

    Xiliang Zheng

    2015-04-01

    Full Text Available We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity, the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics.

  9. The primate fovea: Structure, function and development.

    Science.gov (United States)

    Bringmann, Andreas; Syrbe, Steffen; Görner, Katja; Kacza, Johannes; Francke, Mike; Wiedemann, Peter; Reichenbach, Andreas

    2018-03-30

    A fovea is a pitted invagination in the inner retinal tissue (fovea interna) that overlies an area of photoreceptors specialized for high acuity vision (fovea externa). Although the shape of the vertebrate fovea varies considerably among the species, there are two basic types. The retina of many predatory fish, reptilians, and birds possess one (or two) convexiclivate fovea(s), while the retina of higher primates contains a concaviclivate fovea. By refraction of the incoming light, the convexiclivate fovea may function as image enlarger, focus indicator, and movement detector. By centrifugal displacement of the inner retinal layers, which increases the transparency of the central foveal tissue (the foveola), the primate fovea interna improves the quality of the image received by the central photoreceptors. In this review, we summarize ‒ with the focus on Müller cells of the human and macaque fovea ‒ data regarding the structure of the primate fovea, discuss various aspects of the optical function of the fovea, and propose a model of foveal development. The "Müller cell cone" of the foveola comprises specialized Müller cells which do not support neuronal activity but may serve optical and structural functions. In addition to the "Müller cell cone", structural stabilization of the foveal morphology may be provided by the 'z-shaped' Müller cells of the fovea walls, via exerting tractional forces onto Henle fibers. The spatial distribution of glial fibrillary acidic protein may suggest that the foveola and the Henle fiber layer are subjects to mechanical stress. During development, the foveal pit is proposed to be formed by a vertical contraction of the centralmost Müller cells. After widening of the foveal pit likely mediated by retracting astrocytes, Henle fibers are formed by horizontal contraction of Müller cell processes in the outer plexiform layer and the centripetal displacement of photoreceptors. A better understanding of the molecular, cellular

  10. GROMOS++Software for the Analysis of Biomolecular Simulation Trajectories

    NARCIS (Netherlands)

    Eichenberger, A.P.; Allison, J.R.; Dolenc, J.; Geerke, D.P.; Horta, B.A.C.; Meier, K; Oostenbrink, B.C.; Schmid, N.; Steiner, D; Wang, D.; van Gunsteren, W.F.

    2011-01-01

    GROMOS++ is a set of C++ programs for pre- and postprocessing of molecular dynamics simulation trajectories and as such is part of the GROningen MOlecular Simulation software for (bio)molecular simulation. It contains more than 70 programs that can be used to prepare data for the production of

  11. Improvements to the APBS biomolecular solvation software suite.

    Science.gov (United States)

    Jurrus, Elizabeth; Engel, Dave; Star, Keith; Monson, Kyle; Brandi, Juan; Felberg, Lisa E; Brookes, David H; Wilson, Leighton; Chen, Jiahui; Liles, Karina; Chun, Minju; Li, Peter; Gohara, David W; Dolinsky, Todd; Konecny, Robert; Koes, David R; Nielsen, Jens Erik; Head-Gordon, Teresa; Geng, Weihua; Krasny, Robert; Wei, Guo-Wei; Holst, Michael J; McCammon, J Andrew; Baker, Nathan A

    2018-01-01

    The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pK a values, and an improved web-based visualization tool for viewing electrostatics. © 2017 The Protein Society.

  12. Functions and structures of eukaryotic recombination proteins

    International Nuclear Information System (INIS)

    Ogawa, Tomoko

    1994-01-01

    We have found that Rad51 and RecA Proteins form strikingly similar structures together with dsDNA and ATP. Their right handed helical nucleoprotein filaments extend the B-form DNA double helixes to 1.5 times in length and wind the helix. The similarity and uniqueness of their structures must reflect functional homologies between these proteins. Therefore, it is highly probable that similar recombination proteins are present in various organisms of different evolutional states. We have succeeded to clone RAD51 genes from human, mouse, chicken and fission yeast genes, and found that the homologues are widely distributed in eukaryotes. The HsRad51 and MmRad51 or ChRad51 proteins consist of 339 amino acids differing only by 4 or 12 amino acids, respectively, and highly homologous to both yeast proteins, but less so to Dmcl. All of these proteins are homologous to the region from residues 33 to 240 of RecA which was named ''homologous core. The homologous core is likely to be responsible for functions common for all of them, such as the formation of helical nucleoprotein filament that is considered to be involved in homologous pairing in the recombination reaction. The mouse gene is transcribed at a high level in thymus, spleen, testis, and ovary, at lower level in brain and at a further lower level in some other tissues. It is transcribed efficiently in recombination active tissues. A clear functional difference of Rad51 homologues from RecA was suggested by the failure of heterologous genes to complement the deficiency of Scrad51 mutants. This failure seems to reflect the absence of a compatible partner, such as ScRad52 protein in the case of ScRad51 protein, between different species. Thus, these discoveries play a role of the starting point to understand the fundamental gene targeting in mammalian cells and in gene therapy. (J.P.N.)

  13. Structure-function relationships of human meniscus.

    Science.gov (United States)

    Danso, Elvis K; Oinas, Joonas M T; Saarakkala, Simo; Mikkonen, Santtu; Töyräs, Juha; Korhonen, Rami K

    2017-03-01

    Biomechanical properties of human meniscus have been shown to be site-specific. However, it is not known which meniscus constituents at different depths and locations contribute to biomechanical properties obtained from indentation testing. Therefore, we investigated the composition and structure of human meniscus in a site- and depth-dependent manner and their relationships with tissue site-specific biomechanical properties. Elastic and poroelastic properties were analyzed from experimental stress-relaxation and sinusoidal indentation measurements with fibril reinforced poroelastic finite element modeling. Proteoglycan (PG) and collagen contents, as well as the collagen orientation angle, were determined as a function of tissue depth using microscopic and spectroscopic methods, and they were compared with biomechanical properties. For all the measurement sites (anterior, middle and posterior) of lateral and medial menisci (n=26), PG content and collagen orientation angle increased as a function of tissue depth while the collagen content had an initial sharp increase followed by a decrease across tissue depth. The highest values (pmeniscus. This location had also higher (pmeniscus, higher (pmeniscus) significantly higher (pmeniscus modulus and/or nonlinear permeability. This study suggests that nonlinear biomechanical properties of meniscus, caused by the collagen network and fluid, may be strongly influenced by tissue osmotic swelling from the deep meniscus caused by the increased PG content, leading to increased collagen fibril tension. These nonlinear biomechanical properties are suggested to be further amplified by higher collagen content at all tissue depths and superficial collagen fibril orientation. However, these structure-function relationships are suggested to be highly site-specific. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. 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

  15. Photon-photon collisions and photon structure functions at LEP

    CERN Document Server

    Patt, J

    2000-01-01

    The present knowledge of the structure of the photon based on measurements of photon structure functions is discussed. This review covers recent results on QED structure functions and on the hadronic structure function F/sub 2//sup gamma /. (13 refs).

  16. TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

    Science.gov (United States)

    2017-01-01

    Although deep learning approaches have had tremendous success in image, video and audio processing, computer vision, and speech recognition, their applications to three-dimensional (3D) biomolecular structural data sets have been hindered by the geometric and biological complexity. To address this problem we introduce the element-specific persistent homology (ESPH) method. ESPH represents 3D complex geometry by one-dimensional (1D) topological invariants and retains important biological information via a multichannel image-like representation. This representation reveals hidden structure-function relationships in biomolecules. We further integrate ESPH and deep convolutional neural networks to construct a multichannel topological neural network (TopologyNet) for the predictions of protein-ligand binding affinities and protein stability changes upon mutation. To overcome the deep learning limitations from small and noisy training sets, we propose a multi-task multichannel topological convolutional neural network (MM-TCNN). We demonstrate that TopologyNet outperforms the latest methods in the prediction of protein-ligand binding affinities, mutation induced globular protein folding free energy changes, and mutation induced membrane protein folding free energy changes. Availability: weilab.math.msu.edu/TDL/ PMID:28749969

  17. New insights into apoptosome structure and function.

    Science.gov (United States)

    Dorstyn, Loretta; Akey, Christopher W; Kumar, Sharad

    2018-05-15

    The apoptosome is a platform that activates apical procaspases in response to intrinsic cell death signals. Biochemical and structural studies in the past two decades have extended our understanding of apoptosome composition and structure, while illuminating the requirements for initiator procaspase activation. A number of studies have now provided high-resolution structures for apoptosomes from C. elegans (CED-4), D. melanogaster (Dark), and H. sapiens (Apaf-1), which define critical protein interfaces, including intra and interdomain interactions. This work also reveals interactions of apoptosomes with their respective initiator caspases, CED-3, Dronc and procaspase-9. Structures of the human apoptosome have defined the requirements for cytochrome c binding, which triggers the conversion of inactive Apaf-1 molecules to an extended, assembly competent state. While recent data have provided a detailed understanding of apoptosome formation and procaspase activation, they also highlight important evolutionary differences with functional implications for caspase activation. CARD/CARD interactions in the CED-4, Dark and Apaf-1 apoptosomes. Type I, II and III interfaces that stabilize CARD-CARD interactions are indicated (left column). Note that the Type I interface appears to be unique to Apaf-1/pc-9 CARD interactions. Middle column shows cartoons of the active states of the CARD-CARD disks, illustrating the two CED-4 tetrameric ring layers (top) and the recruitment of 8 Dronc CARDs and between 3-4 pc-9 CARDs, to the Dark and Apaf-1 apoptosomes respectively (middle and lower panels). Ribbon diagrams of the CED-4, Dark and Apaf-1 apoptosomes are shown (right column).

  18. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.

    Science.gov (United States)

    van Zundert, G C P; Rodrigues, J P G L M; Trellet, M; Schmitz, C; Kastritis, P L; Karaca, E; Melquiond, A S J; van Dijk, M; de Vries, S J; Bonvin, A M J J

    2016-02-22

    The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  19. A possible form of the pion's structure function

    International Nuclear Information System (INIS)

    Long Ming; Huang Tao

    1986-01-01

    The pion's structure function behaviour is discussed by using the Fock state expansion of the hadronic wave function in QCD in this paper. As an example, we employ a model wave function of the Fock state in the light-cone and assume a Regge behaviour of a weight function for higher Fock states, and we get a possible form of the pion's structure function. This form is consistent with experimental data of the pion's structure function

  20. Structure-Function Relationships of Ferroelectric Polymers.

    Science.gov (United States)

    Pavlopoulou, Eleni; Maiz, Jon; Spampinato, Nicoletta; Maglione, Mario; Hadziioannou, Georges

    Poly(vinylidene fluoride), PVDF, and its copolymers with trifluoroethylene, P(VDF-co-TrFE) have been long appreciated for their excellent ferroelectric properties. Although they have been mainly studied in the 80s and 90s, understanding their performance is still lacking. Yet the increasing use of P(VDF-co-TrFE) thin films in organic electronic devices during the last ten years revives the need for apprehending the function of these materials. In this work we investigate the structure of P(VDF-co-TrFE) films and correlate it to their ferroelectric properties. Our results show that ferroelectric performance is solely driven by the fraction of polymer that has been crystallized in the ferroelectric phases of PVDF. The relations between remnant polarization, coercive field and dipole switching rate of P(VDF-co-TrFE) with the ferroelectric crystallinity are demonstrated. The French Research Agency (ANR), the Aquitaine Region, Arkema and STMicroelectronics are kindly acknowledged for financial support.

  1. Measuring structure functions at SSC energies

    International Nuclear Information System (INIS)

    Morfin, J.G.; Owens, J.F.

    1985-01-01

    Topics discussed include measuring Λ, tests of QCD using hard scattering processes, and measuring parton distributions. In each case, any opportunities and advantages afforded by the unique features of the SSC are emphasized. The working group on structure functions was charged with investigating two specific questions: (1) How well are the various parton distributions known in the kinematic region relevant to calculations for the SSC. (2) What new information can be learned about parton distributions at the SSC. Especially for this working group, the advantages of having a fixed-target facility at the SSC for the measurement of the parton distributions with multi-TeV leptons, were to be examined. 15 references

  2. Engineering intracellular active transport systems as in vivo biomolecular tools.

    Energy Technology Data Exchange (ETDEWEB)

    Bachand, George David; Carroll-Portillo, Amanda

    2006-11-01

    Active transport systems provide essential functions in terms of cell physiology and metastasis. These systems, however, are also co-opted by invading viruses, enabling directed transport of the virus to and from the cell's nucleus (i.e., the site of virus replication). Based on this concept, fundamentally new approaches for interrogating and manipulating the inner workings of living cells may be achievable by co-opting Nature's active transport systems as an in vivo biomolecular tool. The overall goal of this project was to investigate the ability to engineer kinesin-based transport systems for in vivo applications, specifically the collection of effector proteins (e.g., transcriptional regulators) within single cells. In the first part of this project, a chimeric fusion protein consisting of kinesin and a single chain variable fragment (scFv) of an antibody was successfully produced through a recombinant expression system. The kinesin-scFv retained both catalytic and antigenic functionality, enabling selective capture and transport of target antigens. The incorporation of a rabbit IgG-specific scFv into the kinesin established a generalized system for functionalizing kinesin with a wide range of target-selective antibodies raised in rabbits. The second objective was to develop methods of isolating the intact microtubule network from live cells as a platform for evaluating kinesin-based transport within the cytoskeletal architecture of a cell. Successful isolation of intact microtubule networks from two distinct cell types was demonstrated using glutaraldehyde and methanol fixation methods. This work provides a platform for inferring the ability of kinesin-scFv to function in vivo, and may also serve as a three-dimensional scaffold for evaluating and exploiting kinesin-based transport for nanotechnological applications. Overall, the technology developed in this project represents a first-step in engineering active transport system for in vivo

  3. Structure and functionality of bromine doped graphite.

    Science.gov (United States)

    Hamdan, Rashid; Kemper, A F; Cao, Chao; Cheng, H P

    2013-04-28

    First-principles calculations are used to study the enhanced in-plane conductivity observed experimentally in Br-doped graphite, and to study the effect of external stress on the structure and functionality of such systems. The model used in the numerical calculations is that of stage two doped graphite. The band structure near the Fermi surface of the doped systems with different bromine concentrations is compared to that of pure graphite, and the charge transfer between carbon and bromine atoms is analyzed to understand the conductivity change along different high symmetry directions. Our calculations show that, for large interlayer separation between doped graphite layers, bromine is stable in the molecular form (Br2). However, with increased compression (decreased layer-layer separation) Br2 molecules tend to dissociate. While in both forms, bromine is an electron acceptor. The charge exchange between the graphite layers and Br atoms is higher than that with Br2 molecules. Electron transfer to the Br atoms increases the number of hole carriers in the graphite sheets, resulting in an increase of conductivity.

  4. Structure, Function, and Evolution of Rice Centromeres

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Jiming

    2010-02-04

    The centromere is the most characteristic landmark of eukaryotic chromosomes. Centromeres function as the site for kinetochore assembly and spindle attachment, allowing for the faithful pairing and segregation of sister chromatids during cell division. Characterization of centromeric DNA is not only essential to understand the structure and organization of plant genomes, but it is also a critical step in the development of plant artificial chromosomes. The centromeres of most model eukaryotic species, consist predominantly of long arrays of satellite DNA. Determining the precise DNA boundary of a centromere has proven to be a difficult task in multicellular eukaryotes. We have successfully cloned and sequenced the centromere of rice chromosome 8 (Cen8), representing the first fully sequenced centromere from any multicellular eukaryotes. The functional core of Cen8 spans ~800 kb of DNA, which was determined by chromatin immunoprecipitation (ChIP) using an antibody against the rice centromere-specific H3 histone. We discovered 16 actively transcribed genes distributed throughout the Cen8 region. In addition to Cen8, we have characterized eight additional rice centromeres using the next generation sequencing technology. We discovered four subfamilies of the CRR retrotransposon that is highly enriched in rice centromeres. CRR elements are constitutively transcribed and different CRR subfamilies are differentially processed by RNAi. These results suggest that different CRR subfamilies may play different roles in the RNAi-mediated pathway for formation and maintenance of centromeric chromatin.

  5. The Structural and Functional Organisation of Cognition.

    Directory of Open Access Journals (Sweden)

    Peter John Snow

    2016-10-01

    Full Text Available This paper proposes that what have been historically and contemporarily defined as different domains of human cognition are served by one of four functionally- and structurally-distinct areas of the prefrontal cortex. Their contributions to human intelligence are as follows: (a BA9, enables our emotional intelligence, engaging the psychosocial domain, (b BA47, enables our practical intelligence, engaging the material domain, (c BA46 (or BA46-9/46, enables our abstract intelligence, engaging the hypothetical domain and (d BA10, enables our temporal intelligence, engaging in planning within any of the other three domains. Given their unique contribution to human cognition, it is proposed that these areas be called the, social (BA9, material (BA47, abstract (BA46-9/46 and temporal (BA10 mind. The evidence that BA47 participates strongly in verbal and gestural communication suggests that language evolved primarily as a consequence of the extreme selective pressure for practicality; an observation supported by the functional connectivity between BA47 and orbital areas that negatively reinforce lying. It is further proposed that the abstract mind (BA46-9/46 is the primary seat of metacognition charged with creating adaptive behavioral strategies by generating higher-order concepts (hypotheses from lower-order concepts originating both from our perceptual representations and the other three domains of cognition.

  6. ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design.

    Science.gov (United States)

    Wood, Christopher W; Heal, Jack W; Thomson, Andrew R; Bartlett, Gail J; Ibarra, Amaurys Á; Brady, R Leo; Sessions, Richard B; Woolfson, Derek N

    2017-10-01

    The rational design of biomolecules is becoming a reality. However, further computational tools are needed to facilitate and accelerate this, and to make it accessible to more users. Here we introduce ISAMBARD, a tool for structural analysis, model building and rational design of biomolecules. ISAMBARD is open-source, modular, computationally scalable and intuitive to use. These features allow non-experts to explore biomolecular design in silico. ISAMBARD addresses a standing issue in protein design, namely, how to introduce backbone variability in a controlled manner. This is achieved through the generalization of tools for parametric modelling, describing the overall shape of proteins geometrically, and without input from experimentally determined structures. This will allow backbone conformations for entire folds and assemblies not observed in nature to be generated de novo, that is, to access the 'dark matter of protein-fold space'. We anticipate that ISAMBARD will find broad applications in biomolecular design, biotechnology and synthetic biology. A current stable build can be downloaded from the python package index (https://pypi.python.org/pypi/isambard/) with development builds available on GitHub (https://github.com/woolfson-group/) along with documentation, tutorial material and all the scripts used to generate the data described in this paper. d.n.woolfson@bristol.ac.uk or chris.wood@bristol.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  7. The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.

    Directory of Open Access Journals (Sweden)

    Giulio Caravagna

    Full Text Available After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii a model of enzymatic futile cycle and (iii a genetic toggle switch. In (ii and (iii we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.

  8. The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.

    Science.gov (United States)

    Caravagna, Giulio; Mauri, Giancarlo; d'Onofrio, Alberto

    2013-01-01

    After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i) the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii) a model of enzymatic futile cycle and (iii) a genetic toggle switch. In (ii) and (iii) we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.

  9. Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems

    International Nuclear Information System (INIS)

    Zhou, Peipei; Cai, Shuiming; Liu, Zengrong; Chen, Luonan; Wang, Ruiqi

    2013-01-01

    To understand how a complex biomolecular network functions, a decomposition or a reconstruction process of the network is often needed so as to provide new insights into the regulatory mechanisms underlying various dynamical behaviors and also to gain qualitative knowledge of the network. Unfortunately, it seems that there are still no general rules on how to decompose a complex network into simple modules. An alternative resolution is to decompose a complex network into small modules or subsystems with specified functions such as switches and oscillators and then integrate them by analyzing the interactions between them. The main idea of this approach can be illustrated by considering a bidirectionally coupled network in this paper, i.e., coupled Toggle switch and Repressilator, and analyzing the occurrence of various dynamics, although the theoretical principle may hold for a general class of networks. We show that various biomolecular signals can be shaped by regulating the coupling between the subsystems. The approach presented here can be expected to simplify and analyze even more complex biological networks

  10. Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Peipei [Institute of Systems Biology, Shanghai University, Shanghai 200444 (China); Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu 212013 (China); Cai, Shuiming [Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu 212013 (China); Liu, Zengrong [Institute of Systems Biology, Shanghai University, Shanghai 200444 (China); Chen, Luonan [Key Laboratory of Systems Biology, SIBS-Novo Nordisk Translational Research Center for PreDiabetes, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Collaborative Research Center for Innovative Mathematical Modeling, Institute of Industrial Science, University of Tokyo, Tokyo 153-8505 (Japan); Wang, Ruiqi [Institute of Systems Biology, Shanghai University, Shanghai 200444 (China)

    2013-05-15

    To understand how a complex biomolecular network functions, a decomposition or a reconstruction process of the network is often needed so as to provide new insights into the regulatory mechanisms underlying various dynamical behaviors and also to gain qualitative knowledge of the network. Unfortunately, it seems that there are still no general rules on how to decompose a complex network into simple modules. An alternative resolution is to decompose a complex network into small modules or subsystems with specified functions such as switches and oscillators and then integrate them by analyzing the interactions between them. The main idea of this approach can be illustrated by considering a bidirectionally coupled network in this paper, i.e., coupled Toggle switch and Repressilator, and analyzing the occurrence of various dynamics, although the theoretical principle may hold for a general class of networks. We show that various biomolecular signals can be shaped by regulating the coupling between the subsystems. The approach presented here can be expected to simplify and analyze even more complex biological networks.

  11. QCD dipole prediction for dis and diffractive structure functions

    International Nuclear Information System (INIS)

    Royon, CH.

    1996-01-01

    The F 2 , F G , R = F L /F T proton structure functions are derived in the QCD dipole picture of BFKL dynamics. We get a three parameter fit describing the 1994 H1 proton structure function F 2 data in the low x, moderate Q 2 range. Without any additional parameter, the gluon density and the longitudinal structure functions are predicted. The diffractive dissociation processes are also discussed, and a new prediction for the proton diffractive structure function is obtained. (author)

  12. Report on result 1998. Research and development on fusion area. Part 3 (biomolecular mechanism and design); 1998 nendo seika hokokusho. Yugo ryoiki kenkyu kaihatsu daisan bunsatsu (bimolecular mechanism and design)

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-03-01

    An organism is a molecular mechanical system consisting of nucleic acid, peptide and protein having a self-forming and a self-repairing function. For the purpose of creating cells, tissues and molecular mechanism alternating these biological functions, their basic technology was developed. Concretely, studies were made on three-dimensional cellular structural module engineering and biomolecular mechanism and design. Studies on biological soft tissue resulted in success by giving atmospheric glow discharge treatment to the inner surface of a tubular PVC. An artificial vitreous body was created using PVA hydrogels. In addition, liver cells were successfully cultured for the first time in the world. Studies on biological hard tissue revealed that osteopontin plays a role of a trigger for the initial differentiation of the osteoblast cell. Further, a basic experiment was carried out on the initial response of the cartilage cell. In the research on the molecular mechanism, examination was made on the mechanism of a double-head molecular motor. Examination was also made on the adjustment of the hydrogenase LB film as an electricity/hydrogen energy conversion element and on the biomolecular mechanism and design. (NEDO)

  13. QCD predictions for weak neutral current structure functions

    International Nuclear Information System (INIS)

    Wu Jimin

    1987-01-01

    Employing the analytic expression (to the next leading order) for non-singlet component of structure function which the author got from QCD theory and putting recent experiment result of neutral current structure function at Q 2 = 11 (GeV/C) 2 as input, the QCD prediction for neutral current structure function of their scaling violation behaviours was given

  14. An approach to the structure function for nucleon

    International Nuclear Information System (INIS)

    Long Ming

    1986-01-01

    The structure function for nucleon is discussed by using the method given in a previous paper. The formula are compared with the experimental data from low Q 2 to high Q 2 . The results show that the way that the structure function for nucleon can be obtained from the hadronic wavefunction is a possible approach of investigating structure functions for hadron

  15. Crustal Structure beneath Alaska from Receiver Functions

    Science.gov (United States)

    Zhang, Y.; Li, A.

    2017-12-01

    The crustal structure in Alaska has not been well resolved due to the remote nature of much of the state. The USArray Transportable Array (TA), which is operating in Alaska and northwestern Canada, significantly increases the coverage of broadband seismic stations in the region and allows for a more comprehensive study of the crust. We have analyzed P-receiver functions from earthquake data recorded by 76 stations of the TA and AK networks. Both common conversion point (CCP) and H-K methods are used to estimate the mean crustal thickness. The results from the CCP stacking method show that the Denali fault marks a sharp transition from thick crust in the south to thin crust in the north. The thickest crust up to 52 km is located in the St. Elias Range, which has been formed by oblique collision between the Yakutat microplate and North America. A thick crust of 48 km is also observed beneath the eastern Alaska Range. These observations suggest that high topography in Alaska is largely compensated by the thick crust root. The Moho depth ranges from 28 km to 35 km beneath the northern lowlands and increases to 40-45 km under the Books Range. The preliminary crustal thickness from the H-K method generally agrees with that from the CCP stacking with thicker crust beneath high mountain ranges and thinner crust beneath lowlands and basins. However, the offshore part is not well constrained due to the limited coverage of stations. The mean Vp/Vs ratio is around 1.7 in the Yukon-Tanana terrane and central-northern Alaska. The ratio is about 1.9 in central and southern Alaska with higher values at the Alaska Range, Wrangell Mountains, and St. Elias Range. Further data analyses are needed for obtaining more details of the crustal structure in Alaska to decipher the origin and development of different tectonic terranes.

  16. Protein-Ligand Informatics Force Field (PLIff): Toward a Fully Knowledge Driven "Force Field" for Biomolecular Interactions.

    Science.gov (United States)

    Verdonk, Marcel L; Ludlow, R Frederick; Giangreco, Ilenia; Rathi, Prakash Chandra

    2016-07-28

    The Protein Data Bank (PDB) contains a wealth of data on nonbonded biomolecular interactions. If this information could be distilled down to nonbonded interaction potentials, these would have some key advantages over standard force fields. However, there are some important outstanding issues to address in order to do this successfully. This paper introduces the protein-ligand informatics "force field", PLIff, which begins to address these key challenges ( https://bitbucket.org/AstexUK/pli ). As a result of their knowledge-based nature, the next-generation nonbonded potentials that make up PLIff automatically capture a wide range of interaction types, including special interactions that are often poorly described by standard force fields. We illustrate how PLIff may be used in structure-based design applications, including interaction fields, fragment mapping, and protein-ligand docking. PLIff performs at least as well as state-of-the art scoring functions in terms of pose predictions and ranking compounds in a virtual screening context.

  17. Significance tests for functional data with complex dependence structure

    KAUST Repository

    Staicu, Ana-Maria; Lahiri, Soumen N.; Carroll, Raymond J.

    2015-01-01

    We propose an L (2)-norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a

  18. Dendritic Actin Cytoskeleton: Structure, Functions, and Regulations

    Directory of Open Access Journals (Sweden)

    Anja Konietzny

    2017-05-01

    Full Text Available Actin is a versatile and ubiquitous cytoskeletal protein that plays a major role in both the establishment and the maintenance of neuronal polarity. For a long time, the most prominent roles that were attributed to actin in neurons were the movement of growth cones, polarized cargo sorting at the axon initial segment, and the dynamic plasticity of dendritic spines, since those compartments contain large accumulations of actin filaments (F-actin that can be readily visualized using electron- and fluorescence microscopy. With the development of super-resolution microscopy in the past few years, previously unknown structures of the actin cytoskeleton have been uncovered: a periodic lattice consisting of actin and spectrin seems to pervade not only the whole axon, but also dendrites and even the necks of dendritic spines. Apart from that striking feature, patches of F-actin and deep actin filament bundles have been described along the lengths of neurites. So far, research has been focused on the specific roles of actin in the axon, while it is becoming more and more apparent that in the dendrite, actin is not only confined to dendritic spines, but serves many additional and important functions. In this review, we focus on recent developments regarding the role of actin in dendrite morphology, the regulation of actin dynamics by internal and external factors, and the role of F-actin in dendritic protein trafficking.

  19. Retroviral RNA Dimerization: From Structure to Functions

    Directory of Open Access Journals (Sweden)

    Noé Dubois

    2018-03-01

    Full Text Available The genome of the retroviruses is a dimer composed by two homologous copies of genomic RNA (gRNA molecules of positive polarity. The dimerization process allows two gRNA molecules to be non-covalently linked together through intermolecular base-pairing. This step is critical for the viral life cycle and is highly conserved among retroviruses with the exception of spumaretroviruses. Furthermore, packaging of two gRNA copies into viral particles presents an important evolutionary advantage for immune system evasion and drug resistance. Recent studies reported RNA switches models regulating not only gRNA dimerization, but also translation and packaging, and a spatio-temporal characterization of viral gRNA dimerization within cells are now at hand. This review summarizes our current understanding on the structural features of the dimerization signals for a variety of retroviruses (HIVs, MLV, RSV, BLV, MMTV, MPMV…, the mechanisms of RNA dimer formation and functional implications in the retroviral cycle.

  20. Structure and function of DNA polymerase μ

    International Nuclear Information System (INIS)

    Matsumoto, Takuro; Maezawa, So

    2013-01-01

    DNA polymerases are enzymes playing the central role in DNA metabolism, including DNA replication, DNA repair and recombination. DNA polymerase μ (pol μ DNA polymerase λ (pol λ) and terminal deoxynucleotidyltransferase (TdT) in X family DNA polymerases function in non-homologous end-joining (NHEJ), which is the predonmiant repair pathway for DNA double-strand breaks (DSBs). NHEJ involves enzymes that capture both ends of the broken DNA strand, bring them together in a synaptic DNA-protein complex, and repair the DSB. Pol μ and pol λ fill in the gaps at the junction to maintain the genomic integrity. TdT synthesizes N region at the junction during V(D)J recombination and promotes diversity of immunoglobulin or T-cell receptor gene. Among these three polymerases, the regulatory mechanisms of pol μ remain rather unclear. We have approached the mechanism of pol μ from both sides of structure and cellular dynamics. Here, we propose some new insights into pol μ and the probable NHEJ model including our findings. (author)

  1. Neisserial surface lipoproteins: structure, function and biogenesis.

    Science.gov (United States)

    Hooda, Yogesh; Shin, Hyejin E; Bateman, Thomas J; Moraes, Trevor F

    2017-03-01

    The surface of many Gram-negative bacteria contains lipidated protein molecules referred to as surface lipoproteins or SLPs. SLPs play critical roles in host immune evasion, nutrient acquisition and regulation of the bacterial stress response. The focus of this review is on the SLPs present in Neisseria, a genus of bacteria that colonise the mucosal surfaces of animals. Neisseria contains two pathogens of medical interest, namely Neisseria meningitidis and N. gonorrhoeae. Several SLPs have been identified in Neisseria and their study has elucidated key strategies used by these pathogens to survive inside the human body. Herein, we focus on the identification, structure and function of SLPs that have been identified in Neisseria. We also survey the translocation pathways used by these SLPs to reach the cell surface. Specifically, we elaborate on the strategies used by neisserial SLPs to translocate across the outer membrane with an emphasis on Slam, a novel outer membrane protein that has been implicated in SLP biogenesis. Taken together, the study of SLPs in Neisseria illustrates the widespread roles played by this family of proteins in Gram-negative bacteria. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-02

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  3. QCD dipole predictions for DIS and diffractive structure functions

    International Nuclear Information System (INIS)

    Royon, C.

    1997-01-01

    The proton structure function F 2 , the gluon density F G , and the longitudinal structure function F L are derived in the QCD dipole picture of BFKL dynamics. We use a three parameter fit to describe the 1994 H1 proton structure function F 2 data in the low x, moderate Q 2 range. Without any additional parameter, the gluon density and the longitudinal structure functions are predicted. The diffractive dissociation processes are also discussed within the same framework, and a new prediction for the proton diffractive structure function is obtained

  4. 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.

  5. Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

    Directory of Open Access Journals (Sweden)

    Clarisse Gravina Ricci

    2018-02-01

    Full Text Available Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes.

  6. Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

    Science.gov (United States)

    Ricci, Clarisse Gravina; Li, Bo; Cheng, Li-Tien; Dzubiella, Joachim; McCammon, J. Andrew

    2018-01-01

    Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed) solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes. PMID:29484300

  7. Optimal number of coarse-grained sites in different components of large biomolecular complexes.

    Science.gov (United States)

    Sinitskiy, Anton V; Saunders, Marissa G; Voth, Gregory A

    2012-07-26

    The computational study of large biomolecular complexes (molecular machines, cytoskeletal filaments, etc.) is a formidable challenge facing computational biophysics and biology. To achieve biologically relevant length and time scales, coarse-grained (CG) models of such complexes usually must be built and employed. One of the important early stages in this approach is to determine an optimal number of CG sites in different constituents of a complex. This work presents a systematic approach to this problem. First, a universal scaling law is derived and numerically corroborated for the intensity of the intrasite (intradomain) thermal fluctuations as a function of the number of CG sites. Second, this result is used for derivation of the criterion for the optimal number of CG sites in different parts of a large multibiomolecule complex. In the zeroth-order approximation, this approach validates the empirical rule of taking one CG site per fixed number of atoms or residues in each biomolecule, previously widely used for smaller systems (e.g., individual biomolecules). The first-order corrections to this rule are derived and numerically checked by the case studies of the Escherichia coli ribosome and Arp2/3 actin filament junction. In different ribosomal proteins, the optimal number of amino acids per CG site is shown to differ by a factor of 3.5, and an even wider spread may exist in other large biomolecular complexes. Therefore, the method proposed in this paper is valuable for the optimal construction of CG models of such complexes.

  8. Structural and Functional View of Polypharmacology.

    Science.gov (United States)

    Moya-García, Aurelio; Adeyelu, Tolulope; Kruger, Felix A; Dawson, Natalie L; Lees, Jon G; Overington, John P; Orengo, Christine; Ranea, Juan A G

    2017-08-31

    Protein domains mediate drug-protein interactions and this principle can guide the design of multi-target drugs i.e. polypharmacology. In this study, we associate multi-target drugs with CATH functional families through the overrepresentation of targets of those drugs in CATH functional families. Thus, we identify CATH functional families that are currently enriched in drugs (druggable CATH functional families) and we use the network properties of these druggable protein families to analyse their association with drug side effects. Analysis of selected druggable CATH functional families, enriched in drug targets, show that relatives exhibit highly conserved drug binding sites. Furthermore, relatives within druggable CATH functional families occupy central positions in a human protein functional network, cluster together forming network neighbourhoods and are less likely to be within proteins associated with drug side effects. Our results demonstrate that CATH functional families can be used to identify drug-target interactions, opening a new research direction in target identification.

  9. Molecular Models of Genetic and Organismic Structures

    CERN Document Server

    Baianu, I C

    2004-01-01

    In recent studies we showed that the earlier relational theories of organismic sets (Rashevsky,1967), Metabolic-Replication (M,R)-systems (Rosen,1958)and molecular sets (Bartholomay,1968) share a joint foundation that can be studied within a unified categorical framework of functional organismic structures (Baianu,1980. This is possible because all relational theories have a biomolecular basis, that is, complex structures such as genomes, cells,organs and biological organisms are mathematically represented in terms of biomolecular properties and entities,(that are often implicit in their representation axioms. The definition of organismic sets, for example, requires that certain essential quantities be determined from experiment: these are specified by special sets of values of general observables that are derived from physicochemical measurements(Baianu,1970; Baianu,1980; Baianu et al, 2004a.)Such observables are context-dependent and lead directly to natural transformations in categories and Topoi, that are...

  10. Clustering biomolecular complexes by residue contacts similarity

    NARCIS (Netherlands)

    Garcia Lopes Maia Rodrigues, João; Trellet, Mikaël; Schmitz, Christophe; Kastritis, Panagiotis; Karaca, Ezgi; Melquiond, Adrien S J; Bonvin, Alexandre M J J; Garcia Lopes Maia Rodrigues, João

    Inaccuracies in computational molecular modeling methods are often counterweighed by brute-force generation of a plethora of putative solutions. These are then typically sieved via structural clustering based on similarity measures such as the root mean square deviation (RMSD) of atomic positions.

  11. Inorganic pyrophosphatases: structural diversity serving the function

    Science.gov (United States)

    Samygina, V. R.

    2016-05-01

    The review is devoted to ubiquitous enzymes, inorganic pyrophosphatases, which are essential in all living organisms. Despite the long history of investigations, these enzymes continue to attract interest. The review focuses on the three-dimensional structures of various representatives of this class of proteins. The structural diversity, the relationship between the structure and some properties of pyrophosphatases and various mechanisms of enzyme action related to the structural diversity of these enzymes are discussed. Interactions of pyrophosphatase with other proteins and possible practical applications are considered. The bibliography includes 56 references.

  12. Biomolecular System Design: Architecture, Synthesis, and Simulation

    OpenAIRE

    Chiang , Katherine

    2015-01-01

    The advancements in systems and synthetic biology have been broadening the range of realizable systems with increasing complexity both in vitro and in vivo. Systems for digital logic operations, signal processing, analog computation, program flow control, as well as those composed of different functions – for example an on-site diagnostic system based on multiple biomarker measurements and signal processing – have been realized successfully. However, the efforts to date tend to tackle each de...

  13. A Mapping Between Structural and Functional Brain Networks.

    Science.gov (United States)

    Meier, Jil; Tewarie, Prejaas; Hillebrand, Arjan; Douw, Linda; van Dijk, Bob W; Stufflebeam, Steven M; Van Mieghem, Piet

    2016-05-01

    The relationship between structural and functional brain networks is still highly debated. Most previous studies have used a single functional imaging modality to analyze this relationship. In this work, we use multimodal data, from functional MRI, magnetoencephalography, and diffusion tensor imaging, and assume that there exists a mapping between the connectivity matrices of the resting-state functional and structural networks. We investigate this mapping employing group averaged as well as individual data. We indeed find a significantly high goodness of fit level for this structure-function mapping. Our analysis suggests that a functional connection is shaped by all walks up to the diameter in the structural network in both modality cases. When analyzing the inverse mapping, from function to structure, longer walks in the functional network also seem to possess minor influence on the structural connection strengths. Even though similar overall properties for the structure-function mapping are found for different functional modalities, our results indicate that the structure-function relationship is modality dependent.

  14. Nucleon structure functions, resonance form factors, and duality

    International Nuclear Information System (INIS)

    Davidovsky, V.V.; Struminsky, B.V.

    2003-01-01

    The behavior of nucleon structure functions in the resonance region is explored. For form factors that describe resonance production, expressions are obtained that are dependent on the photon virtuality Q 2 , which have a correct threshold behavior, and which take into account available experimental data on resonance decay. Resonance contributions to nucleon structure functions are calculated. The resulting expressions are used to investigate quark-hadron duality in electron-nucleon scattering by taking the example of the structure function F 2

  15. Nuclear enhanced power corrections to DIS structure functions

    OpenAIRE

    Guo, Xiaofeng; Qiu, Jianwei; Zhu, Wei

    2001-01-01

    We calculate nuclear enhanced power corrections to structure functions measured in deeply inelastic lepton-nucleus scattering in Quantum Chromodynamics (QCD). We find that the nuclear medium enhanced power corrections at order of $O(\\alpha_s/Q^2)$ enhance the longitudinal structure function $F_L$, and suppress the transverse structure function $F_1$. We demonstrate that strong nuclear effects in $\\sigma_A/\\sigma_D$ and $R_A/R_D$, recently observed by HERMES Collaboration, can be explained in ...

  16. Types and Functions of Coastal Structures

    DEFF Research Database (Denmark)

    Burcharth, H. F.; A. Hughes, Steven

    2003-01-01

    Coastal structures are used in coastal defence schemes with the objective of preventing shoreline erosion and flooding of the hinterland. Other objectives include sheltering of harbour basins and harbour entrances against waves, stabilization of navigation channels at inlets, and protection...

  17. Structure and function of yeast alcohol dehydrogenase

    Directory of Open Access Journals (Sweden)

    VLADIMIR LESKOVAC

    2000-04-01

    Full Text Available 1. Introduction 2. Isoenzymes of YADH 3. Substrate specificity 4. Kinetic mechanism 5. Primary structure 6. The active site 7. Mutations in the yeast enzyme 8. Chemical mechanism 9. Binding of coenzymes 10. Hydride transfer

  18. Protein Function Prediction Based on Sequence and Structure Information

    KAUST Repository

    Smaili, Fatima Z.

    2016-01-01

    operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching

  19. Relativistic density functional for nuclear structure

    CERN Document Server

    2016-01-01

    This book aims to provide a detailed introduction to the state-of-the-art covariant density functional theory, which follows the Lorentz invariance from the very beginning and is able to describe nuclear many-body quantum systems microscopically and self-consistently. Covariant density functional theory was introduced in nuclear physics in the 1970s and has since been developed and used to describe the diversity of nuclear properties and phenomena with great success. In order to provide an advanced and updated textbook of covariant density functional theory for graduate students and nuclear physics researchers, this book summarizes the enormous amount of material that has accumulated in the field of covariant density functional theory over the last few decades as well as the latest developments in this area. Moreover, the book contains enough details for readers to follow the formalism and theoretical results, and provides exhaustive references to explore the research literature.

  20. Synthesis, Crystal Structure, Density Function Theory, Molecular ...

    African Journals Online (AJOL)

    Tropical Journal of Pharmaceutical Research February 2016; 15 (2): 385-392 ... tested for its antimicrobial activities and computational studies including density function test (DFT) and docking ... agonists [4], selective dopamine D3 and D4 ...

  1. Second-order QCD analysis of the photon structure function

    International Nuclear Information System (INIS)

    Antoniadis, I.; Grunberg, G.

    1983-01-01

    The QCD predictions for the photon structure function are reexamined with particular emphasis on the small-x behavior. A simple parametrization of the real photon structure function, free of 1/x singularity, is derived. The structure function is found to be sensitive at small x to the non-perturbatively calculable constant term in the n=2 moment, and we show that the problem of a negative structure function can be solved on the basis of the knowledge of this single non-perturbative parameter. (orig.)

  2. iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D.

    Science.gov (United States)

    Liluashvili, Vaja; Kalayci, Selim; Fluder, Eugene; Wilson, Manda; Gabow, Aaron; Gümüs, Zeynep H

    2017-08-01

    Visualizations of biomolecular networks assist in systems-level data exploration in many cellular processes. Data generated from high-throughput experiments increasingly inform these networks, yet current tools do not adequately scale with concomitant increase in their size and complexity. We present an open source software platform, interactome-CAVE (iCAVE), for visualizing large and complex biomolecular interaction networks in 3D. Users can explore networks (i) in 3D using a desktop, (ii) in stereoscopic 3D using 3D-vision glasses and a desktop, or (iii) in immersive 3D within a CAVE environment. iCAVE introduces 3D extensions of known 2D network layout, clustering, and edge-bundling algorithms, as well as new 3D network layout algorithms. Furthermore, users can simultaneously query several built-in databases within iCAVE for network generation or visualize their own networks (e.g., disease, drug, protein, metabolite). iCAVE has modular structure that allows rapid development by addition of algorithms, datasets, or features without affecting other parts of the code. Overall, iCAVE is the first freely available open source tool that enables 3D (optionally stereoscopic or immersive) visualizations of complex, dense, or multi-layered biomolecular networks. While primarily designed for researchers utilizing biomolecular networks, iCAVE can assist researchers in any field. © The Authors 2017. Published by Oxford University Press.

  3. Functional and planning structures of education institutions areas

    OpenAIRE

    Соколова, Юлія Віталіївна; Ковальська, Гелена Леонідівна

    2014-01-01

    The article discusses the main aspects of functional and planning organization of the education institutions. The features of the schools stationing in the city structure and its future extension are also defined. The major functional subdivisions are considered and the role of each of it in the education institution structure is investigated. The ratio of the functional zones depending on the specialization of educational institution is determined. The advantages of the functional zone coope...

  4. MRI to assess renal structure and function.

    Science.gov (United States)

    Artunc, Ferruh; Rossi, Cristina; Boss, Andreas

    2011-11-01

    In addition to excellent anatomical depiction, MRI techniques have expanded to study functional aspects of renal physiology, such as renal perfusion, glomerular filtration rate (GFR) or tissue oxygenation. This review will focus on current developments with an emphasis on clinical applicability. The method of GFR determination is largely heterogeneous and still has weaknesses. However, the technique of employing liver disappearance curves has been shown to be accurate in healthy persons and patients with chronic kidney disease. In potential kidney donors, complete evaluation of kidney anatomy and function can be accomplished in a single-stop investigation. Techniques without contrast media can be utilized to measure renal tissue oxygenation (blood oxygen level-dependent MRI) or perfusion (arterial spin labeling) and could aid in the diagnosis and treatment of ischemic renal diseases, such as renal artery stenosis. Diffusion imaging techniques may provide information on spatially restricted water diffusion and tumor cellularity. Functional MRI opens new horizons in studying renal physiology and pathophysiology in vivo. Although extensively utilized in research, labor-intensive postprocessing and lack of standardization currently limit the clinical applicability of functional MRI. Further studies are necessary to evaluate the clinical value of functional magnetic resonance techniques for early discovery and characterization of kidney disease.

  5. Controlling Function and Structure with DNA

    DEFF Research Database (Denmark)

    Tørring, Thomas

    2011-01-01

    and ideas are presented. The second research topic concerns our contributions to the field of DNA origami. This includes investigations of single molecule reactions on a DNA origami platform. The reaction between an amine and an activated ester, as well as the Huisgen-Meldal-Sharpless reaction were...... investigated on a two dimensional DNA origami platform. This was done by incorporating functional groups on the surface of the origami, and reacting these with biotin analogues carrying the complementary functional groups. Successful reactions could then be observed using atomic force microscopy after addition...... of the protein streptavidin. While the implementation of chemical functionalities on origami can be achieved during automated DNA synthesis, this is laborious and costly. In a separate research project we aimed at improving the accessibility by applying an enzymatic labelling method. We demonstrated that the DNA...

  6. Scanning probe and optical tweezer investigations of biomolecular interactions

    International Nuclear Information System (INIS)

    Rigby-Singleton, Shellie

    2002-01-01

    A complex array of intermolecular forces controls the interactions between and within biological molecules. The desire to empirically explore the fundamental forces has led to the development of several biophysical techniques. Of these, the atomic force microscope (AFM) and the optical tweezers have been employed throughout this thesis to monitor the intermolecular forces involved in biomolecular interactions. The AFM is a well-established force sensing technique capable of measuring biomolecular interactions at a single molecule level. However, its versatility has not been extrapolated to the investigation of a drug-enzyme complex. The energy landscape for the force induced dissociation of the DHFR-methotrexate complex was studied. Revealing an energy barrier to dissociation located ∼0.3 nm from the bound state. Unfortunately, the AFM has a limited range of accessible loading rates and in order to profile the complete energy landscape alternative force sensing instrumentation should be considered, for example the BFP and optical tweezers. Thus, this thesis outlines the development and construction an optical trap capable of measuring intermolecular forces between biomolecules at the single molecule level. To demonstrate the force sensing abilities of the optical set up, proof of principle measurements were performed which investigate the interactions between proteins and polymer surfaces subjected to varying degrees of argon plasma treatment. Complementary data was gained from measurements performed independently by the AFM. Changes in polymer resistance to proteins as a response to changes in polymer surface chemistry were detected utilising both AFM and optical tweezers measurements. Finally, the AFM and optical tweezers were employed as ultrasensitive biosensors. Single molecule investigations of the antibody-antigen interaction between the cardiac troponin I marker and its complementary antibody, reveals the impact therapeutic concentrations of heparin have

  7. Nodal Structure of the Electronic Wigner Function

    DEFF Research Database (Denmark)

    Schmider, Hartmut; Dahl, Jens Peder

    1996-01-01

    On the example of several atomic and small molecular systems, the regular behavior of nodal patterns in the electronic one-particle reduced Wigner function is demonstrated. An expression found earlier relates the nodal pattern solely to the dot-product of the position and the momentum vector......, if both arguments are large. An argument analogous to the ``bond-oscillatory principle'' for momentum densities links the nuclear framework in a molecule to an additional oscillatory term in momenta parallel to bonds. It is shown that these are visible in the Wigner function in terms of characteristic...

  8. Connectivity and functional profiling of abnormal brain structures in pedophilia.

    Science.gov (United States)

    Poeppl, Timm B; Eickhoff, Simon B; Fox, Peter T; Laird, Angela R; Rupprecht, Rainer; Langguth, Berthold; Bzdok, Danilo

    2015-06-01

    Despite its 0.5-1% lifetime prevalence in men and its general societal relevance, neuroimaging investigations in pedophilia are scarce. Preliminary findings indicate abnormal brain structure and function. However, no study has yet linked structural alterations in pedophiles to both connectional and functional properties of the aberrant hotspots. The relationship between morphological alterations and brain function in pedophilia as well as their contribution to its psychopathology thus remain unclear. First, we assessed bimodal connectivity of structurally altered candidate regions using meta-analytic connectivity modeling (MACM) and resting-state correlations employing openly accessible data. We compared the ensuing connectivity maps to the activation likelihood estimation (ALE) maps of a recent quantitative meta-analysis of brain activity during processing of sexual stimuli. Second, we functionally characterized the structurally altered regions employing meta-data of a large-scale neuroimaging database. Candidate regions were functionally connected to key areas for processing of sexual stimuli. Moreover, we found that the functional role of structurally altered brain regions in pedophilia relates to nonsexual emotional as well as neurocognitive and executive functions, previously reported to be impaired in pedophiles. Our results suggest that structural brain alterations affect neural networks for sexual processing by way of disrupted functional connectivity, which may entail abnormal sexual arousal patterns. The findings moreover indicate that structural alterations account for common affective and neurocognitive impairments in pedophilia. The present multimodal integration of brain structure and function analyses links sexual and nonsexual psychopathology in pedophilia. © 2015 Wiley Periodicals, Inc.

  9. Synthesis, Crystal Structure, Density Function Theory, Molecular ...

    African Journals Online (AJOL)

    Tropical Journal of Pharmaceutical Research ... Purpose: To determine the exact structure and antimicrobial activity of 2-(3-(4 phenylpiperazin-1-yl) ... Besides HOMO– LUMO energy gap was performed at B3LYP/6-31G (d,p) level of theory.

  10. Enhanced functional and structural domain assignments using

    Indian Academy of Sciences (India)

    Unknown

    using remote similarity detection procedures for proteins encoded in the genome of Mycobacterium tuberculosis H37Rv” (J. Biosci. 29 (3) 245–. 259, 2004) by Seema Namboori, Natasha Mhatre, Sentivel Sujatha,. Narayanaswamy Srinivasan and Shashi Bhushan Pandit. The three-dimensional structure and subcellular ...

  11. The structure of dual Green functions

    International Nuclear Information System (INIS)

    Green, M.B.

    1976-01-01

    A simple relationship between the position space and momentum space singularity structure of off-shell dual amplitudes is exhibited. This scheme is naturally described in terms of amplitudes which couple to the external sources via pairs of 'confined' states. (Auth.)

  12. 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...

  13. Instrumental biosensors: new perspectives for the analysis of biomolecular interactions.

    Science.gov (United States)

    Nice, E C; Catimel, B

    1999-04-01

    The use of instrumental biosensors in basic research to measure biomolecular interactions in real time is increasing exponentially. Applications include protein-protein, protein-peptide, DNA-protein, DNA-DNA, and lipid-protein interactions. Such techniques have been applied to, for example, antibody-antigen, receptor-ligand, signal transduction, and nuclear receptor studies. This review outlines the principles of two of the most commonly used instruments and highlights specific operating parameters that will assist in optimising experimental design, data generation, and analysis.

  14. Application of Hidden Markov Models in Biomolecular Simulations.

    Science.gov (United States)

    Shukla, Saurabh; Shamsi, Zahra; Moffett, Alexander S; Selvam, Balaji; Shukla, Diwakar

    2017-01-01

    Hidden Markov models (HMMs) provide a framework to analyze large trajectories of biomolecular simulation datasets. HMMs decompose the conformational space of a biological molecule into finite number of states that interconvert among each other with certain rates. HMMs simplify long timescale trajectories for human comprehension, and allow comparison of simulations with experimental data. In this chapter, we provide an overview of building HMMs for analyzing bimolecular simulation datasets. We demonstrate the procedure for building a Hidden Markov model for Met-enkephalin peptide simulation dataset and compare the timescales of the process.

  15. Structural and functional properties of designed globins

    Indian Academy of Sciences (India)

    De novo design of artificial proteins is an essential approach to elucidate the principles of protein architecture and to understand specific functions of natural proteins and also to yield novel molecules for medical and industrial aims. We have designed artificial sequences of 153 amino acids to fit the main-chain framework of ...

  16. Loss functions for structural flood mitigation measures

    African Journals Online (AJOL)

    drinie

    2001-01-01

    Jan 1, 2001 ... for spillways, levees, tramlines, public roads, drains and bridges. Introduction. The aim of this paper is to discuss the ... In the third section the steps that were followed to determine loss functions for ... Wilson's Cannal-, 31/2-, Low Level- and Monzi Bridge, are also maintained by the co-operative. A tramline ...

  17. The structure and function of endophilin proteins

    DEFF Research Database (Denmark)

    Kjaerulff, Ole; Brodin, Lennart; Jung, Anita

    2011-01-01

    Members of the BAR domain protein superfamily are essential elements of cellular traffic. Endophilins are among the best studied BAR domain proteins. They have a prominent function in synaptic vesicle endocytosis (SVE), receptor trafficking and apoptosis, and in other processes that require...

  18. Structural and functional imaging: Particularities in children

    International Nuclear Information System (INIS)

    Chiron, C.; Hertz-Pannier, L.; Chiron, C.; Hertz-Pannier, L.; Chiron, C.; Hertz-Pannier, L.

    2008-01-01

    Surgery of partial epilepsies in childhood has largely benefited from the recent advances of imaging techniques, which carry a triple goal: (1) to contribute to the localization of the epilepsy onset zone, (2) to detect and delineate an underlying lesion, and (3) to study the spatial relationship between the epileptogenic zone and the neighboring functional cortex, in order to select patients and plan the resection. This noninvasive pre-surgical imaging workup must be compared to clinical and electrical data to estimate the postoperative prognosis, while invasive techniques such as SEEG, cortical stimulations, and IAT often remain indispensable in difficult cases, i.e., in cryptogenic epilepsies. As in adults, advances in MRI allow us to detect more and more subtle underlying lesions, but this requires repeating MR studies during early childhood and using adapted sequence parameters to account for ongoing myelination. Ictal SPECT and PET imaging prove especially useful in planning depth electrode placement when video-EEG is not contributive, when MRI looks normal or shows multiple abnormalities, or in cases of discrepant findings. Multimodal imaging greatly enhances the sensitivity of all of these techniques. Finally, functional MRI of motor and language functions provide noninvasive cortical mapping of essential functions, using age-adapted paradigms, in cooperating children from age five to six and from IQs around 60. (authors)

  19. Structure, Function, and Training the Rehabilitation Team.

    Science.gov (United States)

    Settles, Robert B.; Crisler, Jack R.

    The traditional team concept in rehabilitation is a differentiated team in which each member performs a different function. In practice, such teams are rarely cooperative and their additive services are disjointed. Presented is the philosophic rationale for the revitalization of a large rehabilitation center serving mental patients. Reorganization…

  20. Structural and functional imaging: Particularities in children

    Energy Technology Data Exchange (ETDEWEB)

    Chiron, C.; Hertz-Pannier, L. [Hop Necker Enfants Malad, INSERM, Serv Neuropediat, U663, F-75015 Paris (France); Chiron, C.; Hertz-Pannier, L. [UnivParis 05, F-75005 Paris (France); Chiron, C.; Hertz-Pannier, L. [CEA, I2BM, Neurospin, SHFJ, F-91191 Orsay (France)

    2008-07-01

    Surgery of partial epilepsies in childhood has largely benefited from the recent advances of imaging techniques, which carry a triple goal: (1) to contribute to the localization of the epilepsy onset zone, (2) to detect and delineate an underlying lesion, and (3) to study the spatial relationship between the epileptogenic zone and the neighboring functional cortex, in order to select patients and plan the resection. This noninvasive pre-surgical imaging workup must be compared to clinical and electrical data to estimate the postoperative prognosis, while invasive techniques such as SEEG, cortical stimulations, and IAT often remain indispensable in difficult cases, i.e., in cryptogenic epilepsies. As in adults, advances in MRI allow us to detect more and more subtle underlying lesions, but this requires repeating MR studies during early childhood and using adapted sequence parameters to account for ongoing myelination. Ictal SPECT and PET imaging prove especially useful in planning depth electrode placement when video-EEG is not contributive, when MRI looks normal or shows multiple abnormalities, or in cases of discrepant findings. Multimodal imaging greatly enhances the sensitivity of all of these techniques. Finally, functional MRI of motor and language functions provide noninvasive cortical mapping of essential functions, using age-adapted paradigms, in cooperating children from age five to six and from IQs around 60. (authors)

  1. The ABC (Analysing Biomolecular Contacts-database

    Directory of Open Access Journals (Sweden)

    Walter Peter

    2007-03-01

    Full Text Available As protein-protein interactions are one of the basic mechanisms in most cellular processes, it is desirable to understand the molecular details of protein-protein contacts and ultimately be able to predict which proteins interact. Interface areas on a protein surface that are involved in protein interactions exhibit certain characteristics. Therefore, several attempts were made to distinguish protein interactions from each other and to categorize them. One way of classification are the groups of transient and permanent interactions. Previously two of the authors analysed several properties for transient complexes such as the amino acid and secondary structure element composition and pairing preferences. Certainly, interfaces can be characterized by many more possible attributes and this is a subject of intense ongoing research. Although several freely available online databases exist that illuminate various aspects of protein-protein interactions, we decided to construct a new database collecting all desired interface features allowing for facile selection of subsets of complexes. As database-server we applied MySQL and the program logic was written in JAVA. Furthermore several class extensions and tools such as JMOL were included to visualize the interfaces and JfreeChart for the representation of diagrams and statistics. The contact data is automatically generated from standard PDB files by a tcl/tk-script running through the molecular visualization package VMD. Currently the database contains 536 interfaces extracted from 479 PDB files and it can be queried by various types of parameters. Here, we describe the database design and demonstrate its usefulness with a number of selected features.

  2. Orbitofrontal cortex function and structure in depression.

    Science.gov (United States)

    Drevets, Wayne C

    2007-12-01

    The orbitofrontal cortex (OFC) has been implicated in the pathophysiology of major depression by evidence obtained using neuroimaging, neuropathologic, and lesion analysis techniques. The abnormalities revealed by these techniques show a regional specificity, and suggest that some OFC regions which appear cytoarchitectonically distinct also are functionally distinct with respect to mood regulation. For example, the severity of depression correlates inversely with physiological activity in parts of the posterior lateral and medial OFC, consistent with evidence that dysfunction of the OFC associated with cerebrovascular lesions increases the vulnerability for developing the major depressive syndrome. The posterior lateral and medial OFC function may also be impaired in individuals who develop primary mood disorders, as these patients show grey-matter volumetric reductions, histopathologic abnormalities, and altered hemodynamic responses to emotionally valenced stimuli, probabilistic reversal learning, and reward processing. In contrast, physiological activity in the anteromedial OFC situated in the ventromedial frontal polar cortex increases during the depressed versus the remitted phases of major depressive disorder to an extent that is positively correlated with the severity of depression. Effective antidepressant treatment is associated with a reduction in activity in this region. Taken together these data are compatible with evidence from studies in experimental animals indicating that some orbitofrontal and medial prefrontal cortex regions function to inhibit, while others function to enhance, emotional expression. Alterations in the functional balance between these regions and the circuits they form with anatomically related areas of the temporal lobe, striatum, thalamus, and brain stem thus may underlie the pathophysiology of mood disorders, such as major depression.

  3. Overcoming the solubility limit with solubility-enhancement tags: successful applications in biomolecular NMR studies

    International Nuclear Information System (INIS)

    Zhou Pei; Wagner, Gerhard

    2010-01-01

    Although the rapid progress of NMR technology has significantly expanded the range of NMR-trackable systems, preparation of NMR-suitable samples that are highly soluble and stable remains a bottleneck for studies of many biological systems. The application of solubility-enhancement tags (SETs) has been highly effective in overcoming solubility and sample stability issues and has enabled structural studies of important biological systems previously deemed unapproachable by solution NMR techniques. In this review, we provide a brief survey of the development and successful applications of the SET strategy in biomolecular NMR. We also comment on the criteria for choosing optimal SETs, such as for differently charged target proteins, and recent new developments on NMR-invisible SETs.

  4. Phosphatidylinositol 4-kinases: Function, structure, and inhibition

    Czech Academy of Sciences Publication Activity Database

    Bouřa, Evžen; Nencka, Radim

    2015-01-01

    Roč. 337, č. 2 (2015), s. 136-145 ISSN 0014-4827 R&D Projects: GA ČR GJ15-21030Y; GA MŠk LO1302; GA ČR GA15-09310S EU Projects: European Commission(XE) 333916 - STARPI4K Institutional support: RVO:61388963 Keywords : phosphatidylinositol 4-kinase * inhibitor * crystal structure * virus Subject RIV: CC - Organic Chemistry Impact factor: 3.378, year: 2015

  5. Nuclear matrix - structure, function and pathogenesis.

    Science.gov (United States)

    Wasąg, Piotr; Lenartowski, Robert

    2016-12-20

    The nuclear matrix (NM), or nuclear skeleton, is the non-chromatin, ribonucleoproteinaceous framework that is resistant to high ionic strength buffers, nonionic detergents, and nucleolytic enzymes. The NM fulfills a structural role in eukaryotic cells and is responsible for maintaining the shape of the nucleus and the spatial organization of chromatin. Moreover, the NM participates in several cellular processes, such as DNA replication/repair, gene expression, RNA transport, cell signaling and differentiation, cell cycle regulation, apoptosis and carcinogenesis. Short nucleotide sequences called scaffold/matrix attachment regions (S/MAR) anchor the chromatin loops to the NM proteins (NMP). The NMP composition is dynamic and depends on the cell type and differentiation stage or metabolic activity. Alterations in the NMP composition affect anchoring of the S/MARs and thus alter gene expression. This review aims to systematize information about the skeletal structure of the nucleus, with particular emphasis on the organization of the NM and its role in selected cellular processes. We also discuss several diseases that are caused by aberrant NM structure or dysfunction of individual NM elements.

  6. Animal Structures and Functions, Science (Experimental): 5314.13.

    Science.gov (United States)

    Silver, Barbara A.

    This unit of instruction was designed to introduce the student to the relationship between structure and function in the animal kingdom, with emphasis given to: (1) the evolution of physiological systems in the major animal phyla, (2) the complementarity of structure and function, and (3) the concept of homeostasis. The booklet lists the relevant…

  7. Soil-Borne Microbial Functional Structure across Different Land Uses

    NARCIS (Netherlands)

    Kuramae, E.E.; Zhou, J.Z.; Kowalchuk, G.A.; van Veen, J.A..

    2014-01-01

    Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate

  8. QCD analysis of structure functions in terms of Jacobi polynomials

    International Nuclear Information System (INIS)

    Krivokhizhin, V.G.; Kurlovich, S.P.; Savin, I.A.; Sidorov, A.V.; Skachkov, N.B.; Sanadze, V.V.

    1987-01-01

    A new method of QCD-analysis of singlet and nonsinglet structure functions based on their expansion in orthogonal Jacobi polynomials is proposed. An accuracy of the method is studied and its application is demonstrated using the structure function F 2 (x,Q 2 ) obtained by the EMC Collaboration from measurements with an iron target. (orig.)

  9. Soil-borne microbial functional structure across different land uses

    NARCIS (Netherlands)

    Kuramae, Eiko E; Zhou, Jizhong Z; Kowalchuk, George A; van Veen, Johannes A

    2014-01-01

    Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate

  10. Comparison of parton distributions and structure functions for the proton

    International Nuclear Information System (INIS)

    Abramowicz, H.; Charchula, K.; Krawczyk, M.; Levy, A.

    1990-09-01

    A comparative study of the most popular parton parametrizations is presented. The individual parton distributions as well as the F 2 structure function are discussed with a particular emphasis on the low x region, 10 -4 -2 . The predictions of these parametrizations for the F 2 structure function have a wide spread which persists also in the HERA kinematical region. (orig.)

  11. The contact activation proteins: a structure/function overview

    NARCIS (Netherlands)

    Meijers, J. C.; McMullen, B. A.; Bouma, B. N.

    1992-01-01

    In recent years, extensive knowledge has been obtained on the structure/function relationships of blood coagulation proteins. In this overview, we present recent developments on the structure/function relationships of the contact activation proteins: factor XII, high molecular weight kininogen,

  12. Brain Structure-function Couplings (FY11)

    Science.gov (United States)

    2012-01-01

    importance of context in the differential engagement of neural resources during task performance (Foerde et al., 2006), and further stressed that to better...sigmoid function. 4.3.3.1 Neural Mass Region State Space Formally, the NMM el is a dynamical system composed of six coupled first-order differential ...8, 1148–1150. Berger, H. Uber das elektrenkephalogramm des menschen. Archiv fur Psychiatrie und Nervenkrankheiten 1929, 87, 527. Börner, K

  13. Galactosaminoglycan Function and Oligosaccharide Structure Determination

    Directory of Open Access Journals (Sweden)

    Daniela G. Seidler

    2007-01-01

    Full Text Available This review will discuss the importance of sequencing long chondroitin sulfate and dermatan sulfate chains specifically derived from decorin. Decorin is a member of the small leucine-rich repeat proteoglycans and ubiquitously expressed primarily in the skin. Sequence information and diverse function of glycosaminoglycans is further influenced by variable expression through the core protein indicating the importance to analyse glycosaminoglycans from specific proteoglycans.

  14. Structure-function relationships during segregated and integrated network states of human brain functional connectivity.

    Science.gov (United States)

    Fukushima, Makoto; Betzel, Richard F; He, Ye; van den Heuvel, Martijn P; Zuo, Xi-Nian; Sporns, Olaf

    2018-04-01

    Structural white matter connections are thought to facilitate integration of neural information across functionally segregated systems. Recent studies have demonstrated that changes in the balance between segregation and integration in brain networks can be tracked by time-resolved functional connectivity derived from resting-state functional magnetic resonance imaging (rs-fMRI) data and that fluctuations between segregated and integrated network states are related to human behavior. However, how these network states relate to structural connectivity is largely unknown. To obtain a better understanding of structural substrates for these network states, we investigated how the relationship between structural connectivity, derived from diffusion tractography, and functional connectivity, as measured by rs-fMRI, changes with fluctuations between segregated and integrated states in the human brain. We found that the similarity of edge weights between structural and functional connectivity was greater in the integrated state, especially at edges connecting the default mode and the dorsal attention networks. We also demonstrated that the similarity of network partitions, evaluated between structural and functional connectivity, increased and the density of direct structural connections within modules in functional networks was elevated during the integrated state. These results suggest that, when functional connectivity exhibited an integrated network topology, structural connectivity and functional connectivity were more closely linked to each other and direct structural connections mediated a larger proportion of neural communication within functional modules. Our findings point out the possibility of significant contributions of structural connections to integrative neural processes underlying human behavior.

  15. A hydrogel-based versatile screening platform for specific biomolecular recognition in a well plate format.

    Science.gov (United States)

    Beer, Meike V; Rech, Claudia; Diederichs, Sylvia; Hahn, Kathrin; Bruellhoff, Kristina; Möller, Martin; Elling, Lothar; Groll, Jürgen

    2012-04-01

    Precise determination of biomolecular interactions in high throughput crucially depends on a surface coating technique that allows immobilization of a variety of interaction partners in a non-interacting environment. We present a one-step hydrogel coating system based on isocyanate functional six-arm poly(ethylene oxide)-based star polymers for commercially available 96-well microtiter plates that combines a straightforward and robust coating application with versatile bio-functionalization. This system generates resistance to unspecific protein adsorption and cell adhesion, as demonstrated with fluorescently labeled bovine serum albumin and primary human dermal fibroblasts (HDF), and high specificity for the assessment of biomolecular recognition processes when ligands are immobilized on this surface. One particular advantage is the wide range of biomolecules that can be immobilized and convert the per se inert coating into a specifically interacting surface. We here demonstrate the immobilization and quantification of a broad range of biochemically important ligands, such as peptide sequences GRGDS and GRGDSK-biotin, the broadly applicable coupler molecule biocytin, the protein fibronectin, and the carbohydrates N-acetylglucosamine and N-acetyllactosamine. A simplified protocol for an enzyme-linked immunosorbent assay was established for the detection and quantification of ligands on the coating surface. Cell adhesion on the peptide and protein-modified surfaces was assessed using HDF. All coatings were applied using a one-step preparation technique, including bioactivation, which makes the system suitable for high-throughput screening in a format that is compatible with the most routinely used testing systems.

  16. Analysis of Lamellar Structures with Application of Generalized Functions

    Directory of Open Access Journals (Sweden)

    Kipiani Gela

    2016-12-01

    Full Text Available Theory of differential equations in respect of the functional area is based on the basic concepts on generalized functions and splines. There are some basic concepts related to the theory of generalized functions and their properties are considered in relation to the rod systems and lamellar structures. The application of generalized functions gives the possibility to effectively calculate step-variable stiffness lamellar structures. There are also widely applied structures, in that several in which a number of parallel load bearing layers are interconnected by discrete-elastic links. For analysis of system under study, such as design diagrams, there are applied discrete and discrete-continual models.

  17. Photon structure functions at small x in holographic QCD

    International Nuclear Information System (INIS)

    Watanabe, Akira; Li, Hsiang-nan

    2015-01-01

    We investigate the photon structure functions at small Bjorken variable x in the framework of the holographic QCD, assuming dominance of the Pomeron exchange. The quasi-real photon structure functions are expressed as convolution of the Brower–Polchinski–Strassler–Tan (BPST) Pomeron kernel and the known wave functions of the U(1) vector field in the five-dimensional AdS space, in which the involved parameters in the BPST kernel have been fixed in previous studies of the nucleon structure functions. The predicted photon structure functions, as confronted with data, provide a clean test of the BPST kernel. The agreement between theoretical predictions and data is demonstrated, which supports applications of holographic QCD to hadronic processes in the nonperturbative region. Our results are also consistent with those derived from the parton distribution functions of the photon proposed by Glück, Reya, and Schienbein, implying realization of the vector meson dominance in the present model setup.

  18. GH62 arabinofuranosidases: Structure, function and applications

    DEFF Research Database (Denmark)

    Wilkens, Casper; Andersen, Susan; Dumon, Claire

    2017-01-01

    Motivated by industrial demands and ongoing scientific discoveries continuous efforts are made to identify and create improved biocatalysts dedicated to plant biomass conversion. α-1,2 and α-1,3 arabinofuranosyl specific α-l-arabinofuranosidases (EC 3.2.1.55) are debranching enzymes catalyzing...... exclusively α-l-arabinofuranosidases and these are of fungal and bacterial origin. Twenty-two GH62 enzymes out of 223 entries in the CAZy database have been characterized and very recently new knowledge was acquired with regard to crystal structures, substrate specificities, and phylogenetics, which overall...

  19. Structure of DNA-Functionalized Dendrimer Nanoparticles

    OpenAIRE

    Kumar, Mattaparthi Venkata Satish; Maiti, Prabal K

    2012-01-01

    Atomistic molecular dynamics simulations have been carried out to reveal the characteristic features of ethylenediamine (EDA) cored protonated poly amido amine (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) that are functionalized with single stranded DNAs (ssDNAs). The four ssDNA strands that are attached via alkythiolate [-S (CH2)6-] linker molecule to the free amine groups on the surface of the PAMAM dendrimers observed to undergo a rapid conformational change during the 25 ns long sim...

  20. Turner syndrome: neuroimaging findings: structural and functional.

    LENUS (Irish Health Repository)

    Mullaney, Ronan

    2009-01-01

    Neuroimaging studies of Turner syndrome can advance our understanding of the X chromosome in brain development, and the modulatory influence of endocrine factors. There is increasing evidence from neuroimaging studies that TX individuals have significant differences in the anatomy, function, and metabolism of a number of brain regions; including the parietal lobe; cerebellum, amygdala, hippocampus; and basal ganglia; and perhaps differences in "connectivity" between frontal and parieto-occipital regions. Finally, there is preliminary evidence that genomic imprinting, sex hormones and growth hormone have significant modulatory effects on brain maturation in TS.

  1. ALTERNATIVAS BIOMOLECULARES EN EL TRATAMIENTO DE LA OBESIDAD

    Directory of Open Access Journals (Sweden)

    Fernando Lizcano

    2010-09-01

    Full Text Available

    Resumen

    La obesidad se ha convertido en un problema de salud pública que cobija tanto a países desarrollados como a aquellos en vía de desarrollo. En la mayoría de los casos las políticas de salud no han tenido el efecto deseado para reducir la prevalencia de esta patología y muchos de los fármacos útiles para contrarrestar la obesidad no han podido continuar en el mercado debido a serios efectos secundarios. Algunas alternativas terapéuticas más agresivas como la cirugías reductivas han demostrado una utilidad restringida. Incluso, recientes observaciones han puesto de manifiesto las consecuencias a largo plazo de este tipo de intervenciones.

    En la búsqueda de nuevas estrategias para el tratamiento de la obesidad se ha investigado, tanto en la propia célula grasa como en los genes que podrían ser modificados y cuya función está enfocada en regular el gasto calórico y la termogénesis adaptativa. Algunos de estos genes son modificados por factores de transcripción que pueden determinar la característica fenotípica de la célula grasa. Recientemente se ha observado que en la persona adulta es posible evidenciar vestigios de célula grasa parda que puede gastar energía en forma de calor y esta modificación podría ser una alternativa terapéutica en la obesidad. Nuestro grupo de investigación ha observado que mediante la modificación de la función de la proteína del retinoblastoma (pRb se pueden aumentar los genes que estimulan la pérdida calórica en el adipocito.

    Palabras clave: Grasa Parda, Obesidad, transcripción, EID1, transdiferenciación

    BIOMOLECULAR OPTIONS IN TREATING OBESITY

    Abstract

    Obesity is a public health issue for both developed and third world countries. Although many efforts have been made to reverse the trend of this prevalent pathology, no results have been obtained with public health policies in most cases. Furthermore, many medicines approved for

  2. Small catalytic RNA: Structure, function and application

    Energy Technology Data Exchange (ETDEWEB)

    Monforte, Joseph Albert [Univ. of California, Berkeley, CA (United States)

    1991-04-01

    We have utilized a combination of photochemical cross-linking techniques and site-directed mutagenesis to obtain secondary and tertiary structure information for the self-cleaving, self-ligating subsequence of RNA from the negative strand of Satellite Tobacco Ringspot Virus. We have found that the helical regions fold about a hinge to promoting four different possible tertiary interactions, creating a molecular of similar shape to a paperclip. A model suggesting that the ``paperclip`` and ``hammerhead`` RNAs share a similar three dimensional structure is proposed. We have used a self-cleaving RNA molecule related to a subsequence of plant viroids, a ``hammerhead,`` to study the length-dependent folding of RNA produced during transcription by RNA polymerase. We have used this method to determine the length of RNA sequestered within elongating E. coli and T7 RNA polymerase complexes. The data show that for E. coli RNA polymerase 121±s are sequestered within the ternary complex, which is consistent with the presence of an RNA-DNA hybrid within the transcription bubble, as proposed by others. The result for T7 RNA polymerase differs from E. coli RNA polymerase, with only 10{plus_minus}1 nucleotides sequestered within the ternary complex, setting a new upper limit for the minimum RNA-DNA required for a stable elongating complex. Comparisons between E. coli and T7 RNA polymerase are made. The relevance of the results to models or transcription termination, abortive initiation, and initiation to elongation mode transitions are discussed.

  3. Photochirogenesis: Photochemical Models on the Origin of Biomolecular Homochirality

    Directory of Open Access Journals (Sweden)

    Cornelia Meinert

    2010-05-01

    Full Text Available Current research focuses on a better understanding of the origin of biomolecular asymmetry by the identification and detection of the possibly first chiral molecules that were involved in the appearance and evolution of life on Earth. We have reasons to assume that these molecules were specific chiral amino acids. Chiral amino acids have been identified in both chondritic meteorites and simulated interstellar ices. Present research reasons that circularly polarized electromagnetic radiation was identified in interstellar environments and an asymmetric interstellar photon-molecule interaction might have triggered biomolecular symmetry breaking. We review on the possible prebiotic interaction of ‘chiral photons’ in the form of circularly polarized light, with early chiral organic molecules. We will highlight recent studies on enantioselective photolysis of racemic amino acids by circularly polarized light and experiments on the asymmetric photochemical synthesis of amino acids from only one C and one N containing molecules by simulating interstellar environments. Both approaches are based on circular dichroic transitions of amino acids that will be presented as well.

  4. Biomolecular logic systems: applications to biosensors and bioactuators

    Science.gov (United States)

    Katz, Evgeny

    2014-05-01

    The paper presents an overview of recent advances in biosensors and bioactuators based on the biocomputing concept. Novel biosensors digitally process multiple biochemical signals through Boolean logic networks of coupled biomolecular reactions and produce output in the form of YES/NO response. Compared to traditional single-analyte sensing devices, biocomputing approach enables a high-fidelity multi-analyte biosensing, particularly beneficial for biomedical applications. Multi-signal digital biosensors thus promise advances in rapid diagnosis and treatment of diseases by processing complex patterns of physiological biomarkers. Specifically, they can provide timely detection and alert to medical emergencies, along with an immediate therapeutic intervention. Application of the biocomputing concept has been successfully demonstrated for systems performing logic analysis of biomarkers corresponding to different injuries, particularly exemplified for liver injury. Wide-ranging applications of multi-analyte digital biosensors in medicine, environmental monitoring and homeland security are anticipated. "Smart" bioactuators, for example for signal-triggered drug release, were designed by interfacing switchable electrodes and biocomputing systems. Integration of novel biosensing and bioactuating systems with the biomolecular information processing systems keeps promise for further scientific advances and numerous practical applications.

  5. Role of biomolecular logic systems in biosensors and bioactuators

    Science.gov (United States)

    Mailloux, Shay; Katz, Evgeny

    2014-09-01

    An overview of recent advances in biosensors and bioactuators based on biocomputing systems is presented. Biosensors digitally process multiple biochemical signals through Boolean logic networks of coupled biomolecular reactions and produce an output in the form of a YES/NO response. Compared to traditional single-analyte sensing devices, the biocomputing approach enables high-fidelity multianalyte biosensing, which is particularly beneficial for biomedical applications. Multisignal digital biosensors thus promise advances in rapid diagnosis and treatment of diseases by processing complex patterns of physiological biomarkers. Specifically, they can provide timely detection and alert medical personnel of medical emergencies together with immediate therapeutic intervention. Application of the biocomputing concept has been successfully demonstrated for systems performing logic analysis of biomarkers corresponding to different injuries, particularly as exemplified for liver injury. Wide-ranging applications of multianalyte digital biosensors in medicine, environmental monitoring, and homeland security are anticipated. "Smart" bioactuators, for signal-triggered drug release, for example, were designed by interfacing switchable electrodes with biocomputing systems. Integration of biosensing and bioactuating systems with biomolecular information processing systems advances the potential for further scientific innovations and various practical applications.

  6. Structural and Functional Plasticity in the Maternal Brain Circuitry

    Science.gov (United States)

    Pereira, Mariana

    2016-01-01

    Parenting recruits a distributed network of brain structures (and neuromodulators) that coordinates caregiving responses attuned to the young's affect, needs, and developmental stage. Many of these structures and connections undergo significant structural and functional plasticity, mediated by the interplay between maternal hormones and social…

  7. Small catalytic RNA: Structure, function and application

    Energy Technology Data Exchange (ETDEWEB)

    Monforte, J.A.

    1991-04-01

    We have utilized a combination of photochemical cross-linking techniques and site-directed mutagenesis to obtain secondary and tertiary structure information for the self-cleaving, self-ligating subsequence of RNA from the negative strand of Satellite Tobacco Ringspot Virus. We have found that the helical regions fold about a hinge to promoting four different possible tertiary interactions, creating a molecular of similar shape to a paperclip. A model suggesting that the paperclip'' and hammerhead'' RNAs share a similar three dimensional structure is proposed. We have used a self-cleaving RNA molecule related to a subsequence of plant viroids, a hammerhead,'' to study the length-dependent folding of RNA produced during transcription by RNA polymerase. We have used this method to determine the length of RNA sequestered within elongating E. coli and T7 RNA polymerase complexes. The data show that for E. coli RNA polymerase 12{plus minus}1 nucleotides are sequestered within the ternary complex, which is consistent with the presence of an RNA-DNA hybrid within the transcription bubble, as proposed by others. The result for T7 RNA polymerase differs from E. coli RNA polymerase, with only 10{plus minus}1 nucleotides sequestered within the ternary complex, setting a new upper limit for the minimum RNA-DNA required for a stable elongating complex. Comparisons between E. coli and T7 RNA polymerase are made. The relevance of the results to models or transcription termination, abortive initiation, and initiation to elongation mode transitions are discussed.

  8. Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models.

    Directory of Open Access Journals (Sweden)

    2005-08-01

    Full Text Available The bias in protein structure and function space resulting from experimental limitations and targeting of particular functional classes of proteins by structural biologists has long been recognized, but never continuously quantified. Using the Enzyme Commission and the Gene Ontology classifications as a reference frame, and integrating structure data from the Protein Data Bank (PDB, target sequences from the structural genomics projects, structure homology derived from the SUPERFAMILY database, and genome annotations from Ensembl and NCBI, we provide a quantified view, both at the domain and whole-protein levels, of the current and projected coverage of protein structure and function space relative to the human genome. Protein structures currently provide at least one domain that covers 37% of the functional classes identified in the genome; whole structure coverage exists for 25% of the genome. If all the structural genomics targets were solved (twice the current number of structures in the PDB, it is estimated that structures of one domain would cover 69% of the functional classes identified and complete structure coverage would be 44%. Homology models from existing experimental structures extend the 37% coverage to 56% of the genome as single domains and 25% to 31% for complete structures. Coverage from homology models is not evenly distributed by protein family, reflecting differing degrees of sequence and structure divergence within families. While these data provide coverage, conversely, they also systematically highlight functional classes of proteins for which structures should be determined. Current key functional families without structure representation are highlighted here; updated information on the "most wanted list" that should be solved is available on a weekly basis from http://function.rcsb.org:8080/pdb/function_distribution/index.html.

  9. Airway structure and function in Eisenmenger's syndrome.

    Science.gov (United States)

    McKay, K O; Johnson, P R; Black, J L; Glanville, A R; Armour, C L

    1998-10-01

    The responsiveness of airways from patients with Eisenmenger's syndrome (n = 5) was compared with that in airways from organ donors (n = 10). Enhanced contractile responses to cholinergic stimulation were found in airways from patients with Eisenmenger's syndrome. The maximal responses to acetylcholine, carbachol, and parasympathetic nerve stimulation in airway tissue from these patients were 221%, 139%, and 152%, respectively, of the maximal responses obtained in donor tissue. Further, relaxation responses to isoproterenol and levocromakalim were absent (n = 2) or markedly impaired (n = 3) in airways from patients with Eisenmenger's syndrome. This attenuated relaxation response was nonspecific in that it was also absent after vasoactive intestinal peptide, sodium nitroprusside, papaverine, and electrical field application. These observations can most likely be explained by a decrease in intrinsic smooth muscle tone, as precontraction of airways revealed relaxation responses that were equivalent to those obtained in donor tissues. Morphometric analysis of tissues used for the functional studies revealed no differences in the airway dimensions (internal perimeter) or airway wall components (e.g., smooth muscle, cartilage) or total area to explain these observations. Although the mechanism for this observed decrease in intrinsic airway smooth muscle tone is not certain, it may be due to alteration in the substructure of the airway wall or, alternatively, may result from the continued release of depressant factors in the vicinity of the smooth muscle which permanently alters smooth muscle responsiveness.

  10. A structural self-regulation of functioning macromolecules

    International Nuclear Information System (INIS)

    Khristoforov, L.N.

    1998-01-01

    An approach to describing the functional structural changes of macromolecules processing the flows of low-mass agents is formulated. The latter appear as a source of a discrete noise whose defining parameters depend on structural variables. We derive a forward evolution equation and then, by adiabatic elimination, effective Fokker-Planck's equation for the structural modes. Within the dichotomous case, we discuss noise-induced nonequilibrium phase transitions reflecting the regulatory role of the structural subsystem

  11. Pair distribution function and structure factor of spherical particles

    International Nuclear Information System (INIS)

    Howell, Rafael C.; Proffen, Thomas; Conradson, Steven D.

    2006-01-01

    The availability of neutron spallation-source instruments that provide total scattering powder diffraction has led to an increased application of real-space structure analysis using the pair distribution function. Currently, the analytical treatment of finite size effects within pair distribution refinement procedures is limited. To that end, an envelope function is derived which transforms the pair distribution function of an infinite solid into that of a spherical particle with the same crystal structure. Distributions of particle sizes are then considered, and the associated envelope function is used to predict the particle size distribution of an experimental sample of gold nanoparticles from its pair distribution function alone. Finally, complementing the wealth of existing diffraction analysis, the peak broadening for the structure factor of spherical particles, expressed as a convolution derived from the envelope functions, is calculated exactly for all particle size distributions considered, and peak maxima, offsets, and asymmetries are discussed

  12. Significance tests for functional data with complex dependence structure.

    Science.gov (United States)

    Staicu, Ana-Maria; Lahiri, Soumen N; Carroll, Raymond J

    2015-01-01

    We propose an L 2 -norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a multilevel structure of the form groups-clusters or subjects-units, where the unit-level profiles are spatially correlated within the cluster, and the cluster-level data are independent. Orthogonal series expansions are used to approximate the group mean functions and the test statistic is estimated using the basis coefficients. The asymptotic null distribution of the test statistic is developed, under mild regularity conditions. To our knowledge this is the first work that studies hypothesis testing, when data have such complex multilevel functional and spatial structure. Two small-sample alternatives, including a novel block bootstrap for functional data, are proposed, and their performance is examined in simulation studies. The paper concludes with an illustration of a motivating experiment.

  13. Significance tests for functional data with complex dependence structure

    KAUST Repository

    Staicu, Ana-Maria

    2015-01-01

    We propose an L (2)-norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a multilevel structure of the form groups-clusters or subjects-units, where the unit-level profiles are spatially correlated within the cluster, and the cluster-level data are independent. Orthogonal series expansions are used to approximate the group mean functions and the test statistic is estimated using the basis coefficients. The asymptotic null distribution of the test statistic is developed, under mild regularity conditions. To our knowledge this is the first work that studies hypothesis testing, when data have such complex multilevel functional and spatial structure. Two small-sample alternatives, including a novel block bootstrap for functional data, are proposed, and their performance is examined in simulation studies. The paper concludes with an illustration of a motivating experiment.

  14. Cellular regulation of the structure and function of aortic valves

    Directory of Open Access Journals (Sweden)

    Ismail El-Hamamsy

    2010-01-01

    Full Text Available The aortic valve was long considered a passive structure that opens and closes in response to changes in transvalvular pressure. Recent evidence suggests that the aortic valve performs highly sophisticated functions as a result of its unique microscopic structure. These functions allow it to adapt to its hemodynamic and mechanical environment. Understanding the cellular and molecular mechanisms involved in normal valve physiology is essential to elucidate the mechanisms behind valve disease. We here review the structure and developmental biology of aortic valves; we examine the role of its cellular parts in regulating its function and describe potential pathophysiological and clinical implications.

  15. Deep inelastic structure functions in the chiral bag model

    International Nuclear Information System (INIS)

    Sanjose, V.; Vento, V.; Centro Mixto CSIC/Valencia Univ., Valencia

    1989-01-01

    We calculate the structure functions for deep inelastic scattering on baryons in the cavity approximation to the chiral bag model. The behavior of these structure functions is analyzed in the Bjorken limit. We conclude that scaling is satisfied, but not Regge behavior. A trivial extension as a parton model can be achieved by introducing the structure function for the pion in a convolution picture. In this extended version of the model not only scaling but also Regge behavior is satisfied. Conclusions are drawn from the comparison of our results with experimental data. (orig.)

  16. Deep inelastic structure functions in the chiral bag model

    Energy Technology Data Exchange (ETDEWEB)

    Sanjose, V. (Valencia Univ. (Spain). Dept. de Didactica de las Ciencias Experimentales); Vento, V. (Valencia Univ. (Spain). Dept. de Fisica Teorica; Centro Mixto CSIC/Valencia Univ., Valencia (Spain). Inst. de Fisica Corpuscular)

    1989-10-02

    We calculate the structure functions for deep inelastic scattering on baryons in the cavity approximation to the chiral bag model. The behavior of these structure functions is analyzed in the Bjorken limit. We conclude that scaling is satisfied, but not Regge behavior. A trivial extension as a parton model can be achieved by introducing the structure function for the pion in a convolution picture. In this extended version of the model not only scaling but also Regge behavior is satisfied. Conclusions are drawn from the comparison of our results with experimental data. (orig.).

  17. MODY - calculation of ordered structures by symmetry-adapted functions

    Science.gov (United States)

    Białas, Franciszek; Pytlik, Lucjan; Sikora, Wiesława

    2016-01-01

    In this paper we focus on the new version of computer program MODY for calculations of symmetryadapted functions based on the theory of groups and representations. The choice of such a functional frame of coordinates for description of ordered structures leads to a minimal number of parameters which must be used for presentation of such structures and investigations of their properties. The aim of this work is to find those parameters, which are coefficients of a linear combination of calculated functions, leading to construction of different types of structure ordering with a given symmetry. A spreadsheet script for simplification of this work has been created and attached to the program.

  18. Deep inelastic singlet structure functions and scaling violation

    Energy Technology Data Exchange (ETDEWEB)

    Wen-zhu, Li; Bing-xun, Hu

    1984-02-01

    The flavour singlet structure functions of deep inelastic scattering processes can yield more decisive tests of QCD than the non-singlet. We give analytical expression for flavour singlet structure functions through analysing the lepton-nucleon deep inelastic scattering processes by means of QCD and using Jacobi polynomials. This expression contains 4 to 5 parameters and shows the changes of the singlet structure functions with x and Q/sup 2/ very well. In QCD leading order, the conclusion is in reasonable agreement with experimental data.

  19. Characterization of technical surfaces by structure function analysis

    Science.gov (United States)

    Kalms, Michael; Kreis, Thomas; Bergmann, Ralf B.

    2018-03-01

    The structure function is a tool for characterizing technical surfaces that exhibits a number of advantages over Fourierbased analysis methods. So it is optimally suited for analyzing the height distributions of surfaces measured by full-field non-contacting methods. The structure function is thus a useful method to extract global or local criteria like e. g. periodicities, waviness, lay, or roughness to analyze and evaluate technical surfaces. After the definition of line- and area-structure function and offering effective procedures for their calculation this paper presents examples using simulated and measured data of technical surfaces including aircraft parts.

  20. Generalized fluid impulse functions for oscillating marine structures

    Science.gov (United States)

    Janardhanan, K.; Price, W. G.; Wu, Y.

    1992-03-01

    A selection of generalized impulse response functions is presented for a variety of rigid and flexible marine structures (i.e. mono-hull, SWATH, floating drydock and twin dock, fixed flexible pile). These functions are determined from calculated and experimental frequency-dependent hydrodynamic data, and the characteristics of these data depend on the type of structure considered. This information is reflected in the shape and duration of the generalized impulse response functions which are pre-requisites for a generalized integro-differential mathematical model describing the dynamic behaviour of the structures to seaway excitation.

  1. Factor structure of functional state of primary school age children

    Directory of Open Access Journals (Sweden)

    Davidenko O.V.

    2011-02-01

    Full Text Available The examination of primary school children to determine the ranking of significant factors that determine the structure of their functional state depending on the level of physical health. It is shown that the main factor in the structure of the functional state of younger schoolchildren in low-and lower-middle level of physical fitness is selected morpho-functional status, which characterizes the functions of the body at rest. For children with average or above average level of physical fitness is a leading factor in physical fitness of schoolchildren.

  2. Extinction order and altered community structure rapidly disrupt ecosystem functioning.

    Science.gov (United States)

    Larsen, Trond H; Williams, Neal M; Kremen, Claire

    2005-05-01

    By causing extinctions and altering community structure, anthropogenic disturbances can disrupt processes that maintain ecosystem integrity. However, the relationship between community structure and ecosystem functioning in natural systems is poorly understood. Here we show that habitat loss appeared to disrupt ecosystem functioning by affecting extinction order, species richness and abundance. We studied pollination by bees in a mosaic of agricultural and natural habitats in California and dung burial by dung beetles on recently created islands in Venezuela. We found that large-bodied bee and beetle species tended to be both most extinction-prone and most functionally efficient, contributing to rapid functional loss. Simulations confirmed that extinction order led to greater disruption of function than predicted by random species loss. Total abundance declined with richness and also appeared to contribute to loss of function. We demonstrate conceptually and empirically how the non-random response of communities to disturbance can have unexpectedly large functional consequences.

  3. Towards a lattice calculation of the nucleon structure functions

    International Nuclear Information System (INIS)

    Goeckeler, M.; Ilgenfritz, M.; Perlt, H.; Rakow, P.; Schierholz, G.; Forschungszentrum Juelich GmbH; Schiller, A.

    1994-12-01

    We have initiated a programme to compute the lower moments of the unpolarised and polarised deep inelastic structure functions of the nucleon in the quenched approxiation. We review our progress to date. (orig.)

  4. Personification in discourse: linguistic forms, conceptual structures and communicative functions.

    NARCIS (Netherlands)

    Dorst, A.G.

    2011-01-01

    Drawing on examples from a corpus of 14 excerpts from novels, this article aims to present a systematic investigation of the different linguistic forms, conceptual structures and communicative functions of personification in discourse. The Metaphor Identification Procedure (Pragglejaz Group, 2007)

  5. Analysis of the Changing Functional Structure of Major Urban ...

    African Journals Online (AJOL)

    user

    Changes in Urban Functional Structure in Ethiopia. EJBE Vol. ... primary engines of economic growth, social wellbeing, centers of creativity, innovation and ... economic as well as commercial and business activities were confined to the capital ...

  6. Simulation of Protein Structure, Dynamics and Function in Organic Media

    National Research Council Canada - National Science Library

    Daggett, Valerie

    1998-01-01

    The overall goal of our ONR-sponsored research is to pursue realistic molecular modeling strudies pertinnent to the related properties of protein stability, dynamics, structure, function, and folding in aqueous solution...

  7. Nonlinear correction to the longitudinal structure function at small x

    International Nuclear Information System (INIS)

    Boroun, G.R.

    2010-01-01

    We computed the longitudinal proton structure function F L , using the nonlinear Dokshitzer-Gribov-Lipatov-Altarelli-Parisi (NLDGLAP) evolution equation approach at small x. For the gluon distribution, the nonlinear effects are related to the longitudinal structure function. As the very small-x behavior of the gluon distribution is obtained by solving the Gribov, Levin, Ryskin, Mueller and Qiu (GLR-MQ) evolution equation with the nonlinear shadowing term incorporated, we show that the strong rise that corresponds to the linear QCD evolution equations can be tamed by screening effects. Consequently, the obtained longitudinal structure function shows a tamed growth at small x. We computed the predictions for all details of the nonlinear longitudinal structure function in the kinematic range where it has been measured by the H1 Collaboration and made comparisons with the computation by Moch, Vermaseren and Vogt at the second order with input data from the MRST QCD fit. (orig.)

  8. Structure functions in electron-nucleon deep inelastic scattering

    Energy Technology Data Exchange (ETDEWEB)

    Saleem, M.; Fazal-E-Aleem (University of the Punjab, Lahore (Pakistan). Dept. of Physics)

    1982-06-26

    The phenomenological expressions for the structure functions in electron-nucleon deep inelastic scattering are proposed and are shown to satisfy the experimental data as well as a number of sum rules.

  9. Conflict between object structural and functional affordances in peripersonal space.

    Science.gov (United States)

    Kalénine, Solène; Wamain, Yannick; Decroix, Jérémy; Coello, Yann

    2016-10-01

    Recent studies indicate that competition between conflicting action representations slows down planning of object-directed actions. The present study aims to assess whether similar conflict effects exist during manipulable object perception. Twenty-six young adults performed reach-to-grasp and semantic judgements on conflictual objects (with competing structural and functional gestures) and non-conflictual objects (with similar structural and functional gestures) presented at difference distances in a 3D virtual environment. Results highlight a space-dependent conflict between structural and functional affordances. Perceptual judgments on conflictual objects were slower that perceptual judgments on non-conflictual objects, but only when objects were presented within reach. Findings demonstrate that competition between structural and functional affordances during object perception induces a processing cost, and further show that object position in space can bias affordance competition. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Left ventricular structure and function in black normotensive type 2 ...

    African Journals Online (AJOL)

    Keywords: Black normotensive patients, left ventricular function, type 2 DM. Résumé ... sickle cell disease and structural heart disease were excluded ... Pulmonary venous flow (PVF) velocity ... had abnormal ECG pattern compared with 30%.

  11. Experimental investigation of Lagrangian structure functions in turbulence

    DEFF Research Database (Denmark)

    Berg, Jacob; Ott, Søren; Mann, Jakob

    2009-01-01

    Lagrangian properties obtained from a particle tracking velocimetry experiment in a turbulent flow at intermediate Reynolds number are presented. Accurate sampling of particle trajectories is essential in order to obtain the Lagrangian structure functions and to measure intermittency at small...

  12. Kinetic-energy density functional: Atoms and shell structure

    International Nuclear Information System (INIS)

    Garcia-Gonzalez, P.; Alvarellos, J.E.; Chacon, E.

    1996-01-01

    We present a nonlocal kinetic-energy functional which includes an anisotropic average of the density through a symmetrization procedure. This functional allows a better description of the nonlocal effects of the electron system. The main consequence of the symmetrization is the appearance of a clear shell structure in the atomic density profiles, obtained after the minimization of the total energy. Although previous results with some of the nonlocal kinetic functionals have given incipient structures for heavy atoms, only our functional shows a clear shell structure for most of the atoms. The atomic total energies have a good agreement with the exact calculations. Discussion of the chemical potential and the first ionization potential in atoms is included. The functional is also extended to spin-polarized systems. copyright 1996 The American Physical Society

  13. Small-x Resummation and HERA Structure Function Data

    CERN Document Server

    Altarelli, Guido; Forte, Stefano; Altarelli, Guido; Ball, Richard D.; Forte, Stefano

    2001-01-01

    We apply our systematic NLO small x resummation of singlet splitting functions to the scaling violations of structure functions and compare the results with data. We develop various theoretical tools which are needed in order to relate resummed parton distributions to measurable structure functions, and we present results from a variety of fits to HERA data for the structure functions F_2 and F_L using the resummation. The behaviour of the singlet splitting functions at small x and fixed Q^2 is effectively parametrized as x^{-lambda}. We find that, for lambda small or negative, the resummed description of scaling violations may be phenomenologically as good as or even better than the standard next-to-leading order treatment. However, the best fit gluon density and value of alpha_s can be significantly modified by the resummation.

  14. Proton structure functions in the dipole picture of BFKL dynamics

    International Nuclear Information System (INIS)

    Navelet, H.; Peschanski, R.; Wallon, S.; Royon, Ch.

    1996-06-01

    The proton structure functions are derived in the QCD dipole picture. Assuming k T and renormalization-group factorization, deep-inelastic proton scattering is related to deep-inelastic onium scattering. A three parameter fit of the 1994 H1 data in the low-x, moderate Q 2 range has been obtained. The dipole picture of BFKL dynamics is shown to provide a relevant model for quantitatively describing the proton structure functions at HERA. (author)

  15. An introduction about precise measurements of QED γ structure functions

    International Nuclear Information System (INIS)

    Courau, A.

    1989-11-01

    Pure QED processes are theoretically exactly computable. However precise measurements and theoretical expectations of QED γ structure functions within a given experimental acceptance are not so trivial. Yet such a study is quite interesting. It supplies on the one hand a good QED test and, on the other hand, a good exercise for testing the procedure used for the determination of the hadronic γ structure functions

  16. A knowledge representation view on biomedical structure and function.

    Science.gov (United States)

    Schulz, Stefan; Hahn, Udo

    2002-01-01

    In biomedical ontologies, structural and functional considerations are of outstanding importance, and concepts which belong to these two categories are highly interdependent. At the representational level both axes must be clearly kept separate in order to support disciplined ontology engineering. Furthermore, the biaxial organization of physical structure (both by a taxonomic and partonomic order) entails intricate patterns of inference. We here propose a layered encoding of taxonomic, partonomic and functional aspects of biomedical concepts using description logics. PMID:12463912

  17. The photon structure function at large Q2

    International Nuclear Information System (INIS)

    Cordier, A.

    1987-01-01

    LEP II offers the unique opportunity to measure the photon structure function over a large Q 2 range up to ∼ 2000 GeV 2 . Two crucial predictions of QCD can be tested in this experiment: the linear rise in log Q 2 as a consequence of asymptotic freedom, and the large renormalization O(1) of the shape of the structure function due to gluon bremsstrahlung, unperturbed by higher-twist effects

  18. Structural and functional correlates of epileptogenesis — Does gender matter?

    Science.gov (United States)

    Savic, Ivanka; Engel, Jerome

    2016-01-01

    In the majority of neuropsychiatric conditions, marked gender-based differences have been found in the epidemiology, clinical manifestations, and therapy of disease. One possible reason is that sex differences in cerebral morphology, structural and functional connections, render men and women differentially vulnerable to various disease processes. The present review addresses this issue with respect to the functional and structural correlates to some forms of epilepsy. PMID:24943053

  19. Discerning molecular interactions: A comprehensive review on biomolecular interaction databases and network analysis tools.

    Science.gov (United States)

    Miryala, Sravan Kumar; Anbarasu, Anand; Ramaiah, Sudha

    2018-02-05

    Computational analysis of biomolecular interaction networks is now gaining a lot of importance to understand the functions of novel genes/proteins. Gene interaction (GI) network analysis and protein-protein interaction (PPI) network analysis play a major role in predicting the functionality of interacting genes or proteins and gives an insight into the functional relationships and evolutionary conservation of interactions among the genes. An interaction network is a graphical representation of gene/protein interactome, where each gene/protein is a node, and interaction between gene/protein is an edge. In this review, we discuss the popular open source databases that serve as data repositories to search and collect protein/gene interaction data, and also tools available for the generation of interaction network, visualization and network analysis. Also, various network analysis approaches like topological approach and clustering approach to study the network properties and functional enrichment server which illustrates the functions and pathway of the genes and proteins has been discussed. Hence the distinctive attribute mentioned in this review is not only to provide an overview of tools and web servers for gene and protein-protein interaction (PPI) network analysis but also to extract useful and meaningful information from the interaction networks. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Perspective: Markov models for long-timescale biomolecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Schwantes, C. R.; McGibbon, R. T. [Department of Chemistry, Stanford University, Stanford, California 94305 (United States); Pande, V. S., E-mail: pande@stanford.edu [Department of Chemistry, Stanford University, Stanford, California 94305 (United States); Department of Computer Science, Stanford University, Stanford, California 94305 (United States); Department of Structural Biology, Stanford University, Stanford, California 94305 (United States); Biophysics Program, Stanford University, Stanford, California 94305 (United States)

    2014-09-07

    Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is insufficient, as researchers must be able to transform the data in a simulation trajectory into specific scientific insights. Although this analysis step has often been taken for granted, it deserves further attention as large-scale simulations become increasingly routine. In this perspective, we discuss the application of Markov models to the analysis of large-scale biomolecular simulations. We draw attention to recent improvements in the construction of these models as well as several important open issues. In addition, we highlight recent theoretical advances that pave the way for a new generation of models of molecular kinetics.

  1. Techniques of biomolecular quantification through AMS detection of radiocarbon

    International Nuclear Information System (INIS)

    Vogel, S.J.; Turteltaub, K.W.; Frantz, C.; Felton, J.S.; Gledhill, B.L.

    1992-01-01

    Accelerator mass spectrometry offers a large gain over scintillation counting in sensitivity for detecting radiocarbon in biomolecular tracing. Application of this sensitivity requires new considerations of procedures to extract or isolate the carbon fraction to be quantified, to inventory all carbon in the sample, to prepare graphite from the sample for use in the spectrometer, and to derive a meaningful quantification from the measured isotope ratio. These procedures need to be accomplished without contaminating the sample with radiocarbon, which may be ubiquitous in laboratories and on equipment previously used for higher dose, scintillation experiments. Disposable equipment, materials and surfaces are used to control these contaminations. Quantification of attomole amounts of labeled substances are possible through these techniques

  2. Perspective: Markov models for long-timescale biomolecular dynamics

    International Nuclear Information System (INIS)

    Schwantes, C. R.; McGibbon, R. T.; Pande, V. S.

    2014-01-01

    Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is insufficient, as researchers must be able to transform the data in a simulation trajectory into specific scientific insights. Although this analysis step has often been taken for granted, it deserves further attention as large-scale simulations become increasingly routine. In this perspective, we discuss the application of Markov models to the analysis of large-scale biomolecular simulations. We draw attention to recent improvements in the construction of these models as well as several important open issues. In addition, we highlight recent theoretical advances that pave the way for a new generation of models of molecular kinetics

  3. Structure functions of hadrons in the QCD effective theory

    International Nuclear Information System (INIS)

    Shigetani, Takayuki

    1996-01-01

    We study the structure functions of hadrons with the low energy effective theory of QCD. We try to clarify a link between the low energy effective theory, where non-perturbative dynamics is essential, and the high energy deep inelastic scattering experiment. We calculate the leading twist matrix elements of the structure function at the low energy model scale within the effective theory. Calculated structure functions are evoluted to the high momentum scale with the help of the perturbative QCD, and compared with the experimental data. Through the comparison of the model calculations with the experiment, we discuss how the non-perturbative dynamics of the effective theory is reflected in the deep inelastic phenomena. We first evaluate the structure functions of the pseudoscalar mesons using the NJL model. The resulting structure functions show reasonable agreements with experiments. We study then the quark distribution functions of the nucleon using a covariant quark-diquark model. We calculate three leading twist distribution functions, spin-independent f 1 (x), longitudinal spin distribution g 1 (x), and chiral-odd transversity spin distribution h 1 (x). The results for f 1 (x) and g 1 (x) turn out to be consistent with available experiments because of the strong spin-0 diquark correlation. (author)

  4. A density functional study of backbone structures of polydiacetylene: destabilization of butatriene structure

    International Nuclear Information System (INIS)

    Katagiri, Hideki; Shimoi, Yukihiro; Abe, Shuji

    2004-01-01

    Backbone structures of polydiacetylene are studied with first-principles electronic structure method using plane-waves within generalized gradient approximation (GGA) of density functional theory. In spin-restricted calculations a coarse k-point sampling gives a potential energy curve with two local minima corresponding to acetylene and butatriene structures. However, the potential barrier between the two structures rapidly decreases with increasing number of k-points, which results in destabilization of the butatriene structure. Spin polarization effects also destabilize the butatriene structure, inducing atom-centered spin-density-wave state. These potential energies were compared with those obtained by Hartree-Fock, density functional within local density approximation (LDA) and GGA, and hybrid density functional methods using a gaussian basis set. The comparison shows that the density functional methods within LDA and GGA favor the destabilization of the butatriene structure in contrast to the Hartree-Fock method

  5. Myoglobin Structure and Function: A Multiweek Biochemistry Laboratory Project

    Science.gov (United States)

    Silverstein, Todd P.; Kirk, Sarah R.; Meyer, Scott C.; Holman, Karen L. McFarlane

    2015-01-01

    We have developed a multiweek laboratory project in which students isolate myoglobin and characterize its structure, function, and redox state. The important laboratory techniques covered in this project include size-exclusion chromatography, electrophoresis, spectrophotometric titration, and FTIR spectroscopy. Regarding protein structure,…

  6. Heme isomers substantially affect heme's electronic structure and function

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta

    2017-01-01

    Inspection of heme protein structures in the protein data bank reveals four isomers of heme characterized by different relative orientations of the vinyl side chains; remarkably, all these have been reported in multiple protein structures. Density functional theory computations explain this as du...

  7. Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

    Science.gov (United States)

    Lorenz, William A.; Clote, Peter

    2011-01-01

    An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in time and space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1) the number of locally optimal structures is far fewer than the total number of structures – indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2) the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3) the (modified) maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model) can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy. Web server

  8. Computing the partition function for kinetically trapped RNA secondary structures.

    Directory of Open Access Journals (Sweden)

    William A Lorenz

    Full Text Available An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in O(n3 time and O(n2 space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1 the number of locally optimal structures is far fewer than the total number of structures--indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2 the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3 the (modified maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected

  9. The Structure and Function of Male Thomas Langur Loud Calls

    NARCIS (Netherlands)

    Wich, Serge Alexander

    2002-01-01

    This study has addressed the acoustical structure of male loud calls and their function in Thomas langur social organisation. Thomas langurs are medium sized primate that lives in Sumatra, Indonesia. Ome of the characteristics of this species is the loud call of males. Several functions for loud

  10. Hierarchical structure of correlation functions for single jets

    International Nuclear Information System (INIS)

    Lupia, S.; Giovannini, A.; Ugoccioni, R.

    1993-01-01

    Theoretical basis of void scaling function properties of hierarchical structure in rapidity and p T intervals are explored. Their phenomenological consequences are analyzed at single jet level by using Monte Carlo methods in e + e - annihilation. It is found that void scaling function study provides an interesting alternative approach for characterizing single jets of different origin. (orig.)

  11. Hierarchical structure of correlation functions for single jets

    Energy Technology Data Exchange (ETDEWEB)

    Lupia, S. (Dipt. di Fisica Teorica, Univ. di Torino, and INFN, Sezione di Torino (Italy)); Giovannini, A. (Dipt. di Fisica Teorica, Univ. di Torino, and INFN, Sezione di Torino (Italy)); Ugoccioni, R. (Dipt. di Fisica Teorica, Univ. di Torino, and INFN, Sezione di Torino (Italy))

    1993-08-01

    Theoretical basis of void scaling function properties of hierarchical structure in rapidity and p[sub T] intervals are explored. Their phenomenological consequences are analyzed at single jet level by using Monte Carlo methods in e[sup +]e[sup -] annihilation. It is found that void scaling function study provides an interesting alternative approach for characterizing single jets of different origin. (orig.)

  12. Spin-dependent parton distributions and structure functions

    International Nuclear Information System (INIS)

    Bentz, W.; Ito, T.; Cloet, I.C.; Thomas, A.W.; Yazaki, K.

    2008-01-01

    Nuclear parton distributions and structure functions are determined in an effective chiral quark theory. We also discuss an extension of our model to fragmentation functions. Presented at the 20th Few-Body Conference, Pisa, Italy, 10-14 September 2007. (author)

  13. Whole-brain functional connectivity predicted by indirect structural connections

    DEFF Research Database (Denmark)

    Røge, Rasmus; Ambrosen, Karen Marie Sandø; Albers, Kristoffer Jon

    2017-01-01

    Modern functional and diffusion magnetic resonance imaging (fMRI and dMRI) provide data from which macro-scale networks of functional and structural whole brain connectivity can be estimated. Although networks derived from these two modalities describe different properties of the human brain, the...

  14. Network-level structure-function relationships in human neocortex

    NARCIS (Netherlands)

    Miŝic, Bratislav; Betzel, Richard F.; De Reus, Marcel A.; Van Den Heuvel, Martijn P.; Berman, Marc G.; McIntosh, Anthony R.; Sporns, Olaf

    2016-01-01

    The dynamics of spontaneous fluctuations in neural activity are shaped by underlying patterns of anatomical connectivity. While numerous studies have demonstrated edge-wise correspondence between structural and functional connections, much less is known about how large-scale coherent functional

  15. Enhancing the functionality of photovoltaic and photonic biointerfaces through structuration

    OpenAIRE

    Wenzel, Tobias

    2017-01-01

    This two-part thesis focuses on biointerfaces of two different biological systems. It specifically examines the interplay of structure and functionality in these biointerfaces. Part one studies photo-bio-electrochemically active bacteria and the strong dependence of their electrical current generation on electrode structure and pigment organisation. Part two uncovers surprising design principles of photonic structures on flower petals and presents research tools to study disordered optical sy...

  16. Using the structure-function linkage database to characterize functional domains in enzymes.

    Science.gov (United States)

    Brown, Shoshana; Babbitt, Patricia

    2014-12-12

    The Structure-Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu/) is a Web-accessible database designed to link enzyme sequence, structure, and functional information. This unit describes the protocols by which a user may query the database to predict the function of uncharacterized enzymes and to correct misannotated functional assignments. The information in this unit is especially useful in helping a user discriminate functional capabilities of a sequence that is only distantly related to characterized sequences in publicly available databases. Copyright © 2014 John Wiley & Sons, Inc.

  17. Matrix Transfer Function Design for Flexible Structures: An Application

    Science.gov (United States)

    Brennan, T. J.; Compito, A. V.; Doran, A. L.; Gustafson, C. L.; Wong, C. L.

    1985-01-01

    The application of matrix transfer function design techniques to the problem of disturbance rejection on a flexible space structure is demonstrated. The design approach is based on parameterizing a class of stabilizing compensators for the plant and formulating the design specifications as a constrained minimization problem in terms of these parameters. The solution yields a matrix transfer function representation of the compensator. A state space realization of the compensator is constructed to investigate performance and stability on the nominal and perturbed models. The application is made to the ACOSSA (Active Control of Space Structures) optical structure.

  18. Functional clustering in hippocampal cultures: relating network structure and dynamics

    International Nuclear Information System (INIS)

    Feldt, S; Dzakpasu, R; Olariu, E; Żochowski, M; Wang, J X; Shtrahman, E

    2010-01-01

    In this work we investigate the relationship between gross anatomic structural network properties, neuronal dynamics and the resultant functional structure in dissociated rat hippocampal cultures. Specifically, we studied cultures as they developed under two conditions: the first supporting glial cell growth (high glial group), and the second one inhibiting it (low glial group). We then compared structural network properties and the spatio-temporal activity patterns of the neurons. Differences in dynamics between the two groups could be linked to the impact of the glial network on the neuronal network as the cultures developed. We also implemented a recently developed algorithm called the functional clustering algorithm (FCA) to obtain the resulting functional network structure. We show that this new algorithm is useful for capturing changes in functional network structure as the networks evolve over time. The FCA detects changes in functional structure that are consistent with expected dynamical differences due to the impact of the glial network. Cultures in the high glial group show an increase in global synchronization as the cultures age, while those in the low glial group remain locally synchronized. We additionally use the FCA to quantify the amount of synchronization present in the cultures and show that the total level of synchronization in the high glial group is stronger than in the low glial group. These results indicate an interdependence between the glial and neuronal networks present in dissociated cultures

  19. Solving crystal structures with the symmetry minimum function

    International Nuclear Information System (INIS)

    Estermann, M.A.

    1995-01-01

    Unravelling the Patterson function (the auto-correlation function of the crystal structure) (A.L. Patterson, Phys. Rev. 46 (1934) 372) can be the only way of solving crystal structures from neutron and incomplete diffraction data (e.g. powder data) when direct methods for phase determination fail. The negative scattering lengths of certain isotopes and the systematic loss of information caused by incomplete diffraction data invalidate the underlying statistical assumptions made in direct methods. In contrast, the Patterson function depends solely on the quality of the available diffraction data. Simpson et al. (P.G. Simpson et al., Acta Crystallogr. 18 (1965) 169) showed that solving a crystal structure with a particular superposition of origin-shifted Patterson functions, the symmetry minimum function, is advantageous over using the Patterson function alone, for single-crystal X-ray data.This paper describes the extension of the Patterson superposition approach to neutron data and powder data by (a) actively using the negative regions in the Patterson map caused by negative scattering lengths and (b) using maximum entropy Patterson maps (W.I.F. David, Nature 346 (1990) 731). Furthermore, prior chemical knowledge such as bond lengths and angles from known fragments have been included. Two successful structure solutions of a known and a previously unknown structure (M. Hofmann, J. Solid State Chem., in press) illustrate the potential of this new development. ((orig.))

  20. Proceedings of the international advisory committee on 'biomolecular dynamics instrument DNA' and the workshop on 'biomolecular dynamics backscattering spectrometers'

    International Nuclear Information System (INIS)

    Arai, Masatoshi; Aizawa, Kazuya; Nakajima, Kenji; Shibata, Kaoru; Takahashi, Nobuaki

    2008-08-01

    A workshop entitled 'Biomolecular Dynamics Backscattering Spectrometers' was held on February 27th - 29th, 2008 at J-PARC Center, Japan Atomic Energy Agency. This workshop was planned to be held for aiming to realize an innovative neutron backscattering instrument, namely DNA, in the MLF and thus four leading scientists in the field of neutron backscattering instruments were invited as the International Advisory Committee (IAC member: Dr. Dan Neumann (Chair); Prof. Ferenc Mezei; Dr. Hannu Mutka; Dr. Philip Tregenna-Piggott) for DNA from institutes in the United States, France and Switzerland, where backscattering instruments are in-service. It was therefore held in the form of lecture anterior and then in the form of the committee posterior. This report includes the executive summary of the IAC and materials of the presentations in the IAC and the workshop. (author)

  1. Altered resting brain function and structure in professional badminton players.

    Science.gov (United States)

    Di, Xin; Zhu, Senhua; Jin, Hua; Wang, Pin; Ye, Zhuoer; Zhou, Ke; Zhuo, Yan; Rao, Hengyi

    2012-01-01

    Neuroimaging studies of professional athletic or musical training have demonstrated considerable practice-dependent plasticity in various brain structures, which may reflect distinct training demands. In the present study, structural and functional brain alterations were examined in professional badminton players and compared with healthy controls using magnetic resonance imaging (MRI) and resting-state functional MRI. Gray matter concentration (GMC) was assessed using voxel-based morphometry (VBM), and resting-brain functions were measured by amplitude of low-frequency fluctuation (ALFF) and seed-based functional connectivity. Results showed that the athlete group had greater GMC and ALFF in the right and medial cerebellar regions, respectively. The athlete group also demonstrated smaller ALFF in the left superior parietal lobule and altered functional connectivity between the left superior parietal and frontal regions. These findings indicate that badminton expertise is associated with not only plastic structural changes in terms of enlarged gray matter density in the cerebellum, but also functional alterations in fronto-parietal connectivity. Such structural and functional alterations may reflect specific experiences of badminton training and practice, including high-capacity visuo-spatial processing and hand-eye coordination in addition to refined motor skills.

  2. Molecular structures and functional relationships in clostridial neurotoxins.

    Science.gov (United States)

    Swaminathan, Subramanyam

    2011-12-01

    The seven serotypes of Clostridium botulinum neurotoxins (A-G) are the deadliest poison known to humans. They share significant sequence homology and hence possess similar structure-function relationships. Botulinum neurotoxins (BoNT) act via a four-step mechanism, viz., binding and internalization to neuronal cells, translocation of the catalytic domain into the cytosol and finally cleavage of one of the three soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) causing blockage of neurotransmitter release leading to flaccid paralysis. Crystal structures of three holotoxins, BoNT/A, B and E, are available to date. Although the individual domains are remarkably similar, their domain organization is different. These structures have helped in correlating the structural and functional domains. This has led to the determination of structures of individual domains and combinations of them. Crystal structures of catalytic domains of all serotypes and several binding domains are now available. The catalytic domains are zinc endopeptidases and share significant sequence and structural homology. The active site architecture and the catalytic mechanism are similar although the binding mode of individual substrates may be different, dictating substrate specificity and peptide cleavage selectivity. Crystal structures of catalytic domains with substrate peptides provide clues to specificity and selectivity unique to BoNTs. Crystal structures of the receptor domain in complex with ganglioside or the protein receptor have provided information about the binding of botulinum neurotoxin to the neuronal cell. An overview of the structure-function relationship correlating the 3D structures with biochemical and biophysical data and how they can be used for structure-based drug discovery is presented here. Journal compilation © 2011 FEBS. No claim to original US government works.

  3. QCD's Partner Needed for Mass Spectra and Parton Structure Functions

    International Nuclear Information System (INIS)

    Kim, Y.S.

    2009-01-01

    as in the case of the hydrogen atom, bound-state wave functions are needed to generate hadronic spectra. For this purpose, in 1971, Feynman and his students wrote down a Lorentz-invariant harmonic oscillator equation. This differential equation has one set of solutions satisfying the Lorentz-covariant boundary condition. This covariant set generates Lorentz-invariant mass spectra with their degeneracies. Furthermore, the Lorentz-covariant wave functions allow us to calculate the valence parton distribution by Lorentz-boosting the quark-model wave function from the hadronic rest frame. However, this boosted wave function does not give an accurate parton distribution. The wave function needs QCD corrections to make a contact with the real world. Likewise, QCD needs the wave function as a starting point for calculating the parton structure function. (author)

  4. Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics

    KAUST Repository

    Sobhy, M. A.; Elshenawy, M. M.; Takahashi, Masateru; Whitman, B. H.; Walter, N. G.; Hamdan, S. M.

    2011-01-01

    Single-molecule fluorescence imaging is at the forefront of tools applied to study biomolecular dynamics both in vitro and in vivo. The ability of the single-molecule fluorescence microscope to conduct simultaneous multi-color excitation

  5. General quadratic gauge theory: constraint structure, symmetries and physical functions

    Energy Technology Data Exchange (ETDEWEB)

    Gitman, D M [Institute of Physics, University of Sao Paulo (Brazil); Tyutin, I V [Lebedev Physics Institute, Moscow (Russian Federation)

    2005-06-17

    How can we relate the constraint structure and constraint dynamics of the general gauge theory in the Hamiltonian formulation to specific features of the theory in the Lagrangian formulation, especially relate the constraint structure to the gauge transformation structure of the Lagrangian action? How can we construct the general expression for the gauge charge if the constraint structure in the Hamiltonian formulation is known? Whether we can identify the physical functions defined as commuting with first-class constraints in the Hamiltonian formulation and the physical functions defined as gauge invariant functions in the Lagrangian formulation? The aim of the present paper is to consider the general quadratic gauge theory and to answer the above questions for such a theory in terms of strict assertions. To fulfil such a programme, we demonstrate the existence of the so-called superspecial phase-space variables in terms of which the quadratic Hamiltonian action takes a simple canonical form. On the basis of such a representation, we analyse a functional arbitrariness in the solutions of the equations of motion of the quadratic gauge theory and derive the general structure of symmetries by analysing a symmetry equation. We then use these results to identify the two definitions of physical functions and thus prove the Dirac conjecture.

  6. Renormalized sum rules for structure functions of heavy meson decays

    International Nuclear Information System (INIS)

    Grozin, A.G.; Korchemsky, G.P.

    1996-01-01

    We consider the properties of the structure functions of inclusive heavy meson decays B→X c and treat the c quark mass as a free parameter. We show that in two extreme cases of heavy and light c quarks the structure functions of heavy-heavy and heavy-light transitions are given by a Fourier transform of the matrix elements of Wilson lines containing a timelike and a lightlike segment, correspondingly. Using the renormalization properties of Wilson lines we find the dependence of the structure functions on the factorization scale, the structure function of the heavy-heavy transition is renormalized multiplicatively, while that of the heavy-light transition obeys the GLAP-type evolution equation. We propose a generalization of the sum rules for the moments of the structure functions (Bjorken, Voloshin, and the open-quote open-quote third close-quote close-quote sum rules) with a soft exponential factorization cutoff, which correctly incorporates both perturbative and nonperturbative effects. We analyze nonperturbative corrections by first considering infrared renormalon contributions to the Wilson lines. Uncertainties induced by the leading renormalon pole at u=1/2 are exactly canceled by a similar uncertainty in the heavy quark pole mass. The leading nonperturbative corrections associated with the next renormalon at u=1 are parametrized by the matrix element μ π 2 which is proportional to the heavy quark kinetic energy. copyright 1996 The American Physical Society

  7. Cytoscape: a software environment for integrated models of biomolecular interaction networks.

    Science.gov (United States)

    Shannon, Paul; Markiel, Andrew; Ozier, Owen; Baliga, Nitin S; Wang, Jonathan T; Ramage, Daniel; Amin, Nada; Schwikowski, Benno; Ideker, Trey

    2003-11-01

    Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

  8. High-Throughput, Protein-Targeted Biomolecular Detection Using Frequency-Domain Faraday Rotation Spectroscopy.

    Science.gov (United States)

    Murdock, Richard J; Putnam, Shawn A; Das, Soumen; Gupta, Ankur; Chase, Elyse D Z; Seal, Sudipta

    2017-03-01

    A clinically relevant magneto-optical technique (fd-FRS, frequency-domain Faraday rotation spectroscopy) for characterizing proteins using antibody-functionalized magnetic nanoparticles (MNPs) is demonstrated. This technique distinguishes between the Faraday rotation of the solvent, iron oxide core, and functionalization layers of polyethylene glycol polymers (spacer) and model antibody-antigen complexes (anti-BSA/BSA, bovine serum albumin). A detection sensitivity of ≈10 pg mL -1 and broad detection range of 10 pg mL -1 ≲ c BSA ≲ 100 µg mL -1 are observed. Combining this technique with predictive analyte binding models quantifies (within an order of magnitude) the number of active binding sites on functionalized MNPs. Comparative enzyme-linked immunosorbent assay (ELISA) studies are conducted, reproducing the manufacturer advertised BSA ELISA detection limits from 1 ng mL -1 ≲ c BSA ≲ 500 ng mL -1 . In addition to the increased sensitivity, broader detection range, and similar specificity, fd-FRS can be conducted in less than ≈30 min, compared to ≈4 h with ELISA. Thus, fd-FRS is shown to be a sensitive optical technique with potential to become an efficient diagnostic in the chemical and biomolecular sciences. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. A compact hard X-ray source for medical imaging and biomolecular studies

    International Nuclear Information System (INIS)

    Cline, D.B.; Green, M.A.; Kolonko, J.

    1995-01-01

    There are a large number of synchrotron light sources in the world. However, these sources are designed for physics, chemistry, and engineering studies. To our knowledge, none have been optimized for either medical imaging or biomolecular studies. There are special needs for these applications. We present here a preliminary design of a very compact source, small enough for a hospital or a biomolecular laboratory, that is suitable for these applications. (orig.)

  10. Adaptation of brain functional and structural networks in aging.

    Directory of Open Access Journals (Sweden)

    Annie Lee

    Full Text Available The human brain, especially the prefrontal cortex (PFC, is functionally and anatomically reorganized in order to adapt to neuronal challenges in aging. This study employed structural MRI, resting-state fMRI (rs-fMRI, and high angular resolution diffusion imaging (HARDI, and examined the functional and structural reorganization of the PFC in aging using a Chinese sample of 173 subjects aged from 21 years and above. We found age-related increases in the structural connectivity between the PFC and posterior brain regions. Such findings were partially mediated by age-related increases in the structural connectivity of the occipital lobe within the posterior brain. Based on our findings, it is thought that the PFC reorganization in aging could be partly due to the adaptation to age-related changes in the structural reorganization of the posterior brain. This thus supports the idea derived from task-based fMRI that the PFC reorganization in aging may be adapted to the need of compensation for resolving less distinctive stimulus information from the posterior brain regions. In addition, we found that the structural connectivity of the PFC with the temporal lobe was fully mediated by the temporal cortical thickness, suggesting that the brain morphology plays an important role in the functional and structural reorganization with aging.

  11. Adaptation of brain functional and structural networks in aging.

    Science.gov (United States)

    Lee, Annie; Ratnarajah, Nagulan; Tuan, Ta Anh; Chen, Shen-Hsing Annabel; Qiu, Anqi

    2015-01-01

    The human brain, especially the prefrontal cortex (PFC), is functionally and anatomically reorganized in order to adapt to neuronal challenges in aging. This study employed structural MRI, resting-state fMRI (rs-fMRI), and high angular resolution diffusion imaging (HARDI), and examined the functional and structural reorganization of the PFC in aging using a Chinese sample of 173 subjects aged from 21 years and above. We found age-related increases in the structural connectivity between the PFC and posterior brain regions. Such findings were partially mediated by age-related increases in the structural connectivity of the occipital lobe within the posterior brain. Based on our findings, it is thought that the PFC reorganization in aging could be partly due to the adaptation to age-related changes in the structural reorganization of the posterior brain. This thus supports the idea derived from task-based fMRI that the PFC reorganization in aging may be adapted to the need of compensation for resolving less distinctive stimulus information from the posterior brain regions. In addition, we found that the structural connectivity of the PFC with the temporal lobe was fully mediated by the temporal cortical thickness, suggesting that the brain morphology plays an important role in the functional and structural reorganization with aging.

  12. Population structure analysis using rare and common functional variants

    Directory of Open Access Journals (Sweden)

    Ding Lili

    2011-11-01

    Full Text Available Abstract Next-generation sequencing technologies now make it possible to genotype and measure hundreds of thousands of rare genetic variations in individuals across the genome. Characterization of high-density genetic variation facilitates control of population genetic structure on a finer scale before large-scale genotyping in disease genetics studies. Population structure is a well-known, prevalent, and important factor in common variant genetic studies, but its relevance in rare variants is unclear. We perform an extensive population structure analysis using common and rare functional variants from the Genetic Analysis Workshop 17 mini-exome sequence. The analysis based on common functional variants required 388 principal components to account for 90% of the variation in population structure. However, an analysis based on rare variants required 532 significant principal components to account for similar levels of variation. Using rare variants, we detected fine-scale substructure beyond the population structure identified using common functional variants. Our results show that the level of population structure embedded in rare variant data is different from the level embedded in common variant data and that correcting for population structure is only as good as the level one wishes to correct.

  13. Regge behaviour of structure functions and evolution of gluon structure function upto next-to-leading order at low-x

    International Nuclear Information System (INIS)

    Jamil, U.; Sarma, J.K.

    2011-01-01

    Evolution of gluon structure function from Dokshitzer-Gribov-Lipatov-Altarelli-Parisi (DGLAP) evolution equations upto next-to-leading order at low-x is presented assuming the Regge behaviour of structure functions. We compare our results of gluon structure function with GRV 98 global parameterization and show the compatibility of Regge behaviour of structure functions with PQCD. (author)

  14. Ontogenetic functional diversity: size structure of a keystone predator drives functioning of a complex ecosystem.

    Science.gov (United States)

    Rudolf, Volker H W; Rasmussen, Nick L

    2013-05-01

    A central challenge in community ecology is to understand the connection between biodiversity and the functioning of ecosystems. While traditional approaches have largely focused on species-level diversity, increasing evidence indicates that there exists substantial ecological diversity among individuals within species. By far, the largest source of this intraspecific diversity stems from variation among individuals in ontogenetic stage and size. Although such ontogenetic shifts are ubiquitous in natural communities, whether and how they scale up to influence the structure and functioning of complex ecosystems is largely unknown. Here we take an experimental approach to examine the consequences of ontogenetic niche shifts for the structure of communities and ecosystem processes. In particular we experimentally manipulated the stage structure in a keystone predator, larvae of the dragonfly Anax junius, in complex experimental pond communities to test whether changes in the population stage or size structure of a keystone species scale up to alter community structure and ecosystem processes, and how functional differences scale with relative differences in size among stages. We found that the functional role of A. junius was stage-specific. Altering what stages were present in a pond led to concurrent changes in community structure, primary producer biomass (periphyton and phytoplankton), and ultimately altered ecosystem processes (respiration and net primary productivity), indicating a strong, but stage-specific, trophic cascade. Interestingly, the stage-specific effects did not simply scale with size or biomass of the predator, but instead indicated clear ontogenetic niche shifts in ecological interactions. Thus, functional differences among stages within a keystone species scaled up to alter the functioning of entire ecosystems. Therefore, our results indicate that the classical approach of assuming an average functional role of a species can be misleading because

  15. Studying Membrane Protein Structure and Function Using Nanodiscs

    DEFF Research Database (Denmark)

    Huda, Pie

    The structure and dynamic of membrane proteins can provide valuable information about general functions, diseases and effects of various drugs. Studying membrane proteins are a challenge as an amphiphilic environment is necessary to stabilise the protein in a functionally and structurally relevant...... form. This is most typically achieved through the use of detergent based reconstitution systems. However, time and again such systems fail to provide a suitable environment causing aggregation and inactivation. Nanodiscs are self-assembled lipoproteins containing two membrane scaffold proteins...... and a lipid bilayer in defined nanometer size, which can act as a stabiliser for membrane proteins. This enables both functional and structural investigation of membrane proteins in a detergent free environment which is closer to the native situation. Understanding the self-assembly of nanodiscs is important...

  16. Structure and functions of organizational trust in employees’ notions

    Directory of Open Access Journals (Sweden)

    Marina M. Zavartseva

    2016-06-01

    Full Text Available This article investigates the structure and functions of organizational trust, examining the content of employees’ subjective notions about organizational trust and it’s role in organization’s functioning. The combination of direct (R.B.Shaw’s trust assessment survey and indirect (the semantic differential scale; the contentanalysis of the checklist of trust structural components methods was used. Using data on 378 employees of different organizations (commercial, medical, educational we distinguished subjective images of organization in groups with opposite estimation of organizational trust’s level. The study indicated that organizational trust’s structure is not linear, and exposed two main functions of high level of organizational trust – idealization and positive emotional estimation both of actual organization (that is currently place of employment. Obtained data provide basis for express-diagnostic of trust in organization and might be used for design of psychological training aiming high organization’s efficacy.

  17. Structure functions of longitudinal virtual photons at low virtualities

    International Nuclear Information System (INIS)

    Ioffe, B.L.; Shushpanov, I.A.

    1996-01-01

    The structure functions F L 1 and F L 2 of longitudinal virtual photons at low virtualities are calculated in the framework of chiral perturbation theory (ChPT) in the zero and first order of ChPT. It is assumed that the virtuality of a target longitudinal photon p 2 is much less than the virtuality of the hard projectile photon Q 2 and both are less than the characteristic ChPT scale. In this approximation the structure functions are determined by the production of two pions in γγ collisions. The numerical results for F L 2 and F L 1 are presented (the upper index refers to the longitudinal polarization of the virtual target photon). The possibilities of measurements of these structure functions are briefly discussed. copyright 1996 The American Physical Society

  18. Performance analysis, quality function deployment and structured methods

    Science.gov (United States)

    Maier, M. W.

    Quality function deployment, (QFD), an approach to synthesizing several elements of system modeling and design into a single unit, is presented. Behavioral, physical, and performance modeling are usually considered as separate aspects of system design without explicit linkages. Structured methodologies have developed linkages between behavioral and physical models before, but have not considered the integration of performance models. QFD integrates performance models with traditional structured models. In this method, performance requirements such as cost, weight, and detection range are partitioned into matrices. Partitioning is done by developing a performance model, preferably quantitative, for each requirement. The parameters of the model become the engineering objectives in a QFD analysis and the models are embedded in a spreadsheet version of the traditional QFD matrices. The performance model and its parameters are used to derive part of the functional model by recognizing that a given performance model implies some structure to the functionality of the system.

  19. Integrative structure and functional anatomy of a nuclear pore complex

    Science.gov (United States)

    Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D.; Hogan, Joanna A.; Upla, Paula; Chemmama, Ilan E.; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S.; Wang, Junjie; Williams, Rosemary; Unruh, Jay R.; Greenberg, Charles H.; Jacobs, Erica Y.; Yu, Zhiheng; de La Cruz, M. Jason; Mironska, Roxana; Stokes, David L.; Aitchison, John D.; Jarrold, Martin F.; Gerton, Jennifer L.; Ludtke, Steven J.; Akey, Christopher W.; Chait, Brian T.; Sali, Andrej; Rout, Michael P.

    2018-03-01

    Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

  20. Integrative structure and functional anatomy of a nuclear pore complex.

    Science.gov (United States)

    Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D; Hogan, Joanna A; Upla, Paula; Chemmama, Ilan E; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S; Wang, Junjie; Williams, Rosemary; Unruh, Jay R; Greenberg, Charles H; Jacobs, Erica Y; Yu, Zhiheng; de la Cruz, M Jason; Mironska, Roxana; Stokes, David L; Aitchison, John D; Jarrold, Martin F; Gerton, Jennifer L; Ludtke, Steven J; Akey, Christopher W; Chait, Brian T; Sali, Andrej; Rout, Michael P

    2018-03-22

    Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

  1. Class I Cytokine Receptors: Structure and function in the Membrane

    DEFF Research Database (Denmark)

    Bugge, Katrine Østergaard

    bilayer via structural characterizations of TMD representatives. To enable structural studies of these domains, an organic-extraction based strategy for efficient production of isotope-labeled TMDs with or without short intrinsically disordered regions was developed. This strategy successfully provided...... of these challenging domains. Supplemented by a review of the current collection of TMD structures from single-pass transmembrane receptors, the thesis as a whole provides important insights on the structure and function in the membrane as well as highlight the open questions to be addressed in the years to come.......Class I cytokine receptors are involved in important biological functions of both physiological and pathological nature in mammals. However, the molecular details of the cross-membrane signal transduction through these receptors remain obscure. One of the major reasons for this is the lack...

  2. Many Activities, One Structure: Functional Plasticity of Ribozyme Folds

    Directory of Open Access Journals (Sweden)

    Matthew W.L. Lau

    2016-11-01

    Full Text Available Catalytic RNAs, or ribozymes, are involved in a number of essential biological processes, such as replication of RNA genomes and mobile genetic elements, RNA splicing, translation, and RNA degradation. The function of ribozymes requires the formation of active sites decorated with RNA functional groups within defined three-dimensional (3D structures. The genotype (sequence of RNAs ultimately determines what 3D structures they adopt (as a function of their environmental conditions. These 3D structures, in turn, give rise to biochemical activity, which can further elaborate them by catalytic rearrangements or association with other molecules. The fitness landscape of a non-periodic linear polymer, such as RNA, relates its primary structure to a phenotype. Two major challenges in the analysis of ribozymes is to map all possible genotypes to their corresponding catalytic activity (that is, to determine their fitness landscape experimentally, and to understand whether their genotypes and three-dimensional structures can support multiple different catalytic functions. Recently, the combined results of experiments that employ in vitro evolution methods, high-throughput sequencing and crystallographic structure determination have hinted at answers to these two questions: while the fitness landscape of ribozymes is rugged, meaning that their catalytic activity cannot be optimized by a smooth trajectory in sequence space, once an RNA achieves a stable three-dimensional fold, it can be endowed with distinctly different biochemical activities through small changes in genotype. This functional plasticity of highly structured RNAs may be particularly advantageous for the adaptation of organisms to drastic changes in selective pressure, or for the development of new biotechnological tools.

  3. Nucleon structure functions from lattice operator product expansion

    Energy Technology Data Exchange (ETDEWEB)

    Chambers, A.J.; Somfleth, K.; Young, R.D.; Zanotti, J.M. [Adelaide Univ., SA (Australia). CSSM, Dept. of Physics; Horsley, R. [Edinburgh Univ. (United Kingdom). School of Physics and Astronomy; Nakamura, Y. [RIKEN Advanced Institute for Computational Science, Kobe (Japan); Perlt, H.; Schiller, A. [Leipzig Univ. (Germany). Inst. fuer Theoretische Physik; Rakow, P.E.L. [Liverpool Univ. (United Kingdom). Theoretical Physics Div.; Schierholz, G. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2017-03-15

    Deep-inelastic scattering, in the laboratory and on the lattice, is most instructive for understanding how the nucleon is built from quarks and gluons. The long-term goal is to compute the associated structure functions from first principles. So far this has been limited to model calculations. In this Letter we propose a new method to compute the structure functions directly from the virtual, all-encompassing Compton amplitude, utilizing the operator product expansion. This overcomes issues of renormalization and operator mixing, which so far have hindered lattice calculations of power corrections and higher moments.

  4. Photon structure functions with heavy particle mass effects

    Energy Technology Data Exchange (ETDEWEB)

    Uematsu, Tsuneo, E-mail: uematsu@scphys.kyoto-u.jp [Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 (Japan); Maskawa Institute for Science and Culture, Kyoto Sangyo University, Kamigamo, Kita-ku, Kyoto 603-8555 (Japan)

    2013-01-15

    In the framework of the perturbative QCD we investigate heavy particle mass effects on the unpolarized and polarized photon structure functions, F{sub 2}{sup γ} and g{sub 1}{sup γ}, respectively. We present our basic formalism to treat heavy particle mass effects to NLO in perturbative QCD. We also study heavy quark effects on the QCD sum rule for the first moment of g{sub 1}{sup γ}, which is related to axial anomaly. The photon structure function in supersymmetric QCD is also briefly discussed.

  5. Quark-hadron duality of nucleon spin structure function

    International Nuclear Information System (INIS)

    Dong, Y.B.

    2005-01-01

    Bloom-Gilman quark-hadron duality of nuclear spin structure function is studied by comparing the integral of g 1 from perturbative QCD prediction in the scaling region to the moment of g 1 in the resonance region. The spin structure function in the resonance region is estimated by the parametrization forms of non-resonance background and of resonance contributions. The uncertainties of our calculations due to those parametrization forms are discussed. Moreover, the effect of the Δ(1232)-resonance in the first resonance region and the role of the resonances in the second resonance region are explicitly shown. Elastic peak contribution to the duality is also analyzed. (orig.)

  6. The Candida albicans Biofilm Matrix: Composition, Structure and Function.

    Science.gov (United States)

    Pierce, Christopher G; Vila, Taissa; Romo, Jesus A; Montelongo-Jauregui, Daniel; Wall, Gina; Ramasubramanian, Anand; Lopez-Ribot, Jose L

    2017-03-01

    A majority of infections caused by Candida albicans -the most frequent fungal pathogen-are associated with biofilm formation. A salient feature of C. albicans biofilms is the presence of the biofilm matrix. This matrix is composed of exopolymeric materials secreted by sessile cells within the biofilm, in which all classes of macromolecules are represented, and provides protection against environmental challenges. In this review, we summarize the knowledge accumulated during the last two decades on the composition, structure, and function of the C. albicans biofilm matrix. Knowledge of the matrix components, its structure, and function will help pave the way to novel strategies to combat C. albicans biofilm infections.

  7. Structural and functional characterization of human complement factor P

    DEFF Research Database (Denmark)

    Pedersen, Dennis

    not yet been resolved. This PhD-thesis provide structural understanding of the FP mediated stabilization of the AP C3 convertase. Furthermore, functional studies involving oligomeric and monomeric FP variants have helped us to understand the importance of FP oligomerization for the primary functions of FP...... of complement by stabilizing the C3 convertase complex (C3bBb). FP has also been suggested to serve as a pattern recognition molecule for the initiation of the alternative pathway. However, the molecular mechanisms of FP remain unclear due to its oligomeric nature and hence the atomic structure of FP has...

  8. Nucleon structure functions from lattice operator product expansion

    International Nuclear Information System (INIS)

    Chambers, A.J.; Somfleth, K.; Young, R.D.; Zanotti, J.M.; Perlt, H.; Schiller, A.

    2017-03-01

    Deep-inelastic scattering, in the laboratory and on the lattice, is most instructive for understanding how the nucleon is built from quarks and gluons. The long-term goal is to compute the associated structure functions from first principles. So far this has been limited to model calculations. In this Letter we propose a new method to compute the structure functions directly from the virtual, all-encompassing Compton amplitude, utilizing the operator product expansion. This overcomes issues of renormalization and operator mixing, which so far have hindered lattice calculations of power corrections and higher moments.

  9. Nucleon Structure Functions from Operator Product Expansion on the Lattice.

    Science.gov (United States)

    Chambers, A J; Horsley, R; Nakamura, Y; Perlt, H; Rakow, P E L; Schierholz, G; Schiller, A; Somfleth, K; Young, R D; Zanotti, J M

    2017-06-16

    Deep-inelastic scattering, in the laboratory and on the lattice, is most instructive for understanding how the nucleon is built from quarks and gluons. The long-term goal is to compute the associated structure functions from first principles. So far this has been limited to model calculations. In this Letter we propose a new method to compute the structure functions directly from the virtual, all-encompassing Compton amplitude, utilizing the operator product expansion. This overcomes issues of renormalization and operator mixing, which so far have hindered lattice calculations of power corrections and higher moments.

  10. Functional and Structural Brain Changes Associated with Methamphetamine Abuse

    Directory of Open Access Journals (Sweden)

    Bruce R. Russell

    2012-10-01

    Full Text Available Methamphetamine (MA is a potent psychostimulant drug whose abuse has become a global epidemic in recent years. Firstly, this review article briefly discusses the epidemiology and clinical pharmacology of methamphetamine dependence. Secondly, the article reviews relevant animal literature modeling methamphetamine dependence and discusses possible mechanisms of methamphetamine-induced neurotoxicity. Thirdly, it provides a critical review of functional and structural neuroimaging studies in human MA abusers; including positron emission tomography (PET and functional and structural magnetic resonance imaging (MRI. The effect of abstinence from methamphetamine, both short- and long-term within the context of these studies is also reviewed.

  11. Functional Annotation of Ion Channel Structures by Molecular Simulation.

    Science.gov (United States)

    Trick, Jemma L; Chelvaniththilan, Sivapalan; Klesse, Gianni; Aryal, Prafulla; Wallace, E Jayne; Tucker, Stephen J; Sansom, Mark S P

    2016-12-06

    Ion channels play key roles in cell membranes, and recent advances are yielding an increasing number of structures. However, their functional relevance is often unclear and better tools are required for their functional annotation. In sub-nanometer pores such as ion channels, hydrophobic gating has been shown to promote dewetting to produce a functionally closed (i.e., non-conductive) state. Using the serotonin receptor (5-HT 3 R) structure as an example, we demonstrate the use of molecular dynamics to aid the functional annotation of channel structures via simulation of the behavior of water within the pore. Three increasingly complex simulation analyses are described: water equilibrium densities; single-ion free-energy profiles; and computational electrophysiology. All three approaches correctly predict the 5-HT 3 R crystal structure to represent a functionally closed (i.e., non-conductive) state. We also illustrate the application of water equilibrium density simulations to annotate different conformational states of a glycine receptor. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  12. Structural and functional hyperconnectivity within the sensorimotor system in xenomelia.

    Science.gov (United States)

    Hänggi, Jürgen; Vitacco, Deborah A; Hilti, Leonie M; Luechinger, Roger; Kraemer, Bernd; Brugger, Peter

    2017-03-01

    Xenomelia is a rare condition characterized by the persistent and compulsive desire for the amputation of one or more physically healthy limbs. We highlight the neurological underpinnings of xenomelia by assessing structural and functional connectivity by means of whole-brain connectome and network analyses of regions previously implicated in empirical research in this condition. We compared structural and functional connectivity between 13 xenomelic men with matched controls using diffusion tensor imaging combined with fiber tractography and resting state functional magnetic resonance imaging. Altered connectivity in xenomelia within the sensorimotor system has been predicted. We found subnetworks showing structural and functional hyperconnectivity in xenomelia compared with controls. These subnetworks were lateralized to the right hemisphere and mainly comprised by nodes belonging to the sensorimotor system. In the connectome analyses, the paracentral lobule, supplementary motor area, postcentral gyrus, basal ganglia, and the cerebellum were hyperconnected to each other, whereas in the xenomelia-specific network analyses, hyperconnected nodes have been found in the superior parietal lobule, primary and secondary somatosensory cortex, premotor cortex, basal ganglia, thalamus, and insula. Our study provides empirical evidence of structural and functional hyperconnectivity within the sensorimotor system including those regions that are core for the reconstruction of a coherent body image. Aberrant connectivity is a common response to focal neurological damage. As exemplified here, it may affect different brain regions differentially. Due to the small sample size, our findings must be interpreted cautiously and future studies are needed to elucidate potential associations between hyperconnectivity and limb disownership reported in xenomelia.

  13. Structure functions and low Q2 physics at HERA

    International Nuclear Information System (INIS)

    Roeck, A. de; Klein, M.

    1991-12-01

    Important new insights into the hadron structure are expected from the data which will be collected at the electron-proton storage ring HERA at DESY, Hamburg. In this paper the physics opportunities for cross section related measurements at HERA are reviewed. Emphasis is put on the derivation of the proton structure functions, on the QCD effects expected in the newly accessible low χ region and on almost real photoproduction physics. (orig.)

  14. Nondiffraction photoproduction of vector mesons and the photon structure function

    International Nuclear Information System (INIS)

    Badalyan, R.G.; Gulkanyan, H.R.

    1988-01-01

    In the framework of the recombination model of hadron production a self-consistent description of the available data on the inclusive spectra of the nondiffraction photoproduction of vector mesons in the fragmentation region of photons at high energies is obtained. The parameters of parton distribution in the hadron component of a photon are estimated and its structure is compared with the measurements of the photon structure function in γγ-interactions at low Q 2 . 15 refs.; 2 figs.; 1 tab

  15. An effective hierarchical model for the biomolecular covalent bond: an approach integrating artificial chemistry and an actual terrestrial life system.

    Science.gov (United States)

    Oohashi, Tsutomu; Ueno, Osamu; Maekawa, Tadao; Kawai, Norie; Nishina, Emi; Honda, Manabu

    2009-01-01

    Under the AChem paradigm and the programmed self-decomposition (PSD) model, we propose a hierarchical model for the biomolecular covalent bond (HBCB model). This model assumes that terrestrial organisms arrange their biomolecules in a hierarchical structure according to the energy strength of their covalent bonds. It also assumes that they have evolutionarily selected the PSD mechanism of turning biological polymers (BPs) into biological monomers (BMs) as an efficient biomolecular recycling strategy We have examined the validity and effectiveness of the HBCB model by coordinating two complementary approaches: biological experiments using existent terrestrial life, and simulation experiments using an AChem system. Biological experiments have shown that terrestrial life possesses a PSD mechanism as an endergonic, genetically regulated process and that hydrolysis, which decomposes a BP into BMs, is one of the main processes of such a mechanism. In simulation experiments, we compared different virtual self-decomposition processes. The virtual species in which the self-decomposition process mainly involved covalent bond cleavage from a BP to BMs showed evolutionary superiority over other species in which the self-decomposition process involved cleavage from BP to classes lower than BM. These converging findings strongly support the existence of PSD and the validity and effectiveness of the HBCB model.

  16. Linking structural features of protein complexes and biological function.

    Science.gov (United States)

    Sowmya, Gopichandran; Breen, Edmond J; Ranganathan, Shoba

    2015-09-01

    Protein-protein interaction (PPI) establishes the central basis for complex cellular networks in a biological cell. Association of proteins with other proteins occurs at varying affinities, yet with a high degree of specificity. PPIs lead to diverse functionality such as catalysis, regulation, signaling, immunity, and inhibition, playing a crucial role in functional genomics. The molecular principle of such interactions is often elusive in nature. Therefore, a comprehensive analysis of known protein complexes from the Protein Data Bank (PDB) is essential for the characterization of structural interface features to determine structure-function relationship. Thus, we analyzed a nonredundant dataset of 278 heterodimer protein complexes, categorized into major functional classes, for distinguishing features. Interestingly, our analysis has identified five key features (interface area, interface polar residue abundance, hydrogen bonds, solvation free energy gain from interface formation, and binding energy) that are discriminatory among the functional classes using Kruskal-Wallis rank sum test. Significant correlations between these PPI interface features amongst functional categories are also documented. Salt bridges correlate with interface area in regulator-inhibitors (r = 0.75). These representative features have implications for the prediction of potential function of novel protein complexes. The results provide molecular insights for better understanding of PPIs and their relation to biological functions. © 2015 The Protein Society.

  17. High taxonomic variability despite stable functional structure across microbial communities.

    Science.gov (United States)

    Louca, Stilianos; Jacques, Saulo M S; Pires, Aliny P F; Leal, Juliana S; Srivastava, Diane S; Parfrey, Laura Wegener; Farjalla, Vinicius F; Doebeli, Michael

    2016-12-05

    Understanding the processes that are driving variation of natural microbial communities across space or time is a major challenge for ecologists. Environmental conditions strongly shape the metabolic function of microbial communities; however, other processes such as biotic interactions, random demographic drift or dispersal limitation may also influence community dynamics. The relative importance of these processes and their effects on community function remain largely unknown. To address this uncertainty, here we examined bacterial and archaeal communities in replicate 'miniature' aquatic ecosystems contained within the foliage of wild bromeliads. We used marker gene sequencing to infer the taxonomic composition within nine metabolic functional groups, and shotgun environmental DNA sequencing to estimate the relative abundances of these groups. We found that all of the bromeliads exhibited remarkably similar functional community structures, but that the taxonomic composition within individual functional groups was highly variable. Furthermore, using statistical analyses, we found that non-neutral processes, including environmental filtering and potentially biotic interactions, at least partly shaped the composition within functional groups and were more important than spatial dispersal limitation and demographic drift. Hence both the functional structure and taxonomic composition within functional groups of natural microbial communities may be shaped by non-neutral and roughly separate processes.

  18. The γ total cross section and the photon structure functions

    International Nuclear Information System (INIS)

    Alexander, G.

    1986-01-01

    A review on the current experimental status of the photon-photon total hadronic cross section as a function of energy and Q 2 is given in addition to the results obtained for the leptonic and hadronic photon structure functions. The results are discussed in terms of the point-like part of the photon and non-perturbative VDM part. It is shown that the cross section at Q 2 = 0 is well described by VDM derived models

  19. ADVANCED OPTICAL TECHNIQUES TO EXPLORE BRAIN STRUCTURE AND FUNCTION

    OpenAIRE

    Silvestri, L.; Mascaro, A. L. Allegra; Lotti, J.; Sacconi, L.; Pavone, F. S.

    2013-01-01

    Understanding brain structure and function, and the complex relationships between them, is one of the grand challenges of contemporary sciences. Thanks to their flexibility, optical techniques could be the key to explore this complex network. In this manuscript, we briefly review recent advancements in optical methods applied to three main issues: anatomy, plasticity and functionality. We describe novel implementations of light-sheet microscopy to resolve neuronal anatomy in whole fixed brain...

  20. A no extensive statistical model for the nucleon structure function

    International Nuclear Information System (INIS)

    Trevisan, Luis A.; Mirez, Carlos

    2013-01-01

    We studied an application of nonextensive thermodynamics to describe the structure function of nucleon, in a model where the usual Fermi-Dirac and Bose-Einstein energy distribution were replaced by the equivalent functions of the q-statistical. The parameters of the model are given by an effective temperature T, the q parameter (from Tsallis statistics), and two chemical potentials given by the corresponding up (u) and down (d) quark normalization in the nucleon.

  1. Determination of the pion and kaon structure functions

    International Nuclear Information System (INIS)

    Aitkenhead, W.; Barton, D.S.; Brandenburg, G.W.; Busza, W.; Dobrowolski, T.; Friedman, J.I.; Kendall, H.W.; Lyons, T.; Nelson, B.; Rosenson, L.; Toy, W.; Verdier, R.; Votta, L.; Chiaradia, M.T.; DeMarzo, C.; Favuzzi, C.; Germinario, G.; Guerriero, L.; LaVopa, P.; Maggi, G.; Posa, F.; Selvaggi, G.; Spinelli, P.; Waldner, F.; Brenner, A.E.; Carey, D.C.; Elias, J.E.; Garbincius, P.H.; Mikenberg, G.; Polychronakos, V.A.; Meunier, R.; Cutts, D.; Dulude, R.S.; Lanou, R.E. Jr.; Massimo, J.T.

    1980-01-01

    Quark structure functions have been extracted from low-p/sub T/ inclusive hadron production data for the pion and kaon with use of the recombination model. n/sup π/=1.0 +- 0.1 and n/sup K/=2.5 +- 0.6 is obtained, where n is the leading (1-x) power of the nonstrange--valence-quark distribution. Both the pion and kaon nonstrange--sea-quark functions have napprox. =3.5

  2. Normal central retinal function and structure preserved in retinitis pigmentosa.

    Science.gov (United States)

    Jacobson, Samuel G; Roman, Alejandro J; Aleman, Tomas S; Sumaroka, Alexander; Herrera, Waldo; Windsor, Elizabeth A M; Atkinson, Lori A; Schwartz, Sharon B; Steinberg, Janet D; Cideciyan, Artur V

    2010-02-01

    To determine whether normal function and structure, as recently found in forms of Usher syndrome, also occur in a population of patients with nonsyndromic retinitis pigmentosa (RP). Patients with simplex, multiplex, or autosomal recessive RP (n = 238; ages 9-82 years) were studied with static chromatic perimetry. A subset was evaluated with optical coherence tomography (OCT). Co-localized visual sensitivity and photoreceptor nuclear layer thickness were measured across the central retina to establish the relationship of function and structure. Comparisons were made to patients with Usher syndrome (n = 83, ages 10-69 years). Cross-sectional psychophysical data identified patients with RP who had normal rod- and cone-mediated function in the central retina. There were two other patterns with greater dysfunction, and longitudinal data confirmed that progression can occur from normal rod and cone function to cone-only central islands. The retinal extent of normal laminar architecture by OCT corresponded to the extent of normal visual function in patients with RP. Central retinal preservation of normal function and structure did not show a relationship with age or retained peripheral function. Usher syndrome results were like those in nonsyndromic RP. Regional disease variation is a well-known finding in RP. Unexpected was the observation that patients with presumed recessive RP can have regions with functionally and structurally normal retina. Such patients will require special consideration in future clinical trials of either focal or systemic treatment. Whether there is a common molecular mechanism shared by forms of RP with normal regions of retina warrants further study.

  3. Phase sensitive spectral domain interferometry for label free biomolecular interaction analysis and biosensing applications

    Science.gov (United States)

    Chirvi, Sajal

    Biomolecular interaction analysis (BIA) plays vital role in wide variety of fields, which include biomedical research, pharmaceutical industry, medical diagnostics, and biotechnology industry. Study and quantification of interactions between natural biomolecules (proteins, enzymes, DNA) and artificially synthesized molecules (drugs) is routinely done using various labeled and label-free BIA techniques. Labeled BIA (Chemiluminescence, Fluorescence, Radioactive) techniques suffer from steric hindrance of labels on interaction site, difficulty of attaching labels to molecules, higher cost and time of assay development. Label free techniques with real time detection capabilities have demonstrated advantages over traditional labeled techniques. The gold standard for label free BIA is surface Plasmon resonance (SPR) that detects and quantifies the changes in refractive index of the ligand-analyte complex molecule with high sensitivity. Although SPR is a highly sensitive BIA technique, it requires custom-made sensor chips and is not well suited for highly multiplexed BIA required in high throughput applications. Moreover implementation of SPR on various biosensing platforms is limited. In this research work spectral domain phase sensitive interferometry (SD-PSI) has been developed for label-free BIA and biosensing applications to address limitations of SPR and other label free techniques. One distinct advantage of SD-PSI compared to other label-free techniques is that it does not require use of custom fabricated biosensor substrates. Laboratory grade, off-the-shelf glass or plastic substrates of suitable thickness with proper surface functionalization are used as biosensor chips. SD-PSI is tested on four separate BIA and biosensing platforms, which include multi-well plate, flow cell, fiber probe with integrated optics and fiber tip biosensor. Sensitivity of 33 ng/ml for anti-IgG is achieved using multi-well platform. Principle of coherence multiplexing for multi

  4. Soil-borne microbial functional structure across different land uses.

    Science.gov (United States)

    Kuramae, Eiko E; Zhou, Jizhong Z; Kowalchuk, George A; van Veen, Johannes A

    2014-01-01

    Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio. C : N ratio showed a significant positive correlation with clay and soil pH. Fields with low C : N ratio had an overrepresentation of genes for carbon degradation, carbon fixation, metal reductase, and organic remediation categories, while fields with high C : N ratio had an overrepresentation of genes encoding dissimilatory sulfate reductase, methane oxidation, nitrification, and nitrogen fixation. The most abundant genes related to carbon degradation comprised bacterial and fungal cellulases; bacterial and fungal chitinases; fungal laccases; and bacterial, fungal, and oomycete polygalacturonases. The high number of genes related to organic remediation was probably driven by high phosphate content, while the high number of genes for nitrification was probably explained by high total nitrogen content. The functional gene diversity found in different soils did not group the sites accordingly to land management. Rather, the soil factors, C : N ratio, phosphate, and total N, were the main factors driving the differences in functional genes across the fields examined.

  5. Soil-Borne Microbial Functional Structure across Different Land Uses

    Directory of Open Access Journals (Sweden)

    Eiko E. Kuramae

    2014-01-01

    Full Text Available Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio. C : N ratio showed a significant positive correlation with clay and soil pH. Fields with low C : N ratio had an overrepresentation of genes for carbon degradation, carbon fixation, metal reductase, and organic remediation categories, while fields with high C : N ratio had an overrepresentation of genes encoding dissimilatory sulfate reductase, methane oxidation, nitrification, and nitrogen fixation. The most abundant genes related to carbon degradation comprised bacterial and fungal cellulases; bacterial and fungal chitinases; fungal laccases; and bacterial, fungal, and oomycete polygalacturonases. The high number of genes related to organic remediation was probably driven by high phosphate content, while the high number of genes for nitrification was probably explained by high total nitrogen content. The functional gene diversity found in different soils did not group the sites accordingly to land management. Rather, the soil factors, C : N ratio, phosphate, and total N, were the main factors driving the differences in functional genes across the fields examined.

  6. Correlated Heterospectral Lipidomics for Biomolecular Profiling of Remyelination in Multiple Sclerosis

    Directory of Open Access Journals (Sweden)

    Mads S. Bergholt

    2017-12-01

    Full Text Available Analyzing lipid composition and distribution within the brain is important to study white matter pathologies that present focal demyelination lesions, such as multiple sclerosis. Some lesions can endogenously re-form myelin sheaths. Therapies aim to enhance this repair process in order to reduce neurodegeneration and disability progression in patients. In this context, a lipidomic analysis providing both precise molecular classification and well-defined localization is crucial to detect changes in myelin lipid content. Here we develop a correlated heterospectral lipidomic (HSL approach based on coregistered Raman spectroscopy, desorption electrospray ionization mass spectrometry (DESI-MS, and immunofluorescence imaging. We employ HSL to study the structural and compositional lipid profile of demyelination and remyelination in an induced focal demyelination mouse model and in multiple sclerosis lesions from patients ex vivo. Pixelwise coregistration of Raman spectroscopy and DESI-MS imaging generated a heterospectral map used to interrelate biomolecular structure and composition of myelin. Multivariate regression analysis enabled Raman-based assessment of highly specific lipid subtypes in complex tissue for the first time. This method revealed the temporal dynamics of remyelination and provided the first indication that newly formed myelin has a different lipid composition compared to normal myelin. HSL enables detailed molecular myelin characterization that can substantially improve upon the current understanding of remyelination in multiple sclerosis and provides a strategy to assess remyelination treatments in animal models.

  7. Functional RNA structures throughout the Hepatitis C Virus genome.

    Science.gov (United States)

    Adams, Rebecca L; Pirakitikulr, Nathan; Pyle, Anna Marie

    2017-06-01

    The single-stranded Hepatitis C Virus (HCV) genome adopts a set of elaborate RNA structures that are involved in every stage of the viral lifecycle. Recent advances in chemical probing, sequencing, and structural biology have facilitated analysis of RNA folding on a genome-wide scale, revealing novel structures and networks of interactions. These studies have underscored the active role played by RNA in every function of HCV and they open the door to new types of RNA-targeted therapeutics. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. A Quick-responsive DNA Nanotechnology Device for Bio-molecular Homeostasis Regulation.

    Science.gov (United States)

    Wu, Songlin; Wang, Pei; Xiao, Chen; Li, Zheng; Yang, Bing; Fu, Jieyang; Chen, Jing; Wan, Neng; Ma, Cong; Li, Maoteng; Yang, Xiangliang; Zhan, Yi

    2016-08-10

    Physiological processes such as metabolism, cell apoptosis and immune responses, must be strictly regulated to maintain their homeostasis and achieve their normal physiological functions. The speed with which bio-molecular homeostatic regulation occurs directly determines the ability of an organism to adapt to conditional changes. To produce a quick-responsive regulatory system that can be easily utilized for various types of homeostasis, a device called nano-fingers that facilitates the regulation of physiological processes was constructed using DNA origami nanotechnology. This nano-fingers device functioned in linked open and closed phases using two types of DNA tweezers, which were covalently coupled with aptamers that captured specific molecules when the tweezer arms were sufficiently close. Via this specific interaction mechanism, certain physiological processes could be simultaneously regulated from two directions by capturing one biofactor and releasing the other to enhance the regulatory capacity of the device. To validate the universal application of this device, regulation of the homeostasis of the blood coagulant thrombin was attempted using the nano-fingers device. It was successfully demonstrated that this nano-fingers device achieved coagulation buffering upon the input of fuel DNA. This nano-device could also be utilized to regulate the homeostasis of other types of bio-molecules.

  9. A coarse-grained model for the simulations of biomolecular interactions in cellular environments

    International Nuclear Information System (INIS)

    Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

    2014-01-01

    The interactions of bio-molecules constitute the key steps of cellular functions. However, in vivo binding properties differ significantly from their in vitro measurements due to the heterogeneity of cellular environments. Here we introduce a coarse-grained model based on rigid-body representation to study how factors such as cellular crowding and membrane confinement affect molecular binding. The macroscopic parameters such as the equilibrium constant and the kinetic rate constant are calibrated by adjusting the microscopic coefficients used in the numerical simulations. By changing these model parameters that are experimentally approachable, we are able to study the kinetic and thermodynamic properties of molecular binding, as well as the effects caused by specific cellular environments. We investigate the volumetric effects of crowded intracellular space on bio-molecular diffusion and diffusion-limited reactions. Furthermore, the binding constants of membrane proteins are currently difficult to measure. We provide quantitative estimations about how the binding of membrane proteins deviates from soluble proteins under different degrees of membrane confinements. The simulation results provide biological insights to the functions of membrane receptors on cell surfaces. Overall, our studies establish a connection between the details of molecular interactions and the heterogeneity of cellular environments

  10. Keystone taxa as drivers of microbiome structure and functioning.

    Science.gov (United States)

    Banerjee, Samiran; Schlaeppi, Klaus; van der Heijden, Marcel G A

    2018-05-22

    Microorganisms have a pivotal role in the functioning of ecosystems. Recent studies have shown that microbial communities harbour keystone taxa, which drive community composition and function irrespective of their abundance. In this Opinion article, we propose a definition of keystone taxa in microbial ecology and summarize over 200 microbial keystone taxa that have been identified in soil, plant and marine ecosystems, as well as in the human microbiome. We explore the importance of keystone taxa and keystone guilds for microbiome structure and functioning and discuss the factors that determine their distribution and activities.

  11. Structure-function relations in physiology education: Where's the mechanism?

    Science.gov (United States)

    Lira, Matthew E; Gardner, Stephanie M

    2017-06-01

    Physiology demands systems thinking: reasoning within and between levels of biological organization and across different organ systems. Many physiological mechanisms explain how structures and their properties interact at one level of organization to produce emergent functions at a higher level of organization. Current physiology principles, such as structure-function relations, selectively neglect mechanisms by not mentioning this term explicitly. We explored how students characterized mechanisms and functions to shed light on how students make sense of these terms. Students characterized mechanisms as 1 ) processes that occur at levels of organization lower than that of functions; and 2 ) as detailed events with many steps involved. We also found that students produced more variability in how they characterized functions compared with mechanisms: students characterized functions in relation to multiple levels of organization and multiple definitions. We interpret these results as evidence that students see mechanisms as holding a more narrow definition than used in the biological sciences, and that students struggle to coordinate and distinguish mechanisms from functions due to cognitive processes germane to learning in many domains. We offer the instructional suggestion that we scaffold student learning by affording students opportunities to relate and also distinguish between these terms so central to understanding physiology. Copyright © 2017 the American Physiological Society.

  12. On relation of momenta of structure functions of the composite systems with their simultaneous wave functions

    International Nuclear Information System (INIS)

    Linkevich, A.D.; Savrin, V.I.; Sanadze, V.V.; Skachkov, N.B.

    1984-01-01

    Calculation of hadron structure function (SF) comprising point objects is carried out. The obtained hadron SF is expressed by means of simultaneous relativistic wave functions of a composite particle. Exact calculation of hadron SF momenta in simultaneous formulation of quantum field theory off-energy surface is conducted. The given calculation of hadron SF is shown to result in their dependence on momentum transferred square (or square of total vector of energy-momentum of Compton scattering on a quark) whih is determined by the set of simultaneous hadron wave functions as bound state of quark (partons) in the considered case of non-structural quarks

  13. Functional evolution and structural conservation in chimeric cytochromes p450: calibrating a structure-guided approach.

    Science.gov (United States)

    Otey, Christopher R; Silberg, Jonathan J; Voigt, Christopher A; Endelman, Jeffrey B; Bandara, Geethani; Arnold, Frances H

    2004-03-01

    Recombination generates chimeric proteins whose ability to fold depends on minimizing structural perturbations that result when portions of the sequence are inherited from different parents. These chimeric sequences can display functional properties characteristic of the parents or acquire entirely new functions. Seventeen chimeras were generated from two CYP102 members of the functionally diverse cytochrome p450 family. Chimeras predicted to have limited structural disruption, as defined by the SCHEMA algorithm, displayed CO binding spectra characteristic of folded p450s. Even this small population exhibited significant functional diversity: chimeras displayed altered substrate specificities, a wide range in thermostabilities, up to a 40-fold increase in peroxidase activity, and ability to hydroxylate a substrate toward which neither parent heme domain shows detectable activity. These results suggest that SCHEMA-guided recombination can be used to generate diverse p450s for exploring function evolution within the p450 structural framework.

  14. Dose controlled low energy electron irradiator for biomolecular films.

    Science.gov (United States)

    Kumar, S V K; Tare, Satej T; Upalekar, Yogesh V; Tsering, Thupten

    2016-03-01

    We have developed a multi target, Low Energy Electron (LEE), precise dose controlled irradiator for biomolecular films. Up to seven samples can be irradiated one after another at any preset electron energy and dose under UHV conditions without venting the chamber. In addition, one more sample goes through all the steps except irradiation, which can be used as control for comparison with the irradiated samples. All the samples are protected against stray electron irradiation by biasing them at -20 V during the entire period, except during irradiation. Ethernet based communication electronics hardware, LEE beam control electronics and computer interface were developed in house. The user Graphical User Interface to control the irradiation and dose measurement was developed using National Instruments Lab Windows CVI. The working and reliability of the dose controlled irradiator has been fully tested over the electron energy range of 0.5 to 500 eV by studying LEE induced single strand breaks to ΦX174 RF1 dsDNA.

  15. A fast mollified impulse method for biomolecular atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Fath, L., E-mail: lukas.fath@kit.edu [Institute for App. and Num. Mathematics, Karlsruhe Institute of Technology (Germany); Hochbruck, M., E-mail: marlis.hochbruck@kit.edu [Institute for App. and Num. Mathematics, Karlsruhe Institute of Technology (Germany); Singh, C.V., E-mail: chandraveer.singh@utoronto.ca [Department of Materials Science & Engineering, University of Toronto (Canada)

    2017-03-15

    Classical integration methods for molecular dynamics are inherently limited due to resonance phenomena occurring at certain time-step sizes. The mollified impulse method can partially avoid this problem by using appropriate filters based on averaging or projection techniques. However, existing filters are computationally expensive and tedious in implementation since they require either analytical Hessians or they need to solve nonlinear systems from constraints. In this work we follow a different approach based on corotation for the construction of a new filter for (flexible) biomolecular simulations. The main advantages of the proposed filter are its excellent stability properties and ease of implementation in standard softwares without Hessians or solving constraint systems. By simulating multiple realistic examples such as peptide, protein, ice equilibrium and ice–ice friction, the new filter is shown to speed up the computations of long-range interactions by approximately 20%. The proposed filtered integrators allow step sizes as large as 10 fs while keeping the energy drift less than 1% on a 50 ps simulation.

  16. Spin valve sensor for biomolecular identification: Design, fabrication, and characterization

    Science.gov (United States)

    Li, Guanxiong

    Biomolecular identification, e.g., DNA recognition, has broad applications in biology and medicine such as gene expression analysis, disease diagnosis, and DNA fingerprinting. Therefore, we have been developing a magnetic biodetection technology based on giant magnetoresistive spin valve sensors and magnetic nanoparticle (developed for the magnetic nanoparticle detection, assuming the equivalent average field of magnetic nanoparticles and the coherent rotation of spin valve free layer magnetization. Micromagnetic simulations have also been performed for the spin valve sensors. The analytical model and micromagnetic simulations are found consistent with each other and are in good agreement with experiments. The prototype spin valve sensors have been fabricated at both micron and submicron scales. We demonstrated the detection of a single 2.8-mum magnetic microbead by micron-sized spin valve sensors. Based on polymer-mediated self-assembly and fine lithography, a bilayer lift-off process was developed to deposit magnetic nanoparticles onto the sensor surface in a controlled manner. With the lift-off deposition method, we have successfully demonstrated the room temperature detection of monodisperse 16-nm Fe3O 4 nanoparticles in a quantity from a few tens to several hundreds by submicron spin valve sensors, proving the feasibility of the nanoparticle detection. As desired for quantitative biodetection, a fairly linear dependence of sensor signal on the number of nanoparticles has been confirmed. The initial detection of DNA hybridization events labeled by magnetic nanoparticles further proved the magnetic biodetection concept.

  17. Dose controlled low energy electron irradiator for biomolecular films

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, S. V. K., E-mail: svkk@tifr.res.in; Tare, Satej T.; Upalekar, Yogesh V.; Tsering, Thupten [Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005 (India)

    2016-03-15

    We have developed a multi target, Low Energy Electron (LEE), precise dose controlled irradiator for biomolecular films. Up to seven samples can be irradiated one after another at any preset electron energy and dose under UHV conditions without venting the chamber. In addition, one more sample goes through all the steps except irradiation, which can be used as control for comparison with the irradiated samples. All the samples are protected against stray electron irradiation by biasing them at −20 V during the entire period, except during irradiation. Ethernet based communication electronics hardware, LEE beam control electronics and computer interface were developed in house. The user Graphical User Interface to control the irradiation and dose measurement was developed using National Instruments Lab Windows CVI. The working and reliability of the dose controlled irradiator has been fully tested over the electron energy range of 0.5 to 500 eV by studying LEE induced single strand breaks to ΦX174 RF1 dsDNA.

  18. Structure-Function Relations in Physiology Education: Where's the Mechanism?

    Science.gov (United States)

    Lira, Matthew E.; Gardner, Stephanie M.

    2017-01-01

    Physiology demands systems thinking: reasoning within and between levels of biological organization and across different organ systems. Many physiological mechanisms explain how structures and their properties interact at one level of organization to produce emergent functions at a higher level of organization. Current physiology principles, such…

  19. Riparian ecosystems and buffers - multiscale structure, function, and management: introduction

    Science.gov (United States)

    Kathleen A. Dwire; Richard R. Lowrance

    2006-01-01

    Given the importance of issues related to improved understanding and management of riparian ecosystems and buffers, the American Water Resources Association (AWRA) sponsored a Summer Specialty Conference in June 2004 at Olympic Valley, California, entitled 'Riparian Ecosystems and Buffers: Multiscale Structure, Function, and Management.' The primary objective...

  20. What can we learn from polarized structure function data?

    CERN Document Server

    Ball, Richard D.; Altarelli, Guido; Forte, Stefano; Ball, Richard D.; Ridolfi, Giovanni; Altarelli, Guido; Forte, Stefano

    1997-04-20

    We summarise the perturbative QCD analysis of the structure function data for g_1 from longitudinally polarized deep inelastic scattering from proton, deuteron and neutron targets, with particular emphasis on testing sum rules, determining helicity fractions, and extracting the strong coupling from both scaling violations and the Bjorken sum rule.

  1. THE STRUCTURE AND FUNCTION OF DEPARTMENTS OF MEDICINE.

    Science.gov (United States)

    Landefeld, C Seth

    2016-01-01

    The structure and function of departments of medicine are important for several reasons. First, departments of medicine are the biggest departments in virtually every medical school and in most universities with a medical school, and they are the largest professional units in most academic medical centers. In fact, Petersdorf described them as "the linchpins of medical schools" (1). Departments of medicine account for one-fourth or more of the academic medical enterprise: they include about one-fourth of the faculty of medical school, account for roughly one-fourth of the patient care and clinical revenue of academic medical centers, and their faculty perform a disproportionate share of teaching and research, accounting for up to 45% of National Institutes of Health (NIH) - funded research in some medical schools. Second, the department's ability to fulfill its role and advance its mission depends on its structure and function. Finally, lessons learned from examining the structure and function of departments of medicine may guide other departments and schools of medicine themselves in improving their structure and function. This paper describes the issues that face departments of medicine in 2016. I begin by providing the context for these issues with a definition of a department of medicine, describing briefly the history of departments, and stating their mission.

  2. Structural and functional analysis of bovine herpesvirus 1 minor glycoproteins

    NARCIS (Netherlands)

    Baranowski, E.; Keil, G.; Lyaku, J.; Rijsewijk, F.A.M.; Oirschot, van J.T.; Pastoret, P.P.; Thiry, E.

    1996-01-01

    This paper focuses on the structure and functions of bovine herpesvirus 1 minor glycoproteins gH, gE, gG and gp42. It reviews the progress which has been made in their identification and characterization, in the study of their temporal expression and processing in infected cells, and finally in the

  3. Plant functional connectivity – integrating landscape structure and effective dispersal

    NARCIS (Netherlands)

    Auffret, Alistair G.; Rico, Yessica; Bullock, James M.; Hooftman, Danny A.P.; Pakeman, Robin J.; Soons, Merel B.; Suárez-Esteban, Alberto; Traveset, Anna; Wagner, Helene H.; Cousins, Sara A.O.

    2017-01-01

    Dispersal is essential for species to survive the threats of habitat destruction and climate change. Combining descriptions of dispersal ability with those of landscape structure, the concept of functional connectivity has been popular for understanding and predicting species’ spatial responses to

  4. Fabrication of functional structures on thin silicon nitride membranes

    NARCIS (Netherlands)

    Ekkels, P.; Tjerkstra, R.W.; Krijnen, Gijsbertus J.M.; Berenschot, Johan W.; Brugger, J.P.; Elwenspoek, Michael Curt

    A process to fabricate functional polysilicon structures above large (4×4 mm2) thin (200 nm), very flat LPCVD silicon rich nitride membranes was developed. Key features of this fabrication process are the use of low-stress LPCVD silicon nitride, sacrificial layer etching, and minimization of

  5. Joint Modelling of Structural and Functional Brain Networks

    DEFF Research Database (Denmark)

    Andersen, Kasper Winther; Herlau, Tue; Mørup, Morten

    -parametric Bayesian network model which allows for joint modelling and integration of multiple networks. We demonstrate the model’s ability to detect vertices that share structure across networks jointly in functional MRI (fMRI) and diffusion MRI (dMRI) data. Using two fMRI and dMRI scans per subject, we establish...

  6. Muscarinic acetylcholine receptor subtypes: localization and structure/function

    DEFF Research Database (Denmark)

    Brann, M R; Ellis, J; Jørgensen, H

    1993-01-01

    Based on the sequence of the five cloned muscarinic receptor subtypes (m1-m5), subtype selective antibody and cDNA probes have been prepared. Use of these probes has demonstrated that each of the five subtypes has a markedly distinct distribution within the brain and among peripheral tissues...... are described, as well as the implied structures of these functional domains....

  7. Mass-spectrometric exploration of proteome structure and function

    DEFF Research Database (Denmark)

    Aebersold, Ruedi; Mann, Matthias

    2016-01-01

    , the structures and functions of selected proteins have been studied using biochemical and biophysical methods. However, the properties and behaviour of the proteome as an integrated system have largely remained elusive. Powerful mass-spectrometry-based technologies now provide unprecedented insights...

  8. Structural and functional brain connectivity in presymptomatic familial frontotemporal dementia

    NARCIS (Netherlands)

    Dopper, E.G.P.; Rombouts, S.A.R.B.; Jiskoot, L.C.; den Heijer, T.; de Graaf, J.R.A.; de Koning, I.; Hammerschlag, A.R.; Seelaar, H.; Seeley, W.W.; Veer, I.M.; van Buchem, M.A.; Rizzu, P.; van Swieten, J.C.

    2013-01-01

    Objective: We aimed to investigate whether cognitive deficits and structural and functional connectivity changes can be detected before symptom onset in a large cohort of carriers of microtubuleassociated protein tau and progranulin mutations. Methods: In this case-control study, 75 healthy

  9. Structural and functional brain connectivity in presymptomatic familial frontotemporal dementia

    NARCIS (Netherlands)

    E.G.P. Dopper (Elise); S.A.R.B. Rombouts (Serge); L.C. Jiskoot (Lize); T. den Heijer (Tom); J.R.A. de Graaf (Joke); I. de Koning (Inge); M.R. Hammerschlag; H. Seelaar (Harro); W. Seeley (William); I.M. Veer (Ilya); M.A. van Buchem (Mark); P. Rizzu (Patrizia); J.C. van Swieten (John)

    2014-01-01

    textabstractObjective: We aimed to investigate whether cognitive deficits and structural and functional connectivity changes can be detected before symptom onset in a large cohort of carriers of MAPT (microtubule-associated protein tau) or GRN (progranulin) mutations. Methods: In this case-control

  10. Structural and functional brain connectivity in presymptomatic familial frontotemporal dementia

    NARCIS (Netherlands)

    E.G.P. Dopper (Elise); S.A.R.B. Rombouts (Serge); L.C. Jiskoot (Lize); T. den Heijer (Tom); J.R.A. de Graaf (J. Roos); I. de Koning (Inge); M.R. Hammerschlag; H. Seelaar (Harro); W. Seeley (William); I.M. Veer (Ilya); M.A. van Buchem (Mark); P. Rizzu (Patrizia); J.C. van Swieten (John)

    2013-01-01

    textabstractObjective: We aimed to investigate whether cognitive deficits and structural and functional connectivity changes can be detected before symptom onset in a large cohort of carriers of microtubuleassociated protein tau and progranulin mutations. Methods: In this case-control study, 75

  11. Factor Structure, Stability, and Congruence in the Functional Movement Screen

    Science.gov (United States)

    Kelleher, Leila K.; Beach, Tyson A. C.; Frost, David M.; Johnson, Andrew M.; Dickey, James P.

    2018-01-01

    The scoring scheme for the functional movement screen implicitly assumes that the factor structure is consistent, stable, and congruent across different populations. To determine if this is the case, we compared principal components analyses of three samples: a healthy, general population (n = 100), a group of varsity athletes (n = 101), and a…

  12. Imaging structural and functional brain networks in temporal lobe epilepsy

    Science.gov (United States)

    Bernhardt, Boris C.; Hong, SeokJun; Bernasconi, Andrea; Bernasconi, Neda

    2013-01-01

    Early imaging studies in temporal lobe epilepsy (TLE) focused on the search for mesial temporal sclerosis, as its surgical removal results in clinically meaningful improvement in about 70% of patients. Nevertheless, a considerable subgroup of patients continues to suffer from post-operative seizures. Although the reasons for surgical failure are not fully understood, electrophysiological and imaging data suggest that anomalies extending beyond the temporal lobe may have negative impact on outcome. This hypothesis has revived the concept of human epilepsy as a disorder of distributed brain networks. Recent methodological advances in non-invasive neuroimaging have led to quantify structural and functional networks in vivo. While structural networks can be inferred from diffusion MRI tractography and inter-regional covariance patterns of structural measures such as cortical thickness, functional connectivity is generally computed based on statistical dependencies of neurophysiological time-series, measured through functional MRI or electroencephalographic techniques. This review considers the application of advanced analytical methods in structural and functional connectivity analyses in TLE. We will specifically highlight findings from graph-theoretical analysis that allow assessing the topological organization of brain networks. These studies have provided compelling evidence that TLE is a system disorder with profound alterations in local and distributed networks. In addition, there is emerging evidence for the utility of network properties as clinical diagnostic markers. Nowadays, a network perspective is considered to be essential to the understanding of the development, progression, and management of epilepsy. PMID:24098281

  13. Modelling functional and structural impact of non-synonymous ...

    African Journals Online (AJOL)

    ... that could affect protein function and structure. Further wet-lab confirmatory analysis in a pathological association study involving a larger population of goats is required at the DQA1 locus. This would lay a sound foundation for breeding disease-resistant individuals in the future. Keywords: Goats, in silico, mutants, protein, ...

  14. Imaging structural and functional brain networks in temporal lobe epilepsy

    Directory of Open Access Journals (Sweden)

    Boris eBernhardt

    2013-10-01

    Full Text Available Early imaging studies in temporal lobe epilepsy (TLE focused on the search for mesial temporal sclerosis, as its surgical removal results in clinically meaningful improvement in about 70% of patients. Nevertheless, a considerable subgroup of patients continues to suffer from post-operative seizures. Although the reasons for surgical failure are not fully understood, electrophysiological and imaging data suggest that anomalies extending beyond the temporal lobe may have negative impact on outcome. This hypothesis has revived the concept of human epilepsy as a disorder of distributed brain networks. Recent methodological advances in non-invasive neuroimaging have led to quantify structural and functional networks in vivo. While structural networks can be inferred from diffusion MRI tractography and inter-regional covariance patterns of structural measures such as cortical thickness, functional connectivity is generally computed based on statistical dependencies of neurophysiological time-series, measured through functional MRI or electroencephalographic techniques. This review considers the application of advanced analytical methods in structural and functional connectivity analyses in TLE. We will specifically highlight findings from graph-theoretical analysis that allow assessing topological organization of brain networks. These studies have provided compelling evidence that TLE is a system disorder with profound alterations in local and distributed networks. In addition, there is emerging evidence for the utility of network properties as clinical diagnostic markers. Nowadays, a network perspective is considered to be essential to the understanding of the development, progression, and management of epilepsy.

  15. Imaging structural and functional brain networks in temporal lobe epilepsy.

    Science.gov (United States)

    Bernhardt, Boris C; Hong, Seokjun; Bernasconi, Andrea; Bernasconi, Neda

    2013-10-01

    Early imaging studies in temporal lobe epilepsy (TLE) focused on the search for mesial temporal sclerosis, as its surgical removal results in clinically meaningful improvement in about 70% of patients. Nevertheless, a considerable subgroup of patients continues to suffer from post-operative seizures. Although the reasons for surgical failure are not fully understood, electrophysiological and imaging data suggest that anomalies extending beyond the temporal lobe may have negative impact on outcome. This hypothesis has revived the concept of human epilepsy as a disorder of distributed brain networks. Recent methodological advances in non-invasive neuroimaging have led to quantify structural and functional networks in vivo. While structural networks can be inferred from diffusion MRI tractography and inter-regional covariance patterns of structural measures such as cortical thickness, functional connectivity is generally computed based on statistical dependencies of neurophysiological time-series, measured through functional MRI or electroencephalographic techniques. This review considers the application of advanced analytical methods in structural and functional connectivity analyses in TLE. We will specifically highlight findings from graph-theoretical analysis that allow assessing the topological organization of brain networks. These studies have provided compelling evidence that TLE is a system disorder with profound alterations in local and distributed networks. In addition, there is emerging evidence for the utility of network properties as clinical diagnostic markers. Nowadays, a network perspective is considered to be essential to the understanding of the development, progression, and management of epilepsy.

  16. Two-level convolution formula for nuclear structure function

    Science.gov (United States)

    Ma, Boqiang

    1990-05-01

    A two-level convolution formula for the nuclear structure function is derived in considering the nucleus as a composite system of baryon-mesons which are also composite systems of quark-gluons again. The results show that the European Muon Colaboration effect can not be explained by the nuclear effects as nucleon Fermi motion and nuclear binding contributions.

  17. Two-level convolution formula for nuclear structure function

    International Nuclear Information System (INIS)

    Ma Boqiang

    1990-01-01

    A two-level convolution formula for the nuclear structure function is derived in considering the nucleus as a composite system of baryon-mesons which are also composite systems of quark-gluons again. The results show that the European Muon Colaboration effect can not be explained by the nuclear effects as nucleon Fermi motion and nuclear binding contributions

  18. Phenomenological structure functions and Gribov-Lipatov relation

    International Nuclear Information System (INIS)

    Choudhary, D.K.; Misra, A.K.

    1987-01-01

    An analysis of the Giribov-Lipatov relation using the phenomenological forms of the structure function F 2 ep is made. The analysis indicate breakdown of the relation at PETRA energies. Plausible reasons of the breakdown of Gribov-Lipatov relation are discussed together with its phenomenological form. 33 refs., 6 figures. (author)

  19. Structure and Function of a Nonruminant Gut: A Porcine Model

    DEFF Research Database (Denmark)

    Tajima, Kiyoshi; Aminov, Rustam

    2015-01-01

    In many aspects, the anatomical, physiological, and microbial diversity features of the ruminant gut are different from that of the monogastric animals. Thus, the main aim of this chapter is to give a comparative overview of the structure and function of the gastrointestinal tract of a nonruminan...

  20. Structure, function and nutritional potential of milk osteopontin

    DEFF Research Database (Denmark)

    Christensen, Brian Søndergaard; Sørensen, Esben Skipper

    2016-01-01

    in cancer related events. In this article, we review the differences between milk-derived OPN and OPN derived from transformed cells and compare the structure of OPN from human and bovine milk. Furthermore, current knowledge about the function of OPN in milk and recent findings about the effect of orally...

  1. Basic concepts of Density Functional Theory: Electronic structure calculation

    International Nuclear Information System (INIS)

    Sharma, B. Indrajit

    2016-01-01

    We are looking for a material which possesses the required properties as demanded for technological applications. For this we have to repeat the preparation of the appropriate materials and its characterizations. So, before proceeding to experiments, one can study on computer generated structure and predict the properties of the desired material. To do this, a concept of Density Functional Theory comes out. (paper)

  2. The aging lacrimal gland: changes in structure and function.

    Science.gov (United States)

    Rocha, Eduardo M; Alves, Monica; Rios, J David; Dartt, Darlene A

    2008-10-01

    The afferent nerves of the cornea and conjunctiva, efferent nerves of the lacrimal gland, and the lacrimal gland are a functional unit that works cooperatively to produce the aqueous component of tears. A decrease in the lacrimal gland secretory function can lead to dry eye disease. Because aging is a risk factor for dry eye disease, study of the changes in the function of the lacrimal gland functional unit with age is important for developing treatments to prevent dry eye disease. No one mechanism is known to induce the changes that occur with aging, although multiple different mechanisms have been associated with aging. These fall into two theoretical categories: programmed theories of aging (immunological, genetic, apoptotic, and neuroendocrine) and error theories of aging (protein alteration, somatic mutation, etc). Lacrimal glands undergo structural and functional alteration with increasing age. In mouse models of aging, it has been shown that neural stimulation of protein secretion is an early target of aging, accompanied by an increase in mast cells and lipofuscin accumulation. Hyperglycemia and increased lymphocytic infiltration can contribute to this loss of function at older ages. These findings suggest that an increase in oxidative stress may play a role in the loss of lacrimal gland function with age. For the afferent and efferent neural components of the lacrimal gland functional unit, immune or inflammatory mediated decrease in nerve function could contribute to loss of lacrimal gland secretion with age. More research in this area is critically needed.

  3. Measurement of the proton spin structure function g1p

    International Nuclear Information System (INIS)

    Pussieux, T.

    1994-10-01

    In order to check the Bjorken sum rule and confirm the EMC surprising conclusion on the spin structure of the proton, the measurement of the spin structure function of the proton has been performed by the Spin Muon Collaboration via the polarized muon nucleon deep inelastic scattering. The results of the 1993 run are presented within a kinematical range of 0.003 2 = 10 GeV 2 . The first moment of the polarized spin structure function g 1 p is found to be two standard deviations below the Ellis-Jaffe sum rule. Assuming SU(3) for hyperons β decays, the quark spin contribution to the proton spin is extracted. Combining all available data on proton, neutron and deuton, The Bjorken sum rule is confirmed within 10%. (author). 25 refs., 3 figs., 2 tabs

  4. DNA mimic proteins: functions, structures, and bioinformatic analysis.

    Science.gov (United States)

    Wang, Hao-Ching; Ho, Chun-Han; Hsu, Kai-Cheng; Yang, Jinn-Moon; Wang, Andrew H-J

    2014-05-13

    DNA mimic proteins have DNA-like negative surface charge distributions, and they function by occupying the DNA binding sites of DNA binding proteins to prevent these sites from being accessed by DNA. DNA mimic proteins control the activities of a variety of DNA binding proteins and are involved in a wide range of cellular mechanisms such as chromatin assembly, DNA repair, transcription regulation, and gene recombination. However, the sequences and structures of DNA mimic proteins are diverse, making them difficult to predict by bioinformatic search. To date, only a few DNA mimic proteins have been reported. These DNA mimics were not found by searching for functional motifs in their sequences but were revealed only by structural analysis of their charge distribution. This review highlights the biological roles and structures of 16 reported DNA mimic proteins. We also discuss approaches that might be used to discover new DNA mimic proteins.

  5. 2011 Plant Lipids: Structure, Metabolism, & Function Gordon Research Conference

    Energy Technology Data Exchange (ETDEWEB)

    Christopher Benning

    2011-02-04

    This is the second Gordon Research Conference on 'Plant Lipids: Structure, Metabolism & Function'. It covers current topics in lipid structure, metabolism and function in eukaryotic photosynthetic organisms including seed plants, algae, mosses and ferns. Work in photosynthetic bacteria is considered as well as it serves the understanding of specific aspects of lipid metabolism in plants. Breakthroughs are discussed in research on plant lipids as diverse as glycerolipids, sphingolipids, lipids of the cell surface, isoprenoids, fatty acids and their derivatives. The program covers nine concepts at the forefront of research under which afore mentioned plant lipid classes are discussed. The goal is to integrate areas such as lipid signaling, basic lipid metabolism, membrane function, lipid analysis, and lipid engineering to achieve a high level of stimulating interaction among diverse researchers with interests in plant lipids. One Emphasis is on the dynamics and regulation of lipid metabolism during plant cell development and in response to environmental factors.

  6. Structural and functional networks in complex systems with delay.

    Science.gov (United States)

    Eguíluz, Víctor M; Pérez, Toni; Borge-Holthoefer, Javier; Arenas, Alex

    2011-05-01

    Functional networks of complex systems are obtained from the analysis of the temporal activity of their components, and are often used to infer their unknown underlying connectivity. We obtain the equations relating topology and function in a system of diffusively delay-coupled elements in complex networks. We solve exactly the resulting equations in motifs (directed structures of three nodes) and in directed networks. The mean-field solution for directed uncorrelated networks shows that the clusterization of the activity is dominated by the in-degree of the nodes, and that the locking frequency decreases with increasing average degree. We find that the exponent of a power law degree distribution of the structural topology γ is related to the exponent of the associated functional network as α=(2-γ)(-1) for γ<2. © 2011 American Physical Society

  7. DMPD: Structural and functional analyses of bacterial lipopolysaccharides. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 12106784 Structural and functional analyses of bacterial lipopolysaccharides. Carof...html) (.csml) Show Structural and functional analyses of bacterial lipopolysaccharides. PubmedID 12106784 Title Structural and functi...onal analyses of bacterial lipopolysaccharides. Authors

  8. Biomolecular-solvent stereodynamic coupling probed by deuteration

    International Nuclear Information System (INIS)

    Fornili, S.L.; Leone, M.; Madonia, F.; Migliore, M.; Palma-Vittorelli, M.B.; Palma, M.U.; San Biagio, P.L.

    1983-01-01

    Thermodynamic interpretation of experiments with isotopically perturbed solvent supports the view that solvent stereodynamics is directly relevant to thermodynamic stability of biomolecules. According with the current understanding of the structure of the aqueous solvent, in any stereodynamic configuration of the latter, connectivity pathways are identifiable for their topologic and order properties. Perturbing the solvent by isotopic substitution or, e.g., by addition of co-solvents, can therefore be viewed as reinforcing or otherwise perturbing these topologic structures. This microscopic model readily visualizes thermodynamic interpretation. In conclusion, the topologic stereodynamic structures of connectivity pathways in the solvent, as modified by interaction with solutes, acquire a specific thermodynamic and biological significance, and the problem of thermodynamic and functional stability of biomolecules is seen in its full pertinent phase space

  9. Structural and functional cerebral correlates of hypnotic suggestibility.

    Directory of Open Access Journals (Sweden)

    Alexa Huber

    Full Text Available Little is known about the neural bases of hypnotic suggestibility, a cognitive trait referring to the tendency to respond to hypnotic suggestions. In the present magnetic resonance imaging study, we performed regression analyses to assess hypnotic suggestibility-related differences in local gray matter volume, using voxel-based morphometry, and in waking resting state functional connectivity of 10 resting state networks, in 37 healthy women. Hypnotic suggestibility was positively correlated with gray matter volume in portions of the left superior and medial frontal gyri, roughly overlapping with the supplementary and pre-supplementary motor area, and negatively correlated with gray matter volume in the left superior temporal gyrus and insula. In the functional connectivity analysis, hypnotic suggestibility was positively correlated with functional connectivity between medial posterior areas, including bilateral posterior cingulate cortex and precuneus, and both the lateral visual network and the left fronto-parietal network; a positive correlation was also found with functional connectivity between the executive-control network and a right postcentral/parietal area. In contrast, hypnotic suggestibility was negatively correlated with functional connectivity between the right fronto-parietal network and the right lateral thalamus. These findings demonstrate for the first time a correlation between hypnotic suggestibility, the structural features of specific cortical regions, and the functional connectivity during the normal resting state of brain structures involved in imagery and self-monitoring activity.

  10. Structural and functional cerebral correlates of hypnotic suggestibility.

    Science.gov (United States)

    Huber, Alexa; Lui, Fausta; Duzzi, Davide; Pagnoni, Giuseppe; Porro, Carlo Adolfo

    2014-01-01

    Little is known about the neural bases of hypnotic suggestibility, a cognitive trait referring to the tendency to respond to hypnotic suggestions. In the present magnetic resonance imaging study, we performed regression analyses to assess hypnotic suggestibility-related differences in local gray matter volume, using voxel-based morphometry, and in waking resting state functional connectivity of 10 resting state networks, in 37 healthy women. Hypnotic suggestibility was positively correlated with gray matter volume in portions of the left superior and medial frontal gyri, roughly overlapping with the supplementary and pre-supplementary motor area, and negatively correlated with gray matter volume in the left superior temporal gyrus and insula. In the functional connectivity analysis, hypnotic suggestibility was positively correlated with functional connectivity between medial posterior areas, including bilateral posterior cingulate cortex and precuneus, and both the lateral visual network and the left fronto-parietal network; a positive correlation was also found with functional connectivity between the executive-control network and a right postcentral/parietal area. In contrast, hypnotic suggestibility was negatively correlated with functional connectivity between the right fronto-parietal network and the right lateral thalamus. These findings demonstrate for the first time a correlation between hypnotic suggestibility, the structural features of specific cortical regions, and the functional connectivity during the normal resting state of brain structures involved in imagery and self-monitoring activity.

  11. Protein Function Prediction Based on Sequence and Structure Information

    KAUST Repository

    Smaili, Fatima Z.

    2016-05-25

    The number of available protein sequences in public databases is increasing exponentially. However, a significant fraction of these sequences lack functional annotation which is essential to our understanding of how biological systems and processes operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching these predicted models, using global and local similarities, through three independent enzyme commission (EC) and gene ontology (GO) function libraries. The method was tested on 250 “hard” proteins, which lack homologous templates in both structure and function libraries. The results show that this method outperforms the conventional prediction methods based on sequence similarity or threading. Additionally, our method could be improved even further by incorporating protein-protein interaction information. Overall, the method we use provides an efficient approach for automated functional annotation of non-homologous proteins, starting from their sequence.

  12. Surface structure of polymer Gels and emerging functions

    CERN Document Server

    Kobiki, Y

    1999-01-01

    We report the surface structure of polymer gels on a submicrometer scale during the volume phase transition. Sponge-like domains with a mesoscopic scale were directly observed in water by using at atomic force microscope (AFM). The surface structure characterized by the domains is discussed in terms of the root-mean-square roughness and the auto-correlation function, which were calculated from the AFM images. In order to demonstrate the role of surface structure in determining the macroscopic properties of film-like poly (N-isopropylacrylamide: NIPA) gels. It was found that the temperature dependence, as well as the absolute values of the static contact angle, were strongly dependent on the bulk network inhomogeneities. The relation between the mesoscopic structure and the macroscopic properties is qualitatively discussed in terms of not only the changes in the chemical, but also in the physical, surface properties of the NIPA gels in response to a temperature change.

  13. Structural and functional significance of water permeation through cotransporters

    DEFF Research Database (Denmark)

    Zeuthen, Thomas; Gorraitz, Edurne; Her, Ka

    2016-01-01

    Membrane transporters, in addition to their major role as specific carriers for ions and small molecules, can also behave as water channels. However, neither the location of the water pathway in the protein nor their functional importance is known. Here, we map the pathway for water and urea...... through the intestinal sodium/glucose cotransporter SGLT1. Molecular dynamics simulations using the atomic structure of the bacterial transporter vSGLT suggest that water permeates the same path as Na+ and sugar. On a structural model of SGLT1, based on the homology structure of vSGLT, we identified...... to be due to alterations in steric hindrance to water and urea, and/or changes in protein folding caused by mismatching of side chains in the water pathway. Water permeation through SGLT1 and other transporters bears directly on the structural mechanism for the transport of polar solutes through...

  14. Structure to function: Spider silk and human collagen

    Science.gov (United States)

    Rabotyagova, Olena S.

    Nature has the ability to assemble a variety of simple molecules into complex functional structures with diverse properties. Collagens, silks and muscles fibers are some examples of fibrous proteins with self-assembling properties. One of the great challenges facing Science is to mimic these designs in Nature to find a way to construct molecules that are capable of organizing into functional supra-structures by self-assembly. In order to do so, a construction kit consisting of molecular building blocks along with a complete understanding on how to form functional materials is required. In this current research, the focus is on spider silk and collagen as fibrous protein-based biopolymers that can shed light on how to generate nanostructures through the complex process of self-assembly. Spider silk in fiber form offers a unique combination of high elasticity, toughness, and mechanical strength, along with biological compatibility and biodegrability. Spider silk is an example of a natural block copolymer, in which hydrophobic and hydrophilic blocks are linked together generating polymers that organize into functional materials with extraordinary properties. Since silks resemble synthetic block copolymer systems, we adopted the principles of block copolymer design from the synthetic polymer literature to build block copolymers based on spider silk sequences. Moreover, we consider spider silk to be an important model with which to study the relationships between structure and properties in our system. Thus, the first part of this work was dedicated to a novel family of spider silk block copolymers, where we generated a new family of functional spider silk-like block copolymers through recombinant DNA technology. To provide fundamental insight into relationships between peptide primary sequence, block composition, and block length and observed morphological and structural features, we used these bioengineered spider silk block copolymers to study secondary structure

  15. Functional vs. Structural Modularity: do they imply each other?

    Science.gov (United States)

    Toroczkai, Zoltan

    2009-03-01

    While many deterministic and stochastic processes have been proposed to produce heterogeneous graphs mimicking real-world networks, only a handful of studies attempt to connect structure and dynamics with the function(s) performed by the network. In this talk I will present an approach built on the premise that structure, dynamics, and their observed heterogeneity, are implementations of various functions and their compositions. After a brief review of real-world networks where this connection can explicitly be made, I will focus on biological networks. Biological networks are known to possess functionally specialized modules, which perform tasks almost independently of each other. While proposals have been made for the evolutionary emergence of modularity, it is far from clear that adaptation on evolutionary timescales is the sole mechanism leading to functional specialization. We show that non-evolutionary learning can also lead to the formation of functionally specialized modules in a system exposed to multiple environmental constraints. A natural example suggesting that this is possible is the cerebral cortex, where there are clearly delineated functional areas in spite of the largely uniform anatomical construction of the cortical tissue. However, as numerous experiments show, when damaged, regions specialized for a certain function can be retrained to perform functions normally attributed to other regions. We use the paradigm of neural networks to represent a multitasking system, and use several non-evolutionary learning algorithms as mechanisms for phenotypic adaptation. We show that for a network learning to perform multiple tasks, the degree of independence between the tasks dictates the degree of functional specialization emerging in the network. To uncover the functional modules, we introduce a method of node knockouts that explicitly rates the contribution of each node to different tasks (differential robustness). Through a concrete example we also

  16. On the nodal structure of atomic and molecular Wigner functions

    International Nuclear Information System (INIS)

    Dahl, J.P.; Schmider, H.

    1996-01-01

    In previous work on the phase-space representation of quantum mechanics, we have presented detailed pictures of the electronic one-particle reduced Wigner function for atoms and small molecules. In this communication, we focus upon the nodal structure of the function. On the basis of the simplest systems, we present an expression which relates the oscillatory decay of the Wigner function solely to the dot product of the position and momentum vector, if both arguments are large. We then demonstrate the regular behavior of nodal patterns for the larger systems. For the molecular systems, an argument analogous to the open-quotes bond-oscillatory principleclose quotes for momentum densities links the nuclear framework to an additional oscillatory term in momenta parallel to bonds. It is shown that these are visible in the Wigner function in terms of characteristic nodes

  17. Staphylococcal Immune Evasion Proteins: Structure, Function, and Host Adaptation.

    Science.gov (United States)

    Koymans, Kirsten J; Vrieling, Manouk; Gorham, Ronald D; van Strijp, Jos A G

    2017-01-01

    Staphylococcus aureus is a successful human and animal pathogen. Its pathogenicity is linked to its ability to secrete a large amount of virulence factors. These secreted proteins interfere with many critical components of the immune system, both innate and adaptive, and hamper proper immune functioning. In recent years, numerous studies have been conducted in order to understand the molecular mechanism underlying the interaction of evasion molecules with the host immune system. Structural studies have fundamentally contributed to our understanding of the mechanisms of action of the individual factors. Furthermore, such studies revealed one of the most striking characteristics of the secreted immune evasion molecules: their conserved structure. Despite high-sequence variability, most immune evasion molecules belong to a small number of structural categories. Another remarkable characteristic is that S. aureus carries most of these virulence factors on mobile genetic elements (MGE) or ex-MGE in its accessory genome. Coevolution of pathogen and host has resulted in immune evasion molecules with a highly host-specific function and prevalence. In this review, we explore how these shared structures and genomic locations relate to function and host specificity. This is discussed in the context of therapeutic options for these immune evasion molecules in infectious as well as in inflammatory diseases.

  18. Template-assisted growth of nano structured functional materials

    International Nuclear Information System (INIS)

    Ying, K.K.; Nur Ubaidah Saidin; Khuan, N.I.; Suhaila Hani Ilias; Foo, C.T.

    2012-01-01

    Template-assisted growth is an important nano electrochemical deposition technique for synthesizing one-dimensional (1-D) nano structures with uniformly well-controlled shapes and sizes. A good template with well-defined dimensions is imperative for realizing this task. Porous anodic alumina (PAA) has been a favorable candidate for this purpose as it can be tailor-made with precise pore geometries, such as pore length and diameter as well as inter-pore distances, via the anodization of pure aluminium. This paper reports the fabrication of PAA templates and electrochemical synthesis of functional nano structures in the form of nano wires using PAA templates as scaffolds. Axial heterostructure and homogeneous nano wires formed by engineering materials configuration via composition and/ or layer thickness variations were fabricated for different functionalities. X-ray diffraction and imaging techniques were used to alucidate the microstructures, morphologies and chemical compositions of the nano wires produced. Due to their large surface area-to-volume ratios, and therefore high sensitivities, these functional nano structures have useful applications as critical components in nano sensor devices and various areas of nano technology. Potential applications include as hydrogen gas sensors in nuclear power plant for monitoring structural integrity of reactor components and containment building, as well as environmental monitoring of air pollution and leakages of toxic gases and chemicals. (Author)

  19. Nucleon structure functions in noncommutative space-time

    Energy Technology Data Exchange (ETDEWEB)

    Rafiei, A.; Rezaei, Z.; Mirjalili, A. [Yazd University, Physics Department, Yazd (Iran, Islamic Republic of)

    2017-05-15

    In the context of noncommutative space-time we investigate the nucleon structure functions which play an important role in identifying the internal structure of nucleons. We use the corrected vertices and employ new vertices that appear in two approaches of noncommutativity and calculate the proton structure functions in terms of the noncommutative tensor θ{sub μν}. To check our results we plot the nucleon structure function (NSF), F{sub 2}(x), and compare it with experimental data and the results from the GRV, GJR and CT10 parametrization models. We show that with the new vertex that arises the noncommutativity correction will lead to a better consistency between theoretical results and experimental data for the NSF. This consistency will be better for small values of the Bjorken variable x. To indicate and confirm the validity of our calculations we also act conversely. We obtain a lower bound for the numerical values of Λ{sub NC} scale which correspond to recent reports. (orig.)

  20. CLC Chloride Channels and Transporters: Structure, Function, Physiology, and Disease.

    Science.gov (United States)

    Jentsch, Thomas J; Pusch, Michael

    2018-07-01

    CLC anion transporters are found in all phyla and form a gene family of eight members in mammals. Two CLC proteins, each of which completely contains an ion translocation parthway, assemble to homo- or heteromeric dimers that sometimes require accessory β-subunits for function. CLC proteins come in two flavors: anion channels and anion/proton exchangers. Structures of these two CLC protein classes are surprisingly similar. Extensive structure-function analysis identified residues involved in ion permeation, anion-proton coupling and gating and led to attractive biophysical models. In mammals, ClC-1, -2, -Ka/-Kb are plasma membrane Cl - channels, whereas ClC-3 through ClC-7 are 2Cl - /H + -exchangers in endolysosomal membranes. Biological roles of CLCs were mostly studied in mammals, but also in plants and model organisms like yeast and Caenorhabditis elegans. CLC Cl - channels have roles in the control of electrical excitability, extra- and intracellular ion homeostasis, and transepithelial transport, whereas anion/proton exchangers influence vesicular ion composition and impinge on endocytosis and lysosomal function. The surprisingly diverse roles of CLCs are highlighted by human and mouse disorders elicited by mutations in their genes. These pathologies include neurodegeneration, leukodystrophy, mental retardation, deafness, blindness, myotonia, hyperaldosteronism, renal salt loss, proteinuria, kidney stones, male infertility, and osteopetrosis. In this review, emphasis is laid on biophysical structure-function analysis and on the cell biological and organismal roles of mammalian CLCs and their role in disease.

  1. Structural and functional loss in restored wetland ecosystems.

    Directory of Open Access Journals (Sweden)

    David Moreno-Mateos

    2012-01-01

    Full Text Available Wetlands are among the most productive and economically valuable ecosystems in the world. However, because of human activities, over half of the wetland ecosystems existing in North America, Europe, Australia, and China in the early 20th century have been lost. Ecological restoration to recover critical ecosystem services has been widely attempted, but the degree of actual recovery of ecosystem functioning and structure from these efforts remains uncertain. Our results from a meta-analysis of 621 wetland sites from throughout the world show that even a century after restoration efforts, biological structure (driven mostly by plant assemblages, and biogeochemical functioning (driven primarily by the storage of carbon in wetland soils, remained on average 26% and 23% lower, respectively, than in reference sites. Either recovery has been very slow, or postdisturbance systems have moved towards alternative states that differ from reference conditions. We also found significant effects of environmental settings on the rate and degree of recovery. Large wetland areas (>100 ha and wetlands restored in warm (temperate and tropical climates recovered more rapidly than smaller wetlands and wetlands restored in cold climates. Also, wetlands experiencing more (riverine and tidal hydrologic exchange recovered more rapidly than depressional wetlands. Restoration performance is limited: current restoration practice fails to recover original levels of wetland ecosystem functions, even after many decades. If restoration as currently practiced is used to justify further degradation, global loss of wetland ecosystem function and structure will spread.

  2. Nuclear structure functions at a future electron-ion collider

    Science.gov (United States)

    Aschenauer, E. C.; Fazio, S.; Lamont, M. A. C.; Paukkunen, H.; Zurita, P.

    2017-12-01

    The quantitative knowledge of heavy nuclei's partonic structure is currently limited to rather large values of momentum fraction x —robust experimental constraints below x ˜10-2 at low resolution scale Q2 are particularly scarce. This is in sharp contrast to the free proton's structure which has been probed in Deep Inelastic Scattering (DIS) measurements down to x ˜10-5 at perturbative resolution scales. The construction of an electron-ion collider (EIC) with a possibility to operate with a wide variety of nuclei, will allow one to explore the low-x region in much greater detail. In the present paper we simulate the extraction of the nuclear structure functions from measurements of inclusive and charm reduced cross sections at an EIC. The potential constraints are studied by analyzing simulated data directly in a next-to-leading order global fit of nuclear Parton Distribution Functions based on the recent EPPS16 analysis. A special emphasis is placed on studying the impact an EIC would have on extracting the nuclear gluon parton distribution function, the partonic component most prone to nonlinear effects at low Q2. In comparison to the current knowledge, we find that the gluon parton distribution function can be measured at an EIC with significantly reduced uncertainties.

  3. Co-Immobilization of Proteins and DNA Origami Nanoplates to Produce High-Contrast Biomolecular Nanoarrays.

    Science.gov (United States)

    Hager, Roland; Burns, Jonathan R; Grydlik, Martyna J; Halilovic, Alma; Haselgrübler, Thomas; Schäffler, Friedrich; Howorka, Stefan

    2016-06-01

    The biofunctionalization of nanopatterned surfaces with DNA origami nanostructures is an important topic in nanobiotechnology. An unexplored challenge is, however, to co-immobilize proteins with DNA origami at pre-determined substrate sites in high contrast relative to the nontarget areas. The immobilization should, in addition, preferably be achieved on a transparent substrate to allow ultrasensitive optical detection. If successful, specific co-binding would be a step towards stoichiometrically defined arrays with few to individual protein molecules per site. Here, we successfully immobilize with high specificity positively charged avidin proteins and negatively charged DNA origami nanoplates on 100 nm-wide carbon nanoislands while suppressing undesired adsorption to surrounding nontarget areas. The arrays on glass slides achieve unprecedented selectivity factors of up to 4000 and allow ultrasensitive fluorescence read-out. The co-immobilization onto the nanoislands leads to layered biomolecular architectures, which are functional because bound DNA origami influences the number of capturing sites on the nanopatches for other proteins. The novel hybrid DNA origami-protein nanoarrays allow the fabrication of versatile research platforms for applications in biosensing, biophysics, and cell biology, and, in addition, represent an important step towards single-molecule protein arrays. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. [Neutron scatter studies of chromatin structure related to function

    International Nuclear Information System (INIS)

    Bradbury, E.M.

    1990-01-01

    This study is concerned with the application of neutron scatter techniques to the different structural states of nucleosomes and chromatin with the long term objective of understanding how the enormous lengths of DNA are folded into chromosomes. Micrococcal nuclease digestion kinetics have defined two subnucleosome particles; the chromatosome with 168 bp DNA, the histone octamer and one H1 and the nucleosome core particle with 146 bp DNA and the histone octamer. As will be discussed, the structure of the 146 bp DNA core particle is known in solution at low resolution from neutron scatter studies and in crystals. Based on this structure, the authors have a working model for the chromatosome and the mode of binding of H1. In order to define the structure of the nucleosome and also the different orders of chromatin structures they need to know the paths of DNA that link nucleosomes and the factors associated with chromosome functions that act on those DNA paths. The major region for this situation is the inherent variabilities in nucleosome DNA sequences, in the histone subtypes and their states of chemical modification and in the precise locations of nucleosomes. Such variabilities obscure the underlying principles that govern the packaging of DNA into the different structural states of nucleosomes and chromatin. The only way to elucidate these principles is to study the structures of nucleosomes and oligonucleosomes that are fully defined. They have largely achieved these objectives

  5. Application of Functional Use Predictions to Aid in Structure ...

    Science.gov (United States)

    Humans are potentially exposed to thousands of anthropogenic chemicals in commerce. Recent work has shown that the bulk of this exposure may occur in near-field indoor environments (e.g., home, school, work, etc.). Advances in suspect screening analyses (SSA) now allow an improved understanding of the chemicals present in these environments. However, due to the nature of suspect screening techniques, investigators are often left with chemical formula predictions, with the possibility of many chemical structures matching to each formula. Here, newly developed quantitative structure-use relationship (QSUR) models are used to identify potential exposure sources for candidate structures. Previously, a suspect screening workflow was introduced and applied to house dust samples collected from the U.S. Department of Housing and Urban Development’s American Healthy Homes Survey (AHHS) [Rager, et al., Env. Int. 88 (2016)]. This workflow utilized the US EPA’s Distributed Structure-Searchable Toxicity (DSSTox) Database to link identified molecular features to molecular formulas, and ultimately chemical structures. Multiple QSUR models were applied to support the evaluation of candidate structures. These QSURs predict the likelihood of a chemical having a functional use commonly associated with consumer products having near-field use. For 3,228 structures identified as possible chemicals in AHHS house dust samples, we were able to obtain the required descriptors to appl

  6. Structure-function-property-design interplay in biopolymers: spider silk.

    Science.gov (United States)

    Tokareva, Olena; Jacobsen, Matthew; Buehler, Markus; Wong, Joyce; Kaplan, David L

    2014-04-01

    Spider silks have been a focus of research for almost two decades due to their outstanding mechanical and biophysical properties. Recent advances in genetic engineering have led to the synthesis of recombinant spider silks, thus helping to unravel a fundamental understanding of structure-function-property relationships. The relationships between molecular composition, secondary structures and mechanical properties found in different types of spider silks are described, along with a discussion of artificial spinning of these proteins and their bioapplications, including the role of silks in biomineralization and fabrication of biomaterials with controlled properties. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  7. The filamins: organizers of cell structure and function.

    Science.gov (United States)

    Nakamura, Fumihiko; Stossel, Thomas P; Hartwig, John H

    2011-01-01

    Filamin A (FLNa), the first non-muscle actin filament cross-linking protein, was identified in 1975. Thirty five years of FLNa research has revealed its structure in great detail, discovered its isoforms (FLNb and c), and identified over 90 binding partners including channels, receptors, intracellular signaling molecules, and even transcription factors. Due to this diversity, mutations in human FLN genes result in a wide range of anomalies with moderate to lethal consequences. This review focuses on the structure and functions of FLNa in cell migration and adhesion.

  8. Phase Structure and Dynamics of QCD–A Functional Perspective

    International Nuclear Information System (INIS)

    Strodthoff, Nils

    2017-01-01

    The understanding of the phase structure and the fundamental properties of QCD matter from its microscopic description requires appropriate first-principle approaches. Here I review the progress towards a quantitative first-principle continuum approach within the framework of the Functional Renormalization group established by the fQCD collaboration. I focus on recent quantitative results for quenched QCD and Yang-Mills in the vacuum before addressing the calculation of dynamical quantities such as spectral functions and transport coefficients in this framework. (paper)

  9. [Macula structure and function in retinopathy of prematurity].

    Science.gov (United States)

    Kogoleva, L V; Katargina, L A; Rydnitskaia, Ia L

    2011-01-01

    Macula structure and function were studied in 64 patients with retinopathy of prematurity (RP) stage I-III aged 8-17 years old using optical coherence tomography (OCT) and electroretinography. Absence of foveolar depression associated with preservation of fovea layers and normal electroretinography indices were showed to be the evidence of differentiation damage and macula underdevelopment due to immaturity and to have no effect on visual acuity. Preserved or pathologic foveolar depression associated with abnormal OCT findings and central retina electrogenesis damage indicate dysfunction and morphological changes of macula due to not macula underdevelopment because of immaturity only but RP either that can lead to depression, visual function.

  10. Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron.

    Science.gov (United States)

    Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip

    2016-01-01

    Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons.

  11. Approach to kinetic energy density functionals: Nonlocal terms with the structure of the von Weizsaecker functional

    International Nuclear Information System (INIS)

    Garcia-Aldea, David; Alvarellos, J. E.

    2008-01-01

    We propose a kinetic energy density functional scheme with nonlocal terms based on the von Weizsaecker functional, instead of the more traditional approach where the nonlocal terms have the structure of the Thomas-Fermi functional. The proposed functionals recover the exact kinetic energy and reproduce the linear response function of homogeneous electron systems. In order to assess their quality, we have tested the total kinetic energies as well as the kinetic energy density for atoms. The results show that these nonlocal functionals give as good results as the most sophisticated functionals in the literature. The proposed scheme for constructing the functionals means a step ahead in the field of fully nonlocal kinetic energy functionals, because they are capable of giving better local behavior than the semilocal functionals, yielding at the same time accurate results for total kinetic energies. Moreover, the functionals enjoy the possibility of being evaluated as a single integral in momentum space if an adequate reference density is defined, and then quasilinear scaling for the computational cost can be achieved

  12. Super-resolution biomolecular crystallography with low-resolution data.

    Science.gov (United States)

    Schröder, Gunnar F; Levitt, Michael; Brunger, Axel T

    2010-04-22

    X-ray diffraction plays a pivotal role in the understanding of biological systems by revealing atomic structures of proteins, nucleic acids and their complexes, with much recent interest in very large assemblies like the ribosome. As crystals of such large assemblies often diffract weakly (resolution worse than 4 A), we need methods that work at such low resolution. In macromolecular assemblies, some of the components may be known at high resolution, whereas others are unknown: current refinement methods fail as they require a high-resolution starting structure for the entire complex. Determining the structure of such complexes, which are often of key biological importance, should be possible in principle as the number of independent diffraction intensities at a resolution better than 5 A generally exceeds the number of degrees of freedom. Here we introduce a method that adds specific information from known homologous structures but allows global and local deformations of these homology models. Our approach uses the observation that local protein structure tends to be conserved as sequence and function evolve. Cross-validation with R(free) (the free R-factor) determines the optimum deformation and influence of the homology model. For test cases at 3.5-5 A resolution with known structures at high resolution, our method gives significant improvements over conventional refinement in the model as monitored by coordinate accuracy, the definition of secondary structure and the quality of electron density maps. For re-refinements of a representative set of 19 low-resolution crystal structures from the Protein Data Bank, we find similar improvements. Thus, a structure derived from low-resolution diffraction data can have quality similar to a high-resolution structure. Our method is applicable to the study of weakly diffracting crystals using X-ray micro-diffraction as well as data from new X-ray light sources. Use of homology information is not restricted to X

  13. Evolution of biomolecular loadings along a major river system

    Science.gov (United States)

    Freymond, Chantal V.; Kündig, Nicole; Stark, Courcelle; Peterse, Francien; Buggle, Björn; Lupker, Maarten; Plötze, Michael; Blattmann, Thomas M.; Filip, Florin; Giosan, Liviu; Eglinton, Timothy I.

    2018-02-01

    Understanding the transport history and fate of organic carbon (OC) within river systems is crucial in order to constrain the dynamics and significance of land-ocean interactions as a component of the global carbon cycle. Fluvial export and burial of terrestrial OC in marine sediments influences atmospheric CO2 over a range of timescales, while river-dominated sedimentary sequences can provide valuable archives of paleoenvironmental information. While there is abundant evidence that the association of organic matter (OM) with minerals exerts an important influence on its stability as well as hydrodynamic behavior in aquatic systems, there is a paucity of information on where such associations form and how they evolve during fluvial transport. Here, we track total organic carbon (TOC) and terrestrial biomarker concentrations (plant wax-derived long-chain fatty acids (FA), branched glycerol dialkyl glycerol tetraethers (brGDGTs) and lignin-derived phenols) in sediments collected along the entire course of the Danube River system in the context of sedimentological parameters. Mineral-specific surface area-normalized biomarker and TOC concentrations show a systematic decrease from the upper to the lower Danube basin. Changes in OM loading of the available mineral phase correspond to a net decrease of 70-80% of different biomolecular components. Ranges for biomarker loadings on Danube River sediments, corresponding to 0.4-1.5 μgFA/m2 for long-chain (n-C24-32) fatty acids and 17-71 ngbrGDGT/m2 for brGDGTs, are proposed as a benchmark for comparison with other systems. We propose that normalizing TOC as well as biomarker concentrations to mineral surface area provides valuable quantitative constraints on OM dynamics and organo-mineral interactions during fluvial transport from terrigenous source to oceanic sink.

  14. Soft Supercharging of Biomolecular Ions in Electrospray Ionization Mass Spectrometry

    Science.gov (United States)

    Chingin, Konstantin; Xu, Ning; Chen, Huanwen

    2014-06-01

    The charge states of biomolecular ions in ESI-MS can be significantly increased by the addition of low-vapor supercharging (SC) reagents into the spraying solution. Despite the considerable interest from the community, the mechanistic aspects of SC are not well understood and are hotly debated. Arguments that denaturation accounts for the increased charging observed in proteins sprayed from aqueous solutions containing SC reagent have been published widely, but often with incomplete or ambiguous supporting data. In this work, we explored ESI MS charging and SC behavior of several biopolymers including proteins and DNA oligonucleotides. Analytes were ionized from 100 mM ammonium acetate (NH4Ac) aqueous buffer in both positive (ESI+) and negative (ESI-) ion modes. SC was induced either with m-NBA or by the elevated temperature of ESI capillary. For all the analytes studied we, found striking differences in the ESI MS response to these two modes of activation. The data suggest that activation with m-NBA results in more extensive analyte charging with lower degree of denaturation. When working solution with m-NBA was analyzed at elevated temperatures, the SC effect from m-NBA was neutralized. Instead, the net SC effect was similar to the SC effect achieved by thermal activation only. Overall, our observations indicate that SC reagents enhance ESI charging of biomolecules via distinctly different mechanism compared with the traditional approaches based on analyte denaturation. Instead, the data support the hypothesis that the SC phenomenon involves a direct interaction between a biopolymer and SC reagent occurring in evaporating ESI droplets.

  15. Analysis of the proton longitudinal structure function from the gluon distribution function

    International Nuclear Information System (INIS)

    Boroun, G.R.; Rezaei, B.

    2012-01-01

    We make a critical, next-to-leading order, study of the relationship between the longitudinal structure function F L and the gluon distribution proposed in Cooper-Sarkar et al. (Z. Phys. C 39:281, 1988; Acta Phys. Pol. B 34:2911 2003), which is frequently used to extract the gluon distribution from the proton longitudinal structure function at small x. The gluon density is obtained by expanding at particular choices of the point of expansion and compared with the hard Pomeron behavior for the gluon density. Comparisons with H1 data are made and predictions for the proposed best approach are also provided. (orig.)

  16. Myoglobin structure and function: A multiweek biochemistry laboratory project.

    Science.gov (United States)

    Silverstein, Todd P; Kirk, Sarah R; Meyer, Scott C; Holman, Karen L McFarlane

    2015-01-01

    We have developed a multiweek laboratory project in which students isolate myoglobin and characterize its structure, function, and redox state. The important laboratory techniques covered in this project include size-exclusion chromatography, electrophoresis, spectrophotometric titration, and FTIR spectroscopy. Regarding protein structure, students work with computer modeling and visualization of myoglobin and its homologues, after which they spectroscopically characterize its thermal denaturation. Students also study protein function (ligand binding equilibrium) and are instructed on topics in data analysis (calibration curves, nonlinear vs. linear regression). This upper division biochemistry laboratory project is a challenging and rewarding one that not only exposes students to a wide variety of important biochemical laboratory techniques but also ties those techniques together to work with a single readily available and easily characterized protein, myoglobin. © 2015 International Union of Biochemistry and Molecular Biology.

  17. Proton structure functions in the dipole picture of BFKL dynamics

    International Nuclear Information System (INIS)

    Navelet, H.; Wallon, S.

    1996-06-01

    The F 2 , F G , R=F L /F T proton structure functions are derived in the QCD dipole picture. Assuming k T and renormalization-group factorization, we relate deep-inelastic proton scattering to deep-inelastic onium scattering. We get a three-parameter fit of the 1994 H1 data in the low-x, moderate Q 2 range. The ratios F G /F 2 and R are predicted without further adjustment. The dipole picture of BFKL dynamics is shown to provide a relevant model for quantitatively describing the proton structure functions at HERA. The predictions for F 2 and F G are compatible with next-to-leading DGLAP analysis, while R is expected to be significantly lower at very small x. (orig.)

  18. Political ideology: its structure, functions, and elective affinities.

    Science.gov (United States)

    Jost, John T; Federico, Christopher M; Napier, Jaime L

    2009-01-01

    Ideology has re-emerged as an important topic of inquiry among social, personality, and political psychologists. In this review, we examine recent theory and research concerning the structure, contents, and functions of ideological belief systems. We begin by defining the construct and placing it in historical and philosophical context. We then examine different perspectives on how many (and what types of) dimensions individuals use to organize their political opinions. We investigate (a) how and to what extent individuals acquire the discursive contents associated with various ideologies, and (b) the social-psychological functions that these ideologies serve for those who adopt them. Our review highlights "elective affinities" between situational and dispositional needs of individuals and groups and the structure and contents of specific ideologies. Finally, we consider the consequences of ideology, especially with respect to attitudes, evaluations, and processes of system justification.

  19. The adventitia: essential regulator of vascular wall structure and function.

    Science.gov (United States)

    Stenmark, Kurt R; Yeager, Michael E; El Kasmi, Karim C; Nozik-Grayck, Eva; Gerasimovskaya, Evgenia V; Li, Min; Riddle, Suzette R; Frid, Maria G

    2013-01-01

    The vascular adventitia acts as a biological processing center for the retrieval, integration, storage, and release of key regulators of vessel wall function. It is the most complex compartment of the vessel wall and is composed of a variety of cells, including fibroblasts, immunomodulatory cells (dendritic cells and macrophages), progenitor cells, vasa vasorum endothelial cells and pericytes, and adrenergic nerves. In response to vascular stress or injury, resident adventitial cells are often the first to be activated and reprogrammed to influence the tone and structure of the vessel wall; to initiate and perpetuate chronic vascular inflammation; and to stimulate expansion of the vasa vasorum, which can act as a conduit for continued inflammatory and progenitor cell delivery to the vessel wall. This review presents the current evidence demonstrating that the adventitia acts as a key regulator of vascular wall function and structure from the outside in.

  20. Structural and functional characterization of barium zirconium titanate / epoxy composites

    Directory of Open Access Journals (Sweden)

    Filiberto González Garcia

    2011-12-01

    Full Text Available The dielectric behavior of composite materials (barium zirconium titanate / epoxy system was analyzed as a function of ceramic concentration. Structure and morphologic behavior of the composites was investigated by X-ray Diffraction (XRD, Fourier transformed infrared spectroscopy (FT-IR, Raman spectroscopy, field emission scanning electron microscopy (FE-SEM and transmission electron microscopy (TEM analyses. Composites were prepared by mixing the components and pouring them into suitable moulds. It was demonstrated that the amount of inorganic phase affects the morphology of the presented composites. XRD revealed the presence of a single phase while Raman scattering confirmed structural transitions as a function of ceramic concentration. Changes in the ceramic concentration affected Raman modes and the distribution of particles along into in epoxy matrix. Dielectric permittivity and dielectric losses were influenced by filler concentration.