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Sample records for biological structure determination

  1. The potential for biological structure determination with pulsed neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, C.C. [CLRC Rutherford Appleton Laboratory, Chilton Didcot Oxon (United Kingdom)

    1994-12-31

    The potential of pulsed neutron diffraction in structural determination of biological materials is discussed. The problems and potential solutions in this area are outlined, with reference to both current and future sources and instrumentation. The importance of developing instrumentation on pulsed sources in emphasized, with reference to the likelihood of future expansion in this area. The possibilities and limitations of single crystal, fiber and powder diffraction in this area are assessed.

  2. The potential for biological structure determination with pulsed neutrons

    International Nuclear Information System (INIS)

    Wilson, C.C.

    1994-01-01

    The potential of pulsed neutron diffraction in structural determination of biological materials is discussed. The problems and potential solutions in this area are outlined, with reference to both current and future sources and instrumentation. The importance of developing instrumentation on pulsed sources in emphasized, with reference to the likelihood of future expansion in this area. The possibilities and limitations of single crystal, fiber and powder diffraction in this area are assessed

  3. Quantification of the impact of PSI:Biology according to the annotations of the determined structures.

    Science.gov (United States)

    DePietro, Paul J; Julfayev, Elchin S; McLaughlin, William A

    2013-10-21

    Protein Structure Initiative:Biology (PSI:Biology) is the third phase of PSI where protein structures are determined in high-throughput to characterize their biological functions. The transition to the third phase entailed the formation of PSI:Biology Partnerships which are composed of structural genomics centers and biomedical science laboratories. We present a method to examine the impact of protein structures determined under the auspices of PSI:Biology by measuring their rates of annotations. The mean numbers of annotations per structure and per residue are examined. These are designed to provide measures of the amount of structure to function connections that can be leveraged from each structure. One result is that PSI:Biology structures are found to have a higher rate of annotations than structures determined during the first two phases of PSI. A second result is that the subset of PSI:Biology structures determined through PSI:Biology Partnerships have a higher rate of annotations than those determined exclusive of those partnerships. Both results hold when the annotation rates are examined either at the level of the entire protein or for annotations that are known to fall at specific residues within the portion of the protein that has a determined structure. We conclude that PSI:Biology determines structures that are estimated to have a higher degree of biomedical interest than those determined during the first two phases of PSI based on a broad array of biomedical annotations. For the PSI:Biology Partnerships, we see that there is an associated added value that represents part of the progress toward the goals of PSI:Biology. We interpret the added value to mean that team-based structural biology projects that utilize the expertise and technologies of structural genomics centers together with biological laboratories in the community are conducted in a synergistic manner. We show that the annotation rates can be used in conjunction with established metrics, i

  4. Structural Biology Fact Sheet

    Science.gov (United States)

    ... NIGMS NIGMS Home > Science Education > Structural Biology Structural Biology Tagline (Optional) Middle/Main Content Area PDF Version (688 KB) Other Fact Sheets What is structural biology? Structural biology is the study of how biological ...

  5. Integrated Structural Biology for α-Helical Membrane Protein Structure Determination.

    Science.gov (United States)

    Xia, Yan; Fischer, Axel W; Teixeira, Pedro; Weiner, Brian; Meiler, Jens

    2018-04-03

    While great progress has been made, only 10% of the nearly 1,000 integral, α-helical, multi-span membrane protein families are represented by at least one experimentally determined structure in the PDB. Previously, we developed the algorithm BCL::MP-Fold, which samples the large conformational space of membrane proteins de novo by assembling predicted secondary structure elements guided by knowledge-based potentials. Here, we present a case study of rhodopsin fold determination by integrating sparse and/or low-resolution restraints from multiple experimental techniques including electron microscopy, electron paramagnetic resonance spectroscopy, and nuclear magnetic resonance spectroscopy. Simultaneous incorporation of orthogonal experimental restraints not only significantly improved the sampling accuracy but also allowed identification of the correct fold, which is demonstrated by a protein size-normalized transmembrane root-mean-square deviation as low as 1.2 Å. The protocol developed in this case study can be used for the determination of unknown membrane protein folds when limited experimental restraints are available. Copyright © 2018 Elsevier Ltd. All rights reserved.

  6. Neutron structural biology

    International Nuclear Information System (INIS)

    Niimura, Nobuo

    1999-01-01

    Neutron structural biology will be one of the most important fields in the life sciences which will interest human beings in the 21st century because neutrons can provide not only the position of hydrogen atoms in biological macromolecules but also the dynamic molecular motion of hydrogen atoms and water molecules. However, there are only a few examples experimentally determined at present because of the lack of neutron source intensity. Next generation neutron source scheduled in JAERI (Performance of which is 100 times better than that of JRR-3M) opens the life science of the 21st century. (author)

  7. Determining biological fine structure by differential absorption of soft x-rays

    International Nuclear Information System (INIS)

    Panessa-Warren, B.J.; Warren, J.B.

    1979-06-01

    The use of soft x-ray contact microscopy in examining histochemically treated human tissue embedded in plastic and exposed as unstained thin sections is demonstrated. When our preliminary data revealed that we could clearly image not only the histochemical reaction product, but the unstained biological fine structure of the surrounding tissues, we decided to test our hypothesis further and see if we could image unstained biological molecular aggregates as well. For this part of the investigation, we chose to examine hydrated proteoglycan aggregates. Proteoglycans are an essential component of the organic matrix of cartilage, and play a primary role in the retention and maintenance of extracellular water. To avoid any artifacts due to the introduction of exogeneous materials, and examine the proteoglycan aggregates in their hydrated, natural configuration, we made contact x-ray images of isolated proteoglycan aggregates in water

  8. Dyneins: structure, biology and disease

    National Research Council Canada - National Science Library

    King, Stephen M

    2012-01-01

    .... From bench to bedside, Dynein: Structure, Biology and Disease offers research on fundamental cellular processes to researchers and clinicians across developmental biology, cell biology, molecular biology, biophysics, biomedicine...

  9. Neutron structural biology

    International Nuclear Information System (INIS)

    Schoenborn, B.

    1997-01-01

    This is the final report of a one-year, Laboratory Directed Research and Development (LDRD) project at Los Alamos National Laboratory (LANL). We investigated design concepts of neutron scattering capabilities for structural biology at spallation sources. This included the analysis of design parameters for protein crystallography as well as membrane diffraction instruments. These instruments are designed to be general user facilities and will be used by scientists from industry, universities, and other national laboratories

  10. Structure and behavior as determinants: United States nuclear test ban and chemical and biological arms control policy

    International Nuclear Information System (INIS)

    Reich, J.C.

    1991-01-01

    US efforts to control chemical and biological warfare and nuclear testing are examined with the aim of explaining the paucity of US backed agreements in these areas. Two theoretical perspectives, the behavioral and structural approaches, are used to explore US arms control outcomes. In the behavioral approach, the effects of governmental organization and the bargaining dynamics of policy-making elites with different cognitive styles are posited as important influences on US nuclear test ban and chemical and biological arms control policy outcomes. The behavioral perspective accounts for the timing of all US failed and successful entries (with one exception) into nuclear test bans and chemical and biological warfare restraints. A shortcoming of the behavior approach, however, is that it tends to overemphasize the chances for successful US entry into nuclear test and chemical and biological warfare limitations. Analysis of the same events from the structural perspective helps to correct for expectations generated by behavioral variables for a higher success rate than ultimately resulted. In the structural approach, the focus is on the effect of the organization of international politics on US nuclear test ban and chemical and biological arms control policy outcomes

  11. Mathematics, structuralism and biology.

    Science.gov (United States)

    Saunders, P T

    1988-01-01

    A new approach is gaining ground in biology, one that has much in common with the structuralist tradition in other fields. It is very much in the spirit of an earlier view of biology and indeed of science in general. It is also, though this is not generally recognized, in the spirit of twentieth century physics. As in modern physics, however, it is not a question of ignoring all the progress that has been made within the former paradigm. On the contrary, the aim is to use it as a basis for setting out in a somewhat different direction. Complex phenomena do not generally lend themselves to reductionist analyses which seek explanation only in terms of detailed mechanisms, but a proper scientific discussion of structure must make full use of what we have already learned - by whatever means - about the processes that underly the phenomena we are trying to understand.

  12. 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

  13. Structural Molecular Biology 2017 | SSRL

    Science.gov (United States)

    Highlights Training Workshops & Summer Schools Summer Students Structural Molecular Biology Illuminating experimental driver for structural biology research, serving the needs of a large number of academic and — Our Mission The SSRL Structural Molecular Biology program operates as an integrated resource and has

  14. Diffraction Techniques in Structural Biology

    Science.gov (United States)

    Egli, Martin

    2016-01-01

    A detailed understanding of chemical and biological function and the mechanisms underlying the molecular activities ultimately requires atomic-resolution structural data. Diffraction-based techniques such as single-crystal X-ray crystallography, electron microscopy, and neutron diffraction are well established and they have paved the road to the stunning successes of modern-day structural biology. The major advances achieved in the last 20 years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches, and high-speed computing and visualization, now provide specialists and nonspecialists alike with a steady flow of molecular images of unprecedented detail. The present unit combines a general overview of diffraction methods with a detailed description of the process of a single-crystal X-ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis, and quality control. For novices it may serve as a stepping-stone to more in-depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide. PMID:27248784

  15. [Classification of organisms and structuralism in biology].

    Science.gov (United States)

    Vasil'eva, L I

    2001-01-01

    Structuralism in biology is the oldest trend oriented to the search for natural "laws of forms" comparable with laws of growth of crystal, was revived at the end of 20th century on the basis of structuralist thought in socio-humanitarian sciences. The development of principal ideas of the linguistic structuralism in some aspects is similar to that of biological systematics, especially concerning the relationships between "system" and "evolution". However, apart from this general similarity, biological structuralism is strongly focused on familiar problems of the origin of diversity in nature. In their striving for the renovation of existing views, biological structuralists oppose the neo-darwinism emphasizing the existence of "law of forms", that are independent on heredity and genetic "determinism". The trend to develop so-called "rational taxonomy" is also characteristic of biological structuralism but this attempt failed being connected neither with Darwin's historicism nor with Plato's typology.

  16. Structural Biology Guides Antibiotic Discovery

    Science.gov (United States)

    Polyak, Steven

    2014-01-01

    Modern drug discovery programs require the contribution of researchers in a number of specialist areas. One of these areas is structural biology. Using X-ray crystallography, the molecular basis of how a drug binds to its biological target and exerts its mode of action can be defined. For example, a drug that binds into the active site of an…

  17. Inference problems in structural biology

    DEFF Research Database (Denmark)

    Olsson, Simon

    The structure and dynamics of biological molecules are essential for their function. Consequently, a wealth of experimental techniques have been developed to study these features. However, while experiments yield detailed information about geometrical features of molecules, this information is of...

  18. Neutron structural biology

    Energy Technology Data Exchange (ETDEWEB)

    Niimura, Nobuo [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    1998-03-01

    Neutron diffraction provides an experimental method of directly locating hydrogen atoms in protein which play important roles in physiological functions. However, there are relatively few examples of neutron crystallography in biology since it takes a lot of time to collect a sufficient number of Bragg reflections due to the low flux of neutrons illuminating the sample. In order to overcome the flux problem, we have successfully developed the neutron IP, where the neutron converter, {sup 6}Li or Gd, was mixed with a photostimulated luminescence material on flexible plastic support. Neutron Laue diffraction 2A data from tetragonal lysozyme were collected for 10 days with neutron imaging plates, and 960 hydrogen atoms in the molecule and 157 bound water molecules were identified. These results explain the proposed hydrolysis mechanism of the sugar by the lysozyme molecule and that lysozyme is less active at pH7.0. (author)

  19. Structural biological composites: An overview

    Science.gov (United States)

    Meyers, Marc A.; Lin, Albert Y. M.; Seki, Yasuaki; Chen, Po-Yu; Kad, Bimal K.; Bodde, Sara

    2006-07-01

    Biological materials are complex composites that are hierarchically structured and multifunctional. Their mechanical properties are often outstanding, considering the weak constituents from which they are assembled. They are for the most part composed of brittle (often, mineral) and ductile (organic) components. These complex structures, which have risen from millions of years of evolution, are inspiring materials scientists in the design of novel materials. This paper discusses the overall design principles in biological structural composites and illustrates them for five examples; sea spicules, the abalone shell, the conch shell, the toucan and hornbill beaks, and the sheep crab exoskeleton.

  20. [Network structures in biological systems].

    Science.gov (United States)

    Oleskin, A V

    2013-01-01

    Network structures (networks) that have been extensively studied in the humanities are characterized by cohesion, a lack of a central control unit, and predominantly fractal properties. They are contrasted with structures that contain a single centre (hierarchies) as well as with those whose elements predominantly compete with one another (market-type structures). As far as biological systems are concerned, their network structures can be subdivided into a number of types involving different organizational mechanisms. Network organization is characteristic of various structural levels of biological systems ranging from single cells to integrated societies. These networks can be classified into two main subgroups: (i) flat (leaderless) network structures typical of systems that are composed of uniform elements and represent modular organisms or at least possess manifest integral properties and (ii) three-dimensional, partly hierarchical structures characterized by significant individual and/or intergroup (intercaste) differences between their elements. All network structures include an element that performs structural, protective, and communication-promoting functions. By analogy to cell structures, this element is denoted as the matrix of a network structure. The matrix includes a material and an immaterial component. The material component comprises various structures that belong to the whole structure and not to any of its elements per se. The immaterial (ideal) component of the matrix includes social norms and rules regulating network elements' behavior. These behavioral rules can be described in terms of algorithms. Algorithmization enables modeling the behavior of various network structures, particularly of neuron networks and their artificial analogs.

  1. Gallium determination in biological samples

    International Nuclear Information System (INIS)

    Stulzaft, O.; Maziere, B.; Ly, S.

    1980-01-01

    A sensitive, simple and time-saving method has been developed for the neutron activation analysis of gallium at concentrations around 10 -4 ppm in biological tissues. After a 24-hour irradiation in a thermal neutron flux of 2.8x10 13 nxcm -2 xs -1 and a purification by ion-exchange chromatography to eliminate troublesome elements such as sodium, iron and copper, the 72 Ga activity is measured with enough accuracy for the method to be applicable in animal physiology and clinical toxicology. (author)

  2. Dissipative structures and biological rhythms

    Science.gov (United States)

    Goldbeter, Albert

    2017-10-01

    Sustained oscillations abound in biological systems. They occur at all levels of biological organization over a wide range of periods, from a fraction of a second to years, and with a variety of underlying mechanisms. They control major physiological functions, and their dysfunction is associated with a variety of physiological disorders. The goal of this review is (i) to give an overview of the main rhythms observed at the cellular and supracellular levels, (ii) to briefly describe how the study of biological rhythms unfolded in the course of time, in parallel with studies on chemical oscillations, (iii) to present the major roles of biological rhythms in the control of physiological functions, and (iv) the pathologies associated with the alteration, disappearance, or spurious occurrence of biological rhythms. Two tables present the main examples of cellular and supracellular rhythms ordered according to their period, and their role in physiology and pathophysiology. Among the rhythms discussed are neural and cardiac rhythms, metabolic oscillations such as those occurring in glycolysis in yeast, intracellular Ca++ oscillations, cyclic AMP oscillations in Dictyostelium amoebae, the segmentation clock that controls somitogenesis, pulsatile hormone secretion, circadian rhythms which occur in all eukaryotes and some bacteria with a period close to 24 h, the oscillatory dynamics of the enzymatic network driving the cell cycle, and oscillations in transcription factors such as NF-ΚB and tumor suppressors such as p53. Ilya Prigogine's concept of dissipative structures applies to temporal oscillations and allows us to unify within a common framework the various rhythms observed at different levels of biological organization, regardless of their period and underlying mechanism.

  3. Structural Biology: Practical NMR Applications

    CERN Document Server

    Teng, Quincy

    2005-01-01

    This textbook begins with an overview of NMR development and applications in biological systems. It describes recent developments in instrument hardware and methodology. Chapters highlight the scope and limitation of NMR methods. While detailed math and quantum mechanics dealing with NMR theory have been addressed in several well-known NMR volumes, chapter two of this volume illustrates the fundamental principles and concepts of NMR spectroscopy in a more descriptive manner. Topics such as instrument setup, data acquisition, and data processing using a variety of offline software are discussed. Chapters further discuss several routine stategies for preparing samples, especially for macromolecules and complexes. The target market for such a volume includes researchers in the field of biochemistry, chemistry, structural biology and biophysics.

  4. Determinants of capital structure.

    Science.gov (United States)

    McCue, M J; Ozcan, Y A

    1992-01-01

    This study analyzes the determinants of hospital capital structure in a new market setting that are created by the financial pressures of prospective payment and the intense price competition among hospitals. Using California data, the study found hospital system affiliation, bed size, growth rate in revenues, operating risk, and asset structure affected both short- and long-term debt borrowings. In addition, percentage of uncompensated care, profitability, and payer mix influenced short-term borrowings while market conditions and ownership affected long-term borrowings. Most significant of all is the finding that smaller hospitals tend to borrow more, possibly because they cannot generate funds internally.

  5. Track structure in biological models.

    Science.gov (United States)

    Curtis, S B

    1986-01-01

    High-energy heavy ions in the galactic cosmic radiation (HZE particles) may pose a special risk during long term manned space flights outside the sheltering confines of the earth's geomagnetic field. These particles are highly ionizing, and they and their nuclear secondaries can penetrate many centimeters of body tissue. The three dimensional patterns of ionizations they create as they lose energy are referred to as their track structure. Several models of biological action on mammalian cells attempt to treat track structure or related quantities in their formulation. The methods by which they do this are reviewed. The proximity function is introduced in connection with the theory of Dual Radiation Action (DRA). The ion-gamma kill (IGK) model introduces the radial energy-density distribution, which is a smooth function characterizing both the magnitude and extension of a charged particle track. The lethal, potentially lethal (LPL) model introduces lambda, the mean distance between relevant ion clusters or biochemical species along the track. Since very localized energy depositions (within approximately 10 nm) are emphasized, the proximity function as defined in the DRA model is not of utility in characterizing track structure in the LPL formulation.

  6. Communication on the structure of biological networks

    Indian Academy of Sciences (India)

    Introduction. Over the past few years, network science has drawn attention from a large number of ... The qualitative properties of biological networks cannot ... Here, we study the underlying undirected structure of empirical biological networks.

  7. Structure Biology of Membrane Bound Enzymes

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Dax [Johns Hopkins Univ., Baltimore, MD (United States). School of Medicine. Dept. of Physiology

    2016-11-30

    The overall goal of the proposed research is to understand the membrane-associated active processes catalyzed by an alkane $\\square$-hydroxylase (AlkB) from eubacterium Pseudomonase oleovorans. AlkB performs oxygenation of unactivated hydrocarbons found in crude oils. The enzymatic reaction involves energy-demanding steps in the membrane with the uses of structurally unknown metal active sites featuring a diiron [FeFe] center. At present, a critical barrier to understanding the membrane-associated reaction mechanism is the lack of structural information. The structural biology efforts have been challenged by technical difficulties commonly encountered in crystallization and structural determination of membrane proteins. The specific aims of the current budget cycle are to crystalize AlkB and initiate X-ray analysis to set the stage for structural determination. The long-term goals of our structural biology efforts are to provide an atomic description of AlkB structure, and to uncover the mechanisms of selective modification of hydrocarbons. The structural information will help elucidating how the unactivated C-H bonds of saturated hydrocarbons are oxidized to initiate biodegradation and biotransformation processes. The knowledge gained will be fundamental to biotechnological applications to biofuel transformation of non-edible oil feedstock. Renewable biodiesel is a promising energy carry that can be used to reduce fossil fuel dependency. The proposed research capitalizes on prior BES-supported efforts on over-expression and purification of AlkB to explore the inner workings of a bioenergy-relevant membrane-bound enzyme.

  8. Structural Identifiability of Dynamic Systems Biology Models.

    Science.gov (United States)

    Villaverde, Alejandro F; Barreiro, Antonio; Papachristodoulou, Antonis

    2016-10-01

    A powerful way of gaining insight into biological systems is by creating a nonlinear differential equation model, which usually contains many unknown parameters. Such a model is called structurally identifiable if it is possible to determine the values of its parameters from measurements of the model outputs. Structural identifiability is a prerequisite for parameter estimation, and should be assessed before exploiting a model. However, this analysis is seldom performed due to the high computational cost involved in the necessary symbolic calculations, which quickly becomes prohibitive as the problem size increases. In this paper we show how to analyse the structural identifiability of a very general class of nonlinear models by extending methods originally developed for studying observability. We present results about models whose identifiability had not been previously determined, report unidentifiabilities that had not been found before, and show how to modify those unidentifiable models to make them identifiable. This method helps prevent problems caused by lack of identifiability analysis, which can compromise the success of tasks such as experiment design, parameter estimation, and model-based optimization. The procedure is called STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition), and it is implemented in a MATLAB toolbox which is available as open source software. The broad applicability of this approach facilitates the analysis of the increasingly complex models used in systems biology and other areas.

  9. The use of anomalous scattering of uranium for the determination of biological macromolecules structures - From hard to soft X-rays

    International Nuclear Information System (INIS)

    Chesne-Seck, M.L.

    2002-01-01

    In order to solve biological macromolecules structures, structure factor phases must be derived from the intensities diffracted by the crystal. The SAD and the MAD methods make use of variations in scattering factors measured at specific absorption edges of heavy atoms, bound to the protein. The phasing power depends on the occupancy of the binding sites and on the variations of the scattering factors at the absorption edge that is used. With uranyl, numerous sites with low occupancies are usually obtained. We used new colored uranyl complexes, which give higher occupancies, to solve de novo the lysozyme structure and an unknown structure. We have developed the use of the My absorption edge of uranium (λ = 3,5 Angstroms), where a variation of 120 electrons is observed in the scattering factors. With a helium atmosphere to limit the X-rays absorption, we have collected three data sets, on a single image. Data were processed both with 'classical' and specific programs. (author) [fr

  10. Computational structural biology: methods and applications

    National Research Council Canada - National Science Library

    Schwede, Torsten; Peitsch, Manuel Claude

    2008-01-01

    ... sequencing reinforced the observation that structural information is needed to understand the detailed function and mechanism of biological molecules such as enzyme reactions and molecular recognition events. Furthermore, structures are obviously key to the design of molecules with new or improved functions. In this context, computational structural biology...

  11. Structural Studies of Biological Solids Using NMR

    Science.gov (United States)

    Ramamoorthy, Ayyalusamy

    2011-03-01

    High-resolution structure and dynamics of biological molecules are important in understanding their function. While studies have been successful in solving the structures of water-soluble biomolecules, it has been proven difficult to determine the structures of membrane proteins and fibril systems. Recent studies have shown that solid-state NMR is a promising technique and could be highly valuable in studying such non-crystalline and non-soluble biosystems. I will present strategies to study the structures of such challenging systems and also about the applications of solid-state NMR to study the modes of membrane-peptide interactions for a better assessment of the prospects of antimicrobial peptides as substitutes to antibiotics in the control of human disease. Our studies on the mechanism of membrane disruption by LL-37 (a human antimicrobial peptide), analogs of the naturally occurring antimicrobial peptide magainin2 extracted from the skin of the African frog Xenopus Laevis, and pardaxin will be presented. Solid-state NMR experiments were used to determine the secondary structure, dynamics and topology of these peptides in lipid bilayers. Similarities and difference in the cell-lysing mechanism, and their dependence on the membrane composition, of these peptides will be discussed. Atomic-level resolution NMR structures of amyloidogenic proteins revealing the misfolding pathway and early intermediates that play key roles in amyloid toxicity will also be presented.

  12. Structural biology of the sequestration and transport of heavy metal toxins: NMR structure determination of proteins containing the -Cys-X-Y-Cys-metal binding motifs. 1998 annual progress report

    International Nuclear Information System (INIS)

    Opella, S.J.

    1998-01-01

    'The overall goal of the research is to apply the methods of structural biology, which have been previously used primarily in biomedical applications, to bioremediation. The authors are doing this by using NMR spectroscopy to determine the structures of proteins involved in the bacterial mercury detoxification system. The research is based on the premise that the proteins encoded in the genes of the bacterial detoxification system are an untapped source of reagents and, more fundamentally, chemical strategies that can be used to remove heavy metal toxins from the environment. The initial goals are to determine the structures of the proteins of the bacterial mercury detoxification systems responsible for the sequestration and transport of the Hg(II) ions in to the cell where reduction to Hg(O) occurs. These proteins are meP, which is water soluble and can be investigated with multidimensional solution NMR methods, and merT, the transport protein in the membrane that requires solid-state NMR methods. As of June 1998, this report summarizes work after about one and half years of the three-year award. The authors have made significant accomplishments in three aspects of the NMR studies of the proteins of the bacterial mercury detoxification system.'

  13. Structural biology at York Structural Biology Laboratory; laboratory information management systems for structural genomics

    Czech Academy of Sciences Publication Activity Database

    Dohnálek, Jan

    2005-01-01

    Roč. 12, č. 1 (2005), s. 3 ISSN 1211-5894. [Meeting of Structural Biologists /4./. 10.03.2005-12.03.2005, Nové Hrady] R&D Projects: GA MŠk(CZ) 1K05008 Keywords : structural biology * LIMS * structural genomics Subject RIV: CD - Macromolecular Chemistry

  14. Applications of contact predictions to structural biology

    Directory of Open Access Journals (Sweden)

    Felix Simkovic

    2017-05-01

    Full Text Available Evolutionary pressure on residue interactions, intramolecular or intermolecular, that are important for protein structure or function can lead to covariance between the two positions. Recent methodological advances allow much more accurate contact predictions to be derived from this evolutionary covariance signal. The practical application of contact predictions has largely been confined to structural bioinformatics, yet, as this work seeks to demonstrate, the data can be of enormous value to the structural biologist working in X-ray crystallography, cryo-EM or NMR. Integrative structural bioinformatics packages such as Rosetta can already exploit contact predictions in a variety of ways. The contribution of contact predictions begins at construct design, where structural domains may need to be expressed separately and contact predictions can help to predict domain limits. Structure solution by molecular replacement (MR benefits from contact predictions in diverse ways: in difficult cases, more accurate search models can be constructed using ab initio modelling when predictions are available, while intermolecular contact predictions can allow the construction of larger, oligomeric search models. Furthermore, MR using supersecondary motifs or large-scale screens against the PDB can exploit information, such as the parallel or antiparallel nature of any β-strand pairing in the target, that can be inferred from contact predictions. Contact information will be particularly valuable in the determination of lower resolution structures by helping to assign sequence register. In large complexes, contact information may allow the identity of a protein responsible for a certain region of density to be determined and then assist in the orientation of an available model within that density. In NMR, predicted contacts can provide long-range information to extend the upper size limit of the technique in a manner analogous but complementary to experimental

  15. On the Concept "Microscope": Biology Student Teachers' Cognitive Structure

    Science.gov (United States)

    Kurt, Hakan; Ekici, Gulay; Aktas, Murat; Aksu, Ozlem

    2013-01-01

    The purpose of the current study is to determine biology student teachers' cognitive structures on the concept of microscope. Qualitative research methodology has been applied in the study. The data were collected from biology student teachers. Free word association test and drawing-writing test were used to collect data. The data collected were…

  16. Biology Student Teachers' Cognitive Structure about "Living Thing"

    Science.gov (United States)

    Kurt, Hakan

    2013-01-01

    The current study aims to determine biology student teachers' cognitive structure on the concept of "living thing" through revealing their conceptual framework. Qualitative research method was applied in this study. The data were collected from 44 biology student teachers. A free word association test was used as a data collection…

  17. System for determining sizes of biological macromolecules

    International Nuclear Information System (INIS)

    Nelson, R.M.; Danby, P.C.

    1987-01-01

    An electrophoresis system for determining the sizes of radiolabelled biological macromolecules is described. It comprises a cell containing an electrophoresis gel and having at least one lane, a voltage source connected across the gel for effecting the movement of macromolecules in the lane, a detector fixed relative to the moving molecules for generating electrical pulses responsive to signals emitted by the radiolabelled molecules; a pulse processor for counting the pulse rate, and a computational device for comparing the pulse rate to a predetermined value. (author)

  18. CSMB | Center For Structural Molecular Biology

    Data.gov (United States)

    Federal Laboratory Consortium — The Center for Structural Molecular Biologyat ORNL is dedicated to developing instrumentation and methods for determining the 3-dimensional structures of proteins,...

  19. Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

    DEFF Research Database (Denmark)

    Chang, Roger L.; Andrews, Kathleen; Kim, Donghyuk

    2013-01-01

    Improve the System A "systems biology" approach may clarify, for example, how particular proteins determine sensitivity of bacteria to extremes of temperature. Chang et al. (p. 1220) integrated information on protein structure with a model of metabolism, thus associating the protein structure of ...

  20. Structural Biology for A-Level Students

    Science.gov (United States)

    Philip, Judith

    2013-01-01

    The relationship between the structure and function of proteins is an important area in biochemistry. Pupils studying A-level Biology are introduced to the four levels of protein structure (primary, secondary, tertiary and quaternary) and how these can be used to describe the progressive folding of a chain of amino acid residues to a final,…

  1. Structured population models in biology and epidemiology

    CERN Document Server

    Ruan, Shigui

    2008-01-01

    This book consists of six chapters written by leading researchers in mathematical biology. These chapters present recent and important developments in the study of structured population models in biology and epidemiology. Topics include population models structured by age, size, and spatial position; size-structured models for metapopulations, macroparasitc diseases, and prion proliferation; models for transmission of microparasites between host populations living on non-coincident spatial domains; spatiotemporal patterns of disease spread; method of aggregation of variables in population dynamics; and biofilm models. It is suitable as a textbook for a mathematical biology course or a summer school at the advanced undergraduate and graduate level. It can also serve as a reference book for researchers looking for either interesting and specific problems to work on or useful techniques and discussions of some particular problems.

  2. West-Life, Tools for Integrative Structural Biology

    CERN Multimedia

    CERN. Geneva

    2018-01-01

    Structural biology is part of molecular biology focusing on determining structure of macromolecules inside living cells and cell membranes. As macromolecules determines most of the functions of cells the structural knowledge is very useful for further research in metabolism, physiology to application in pharmacology etc. As macromolecules are too small to be observed directly by light microscope, there are other methods used to determine the structure including nuclear magnetic resonance (NMR), X-Ray crystalography, cryo electron microscopy and others. Each method has it's advantages and disadvantages in the terms of availability, sample preparation, resolution. West-Life project has ambition to facilitate integrative approach using multiple techniques mentioned above. As there are already lot of software tools to process data produced by the techniques above, the challenge is to integrate them together in a way they can be used by experts in one technique but not experts in other techniques. One product ...

  3. Determination of Biological Oxygen Demand Rate Constant and ...

    African Journals Online (AJOL)

    Determination of Biological Oxygen Demand Rate Constant and Ultimate Biological Oxygen Demand for Liquid Waste Generated from Student Cafeteria at Jimma University: A Tool for Development of Scientific Criteria to Protect Aquatic Health in the Region.

  4. DNA in a Tunnel: A Comfy Spot for Recognition - or -The Structure of BsoBI Complexed with DNA. What can we Learn about Function via Structure Determination and how can this be Applied to Bone or Muscle Biology?

    Science.gov (United States)

    vanderWoerd, Mark

    2004-01-01

    The structure and function of a biologically active molecule are related. To understand its function, it is necessary (but not always sufficient) to know the structure of the molecule. There are many ways of relating the molecular function with the structure. Mutation analysis can identify pertinent amino acids of an enzyme, or alternatively structure comparison of the of two similar molecules with different function may lead to understanding which parts are responsible for a functional aspect, or a series of "structural cartoons" - enzyme structure, enzyme plus substrate, enzyme with transition state analog, and enzyme with product - may give insight in the function of a molecule. As an example we will discuss the structure and function of the restriction enzyme BsoBI from Bacillus stearothemzophilus in complex with its cognate DNA. The enzyme forms a unique complex with DNA in that it completely encircles the DNA. The structure reveals the enzyme-DNA contacts, how the DNA is distorted compared with the canonical forms, and elegantly shows how two distinct DNA sequences can be recognized with the same efficiency. Based on the structure we may also propose a hypothesis how the enzymatic mechanism works. The knowledge gained thru studies such as this one can be used to alter the function by changing the molecular structure. Usually this is done by design of inhibitors specifically active against and fitting into an active site of the enzyme of choice. In the case of BsoBI one of the objectives of the study was to alter the enzyme specificity. In bone biology there are many candidates available for molecular study in order to explain, alter, or (temporarily) suspend activity. For example, the understanding of a pathway that negatively regulates bone formation may be a good target for drug design to stimulate bone formation and have good potential as the basis for new countermeasures against bone loss. In principle the same approach may aid muscle atrophy, radiation

  5. Biological activity of antitumoural MGBG: the structural variable.

    Science.gov (United States)

    Marques, M P M; Gil, F P S C; Calheiros, R; Battaglia, V; Brunati, A M; Agostinelli, E; Toninello, A

    2008-05-01

    The present study aims at determining the structure-activity relationships (SAR's) ruling the biological function of MGBG (methylglyoxal bis(guanylhydrazone)), a competitive inhibitor of S-adenosyl-L-methionine decarboxylase displaying anticancer activity, involved in the biosynthesis of the naturally occurring polyamines spermidine and spermine. In order to properly understand its biochemical activity, MGBG's structural preferences at physiological conditions were ascertained, by quantum mechanical (DFT) calculations.

  6. Advances in Structural Biology and the Application to Biological Filament Systems.

    Science.gov (United States)

    Popp, David; Koh, Fujiet; Scipion, Clement P M; Ghoshdastider, Umesh; Narita, Akihiro; Holmes, Kenneth C; Robinson, Robert C

    2018-04-01

    Structural biology has experienced several transformative technological advances in recent years. These include: development of extremely bright X-ray sources (microfocus synchrotron beamlines and free electron lasers) and the use of electrons to extend protein crystallography to ever decreasing crystal sizes; and an increase in the resolution attainable by cryo-electron microscopy. Here we discuss the use of these techniques in general terms and highlight their application for biological filament systems, an area that is severely underrepresented in atomic resolution structures. We assemble a model of a capped tropomyosin-actin minifilament to demonstrate the utility of combining structures determined by different techniques. Finally, we survey the methods that attempt to transform high resolution structural biology into more physiological environments, such as the cell. Together these techniques promise a compelling decade for structural biology and, more importantly, they will provide exciting discoveries in understanding the designs and purposes of biological machines. © 2018 The Authors. BioEssays Published by WILEY Periodicals, Inc.

  7. Crystal structure determination of Efavirenz

    International Nuclear Information System (INIS)

    Popeneciu, Horea; Dumitru, Ristoiu; Tripon, Carmen; Borodi, Gheorghe; Pop, Mihaela Maria

    2015-01-01

    Needle-shaped single crystals of the title compound, C 14 H 9 ClF 3 NO 2 , were obtained from a co-crystallization experiment of Efavirenz with maleic acid in a (1:1) ratio, using methanol as solvent. Crystal structure determination at room temperature revealed a significant anisotropy of the lattice expansion compared to the previously reported low-temperature structure. In both low- and room temperature structures the cyclopropylethynyl fragment in one of the asymmetric unit molecules is disordered. While at low-temperature only one C atom exhibits positional disorder, at room temperature the disorder is present for two C atoms of the cyclopropane ring

  8. The JCSG high-throughput structural biology pipeline

    International Nuclear Information System (INIS)

    Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wooley, John; Wüthrich, Kurt; Wilson, Ian A.

    2010-01-01

    The Joint Center for Structural Genomics high-throughput structural biology pipeline has delivered more than 1000 structures to the community over the past ten years and has made a significant contribution to the overall goal of the NIH Protein Structure Initiative (PSI) of expanding structural coverage of the protein universe. The Joint Center for Structural Genomics high-throughput structural biology pipeline has delivered more than 1000 structures to the community over the past ten years. The JCSG has made a significant contribution to the overall goal of the NIH Protein Structure Initiative (PSI) of expanding structural coverage of the protein universe, as well as making substantial inroads into structural coverage of an entire organism. Targets are processed through an extensive combination of bioinformatics and biophysical analyses to efficiently characterize and optimize each target prior to selection for structure determination. The pipeline uses parallel processing methods at almost every step in the process and can adapt to a wide range of protein targets from bacterial to human. The construction, expansion and optimization of the JCSG gene-to-structure pipeline over the years have resulted in many technological and methodological advances and developments. The vast number of targets and the enormous amounts of associated data processed through the multiple stages of the experimental pipeline required the development of variety of valuable resources that, wherever feasible, have been converted to free-access web-based tools and applications

  9. Structural determination of organic compounds

    International Nuclear Information System (INIS)

    Kintzinger, J.P.

    1991-01-01

    This paper reports that the current methods available in high-field NMR spectroscopy are such that the tridimensional structure determination of any rigid molecule containing only carbon and hydrogen atoms may be achieved. The connectivities between carbon-carbon, carbon-hydrogen, and hydrogen-hydrogen atoms are determined by multipulse and two-dimensional (2D) experiments. These connectivity patterns or maps allow a step-by-step reconstruction of the molecular structures. From the carbon-carbon connectivity map, the carbon framework of the molecule is obtained, whereas the carbon-hydrogen pattern allows determination of the positions of the hydrogen atoms on their corresponding carbon atoms. High-field spectrometers are then necessary to remove fortuitous degeneracy and to reduce the proton spectra to a nearly first-order one, allowing an easy measurement of the chemical shifts and the coupling constants

  10. Capacitive Structures for Gas and Biological Sensing

    KAUST Repository

    Sapsanis, Christos

    2015-04-01

    The semiconductor industry was benefited by the advances in technology in the last decades. This fact has an impact on the sensors field, where the simple transducer was evolved into smart miniaturized multi-functional microsystems. However, commercially available gas and biological sensors are mostly bulky, expensive, and power-hungry, which act as obstacles to mass use. The aim of this work is gas and biological sensing using capacitive structures. Capacitive sensors were selected due to its design simplicity, low fabrication cost, and no DC power consumption. In the first part, the dominant structure among interdigitated electrodes (IDEs), fractal curves (Peano and Hilbert) and Archimedean spiral was investigated from capacitance density perspective. The investigation consists of geometrical formula calculations, COMSOL Multiphysics simulations and cleanroom fabrication of the capacitors on a silicon substrate. Moreover, low-cost fabrication on flexible plastic PET substrate was conducted outside cleanroom with rapid prototyping using a maskless laser etching. The second part contains the humidity, Volatile Organic compounds (VOCs) and Ammonia sensing of polymers, Polyimide and Nafion, and metal-organic framework (MOF), Cu(bdc)2.xH2O using IDEs and tested in an automated gas setup for experiment control and data extraction. The last part includes the biological sensing of C - reactive protein (CRP) quantification, which is considered as a biomarker of being prone to cardiac diseases and Bovine serum albumin (BSA) protein quantification, which is used as a reference for quantifying unknown proteins.

  11. New pyrrole inhibitors of monoamine oxidase: synthesis, biological evaluation, and structural determinants of MAO-A and MAO-B selectivity.

    Science.gov (United States)

    La Regina, Giuseppe; Silvestri, Romano; Artico, Marino; Lavecchia, Antonio; Novellino, Ettore; Befani, Olivia; Turini, Paola; Agostinelli, Enzo

    2007-03-08

    A series of new pyrrole derivatives have been synthesized and evaluated for their monoamine oxidase (MAO) A and B inhibitory activity and selectivity. N-Methyl,N-(benzyl),N-(pyrrol-2-ylmethyl)amine (7) and N-(2-benzyl),N-(1-methylpyrrol-2-ylmethyl)amine (18) were the most selective MAO-B (7, SI = 0.0057) and MAO-A (18, SI = 12500) inhibitors, respectively. Docking and molecular dynamics simulations gave structural insights into the MAO-A and MAO-B selectivity. Compound 18 forms an H-bond with Gln215 through its protonated amino group into the MAO-A binding site. This H-bond is absent in the 7/MAO-A complex. In contrast, compound 7 places its phenyl ring into an aromatic cage of the MAO-B binding pocket, where it forms charge-transfer interactions. The slightly different binding pose of 18 into the MAO-B active site seems to be forced by a bulkier Tyr residue, which replaces a smaller Ile residue present in MAO-A.

  12. Structural Interfaces and Attachments in Biology

    CERN Document Server

    Birman, Victor; Genin, Guy

    2013-01-01

    Attachment of dissimilar materials in engineering and surgical practice is a perennial challenge. Bimaterial attachment sites are common locations for injury, repeated injury, and mechanical failure. Nature presents several highly effective solutions to the challenge of bimaterial attachment that differ from those found in engineering practice. Structural Interfaces and Attachments in Biology describes the attachment of dissimilar materials from multiple perspectives. The text will simultaneously elucidate natural bimaterial attachments and outline engineering principles underlying successful attachments to the communities of tissue engineers and surgeons. Included an in-depth analysis of the biology of attachments in the body and mechanisms by which robust attachments are formed, a review of current concepts of attaching dissimilar materials in surgical practice and a discussion of bioengineering approaches that are currently being developed. This book also: Provides the first comprehensive treatment of phys...

  13. STRUCTURES AND BIOLOGICAL ACTIVITY OF CUPROPHYLLINS

    Directory of Open Access Journals (Sweden)

    Martynov A.V.

    2017-06-01

    Full Text Available Chlorophylls (a, b are the porphyrin compounds and most common chemical in the plant’s world. In fact, these compounds are an obligatory intermediate product both in energy metabolism and in plant catabolism. At the same time, currently there are few pharmaceutical preparations on the pharmaceutical market based on chlorophylls. Dyes based on hydrolyzed chlorophyll are successfully used in the food industry. Commercial chlorophylline is a copper complex of hydrolyzed chlorophylls. As shown earlier in TLC, the chlorophyllin mixture contains a large number of different compounds. It is like water-soluble saponified derivatives in the form of sodium-magnesium complexes, and similar structures in the form of a complex with copper. The latter are more brightly colored, soluble in water and widely used as coloring agents in cooking. In this case, if the initial chlorophyll was not found to have a pronounced biological activity, the substituted derivatives in the form of copper complexes possessed a number of new unique biological properties. Non-hydrolyzed hydrophobic cuprophylline obtained from eucalyptus leaves possessed high antimicrobial activity to most strains of staphylococci, inclusion resistant to antimicrobials and multiresistant strains. This drug is called Chlorophyllipt, it is allowed to be used as a medicinal product and is one of the oldest antibacterial drugs from plants on the market. It is marketed as ethanoic and oily solutions for topical use, and as an alcohol solution for intravenous injections. Its main purpose is the fight against staphylococcal infections. Recently, found that the oral administration of chlorophyllipt activates cellular immunity and indirectly exhibits antiviral activity. Another compound of cuprophyllin is water-soluble chlorophyllin. Some authors show the variability of the structure and biological activity of cuprophyllins. Different derivatives of chlorophyll have different biological activity

  14. Determinants of Glycosaminoglycan (GAG Structure

    Directory of Open Access Journals (Sweden)

    Kristian Prydz

    2015-08-01

    Full Text Available Proteoglycans (PGs are glycosylated proteins of biological importance at cell surfaces, in the extracellular matrix, and in the circulation. PGs are produced and modified by glycosaminoglycan (GAG chains in the secretory pathway of animal cells. The most common GAG attachment site is a serine residue followed by a glycine (-ser-gly-, from which a linker tetrasaccharide extends and may continue as a heparan sulfate, a heparin, a chondroitin sulfate, or a dermatan sulfate GAG chain. Which type of GAG chain becomes attached to the linker tetrasaccharide is influenced by the structure of the protein core, modifications occurring to the linker tetrasaccharide itself, and the biochemical environment of the Golgi apparatus, where GAG polymerization and modification by sulfation and epimerization take place. The same cell type may produce different GAG chains that vary, depending on the extent of epimerization and sulfation. However, it is not known to what extent these differences are caused by compartmental segregation of protein cores en route through the secretory pathway or by differential recruitment of modifying enzymes during synthesis of different PGs. The topic of this review is how different aspects of protein structure, cellular biochemistry, and compartmentalization may influence GAG synthesis.

  15. 2010 Diffraction Methods in Structural Biology

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Ana Gonzalez

    2011-03-10

    Advances in basic methodologies have played a major role in the dramatic progress in macromolecular crystallography over the past decade, both in terms of overall productivity and in the increasing complexity of the systems being successfully tackled. The 2010 Gordon Research Conference on Diffraction Methods in Structural Biology will, as in the past, focus on the most recent developments in methodology, covering all aspects of the process from crystallization to model building and refinement, complemented by examples of structural highlights and complementary methods. Extensive discussion will be encouraged and it is hoped that all attendees will participate by giving oral or poster presentations, the latter using the excellent poster display area available at Bates College. The relatively small size and informal atmosphere of the meeting provides an excellent opportunity for all participants, especially younger scientists, to meet and exchange ideas with leading methods developers.

  16. Structure determination of enterovirus 71

    Energy Technology Data Exchange (ETDEWEB)

    Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G. (Purdue); (Sentinext)

    2013-02-20

    Enterovirus 71 is a picornavirus that causes hand, foot and mouth disease but may induce fatal neurological illness in infants and young children. Enterovirus 71 crystallized in a body-centered orthorhombic space group with two particles in general orientations in the crystallographic asymmetric unit. Determination of the particle orientations required that the locked rotation function excluded the twofold symmetry axes from the set of icosahedral symmetry operators. This avoided the occurrence of misleading high rotation-function values produced by the alignment of icosahedral and crystallographic twofold axes. Once the orientations and positions of the particles had been established, the structure was solved by molecular replacement and phase extension.

  17. Study of phosphors determination in biological samples

    International Nuclear Information System (INIS)

    Oliveira, Rosangela Magda de.

    1994-01-01

    In this paper, phosphors determination by neutron activation analysis in milk and bone samples was studied employing both instrumental and radiochemical separation methods. The analysis with radiochemistry separation consisted of the simultaneous irradiation of the samples and standards during 30 minutes, dissolution of the samples, hold back carrier, addition precipitation of phosphorus with ammonium phosphomolibdate (A.M.P.) and phosphorus-32 by counting by using Geiger-Mueller detector. The instrumental analysis consisted of the simultaneous irradiation of the samples and standards during 30 minutes, transfer of the samples into a counting planchet and measurement of the beta radiation emitted by phosphorus-32, after a suitable decay period. After the phosphorus analysis methods were established they were applied to both commercial milk and animal bone samples, and data obtained in the instrumental and radiochemical separation methods for each sample, were compared between themselves. In this work, it became possible to obtain analysis methods for phosphorus that can be applied independently of the sample quantity available, and the phosphorus content in the samples or interference that can be present in them. (author). 51 refs., 7 figs., 4 tabs

  18. Structural Basis of Biological Nitrile Reduction*

    Science.gov (United States)

    Chikwana, Vimbai M.; Stec, Boguslaw; Lee, Bobby W. K.; de Crécy-Lagard, Valérie; Iwata-Reuyl, Dirk; Swairjo, Manal A.

    2012-01-01

    The enzyme QueF catalyzes the reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1), the only nitrile reduction reaction known in biology. We describe here two crystal structures of Bacillus subtilis QueF, one of the wild-type enzyme in complex with the substrate preQ0, trapped as a covalent thioimide, a putative intermediate in the reaction, and the second of the C55A mutant in complex with the substrate preQ0 bound noncovalently. The QueF enzyme forms an asymmetric tunnel-fold homodecamer of two head-to-head facing pentameric subunits, harboring 10 active sites at the intersubunit interfaces. In both structures, a preQ0 molecule is bound at eight sites, and in the wild-type enzyme, it forms a thioimide covalent linkage to the catalytic residue Cys-55. Both structural and transient kinetic data show that preQ0 binding, not thioimide formation, induces a large conformational change in and closure of the active site. Based on these data, we propose a mechanism for the activation of the Cys-55 nucleophile and subsequent hydride transfer. PMID:22787148

  19. INAA Application for Trace Element Determination in Biological Reference Material

    Science.gov (United States)

    Atmodjo, D. P. D.; Kurniawati, S.; Lestiani, D. D.; Adventini, N.

    2017-06-01

    Trace element determination in biological samples is often used in the study of health and toxicology. Determination change to its essentiality and toxicity of trace element require an accurate determination method, which implies that a good Quality Control (QC) procedure should be performed. In this study, QC for trace element determination in biological samples was applied by analyzing the Standard Reference Material (SRM) Bovine muscle 8414 NIST using Instrumental Neutron Activation Analysis (INAA). Three selected trace element such as Fe, Zn, and Se were determined. Accuracy of the elements showed as %recovery and precision as %coefficient of variance (%CV). The result showed that %recovery of Fe, Zn, and Se were in the range between 99.4-107%, 92.7-103%, and 91.9-112%, respectively, whereas %CV were 2.92, 3.70, and 5.37%, respectively. These results showed that INAA method is precise and accurate for trace element determination in biological matrices.

  20. Sulfated oligosaccharide structures, as determined by NMR techniques

    International Nuclear Information System (INIS)

    Noseda, M.D.; Duarte, M.E.R.; Tischer, C.A.; Gorin, P.A.J.; Cerezo, A.S.

    1997-01-01

    Carrageenans are sulfated polysaccharides, produced by red seaweeds (Rhodophyta), that have important biological and physico-chemical properties. Using partial autohydrolysis, we obtained sulfated oligosaccharides from a λ-carrageenan (Noseda and Cerezo, 1993). These oligosaccharides are valuable not only for the study of the structures of the parent carrageenans but also for their possible biological activities. In this work we determined the chemical structure of one of the sulfated oligosaccharides using 1D and 2D NMR techniques. (author)

  1. Biologically inspired autonomous structural materials with controlled toughening and healing

    Science.gov (United States)

    Garcia, Michael E.; Sodano, Henry A.

    2010-04-01

    The field of structural health monitoring (SHM) has made significant contributions in the field of prognosis and damage detection in the past decade. The advantageous use of this technology has not been integrated into operational structures to prevent damage from propagating or to heal injured regions under real time loading conditions. Rather, current systems relay this information to a central processor or human operator, who then determines a course of action such as altering the mission or scheduling repair maintenance. Biological systems exhibit advanced sensory and healing traits that can be applied to the design of material systems. For instance, bone is the major structural component in vertebrates; however, unlike modern structural materials, bone has many properties that make it effective for arresting the propagation of cracks and subsequent healing of the fractured area. The foremost goal for the development of future adaptive structures is to mimic biological systems, similar to bone, such that the material system can detect damage and deploy defensive traits to impede damage from propagating, thus preventing catastrophic failure while in operation. After sensing and stalling the propagation of damage, the structure must then be repaired autonomously using self healing mechanisms motivated by biological systems. Here a novel autonomous system is developed using shape memory polymers (SMPs), that employs an optical fiber network as both a damage detection sensor and a network to deliver stimulus to the damage site initiating adaptation and healing. In the presence of damage the fiber optic fractures allowing a high power laser diode to deposit a controlled level of thermal energy at the fractured sight locally reducing the modulus and blunting the crack tip, which significantly slows the crack growth rate. By applying a pre-induced strain field and utilizing the shape memory recovery effect, thermal energy can be deployed to close the crack and return

  2. Determination of chromium in biological matrices by neutron activation

    International Nuclear Information System (INIS)

    McClendon, L.T.

    1978-01-01

    Chromium is recognized to be an essential trace element in several biological systems. It exists in many biological materials in a variety of chemical forms and very low concentration levels which cause problems for many analytical techniques. Both instrumental and destructive neutron activation analysis were used to determine the chromium concentration in Orchard Leaves, SRM 1571, Brewers Yeast, SRM 1569, and Bovine Liver, SRM 1577. Some of the problems inherent with determining chromium in certain biological matrices and the data obtained here at the National Bureau of Standards using this technique are discussed. The results obtained from dissolution of brewers yeast in a closed system as described in the DNAA procedure are in good agreement with the INAA results. The same phenomenon existed in the determination of chromium in bovine liver. The radiochemical procedure described for chromium (DNAA) provides the analyst with a simple, rapid and selective technique for chromium determination in a variety of matrices. (T.G.)

  3. J D Bernal and the genesis of structural biology

    Science.gov (United States)

    Caffrey, Martin

    2007-02-01

    I was invited to participate in this Symposium a month or so before the event. At that time however, I knew little about J D Bernal. I vaguely remembered a brief conversation on the topic over a decade ago with Professor Vittorio Luzzati as we ambled around the gardens at the Palace of Varsailles. Vittorio likely knew Bernal through his friend Rosalind Franklin who worked with Bernal at Birbeck College. But beyond that I knew nothing about the man or his science. And so it was most fortunate that Andrew Brown's book J D Bernal: The Sage of Science appeared in 2005 and I was able to call on it. Indeed, much of the material included in this chapter is based on that source and on Dorothy Hodgkin's biographic memoir of J D Bernal, her postgraduate supervisor. Given that this chapter is to be published in a Physics journal I thought it appropriate to provide some background to the theme of my presentation, structural biology. Accordingly, I will begin with an introduction to proteins, one of structural biology's central characters, and to which Bernal devoted much energy and attention. How the molecular structure of a protein determines its activity and function will then be described. Bernal's major contribution in this area was to X-ray crystallography, the primary method by which a protein's structure is determined. The method, and aspects of its development, will be described. I will also make reference to some of Bernal's additional contributions in related fields. Finally, Vincent Casey, the symposium organizer, asked that I comment on how structural biology might impact on society. I will attempt to address that at the close of my presentation.

  4. J D Bernal and the genesis of structural biology

    International Nuclear Information System (INIS)

    Caffrey, Martin

    2007-01-01

    I was invited to participate in this Symposium a month or so before the event. At that time however, I knew little about J D Bernal. I vaguely remembered a brief conversation on the topic over a decade ago with Professor Vittorio Luzzati as we ambled around the gardens at the Palace of Varsailles. Vittorio likely knew Bernal through his friend Rosalind Franklin who worked with Bernal at Birbeck College. But beyond that I knew nothing about the man or his science. And so it was most fortunate that Andrew Brown's book J D Bernal: The Sage of Science appeared in 2005 and I was able to call on it. Indeed, much of the material included in this chapter is based on that source and on Dorothy Hodgkin's biographic memoir of J D Bernal, her postgraduate supervisor. Given that this chapter is to be published in a Physics journal I thought it appropriate to provide some background to the theme of my presentation, structural biology. Accordingly, I will begin with an introduction to proteins, one of structural biology's central characters, and to which Bernal devoted much energy and attention. How the molecular structure of a protein determines its activity and function will then be described. Bernal's major contribution in this area was to X-ray crystallography, the primary method by which a protein's structure is determined. The method, and aspects of its development, will be described. I will also make reference to some of Bernal's additional contributions in related fields. Finally, Vincent Casey, the symposium organizer, asked that I comment on how structural biology might impact on society. I will attempt to address that at the close of my presentation

  5. Structural Biology in the context of EGEE

    CERN Document Server

    García, D; Carazo, J M; Valverde, J R; Moscicki, J; Muraru, A

    2007-01-01

    Electron microscopy (EM) is a crucial technique, which allows Structural Biology researchers to characterize macromolecular assemblies in distinct functional states. Image processing in three dimensional EM (3D-EM) is used by a flourishing community (exemplarized by the EU funded 3D-EM NoE) and is characterized by voluminous data and large computing requirements, making this a problem well suited for Grid computing and the EGEE infrastructure. There are various steps in the 3D-EM refinement process that may benefit from Grid computing. To start with, large numbers of experimental images need to be averaged. Nowadays, typically tens of thousands of images are used, while future studies may routinely employ millions of images. Our group has been developing Xmipp, a package for single-particle 3D-EM image processing. Using Xmipp, the classification of 91,000 ribosome projections into 4 classes took more than 2500 CPU hours using the resources of the MareNostrum supercomputer at the Barcelona Supercomputing Centr...

  6. Structural biology by NMR: structure, dynamics, and interactions.

    Directory of Open Access Journals (Sweden)

    Phineus R L Markwick

    2008-09-01

    Full Text Available The function of bio-macromolecules is determined by both their 3D structure and conformational dynamics. These molecules are inherently flexible systems displaying a broad range of dynamics on time-scales from picoseconds to seconds. Nuclear Magnetic Resonance (NMR spectroscopy has emerged as the method of choice for studying both protein structure and dynamics in solution. Typically, NMR experiments are sensitive both to structural features and to dynamics, and hence the measured data contain information on both. Despite major progress in both experimental approaches and computational methods, obtaining a consistent view of structure and dynamics from experimental NMR data remains a challenge. Molecular dynamics simulations have emerged as an indispensable tool in the analysis of NMR data.

  7. The Structure and Function of Biological Networks

    Science.gov (United States)

    Wu, Daniel Duanqing

    2010-01-01

    Biology has been revolutionized in recent years by an explosion in the availability of data. Transforming this new wealth of data into meaningful biological insights and clinical breakthroughs requires a complete overhaul both in the questions being asked and the methodologies used to answer them. A major challenge in organizing and understanding…

  8. Structure and Biological Activity of Pathogen-like Synthetic Nanomedicines

    Science.gov (United States)

    Lőrincz, Orsolya; Tőke, Enikő R.; Somogyi, Eszter; Horkay, Ferenc; Chandran, Preethi; Douglas, Jack F.; Szebeni, János; Lisziewicz, Julianna

    2011-01-01

    Here we characterize the structure, stability and intracellular mode-of-action of DermaVir nanomedicine that is under clinical development for the treatment of HIV/AIDS. This nanomedicine is comprised of pathogen-like pDNA/PEIm nanoparticles (NPs) having the structure and function resembling spherical viruses that naturally evolved to deliver nucleic acids to the cells. Atomic force microscopy demonstrated spherical 100–200nm NPs with a smooth polymer surface protecting the pDNA in the core. Optical-absorption determined both the NP structural stability and biological activity relevant to their ability to escape from the endosome and release the pDNA at the nucleus. Salt, pH and temperature influence the nanomedicine shelf-life and intracellular stability. This approach facilitates the development of diverse polyplex nanomedicines where the delivered pDNA-expressed antigens induce immune responses to kill infected cells. PMID:21839051

  9. Structural Biology and Molecular Applications Research

    Science.gov (United States)

    Part of NCI's Division of Cancer Biology's research portfolio, research and development in this area focuses on enabling technologies, models, and methodologies to support basic and applied cancer research.

  10. Determination of trace elements in KRISS biological CRMs by INAA

    International Nuclear Information System (INIS)

    Cho, Kyung Haeng; Park, Kwang Won; Zeisler, Rolf

    2005-01-01

    Two biological Certified Reference Materials (CRMs), KRISS 108-04-001 (oyster tissue) and 108-05-001 (water dropwort stem), were prepared by Korea Research Institute of Standards and Science (KRISS) during FY '01. The certified values of these materials had been determined by Isotope Dilution Mass Spectrometry (IDMS) for six elements (Cd, Cr, Cu, Fe, Pb and Zn). Additional analytical works are now progressing to certify the concentrations of a number of the environmental and nutrimental elements in these CRMs. The certified values in a CRM are usually determined by using a single primary method with confirmation by other method(s) or using two independent critically-evaluated methods. Instrumental Neutron Activation Analysis (INAA) plays an important role in determination of certified values. INAA procedure was used in determination of 20 elements in these two biological CRMs to acquire the concentration information and the results were compared with KRISS certified values

  11. Hydrological structure and biological productivity of the tropical Indian Ocean

    Digital Repository Service at National Institute of Oceanography (India)

    Muraleedharan, U.D.; Muraleedharan, P.M.

    Hydrological structure analyses of regions in the tropical Atlantic Ocean have consistently revealed the existence of a typical tropical structure characterized by a nitrate-depleted mixed layer above the thermocline. The important biological...

  12. The determination of copper in biological materials by flame spectrophotometry

    Science.gov (United States)

    Newman, G. E.; Ryan, M.

    1962-01-01

    A method for the determination of the copper content of biological materials by flame spectrophotometry is described. The effects of interference by ions such as sodium and phosphate were eliminated by isolating copper as the dithizonate in CCl4. Results obtained for the urinary excretion of copper by a patient with Wilson's disease before and after treatment with penicillamine are reported. PMID:14479334

  13. Method of 10B determination in biological specimens

    International Nuclear Information System (INIS)

    Nikitina, R.G.; Frolova, E.I.

    1981-01-01

    The paper is concerned with the methods of 10 B determination in biological specimens (blood, skin and tissues of rats). On the basis of investigations conducted there have been proposed films based on cellulose triacetate with optimal characteristics in terms of their possible utilization as solid detectors to record α-particles and recoil nuclei. The conditions of film staining are also discussed

  14. Structural biology facilities at Brookhaven National Laboratory`s high flux beam reactor

    Energy Technology Data Exchange (ETDEWEB)

    Korszun, Z.R.; Saxena, A.M.; Schneider, D.K. [Brookhaven National Laboratory, Upton, NY (United States)

    1994-12-31

    The techniques for determining the structure of biological molecules and larger biological assemblies depend on the extent of order in the particular system. At the High Flux Beam Reactor at the Brookhaven National Laboratory, the Biology Department operates three beam lines dedicated to biological structure studies. These beam lines span the resolution range from approximately 700{Angstrom} to approximately 1.5{Angstrom} and are designed to perform structural studies on a wide range of biological systems. Beam line H3A is dedicated to single crystal diffraction studies of macromolecules, while beam line H3B is designed to study diffraction from partially ordered systems such as biological membranes. Beam line H9B is located on the cold source and is designed for small angle scattering experiments on oligomeric biological systems.

  15. [Progress on Determination and Analysis of Zopiclone in Biological Samples].

    Science.gov (United States)

    Shu, C X; Gong, D; Zhang, L P; Zhao, J X

    2017-12-01

    As a new hypnotic, zopiclone is widely used in clinical treatment. There are many methods for determination of zopiclone, including spectrophotometry, chromatography and chromatography mass spectrum, etc. Present paper reviews different kinds of biological samples associated with zopiclone, extraction and purification methods, and determination and analysis methods, which aims to provide references for the relevant research and practice. Copyright© by the Editorial Department of Journal of Forensic Medicine.

  16. Solution NMR structure determination of proteins revisited

    International Nuclear Information System (INIS)

    Billeter, Martin; Wagner, Gerhard; Wuethrich, Kurt

    2008-01-01

    This 'Perspective' bears on the present state of protein structure determination by NMR in solution. The focus is on a comparison of the infrastructure available for NMR structure determination when compared to protein crystal structure determination by X-ray diffraction. The main conclusion emerges that the unique potential of NMR to generate high resolution data also on dynamics, interactions and conformational equilibria has contributed to a lack of standard procedures for structure determination which would be readily amenable to improved efficiency by automation. To spark renewed discussion on the topic of NMR structure determination of proteins, procedural steps with high potential for improvement are identified

  17. Macromolecular structure determination in the post-genome era

    CERN Document Server

    Kuhn, P

    2001-01-01

    Recent advances in genetics, molecular biology and crystallographic instrumentation and methodology have led to a revolution in the field of Structural Molecular Biology (SMB). These combined advances have paved the way to a more complete and detailed understanding of the biological macromolecules that make up an organism, both in terms of their individual functions and also the interactions between them. In this paper we describe a large-scale, genomic approach to the three-dimensional structure determination of macromolecules and their complexes, using high-throughput methodology to streamline all aspects of the process. This task requires the development of automated high-intensity synchrotron beam lines for X-ray diffraction data collection from single crystal samples. Furthermore, these beam lines must be operated within a sophisticated software and hardware environment, which is capable of delivering a completely automated structure determination pipeline. The SMB resource at SSRL is developing a system...

  18. Structure of catalase determined by MicroED

    Science.gov (United States)

    Nannenga, Brent L; Shi, Dan; Hattne, Johan; Reyes, Francis E; Gonen, Tamir

    2014-01-01

    MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination. DOI: http://dx.doi.org/10.7554/eLife.03600.001 PMID:25303172

  19. Structural biology of the sequestration and transport of heavy metal toxins: NMR structure determination of proteins containing the -Cys-X-Y-Cys-metal binding motifs. 1997 annual progress report

    International Nuclear Information System (INIS)

    Opella, S.J.

    1997-01-01

    'There are enormous amounts of heavy metals in the environment, much of it in the form of organometallic compounds resulting from various types of industrial and military waste. Nearly all of these metals and compounds are highly toxic to biological organisms including humans. However, some bacteria thrive in the presence of high concentrations of heavy metal toxins because they possess efficient mechanisms for the detoxification of these metals and compounds. Heavy metals appear to be universally toxic because of their non-selective chemistry, for example Hg(II) reacts with essentially all exposed sulfhydryl groups on proteins, thus, it may seem surprising that any organism at all can survive these chemical insults much less those that grow in a toxic milieu. However, the prebiotic environment was undoubtedly heavily polluted with heavy metals from geological processes, and the most primitive organisms simply had to evolve mechanisms for dealing with them if they were going to be able to utilize Cys, His, and the other amino acids that contribute to metal binding sites in their proteins. Genes associated with bacterial resistance to Ag, AsO 2 , AsO 4 , Bi, Cd, Co, CrO 4 , Cu, Hg, iNi, TeO 3 , TI, Pb, Zn, and other metals of environmental concern have been described (Silver, 1992; Silver and Walderhaug, 1995).'

  20. Structure, reactivity, and biological properties of hidantoines

    International Nuclear Information System (INIS)

    Oliveira, Silvania Maria de; Silva, Joao Bosco Paraiso da; Hernandes, Marcelo Zaldini; Lima, Maria do Carmo Alves de; Galdino, Suely Lins; Pitta, Ivan da Rocha

    2008-01-01

    Hydantoin (imidazolidine-2,4-dione) is a 2,4-diketotetrahydroimidazole discovered by Baeyer in 1861. Thiohydantoins and derivatives were prepared, having chemical properties similar to the corresponding carbonyl compounds. Some biological activities (antimicrobial, anticonvulsant, schistosomicidal) are attributed to the chemical reactivity and consequent affinity of hydantoinic rings towards biomacromolecules. Therefore, knowledge about the chemistry of hydantoins has increased enormously. In this review, we present important aspects such as reactivity of hydantoins, acidity of hydantoins, spectroscopy and crystallographic properties, and biological activities of hydantoin and its derivatives. (author)

  1. On the Concept of "Respiration": Biology Student Teachers' Cognitive Structures and Alternative Conceptions

    Science.gov (United States)

    Kurt, Hakan; Ekici, Gulay; Aktas, Murat; Aksu, Ozlem

    2013-01-01

    In researches, the subject of respiration has been determined to be among subjects about whom participants from all educational levels struggle to form their cognitive structures and have many alternative conceptions. This research was carried out in order to determine biology student teachers' cognitive structures and alternative conceptions…

  2. Identification of Bacteria and Determination of Biological Indicators

    Science.gov (United States)

    Venkateswaran, Kasthuri; La Duc, Myron T.; Vaishampayan, Parag A.

    2009-01-01

    The ultimate goal of planetary protection research is to develop superior strategies for inactivating resistance bearing micro-organisms like Rummeli - bacillus stabekisii. By first identifying the particular physiologic pathway and/or structural component of the cell/spore that affords it such elevated tolerance, eradication regimes can then be designed to target these resistance-conferring moieties without jeopardizing the structural integrity of spacecraft hardware. Furthermore, hospitals and government agencies frequently use biological indicators to ensure the efficacy of a wide range of sterilization processes. The spores of Rummelibacillus stabekisii, which are far more resistant to many of such perturbations, could likely serve as a more significant biological indicator for potential survival than those being used currently.

  3. Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course

    Science.gov (United States)

    Ziegler, Brittany; Montplaisir, Lisa

    2014-01-01

    Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students' perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest…

  4. Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course

    OpenAIRE

    Ziegler, Brittany; Montplaisir, Lisa

    2014-01-01

    Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students’ perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest approach. Significant differences in students’ perception of their knowledge and their determined knowledge exist at the beginning (pretest) and end (postte...

  5. Laser-matter structuration of optical and biological materials

    Energy Technology Data Exchange (ETDEWEB)

    Hallo, L., E-mail: hallo@celia.u-bordeaux1.fr [CELIA, Universite Bordeaux 1 (France); Mezel, C., E-mail: candice.mezel@cea.fr [CELIA, Universite Bordeaux 1 (France); CEA Le Ripault, 37260 Monts (France); Guillemot, F., E-mail: fabien.guillemot@inserm.fr [UMR 577 INSERM, Universite Bordeaux 2 (France); Chimier, B., E-mail: chimier@celia.u-bordeaux1.fr [CELIA, Universite Bordeaux 1 (France); Bourgeade, A., E-mail: antoine.bourgeade@cea.fr [CEA-CESTA, Le Barp (France); Regan, C., E-mail: regan@celia.u-bordeaux1.fr [CELIA, Universite Bordeaux 1 (France); Duchateau, G., E-mail: duchateau@celia.u-bordeaux1.fr [CELIA, Universite Bordeaux 1 (France); Souquet, A., E-mail: agnes.souquet@inserm.fr [UMR 577 INSERM, Universite Bordeaux 2 (France); Hebert, D., E-mail: david.hebert@cea.fr [CEA-CESTA, Le Barp (France)

    2012-09-15

    Highlights: Black-Right-Pointing-Pointer In this study we model nanomaterial structuring. Black-Right-Pointing-Pointer The laser energy deposition is discussed first. Black-Right-Pointing-Pointer Full and approximate models are discussed. Black-Right-Pointing-Pointer Dynamic material response is addressed via hydrodynamics. Black-Right-Pointing-Pointer Sild effects are accounted for - Abstract: Interaction of ultrafast laser, i.e. from the femtosecond (fs) to the nanosecond (ns) regime, with initially transparent matter may produce very high energy density hot spots in the bulk as well as at the material surface, depending on focusing conditions. In the fs regime, absorption is due to ionisation of the dielectric, which enables absorption process to begin, and then hydrodynamic to take place. In the ns regime both absorption and hydrodynamic are coupled to each other, which complexifies considerably the comprehension but matter structuration looks similar. A numerical tool including solution of 3D Maxwell equations and a rate equation for free electrons is first compared to some available simple models of laser energy absorption. Then, subsequent material deformation, i.e. structuration, is determined by solving hydrodynamic equations, including or not solid behaviour. We show that nature of the final structures strongly depends on the amount of deposited energy and on the shape of the absorption zone. Then we address some problems related to laser-matter structuration of optical and biological materials in the fs, ps and ns regimes.

  6. Sulfated oligosaccharide structures, as determined by NMR techniques

    Energy Technology Data Exchange (ETDEWEB)

    Noseda, M.D.; Duarte, M.E.R.; Tischer, C.A.; Gorin, P.A.J. [Parana Univ., Curitiba, PR (Brazil). Dept. De Bioquimica; Cerezo, A.S. [Buenos Aires Univ. Nacional (Argentina). Dept. de Quimica Organica

    1997-12-31

    Carrageenans are sulfated polysaccharides, produced by red seaweeds (Rhodophyta), that have important biological and physico-chemical properties. Using partial autohydrolysis, we obtained sulfated oligosaccharides from a {lambda}-carrageenan (Noseda and Cerezo, 1993). These oligosaccharides are valuable not only for the study of the structures of the parent carrageenans but also for their possible biological activities. In this work we determined the chemical structure of one of the sulfated oligosaccharides using 1D and 2D NMR techniques. (author) 4 refs., 8 figs., 1 tabs.

  7. 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.

  8. Communication on the structure of biological networks

    Indian Academy of Sciences (India)

    Networks are widely used to represent interaction pattern among the components in complex systems. Structures of real networks from different domains may vary quite significantly. As there is an interplay between network architecture and dynamics, structure plays an important role in communication and spreading of ...

  9. Determining environmental causes of biological effects: the need for a mechanistic physiological dimension in conservation biology.

    Science.gov (United States)

    Seebacher, Frank; Franklin, Craig E

    2012-06-19

    The emerging field of Conservation Physiology links environmental change and ecological success by the application of physiological theory, approaches and tools to elucidate and address conservation problems. Human activity has changed the natural environment to a point where the viability of many ecosystems is now under threat. There are already many descriptions of how changes in biological patterns are correlated with environmental changes. The next important step is to determine the causative relationship between environmental variability and biological systems. Physiology provides the mechanistic link between environmental change and ecological patterns. Physiological research, therefore, should be integrated into conservation to predict the biological consequences of human activity, and to identify those species or populations that are most vulnerable.

  10. Growth and development and their environmental and biological determinants.

    Science.gov (United States)

    da Rocha Neves, Kelly; de Souza Morais, Rosane Luzia; Teixeira, Romero Alves; Pinto, Priscilla Avelino Ferreira

    2016-01-01

    To investigate child growth, cognitive/language development, and their environmental and biological determinants. This was a cross-sectional, predictive correlation study with all 92 children aged 24-36 months who attended the municipal early childhood education network in a town in the Vale do Jequitinhonha region, in 2011. The socioeconomic profile was determined using the questionnaire of the Associação Brasileira de Empresas de Pesquisa. The socio-demographicand maternal and child health profiles were created through a self-prepared questionnaire. The height-for-age indicator was selected to represent growth. Cognitive/language development was assessed through the Bayley Scale of Infant and Toddler Development. The quality of educational environments was assessed by Infant/Toddler Environment Scale; the home environment was assessed by the Home Observation for Measurement of the Environment. The neighborhood quality was determined by a self-prepared questionnaire. A multivariate linear regression analysis was performed. Families were predominantly from socioeconomic class D, with low parental education. The prevalence of stunted growth was 14.1%; cognitive and language development were below average at 28.6% and 28.3%, respectively. Educational institutions were classified as inadequate, and 69.6% of homes were classified as presenting a risk for development. Factors such as access to parks and pharmacies and perceived security received the worst score regarding neighborhood environment. Biological variables showed a greater association with growth and environmental variables with development. The results showed a high prevalence of stunting and below-average results for cognitive/language development among the participating children. Both environmental and biological factors were related to growth and development. However, biological variables showed a greater association with growth, whereas environmental variables were associated with development

  11. Growth and development and their environmental and biological determinants

    Directory of Open Access Journals (Sweden)

    Kelly da Rocha Neves

    2016-06-01

    Full Text Available Abstract Objective To investigate child growth, cognitive/language development, and their environmental and biological determinants. Methods This was a cross-sectional, predictive correlation study with all 92 children aged 24-36 months who attended the municipal early childhood education network in a town in the Vale do Jequitinhonha region, in 2011. The socioeconomic profile was determined using the questionnaire of the Associação Brasileira de Empresas de Pesquisa. The socio-demographicand maternal and child health profiles were created through a self-prepared questionnaire. The height-for-age indicator was selected to represent growth. Cognitive/language development was assessed through the Bayley Scale of Infant and Toddler Development. The quality of educational environments was assessed by Infant/Toddler Environment Scale; the home environment was assessed by the Home Observation for Measurement of the Environment. The neighborhood quality was determined by a self-prepared questionnaire. A multivariate linear regression analysis was performed. Results Families were predominantly from socioeconomic class D, with low parental education. The prevalence of stunted growth was 14.1%; cognitive and language development were below average at 28.6% and 28.3%, respectively. Educational institutions were classified as inadequate, and 69.6% of homes were classified as presenting a risk for development. Factors such as access to parks and pharmacies and perceived security received the worst score regarding neighborhood environment. Biological variables showed a greater association with growth and environmental variables with development. Conclusion The results showed a high prevalence of stunting and below-average results for cognitive/language development among the participating children. Both environmental and biological factors were related to growth and development. However, biological variables showed a greater association with growth, whereas

  12. Deciphering complement mechanisms: The contributions of structural biology.

    NARCIS (Netherlands)

    Arlaud, G.J.; Barlow, P.N.; Gaboriaud, C.; Gros, P.; Narayana, S.V.L.

    2007-01-01

    Since the resolution of the first three-dimensional structure of a complement component in 1980, considerable efforts have been put into the investigation of this system through structural biology techniques, resulting in about a hundred structures deposited in the Protein Data Bank by the beginning

  13. Neutron scattering for the analysis of biological structures. Brookhaven symposia in biology. Number 27

    Energy Technology Data Exchange (ETDEWEB)

    Schoenborn, B P [ed.

    1976-01-01

    Sessions were included on neutron scattering and biological structure analysis, protein crystallography, neutron scattering from oriented systems, solution scattering, preparation of deuterated specimens, inelastic scattering, data analysis, experimental techniques, and instrumentation. Separate entries were made for the individual papers.

  14. An Error Analysis of Structured Light Scanning of Biological Tissue

    DEFF Research Database (Denmark)

    Jensen, Sebastian Hoppe Nesgaard; Wilm, Jakob; Aanæs, Henrik

    2017-01-01

    This paper presents an error analysis and correction model for four structured light methods applied to three common types of biological tissue; skin, fat and muscle. Despite its many advantages, structured light is based on the assumption of direct reflection at the object surface only......, statistical linear model based on the scan geometry. As such, scans can be corrected without introducing any specially designed pattern strategy or hardware. We can effectively reduce the error in a structured light scanner applied to biological tissue by as much as factor of two or three........ This assumption is violated by most biological material e.g. human skin, which exhibits subsurface scattering. In this study, we find that in general, structured light scans of biological tissue deviate significantly from the ground truth. We show that a large portion of this error can be predicted with a simple...

  15. Orientation determination of interfacial beta-sheet structures in situ.

    Science.gov (United States)

    Nguyen, Khoi Tan; King, John Thomas; Chen, Zhan

    2010-07-01

    Structural information such as orientations of interfacial proteins and peptides is important for understanding properties and functions of such biological molecules, which play crucial roles in biological applications and processes such as antimicrobial selectivity, membrane protein activity, biocompatibility, and biosensing performance. The alpha-helical and beta-sheet structures are the most widely encountered secondary structures in peptides and proteins. In this paper, for the first time, a method to quantify the orientation of the interfacial beta-sheet structure using a combined attenuated total reflectance Fourier transformation infrared spectroscopic (ATR-FTIR) and sum frequency generation (SFG) vibrational spectroscopic study was developed. As an illustration of the methodology, the orientation of tachyplesin I, a 17 amino acid peptide with an antiparallel beta-sheet, adsorbed to polymer surfaces as well as associated with a lipid bilayer was determined using the regular and chiral SFG spectra, together with polarized ATR-FTIR amide I signals. Both the tilt angle (theta) and the twist angle (psi) of the beta-sheet at interfaces are determined. The developed method in this paper can be used to obtain in situ structural information of beta-sheet components in complex molecules. The combination of this method and the existing methodology that is currently used to investigate alpha-helical structures will greatly broaden the application of optical spectroscopy in physical chemistry, biochemistry, biophysics, and structural biology.

  16. Spatial Structures and Regulation in Biological Systems

    DEFF Research Database (Denmark)

    Yde, Pernille

    , and the other is the spatial regulation of biological systems, here related to different aspects of the inflammatory response. All systems are studied using computational modelling and mathematical analysis. The first part of the thesis explores different protein aggregation scenarios. In Chapter 1, we consider...... a previously studied and very general aggregation model describing frangible linear filaments. This model is especially relevant for the growth of amyloid fibres, that have been related to a number of serious human diseases, and which are known to grow in an accelerated self-enhanced manner.We derive...... model of the tissue and show how coupled cells are able to function as an excitable medium and propagate waves of high cytokine concentration through the tissue. If the internal regulation in the cells is over-productive, the model predicts a continuous amplification of cytokines, which spans the entire...

  17. Monte Carlo determination of heteroepitaxial misfit structures

    DEFF Research Database (Denmark)

    Baker, J.; Lindgård, Per-Anker

    1996-01-01

    We use Monte Carlo simulations to determine the structure of KBr overlayers on a NaCl(001) substrate, a system with large (17%) heteroepitaxial misfit. The equilibrium relaxation structure is determined for films of 2-6 ML, for which extensive helium-atom scattering data exist for comparison...

  18. The normative structure of mathematization in systematic biology.

    Science.gov (United States)

    Sterner, Beckett; Lidgard, Scott

    2014-06-01

    We argue that the mathematization of science should be understood as a normative activity of advocating for a particular methodology with its own criteria for evaluating good research. As a case study, we examine the mathematization of taxonomic classification in systematic biology. We show how mathematization is a normative activity by contrasting its distinctive features in numerical taxonomy in the 1960s with an earlier reform advocated by Ernst Mayr starting in the 1940s. Both Mayr and the numerical taxonomists sought to formalize the work of classification, but Mayr introduced a qualitative formalism based on human judgment for determining the taxonomic rank of populations, while the numerical taxonomists introduced a quantitative formalism based on automated procedures for computing classifications. The key contrast between Mayr and the numerical taxonomists is how they conceptualized the temporal structure of the workflow of classification, specifically where they allowed meta-level discourse about difficulties in producing the classification. Copyright © 2014. Published by Elsevier Ltd.

  19. Cation-π interactions in structural biology

    OpenAIRE

    Gallivan, Justin P.; Dougherty, Dennis A.

    1999-01-01

    Cation-pi interactions in protein structures are identified and evaluated by using an energy-based criterion for selecting significant sidechain pairs. Cation-pi interactions are found to be common among structures in the Protein Data Bank, and it is clearly demonstrated that, when a cationic sidechain (Lys or Arg) is near an aromatic sidechain (Phe, Tyr, or Trp), the geometry is biased toward one that would experience a favorable cation-pi interaction. The sidechain of Arg is more likely tha...

  20. The Diamond Light Source and the challenges ahead for structural biology: some informal remarks.

    Science.gov (United States)

    Ramakrishnan, V

    2015-03-06

    The remarkable advances in structural biology in the past three decades have led to the determination of increasingly complex structures that lie at the heart of many important biological processes. Many of these advances have been made possible by the use of X-ray crystallography using synchrotron radiation. In this short article, some of the challenges and prospects that lie ahead will be summarized. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  1. Macromolecular structure determination in the post-genome era

    International Nuclear Information System (INIS)

    Kuhn, P.; Soltis, S.M.

    2001-01-01

    Recent advances in genetics, molecular biology and crystallographic instrumentation and methodology have led to a revolution in the field of Structural Molecular Biology (SMB). These combined advances have paved the way to a more complete and detailed understanding of the biological macromolecules that make up an organism, both in terms of their individual functions and also the interactions between them. In this paper we describe a large-scale, genomic approach to the three-dimensional structure determination of macromolecules and their complexes, using high-throughput methodology to streamline all aspects of the process. This task requires the development of automated high-intensity synchrotron beam lines for X-ray diffraction data collection from single crystal samples. Furthermore, these beam lines must be operated within a sophisticated software and hardware environment, which is capable of delivering a completely automated structure determination pipeline. The SMB resource at SSRL is developing a system for the structure determination steps of this process, starting with the initial characterization of the frozen sample, followed by data collection, data reduction, phase determination, and model building. This paper focuses on the data collection elements of this high-throughput system

  2. Augmenting Plant Immune Responses and Biological Control by Microbial Determinants

    Directory of Open Access Journals (Sweden)

    Sang Moo Lee

    2015-09-01

    Full Text Available Plant have developed sophisticated defence mechanisms against microbial pathogens. The recent accumulated information allow us to understand the nature of plant immune responses followed by recognition of microbial factors/determinants through cutting-edge genomics and multi-omics techniques. However, the practical approaches to sustain plant health using enhancement of plant immunity is yet to be fully appreciated. Here, we overviewed the general concept and representative examples on the plant immunity. The fungal, bacterial, and viral determinants that was previously reported as the triggers of plant immune responses are introduced and described as the potential protocol of biological control. Specifically, the role of chitin, glucan, lipopolysaccharides/extracellular polysaccharides, microbe/pathogen-associated molecular pattern, antibiotics, mimic-phytohormones, N-acyl homoserine lactone, harpin, vitamins, and volatile organic compounds are considered. We hope that this review stimulates scientific community and farmers to broaden their knowledge on the microbial determinant-based biological control and to apply the technology on the integrated pest management program.

  3. Determination of platinum in biological samples by NAA

    International Nuclear Information System (INIS)

    Okada, Yukiko; Hirai, Shoji; Sakurai, Hiromu; Haraguchi, Hiroki.

    1990-01-01

    Recently, a Pt compound, Cisplatin (cis-dichlorodiamine platinum) has been used therapeutically as an effective anti-malignant-cancer drug. However, since this drug has a harmful aftereffect on kidney, an urgent study of how to reduce its toxicity without influencing the therapeutic effect is needed. We have to understand the behavior of Pt in biological organs in order to elucidate the mechanism of its toxicity reduction. In this study, the analytical conditions for the determination of Pt in biological samples by neutron activation analysis, such as cooling time, counting time and sample weight, are optimized. Freeze-dried samples of the liver, kidney and whole blood of a rat treated with Cisplatin were prepared to evaluate the precision of the analysis and the lower limit of determination. 199 Au (t 1/2 = 3.15 d) produced from 199 Pt (n, γ, β - ) was selected as the analytical radionuclide. A concentration of ca. 1 ppm Pt was determinable under the optimal conditions: a cooling time of 5 d and a counting time of 1 h. Pt in the respective organs of the control rat was not detected under the same analytical conditions. The concentrations of Pt in the liver, kidney, spleen, pancreas and lung of a rat treated with both Cisplatin and sodium selenite were higher than those of a rat treated only with Cisplatin. (author)

  4. Routine Determination of Arsenic in Biological Materials. RCN Report

    International Nuclear Information System (INIS)

    Kroon, J.J.; Das, H.A.

    1970-08-01

    This text describes a routine procedure for the determination of arsenic in biological materials by neutron activation analysis. Unlike most methods published in literature the present analysis is not based on chemical separation by destination. After a first purification by anion-exchange the 76 As-activity (T1/2 = 26,4 h) is isolated by precipitation as the metal. The method was tested by analysis of the standard kale powder. This material was prepared and issued by Bowen in 1966, to provide a reliable standard for the intercomparison of various methods. (author)

  5. Flame Spectrophotometric Determination of Strontium in Water and Biological Material

    Energy Technology Data Exchange (ETDEWEB)

    Joensson, G

    1964-10-15

    A flame spectrophotometric method has been developed for the determination of strontium in biological material and water samples. Strontium is determined in the presence of calcium at a wavelength of 4607 A. The intensity of the strontium emission from the sample is increased if n-butanol is added to a solution of the sample in water. With a 6 vol% solution of n-butanol in water, an optimum intensity of 3.5 times that obtained with pure water solution is obtained. Anions and alkali metals which might interfere with the flame spectrophotometric determination are separated from the sample by a simple ion exchange operation. The method allows determination of strontium in solutions down to 0.1{mu}g/ml. In this case the standard deviation is 3.1 % and with a strontium concentration of 1 {mu}g/ml the deviation is 0.9 %. This method has been used for the determination of strontium in samples of varying composition such as bone, meat and skin from fishes, samples of human bones, shell-fish, milk, and water, in which case Sr quantities of 5{mu}g were determined with an analytical error of less than 5 % and Sr{sub q}uantities greater than 10 {mu}g with an error of less than 3 %.

  6. Flame Spectrophotometric Determination of Strontium in Water and Biological Material

    International Nuclear Information System (INIS)

    Joensson, G.

    1964-10-01

    A flame spectrophotometric method has been developed for the determination of strontium in biological material and water samples. Strontium is determined in the presence of calcium at a wavelength of 4607 A. The intensity of the strontium emission from the sample is increased if n-butanol is added to a solution of the sample in water. With a 6 vol% solution of n-butanol in water, an optimum intensity of 3.5 times that obtained with pure water solution is obtained. Anions and alkali metals which might interfere with the flame spectrophotometric determination are separated from the sample by a simple ion exchange operation. The method allows determination of strontium in solutions down to 0.1μg/ml. In this case the standard deviation is 3.1 % and with a strontium concentration of 1 μg/ml the deviation is 0.9 %. This method has been used for the determination of strontium in samples of varying composition such as bone, meat and skin from fishes, samples of human bones, shell-fish, milk, and water, in which case Sr quantities of 5μg were determined with an analytical error of less than 5 % and Sr q uantities greater than 10 μg with an error of less than 3 %

  7. Analytical methodologies for the determination of benzodiazepines in biological samples.

    Science.gov (United States)

    Persona, Karolina; Madej, Katarzyna; Knihnicki, Paweł; Piekoszewski, Wojciech

    2015-09-10

    Benzodiazepine drugs belong to important and most widely used medicaments. They demonstrate such therapeutic properties as anxiolytic, sedative, somnifacient, anticonvulsant, diastolic and muscle relaxant effects. However, despite the fact that benzodiazepines possess high therapeutic index and are considered to be relatively safe, their use can be dangerous when: (1) co-administered with alcohol, (2) co-administered with other medicaments like sedatives, antidepressants, neuroleptics or morphine like substances, (3) driving under their influence, (4) using benzodiazepines non-therapeutically as drugs of abuse or in drug-facilitated crimes. For these reasons benzodiazepines are still studied and determined in a variety of biological materials. In this article, sample preparation techniques which have been applied in analysis of benzodiazepine drugs in biological samples have been reviewed and presented. The next part of the article is focused on a review of analytical methods which have been employed for pharmacological, toxicological or forensic study of this group of drugs in the biological matrices. The review was preceded by a description of the physicochemical properties of the selected benzodiazepines and two, very often coexisting in the same analyzed samples, sedative-hypnotic drugs. Copyright © 2015. Published by Elsevier B.V.

  8. Neutron activation analysis on determination of arsenic in biological matrixes

    Energy Technology Data Exchange (ETDEWEB)

    Menezes, Maria Angela de B.C.; Silva, Maria Aparecida, E-mail: menezes@cdtn.br, E-mail: cida@cdtn.br [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil)

    2013-07-01

    Aiming at giving support to the Worker's Health Awareness Program of the Municipal Department of Health of Belo Horizonte, an assessment related arsenic was carried out in two galvanising factories by means of hair and toenail samples analysis as biomonitors. The arsenic was determined in all matrixes from the factories where gold electrodeposition process was applied. This is because arsenic salts are usually added to gold bath to improve the metal covering. The high concentration results surprised the health surveillance professionals, and alerted for the need of assessing the influence of a long-term exposure. Studies concerning galvanising process have usually been developed broaching many aspects, but so far few works has pointed out the detection and measurement of other elements like arsenic. The k{sub 0}-Instrumental Neutron Activation method was applied confirming to be a suitable technique on determination of arsenic in biological matrixes. (author)

  9. Neutron activation analysis on determination of arsenic in biological matrixes

    International Nuclear Information System (INIS)

    Menezes, Maria Angela de B.C.; Silva, Maria Aparecida

    2013-01-01

    Aiming at giving support to the Worker's Health Awareness Program of the Municipal Department of Health of Belo Horizonte, an assessment related arsenic was carried out in two galvanising factories by means of hair and toenail samples analysis as biomonitors. The arsenic was determined in all matrixes from the factories where gold electrodeposition process was applied. This is because arsenic salts are usually added to gold bath to improve the metal covering. The high concentration results surprised the health surveillance professionals, and alerted for the need of assessing the influence of a long-term exposure. Studies concerning galvanising process have usually been developed broaching many aspects, but so far few works has pointed out the detection and measurement of other elements like arsenic. The k 0 -Instrumental Neutron Activation method was applied confirming to be a suitable technique on determination of arsenic in biological matrixes. (author)

  10. XFELs open a new era in structural chemical biology

    OpenAIRE

    Fromme, Petra

    2015-01-01

    X-ray crystallography, the workhorse of structural biology, has been revolutionized by the advent of serial femtosecond crystallography using X-ray free electron lasers. Here, the fast pace and history of discoveries are discussed together with current challenges and the method’s great potential to make new structural discoveries, such as the ability to generate molecular movies of biomolecules at work.

  11. Isolation, structural determination, and evaluation of the biological activity of 20(S)-25-methoxyl-dammarane-3beta, 12beta, 20-triol [20(S)-25-OCH3-PPD], a novel natural product from Panax notoginseng.

    Science.gov (United States)

    Zhao, Y; Wang, W; Han, L; Rayburn, E R; Hill, D L; Wang, H; Zhang, R

    2007-01-01

    Ginseng has been used extensively for medicinal purposes, with suggested utility for indications as diverse as diabetes, cardiovascular disease and cancer. Herein we report the discovery and characterization of 20(S)-25-OCH3-PPD, a ginsenoside that inhibits growth and survival of cancer cells. The novel dammarane triterpene sapogenin (C31H56O4; molecular weight 492) was isolated from the total hydrolyzed saponins extracted from the leaves of Panax notoginseng using conventional and reverse-phase silica gel chromatography. Based on physicochemical characteristics and NMR data, the compound was identified as 20(S)-25-OCH3-PPD. The biological activities of 20(S)-25-OCH3-PPD and its known analogs, 20(S)-PPD and Rg3, were evaluated in 12 human cancer cell lines. In all cell lines, the order of cytotoxicity of the test compounds was 20(S)-25-OCH3-PPD > 20(S)-PPD > Rg3. 20(S)-25-OCH3-PPD also induced apoptosis and cell cycle arrest in the G1 phase, and inhibited proliferation in breast cancer cell lines, demonstrating its potent biological effects. In regard to cytotoxicity, the IC50 values of 20(S)-25-OCH3-PPD for most cell lines were in the lower microM range, a 5-15-fold greater cytotoxicity relative to 20(S)-PPD and a 10-100-fold increase over Rg3. These findings suggest a structure-activity relationship among dammarane-type sapogenins. The data presented here may provide a basis for the future development of 20(S)-25-OCH3-PPD as a novel anti-cancer agent.

  12. Effective Elastic Modulus of Structured Adhesives: From Biology to Biomimetics

    Directory of Open Access Journals (Sweden)

    Xin Wang

    2017-06-01

    Full Text Available Micro- and nano-hierarchical structures (lamellae, setae, branches, and spatulae on the toe pads of many animals play key roles for generating strong but reversible adhesion for locomotion. The hierarchical structure possesses significantly reduced, effective elastic modulus (Eeff, as compared to the inherent elastic modulus (Einh of the corresponding biological material (and therefore contributes to a better compliance with the counterpart surface. Learning from nature, three types of hierarchical structures (namely self-similar pillar structure, lamella–pillar hybrid structure, and porous structure have been developed and investigated.

  13. Structural determinants of students' employability: Influence of ...

    African Journals Online (AJOL)

    Structural determinants of students' employability: Influence of career ... greatest influence on students' employability, followed by decision-making skills, and ... efforts in developing app-ropriate strategies so as to engage undergraduates with ...

  14. Hierarchical structure of biological systems: a bioengineering approach.

    Science.gov (United States)

    Alcocer-Cuarón, Carlos; Rivera, Ana L; Castaño, Victor M

    2014-01-01

    A general theory of biological systems, based on few fundamental propositions, allows a generalization of both Wierner and Berthalanffy approaches to theoretical biology. Here, a biological system is defined as a set of self-organized, differentiated elements that interact pair-wise through various networks and media, isolated from other sets by boundaries. Their relation to other systems can be described as a closed loop in a steady-state, which leads to a hierarchical structure and functioning of the biological system. Our thermodynamical approach of hierarchical character can be applied to biological systems of varying sizes through some general principles, based on the exchange of energy information and/or mass from and within the systems.

  15. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

  16. Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course

    Science.gov (United States)

    Montplaisir, Lisa

    2014-01-01

    Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students’ perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest approach. Significant differences in students’ perception of their knowledge and their determined knowledge exist at the beginning (pretest) and end (posttest) of the course. Alignment between student perception and determined knowledge was significantly more accurate on the posttest compared with the pretest. Students whose determined knowledge was in the upper quartile had significantly better alignment between their perception and determined knowledge on the pre- and posttest than students in the lower quartile. No difference exists between how students perceived their knowledge between upper- and lower-quartile students. There was a significant difference in alignment of perception and determined knowledge between males and females on the posttest, with females being more accurate in their perception of knowledge. This study provides evidence of discrepancies that exist between what students perceive they know and what they actually know. PMID:26086662

  17. Biogastronomy: Factors that determine the biological response to meal ingestion.

    Science.gov (United States)

    Pribic, T; Azpiroz, F

    2018-02-02

    The biological response to a meal includes physiological changes, primarily related to the digestive process, and a sensory experience, involving sensations related to the homeostatic control of food consumption, eg, satiety and fullness, with a hedonic dimension, ie associated with changes in digestive well-being and mood. The responses to a meal include a series of events before, during and after ingestion. While much attention has been paid to the events before and during ingestion, relatively little is known about the postprandial sensations, which are key to the gastronomical experience. The aim of this narrative review is to provide a comprehensive overview and to define the framework to investigate the factors that determine the postprandial experience. Based on a series of proof-of-concept studies and related information, we propose that the biological responses to a meal depend on the characteristics of the meal, primarily its palatability and composition, and the responsiveness of the guest, which may be influenced by multiple previous and concurrent conditioning factors. This information provides the scientific backbone to the development of personalized gastronomy. © 2018 John Wiley & Sons Ltd.

  18. Problems in the determination of chromium in biological materials

    International Nuclear Information System (INIS)

    Behne, D.; Braetter, P.; Gessner, H.; Hube, G.; Mertz, W.; Roesick, U.

    1976-01-01

    The effects of sample preparation on the analysis of chromium in biological matter have been investigated using brewer's yeast as a test material. The apparent chromium content of the yeast as determined by flameless atomic absorption spectrometry was significantly higher after destruction of the organic matter with HNO 3 in a closed pressure vessel than after wet-ashing in open vessels and after direct introduction of the sample into the graphite furnace. The results obtained by neutron activation analysis without any sample preparation, which corresponded to the atomic absorption values after digestion in the pressure vessel, showed that considerable errors arise in the other methods of sample treatment. Chromium analysis of dried and ashed yeast suggest that losses of volatile chromium compounds may occur during heating. (orig.) [de

  19. In cellulo structure determination of a novel cypovirus polyhedrin

    International Nuclear Information System (INIS)

    Axford, Danny; Ji, Xiaoyun; Stuart, David I.; Sutton, Geoff

    2014-01-01

    The crystal structure of a previously unsolved type of cypovirus polyhedrin has been determined from data collected directly from frozen live insect cells. This work demonstrates that with the use of a microfocus synchrotron beam the structure of a novel viral polyhedrin could be successfully determined from microcrystals within cells, removing the preparatory step of sample isolation and maintaining a favourable biological environment. The data obtained are of high quality, comparable to that obtained from isolated crystals, and enabled a facile structure determination. A small but significant difference is observed between the unit-cell parameters and the mosaic spread of in cellulo and isolated crystals, suggesting that even these robust crystals are adversely affected by removal from the cell

  20. Structure determination by X-ray crystallography

    CERN Document Server

    Ladd, M F C

    1995-01-01

    X-ray crystallography provides us with the most accurate picture we can get of atomic and molecular structures in crystals. It provides a hard bedrock of structural results in chemistry and in mineralogy. In biology, where the structures are not fully crystalline, it can still provide valuable results and, indeed, the impact here has been revolutionary. It is still an immense field for young workers, and no doubt will provide yet more striking develop­ ments of a major character. It does, however, require a wide range of intellectual application, and a considerable ability in many fields. This book will provide much help. It is a very straightforward and thorough guide to every aspect of the subject. The authors are experienced both as research workers themselves and as teachers of standing, and this is shown in their clarity of exposition. There are plenty of iliustrations and worked examples to aid the student to obtain a real grasp of the subject.

  1. Capital Structure Determinants and Governance Structure Variety in Franchising

    NARCIS (Netherlands)

    T. Jiang (Tao)

    2009-01-01

    textabstractThis thesis investigates two questions: the determinants of capital structure in franchising and its subsequent impact on the franchise financing decisions; and the efficient governance structure choice in franchising. We posit that firms franchise in order to benefit from the reduced

  2. Aspartate and glutamate mimetic structures in biologically active compounds.

    Science.gov (United States)

    Stefanic, Peter; Dolenc, Marija Sollner

    2004-04-01

    Glutamate and aspartate are frequently recognized as key structural elements for the biological activity of natural peptides and synthetic compounds. The acidic side-chain functionality of both the amino acids provides the basis for the ionic interaction and subsequent molecular recognition by specific receptor sites that results in the regulation of physiological or pathophysiological processes in the organism. In the development of new biologically active compounds that possess the ability to modulate these processes, compounds offering the same type of interactions are being designed. Thus, using a peptidomimetic design approach, glutamate and aspartate mimetics are incorporated into the structure of final biologically active compounds. This review covers different bioisosteric replacements of carboxylic acid alone, as well as mimetics of the whole amino acid structure. Amino acid analogs presented include those with different distances between anionic moieties, and analogs with additional functional groups that result in conformational restriction or alternative interaction sites. The article also provides an overview of different cyclic structures, including various cycloalkane, bicyclic and heterocyclic analogs, that lead to conformational restriction. Higher di- and tripeptide mimetics in which carboxylic acid functionality is incorporated into larger molecules are also reviewed. In addition to the mimetic structures presented, emphasis in this article is placed on their steric and electronic properties. These mimetics constitute a useful pool of fragments in the design of new biologically active compounds, particularly in the field of RGD mimetics and excitatory amino acid agonists and antagonists.

  3. From crystallography to structural biology, a century of discoveries

    Directory of Open Access Journals (Sweden)

    Montoya, Guillermo

    2015-04-01

    Full Text Available From crystallography, the technique mostly used to study the structure of matter, the field mutated into structural biology, has mutated in life sciences into structural biology, which has been developed as an essential and rather successful area of research to fully understand the workings of cellular pathways. The application of physical approaches to biological systems has been crucial to comprehend the structure and function of the biological components of living organisms. In this assay the author walks the reader through the last century, which has witnessed how this life sciences research area was born and moved towards larger assemblies in the core of crucial biological problems. The influence of research in physics, biochemistry and molecular biology has been key in the successes and large body of seminal results obtained by structural biologists. The author proposes that the future of this area implies the integration of its results at the cellular level apart of using more quantitative approaches to describe biological processes.La cristalografía, la técnica más ampliamente usada para estudiar la estructura de la materia, ha evolucionado en las ciencias de la vida hacia la biología estructural, una exitosa área de investigación encaminada a comprender el funcionamiento de los procesos celulares. La aplicación de aproximaciones físicas a sistemas biológicos es clave para entender la estructura y funcionamiento de los componentes de los organismos. En este artículo el autor ofrece al lector un paseo por la evolución de esta área de conocimiento durante el siglo XX, desde su nacimiento hasta el análisis de grandes complejos macromoleculares, protagonistas importantes en diversos procesos biológicos. La influencia de investigaciones en física, bioquímica y biología molecular ha sido clave para los numerosos éxitos alcanzados por biólogos estructurales. El autor sostiene que el futuro de esta disciplina pasa por la

  4. A biological radioimmunological microassay to determine hypophysiotropic factors

    International Nuclear Information System (INIS)

    Sand, T.

    1980-01-01

    The thesis presented there describes a combined biological-radioimmunological assay for hypophysiotropic substances. The secretion reaction of adenohypophysial rat cells cultured by a long-term monolayer technique is used as a measure of hypophysiotropic activity. For hypophysial hormones released into the culture medium are then determined directly with the aid of specific radio immunoassay. This method can also be used for substances not yet characterized chemically or for tissue extracts, as shown here using hypothalamus stalk median eminance extract as example. The method is technically quite simple and economical. At the same time the technique is exact and reliable and offers, for TRH and LHRH determination, a degree of sensitivity in the pg range similar to that obtained by radioimmunological methods. The sensitivity towards CRH activity exceeds that obtained by other methods to date. From a morphological viewpoint and from comparisons of spontaneous secretion behaviour (or stimulation reactions following TRH, LHRH, dopamine and vasopressin application) with in-vivo findings it was shown that the long-term cell cultures were intact and that, overall, the culture model used closely approximates in its functional behaviour the physiological situation. (orig./MG) [de

  5. Taking MAD to the extreme: ultrafast protein structure determination

    International Nuclear Information System (INIS)

    Walsh, M.A.; Dementieva, I.; Evans, G.; Sanishvili, R.; Joachimiak, A.

    1999-01-01

    Multiwavelength anomalous diffraction data were measured in 23 min from a 16 kDa selenomethionyl-substituted protein, producing experimental phases to 2.25 (angstrom) resolution. The data were collected on a mosaic 3 x 3 charge-coupled device using undulator radiation from the Structural Biology Center 19ID beamline at the Argonne National Laboratory's Advanced Photon Source. The phases were independently obtained semiautomatically by two crystallographic program suites, CCP4 and CNS. The quality and speed of this data acquisition exemplify the opportunities at third-generation synchrotron sources for high-throughput protein crystal structure determination

  6. Study of nanoscale structural biology using advanced particle beam microscopy

    Science.gov (United States)

    Boseman, Adam J.

    This work investigates developmental and structural biology at the nanoscale using current advancements in particle beam microscopy. Typically the examination of micro- and nanoscale features is performed using scanning electron microscopy (SEM), but in order to decrease surface charging, and increase resolution, an obscuring conductive layer is applied to the sample surface. As magnification increases, this layer begins to limit the ability to identify nanoscale surface structures. A new technology, Helium Ion Microscopy (HIM), is used to examine uncoated surface structures on the cuticle of wild type and mutant fruit flies. Corneal nanostructures observed with HIM are further investigated by FIB/SEM to provide detailed three dimensional information about internal events occurring during early structural development. These techniques are also used to reconstruct a mosquito germarium in order to characterize unknown events in early oogenesis. Findings from these studies, and many more like them, will soon unravel many of the mysteries surrounding the world of developmental biology.

  7. Topography and biological noise determine acoustic detectability on coral reefs

    KAUST Repository

    Cagua, Edgar F.

    2013-08-19

    Acoustic telemetry is an increasingly common tool for studying the movement patterns, behavior and site fidelity of marine organisms, but to accurately interpret acoustic data, the variability, periodicity and range of detectability between acoustic tags and receivers must be understood. The relative and interactive effects of topography with biological and environmental noise have not been quantified on coral reefs. We conduct two long-term range tests (1- and 4-month duration) on two different reef types in the central Red Sea to determine the relative effect of distance, depth, topography, time of day, wind, lunar phase, sea surface temperature and thermocline on detection probability. Detectability, as expected, declines with increasing distance between tags and receivers, and we find average detection ranges of 530 and 120 m, using V16 and V13 tags, respectively, but the topography of the reef can significantly modify this relationship, reducing the range by ~70 %, even when tags and receivers are in line-of-sight. Analyses that assume a relationship between distance and detections must therefore be used with care. Nighttime detection range was consistently reduced in both locations, and detections varied by lunar phase in the 4-month test, suggesting a strong influence of biological noise (reducing detection probability up to 30 %), notably more influential than other environmental noises, including wind-driven noise, which is normally considered important in open-water environments. Analysis of detections should be corrected in consideration of the diel patterns we find, and range tests or sentinel tags should be used for more than 1 month to quantify potential changes due to lunar phase. Some studies assume that the most usual factor limiting detection range is weather-related noise; this cannot be extrapolated to coral reefs. © 2013 Springer-Verlag Berlin Heidelberg.

  8. Advances on surface structural determination by LEED

    International Nuclear Information System (INIS)

    Soares, Edmar A; De Carvalho, Vagner E; De Castilho, Caio M C

    2011-01-01

    In the last 40 years, low energy electron diffraction (LEED) has proved to be the most reliable quantitative technique for surface structural determination. In this review, recent developments related to the theory that gives support to LEED structural determination are discussed under a critical analysis of the main theoretical approximation-the muffin-tin calculation. The search methodologies aimed at identifying the best matches between theoretical and experimental intensity versus voltage curves are also considered, with the most recent procedures being reviewed in detail. (topical review)

  9. Biological, Histological and Ultra-Structural Studies of Female Mullet ...

    African Journals Online (AJOL)

    Biological, Histological and Ultra-Structural Studies of Female Mullet, Mugil cephalus , Ovaries Collected from Different Habitats during Annual Reproductive Cycle. ... 35 and 52 cm, respectively; whereas, the total number of ripe ova in brackish water fish ranged from 0.57±0.14 to 3.81±0.59 x106 for the same length groups.

  10. Recent progress in structural biology: lessons from our research history.

    Science.gov (United States)

    Nitta, Ryo; Imasaki, Tsuyoshi; Nitta, Eriko

    2018-05-16

    The recent 'resolution revolution' in structural analyses of cryo-electron microscopy (cryo-EM) has drastically changed the research strategy for structural biology. In addition to X-ray crystallography and nuclear magnetic resonance spectroscopy, cryo-EM has achieved the structural analysis of biological molecules at near-atomic resolution, resulting in the Nobel Prize in Chemistry 2017. The effect of this revolution has spread within the biology and medical science fields affecting everything from basic research to pharmaceutical development by visualizing atomic structure. As we have used cryo-EM as well as X-ray crystallography since 2000 to elucidate the molecular mechanisms of the fundamental phenomena in the cell, here we review our research history and summarize our findings. In the first half of the review, we describe the structural mechanisms of microtubule-based motility of molecular motor kinesin by using a joint cryo-EM and X-ray crystallography method. In the latter half, we summarize our structural studies on transcriptional regulation by X-ray crystallography of in vitro reconstitution of a multi-protein complex.

  11. X-ray lasers for structural and dynamic biology

    International Nuclear Information System (INIS)

    Spence, J C H; Weierstall, U; Chapman, H N

    2012-01-01

    Research opportunities and techniques are reviewed for the application of hard x-ray pulsed free-electron lasers (XFEL) to structural biology. These include the imaging of protein nanocrystals, single particles such as viruses, pump–probe experiments for time-resolved nanocrystallography, and snapshot wide-angle x-ray scattering (WAXS) from molecules in solution. The use of femtosecond exposure times, rather than freezing of samples, as a means of minimizing radiation damage is shown to open up new opportunities for the molecular imaging of biochemical reactions at room temperature in solution. This is possible using a ‘diffract-and-destroy’ mode in which the incident pulse terminates before radiation damage begins. Methods for delivering hundreds of hydrated bioparticles per second (in random orientations) to a pulsed x-ray beam are described. New data analysis approaches are outlined for the correlated fluctuations in fast WAXS, for protein nanocrystals just a few molecules on a side, and for the continuous x-ray scattering from a single virus. Methods for determining the orientation of a molecule from its diffraction pattern are reviewed. Methods for the preparation of protein nanocrystals are also reviewed. New opportunities for solving the phase problem for XFEL data are outlined. A summary of the latest results is given, which now extend to atomic resolution for nanocrystals. Possibilities for time-resolved chemistry using fast WAXS (solution scattering) from mixtures is reviewed, toward the general goal of making molecular movies of biochemical processes. (key issues reviews)

  12. A method to determine site-specific, anisotropic fracture toughness in biological materials

    International Nuclear Information System (INIS)

    Bechtle, Sabine; Özcoban, Hüseyin; Yilmaz, Ezgi D.; Fett, Theo; Rizzi, Gabriele; Lilleodden, Erica T.; Huber, Norbert; Schreyer, Andreas; Swain, Michael V.; Schneider, Gerold A.

    2012-01-01

    Many biological materials are hierarchically structured, with highly anisotropic structures and properties on several length scales. To characterize the mechanical properties of such materials, detailed testing methods are required that allow precise and site-specific measurements on several length scales. We propose a fracture toughness measurement technique based on notched focused ion beam prepared cantilevers of lower and medium micron size scales. Using this approach, site-specific fracture toughness values in dental enamel were determined. The usefulness and challenges of the method are discussed.

  13. Representing Personal Determinants in Causal Structures.

    Science.gov (United States)

    Bandura, Albert

    1984-01-01

    Responds to Staddon's critique of the author's earlier article and addresses issues raised by Staddon's (1984) alternative models of causality. The author argues that it is not the formalizability of causal processes that is the issue but whether cognitive determinants of behavior are reducible to past stimulus inputs in causal structures.…

  14. Neutron scattering applications in structural biology: now and the future

    Energy Technology Data Exchange (ETDEWEB)

    Trewhella, J [Los Alamos National Lab., NM (United States)

    1996-05-01

    Neutrons have an important role to play in structural biology. Neutron crystallography, small-angle neutron scattering and inelastic neutron scattering techniques all contribute unique information on biomolecular structures. In particular, solution scattering techniques give critical information on the conformations and dispositions of the components of complex assemblies under a wide variety of relevant conditions. The power of these methods is demonstrated here by studies of protein/DNA complexes, and Ca{sup 2+}-binding proteins complexed with their regulatory targets. In addition, we demonstrate the utility of a new structural approach using neutron resonance scattering. The impact of biological neutron scattering to date has been constrained principally by the available fluxes at neutron sources and the true potential of these approaches will only be realized with the development of new more powerful neutron sources. (author)

  15. Fluorine determinations in biological materials by instrumental neutron activation analysis

    International Nuclear Information System (INIS)

    Demiralp, R.; Guinn, V.P.; Becker, D.A.

    1992-01-01

    Exploratory studies were carried out at the University of California, Irvine on several freeze-dried human diet materials and on two freeze-dried vegetation materials - all prospective reference materials. The University of California, Irvine equipment includes a 250-kW TRIGA Mark 1 reactor, 2.5 x 10 12 n/cm 2 ·s thermal flux, 3-s sample transfer time, and a typical 18% Ge(Li)/4,096-channel gamma-ray spectrometer with a detector resolution of 3.3 keV at 1,332 keV. In these exploratory studies, it was found that it was not feasible to measure fluorine with adequate precision or accuracy at fluorine concentrations much less than ∼100 ppm. These initial studies, however, defined the magnitudes of the various difficulties. One good outcome of these studies was the demonstration that the otherwise excellent Teflon-mill brittle-fracture method for homogenizing freeze-dried biological samples was not suitable if fluorine was to be determined. Abrasion of the Teflon increased the fluorine content of a human diet sample about sevenfold (compared with similar treatment of the same material in an all-titanium mill)

  16. Building bridges between cellular and molecular structural biology.

    Science.gov (United States)

    Patwardhan, Ardan; Brandt, Robert; Butcher, Sarah J; Collinson, Lucy; Gault, David; Grünewald, Kay; Hecksel, Corey; Huiskonen, Juha T; Iudin, Andrii; Jones, Martin L; Korir, Paul K; Koster, Abraham J; Lagerstedt, Ingvar; Lawson, Catherine L; Mastronarde, David; McCormick, Matthew; Parkinson, Helen; Rosenthal, Peter B; Saalfeld, Stephan; Saibil, Helen R; Sarntivijai, Sirarat; Solanes Valero, Irene; Subramaniam, Sriram; Swedlow, Jason R; Tudose, Ilinca; Winn, Martyn; Kleywegt, Gerard J

    2017-07-06

    The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

  17. Capital Structure Determinants and Governance Structure Variety in Franchising

    OpenAIRE

    Jiang, Tao

    2009-01-01

    textabstractThis thesis investigates two questions: the determinants of capital structure in franchising and its subsequent impact on the franchise financing decisions; and the efficient governance structure choice in franchising. We posit that firms franchise in order to benefit from the reduced franchisees’ operational risks by limiting the debt level, such that the franchisor can bear more debt and gain tax-deduction benefits. Specific hypotheses are based on various theories like resource...

  18. Sharing Structure and Function in Biological Design with SBOL 2.0.

    Science.gov (United States)

    Roehner, Nicholas; Beal, Jacob; Clancy, Kevin; Bartley, Bryan; Misirli, Goksel; Grünberg, Raik; Oberortner, Ernst; Pocock, Matthew; Bissell, Michael; Madsen, Curtis; Nguyen, Tramy; Zhang, Michael; Zhang, Zhen; Zundel, Zach; Densmore, Douglas; Gennari, John H; Wipat, Anil; Sauro, Herbert M; Myers, Chris J

    2016-06-17

    The Synthetic Biology Open Language (SBOL) is a standard that enables collaborative engineering of biological systems across different institutions and tools. SBOL is developed through careful consideration of recent synthetic biology trends, real use cases, and consensus among leading researchers in the field and members of commercial biotechnology enterprises. We demonstrate and discuss how a set of SBOL-enabled software tools can form an integrated, cross-organizational workflow to recapitulate the design of one of the largest published genetic circuits to date, a 4-input AND sensor. This design encompasses the structural components of the system, such as its DNA, RNA, small molecules, and proteins, as well as the interactions between these components that determine the system's behavior/function. The demonstrated workflow and resulting circuit design illustrate the utility of SBOL 2.0 in automating the exchange of structural and functional specifications for genetic parts, devices, and the biological systems in which they operate.

  19. Biological condition gradient: Applying a framework for determining the biological integrity of coral reefs

    Science.gov (United States)

    The goals of the U.S. Clean Water Act (CWA) are to restore and maintain the chemical, physical and biological integrity of water resources. Although clean water is a goal, another is to safeguard biological communities by defining levels of biological integrity to protect aquatic...

  20. Melatonin charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone: Molecular structure, DFT studies, thermal analyses, evaluation of biological activity and utility for determination of melatonin in pure and dosage forms

    Science.gov (United States)

    Mohamed, Gehad G.; Hamed, Maher M.; Zaki, Nadia G.; Abdou, Mohamed M.; Mohamed, Marwa El-Badry; Abdallah, Abanoub Mosaad

    2017-07-01

    A simple, accurate and fast spectrophotometric method for the quantitative determination of melatonin (ML) drug in its pure and pharmaceutical forms was developed based on the formation of its charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as an electron acceptor. The different conditions for this method were optimized accurately. The Lambert-Beer's law was found to be valid over the concentration range of 4-100 μg mL- 1 ML. The solid form of the CT complex was structurally characterized by means of different spectral methods. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations were carried out. The different quantum chemical parameters of the CT complex were calculated. Thermal properties of the CT complex and its kinetic thermodynamic parameters were studied, as well as its antimicrobial and antifungal activities were investigated. Molecular docking studies were performed to predict the binding modes of the CT complex components towards E. coli bacterial RNA and the receptor of breast cancer mutant oxidoreductase.

  1. Evolutionary biology and the determinants of morality 2 | Odozor ...

    African Journals Online (AJOL)

    This second essay continues the reflection on this problem through an exploration of the extra-biological factors and how they effect human moral development—a facet which is only too obvious, but which the evolutionary approach sidelines in its desperate effort to put up purely biological accounts of morality and ethics.

  2. Growth and development and their environmental and biological determinants

    Directory of Open Access Journals (Sweden)

    Kelly da Rocha Neves

    2016-05-01

    Conclusion: The results showed a high prevalence of stunting and below‐average results for cognitive/language development among the participating children. Both environmental and biological factors were related to growth and development. However, biological variables showed a greater association with growth, whereas environmental variables were associated with development.

  3. Determination of azide in biological fluids by use of electron paramagnetic resonance

    International Nuclear Information System (INIS)

    Minakata, Kayoko; Suzuki, Osamu

    2005-01-01

    A simple and sensitive method has been developed for the determination of azide ion (N 3 - ) in biological fluids and beverages. The procedure was based on the formation of a ternary complex Cu(N 3 ) 2 (4-methylpyridine) x in benzene, followed by its detection by electron paramagnetic resonance. The complex in benzene showed a characteristic four-peak hyperfine structure with a g-value of 2.115 at room temperature. Cu 2+ reacted with N 3 - most strongly among common metals found in biological fluids. Several anions and metal ions in biological fluids did not interfere with the determination of N 3 - in the presence of large amounts of Cu 2+ and oxidants. In the present method, N 3 - at the concentration from 5 μM to 2 mM in 100 μl solution could be determined with the detection limit of 20 ng. The recoveries were more than 95% for N 3 - added to 100 μl of blood, urine, milk and beverages at 200 μM. Our method is recommendable because it takes less than 10 min to determine N 3 - and the produced complex is quite stable

  4. Databases, Repositories, and Other Data Resources in Structural Biology.

    Science.gov (United States)

    Zheng, Heping; Porebski, Przemyslaw J; Grabowski, Marek; Cooper, David R; Minor, Wladek

    2017-01-01

    Structural biology, like many other areas of modern science, produces an enormous amount of primary, derived, and "meta" data with a high demand on data storage and manipulations. Primary data come from various steps of sample preparation, diffraction experiments, and functional studies. These data are not only used to obtain tangible results, like macromolecular structural models, but also to enrich and guide our analysis and interpretation of various biomedical problems. Herein we define several categories of data resources, (a) Archives, (b) Repositories, (c) Databases, and (d) Advanced Information Systems, that can accommodate primary, derived, or reference data. Data resources may be used either as web portals or internally by structural biology software. To be useful, each resource must be maintained, curated, as well as integrated with other resources. Ideally, the system of interconnected resources should evolve toward comprehensive "hubs", or Advanced Information Systems. Such systems, encompassing the PDB and UniProt, are indispensable not only for structural biology, but for many related fields of science. The categories of data resources described herein are applicable well beyond our usual scientific endeavors.

  5. Simultaneous determination of protein structure and dynamics

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, M. A.

    2005-01-01

    at the atomic level about the structural and dynamical features of proteins-with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout......We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy-for obtaining experimental information...... the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant...

  6. Transmission electron microscopy in molecular structural biology: A historical survey.

    Science.gov (United States)

    Harris, J Robin

    2015-09-01

    In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Synthesis, crystal structure and biological activity of novel diester cyclophanes

    International Nuclear Information System (INIS)

    Zhang, Pengfei; Yang, Bingqin; Fang, Xianwen; Cheng, Zhao; Yang, Meipan

    2012-01-01

    A series of novel diester cyclophanes was synthesized by esterification of 1,2-benzenedicarbonyl chloride with eight different diols under high dilution conditions. The structures of the compounds were verified by elemental analysis, 1 H nuclear magnetic resonance (NMR), IR spectroscopy and high resolution mass spectrometry (HRMS). The crystal structures of two compounds were characterized by single crystal X-ray diffractometry (XRD). All the new cyclophanes were evaluated for biological activities and the results showed that some of these compounds have low antibacterial or antifungal activities (author)

  8. Synthesis, crystal structure and biological activity of novel diester cyclophanes

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Pengfei; Yang, Bingqin; Fang, Xianwen; Cheng, Zhao; Yang, Meipan, E-mail: yangbq@nwu.edu.cn [Department of Chemistry, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, Northwest University, Shaanxi (China)

    2012-10-15

    A series of novel diester cyclophanes was synthesized by esterification of 1,2-benzenedicarbonyl chloride with eight different diols under high dilution conditions. The structures of the compounds were verified by elemental analysis, {sup 1}H nuclear magnetic resonance (NMR), IR spectroscopy and high resolution mass spectrometry (HRMS). The crystal structures of two compounds were characterized by single crystal X-ray diffractometry (XRD). All the new cyclophanes were evaluated for biological activities and the results showed that some of these compounds have low antibacterial or antifungal activities (author)

  9. Language structure is partly determined by social structure.

    Directory of Open Access Journals (Sweden)

    Gary Lupyan

    Full Text Available BACKGROUND: Languages differ greatly both in their syntactic and morphological systems and in the social environments in which they exist. We challenge the view that language grammars are unrelated to social environments in which they are learned and used. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a statistical analysis of >2,000 languages using a combination of demographic sources and the World Atlas of Language Structures--a database of structural language properties. We found strong relationships between linguistic factors related to morphological complexity, and demographic/socio-historical factors such as the number of language users, geographic spread, and degree of language contact. The analyses suggest that languages spoken by large groups have simpler inflectional morphology than languages spoken by smaller groups as measured on a variety of factors such as case systems and complexity of conjugations. Additionally, languages spoken by large groups are much more likely to use lexical strategies in place of inflectional morphology to encode evidentiality, negation, aspect, and possession. Our findings indicate that just as biological organisms are shaped by ecological niches, language structures appear to adapt to the environment (niche in which they are being learned and used. As adults learn a language, features that are difficult for them to acquire, are less likely to be passed on to subsequent learners. Languages used for communication in large groups that include adult learners appear to have been subjected to such selection. Conversely, the morphological complexity common to languages used in small groups increases redundancy which may facilitate language learning by infants. CONCLUSIONS/SIGNIFICANCE: We hypothesize that language structures are subjected to different evolutionary pressures in different social environments. Just as biological organisms are shaped by ecological niches, language structures appear to adapt to the

  10. Structural identifiability of cyclic graphical models of biological networks with latent variables.

    Science.gov (United States)

    Wang, Yulin; Lu, Na; Miao, Hongyu

    2016-06-13

    Graphical models have long been used to describe biological networks for a variety of important tasks such as the determination of key biological parameters, and the structure of graphical model ultimately determines whether such unknown parameters can be unambiguously obtained from experimental observations (i.e., the identifiability problem). Limited by resources or technical capacities, complex biological networks are usually partially observed in experiment, which thus introduces latent variables into the corresponding graphical models. A number of previous studies have tackled the parameter identifiability problem for graphical models such as linear structural equation models (SEMs) with or without latent variables. However, the limited resolution and efficiency of existing approaches necessarily calls for further development of novel structural identifiability analysis algorithms. An efficient structural identifiability analysis algorithm is developed in this study for a broad range of network structures. The proposed method adopts the Wright's path coefficient method to generate identifiability equations in forms of symbolic polynomials, and then converts these symbolic equations to binary matrices (called identifiability matrix). Several matrix operations are introduced for identifiability matrix reduction with system equivalency maintained. Based on the reduced identifiability matrices, the structural identifiability of each parameter is determined. A number of benchmark models are used to verify the validity of the proposed approach. Finally, the network module for influenza A virus replication is employed as a real example to illustrate the application of the proposed approach in practice. The proposed approach can deal with cyclic networks with latent variables. The key advantage is that it intentionally avoids symbolic computation and is thus highly efficient. Also, this method is capable of determining the identifiability of each single parameter and

  11. High Resolution Powder Diffraction and Structure Determination

    International Nuclear Information System (INIS)

    Cox, D. E.

    1999-01-01

    It is clear that high-resolution synchrotrons X-ray powder diffraction is a very powerful and convenient tool for material characterization and structure determination. Most investigations to date have been carried out under ambient conditions and have focused on structure solution and refinement. The application of high-resolution techniques to increasingly complex structures will certainly represent an important part of future studies, and it has been seen how ab initio solution of structures with perhaps 100 atoms in the asymmetric unit is within the realms of possibility. However, the ease with which temperature-dependence measurements can be made combined with improvements in the technology of position-sensitive detectors will undoubtedly stimulate precise in situ structural studies of phase transitions and related phenomena. One challenge in this area will be to develop high-resolution techniques for ultra-high pressure investigations in diamond anvil cells. This will require highly focused beams and very precise collimation in front of the cell down to dimensions of 50 (micro)m or less. Anomalous scattering offers many interesting possibilities as well. As a means of enhancing scattering contrast it has applications not only to the determination of cation distribution in mixed systems such as the superconducting oxides discussed in Section 9.5.3, but also to the location of specific cations in partially occupied sites, such as the extra-framework positions in zeolites, for example. Another possible application is to provide phasing information for ab initio structure solution. Finally, the precise determination of f as a function of energy through an absorption edge can provide useful information about cation oxidation states, particularly in conjunction with XANES data. In contrast to many experiments at a synchrotron facility, powder diffraction is a relatively simple and user-friendly technique, and most of the procedures and software for data analysis

  12. Tensegrity I. Cell structure and hierarchical systems biology

    Science.gov (United States)

    Ingber, Donald E.

    2003-01-01

    In 1993, a Commentary in this journal described how a simple mechanical model of cell structure based on tensegrity architecture can help to explain how cell shape, movement and cytoskeletal mechanics are controlled, as well as how cells sense and respond to mechanical forces (J. Cell Sci. 104, 613-627). The cellular tensegrity model can now be revisited and placed in context of new advances in our understanding of cell structure, biological networks and mechanoregulation that have been made over the past decade. Recent work provides strong evidence to support the use of tensegrity by cells, and mathematical formulations of the model predict many aspects of cell behavior. In addition, development of the tensegrity theory and its translation into mathematical terms are beginning to allow us to define the relationship between mechanics and biochemistry at the molecular level and to attack the larger problem of biological complexity. Part I of this two-part article covers the evidence for cellular tensegrity at the molecular level and describes how this building system may provide a structural basis for the hierarchical organization of living systems--from molecule to organism. Part II, which focuses on how these structural networks influence information processing networks, appears in the next issue.

  13. Analysis of the Causes and Recommendations on Elimination of Biological Damage of Structures During the Repair and Reconstruction of the State Biological Museum in Moscow

    Directory of Open Access Journals (Sweden)

    Kamskov Viktor

    2017-01-01

    Full Text Available The article presents the results of mycological research on buildings of the State Biological Museum located in Moscow. Over time, the building maintenance conditions have worsened, in particular because of construction of high-rise buildings in the immediate vicinity of the museum, as well as construction of a greenhouse above the underground passage tunnel between buildings 1 and 2. Over the years, the temperature gradients, high humidity, wear and damage of wall waterproofing and foundations have caused leaks in the underpass tunnel and the biological corrosion of stone, wood and metal structures in indoor exhibition halls. In this connection, part of the survey was to determine the types and size of biological lesions in structures, determination of the causes of biological damage, and the development of measures to eliminate the mycological problems during repair and reconstruction works in the museum.

  14. Biological psychological and social determinants of old age: Bio-psycho-social aspects of human aging

    Directory of Open Access Journals (Sweden)

    Małgorzata Dziechciaż

    2014-11-01

    Full Text Available Biological psychological and social determinants of old age: Bio-psycho-social aspects of human aging. The aging of humans is a physiological and dynamic process ongoing with time. In accordance with most gerontologists’ assertions it starts in the fourth decade of life and leads to death. The process of human aging is complex and individualized, occurs in the biological, psychological and social sphere. Biological aging is characterized by progressive age-changes in metabolism and physicochemical properties of cells, leading to impaired self-regulation, regeneration, and to structural changes and functional tissues and organs. It is a natural and irreversible process which can run as successful aging, typical or pathological. Biological changes that occur with age in the human body affect mood, attitude to the environment, physical condition and social activity, and designate the place of seniors in the family and society. Psychical ageing refers to human awareness and his adaptability to the ageing process. Among adaptation attitudes we can differentiate: constructive, dependence, hostile towards others and towards self attitudes. With progressed age, difficulties with adjustment to the new situation are increasing, adverse changes in the cognitive and intellectual sphere take place, perception process involutes, perceived sensations and information received is lowered, and thinking processes change. Social ageing is limited to the role of an old person is culturally conditioned and may change as customs change. Social ageing refers to how a human being perceives the ageing process and how society sees it.

  15. Determination of biologically active phenols and polyphenols in various objects by chromatographic techniques

    International Nuclear Information System (INIS)

    Kochetova, M V; Semenistaya, E N; Larionov, Oleg G; Revina, A A

    2007-01-01

    Chromatographic techniques for determination of biologically active phenols and polyphenols are considered. Various methods for sample preparation and detection are compared. The advantages of high performance liquid chromatography with spectrophotometric detection for determination of antioxidants are demonstrated. Data on determination of biologically active phenols and polyphenols published in the period from 1995 to 2005 are analysed.

  16. A routine chromium determination in biological materials; application to various reference materials and standard reference materials

    International Nuclear Information System (INIS)

    Tjioe, P.S.; Goeij, J.J.M. de; Volkers, K.J.

    1979-01-01

    The determination limit under standard working conditions of chromium in biological materials is discussed. Neutron activation analysis and atomic spectrometry have been described for some analytical experiences with NBS SRM 1577 reference material. The chromium determination is a part of a larger multi-element scheme for the determination of 12 elements in biological materials

  17. Structure, function, and behaviour of computational models in systems biology.

    Science.gov (United States)

    Knüpfer, Christian; Beckstein, Clemens; Dittrich, Peter; Le Novère, Nicolas

    2013-05-31

    Systems Biology develops computational models in order to understand biological phenomena. The increasing number and complexity of such "bio-models" necessitate computer support for the overall modelling task. Computer-aided modelling has to be based on a formal semantic description of bio-models. But, even if computational bio-models themselves are represented precisely in terms of mathematical expressions their full meaning is not yet formally specified and only described in natural language. We present a conceptual framework - the meaning facets - which can be used to rigorously specify the semantics of bio-models. A bio-model has a dual interpretation: On the one hand it is a mathematical expression which can be used in computational simulations (intrinsic meaning). On the other hand the model is related to the biological reality (extrinsic meaning). We show that in both cases this interpretation should be performed from three perspectives: the meaning of the model's components (structure), the meaning of the model's intended use (function), and the meaning of the model's dynamics (behaviour). In order to demonstrate the strengths of the meaning facets framework we apply it to two semantically related models of the cell cycle. Thereby, we make use of existing approaches for computer representation of bio-models as much as possible and sketch the missing pieces. The meaning facets framework provides a systematic in-depth approach to the semantics of bio-models. It can serve two important purposes: First, it specifies and structures the information which biologists have to take into account if they build, use and exchange models. Secondly, because it can be formalised, the framework is a solid foundation for any sort of computer support in bio-modelling. The proposed conceptual framework establishes a new methodology for modelling in Systems Biology and constitutes a basis for computer-aided collaborative research.

  18. Physical and biological factors determining the effective proton range

    International Nuclear Information System (INIS)

    Grün, Rebecca; Friedrich, Thomas; Krämer, Michael; Scholz, Michael; Zink, Klemens; Durante, Marco; Engenhart-Cabillic, Rita

    2013-01-01

    Purpose: Proton radiotherapy is rapidly becoming a standard treatment option for cancer. However, even though experimental data show an increase of the relative biological effectiveness (RBE) with depth, particularly at the distal end of the treatment field, a generic RBE of 1.1 is currently used in proton radiotherapy. This discrepancy might affect the effective penetration depth of the proton beam and thus the dose to the surrounding tissue and organs at risk. The purpose of this study was thus to analyze the impact of a tissue and dose dependent RBE of protons on the effective range of the proton beam in comparison to the range based on a generic RBE of 1.1.Methods: Factors influencing the biologically effective proton range were systematically analyzed by means of treatment planning studies using the Local Effect Model (LEM IV) and the treatment planning software TRiP98. Special emphasis was put on the comparison of passive and active range modulation techniques.Results: Beam energy, tissue type, and dose level significantly affected the biological extension of the treatment field at the distal edge. Up to 4 mm increased penetration depth as compared to the depth based on a constant RBE of 1.1. The extension of the biologically effective range strongly depends on the initial proton energy used for the most distal layer of the field and correlates with the width of the distal penumbra. Thus, the range extension, in general, was more pronounced for passive as compared to active range modulation systems, whereas the maximum RBE was higher for active systems.Conclusions: The analysis showed that the physical characteristics of the proton beam in terms of the width of the distal penumbra have a great impact on the RBE gradient and thus also the biologically effective penetration depth of the beam

  19. Micro-buckling in the nanocomposite structure of biological materials

    Science.gov (United States)

    Su, Yewang; Ji, Baohua; Hwang, Keh-Chih; Huang, Yonggang

    2012-10-01

    Nanocomposite structure, consisting of hard mineral and soft protein, is the elementary building block of biological materials, where the mineral crystals are arranged in a staggered manner in protein matrix. This special alignment of mineral is supposed to be crucial to the structural stability of the biological materials under compressive load, but the underlying mechanism is not yet clear. In this study, we performed analytical analysis on the buckling strength of the nanocomposite structure by explicitly considering the staggered alignment of the mineral crystals, as well as the coordination among the minerals during the buckling deformation. Two local buckling modes of the nanostructure were identified, i.e., the symmetric mode and anti-symmetric mode. We showed that the symmetric mode often happens at large aspect ratio and large volume fraction of mineral, while the anti-symmetric happens at small aspect ratio and small volume fraction. In addition, we showed that because of the coordination of minerals with the help of their staggered alignment, the buckling strength of these two modes approached to that of the ideally continuous fiber reinforced composites at large aspect ratio given by Rosen's model, insensitive to the existing "gap"-like flaws between mineral tips. Furthermore, we identified a mechanism of buckling mode transition from local to global buckling with increase of aspect ratio, which was attributed to the biphasic dependence of the buckling strength on the aspect ratio. That is, for small aspect ratio, the local buckling strength is smaller than that of global buckling so that it dominates the buckling behavior of the nanocomposite; for comparatively larger aspect ratio, the local buckling strength is higher than that of global buckling so that the global buckling dominates the buckling behavior. We also found that the hierarchical structure can effectively enhance the buckling strength, particularly, this structural design enables

  20. How structure determines correlations in neuronal networks.

    Directory of Open Access Journals (Sweden)

    Volker Pernice

    2011-05-01

    Full Text Available Networks are becoming a ubiquitous metaphor for the understanding of complex biological systems, spanning the range between molecular signalling pathways, neural networks in the brain, and interacting species in a food web. In many models, we face an intricate interplay between the topology of the network and the dynamics of the system, which is generally very hard to disentangle. A dynamical feature that has been subject of intense research in various fields are correlations between the noisy activity of nodes in a network. We consider a class of systems, where discrete signals are sent along the links of the network. Such systems are of particular relevance in neuroscience, because they provide models for networks of neurons that use action potentials for communication. We study correlations in dynamic networks with arbitrary topology, assuming linear pulse coupling. With our novel approach, we are able to understand in detail how specific structural motifs affect pairwise correlations. Based on a power series decomposition of the covariance matrix, we describe the conditions under which very indirect interactions will have a pronounced effect on correlations and population dynamics. In random networks, we find that indirect interactions may lead to a broad distribution of activation levels with low average but highly variable correlations. This phenomenon is even more pronounced in networks with distance dependent connectivity. In contrast, networks with highly connected hubs or patchy connections often exhibit strong average correlations. Our results are particularly relevant in view of new experimental techniques that enable the parallel recording of spiking activity from a large number of neurons, an appropriate interpretation of which is hampered by the currently limited understanding of structure-dynamics relations in complex networks.

  1. Exploring biological network structure with clustered random networks

    Directory of Open Access Journals (Sweden)

    Bansal Shweta

    2009-12-01

    Full Text Available Abstract Background Complex biological systems are often modeled as networks of interacting units. Networks of biochemical interactions among proteins, epidemiological contacts among hosts, and trophic interactions in ecosystems, to name a few, have provided useful insights into the dynamical processes that shape and traverse these systems. The degrees of nodes (numbers of interactions and the extent of clustering (the tendency for a set of three nodes to be interconnected are two of many well-studied network properties that can fundamentally shape a system. Disentangling the interdependent effects of the various network properties, however, can be difficult. Simple network models can help us quantify the structure of empirical networked systems and understand the impact of various topological properties on dynamics. Results Here we develop and implement a new Markov chain simulation algorithm to generate simple, connected random graphs that have a specified degree sequence and level of clustering, but are random in all other respects. The implementation of the algorithm (ClustRNet: Clustered Random Networks provides the generation of random graphs optimized according to a local or global, and relative or absolute measure of clustering. We compare our algorithm to other similar methods and show that ours more successfully produces desired network characteristics. Finding appropriate null models is crucial in bioinformatics research, and is often difficult, particularly for biological networks. As we demonstrate, the networks generated by ClustRNet can serve as random controls when investigating the impacts of complex network features beyond the byproduct of degree and clustering in empirical networks. Conclusion ClustRNet generates ensembles of graphs of specified edge structure and clustering. These graphs allow for systematic study of the impacts of connectivity and redundancies on network function and dynamics. This process is a key step in

  2. Structural valve deterioration in the Mitroflow biological heart valve prosthesis

    DEFF Research Database (Denmark)

    Issa, Issa Farah; Poulsen, Steen Hvitfeldt; Waziri, Farhad

    2018-01-01

    OBJECTIVES: Concern has been raised regarding the long-term durability of the Mitroflow biological heart valve prosthesis. Our aim was to assess the incidence of structural valve degeneration (SVD) for the Mitroflow bioprosthesis in a nationwide study in Denmark including all patients alive......: A total of 173 patients were diagnosed with SVD by echocardiography. Of these, 64 (11%) patients had severe SVD and 109 (19%) patients moderate SVD. Severe SVD was associated with the age of the prosthesis and small prosthesis size [Size 21: hazard ratio (95% confidence interval, CI) 2.72 (0.97-8.56), P...

  3. Using systems and structure biology tools to dissect cellular phenotypes.

    Science.gov (United States)

    Floratos, Aris; Honig, Barry; Pe'er, Dana; Califano, Andrea

    2012-01-01

    The Center for the Multiscale Analysis of Genetic Networks (MAGNet, http://magnet.c2b2.columbia.edu) was established in 2005, with the mission of providing the biomedical research community with Structural and Systems Biology algorithms and software tools for the dissection of molecular interactions and for the interaction-based elucidation of cellular phenotypes. Over the last 7 years, MAGNet investigators have developed many novel analysis methodologies, which have led to important biological discoveries, including understanding the role of the DNA shape in protein-DNA binding specificity and the discovery of genes causally related to the presentation of malignant phenotypes, including lymphoma, glioma, and melanoma. Software tools implementing these methodologies have been broadly adopted by the research community and are made freely available through geWorkbench, the Center's integrated analysis platform. Additionally, MAGNet has been instrumental in organizing and developing key conferences and meetings focused on the emerging field of systems biology and regulatory genomics, with special focus on cancer-related research.

  4. Data publication with the structural biology data grid supports live analysis

    NARCIS (Netherlands)

    Meyer, Peter A.; Socias, Stephanie; Key, Jason; Ransey, Elizabeth; Tjon, Emily C.; Buschiazzo, Alejandro; Lei, Ming; Botka, Chris; Withrow, James; Neau, David; Rajashankar, Kanagalaghatta; Anderson, Karen S.; Baxter, Richard H.; Blacklow, Stephen C.; Boggon, Titus J.; Bonvin, Alexandre M J J|info:eu-repo/dai/nl/113691238; Borek, Dominika; Brett, Tom J.; Caflisch, Amedeo; Chang, Chung I.; Chazin, Walter J.; Corbett, Kevin D.; Cosgrove, Michael S.; Crosson, Sean; Dhe-Paganon, Sirano; Di Cera, Enrico; Drennan, Catherine L.; Eck, Michael J.; Eichman, Brandt F.; Fan, Qing R.; Ferré-D'Amaré, Adrian R.; Fromme, J. Christopher; Garcia, K. Christopher; Gaudet, Rachelle; Gong, Peng; Harrison, Stephen C.; Heldwein, Ekaterina E.; Jia, Zongchao; Keenan, Robert J.; Kruse, Andrew C.; Kvansakul, Marc; McLellan, Jason S.; Modis, Yorgo; Nam, Yunsun; Otwinowski, Zbyszek; Pai, Emil F.; Pereira, Pedro José Barbosa; Petosa, Carlo; Raman, C. S.; Rapoport, Tom A.; Roll-Mecak, Antonina; Rosen, Michael K.; Rudenko, Gabby; Schlessinger, Joseph; Schwartz, Thomas U.; Shamoo, Yousif; Sondermann, Holger; Tao, Yizhi J.; Tolia, Niraj H.; Tsodikov, Oleg V.; Westover, Kenneth D.; Wu, Hao; Foster, Ian; Fraser, James S.; Maia, Filipe R N C; Gonen, Tamir; Kirchhausen, Tom; Diederichs, Kay; Crosas, Mercé; Sliz, Piotr

    2016-01-01

    Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology

  5. Synthesis, crystal structure determination, biological screening and docking studies of N1-substituted derivatives of 2,3-dihydroquinazolin-4(1H)-one as inhibitors of cholinesterases.

    Science.gov (United States)

    Sultana, Nargis; Sarfraz, Muhammad; Tanoli, Saba Tahir; Akram, Muhammad Safwan; Sadiq, Abdul; Rashid, Umer; Tariq, Muhammad Ilyas

    2017-06-01

    Pursuing the strategy of developing potent AChE inhibitors, we attempted to carry out the N 1 -substitution of 2,3-dihydroquinazolin-4(1H)-one core. A set of 32 N-alkylated/benzylated quinazoline derivatives were synthesized, characterized and evaluated for their inhibition against cholinesterases. N-alkylation of the series of the compounds reported previously (N-unsubstituted) resulted in improved activity. All the compounds showed inhibition of both enzymes in the micromolar to submicromolar range. Structure activity relationship (SAR) of the 32 derivatives showed that N-benzylated compounds possess good activity than N-alkylated compounds. N-benzylated compounds 2ad and 2af were found very active with their IC 50 values toward AChE in submicromolar range (0.8µM and 0.6µM respectively). Binding modes of the synthesized compounds were explored by using GOLD (Genetic Optimization for Ligand Docking) suit v5.4.1. Computational predictions of ADMET studies reveal that all the compounds have good pharmacokinetic properties with no AMES toxicity and carcinogenicity. Moreover, all the compounds are predicted to be absorbed in human intestine and also have the ability to cross blood brain barrier. Overall, the synthesized compounds have established a structural foundation for the design of new inhibitors of cholinesterase. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Synchrotron radiation and structure biology. From the instrumentation view point

    International Nuclear Information System (INIS)

    Sakabe, N.

    1996-01-01

    Structure Biology is based on a three dimensional macromolecule structures, the most of which are studied by x-ray crystal structure analysis. Synchrotron radiation X-rays are quite strong, tunable, very parallel and pico-second order bunch and are very suitable for diffraction data collection of macromolecular crystals. To collect accurate data at high resolution from large unit cell protein crystals using SR, we made screenless large Weissenberg cameras with imaging plates at the PF. 146 research projects using this data collection system were running in 1995. They include 51 projects from 11 overseas countries. Recently we have developed user-friendly type Weissenberg camera for the structure biology project of TARA (Tsukuba Advanced Research Alliance), and installed it at BL6B of the PF. Cylindrical cassette radius of this new camera is 575.7mm and two large format (400x800mm) imaging plates (IP) can be fixed into the cassette by suction from back side. However, the system is not automatic and manual tasks to be performed are heavy. Therefore an automation of the system is very urgent to maintain accuracy and resolution. We are now developing a high accuracy, high resolution and high speed automated data collection system. This fully automated system consists of a camera, an IP reader equipped with 8 reading heads, an IP eraser, and a cassette transportation mechanism. In the new system, one imaging plate is fixed inside of a movable cylindrical cassette. The cassette presenting 16 rectangular holes, direct beam injection of i.e. 1.0A X-rays would produce 8 images of data at 2.6A resolutions. As 2 cassettes can be used simultaneously on the cassette transportation system, one cassette is being read while the other one is being exposed, therefore completely removing the reading bottleneck problem. This system therefore permits to use the radiation with the maximum of efficiency, and reduce the manpower necessary for data recording. (author)

  7. Spectrophotometric determination of vanadium in environmental and biological samples

    International Nuclear Information System (INIS)

    Rekha, D.; Krishnapriya, B.; Subrahmanyam, P.; Reddyprasad, P.; Dilip Kumar, J.; Chiranjeevi, P.

    2007-01-01

    The method is based on oxidation of p-nitro aniline by vanadium (V) followed by coupling reaction with N-(1-naphthalene-1-y1)ethane-1, 2-diaminedihydrochloride (NEDA) in basic medium of pH 8 to give purple colored derivative. The derivative having an λ max 525nm is stable for 10 days. Beer's law is obeyed for vanadium (V) in the concentration range of 0.03-4.5 μg ml -1 . The proposed method was successfully applied to the analysis of vanadium in environmental and biological samples. (author)

  8. [Determination of glutamic acid in biological material by capillary electrophoresis].

    Science.gov (United States)

    Narezhnaya, E; Krukier, I; Avrutskaya, V; Degtyareva, A; Igumnova, E A

    2015-01-01

    The conditions for the identification and determination of Glutamic acid by capillary zone electrophoresis without their preliminary derivatization have been optimized. The effect of concentration of buffer electrolyte and pH on determination of Glutamic acid has been investigated. It is shown that the 5 Mm borate buffer concentration and a pH 9.15 are optimal. Quantitative determination of glutamic acid has been carried out using a linear dependence between the concentration of the analyte and the area of the peak. The accuracy and reproducibility of the determination are confirmed by the method "introduced - found". Glutamic acid has been determined in the placenta homogenate. The duration of analysis doesn't exceed 30 minutes. The results showed a decrease in the level of glutamic acid in cases of pregnancy complicated by placental insufficiency compared with the physiological, and this fact allows to consider the level of glutamic acid as a possible marker of complicated pregnancy.

  9. 78 FR 55326 - Determinations Regarding Use of Chemical Weapons in Syria Under the Chemical and Biological...

    Science.gov (United States)

    2013-09-10

    ... DEPARTMENT OF STATE [Public Notice 8460] Determinations Regarding Use of Chemical Weapons in Syria Under the Chemical and Biological Weapons Control and Warfare Elimination Act of 1991 AGENCY: Bureau of... Government has determined on August 2, pursuant to Section 306(a) of the Chemical and Biological Weapons...

  10. Structure determination by X-ray crystallography

    CERN Document Server

    Ladd, M F C

    1977-01-01

    Crystallography may be described as the science of the structure of materi­ als, using this word in its widest sense, and its ramifications are apparent over a broad front of current scientific endeavor. It is not surprising, therefore, to find that most universities offer some aspects of crystallography in their undergraduate courses in the physical sciences. It is the principal aim of this book to present an introduction to structure determination by X-ray crystal­ lography that is appropriate mainly to both final-year undergraduate studies in crystallography, chemistry, and chemical physics, and introductory post­ graduate work in this area of crystallography. We believe that the book will be of interest in other disciplines, such as physics, metallurgy, biochemistry, and geology, where crystallography has an important part to play. In the space of one book, it is not possible either to cover all aspects of crystallography or to treat all the subject matter completely rigorously. In particular, certain ...

  11. The importance of correct tautomeric structures for biological molecules

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Mortensen, John; Kamounah, Fadhil S.

    2015-01-01

    The structures of usnic acid and tetracycline are determined using deuterium isotope effects on 13C chemical shifts in a water environment. In case of usnic acid this is achieved by synthesizing a more water soluble usnic acid with a PEG linker. In the usnic acid case an enolic b-triketone (C-1, ...

  12. Determination of 18O concentrations in microsamples of biological fluids

    International Nuclear Information System (INIS)

    Cohen, D.D.; Bradshaw, S.D.; Bradshaw, F.J.

    1990-01-01

    The 18 O(p, α) 15 N reaction has been developed for the analysis of microsamples of biological fluids containing 18 O-enriched water. Samples as small as 50 μl have been used. Well characterized Ta 2 O 5 targets were prepared from these fluids and irradiated with several hundred nA of protons from the 3 MV Van de Graaff at Lucas Heights. The broad (47 keV) 846 kV resonance in this reaction was used to measure 18 O concentrations down to natural backgrounds (0.2 at.%) in a few minutes of accelerator running time. Concentrations of 18 O from 0 to 5 at.% were measured in body fluids in small Australian lizards directly after doping with 18 O-enriched water and then again after several days of roaming around in their natural desert environments. The changes in these levels were related to the metabolic rates of these animals. (orig.)

  13. A lightweight, biological structure with tailored stiffness: The feather vane.

    Science.gov (United States)

    Sullivan, Tarah N; Pissarenko, Andreï; Herrera, Steven A; Kisailus, David; Lubarda, Vlado A; Meyers, Marc A

    2016-09-01

    The flying feathers of birds are keratinous appendages designed for maximum performance with a minimum weight penalty. Thus, their design contains ingenious combinations of components that optimize lift, stiffness, aerodynamics, and damage resistance. This design involves two main parts: a central shaft that prescribes stiffness and lateral vanes which allows for the capture of air. Within the feather vane, barbs branch from the shaft and barbules branch from barbs, forming a flat surface which ensures lift. Microhooks at the end of barbules hold barbs tightly together, providing the close-knit, unified structure of the feather vane and enabling a repair of the structure through the reattachment of un-hooked junctions. Both the shaft and barbs are lightweight biological structures constructed of keratin using the common motif of a solid shell and cellular interior. The cellular core increases the resistance to buckling with little added weight. Here we analyze the detailed structure of the feather barb and, for the first time, explain its flexural stiffness in terms of the mechanics of asymmetric foam-filled beams subjected to bending. The results are correlated and validated with finite element modeling. We compare the flexure of single barbs as well as arrays of barbs and find that the interlocking adherence of barbs to one another enables a more robust structure due to minimized barb rotation during deflection. Thus, the flexure behavior of the feather vane can be tailored by the adhesive hooking between barbs, creating a system that mitigates damage. A simplified three-dimensional physical model for this interlocking mechanism is constructed by additive manufacturing. The exceptional architecture of the feather vane will motivate the design of bioinspired structures with tailored and unique properties ranging from adhesives to aerospace materials. Despite its importance to bird flight, literature characterizing the feather vane is extremely limited. The feather

  14. Thorium determination in water and biological materials by fission track

    International Nuclear Information System (INIS)

    Melo Ferreira, A.C. de.

    1989-01-01

    As a segment of a research programme on the study of bioaccumulation of radionuclides, in animals and vegetables from Morro do Ferro, Pocos de Caldas, MG, a fission track method for the determination of low levels of thorium in environmental samples was developed as an alternative for alpha spectroscopy. The study was carried out in early alpha spectroscopy samples, containing high levels of 228 Th activity, which makes difficult the 232 Th determination. A dry way method for thorium evaluation was developed. Pieces of membrane filters, containing La F 3 (Th), coupled to Makrofol detectors, were irradiated in the core of a research reactor, IEA-R1 (IPEN). (author)

  15. Amines as extracting agents for the quantitative determinations of actinides in biological samples

    International Nuclear Information System (INIS)

    Singh, N.P.

    1987-01-01

    The use of amines (primary, secondary and tertiary chains and quaternary ammonium salts) as extracting agents for the quantitative determination of actinides in biological samples is reviewed. Among the primary amines, only Primene JM-T is used to determine Pu in urine and bone. No one has investigated the possibility of using secondary amines to quantitatively extract actinides from biological samples. Among the tertiary amines, tri-n-octylamine, tri-iso-octylamine, tyricaprylamine (Alamine) and trilaurylamine (tridodecylamine) are used extensively to extract and separate the actinides from biological samples. Only one quaternary ammonium salt, methyltricapryl ammonium chloride (Aliquat-336), is used to extract Pu from biological samples. (author) 28 refs

  16. The High-Strain Rate Loading of Structural Biological Materials

    Science.gov (United States)

    Proud, W. G.; Nguyen, T.-T. N.; Bo, C.; Butler, B. J.; Boddy, R. L.; Williams, A.; Masouros, S.; Brown, K. A.

    2015-10-01

    The human body can be subjected to violent acceleration as a result of explosion caused by military ordinance or accident. Blast waves cause injury and blunt trauma can be produced by violent impact of objects against the human body. The long-term clinical manifestations of blast injury can be significantly different in nature and extent to those suffering less aggressive insult. Similarly, the damage seen in lower limbs from those injured in explosion incidents is in general more severe than those falling from height. These phenomena increase the need for knowledge of the short- and long-term effect of transient mechanical loading to the biological structures of the human body. This paper gives an overview of some of the results of collaborative investigation into blast injury. The requirement for time-resolved data, appropriate mechanical modeling, materials characterization and biological effects is presented. The use of a range of loading platforms, universal testing machines, drop weights, Hopkinson bars, and bespoke traumatic injury simulators are given.

  17. Structural and Biological Assessment of Zinc Doped Hydroxyapatite Nanoparticles

    Directory of Open Access Journals (Sweden)

    Cristina Liana Popa

    2016-01-01

    Full Text Available The aim of the current research work was to study the physicochemical and biological properties of synthesized zinc doped hydroxyapatite (ZnHAp nanoparticles with Zn concentrations xZn=0 (HAp, xZn=0.07 (7ZnHAp, and xZn=0.1 (10ZnHAp for potential use in biological applications. The morphology, size, compositions, and incorporation of zinc into hydroxyapatite were characterized by scanning electron microscopy (SEM, transmission electron microscopy (TEM, Fourier Transform Infrared Spectroscopy (FTIR, Raman scattering, and X-Ray Photoelectron Spectroscopy (XPS. In addition, the cytotoxicity of ZnHAp nanoparticles was tested on both E. coli bacteria and human hepatocarcinoma cell line HepG2. The results showed that ZnHAp nanoparticles (HAp, 7ZnHAp, and 10ZnHAp have slightly elongated morphologies with average diameters between 25 nm and 18 nm. On the other hand, a uniform and homogeneous distribution of the constituent elements (calcium, phosphorus, zinc, and oxygen in the ZnHAp powder was noticed. Besides, FTIR and Raman analyses confirmed the proper hydroxyapatite structure of the synthesized ZnHAp nanoparticles with the signature of phosphate, carbonate, and hydroxyl groups. Moreover, it can be concluded that Zn doping at the tested concentrations is not inducing a specific prokaryote or eukaryote toxicity in HAp compounds.

  18. Data acquisition and analysis at the Structural Biology Center

    International Nuclear Information System (INIS)

    Westbrook, M.L.; Coleman, T.A.; Daly, R.T.; Pflugrath, J.W.

    1996-01-01

    The Structural Biology Center (SBC), a national user facility for macromolecular crystallography located at Argonne National Laboratory's Advanced Photon Source, is currently being built and commissioned. SBC facilities include a bending-magnet beamline, an insertion-device beamline, laboratory and office space adjacent to the beamlines, and associated instrumentation, experimental apparatus, and facilities. SBC technical facilities will support anomalous dispersion phasing experiments, data collection from microcrystals, data collection from crystals with large molecular structures and rapid data collection from multiple related crystal structures for protein engineering and drug design. The SBC Computing Systems and Software Engineering Group is tasked with developing the SBC Control System, which includes computing systems, network, and software. The emphasis of SBC Control System development has been to provide efficient and convenient beamline control, data acquisition, and data analysis for maximal facility and experimenter productivity. This paper describes the SBC Control System development, specifically data acquisition and analysis at the SBC, and the development methods used to meet this goal

  19. Nitrate biosensors and biological methods for nitrate determination.

    Science.gov (United States)

    Sohail, Manzar; Adeloju, Samuel B

    2016-06-01

    The inorganic nitrate (NO3‾) anion is present under a variety of both natural and artificial environmental conditions. Nitrate is ubiquitous within the environment, food, industrial and physiological systems and is mostly present as hydrated anion of a corresponding dissolved salt. Due to the significant environmental and toxicological effects of nitrate, its determination and monitoring in environmental and industrial waters are often necessary. A wide range of analytical techniques are available for nitrate determination in various sample matrices. This review discusses biosensors available for nitrate determination using the enzyme nitrate reductase (NaR). We conclude that nitrate determination using biosensors is an excellent non-toxic alternative to all other available analytical methods. Over the last fifteen years biosensing technology for nitrate analysis has progressed very well, however, there is a need to expedite the development of nitrate biosensors as a suitable alternative to non-enzymatic techniques through the use of different polymers, nanostructures, mediators and strategies to overcome oxygen interference. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Nonoxidized, biologically active parathyroid hormone determines mortality in hemodialysis patients

    DEFF Research Database (Denmark)

    Tepel, Martin; Armbruster, Franz Paul; Grön, Hans Jürgen

    2013-01-01

    Background: It was shown that nonoxidized PTH (n-oxPTH) is bioactive, whereas the oxidation of PTH results in a loss of biological activity. Methods: In this study we analyzed the association of n-oxPTH on mortality in hemodialysis patients using a recently developed assay system. Results......: Hemodialysis patients (224 men, 116 women) had a median age of 66 years. One hundred seventy patients (50%) died during the follow-up period of 5 years. Median n-oxPTH levels were higher in survivors (7.2 ng/L) compared with deceased patients (5.0 ng/L; P = .002). Survival analysis showed an increased survival...... in the highest n-oxPTH tertile compared with the lowest n-oxPTH tertile (χ(2), 14.3; P = .0008). Median survival was 1702 days in the highest n-oxPTH tertile, whereas it was only 453 days in the lowest n-oxPTH tertile. Multivariable-adjusted Cox regression showed that higher age increased odds for death, whereas...

  1. Temporal change in biological community structure in the Fountain Creek basin, Colorado, 2001-2008

    Science.gov (United States)

    Zuellig, Robert E.; Bruce, James F.; Stogner, Sr., Robert W.

    2010-01-01

    In 2001, the U.S. Geological Survey, in cooperation with Colorado Springs City Engineering, began a study to better understand the relations between environmental characteristics and biological communities in the Fountain Creek basin in order to aide water-resource management and guide future monitoring activities. To accomplish this task, environmental (streamflow, habitat, and water chemistry) and biological (fish and macroinvertebrate) data were collected annually at 24 sites over a 6- or 8-year period (fish, 2003 to 2008; macroinvertebrates, 2001 to 2008). For this report, these data were first analyzed to determine the presence of temporal change in macroinvertebrate and fish community structure among years using nonparametric multivariate statistics. Where temporal change in the biological communities was found, these data were further analyzed using additional nonparametric multivariate techniques to determine which subset of selected streamflow, habitat, or water-chemistry variables best described site-specific changes in community structure relative to a gradient of urbanization. This study identified significant directional patterns of temporal change in macroinvertebrate and fish community structure at 15 of 24 sites in the Fountain Creek basin. At four of these sites, changes in environmental variables were significantly correlated with the concurrent temporal change identified in macroinvertebrate and fish community structure (Monument Creek above Woodmen Road at Colorado Springs, Colo.; Monument Creek at Bijou Street at Colorado Springs, Colo.; Bear Creek near Colorado Springs, Colo.; Fountain Creek at Security, Colo.). Combinations of environmental variables describing directional temporal change in the biota appeared to be site specific as no single variable dominated the results; however, substrate composition variables (percent substrate composition composed of sand, gravel, or cobble) collectively were present in 80 percent of the environmental

  2. Structural Diversity and Biological Activities of the Cyclodipeptides from Fungi

    Directory of Open Access Journals (Sweden)

    Xiaohan Wang

    2017-11-01

    Full Text Available Cyclodipeptides, called 2,5-diketopiperazines (2,5-DKPs, are obtained by the condensation of two amino acids. Fungi have been considered to be a rich source of novel and bioactive cyclodipeptides. This review highlights the occurrence, structures and biological activities of the fungal cyclodipeptides with the literature covered up to July 2017. A total of 635 fungal cyclodipeptides belonging to the groups of tryptophan-proline, tryptophan-tryptophan, tryptophan–Xaa, proline–Xaa, non-tryptophan–non-proline, and thio-analogs have been discussed and reviewed. They were mainly isolated from the genera of Aspergillus and Penicillium. More and more cyclodipeptides have been isolated from marine-derived and plant endophytic fungi. Some of them were screened to have cytotoxic, phytotoxic, antimicrobial, insecticidal, vasodilator, radical scavenging, antioxidant, brine shrimp lethal, antiviral, nematicidal, antituberculosis, and enzyme-inhibitory activities to show their potential applications in agriculture, medicinal, and food industry.

  3. Aromatic-Aromatic Interactions in Biological System: Structure Activity Relationships

    International Nuclear Information System (INIS)

    Rajagopal, Appavu; Deepa, Mohan; Govindaraju, Munisamy

    2016-01-01

    While, intramolecular hydrogen bonds have attracted the greatest attention in studies of peptide conformations, the recognition that several other weakly polar interactions may be important determinants of folded structure has been growing. Burley and Petsko provided a comprehensive overview of the importance of weakly polar interactions, in shaping protein structures. The interactions between aromatic rings, which are spatially approximate, have attracted special attention. A survey of the proximal aromatic residue pairs in proteins, allowed Burley and Petsko to suggest that, “phenyl ring centroids are separated by a preferential distance of between 4.5 and 7 Å, and dihedral angles approximately 90° are most common”

  4. Aromatic-Aromatic Interactions in Biological System: Structure Activity Relationships

    Energy Technology Data Exchange (ETDEWEB)

    Rajagopal, Appavu; Deepa, Mohan [Molecular Biophysics Unit, Indian Institute of Sciences-Bangalore, Karnataka (India); Govindaraju, Munisamy [Bio-Spatial Technology Research Unit, Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu (India)

    2016-02-26

    While, intramolecular hydrogen bonds have attracted the greatest attention in studies of peptide conformations, the recognition that several other weakly polar interactions may be important determinants of folded structure has been growing. Burley and Petsko provided a comprehensive overview of the importance of weakly polar interactions, in shaping protein structures. The interactions between aromatic rings, which are spatially approximate, have attracted special attention. A survey of the proximal aromatic residue pairs in proteins, allowed Burley and Petsko to suggest that, “phenyl ring centroids are separated by a preferential distance of between 4.5 and 7 Å, and dihedral angles approximately 90° are most common”.

  5. Core/Shell Structured Magnetic Nanoparticles for Biological Applications

    International Nuclear Information System (INIS)

    Park, Jeong Chan; Jung, Myung Hwan

    2013-01-01

    Magnetic nanoparticles have been widely used for biomedical applications, such as magnetic resonance imaging (MRI), hyperthermia, drug delivery and cell signaling. The surface modification of the nanomaterials is required for biomedical use to give physiogical stability, surface reactivity and targeting properties. Among many approaches for the surface modification with materials, such as polymers, organic ligands and metals, one of the most attractive ways is using metals. The fabrication of metal-based, monolayer-coated magnetic nanoparticles has been intensively studied. However, the synthesis of metal-capped magnetic nanoparticles with monodispersities and controllable sizes is still challenged. Recently, gold-capped magnetic nanoparticles have been reported to increase stability and to provide biocompatibility. Magnetic nanoparticle with gold coating is an attractive system, which can be stabilized in biological conditions and readily functionalized in biological conditions and readily functionalized through well-established surface modification (Au-S) chemistry. The Au coating offers plasmonic properties to magnetic nanoparticles. This makes the magnetic/Au core/shell combinations interesting for magnetic and optical applications. Herein, the synthesis and characterization of gold capped-magnetic core structured nanomaterials with different gold sources, such as gold acetate and chloroauric acid have been reported. The core/shell nanoparticles were transferred from organic to aqueous solutions for biomedical applications. Magnetic core/shell structured nanoparticles have been prepared and transferred from organic phase to aqueous solutions. The resulting Au-coated magnetic core nanoparticles might be an attractive system for biomedical applications, which are needed both magnetic resonance imaging and optical imaging

  6. RNAA determination of As, Cd and Zn in biological materials

    International Nuclear Information System (INIS)

    Taskaev, E.; Penev, I.; Kinova, L.

    1985-01-01

    In connection with the IAEA project 3739/RB the elements Hg, As, Cd and Zn in human spleen, kidney, heart, liver, SRM Bovine Liver 1577a and Bowen's Kale. The consecutive extraction have been chosen as the most rational approach determining these elements in a single specimen. Aiming at getting reliable results well established systems were used (ditizone to separate Hg, Cu and DEDTC to extract As, Cd and Zn). Special attention was paid to the accuracy of the determination. Monitoring, optimization and cooling time and control of chemical yield were carried out in each case. The samples were irradiated in the vertical channel of the IRT-2000 reactor in Sofia, in thermal neutron flux of about 5.10 12 n.cm -2 .s -1 for 24 h. Iron monitor was used and cooling time varied from 20 h to 30 h

  7. Determination of palladium in biological samples applying nuclear analytical techniques

    International Nuclear Information System (INIS)

    Cavalcante, Cassio Q.; Sato, Ivone M.; Salvador, Vera L. R.; Saiki, Mitiko

    2008-01-01

    This study presents Pd determinations in bovine tissue samples containing palladium prepared in the laboratory, and CCQM-P63 automotive catalyst materials of the Proficiency Test, using instrumental thermal and epithermal neutron activation analysis and energy dispersive X-ray fluorescence techniques. Solvent extraction and solid phase extraction procedures were also applied to separate Pd from interfering elements before the irradiation in the nuclear reactor. The results obtained by different techniques were compared against each other to examine sensitivity, precision and accuracy. (author)

  8. Using the Cambridge structure database of organic and organometalic compounds in structure biology

    Czech Academy of Sciences Publication Activity Database

    Hašek, Jindřich

    2010-01-01

    Roč. 17, 1a (2010), b24-b26 ISSN 1211-5894. [Discussions in Structural Molecular Biology /8./. Nové Hrady, 18.03.2010-20.03.2010] R&D Projects: GA AV ČR IAA500500701; GA ČR GA305/07/1073 Institutional research plan: CEZ:AV0Z40500505 Keywords : organic chemistry * Cambridge Structure Data base * molecular structure Subject RIV: CD - Macromolecular Chemistry http://xray.cz/ms/bul2010-1a/friday2.pdf

  9. Overcoming bottlenecks in the membrane protein structural biology pipeline.

    Science.gov (United States)

    Hardy, David; Bill, Roslyn M; Jawhari, Anass; Rothnie, Alice J

    2016-06-15

    Membrane proteins account for a third of the eukaryotic proteome, but are greatly under-represented in the Protein Data Bank. Unfortunately, recent technological advances in X-ray crystallography and EM cannot account for the poor solubility and stability of membrane protein samples. A limitation of conventional detergent-based methods is that detergent molecules destabilize membrane proteins, leading to their aggregation. The use of orthologues, mutants and fusion tags has helped improve protein stability, but at the expense of not working with the sequence of interest. Novel detergents such as glucose neopentyl glycol (GNG), maltose neopentyl glycol (MNG) and calixarene-based detergents can improve protein stability without compromising their solubilizing properties. Styrene maleic acid lipid particles (SMALPs) focus on retaining the native lipid bilayer of a membrane protein during purification and biophysical analysis. Overcoming bottlenecks in the membrane protein structural biology pipeline, primarily by maintaining protein stability, will facilitate the elucidation of many more membrane protein structures in the near future. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

  10. Vestigial Biological Structures: A Classroom-Applicable Test of Creationist Hypotheses

    Science.gov (United States)

    Senter, Phil; Ambrocio, Zenis; Andrade, Julia B.; Foust, Katanya K.; Gaston, Jasmine E.; Lewis, Ryshonda P.; Liniewski, Rachel M.; Ragin, Bobby A.; Robinson, Khanna L.; Stanley, Shane G.

    2015-01-01

    Lists of vestigial biological structures in biology textbooks are so short that some young-Earth creationist authors claim that scientists have lost confidence in the existence of vestigial structures and can no longer identify any verifiable ones. We tested these hypotheses with a method that is easily adapted to biology classes. We used online…

  11. The Effect of Knowledge Linking Levels in Biology Lessons upon Students' Knowledge Structure

    Science.gov (United States)

    Wadouh, Julia; Liu, Ning; Sandmann, Angela; Neuhaus, Birgit J.

    2014-01-01

    Knowledge structure is an important aspect for defining students' competency in biology learning, but how knowledge structure is influenced by the teaching process in naturalistic biology classroom settings has scarcely been empirically investigated. In this study, 49 biology lessons in the teaching unit "blood and circulatory system" in…

  12. Determination of methylmercury salts in various kinds of biological material

    Energy Technology Data Exchange (ETDEWEB)

    Westoeoe, G

    1968-01-01

    The cysteine acetate modification of the method for determining methylmercury salts in foods, which was useful for analysis of fish, egg white, and meat, was not efficient when applied to egg yolk with low methylmercury content, liver, sediments in aquaria, or sludge. Therefore some modifications of the procedure have been investigated. A combination of the mercuric chloride and cysteine acetate procedures gave good results for sediments in aquaria and sludge and could also be used for, e.g., fish, egg white, bile, kidney, blood, meat, and moss. Precipitation of the proteins with molybdic acid at the first extraction improved the results for liver but not for egg yolk. For egg yolk an increase of the concentration of the cysteine acetate solution from 1 to 10% gave 90% recovery of added methylmercury, repeated extractions 100% recovery. 5 references, 2 tables.

  13. Determination of uranium in biological objects using adsorption

    International Nuclear Information System (INIS)

    Zakharova, Eh.A.; Filichkina, O.G.; Pikula, N.P.; Slepchenko, G.B.

    2002-01-01

    A method of U 6+ (0.0001-0.005 mg/liter) determination in urine using adsorption cathode voltammetry is presented. The signal was measured using supporting 0.01 M KCl + 5 x 10 -5 M oxyquinoline + 1x10 -4 M trilon B at pH 6.8 - 7.0. A stationary mercury film electrode on a silver substrate was restituted mechanically and electrochemically. The interfering matrix effect was eliminated using wet mineralization and calcination of the samples (up to 100 ml) and subsequent isolation of oxyquinolinate complex of uranyl with chloroform. The total error, within which the error falls with the probability p=0.95, is ±33%. A systematic error attributed to partial isolation is eliminated via a correction coefficient equal to 1.3 [ru

  14. Ab Initio Calculations of the Electronic Structures and Biological Functions of Protein Molecules

    Science.gov (United States)

    Zheng, Haoping

    2003-04-01

    The self-consistent cluster-embedding (SCCE) calculation method reduces the computational effort from M3 to about M1 (M is the number of atoms in the system) with unchanged calculation precision. So the ab initio, all-electron calculation of the electronic structure and biological function of protein molecule becomes a reality, which will promote new proteomics considerably. The calculated results of two real protein molecules, the trypsin inhibitor from the seeds of squash Cucurbita maxima (CMTI-I, 436 atoms) and the Ascaris trypsin inhibitor (912 atoms, two three-dimensional structures), are presented. The reactive sites of the inhibitors are determined and explained. The precision of structure determination of inhibitors are tested theoretically.

  15. The Learning of Biology: A Structural Basis for Future Research

    Science.gov (United States)

    Murray, Darrel L.

    1977-01-01

    This article reviews recent research studies and experiences relating the learning theories of Ausubel to biology instruction. Also some suggestions are made for future research on the learning of biology. (MR)

  16. From structure of the complex to understanding of the biology

    Energy Technology Data Exchange (ETDEWEB)

    Rossmann, Michael G., E-mail: mr@purdue.edu [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Arisaka, Fumio [Graduate School and School of Bioscience and Biotechnology, Tokyo Institute of Technology, 5249 Nagatsuta-cho, Yokohama 226-8501-B39 (Japan); Battisti, Anthony J.; Bowman, Valorie D.; Chipman, Paul R.; Fokine, Andrei; Hafenstein, Susan [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Kanamaru, Shuji [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Graduate School and School of Bioscience and Biotechnology, Tokyo Institute of Technology, 5249 Nagatsuta-cho, Yokohama 226-8501-B39 (Japan); Kostyuchenko, Victor A. [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Mesyanzhinov, Vadim V.; Shneider, Mikhail M. [Laboratory of Molecular Bioengineering, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya Street, Moscow, 117997 (Russian Federation); Morais, Marc C.; Leiman, Petr G. [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Palermo, Laura M.; Parrish, Colin R. [James A. Baker Institute, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853 (United States); Xiao, Chuan [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States)

    2007-01-01

    The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques. The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy (cryo-EM) single-particle reconstructions. Both techniques lean heavily on imposing icosahedral symmetry, thereby obscuring any deviation from the assumed symmetry. However, tailed bacteriophages have icosahedral or prolate icosahedral heads that have one obvious unique vertex where the genome can enter for DNA packaging and exit when infecting a host cell. The presence of the tail allows cryo-EM reconstructions in which the special vertex is used to orient the head in a unique manner. Some very large dsDNA icosahedral viruses also develop special vertices thought to be required for infecting host cells. Similarly, preliminary cryo-EM data for the small ssDNA canine parvovirus complexed with receptor suggests that these viruses, previously considered to be accurately icosahedral, might have some asymmetric properties that generate one preferred receptor-binding site on the viral surface. Comparisons are made between rhinoviruses that bind receptor molecules uniformly to all 60 equivalent binding sites, canine parvovirus, which appears to have a preferred receptor-binding site, and bacteriophage T4, which gains major biological advantages on account of its unique vertex and tail organelle.

  17. From structure of the complex to understanding of the biology

    International Nuclear Information System (INIS)

    Rossmann, Michael G.; Arisaka, Fumio; Battisti, Anthony J.; Bowman, Valorie D.; Chipman, Paul R.; Fokine, Andrei; Hafenstein, Susan; Kanamaru, Shuji; Kostyuchenko, Victor A.; Mesyanzhinov, Vadim V.; Shneider, Mikhail M.; Morais, Marc C.; Leiman, Petr G.; Palermo, Laura M.; Parrish, Colin R.; Xiao, Chuan

    2007-01-01

    The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques. The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy (cryo-EM) single-particle reconstructions. Both techniques lean heavily on imposing icosahedral symmetry, thereby obscuring any deviation from the assumed symmetry. However, tailed bacteriophages have icosahedral or prolate icosahedral heads that have one obvious unique vertex where the genome can enter for DNA packaging and exit when infecting a host cell. The presence of the tail allows cryo-EM reconstructions in which the special vertex is used to orient the head in a unique manner. Some very large dsDNA icosahedral viruses also develop special vertices thought to be required for infecting host cells. Similarly, preliminary cryo-EM data for the small ssDNA canine parvovirus complexed with receptor suggests that these viruses, previously considered to be accurately icosahedral, might have some asymmetric properties that generate one preferred receptor-binding site on the viral surface. Comparisons are made between rhinoviruses that bind receptor molecules uniformly to all 60 equivalent binding sites, canine parvovirus, which appears to have a preferred receptor-binding site, and bacteriophage T4, which gains major biological advantages on account of its unique vertex and tail organelle

  18. Polyphenols from Bee Pollen: Structure, Absorption, Metabolism and Biological Activity

    Directory of Open Access Journals (Sweden)

    Anna Rzepecka-Stojko

    2015-12-01

    Full Text Available Bee pollen constitutes a natural source of antioxidants such as phenolic acids and flavonoids, which are responsible for its biological activity. Research has indicated the correlation between dietary polyphenols and cardioprotective, hepatoprotective, anti-inflammatory, antibacterial, anticancerogenic, immunostimulating, antianaemic effects, as well as their beneficial influence on osseous tissue. The beneficial effects of bee pollen on health result from the presence of phenolic acids and flavonoids which possess anti-inflammatory properties, phytosterol and linolenic acid which play an anticancerogenic role, and polysaccharides which stimulate immunological activity. Polyphenols are absorbed in the alimentary tract, metabolised by CYP450 enzymes, and excreted with urine and faeces. Flavonoids and phenolic acids are characterised by high antioxidative potential, which is closely related to their chemical structure. The high antioxidant potential of phenolic acids is due to the presence and location of hydroxyl groups, a carboxyl group in the immediate vicinity of ortho-diphenolic substituents, and the ethylene group between the phenyl ring and the carboxyl group. As regards flavonoids, essential structural elements are hydroxyl groups at the C5 and C7 positions in the A ring, and at the C3′ and C4′ positions in the B ring, and a hydroxyl group at the C3 position in the C ring. Furthermore, both, the double bond between C2 and C3, and a ketone group at the C4 position in the C ring enhance the antioxidative potential of these compounds. Polyphenols have an ideal chemical structure for scavenging free radicals and for creating chelates with metal ions, which makes them effective antioxidants in vivo.

  19. Determination of fluorine in biological materials: reaction paper.

    Science.gov (United States)

    Ophaug, R

    1994-06-01

    Although the fluorine in human tissues may exist in both inorganic and organic (covalently bound) forms, the inorganic fraction is clearly the most relevant for assessing human exposure to, and utilization of, environmental fluoride. There is now general agreement that the inorganic fraction of total tissue fluorine can be accurately determined by a variety of analytical techniques. One of the basic questions considered at this workshop is whether the analysis of a specific tissue or body fluid can provide an estimate of how much of the fluoride to which an individual is exposed actually enters and accumulates in the body. The analysis of hair and nails has been used as an indicator of exposure and utilization for several trace elements, including fluoride. Due to methodological uncertainties regarding sampling and pre-analysis treatment, however, it is presently not possible clearly to distinguish fluoride which is incorporated into hair and nails during formation (endogenous) from that which becomes associated with the tissues following exposure to the environment (exogenous). Consequently, although the fluoride content of hair and nails is clearly increased by environmental exposure to fluoride, the conclusion that these tissues are suitable indicators of fluoride utilization and accumulation in the body is premature.

  20. Specific determination of clinical and toxicological important substances in biological samples by LC-MS

    International Nuclear Information System (INIS)

    Mitulovic, G.

    2001-02-01

    This thesis of this dissertation is the specific determination of clinical and toxicological important substances in biological samples by LC-MS. Nicotine was determined in serum after application of nicotine plaster and nicotine nasal spray with HPLC-ESI-MS. Cotinine was determined direct in urine with HPLC-ESI-MS. Short time anesthetics were determined in blood and cytostatics were determined in liquor with HPLC-ESI-MS. (botek)

  1. Overcoming barriers to membrane protein structure determination.

    Science.gov (United States)

    Bill, Roslyn M; Henderson, Peter J F; Iwata, So; Kunji, Edmund R S; Michel, Hartmut; Neutze, Richard; Newstead, Simon; Poolman, Bert; Tate, Christopher G; Vogel, Horst

    2011-04-01

    After decades of slow progress, the pace of research on membrane protein structures is beginning to quicken thanks to various improvements in technology, including protein engineering and microfocus X-ray diffraction. Here we review these developments and, where possible, highlight generic new approaches to solving membrane protein structures based on recent technological advances. Rational approaches to overcoming the bottlenecks in the field are urgently required as membrane proteins, which typically comprise ~30% of the proteomes of organisms, are dramatically under-represented in the structural database of the Protein Data Bank.

  2. Single molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update

    Science.gov (United States)

    Widom, Julia R.; Dhakal, Soma; Heinicke, Laurie A.; Walter, Nils G.

    2015-01-01

    Toxicology is the highly interdisciplinary field studying the adverse effects of chemicals on living organisms. It requires sensitive tools to detect such effects. After their initial implementation during the 1990s, single-molecule fluorescence detection tools were quickly recognized for their potential to contribute greatly to many different areas of scientific inquiry. In the intervening time, technical advances in the field have generated ever-improving spatial and temporal resolution, and have enabled the application of single-molecule fluorescence to increasingly complex systems, such as live cells. In this review, we give an overview of the optical components necessary to implement the most common versions of single-molecule fluorescence detection. We then discuss current applications to enzymology and structural studies, systems biology, and nanotechnology, presenting the technical considerations that are unique to each area of study, along with noteworthy recent results. We also highlight future directions that have the potential to revolutionize these areas of study by further exploiting the capabilities of single-molecule fluorescence microscopy. PMID:25212907

  3. determination of verticality of reservoir engineering structure

    African Journals Online (AJOL)

    user

    applications is 3D survey and management of oil and gas facilities and other engineering structures. This recent .... also affect ground water contamination. 2. VERTICALITY ...... The soil, water and concrete in a Reservoir at the foundation bed ...

  4. DETERMINANTS OF FINANCIAL STRUCTURE OF GREEK COMPANIES

    Directory of Open Access Journals (Sweden)

    Gargalis PANAGIOTIS

    2016-06-01

    Full Text Available Capital structure is essential for the survival, growth and performance of a firm. There has been a growing interest worldwide in identifying the factors associated with debt leverage. This article aims to investigate the factors affecting the capital structure of companies listed on the Athens Stock Exchange (ASE. The data set used is composed of indicators reflecting the financial position and performance of 40 firms listed on the ASE in 2014. Using a regression model we estimate in what extent the financial structure of companies is affected by performance indicators and other specific factors like the field of activity or the size of the firms. The results obtained show an important influence of share of tangible assets in total assets of the company on the financial leverage, as main variable selected in order to reflect the capital structure of Greek companies.

  5. Labelling of biological structures with technetium 99 m

    International Nuclear Information System (INIS)

    Bernardo Filho, M.

    1988-01-01

    The labelling of red blood cells (RBC) with technetium 99m ( 99m Tc) depends on several factors, as the stannous ion (Sn ++ ) concentration, the time and temperature of incubation, the anticoagulant utilized, the presence of plasma proteins (PP) and others. Although the blinding of 99m Tc with hemoglobin and PP are similar, they appear to have specific characteristics as demonstrated by precipitation with alcohol, acetone, trichloroacetic acid, hydrochloric acid and mercury chloride. The bacterial cultures labeled with Technetium- 99m , at optimal Sn ++ ion concentration, presents a large stability and their viability is not altered by this treatment. The electrophoretic mobility, the hydrophobicity, the cationized ferritin distribution and the adherence to human buccal epithelial cells are not modified either. The possibility of labelling with 99m Tc of planaria and cercariae of Schistossoma mansoni evaluative cycle increases the utilization of this radionuclide to an experimental level. The results described with the labelling of these biological structures with 99m Tc demonstrated that stable labeled and viable operations are obtained. (author)

  6. Analysis of the causes and recommendations on elimination of biological damage of structures during the repair and reconstruction of the State Biological Museum in Moscow.

    Directory of Open Access Journals (Sweden)

    Kamskov Victor

    2017-01-01

    Full Text Available The article presents the results of mycological research on buildings of the State Biological Museum located in Moscow. The problems have been considered as for a complex of buildings of the State Biological Museum built in the late nineteenth century which, to the present time, has been operated almost in its original form. Over time, the building maintenance conditions have worsened, in particular because of construction of high-rise buildings in the immediate vicinity of the museum, as well as construction of a greenhouse above the underground passage tunnel between buildings 1 and 2. Over the years, the temperature gradients, high humidity, wear and damage of wall waterproofing and foundations have caused leaks in the underpass tunnel and the biological corrosion of stone, wood and metal structures in indoor exhibition halls. In this connection, part of the survey was to determine the types and size of biological lesions in structures, determination of the causes of biological damage, and the development of measures to eliminate the mycological problems during repair and reconstruction works in the museum.

  7. Science achievement determinants: factorial structure of family ...

    African Journals Online (AJOL)

    The family plays an important role in determining the academic achievement ... parents' assistance, expectation, and encouragement in their children's mathematics ... suggested that cultural upbringing is a strong factor contributing to the.

  8. Structural determinants in the bulk heterojunction.

    Science.gov (United States)

    Acocella, Angela; Höfinger, Siegfried; Haunschmid, Ernst; Pop, Sergiu C; Narumi, Tetsu; Yasuoka, Kenji; Yasui, Masato; Zerbetto, Francesco

    2018-02-21

    Photovoltaics is one of the key areas in renewable energy research with remarkable progress made every year. Here we consider the case of a photoactive material and study its structural composition and the resulting consequences for the fundamental processes driving solar energy conversion. A multiscale approach is used to characterize essential molecular properties of the light-absorbing layer. A selection of bulk-representative pairs of donor/acceptor molecules is extracted from the molecular dynamics simulation of the bulk heterojunction and analyzed at increasing levels of detail. Significantly increased ground state energies together with an array of additional structural characteristics are identified that all point towards an auxiliary role of the material's structural organization in mediating charge-transfer and -separation. Mechanistic studies of the type presented here can provide important insights into fundamental principles governing solar energy conversion in next-generation photovoltaic devices.

  9. Some structural determinants of melody recall.

    Science.gov (United States)

    Boltz, M

    1991-05-01

    Sophisticated musicians were asked to recall, using musical notation, a set of unfamiliar folk tunes that varied in rhythmic structure and referents of tonality. The results showed that memory was facilitated by tonic triad members marking phrase endings, but only when their presence was highlighted by a corresponding pattern of temporal accents. Conversely, recall significantly declined when tonal information was either absent or obscured by rhythmic structure. Error analyses further revealed that the retention of overall pitch contour and information at phrase ending points varied as a function of these manipulations. The results are discussed in terms of a framework that links the acts of perceiving and remembering to a common attentional scheme.

  10. Overcoming barriers to membrane protein structure determination

    NARCIS (Netherlands)

    Bill, Roslyn M.; Henderson, Peter J. F.; Iwata, So; Kunji, Edmund R. S.; Michel, Hartmut; Neutze, Richard; Newstead, Simon; Poolman, Bert; Tate, Christopher G.; Vogel, Horst

    After decades of slow progress, the pace of research on membrane protein structures is beginning to quicken thanks to various improvements in technology, including protein engineering and microfocus X-ray diffraction. Here we review these developments and, where possible, highlight generic new

  11. Structural determination and gynecological tumor diagnosis using ...

    African Journals Online (AJOL)

    covalent bonding patterns and branched structures. Studies have shown that changes in protein glycosylation at the cell surface during tumorigenesis are closely related to the occurrence and development of some cancers, including pancreatic cancer, mammary cancer, prostatic cancer, colon cancer, and gastric cancer [1].

  12. Determining the structure of Carbon-60

    International Nuclear Information System (INIS)

    Wif, D.

    1994-01-01

    Carbon-60 is the most stable and best known of the carbon cage structures known collectively as the fullerenes. It is a remarkable molecule that forms a fascinating solid. Although the molecular shape of C sub 6 sub 0 is familiar - it is simply the shape of a soccer ball with 12 pentagons and 20 hexagons - the manner in which it forms a crystal structure is by no means obvious. This talk will focus on the insights which neutron scattering at ISIS has brought to our understanding of solid C sub6 sub 0. At room temperature, the structure may be regarded as forming as essentially ideal cubic-close packed molecular b ubble-raft : each molecule is reorienting so rapidly that a time-averaged picture, over as little as a nanosecond, reveals a closely spherical shell of atomic density. At 260 K, a rather unusual structural transition occurs. The molecules order but still retain cubic symmetry. Although this may not appear to be a rather dramatic change, detailed considerations show that a profound transition has occurred that bears close similarities to a solid-liquid phase transition but in two dimensions. Below 260 K, reorientation still occurs but at a dramatically reduced rate as the temperature is lowered. Indeed at around 90 K, The reorientation is so slow that thermodynamic equilibrium cannot be achieved in a reasonable timescale an orientational glass transition occurs. Although the behaviour of solid C sub 6 sub 0 undergoes dramatic changes as a function of temperature, a coherent description has evolved in which neutron scattering plays a central role. Close analogies are to be found in the study of systems as diverse as solid H sub 2 and human-rhinovirus structures. These analogies and the central role played by neutron scattering at ISIS will be emphasised in this paper. 5 figs., 10 refs. (author)

  13. Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea.

    Science.gov (United States)

    Tolar, Bradley B; Herrmann, Jonathan; Bargar, John R; van den Bedem, Henry; Wakatsuki, Soichi; Francis, Christopher A

    2017-10-01

    Knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowledge of key N-cycling enzymes from ecologically relevant ammonia oxidizers is unfortunately extremely limited. Here, we discuss the challenges and opportunities for examining the ecology of ammonia-oxidizing organisms, particularly uncultivated Thaumarchaeota, through (meta)genome-driven structural biology of the enzymes ammonia monooxygenase (AMO) and nitrite reductase (NirK). © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  14. Vascular structure determines pulmonary blood flow distribution

    Science.gov (United States)

    Hlastala, M. P.; Glenny, R. W.

    1999-01-01

    Scientific knowledge develops through the evolution of new concepts. This process is usually driven by new methodologies that provide observations not previously available. Understanding of pulmonary blood flow determinants advanced significantly in the 1960s and is now changing rapidly again, because of increased spatial resolution of regional pulmonary blood flow measurements.

  15. Flowering biology and nectary structure of Melissa officinalis L.

    Directory of Open Access Journals (Sweden)

    Mirosława Chwil

    2012-12-01

    Full Text Available The present study on lemon balm (Melissa officinalis L. covered flowering biology, monitoring of pollinating insects and floral nectary structure. The micromorphology of epidermal cells of the nectary was investigated using scanning electron microscopy. The nectariferous tissues were observed using light microscopy based on semi-thin sections. Lemon balm flowered from the second decade of June until September. Buds opened from early morning hours until noon. Flowers lived for 24 hours, on the average. Their primary pollinator was the honey bee. The beginning of nectar secretion was found to be at the bud swell stage. The automorphic nectary forms a disc with four protrusions at the base of the nectary. Three smaller ones and one larger than the other ones were distinguished among them. No stomata were found on the lower protuberances, whereas on the highest part anomocytic stomata were present, the number of which was 15. The stomata exhibited different development stages and they were situated above other epidermal cells. In their outline, they were ellipsoidally shaped (18 × 23 µm and they had average-sized cuticular ledges. They produced a smooth cuticle and wax granules. In cross section, the nectary tissues were composed of a singlelayered epidermis and 9 - 11 layers of the nectary parenchyma. Their thickness was 198 µm. In longitudinal section, the height of the nectary was within a range of 354 - 404 µm. The epidermal cells produced thin outer cell walls. Some of them were completely filled with strongly stained cytoplasm, whereas others showed a high degree of vacuolisation. But the nectary parenchyma cells were marked by poorly stained cytoplasm, a large nucleus and vacuolisation of varying degree.

  16. An independent accurate reference method for the determination of chromium in biological materials

    NARCIS (Netherlands)

    Lagerwaard, A.; Woittiez, J.R.W.; de Goeij, J.J.M.

    1994-01-01

    A method for the determination of Cr in biological materials with high accuracy is reported for use as an independent reference method. It is based on radiochemical neutron activation analysis (RNAA) in combination with an individual yield determination based on the online yield principle. A

  17. X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

    Science.gov (United States)

    Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

    2016-04-01

    Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

  18. Biyoloji Öğretmen Adaylarının “Bakteri” Konusundaki Bilişsel Yapılarının Ve Alternatif Kavramlarının Belirlenmesi Determining Biology Student Teachers’ Cognitive Structure And Alternative Concepts On The Concept Of “Bacteria”

    Directory of Open Access Journals (Sweden)

    Hakan KURT

    2013-09-01

    Full Text Available To understand how students transfer knowledge to their minds and how they structure this knowledge is one of the most important issues that researchers are interested in. Constructive learning approach indicates that individuals construct knowledge actively through associating this knowledge with pre-existing knowledge and previous experiences (Anderson 1992; Bodner 1986; Mills, Shaw, Van Horne, Zhang and Boughman, 2008. According to this approach, due to the associations with previous experiences, the existing cognitive structures in mind affect individuals' perceptions of new events and the new cognitive structures that they will construct. It is, then, possible that a weak cognitive structure will affect the process of constructing new knowledge in mind adversely, and thus, leading to failure to construct new knowledge meaningfully (Tsai and Huang 2002; Vosniadou, Ioannides, Dimitrakopoulou and Papademetriou, 2001.In this respect, rather than merely dealing with what knowledge students have, researchers have headed towards several techniques (Vance, Miller and Hand, 1995. Bahar (2003 provides these strategies as follows: word association, structured grid, diagnostic tree, concept maps, texts of conceptual change, analogy, and predict-observe-explain. Of the techniques that investigate students’ cognitive structure, word association techniques is the most commonly used and oldest one, which was used as a data collection instrument in this study (Bahar, Johnstone and Sutcliffe, 1999; Hovardas and Korfiatis, 2006; Özatlı and Bahar, 2010; White and Gunstone, 2000. The aim of the current study is to determine biology student teachers’ cognitive structure on the concept of bacteria. However, to the best knowledge of the author, there is not any study in the literature that uses the free word association test and the drawing technique to investigate biology student teachers’ cognitive structure on the concept of bacteria.Qualitative research

  19. Strategies for structuring interdisciplinary education in Systems Biology

    DEFF Research Database (Denmark)

    Cvijovic, Marija; Höfer, Thomas; Aćimović, Jure

    2016-01-01

    function by employing experimental data, mathematical models and computational simulations. As Systems Biology is inherently multidisciplinary, education within this field meets numerous hurdles including departmental barriers, availability of all required expertise locally, appropriate teaching material...... and example curricula. As university education at the Bachelor’s level is traditionally built upon disciplinary degrees, we believe that the most effective way to implement education in Systems Biology would be at the Master’s level, as it offers a more flexible framework. Our team of experts and active...... performers of Systems Biology education suggest here (i) a definition of the skills that students should acquire within a Master’s programme in Systems Biology, (ii) a possible basic educational curriculum with flexibility to adjust to different application areas and local research strengths, (iii...

  20. Three-Dimensional Structure Determination of Botulinum Toxin

    National Research Council Canada - National Science Library

    Stevens, Ray

    1997-01-01

    ...) Based on the structure of the neurotoxin, understand the toxins mechanism of action. We have accomplished the first goal of determining the three-dimensional structure of the 150 kD botulinum neurotoxin serotype...

  1. Three-Dimensional Structure Determination of Botulinum Toxin

    National Research Council Canada - National Science Library

    Stevens, Ray

    1998-01-01

    ...) Based on the structure of the neurotoxin, understand the toxins mechanism of action. We have accomplished the first goal of determining the three-dimensional structure of the 150 kD botulinum neurotoxin serotype...

  2. The chemical structures, plant origins, ethnobotany and biological activities of homoisoflavanones.

    Science.gov (United States)

    du Toit, Karen; Drewes, Siegfried E; Bodenstein, Johannes

    2010-03-01

    This work reviews the four basic structural types of homoisoflavanones. The relationships between the various structures of homoisoflavanones and their plant origins, ethnobotany and biological activities are put into perspective.

  3. The determinants of capital structure: evidence from Dutch panel data

    OpenAIRE

    Chen, Linda H.; Lensink, Robert; Sterken, Elmer

    1999-01-01

    This paper studies the determinants of capital structure choice of Dutch firms. Our main objective is to investigate whether and to what extent the main capital structure theories can explain capital structure choice of Dutch firms. A better understanding of the capital structure determinants in a rela-tively small yet open industrialized economy is essential not only for enrich-ing empirical studies in this field, but also for the purpose of cross country asset evaluation. By estimating a pa...

  4. The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.

    Science.gov (United States)

    Rose, Peter W; Prlić, Andreas; Bi, Chunxiao; Bluhm, Wolfgang F; Christie, Cole H; Dutta, Shuchismita; Green, Rachel Kramer; Goodsell, David S; Westbrook, John D; Woo, Jesse; Young, Jasmine; Zardecki, Christine; Berman, Helen M; Bourne, Philip E; Burley, Stephen K

    2015-01-01

    The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. Semiexperimental equilibrium structures for building blocks of organic and biological molecules: the B2PLYP route.

    Science.gov (United States)

    Penocchio, Emanuele; Piccardo, Matteo; Barone, Vincenzo

    2015-10-13

    The B2PLYP double hybrid functional, coupled with the correlation-consistent triple-ζ cc-pVTZ (VTZ) basis set, has been validated in the framework of the semiexperimental (SE) approach for deriving accurate equilibrium structures of molecules containing up to 15 atoms. A systematic comparison between new B2PLYP/VTZ results and several equilibrium SE structures previously determined at other levels, in particular B3LYP/SNSD and CCSD(T) with various basis sets, has put in evidence the accuracy and the remarkable stability of such model chemistry for both equilibrium structures and vibrational corrections. New SE equilibrium structures for phenylacetylene, pyruvic acid, peroxyformic acid, and phenyl radical are discussed and compared with literature data. Particular attention has been devoted to the discussion of systems for which lack of sufficient experimental data prevents a complete SE determination. In order to obtain an accurate equilibrium SE structure for these situations, the so-called templating molecule approach is discussed and generalized with respect to our previous work. Important applications are those involving biological building blocks, like uracil and thiouracil. In addition, for more general situations the linear regression approach has been proposed and validated.

  6. 75 FR 33312 - Indexing Structured Product Labeling for Human Prescription Drug and Biological Products; Request...

    Science.gov (United States)

    2010-06-11

    ...] Indexing Structured Product Labeling for Human Prescription Drug and Biological Products; Request for... Biologics Evaluation and Research (CBER) are indexing certain categories of information in product labeling for use as terms to search repositories of approved prescription medical product structured product...

  7. Determining building interior structures using compressive sensing

    Science.gov (United States)

    Lagunas, Eva; Amin, Moeness G.; Ahmad, Fauzia; Nájar, Montse

    2013-04-01

    We consider imaging of the building interior structures using compressive sensing (CS) with applications to through-the-wall imaging and urban sensing. We consider a monostatic synthetic aperture radar imaging system employing stepped frequency waveform. The proposed approach exploits prior information of building construction practices to form an appropriate sparse representation of the building interior layout. We devise a dictionary of possible wall locations, which is consistent with the fact that interior walls are typically parallel or perpendicular to the front wall. The dictionary accounts for the dominant normal angle reflections from exterior and interior walls for the monostatic imaging system. CS is applied to a reduced set of observations to recover the true positions of the walls. Additional information about interior walls can be obtained using a dictionary of possible corner reflectors, which is the response of the junction of two walls. Supporting results based on simulation and laboratory experiments are provided. It is shown that the proposed sparsifying basis outperforms the conventional through-the-wall CS model, the wavelet sparsifying basis, and the block sparse model for building interior layout detection.

  8. Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs

    Directory of Open Access Journals (Sweden)

    Theis Fabian J

    2010-10-01

    Full Text Available Abstract Background Extensive and automated data integration in bioinformatics facilitates the construction of large, complex biological networks. However, the challenge lies in the interpretation of these networks. While most research focuses on the unipartite or bipartite case, we address the more general but common situation of k-partite graphs. These graphs contain k different node types and links are only allowed between nodes of different types. In order to reveal their structural organization and describe the contained information in a more coarse-grained fashion, we ask how to detect clusters within each node type. Results Since entities in biological networks regularly have more than one function and hence participate in more than one cluster, we developed a k-partite graph partitioning algorithm that allows for overlapping (fuzzy clusters. It determines for each node a degree of membership to each cluster. Moreover, the algorithm estimates a weighted k-partite graph that connects the extracted clusters. Our method is fast and efficient, mimicking the multiplicative update rules commonly employed in algorithms for non-negative matrix factorization. It facilitates the decomposition of networks on a chosen scale and therefore allows for analysis and interpretation of structures on various resolution levels. Applying our algorithm to a tripartite disease-gene-protein complex network, we were able to structure this graph on a large scale into clusters that are functionally correlated and biologically meaningful. Locally, smaller clusters enabled reclassification or annotation of the clusters' elements. We exemplified this for the transcription factor MECP2. Conclusions In order to cope with the overwhelming amount of information available from biomedical literature, we need to tackle the challenge of finding structures in large networks with nodes of multiple types. To this end, we presented a novel fuzzy k-partite graph partitioning

  9. Configuration of biological wastewater treatment line and influent composition as the main factors driving bacterial community structure of activated sludge

    OpenAIRE

    Jaranowska, Paulina; Cydzik-Kwiatkowska, Agnieszka; Zieli?ska, Magdalena

    2013-01-01

    The structure of microbial consortia in wastewater treatment facilities is a resultant of environmental conditions created by the operational parameters of the purification process. In the research, activated sludge from nine Polish wastewater treatment plants (WWTPs) was investigated at a molecular level to determine the impact of the complexity of biological treatment line and the influent composition on the species structure and the diversity of bacterial consortia. The community fingerpri...

  10. Microwave Determination of the Structure of Pyridine

    Energy Technology Data Exchange (ETDEWEB)

    Bak, B.; Hansen, L.; Rastrup-Andersen, J. [Chemical Laboratory of the University of Copenhagen, Copenhagen (Denmark)

    1954-12-15

    2‐, 3‐, and 4‐mono‐deutero‐pyridine have been prepared and the microwave spectra recorded. For each of the isotopic species 11—12 transitions (Q‐ and R‐branch lines) were localized, a number of which could be identified by their Stark effect. For all three species rotational constants of high precision were calculated. The material so provided in connection with known rotational constants for ordinary pyridine is insufficient for a complete determination of the ten geometrical parameters of the molecule. Seven models with a choice of C – H distances close to the correct value (1.075‐1.085 A) were considered one of which was shown to be consistent with electron‐diffraction work and current valence theory. In this model d(N – C(2)) = 1.340±0.005; d(C(2) – C(3)) = 1.390±0.005; d(C(3) – C(4)) = 1.400±0.005 A. The valence angles in the aromatic ring (starting with the C(6) – N – C(2) angle) are: 116° 42′; 124° 00′; 118° 36′; 118° 06′.

  11. Quantitative HPLC determination of [99mTc]-pertechnetate in radiopharmaceuticals and biological samples: Pt. 1

    International Nuclear Information System (INIS)

    Tianze Zhou; Hirth, W.W.; Heineman, W.R.; Deutsch, Edward

    1988-01-01

    Techniques have been developed which allow HPLC (high performance liquid chromatography) to be used for the quantitative determination of [ 99m Tc]pertechnetate in radiopharmaceuticals and biological samples. An instrumental technique accounts for 99m Tc species which do not elute from the HPLC column, while a chemical technique obviates interferences caused by Sn(II). These two techniques are incorporated into an anion exchange HPLC procedure which is applied to the determination of [ 99m Tc]pertechnetate in 99m Tc-diphosphonate radiopharmaceuticals and biological samples. (author)

  12. Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

    Science.gov (United States)

    Westbrook, John D; Feng, Zukang; Persikova, Irina; Sala, Raul; Sen, Sanchayita; Berrisford, John M; Swaminathan, G Jawahar; Oldfield, Thomas J; Gutmanas, Aleksandras; Igarashi, Reiko; Armstrong, David R; Baskaran, Kumaran; Chen, Li; Chen, Minyu; Clark, Alice R; Di Costanzo, Luigi; Dimitropoulos, Dimitris; Gao, Guanghua; Ghosh, Sutapa; Gore, Swanand; Guranovic, Vladimir; Hendrickx, Pieter M S; Hudson, Brian P; Ikegawa, Yasuyo; Kengaku, Yumiko; Lawson, Catherine L; Liang, Yuhe; Mak, Lora; Mukhopadhyay, Abhik; Narayanan, Buvaneswari; Nishiyama, Kayoko; Patwardhan, Ardan; Sahni, Gaurav; Sanz-García, Eduardo; Sato, Junko; Sekharan, Monica R; Shao, Chenghua; Smart, Oliver S; Tan, Lihua; van Ginkel, Glen; Yang, Huanwang; Zhuravleva, Marina A; Markley, John L; Nakamura, Haruki; Kurisu, Genji; Kleywegt, Gerard J; Velankar, Sameer; Berman, Helen M; Burley, Stephen K

    2018-01-01

    Abstract The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands. The worldwide PDB (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR principles: Findability, Accessibility, Interoperability and Reusability. The wwPDB recently developed OneDep, a unified tool for deposition, validation and biocuration of structures of biological macromolecules. All data deposited to the PDB undergo critical review by wwPDB Biocurators. This article outlines the importance of biocuration for structural biology data deposited to the PDB and describes wwPDB biocuration processes and the role of expert Biocurators in sustaining a high-quality archive. Structural data submitted to the PDB are examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources and validated for scientific/technical accuracy. We illustrate how biocuration is integral to PDB data archiving, as it facilitates accurate, consistent and comprehensive representation of biological structure data, allowing efficient and effective usage by research scientists, educators, students and the curious public worldwide. Database URL: https://www.wwpdb.org/ PMID:29688351

  13. Biological Membrane Ion Channels Dynamics, Structure, and Applications

    CERN Document Server

    Chung, Shin-Ho; Krishnamurthy, Vikram

    2007-01-01

    Ion channels are biological nanotubes that are formed by membrane proteins. Because ion channels regulate all electrical activities in living cells, understanding their mechanisms at a molecular level is a fundamental problem in biology. This book deals with recent breakthroughs in ion-channel research that have been brought about by the combined effort of experimental biophysicists and computational physicists, who together are beginning to unravel the story of these exquisitely designed biomolecules. With chapters by leading experts, the book is aimed at researchers in nanodevices and biosensors, as well as advanced undergraduate and graduate students in biology and the physical sciences. Key Features Presents the latest information on the molecular mechanisms of ion permeation through membrane ion channels Uses schematic diagrams to illustrate important concepts in biophysics Written by leading researchers in the area of ion channel investigations

  14. Micro-scale NMR Experiments for Monitoring the Optimization of Membrane Protein Solutions for Structural Biology.

    Science.gov (United States)

    Horst, Reto; Wüthrich, Kurt

    2015-07-20

    Reconstitution of integral membrane proteins (IMP) in aqueous solutions of detergent micelles has been extensively used in structural biology, using either X-ray crystallography or NMR in solution. Further progress could be achieved by establishing a rational basis for the selection of detergent and buffer conditions, since the stringent bottleneck that slows down the structural biology of IMPs is the preparation of diffracting crystals or concentrated solutions of stable isotope labeled IMPs. Here, we describe procedures to monitor the quality of aqueous solutions of [ 2 H, 15 N]-labeled IMPs reconstituted in detergent micelles. This approach has been developed for studies of β-barrel IMPs, where it was successfully applied for numerous NMR structure determinations, and it has also been adapted for use with α-helical IMPs, in particular GPCRs, in guiding crystallization trials and optimizing samples for NMR studies (Horst et al ., 2013). 2D [ 15 N, 1 H]-correlation maps are used as "fingerprints" to assess the foldedness of the IMP in solution. For promising samples, these "inexpensive" data are then supplemented with measurements of the translational and rotational diffusion coefficients, which give information on the shape and size of the IMP/detergent mixed micelles. Using microcoil equipment for these NMR experiments enables data collection with only micrograms of protein and detergent. This makes serial screens of variable solution conditions viable, enabling the optimization of parameters such as the detergent concentration, sample temperature, pH and the composition of the buffer.

  15. The structural biology center at the APS: an integrated user facility for macromolecular crystallography

    International Nuclear Information System (INIS)

    Rosenbaum, G.; Westbrook, E.M.

    1997-01-01

    The Structural Biology Center (SBC) has developed and operates a sector (undulator and bending magnet) of the APS as a user facility for macromolecular crystallography. Crystallographically determined structures of proteins, nucleic acids and their complexes with proteins, viruses, and complexes between macromolecules and small ligands have become of central importance in molecular and cellular biology. Major design goals were to make the extremely high brilliance of the APS available for brilliance limited studies, and to achieve a high throughput of less demanding studies, as well as optimization for MAS-phasing. Crystal samples will include extremely small crystals, crystals with large unit cells (viruses, ribosomes, etc.) and ensembles of closely similar crystal structures for drug design, protein engineering, etc. Data are recorded on a 3000x3000 pixel CCD-area detector (optionally on image plates). The x-ray optics of both beamlines has been designed to produce a highly demagnified image of the source in order to match the focal size with the sizes of the sample and the resolution element of the detector. Vertical focusing is achieved by a flat, cylindrically bent mirror. Horizontal focusing is achieved by sagitally bending the second crystal of the double crystal monochromator. Monochromatic fluxes of 1.3 * 10 13 ph/s into focal sizes of 0.08 mm (horizontal)x0.04 mm (vertical) FWHM (flux density 3.5 * 10 15 ph/s/mm 2 ) have been recorded.copyright 1997 American Institute of Physics

  16. The in vivo structure of biological membranes and evidence for lipid domains

    Energy Technology Data Exchange (ETDEWEB)

    Nickels, Jonathan D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States); Chatterjee, Sneha [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Stanley, Christopher B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Qian, Shuo [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Cheng, Xiaolin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States); Myles, Dean A. A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Standaert, Robert F. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States); Elkins, James G. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States); Katsaras, John [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States); Lopez, Daniel [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)

    2017-05-23

    Examining the fundamental structure and processes of living cells at the nanoscale poses a unique analytical challenge, as cells are dynamic, chemically diverse, and fragile. A case in point is the cell membrane, which is too small to be seen directly with optical microscopy and provides little observational contrast for other methods. As a consequence, nanoscale characterization of the membrane has been performed ex vivo or in the presence of exogenous labels used to enhance contrast and impart specificity. Here, we introduce an isotopic labeling strategy in the gram-positive bacterium Bacillus subtilis to investigate the nanoscale structure and organization of its plasma membrane in vivo. Through genetic and chemical manipulation of the organism, we labeled the cell and its membrane independently with specific amounts of hydrogen (H) and deuterium (D). These isotopes have different neutron scattering properties without altering the chemical composition of the cells. From neutron scattering spectra, we confirmed that the B. subtilis cell membrane is lamellar and determined that its average hydrophobic thickness is 24.3 ± 0.9 Ångstroms (Å). Furthermore, by creating neutron contrast within the plane of the membrane using a mixture of H- and D-fatty acids, we detected lateral features smaller than 40 nm that are consistent with the notion of lipid rafts. These experiments—performed under biologically relevant conditions—answer long-standing questions in membrane biology and illustrate a fundamentally new approach for systematic in vivo investigations of cell membrane structure.

  17. Protein structure determination by exhaustive search of Protein Data Bank derived databases.

    Science.gov (United States)

    Stokes-Rees, Ian; Sliz, Piotr

    2010-12-14

    Parallel sequence and structure alignment tools have become ubiquitous and invaluable at all levels in the study of biological systems. We demonstrate the application and utility of this same parallel search paradigm to the process of protein structure determination, benefitting from the large and growing corpus of known structures. Such searches were previously computationally intractable. Through the method of Wide Search Molecular Replacement, developed here, they can be completed in a few hours with the aide of national-scale federated cyberinfrastructure. By dramatically expanding the range of models considered for structure determination, we show that small (less than 12% structural coverage) and low sequence identity (less than 20% identity) template structures can be identified through multidimensional template scoring metrics and used for structure determination. Many new macromolecular complexes can benefit significantly from such a technique due to the lack of known homologous protein folds or sequences. We demonstrate the effectiveness of the method by determining the structure of a full-length p97 homologue from Trichoplusia ni. Example cases with the MHC/T-cell receptor complex and the EmoB protein provide systematic estimates of minimum sequence identity, structure coverage, and structural similarity required for this method to succeed. We describe how this structure-search approach and other novel computationally intensive workflows are made tractable through integration with the US national computational cyberinfrastructure, allowing, for example, rapid processing of the entire Structural Classification of Proteins protein fragment database.

  18. Structural and Biological Assessment of Zinc Doped Hydroxyapatite Nanoparticles

    OpenAIRE

    Popa , Cristina ,; Deniaud , Aurélien; Michaud-Soret , Isabelle; Guégan , Régis; Motelica-Heino , Mikael; Predoi , Daniela

    2016-01-01

    International audience; The aim of the current research work was to study the physicochemical and biological properties of synthesized zinc doped hydroxyapatite (ZnHAp) nanoparticles with Zn concentrations í µí±¥ Zn = 0 (HAp), í µí±¥ Zn = 0.07 (7ZnHAp), and í µí±¥ Zn = 0.1 (10ZnHAp) for potential use in biological applications. The morphology, size, compositions, and incorporation of zinc into hydroxyapatite were characterized by scanning electron microscopy (SEM), transmission electron micro...

  19. The Protein Data Bank and Its Uses in Structural Biology Education

    Directory of Open Access Journals (Sweden)

    Judith Voet

    2004-05-01

    Full Text Available The Protein Data Bank (PDB is a repository for the structures of proteins and nucleic acids. Itcontains les of their 3-dimensional coordinates, information on how these structures were determinedand references to the journal articles describing them. The PDB was established in 1971 by HelenBerman (it s present director and has grown exponentially so that it now contains 25,000 data lesrepresenting X-ray crystallographic, NMR and other structure determinations. Database queryingand data miningtools and resources at the PDB make it possible to search, compare and infer orpredict the function of newly identied proteins. Computer graphics capabilities make it possible foranyone to easily visualize and study the structural data. The capability to present beautiful graphicrepresentations of the 3-dimesnional structures of proteins and nucleic acids has been a boon to theeducation community. Communicating an understanding of these structures and the chemical forcesdetermining them and their interactions is one of the major aims of biochemistry and molecular biologyeducation. The ability to teach these principles visually has made a great dierence in our abilityto excite our students and provide them with physical interpretations for some abstract concepts inbiochemistry and molecular biology. In this talk we will explore some of the ways that the education community uses the PDB.

  20. Determination of atomic cluster structure with cluster fusion algorithm

    DEFF Research Database (Denmark)

    Obolensky, Oleg I.; Solov'yov, Ilia; Solov'yov, Andrey V.

    2005-01-01

    We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters.......We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters....

  1. [Environmental and biological determinants of neuropsychomotor development in a sample of children in Canoas/RS].

    Science.gov (United States)

    Pilz, Elsa Maria Luz; Schermann, Lígia Braun

    2007-01-01

    The object of this study is to determine the prevalence of potential delays in neuropsychomotor development and their possible association with, on one hand, environmental and biological factors, and maternal competence on the other, in a sample of children up to six years old living in Canoas, in Rio Grande do Sul state. A questionnaire was submitted to mothers including questions on social, economic and reproduction factors; child's conditions at birth; child's pathologies; family structure; child care and elements on maternal competence. The potential for neuropsychomotor development delay was assessed by the Denver II Test. Forty clusters were visited in Canoas, a city in Rio Grande do Sul state, in accordance with the cluster probabilistic sampling process. From 197 children assessed by this analytical cross-section study, there was a 27% (n=53) prevalence of potential delay in neuropsychomotor development. The multivariate analysis showed that factors associated with potential development delays were: low income (or = 9,3); mothers with less than 18-month intervals between pregnancies (or=3,9) ; and lack of support from child's father (or=7,0). These results support the importance of implementing income generating programs, health education, and family planning in order to prevent child development delays.

  2. Non-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination.

    Science.gov (United States)

    Didenko, Tatiana; Proudfoot, Andrew; Dutta, Samit Kumar; Serrano, Pedro; Wüthrich, Kurt

    2015-08-24

    High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in the efficiency of NMR structure determination by advances in NMR experiments and automation of data handling therefore attracts continued interest. Here, non-uniform sampling (NUS) of 3D heteronuclear-resolved [(1)H,(1)H]-NOESY data yielded two- to three-fold savings of instrument time for structure determinations of soluble proteins. With the 152-residue protein NP_372339.1 from Staphylococcus aureus and the 71-residue protein NP_346341.1 from Streptococcus pneumonia we show that high-quality structures can be obtained with NUS NMR data, which are equally well amenable to robust automated analysis as the corresponding uniformly sampled data. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Polysaccharies of higher fungi: Biological role, structure and antioxidative activity

    NARCIS (Netherlands)

    Kozarski, M.S.; Klaus, A.; Niksic, M.; Griensven, van L.J.L.D.; Vrvic, M.M.; Jakovljevic, D.M.

    2014-01-01

    The fungal polysaccharides attract a lot of attention due to their multiple challenging bio-logical properties, such as: anti-tumor, anti-viral, anticomplementary, anticoagulant, hypo-lipidemic, immunomodulatory and immune-stimulatory activities, which all together make them suitable for application

  4. Systems Biology Markup Language (SBML Level 2 Version 5: Structures and Facilities for Model Definitions

    Directory of Open Access Journals (Sweden)

    Hucka Michael

    2015-06-01

    Full Text Available Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

  5. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

    Science.gov (United States)

    Hucka, Michael; Bergmann, Frank T; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M; Le Novère, Nicolas; Myers, Chris J; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Waltemath, Dagmar; Wilkinson, Darren J

    2015-09-04

    Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org.

  6. Simultaneous Determination of Arsenic, Manganese, and Selenium in Biological Materials by Neutron-Activation Analysis

    DEFF Research Database (Denmark)

    Heydorn, Kaj; Damsgaard, Else

    1973-01-01

    A new method was developed for the simultaneous determination of arsenic, manganese, and selenium in biological material by thermal-neutron activation analysis. The use of 81 mSe as indicator for selenium permitted a reduction of activation time to 1 hr for a 1 g sample, and the possibility of loss...

  7. Selenium determination in biological material by atomic absorption spectrophotometry in graphite furnace and using vapor generation

    International Nuclear Information System (INIS)

    Carvalho Vidal, M. de F. de.

    1984-01-01

    The applicability of the atomic absorption spectrophotometry to the determination of selenium in biological material using vapor generation and electrothermal atomization in the graphite furnace was investigated. Instrumental parameters and the analytical conditions of the methods were studied. Decomposition methods for the samples were tested, and the combustion in the Wickbold apparatus was chosen. (author) [pt

  8. Genetic Diseases and Genetic Determinism Models in French Secondary School Biology Textbooks

    Science.gov (United States)

    Castera, Jeremy; Bruguiere, Catherine; Clement, Pierre

    2008-01-01

    The presentation of genetic diseases in French secondary school biology textbooks is analysed to determine the major conceptions taught in the field of human genetics. References to genetic diseases, and the processes by which they are explained (monogeny, polygeny, chromosomal anomaly and environmental influence) are studied in recent French…

  9. Determination of carbon-14 content in biological materials and its application to vinegars

    International Nuclear Information System (INIS)

    Grau Malonda, A.; Martin-Casallo, M.T.; Chereguini, S.

    1976-01-01

    A radiometric method for the determination of synthetic acetic acid in the presence of biological vinegar has been developed. The activity of 1 4C is measured by liquid scintillation counting and the sensitivity is optimized by taking into account the composition of several liquid scintillation solutions and the concentration of their components. (author) [es

  10. Determination of trace elements in biological material by neutron activation analysis

    International Nuclear Information System (INIS)

    Tran Van, L.; Teherani, D.K.

    1989-01-01

    Eighteen trace elements in biological materials [grass (Imperata cylindrica), mimosa plant (Mimosa pudica), rice] by neutron activation method were determined. In the comparative analysis the content of the same element was different in each material, although they were collected at the same place and the same sampling method was applied. (author) 4 refs.; 1 fig.; 1 tab

  11. Determination of arsenic in biological materials using ammonium molybdate labelled with 99Mo

    International Nuclear Information System (INIS)

    Maruyama, Y.; Nagaoka, Y.

    1983-01-01

    A new radiometric method for the determination of arsenic in biological materials has been developed. An excess of ammonium molybdate labelled with 99 Mo was added to the sample solution and the arsenomolybdic acid formed was extracted into n-butyl alcohol and ethyl acetate mixture. The activity of the organic phase was directly proportional to the amount of arsenic. The method was applied for the determination of arsenic in Orchard Leaves obtained from the National Bureau of Standards. (author)

  12. Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids.

    Science.gov (United States)

    Sales, Mark; Plecs, Joseph J; Holton, James M; Alber, Tom

    2007-10-01

    The previous design of an unprecedented family of two-, three-, and four-helical, right-handed coiled coils utilized nonbiological amino acids to efficiently pack spaces in the oligomer cores. Here we show that a stable, right-handed parallel tetrameric coiled coil, called RH4B, can be designed entirely using biological amino acids. The X-ray crystal structure of RH4B was determined to 1.1 Angstrom resolution using a designed metal binding site to coordinate a single Yb(2+) ion per 33-amino acid polypeptide chain. The resulting experimental phases were particularly accurate, and the experimental electron density map provided an especially clear, unbiased view of the molecule. The RH4B structure closely matched the design, with equivalent core rotamers and an overall root-mean-square deviation for the N-terminal repeat of the tetramer of 0.24 Angstrom. The clarity and resolution of the electron density map, however, revealed alternate rotamers and structural differences between the three sequence repeats in the molecule. These results suggest that the RH4B structure populates an unanticipated variety of structures.

  13. Rapid and reliable protein structure determination via chemical shift threading.

    Science.gov (United States)

    Hafsa, Noor E; Berjanskii, Mark V; Arndt, David; Wishart, David S

    2018-01-01

    Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .

  14. Determination of drugs in biological fluids by direct injection of samples for liquid-chromatographic analysis.

    Science.gov (United States)

    Mullett, Wayne M

    2007-03-10

    The analysis of drugs in various biological fluids is an important criterion for the determination of the physiological performance of a drug. After sampling of the biological fluid, the next step in the analytical process is sample preparation. The complexity of biological fluids adds to the challenge of direct determination of the drug by chromatographic analysis, therefore demanding a sample preparation step that is often time-consuming, tedious, and frequently overlooked. However, direct on-line injection methods offer the advantage of reducing sample preparation steps and enabling effective pre-concentration and clean-up of biological fluids. These procedures can be automated and therefore reduce the requirements for handling potentially infectious biomaterial, improve reproducibility, and minimize sample manipulations and potential contamination. The objective of this review is to present an overview of the existing literature with emphasis on advances in automated sample preparation methods for liquid-chromatographic methods. More specifically, this review concentrates on the use of direct injection techniques, such as restricted-access materials, turbulent-flow chromatography and other automated on-line solid-phase extraction (SPE) procedures. It also includes short overviews of emerging automated extraction-phase technologies, such as molecularly imprinted polymers, in-tube solid-phase micro-extraction, and micro-extraction in a packed syringe for a more selective extraction of analytes from complex samples, providing further improvements in the analysis of biological materials. Lastly, the outlook for these methods and potential new applications for these technologies are briefly discussed.

  15. Insights into the structural biology of Gaucher disease.

    Science.gov (United States)

    Smith, Laura; Mullin, Stephen; Schapira, Anthony H V

    2017-12-01

    Gaucher disease, the most common lysosomal storage disorder, is caused by mutations in the gene encoding the acid-β-glucosidase lysosomal hydrolase enzyme that cleaves glucocerebroside into glucose and ceramide. Reduced enzyme activity and impaired structural stability arise due to >300 known disease-causing mutations. Several of these mutations have also been associated with an increased risk of Parkinson disease (PD). Since the discovery of the acid-β-glucosidase X-ray structure, there have been major advances in our understanding of the structural properties of the protein. Analysis of specific residues has provided insight into their functional and structural importance and provided insight into the pathogenesis of Gaucher disease and the contribution to PD. Disease-causing mutations are positioned throughout the acid-β-glucosidase structure, with many located far from the active site and thus retaining some enzymatic activity however, thus far no clear relationship between mutation location and disease severity has been established. Here, we review the crystal structure of acid-β-glucosidase, while highlighting important structural aspects of the protein in detail. This review discusses the structural stability of acid-β-glucosidase, which can be altered by pH and glycosylation, and explores the relationship between known Gaucher disease and PD mutations, structural stability and disease severity. Copyright © 2017. Published by Elsevier Inc.

  16. Procedure for developing biological input for the design, location, or modification of water-intake structures

    Energy Technology Data Exchange (ETDEWEB)

    Neitzel, D.A.; McKenzie, D.H.

    1981-12-01

    To minimize adverse impact on aquatic ecosystems resulting from the operation of water intake structures, design engineers must have relevant information on the behavior, physiology and ecology of local fish and shellfish. Identification of stimulus/response relationships and the environmental factors that influence them is the first step in incorporating biological information in the design, location or modification of water intake structures. A procedure is presented in this document for providing biological input to engineers who are designing, locating or modifying a water intake structure. The authors discuss sources of stimuli at water intakes, historical approaches in assessing potential/actual impact and review biological information needed for intake design.

  17. Of arrows and flows. Causality, determination, and specificity in the Central Dogma of molecular biology.

    Science.gov (United States)

    Fantini, Bernardino

    2006-01-01

    From its first proposal, the Central Dogma had a graphical form, complete with arrows of different types, and this form quickly became its standard presentation. In different scientific contexts, arrows have different meanings and in this particular case the arrows indicated the flow of information among different macromolecules. A deeper analysis illustrates that the arrows also imply a causal statement, directly connected to the causal role of genetic information. The author suggests a distinction between two different kinds of causal links, defined as 'physical causality' and 'biological determination', both implied in the production of biological specificity.

  18. Application of genetic algorithms for determination biological half-life of 137 Cs in milk

    International Nuclear Information System (INIS)

    Pantelic, G.

    1998-01-01

    Genetic algorithm an optimization method involving natural selection mechanisms, was used to determine biological half-life of sup 1 sup 3 sup 7 Cs in the milk, after the Chernobyl accident, based on a two compartment linear system model. Genetic algorithms operate on populations of strings. Reproduction, crossover and mutation are applied to successive string population to create new string population. A model parameter estimation is performed by minimizing square differences between fitting function and experimental data. The calculated biological half-life of sup 1 sup 3 sup 7 Cs in milk is (32(+(-) days (author)

  19. Determination of silicon in biological and botanical reference materials by epithermal INAA and Compton suppression

    International Nuclear Information System (INIS)

    Landsberger, S.; Peshev, S.; Becker, D.A.

    1994-01-01

    Silicon determination in sixteen botanical and biological standard reference materials is described using the 29 Si(n, p) 29 Al reaction through instrumental epithermal neutron activation analysis and Compton suppression gamma-ray spectroscopy. By simultaneous utilization of both cadmium and boron epithermal filters along with anticoincidence gamma-counting, detection limits as low as 12 ppm were obtained for certain matrices, much lower than previously reported values for this type of analysis. The method is applicable to many botanical and biological matrices and is attractive with its interference free, purely instrumental nature, compared with methods using the 28 Si(n, p) 28 Al reaction or chemical separation techniques. ((orig.))

  20. Possibilities of nondestructive determination of fluorine in coal and biological materials by IPAA

    International Nuclear Information System (INIS)

    Randa, Zdenek; Mizera, Jiri; Chvatil, David

    2009-01-01

    The possibilities of nondestructive determination of fluorine in coal and biological materials by instrumental photon activation analysis (IPAA) were studied. The determination was based on counting the non-specific 511 keV annihilation gamma rays of 18 F, a pure positron emitter which is the product of the photonuclear reaction 19 F(γ, n) 18 F. The simultaneous formation of some additional positron emitters, particularly 45 Ti and 34m Cl, is an interfering factor. When using correction standards for Ti and Cl and optimization of the beam energy and irradiation-decay-counting times, fluorine could be determined by IPAA in selected coal and biological samples at the ten ppm level. The feasibility of additional optimization for further improvements of the proposed IPAA procedure are discussed

  1. Determination of chorionic gonadotrophin. Comparison of biological, immunological and radioimmunological methods

    International Nuclear Information System (INIS)

    Munier, M.-P.

    1978-07-01

    Three types of analysis were used to quantify chorionic gonadotrophic hormone: biological determination (rana-reaction); immunological determination (simplified pregnosticon test of the Organon Teknika laboratories); radioimmunological determination (Commissariat a l'Energie Atomique - CEA kits). While the immunochemical technique is specially suited to analysis of the urine, the radioimmunological measurement is carried out on the plasma. This method is extremely sensitive; when traditional biological and immunological methods are used the quantity of CGH detectable is of the order of some hundreds or at best a few tens of international units. The radioimmunological method is a thousand times more sensitive and can therefore measure CGH in amounts of the milli-unit order. Until recently it was not specific enough to differentiate between CGH and LH, but not long ago a β CGH-specific antibody was discovered and it is now possible to detect small amounts of CGH in the presence of LH [fr

  2. De novo protein structure determination using sparse NMR data

    International Nuclear Information System (INIS)

    Bowers, Peter M.; Strauss, Charlie E.M.; Baker, David

    2000-01-01

    We describe a method for generating moderate to high-resolution protein structures using limited NMR data combined with the ab initio protein structure prediction method Rosetta. Peptide fragments are selected from proteins of known structure based on sequence similarity and consistency with chemical shift and NOE data. Models are built from these fragments by minimizing an energy function that favors hydrophobic burial, strand pairing, and satisfaction of NOE constraints. Models generated using this procedure with ∼1 NOE constraint per residue are in some cases closer to the corresponding X-ray structures than the published NMR solution structures. The method requires only the sparse constraints available during initial stages of NMR structure determination, and thus holds promise for increasing the speed with which protein solution structures can be determined

  3. Determination of the three-dimensional structure for weakly aligned biomolecules by NMR spectroscopy

    International Nuclear Information System (INIS)

    Shahkhatuni, Astghik A; Shahkhatuni, Aleksan G

    2002-01-01

    The key achievements and the potential of NMR spectroscopy for weakly aligned biomolecules are considered. Due to weak alignment, it becomes possible to determine a number of NMR parameters dependent on the orientation of biomolecules, which are averaged to zero in usual isotropic media. The addition of new orientational constraints to standard procedures of 3D structure determination markedly increases the achievable accuracy. The possibility of structure determination for biomolecules using only orientation-dependent parameters without invoking other NMR data is discussed. The methods of orientation, experimental techniques, and calculation methods are systematised. The main results obtained and the prospects of using NMR spectroscopy of weakly aligned systems to study different classes of biomolecules and to solve various problems of molecular biology are analysed. Examples of biomolecules whose structures have been determined using orientation-dependent parameters are given. The bibliography includes 508 references.

  4. Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction.

    Science.gov (United States)

    Fromm, S A; Sachse, C

    2016-01-01

    Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method. © 2016 Elsevier Inc. All rights reserved.

  5. Yeast prions: structure, biology, and prion-handling systems.

    Science.gov (United States)

    Wickner, Reed B; Shewmaker, Frank P; Bateman, David A; Edskes, Herman K; Gorkovskiy, Anton; Dayani, Yaron; Bezsonov, Evgeny E

    2015-03-01

    A prion is an infectious protein horizontally transmitting a disease or trait without a required nucleic acid. Yeast and fungal prions are nonchromosomal genes composed of protein, generally an altered form of a protein that catalyzes the same alteration of the protein. Yeast prions are thus transmitted both vertically (as genes composed of protein) and horizontally (as infectious proteins, or prions). Formation of amyloids (linear ordered β-sheet-rich protein aggregates with β-strands perpendicular to the long axis of the filament) underlies most yeast and fungal prions, and a single prion protein can have any of several distinct self-propagating amyloid forms with different biological properties (prion variants). Here we review the mechanism of faithful templating of protein conformation, the biological roles of these prions, and their interactions with cellular chaperones, the Btn2 and Cur1 aggregate-handling systems, and other cellular factors governing prion generation and propagation. Human amyloidoses include the PrP-based prion conditions and many other, more common amyloid-based diseases, several of which show prion-like features. Yeast prions increasingly are serving as models for the understanding and treatment of many mammalian amyloidoses. Patients with different clinical pictures of the same amyloidosis may be the equivalent of yeasts with different prion variants. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  6. Determination of the dynamical behaviour of biological materials during impact using a pendulum device

    Science.gov (United States)

    Van Zeebroeck, M.; Tijskens, E.; Van Liedekerke, P.; Deli, V.; De Baerdemaeker, J.; Ramon, H.

    2003-09-01

    A pendulum device has been developed to measure contact force, displacement and displacement rate of an impactor during its impact on the sample. Displacement, classically measured by double integration of an accelerometer, was determined in an alternative way using a more accurate incremental optical encoder. The parameters of the Kuwabara-Kono contact force model for impact of spheres have been estimated using an optimization method, taking the experimentally measured displacement, displacement rate and contact force into account. The accuracy of the method was verified using a rubber ball. Contact force parameters for the Kuwabara-Kono model have been estimated with success for three biological materials, i.e., apples, tomatoes and potatoes. The variability in the parameter estimations for the biological materials was quite high and can be explained by geometric differences (radius of curvature) and by biological variation of mechanical tissue properties.

  7. Biophysical and biological factors determining the ability to achieve long-term cryobiological preservation

    Energy Technology Data Exchange (ETDEWEB)

    Mazur, P. [Oak Ridge National Lab., TN (United States). Life Sciences Div.

    1997-12-01

    The BESTCapsule will maintain appropriate biological specimens for decades or centuries at cryogenic temperatures in the living state. Maintenance at temperatures below {approximately} {minus}140 C is not a problem. No ordinary chemical reactions in aqueous solutions can occur. The only source of damage will be the slow accumulation of physical damage to DNA from background ionizing radiation. But this source of damage should not become serious in less than a millennium. Rather, the main problem in cryopreservation is to devise procedures for cooling the biological specimens to {minus}196 C and returning them to normal temperatures without inflicting lethal injury. Regardless of the cell type, there are certain encompassing biophysical factors and constraints that determine whether they will survive or die during freezing and thawing. Superimposed on these may be special biological factors that apply to specific cell types. This paper will emphasize the former and give illustrative examples of the latter.

  8. Advanced photonic structures for biological and chemical detection

    CERN Document Server

    Fan, Xudong

    2009-01-01

    One of a series of books on Integrated Microanalytical Systems, this text discusses the latest applications of photonic technologies in bio/chemical sensing. The book is divided into four sections, each one being based on photonic structures.

  9. Proceedings of the 182nd basic science seminar (The workshop on neutron structural biology ) 'New frontiers of structural biology advanced by solution scattering'

    International Nuclear Information System (INIS)

    Fujiwara, Satoru

    2001-03-01

    182nd advanced science seminar (the workshop on neutron structural biology) was held in February 9-10, 2000 at Tokai. Thirty-six participants from universities, research institutes, and private companies took part in the workshop, and total of 24 lectures were given. This proceedings collects abstracts, the figures and tables, which the speakers used in their lectures. The proceedings contains two reviews from the point of view of x-ray and neutron scatterings, and six subjects (21 papers) including neutron and x-ray scattering in the era of structure genomics, structural changes detected with solution scattering, a new way in structural biology opened by neutron crystallography and neutron scattering, x-ray sources and detectors, simulation and solution scattering, and neutron sources and detectors. (Kazumata, Y.)

  10. Proceedings of the 182nd basic science seminar (The workshop on neutron structural biology ) 'New frontiers of structural biology advanced by solution scattering'

    Energy Technology Data Exchange (ETDEWEB)

    Fujiwara, Satoru (ed.) [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    2001-03-01

    182nd advanced science seminar (the workshop on neutron structural biology) was held in February 9-10, 2000 at Tokai. Thirty-six participants from universities, research institutes, and private companies took part in the workshop, and total of 24 lectures were given. This proceedings collects abstracts, the figures and tables, which the speakers used in their lectures. The proceedings contains two reviews from the point of view of x-ray and neutron scatterings, and six subjects (21 papers) including neutron and x-ray scattering in the era of structure genomics, structural changes detected with solution scattering, a new way in structural biology opened by neutron crystallography and neutron scattering, x-ray sources and detectors, simulation and solution scattering, and neutron sources and detectors. (Kazumata, Y.)

  11. First-Year Biology Students' Understandings of Meiosis: An Investigation Using a Structural Theoretical Framework

    Science.gov (United States)

    Quinn, Frances; Pegg, John; Panizzon, Debra

    2009-01-01

    Meiosis is a biological concept that is both complex and important for students to learn. This study aims to explore first-year biology students' explanations of the process of meiosis, using an explicit theoretical framework provided by the Structure of the Observed Learning Outcome (SOLO) model. The research was based on responses of 334…

  12. Quinones from plants of northeastern Brazil: structural diversity, chemical transformations, NMR data and biological activities.

    Science.gov (United States)

    Lemos, Telma L G; Monte, Francisco J Q; Santos, Allana Kellen L; Fonseca, Aluisio M; Santos, Hélcio S; Oliveira, Mailcar F; Costa, Sonia M O; Pessoa, Otilia D L; Braz-Filho, Raimundo

    2007-05-20

    The present review focus in quinones found in species of Brazilian northeastern Capraria biflora, Lippia sidoides, Lippia microphylla and Tabebuia serratifolia. The review cover ethnopharmacological aspects including photography of species, chemical structure feature, NMR datea and biological properties. Chemical transformations of lapachol to form enamine derivatives and biological activities are discussed.

  13. Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules.

    Science.gov (United States)

    Vallat, Brinda; Webb, Benjamin; Westbrook, John D; Sali, Andrej; Berman, Helen M

    2018-04-09

    Essential processes in biology are carried out by large macromolecular assemblies, whose structures are often difficult to determine by traditional methods. Increasingly, researchers combine measured data and computed information from several complementary methods to obtain "hybrid" or "integrative" structural models of macromolecules and their assemblies. These integrative/hybrid (I/H) models are not archived in the PDB because of the absence of standard data representations and processing mechanisms. Here we present the development of data standards and a prototype system for archiving I/H models. The data standards provide the definitions required for representing I/H models that span multiple spatiotemporal scales and conformational states, as well as spatial restraints derived from different experimental techniques. Based on these data definitions, we have built a prototype system called PDB-Dev, which provides the infrastructure necessary to archive I/H structural models. PDB-Dev is now accepting structures and is open to the community for new submissions. Copyright © 2018 Elsevier Ltd. All rights reserved.

  14. Superhydrophobic hierarchically structured surfaces in biology: evolution, structural principles and biomimetic applications.

    Science.gov (United States)

    Barthlott, W; Mail, M; Neinhuis, C

    2016-08-06

    A comprehensive survey of the construction principles and occurrences of superhydrophobic surfaces in plants, animals and other organisms is provided and is based on our own scanning electron microscopic examinations of almost 20 000 different species and the existing literature. Properties such as self-cleaning (lotus effect), fluid drag reduction (Salvinia effect) and the introduction of new functions (air layers as sensory systems) are described and biomimetic applications are discussed: self-cleaning is established, drag reduction becomes increasingly important, and novel air-retaining grid technology is introduced. Surprisingly, no evidence for lasting superhydrophobicity in non-biological surfaces exists (except technical materials). Phylogenetic trees indicate that superhydrophobicity evolved as a consequence of the conquest of land about 450 million years ago and may be a key innovation in the evolution of terrestrial life. The approximate 10 million extant species exhibit a stunning diversity of materials and structures, many of which are formed by self-assembly, and are solely based on a limited number of molecules. A short historical survey shows that bionics (today often called biomimetics) dates back more than 100 years. Statistical data illustrate that the interest in biomimetic surfaces is much younger still. Superhydrophobicity caught the attention of scientists only after the extreme superhydrophobicity of lotus leaves was published in 1997. Regrettably, parabionic products play an increasing role in marketing.This article is part of the themed issue 'Bioinspired hierarchically structured surfaces for green science'. © 2016 The Author(s).

  15. Superhydrophobic hierarchically structured surfaces in biology: evolution, structural principles and biomimetic applications

    Science.gov (United States)

    Mail, M.; Neinhuis, C.

    2016-01-01

    A comprehensive survey of the construction principles and occurrences of superhydrophobic surfaces in plants, animals and other organisms is provided and is based on our own scanning electron microscopic examinations of almost 20 000 different species and the existing literature. Properties such as self-cleaning (lotus effect), fluid drag reduction (Salvinia effect) and the introduction of new functions (air layers as sensory systems) are described and biomimetic applications are discussed: self-cleaning is established, drag reduction becomes increasingly important, and novel air-retaining grid technology is introduced. Surprisingly, no evidence for lasting superhydrophobicity in non-biological surfaces exists (except technical materials). Phylogenetic trees indicate that superhydrophobicity evolved as a consequence of the conquest of land about 450 million years ago and may be a key innovation in the evolution of terrestrial life. The approximate 10 million extant species exhibit a stunning diversity of materials and structures, many of which are formed by self-assembly, and are solely based on a limited number of molecules. A short historical survey shows that bionics (today often called biomimetics) dates back more than 100 years. Statistical data illustrate that the interest in biomimetic surfaces is much younger still. Superhydrophobicity caught the attention of scientists only after the extreme superhydrophobicity of lotus leaves was published in 1997. Regrettably, parabionic products play an increasing role in marketing. This article is part of the themed issue ‘Bioinspired hierarchically structured surfaces for green science’. PMID:27354736

  16. Determinants of capital structure and financial crisis impact: evidence

    OpenAIRE

    Proença, Pedro Miguel Correia

    2012-01-01

    Mestrado em contabilidade The objectives of this empirical work are to investigate the determinants of Portuguese SMEs capital structure, evaluate whether and how the impacts of those determinants affect the debt ratios and examine the effects of financial crisis and industry on Portuguese SMEs capital structure. The sample used considers the period 2007-2010, resulting in 12.857 Portugues e SMEs per year observations. R...

  17. Neutron scattering and diffraction instrument for structural study on biology in Japan

    Energy Technology Data Exchange (ETDEWEB)

    Niimura, Nobuo [Japan Atomic Energy Research Inst., Ibaraki-ken (Japan)

    1994-12-31

    Neutron scattering and diffraction instruments in Japan which can be used for structural studies in biology are briefly introduced. Main specifications and general layouts of the instruments are shown.

  18. Structural Molecular Biology-A Personal Reflection on the Occasion of John Kendrew's 100th Birthday.

    Science.gov (United States)

    Cramer, Patrick

    2017-08-18

    Here, I discuss the development and future of structural molecular biology, concentrating on the eukaryotic transcription machinery and reflecting on John Kendrew's legacy from a personal perspective. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. ssbio: a Python framework for structural systems biology.

    Science.gov (United States)

    Mih, Nathan; Brunk, Elizabeth; Chen, Ke; Catoiu, Edward; Sastry, Anand; Kavvas, Erol; Monk, Jonathan M; Zhang, Zhen; Palsson, Bernhard O

    2018-06-15

    Working with protein structures at the genome-scale has been challenging in a variety of ways. Here, we present ssbio, a Python package that provides a framework to easily work with structural information in the context of genome-scale network reconstructions, which can contain thousands of individual proteins. The ssbio package provides an automated pipeline to construct high quality genome-scale models with protein structures (GEM-PROs), wrappers to popular third-party programs to compute associated protein properties, and methods to visualize and annotate structures directly in Jupyter notebooks, thus lowering the barrier of linking 3D structural data with established systems workflows. ssbio is implemented in Python and available to download under the MIT license at http://github.com/SBRG/ssbio. Documentation and Jupyter notebook tutorials are available at http://ssbio.readthedocs.io/en/latest/. Interactive notebooks can be launched using Binder at https://mybinder.org/v2/gh/SBRG/ssbio/master?filepath=Binder.ipynb. Supplementary data are available at Bioinformatics online.

  20. Chemical preparation of biological materials for accurate chromium determination by isotope dilution mass spectrometry

    International Nuclear Information System (INIS)

    Dunstan, L.P.; Garner, E.L.

    1977-01-01

    The current interest in trace elements in biological materials has created a need for accurate methods of analysis. The source of discrepancies and variations in chromium concentration determinations is often traceable to inadequate methods of sample preparation. Any method of Cr analysis that requires acid digestion of a biological matrix must take into consideration the existence or formation of a volatile Cr component. In addition, because Cr is often present at concentrations less than 1 μg/g, the analytical blank becomes a potential source of error. Chemical procedures have been developed for the digestion of the biological matrix and the separation of Cr without either large analytical blanks or significant losses by volatilization. These procedures have been used for the analysis of NBS Standard Reference Material (SRM) 1569 Brewers Yeast; SRM 1577 Bovine Liver; SRM 1570 Spinach and other biological materials including human hair and nails. At this time, samples containing 1 μg of Cr can be determined with an estimated accuracy of 2 percent

  1. Pili and flagella biology, structure, and biotechnological applications.

    Science.gov (United States)

    Van Gerven, Nani; Waksman, Gabriel; Remaut, Han

    2011-01-01

    Bacteria and Archaea expose on their outer surfaces a variety of thread-like proteinaceous organelles with which they interact with their environments. These structures are repetitive assemblies of covalently or non-covalently linked protein subunits, organized into filamentous polymers known as pili ("hair"), flagella ("whips") or injectisomes ("needles"). They serve different roles in cell motility, adhesion and host invasion, protein and DNA secretion and uptake, conductance, or cellular encapsulation. Here we describe the functional, morphological and genetic diversity of these bacterial filamentous protein structures. The organized, multi-copy build-up and/or the natural function of pili and flagella have lead to their biotechnological application as display and secretion tools, as therapeutic targets or as molecular motors. We review the documented and potential technological exploitation of bacterial surface filaments in light of their structural and functional traits. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. A Comprehensive Experiment for Molecular Biology: Determination of Single Nucleotide Polymorphism in Human REV3 Gene Using PCR-RFLP

    Science.gov (United States)

    Zhang, Xu; Shao, Meng; Gao, Lu; Zhao, Yuanyuan; Sun, Zixuan; Zhou, Liping; Yan, Yongmin; Shao, Qixiang; Xu, Wenrong; Qian, Hui

    2017-01-01

    Laboratory exercise is helpful for medical students to understand the basic principles of molecular biology and to learn about the practical applications of molecular biology. We have designed a lab course on molecular biology about the determination of single nucleotide polymorphism (SNP) in human REV3 gene, the product of which is a subunit of…

  3. SPring-8 Structural Biology Beamlines / Current Status of Public Beamlines for Protein Crystallography at SPring-8

    International Nuclear Information System (INIS)

    Kawamoto, Masahide; Hasegawa, Kazuya; Shimizu, Nobutaka; Sakai, Hisanobu; Shimizu, Tetsuya; Nisawa, Atsushi; Yamamoto, Masaki

    2007-01-01

    SPring-8 has 2 protein crystallography beamlines for public use, BL38B1 (Structural Biology III) and BL41XU (Structural Biology I). The BL38B1 is a bending magnet beamline for routine data collection, and the BL41XU is an undulator beamline specially customized for micro beam and ultra-high resolutional experiment. The designs and the performances of each beamline are presented

  4. Transaction cost determinants of credit governance structures of ...

    African Journals Online (AJOL)

    This paper explores transaction cost determinants of credit governance structures (CGS) of commercial banks in Tanzania. Descriptive statistics, linear regression model, binary and multinomial logistic regression models were employed for analysis. Findings revealed four modes of credit governance structures that are ...

  5. The Determinants of Capital Structure: Some Evidence from Banks

    OpenAIRE

    Heider, Florian; Gropp, Reint

    2008-01-01

    This paper documents that standard cross-sectional determinants of firm leverage also apply to the capital structure of large banks in the United States and Europe. We find a remarkable consistency in sign, significance and economic magnitude. Like non-financial firms, banks appear to have stable capital structures at levels that are specific to each individual bank. The results suggest that capital requirements may only be of second-order importance for banks’ capital structures and confirm ...

  6. On the accuracy of protein determination in large biological samples by prompt gamma neutron activation analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kasviki, K. [Institute of Nuclear Technology and Radiation Protection, NCSR ' Demokritos' , Aghia Paraskevi, Attikis 15310 (Greece); Medical Physics Laboratory, Medical School, University of Ioannina, Ioannina 45110 (Greece); Stamatelatos, I.E. [Institute of Nuclear Technology and Radiation Protection, NCSR ' Demokritos' , Aghia Paraskevi, Attikis 15310 (Greece)], E-mail: ion@ipta.demokritos.gr; Yannakopoulou, E. [Institute of Physical Chemistry, NCSR ' Demokritos' , Aghia Paraskevi, Attikis 15310 (Greece); Papadopoulou, P. [Institute of Technology of Agricultural Products, NAGREF, Lycovrissi, Attikis 14123 (Greece); Kalef-Ezra, J. [Medical Physics Laboratory, Medical School, University of Ioannina, Ioannina 45110 (Greece)

    2007-10-15

    A prompt gamma neutron activation analysis (PGNAA) facility has been developed for the determination of nitrogen and thus total protein in large volume biological samples or the whole body of small animals. In the present work, the accuracy of nitrogen determination by PGNAA in phantoms of known composition as well as in four raw ground meat samples of about 1 kg mass was examined. Dumas combustion and Kjeldahl techniques were also used for the assessment of nitrogen concentration in the meat samples. No statistically significant differences were found between the concentrations assessed by the three techniques. The results of this work demonstrate the applicability of PGNAA for the assessment of total protein in biological samples of 0.25-1.5 kg mass, such as a meat sample or the body of small animal even in vivo with an equivalent radiation dose of about 40 mSv.

  7. On the accuracy of protein determination in large biological samples by prompt gamma neutron activation analysis

    International Nuclear Information System (INIS)

    Kasviki, K.; Stamatelatos, I.E.; Yannakopoulou, E.; Papadopoulou, P.; Kalef-Ezra, J.

    2007-01-01

    A prompt gamma neutron activation analysis (PGNAA) facility has been developed for the determination of nitrogen and thus total protein in large volume biological samples or the whole body of small animals. In the present work, the accuracy of nitrogen determination by PGNAA in phantoms of known composition as well as in four raw ground meat samples of about 1 kg mass was examined. Dumas combustion and Kjeldahl techniques were also used for the assessment of nitrogen concentration in the meat samples. No statistically significant differences were found between the concentrations assessed by the three techniques. The results of this work demonstrate the applicability of PGNAA for the assessment of total protein in biological samples of 0.25-1.5 kg mass, such as a meat sample or the body of small animal even in vivo with an equivalent radiation dose of about 40 mSv

  8. Structure Building Predicts Grades in College Psychology and Biology

    Science.gov (United States)

    Arnold, Kathleen M.; Daniel, David B.; Jensen, Jamie L.; McDaniel, Mark A.; Marsh, Elizabeth J.

    2016-01-01

    Knowing what skills underlie college success can allow students, teachers, and universities to identify and to help at-risk students. One skill that may underlie success across a variety of subject areas is structure building, the ability to create mental representations of narratives (Gernsbacher, Varner, & Faust, 1990). We tested if…

  9. Track structure in radiation biology: theory and applications.

    Science.gov (United States)

    Nikjoo, H; Uehara, S; Wilson, W E; Hoshi, M; Goodhead, D T

    1998-04-01

    A brief review is presented of the basic concepts in track structure and the relative merit of various theoretical approaches adopted in Monte-Carlo track-structure codes are examined. In the second part of the paper, a formal cluster analysis is introduced to calculate cluster-distance distributions. Total experimental ionization cross-sections were least-square fitted and compared with the calculation by various theoretical methods. Monte-Carlo track-structure code Kurbuc was used to examine and compare the spectrum of the secondary electrons generated by using functions given by Born-Bethe, Jain-Khare, Gryzinsky, Kim-Rudd, Mott and Vriens' theories. The cluster analysis in track structure was carried out using the k-means method and Hartigan algorithm. Data are presented on experimental and calculated total ionization cross-sections: inverse mean free path (IMFP) as a function of electron energy used in Monte-Carlo track-structure codes; the spectrum of secondary electrons generated by different functions for 500 eV primary electrons; cluster analysis for 4 MeV and 20 MeV alpha-particles in terms of the frequency of total cluster energy to the root-mean-square (rms) radius of the cluster and differential distance distributions for a pair of clusters; and finally relative frequency distribution for energy deposited in DNA, single-strand break and double-strand breaks for 10MeV/u protons, alpha-particles and carbon ions. There are a number of Monte-Carlo track-structure codes that have been developed independently and the bench-marking presented in this paper allows a better choice of the theoretical method adopted in a track-structure code to be made. A systematic bench-marking of cross-sections and spectra of the secondary electrons shows differences between the codes at atomic level, but such differences are not significant in biophysical modelling at the macromolecular level. Clustered-damage evaluation shows: that a substantial proportion of dose ( 30%) is

  10. Connecting Structure-Property and Structure-Function Relationships across the Disciplines of Chemistry and Biology: Exploring Student Perceptions

    Science.gov (United States)

    Kohn, Kathryn P.; Underwood, Sonia M.; Cooper, Melanie M.

    2018-01-01

    While many university students take science courses in multiple disciplines, little is known about how they perceive common concepts from different disciplinary perspectives. Structure-property and structure-function relationships have long been considered important explanatory concepts in the disciplines of chemistry and biology, respectively.…

  11. Labor Market Structure and Salary Determination among Professional Basketball Players.

    Science.gov (United States)

    Wallace, Michael

    1988-01-01

    The author investigates the labor market structure and determinants of salaries for professional basketball players. An expanded version of the resource perspective is used. A three-tiered model of labor market segmentation is revealed for professional basketball players, but other variables also are important in salary determination. (Author/CH)

  12. Denotational, Causal, and Operational Determinism in Event Structures

    NARCIS (Netherlands)

    Rensink, Arend; Kirchner, H.

    1996-01-01

    Determinism of labelled transition systems and trees is a concept of theoretical and practical importance. We study its generalisation to event structures. It turns out that the result depends on what characterising property of tree determinism one sets out to generalise. We present three distinct

  13. Denotational, Causal, and Operational Determinism in Event Structures

    NARCIS (Netherlands)

    Rensink, Arend

    Determinism is a theoretically and practically important concept in labelled transition systems and trees. We study its generalisation to event structures. It turns out that the result depends on what characterising property of tree determinism one sets out to generalise. We present three distinct

  14. Determination of biological transport of oxygen-15 and carbon-11 generated in rats

    International Nuclear Information System (INIS)

    Archambeau, B.; Bennett, G.W.; Archambeau, J.O.

    1976-02-01

    The distribution of induced 15 O and 11 C activity in live and dead rats was determined following local irradiation with a 32 MeV proton beam. Results indicate that rapid biological redistribution of some of the induced activity occurs within a minute following irradiation. Sufficient activity remains, bound in the intracellular water, to define the proton beam in tissue. Thus, mapping of the induced 15 O activity proves to be a valid means of beam localization

  15. Determination of trace metals in Cladophora glomerata: C. glomerata as a potential biological monitor

    Energy Technology Data Exchange (ETDEWEB)

    Keeny, W.L.; Breck, W.G.; Vanloon, G.W.; Page, J.A.

    1976-01-01

    A differential pulse anodic stripping voltammetry method has been developed for the determination of Zn, Cd, Pb and Cu in Cladophora glomerata. The method has been applied to samples taken in August from a remote island in Lake Ontario (Main Duck) and a shore site near Kingston, Ontario (Deadman Bay). It is postulated that C. glomerata can act as a biological monitor, concentrating the trace metals present in the aqueous environment with a reasonably constant CF for each element.

  16. STRUCTURAL BIOLOGY AND MOLECULAR MEDICINE RESEARCH PROGRAM (LSBMM)

    International Nuclear Information System (INIS)

    Eisenberg, David S.

    2008-01-01

    The UCLA-DOE Institute of Genomics and Proteomics is an organized research unit of the University of California, sponsored by the Department of Energy through the mechanism of a Cooperative Agreement. Today the Institute consists of 10 Principal Investigators and 7 Associate Members, developing and applying technologies to promote the biological and environmental missions of the Department of Energy, and 5 Core Technology Centers to sustain this work. The focus is on understanding genomes, pathways and molecular machines in organisms of interest to DOE, with special emphasis on developing enabling technologies. Since it was founded in 1947, the UCLA-DOE Institute has adapted its mission to the research needs of DOE and its progenitor agencies as these research needs have changed. The Institute started as the AEC Laboratory of Nuclear Medicine, directed by Stafford Warren, who later became the founding Dean of the UCLA School of Medicine. In this sense, the entire UCLA medical center grew out of the precursor of our Institute. In 1963, the mission of the Institute was expanded into environmental studies by Director Ray Lunt. I became the third director in 1993, and in close consultation with David Galas and John Wooley of DOE, shifted the mission of the Institute towards genomics and proteomics. Since 1993, the Principal Investigators and Core Technology Centers are entirely new, and the Institute has separated from its former division concerned with PET imaging. The UCLA-DOE Institute shares the space of Boyer Hall with the Molecular Biology Institute, and assumes responsibility for the operation of the main core facilities. Fig. 1 gives the organizational chart of the Institute. Some of the benefits to the public of research carried out at the UCLA-DOE Institute include the following: The development of publicly accessible, web-based databases, including the Database of Protein Interactions, and the ProLinks database of genomicly inferred protein function linkages

  17. Analytic determination of the activation of essential and toxic trace elements in biological material

    International Nuclear Information System (INIS)

    Schelenz, R.

    1980-01-01

    A neutron activation-analysis technique for the multielement determination in biological material was developed. The individual steps of this procedure comprise radiochemical and also instrumental analytic techniques. After radiochemical separation 34 elements can be determined, after only instrumental procedures 26 elements can be detected in biological material. The radiochemical analysis of 34 elements lasts 4 days. Tracer investigations on the radionuclide retention of the anorganic separators HAP, TiP and ZP in 9N aqueous HNO 3 solution indicated that apart from Na-24, K-42 and P-32 the radionuclides Cs-134, Rb-86 and Se-75 are almost quantitatively adsorbed at the separators. For the remaining investigated radionuclides different but well-reproducible retention values resulted. The pH-value only slightly influences the extent of the radionuclide retention. Kinetic investigations on the radiochemical precipitation of some radionuclides on Cu and Cu(Hg)sub(x) were carried out. The depositing of the radionuclides Ag-110m, Hg-203 and Se-75 at 0 0 C and room temperature on Cu(Hg)sub(x) and Cu foil is a first order reaction. The half-life periods and the velocity constants of the depositing on Cu and Cu(Hg)sub(x) were determined for the investigated radionuclides in dependency of the temperature. The technique was examined by means of international biological multielement standards of known element combinations. The realisation of ring tests for the multielement determination in potatoe and milk powder showed that this method provides precise results. The applicability of the radiochemical method was confirmed by the simultaneous determination of 25 elements in overall nutrition samples. The instrumental technique was applied for the multielement determination in human hair (of the head) and in river water. (orig./MG) [de

  18. Molecular mechanisms of temperature-dependent sex determination in the context of ecological developmental biology.

    Science.gov (United States)

    Matsumoto, Yuiko; Crews, David

    2012-05-06

    Temperature-dependent sex determination (TSD) is a prime example of phenotypic plasticity in that gonadal sex is determined by the temperature of the incubating egg. In the red-eared slider turtle (Trachemys scripta), the effect of temperature can be overridden by exogenous ligands, i.e., sex steroid hormones and steroid metabolism enzyme inhibitors, during the temperature-sensitive period (TSP) of development. Precisely how the physical signal of temperature is transduced into a biological signal that ultimately results in sex determination remains unknown. In this review, we discuss the sex determining pathway underlying TSD by focusing on two candidate sex determining genes, Forkhead box protein L2 (FoxL2) and Doublesex mab3- related transcription factor 1 (Dmrt1). They appear to be involved in transducing the environmental temperature signal into a biological signal that subsequently determines gonadal sex. FoxL2 and Dmrt1 exhibit gonad-typical patterns of expression in response to temperature during the TSP in the red-eared slider turtle. Further, the biologically active ligands regulate the expression of FoxL2 and Dmrt1 during development to modify gonad trajectory. The precise regulatory mechanisms of expression of these genes by temperature or exogenous ligands are not clear. However, the environment often influences developmental gene expression by altering the epigenetic status in regulatory regions. Here, we will discuss if the regulation of FoxL2 and Dmrt1 expression by environment is mediated through epigenetic mechanisms during development in species with TSD. Published by Elsevier Ireland Ltd.

  19. Integral membrane protein structure determination using pseudocontact shifts

    Energy Technology Data Exchange (ETDEWEB)

    Crick, Duncan J.; Wang, Jue X. [University of Cambridge, Department of Biochemistry (United Kingdom); Graham, Bim; Swarbrick, James D. [Monash University, Monash Institute of Pharmaceutical Sciences (Australia); Mott, Helen R.; Nietlispach, Daniel, E-mail: dn206@cam.ac.uk [University of Cambridge, Department of Biochemistry (United Kingdom)

    2015-04-15

    Obtaining enough experimental restraints can be a limiting factor in the NMR structure determination of larger proteins. This is particularly the case for large assemblies such as membrane proteins that have been solubilized in a membrane-mimicking environment. Whilst in such cases extensive deuteration strategies are regularly utilised with the aim to improve the spectral quality, these schemes often limit the number of NOEs obtainable, making complementary strategies highly beneficial for successful structure elucidation. Recently, lanthanide-induced pseudocontact shifts (PCSs) have been established as a structural tool for globular proteins. Here, we demonstrate that a PCS-based approach can be successfully applied for the structure determination of integral membrane proteins. Using the 7TM α-helical microbial receptor pSRII, we show that PCS-derived restraints from lanthanide binding tags attached to four different positions of the protein facilitate the backbone structure determination when combined with a limited set of NOEs. In contrast, the same set of NOEs fails to determine the correct 3D fold. The latter situation is frequently encountered in polytopical α-helical membrane proteins and a PCS approach is thus suitable even for this particularly challenging class of membrane proteins. The ease of measuring PCSs makes this an attractive route for structure determination of large membrane proteins in general.

  20. cellPACK: a virtual mesoscope to model and visualize structural systems biology.

    Science.gov (United States)

    Johnson, Graham T; Autin, Ludovic; Al-Alusi, Mostafa; Goodsell, David S; Sanner, Michel F; Olson, Arthur J

    2015-01-01

    cellPACK assembles computational models of the biological mesoscale, an intermediate scale (10-100 nm) between molecular and cellular biology scales. cellPACK's modular architecture unites existing and novel packing algorithms to generate, visualize and analyze comprehensive three-dimensional models of complex biological environments that integrate data from multiple experimental systems biology and structural biology sources. cellPACK is available as open-source code, with tools for validation of models and with 'recipes' and models for five biological systems: blood plasma, cytoplasm, synaptic vesicles, HIV and a mycoplasma cell. We have applied cellPACK to model distributions of HIV envelope protein to test several hypotheses for consistency with experimental observations. Biologists, educators and outreach specialists can interact with cellPACK models, develop new recipes and perform packing experiments through scripting and graphical user interfaces at http://cellPACK.org/.

  1. Structural determination of intact proteins using mass spectrometry

    Science.gov (United States)

    Kruppa, Gary [San Francisco, CA; Schoeniger, Joseph S [Oakland, CA; Young, Malin M [Livermore, CA

    2008-05-06

    The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

  2. BIRTHDAY CAKE ACTIVITY STRUCTURED ARRANGEMENT FOR HELPING CHILDREN DETERMINING QUANTITIES

    Directory of Open Access Journals (Sweden)

    Neni Mariana

    2010-07-01

    Full Text Available Few researches have been concerned about relation between children’s spatialthinking and number sense. Narrowing for this small research, we focused onone component of spatial thinking, that is structuring objects, and onecomponent of number senses, that is cardinality by determining quantities. Thisstudy focused on a design research that was conducted in Indonesia in which weinvestigated pre-school children’s (between 2 and 3.5 years old ability inmaking structured arrangement and their ability to determine the quantities bylooking at the arrangements. The result shows us that some of the children wereable to make such arrangement. However, the children found difficulties eitherto determine quantities from those arrangements or to compare some structuresto easily recognize number of objects.Keywords: structures, structured arrangement, cardinality DOI: http://dx.doi.org/10.22342/jme.1.1.790.53-70

  3. Structural Biology of CI from Phage TP901-1

    DEFF Research Database (Denmark)

    Rasmussen, Kim Krighaar

    (CTD), separated by a linker of various lengths. The NTD is responsible for DNA binding and the CTD is responsible for oligomerization of the CI protein. A Helix-turn-Helix motif is usually responsible for DNA binding. This thesis presents a structural characterization of the CI repressor from TP901...... condition of the CTD, responsible for the arrangement of the hexameric CI repressor. The arrangement of the CI repressor for TP901-1 has previously been described to have 32 point group symmetry based on SAXS studies. The CTD crystallizes with P3121 or P3221 symmetry with one molecule in the asymmetric unit......-length CI can only be answered unambiguously by solving the CTD crystal structure or by use of alternative techniques on the full-length CI....

  4. Energy group structure determination using particle swarm optimization

    International Nuclear Information System (INIS)

    Yi, Ce; Sjoden, Glenn

    2013-01-01

    Highlights: ► Particle swarm optimization is applied to determine broad group structure. ► A graph representation of the broad group structure problem is introduced. ► The approach is tested on a fuel-pin model. - Abstract: Multi-group theory is widely applied for the energy domain discretization when solving the Linear Boltzmann Equation. To reduce the computational cost, fine group cross libraries are often down-sampled into broad group cross section libraries. Cross section data collapsing generally involves two steps: Firstly, the broad group structure has to be determined; secondly, a weighting scheme is used to evaluate the broad cross section library based on the fine group cross section data and the broad group structure. A common scheme is to average the fine group cross section weighted by the fine group flux. Cross section collapsing techniques have been intensively researched. However, most studies use a pre-determined group structure, open based on experience, to divide the neutron energy spectrum into thermal, epi-thermal, fast, etc. energy range. In this paper, a swarm intelligence algorithm, particle swarm optimization (PSO), is applied to optimize the broad group structure. A graph representation of the broad group structure determination problem is introduced. And the swarm intelligence algorithm is used to solve the graph model. The effectiveness of the approach is demonstrated using a fuel-pin model

  5. The use of a single technique for the separation and determination of actinides in biological materials

    International Nuclear Information System (INIS)

    Camera, V.; Giubileo.

    1975-01-01

    For the radiotoxicological survey of workers exposed to different types of alpha-emitting contaminants, a procedure was developed which permits the estimate of Th, Pa, U, Np, Pu, Am and Cm in biological samples with a single technique. The radionuclides are extracted on a column by tri-n-octylphosphine oxide and separated by elution at different pH values. Afterwards, the quantitative determinations are done by physical methods (alpha counting or spectrometry). In the case of an accident it is possible to use a simplification of the procedure (extraction in a beaker) for checks. A procedure for the rapid determination of actinides in faeces and in nasal secretions is described

  6. Generation of structurally novel short carotenoids and study of their biological activity.

    Science.gov (United States)

    Kim, Se H; Kim, Moon S; Lee, Bun Y; Lee, Pyung C

    2016-02-23

    Recent research interest in phytochemicals has consistently driven the efforts in the metabolic engineering field toward microbial production of various carotenoids. In spite of systematic studies, the possibility of using C30 carotenoids as biologically functional compounds has not been explored thus far. Here, we generated 13 novel structures of C30 carotenoids and one C35 carotenoid, including acyclic, monocyclic, and bicyclic structures, through directed evolution and combinatorial biosynthesis, in Escherichia coli. Measurement of radical scavenging activity of various C30 carotenoid structures revealed that acyclic C30 carotenoids showed higher radical scavenging activity than did DL-α-tocopherol. We could assume high potential biological activity of the novel structures of C30 carotenoids as well, based on the neuronal differentiation activity observed for the monocyclic C30 carotenoid 4,4'-diapotorulene on rat bone marrow mesenchymal stem cells. Our results demonstrate that a series of structurally novel carotenoids possessing biologically beneficial properties can be synthesized in E. coli.

  7. Development of XAFS Into a Structure Determination Technique

    Science.gov (United States)

    Stern, E. A.

    After the detection of diffraction of x-rays by M. Laue in 1912, the technique was soon applied to structure determination by Bragg within a year. On the other hand, although the edge steps in X-Ray absorption were discovered even earlier by Barkla and both the near edge (XANES) and extended X-Ray fine structure (EXAFS) past the edge were detected by 1929, it still took over 40 years to realize the structure information contained in this X-Ray absorption fine structure (XAFS). To understand this delay a brief historical review of the development of the scientific ideas that transformed XAFS into the premiere technique for local structure determination is given. The development includes both advances in theoretical understanding and calculational capabilities, and in experimental facilities, especially synchrotron radiation sources. The present state of the XAFS technique and its capabilities are summarized.

  8. Structural biology data archiving: where we are and what lies ahead.

    Science.gov (United States)

    Kleywegt, Gerard J; Velankar, Sameer; Patwardhan, Ardan

    2018-05-10

    For almost 50 years, structural biology has endeavoured to conserve and share its experimental data and their interpretations (usually, atomistic models) through global public archives such as the Protein Data Bank (PDB), Electron Microscopy Data Bank (EMDB) and Biologic Magnetic Resonance Bank (BMRB). These archives are treasure troves of freely accessible data that document our quest for molecular or atomic understanding of biological function and processes in health and disease. They have prepared the field to tackle new archiving challenges as more and more (combinations of) techniques are being utilised to elucidate structure at ever increasing length scales. Furthermore, the field has made substantial efforts to develop validation methods that help users to assess the reliability of structures and to identify the most appropriate data for their needs. In this Review, we present an overview of public data archives in structural biology and discuss the importance of validation for users and producers of structural data. Finally, we sketch our efforts to integrate structural data with bioimaging data and with other sources of biological data. This will make relevant structural information available and more easily discoverable for a wide range of scientists. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  9. Monoalkylated barbiturate derivatives: X-ray crystal structure, theoretical studies, and biological activities

    Science.gov (United States)

    Barakat, Assem; Al-Majid, Abdullah Mohammed; Soliman, Saied M.; Islam, Mohammad Shahidul; Ghawas, Hussain Mansur; Yousuf, Sammer; Choudhary, M. Iqbal; Wadood, Abdul

    2017-08-01

    Barbiturate derivatives are privileged structures with a broad range of pharmaceutical applications. We prepared a series of 5-monoalkylated barbiturate derivatives (3a-l) and evaluated, in vitro, their antioxidant (DPPH assay), and α-glucosidase inhibitory activities. Compounds 3a-l were synthesized via Michael addition. The structure of compound 3k was determined using X-ray single-crystal diffraction, and geometric parameters were calculated using density functional theory at the B3LYP/6-311G(d,p) level of theory. Further, the structural analysis of 3k were also investigated. Biological studies revealed that compounds 3b (IC50 = 133.1 ± 3.2 μM), 3d (IC50 = 305 ± 7.7 μM), and 3e (IC50 = 184 ± 2.3 μM) have potent α-glucosidase enzyme inhibitors and showed greater activity than the standard drug acarbose (IC50 = 841 ± 1.73 μM). Compounds 3a-3i were found to show weak antioxidant activity against 1,1-diphenyl-2-picryl-hydrazyl (DPPH) radicals (IC50 = 91 ± 0.75 to 122 ± 1.0 μM) when tested against a standard antioxidant, gallic acid (IC50 = 23 ± 0.43 μM).

  10. Impact parameter determination for the passage of cosmic heavy ions through mesoscopic biological test organisms

    International Nuclear Information System (INIS)

    Facius, R.; Reitz, G.; Buecker, H.; Nevzgodina, L.V.; Maximova, E.N.

    1992-01-01

    Seeds of the plant Lactuca sativa as a prototype of a mesoscopic, i.e. neither micro- nor truly macroscopic, biological test organism, were exposed during the Biocosmos 9 mission to cosmic heavy ions within stacks of visual track detectors in order to explore the not yet properly understood radiobiological effects of single heavy ions. In such an investigation, the establishment of the geometrical correlation between the ion trajectories and the location of radiation-sensitive biological substructures is an essential task. We describe how this was achieved for biological test organisms, whose location and orientation had to be derived from contact photographs displaying their outlines and those of the holder plates only. The overall qualitative and quantitative precision achieved, as well as the contributing sources of uncertainties are discussed in detail. A precision of ≅ 10μm was accomplished for the coordinates of particle trajectories, which is near the limit set by the mechanical precision and stability of the detector material. The precision of the impact parameter is limited by the uncertainty in the location of the internal structures, which at best is around 50 and at worst around 150 μm, but is still acceptable when compared with the extension of the sensitive structures. (author)

  11. Impact parameter determination for the passage of cosmic heavy ions through mesoscopic biological test organisms

    Energy Technology Data Exchange (ETDEWEB)

    Facius, R.; Reitz, G.; Buecker, H. (Deutsche Forschungsanstalt fuer Luft- und Raumfahrt e.V. (DLR), Koeln (Germany)); Nevzgodina, L.V.; Maximova, E.N. (Institute of Biomedical Problems, Moscow (USSR))

    1992-01-01

    Seeds of the plant Lactuca sativa as a prototype of a mesoscopic, i.e. neither micro- nor truly macroscopic, biological test organism, were exposed during the Biocosmos 9 mission to cosmic heavy ions within stacks of visual track detectors in order to explore the not yet properly understood radiobiological effects of single heavy ions. In such an investigation, the establishment of the geometrical correlation between the ion trajectories and the location of radiation-sensitive biological substructures is an essential task. We describe how this was achieved for biological test organisms, whose location and orientation had to be derived from contact photographs displaying their outlines and those of the holder plates only. The overall qualitative and quantitative precision achieved, as well as the contributing sources of uncertainties are discussed in detail. A precision of {approx equal} 10{mu}m was accomplished for the coordinates of particle trajectories, which is near the limit set by the mechanical precision and stability of the detector material. The precision of the impact parameter is limited by the uncertainty in the location of the internal structures, which at best is around 50 and at worst around 150 {mu}m, but is still acceptable when compared with the extension of the sensitive structures. (author).

  12. Modeling cell-in-cell structure into its biological significance

    OpenAIRE

    He, M-f; Wang, S; Wang, Y; Wang, X-n

    2013-01-01

    Although cell-in-cell structure was noted 100 years ago, the molecular mechanisms of ?entering' and the destination of cell-in-cell remain largely unclear. It takes place among the same type of cells (homotypic cell-in-cell) or different types of cells (heterotypic cell-in-cell). Cell-in-cell formation affects both effector cells and their host cells in multiple aspects, while cell-in-cell death is under more intensive investigation. Given that cell-in-cell has an important role in maintainin...

  13. Mass determination based on electron scattering in electron probe X-ray microanalysis of thin biological specimens

    International Nuclear Information System (INIS)

    Linders, P.W.J.

    1984-01-01

    This thesis describes the development of a method for mass determination of thin biological objects by quantitative electron microscopy. The practical realization of the mass determination consists of photographical recording with subsequent densitometry. (Auth.)

  14. Capital Structure Determinants of Small and Medium Enterprises in Croatia

    Directory of Open Access Journals (Sweden)

    Nataša Šarlija

    2016-09-01

    Full Text Available Most of the research about capital structure is focused towards two theories: trade off theory (TOT and pecking order theory (POT. The idea is to explore which theory works better in certain conditions and identify the key determinants that affect the capital structure of the company. However, in different countries different determinants with opposite relation to the leverage are found to be significant. Besides, most of the previous researches are oriented on listed companies. The aim of this paper is to analyse the capital structure of small and medium enterprises in Croatia through the analysis of the fundamental determinants of the capital structure. The research was conducted on a data sample of 500 SMEs in Croatia in the period of 2005–2011. On the unbalanced panel data set a linear regression is applied. Influence of determinants on leverage is estimated by a static panel model with random effect and with fixed effect estimation. Four capital structure determinants are analysed: growth, size, profitability and tangible assets. The results of this research support the pecking order theory confirming that SMEs in Croatia are primarily financed frominternally generated funds that affect profitability, growth, tangible assets and enterprise size.

  15. Acoustic fine structure may encode biologically relevant information for zebra finches.

    Science.gov (United States)

    Prior, Nora H; Smith, Edward; Lawson, Shelby; Ball, Gregory F; Dooling, Robert J

    2018-04-18

    The ability to discriminate changes in the fine structure of complex sounds is well developed in birds. However, the precise limit of this discrimination ability and how it is used in the context of natural communication remains unclear. Here we describe natural variability in acoustic fine structure of male and female zebra finch calls. Results from psychoacoustic experiments demonstrate that zebra finches are able to discriminate extremely small differences in fine structure, which are on the order of the variation in acoustic fine structure that is present in their vocal signals. Results from signal analysis methods also suggest that acoustic fine structure may carry information that distinguishes between biologically relevant categories including sex, call type and individual identity. Combined, our results are consistent with the hypothesis that zebra finches can encode biologically relevant information within the fine structure of their calls. This study provides a foundation for our understanding of how acoustic fine structure may be involved in animal communication.

  16. Carcinogenesis: alterations in reciprocal interactions of normal functional structure of biologic systems.

    Science.gov (United States)

    Davydyan, Garri

    2015-12-01

    The evolution of biologic systems (BS) includes functional mechanisms that in some conditions may lead to the development of cancer. Using mathematical group theory and matrix analysis, previously, it was shown that normally functioning BS are steady functional structures regulated by three basis regulatory components: reciprocal links (RL), negative feedback (NFB) and positive feedback (PFB). Together, they form an integrative unit maintaining system's autonomy and functional stability. It is proposed that phylogenetic development of different species is implemented by the splitting of "rudimentary" characters into two relatively independent functional parts that become encoded in chromosomes. The functional correlate of splitting mechanisms is RL. Inversion of phylogenetic mechanisms during ontogenetic development leads cell differentiation until cells reach mature states. Deterioration of reciprocal structure in the genome during ontogenesis gives rise of pathological conditions characterized by unsteadiness of the system. Uncontrollable cell proliferation and invasive cell growth are the leading features of the functional outcomes of malfunctioning systems. The regulatory element responsible for these changes is RL. In matrix language, pathological regulation is represented by matrices having positive values of diagonal elements ( TrA  > 0) and also positive values of matrix determinant ( detA  > 0). Regulatory structures of that kind can be obtained if the negative entry of the matrix corresponding to RL is replaced with the positive one. To describe not only normal but also pathological states of BS, a unit matrix should be added to the basis matrices representing RL, NFB and PFB. A mathematical structure corresponding to the set of these four basis functional patterns (matrices) is a split quaternion (coquaternion). The structure and specific role of basis elements comprising four-dimensional linear space of split quaternions help to understand what

  17. Structure and Oxidation of Pyrrole Adducts Formed between Aflatoxin B2a and Biological Amines.

    Science.gov (United States)

    Rushing, Blake R; Selim, Mustafa I

    2017-06-19

    Aflatoxin B 2a has been shown to bind to proteins through a dialdehyde intermediate under physiological conditions. The proposed structure of this adduct has been published showing a Schiff base interaction, but adequate verification using structural elucidation instrumental techniques has not been performed. In this work, we synthesized the aflatoxin B 2a amino acid adduct under alkaline conditions, and the formation of a new product was determined using high performance liquid chromatography-time-of-flight mass spectrometry. The resulting accurate mass was used to generate a novel proposed chemical structure of the adduct in which the dialdehyde forms a pyrrole ring with primary amines rather than the previously proposed Schiff base interaction. The pyrrole structure was confirmed using 1 H, 13 C, correlation spectroscopy, heteronuclear single quantum correlation, and heteronuclear multiple bond correlation NMR and tandem mass spectrometry. Reaction kinetics show that the reaction is overall second order and that the rate increases as pH increases. Additionally, this study shows for the first time that aflatoxin B 2a dialdehyde forms adducts with phosphatidylethanolamines and does so through pyrrole ring formation, which makes it the first aflatoxin-lipid adduct to be structurally identified. Furthermore, oxidation of the pyrrole adduct produced a product that was 16 m/z heavier. When the aflatoxin B 2a -lysine (ε) adduct was oxidized, it gave a product with an accurate mass, mass fragmentation pattern, and 1 H NMR spectrum that match aflatoxin B 1 -lysine, which suggest the transformation of the pyrrole ring to a pyrrolin-2-one ring. These data give new insight into the fate and chemical properties of biological adducts formed from aflatoxin B 2a as well as possible interferences with known aflatoxin B 1 exposure biomarkers.

  18. COMPLEMENTARY SEX DETERMINATION IN HYMENOPTERAN PARASITOIDS AND ITS IMPLICATIONS FOR BIOLOGICAL CONTROL

    Institute of Scientific and Technical Information of China (English)

    WUZhishan; KeithR.Hopper; PaulJ.Ode; RogerW.Fuester; CHENJia-hua; GeorgeE.Heimpel

    2003-01-01

    In haplodiploid Hymenoptera, unfertilized eggs produce haploid males while fertilized eggs lead to diploid females under most circumstances. Diploid males can also be produced from fertilization under a system of sex determination known as complementary sex determination (CSD). Under single-locus CSD, sex is determined by multiple alleles at a single sex locus. Individuals heterozygous at the sex locus are female while hemizygous and homozygous individuals develop as haploid and diploid males, respectively. In multiple-locus CSD, two or more loci, each with two or more alleles, determine sex. Diploid individuals are female if one or more sex loci are het-erozygous, while a diploid is male only if homozygous at all sex loci. Diploid males are known to occur in 43 hym-enopteran species and single-locus CSD has been demonstrated in 22 of these species. Diploid males are either developmentally inviable or sterile, so their production constitutes a genetic load. Because diploid male production is more likely under inbreeding, CSD is a form of inbreeding depression. It is crucial to preserve the diversity of sex alleles and reduce the loss of genetic variation in biological control. In the parasitoid species with single-locus CSD, certain precautionary procedures can prevent negative effects of single-locus CSD on biological control.

  19. Sensitive kinetic spectrophotometric determination of captopril and ethamsylate in pharmaceutical preparations and biological fluids.

    Science.gov (United States)

    El-Shabrawy, Y; El-Enany, N; Salem, K

    2004-10-01

    A highly sensitive kinetic spectrophotometric method was developed for the determination of captopril (CPL) and ethamsylate (ESL) in pharmaceutical preparations and biological fluids. The method is based on a catalytic acceleration of the reaction between sodium azide and iodine in an aqueous solution. Concentration range of 0.1-1.5 microg ml(-1) for CPL and 0.3-3 microg ml(-1) for ESL was determined by measuring the decrease in the absorbance of iodine at 348 nm by a fixed time method. The decrease in absorbance after 5 min was markedly correlated to the concentration. The relative standard deviations obtained were 1.30 and 1.87 for CPL and ESL, respectively, in pure forms. Correlation coefficients were 0.9997 and 0.9999 for CPL and ESL, respectively. The detection limits were determined as (S/N = 3) were 20 ng ml(-1) for CPL and 50 ng ml(-1) for ESL. The proposed procedure was successively applied for the determination of both drugs in pharmaceutical preparations and in biological fluids.

  20. The determination of iodine in biological media using radioactivation analysis (1962)

    International Nuclear Information System (INIS)

    Comar, D.

    1962-06-01

    The object of this study is to show that the application of radioactivation analysis to the determination of iodine in biological media makes it possible to measure iodine concentrations of the order of 0.0001 μg. After a review of the chemical methods with a mention of the difficulties they present, the optimum conditions for the determination of iodine in biological liquids are given. Three methods are described: - the first consists of a chemical treatment which liberates the protein bound iodine in an inorganic form. After distillation this iodine is irradiated in a flux of thermal neutrons. The induced radioactivity is compared to that of a standard sample irradiated in the same conditions by γ spectrometry. - the second method which is of more general application consists in irradiating the sample and then extracting the iodine; its induced radio-activity is then measured by β-counting. - the third method measures the iodine directly in the thyroid tissue by anti-compton spectrometry. The sensitivity, the reproducibility and the accuracy are discussed. Some applications are described: determination of iodine in its various organic forms in serum, determination of iodine in urines, in food-stuffs, etc., in the thyroid tissue, etc. (author) [fr

  1. Birthday Cake Activity Structured Arrangement for Helping Children Determining Quantities

    Directory of Open Access Journals (Sweden)

    Neni Mariana

    2010-07-01

    Full Text Available Few researches have been concerned about relation between children’s spatial thinking and number sense. Narrowing for this small research, we focused on one component of spatial thinking, that is structuring objects, and one component of number senses, that is cardinality by determining quantities. This study focused on a design research that was conducted in Indonesia in which we investigated pre-school children’s (between 2 and 3.5 years old ability in making structured arrangement and their ability to determine the quantities by looking at the arrangements. The result shows us that some of the children were able to make such arrangement. However, the children found difficulties either to determine quantities from those arrangements or to compare some structures to easily recognize number of objects.

  2. Differential determination of 203Hg and 14C or 35S in double labelled biological samples

    International Nuclear Information System (INIS)

    Bem, E.M.; Bem, H.; Reimschussel, W.

    1979-01-01

    The differential determination of 203 Hg and 14 C or 35 S in double labelled biological samples is presented. The biological samples were mineralized with 70% HClO 4 and 30% H 2 O 2 in glass vials, MILLI-6. The γ-activity of 203 Hg was measured on a well scintillation counter. The total activity, due to 203 Hg and 14 C or 35 S, was measured by the liquid scintillation technique after addition of Aquasol into the same vials. The method of external standard channel ratio was used for standardization. Very good recoveries were obtained: 100+-0.7% for 203 Hg and 94.6-101.0% for 14 C and 35 S. This method could be used for other β, γ and β-active nuclides with similar β-spectra. (author)

  3. Development of capillary electrophoresis methods for quantitative determination of taurine in vehicle system and biological media.

    Science.gov (United States)

    da Silva, Dayse L P; Rüttinger, Hans H; Mrestani, Yahia; Baum, Walter F; Neubert, Reinhard H H

    2006-06-01

    CE methods have been developed for the determination of taurine in pharmaceutical formulation (microemulsion) and in biological media such as sweat. The CE system with end-column pulsed amperometric detection has been found to be an interesting method in comparison with UV and fluorescence detection for its simplicity and rapidity. A gold-disk electrode of 100 mm diameter was used as the working electrode. The effects of a field decoupler at the end of the capillary, separation voltage, injection and pressure times were investigated. A detection limit of 4 x 10(-5) mol/L was reached using integrated pulsed amperometric detection, a method successfully applied to taurine analysis of the biological samples such as sweat. For taurine analysis of oil-in-water microemulsion, fluorescence detector was the favored method, the detection limit of which was 4 x 10(-11) mol/L.

  4. Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation.

    Science.gov (United States)

    Villaverde, Alejandro F; Banga, Julio R

    2017-11-01

    The concept of dynamical compensation has been recently introduced to describe the ability of a biological system to keep its output dynamics unchanged in the face of varying parameters. However, the original definition of dynamical compensation amounts to lack of structural identifiability. This is relevant if model parameters need to be estimated, as is often the case in biological modelling. Care should we taken when using an unidentifiable model to extract biological insight: the estimated values of structurally unidentifiable parameters are meaningless, and model predictions about unmeasured state variables can be wrong. Taking this into account, we explore alternative definitions of dynamical compensation that do not necessarily imply structural unidentifiability. Accordingly, we show different ways in which a model can be made identifiable while exhibiting dynamical compensation. Our analyses enable the use of the new concept of dynamical compensation in the context of parameter identification, and reconcile it with the desirable property of structural identifiability.

  5. Nucleic acid helix structure determination from NMR proton chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Werf, Ramon M. van der; Tessari, Marco; Wijmenga, Sybren S., E-mail: S.Wijmenga@science.ru.nl [Radboud University Nijmegen, Department of Biophysical Chemistry, Institute of Molecules and Materials (Netherlands)

    2013-06-15

    We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.

  6. Neutron diffractometers for structural biology at spallation neutron sources

    Energy Technology Data Exchange (ETDEWEB)

    Schoenborn, B.P.; Pitcher, E. [Los Alamos National Laboratory, NM (United States)

    1994-12-31

    Spallation neutron sources are ideal for diffraction studies of proteins and oriented molecular complexes. With spoliation neutrons and their time dependent wavelength structure, it is easy to electronically select data with an optimal wavelength bandwidth and cover the whole Laue spectrum as time (wavelength) resolved snapshots. This optimized data quality with best peak-to-background ratios and provides adequate spatial and energy resolution to eliminate peak overlaps. The application of this concept will use choppers to select the desired Laue wavelength spectrum and employ focusing optics and large cylindrical {sup 3}He detectors to optimize data collection rates. Such a diffractometer will cover a Laue wavelength range from 1 to 5{Angstrom} with a flight path length of 10m and an energy resolution of 0.25{Angstrom}. Moderator concepts for maximal flux distribution within this energy range will be discussed using calculated flux profiles. Since the energy resolution required for such timed data collection in this super Laue techniques is not very high, the use of a linac only (LAMPF) spoliation target is an exciting possibility with an order of magnitude increase in flux.

  7. Neutron diffractometers for structural biology at spallation neutron sources

    International Nuclear Information System (INIS)

    Schoenborn, B.P.; Pitcher, E.

    1994-01-01

    Spallation neutron sources are ideal for diffraction studies of proteins and oriented molecular complexes. With spoliation neutrons and their time dependent wavelength structure, it is easy to electronically select data with an optimal wavelength bandwidth and cover the whole Laue spectrum as time (wavelength) resolved snapshots. This optimized data quality with best peak-to-background ratios and provides adequate spatial and energy resolution to eliminate peak overlaps. The application of this concept will use choppers to select the desired Laue wavelength spectrum and employ focusing optics and large cylindrical 3 He detectors to optimize data collection rates. Such a diffractometer will cover a Laue wavelength range from 1 to 5 Angstrom with a flight path length of 10m and an energy resolution of 0.25 Angstrom. Moderator concepts for maximal flux distribution within this energy range will be discussed using calculated flux profiles. Since the energy resolution required for such timed data collection in this super Laue techniques is not very high, the use of a linac only (LAMPF) spoliation target is an exciting possibility with an order of magnitude increase in flux

  8. Synthesis, crystal structure and biological activity of n-(5-(o-tolyl)-1, 3, 4-thiadiazol-2-yl)cyclopropanecarboxamide

    International Nuclear Information System (INIS)

    Tong, J.Y.; Sun, N.B.; Wu, H.K.

    2013-01-01

    A new 1, 3, 4-thiadiazole compound, N-(5-(o-tolyl)-1,3,4-thiadiazol-2-yl) cyclopropanecarboxamide, was synthesized and its structure was confirmed by 1H NMR, MS and HRMS. The single crystal structure of the title compound was determined by X-ray diffraction. The preliminary biological test showed that the synthesized compound has moderate herbicidal activity against Brassica campestris and fungicidal activities against Sclerotinia sclerotiorum(Lib.) de Bary, Rhizoctonia solanii, Fusarium oxysporum, Corynespora cassiicola, and Botrytis cinerea. (author)

  9. Determinants of Capital Structure in Non-Financial Companies

    OpenAIRE

    Kühnhausen, Fabian; Stieber, Harald W.

    2014-01-01

    In this paper, we evaluate firm-, industry- and country-specific factors determining a firm's capital structure. The empirical validity of several capital structure theories has been ambiguous so far. We shed light on the main drivers of leverage and depict differences in industry and country characteristics. Using a short panel data set with a large cross-section, we are able to show that firm size, industry leverage, industry growth and tax shield positively affect leverage ratios, while pr...

  10. A study on determinants of capital structure in India

    Directory of Open Access Journals (Sweden)

    Anshu Handoo

    2014-09-01

    Full Text Available The paper identifies the most important determinants of capital structure of 870 listed Indian firms comprising both private sector companies and government companies for the period 2001–2010. Ten independent variables and three dependent variables have been tested using regression analysis. It has been concluded that factors such as profitability, growth, asset tangibility, size, cost of debt, tax rate, and debt serving capacity have significant impact on the leverage structure chosen by firms in the Indian context.

  11. Determinants of Market Structure and the Airline Industry

    Science.gov (United States)

    Raduchel, W.

    1972-01-01

    The general economic determinants of market structure are outlined with special reference to the airline industry. Included are the following facets: absolute size of firms; distributions of firms by size; concentration; entry barriers; product and service differentiation; diversification; degrees of competition; vertical integration; market boundaries; and economies of scale. Also examined are the static and dynamic properties of market structure in terms of mergers, government policies, and economic growth conditions.

  12. Population Genetic Structure of Glycyrrhiza inflata B. (Fabaceae) Is Shaped by Habitat Fragmentation, Water Resources and Biological Characteristics.

    Science.gov (United States)

    Yang, Lulu; Chen, Jianjun; Hu, Weiming; Yang, Tianshun; Zhang, Yanjun; Yukiyoshi, Tamura; Zhou, Yanyang; Wang, Ying

    2016-01-01

    Habitat fragmentation, water resources and biological characteristics are important factors that shape the genetic structure and geographical distribution of desert plants. Analysis of the relationships between these factors and population genetic variation should help to determine the evolutionary potential and conservation strategies for genetic resources for desert plant populations. As a traditional Chinese herb, Glycyrrhiza inflata B. (Fabaceae) is restricted to the fragmented desert habitat in China and has undergone a dramatic decline due to long-term over-excavation. Determining the genetic structure of the G. inflata population and identifying a core collection could help with the development of strategies to conserve this species. We investigated the genetic variation of 25 G. inflata populations based on microsatellite markers. A high level of population genetic divergence (FST = 0.257), population bottlenecks, reduced gene flow and moderate genetic variation (HE = 0.383) were detected. The genetic distances between the populations significantly correlated with the geographical distances, and this suggests that habitat fragmentation has driven a special genetic structure of G. inflata in China through isolation by distance. STRUCTURE analysis showed that G. inflata populations were structured into three clusters and that the populations belonged to multiple water systems, which suggests that water resources were related to the genetic structure of G. inflata. In addition, the biological characteristics of the perennial species G. inflata, such as its long-lived seeds, asexual reproduction, and oasis ecology, may be related to its resistance to habitat fragmentation. A core collection of G. inflata, that included 57 accessions was further identified, which captured the main allelic diversity of G. inflata. Recent habitat fragmentation has accelerated genetic divergence. The population genetic structure of G. inflata has been shaped by habitat

  13. Generative probabilistic models extend the scope of inferential structure determination

    DEFF Research Database (Denmark)

    Olsson, Simon; Boomsma, Wouter; Frellsen, Jes

    2011-01-01

    demonstrate that the use of generative probabilistic models instead of physical forcefields in the Bayesian formalism is not only conceptually attractive, but also improves precision and efficiency. Our results open new vistas for the use of sophisticated probabilistic models of biomolecular structure......Conventional methods for protein structure determination from NMR data rely on the ad hoc combination of physical forcefields and experimental data, along with heuristic determination of free parameters such as weight of experimental data relative to a physical forcefield. Recently, a theoretically...

  14. Rotational characterization of methyl methacrylate: Internal dynamics and structure determination

    Science.gov (United States)

    Herbers, Sven; Wachsmuth, Dennis; Obenchain, Daniel A.; Grabow, Jens-Uwe

    2018-01-01

    Rotational constants, Watson's S centrifugal distortion coefficients, and internal rotation parameters of the two most stable conformers of methyl methacrylate were retrieved from the microwave spectrum. Splittings of rotational energy levels were caused by two non equivalent methyl tops. Constraining the centrifugal distortion coefficients and internal rotation parameters to the values of the main isotopologues, the rotational constants of all single substituted 13C and 18O isotopologues were determined. From these rotational constants the substitution structures and semi-empirical zero point structures of both conformers were precisely determined.

  15. Organizational Structure as a Determinant of Job Burnout.

    Science.gov (United States)

    Bilal, Atif; Ahmed, Hafiz Mushtaq

    2017-03-01

    This exploratory study determined the impact of organizational structure, particularly participation in decision making, instrumental communication, formalization, integration, and promotional opportunity, on burnout among Pakistani pediatric nurses. Data were collected from pediatric nurses working for Punjab's largest state-run hospital. The findings revealed that participation in decision making, instrumental communication, and promotional opportunity prevented burnout. Formalization contributed to burnout but integration was not related to burnout. Quite interestingly, except for supervisory status, most control variables for this study were not significantly related to emotional burnout. Hence, the hypothesis that organizational structure is a determinant of job burnout was accepted.

  16. Synthetical bone-like and biological hydroxyapatites: a comparative study of crystal structure and morphology

    Energy Technology Data Exchange (ETDEWEB)

    Markovic, Smilja; Veselinovic, Ljiljana; Lukic, Miodrag J; Ignjatovic, Nenad; Uskokovic, Dragan [Institute of Technical Sciences of the Serbian Academy of Sciences and Arts, Knez Mihailova 35/IV, 11001 Belgrade (Serbia); Karanovic, Ljiljana [Laboratory for Crystallography, Faculty of Mining and Geology, University of Belgrade, Dusina 7, 11000 Belgrade (Serbia); Bracko, Ines, E-mail: dragan.uskokovic@itn.sanu.ac.rs [Jozef Stefan Institute, Jamova 39, 1000 Ljubljana (Slovenia)

    2011-08-15

    Phase composition, crystal structure and morphology of biological hydroxyapatite (BHAp) extracted from human mandible bone, and carbonated hydroxyapatite (CHAp), synthesized by the chemical precipitation method, were studied by x-ray powder diffraction (XRD), Fourier transform infrared (FTIR) and Raman (R) spectroscopy techniques, combined with transmission electron microscopy (TEM). Structural and microstructural parameters were determined through Rietveld refinement of recorded XRD data, performed using the FullProf computing program, and TEM. Microstructural analysis shows anisotropic extension along the [0 0 l] crystallographic direction (i.e. elongated crystallites shape) of both investigated samples. The average crystallite sizes of 10 and 8 nm were estimated for BHAp and CHAp, respectively. The FTIR and R spectroscopy studies show that carbonate ions substitute both phosphate and hydroxyl ions in the crystal structure of BHAp as well as in CHAp, indicating that both of them are mixed AB-type of CHAp. The thermal behaviour and carbonate content were analysed using thermogravimetric and differential thermal analysis. The carbonate content of about 1 wt.% and phase transition, at near 790 {sup 0}C, from HAp to {beta}-tricalcium phosphate were determined in both samples. The quality of synthesized CHAp powder, particularly, the particle size distribution and uniformity of morphology, was analysed by a particle size analyser based on laser diffraction and field emission scanning electron microscopy, respectively. These data were used to discuss similarity between natural and synthetic CHAp. Good correlation between the unit cell parameters, average crystallite size, morphology, carbonate content and crystallographic positions of carbonate ions in natural and synthetic HAp samples was found.

  17. Synthetical bone-like and biological hydroxyapatites: a comparative study of crystal structure and morphology

    International Nuclear Information System (INIS)

    Markovic, Smilja; Veselinovic, Ljiljana; Lukic, Miodrag J; Ignjatovic, Nenad; Uskokovic, Dragan; Karanovic, Ljiljana; Bracko, Ines

    2011-01-01

    Phase composition, crystal structure and morphology of biological hydroxyapatite (BHAp) extracted from human mandible bone, and carbonated hydroxyapatite (CHAp), synthesized by the chemical precipitation method, were studied by x-ray powder diffraction (XRD), Fourier transform infrared (FTIR) and Raman (R) spectroscopy techniques, combined with transmission electron microscopy (TEM). Structural and microstructural parameters were determined through Rietveld refinement of recorded XRD data, performed using the FullProf computing program, and TEM. Microstructural analysis shows anisotropic extension along the [0 0 l] crystallographic direction (i.e. elongated crystallites shape) of both investigated samples. The average crystallite sizes of 10 and 8 nm were estimated for BHAp and CHAp, respectively. The FTIR and R spectroscopy studies show that carbonate ions substitute both phosphate and hydroxyl ions in the crystal structure of BHAp as well as in CHAp, indicating that both of them are mixed AB-type of CHAp. The thermal behaviour and carbonate content were analysed using thermogravimetric and differential thermal analysis. The carbonate content of about 1 wt.% and phase transition, at near 790 0 C, from HAp to β-tricalcium phosphate were determined in both samples. The quality of synthesized CHAp powder, particularly, the particle size distribution and uniformity of morphology, was analysed by a particle size analyser based on laser diffraction and field emission scanning electron microscopy, respectively. These data were used to discuss similarity between natural and synthetic CHAp. Good correlation between the unit cell parameters, average crystallite size, morphology, carbonate content and crystallographic positions of carbonate ions in natural and synthetic HAp samples was found.

  18. Determination of rhenium in biological and environmental samples by radiochemical neutron activation analysis

    International Nuclear Information System (INIS)

    Kucera, J.; Mizera, J.; Randa, Z.; Byrne, A.R.; Lucanikova, M.

    2006-01-01

    Radiochemical neutron activation procedures using liquid-liquid extraction with tetraphenylarsonium chloride in chloroform from 1 M HCl and solid extraction with ALIQUAT 336 incorporated in a polyacrylonitrile binding matrix from 0.1 M HCl were developed for accurate determination of rhenium in biological and environmental samples at the sub-ng.g -1 level. Concentrations of Re in the range of 0.1 to 2.4 ng.g -1 were determined in several botanical reference materials (RM), while in a RM of road dust a value of approx. 10 ng.g -1 was found. Significantly elevated values of Re, up to 90 ng.g -1 , were found in seaweed (brown algae). Results for Re in the brown algae Fucus vesiculosus in which elevated 99 Tc values had previously been determined suggest possible competition between Re and Tc in the accumulation process. (author)

  19. Synthesis, structural, spectroscopic and biological studies of Schiff base complexes

    Science.gov (United States)

    Diab, M. A.; El-Sonbati, A. Z.; Shoair, A. F.; Eldesoky, A. M.; El-Far, N. M.

    2017-08-01

    Schiff base ligand 4-((pyridin-2- yl)methyleneamino)-1,2-dihydro-2,3-dimethyl-1-phenylpyrazol-5-one (PDMP) and its complexes were prepared and characterized on the basis of elemental analysis, IR, mass spectra and thermogravimetric analysis. All results confirm that the complexes have 1:1 (M: PMDP) stoichiometric formula [M(PMDP)Cl2H2O ] (M = Cu(II), Co(II), Ni(II) and Mn(II)), [Cd(PMDP)Cl2] and the ligand behaves as a bi/tridentate forming five-membered chelating ring towards the metal ions, bonding through azomethine nitrogen/exocyclic carbonyl oxygen, azomethine pyridine nitrogen and exocyclic carbonyl oxygen. The shift in the band positions of the groups involved in coordination has been utilized to estimate the metal-nitrogen and/or oxygen bond lengths. The complexes of Co(II), Ni(II) and Cu(II) are paramagnetic and the magnetic as well as spectral data suggest octahedral geometry, whereas the Cd(II) complex is tetrahedral. The XRD studies show that both the ligand and its metal complexes (1 and 3) show polycrystalline with crystal structure. Molecular docking was used to predict the binding between PMDP ligand and the receptors. The corrosion inhibition of mild steel in 2 M HCl solution by PDMP was explored utilizing potentiodynamic polarization, electrochemical impedance spectroscopy (EIS) and (EFM) electrochemical frequency modulation method. Potentiodynamic polarization demonstrated that PDMP compound is mixed-type inhibitor. EIS spectra exhibit one capacitive loop and confirm the protective ability. The percentage of inhibition efficiency was found to increase with increasing the inhibitor concentration.

  20. Invited review: Caseins and the casein micelle: their biological functions, structures, and behavior in foods.

    Science.gov (United States)

    Holt, C; Carver, J A; Ecroyd, H; Thorn, D C

    2013-10-01

    A typical casein micelle contains thousands of casein molecules, most of which form thermodynamically stable complexes with nanoclusters of amorphous calcium phosphate. Like many other unfolded proteins, caseins have an actual or potential tendency to assemble into toxic amyloid fibrils, particularly at the high concentrations found in milk. Fibrils do not form in milk because an alternative aggregation pathway is followed that results in formation of the casein micelle. As a result of forming micelles, nutritious milk can be secreted and stored without causing either pathological calcification or amyloidosis of the mother's mammary tissue. The ability to sequester nanoclusters of amorphous calcium phosphate in a stable complex is not unique to caseins. It has been demonstrated using a number of noncasein secreted phosphoproteins and may be of general physiological importance in preventing calcification of other biofluids and soft tissues. Thus, competent noncasein phosphoproteins have similar patterns of phosphorylation and the same type of flexible, unfolded conformation as caseins. The ability to suppress amyloid fibril formation by forming an alternative amorphous aggregate is also not unique to caseins and underlies the action of molecular chaperones such as the small heat-shock proteins. The open structure of the protein matrix of casein micelles is fragile and easily perturbed by changes in its environment. Perturbations can cause the polypeptide chains to segregate into regions of greater and lesser density. As a result, the reliable determination of the native structure of casein micelles continues to be extremely challenging. The biological functions of caseins, such as their chaperone activity, are determined by their composition and flexible conformation and by how the casein polypeptide chains interact with each other. These same properties determine how caseins behave in the manufacture of many dairy products and how they can be used as functional

  1. High-throughput determination of RNA structure by proximity ligation.

    Science.gov (United States)

    Ramani, Vijay; Qiu, Ruolan; Shendure, Jay

    2015-09-01

    We present an unbiased method to globally resolve RNA structures through pairwise contact measurements between interacting regions. RNA proximity ligation (RPL) uses proximity ligation of native RNA followed by deep sequencing to yield chimeric reads with ligation junctions in the vicinity of structurally proximate bases. We apply RPL in both baker's yeast (Saccharomyces cerevisiae) and human cells and generate contact probability maps for ribosomal and other abundant RNAs, including yeast snoRNAs, the RNA subunit of the signal recognition particle and the yeast U2 spliceosomal RNA homolog. RPL measurements correlate with established secondary structures for these RNA molecules, including stem-loop structures and long-range pseudoknots. We anticipate that RPL will complement the current repertoire of computational and experimental approaches in enabling the high-throughput determination of secondary and tertiary RNA structures.

  2. Track Detection Technique Using CR-39 for Determining Depleted Uranium in Biological Specimens

    International Nuclear Information System (INIS)

    Murbat, S.M.

    2013-01-01

    Track detecting technique using CR-39 track detector has been implemented for determining depleted uranium concentration in biological specimens (tissues, bones, and blood) of patients infected with cancer diseases. Results were compared with specimens of patients infected with conventional diseases (noncancerous). Specimens were collected from middle and south of Iraq have been contaminated with depleted uranium in the Gulf war in 1991. Results show that this technique is efficient for determining depleted uranium concentration in biological specimens. It was found that all studies samples determine for patients infected with cancer diseases contain a high concentration of depleted uranium (more than the international standard) comparing with noncancerous diseases. Moreover, it was found that persons infected with Leukemia show more sensitive to uranium concentrations to induce the diseases (66-202 ppb), while (116- 1910 ppb) concentrations were needed for inducing cancer diseases in organs and tissues. Result confirmed the correlation between cancerous diseases and the munitions made of depleted uranium used in the Gulf war in 1991 leads to contaminate the Iraqi environment and causes a high risk against people in Iraq.

  3. Heavy water effects on the structure, functions and behavior of biological systems

    International Nuclear Information System (INIS)

    Buzgariu, Wanda; Caloianu, Maria; Moldovan, Lucia; Titescu, G.

    2003-01-01

    The H 2 O substitution for D 2 O either in environment or in the culture medium of the living systems generates changes in their main functions and composition. In this paper some of the heavy water effects in biological systems such as structural and functional changes were reviewed: normal cell architecture alterations, cell division and membrane functions disturbance, muscular contractility and the perturbations of biological oscillators such as circadian rhythm, heart rate, respiratory cycle, tidal and ultradian rhythm. (authors)

  4. Liquid chromatographic determination of CPZEN-45, a novel anti-tubercular drug, in biological samples.

    Science.gov (United States)

    Hanif, S N M; Hickey, A J; Garcia-Contreras, L

    2014-01-01

    CPZEN-45 is a new drug candidate being considered for the treatment of tuberculosis (TB). The aim of this study was to develop and validate a reverse-phase high-performance liquid chromatographic (HPLC) method suitable to determine CPZEN-45 concentrations in biological samples. CPZEN-45 was extracted from biological fluids and tissues (plasma, lung and spleen from guinea pig) by sequential extraction with acetonitrile and quantified by a Waters HPLC Alliance System coupled with a ZORBAX Bonus-RP column, guard column and UV detection at 263nm. The mobile phase was 20:80 acetonitrile:ultrapure-water with 0.05% TFA. The CPZEN-45 peak was eluted at 5.1min with no interference from the inherent peaks of plasma, bronchoalveolar lavage (BAL), lung or spleen tissues. Recovery of CPZEN-45 from biological samples was >96% of the spiked amount. The limit of detection was 0.05μg/ml and the limit of quantitation was 0.29μg/ml which was more than 5 and 21 times lower than the reported minimal inhibitory concentration of CPZEN-45 (MIC=1.56μg/ml for Mycobacterium tuberculosis and 6.25μg/ml for MDR-TB, respectively). Thus, HPLC method was deemed reliable, sensitive, reproducible and accurate for the determination of CPZEN-45 concentrations in plasma, BAL, lung and spleen tissues. Therefore, this method was used in subsequent studies in the guinea pig model to determine the disposition of CPZEN-45 after administration of solutions by the IV and SC routes. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. Structure determination of helical filaments by solid-state NMR spectroscopy

    Science.gov (United States)

    Ahmed, Mumdooh; Spehr, Johannes; König, Renate; Lünsdorf, Heinrich; Rand, Ulfert; Lührs, Thorsten; Ritter, Christiane

    2016-01-01

    The controlled formation of filamentous protein complexes plays a crucial role in many biological systems and represents an emerging paradigm in signal transduction. The mitochondrial antiviral signaling protein (MAVS) is a central signal transduction hub in innate immunity that is activated by a receptor-induced conversion into helical superstructures (filaments) assembled from its globular caspase activation and recruitment domain. Solid-state NMR (ssNMR) spectroscopy has become one of the most powerful techniques for atomic resolution structures of protein fibrils. However, for helical filaments, the determination of the correct symmetry parameters has remained a significant hurdle for any structural technique and could thus far not be precisely derived from ssNMR data. Here, we solved the atomic resolution structure of helical MAVSCARD filaments exclusively from ssNMR data. We present a generally applicable approach that systematically explores the helical symmetry space by efficient modeling of the helical structure restrained by interprotomer ssNMR distance restraints. Together with classical automated NMR structure calculation, this allowed us to faithfully determine the symmetry that defines the entire assembly. To validate our structure, we probed the protomer arrangement by solvent paramagnetic resonance enhancement, analysis of chemical shift differences relative to the solution NMR structure of the monomer, and mutagenesis. We provide detailed information on the atomic contacts that determine filament stability and describe mechanistic details on the formation of signaling-competent MAVS filaments from inactive monomers. PMID:26733681

  6. Determination of phosphorus in biological samples by thermal neutron activation followed by β--counting

    International Nuclear Information System (INIS)

    Weginwar, R.G.; Samudralwar, D.L.; Garg, A.N.

    1989-01-01

    Phosphorus was determined using the β - emitter 32 P by instrumental neutron activation analysis (INAA) in several NBS and IAEA standards, and in samples of biological origin such as human and animal blood, cancerous tissue, edible plant leaves, diets, milk samples, etc. The method involves thermal neutron irradiation (for 2-10 h in a reactor) followed by β - counting on an end-window gas flow proportional counter using aluminium filter. The results are within ±10% of the certified values in most cases. (author) 29 refs.; 3 tabs

  7. Method for determining the biological effects of air pollution by transplanted lichens

    Energy Technology Data Exchange (ETDEWEB)

    Schoenbeck, H

    1969-01-01

    The natural sensitivity of the leaf Parmelia physodes to air pollutants can be used for their detection. For this purpose the lichens are transplanted in many parallel lines onto boards made of wood or of any other material (lichen exposure boards) and are exposed in the area to be investigated at a height of 1.50 m. Their reactions are recorded photographically at definite intervals. The biological test values determined permit evidence of the existing emission load to be obtained, which can then be used in addition to the chemical air analysis.

  8. A Fast Radiochemical Method for the Determination of Some Essential Trace Elements in Biology and Medicine

    International Nuclear Information System (INIS)

    Samsahl, K.

    1964-12-01

    A method has been developed for the determination with neutron-activation analysis of the following trace elements in soft biological tissues: Br, Ca, Cl, Cu, K, Mg, Mn, Mo, Na, P, Sr and Zn. The method consists in performing a short-term irradiation of the samples with a high thermal neutron flux, followed by fast chemical separations and gamma-spectrometric measurements. The chemical separations and the measurements of short-lived nuclides from a run are finished within 70 min, after the end of irradiation

  9. Ionometric determination of boron in natural, waste waters and biological materials

    International Nuclear Information System (INIS)

    Yakimov, V.P.; Markova, O.L.

    1992-01-01

    Method have been developed for the determination of boron in natural, waste waters and biological materials using direct potentiometry with a BF 4 - selective electrode. In order to estimate the matrix effects in plotting the calibration graphs, it is recommended to and the test water or solution of biomaterial mineralizates, containing boron in electrode-inactive form, to the calibration solutions before e.m.f. measurements version of boron into tetrafluoroborate in solid phase on heating the mineralized samples with ammonium bifluoride at 150-180 deg C

  10. A neural network based approach for determination of optical scattering and absorption coefficients of biological tissue

    International Nuclear Information System (INIS)

    Warncke, D; Lewis, E; Leahy, M; Lochmann, S

    2009-01-01

    The propagation of light in biological tissue depends on the absorption and reduced scattering coefficient. The aim of this project is the determination of these two optical properties using spatially resolved reflectance measurements. The sensor system consists of five laser sources at different wavelengths, an optical fibre probe and five photodiodes. For these kinds of measurements it has been shown that an often used solution of the diffusion equation can not be applied. Therefore a neural network is being developed to extract the needed optical properties out of the reflectance data. Data sets for the training, validation and testing process are provided by Monte Carlo Simulations.

  11. A Fast Radiochemical Method for the Determination of Some Essential Trace Elements in Biology and Medicine

    Energy Technology Data Exchange (ETDEWEB)

    Samsahl, K

    1964-12-15

    A method has been developed for the determination with neutron-activation analysis of the following trace elements in soft biological tissues: Br, Ca, Cl, Cu, K, Mg, Mn, Mo, Na, P, Sr and Zn. The method consists in performing a short-term irradiation of the samples with a high thermal neutron flux, followed by fast chemical separations and gamma-spectrometric measurements. The chemical separations and the measurements of short-lived nuclides from a run are finished within 70 min, after the end of irradiation.

  12. Evaluation of Botanical Reference Materials for the Determination of Vanadium in Biological Samples

    DEFF Research Database (Denmark)

    Heydorn, Kaj; Damsgaard, Else

    1982-01-01

    Three botanical reference materials prepared by the National Bureau of Standards have been studied by neutron activation analysis to evaluate their suitability with respect to the determination of vanadium in biological samples. Various decomposition methods were applied in connection with chemic....... A reference value of 1.15 mg/kg of this material is recommended, based on results from 3 different methods. All three materials are preferable to SRM 1571 Orchard Leaves, while Bowen's Kale remains the material of choice because of its lower concentration....

  13. NBS SRM 1569 Brewer's Yeast: Is it an adequate standard reference material for testing a chromium determination in biological materials tion in biological materials

    International Nuclear Information System (INIS)

    Goeij, J.J.M. de; Volkers, K.J.; Tjioe, P.S.; Kroon, J.J.

    1978-01-01

    Some analytical experiences with NBS SRM 1569 Brewer's Yeast are presented. Against this background the adequacy of this standard reference material for the determination of chromium in biological materials is discussed. Authors have three main objections. Due to its high content of insoluble chromium-containing particles, SRM 1569 is not typical for biological materials, possibly not even for Brewer's Yeast. The chromium level of SRM 1569 is not typical for the chromium levels normally encountered in pure biological materials. The major fraction (69 +- 3 percent) of the chromium is present in a form which is insoluble under the conditions used in Author's analysis. (T.I.)

  14. Direct electron crystallographic determination of zeolite zonal structures

    International Nuclear Information System (INIS)

    Dorset, Douglas L.; Gilmore, Christopher J.; Jorda, Jose Luis; Nicolopoulos, Stavros

    2007-01-01

    The prospect for improving the success of ab initio zeolite structure investigations with electron diffraction data is evaluated. First of all, the quality of intensities obtained by precession electron diffraction at small hollow cone illumination angles is evaluated for seven representative materials: ITQ-1, ITQ-7, ITQ-29, ZSM-5, ZSM-10, mordenite, and MCM-68. It is clear that, for most examples, an appreciable fraction of a secondary scattering perturbation is removed by precession at small angles. In one case, ZSM-10, it can also be argued that precession diffraction produces a dramatically improved 'kinematical' data set. There seems to no real support for application of a Lorentz correction to these data and there is no reason to expect for any of these samples that a two-beam dynamical scattering relationship between structure factor amplitude and observed intensity should be valid. Removal of secondary scattering by the precession mode appears to facilitate ab initio structure analysis. Most zeolite structures investigated could be solved by maximum entropy and likelihood phasing via error-correcting codes when precession data were used. Examples include the projected structure of mordenite that could not be determined from selected area data alone. One anomaly is the case of ZSM-5, where the best structure determination in projection is made from selected area diffraction data. In a control study, the zonal structure of SSZ-48 could be determined from selected area diffraction data by either maximum entropy and likelihood or traditional direct methods. While the maximum entropy and likelihood approach enjoys some advantages over traditional direct methods (non-dependence on predicted phase invariant sums), some effort must be made to improve the figures of merit used to identify potential structure solutions

  15. Determination of Biological Treatability Processes of Textile Wastewater and Implementation of a Fuzzy Logic Model

    Directory of Open Access Journals (Sweden)

    Harun Akif Kabuk

    2015-01-01

    Full Text Available This study investigated the biological treatability of textile wastewater. For this purpose, a membrane bioreactor (MBR was utilized for biological treatment after the ozonation process. Due to the refractory organic contents of textile wastewater that has a low biodegradability capacity, ozonation was implemented as an advanced oxidation process prior to the MBR system to increase the biodegradability of the wastewater. Textile wastewater, oxidized by ozonation, was fed to the MBR at different hydraulic retention times (HRT. During the process, color, chemical oxygen demand (COD, and biochemical oxygen demand (BOD removal efficiencies were monitored for 24-hour, 12-hour, 6-hour, and 3-hour retention times. Under these conditions, 94% color, 65% COD, and 55% BOD removal efficiencies were obtained in the MBR system. The experimental outputs were modeled with multiple linear regressions (MLR and fuzzy logic. MLR results suggested that color removal is more related to COD removal relative to BOD removal. A surface map of this issue was prepared with a fuzzy logic model. Furthermore, fuzzy logic was employed to the whole modeling of the biological system treatment. Determination coefficients for COD, BOD, and color removal efficiencies were 0.96, 0.97, and 0.92, respectively.

  16. Disclosure Level of CPC 29 Biological Assets: Analysis of Determining Factors in Brazilian companies

    Directory of Open Access Journals (Sweden)

    Daniel Ramos Nogueira

    2017-04-01

    Full Text Available The research question guiding this research is "What are the Determining Factors of CPC 29 Disclosure in Brazilian Companies?". In this aspect, the research objective was to evaluate the main factors that affect the disclosure of information related to biological assets. For this, 5 variables highlighted in the literature were selected as evidence influencers. The sample was composed of Brazilian companies with biological assets in the Balance Sheet. From this list, financial statements, explanatory notes, corporate management level and independent auditing company for the 6 years (2010 to 2015 were collected. With the collected information, the dependent variable (Disclosure level of CPC 29 and the independent variables of each year were verified. At the end (after exclusions, 100 observations were analyzed. The results indicated that the variables Size, Representativeness of Biological Assets and Effectiveness of OCPC 07 positively impacted the level of Disclosure. The first two confirmed the predicted hypothesis and OCPC 07 presented a relation that was different from what was expected, showing an increase and not a reduction in the number of disclosures in the years 2014 and 2015.

  17. Quantitative determination of nitrogen biological fixation by the N-15 isotopic method

    International Nuclear Information System (INIS)

    Basantes, Emilio; Trivelin, Paulo; Mui Tsai, Siu

    1993-01-01

    In order to quantify the biological nitrogen fixation (BNF) and to evaluate the mycorrhiza effect in the BNF, an experiment was carried on by applying 1 5 N -ammonium sulphate and mycorrhiza fungi to the soil. The treatments included legumes: mucuna negra(Stizolobium atterrinum Piper et Tracv) and caupi (Vigna unguiculoata L. Walp). Two control plants: non nodulating soybean (Glycine max L.Merril) and rice (Oryza sativa), were used for measuring the fixed N in the legumes by isotope dilution method. Both legumes and control plants assimmilated the same ammounts of nitrogen from the soil and fertilizer. The greater N content in the legumnes was determined as coming from the fixed nitrogen. Rice and non nodulating soybean showed to be good controls for measuring biological nitrogen fixation using isotopic dilution method. The values of fixed nitrogen for legumes calculated using rice as control plant were slightly greater than those with non nodulating soybean, nevertheless there were no significant statistical differences between the values. The mucuna fixed more N than caupi in both mycorrhiza treatments (76.7, 66.6 and 56. 7 per cent of N fixed, respectively). The mycorrhiza increased dry matter yield (13.84 per cent), accumulation of N in the plant(14.85 per cent N) and the biological N fixation (16.06 per cent N-fixed) in caupi

  18. Document boundary determination using structural and lexical analysis

    Science.gov (United States)

    Taghva, Kazem; Cartright, Marc-Allen

    2009-01-01

    The document boundary determination problem is the process of identifying individual documents in a stack of papers. In this paper, we report on a classification system for automation of this process. The system employs features based on document structure and lexical content. We also report on experimental results to support the effectiveness of this system.

  19. New method to determine structures in thermonuclear plasmas

    International Nuclear Information System (INIS)

    Tanzi, C.P.

    1998-01-01

    The information from tomographic methods is not always sufficient to determine fast changing structures, e.g. very hot plasmas. A new method has been developed by means of which, among other things, physical mechanisms of plasma instability can be disentangled. 4 refs

  20. Dynamic Capital Structure: Dynamics, Determinants and Speed of Adjustment

    NARCIS (Netherlands)

    Tamirat, A.S.; Trujillo Barrera, A.A.; Pennings, J.M.E.

    2017-01-01

    The corporate finance literature has focused on explaining the determinants of firms target capital structure and speed of adjustment using the well-established theories such as pecking order, signaling and trade-off theories. However, less attention has been paid to understanding the financing

  1. Farm Target Capital Structure: Dynamics, Determinants and Speed of Adjustment

    NARCIS (Netherlands)

    Tamirat, A.S.; Trujillo Barrera, A.A.; Pennings, J.M.E.

    2017-01-01

    The corporate finance literature has focused on explaining the determinants of firms target capital structure and speed of adjustment using the well-established theories such as pecking order, signaling and trade-off theories. However, less attention has been paid to understanding the financing

  2. A Laboratory Exercise in the Determination of Carbohydrate Structures.

    Science.gov (United States)

    White, Bernard J.; Robyt, John F.

    1988-01-01

    Describes an experiment in which students are given a naturally occurring oligosaccharide as an unknown and are asked to determine both its monosaccharide composition and its structure. Discusses methods and experimental techniques including thin layer chromatography and the use of enzymes. (CW)

  3. Determining modulus of elasticity of ancient structural timber

    Science.gov (United States)

    Houjiang Zhang; Lei Zhu; Yanliang Sun; Xiping Wang; Haicheng Yan

    2011-01-01

    During maintenance of ancient timber architectures, it is important to determine mechanical properties of the wood component materials non-destructively and effectively, so that degraded members may be replaced or repaired to avoid structural failure. Experimental materials are four larch (Larix principis-rupprechtii Mayr.) components, which were taken down from the...

  4. Birthday Cake Activity Structured Arrangement for Helping Children Determining Quantities

    Science.gov (United States)

    Mariana, Neni

    2010-01-01

    Few researches have been concerned about relation between children's spatial thinking and number sense. Narrowing for this small research, we focused on one component of spatial thinking, that is structuring objects, and one component of number senses, that is cardinality by determining quantities. This study focused on a design research that was…

  5. From bacterial to human dihydrouridine synthase: automated structure determination

    Energy Technology Data Exchange (ETDEWEB)

    Whelan, Fiona, E-mail: fiona.whelan@york.ac.uk; Jenkins, Huw T., E-mail: fiona.whelan@york.ac.uk [The University of York, Heslington, York YO10 5DD (United Kingdom); Griffiths, Samuel C. [University of Oxford, Headington, Oxford OX3 7BN (United Kingdom); Byrne, Robert T. [Ludwig-Maximilians-University Munich, Feodor-Lynen-Strasse 25, 81377 Munich (Germany); Dodson, Eleanor J.; Antson, Alfred A., E-mail: fiona.whelan@york.ac.uk [The University of York, Heslington, York YO10 5DD (United Kingdom)

    2015-06-30

    The crystal structure of a human dihydrouridine synthase, an enzyme associated with lung cancer, with 18% sequence identity to a T. maritima enzyme, has been determined at 1.9 Å resolution by molecular replacement after extensive molecular remodelling of the template. The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1–340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr-rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain–domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer.

  6. From bacterial to human dihydrouridine synthase: automated structure determination

    International Nuclear Information System (INIS)

    Whelan, Fiona; Jenkins, Huw T.; Griffiths, Samuel C.; Byrne, Robert T.; Dodson, Eleanor J.; Antson, Alfred A.

    2015-01-01

    The crystal structure of a human dihydrouridine synthase, an enzyme associated with lung cancer, with 18% sequence identity to a T. maritima enzyme, has been determined at 1.9 Å resolution by molecular replacement after extensive molecular remodelling of the template. The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1–340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr-rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain–domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer

  7. Using photoelectron diffraction to determine complex molecular adsorption structures

    International Nuclear Information System (INIS)

    Woodruff, D P

    2010-01-01

    Backscattering photoelectron diffraction, particularly in the energy-scan mode, is now an established technique for determining in a quantitative fashion the local structure of adsorbates on surfaces, and has been used successfully for ∼100 adsorbate phases. The elemental and chemical-state specificity afforded by the characteristic core level photoelectron binding energies means that it has particular advantages for molecular adsorbates, as the local geometry of inequivalent atoms in the molecule can be determined in a largely independent fashion. On the other hand, polyatomic molecules present a general problem for all methods of surface structure determination in that a mismatch of intramolecular distances with interatomic distances on the substrate surface means that the atoms in the adsorbed molecule are generally in low-symmetry sites. The quantities measured experimentally then represent an incoherent sum of the properties of each structural domain that is inequivalent with respect to the substrate point group symmetry. This typically leads to greater ambiguity or precision in the structural solutions. The basic principles of the method are described and illustrated with a simple example involving molecule/substrate bonding through only one constituent atom (TiO 2 -(110)/H 2 O). This example demonstrates the importance of obtaining quantitative local structural information. Further examples illustrate both the successes and the problems of this approach when applied to somewhat more complex molecular adsorbates.

  8. Design, modeling and control of a pneumatically actuated manipulator inspired by biological continuum structures

    International Nuclear Information System (INIS)

    Kang, Rongjie; Zheng Tianjiang; Guglielmino, Emanuele; Caldwell, Darwin G; Branson, David T

    2013-01-01

    Biological tentacles, such as octopus arms, have entirely flexible structures and virtually infinite degrees of freedom (DOF) that allow for elongation, shortening and bending at any point along the arm length. The amazing dexterity of biological tentacles has driven the growing implementation of continuum manipulators in robotic systems. This paper presents a pneumatic manipulator inspired by biological continuum structures in some of their key features and functions, such as continuum morphology, intrinsic compliance and stereotyped motions with hyper redundant DOF. The kinematics and dynamics of the manipulator are formulated and identified, and a hierarchical controller taking inspiration from the structure of an octopus nervous system is used to relate desired stereotyped motions to individual actuator inputs. Simulations and experiments are carried out to validate the model and prototype where good agreement was found between the two. (paper)

  9. The diverse and expanding role of mass spectrometry in structural and molecular biology.

    Science.gov (United States)

    Lössl, Philip; van de Waterbeemd, Michiel; Heck, Albert Jr

    2016-12-15

    The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes. © 2016 The Authors. Published under the terms of the CC BY NC ND 4.0 license.

  10. DOE EPSCoR Initiative in Structural and computational Biology/Bioinformatics

    Energy Technology Data Exchange (ETDEWEB)

    Wallace, Susan S.

    2008-02-21

    The overall goal of the DOE EPSCoR Initiative in Structural and Computational Biology was to enhance the competiveness of Vermont research in these scientific areas. To develop self-sustaining infrastructure, we increased the critical mass of faculty, developed shared resources that made junior researchers more competitive for federal research grants, implemented programs to train graduate and undergraduate students who participated in these research areas and provided seed money for research projects. During the time period funded by this DOE initiative: (1) four new faculty were recruited to the University of Vermont using DOE resources, three in Computational Biology and one in Structural Biology; (2) technical support was provided for the Computational and Structural Biology facilities; (3) twenty-two graduate students were directly funded by fellowships; (4) fifteen undergraduate students were supported during the summer; and (5) twenty-eight pilot projects were supported. Taken together these dollars resulted in a plethora of published papers, many in high profile journals in the fields and directly impacted competitive extramural funding based on structural or computational biology resulting in 49 million dollars awarded in grants (Appendix I), a 600% return on investment by DOE, the State and University.

  11. Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins

    Science.gov (United States)

    Kinjo, Akira R.; Nakamura, Haruki

    2012-01-01

    Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures. PMID:22347478

  12. Direct experimental determination of the atomic structure at internal interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Browning, N.D. [Oak Ridge National Lab., TN (United States)]|[Illinois Univ., Chicago, IL (United States); Pennycook, S.J. [Oak Ridge National Lab., TN (United States)

    1995-07-01

    A crucial first step in understanding the effect that internal interfaces have on the properties of materials is the ability to determine the atomic structure at the interface. As interfaces can contain atomic disorder, dislocations, segregated impurities and interphases, sensitivity to all of these features is essential for complete experimental characterization. By combining Z-contrast imaging and electron energy loss spectroscopy (EELS) in a dedicated scanning transmission electron microscope (STEM), the ability to probe the structure, bonding and composition at interfaces with the necessary atomic resolution has been obtained. Experimental conditions can be controlled to provide, simultaneously, both incoherent imaging and spectroscopy. This enables interface structures observed in the image to be interpreted intuitively and the bonding in a specified atomic column to be probed directly by EELS. The bonding and structure information can then be correlated using bond-valence sum analysis to produce structural models. This technique is demonstrated for 25{degrees}, 36{degrees} and 67{degrees} symmetric and 45{degrees} and 25{degrees} asymmetric [001] tilt grain boundaries in SrTiO{sub 3} The structures of both types of boundary were found to contain partially occupied columns in the boundary plane. From these experimental results, a series of structural units were identified which could be combined, using continuity of gain boundary structure principles, to construct all [001] tilt boundaries in SrTiO{sub 3}. Using these models, the ability of this technique to address the issues of vacancies and dopant segregation at grain boundaries in electroceramics is discussed.

  13. Global search in photoelectron diffraction structure determination using genetic algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Viana, M L [Departamento de Fisica, Icex, UFMG, Belo Horizonte, Minas Gerais (Brazil); Muino, R Diez [Donostia International Physics Center DIPC, Paseo Manuel de Lardizabal 4, 20018 San Sebastian (Spain); Soares, E A [Departamento de Fisica, Icex, UFMG, Belo Horizonte, Minas Gerais (Brazil); Hove, M A Van [Department of Physics and Materials Science, City University of Hong Kong, Hong Kong (China); Carvalho, V E de [Departamento de Fisica, Icex, UFMG, Belo Horizonte, Minas Gerais (Brazil)

    2007-11-07

    Photoelectron diffraction (PED) is an experimental technique widely used to perform structural determinations of solid surfaces. Similarly to low-energy electron diffraction (LEED), structural determination by PED requires a fitting procedure between the experimental intensities and theoretical results obtained through simulations. Multiple scattering has been shown to be an effective approach for making such simulations. The quality of the fit can be quantified through the so-called R-factor. Therefore, the fitting procedure is, indeed, an R-factor minimization problem. However, the topography of the R-factor as a function of the structural and non-structural surface parameters to be determined is complex, and the task of finding the global minimum becomes tough, particularly for complex structures in which many parameters have to be adjusted. In this work we investigate the applicability of the genetic algorithm (GA) global optimization method to this problem. The GA is based on the evolution of species, and makes use of concepts such as crossover, elitism and mutation to perform the search. We show results of its application in the structural determination of three different systems: the Cu(111) surface through the use of energy-scanned experimental curves; the Ag(110)-c(2 x 2)-Sb system, in which a theory-theory fit was performed; and the Ag(111) surface for which angle-scanned experimental curves were used. We conclude that the GA is a highly efficient method to search for global minima in the optimization of the parameters that best fit the experimental photoelectron diffraction intensities to the theoretical ones.

  14. CAPITAL STRUCTURE DETERMINANTS: EVIDENCE FROM PALESTINE AND EGYPT STOCK EXCHANGES

    Directory of Open Access Journals (Sweden)

    Abdul Razak Abdul Hadi

    2017-04-01

    Full Text Available Abstract -This study is driven by the motivation to examine the capital structure determinants for Palestine Stock Exchange (PEX and Egypt Stock Exchange (EGX. Within the framework of capital structure theories, this study uses Generalized Method of Moments (GMM,1982 as an estimation model employing quarterly panel data analysis during the observed period from 2008 till 2012. The test results from GMM indicate that all the examined determinants have significant relationship with leverage. It has a negative value with liquidity, non-debt tax shield, profitability, size and growth. The Egyptian firms have some uniqueness in its trend. Current assets, debt ratio and liquidity behave positively with leverage except for growth. The other tested determinants in Egyptian companies are found to be not significant.

  15. A Self-Assisting Protein Folding Model for Teaching Structural Molecular Biology.

    Science.gov (United States)

    Davenport, Jodi; Pique, Michael; Getzoff, Elizabeth; Huntoon, Jon; Gardner, Adam; Olson, Arthur

    2017-04-04

    Structural molecular biology is now becoming part of high school science curriculum thus posing a challenge for teachers who need to convey three-dimensional (3D) structures with conventional text and pictures. In many cases even interactive computer graphics does not go far enough to address these challenges. We have developed a flexible model of the polypeptide backbone using 3D printing technology. With this model we have produced a polypeptide assembly kit to create an idealized model of the Triosephosphate isomerase mutase enzyme (TIM), which forms a structure known as TIM barrel. This kit has been used in a laboratory practical where students perform a step-by-step investigation into the nature of protein folding, starting with the handedness of amino acids to the formation of secondary and tertiary structure. Based on the classroom evidence we collected, we conclude that these models are valuable and inexpensive resource for teaching structural molecular biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. How Clean is Safe? Improving the Effectiveness of Decontamination of Structures and People Following Chemical and Biological Incidents

    Energy Technology Data Exchange (ETDEWEB)

    Vogt (Sorensen), B.M.

    2003-04-03

    This report describes a U.S. Department of Energy, (DOE) Chemical and Biological National Security Program project that sought to establish what is known about decontamination of structures, objects, and people following an exposure to chemical or biological materials. Specifically we sought to identify the procedures and protocols used to determine when and how people or buildings are considered ''clean'' following decontamination. To fulfill this objective, the study systematically examined reported decontamination experiences to determine what procedures and protocols are currently employed for decontamination, the timeframe involved to initiate and complete the decontamination process, how the contaminants were identified, the factors determining when people were (or were not) decontaminated, the problems encountered during the decontamination process, how response efforts of agencies were coordinated, and the perceived social psychological effects on people who were decontaminated or who participated in the decontamination process. Findings and recommendations from the study are intended to aid decision-making and to improve the basis for determining appropriate decontamination protocols for recovery planners and policy makers for responding to chemical and biological events.

  17. Analytical Methodologies for the Determination of Endocrine Disrupting Compounds in Biological and Environmental Samples

    Directory of Open Access Journals (Sweden)

    Zoraida Sosa-Ferrera

    2013-01-01

    Full Text Available Endocrine-disruptor compounds (EDCs can mimic natural hormones and produce adverse effects in the endocrine functions by interacting with estrogen receptors. EDCs include both natural and synthetic chemicals, such as hormones, personal care products, surfactants, and flame retardants, among others. EDCs are characterised by their ubiquitous presence at trace-level concentrations and their wide diversity. Since the discovery of the adverse effects of these pollutants on wildlife and human health, analytical methods have been developed for their qualitative and quantitative determination. In particular, mass-based analytical methods show excellent sensitivity and precision for their quantification. This paper reviews recently published analytical methodologies for the sample preparation and for the determination of these compounds in different environmental and biological matrices by liquid chromatography coupled with mass spectrometry. The various sample preparation techniques are compared and discussed. In addition, recent developments and advances in this field are presented.

  18. Development of radiochemical separation method for determination of toxic elements in biological samples

    International Nuclear Information System (INIS)

    Maihara, V.A.; Vasconcellos, M.B.A.; Favaro, D.I.T.; Armelin, M.J.A.

    1990-01-01

    In order to determine Hg, Sb, As and Se in biological materials by neutron activation analysis, a radiochemical separation was developed. The chemical separation procedure used was based on the digestion of the irradiated sample in a mixture of H NO 3 and H 2 SO 4 in a teflon bomb, at 130 0 C for 1 to 4 hours. After the dissolution of organic matter, Hg and Sb were retained by a Dowex 2-X8 resin column in 6 M HCl. The effluent was passed through a TDO, tin dioxide column which retains As and Se in 3 M HCl medium. Radioactive tracers of these elements were used to determine the yields of the separation process. Certified reference materials were analyzed to check the precision and accuracy of the method. (author)

  19. Development of a radiochemical separation method for toxic elements determination from biologic samples

    International Nuclear Information System (INIS)

    Malhara, V.A.; Vasconcellos, M.B.A.; Favaro, D.I.T.; Armelin, M.J.A.

    1990-01-01

    In order to determine Hg, Sb, As and Se in biological materials by neutron activation analysis, a radiochemical separation was developed. The chemical separation procedure used was based on the digestion of the irradiated sample in a mixture of HNO 3 and H 2 SO 4 in a teflon bomb, at 130 0 C for 1 to 4 hours. After the dissolution of organic matter, Hg and Sb were retained by a Dowex 2-XB resin column in 6M HCI. The efluent was passed through a TDO, tin dioxide column which retains As and Se in 3M HCI medium. Radioactive tracers of these elements were used to determine the yields of the separation process. Certified reference materials were analyzed to check the precision and accuracy of the method. (author)

  20. Ultratrace determination of platinum in biological materials via neutron activation and radiochemical separation

    International Nuclear Information System (INIS)

    Zeisler, R.; Greenberg, R.R.

    1982-01-01

    A neutron activation analysis scheme based upon a radiochemical separation of the activation products has been developed. The method utilizes the inherent sensitivity of the activation reaction 198 Pt(n,ν) 199 Pt and counting of the daughter nuclide 199 Au. This nuclide is radiochemically separated from interfering activities by homogeneous precipitation as elemental gold. The remaining interference of the secondary reaction 197 Au(n,ν) 198 Au(n,ν) 199 Au from gold in the samples is quantitatively assessed and corrected. During this process accurate gold concentrations in the samples are obtained at ultratrace levels. The analysis scheme is applied to gold and platinum determinations in biological Standard Reference Materials and human liver specimens. Gold and platinum are determined at concentrations of 5x10 - 11 g/g, and at higher levels. (author)

  1. Activation analytical determination of essential and toxic trace elements in biological material

    International Nuclear Information System (INIS)

    Schelenz, R.

    1980-01-01

    In order to determine the essential trace elements Hg, Ag, Cu and Se in food (potatoes, milk powder) and biological standard materials (fruit tree leaves), simple, fast radiochemical separation methods are worked out. Following oxidative decomposition and destillation of Hg, the elements silver, copper and selenium are found in the destillation residue and can be electrochemically enriched on an amalgamated Cu foil (determination of Ag and Se in the concentration range of 10 -9 to 10 -8 g, of Cu in the range of 10 -12 to 10 -10 g), whilst the matrix elements Na, K, P are adsorbed on a column with 3 different inorganic ion exchangers. The eluate of the ion exchanger can be added directly to the multielement gamma spectroscopy. The possiblity of working purely instrumentally is demonstrated by 2 examples: multielement analysis of human hair and river water. (RB) [de

  2. The application of extraction chromatography to the determination of radionuclides in biological and environmental samples

    International Nuclear Information System (INIS)

    Testa, C.; Delle Site, A.

    1976-01-01

    The paper describe the application of extraction chromatography to the determination of several alpha and beta emitters in biological and environmental samples. Both column extraction chromatography and batch extraction process have been used to isolate the radionuclides from the samples. The effect of several parameters (extractant concentration, support granulometry, stirring time, temperature, presence of a complexing agent) on the extraction and elution has been examined. The application of redox extraction chromatography is also described. A very simple and rapid determination of the activity retained on the column can be obtained by transferring the slurry to a counting vial and by adding the scintillation liquid for a direct detection of the α or β emission. The counting efficiencies obtained with this technique are compared with those obtained with ion exchange resins. The organic polymers used for the extraction chromatography give about 100% counting efficiency. The conventional ion exchange resin cannot be used to this purpose because of their strong light absorption. (T.G.)

  3. ANALYTICAL TECHNIQUES FOR THE DETERMINATION OF MELOXICAM IN PHARMACEUTICAL FORMULATIONS AND BIOLOGICAL SAMPLES

    Directory of Open Access Journals (Sweden)

    Aisha Noreen

    2016-06-01

    Full Text Available Meloxicam (MX belongs to the family of oxicams which is the most important group of non steroidal anti-inflammatory drugs (NSAIDs and is widely used for their analgesics and antipyretic activities. It inhibits both COX-I and COX-II enzymes with less gastric and local tissues irritation. A number of analytical techniques have been used for the determination of MX in pharmaceutical as well as in biological fluids. These techniques include titrimetry, spectrometry, chromatography, flow injection spectrometry, fluorescence spectrometry, capillary zone electrophoresis and electrochemical techniques. Many of these techniques have also been used for the simultaneous determination of MX with other compounds. A comprehensive review of these analytical techniques has been done which could be useful for the analytical chemists and quality control pharmacists.

  4. Analytical Strategies for the Determination of Norepinephrine Reuptake Inhibitors in Pharmaceutical Formulations and Biological Fluids.

    Science.gov (United States)

    Saka, Cafer

    2016-01-01

    Norepinephrine reuptake inhibitors (NRIs) are a class of antidepressant drugs that act as reuptake inhibitors for the neurotransmitters norepinephrine and epinephrine. The present review provides an account of analytical methods published in recent years for the determination of NRI drugs. NRIs are atomoxetine, reboxetine, viloxazine and maprotiline. NRIs with less activity at other sites are mazindol, bupropion, tapentadol, and teniloxazine. This review focuses on the analytical methods including chromatographic, spectrophotometric, electroanalytical, and electrophoresis techniques for NRI analysis from pharmaceutical formulations and biological samples. Among all of the published methods, liquid chromatography with UV-vis or MS-MS detection is the most popular technique. The most the common sample preparation techniques in the analytical methods for NRIs include liquid-liquid extraction and solid-phase extraction. Besides the analytical methods for single components, some of the simultaneous determinations are also included in this review.

  5. CyBy(2): a structure-based data management tool for chemical and biological data.

    Science.gov (United States)

    Höck, Stefan; Riedl, Rainer

    2012-01-01

    We report the development of a powerful data management tool for chemical and biological data: CyBy(2). CyBy(2) is a structure-based information management tool used to store and visualize structural data alongside additional information such as project assignment, physical information, spectroscopic data, biological activity, functional data and synthetic procedures. The application consists of a database, an application server, used to query and update the database, and a client application with a rich graphical user interface (GUI) used to interact with the server.

  6. Mass spectrometry in structural biology and biophysics architecture, dynamics, and interaction of biomolecules

    CERN Document Server

    Kaltashov, Igor A; Desiderio, Dominic M; Nibbering, Nico M

    2012-01-01

    The definitive guide to mass spectrometry techniques in biology and biophysics The use of mass spectrometry (MS) to study the architecture and dynamics of proteins is increasingly common within the biophysical community, and Mass Spectrometry in Structural Biology and Biophysics: Architecture, Dynamics, and Interaction of Biomolecules, Second Edition provides readers with detailed, systematic coverage of the current state of the art. Offering an unrivalled overview of modern MS-based armamentarium that can be used to solve the most challenging problems in biophysics, structural biol

  7. Resilience of caregivers of people with dementia: a systematic review of biological and psychosocial determinants

    Directory of Open Access Journals (Sweden)

    Rachel Dias

    2015-03-01

    Full Text Available Introduction: Although caregivers of people with dementia may face difficulties, some positive feelings of caregiving may be associated with resilience.Objective: This study systematically reviewed the definitions, methodological approaches and determinant models associated with resilience among caregivers of people with dementia.Methods: Search for articles published between 2003 and 2014 in ISI, PubMed/MEDLINE, SciELO and Lilacs using the search terms resilience, caregivers and dementia.Results and conclusions: Resilience has been defined as positive adaptation to face adversity, flexibility, psychological well-being, strength, healthy life, burden, social network and satisfaction with social support. No consensus was found about the definition of resilience associated with dementia. We classified the determinant variables into biological, psychological and social models. Higher levels of resilience were associated with lower depression rates and greater physical health. Other biological factors associated with higher levels of resilience were older age, African-American ethnicity and female sex. Lower burden, stress, neuroticism and perceived control were the main psychological factors associated with resilience. Social support was a moderating factor of resilience, and different types of support seemed to relieve the physical and mental overload caused by stress.

  8. Resilience of caregivers of people with dementia: a systematic review of biological and psychosocial determinants.

    Science.gov (United States)

    Dias, Rachel; Santos, Raquel Luiza; Sousa, Maria Fernanda Barroso de; Nogueira, Marcela Moreira Lima; Torres, Bianca; Belfort, Tatiana; Dourado, Marcia Cristina Nascimento

    2015-01-01

    Although caregivers of people with dementia may face difficulties, some positive feelings of caregiving may be associated with resilience. This study systematically reviewed the definitions, methodological approaches and determinant models associated with resilience among caregivers of people with dementia. Search for articles published between 2003 and 2014 in ISI, PubMed/MEDLINE, SciELO and Lilacs using the search terms resilience, caregivers and dementia. Resilience has been defined as positive adaptation to face adversity, flexibility, psychological well-being, strength, healthy life, burden, social network and satisfaction with social support. No consensus was found about the definition of resilience associated with dementia. We classified the determinant variables into biological, psychological and social models. Higher levels of resilience were associated with lower depression rates and greater physical health. Other biological factors associated with higher levels of resilience were older age, African-American ethnicity and female sex. Lower burden, stress, neuroticism and perceived control were the main psychological factors associated with resilience. Social support was a moderating factor of resilience, and different types of support seemed to relieve the physical and mental overload caused by stress.

  9. Recent advances in the determination of tocopherols in biological fluids: from sample pretreatment and liquid chromatography to clinical studies.

    Science.gov (United States)

    Cervinkova, Barbora; Krcmova, Lenka Kujovska; Solichova, Dagmar; Melichar, Bohuslav; Solich, Petr

    2016-04-01

    Vitamin E comprises eight related compounds: α-, β-, γ-, δ-tocopherols and α-, β-, γ-, δ-tocotrienols. In the past, α-tocopherol has been the isomer that was studied most, and its anti-inflammatory and anti-proliferative effects have been described. Therefore, many prevention trials have investigated the effect of α-tocopherol on human health. Current research studies have also defined the important roles of other tocopherols, such as anti-inflammatory, anti-proliferative and cancer preventative effects. Knowledge of the individual tocopherols could help to understand their roles in various metabolic pathways. This review summarizes the recent trends in sample pretreatment, liquid chromatography and selected applications of the determination of tocopherols in various biological materials. The relationship between tocopherol isomers and serious diseases is also described. Graphical Abstract Article structure.

  10. X-ray structure determination and deuteration of nattokinase

    International Nuclear Information System (INIS)

    Yanagisawa, Yasuhide; Chatake, Toshiyuki; Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki; Kawaguchi, Akio; Chiba-Kamosida, Kaori; Ogawa, Megumi; Adachi, Tatsumi; Morimoto, Yukio

    2013-01-01

    X-ray structure determination and deuteration of nattokinase were performed to facilitate neutron crystallographic analysis. Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D 2 O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D 2 O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis

  11. X-ray structure determination and deuteration of nattokinase

    Energy Technology Data Exchange (ETDEWEB)

    Yanagisawa, Yasuhide [Chiba Institute of Science, 15-8 Shiomi-cho, Cho-shi, Chiba 288-025 (Japan); Chatake, Toshiyuki [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan); Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki [Kurashiki University of Science and the Arts, 2640 Nishinoura, Tsurajima-cho, Kurashiki, Okayama 712-8505 (Japan); Kawaguchi, Akio [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan); Chiba-Kamosida, Kaori [Nippon Advanced Technology Co. Ltd, J-PARC, 2-4 Shirane Shirakata, Tokai, Ibaraki 319-1195 (Japan); Ogawa, Megumi; Adachi, Tatsumi [Chiba Institute of Science, 15-8 Shiomi-cho, Cho-shi, Chiba 288-025 (Japan); Morimoto, Yukio [Kyoto University, Asashironishi 2, Kumatori, Osaka 590-0494 (Japan)

    2013-11-01

    X-ray structure determination and deuteration of nattokinase were performed to facilitate neutron crystallographic analysis. Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D{sub 2}O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D{sub 2}O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis.

  12. Overconfidence, Managerial Optimism, and the Determinants of Capital Structure

    Directory of Open Access Journals (Sweden)

    Alexandre di Miceli da Silveira

    2008-12-01

    Full Text Available This research examines the determinants of the capital structure of firms introducing a behavioral perspective that has received little attention in corporate finance literature. The following central hypothesis emerges from a set of recently developed theories: firms managed by optimistic and/or overconfident people will choose more levered financing structures than others, ceteris paribus. We propose different proxies for optimism/overconfidence, based on the manager’s status as an entrepreneur or non-entrepreneur, an idea that is supported by theories and solid empirical evidence, as well as on the pattern of ownership of the firm’s shares by its manager. The study also includes potential determinants of capital structure used in earlier research. We use a sample of Brazilian firms listed in the Sao Paulo Stock Exchange (Bovespa in the years 1998 to 2003. The empirical analysis suggests that the proxies for the referred cognitive biases are important determinants of capital structure. We also found as relevant explanatory variables: profitability, size, dividend payment and tangibility, as well as some indicators that capture the firms’ corporate governance standards. These results suggest that behavioral approaches based on human psychology research can offer relevant contributions to the understanding of corporate decision making.

  13. Defining and detecting structural sensitivity in biological models: developing a new framework.

    Science.gov (United States)

    Adamson, M W; Morozov, A Yu

    2014-12-01

    When we construct mathematical models to represent biological systems, there is always uncertainty with regards to the model specification--whether with respect to the parameters or to the formulation of model functions. Sometimes choosing two different functions with close shapes in a model can result in substantially different model predictions: a phenomenon known in the literature as structural sensitivity, which is a significant obstacle to improving the predictive power of biological models. In this paper, we revisit the general definition of structural sensitivity, compare several more specific definitions and discuss their usefulness for the construction and analysis of biological models. Then we propose a general approach to reveal structural sensitivity with regards to certain system properties, which considers infinite-dimensional neighbourhoods of the model functions: a far more powerful technique than the conventional approach of varying parameters for a fixed functional form. In particular, we suggest a rigorous method to unearth sensitivity with respect to the local stability of systems' equilibrium points. We present a method for specifying the neighbourhood of a general unknown function with [Formula: see text] inflection points in terms of a finite number of local function properties, and provide a rigorous proof of its completeness. Using this powerful result, we implement our method to explore sensitivity in several well-known multicomponent ecological models and demonstrate the existence of structural sensitivity in these models. Finally, we argue that structural sensitivity is an important intrinsic property of biological models, and a direct consequence of the complexity of the underlying real systems.

  14. The Widespread Prevalence and Functional Significance of Silk-Like Structural Proteins in Metazoan Biological Materials.

    Directory of Open Access Journals (Sweden)

    Carmel McDougall

    Full Text Available In nature, numerous mechanisms have evolved by which organisms fabricate biological structures with an impressive array of physical characteristics. Some examples of metazoan biological materials include the highly elastic byssal threads by which bivalves attach themselves to rocks, biomineralized structures that form the skeletons of various animals, and spider silks that are renowned for their exceptional strength and elasticity. The remarkable properties of silks, which are perhaps the best studied biological materials, are the result of the highly repetitive, modular, and biased amino acid composition of the proteins that compose them. Interestingly, similar levels of modularity/repetitiveness and similar bias in amino acid compositions have been reported in proteins that are components of structural materials in other organisms, however the exact nature and extent of this similarity, and its functional and evolutionary relevance, is unknown. Here, we investigate this similarity and use sequence features common to silks and other known structural proteins to develop a bioinformatics-based method to identify similar proteins from large-scale transcriptome and whole-genome datasets. We show that a large number of proteins identified using this method have roles in biological material formation throughout the animal kingdom. Despite the similarity in sequence characteristics, most of the silk-like structural proteins (SLSPs identified in this study appear to have evolved independently and are restricted to a particular animal lineage. Although the exact function of many of these SLSPs is unknown, the apparent independent evolution of proteins with similar sequence characteristics in divergent lineages suggests that these features are important for the assembly of biological materials. The identification of these characteristics enable the generation of testable hypotheses regarding the mechanisms by which these proteins assemble and direct the

  15. On the holistic approach in cellular and cancer biology: nonlinearity, complexity, and quasi-determinism of the dynamic cellular network.

    Science.gov (United States)

    Waliszewski, P; Molski, M; Konarski, J

    1998-06-01

    A keystone of the molecular reductionist approach to cellular biology is a specific deductive strategy relating genotype to phenotype-two distinct categories. This relationship is based on the assumption that the intermediary cellular network of actively transcribed genes and their regulatory elements is deterministic (i.e., a link between expression of a gene and a phenotypic trait can always be identified, and evolution of the network in time is predetermined). However, experimental data suggest that the relationship between genotype and phenotype is nonbijective (i.e., a gene can contribute to the emergence of more than just one phenotypic trait or a phenotypic trait can be determined by expression of several genes). This implies nonlinearity (i.e., lack of the proportional relationship between input and the outcome), complexity (i.e. emergence of the hierarchical network of multiple cross-interacting elements that is sensitive to initial conditions, possesses multiple equilibria, organizes spontaneously into different morphological patterns, and is controlled in dispersed rather than centralized manner), and quasi-determinism (i.e., coexistence of deterministic and nondeterministic events) of the network. Nonlinearity within the space of the cellular molecular events underlies the existence of a fractal structure within a number of metabolic processes, and patterns of tissue growth, which is measured experimentally as a fractal dimension. Because of its complexity, the same phenotype can be associated with a number of alternative sequences of cellular events. Moreover, the primary cause initiating phenotypic evolution of cells such as malignant transformation can be favored probabilistically, but not identified unequivocally. Thermodynamic fluctuations of energy rather than gene mutations, the material traits of the fluctuations alter both the molecular and informational structure of the network. Then, the interplay between deterministic chaos, complexity, self

  16. Experimental determination of the structure of H3+

    International Nuclear Information System (INIS)

    Gaillard, M.J.; Gemmell, D.S.; Goldring, G.; Levine, I.; Pietsch, W.J.; Poizat, J.C.; Ratkowski, A.J.; Remillieux, J.; Vager, Z.; Zabransky, B.J.

    1978-01-01

    Three different measurements on the structure of the H 3 + molecular ion are reported. The measurements all make use of a new technique: the foil-induced dissociation of a fast molecular-ion beam. It is shown that the structure is equilaterally triangular in shape. The most probable length of side of the triangle is determined by the three measurements to be 0.97 +- 0.03 A, 0.95 +- 0.06 A, and 1.2 +- 0.2 A, respectively

  17. Implantation measurements to determine tritium permeation in first wall structures

    International Nuclear Information System (INIS)

    Holland, D.F.; Causey, R.A.

    1983-01-01

    A principal safety concern for a D-T burning fusion reactor is release of tritium during routine operation. Tritium implantation into first wall structures, and subsequent permeation into coolants, is potentially an important source of tritium loss. This paper reports on an experiment in which an ion accelerator was used to implant deuterium atoms in a stainless steel disk to simulate tritium implantation in first wall structures. The permeation rate was measured under various operating conditions. These results were used in the TMAP computer code to determine potential tritium loss rates for fusion reactors

  18. DETERMINANT FACTORS OF THE CAPITAL STRUCTURE OF BRAZILIAN TECHNOLOGY COMPANIES

    Directory of Open Access Journals (Sweden)

    Camila Freitas Sant´Ana

    2015-12-01

    Full Text Available The purpose of this study is to identify determinant factors of the capital structure of Brazilian technology companies. The research was characterized as descriptive, document and quantitative, consisting of 21 companies in the communications, telecommunications and digital industry, according to the Exame magazine ranking. The analysis was established from 2009 to 2013 using panel data regression. The results indicate that the growth rate of capital and control type have a positive relationship with the general and long-term debt. However, it was found that company size, profitability and type of capital point to a negative relationship with the capital structure.

  19. A novel visible spectrophotometric method for the determination of ethamsylate in pharmaceutical preparations and biological samples

    Science.gov (United States)

    Zhang, Meiyun; Zhang, Yan; Li, Quanmin

    2010-03-01

    A highly sensitive visible spectrophotometric method has been developed to determine ethamsylate in this paper, which is based on using Cu(II) as spectroscopic probe reagent. The study indicates that in the presence of SCN - and KNO 3, Cu(II) is reduced to Cu(I) by ethamsylate at pH 5.0, and the in situ formed Cu(I) reacts with SCN - to form into the white emulsion CuSCN that could be stayed upon the surface of water. According to the amount of residual Cu(II), the amount of ethamsylate can be indirectly determined. Under the optimal conditions, Beer's law is applicable in the range of 0.2-9.0 μg/mL (7.60 × 10 -7-3.42 × 10 -5 mol/L) for aqueous standard solution of ethamsylate with linear correlation coefficient of 0.9998. The detection limit and relative standard deviation are 0.12 μg/mL and 1.5%, respectively. And the molar absorption coefficient of the indirect determination of ethamsylate is 1.0 × 10 5 L/mol cm. The method is successfully applied to determine ethamsylate in pharmaceutical preparations and biological samples.

  20. Optimization and validation of spectrophotometric methods for determination of finasteride in dosage and biological forms

    Science.gov (United States)

    Amin, Alaa S.; Kassem, Mohammed A.

    2012-01-01

    Aim and Background: Three simple, accurate and sensitive spectrophotometric methods for the determination of finasteride in pure, dosage and biological forms, and in the presence of its oxidative degradates were developed. Materials and Methods: These methods are indirect, involve the addition of excess oxidant potassium permanganate for method A; cerric sulfate [Ce(SO4)2] for methods B; and N-bromosuccinimide (NBS) for method C of known concentration in acid medium to finasteride, and the determination of the unreacted oxidant by measurement of the decrease in absorbance of methylene blue for method A, chromotrope 2R for method B, and amaranth for method C at a suitable maximum wavelength, λmax: 663, 528, and 520 nm, for the three methods, respectively. The reaction conditions for each method were optimized. Results: Regression analysis of the Beer plots showed good correlation in the concentration ranges of 0.12–3.84 μg mL–1 for method A, and 0.12–3.28 μg mL–1 for method B and 0.14 – 3.56 μg mL–1 for method C. The apparent molar absorptivity, Sandell sensitivity, detection and quantification limits were evaluated. The stoichiometric ratio between the finasteride and the oxidant was estimated. The validity of the proposed methods was tested by analyzing dosage forms and biological samples containing finasteride with relative standard deviation ≤ 0.95. Conclusion: The proposed methods could successfully determine the studied drug with varying excess of its oxidative degradation products, with recovery between 99.0 and 101.4, 99.2 and 101.6, and 99.6 and 101.0% for methods A, B, and C, respectively. PMID:23781478

  1. Generation of structurally novel short carotenoids and study of their biological activity

    DEFF Research Database (Denmark)

    Kim, Se Hyeuk; Kim, Moon S.; Lee, Bun Y.

    2016-01-01

    Recent research interest in phytochemicals has consistently driven the efforts in the metabolic engineering field toward microbial production of various carotenoids. In spite of systematic studies, the possibility of using C30 carotenoids as biologically functional compounds has not been explored...... thus far. Here, we generated 13 novel structures of C30 carotenoids and one C35 carotenoid, including acyclic, monocyclic, and bicyclic structures, through directed evolution and combinatorial biosynthesis, in Escherichia coli. Measurement of radical scavenging activity of various C30 carotenoid...... structures revealed that acyclic C30 carotenoids showed higher radical scavenging activity than did DL-atocopherol. We could assume high potential biological activity of the novel structures of C30 carotenoids as well, based on the neuronal differentiation activity observed for the monocyclic C30 carotenoid...

  2. Function of dynamic models in systems biology: linking structure to behaviour.

    Science.gov (United States)

    Knüpfer, Christian; Beckstein, Clemens

    2013-10-08

    Dynamic models in Systems Biology are used in computational simulation experiments for addressing biological questions. The complexity of the modelled biological systems and the growing number and size of the models calls for computer support for modelling and simulation in Systems Biology. This computer support has to be based on formal representations of relevant knowledge fragments. In this paper we describe different functional aspects of dynamic models. This description is conceptually embedded in our "meaning facets" framework which systematises the interpretation of dynamic models in structural, functional and behavioural facets. Here we focus on how function links the structure and the behaviour of a model. Models play a specific role (teleological function) in the scientific process of finding explanations for dynamic phenomena. In order to fulfil this role a model has to be used in simulation experiments (pragmatical function). A simulation experiment always refers to a specific situation and a state of the model and the modelled system (conditional function). We claim that the function of dynamic models refers to both the simulation experiment executed by software (intrinsic function) and the biological experiment which produces the phenomena under investigation (extrinsic function). We use the presented conceptual framework for the function of dynamic models to review formal accounts for functional aspects of models in Systems Biology, such as checklists, ontologies, and formal languages. Furthermore, we identify missing formal accounts for some of the functional aspects. In order to fill one of these gaps we propose an ontology for the teleological function of models. We have thoroughly analysed the role and use of models in Systems Biology. The resulting conceptual framework for the function of models is an important first step towards a comprehensive formal representation of the functional knowledge involved in the modelling and simulation process

  3. Dispensing processes impact apparent biological activity as determined by computational and statistical analyses.

    Directory of Open Access Journals (Sweden)

    Sean Ekins

    Full Text Available Dispensing and dilution processes may profoundly influence estimates of biological activity of compounds. Published data show Ephrin type-B receptor 4 IC50 values obtained via tip-based serial dilution and dispensing versus acoustic dispensing with direct dilution differ by orders of magnitude with no correlation or ranking of datasets. We generated computational 3D pharmacophores based on data derived by both acoustic and tip-based transfer. The computed pharmacophores differ significantly depending upon dispensing and dilution methods. The acoustic dispensing-derived pharmacophore correctly identified active compounds in a subsequent test set where the tip-based method failed. Data from acoustic dispensing generates a pharmacophore containing two hydrophobic features, one hydrogen bond donor and one hydrogen bond acceptor. This is consistent with X-ray crystallography studies of ligand-protein interactions and automatically generated pharmacophores derived from this structural data. In contrast, the tip-based data suggest a pharmacophore with two hydrogen bond acceptors, one hydrogen bond donor and no hydrophobic features. This pharmacophore is inconsistent with the X-ray crystallographic studies and automatically generated pharmacophores. In short, traditional dispensing processes are another important source of error in high-throughput screening that impacts computational and statistical analyses. These findings have far-reaching implications in biological research.

  4. Large, dynamic, multi-protein complexes: a challenge for structural biology

    Czech Academy of Sciences Publication Activity Database

    Rozycki, B.; Bouřa, Evžen

    2014-01-01

    Roč. 26, č. 46 (2014), 463103/1-463103/11 ISSN 0953-8984 R&D Projects: GA MŠk LO1302 EU Projects: European Commission(XE) 333916 - STARPI4K Institutional support: RVO:61388963 Keywords : protein structure * multi-protein complexes * hybrid methods of structural biology Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.346, year: 2014

  5. Determining the helicity structure of third generation resonances

    International Nuclear Information System (INIS)

    Papaefstathiou, Andreas

    2011-11-01

    We examine methods that have been proposed for determining the helicity structure of decays of new resonances to third generation quarks and/or leptons. We present analytical and semi-analytical predictions and assess the applicability of the relevant variables in realistic reconstruction scenarios using Monte Carlo-generated events, including the effects of QCD radiation and multiple parton interactions, combinatoric ambiguities and fast detector simulation. (orig.)

  6. Determination of the Basin Structure Beneath European Side of Istanbul

    Science.gov (United States)

    Karabulut, Savas; Cengiz Cinku, Mulla; Thomas, Michael; Lamontagne, Maurice

    2016-04-01

    Istanbul (near North Anatolian Fault Zone:NAFZ, Turkey) is located in northern part of Sea of Marmara, an area that has been influenced by possible Marmara Earthquakes. The general geology of Istanbul divided into two stratigraphic unit such as sedimentary (from Oligocene to Quaternary Deposits) and bedrock (Paleozoic and Eocene). The bedrock units consists of sand stone, clay stone to Paleozoic age and limestone to Eocene age and sedimentary unit consist of sand, clay, mil and gravel from Oligocene to Quaternary age. Earthquake disaster mitigation studies divided into two important phases, too. Firstly, earthquake, soil and engineering structure problems identify for investigation area, later on strategic emergency plan can prepare for these problems. Soil amplification play important role the disaster mitigation and the site effect analysis and basin structure is also a key parameter for determining of site effect. Some geophysical, geological and geotechnical measurements are requeired to defined this relationship. Istanbul Megacity has been waiting possible Marmara Earthquake and their related results. In order to defined to possible damage potential related to site effect, gravity measurements carried out for determining to geological structure, basin geometry and faults in Istanbul. Gravity data were collected at 640 sites by using a Scientrex CG-5 Autogravity meter Standard corrections applied to the gravity data include those for instrumental drift, Earth tides and latitude, and the free-air and Bouguer corrections. The corrected gravity data were imported into a Geosoft database to create a grid and map of the Bouguer gravity anomaly (grid cell size of 200 m). As a previously results, we determined some lineminants, faults and basins beneath Istanbul City. Especially, orientation of faults were NW-SE direction and some basin structures determined on between Buyukcekmece and Kucukcekmece Lake.

  7. Breaking Frontiers: Submicron Structures in Physics and Biology - 52 Zakopane School of Physics

    International Nuclear Information System (INIS)

    2008-01-01

    The 52 Zakopane School of Physics held in Zakopane from 19 to 24 May 2008. The main task of the symposium was to present the newest results of research in field of submicron structures in physics, biology and medicine. Some new technologies as well as their applications are also presented

  8. Breaking Frontiers: Submicron Structures in Physics and Biology - 52 Zakopane School of Physics

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2008-07-01

    The 52 Zakopane School of Physics held in Zakopane from 19 to 24 May 2008. The main task of the symposium was to present the newest results of research in field of submicron structures in physics, biology and medicine. Some new technologies as well as their applications are also presented.

  9. MOTIVATION INTERNALIZATION AND SIMPLEX STRUCTURE IN SELF-DETERMINATION THEORY.

    Science.gov (United States)

    Ünlü, Ali; Dettweiler, Ulrich

    2015-12-01

    Self-determination theory, as proposed by Deci and Ryan, postulated different types of motivation regulation. As to the introjected and identified regulation of extrinsic motivation, their internalizations were described as "somewhat external" and "somewhat internal" and remained undetermined in the theory. This paper introduces a constrained regression analysis that allows these vaguely expressed motivations to be estimated in an "optimal" manner, in any given empirical context. The approach was even generalized and applied for simplex structure analysis in self-determination theory. The technique was exemplified with an empirical study comparing science teaching in a classical school class versus an expeditionary outdoor program. Based on a sample of 84 German pupils (43 girls, 41 boys, 10 to 12 years old), data were collected using the German version of the Academic Self-Regulation Questionnaire. The science-teaching format was seen to not influence the pupils' internalization of identified regulation. The internalization of introjected regulation differed and shifted more toward the external pole in the outdoor teaching format. The quantification approach supported the simplex structure of self-determination theory, whereas correlations may disconfirm the simplex structure.

  10. Determinants of capital structure: evidence from the Czech automotive industry

    Directory of Open Access Journals (Sweden)

    Pavlína Pinková

    2012-01-01

    Full Text Available The objective of the paper is to identify the determinants influencing the capital structure of large and medium-sized enterprises of the automotive industry in the Czech Republic. The sample consists of 100 companies belonging to NACE division 29. The data come from financial statements of selected companies and cover a period from 2006 to 2010. For the purpose of the paper quantitative research is used. The selection of appropriate dependent and independent is realized on the basis of secondary research on studies of capital structure. The analysis of variance, correlation and regression analyses have been performed to see the nature of relationship between variables. Size, tangibility, profitability and liquidity appear to be relevant determinants of capital structure. Growth is not a statistically significant determinant of leverage. It has been observed that the maturity of debt has to be considered, since the investigation of total debt only does not provide precious results. The findings do not unequivocally support either the static trade-off theory or the pecking order theory.

  11. Local magnetic structure determination using polarized neutron holography

    International Nuclear Information System (INIS)

    Szakál, Alex; Markó, Márton; Cser, László

    2015-01-01

    A unique and important property of the neutron is that it possesses magnetic moment. This property is widely used for determination of magnetic structure of crystalline samples observing the magnetic components of the diffraction peaks. Investigations of diffraction patterns give information only about the averaged structure of a crystal but for discovering of local spin arrangement around a specific (e.g., impurity) nucleus remains still a challenging problem. Neutron holography is a useful tool to investigate the local structure around a specific nucleus embedded in a crystal lattice. The method has been successfully applied experimentally in several cases using non-magnetic short range interaction of the neutron and the nucleus. A mathematical model of the hologram using interaction between magnetic moment of the atom and the neutron spin for polarized neutron holography is provided. Validity of a polarized neutron holographic experiment is demonstrated by applying the proposed method on model systems

  12. DNA nanotubes for NMR structure determination of membrane proteins.

    Science.gov (United States)

    Bellot, Gaëtan; McClintock, Mark A; Chou, James J; Shih, William M

    2013-04-01

    Finding a way to determine the structures of integral membrane proteins using solution nuclear magnetic resonance (NMR) spectroscopy has proved to be challenging. A residual-dipolar-coupling-based refinement approach can be used to resolve the structure of membrane proteins up to 40 kDa in size, but to do this you need a weak-alignment medium that is detergent-resistant and it has thus far been difficult to obtain such a medium suitable for weak alignment of membrane proteins. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400-nm-long six-helix bundles, each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, toward collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes using counter ions and small DNA-binding molecules. This detergent-resistant liquid-crystal medium offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility and structural programmability. Production of sufficient nanotubes for four or five NMR experiments can be completed in 1 week by a single individual.

  13. Structural determinants and mechanism of HIV-1 genome packaging.

    Science.gov (United States)

    Lu, Kun; Heng, Xiao; Summers, Michael F

    2011-07-22

    Like all retroviruses, the human immunodeficiency virus selectively packages two copies of its unspliced RNA genome, both of which are utilized for strand-transfer-mediated recombination during reverse transcription-a process that enables rapid evolution under environmental and chemotherapeutic pressures. The viral RNA appears to be selected for packaging as a dimer, and there is evidence that dimerization and packaging are mechanistically coupled. Both processes are mediated by interactions between the nucleocapsid domains of a small number of assembling viral Gag polyproteins and RNA elements within the 5'-untranslated region of the genome. A number of secondary structures have been predicted for regions of the genome that are responsible for packaging, and high-resolution structures have been determined for a few small RNA fragments and protein-RNA complexes. However, major questions regarding the RNA structures (and potentially the structural changes) that are responsible for dimeric genome selection remain unanswered. Here, we review efforts that have been made to identify the molecular determinants and mechanism of human immunodeficiency virus type 1 genome packaging. Copyright © 2011 Elsevier Ltd. All rights reserved.

  14. High voltage electric field effects on structure and biological characteristics of barley seeds

    Energy Technology Data Exchange (ETDEWEB)

    Khazaei, J. [Tehran Univ., Tehran (Iran, Islamic Republic of). Dept. of Agrotechnology, Univ. College of Abouraihan; Aliabadi, E. [Tehran Univ., Tehran (Iran, Islamic Republic of). Dept. of Crop Production Horticulture, Univ. College of Aburaihan; Shayegani, A.A. [Tehran Univ., Tehran (Iran, Islamic Republic of). Univ. College of Engineering

    2010-07-01

    Electric biostimulation of seeds is a pre-sowing treatment in which an electric field is applied to seeds to increase germination of non standard seeds. This paper reported on a study that examined the effects of AC electric field and exposure time on the structure and biological characteristics of barley seeds. The objective was to determine the potential to accelerate seed germination, plant growth and root development by the electric field strength and exposure time. Makooei cultivar barley seeds were used in this study. The effect of electric field strength (at 2, 4, 9, and 14 kV/m) and exposure time (at 15, 45, 80, and 150 min) on seed germination was studied along with height of seedling, length or root, height of stem, length of leaves, earliness, dry weight and wet weight of seedling. The treated seeds were stored for a month in a refrigerator at 5 degrees C prior to the germination experiments. The initial germination percent of the seed was 81 per cent. The treatment of barley seeds in an AC electric field had a positive effect on all investigated parameters. The germination percent of the treated seed increased to 94.5 per cent . The seeds exposed for long periods of time (45 to 150 min) showed better germination than the seeds exposed to lower exposure times. Dry and wet weights of seedling increased 143.4 per cent and 45.7 per cent, respectively.

  15. Structural, spectroscopic and biological investigation of copper oxides nanoparticles with various capping agents

    Energy Technology Data Exchange (ETDEWEB)

    Nowak, A., E-mail: ana.maria.nowak@gmail.com [A. Chelkowski Institute of Physics, University of Silesia, Katowice (Poland); Szade, J.; Talik, E.; Ratuszna, A. [A. Chelkowski Institute of Physics, University of Silesia, Katowice (Poland); Ostafin, M. [Agricultural University of Cracow, Department of Microbiology, Krakow (Poland); Peszke, J. [A. Chelkowski Institute of Physics, University of Silesia, Katowice (Poland)

    2014-06-01

    Powder composed of copper oxides nanoparticles with various capping agents has been synthesized and characterized with the use of X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and X-ray diffraction (XRD). Polyvinyl alcohol (PVA), glycol propylene, glycerin and glycerin plus ammonia were used as capping agents. The scanning electron microscopy (SEM) studies showed that nanoparticles form agglomerates with the size from 80 to 120 nm while particles size determined from the XRD experiment was in the range from 7 to 21 nm. XPS and XRD experiments revealed that depending on capping and reducing agents used in the synthesis nanoparticles are composed of Cu{sub 2}O, CuO or a mixture of them. The biological activity test performed for a selected sample where the capping agent was glycerin plus ammonia has shown promising killing/inhibiting behavior, very effective especially for Gram negatives bacteria. - Highlights: • We obtained copper oxide nanoparticles in a powder form. • Several capping agents were tested. • Structural and chemical tests showed that the main component were Cu{sub 2}O and CuO. • The size of nanoparticles was in the range 7–21 nm. • Nanoparticles with glycerin and ammonia capping agent showed good antibacterial properties.

  16. Optimization of polysaccharides extraction from watermelon rinds: Structure, functional and biological activities.

    Science.gov (United States)

    Romdhane, Molka Ben; Haddar, Anissa; Ghazala, Imen; Jeddou, Khawla Ben; Helbert, Claire Boisset; Ellouz-Chaabouni, Semia

    2017-02-01

    In the present work, optimization of hot water extraction, structural characteristics, functional properties, and biological activities of polysaccharides extracted from watermelon rinds (WMRP) were investigated. The physicochemical characteristics and the monosaccharide composition of these polysaccharides were then determined using chemical composition analysis, Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM) and gas chromatography-flame ionization detection (GC-FID). SEM images showed that extracted polysaccharides had a rough surface with many cavities. GC-FID results proved that galactose was the dominant sugar in the extracted polysaccharides, followed by arabinose, glucose, galacturonic acid, rhamnose, mannose, xylose and traces of glucuronic acid. The findings revealed that WMRP displayed excellent antihypertensive and antioxidant activities. Those polysaccharides had also a protection effect against hydroxyl radical-induced DNA damage. Functional properties of extracted polysaccharides were also evaluated. WMRP showed good interfacial dose-dependent proprieties. Overall, the results suggested that WMRP presents a promising natural source of antioxidants and antihypertensive agents. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Biological and chemical tests of contaminated soils to determine bioavailability and environmentally acceptable endpoints (EAE)

    International Nuclear Information System (INIS)

    Montgomery, C.R.; Menzie, C.A.; Pauwells, S.J.

    1995-01-01

    The understanding of the concept of bioavailability of soil contaminants to receptors and its use in supporting the development of EAE is growing but still incomplete. Nonetheless, there is increased awareness of the importance of such data to determine acceptable cleanup levels and achieve timely site closures. This presentation discusses a framework for biological and chemical testing of contaminated soils developed as part of a Gas Research Institute (GRI) project entitled ''Environmentally Acceptable Endpoints in Soil Using a Risk Based Approach to Contaminated Site Management Based on Bioavailability of Chemicals in Soil.'' The presentation reviews the GRI program, and summarizes the findings of the biological and chemical testing section published in the GRI report. The three primary components of the presentation are: (1) defining the concept of bioavailability within the existing risk assessment paradigm, (2) assessing the usefulness of the existing tests to measure bioavailability and test frameworks used to interpret these measurements, and (3) suggesting how a small selection of relevant tests could be incorporated into a flexible testing scheme for soils to address this issue

  18. Bioanalytical methods for the determination of cocaine and metabolites in human biological samples.

    Science.gov (United States)

    Barroso, M; Gallardo, E; Queiroz, J A

    2009-08-01

    Determination of cocaine and its metabolites in biological specimens is of great importance, not only in clinical and forensic toxicology, but also in workplace drug testing. These compounds are normally screened for using sensitive immunological methods. However, screening methods are unspecific and, therefore, the posterior confirmation of presumably positive samples by a specific technique is mandatory. Although GC-MS-based techniques are still the most commonly used for confirmation purposes of cocaine and its metabolites in biological specimens, the advent of LC-MS and LC-MS/MS has enabled the detection of even lower amounts of these drugs, which assumes particular importance when sample volume available is small, as frequently occurs with oral fluid. This paper will review recently-published papers that describe procedures for detection of cocaine and metabolites, not only in the most commonly used specimens, such as blood and urine, but also in other 'alternative' matrices (e.g., oral fluid and hair) with a special focus on sample preparation and chromatographic analysis.

  19. DETERMINATION OF EDUCATIONAL EFFICIENCY AND STUDENTS’ INVOLVEMENT IN THE FLIPPED BIOLOGY CLASSROOM IN PRIMARY SCHOOL

    Directory of Open Access Journals (Sweden)

    Vera S. Županec

    2018-02-01

    Full Text Available The Flipped Classroom (FC is a teaching approach in which students gain the first-exposure learning with online materials outside the classroom, and then, in the classroom, they focus on interactive or engaging exercises. Despite its considerable publicity, the studies focused on the FC in primary education are deficient. The aim of this research is to determine efficiency and students’ involvement in the flipped Biology classroom in primary school, compared to the conventional classroom (CC approach. Educational efficiency and students’ involvement are measured by combining the values of the students’ performance and mental effort on the test. Each task in the test was followed by the 5-point Likert scale for evaluation of invested mental effort. The total sample of this research included 112 students, aged from 12 to 13. The results show that the FC approach contributes to the reduction of the students’ mental effort and an increase in the students’ performance. On the basis of calculated efficiency and students’ involvement of applied teaching approaches, it was concluded that the FC represents a feasible and efficient approach to Biology primary education.

  20. Experience of an inter-laboratory exercise for the determination of Carbon-14 in biological samples

    International Nuclear Information System (INIS)

    Baburajan, A.; Rajaram, S.; D'Souza, Renita Shiny; Nayak, Rasmi; Karunakara, N.; Ravi, P.M.; Tripathi, R.M.

    2018-01-01

    Carbon-14 is one of the naturally occurring cosmogenic nuclide with long half life of 5730 y and beta energy, E max : 156 keV produced continuously in the outer atmosphere. It is also produced by the anthropogenic activities like nuclear weapon test, nuclear power plant etc. contributing to the atmospheric inventory. The 14 CO 2 gets incorporated with the plant species during photosynthesis and ultimately reaches to man through food chain. It is important to accurately quantify the level of 14 C in different biological matrices for the computation of radiation dose due to ingestion. There are different methods available for the determination of 14 C in biological samples. The oxidation of the dried sample is one of the methods used for liberating the 14 CO 2 and which in turn re-absorbed using Carbo Sorb and subjected to Liquid scintillation analyses with Permaflour scintillator solution. The paper deals with the quality assurance programme initiated by ESL, Tarapur along with ESL, Kalpakkam and CARER, Mangalore University and share the experience of the inter-laboratory comparison exercise

  1. Determination of zinc stable isotopes in biological materials using isotope dilution inductively coupled plasma mass spectrometry

    International Nuclear Information System (INIS)

    Patterson, K.Y.; Veillon, Claude

    1992-01-01

    A method is described for using isotope dilution to determine both the amount of natural zinc and enriched isotopes of zinc in biological samples. Isotope dilution inductively coupled plasma mass spectrometry offers a way to quantify not only the natural zinc found in a sample but also the enriched isotope tracers of zinc. Accurate values for the enriched isotopes and natural zinc are obtained by adjusting the mass count rate data for measurable instrumental biases. Analytical interferences from the matrix are avoided by extracting the zinc from the sample matrix using diethylammonium diethyldithiocarbamate. The extraction technique separates the zinc from elements which form interfering molecular ions at the same nominal masses as the zinc isotopes. Accuracy of the method is verified using standard reference materials. The detection limit is 0.06 μg Zn per sample. Precision of the abundance ratios range from 0.3-0.8%. R.S.D. for natural zinc concentrations is about 200-600 μg g -1 . The accuracy and precision of the measurements make it possible to follow enriched isotopic tracers of zinc in biological samples in metabolic tracer studies. (author). 19 refs.; 1 fig., 4 tabs

  2. The determination of plutonium alpha activity in urine, faeces and biological materials

    International Nuclear Information System (INIS)

    Bains, M.E.D.

    1963-07-01

    Methods have been developed for the determination of plutonium alpha activity in urine, faeces and biological materials. The chemical stages involved give practically complete separation of all extraneous material from the plutonium, which is electrodeposited on to a 0.5 inch stainless steel disc to produce a thin high resolution source. The limit of detection is 0.025 μμc/sample (sixteen-hour count) when the sources are counted in a small scintillator counter, but is lowest when counted in a counter which counts particles of energy 5.05-5.25 MeV only, and which therefore discriminates against small quantities of α-active materials introduced with the reagents in the final electrodeposition stage of the process. (Any such alpha activity may readily be identified by alpha pulse height analysis). (author)

  3. Isolation of thymus gland fractions and the determination of their biological activity

    Directory of Open Access Journals (Sweden)

    MILENA RADETA

    2007-03-01

    Full Text Available A calf thymus extract was prepared and fractionated into lipid and non-lipid fractions. The non-lipid fraction was isolated from the calf thymus extract using the Folch method. The components isolated from the non-lipid fraction were characterized by IR, NMR, biuret and HPLC method. The results of the analyses indicated the presence of peptides. The lipid fraction contained phospholipids, glycolipids and neutral lipids. The biological activity of both the isolated lipid and peptide fractions was determined by the in vivo hemolytic plaques method in Wistar rats with an involuted thymus. The peptide and phospholipid fractions of the thymus extract showed a significant increase of hemolytic plaques. The glycolipid and neutral lipid fraction failed to express a significant immunological response.

  4. Determination of selenium in biological material by instrumental neutron activation analysis using 77m Se radioisotope

    International Nuclear Information System (INIS)

    Vasconcellos, Marina B.A.; Moreira, Edson G.; Catharino, Marilia G.M.; Tokura, Alexandra M.; Saiki, Mitiko

    1999-01-01

    Selenium is an essential element in human diet due to its relation to the protection against carcinogenic substances, heart disease, hypertension, sexual performance enhancement, and others. In this work Se concentration in samples of the biological certificate reference materials Human Hair BCR-CRM 397, Spiked Human Hair IAEA-085, Unspiked Human Hair IAEA-086; Dogfish Liver DOLT-1 and Dogfish Muscle DORM-1 were determined in order to improve the instrumental neutron activation analysis, INAA, method using 77m Se radioisotope. The application of this method allows the analysis of a large number of samples of samples with reduced time of experimental and cost. the best results were obtained with the reactor operating at 5 MW and time of irradiation between 10 and 20 s. In these experimental conditions the relative standard deviation and error were generally lower than 10%. (author)

  5. Method for determination of radioactive iodine isotopes in environmental objects and biologic materials

    International Nuclear Information System (INIS)

    Dubynin, O.D.; Pogodin, R.I.

    1981-01-01

    The method proposed for determination of radioactive iodine isotopes content in environmental objects and biologic materials is based on the extraction of iodine with carbon tetrachloride and subsequent precipitation of bismuthyl iodine (BiOI) in perchloric medium. Sample preparation for analysis is carried out using conventional alkaline ashing methods. Quantitative iodine separation is hampered if macroquantities of Cl - , Br - , SO 4 2 - , SO 8 2 - , Cr 2 O 7 2 - and other ions are present in the solution. Iodine extraction is carried out before its precipitation. Separated iodine preparation activity is measured using scintillation (NaI) Tl gamma spectrometer. The method's sensitivity when measuring iodine-131 preparations makes up 0.07 Bq per 1 sample with the error +-25 %

  6. Evaluation of botanical reference materials for the determination of vanadium in biological samples

    International Nuclear Information System (INIS)

    Heydorn, K.; Damsgaard, E.

    1982-01-01

    Three botanical reference materials prepared by the National Bureau of Standards have been studied by neutron activation analysis to evaluate their suitability with respect to the determination of vanadium in biological samples. Various decomposition methods were applied in connection with chemical or radiochemical separations, and results for vanadium were compared with those found by purely instrumental neutron activation analysis. Significantly lower results indicate losses or incomplete dissolution, which makes SRM 1575 Pine Needles and SRM 1573 Tomato Leaves less satisfactory than SRM 1570 Spinach. A reference value of 1.15 mg/kg of this material is recommended, based on results from 3 different methods. All three materials are preferable to SRM 1571 Orchard Leaves, while Bowen's Kale remains the material of choice because of its lower concentration. (author)

  7. Applicability of discovery science approach to determine biological effects of mobile phone radiation.

    Science.gov (United States)

    Leszczynski, Dariusz; Nylund, Reetta; Joenväärä, Sakari; Reivinen, Jukka

    2004-02-01

    We argue that the use of high-throughput screening techniques, although expensive and laborious, is justified and necessary in studies that examine biological effects of mobile phone radiation. The "case of hsp27 protein" presented here suggests that even proteins with only modestly altered (by exposure to mobile phone radiation) expression and activity might have an impact on cell physiology. However, this short communication does not attempt to present the full scientific evidence that is far too large to be presented in a single article and that is being prepared for publication in three separate research articles. Examples of the experimental evidence presented here were designed to show the flow of experimental process demonstrating that the use of high-throughput screening techniques might help in rapid identification of the responding proteins. This, in turn, can help in speeding up of the process of determining whether these changes might affect human health.*

  8. Determination of 25 elements in biological standard reference materials by neutron activation analysis

    International Nuclear Information System (INIS)

    Guzzi, G.; Pietra, R.; Sabbioni, E.

    1974-12-01

    Standard and Certified Reference Materials programme of the JRC includes the determination of trace elements in complex biological samples delivered by the U.S. National Bureau of Standards: Bovine liver (NBS SRM 1577), Orchard Leaves (NBS SRM 1571) and Tomato Leaves. The study has been performed by the use of neutron activation analysis. Due to the very low concentration of some elements, radiochemical groups or elemental separation procedures were necessary. The paper describes the techniques used to analyse 25 elements. Computer assisted instrumental neutron activation analysis with high resolution Ge(Li) spectrometry was considerably advantageous in the determination of Na, K, Cl, Mn, Fe, Rb and Co and in some cases of Ca, Zn, Cs, Sc, and Cr. For low contents of Ca, Mg, Ni and Si special chemical separation schemes, followed by Cerenkov counting have been developped. Two other separation procedures allowing the determination of As, Cd, Ga, Hg, Mo, Cu, Sr Se, Ba and P have been set up. The first, the simplified one involves the use of high resolution Ge(Li) detectors, the second, the more complete one involves a larger number of shorter measurements performed by simpler and more sensitive techniques, such as NaI(Tl) scintillation spectrometry and Cerenkov counting. The results obtained are presented and discussed

  9. Analytical applications of oscillatory chemical reactions: determination of some pharmaceuticaly and biologically important compounds

    Directory of Open Access Journals (Sweden)

    Pejić Nataša D.

    2012-01-01

    Full Text Available Novel analytical methods for quantitive determination of analytes based on perturbations of oscillatory chemical reactions realized under open reactor conditions (continuosly fed well stirred tank reactor, CSTR, have been developed in the past twenty years. The proposed kinetic methods are generally based on the ability of the analyzed substances to change the kinetics of the chemical reactions matrix. The unambiguous correlation of quantitative characteristics of perturbations, and the amount (concentration of analyte expressed as a regression equation, or its graphics (calibration curve, enable the determination of the unknown analyte concentration. Attention is given to the development of these methods because of their simple experimental procedures, broad range of linear regression ( 10-7 10-4 mol L-1 and low limits of detection of analytes ( 10-6 10-8 mol L1, in some cases even lower than 10-12 mol L-1. Therefore, their application is very convenient for routine analysis of various inorganic and organic compounds as well as gases. This review summarizes progress made in the past 5 years on quantitative determination of pharmaceutically and biologically important compounds.

  10. Preconcentration and determination of heavy metals in water, sediment and biological samples

    Directory of Open Access Journals (Sweden)

    Shirkhanloo Hamid

    2011-01-01

    Full Text Available In this study, a simple, sensitive and accurate column preconcentration method was developed for the determination of Cd, Cu and Pb ions in river water, urine and sediment samples by flame atomic absorption spectrometry. The procedure is based on the retention of the analytes on a mixed cellulose ester membrane (MCEM column from buffered sample solutions and then their elution from the column with nitric acid. Several parameters, such as pH of the sample solution, volume of the sample and eluent and flow rates of the sample were evaluated. The effects of diverse ions on the preconcentration were also investigated. The recoveries were >95 %. The developed method was applied to the determination of trace metal ions in river water, urine and sediment samples, with satisfactory results. The 3δ detection limits for Cu, Pb and Cd were found to be 2, 3 and 0.2 μg dm−3, respectively. The presented procedure was successfully applied for determination of the copper, lead and cadmium contents in real samples, i.e., river water and biological samples.

  11. Determination of total mercury and methylmercury in biological samples by photochemical vapor generation

    Energy Technology Data Exchange (ETDEWEB)

    Vieira, Mariana A.; Ribeiro, Anderson S.; Curtius, Adilson J. [Universidade Federal de Santa Catarina, Departamento de Quimica, Florianopolis, SC (Brazil); Sturgeon, Ralph E. [National Research Council Canada, Institute for National Measurement Standards, Ottawa, ON (Canada)

    2007-06-15

    Cold vapor atomic absorption spectrometry (CV-AAS) based on photochemical reduction by exposure to UV radiation is described for the determination of methylmercury and total mercury in biological samples. Two approaches were investigated: (a) tissues were digested in either formic acid or tetramethylammonium hydroxide (TMAH), and total mercury was determined following reduction of both species by exposure of the solution to UV irradiation; (b) tissues were solubilized in TMAH, diluted to a final concentration of 0.125% m/v TMAH by addition of 10% v/v acetic acid and CH{sub 3}Hg{sup +} was selectively quantitated, or the initial digests were diluted to 0.125% m/v TMAH by addition of deionized water, adjusted to pH 0.3 by addition of HCl and CH{sub 3}Hg{sup +} was selectively quantitated. For each case, the optimum conditions for photochemical vapor generation (photo-CVG) were investigated. The photochemical reduction efficiency was estimated to be {proportional_to}95% by comparing the response with traditional SnCl{sub 2} chemical reduction. The method was validated by analysis of several biological Certified Reference Materials, DORM-1, DORM-2, DOLT-2 and DOLT-3, using calibration against aqueous solutions of Hg{sup 2+}; results showed good agreement with the certified values for total and methylmercury in all cases. Limits of detection of 6 ng/g for total mercury using formic acid, 8 ng/g for total mercury and 10 ng/g for methylmercury using TMAH were obtained. The proposed methodology is sensitive, simple and inexpensive, and promotes ''green'' chemistry. The potential for application to other sample types and analytes is evident. (orig.)

  12. Determination of tin in biological reference materials by atomic absorption spectrophotometry and neutron activation analysis

    International Nuclear Information System (INIS)

    Chiba, M.; Iyengar, V.; Gills, T.

    1991-01-01

    Because of a lack of reliable analytical techniques for the determination of tin in biological materials, there have been no reference materials certified for this element. However, the authors' experience has shown that it is feasible to use both atomic absorption and nuclear activation techniques at least for selected matrices. Therefore, an investigation was undertaken to determine tin in several biological materials such as non-fat milk powder (NBS-SRM-1549), citrus leaves (NBS-SRM-1572), total diet (NIST-SRM-1548), mixed diet (NBS-RM-8431), and USDIET-I by atomic absorption spectrophotometry (AAS) and neutron activation analysis (NAA). AAS-ashed samples were extracted with MIBK and assayed using a Perkin Elmer model 5000 apparatus. NAA was carried out by irradiating the samples at the NIST reactor in the RT-4 facility and counting with the help of a Ge(Li) detector connected to a multichannel analyzer. The concentration of tin measured by both AAS and NAA agree well for USDIET-I, total diet, citrus leaves and non-fat milk powder (the concentration ranges for tin in these matrices were from 0.0025 to 3.8 micro g/g). However, in the case of mixed diet (RM-8431), the mean values found were 47 ± 5.6 (n = 19) by AAS and 55.5 ± 2.5 (n = 6) by INAA. Since RM-8431 is not certified it is difficult to draw conclusions. For apple and peach leaves, a distillation step was required. The results were apple leaves 0.085 ± 0.015 (n = 10) by AAS and < 0.2 (n = 3) by RNAA; for peach leaves 0.077 ± 0.02 (n = 9) by AAS and < 0.1 (n = 3) by RNAA. All concentrations are expressed in micro g/g dry weight

  13. Mixing regime as a key factor to determine DON formation in drinking water biological treatment.

    Science.gov (United States)

    Lu, Changqing; Li, Shuai; Gong, Song; Yuan, Shoujun; Yu, Xin

    2015-11-01

    Dissolved organic nitrogen (DON) can act as precursor of nitrogenous disinfection by-products formed during chlorination disinfection. The performances of biological fluidized bed (continuous stirred tank reactor, CSTR) and bio-ceramic filters (plug flow reactor, PFR) were compared in this study to investigate the influence of mixing regime on DON formation in drinking water treatment. In the shared influent, DON ranged from 0.71mgL(-1) to 1.20mgL(-1). The two biological fluidized bed reactors, named BFB1 (mechanical stirring) and BFB2 (air agitation), contained 0.12 and 0.19mgL(-1) DON in their effluents, respectively. Meanwhile, the bio-ceramic reactors, labeled as BCF1 (no aeration) and BCF2 (with aeration), had 1.02 and 0.81mgL(-1) DON in their effluents, respectively. Comparative results showed that the CSTR mixing regime significantly reduced DON formation. This particular reduction was further investigated in this study. The viable/total microbial biomass was determined with propidium monoazide quantitative polymerase chain reaction (PMA-qPCR) and qPCR, respectively. The results of the investigation demonstrated that the microbes in BFB2 had higher viability than those in BCF2. The viable bacteria decreased more sharply than the total bacteria along the media depth in BCF2, and DON in BCF2 accumulated in the deeper media. These phenomena suggested that mixing regime determined DON formation by influencing the distribution of viable, total biomass, and ratio of viable biomass to total biomass. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. TLC-spectrophometric separation and trace determination of monocrotophos and dichlorvos in enviromental and biological samples.

    Science.gov (United States)

    Janghel, Etesh K; Rai, J K; Khan, S; Rai, M K; Gupta, V K

    2007-04-01

    Organophosphorus insecticides, monocrotophos and dichlrovos are increasingly being used in agriculture to control insects on a wide range of crops. Their ready access has resulted in misuse in many instances of homicidal and suicidal poisoning cases. This paper describes about a chromogenic spray reagent for the detection/determination of monocrophos and dichlrovos in environmental and biological samples by TLC and spectrophotometric method. Monocrotophos and dichlorvos on alkaline hydrolysis yield N-methyl acetoacetamide and dichlroacetaldehyde respectively, which in turn react with diazotized p-amino acetophenone to give red-violet and red coloured compounds. Other organophosphorus insecticides do not give this reaction. Moreover, organochlorine and synthetic pyrethroid insecticides and constituents of viscera (amino acids, peptides, proteins etc), which are generally coextracted with the insecticides, do not interfere. However, phenolic compounds and hydrolysed product of carbamate insecticides may interfere and differentiate from monocrotophos and dichlrovos by Rf values. The lower limit of detection is 0.2 mg for monocrotophos and 0.1 mg for dichlorovos. The absorption maxima of the reddish-violet and red colour formed by monocrotophos and dichlrovos, are measured at 560 nm and 540 nm respectively. Beer's Law is obeyed over the concentration range of 1.2 to 6.8 mg and 6.2 to 35 mg in the final solution volume of 25 mL. The molar absorptivity and Sandell's sensitivity of monocrotophos and dichlrovos were found to be 7.1 x 10(5) (+100) 1 mole(-1) cm(-1) and 0.008 mg cm(-2), 1.2 x 10(5) 1 mole(-1) cm(-1) and 0.003 mg cm(-2) respectively. The standard deviation and relative standard deviation were found be +/- 0.005 and 2.05% +/- 0.007 and 2.02% respectively. The developed method has been successfully applied to the detection and determination of monocrotophos and dichlrovos in environmental and biological samples.

  15. German National Proficiency Scales in Biology: Internal Structure, Relations to General Cognitive Abilities and Verbal Skills

    Science.gov (United States)

    KÖLLER, OLAF

    2016-01-01

    ABSTRACT National and international large‐scale assessments (LSA) have a major impact on educational systems, which raises fundamental questions about the validity of the measures regarding their internal structure and their relations to relevant covariates. Given its importance, research on the validity of instruments specifically developed for LSA is still sparse, especially in science and its subdomains biology, chemistry, and physics. However, policy decisions for the improvement of educational quality based on LSA can only be helpful if valid information on students’ achievement levels is provided. In the present study, the nature of the measurement instruments based on the German Educational Standards in Biology is examined. On the basis of data from 3,165 students in Grade 10, we present dimensional analyses and report the relationship between different subdimensions of biology literacy and cognitive covariates such as general cognitive abilities and verbal skills. A theory‐driven two‐dimensional model fitted the data best. Content knowledge and scientific inquiry, two subdimensions of biology literacy, are highly correlated and show differential correlational patterns to the covariates. We argue that the underlying structure of biology should be incorporated into curricula, teacher training and future assessments. PMID:27818532

  16. A Glimpse of Membrane Transport through Structures-Advances in the Structural Biology of the GLUT Glucose Transporters.

    Science.gov (United States)

    Yan, Nieng

    2017-08-18

    The cellular uptake of glucose is an essential physiological process, and movement of glucose across biological membranes requires specialized transporters. The major facilitator superfamily glucose transporters GLUTs, encoded by the SLC2A genes, have been a paradigm for functional, mechanistic, and structural understanding of solute transport in the past century. This review starts with a glimpse into the structural biology of membrane proteins and particularly membrane transport proteins, enumerating the landmark structures in the past 25years. The recent breakthrough in the structural elucidation of GLUTs is then elaborated following a brief overview of the research history of these archetypal transporters, their functional specificity, and physiological and pathophysiological significances. Structures of GLUT1, GLUT3, and GLUT5 in distinct transport and/or ligand-binding states reveal detailed mechanisms of the alternating access transport cycle and substrate recognition, and thus illuminate a path by which structure-based drug design may be applied to help discover novel therapeutics against several debilitating human diseases associated with GLUT malfunction and/or misregulation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Configuration of biological wastewater treatment line and influent composition as the main factors driving bacterial community structure of activated sludge.

    Science.gov (United States)

    Jaranowska, Paulina; Cydzik-Kwiatkowska, Agnieszka; Zielińska, Magdalena

    2013-07-01

    The structure of microbial consortia in wastewater treatment facilities is a resultant of environmental conditions created by the operational parameters of the purification process. In the research, activated sludge from nine Polish wastewater treatment plants (WWTPs) was investigated at a molecular level to determine the impact of the complexity of biological treatment line and the influent composition on the species structure and the diversity of bacterial consortia. The community fingerprints and technological data were subjected to the canonical correspondence and correlation analyses. The number of separated biological processes realized in the treatment line and the presence of industrial wastewater in the influent were the key factors determining the species structure of total and ammonia-oxidizing bacteria in biomass. The N2O-reducers community composition depended significantly on the design of the facility; the highest species richness of denitrifiers was noted in the WWTPs with separated denitrification tanks. The contribution of industrial streams to the inflow affected the diversity of total and denitrifying bacterial consortia and diminished the diversity of ammonia oxidizers. The obtained data are valuable for engineers since they revealed the main factors, including the design of wastewater treatment plant, influencing the microbial groups critical for the stability of purification processes.

  18. ALOUD: Adult Learning Open University Determinants Study: Association between biological and psychological determinants and study success in adult formal distance education

    NARCIS (Netherlands)

    De Groot, Renate; Neroni, Joyce; Gijselaers, Jérôme; Kirschner, Paul A.

    2012-01-01

    De Groot, R. H. M., Neroni, J., Gijselaers, J., & Kirschner, P. A. (2012, 6 December). ALOUD: Adult Learning Open University Determinants Study: Associations between biological and psychological determinants and study success in adult formal distance education. Presented at the Open University for

  19. Defining an essence of structure determining residue contacts in proteins.

    Science.gov (United States)

    Sathyapriya, R; Duarte, Jose M; Stehr, Henning; Filippis, Ioannis; Lappe, Michael

    2009-12-01

    The network of native non-covalent residue contacts determines the three-dimensional structure of a protein. However, not all contacts are of equal structural significance, and little knowledge exists about a minimal, yet sufficient, subset required to define the global features of a protein. Characterisation of this "structural essence" has remained elusive so far: no algorithmic strategy has been devised to-date that could outperform a random selection in terms of 3D reconstruction accuracy (measured as the Ca RMSD). It is not only of theoretical interest (i.e., for design of advanced statistical potentials) to identify the number and nature of essential native contacts-such a subset of spatial constraints is very useful in a number of novel experimental methods (like EPR) which rely heavily on constraint-based protein modelling. To derive accurate three-dimensional models from distance constraints, we implemented a reconstruction pipeline using distance geometry. We selected a test-set of 12 protein structures from the four major SCOP fold classes and performed our reconstruction analysis. As a reference set, series of random subsets (ranging from 10% to 90% of native contacts) are generated for each protein, and the reconstruction accuracy is computed for each subset. We have developed a rational strategy, termed "cone-peeling" that combines sequence features and network descriptors to select minimal subsets that outperform the reference sets. We present, for the first time, a rational strategy to derive a structural essence of residue contacts and provide an estimate of the size of this minimal subset. Our algorithm computes sparse subsets capable of determining the tertiary structure at approximately 4.8 A Ca RMSD with as little as 8% of the native contacts (Ca-Ca and Cb-Cb). At the same time, a randomly chosen subset of native contacts needs about twice as many contacts to reach the same level of accuracy. This "structural essence" opens new avenues in the

  20. Synthesis, structural studies and biological properties of new TBA analogues containing an acyclic nucleotide.

    Science.gov (United States)

    Coppola, Teresa; Varra, Michela; Oliviero, Giorgia; Galeone, Aldo; D'Isa, Giuliana; Mayol, Luciano; Morelli, Elena; Bucci, Maria-Rosaria; Vellecco, Valentina; Cirino, Giuseppe; Borbone, Nicola

    2008-09-01

    A new modified acyclic nucleoside, namely N(1)-(3-hydroxy-2-hydroxymethyl-2-methylpropyl)-thymidine, was synthesized and transformed into a building block useful for oligonucleotide (ON) automated synthesis. A series of modified thrombin binding aptamers (TBAs) in which the new acyclic nucleoside replaces, one at the time, the thymidine residues were then synthesized and characterized by UV, CD, MS, and (1)H NMR. The biological activity of the resulting TBAs was tested by Prothrombin Time assay (PT assay) and by purified fibrinogen clotting assay. From a structural point of view, nearly all the new TBA analogues show a similar behavior as the unmodified counterpart, being able to fold into a bimolecular or monomolecular quadruplex structure depending on the nature of monovalent cations (sodium or potassium) coordinated in the quadruplex core. From the comparison of structural and biological data, some important structure-activity relationships emerged, particularly when the modification involved the TT loops. In agreement with previous studies we found that the folding ability of TBA analogues is more affected by modifications involving positions 4 and 13, rather than positions 3 and 12. On the other hand, the highest anti-thrombin activities were detected for aptamers containing the modification at T13 or T12 positions, thus indicating that the effects produced by the introduction of the acyclic nucleoside on the biological activity are not tightly connected with structure stabilities. It is noteworthy that the modification at T7 produces an ON being more stable and active than the natural TBA.

  1. Form and function: Perspectives on structural biology and resources for the future

    International Nuclear Information System (INIS)

    Vaughan, D.

    1990-12-01

    The purpose of this study is largely to explore and expand on the thesis that biological structures and their functions are suited to. Form indeed follows function and if we are to understand the workings of a living system, with all that such an understanding promises, we must first seek to describe the structure of its parts. Descriptions of a few achievements of structural biology lay the groundwork, but the substance of this booklet is a discussion of important questions yet unanswered and opportunities just beyond our grasp. The concluding pages then outline a course of action in which the Department of Energy would exercise its responsibility to develop the major resources needed to extend our reach and to answer some of those unanswered questions. 22 figs

  2. Adapting federated cyberinfrastructure for shared data collection facilities in structural biology.

    Science.gov (United States)

    Stokes-Rees, Ian; Levesque, Ian; Murphy, Frank V; Yang, Wei; Deacon, Ashley; Sliz, Piotr

    2012-05-01

    Early stage experimental data in structural biology is generally unmaintained and inaccessible to the public. It is increasingly believed that this data, which forms the basis for each macromolecular structure discovered by this field, must be archived and, in due course, published. Furthermore, the widespread use of shared scientific facilities such as synchrotron beamlines complicates the issue of data storage, access and movement, as does the increase of remote users. This work describes a prototype system that adapts existing federated cyberinfrastructure technology and techniques to significantly improve the operational environment for users and administrators of synchrotron data collection facilities used in structural biology. This is achieved through software from the Virtual Data Toolkit and Globus, bringing together federated users and facilities from the Stanford Synchrotron Radiation Lightsource, the Advanced Photon Source, the Open Science Grid, the SBGrid Consortium and Harvard Medical School. The performance and experience with the prototype provide a model for data management at shared scientific facilities.

  3. Form and function: Perspectives on structural biology and resources for the future

    Energy Technology Data Exchange (ETDEWEB)

    Vaughan, D. (ed.)

    1990-12-01

    The purpose of this study is largely to explore and expand on the thesis that biological structures and their functions are suited to. Form indeed follows function and if we are to understand the workings of a living system, with all that such an understanding promises, we must first seek to describe the structure of its parts. Descriptions of a few achievements of structural biology lay the groundwork, but the substance of this booklet is a discussion of important questions yet unanswered and opportunities just beyond our grasp. The concluding pages then outline a course of action in which the Department of Energy would exercise its responsibility to develop the major resources needed to extend our reach and to answer some of those unanswered questions. 22 figs.

  4. Bidimensional microdosimetry as a tool for evaluating biological response and target structure

    International Nuclear Information System (INIS)

    Booz, J.; Schmitz, Th.; Feinendegen, L.E.; Olko, P.

    1992-01-01

    The paper addresses the issue of the relevance of microdosimetric spectra for quantifying the effects of low-level exposures to radiation. Biological response functions derived to date from numerical analyses of radiobiological and microdosimetric observations refer to uniform targets of a preassumed size. The characteristic two-modal shape of functions obtained for several endpoints reflects the importance of two different pathways of damage formation, each of them related in fact to different target sizes. The correlated energy deposition distributions in such a bidimensional system are suggested as a more appropriate physical input for analysing biological response and target structure. (author)

  5. HIV INFECTION AMONG FEMALE SEX WORKERS IN CONCENTRATED AND HIGH PREVALENCE EPIDEMICS: WHY A STRUCTURAL DETERMINANTS FRAMEWORK IS NEEDED

    Science.gov (United States)

    Shannon, Kate; Goldenberg, Shira M.; Deering, Kathleen N.; Strathdee, Steffanie A.

    2014-01-01

    Purpose of review This article reviews the current state of the epidemiological literature on female sex work and HIV from the past 18 months. We offer a conceptual framework for structural HIV determinants and sex work that unpacks intersecting structural, interpersonal, and individual biological and behavioural factors. Recent findings Our review suggests that despite the heavy HIV burden among female sex workers (FSWs) globally, data on the structural determinants shaping HIV transmission dynamics have only begun to emerge. Emerging research suggests that factors operating at macrostructural (e.g., migration, stigma, criminalized laws), community organization (e.g., empowerment) and work environment levels (e.g., violence, policing, access to condoms HIV testing, HAART) act dynamically with interpersonal (e.g., dyad factors, sexual networks) and individual biological and behavioural factors to confer risks or protections for HIV transmission in female sex work. Summary Future research should be guided by a Structural HIV Determinants Framework to better elucidate the complex and iterative effects of structural determinants with interpersonal and individual biological and behavioural factors on HIV transmission pathways among FSWs, and meet critical gaps in optimal access to HIV prevention, treatment, and care for FSWs globally. PMID:24464089

  6. Synthesis and Structural Determination of Temocapril Sulfoxide Hydrochlorides

    International Nuclear Information System (INIS)

    Seong, Seok Bong; Moon, Jong Taik; Kim, Jung Ahn; Choo, Dong Joon; Lee, Jae Yeol

    2012-01-01

    Impurity (or related substance) control in pharmaceutical products is a primary goal of drug development. Stringent international regulatory requirements have been in place for several years as outlined in the International Conference on Harmonization (ICH) Guidelines Q3A (R), Q3B (R) and Q3C. According to ICH guidelines, impurities associated with the manufacture of a drug substance, also known as an active pharmaceutical ingredient (API), are classified into the following categories: (1) organic impurities (process and drug-related); (2) inorganic impurities (3) residual solvents. Many potential impurities result from the API manufacturing process including starting materials, isomers, intermediates, reagents, solvents, catalysts and reaction by-products. These potential impurities should be investigated to determine process control mechanisms for their removal and the need for specification controls at appropriate points in the process. The suggested structures of the impurities can be synthesized and will provide the final evidence for their structures, previously determined by spectroscopic methods. Therefore it is essential to know the structure of these impurities in the bulk drug in order to alter the reaction condition and to reduce the quantity of impurity to an acceptable level. Isolation, identification and quantification of impurities help the pharmaceutical company to obtain a pure substance with less toxicity and safety in drug therapy

  7. Assessment of carotid plaque vulnerability using structural and geometrical determinants

    International Nuclear Information System (INIS)

    Li, Z.Y.; Tang, T.; U-King-Im, J.; Graves, M.; Gillard, J.H.; Sutcliffe, M.

    2008-01-01

    Because many acute cerebral ischemic events are caused by rupture of vulnerable carotid atheroma and subsequent thrombosis, the present study used both idealized and patient-specific carotid atheromatous plaque models to evaluate the effect of structural determinants on stress distributions within plaque. Using a finite element method, structural analysis was performed using models derived from in vivo high-resolution magnetic resonance imaging (MRI) of carotid atheroma in 40 non-consecutive patients (20 symptomatic, 20 asymptomatic). Plaque components were modeled as hyper-elastic materials. The effects of varying fibrous cap thickness, lipid core size and lumen curvature on plaque stress distributions were examined. Lumen curvature and fibrous cap thickness were found to be major determinants of plaque stress. The size of the lipid core did not alter plaque stress significantly when the fibrous cap was relatively thick. The correlation between plaque stress and lumen curvature was significant for both symptomatic (p=0.01; correlation coefficient: 0.689) and asymptomatic patients (p=0.01; correlation coefficient: 0.862). Lumen curvature in plaques of symptomatic patients was significantly larger than those of asymptomatic patients (1.50±1.0 mm -1 vs 1.25±0.75 mm -1 ; p=0.01). Specific plaque morphology (large lumen curvature and thin fibrous cap) is closely related to plaque vulnerability. Structural analysis using high-resolution MRI of carotid atheroma may help in detecting vulnerable atheromatous plaque and aid the risk stratification of patients with carotid disease. (author)

  8. X-ray structure determination and deuteration of nattokinase.

    Science.gov (United States)

    Yanagisawa, Yasuhide; Chatake, Toshiyuki; Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki; Kawaguchi, Akio; Chiba-Kamosida, Kaori; Ogawa, Megumi; Adachi, Tatsumi; Morimoto, Yukio

    2013-11-01

    Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D2O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D2O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis.

  9. Ultra-Structure database design methodology for managing systems biology data and analyses

    Directory of Open Access Journals (Sweden)

    Hemminger Bradley M

    2009-08-01

    Full Text Available Abstract Background Modern, high-throughput biological experiments generate copious, heterogeneous, interconnected data sets. Research is dynamic, with frequently changing protocols, techniques, instruments, and file formats. Because of these factors, systems designed to manage and integrate modern biological data sets often end up as large, unwieldy databases that become difficult to maintain or evolve. The novel rule-based approach of the Ultra-Structure design methodology presents a potential solution to this problem. By representing both data and processes as formal rules within a database, an Ultra-Structure system constitutes a flexible framework that enables users to explicitly store domain knowledge in both a machine- and human-readable form. End users themselves can change the system's capabilities without programmer intervention, simply by altering database contents; no computer code or schemas need be modified. This provides flexibility in adapting to change, and allows integration of disparate, heterogenous data sets within a small core set of database tables, facilitating joint analysis and visualization without becoming unwieldy. Here, we examine the application of Ultra-Structure to our ongoing research program for the integration of large proteomic and genomic data sets (proteogenomic mapping. Results We transitioned our proteogenomic mapping information system from a traditional entity-relationship design to one based on Ultra-Structure. Our system integrates tandem mass spectrum data, genomic annotation sets, and spectrum/peptide mappings, all within a small, general framework implemented within a standard relational database system. General software procedures driven by user-modifiable rules can perform tasks such as logical deduction and location-based computations. The system is not tied specifically to proteogenomic research, but is rather designed to accommodate virtually any kind of biological research. Conclusion We find

  10. Determination of parathion in biological fluids by means of direct solid-phase microextraction.

    Science.gov (United States)

    Gallardo, E; Barroso, M; Margalho, C; Cruz, A; Vieira, D N; López-Rivadulla, M

    2006-11-01

    A new and simple procedure for the determination of parathion in human whole blood and urine using direct immersion (DI) solid-phase microextraction (SPME) and gas chromatography/mass spectrometry (GC/MS) is presented. This technique was developed using only 100 microL of sample, and ethion was used as internal standard (IS). A 65-microm Carbowax/divinylbenzene (CW/DVB) SPME fibre was selected for sampling, and the main parameters affecting the SPME process such as extraction temperature, adsorption and desorption time, salt addition, agitation and pH effect were optimized to enhance the sensitivity of the method. This optimization was also performed to allow the qualitative determination of parathion's main metabolite, paraoxon, in blood. The limits of detection and quantitation for parathion were 3 and 10 ng/mL for urine and 25 and 50 ng/mL for blood, respectively. For paraoxon, the limit of detection was 50 ng/mL in blood. The method showed linearity between the LOQ and 50 microg/mL for both matrices, with correlation coefficients ranging from 0.9954 to 0.9999. Precision and accuracy were in conformity with the criteria normally accepted in bioanalytical method validation. The mean absolute recoveries were 35.1% for urine and 6.7% for blood. Other parameters such as dilution of sample and stability were also validated. Its simplicity and the fact that only 100 microL of sample is required to accomplish the analysis make this method useful in forensic toxicology laboratories to determine this compound in intoxications, and it can be considered an alternative to other methods normally used for the determination of this compound in biological media.

  11. A use of Ramachandran potentials in protein solution structure determinations

    International Nuclear Information System (INIS)

    Bertini, Ivano; Cavallaro, Gabriele; Luchinat, Claudio; Poli, Irene

    2003-01-01

    A strategy is developed to use database-derived φ-ψ constraints during simulated annealing procedures for protein solution structure determination in order to improve the Ramachandran plot statistics, while maintaining the agreement with the experimental constraints as the sole criterion for the selection of the family. The procedure, fully automated, consists of two consecutive simulated annealing runs. In the first run, the database-derived φ-ψ constraints are enforced for all aminoacids (but prolines and glycines). A family of structures is then selected on the ground of the lowest violations of the experimental constraints only, and the φ-ψ values for each residue are examined. In the second and final run, the database-derived φ-ψ constraints are enforced only for those residues which in the first run have ended in one and the same favored φ-ψ region. For residues which are either spread over different favored regions or concentrated in disallowed regions, the constraints are not enforced. The final family is then selected, after the second run, again only based on the agreement with the experimental constraints. This automated approach was implemented in DYANA and was tested on as many as 12 proteins, including some containing paramagnetic metals, whose structures had been previously solved in our laboratory. The quality of the structures, and of Ramachandran plot statistics in particular, was notably improved while preserving the agreement with the experimental constraints

  12. What determines the structures of native folds of proteins?

    International Nuclear Information System (INIS)

    Trovato, Antonio; Hoang, Trinh X; Banavar, Jayanth R; Maritan, Amos; Seno, Flavio

    2005-01-01

    We review a simple physical model (Hoang et al 2004 Proc. Natl Acad. Sci. USA 101 7960, Banavar et al 2004 Phys. Rev. E at press) which captures the essential physico-chemical ingredients that determine protein structure, such as the inherent anisotropy of a chain molecule, the geometrical and energetic constraints placed by hydrogen bonds, sterics, and hydrophobicity. Within this framework, marginally compact conformations resembling the native state folds of proteins emerge as competing minima in the free energy landscape. Here we demonstrate that a hydrophobic-polar (HP) sequence composed of regularly repeated patterns has as its ground state a β-helical structure remarkably similar to a known architecture in the Protein Data Bank

  13. Host Proteins Determine MRSA Biofilm Structure and Integrity

    DEFF Research Database (Denmark)

    Dreier, Cindy; Nielsen, Astrid; Jørgensen, Nis Pedersen

    Human extracellular matrix (hECM) proteins aids the initial attachment and initiation of an infection, by specific binding to bacterial cell surface proteins. However, the importance of hECM proteins in structure, integrity and antibiotic resilience of a biofilm is unknown. This study aims...... to determine how specific hECM proteins affect S. aureus USA300 JE2 biofilms. Biofilms were grown in the presence of synovial fluid from rheumatoid arteritis patients to mimic in vivo conditions, where bacteria incorporate hECM proteins into the biofilm matrix. Difference in biofilm structure, with and without...... addition of hECM to growth media, was visualized by confocal laser scanning microscopy. Two enzymatic degradation experiments were used to study biofilm matrix composition and importance of hECM proteins: enzymatic removal of specific hECM proteins from growth media, before biofilm formation, and enzymatic...

  14. Application of ion mobility spectrometry for the determination of tramadol in biological samples

    Directory of Open Access Journals (Sweden)

    Ali Sheibani

    2014-12-01

    Full Text Available In this study, a simple and rapid ion mobility spectrometry (IMS method has been described for the determination of tramadol. The operating instrumental parameters that could influence IMS were investigated and optimized (temperature; injection: 220 and IMS cell: 190°C, flow rate; carrier: 300 and drift: 600 mL/minute, voltage; corona: 2300 and drift: 7000 V, pulse width: 100 μs. Under optimum conditions, the calibration curves were linear within two orders of magnitude with R2 ≥ 0.998 for the determination of tramadol in human plasma, saliva, serum, and urine samples. The limits of detection and the limits of quantitation were between 0.1 and 0.3 and 0.3 and 1 ng/mL, respectively. The relative standard deviations were between 7.5 and 8.8%. The recovery results (90–103.9% indicate that the proposed method can be applied for tramadol analysis in different biological samples.

  15. Determination of traces of lithium in biological, environmental and metal samples by neutron activation analysis

    International Nuclear Information System (INIS)

    Yang, J.Y.; Tseng, C.L.; Lo, J.M.; Yang, M.H.

    1985-01-01

    Lithium in environmental, biological and metal samples was determined by neutron activation analysis via the 6 Li(n,α)T and 16 O(T,n) 18 F reactions. The samples were converted to aqueous solutions either by dissolution or by digestion and their aliquots were irradiated in a nuclear reactor for 2 h. The irradiated sample solution, was placed in a ZrO 2 column on which the 18 F nuclide was adsorbed. Most of the coexisting nuclides 24 Na, 82 Br, 38 Cl, 64 Cu, etc. were separated by elution with pH 1proportional3 solution. The column was subjected to a Ge(Li) detector for γ-ray spectrometry. The lithium content in the sample was estimated from the 18 F activity obtained. The matrix effect can be eliminated by either strong dilution of the samples in aqueous medium or by the method of standard addition. Lithium can be determined with high precision and accuracy in sub-ppm samples. (orig.) [de

  16. Simultaneous determination of arsenic, copper, manganese, selenium, and zinc in biological materials by neutron activation analysis

    International Nuclear Information System (INIS)

    Damsgaard, E.; Heydorn, K.

    1976-08-01

    A method for the simultaneous determination of arsenic, copper, manganese, selenium, and zinc in biological material was developed by the incorporation of separation procedures for copper and zinc into an existing procedure. Investigation of the performance characteristics of the method was carried out with reference to copper and zinc. For certain materials characterized by a high Cu/Zn ratio, or a high zinc content, or both, such as liver, copper ihterferes in the determination of zinc thus requiring a small correction by an iterative procedure. Blank values for copper depend on the rinsing of the irradiation container, and a single rinsing with redistilled water was found superior to other rinsing procedures. Nuclear interference was negligible. The accuracy of the method was checked by analysis of Standard Reference Materials and the precision verified by analysis of Intercomparison Samples. Results are presented for 5 male foetuses of 3-5 months' gestational age. The distribution of arsenic, manganese and selenium is similar to that previously reported for adults. With the exception of liver, concentrations of copper in foetal organs were lower than values in the literature indicate. (author)

  17. Study on Solid Phase Extraction and Spectrophotometric Determination of Nickel in Waters and Biological Samples

    International Nuclear Information System (INIS)

    Hu, Qiufen; Yang, Guangyu; Huang, Zhangjie; Yin, Jiayuan

    2004-01-01

    A sensitive, selective and rapid method for the determination of nickel based on the rapid reaction of nickel(II) with QADMAA and the solid phase extraction of the Ni(II)-QADMAA chelate with C 18 membrane disks has been developed. In the presence of pH 6.0 buffer solution and sodium dodecyl sulfonate (SDS) medium, QADMAA reacts with nickel to form a violet complex of a molar ratio of 1 : 2 (nickel to QADMAA). This chelate was enriched by solid phase extraction with C 18 membrane disks. An enrichment factor of 50 was obtained by elution of the chelates form the disks with the minimal amount of isopentyl alcohol. The molar absorptivity of the chelate was 1.32 x 10 5 L mol -1 cm -1 at 590 nm in the measured solution. Beer's law was obeyed in the range of 0.01-0.6 μg/mL. This method was applied to the determination of nickel in water and biological samples with good results

  18. Purification and primary structure determination of human lysosomal dipeptidase.

    Science.gov (United States)

    Dolenc, Iztok; Mihelic, Marko

    2003-02-01

    The lysosomal metallopeptidase is an enzyme that acts preferentially on dipeptides with unsubstituted N- and C-termini. Its activity is highest in slightly acidic pH. Here we describe the isolation and characterization of lysosomal dipeptidase from human kidney. The isolated enzyme has the amino-terminal sequence DVAKAIINLAVY and is a homodimer with a molecular mass of 100 kDa. So far no amino acid sequence has been determined for this metallopeptidase. The complete primary structure as deduced from the nucleotide sequence revealed that the isolated dipeptidase is similar to blood plasma glutamate carboxypeptidase.

  19. Structure determination of spider silk from X-ray images

    Energy Technology Data Exchange (ETDEWEB)

    Ulrich, Stephan; Zippelius, Annette [Universitaet Goettingen, Institut fuer Theoretische Physik (Germany); Meling, Martin [Max-Planck-Institut fuer biophysikalische Chemie, Goettingen (Germany); Glisovic, Anja; Salditt, Tim [Universitaet Goettingen, Institut fuer Roentgenphysik (Germany)

    2008-07-01

    Spider silk consists of interconnected crystallites, which are typically aligned along the fiber axis. We present a method to systematically determine the structure of these crystallites. Hereby we introduce a model that calculates the scattering function G(q) which is fitted to the measured X-ray image (silk from nephila clavipes). With it, the crystallites' size, the constitution and dimensions of their unit cell, as well as their tilt with respect to the fiber axis is identified, and furthermore the effect of coherent scattering from different crystallites is investigated. The shown methods and the presented model can easily be generalized to a wide class of composite materials.

  20. Shallow lunar structure determined from the passive seismic experiment

    International Nuclear Information System (INIS)

    Nakamura, Y.; Dorman, J.; Duennebier, F.; Lammlein, D.; Latham, G.

    1975-01-01

    Data relevant to the shallow structure of the Moon obtained at the Apollo seismic stations are compared with previously published results of the active seismic experiments. It is concluded that the lunar surface is covered by a layer of low seismic velocity (Vsub(p) approximately equal to 100 ms -1 ), which appears to be equivalent to the lunar regolith defined previously by geological observations. This layer is underlain by a zone of distinctly higher seismic velocity at all of the Apollo landing sites. The regolith thicknesses at the Apollo 11, 12, and 15 sites are estimated from the shear-wave resonance to be 4.4, 3.7, and 4.4m, respectively. These thicknesses and those determined at the other Apollo sites by the active seismic experiments appear to be correlated with the age determinations and the abundances of extra-lunar components at the sites. (Auth.)

  1. Computational tools for experimental determination and theoretical prediction of protein structure

    Energy Technology Data Exchange (ETDEWEB)

    O`Donoghue, S.; Rost, B.

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. The authors intend to review the state of the art in the experimental determination of protein 3D structure (focus on nuclear magnetic resonance), and in the theoretical prediction of protein function and of protein structure in 1D, 2D and 3D from sequence. All the atomic resolution structures determined so far have been derived from either X-ray crystallography (the majority so far) or Nuclear Magnetic Resonance (NMR) Spectroscopy (becoming increasingly more important). The authors briefly describe the physical methods behind both of these techniques; the major computational methods involved will be covered in some detail. They highlight parallels and differences between the methods, and also the current limitations. Special emphasis will be given to techniques which have application to ab initio structure prediction. Large scale sequencing techniques increase the gap between the number of known proteins sequences and that of known protein structures. They describe the scope and principles of methods that contribute successfully to closing that gap. Emphasis will be given on the specification of adequate testing procedures to validate such methods.

  2. Simple Sensitive Spectrophotometric Determination of Vanadium in Biological and Environmental Samples

    Directory of Open Access Journals (Sweden)

    B. Krishna Priya

    2006-01-01

    Full Text Available Novel, rapid, highly sensitive and selective spectrophotometric method for the determination of traces of vanadium (V in environmental and biological samples, pharmaceutical and steel samples was studied. The method is based on oxidation of 2,4- dinitro phenyl hydrazine(2,4-DNPH by vanadium (V followed by coupling reaction with N-(1-naphthalene-1-ylethane-1,2-diamine-dihydrochloride (NEDA in acidic medium to give red colored derivative or on oxidation of 4-Amino Pyridine by vanadium (V followed by coupling reaction with NEDA in basic medium to give pink colored derivative. The red colored derivative having an λmax 495 nm which is stable for 8 days and the pink colored derivative with 525 nm is stable for more than 7 days at 350C. Beer's law is obeyed for vanadium (V in the concentration range of 0.02 - 3.5 μg mL–1 (red derivative and 0.03 – 4.5 μg mL–1 (pink derivative at the wave length of maximum absorption. The optimum reaction conditions and other analytical parameters were investigated to enhance the sensitivity of the present method. The detailed study of various interferences made the method more selective. The proposed method was successfully applied to the analysis of vanadium in natural water samples, plant material, soil samples, synthetic mixtures, pharmaceutical samples and biological samples. The results obtained were agreed with the reported methods at the 95 % confidence level. The performance of proposed method was evaluated in terms of Student's t-test and Variance ratio f-test which indicates the significance of proposed method over reported method.

  3. Study to Determine the Biological Feasibility of a New Fish Tagging System : Annual Report 1983.

    Energy Technology Data Exchange (ETDEWEB)

    Prentice, Earl F.; Park, D.L.

    1984-05-01

    Pacific salmon are tagged or marked as a critical part of numerous research and management studies. A new tag called the PIT (passive integrated transponder) tag measuring 7.5 mm long by 1.5 mm in diameter has a great potential for marking fish if it proves to be biologically compatible. A study was conducted to evaluate the potential of the PIT tag for marking salmonids. The objectives of the first year's research were to determine: (1) the anatomical areas in which the tag could be placed; (2) tissue response to the tag; and (3) tag retention. Juvenile coho, Oncorhynchus kisutch, and chinook O. tshawytscha, salmon and adult chinook salmon held at Manchester or Big Beef Creek, Washington, were used as test animals. Juvenile salmon were injected with sham PIT tags in the body cavity and opercular, dorsal, and caudal masculature. The fish ranged in length from 126 to 212 mm. Observations based on three tests, from 44 to 102 days long, indicated that the dorsal musculature and body cavity were the best locations to inject the tag from biological and social standpoints. Sham PIT tags were injected into the nose; body cavity; and opercular, dorsal, and caudal musculature of jack chinook salmon. The test was conducted for 23 days. Although all five anatomical areas were acceptable from a technical standpoint, the body cavity appeared to be the best area for tag placement. Initial test results with the Sham PIT tag were very encouraging. Apparently the PIT tag can be successfully injected into and carried by salmon, making it a potentially useful tool for fisheries biologists. 5 refs., 8 figs., 6 tabs.

  4. Evaluation rate of aging person based on determination of biological age

    Directory of Open Access Journals (Sweden)

    V. Fil

    2015-01-01

    2Kazimierz Wielki University, Bydgoszcz, Poland   Abstract The article considers the value of biological and passport age of student youth. In experiment participated 140 students aged 17-19 years. Calculated their biological age. Reviewed pace of aging of the body of students. Detected indexes that have the strongest relationship with indicators of biological age. The results compared with researchers of other regions of Ukraine.   Keywords: chronological (passport age, biological age, appropriate biological age, pulse blood pressure, rate of aging, static balancing, self-reported level of health.

  5. Shifting to structures in physics and biology: a prophylactic for promiscuous realism.

    Science.gov (United States)

    French, Steven

    2011-06-01

    Within the philosophy of science, the realism debate has been revitalised by the development of forms of structural realism. These urge a shift in focus from the object oriented ontologies that come and go through the history of science to the structures that remain through theory change. Such views have typically been elaborated in the context of theories of physics and are motivated by, first of all, the presence within such theories of mathematical equations that allow straightforward representation of the relevant structures; and secondly, the implications of such theories for the individuality and identity of putative objects. My aim in this paper is to explore the possibility of extending such views to biological theories. An obvious concern is that within the context of the latter it is typically insisted that we cannot find the kinds of highly mathematised structures that structural realism can point to in physics. I shall indicate how the model-theoretic approach to theories might help allay such concerns. Furthermore, issues of identity and individuality also arise within biology. Thus Dupré has recently noted that there exists a 'General Problem of Biological Individuality' which relates to the issue of how one divides 'massively integrated and interconnected' systems into discrete components. In response Dupré advocates a form of 'Promiscuous Realism' that holds, for example, that there is no unique way of dividing the phylogenetic tree into kinds. Instead I shall urge serious consideration of those aspects of the work of Dupré and others that lean towards a structuralist interpretation. By doing so I hope to suggest possible ways in which a structuralist stance might be extended to biology. Copyright © 2010 Elsevier Ltd. All rights reserved.

  6. Cell-free protein synthesis for structure determination by X-ray crystallography.

    Science.gov (United States)

    Watanabe, Miki; Miyazono, Ken-ichi; Tanokura, Masaru; Sawasaki, Tatsuya; Endo, Yaeta; Kobayashi, Ichizo

    2010-01-01

    Structure determination has been difficult for those proteins that are toxic to the cells and cannot be prepared in a large amount in vivo. These proteins, even when biologically very interesting, tend to be left uncharacterized in the structural genomics projects. Their cell-free synthesis can bypass the toxicity problem. Among the various cell-free systems, the wheat-germ-based system is of special interest due to the following points: (1) Because the gene is placed under a plant translational signal, its toxic expression in a bacterial host is reduced. (2) It has only little codon preference and, especially, little discrimination between methionine and selenomethionine (SeMet), which allows easy preparation of selenomethionylated proteins for crystal structure determination by SAD and MAD methods. (3) Translation is uncoupled from transcription, so that the toxicity of the translation product on DNA and its transcription, if any, can be bypassed. We have shown that the wheat-germ-based cell-free protein synthesis is useful for X-ray crystallography of one of the 4-bp cutter restriction enzymes, which are expected to be very toxic to all forms of cells retaining the genome. Our report on its structure represents the first report of structure determination by X-ray crystallography using protein overexpressed with the wheat-germ-based cell-free protein expression system. This will be a method of choice for cytotoxic proteins when its cost is not a problem. Its use will become popular when the crystal structure determination technology has evolved to require only a tiny amount of protein.

  7. Molecular structure descriptors in the computer-aided design of biologically active compounds

    International Nuclear Information System (INIS)

    Raevsky, Oleg A

    1999-01-01

    The current state of description of molecular structure in computer-aided molecular design of biologically active compounds by means of descriptors is analysed. The information contents of descriptors increases in the following sequence: element-level descriptors-structural formulae descriptors-electronic structure descriptors-molecular shape descriptors-intermolecular interaction descriptors. Each subsequent class of descriptors normally covers information contained in the previous-level ones. It is emphasised that it is practically impossible to describe all the features of a molecular structure in terms of any single class of descriptors. It is recommended to optimise the number of descriptors used by means of appropriate statistical procedures and characteristics of structure-property models based on these descriptors. The bibliography includes 371 references.

  8. Human Development VII: A Spiral Fractal Model of Fine Structure of Physical Energy Could Explain Central Aspects of Biological Information, Biological Organization and Biological Creativity

    Directory of Open Access Journals (Sweden)

    Søren Ventegodt

    2006-01-01

    Full Text Available In this paper we have made a draft of a physical fractal essence of the universe, a sketch of a new cosmology, which we believe to lay at the root of our new holistic biological paradigm. We present the fractal roomy spiraled structures and the energy-rich dancing “infinite strings” or lines of the universe that our hypothesis is based upon. The geometric language of this cosmology is symbolic and both pre-mathematical and pre-philosophical. The symbols are both text and figures, and using these we step by step explain the new model that at least to some extent is able to explain the complex informational system behind morphogenesis, ontogenesis, regeneration and healing. We suggest that it is from this highly dynamic spiraled structure that organization of cells, organs, and the wholeness of the human being including consciousness emerge. The model of ““dancing fractal spirals” carries many similarities to premodern cultures descriptions of the energy of the life and universe. Examples are the Native American shamanistic descriptions of their perception of energy and the old Indian Yogis descriptions of the life-energy within the body and outside. Similar ideas of energy and matter are found in the modern superstring theories. The model of the informational system of the organism gives new meaning to Bateson’s definition of information: “A difference that makes a difference”, and indicates how information-directed self-organization can exist on high structural levels in living organisms, giving birth to their subjectivity and consciousness.

  9. Structural biology studies of CagA from Helicobacter pylori and histone chaperone CIA/ASF1

    International Nuclear Information System (INIS)

    Senda, Toshiya

    2015-01-01

    Crystal structures of proteins and their complexes have become critical information for molecular-based life science. Biochemical and biological analysis based on tertiary structural information is a powerful tool to unveil complex molecular processes in the cell. Here, we present two examples of the structure-based life science study, structural biology studies of CagA, an effector protein from Helicobacter pylori, and histone chaperone CIA/ASF1, which is involved in transcription initiation. (author)

  10. X-ray structure analyses of biological molecules and particles in Japan. A brief history and future prospect

    International Nuclear Information System (INIS)

    Nakasako, Masayoshi; Yamamoto, Masaki

    2015-01-01

    In Japan, X-ray structure analyses of molecules and particles from biology started in the 1970s. The structure analysis methods have been developed through the innovation of various techniques in advance, and have contributed for understanding the elementary and microscopic processes in life. Here we summarize briefly the history of X-ray structure analyses for structural biology in Japan and think about the prospect. (author)

  11. Independent component analysis reveals new and biologically significant structures in micro array data

    Directory of Open Access Journals (Sweden)

    Veerla Srinivas

    2006-06-01

    Full Text Available Abstract Background An alternative to standard approaches to uncover biologically meaningful structures in micro array data is to treat the data as a blind source separation (BSS problem. BSS attempts to separate a mixture of signals into their different sources and refers to the problem of recovering signals from several observed linear mixtures. In the context of micro array data, "sources" may correspond to specific cellular responses or to co-regulated genes. Results We applied independent component analysis (ICA to three different microarray data sets; two tumor data sets and one time series experiment. To obtain reliable components we used iterated ICA to estimate component centrotypes. We found that many of the low ranking components indeed may show a strong biological coherence and hence be of biological significance. Generally ICA achieved a higher resolution when compared with results based on correlated expression and a larger number of gene clusters with significantly enriched for gene ontology (GO categories. In addition, components characteristic for molecular subtypes and for tumors with specific chromosomal translocations were identified. ICA also identified more than one gene clusters significant for the same GO categories and hence disclosed a higher level of biological heterogeneity, even within coherent groups of genes. Conclusion Although the ICA approach primarily detects hidden variables, these surfaced as highly correlated genes in time series data and in one instance in the tumor data. This further strengthens the biological relevance of latent variables detected by ICA.

  12. In silico determination of intracellular glycosylation and phosphorylation sites in human selectins: Implications for biological function

    DEFF Research Database (Denmark)

    Ahmad, I.; Hoessli, D.C.; Gupta, Ramneek

    2007-01-01

    Post-translational modifications provide the proteins with the possibility to perform functions in addition to those determined by their primary sequence. However, analysis of multifunctional protein structures in the environment of cells and body fluids is made especially difficult by the presence...... both modifications are likely to occur can also be predicted (YinYang sites), to suggest further functional versatility. Structural modifications of hydroxyl groups of P-, E-, and L-selectins have been predicted and possible functions resulting from such modifications are proposed. Functional changes...... of the three selectins are based on the assumption that transitory and reversible protein modifications by phosphate and O-GlcNAc cause specific conformational changes and generate binding sites for other proteins. The computer-assisted prediction of glycosylation and phosphorylation sites in selectins should...

  13. Single Fluorescent Molecules as Nano-Illuminators for Biological Structure and Function

    Science.gov (United States)

    Moerner, W. E.

    2011-03-01

    Since the first optical detection and spectroscopy of a single molecule in a solid (Phys. Rev. Lett. {62}, 2535 (1989)), much has been learned about the ability of single molecules to probe local nanoenvironments and individual behavior in biological and nonbiological materials in the absence of ensemble averaging that can obscure heterogeneity. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic imaging of individual fluorophores leads naturally to superlocalization, or determination of the position of the molecule with precision beyond the optical diffraction limit, simply by digitization of the point-spread function from the single emitter. For example, the shape of single filaments in a living cell can be extracted simply by allowing a single molecule to move through the filament (PNAS {103}, 10929 (2006)). The addition of photoinduced control of single-molecule emission allows imaging beyond the diffraction limit (super-resolution) and a new array of acronyms (PALM, STORM, F-PALM etc.) and advances have appeared. We have used the native blinking and switching of a common yellow-emitting variant of green fluorescent protein (EYFP) reported more than a decade ago (Nature {388}, 355 (1997)) to achieve sub-40 nm super-resolution imaging of several protein structures in the bacterium Caulobacter crescentus: the quasi-helix of the actin-like protein MreB (Nat. Meth. {5}, 947 (2008)), the cellular distribution of the DNA binding protein HU (submitted), and the recently discovered division spindle composed of ParA filaments (Nat. Cell Biol. {12}, 791 (2010)). Even with these advances, better emitters would provide more photons and improved resolution, and a new photoactivatable small-molecule emitter has recently been synthesized and targeted to specific structures in living cells to provide super-resolution images (JACS {132}, 15099 (2010)). Finally, a new optical method for extracting three-dimensional position information based on

  14. Cadmium determination in biological samples using neutron activation analysis with radiochemical separations

    International Nuclear Information System (INIS)

    Munoz A, Luis; Gras R, Nuri

    2005-01-01

    Chile has 7500 km of coastline on the Southern Pacific ocean,with about 4500 km of continental coastline that contains a variety of different geographical zones.This variety means that there is a great diversity of marine resources such as fish, shellfish and seaweeds. The utilization of these resources has been increasing in recent years making this sector an economically important one. The catch as of May 2002 came to 1.9 million tons and exports of the different species amounted to US$611.5 million as of April.But this important economic resource is being threatened by the technical demands imposed by importing countries, mainly the specific requirements for sanitary certification for fishery export products, depending on the markets of destination. The chemical element cadmium is one of the most strictly controlled elements due some shellfish accumulate a large amount of this element and to its high toxicity. The Chilean standard's analytical procedures for cadmium determination in hydro biological products, which must be met by laboratories that certify and control these products for export, are now being evaluated. Through its Chemical Metrology Unit, the Chilean Nuclear Energy Commission is strongly supporting this sector by preparing the secondary reference or control materials, and it has developed and implemented nuclear analytical methods for the certification of these materials, which will be used mostly in collaborative studies. This work describes the methodology developed for the determination of cadmium in biological samples, particularly in shellfish and fish. The method is based on neutron activation analysis with radiochemical separations, using the radioisotopes 115 Cd and 115m In, generated in the samples by bombarding with neutrons in a nuclear reactor. The samples were digested at 110 o C with H 2 SO 4 and H 2 O 2 and then the radioactive cadmium element was separated from the other elements present in the samples using a Bio Rad AG 2-X8

  15. Shell and membrane theories in mechanics and biology from macro- to nanoscale structures

    CERN Document Server

    Mikhasev, Gennadi

    2015-01-01

    This book presents the latest results related to shells  characterize and design shells, plates, membranes and other thin-walled structures, a multidisciplinary approach from macro- to nanoscale is required which involves the classical disciplines of mechanical/civil/materials engineering (design, analysis, and properties) and physics/biology/medicine among others. The book contains contributions of a meeting of specialists (mechanical engineers, mathematicians, physicists and others) in such areas as classical and non-classical shell theories. New trends with respect to applications in mechanical, civil and aero-space engineering, as well as in new branches like medicine and biology are presented which demand improvements of the theoretical foundations of these theories and a deeper understanding of the material behavior used in such structures.

  16. Survey of currently available reference materials for use in connection with the determination of trace elements in biological materials

    International Nuclear Information System (INIS)

    Parr, R.M.

    1983-09-01

    Elemental analysis of biological materials is at present the subject of intensive study by many different research groups throughout the world, in view of the importance of these trace elements in health and medical diagnosis. IAEA and other organizations are now making a variety of suitable reference materials available for use in connection with the determination of trace elements in biological materials. To help analysts in making a selection from among these various materials, the present report provides a brief survey of data for all such biological reference materials known to the author. These data are compiled by the author from January 1982 to June 1983

  17. Simple surface structure determination from Fourier transforms of angle-resolved photoemission extended fine structure

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Y. [Pennsylvania State Univ., University Park, PA (United States)]|[Lawrence Berkeley Lab., CA (United States); Shirley, D.A. [Pennsylvania State Univ., University Park, PA (United States)

    1995-02-01

    The authors show by Fourier analyses of experimental data, with no further treatment, that the positions of all the strong peaks in Fourier transforms of angle-resolved photoemission extended fine structure (ARPEFS) from adsorbed surfaces can be explicitly predicted from a trial structure with an accuracy of about {+-} 0.3 {angstrom} based on a single-scattering cluster model together with the concept of a strong backscattering cone, and without any additional analysis. This characteristic of ARPEFS Fourier transforms can be developed as a simple method for determining the structures of adsorbed surfaces to an accuracy of about {+-} 0.1 {angstrom}.

  18. Determination of the Fatty Acid Content of Biological Membranes: A Highly Versatile GC-MS Experiment

    Science.gov (United States)

    Schultz, Emeric; Pugh, Michael Eugene

    2001-07-01

    The experiment involves the GC-MS of fatty acid methyl esters (FAMEs) obtained from bacterial membranes. It takes about 2 h, from cell harvest to injection. This experiment is done in a lab course for non-science majors and in biochemistry. For non-science majors the focus is on GC-MS as a technique for fingerprinting and on the underlying basis of that fingerprinting. In biochemistry the focus is on the composition of membranes and how this changes with temperature--specifically how the ratio of saturated to unsaturated fatty acids changes to maintain constant cell fluidity. Combined with a parallel DNA experiment, the two major types of intermolecular forces important for the structure and function of biomolecules are compared. How this versatile experiment could be adapted in other chemistry courses is presented. The experiment has obvious appeal to biology majors, can be used to develop several important chemistry concepts, involves teamwork, and employs an important instrument. It could be used in the laboratory portion of a course other than biochemistry to fulfill the new ACS biochemistry requirement.

  19. Cold Spring Harbor symposia on quantitative biology. Volume XLVII, Part 1. Structures of DNA

    International Nuclear Information System (INIS)

    Anon.

    1983-01-01

    The proceedings for the 47th Annual Cold Spring Harbor Symposia on Quantitative Biology are presented. This symposium focused on the Structure of DNA. Topics presented covered research in the handedness of DNA, conformational analysis, chemically modified DNA, chemical synthesis of DNA, DNA-protein interactions, DNA within nucleosomes, DNA methylation, DNA replication, gyrases and topoisomerases, recombining and mutating DNA, transcription of DNA and its regulation, the organization of genes along DNA, repetitive DNA and pseudogenes, and origins of replication, centromeres, and teleomeres

  20. Sea Cucumber Glycosides: Chemical Structures, Producing Species and Important Biological Properties.

    Science.gov (United States)

    Mondol, Muhammad Abdul Mojid; Shin, Hee Jae; Rahman, M Aminur; Islam, Mohamad Tofazzal

    2017-10-17

    Sea cucumbers belonging to echinoderm are traditionally used as tonic food in China and other Asian countries. They produce abundant biologically active triterpene glycosides. More than 300 triterpene glycosides have been isolated and characterized from various species of sea cucumbers, which are classified as holostane and nonholostane depending on the presence or absence of a specific structural unit γ(18,20)-lactone in the aglycone. Triterpene glycosides contain a carbohydrate chain up to six monosaccharide units mainly consisting of d-xylose, 3-O-methy-d-xylose, d-glucose, 3-O-methyl-d-glucose, and d-quinovose. Cytotoxicity is the common biological property of triterpene glycosides isolated from sea cucumbers. Besides cytotoxicity, triterpene glycosides also exhibit antifungal, antiviral and hemolytic activities. This review updates and summarizes our understanding on diverse chemical structures of triterpene glycosides from various species of sea cucumbers and their important biological activities. Mechanisms of action and structural-activity relationships (SARs) of sea cucumber glycosides are also discussed briefly.

  1. Correlative Structural Biology: How to Investigate the Fine Details of Viral Structure

    Directory of Open Access Journals (Sweden)

    Elizabeth R. Wright

    2010-01-01

    Full Text Available Commentary on Byeon, I.J.; Meng, X.; Jung, J.; Zhao, G.; Yang, R.; Ahn, J.; Shi, J.; Concel, J.; Aiken, C.; Zhang, P.; Gronenborn, A.M. Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function. Cell 2009, 139, 780-790.

  2. Study on the determination of palladium in biological samples by the method of neutron activation analysis

    International Nuclear Information System (INIS)

    Cavalcante, Cassio Queiroz

    2007-01-01

    Palladium is one of platinum group elements present in the nature at very low concentrations. However with the use of this element in the automobile catalyzers Pd became a new pollutant. Besides, Pd has been studied in the preparation of new antitumour drugs. Consequently, there is a need to determine Pd concentrations in biological and environmental samples. This study presents palladium results obtained in the analysis of biological samples and reference materials using instrumental thermal and epithermal neutron activation analysis (INAA and ENAA). The solvent extraction and solid phase extraction separation methods were also applied before ENAA. The samples analyzed in this study were, reference material BCR 723 - Palladium, Platinum and Rhodium in road dust, CCQM-P63 automotive catalyst material of the Proficiency Test and bovine tissue samples containing palladium prepared in the laboratory. Samples and palladium synthetic standard were irradiated at the IEA-R1 nuclear research reactor under thermal neutron flux of about 4 x 10 12 n cm-2 s-1, during a period of 4 and 16 h for INAA and ENAA, respectively. The induced gamma activity of 109 Pd to the sample and standard was measured using a hyper pure Ge detector coupled to a gamma ray spectrometer. The palladium concentration was calculated by comparative method. The gamma ray energy of 109 Pd radioisotope measured was of 88.0 keV, located in a spectrum region of low energy where occurs the interference of X rays, 'Bremsstrahlung' radiations, as well as Compton effect of 24 Na. The pre-separation of palladium from interfering elements by solvent extraction was performed using dimethylglyoxime complexant and chloroform as diluent. In the case of the pre separation procedure using solid reversed phase column, the palladium was retained using N,N-diethyl-N'-benzoyl thiourea complexant and eluted using ethanol. Aliquots of the resulting solutions from the pre-separations, free of interfering elements, were

  3. Determination of copper in biological materials by neutron activation analysis using short-lived 66Cu

    International Nuclear Information System (INIS)

    Dybczynski, R.; Danko, B.; Kaczorowski, J.

    1989-01-01

    A method for determination of copper traces in biological materials based on neutron activation employing 65 Cu(n, γ) 66 Cu reaction and preconcentration by extraction chromatography has been devised. The 200-500 mg samples after wet digestion and evaporation were dissolved in glycine solution and after pH adjusting to ca. 4.4 were passed through the column with Lix 64N on Bio Beads SM-1 for isolation of copper traces from the matrix elements. Other cations were selectively eluted with 0.1 mol x 1 -1 (glycine-HNO 3 ) buffer, 1 mol x 1 -1 in NH 4 NO 3 (pH = 3.6). The resin bed with quantitatively retained copper was sealed in the PE bag and irradiated together with Cu standards in EWA reactor using pneumatic tube facility. The activity of the short-lived 66 Cu was measured in samples and standard by gamma-ray spectrometry with Ge(Li) detector. Good accuracy of the method was confirmed by analysis of the following certified reference materials: NBS 1571 Orchad leaves, IAEA H-4 Animal muscle, IAEA V-8 Rye flour, IAEA A-11 milk powder. The detection limit amounted to 0.34 mg/kg, for the sample weight of 500 mg. (author)

  4. Direct determination of uranium in soil, rock, ore and biological samples by laser-induced fluorometry

    International Nuclear Information System (INIS)

    Li Qingzhen; Zhang Yanan

    1993-03-01

    A laser-induced fluorometric method with modified J-22 anti-interferent fluorescent reagent for directly determining the uranium in soil, rock, ore, geochemical, biological and other samples has been studied. The effects of external ions and dilution law of sample are examined in detail. A method for correcting inner effect is proposed. A mixed solution of 0.25% NaOH-10% J-22 is prepared which can be added to the sample cuvette for direct measurement without any pre-adjustment of acidity. Therefore, it is much simpler for operation and reduces the loss and contamination of uranium. By changing the laser fluorometer sensitivity (400 ∼ 200), up to 3000 ng uranium in the cuvette can be detected. Thus, both analytical accuracy and detectable range are improved. This method is simple, rapid, accurate and applicable to various uranium-bearing samples. The detection limit is better than 0.05 μgU/g. The relative standard deviation is ≤+-5% for the rock reference samples of 0.95, 84.8, 669 and 7240 μgU/g

  5. Simultaneous determination of octylphenol, nonylphenol, Bis(2-ethylehxyl) phathalate in biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Kim, J.H. [Jeonju University, Chonju (Korea)

    2001-04-01

    A comprehensive analytical method of endocrine disruptors[i.e., nonylphenol (NP), octylphenol (OP), bis (2-ethylhexyl) phthalate (BEHP) in meat or pork samples was developed. The method employed closed culture tube extraction with dichloromethane and solvent exchange to iso-hexane and SPE 92g) aminopropyl column, followed by determination on gas chromatography linked to mass spectrometry (GC/MS) operated in the single ion monitoring (SIM) mode. For the multipoint recovery of nonylphenol, octylphenol and bis (2-ethylhexyl) phthalate OP, NP were shown good recoveries in 0.125 {approx} 1.25 {mu}g/g range of concentration, and BEHP more good recoveries on 0.0125 {approx} 12.5 {mu}g/g wide range of concentration. The present method was applied to beef or pork samples of mart and butcher in Cheonju city and near cheonju. The range of concentrations was respectively, 0.06 {approx} 0.24 {mu}g/g in bis (2-ethylhexyl)phthalate (BEHP), but octylphenol (OP) was not dec ted in any samples. This method provides a powerful analytical tool to investigate a wide range of endocrine disruptors in biological samples of limited quantity. (author). 24 refs., 5 tabs., 3 figs.

  6. Sensitivity improvements, in the determination of mercury in biological tissues by neutron activation analysis

    Energy Technology Data Exchange (ETDEWEB)

    Cornett, C R; Samudralwar, D L; Ehmann, W D [Kentucky Univ., Lexington, KY (United States). Dept. of Chemistry; Markesbery, W R [Kentucky Univ., Lexington, KY (United States)

    1995-08-01

    The possible association of dental amalgam surface exposure, brain mercury (Hg) levels, and pathological markers of Alzheimer`s disease (AD) in the brain is the subject of an on-going study in our laboratory. Two radiochemical neutron activation analysis methods and the use of instrumental neutron activation analysis (INAA) with Compton suppression spectrometry have been evaluated for improving our INAA Hg detection limit (2.8{+-}0.6 ng/g, wet-weight basis) in human tissue. Large numbers of samples dictated the use of a purely instrumental method or rapid, simple radiochemical separations. Human brain tissues and NIST biological standards were analyzed using a precipitation of Hg{sub 2}Cl{sub 2}, a solvent extraction utilizing sodium diethyldithiocarbomate, conventional INAA, and INAA with Compton suppression. The radiochemical precipitation of Hg{sub 2}Cl{sub 2} proved to be the most useful method for use in our study because it provided a simultaneous, quantitative determination of silver (Ag) and a Hg detection limit in brain tissue of 1.6{+-}0.1 ng/g (wet-weight basis). (author). 12 refs., 2 tabs.

  7. Structure determination by photoelectron diffraction of small molecules on surfaces

    International Nuclear Information System (INIS)

    Booth, N.A.

    1998-05-01

    The synchrotron radiation based technique of Photoelectron Diffraction (PhD) has been applied to three adsorption systems. Structure determinations, are presented for each system which involve the adsorption of small molecules on the low index {110} plane of single crystal Cu and Ni substrates. For the NH 3 -Cu(110) system PhD was successful in determining a N-Cu bondlength of 2.05 ± 0.03 A as well as values for the anisotropic vibrational amplitudes of the N and an expansion of the 1st to 2nd Cu substrate layer spacing from the bulk value of 0.08 ± 0.08 A. The most significant and surprising structural parameter determined for this system was that the N atom occupies an asymmetric adsorption site. Rather than being situated in the expected high symmetry atop site the N atom was found to be offset parallel to the surface by 0.37 ± 0.12 A in the [001] azimuth. In studying the glycine-Cu(110) system the adsorption structure of an amino-acid has been quantified. The local adsorption geometries of all the atoms involved in the molecule to surface bond have been determined. The glycine molecule is found to be bonded to the surface via both its amino and carboxylate functional groups. The molecule straddles two [11-bar0] rows of the Cu substrate. The two O atoms are found to be in identical sites both approximately atop Cu atoms on the [11-bar0] rows offset parallel to the surface by 0.80 ± 0.05 A in the [001] azimuth, the O-Cu bondlength was found to be 2.03 ± 0.05 A. The N atom was also found to adsorb in an approximately atop geometry but offset parallel to the surface by 0.24 ± 0.10A in the [11-bar0] direction, the N-Cu bondlength was found to be 2.05± 0.05 A. PhD was unsuccessful in determining the positions of the two C atoms that form a bridge between the two functional groups bonded to the surface due to difficulties in separating the two inequivalent contributions to the final intensity modulation function. For the CN-Ni(110) system both PhD and Near Edge

  8. C-glucosidic ellagitannins from Lythri herba (European Pharmacopoeia): chromatographic profile and structure determination.

    Science.gov (United States)

    Piwowarski, Jakub P; Kiss, Anna K

    2013-01-01

    Lythri herba, a pharmacopoeial plant material (European Pharmacopoea), is obtained from flowering parts of purple loosestrife (Lythrum salicaria L.). Although extracts from this plant material have been proven to possess some interesting biological activities and its pharmacopoeial standardisation is based on total tannin content determination, the phytochemical characterisation of this main group of compounds has not yet been fully conducted. To isolate ellagitannins from Lythri herba, determine their structures and develop chromatographic methods for their qualitative analysis. Five C-glucosidic ellagitannins - monomeric- vescalagin and castalagin together with new dimeric structures - salicarinins A-C, composed of vescalagin and stachyurin, vescalagin and casuarinin, castalagin and casuarinin units connected via formation of valoneoyl group, were isolated using column chromatography and preparative HPLC. Structures were determined according to (1) H and (13) C-NMR (one- and two-dimensional), electrospray ionisation-time of flight (ESI-TOF), electrospray ionisation-ion trap (ESI-MS(n) ) and circular dichroism (CD) spectra, together with acidic hydrolysis products analysis. HPTLC on RP-18 modified plates and HPLC-DAD-MS(n) on RP-18 column methods were developed for separation of the five main ellagitannins. Copyright © 2012 John Wiley & Sons, Ltd.

  9. Expression of recombinant glycoproteins in mammalian cells: towards an integrative approach to structural biology.

    Science.gov (United States)

    Aricescu, A Radu; Owens, Raymond J

    2013-06-01

    Mammalian cells are rapidly becoming the system of choice for the production of recombinant glycoproteins for structural biology applications. Their use has enabled the structural investigation of a whole new set of targets including large, multi-domain and highly glycosylated eukaryotic cell surface receptors and their supra-molecular assemblies. We summarize the technical advances that have been made in mammalian expression technology and highlight some of the structural insights that have been obtained using these methods. Looking forward, it is clear that mammalian cell expression will provide exciting and unique opportunities for an integrative approach to the structural study of proteins, especially of human origin and medically relevant, by bridging the gap between the purified state and the cellular context. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. Biological and structure-activity evaluation of chalcone derivatives against bacteria and fungi

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Wender A.; Andrade, Carlos Kleber Z.; Napolitano, Hamilton B., E-mail: wender@unb.br, E-mail: ckleber@unb.br [Universidade de Brasilia (LaQMOS/UnB), DF (Brazil). Inst. de Quimica; Vencato, Ivo; Castro, Miriam R.C. de; Camargo, Ademir J. [Universidade Estadual de Goias (UEG), Anapolis, GO (Brazil). Ciencias Exatas e Tecnologicas; Lariucci, Carlito [Universidade Estadual de Goias (UEG), Goiania, GO (Brazil). Inst. de Fisica

    2013-01-15

    The present work describes the antibacterial and antifungal activities of several chalcones obtained by a straight Claisen-Schmidt aldol condensation determined by the minimal inhibitory concentration against different microorganisms (Gram-positive and Gram-negative bacteria and fungi). Solid state crystal structures of seven chalcones were determined by X-ray diffraction (XRD) analysis. Chemometric studies were carried out in order to identify a potential structure activity relationship. (author)

  11. 3D high-resolution two-photon crosslinked hydrogel structures for biological studies.

    Science.gov (United States)

    Brigo, Laura; Urciuolo, Anna; Giulitti, Stefano; Della Giustina, Gioia; Tromayer, Maximilian; Liska, Robert; Elvassore, Nicola; Brusatin, Giovanna

    2017-06-01

    Hydrogels are widely used as matrices for cell growth due to the their tuneable chemical and physical properties, which mimic the extracellular matrix of natural tissue. The microfabrication of hydrogels into arbitrarily complex 3D structures is becoming essential for numerous biological applications, and in particular for investigating the correlation between cell shape and cell function in a 3D environment. Micrometric and sub-micrometric resolution hydrogel scaffolds are required to deeply investigate molecular mechanisms behind cell-matrix interaction and downstream cellular processes. We report the design and development of high resolution 3D gelatin hydrogel woodpile structures by two-photon crosslinking. Hydrated structures of lateral linewidth down to 0.5µm, lateral and axial resolution down to a few µm are demonstrated. According to the processing parameters, different degrees of polymerization are obtained, resulting in hydrated scaffolds of variable swelling and deformation. The 3D hydrogels are biocompatible and promote cell adhesion and migration. Interestingly, according to the polymerization degree, 3D hydrogel woodpile structures show variable extent of cell adhesion and invasion. Human BJ cell lines show capability of deforming 3D micrometric resolved hydrogel structures. The design and development of high resolution 3D gelatin hydrogel woodpile structures by two-photon crosslinking is reported. Significantly, topological and mechanical conditions of polymerized gelatin structures were suitable for cell accommodation in the volume of the woodpiles, leading to a cell density per unit area comparable to the bare substrate. The fabricated structures, presenting micrometric features of high resolution, are actively deformed by cells, both in terms of cell invasion within rods and of cell attachment in-between contiguous woodpiles. Possible biological targets for this 3D approach are customized 3D tissue models, or studies of cell adhesion

  12. Diffusion-advection within dynamic biological gaps driven by structural motion

    Science.gov (United States)

    Asaro, Robert J.; Zhu, Qiang; Lin, Kuanpo

    2018-04-01

    To study the significance of advection in the transport of solutes, or particles, within thin biological gaps (channels), we examine theoretically the process driven by stochastic fluid flow caused by random thermal structural motion, and we compare it with transport via diffusion. The model geometry chosen resembles the synaptic cleft; this choice is motivated by the cleft's readily modeled structure, which allows for well-defined mechanical and physical features that control the advection process. Our analysis defines a Péclet-like number, AD, that quantifies the ratio of time scales of advection versus diffusion. Another parameter, AM, is also defined by the analysis that quantifies the full potential extent of advection in the absence of diffusion. These parameters provide a clear and compact description of the interplay among the well-defined structural, geometric, and physical properties vis-a ̀-vis the advection versus diffusion process. For example, it is found that AD˜1 /R2 , where R is the cleft diameter and hence diffusion distance. This curious, and perhaps unexpected, result follows from the dependence of structural motion that drives fluid flow on R . AM, on the other hand, is directly related (essentially proportional to) the energetic input into structural motion, and thereby to fluid flow, as well as to the mechanical stiffness of the cleftlike structure. Our model analysis thus provides unambiguous insight into the prospect of competition of advection versus diffusion within biological gaplike structures. The importance of the random, versus a regular, nature of structural motion and of the resulting transient nature of advection under random motion is made clear in our analysis. Further, by quantifying the effects of geometric and physical properties on the competition between advection and diffusion, our results clearly demonstrate the important role that metabolic energy (ATP) plays in this competitive process.

  13. The Relative Importance of Spatial Versus Temporal Structure in the Perception of Biological Motion: An Event-Related Potential Study

    Science.gov (United States)

    Hirai, Masahiro; Hiraki, Kazuo

    2006-01-01

    We investigated how the spatiotemporal structure of animations of biological motion (BM) affects brain activity. We measured event-related potentials (ERPs) during the perception of BM under four conditions: normal spatial and temporal structure; scrambled spatial and normal temporal structure; normal spatial and scrambled temporal structure; and…

  14. Production, purification, crystallization and structure determination of H-1 Parvovirus

    International Nuclear Information System (INIS)

    Halder, Sujata; Nam, Hyun-Joo; Govindasamy, Lakshmanan; Vogel, Michèle; Dinsart, Christiane; Salomé, Nathalie; McKenna, Robert; Agbandje-McKenna, Mavis

    2012-01-01

    The production, purification, crystallization and crystallographic analysis of H-1 Parvovirus, a gene-therapy vector, are reported. Crystals of H-1 Parvovirus (H-1PV), an antitumor gene-delivery vector, were obtained for DNA-containing capsids and diffracted X-rays to 2.7 Å resolution using synchrotron radiation. The crystals belonged to the monoclinic space group P2 1 , with unit-cell parameters a = 255.4, b = 350.4, c = 271.6 Å, β = 90.34°. The unit cell contained two capsids, with one capsid per crystallographic asymmetric unit. The H-1PV structure has been determined by molecular replacement and is currently being refined

  15. Integrating NOE and RDC using sum-of-squares relaxation for protein structure determination.

    Science.gov (United States)

    Khoo, Y; Singer, A; Cowburn, D

    2017-07-01

    We revisit the problem of protein structure determination from geometrical restraints from NMR, using convex optimization. It is well-known that the NP-hard distance geometry problem of determining atomic positions from pairwise distance restraints can be relaxed into a convex semidefinite program (SDP). However, often the NOE distance restraints are too imprecise and sparse for accurate structure determination. Residual dipolar coupling (RDC) measurements provide additional geometric information on the angles between atom-pair directions and axes of the principal-axis-frame. The optimization problem involving RDC is highly non-convex and requires a good initialization even within the simulated annealing framework. In this paper, we model the protein backbone as an articulated structure composed of rigid units. Determining the rotation of each rigid unit gives the full protein structure. We propose solving the non-convex optimization problems using the sum-of-squares (SOS) hierarchy, a hierarchy of convex relaxations with increasing complexity and approximation power. Unlike classical global optimization approaches, SOS optimization returns a certificate of optimality if the global optimum is found. Based on the SOS method, we proposed two algorithms-RDC-SOS and RDC-NOE-SOS, that have polynomial time complexity in the number of amino-acid residues and run efficiently on a standard desktop. In many instances, the proposed methods exactly recover the solution to the original non-convex optimization problem. To the best of our knowledge this is the first time SOS relaxation is introduced to solve non-convex optimization problems in structural biology. We further introduce a statistical tool, the Cramér-Rao bound (CRB), to provide an information theoretic bound on the highest resolution one can hope to achieve when determining protein structure from noisy measurements using any unbiased estimator. Our simulation results show that when the RDC measurements are

  16. Determination of haplotypes at structurally complex regions using emulsion haplotype fusion PCR.

    Science.gov (United States)

    Tyson, Jess; Armour, John A L

    2012-12-11

    Genotyping and massively-parallel sequencing projects result in a vast amount of diploid data that is only rarely resolved into its constituent haplotypes. It is nevertheless this phased information that is transmitted from one generation to the next and is most directly associated with biological function and the genetic causes of biological effects. Despite progress made in genome-wide sequencing and phasing algorithms and methods, problems assembling (and reconstructing linear haplotypes in) regions of repetitive DNA and structural variation remain. These dynamic and structurally complex regions are often poorly understood from a sequence point of view. Regions such as these that are highly similar in their sequence tend to be collapsed onto the genome assembly. This is turn means downstream determination of the true sequence haplotype in these regions poses a particular challenge. For structurally complex regions, a more focussed approach to assembling haplotypes may be required. In order to investigate reconstruction of spatial information at structurally complex regions, we have used an emulsion haplotype fusion PCR approach to reproducibly link sequences of up to 1kb in length to allow phasing of multiple variants from neighbouring loci, using allele-specific PCR and sequencing to detect the phase. By using emulsion systems linking flanking regions to amplicons within the CNV, this led to the reconstruction of a 59kb haplotype across the DEFA1A3 CNV in HapMap individuals. This study has demonstrated a novel use for emulsion haplotype fusion PCR in addressing the issue of reconstructing structural haplotypes at multiallelic copy variable regions, using the DEFA1A3 locus as an example.

  17. Determination of haplotypes at structurally complex regions using emulsion haplotype fusion PCR

    Directory of Open Access Journals (Sweden)

    Tyson Jess

    2012-12-01

    Full Text Available Abstract Background Genotyping and massively-parallel sequencing projects result in a vast amount of diploid data that is only rarely resolved into its constituent haplotypes. It is nevertheless this phased information that is transmitted from one generation to the next and is most directly associated with biological function and the genetic causes of biological effects. Despite progress made in genome-wide sequencing and phasing algorithms and methods, problems assembling (and reconstructing linear haplotypes in regions of repetitive DNA and structural variation remain. These dynamic and structurally complex regions are often poorly understood from a sequence point of view. Regions such as these that are highly similar in their sequence tend to be collapsed onto the genome assembly. This is turn means downstream determination of the true sequence haplotype in these regions poses a particular challenge. For structurally complex regions, a more focussed approach to assembling haplotypes may be required. Results In order to investigate reconstruction of spatial information at structurally complex regions, we have used an emulsion haplotype fusion PCR approach to reproducibly link sequences of up to 1kb in length to allow phasing of multiple variants from neighbouring loci, using allele-specific PCR and sequencing to detect the phase. By using emulsion systems linking flanking regions to amplicons within the CNV, this led to the reconstruction of a 59kb haplotype across the DEFA1A3 CNV in HapMap individuals. Conclusion This study has demonstrated a novel use for emulsion haplotype fusion PCR in addressing the issue of reconstructing structural haplotypes at multiallelic copy variable regions, using the DEFA1A3 locus as an example.

  18. Structure of HIV-1 protease determined by neutron crystallography

    International Nuclear Information System (INIS)

    Adachi, Motoyasu; Kuroki, Ryota

    2009-01-01

    HIV-1 protease is an aspartic protease, and plays an essential role in replication of HIV. To develop HIV-1 protease inhibitors through structure-based drug design, it is necessary to understand the catalytic mechanism and inhibitor recognition of HIV-1 protease. We have determined the crystal structure of HIV-1 protease in complex with KNI-272 to 1.9 A resolution by neutron crystallography in combination with 1.4 A resolution X-ray diffraction data. The results show that the carbonyl group of hydroxymethylcarbonyl (HMC) in KNI-272 forms a hydrogen bonding interaction with protonated Asp 25 and the hydrogen atom from the hydroxyl group of HMC forms a hydrogen bonding interaction with the deprotonated Asp125. This is the first neutron report for HIV-1/inhibitor complex and shows directly the locations of key hydrogen atoms in catalysis and in the binding of a transition-state analog. The results confirm key aspect of the presumed catalytic mechanism of HIV-1 protease and will aid in the further development of protease inhibitors. (author)

  19. Determination of subsurface geological structure with borehole gravimetry

    International Nuclear Information System (INIS)

    Clark, S.R.; Hearst, J.R.

    1983-07-01

    Conventional gamma-gamma and gravimetric density measurements are routinely gathered for most holes used for underground nuclear tests. The logs serve to determine the subsurface structural geology near the borehole. The gamma-gamma density log measures density of the rock within about 15 cm of the borehole wall. The difference in gravity measured at two depths in a borehole can be interpreted in terms of the density of an infinite, homogeneous, horizontal bed between those depths. When the gravimetric density matches the gamma-gamma density over a given interval it is assumed that the bed actualy exists, and that rocks far from the hole must be the same as those encountered adjacent to the borehole. Conversely, when the gravimetric density differs from the gamma-gamma density it is apparent that the gravimeter is being influenced by a rock mass of different density than that at the hole wall. This mismatch can be a powerful tool to deduce the local structural geology. The geology deduced from gravity mesurements in emplacement hole, U4al, and the associated exploratory hole, UE4al, is an excellent example of the power of the method

  20. Determination of scattering structures from spatial coherence measurements.

    Science.gov (United States)

    Zarubin, A M

    1996-03-01

    A new method of structure determination and microscopic imaging with short-wavelength radiations (charged particles, X-rays, neutrons), based on measurements of the modulus and the phase of the degree of spatial coherence of the scattered radiation, is developed. The underlying principle of the method--transfer of structural information about the scattering potential via spatial coherence of the secondary (scattering) source of radiation formed by this potential--is expressed by the generalization of the van Cittert-Zernike theorem to wave and particle scattering [A.M. Zarubin, Opt. Commun. 100 (1993) 491; Opt. Commun. 102 (1993) 543]. Shearing interferometric techniques are proposed for implementing the above measurements; the limits of spatial resolution attainable by reconstruction of the absolute square of a 3D scattering potential and its 2D projections from the measurements are analyzed. It is shown theoretically that 3D imaging with atomic resolution can be realized in a "synthetic aperture" electron or ion microscope and that a 3D resolution of about 6 nm can be obtained with a "synthetic aperture" X-ray microscope. A proof-of-principle optical experiment is presented.