WorldWideScience

Sample records for biological structure determination

  1. The potential for biological structure determination with pulsed neutrons

    International Nuclear Information System (INIS)

    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

    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.

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

    OpenAIRE

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

    2013-01-01

    Background 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 ...

  4. Compressed Sensing Electron Tomography for Determining Biological Structure

    Science.gov (United States)

    Guay, Matthew D.; Czaja, Wojciech; Aronova, Maria A.; Leapman, Richard D.

    2016-06-01

    There has been growing interest in applying compressed sensing (CS) theory and practice to reconstruct 3D volumes at the nanoscale from electron tomography datasets of inorganic materials, based on known sparsity in the structure of interest. Here we explore the application of CS for visualizing the 3D structure of biological specimens from tomographic tilt series acquired in the scanning transmission electron microscope (STEM). CS-ET reconstructions match or outperform commonly used alternative methods in full and undersampled tomogram recovery, but with less significant performance gains than observed for the imaging of inorganic materials. We propose that this disparity stems from the increased structural complexity of biological systems, as supported by theoretical CS sampling considerations and numerical results in simulated phantom datasets. A detailed analysis of the efficacy of CS-ET for undersampled recovery is therefore complicated by the structure of the object being imaged. The numerical nonlinear decoding process of CS shares strong connections with popular regularized least-squares methods, and the use of such numerical recovery techniques for mitigating artifacts and denoising in reconstructions of fully sampled datasets remains advantageous. This article provides a link to the software that has been developed for CS-ET reconstruction of electron tomographic data sets.

  5. Structural Biology Fact Sheet

    Science.gov (United States)

    ... Home > Science Education > Structural Biology Fact Sheet Structural Biology Fact Sheet Tagline (Optional) Middle/Main Content Area What is structural biology? Structural biology is a field of science focused ...

  6. Neutron structural biology

    International Nuclear Information System (INIS)

    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. Sample preparation of biological macromolecular assemblies for the determination of high-resolution structures by cryo-electron microscopy.

    Science.gov (United States)

    Stark, Holger; Chari, Ashwin

    2016-02-01

    Single particle cryo-EM has recently developed into a powerful tool to determine the 3D structure of macromolecular complexes at near-atomic resolution, which allows structural biologists to build atomic models of proteins. All technical aspects of cryo-EM technology have been considerably improved over the last two decades, including electron microscopic hardware, image processing software and the ever growing speed of computers. This leads to a more widespread use of the technique, and it can be anticipated that further automation of electron microscopes and image processing tools will soon fully shift the focus away from the technological aspects, onto biological questions that can be answered. In single particle cryo-EM, no crystals of a macromolecule are required. In contrast to X-ray crystallography, this significantly facilitates structure determination by cryo-EM. Nevertheless, a relatively high level of biochemical control is still essential to obtain high-resolution structures by cryo-EM, and it can be anticipated that the success of the cryo-EM technology goes hand in hand with further developments of sample purification and preparation techniques. This will allow routine high-resolution structure determination of the many macromolecular complexes of the cell that until now represent evasive targets for X-ray crystallographers. Here we discuss the various biochemical tools that are currently available and the existing sample purification and preparation techniques for cryo-EM grid preparation that are needed to obtain high-resolution images for structure determination. PMID:26671943

  8. Efficient, sparse biological network determination

    Directory of Open Access Journals (Sweden)

    Papachristodoulou Antonis

    2009-02-01

    Full Text Available Abstract Background Determining the interaction topology of biological systems is a topic that currently attracts significant research interest. Typical models for such systems take the form of differential equations that involve polynomial and rational functions. Such nonlinear models make the problem of determining the connectivity of biochemical networks from time-series experimental data much harder. The use of linear dynamics and linearization techniques that have been proposed in the past can circumvent this, but the general problem of developing efficient algorithms for models that provide more accurate system descriptions remains open. Results We present a network determination algorithm that can treat model descriptions with polynomial and rational functions and which does not make use of linearization. For this purpose, we make use of the observation that biochemical networks are in general 'sparse' and minimize the 1-norm of the decision variables (sum of weighted network connections while constraints keep the error between data and the network dynamics small. The emphasis of our methodology is on determining the interconnection topology rather than the specific reaction constants and it takes into account the necessary properties that a chemical reaction network should have – something that techniques based on linearization can not. The problem can be formulated as a Linear Program, a convex optimization problem, for which efficient algorithms are available that can treat large data sets efficiently and uncertainties in data or model parameters. Conclusion The presented methodology is able to predict with accuracy and efficiency the connectivity structure of a chemical reaction network with mass action kinetics and of a gene regulatory network from simulation data even if the dynamics of these systems are non-polynomial (rational and uncertainties in the data are taken into account. It also produces a network structure that can

  9. Preparation, Purification, and Secondary Structure Determination of Bacillus Circulans Xylanase. A Molecular Laboratory Incorporating Aspects of Molecular Biology, Biochemistry, and Biophysical Chemistry

    Science.gov (United States)

    Russo, Sal; Gentile, Lisa

    2006-01-01

    A project module designed for biochemistry or cellular and molecular biology student which involves determining the secondary structure of Bacillus circulans xylanase (BCX) by circular dichroism (CD) spectroscopy under conditions that compromise its stabilizing intramolecular forces is described. The lab model enhanced students knowledge of the…

  10. [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. PMID:11605547

  11. 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…

  12. 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...

  13. 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)

  14. [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.

  15. Structural Biology of The sequestration & Transport of Heavy Metal Toxins: NMR Structure Determination of Proteins Containing the CYS-X-Y-Metal Binding Motif

    Energy Technology Data Exchange (ETDEWEB)

    Stanley J. Opella

    2004-03-10

    The support from the Department of Energy enabled us to initiate research on several proteins from the bacterial mercury detoxification system; in particular, we were able to determine the structures of MerP and related metal binding sequences. We have also worked on the membrane transport proteins MerF and MerT.

  16. [Sodium determination in biological fluids].

    Science.gov (United States)

    Cristol, J-P; Balint, B; Canaud, B; Daurés, M-F

    2007-09-01

    Electrolyte disorders are frequently observed in nephrology and intensive care unit department and Na determination is routinely performed in biochemistry laboratories. Three methods are currently available. Flame photometry remains the reference method. With this method the serum sample is diluted before the actual measurement is obtained. Results are expressed as molarity (per Liter of plasma). Potentiometric methods have an increasing importance due to the advances in ion sensitive (selective) electrodes (ISE). Whereas the instruments for routine chemical analysis typically use indirect potentiometry (involving te dilution of samples) to measure sodium levels, the equipment for measuring arterial blood gases use direct potentiometry without any dilution. Thus, results obtained with indirect potentiometry are expressed in molarity (per liter of plasma) while results obtained with direct potentiometry are initially given in morality (per kg of plasma water) then converted in molarity. Analytical performances are in all cases satisfactory and therefore all the methods could be used in both normal and pathological ranges. Methods involving sample dilution such as flame photometry or indirect potentiometry, the serum sodium value would be expected to be low in case of decrease plasma water (pseudohyponatremia). By contrast, with direct potentiometry where no sample dilution takes place, no interference would be expected since the activity of sodium in the water phase only is being measured. Thus, the classical pseudohyponatremia observed with hyperlipemia or paraproteinemia are not further observed with direct potentiometry. These differences in methodology should be taken into account to explain discrepancies between results obtained with classical biochemistry analyser and with blood gas apparatus.

  17. 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.

  18. Diffraction structural biology – a new horizon

    Energy Technology Data Exchange (ETDEWEB)

    Yamane, Takashi [Nagoya Industrial Science Research Institute, 1-13 Yotsuya-dori, Chikusa-ku, Nagoya 464-0819 (Japan); Helliwell, John R. [University of Manchester, Manchester M13 9PL (United Kingdom); Johnson, John E. [Scripps Research Institute, San Diego, CA (United States); Yasuoka, Noritake, E-mail: nori-yasuoka@nifty.com [AIST Kansai Center, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577 (Japan); Sakabe, Noriyoshi [Photon Factory, KEK, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan)

    2013-11-01

    An introductory overview to the special issue papers on diffraction structural biology in this issue of the journal. An introductory overview to the special issue papers on diffraction structural biology in this issue of the journal.

  19. 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.

  20. 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. PMID:11537218

  1. Ice breaking in GPCR structural biology

    Institute of Scientific and Technical Information of China (English)

    Qiang ZHAO; Bei-li WU

    2012-01-01

    G-protein-coupled receptors (GPCRs) are one of the most challenging targets in structural biology.To successfully solve a high-resolution GPCR structure,several experimental obstacles must be overcome,including expression,extraction,purification,and crystallization.As a result,there are only a handful of unique structures reported from this protein superfamily,which consists of over 800 members.In the past few years,however,there has been an increase in the amount of solved GPCR structures,and a few high-impact structures have been determined:the peptide receptor CXCR4,the agonist bound receptors,and the GPCR-G protein complex.The dramatic progress in GPCR structural studies is not due to the development of any single technique,buta combination of new techniques,new tools and new concepts.Here,we summarize the progress made for GPCR expression,purification,and crystalliza-tion,and we highlight the technical advances that will facilitate the future determination of GPCR structures.

  2. 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.

  3. Determining biological fine structure by differential absorption of soft x-rays. [Ultrastructural studies of nerve fibers using scanning electron microscopy without need for staining or osmication

    Energy Technology Data Exchange (ETDEWEB)

    Panessa-Warren, Barbara J.; Warren, John 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.

  4. 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,...

  5. 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 ...

  6. Visualizing ensembles in structural biology.

    Science.gov (United States)

    Melvin, Ryan L; Salsbury, Freddie R

    2016-06-01

    Displaying a single representative conformation of a biopolymer rather than an ensemble of states mistakenly conveys a static nature rather than the actual dynamic personality of biopolymers. However, there are few apparent options due to the fixed nature of print media. Here we suggest a standardized methodology for visually indicating the distribution width, standard deviation and uncertainty of ensembles of states with little loss of the visual simplicity of displaying a single representative conformation. Of particular note is that the visualization method employed clearly distinguishes between isotropic and anisotropic motion of polymer subunits. We also apply this method to ligand binding, suggesting a way to indicate the expected error in many high throughput docking programs when visualizing the structural spread of the output. We provide several examples in the context of nucleic acids and proteins with particular insights gained via this method. Such examples include investigating a therapeutic polymer of FdUMP (5-fluoro-2-deoxyuridine-5-O-monophosphate) - a topoisomerase-1 (Top1), apoptosis-inducing poison - and nucleotide-binding proteins responsible for ATP hydrolysis from Bacillus subtilis. We also discuss how these methods can be extended to any macromolecular data set with an underlying distribution, including experimental data such as NMR structures. PMID:27179343

  7. Visualizing ensembles in structural biology.

    Science.gov (United States)

    Melvin, Ryan L; Salsbury, Freddie R

    2016-06-01

    Displaying a single representative conformation of a biopolymer rather than an ensemble of states mistakenly conveys a static nature rather than the actual dynamic personality of biopolymers. However, there are few apparent options due to the fixed nature of print media. Here we suggest a standardized methodology for visually indicating the distribution width, standard deviation and uncertainty of ensembles of states with little loss of the visual simplicity of displaying a single representative conformation. Of particular note is that the visualization method employed clearly distinguishes between isotropic and anisotropic motion of polymer subunits. We also apply this method to ligand binding, suggesting a way to indicate the expected error in many high throughput docking programs when visualizing the structural spread of the output. We provide several examples in the context of nucleic acids and proteins with particular insights gained via this method. Such examples include investigating a therapeutic polymer of FdUMP (5-fluoro-2-deoxyuridine-5-O-monophosphate) - a topoisomerase-1 (Top1), apoptosis-inducing poison - and nucleotide-binding proteins responsible for ATP hydrolysis from Bacillus subtilis. We also discuss how these methods can be extended to any macromolecular data set with an underlying distribution, including experimental data such as NMR structures.

  8. 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,…

  9. [Our investigation on the chemistry of biologically active natural products. With the object of exploitation for structure determination methods, and elucidation of vital function].

    Science.gov (United States)

    Komori, T

    1993-03-01

    Our investigation on the chemistry of biologically active natural products during the last 40 years since 1953 are reviewed in this paper. The following subjects are discussed: I. photochemical relationship between rhodopsin and compounds related to areca alkaloid, II. furanoid diterpenoid constituents from dioscoreaceae plants and colombo root, III. field desorption and fast atom bombardment mass spectrometry of biologically active natural glycosides and glycosphingolipids, IV. investigation of biologically active marine natural products, 1) constituents of steroid glycoside sulfates from Asteroidea, 2) spine toxins from Acanthaster planci, 3) constituents of triterpenoid glycoside sulfates from Holothuroidea, 4) constituents of isoprenoids from Opisthobranchia and Octocorallia, 5) constituents of glycosphingolipids from Asteroidea. PMID:8509990

  10. 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.

  11. A glimpse of structural biology through X-ray crystallography.

    Science.gov (United States)

    Shi, Yigong

    2014-11-20

    Since determination of the myoglobin structure in 1957, X-ray crystallography, as the anchoring tool of structural biology, has played an instrumental role in deciphering the secrets of life. Knowledge gained through X-ray crystallography has fundamentally advanced our views on cellular processes and greatly facilitated development of modern medicine. In this brief narrative, I describe my personal understanding of the evolution of structural biology through X-ray crystallography-using as examples mechanistic understanding of protein kinases and integral membrane proteins-and comment on the impact of technological development and outlook of X-ray crystallography.

  12. Eddy Current Probe for Biological Structures Identification

    International Nuclear Information System (INIS)

    The new eddy current probe for conductivity measurement of biological structures was presented. The probe operation principle is based on the differential pick-up. After theoretical analysis results of experiments have been presented. For experiments fruits and meat, have been used. (author)

  13. Xanthane sesquiterpenoids: structure, synthesis and biological activity.

    Science.gov (United States)

    Vasas, Andrea; Hohmann, Judit

    2011-04-01

    The aim of this review is to survey the naturally occurring xanthanes and xanthanolides, their structures, biological activities, structure–activity relationships and synthesis. There has been no comprehensive review of this topic previously. On the basis of 126 references, 112 compounds are summarized. PMID:21321751

  14. 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

  15. Glycosides from Marine Sponges (Porifera, Demospongiae: Structures, Taxonomical Distribution, Biological Activities and Biological Roles

    Directory of Open Access Journals (Sweden)

    Valentin A. Stonik

    2012-08-01

    Full Text Available Literature data about glycosides from sponges (Porifera, Demospongiae are reviewed. Structural diversity, biological activities, taxonomic distribution and biological functions of these natural products are discussed.

  16. Glycosides from Marine Sponges (Porifera, Demospongiae): Structures, Taxonomical Distribution, Biological Activities and Biological Roles

    OpenAIRE

    Stonik, Valentin A.; Makarieva, Tatyana N.; Kalinin, Vladimir I.; Krasokhin, Vladimir B.; Natalia V. Ivanchina

    2012-01-01

    Literature data about glycosides from sponges (Porifera, Demospongiae) are reviewed. Structural diversity, biological activities, taxonomic distribution and biological functions of these natural products are discussed.

  17. Communication on the structure of biological networks

    Indian Academy of Sciences (India)

    Deyasi Krishanu; Upadhyay Shashankaditya; Banerjee Anirban

    2016-03-01

    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 information in a network. Here we investigate the underlying undirected topology of different biological networks which support faster spreading of information and are better in communication. We analyse the good expansion property by using the spectral gap and communicability between nodes. Different epidemic models are also used to study the transmission of information in terms of spreading of disease through individuals (nodes)in those networks. Moreover, we explore the structural conformation and properties which may be responsible for better communication. Among all biological networks studied here, the undirected structure of neuronal networks not only possesses the small-world property but the same is also expressed remarkably to a higher degree compared to any randomly generated network which possesses the same degree sequence. A relatively high percentage of nodes, in neuronal networks, form a higher core in their structure. Our study shows that the underlying undirected topology in neuronal networks, in a significant way, is qualitatively different from the same in other biologicalnetworks and that they may have evolved in such a way that they inherit a (undirected) structure which is excellent and robust in communication.

  18. Landscape Structure and Biological Control in Agroecosystems

    OpenAIRE

    Thies, Carsten; Tscharntke, Teja

    1999-01-01

    Biological pest control has primarily relied on local improvements in populations of natural enemies, but landscape structure may also be important. This is shown here with experiments at different spatial scales using the rape pollen beetle (Meligethes aeneus), an important pest on oilseed rape (Brassica napus). The presence of old field margin strips along rape fields was associated with increased mortality of pollen beetles resulting from parasitism and adjacent, large, old fallow habit...

  19. 2004 Reversible Associations in Structure & Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    Edward Eisenstein Nancy Ryan Gray

    2005-03-23

    The Gordon Research Conference (GRC) on 2004 Gordon Research Conference on Reversible Associations in Structure & Molecular Biology was held at Four Points Sheraton, CA, 1/25-30/2004. The Conference was well attended with 82 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students.

  20. Landscape structure and biological control in agroecosystems

    Science.gov (United States)

    Thies; Tscharntke

    1999-08-01

    Biological pest control has primarily relied on local improvements in populations of natural enemies, but landscape structure may also be important. This is shown here with experiments at different spatial scales using the rape pollen beetle (Meligethes aeneus), an important pest on oilseed rape (Brassica napus). The presence of old field margin strips along rape fields was associated with increased mortality of pollen beetles resulting from parasitism and adjacent, large, old fallow habitats had an even greater effect. In structurally complex landscapes, parasitism was higher and crop damage was lower than in simple landscapes with a high percentage of agricultural use. PMID:10436158

  1. ALOUD biological: Adult Learning Open University Determinants study - Association of biological determinants with study success in formal lifelong learners

    NARCIS (Netherlands)

    Gijselaers, Jérôme; De Groot, Renate; Kirschner, Paul A.

    2012-01-01

    Gijselaers, H. J. M., De Groot, R. H. M., & Kirschner, P. A. (2012, 15 March). ALOUD biological: Adult Learning Open University Determinants study - Association of biological determinants with study success in formal lifelong learners. Presentation given at the plenary meeting of Learning & Cognitio

  2. 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.

  3. Determination of Uranium Oxides Structure

    International Nuclear Information System (INIS)

    Determination of uranium oxides structure have been worked using XRD (X-Ray Diffractometer). Where the diffraction patterns were analyzed by Rietan method. The samples that analysis were UO2,07; UO2,06; UO2,15; UO2,27 and U3O8 compound. Rietan refinement of the diffraction patterns showed cubic structures for UO2,07 and UO2,06, with a = 5,4663 A and 5,4638 A, respectively. UO2,15 compound was found to be a mixture of cubic, a = 5,4637 A and tetragonal structures, a = 5,454 A and c = 5,409 A. The structures of UO2,27 and U3O8 were found to be tetragonal and orthorhombic, respectively with a 5,4717 A and c = 5,407 A for the tetragonal structure, while a 6,7147 A, b = 11, 9506 A and c = 4,1448 A for the orthorhombic one. It was concluded from this investigation that large amounts of x oxygen atoms in UO2+x, transforms the cubic structure gradually to tetragonal and finely to orthorhombic structure. Sample of PPNY's UO2 had cubic structure, so that the structure specification as which expected. (author)

  4. Developmental biology of sex determination : establishing a basis for systems approach

    OpenAIRE

    Segerståhl, Margareta

    2008-01-01

    The existence of males and females is a fundamental aspect of animal biology but the developmental mechanisms of sex determination and sexual differentiation exhibit surprising evolutionary diversity. Depending on the species, sex determination mechanisms range from genetic sex chromosome effects to environmental temperature effects and even to social cues that derive from local population structure. Many genes and molecules that play a role in sex determination biology have been identified, ...

  5. 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...

  6. Determination of cadmium in biological samples.

    Science.gov (United States)

    Klotz, Katrin; Weistenhöfer, Wobbeke; Drexler, Hans

    2013-01-01

    Analyses of cadmium concentrations in biological material are performed using inductively coupled plasma mass spectrometry (ICP-MS) and atomic absorption spectrometry (AAS), but also electrochemical methods, neutron activation analysis (NAA), and X-ray fluorescence spectrometry (XRF). The predominant sample matrices include blood, plasma, serum, and urine, as well as hair, saliva, and tissue of kidney cortex, lung, and liver. While cadmium in blood reveals rather the recent exposure situation, cadmium in urine reflects the body burden and is an indicator for the cumulative long term exposure.After chronic exposure, cadmium accumulates in the human body and causes kidney diseases, especially lesions of proximal tubular cells. A tubular proteinuria causes an increase in urinary excretion of microproteins. Excretions of retinol binding protein (RBP), β2-microglobulin (β2-M), and α1-microglobulin are validated biomarkers for analyzing cadmium effects. For this purpose, immunological procedures such as ELISA, and radio- and latex-immunoassays are used.However, proteinuria is not specific to cadmium, but can also occur after exposure to other nephrotoxic agents or due to various kidney diseases. In summary, cadmium in urine and blood are the most specific biomarkers of cadmium exposure. A combination of parameters of exposure (cadmium in blood, cadmium in urine) and parameters of effect (e.g., β2-M, RBP) is required to reveal cadmium-induced nephrological effects. PMID:23430771

  7. The structural biology of phenazine biosynthesis.

    Science.gov (United States)

    Blankenfeldt, Wulf; Parsons, James F

    2014-12-01

    The phenazines are a class of over 150 nitrogen-containing aromatic compounds of bacterial and archeal origin. Their redox properties not only explain their activity as broad-specificity antibiotics and virulence factors but also enable them to function as respiratory pigments, thus extending their importance to the primary metabolism of phenazine-producing species. Despite their discovery in the mid-19th century, the molecular mechanisms behind their biosynthesis have only been unraveled in the last decade. Here, we review the contribution of structural biology that has led to our current understanding of phenazine biosynthesis. PMID:25215885

  8. Ultrasonic determination of steel structures

    International Nuclear Information System (INIS)

    In the research project 'Determination of steel structures by means of ultrasound' methods are developed for the non-destructive structure characterization with scattered ultrasound. Measurements were made at about 200 steel samples with frequencies between 5 and 20 Mc/sec. In the range of 0,05 <= d/lambda <= 0,5 (d=mean grain size, lambda = wavelength of the ultrasound pulse) known theories can be applied for the quantitative grain size determination and with an accuracy of +-15% the results agree with the metallographically measured values. The best method for this is the combination of two measurements with two different frequencies. Advantages are given by the measurement of the multiple scattering which is leading to the scattering coefficient and to the grain size with one measurement only and without assumptions concerning other parameters of ultrasound propagation. A structure characterization concerning the homogeneity inside the material is possible, too, because of the time (i.e. sound path-)-dependent scattering measurement. It is able to control the structure of monophasic steels with grain sizes between ASTM 1 and ASTM 11. Today problems unsolved are the martensitic steels, the multiphasic structures

  9. Electron crystallography--the waking beauty of structural biology.

    Science.gov (United States)

    Pope, Christopher R; Unger, Vinzenz M

    2012-08-01

    Since its debut in the mid 1970s, electron crystallography has been a valuable alternative in the structure determination of biological macromolecules. Its reliance on single-layered or double-layered two-dimensionally ordered arrays and the ability to obtain structural information from small and disordered crystals make this approach particularly useful for the study of membrane proteins in a lipid bilayer environment. Despite its unique advantages, technological hurdles have kept electron crystallography from reaching its full potential. Addressing the issues, recent initiatives developed high-throughput pipelines for crystallization and screening. Adding progress in automating data collection, image analysis and phase extension methods, electron crystallography is poised to raise its profile and may lead the way in exploring the structural biology of macromolecular complexes.

  10. 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.

  11. Crystal structure determination of Efavirenz

    Energy Technology Data Exchange (ETDEWEB)

    Popeneciu, Horea, E-mail: horea.popeneciu@itim-cj.ro; Dumitru, Ristoiu [College of Environmental Science on Engineering Babes Bolyai University, 30 Fantanele, 400294 Cluj Napoca (Romania); Tripon, Carmen, E-mail: horea.popeneciu@itim-cj.ro; Borodi, Gheorghe, E-mail: horea.popeneciu@itim-cj.ro; Pop, Mihaela Maria, E-mail: mihaelapop@teracrystal.com

    2015-12-23

    Needle-shaped single crystals of the title compound, C{sub 14}H{sub 9}ClF{sub 3}NO{sub 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.

  12. Some Limitations of BIOLOG System for Determining Soil Microbial Community

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A laboratory experiment was conducted to evaluate the effect of triphenyltetrazolium chloride (TTC)on soil microorganisms and the availability of pH characterization medium in BIOLOG plates. Applicationof TTC decreased the color development sharply and resulted in a great biocidal effect on the growth andreproduction of soil microorganisms, indicating that TTC can affect the discrimination on soil microbialcommunity. The microtitration plates with 21 carbon sources and two different pH levels (4.7 and 7.0) wereused to determine microbial community structure of eight red soils. The average utilization (average wellcolour development) of the carbon sources in the plates with different pH levels generally followed the samesigmoidal pattern as that in the traditional BIOLOG plates, but the pH 4.7 plates increased the discrimination of this technique, compared with the pH 7.0 plates. Since most tested soils are acid, it seemed that it's better to use a suitable pH characterization medium for a specific soil in the sole carbon source test.

  13. 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.

  14. Insights into the biology of Escherichia coli through structural proteomics.

    Science.gov (United States)

    Matte, Allan; Jia, Zongchao; Sunita, S; Sivaraman, J; Cygler, Miroslaw

    2007-09-01

    Escherichia coli has historically been an important organism for understanding a multitude of biological processes, and represents a model system as we attempt to simulate the workings of living cells. Many E. coli strains are also important human and animal pathogens for which new therapeutic strategies are required. For both reasons, a more complete and comprehensive understanding of the protein structure complement of E. coli is needed at the genome level. Here, we provide examples of insights into the mechanism and function of bacterial proteins that we have gained through the Bacterial Structural Genomics Initiative (BSGI), focused on medium-throughput structure determination of proteins from E. coli. We describe the structural characterization of several enzymes from the histidine biosynthetic pathway, the structures of three pseudouridine synthases, enzymes that synthesize one of the most abundant modified bases in RNA, as well as the combined use of protein structure and focused functional analysis to decipher functions for hypothetical proteins. Together, these results illustrate the power of structural genomics to contribute to a deeper biological understanding of bacterial processes.

  15. Biomolecular Structure Determination with Divide and Concur

    Science.gov (United States)

    Kallus, Yoav; Elser, Veit

    2009-03-01

    Divide and concur (D-C) is a general computational approach, designed for the solution of highly frustrated problems. Recently applied to the problems of disk packing, the kissing number problem, and 3-SAT, it was competitive or outperformed special-purpose methods.ootnotetextS. Gravel and V. Elser, Phys. Rev. E 78, 036706 (2008) We present a method for applying the D-C framework to the problem of biomolecular structure determination. From a list of geometric constraints on groups of atoms in the molecule, we construct a deterministic iterative map that efficiently searches for structures simultaneously satisfying all constraints. As our method eschews an energy function and its minimization to focus on geometric constraints, it can very naturally integrate with the geometric constraints due to chemistry and physics, experimental constraints due to NMR data or many other experimental or biological hints. We present some results of our method.

  16. Structure and biological functions of fungal cerebrosides

    Directory of Open Access Journals (Sweden)

    Barreto-Bergter Eliana

    2004-01-01

    Full Text Available Ceramide monohexosides (CMHs, cerebrosides are glycosphingolipids composed of a hydrophobic ceramide linked to one sugar unit. In fungal cells, CMHs are very conserved molecules consisting of a ceramide moiety containing 9-methyl-4,8-sphingadienine in amidic linkage to 2-hydroxyoctadecanoic or 2-hydroxyhexadecanoic acids, and a carbohydrate portion consisting of one residue of glucose or galactose. 9-Methyl 4,8-sphingadienine-containing ceramides are usually glycosylated to form fungal cerebrosides, but the recent description of a ceramide dihexoside (CDH presenting phytosphingosine in Magnaporthe grisea suggests the existence of alternative pathways of ceramide glycosylation in fungal cells. Along with their unique structural characteristics, fungal CMHs have a peculiar subcellular distribution and striking biological properties. In Pseudallescheria boydii, Candida albicans, Cryptococcus neoformans, Aspergillus nidulans, A. fumigatus, and Schizophyllum commune, CMHs are apparently involved in morphological transitions and fungal growth. The elucidation of structural and functional aspects of fungal cerebrosides may therefore contribute to the design of new antifungal agents inhibiting growth and differentiation of pathogenic species.

  17. Development of methods for determining aflatoxins in biological material

    OpenAIRE

    Kussak, Anders

    1995-01-01

    In this thesis, it is shown how aflatoxins can be determined in biological material. The thesis is a summary of five papers. Aflatoxins are carcinogenic mycotoxins produced by Aspergillus moulds. Methods were developed for the determination of aflatoxins in samples of airborne dust and human urine collected at feed factories. For the dust samples from such agricultural products as copra, cotton seed and maize, methods were developed for the determination of aflatoxins B1, B2, G1 and G2. For u...

  18. 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.

  19. Structural biology computing: Lessons for the biomedical research sciences.

    Science.gov (United States)

    Morin, Andrew; Sliz, Piotr

    2013-11-01

    The field of structural biology, whose aim is to elucidate the molecular and atomic structures of biological macromolecules, has long been at the forefront of biomedical sciences in adopting and developing computational research methods. Operating at the intersection between biophysics, biochemistry, and molecular biology, structural biology's growth into a foundational framework on which many concepts and findings of molecular biology are interpreted1 has depended largely on parallel advancements in computational tools and techniques. Without these computing advances, modern structural biology would likely have remained an exclusive pursuit practiced by few, and not become the widely practiced, foundational field it is today. As other areas of biomedical research increasingly embrace research computing techniques, the successes, failures and lessons of structural biology computing can serve as a useful guide to progress in other biomedically related research fields.

  20. Structural biology of bacterial RNA polymerase.

    Science.gov (United States)

    Murakami, Katsuhiko S

    2015-05-11

    Since its discovery and characterization in the early 1960s (Hurwitz, J. The discovery of RNA polymerase. J. Biol. Chem. 2005, 280, 42477-42485), an enormous amount of biochemical, biophysical and genetic data has been collected on bacterial RNA polymerase (RNAP). In the late 1990s, structural information pertaining to bacterial RNAP has emerged that provided unprecedented insights into the function and mechanism of RNA transcription. In this review, I list all structures related to bacterial RNAP (as determined by X-ray crystallography and NMR methods available from the Protein Data Bank), describe their contributions to bacterial transcription research and discuss the role that small molecules play in inhibiting bacterial RNA transcription.

  1. Structural Biology of Bacterial RNA Polymerase

    Directory of Open Access Journals (Sweden)

    Katsuhiko S. Murakami

    2015-05-01

    Full Text Available Since its discovery and characterization in the early 1960s (Hurwitz, J. The discovery of RNA polymerase. J. Biol. Chem. 2005, 280, 42477–42485, an enormous amount of biochemical, biophysical and genetic data has been collected on bacterial RNA polymerase (RNAP. In the late 1990s, structural information pertaining to bacterial RNAP has emerged that provided unprecedented insights into the function and mechanism of RNA transcription. In this review, I list all structures related to bacterial RNAP (as determined by X-ray crystallography and NMR methods available from the Protein Data Bank, describe their contributions to bacterial transcription research and discuss the role that small molecules play in inhibiting bacterial RNA transcription.

  2. 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...

  3. Lipids in the structure and functions of biological membranes

    Directory of Open Access Journals (Sweden)

    Kuznetsov V.I.

    2014-06-01

    Full Text Available Lipids are one of the main components of cellular membranes. Lipids make up 30-55% of the cell content depending on the types of cells. Phospholipids, sphingomyelins, cholesterol, etc. are characteristic to cellular membranes. The composition of lipids of the both sides of the membranes differs. This fact determines asymmetry of the structure of bili-pid layer. The reason for many pathologies is the changes in the properties of cellular membranes with the modification of their components. The study of structure and functioning of cellular biomembranes is essential for many researchers. The condition of membranes, their quality, their quantitative composition and modification under the influence of different factors as well as their interaction with carbohydrate and protein component are of great importance for the functioning of both membranes, cells and the body in general. Analysis and structuring of lipids and their functions in biological membranes are studied.

  4. The JCSG high-throughput structural biology pipeline.

    Science.gov (United States)

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

    2010-10-01

    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. 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.

  5. 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…

  6. 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.

  7. Biology of sexuality inborn determinants of human sexual response.

    Science.gov (United States)

    Goodman, R E

    1983-09-01

    Opinions vary on the relative importance of biological and learning processes in the aetiology of sexual expression and deviance. The structure of personality, consistency of fantasy patterns, and the familial nature of homosexuality hint at a biological anlage. Research with the HY-antigen complex and X chromosome, and the elucidation of the interactions of intrauterine testosterone and its products with the foetal brain and neurotransmitters, have given us new models to understand the programming of sexuality. However, gonadotrophin feedback is not relevant as an indicator of brain feminization in primates and man. Finally, the interaction of masculinization and defeminization provides us with a model for understanding homosexual behaviour. PMID:6138111

  8. Determination of hair structure and shape.

    Science.gov (United States)

    Schlake, Thomas

    2007-04-01

    The hair follicle attracted significant attention as a model for the investigation of diverse biological problems. Whereas its morphology and the structure of the hair shaft are known in detail, the molecular biology of this miniorgan is significantly less characterised. Many efforts focussed on the development of the hair follicle and its stem cell reservoir; by contrast, the follicular product, the hair, which is interesting not only in terms of cosmetics was neglected. This review highlights our current knowledge of the control of hair structure and shape with emphasis on mouse hair follicle biology and discusses continuing problems.

  9. RNA triplexes: from structural principles to biological and biotech applications.

    Science.gov (United States)

    Devi, Gitali; Zhou, Yuan; Zhong, Zhensheng; Toh, Desiree-Faye Kaixin; Chen, Gang

    2015-01-01

    The diverse biological functions of RNA are determined by the complex structures of RNA stabilized by both secondary and tertiary interactions. An RNA triplex is an important tertiary structure motif that is found in many pseudoknots and other structured RNAs. A triplex structure usually forms through tertiary interactions in the major or minor groove of a Watson-Crick base-paired stem. A major-groove RNA triplex structure is stable in isolation by forming consecutive major-groove base triples such as U·A-U and C(+) ·G-C. Minor-groove RNA triplexes, e.g., A-minor motif triplexes, are found in almost all large structured RNAs. As double-stranded RNA stem regions are often involved in biologically important tertiary triplex structure formation and protein binding, the ability to sequence specifically target any desired RNA duplexes by triplex formation would have great potential for biomedical applications. Programmable chemically modified triplex-forming oligonucleotides (TFOs) and triplex-forming peptide nucleic acids (PNAs) have been developed to form TFO·RNA2 and PNA·RNA2 triplexes, respectively, with enhanced binding affinity and sequence specificity at physiological conditions. Here, we (1) provide an overview of naturally occurring RNA triplexes, (2) summarize the experimental methods for studying triplexes, and (3) review the development of TFOs and triplex-forming PNAs for targeting an HIV-1 ribosomal frameshift-inducing RNA, a bacterial ribosomal A-site RNA, and a human microRNA hairpin precursor, and for inhibiting the RNA-protein interactions involving human RNA-dependent protein kinase and HIV-1 viral protein Rev. PMID:25146348

  10. 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...

  11. 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.

  12. 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…

  13. 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…

  14. 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…

  15. Serial femtosecond crystallography: A revolution in structural biology.

    Science.gov (United States)

    Martin-Garcia, Jose M; Conrad, Chelsie E; Coe, Jesse; Roy-Chowdhury, Shatabdi; Fromme, Petra

    2016-07-15

    Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein.

  16. Serial femtosecond crystallography: A revolution in structural biology.

    Science.gov (United States)

    Martin-Garcia, Jose M; Conrad, Chelsie E; Coe, Jesse; Roy-Chowdhury, Shatabdi; Fromme, Petra

    2016-07-15

    Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein. PMID:27143509

  17. 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.

  18. 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

    Energy Technology Data Exchange (ETDEWEB)

    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{sub 2}, AsO{sub 4}, Bi, Cd, Co, CrO{sub 4}, Cu, Hg, iNi, TeO{sub 3}, TI, Pb, Zn, and other metals of environmental concern have been described (Silver, 1992; Silver and Walderhaug, 1995).'

  19. Visualising Knowledge Structures in Biology: Discipline, Curriculum and Student Understanding

    Science.gov (United States)

    Kinchin, Ian M.

    2011-01-01

    Concept mapping is discussed as a tool for the visualisation of knowledge structures that can be exploited within biological education. Application of this tool makes it possible to relate the structure of the curriculum to the structure of the discipline, in order to support the development of robust student knowledge structures in ways that…

  20. 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...

  1. 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.

  2. Automating the determination of 3D protein structure

    Energy Technology Data Exchange (ETDEWEB)

    Rayl, K.D.

    1993-12-31

    The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.

  3. Chirality as a physical aspect of structure formation in biological macromolecular systems

    Science.gov (United States)

    Malyshko, E. V.; Tverdislov, V. A.

    2016-08-01

    A novel regularity of hierarchical structures is found in the formation of chiral biological macromolecular systems. The formation of structures with alternating chirality (helical structures) serves as an instrument of stratification. The ability of a carbon atom to form chiral compounds is an important factor that determined the carbon basis of living systems on the Earth as well as their development through a series of chiral bifurcations. In the course of biological evolution, the helical structures became basic elements of the molecular machines in the cell. The discreteness of structural levels allowed the mechanical degrees of freedom formation in the molecular machines in the cell.

  4. 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.

  5. Identifying and Visualizing Macromolecular Flexibility in Structural Biology.

    Science.gov (United States)

    Palamini, Martina; Canciani, Anselmo; Forneris, Federico

    2016-01-01

    Structural biology comprises a variety of tools to obtain atomic resolution data for the investigation of macromolecules. Conventional structural methodologies including crystallography, NMR and electron microscopy often do not provide sufficient details concerning flexibility and dynamics, even though these aspects are critical for the physiological functions of the systems under investigation. However, the increasing complexity of the molecules studied by structural biology (including large macromolecular assemblies, integral membrane proteins, intrinsically disordered systems, and folding intermediates) continuously demands in-depth analyses of the roles of flexibility and conformational specificity involved in interactions with ligands and inhibitors. The intrinsic difficulties in capturing often subtle but critical molecular motions in biological systems have restrained the investigation of flexible molecules into a small niche of structural biology. Introduction of massive technological developments over the recent years, which include time-resolved studies, solution X-ray scattering, and new detectors for cryo-electron microscopy, have pushed the limits of structural investigation of flexible systems far beyond traditional approaches of NMR analysis. By integrating these modern methods with powerful biophysical and computational approaches such as generation of ensembles of molecular models and selective particle picking in electron microscopy, more feasible investigations of dynamic systems are now possible. Using some prominent examples from recent literature, we review how current structural biology methods can contribute useful data to accurately visualize flexibility in macromolecular structures and understand its important roles in regulation of biological processes.

  6. Structural determinants of hospital closure.

    Science.gov (United States)

    Longo, D R; Chase, G A

    1984-05-01

    In a retrospective case-control study, structural characteristics of hospitals that closed during the years 1976-1980 were contrasted with three comparison groups: hospitals that were acquired in a merger; hospitals that joined a multihospital system; and hospitals that remained autonomously opened, to investigate these characteristics as predictors of closure. Characteristics investigated included environmental, structural, and process variables. The independent variables were measured 5 years prior to outcome. Findings indicate that closed hospitals resemble hospitals acquired in a merger ("failure"), and likewise autonomous hospitals resemble hospitals that join a multihospital system ("success"). The most important predictors of hospital failure were the physician-to-population ratio, the East North Central and West North Central census regions, the level of diversification, low occupancy rate, location in a standard metropolitan statistical area, the chief executive officer's lack of affiliation in the American College of Hospital Administrators, profit status, bed size of less than 50, and presence in a state with a rate-setting agency. Surprisingly, this study shows the bed-to-population ratio to be unrelated to closure. In addition, the findings strongly support the open-system perspective, which, unlike the closed-system perspective, is concerned with the vulnerability of the organization to the uncontrollable and often unpredictable influences of the environment.

  7. Biology content cognitive structure: From science student to science teacher

    Science.gov (United States)

    Hauslein, Patricia L.; Good, Ronald G.; Cummins, Catherine L.

    The F-Sort of Biology Concepts was used to assess understanding of the relationships among 37 biology concepts by five groups: Preservice secondary science teachers, in-service biology teachers with 1-3 years of teaching experience, in-service biology teachers with 5 or more years of experience, scientists in any biological science field, and college seniors majoring in biology. Data collected from the F-sort were analyzed using latent partition analysis and alpha factor analysis with additional interpretation from multidimensional scaling. The subjects were asked to think aloud as they performed the F-sort and each session was audiotaped for later analysis. These analyses indicated that the biology major and experienced secondary science teachers were separated from the scientists by a dimension based on a deep-versus-surface structure understanding of the concepts. A second axis shows that scientists are separated from other groups by a fluid-versus-fixed cognitive structure dimension. That is, both experienced teachers and scientists were found to have well-constructed and ordered cognitive structures, but scientists were much more likely to see an item having a place in two or more categories, whereas experienced teachers tended to focus on only one aspect of an item, and therefore understanding that it rightfully belonged in only one category. It appears that teachers restructure their science knowledge as they become more experienced. There is an apparent transition from poorly organized to highly organized cognitive structures for biology concepts when comparing preservice, novice, and experienced teachers, respectively. The transition does not seem to be one achieving a deeper understanding of the biology concepts or to a greater degree of integration of the concepts, but rather a transition from a fairly large, loosely organized pool of biology concepts to one which is highly structured but limited to the expectations of the established curriculum. The

  8. Macromolecular structure determination in the post-genome era

    International Nuclear Information System (INIS)

    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

  9. MOTOR: model assisted software for NMR structure determination.

    Science.gov (United States)

    Schieborr, Ulrich; Sreeramulu, Sridhar; Elshorst, Bettina; Maurer, Marcus; Saxena, Krishna; Stehle, Tanja; Kudlinzki, Denis; Gande, Santosh Lakshmi; Schwalbe, Harald

    2013-11-01

    Eukaryotic proteins with important biological function can be partially unstructured, conformational flexible, or heterogenic. Crystallization trials often fail for such proteins. In NMR spectroscopy, parts of the polypeptide chain undergoing dynamics in unfavorable time regimes cannot be observed. De novo NMR structure determination is seriously hampered when missing signals lead to an incomplete chemical shift assignment resulting in an information content of the NOE data insufficient to determine the structure ab initio. We developed a new protein structure determination strategy for such cases based on a novel NOE assignment strategy utilizing a number of model structures but no explicit reference structure as it is used for bootstrapping like algorithms. The software distinguishes in detail between consistent and mutually exclusive pairs of possible NOE assignments on the basis of different precision levels of measured chemical shifts searching for a set of maximum number of consistent NOE assignments in agreement with 3D space. Validation of the method using the structure of the low molecular-weight-protein tyrosine phosphatase A (MptpA) showed robust results utilizing protein structures with 30-45% sequence identity and 70% of the chemical shift assignments. About 60% of the resonance assignments are sufficient to identify those structural models with highest conformational similarity to the real structure. The software was benchmarked by de novo solution structures of fibroblast growth factor 21 (FGF21) and the extracellular fibroblast growth factor receptor domain FGFR4 D2, which both failed in crystallization trials and in classical NMR structure determination. PMID:23852655

  10. Structural biology applications of solid state MAS DNP NMR

    Science.gov (United States)

    Akbey, Ümit; Oschkinat, Hartmut

    2016-08-01

    Dynamic Nuclear Polarization (DNP) has long been an aim for increasing sensitivity of nuclear magnetic resonance (NMR) spectroscopy, delivering spectra in shorter experiment times or of smaller sample amounts. In recent years, it has been applied in magic angle spinning (MAS) solid-state NMR to a large range of samples, including biological macromolecules and functional materials. New research directions in structural biology can be envisaged by DNP, facilitating investigations on very large complexes or very heterogeneous samples. Here we present a summary of state of the art DNP MAS NMR spectroscopy and its applications to structural biology, discussing the technical challenges and factors affecting DNP performance.

  11. Self-Reference, Biologic and the Structure of Reproduction

    CERN Document Server

    Kauffman, Louis H

    2015-01-01

    This paper concentrates on relationships of formal systems with biology. The paper is based on previous papers by the author. We have freely used texts of those papers where the formulations are of use, and we have extended the concepts and discussions herein considerably beyond the earlier work. We concentrate on formal systems not only for the sake of showing how there is a fundamental mathematical structure to biology, but also to consider and reconsider philosophical and phenomenological points of view in relation to natural science and mathematics. The relationship with phenomenology comes about in the questions that arise about the nature of the observer in relation to the observed that arise in philosophy, but also in science in the very act of determining the context and models upon which it shall be based.We examine the schema behind the reproduction of DNA. The DNA molecule consists of two interwound strands, the Watson Strand (W) and the Crick Strand (C). The two strands are bonded to each other vi...

  12. The NIGMS X6A East Coast Structural Biology Facility

    International Nuclear Information System (INIS)

    The X6A facility at the National Synchrotron Light Source (NSLS) is a dedicated macromolecular crystallography beam line funded by the National Institute of General Medical Sciences. The facility serves expert and non-expert crystallographers from protein purification to the determination of atomic coordinates. The X6A facility consists of an experimental station and an associated laboratory for sample preparation. The X6A beam line optics include an NSLS design Si(111) channel-cut monochromator and an Oxford Danfysik toroidal focusing mirror. The end station consists of a CrystalLogic Kappa diffractometer and an ADSC 210 CCD detector. Standard crystallographic packages are available to assist the users for data analysis. An automated sample changer will be added in the near future to the end station. The associated laboratory is fully equipped for all aspects of protein purification and crystallization. The beam line is currently available for users (http://protein.nsls.bnl.gov). The main goal of the X6A effort is to provide the basic tools to researchers who would like to use macromolecular crystallography and structural biology to address important biological questions

  13. Mass Spec Studio for Integrative Structural Biology

    NARCIS (Netherlands)

    Rey, Martial; Sarpe, Vladimir; Burns, Kyle M.; Buse, Joshua; Baker, Charles A. H.; van Dijk, Marc; Wordeman, Linda; Bonvin, Alexandre M. J. J.; Schriemer, David C.

    2014-01-01

    The integration of biophysical data from multiple sources is critical for developing accurate structural models of large multiprotein systems and their regulators. Mass spectrometry (MS) can be used to measure the insertion location for a wide range of topographically sensitive chemical probes, and

  14. Wham: Identifying Structural Variants of Biological Consequence.

    Science.gov (United States)

    Kronenberg, Zev N; Osborne, Edward J; Cone, Kelsey R; Kennedy, Brett J; Domyan, Eric T; Shapiro, Michael D; Elde, Nels C; Yandell, Mark

    2015-12-01

    Existing methods for identifying structural variants (SVs) from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics) to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools-Lumpy, Delly and SoftSearch-and demonstrate Wham's ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham), with documentation on a wiki (http://zeeev.github.io/wham/). For community support please post questions to https://www.biostars.org/.

  15. Wham: Identifying Structural Variants of Biological Consequence.

    Directory of Open Access Journals (Sweden)

    Zev N Kronenberg

    2015-12-01

    Full Text Available Existing methods for identifying structural variants (SVs from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools-Lumpy, Delly and SoftSearch-and demonstrate Wham's ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham, with documentation on a wiki (http://zeeev.github.io/wham/. For community support please post questions to https://www.biostars.org/.

  16. Optimizing an emperical scoring function for transmembrane protein structure determination.

    Energy Technology Data Exchange (ETDEWEB)

    Young, Malin M.; Sale, Kenneth L.; Gray, Genetha Anne; Kolda, Tamara Gibson

    2003-10-01

    We examine the problem of transmembrane protein structure determination. Like many other questions that arise in biological research, this problem cannot be addressed by traditional laboratory experimentation alone. An approach that integrates experiment and computation is required. We investigate a procedure which states the transmembrane protein structure determination problem as a bound constrained optimization problem using a special empirical scoring function, called Bundler, as the objective function. In this paper, we describe the optimization problem and some of its mathematical properties. We compare and contrast results obtained using two different derivative free optimization algorithms.

  17. Structure Determination of Natural Products by Mass Spectrometry

    Science.gov (United States)

    Biemann, Klaus

    2015-07-01

    I review laboratory research on the development of mass spectrometric methodology for the determination of the structure of natural products of biological and medical interest, which I conducted from 1958 to the end of the twentieth century. The methodology was developed by converting small peptides to their corresponding polyamino alcohols to make them amenable to mass spectrometry, thereby making it applicable to whole proteins. The structures of alkaloids were determined by analyzing the fragmentation of a known alkaloid and then using the results to deduce the structures of related compounds. Heparin-like structures were investigated by determining their molecular weights from the mass of protonated molecular ions of complexes with highly basic, synthetic peptides. Mass spectrometry was also employed in the analysis of lunar material returned by the Apollo missions. A miniaturized gas chromatograph mass spectrometer was sent to Mars on board of the two Viking 1976 spacecrafts.

  18. Optical manipulation of microparticles and biological structures

    Science.gov (United States)

    Gahagan, Kevin Thomas

    1998-06-01

    We report experimental and theoretical investigations of the trapping of microparticles and biological objects using radiation pressure. Part I of this thesis presents a technique for trapping both low and high index microparticles using a single, stationary focused laser beam containing an optical vortex. Advantages of this vortex trap include the ease of implementation, a lower exposure level for high-index particles compared to a standard Gaussian beam trap, and the ability to isolate individual low-index particles in concentrated dispersions. The vortex trap is modeled using ray-tracing methods and a more precise electromagnetic model, which is accurate for particles less than 10 μm in diameter. We have measured the stable equilibrium position for two low-index particle systems (e.g., hollow glass spheres (HGS) in water, and water droplets in acetophenone (W/A)). The strength of the trap was measured for the HGS system along the longitudinal and transverse directions. We also demonstrate simultaneous trapping of a low and high index particle with a vortex beam. The stability of this dual-particle trap is found to depend on the relative particle size, the divergence angle of the beam, and the depth of the particles within the trapping chamber. Part II presents results from an interdisciplinary and collaborative investigation of an all-optical genetic engineering technique whereby Agrobacterium rhizogenes were inserted through a laser-ablated hole in the cell wall of the plant, Gingko biloba. We describe a protocol which includes the control of osmotic conditions, culturing procedures, viability assays and laser microsurgery. We succeeded in placing up to twelve viable bacteria into a single plant cell using this technique. The bacteria are believed to be slightly heated by the Gaussian beam trap. A numerical model is presented predicting a temperature rise of just a few degrees. Whereas G. biloba and A. rhitogenes were chosen for this study because of Ginkgo

  19. Simultaneous determination of protein structure and dynamics

    DEFF Research Database (Denmark)

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

    2005-01-01

    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 at...

  20. Simultaneous determination of salicylic acid and salicylamide in biological fluids

    Science.gov (United States)

    Murillo Pulgarín, J. A.; Alañón Molina, A.; Sánchez-Ferrer Robles, I.

    2011-09-01

    A new methodology for the simultaneous determination of salicylic acid and salicylamide in biological fluids is proposed. The strong overlapping of the fluorescence spectra of both analytes makes impossible the conventional fluorimetric determination. For that reason, the use of fluorescence decay curves to resolve mixtures of analytes is proposed; this is a novel technique that provides the benefits in selectivity and sensitivity of the fluorescence decay curves. In order to assess the goodness of the proposed method, a prediction set of synthetic samples were analyzed obtaining recuperation percentages between 98.2 and 104.6%. Finally, a study of the detection limits was done using a new criterion resulting in values for the detection limits of 8.2 and 11.6 μg L -1 for salicylic acid and salicylamide respectively. The validity of the method was tested in human serum and human urine spiked with aliquots of the analytes. Recoveries obtained were 96.2 and 94.5% for salicylic acid and salicylamide respectively.

  1. Some problems of ultrasonic and laser cutting of biological structures

    Science.gov (United States)

    Gudra, T.; Muc, S.

    2008-02-01

    The paper presents the influence of the laser and ultrasonic cutter on biological structures and some problems bound up with the applications of lasers and ultrasounds in surgery. The advantages and disadvantages of contact and noncontact applications of the Nd:YAG laser were presented as well as the usefulness of the ultrasonic cutter for selective cutting of various tissues. The benefits resulting from a combination of the two technologies were discussed, and initial tests of the laser-ultrasonic cutter operation were performed, pointing to the possibility of improving the cutting of biological structures.

  2. 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.

  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. 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.

  5. 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.

  6. 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 fr

  7. Analysis and Design of Biological Materials and Structures

    CERN Document Server

    Öchsner, Andreas; Altenbach, Holm

    2012-01-01

    This collection provides researchers and scientists with advanced analyses and materials design techniques in Biomaterials and presents mechanical studies of biological structures. In 16 contributions well known experts present their research on Stress and Strain Analysis, Material Properties, Fluid and Gas mechanics and they show related problems.

  8. The Evolving Contribution of Mass Spectrometry to Integrative Structural Biology

    Science.gov (United States)

    Faini, Marco; Stengel, Florian; Aebersold, Ruedi

    2016-06-01

    Protein complexes are key catalysts and regulators for the majority of cellular processes. Unveiling their assembly and structure is essential to understanding their function and mechanism of action. Although conventional structural techniques such as X-ray crystallography and NMR have solved the structure of important protein complexes, they cannot consistently deal with dynamic and heterogeneous assemblies, limiting their applications to small scale experiments. A novel methodological paradigm, integrative structural biology, aims at overcoming such limitations by combining complementary data sources into a comprehensive structural model. Recent applications have shown that a range of mass spectrometry (MS) techniques are able to generate interaction and spatial restraints (cross-linking MS) information on native complexes or to study the stoichiometry and connectivity of entire assemblies (native MS) rapidly, reliably, and from small amounts of substrate. Although these techniques by themselves do not solve structures, they do provide invaluable structural information and are thus ideally suited to contribute to integrative modeling efforts. The group of Brian Chait has made seminal contributions in the use of mass spectrometric techniques to study protein complexes. In this perspective, we honor the contributions of the Chait group and discuss concepts and milestones of integrative structural biology. We also review recent examples of integration of structural MS techniques with an emphasis on cross-linking MS. We then speculate on future MS applications that would unravel the dynamic nature of protein complexes upon diverse cellular states.

  9. Clustering and rule-based classifications of chemical structures evaluated in the biological activity space.

    Science.gov (United States)

    Schuffenhauer, Ansgar; Brown, Nathan; Ertl, Peter; Jenkins, Jeremy L; Selzer, Paul; Hamon, Jacques

    2007-01-01

    Classification methods for data sets of molecules according to their chemical structure were evaluated for their biological relevance, including rule-based, scaffold-oriented classification methods and clustering based on molecular descriptors. Three data sets resulting from uniformly determined in vitro biological profiling experiments were classified according to their chemical structures, and the results were compared in a Pareto analysis with the number of classes and their average spread in the profile space as two concurrent objectives which were to be minimized. It has been found that no classification method is overall superior to all other studied methods, but there is a general trend that rule-based, scaffold-oriented methods are the better choice if classes with homogeneous biological activity are required, but a large number of clusters can be tolerated. On the other hand, clustering based on chemical fingerprints is superior if fewer and larger classes are required, and some loss of homogeneity in biological activity can be accepted.

  10. The determinism and boundedness of self-assembling structures

    CERN Document Server

    Tesoro, S

    2016-01-01

    Self-assembly processes are widespread in nature, and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Among the most important of these properties are whether the self-assembly is deterministic or nondeterministic, and whether it is bound or unbound. The former tells us whether the same set of building blocks always generates the same structure, and the latter whether it grows indefinitely. These properties are highly relevant in the context of protein structures, as the difference between deterministic protein self-assembly and nondeterministic protein aggregation is central to a number of diseases. Here we introduce a graph-based approach that can determine, with a few restrictions, whether a set of self-assembly building blocks is deterministic or nondeterministic, and whether it is bound or unbound. We apply this methodology to a previously studied lattice self-assembly model and discuss generalisatio...

  11. A structural determinant required for RNA editing

    Science.gov (United States)

    Tian, Nan; Yang, Yun; Sachsenmaier, Nora; Muggenhumer, Dominik; Bi, Jingpei; Waldsich, Christina; Jantsch, Michael F.; Jin, Yongfeng

    2011-01-01

    RNA editing by adenosine deaminases acting on RNAs (ADARs) can be both specific and non-specific, depending on the substrate. Specific editing of particular adenosines may depend on the overall sequence and structural context. However, the detailed mechanisms underlying these preferences are not fully understood. Here, we show that duplex structures mimicking an editing site in the Gabra3 pre-mRNA unexpectedly fail to support RNA editing at the Gabra3 I/M site, although phylogenetic analysis suggest an evolutionarily conserved duplex structure essential for efficient RNA editing. These unusual results led us to revisit the structural requirement for this editing by mutagenesis analysis. In vivo nuclear injection experiments of mutated editing substrates demonstrate that a non-conserved structure is a determinant for editing. This structure contains bulges either on the same or the strand opposing the edited adenosine. The position of these bulges and the distance to the edited base regulate editing. Moreover, elevated folding temperature can lead to a switch in RNA editing suggesting an RNA structural change. Our results indicate the importance of RNA tertiary structure in determining RNA editing. PMID:21427087

  12. Advances on surface structural determination by LEED

    Energy Technology Data Exchange (ETDEWEB)

    Soares, Edmar A; De Carvalho, Vagner E [Departamento de Fisica, ICEX, Universidade Federal de Minas Gerais, 31270-090, Belo Horizonte, MG (Brazil); De Castilho, Caio M C, E-mail: edmar@fisica.ufmg.br [Grupo de Fisica de SuperfIcies e Materiais, Instituto de Fisica and Instituto Nacional de Ciencia e Tecnologia em Energia e Ambiente (CIENAM)INCT-E and A, Universidade Federal da Bahia, Campus Universitario da Federacao, 40170-115, Salvador, BA (Brazil)

    2011-08-03

    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)

  13. DETERMINANTS OF BANK BOARD STRUCTURE IN GHANA

    OpenAIRE

    Michael Adusei

    2012-01-01

    The paper investigates the determinants of bank board structure in Ghana and finds that the Scope of Operations Hypothesis could explain the variation in board size but not board independence. On the other hand, the Board Monitoring Hypothesis could only explain the variation in board independence but not board size. The study also finds that cost-income ratio, foreign majority ownership structure and Ghana Stock Exchange listing status are positively and significantly associated with large b...

  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. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes...... chemical shifts. The method is benchmarked on folding simulations of five small proteins. In four cases the resulting structures are in excellent agreement with experimental data, the fifth case fail likely due to inaccuracies in the energy function. For the Chymotrypsin Inhibitor protein, a structure...

  16. A structural biology perspective on NMDA receptor pharmacology and function.

    Science.gov (United States)

    Regan, Michael C; Romero-Hernandez, Annabel; Furukawa, Hiro

    2015-08-01

    N-methyld-aspartate receptors (NMDARs) belong to the large family of ionotropic glutamate receptors (iGluRs), which are critically involved in basic brain functions as well as multiple neurological diseases and disorders. The NMDARs are large heterotetrameric membrane protein complexes. The extensive extracellular domains recognize neurotransmitter ligands and allosteric compounds and translate the binding information to regulate activity of the transmembrane ion channel. Here, we review recent advances in the structural biology of NMDARs with a focus on pharmacology and function. Structural analysis of the isolated extracellular domains in combination with the intact heterotetrameric NMDAR structure provides important insights into how this sophisticated ligand-gated ion channel may function.

  17. Précis of "Lifelines: biology, freedom, determinism".

    Science.gov (United States)

    Rose, S

    1999-10-01

    There are many ways of describing and explaining the properties of living systems; causal, functional, and reductive accounts are necessary but no one account has primacy. The history of biology as a discipline has given excessive authority to reductionism, which collapses higher level accounts, such as social or behavioural ones, into molecular ones. Such reductionism becomes crudely ideological when applied to the human condition, with its claims for genes "for" everything from sexual orientation to compulsive shopping. The current enthusiasm for genetics and ultra-Darwinist accounts, with their selfish-gene metaphors for living processes, misunderstand both the phenomena of development and the interactive role that DNA and the fluid genome play in the cellular orchestra. DNA is not a blueprint, and the four dimensions of life (three of space, one of time) cannot be read off from its one-dimensional strand. Both developmental and evolutionary processes are more than merely instructive or selective; the organism constructs itself, a process known as autopoiesis, through a lifeline trajectory. Because organisms are thermodynamically open systems, living processes are homeodynamic, not homeostatic. The self-organising membrane-bound and energy-utilising metabolic web of the cell must have evolved prior to socalled naked replicators. Evolution is constrained by physics, chemistry, and structure; not all change is powered by natural selection, and not all phenotypes are adaptive. Finally, therefore, living processes are radically indeterminate; like all other living organisms, but to an even greater degree, we make our own future, though in circumstances not of our own choosing. PMID:11301572

  18. 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.…

  19. Biological determinants of aldosterone-induced cardiac fibrosis in rats.

    Science.gov (United States)

    Robert, V; Silvestre, J S; Charlemagne, D; Sabri, A; Trouvé, P; Wassef, M; Swynghedauw, B; Delcayre, C

    1995-12-01

    To determine the events leading to cardiac fibrosis in aldosterone-salt hypertensive rats, we studied protein and mRNA accumulation of procollagens I and III for 60 days. After 3 and 7 days of treatment systolic pressure was normal, and no histological or biochemical changes were seen in rat hearts. At day 15 arterial pressure was raised (+40%) and left ventricular hypertrophy was +15%. Cardiac examination after hemalun-eosin staining and immunolabeling with anticollagen I and III antibodies showed no structural alterations, but an 83% increase in right ventricular type III procollagen mRNA levels was found. At 30 and 60 days we found progressive cardiac fibrosis, with inflammatory cells, myocyte necrosis, and elevation of both types I and III procollagen mRNA levels in both ventricles. To determine whether aldosterone had effects on Na,K-ATPase that might lead to ionic disturbances and induce myocyte necrosis, we studied the major cardiac Na,K-ATPase isoform genes. Although Na,K-ATPase alpha 1- and beta 1-subunit mRNA levels were elevated in kidney at day 1, neither of these cardiac transcripts nor the specific alpha 2 isoform was altered between 1 and 15 days. These results show that accumulation of procollagen mRNAs occurs before collagen deposition. Cardiac alterations are late and not preceded by changes in Na,K-ATPase cardiac gene expression, precluding a direct modulation of cardiac collagen synthesis and Na,K-ATPase by aldosterone. PMID:7490157

  20. Correlation of transverse relaxation time with structure of biological tissue

    Science.gov (United States)

    Furman, Gregory B.; Meerovich, Victor M.; Sokolovsky, Vladimir L.

    2016-09-01

    Transverse spin-spin relaxation of liquids entrapped in nanocavities with different orientational order is theoretically investigated. Based on the bivariate normal distribution of nanocavities directions, we have calculated the anisotropy of the transverse relaxation time for biological systems, such as collagenous tissues, articular cartilage, and tendon. In the framework of the considered model, the dipole-dipole interaction is determined by a single coupling constant. The calculation results for the transverse relaxation time explain the angular dependence observed in MRI experiments with biological objects. The good agreement with the experimental data is obtained by adjustment of only one parameter which characterizes the disorder in fiber orientations. The relaxation time is correlated with the degree of ordering in biological tissues. Thus, microstructure of the tissues can be revealed from the measurement of relaxation time anisotropy. The clinical significance of the correlation, especially in the detection of damage must be evaluated in a large prospective clinical trials.

  1. Depth Determination of an Abnormal Heat Source in Biological Tissues

    Institute of Scientific and Technical Information of China (English)

    WANG Qing-Hua; LI Zhen-Hua; LAI Jian-Cheng; HE An-Zhi

    2011-01-01

    We deduce the surface temperature distribution generated by the inner point heat source in biological tissues and propose a graphic method to retrieve the depth of the point heat source. The practical surface temperature distribution can be regarded as the convolution of the temperature distribution of the inner point heat source with the heat source shape function. The depth of an abnormal heat source in biological tissues can be retrieved by using the graphic method combined with the blind deconvolution scheme.%We deduce the surface temperature distribution generated by the inner point heat source in biological tissues and propose a graphic method to retrieve the depth of the point heat source.The practical surface temperature distribution can be regarded as the convolution of the temperature distribution of the inner point heat source with the heat source shape function.The depth of an abnormal heat source in biological tissues can be retrieved by using the graphic method combined with the blind deconvolution scheme.Surface temperature distribution of the biological tissues is closely related to the neighboring metabolic heat production,blood circulation in an organism and environmental temperature.[1] The abnormal metabolic performances of a local region in biological tissue imply malignant changes occurring,which can be distinguished from the variance of surface temperature.Modern development of thermal infrared (TIR) imaging has made the surface temperature measurement of biological tissue easier.Nowadays,several types of tumors,e.g.skin or breast can be recognized with TIR imaging.[2] The diagnostics with TIR imaging require more experienced operators and can not accurately ascertain the site of pathological changes,which limits the value of this technology.Therefore ascertaining the depth of inner heat source in biological body has the extremely important clinical value.

  2. Polysaccharides of higher fungi: Biological role, structure, and antioxidative activity

    Directory of Open Access Journals (Sweden)

    Kozarski Maja S.

    2014-01-01

    Full Text Available Fungal polysaccharides attract a lot of attention due to their multiple challenging biological properties, such as: anti-tumor, anti-viral, anticomplementary, anticoagulant, hypolipidemic and immunomodulatory and immune-stimulatory activities, which all together make them suitable for application in many quite distinctive areas, such as food industry, biomedicine, cosmetology, agriculture, environmental protection and waste water management. This article presents results with respect to biological properties, structure and procedures related to the isolation and activation of polysaccharides of higher fungi. It is considered and presented along with a review of the critical antioxidative activity and possible influence of the structural composition of polysaccharide extracts (isolated from these higher fungi upon their antioxidative properties.

  3. Structure and mechanics of interfaces in biological materials

    Science.gov (United States)

    Barthelat, Francois; Yin, Zhen; Buehler, Markus J.

    2016-04-01

    Hard biological materials — for example, seashells, bone or wood — fulfil critical structural functions and display unique and attractive combinations of stiffness, strength and toughness, owing to their intricate architectures, which are organized over several length scales. The size, shape and arrangement of the ‘building blocks’ of which these materials are made are essential for defining their properties and their exceptional performance, but there is growing evidence that their deformation and toughness are also largely governed by the interfaces that join these building blocks. These interfaces channel nonlinear deformations and deflect cracks into configurations in which propagation is more difficult. In this Review, we discuss comparatively the composition, structure and mechanics of a set of representative biological interfaces in nacre, bone and wood, and show that these interfaces possess unusual mechanical characteristics, which can encourage the development of advanced bioinspired composites. Finally, we highlight recent examples of synthetic materials inspired from the mechanics and architecture of natural interfaces.

  4. Aromatic rings in chemical and biological recognition: energetics and structures.

    Science.gov (United States)

    Salonen, Laura M; Ellermann, Manuel; Diederich, François

    2011-05-16

    This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations. PMID:21538733

  5. Chemical and structural features influencing the biological activity of curcumin.

    Science.gov (United States)

    Priyadarsini, K Indira

    2013-01-01

    Curcumin, a polyphenolic natural product, exhibits therapeutic activity against a number of diseases, attributed mainly to its chemical structure and unique physical, chemical, and biological properties. It is a diferuloyl methane molecule [1,7-bis (4-hydroxy-3- methoxyphenyl)-1,6-heptadiene-3,5-dione)] containing two ferulic acid residues joined by a methylene bridge. It has three important functionalities: an aromatic o-methoxy phenolic group, α, β-unsaturated β-diketo moiety and a seven carbon linker. Extensive research in the last two decades has provided evidence for the role of these different functional groups in its crucial biological activities. A few highlights of chemical structural features associated with the biological activity of curcumin are: The o-methoxyphenol group and methylenic hydrogen are responsible for the antioxidant activity of curcumin, and curcumin donates an electron/ hydrogen atom to reactive oxygen species. Curcumin interacts with a number of biomolecules through non-covalent and covalent binding. The hydrogen bonding and hydrophobicity of curcumin, arising from the aromatic and tautomeric structures along with the flexibility of the linker group are responsible for the non-covalent interactions. The α, β-unsaturated β-diketone moiety covalently interacts with protein thiols, through Michael reaction. The β-diketo group forms chelates with transition metals, there by reducing the metal induced toxicity and some of the metal complexes exhibit improved antioxidant activity as enzyme mimics. New analogues with improved activity are being developed with modifications on specific functional groups of curcumin. The physico-chemical and structural features associated with some of the biological activities of curcumin and important analogues are summarized in this article. PMID:23116315

  6. The Structural Biology of CRISPR-Cas Systems

    OpenAIRE

    Jiang, Fuguo; Doudna, Jennifer A.

    2015-01-01

    Prokaryotic CRISPR-Cas genomic loci encode RNA-mediated adaptive immune systems that bear some functional similarities with eukaryotic RNA interference. Acquired and heritable immunity against bacteriophage and plasmids begins with integration of ~30 base pair foreign DNA sequences into the host genome. CRISPR-derived transcripts assemble with CRISPR-associated (Cas) proteins to target complementary nucleic acids for degradation. Here we review recent advances in the structural biology of the...

  7. 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.

  8. Application of Nuclear Magnetic Resonance and Hybrid Methods to Structure Determination of Complex Systems.

    Science.gov (United States)

    Prischi, Filippo; Pastore, Annalisa

    2016-01-01

    The current main challenge of Structural Biology is to undertake the structure determination of increasingly complex systems in the attempt to better understand their biological function. As systems become more challenging, however, there is an increasing demand for the parallel use of more than one independent technique to allow pushing the frontiers of structure determination and, at the same time, obtaining independent structural validation. The combination of different Structural Biology methods has been named hybrid approaches. The aim of this review is to critically discuss the most recent examples and new developments that have allowed structure determination or experimentally-based modelling of various molecular complexes selecting them among those that combine the use of nuclear magnetic resonance and small angle scattering techniques. We provide a selective but focused account of some of the most exciting recent approaches and discuss their possible further developments.

  9. Magnetic Micro/Nano Structures for Biological Manipulation

    Science.gov (United States)

    Huang, Chen-Yu; Hsieh, Teng-Fu; Chang, Wei-Chieh; Yeh, Kun-Chieh; Hsu, Ming-Shinn; Chang, Ching-Ray; Chen, Jiann-Yeu; Wei, Zung-Hang

    2016-05-01

    Biomanipulation based on micro/nano structures is an attractive approach for biotechnology. To manipulate biological systems by magnetic forces, the magnetic labeling technology utilized magnetic nanoparticles (MNPs) as a common rule. Ferrofluid, well-dispersed MNPs, can be used for magnetic modification of the surface or as molds to form organized microstructures. For magnetic-based micro/nano structures, different methods to modulate magnetic field at the microscale have been developed. Specifically, this review focused on a new strategy which uses the concept of micromagnetism of patterned magnetic thin film with specific domain walls configurations to generate stable magnetic poles for cell patterning.

  10. 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)

  11. Biologic

    CERN Document Server

    Kauffman, L H

    2002-01-01

    In this paper we explore the boundary between biology and the study of formal systems (logic). In the end, we arrive at a summary formalism, a chapter in "boundary mathematics" where there are not only containers but also extainers ><, entities open to interaction and distinguishing the space that they are not. The boundary algebra of containers and extainers is to biologic what boolean algebra is to classical logic. We show how this formalism encompasses significant parts of the logic of DNA replication, the Dirac formalism for quantum mechanics, formalisms for protein folding and the basic structure of the Temperley Lieb algebra at the foundations of topological invariants of knots and links.

  12. Cooperativity governs the size and structure of biological interfaces.

    Science.gov (United States)

    Qin, Zhao; Buehler, Markus J

    2012-11-15

    Interfaces, defined as the surface of interactions between two parts of a system at a discontinuity, are very widely found in nature. While it is known that the specific structure of an interface plays an important role in defining its properties, it is less clear whether or not there exist universal scaling laws that govern the structural evolution of a very broad range of natural interfaces. Here we show that cooperativity of interacting elements, leading to great strength at low material use, is a key concept that governs the structural evolution of many natural interfaces. We demonstrate this concept for the cases of β-sheet proteins in spider silk, gecko feet, legs of caterpillars, and self-assembling of penguins into huddles, which range in scales from the submolecular to the macroscopic level. A general model is proposed that explains the size and structure of biological interfaces from a fundamental point of view.

  13. Robust structural analysis of native biological macromolecules from multi-crystal anomalous diffraction data

    International Nuclear Information System (INIS)

    Anomalous diffraction signals from typical native macromolecules are very weak, frustrating their use in structure determination. Here, native SAD procedures are described for enhancing the signal to noise in anomalous diffraction by using multiple crystals are described. Five applications demonstrate that truly routine structure determination is possible without the need for heavy atoms. Structure determinations for biological macromolecules that have no known structural antecedents typically involve the incorporation of heavier atoms than those found natively in biological molecules. Currently, selenomethionyl proteins analyzed using single- or multi-wavelength anomalous diffraction (SAD or MAD) data predominate for such de novo analyses. Naturally occurring metal ions such as zinc or iron often suffice in MAD or SAD experiments, and sulfur SAD has been an option since it was first demonstrated using crambin 30 years ago; however, SAD analyses of structures containing only light atoms (Zmax ≤ 20) have not been common. Here, robust procedures for enhancing the signal to noise in measurements of anomalous diffraction by combining data collected from several crystals at a lower than usual X-ray energy are described. This multi-crystal native SAD method was applied in five structure determinations, using between five and 13 crystals to determine substructures of between four and 52 anomalous scatterers (Z ≤ 20) and then the full structures ranging from 127 to 1200 ordered residues per asymmetric unit at resolutions from 2.3 to 2.8 Å. Tests were devised to assure that all of the crystals used were statistically equivalent. Elemental identities for Ca, Cl, S, P and Mg were proven by f′′ scattering-factor refinements. The procedures are robust, indicating that truly routine structure determination of typical native macromolecules is realised. Synchrotron beamlines that are optimized for low-energy X-ray diffraction measurements will facilitate such direct

  14. Biomolecular Deuteration for Neutron Structural Biology and Dynamics.

    Science.gov (United States)

    Haertlein, Michael; Moulin, Martine; Devos, Juliette M; Laux, Valerie; Dunne, Orla; Forsyth, V Trevor

    2016-01-01

    Neutron scattering studies provide important information in structural biology that is not accessible using other approaches. The uniqueness of the technique, and its complementarity with X-ray scattering, is greatest when full use is made of deuterium labeling. The ability to produce tailor-made deuterium-labeled biological macromolecules allows neutron studies involving solution scattering, crystallography, reflection, and dynamics to be optimized in a manner that has major impact on the scope, quality, and throughput of work in these areas. Deuteration facilities have now been developed at many neutron centres throughout the world; these are having a crucial effect on neutron studies in the life sciences and on biologically related studies in soft matter. This chapter describes methods that have been developed for the efficient production of deuterium-labeled samples for a wide range of neutron scattering applications. Examples are given that illustrate the use of these samples for each of the main techniques. Perspectives for biological deuterium labeling are discussed in relation to developments at current facilities and those that are planned in the future.

  15. Physical and biological factors determining the effective proton range

    Energy Technology Data Exchange (ETDEWEB)

    Grün, Rebecca [Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt 64291 (Germany); Institute of Medical Physics and Radiation Protection, University of Applied Sciences Gießen, Gießen 35390 (Germany); Medical Faculty of Philipps-University Marburg, Marburg 35032 (Germany); Friedrich, Thomas; Krämer, Michael; Scholz, Michael [Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt 64291 (Germany); Zink, Klemens [Institute of Medical Physics and Radiation Protection, University of Applied Sciences Gießen, Gießen 35390, Germany and Department of Radiotherapy and Radiation Oncology, University Medical Center Giessen and Marburg, Marburg 35043 (Germany); Durante, Marco [Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt 64291, Germany and Department of Condensed Matter Physics, Darmstadt University of Technology, Darmstadt 64289 (Germany); Engenhart-Cabillic, Rita [Medical Faculty of Philipps-University Marburg, Marburg 35032, Germany and Department of Radiotherapy and Radiation Oncology, University Medical Center Giessen and Marburg, Marburg 35043 (Germany)

    2013-11-15

    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.

  16. 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.

  17. Synthesis, structure and biological properties of active spirohydantoin derivatives

    Directory of Open Access Journals (Sweden)

    Lazić Anita M.

    2016-01-01

    Full Text Available Spirohidantoins represent an pharmacologically important class of heterocycles since many derivatives have been recognized that display interesting activities against a wide range of biological targets. First synthesis of cycloalkanespiro-5-hydantoins was performed by Bucherer and Lieb 1934 by the reaction of cycloalkanone, potassium cyanide and ammonium-carbonate at reflux in a mixture of ethanol and water. QSAR (Quantitative Structure-Activity Relationship studies showed that a wide range of biological activities of spirohydantoin derivatives strongly depend upon their structure. This paper describes different methods of synthesis of spirohydantoin derivatives, their physico-chemical properties and biological activity. It emphasizes the importance of cycloalkanespiro-5-hydantoins with anticonvulsant, antiproliferative, antipsychotic, antimicrobial and antiinflammatory properties as well as their importance in the treatment of diabetes. Numerous spirohydantoin compounds exhibit physiological activity such as serotonin and fibrinogen antagonist, inhibitors of the glycine binding site of the NMDA receptor also, antagonist of leukocyte cell adhesion, acting as allosteric inhibitors of the protein-protein interactions. Some spirohydantoin derivatives have been identified as antitumor agents. Their activity depends on the substituent presented at position N-3 of the hydantoin ring and increases in order alkene > ester > ether. Besides that, compounds that contain two electron withdrawing groups (e.g. fluorine or chlorine on the third and fourth position of the phenyl ring are better antitumor agents than compounds with a single electron withdrawing group. [Projekat Ministarstva nauke Republike Srbije, br. 172013

  18. High Resolution Powder Diffraction and Structure Determination

    Energy Technology Data Exchange (ETDEWEB)

    Cox, D. E.

    1999-04-23

    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

  19. Image-based surface matching algorithm oriented to structural biology.

    Science.gov (United States)

    Merelli, Ivan; Cozzi, Paolo; D'Agostino, Daniele; Clematis, Andrea; Milanesi, Luciano

    2011-01-01

    Emerging technologies for structure matching based on surface descriptions have demonstrated their effectiveness in many research fields. In particular, they can be successfully applied to in silico studies of structural biology. Protein activities, in fact, are related to the external characteristics of these macromolecules and the ability to match surfaces can be important to infer information about their possible functions and interactions. In this work, we present a surface-matching algorithm, based on encoding the outer morphology of proteins in images of local description, which allows us to establish point-to-point correlations among macromolecular surfaces using image-processing functions. Discarding methods relying on biological analysis of atomic structures and expensive computational approaches based on energetic studies, this algorithm can successfully be used for macromolecular recognition by employing local surface features. Results demonstrate that the proposed algorithm can be employed both to identify surface similarities in context of macromolecular functional analysis and to screen possible protein interactions to predict pairing capability. PMID:21566253

  20. Use of reverse micelles in membrane protein structural biology

    Energy Technology Data Exchange (ETDEWEB)

    Van Horn, Wade D. [Vanderbilt University School of Medicine, Department of Biochemistry and Center for Structural Biology (United States); Ogilvie, Mark E.; Flynn, Peter F. [University of Utah, Department of Chemistry (United States)], E-mail: peter.flynn@utah.edu

    2008-03-15

    Membrane protein structural biology is a rapidly developing field with fundamental importance for elucidating key biological and biophysical processes including signal transduction, intercellular communication, and cellular transport. In addition to the intrinsic interest in this area of research, structural studies of membrane proteins have direct significance on the development of therapeutics that impact human health in diverse and important ways. In this article we demonstrate the potential of investigating the structure of membrane proteins using the reverse micelle forming surfactant dioctyl sulfosuccinate (AOT) in application to the prototypical model ion channel gramicidin A. Reverse micelles are surfactant based nanoparticles which have been employed to investigate fundamental physical properties of biomolecules. The results of this solution NMR based study indicate that the AOT reverse micelle system is capable of refolding and stabilizing relatively high concentrations of the native conformation of gramicidin A. Importantly, pulsed-field-gradient NMR diffusion and NOESY experiments reveal stable gramicidin A homodimer interactions that bridge reverse micelle particles. The spectroscopic benefit of reverse micelle-membrane protein solubilization is also explored, and significant enhancement over commonly used micelle based mimetic systems is demonstrated. These results establish the effectiveness of reverse micelle based studies of membrane proteins, and illustrate that membrane proteins solubilized by reverse micelles are compatible with high resolution solution NMR techniques.

  1. Biological insights from topology independent comparison of protein 3D structures.

    Science.gov (United States)

    Nguyen, Minh N; Madhusudhan, M S

    2011-08-01

    Comparing and classifying the three-dimensional (3D) structures of proteins is of crucial importance to molecular biology, from helping to determine the function of a protein to determining its evolutionary relationships. Traditionally, 3D structures are classified into groups of families that closely resemble the grouping according to their primary sequence. However, significant structural similarities exist at multiple levels between proteins that belong to these different structural families. In this study, we propose a new algorithm, CLICK, to capture such similarities. The method optimally superimposes a pair of protein structures independent of topology. Amino acid residues are represented by the Cartesian coordinates of a representative point (usually the C(α) atom), side chain solvent accessibility, and secondary structure. Structural comparison is effected by matching cliques of points. CLICK was extensively benchmarked for alignment accuracy on four different sets: (i) 9537 pair-wise alignments between two structures with the same topology; (ii) 64 alignments from set (i) that were considered to constitute difficult alignment cases; (iii) 199 pair-wise alignments between proteins with similar structure but different topology; and (iv) 1275 pair-wise alignments of RNA structures. The accuracy of CLICK alignments was measured by the average structure overlap score and compared with other alignment methods, including HOMSTRAD, MUSTANG, Geometric Hashing, SALIGN, DALI, GANGSTA(+), FATCAT, ARTS and SARA. On average, CLICK produces pair-wise alignments that are either comparable or statistically significantly more accurate than all of these other methods. We have used CLICK to uncover relationships between (previously) unrelated proteins. These new biological insights include: (i) detecting hinge regions in proteins where domain or sub-domains show flexibility; (ii) discovering similar small molecule binding sites from proteins of different folds and (iii

  2. Determinants of Capital Structure in Nigeria

    Directory of Open Access Journals (Sweden)

    Oladele John AKINYOMI

    2013-08-01

    Full Text Available Capital structure represents one of the most discussed concepts in financial management. Capital structure refers to how a company finances its operations whether through shareholders equity-fund or debt or a combination of both. Various internal and external factors contribute to the choice of these sources of fund. The external factors include factors such as tax policy, capital market conditions and tax policy, among others. Meanwhile, the internal factors are those that relate to individual firm characteristics. This study examines the determinants of capital structure in Nigeria using the descriptive research design. The population comprised of the eighty-six manufacturing firms that are listed in the Nigerian Stock Exchange. The sample firms were selected using the simple random sampling method. Secondary data obtained from the annual accounts of 24 randomly selected manufacturing firms for 10 years period culminating in 240 firm-year observations. The results of the regression analysis revealed that leverage (a measure of capital structure has a negative relationship with firm size and tax on one hand and a positive relationship with tangibility of assets, profitability and growth on the other hand. However, only with tangibility of assets and firm size that significant relationship is established. It is recommended for future researchers to carry out similar studies in multiple sectors.

  3. 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

  4. Computer structures perspective on switching dynamics of simple biological systems

    OpenAIRE

    Moškon, Miha

    2012-01-01

    Synthetic biology is a rapidly evolving discipline that copes with the modifications of existent and with the construction of new biological systems with novel functionalities. Its interdisciplinarity arises from combining of engineering and biological sciences. Biological computing is a relatively new research field that is analyzing the possibilities of constructing a biological computer. Synthetic biology approaches can also be used in order to build biological computer. Certain levels of ...

  5. 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; 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 Dat

  6. 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.

  7. Similarities Between Biological and Social Networks in Their Structural Organization

    Science.gov (United States)

    Kahng, Byungnam; Lee, Deokjae; Kim, Pureun

    A branching tree is a tree that is generated through a multiplicative branching process starting from a root. A critical branching tree is a branching tree in which the mean branching number of each node is 1, so that the number of offspring neither decays to zero nor flourishes as the branching process goes on. Moreover, a scale-free branching tree is a branching tree in which the number of offspring is heterogeneous, and its distribution follows a power law. Here we examine three structures, two from biology (a phylogenetic tree and the skeletons of a yeast protein interaction network) and one from social science (a coauthorship network), and find that all these structures are scale-free critical branching trees. This suggests that evolutionary processes in such systems take place in bursts and in a self-organized manner.

  8. Exploiting Microbeams for Membrane Protein Structure Determination.

    Science.gov (United States)

    Warren, Anna J; Axford, Danny; Paterson, Neil G; Owen, Robin L

    2016-01-01

    A reproducible, and sample independent means of predictably obtaining large, well-ordered crystals has proven elusive in macromolecular crystallography. In the structure determination pipeline, crystallisation often proves to be a rate-limiting step, and the process of obtaining even small or badly ordered crystals can prove time-consuming and laborious. This is particularly true in the field of membrane protein crystallography and this is reflected in the limited number of unique membrane protein structures deposited in the protein data bank (less than 650 by June 2016 - http://blanco.biomol.uci.edu/mpstruc ). Over recent years the requirement for, and time and cost associated with obtaining, large crystals has been partially alleviated through the development of beamline instrumentation allowing data collection, and structure solution, from ever-smaller crystals. Advances in several areas have led to a step change in what might be considered achievable during a synchrotron trip over the last decade. This chapter will briefly review the current status of the field, the tools available to ease data collection and processing, and give some examples of exploitation of these for membrane protein microfocus macromolecular crystallography. PMID:27553238

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

    Energy Technology Data Exchange (ETDEWEB)

    Sakabe, N. [Tsukuba Univ., Ibaraki (Japan). Inst. of Applied Biochemistry

    1996-12-31

    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)

  10. 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....... Conclusions: The predictive power of n-oxPTH and iPTH on the mortality of hemodialysis patients differs substantially. Measurements of n-oxPTH may reflect the hormone status more precisely. The iPTH-associated mortality is most likely describing oxidative stress-related mortality....

  11. Mass spectrometric determination of early and advanced glycation in biology.

    Science.gov (United States)

    Rabbani, Naila; Ashour, Amal; Thornalley, Paul J

    2016-08-01

    Protein glycation in biological systems occurs predominantly on lysine, arginine and N-terminal residues of proteins. Major quantitative glycation adducts are found at mean extents of modification of 1-5 mol percent of proteins. These are glucose-derived fructosamine on lysine and N-terminal residues of proteins, methylglyoxal-derived hydroimidazolone on arginine residues and N(ε)-carboxymethyl-lysine residues mainly formed by the oxidative degradation of fructosamine. Total glycation adducts of different types are quantified by stable isotopic dilution analysis liquid chromatography-tandem mass spectrometry (LC-MS/MS) in multiple reaction monitoring mode. Metabolism of glycated proteins is followed by LC-MS/MS of glycation free adducts as minor components of the amino acid metabolome. Glycated proteins and sites of modification within them - amino acid residues modified by the glycating agent moiety - are identified and quantified by label-free and stable isotope labelling with amino acids in cell culture (SILAC) high resolution mass spectrometry. Sites of glycation by glucose and methylglyoxal in selected proteins are listed. Key issues in applying proteomics techniques to analysis of glycated proteins are: (i) avoiding compromise of analysis by formation, loss and relocation of glycation adducts in pre-analytic processing; (ii) specificity of immunoaffinity enrichment procedures, (iii) maximizing protein sequence coverage in mass spectrometric analysis for detection of glycation sites, and (iv) development of bioinformatics tools for prediction of protein glycation sites. Protein glycation studies have important applications in biology, ageing and translational medicine - particularly on studies of obesity, diabetes, cardiovascular disease, renal failure, neurological disorders and cancer. Mass spectrometric analysis of glycated proteins has yet to find widespread use clinically. Future use in health screening, disease diagnosis and therapeutic monitoring, and

  12. 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, C...

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

    International Nuclear Information System (INIS)

    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 F3 (Th), coupled to Makrofol detectors, were irradiated in the core of a research reactor, IEA-R1 (IPEN). (author)

  14. Energy and time determine scaling in biological and computer designs.

    Science.gov (United States)

    Moses, Melanie; Bezerra, George; Edwards, Benjamin; Brown, James; Forrest, Stephanie

    2016-08-19

    Metabolic rate in animals and power consumption in computers are analogous quantities that scale similarly with size. We analyse vascular systems of mammals and on-chip networks of microprocessors, where natural selection and human engineering, respectively, have produced systems that minimize both energy dissipation and delivery times. Using a simple network model that simultaneously minimizes energy and time, our analysis explains empirically observed trends in the scaling of metabolic rate in mammals and power consumption and performance in microprocessors across several orders of magnitude in size. Just as the evolutionary transitions from unicellular to multicellular animals in biology are associated with shifts in metabolic scaling, our model suggests that the scaling of power and performance will change as computer designs transition to decentralized multi-core and distributed cyber-physical systems. More generally, a single energy-time minimization principle may govern the design of many complex systems that process energy, materials and information.This article is part of the themed issue 'The major synthetic evolutionary transitions'. PMID:27431524

  15. 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 ...

  16. Crystal structure determination of Jatrorrhizine chloride

    Institute of Scientific and Technical Information of China (English)

    LEI XianRong; YANG JianHua; LIN Xiang; DAI Qin; CHENG Qiang; GUO LingHong; LI Hui

    2009-01-01

    Optimum resolution data of powder X-ray diffraction (PXRD) for Jatrorrhizine (Jat) were collected by an X' Pert Pro MPD diffractometer with an X'celerator detector under the stepwise scanning condition as 8.255 ms and 0.00836°per step,2θrange of 50°-80° and total scanning period of 8-10 min. Indexing of the crystal system and a search of the space group from the powder X-ray diffraction data were conducted by the computational crystallography method. The pilot crystal models of Jat were globally optimized with Monte Carlo method and then refined with the Rietveld method. In parallel with PXRD test,single crystals of Jat were cultured in an aqueous solution by a slow-decreasing temperature method,then its crystal structure was determined by single crystal X-ray diffraction (SCXRD). Both crystal structures from PXRD and SCXRD are identical. The results show that the crystal structure of Jat belongs to a monoclinic system and the space group P21/c. The parameters of cell dimensions from PXRD are a=7.69(A),b= 12.55(A),c=20.89(A),β=106.53°,Z=4,and V=1933.4(A)3,meanwhile the parameters from SCXRD are a=7.72(A),b=12.61(A),c=20.99(A),β=106.38°,Z=4,and V=1961.3(A)3.

  17. Logical Reduction of Biological Networks to Their Most Determinative Components.

    Science.gov (United States)

    Matache, Mihaela T; Matache, Valentin

    2016-07-01

    Boolean networks have been widely used as models for gene regulatory networks, signal transduction networks, or neural networks, among many others. One of the main difficulties in analyzing the dynamics of a Boolean network and its sensitivity to perturbations or mutations is the fact that it grows exponentially with the number of nodes. Therefore, various approaches for simplifying the computations and reducing the network to a subset of relevant nodes have been proposed in the past few years. We consider a recently introduced method for reducing a Boolean network to its most determinative nodes that yield the highest information gain. The determinative power of a node is obtained by a summation of all mutual information quantities over all nodes having the chosen node as a common input, thus representing a measure of information gain obtained by the knowledge of the node under consideration. The determinative power of nodes has been considered in the literature under the assumption that the inputs are independent in which case one can use the Bahadur orthonormal basis. In this article, we relax that assumption and use a standard orthonormal basis instead. We use techniques of Hilbert space operators and harmonic analysis to generate formulas for the sensitivity to perturbations of nodes, quantified by the notions of influence, average sensitivity, and strength. Since we work on finite-dimensional spaces, our formulas and estimates can be and are formulated in plain matrix algebra terminology. We analyze the determinative power of nodes for a Boolean model of a signal transduction network of a generic fibroblast cell. We also show the similarities and differences induced by the alternative complete orthonormal basis used. Among the similarities, we mention the fact that the knowledge of the states of the most determinative nodes reduces the entropy or uncertainty of the overall network significantly. In a special case, we obtain a stronger result than in previous

  18. Strategies for structuring interdisciplinary education in Systems Biology

    DEFF Research Database (Denmark)

    Cvijovic, Marija; Höfer, Thomas; Aćimović, Jure;

    2016-01-01

    Systems Biology is an approach to biology and medicine that has the potential to lead to a better understanding of how biological properties emerge from the interaction of genes, proteins, molecules, cells and organisms. The approach aims at elucidating how these interactions govern biological fu...

  19. Determination of Alkali Ions in Biological and Environmental Samples.

    Science.gov (United States)

    Hauser, Peter C

    2016-01-01

    An overview of the common methods for the determination of the alkali metals is given. These are drawn from all of the three principle branches of quantitative analysis and consist mainly of optical atomic spectrometric methods, ion-selective electrodes, and the separation methods of ion-chromatography and capillary electrophoresis. Their main characteristics and performance parameters are discussed. Important specific applications are also examined, namely clinical analysis, single cell analysis, the analysis of soil samples and hydroponic nutrient solutions, as well as the detection of the radioactive (137)Cs isotope. PMID:26860298

  20. 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.

  1. 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.

  2. 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”.

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

    Directory of Open Access Journals (Sweden)

    Rajagopal Appavu

    2016-03-01

    Full Text Available 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

    International Nuclear Information System (INIS)

    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. Data acquisition and analysis at the Structural Biology Center

    International Nuclear Information System (INIS)

    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

  6. Structure, Function, and Biology of the Enterococcus faecalis Cytolysin

    Directory of Open Access Journals (Sweden)

    Daria Van Tyne

    2013-04-01

    Full Text Available Enterococcus faecalis is a Gram-positive commensal member of the gut microbiota of a wide range of organisms. With the advent of antibiotic therapy, it has emerged as a multidrug resistant, hospital-acquired pathogen. Highly virulent strains of E. faecalis express a pore-forming exotoxin, called cytolysin, which lyses both bacterial and eukaryotic cells in response to quorum signals. Originally described in the 1930s, the cytolysin is a member of a large class of lanthionine-containing bacteriocins produced by Gram-positive bacteria. While the cytolysin shares some core features with other lantibiotics, it possesses unique characteristics as well. The current understanding of cytolysin biosynthesis, structure/function relationships, and contribution to the biology of E. faecalis are reviewed, and opportunities for using emerging technologies to advance this understanding are discussed.

  7. Adult Learning Open University Determinants study (ALOUD): Biological lifestyle factors associated with study success

    NARCIS (Netherlands)

    Gijselaers, Jérôme; De Groot, Renate; Kirschner, Paul A.

    2012-01-01

    Gijselaers, H. J. M., De Groot, R. H. M., & Kirschner, P. A. (2012, 7 November). Adult Learning Open University Determinants study (ALOUD): Biological lifestyle factors associated with study success. Poster presentation at the International ICO Fall School, Girona, Spain.

  8. 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…

  9. Determining structure and function in nanomaterial biocomposites

    Science.gov (United States)

    Griffin, David M.

    Polymeric biomaterials represent the leading technologies available today for the repair of tissue damage and for targeted drug delivery. Perhaps the most valuable aspect of polymer-based systems is the extent to which their physical properties (e.g. elasticity, porosity, etc.) can be controlled and tuned by regulating experimental parameters during their synthesis. Biomaterial performance can be improved further still by including supplementary components resulting in a composite material. Synergetic interactions between the constituents of composite materials often results in bulk physical properties that are substantially more than the sum of individual parts. Through understanding and exploiting these sympathetic relationships, novel biocomposites can be developed which exhibit improved efficacy and biocompatibility. Here we report on the synthesis strategies and characterization of novel biocomposites from our laboratory. We look specifically at hydrogel composites containing a physically-associated network of PluronicRTM block copolymer along with a calcium-phosphate mineral component. Rheological results show that composites containing an in situ deposited mineral exhibit a significantly higher elastic modulus than composites of similar composition formed by conventional means. Moreover, analysis of the calcium-phosphate phase of in situ composites revealed that system parameters such as acidity play an integral role in determining the size and stability of the resultant mineral and subsequently the materials' expected in vivo performance. Changes to the structure in PluronicRTM/calcium-phosphate composite hydrogels during dehydration was investigated to provide a look into the mechanisms involved in composite formation. Small angle X-ray scattering analysis of these systems shows that hydrogen bonding interactions between phosphate ions and the polyethylene oxide (PEO) polymer block significantly impact the nanoscale structure and long-range order contained

  10. Structural and biological properties of carbon nanotube composite films

    Energy Technology Data Exchange (ETDEWEB)

    Narayan, Roger J. [School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0245 (United States)]. E-mail: roger.narayan@mse.gatech.edu; Berry, C.J. [Environmental Biotechnology Section, Savannah River National Laboratory, Aiken, SC 29808 (United States); Brigmon, R.L. [Environmental Biotechnology Section, Savannah River National Laboratory, Aiken, SC 29808 (United States)

    2005-11-20

    Carbon nanotube composite films have been developed that exhibit unusual structural and biological properties. These novel materials have been created by pulsed laser ablation of graphite and bombardment of nitrogen ions at temperatures between 600 and 700 deg. C. High-resolution transmission electron microscopy and radial distribution function analysis demonstrate that this material consists of sp{sup 2}-bonded concentric ribbons that are wrapped approximately 15 deg. normal to the silicon substrate. The interlayer order in this material extends to approximately 15-30 A. X-ray photoelectron spectroscopy and Raman spectroscopy data suggest that this material is predominantly trigonally coordinated. The carbon nanotube composite structure results from the use of energetic ions, which allow for non-equilibrium growth of graphitic planes. In vitro testing has revealed significant antimicrobial activity of carbon nanotube composite films against Staphylococcus aureus and Staphylococcus warneri colonization. Carbon nanotube composite films may be useful for inhibiting microorganism attachment and biofilm formation in hemodialysis catheters and other medical devices.

  11. 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.

  12. 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.

  13. STUDIES OF RELATIONSHIPS BETWEEN MOLECULAR STRUCTURE AND BIOLOGICAL ACTIVITY BY PATTERN RECOGNITION METHODS

    Science.gov (United States)

    The attempt to rationalize the connections between the molecular structures of organic compounds and their biological activities comprises the field of structure-activity relations (SAR) studies. Correlations between structure and activity are important for the understanding and ...

  14. OpenStructure: an integrated software framework for computational structural biology

    Science.gov (United States)

    Biasini, M.; Schmidt, T.; Bienert, S.; Mariani, V.; Studer, G.; Haas, J.; Johner, N.; Schenk, A. D.; Philippsen, A.; Schwede, T.

    2013-01-01

    Research projects in structural biology increasingly rely on combinations of heterogeneous sources of information, e.g. evolutionary information from multiple sequence alignments, experimental evidence in the form of density maps and proximity constraints from proteomics experiments. The OpenStructure software framework, which allows the seamless integration of information of different origin, has previously been introduced. The software consists of C++ libraries which are fully accessible from the Python programming language. Additionally, the framework provides a sophisticated graphics module that interactively displays molecular structures and density maps in three dimensions. In this work, the latest developments in the OpenStructure framework are outlined. The extensive capabilities of the framework will be illustrated using short code examples that show how information from molecular-structure coordinates can be combined with sequence data and/or density maps. The framework has been released under the LGPL version 3 license and is available for download from http://www.openstructure.org. PMID:23633579

  15. OpenStructure: an integrated software framework for computational structural biology.

    Science.gov (United States)

    Biasini, M; Schmidt, T; Bienert, S; Mariani, V; Studer, G; Haas, J; Johner, N; Schenk, A D; Philippsen, A; Schwede, T

    2013-05-01

    Research projects in structural biology increasingly rely on combinations of heterogeneous sources of information, e.g. evolutionary information from multiple sequence alignments, experimental evidence in the form of density maps and proximity constraints from proteomics experiments. The OpenStructure software framework, which allows the seamless integration of information of different origin, has previously been introduced. The software consists of C++ libraries which are fully accessible from the Python programming language. Additionally, the framework provides a sophisticated graphics module that interactively displays molecular structures and density maps in three dimensions. In this work, the latest developments in the OpenStructure framework are outlined. The extensive capabilities of the framework will be illustrated using short code examples that show how information from molecular-structure coordinates can be combined with sequence data and/or density maps. The framework has been released under the LGPL version 3 license and is available for download from http://www.openstructure.org.

  16. 78 FR 55326 - Determinations Regarding Use of Chemical Weapons in Syria Under the Chemical and Biological...

    Science.gov (United States)

    2013-09-10

    ... Determinations Regarding Use of Chemical Weapons in Syria Under the Chemical and Biological Weapons Control and..., 22 U.S.C. 5604(a), that the Government of Syria has used chemical weapons in violation of... Under Secretary of State for Political Affairs: (1) Determined that the Government of Syria has...

  17. 9 CFR 113.29 - Determination of moisture content in desiccated biological products.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Determination of moisture content in desiccated biological products. 113.29 Section 113.29 Animals and Animal Products ANIMAL AND PLANT HEALTH... VECTORS STANDARD REQUIREMENTS Standard Procedures § 113.29 Determination of moisture content in...

  18. Labelling of biological structures with technetium 99 m

    International Nuclear Information System (INIS)

    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)

  19. Structural Determinants of Juvenile Offenses in School.

    Science.gov (United States)

    Kowalski, Gregory S.; And Others

    1983-01-01

    Using multiple regression techniques, evaluates the relative contributions of community structure, school structure, and crime prevention efforts to delinquency in public schools. Finds that distance from central business district, school size, and region are of predictive value, when crimes against persons, property, and perceived crime are…

  20. The Most Important Concept of Transport and Circulatory Systems: Turkish Biology Student Teachers' Cognitive Structure

    Science.gov (United States)

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

    2013-01-01

    The purpose of this study is to determine biology student teachers' cognitive structure with regard to "Blood". Qualitative research method has been used. The free word association test and the draw-write technique have been used in collection of data. The data obtained have been evaluated and divided into categories based on…

  1. Solid state structures of cadmium complexes with relevance for biological systems.

    Science.gov (United States)

    Carballo, Rosa; Castiñeiras, Alfonso; Domínguez-Martín, Alicia; García-Santos, Isabel; Niclós-Gutiérrez, Juan

    2013-01-01

    This chapter provides a review of the literature on structural information from crystal structures determined by X-ray diffractometry of cadmium(II) complexes containing ligands of potential biological interest. These ligands fall into three broad classes, (i) those containing N-donors such as purine or pyrimidine bases and derivatives of adenine, guanine or cytosine, (ii) those containing carboxylate groups such as α-amino acids, in particular the twenty essential ones, the water soluble vitamins (B-complex) or the polycarboxylates of EDTA type ligands, and (iii) S-donors such as thiols/thiolates or dithiocarbamates. A crystal and molecular structural analysis has been carried out for some representative complexes of these ligands, specifically addressing the coordination mode of ligands, the coordination environment of cadmium and, in some significant cases, the intermolecular interactions. PMID:23430774

  2. WAY TO DETERMINE STIFFNESS FUNCTION OF STRUCTURE

    Institute of Scientific and Technical Information of China (English)

    WANG De-ming; GAI Bing-zheng

    2005-01-01

    For calculating the stiffness function of a structure, the differential equation of the vibration of the structure was divided into the differential equation on the original stiffness function that was known, and Fredholm integral equation of the first kind on the undetermined stiffness function that was unknown. And the stable solutions of the integral equation, when the smooth factor was equal to zero, was solved by the extrapolation with p smooth factors. So the stiffness function of the structure is obtained. Applied examples show that the method is feasible and effective.

  3. Determining crystal structures through crowdsourcing and coursework

    Science.gov (United States)

    2016-09-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

  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. Modelling and interpreting biologically crusted dryland soil sub-surface structure using automated micropenetrometry

    Science.gov (United States)

    Hoon, Stephen R.; Felde, Vincent J. M. N. L.; Drahorad, Sylvie L.; Felix-Henningsen, Peter

    2015-04-01

    Soil penetrometers are used routinely to determine the shear strength of soils and deformable sediments both at the surface and throughout a depth profile in disciplines as diverse as soil science, agriculture, geoengineering and alpine avalanche-safety (e.g. Grunwald et al. 2001, Van Herwijnen et al. 2009). Generically, penetrometers comprise two principal components: An advancing probe, and a transducer; the latter to measure the pressure or force required to cause the probe to penetrate or advance through the soil or sediment. The force transducer employed to determine the pressure can range, for example, from a simple mechanical spring gauge to an automatically data-logged electronic transducer. Automated computer control of the penetrometer step size and probe advance rate enables precise measurements to be made down to a resolution of 10's of microns, (e.g. the automated electronic micropenetrometer (EMP) described by Drahorad 2012). Here we discuss the determination, modelling and interpretation of biologically crusted dryland soil sub-surface structures using automated micropenetrometry. We outline a model enabling the interpretation of depth dependent penetration resistance (PR) profiles and their spatial differentials using the model equations, σ {}(z) ={}σ c0{}+Σ 1n[σ n{}(z){}+anz + bnz2] and dσ /dz = Σ 1n[dσ n(z) /dz{} {}+{}Frn(z)] where σ c0 and σ n are the plastic deformation stresses for the surface and nth soil structure (e.g. soil crust, layer, horizon or void) respectively, and Frn(z)dz is the frictional work done per unit volume by sliding the penetrometer rod an incremental distance, dz, through the nth layer. Both σ n(z) and Frn(z) are related to soil structure. They determine the form of σ {}(z){} measured by the EMP transducer. The model enables pores (regions of zero deformation stress) to be distinguished from changes in layer structure or probe friction. We have applied this method to both artificial calibration soils in the

  6. The structure, occurrence and biological activity of ellagitannins: a general review

    Directory of Open Access Journals (Sweden)

    Lidia Lipińska

    2014-09-01

    Full Text Available The present paper deals with the structure, occurrence and biological activity of ellagitannins. Ellagitannins belong to the class of hydrolysable tannins, they are esters of hexahydroxydiphenoic acid and monosaccharide (most commonly glucose. Ellagitannins are slowly hydrolysed in the digestive tract, releasing the ellagic acid molecule. Their chemical structure determines physical and chemical properties and biological activity. Ellagitannins occur naturally in some fruits (pomegranate, strawberry, blackberry, raspberry, nuts (walnuts, almonds, and seeds. They form a diverse group of bioactive polyphenols with anti-infl ammatory, anticancer, antioxidant and antimicrobial (antibacterial, antifungal and antiviral activity. Furthermore, they improve the health of blood vessels. The paper discusses the metabolism and bioavailability of ellagitannins and ellagic acid. Ellagitannins are metabolized in the gastrointestinal tract by intestinal microbiota. They are stable in the stomach and undergo neither hydrolysis to free ellagic acid nor degradation. In turn, ellagic acid can be absorbed in the stomach. This paper shows the role of cancer cell lines in the studies of ellagitannins and ellagic acid metabolism. The biological activity of these compounds is broad and thus the focus is on their antimicrobial, anti-inflammatory and antitumor properties. Ellagitannins exhibit antimicrobial activity against fungi, viruses, and importantly, bacteria, including antibiotic-resistant strains such as methicillinresistant Staphylococcus aureus.

  7. 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

    2016-01-01

    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. PMID:27070998

  8. Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology.

    Science.gov (United States)

    Belsom, Adam; Schneider, Michael; Fischer, Lutz; Brock, Oliver; Rappsilber, Juri

    2016-03-01

    Chemical cross-linking combined with mass spectrometry has proven useful for studying protein-protein interactions and protein structure, however the low density of cross-link data has so far precluded its use in determining structures de novo. Cross-linking density has been typically limited by the chemical selectivity of the standard cross-linking reagents that are commonly used for protein cross-linking. We have implemented the use of a heterobifunctional cross-linking reagent, sulfosuccinimidyl 4,4'-azipentanoate (sulfo-SDA), combining a traditional sulfo-N-hydroxysuccinimide (sulfo-NHS) ester and a UV photoactivatable diazirine group. This diazirine yields a highly reactive and promiscuous carbene species, the net result being a greatly increased number of cross-links compared with homobifunctional, NHS-based cross-linkers. We present a novel methodology that combines the use of this high density photo-cross-linking data with conformational space search to investigate the structure of human serum albumin domains, from purified samples, and in its native environment, human blood serum. Our approach is able to determine human serum albumin domain structures with good accuracy: root-mean-square deviation to crystal structure are 2.8/5.6/2.9 Å (purified samples) and 4.5/5.9/4.8Å (serum samples) for domains A/B/C for the first selected structure; 2.5/4.9/2.9 Å (purified samples) and 3.5/5.2/3.8 Å (serum samples) for the best out of top five selected structures. Our proof-of-concept study on human serum albumin demonstrates initial potential of our approach for determining the structures of more proteins in the complex biological contexts in which they function and which they may require for correct folding. Data are available via ProteomeXchange with identifier PXD001692.

  9. The structural molecular biology network of the State of São Paulo, Brazil

    Directory of Open Access Journals (Sweden)

    João A.R.G. Barbosa

    2006-06-01

    Full Text Available This article describes the achievements of the Structural Molecular Biology Network (SMolBNet, a collaborative program of structural molecular biology, centered in the State of São Paulo, Brazil, and supported by São Paulo State Funding Agency (FAPESP. It gathers twenty scientific groups and is coordinated by the scientific staff of the Center of Structural Molecular Biology, at the National Laboratory of Synchrotron Light (LNLS, in Campinas. The SMolBNet program has been aimed at 1 solving the structure of proteins of interest related to the research projects of the groups. In some cases, the choice has been to select proteins of unknown function or of possible novel structure obtained from the sequenced genomes of the FAPESP genomic program; 2 providing the groups with training in all the steps of the protein structure determination: gene cloning, protein expression, protein purification, protein crystallization and structure determination. Having begun in 2001, the program has been successful in both aims. Here, four groups reveal their participation in the program and describe the structural aspects of the proteins they have selected to study.Esse artigo descreve realizações do Programa SMolBNet (Rede de Biologia Molecular Estrutural do Estado de São Paulo, apoiado pela FAPESP (Fundação de Apoio à Pesquisa do Estado de São Paulo. Ele reúne vinte grupos de pesquisa e é coordenado pelos pesquisadores do Laboratório Nacional de Luz Síncrotron (LNLS, em Campinas. O Programa SMolBNet tem como metas: Elucidar a estrutura tridimensional de proteínas de interesse aos grupos de pesquisa componentes do Programa; Prover os grupos com treinamento em todas as etapas de determinação de estrutura: clonagem gênica, expressão de proteínas, purificação de proteínas, cristalização de proteínas e elucidação de suas estruturas. Tendo começado em 2001, o Programa alcançou sucesso em ambas as metas. Neste artigo, quatro dos grupos

  10. Automated Structure-Activity Relationship Mining: Connecting Chemical Structure to Biological Profiles.

    Science.gov (United States)

    Wawer, Mathias J; Jaramillo, David E; Dančík, Vlado; Fass, Daniel M; Haggarty, Stephen J; Shamji, Alykhan F; Wagner, Bridget K; Schreiber, Stuart L; Clemons, Paul A

    2014-06-01

    Understanding the structure-activity relationships (SARs) of small molecules is important for developing probes and novel therapeutic agents in chemical biology and drug discovery. Increasingly, multiplexed small-molecule profiling assays allow simultaneous measurement of many biological response parameters for the same compound (e.g., expression levels for many genes or binding constants against many proteins). Although such methods promise to capture SARs with high granularity, few computational methods are available to support SAR analyses of high-dimensional compound activity profiles. Many of these methods are not generally applicable or reduce the activity space to scalar summary statistics before establishing SARs. In this article, we present a versatile computational method that automatically extracts interpretable SAR rules from high-dimensional profiling data. The rules connect chemical structural features of compounds to patterns in their biological activity profiles. We applied our method to data from novel cell-based gene-expression and imaging assays collected on more than 30,000 small molecules. Based on the rules identified for this data set, we prioritized groups of compounds for further study, including a novel set of putative histone deacetylase inhibitors.

  11. 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.

  12. 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, C......-14 and C-3) tautomeric equilibrium is at hand below pH 5. At pH 7.4 it exists as a mono anion. In case of tetracycline equilibrium between a zwitter ion and a neutral form is found together with an amide functional group and a hydrogen bonded enolic b-diketone system shifted strongly towards one...

  13. Structure-biological activity relationship of synthetic trihydroxilated chalcones

    Directory of Open Access Journals (Sweden)

    Devia Cristina M.

    1998-01-01

    Full Text Available The bacteriostatic activity of 2?,4?,2-trihydroxychalcone; 2?,4?,3-trihydroxychalcone and 2?,4?,4-trihydroxychalcone, prepared by condensation of 2,4-dihydroxyacetophenone and benzaldehyde substituted, against Staphylococcus aureus ATCC 25923 was assayed by agar plate method. The three compounds presented important inhibition halos. In order to elucidate structure-activity relationships, the minimal inhibitory concentrations against S. aureus were determined by the broth dilution method and the results obtained were compared to that of 2',4'-dihydroxychalcone. The sequence observed was: MIC 2?,4?,3-(OH3 > MIC 2?,4?-(OH2 > MIC 2?,4?,4-(OH3 > > MIC 2?,4?,2-(OH3. These results showed that the introduction of an electron donating group (-OH in the aromatic B-ring causes an increase in bioactivity, and that the intensity of action depends on the position of the OH substitute.

  14. 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

  15. Structural biology of human H3K9 methyltransferases.

    Directory of Open Access Journals (Sweden)

    Hong Wu

    Full Text Available UNLABELLED: SET domain methyltransferases deposit methyl marks on specific histone tail lysine residues and play a major role in epigenetic regulation of gene transcription. We solved the structures of the catalytic domains of GLP, G9a, Suv39H2 and PRDM2, four of the eight known human H3K9 methyltransferases in their apo conformation or in complex with the methyl donating cofactor, and peptide substrates. We analyzed the structural determinants for methylation state specificity, and designed a G9a mutant able to tri-methylate H3K9. We show that the I-SET domain acts as a rigid docking platform, while induced-fit of the Post-SET domain is necessary to achieve a catalytically competent conformation. We also propose a model where long-range electrostatics bring enzyme and histone substrate together, while the presence of an arginine upstream of the target lysine is critical for binding and specificity. ENHANCED VERSION: This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

  16. Determinants of the detrital arthropod community structure

    DEFF Research Database (Denmark)

    Lessard, J.P.; Sackett, Tara E.; Reynolds, William N.;

    2011-01-01

    Understanding the factors that shape community structure, and whether those factors vary geographically, has a long history in ecology. Because the abiotic environment often varies in predictable ways along elevational gradients, montane systems are ideal to study geographic variation in the dete...

  17. Determining the structure of Carbon-60

    International Nuclear Information System (INIS)

    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 bubble-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)

  18. Modelling the structure and dynamics of biological pathways

    OpenAIRE

    O'Hara, Laura; Livigni, Alessandra; Theocharidis, Thanos; Boyer, Benjamin; Angus, Tim; Wright, Derek; Chen, Sz-Hau; Raza, Sobia; Barnett, Mark; Digard, Paul; Smith, Lee; Freeman, Thomas

    2016-01-01

    There is a need for formalised diagrams that both summarise current biological pathway knowledge and support modelling approaches that explain and predict their behaviour. Here we present a new, freely-available modelling framework that includes: a biologist-friendly pathway modelling language (mEPN); a simple but sophisticated method to support model parameterisation using accessible biological information, a stochastic flow algorithm that simulates the dynamics of pathway activity, and a 3D...

  19. 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. PMID:1861610

  20. What Determines the Likelihood of Structural Reforms?

    OpenAIRE

    Agnello, Luca; Castro, Vitor; Jalles, João Tovar; Sousa, Ricardo M.

    2014-01-01

    We use data for a panel of 60 countries over the period 1980-2005 to investigate the main drivers of the likelihood of structural reforms. We find that: (i) external debt crises are the main trigger of financial and banking reforms; (ii) inflation and banking crises are the key drivers of external capital account reforms; (iii) banking crises also hasten financial reforms; and (iv) economic recessions play an important role in promoting the necessary consensus for financial, capital, banking ...

  1. Structure and determinants of consumer expenditures

    OpenAIRE

    Stejskal, Ladislav; Stávková, Jana

    2011-01-01

    The local and worldwide present economic situation is often judged and discussed on the basis of the consumer expenditures development. Consumer expenditures or a buying behaviour outcome of each individual market subject is in marketing defined as a product and service seeking, from that consumers expect satisfying of their needs. On the basis of the introduced determination authors conducted a marketing research. Results in combination with a marketing insight into consumer expenditures rea...

  2. Synthesis, Crystal Structure and Biological Activites of Rotenone O-Alkyl Oximes

    Institute of Scientific and Technical Information of China (English)

    CHEN Xiao-dong; WANG Chao; HU Ai-xi; YE Jiao; ZHANG Cui-yang

    2012-01-01

    A series of rotenone O-alkyl oxime derivatives was designed and synthesized.Their structures were confirmed by elemental analyses,Fourier transform infrared(FTIR) and 1H NMR spectral studies,and the typical crystal structure of rotenone O-ethyl oxime(3b) was determined by X-ray diffraction.The preliminary biological activities of the new compounds were evaluated.The results of bioassays indicate that the title compounds exhibit moderate insecticidal and bactericidal activities.Among the synthesized compounds,compound 3q exhibited 90.0% mortality against M.separata at 1000 μg/mL.Compounds 3b and 3g exhibited both 90.0% inhibition rate against R.solani at 500 μg/mL,respectively.

  3. Teachers' conceptions of biological determinism in five countries: Denmark, Estonia, Finland, France and Italy

    OpenAIRE

    Clément, Pierre, 1809-1870.; Castéra, Jérémy

    2013-01-01

    e-book: http://www.esera.org/media/eBook_2013/strand%2012/Pierre_Clement_09Jan2014.pdf International audience The interaction between the genome and its environment (epigenetics) is a new paradigm in biology. Nevertheless, the notion of genetic determinism is still present in syllabuses and textbooks. What about teachers' conceptions? We analyzed the teachers' conceptions related to the genetic determinism of human performances in five European countries, using 24 questions of the Biohe...

  4. X-ray spectrometric determination of thorium in bone and other biological materials

    International Nuclear Information System (INIS)

    An x-ray spectrometric method has been developed for the determination of thorium in bone and other biological materials. The limit of detection at the 95% confidence level is 20 ng. This corresponds to a concentration of 2 ppb in a 10-g sample of bone ash

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

    International Nuclear Information System (INIS)

    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)

  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. Intracellular biology and virulence determinants of Francisella tularensis revealed by transcriptional profiling inside macrophages

    OpenAIRE

    Wehrly, Tara D.; Chong, Audrey; Virtaneva, Kimmo; Sturdevant, Dan E.; Child, Robert; Edwards, Jessica A.; Brouwer, Dedeke; Nair, Vinod; Fischer, Elizabeth R.; Wicke, Luke; Curda, Alissa J.; Kupko, John J.; Martens, Craig; Crane, Deborah D.; Bosio, Catharine M.

    2009-01-01

    The highly infectious bacterium Francisella tularensis is a facultative intracellular pathogen, whose virulence requires proliferation inside host cells, including macrophages. Here we have performed a global transcriptional profiling of the highly virulent F. tularensis subsp. tularensis Schu S4 strain during its intracellular cycle within primary murine macrophages, to characterize its intracellular biology and identify pathogenic determinants based on their intracellular expression profile...

  8. Sex determination meltdown upon biological control introduction of the parasitoid Cotesia rubecula?

    NARCIS (Netherlands)

    de Boer, Jetske G.; Kuijper, Bram; Heimpel, George E.; Beukeboom, Leo W.

    2012-01-01

    Natural enemies may go through genetic bottlenecks during the process of biological control introductions. Such bottlenecks are expected to be particularly detrimental in parasitoid Hymenoptera that exhibit complementary sex determination (CSD). CSD is associated with a severe form of inbreeding dep

  9. 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.

  10. Development of dispersive anomalous diffraction, application to the study of inorganic modulated structures and biological macromolecules

    International Nuclear Information System (INIS)

    X-ray diffraction has been developed since the beginning of the century for the determination of crystallographic structures. Most complex structures (proteins, incommensurate crystals...) require the use of anomalous diffraction, i.e. the measurement of diffracted intensities at several wavelengths around the absorption edge of one element of the crystal. This technique allows the determination of the phase of the structure factor, as well as the positions of the anomalous atoms. In this thesis, we present the Dispersive Anomalous Diffraction (DAD) method, which allows the simultaneous measure of diffracted intensities at a number of wavelengths for many reflections. Two collection modes can be used, either continuous (DDAFS-Dispersive Diffraction Anomalous Fine Structure) or discrete (SMAD-Simultaneous Multiwavelength Anomalous Diffraction. A specific procedure and a program (DAD) have been developed for the quantitative analysis of dispersive diffraction images. This program also allows the analysis of monochromatic diffraction images, with satellite reflections near main diffraction peaks. We present the first two quantitative experiments in dispersive diffraction for biological compounds. Our results show that the use of SMAD for structure determination is possible, although several improvements are still necessary for both data collection and analysis. An important point in this thesis is the study of quasi-1D compound (TaSe4)2I: this crystal exhibits a Peierls transition, for which no condensation of the metallic atoms was shown for the last 15 years. Our study has characterized the domain structure of this material, and anomalous diffraction has shown in a specific way the tetramerisation of tantalum atoms, which exists along the already-known acoustic modulation. (author)

  11. 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

  12. Photoelectron holography applied to surface structural determination

    Energy Technology Data Exchange (ETDEWEB)

    Petersen, B.L.

    1995-05-01

    Photoemitted electron waves are used as coherent source waves for angstrom-scale holographic imaging of local atomic geometry at surfaces. Electron angular distribution patterns are collected above a sample surface and serve as a record of the interference between source wave and waves scattered from surrounding ion cores. Using a mathematical imaging integral transformation, the three-dimensional structural information is obtained directly from these collected patterns. Patterns measured with different electron kinetic energies are phase-summed for image improvement. Pt (111) surface is used as a model system. A pattern 9.6{angstrom}{sup {minus}1} (351 eV) is used to generate a full 3-D image of atom locations around an emitter with nearest neighbors within 0.l{angstrom} of the expected bulk positions. Atoms several layers beyond the nearest neighbors are also apparent. Twin-image reduction and artifact suppression is obtained by phase-summing eight patterns measured from 8.8 to 10.2{angstrom}{sup {minus}1} (295 to 396 eV). 32 were measured in 0.2{angstrom}{sup {minus}1} steps from 6.0 to 12.2{angstrom}{sup {minus}1} (137 to 567 eV) are presented here. Simple models of two-slit interference are compared with electron scattering to illuminate understanding of holographic recording of the structural information. This also shows why it sometimes fails due to destructive interferences. Simple theoretical models of electron scattering are compared to experiment to show the origin of the structural information and the differences that result from atomic scattering and from the source wave. Experimental parameters and their relation to imaging is discussed. Comparison is made to the Pt pattern measured at 351 eV using the simple theoretical model. The remaining data set is also modeled, and the eight appropriate theoretical patterns are used to regenerate the multiple-wavenumber experimental result. A clean Cu (001) surface is also measured and imaged.

  13. Technical and biological variance structure in mRNA-Seq data: life in the real world

    Directory of Open Access Journals (Sweden)

    Oberg Ann L

    2012-07-01

    Full Text Available Abstract Background mRNA expression data from next generation sequencing platforms is obtained in the form of counts per gene or exon. Counts have classically been assumed to follow a Poisson distribution in which the variance is equal to the mean. The Negative Binomial distribution which allows for over-dispersion, i.e., for the variance to be greater than the mean, is commonly used to model count data as well. Results In mRNA-Seq data from 25 subjects, we found technical variation to generally follow a Poisson distribution as has been reported previously and biological variability was over-dispersed relative to the Poisson model. The mean-variance relationship across all genes was quadratic, in keeping with a Negative Binomial (NB distribution. Over-dispersed Poisson and NB distributional assumptions demonstrated marked improvements in goodness-of-fit (GOF over the standard Poisson model assumptions, but with evidence of over-fitting in some genes. Modeling of experimental effects improved GOF for high variance genes but increased the over-fitting problem. Conclusions These conclusions will guide development of analytical strategies for accurate modeling of variance structure in these data and sample size determination which in turn will aid in the identification of true biological signals that inform our understanding of biological systems.

  14. Structural and institutional determinants of investment activity in Africa

    OpenAIRE

    Chuku, Chuku; Onye, Kenneth; Ajah, Hycent

    2015-01-01

    This paper considers the structural and institutional determinants of investment activity in selected African countries within a neoclassical framework. Generalized method of moments and a family of panel data estimation techniques are utilized in addition to nonparametric kernel regression techniques to uncover the relationship. Three main findings emerge; (i) financial openness and institutional quality are reasonably robust structural and institutional determinants of investment activity...

  15. Simultaneous determination of arsenic and selenium in biological samples by HG-AFS

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Hanwen; Liu, Zhanfeng; Shi, Hongmei [Hebei University, College of Chemistry and Environmental Science, Baoding (China); Wu, Wenjuan [Third Hospital of Hebei Medical University, Department of Radiology, Shijiazhuang 050051 (China); Li, Liqing [Hebei University, College of Chemistry and Environmental Science, Baoding (China); Taishan College, Department of Chemistry, Shan Dong Taian (China)

    2005-06-01

    A new method is proposed for simultaneous determination of traces of arsenic (As) and selenium (Se) in biological samples by hydride-generation double-channel non-dispersive atomic-fluorescence spectrometry (HG-AFS) from tartaric acid media. The effects of analytical conditions on fluorescence signal intensity were investigated and optimized. Interferences from coexisting ions were evaluated. Under optimum conditions linear response ranges above 20 {mu}g L{sup -1} for As and 32 {mu}g L{sup -1} for Se were obtained with detection limits of 0.13 and 0.12 {mu}g L{sup -1}, respectively. The precision for elevenfold determination of As at the 4 {mu}g L{sup -1} level and of Se at the 8 {mu}g L{sup -1} level were 2.7 and 1.9% (RSD), respectively. Recoveries of 92.5-95.5% for As and 101.2-108.4% for Se were obtained for four biological samples and two certified biological reference materials. The proposed method has the advantages of simple operation, high sensitivity, and high efficiency; it was successfully used for simultaneous determination of As and Se in biological samples. (orig.)

  16. A review on determination of steroids in biological samples exploiting nanobio-electroanalytical methods.

    Science.gov (United States)

    Yadav, Saurabh K; Chandra, Pranjal; Goyal, Rajendra N; Shim, Yoon-Bo

    2013-01-31

    The applications of nanomaterial modified sensors, molecularly imprinting polymer based, aptamer based, and immunosensors have been described in the determination of steroids using electroanalytical techniques. After a brief description of the steroids and assays in biological fluids, the principles of electrochemical detection with the advantages and the limitations of the various sensors are presented. The nanomaterial modified sensors catalyze the oxidation/reduction of steroids and are suitable for sensing them in environmental samples and biological fluids. The determination of steroids based on their reduction has been found more useful in comparison to oxidation as the common metabolites present in the biological fluids do not undergo reduction in the usual potential window and hence, do not interfere in the determination. The sensors based on immunosensors and aptamers were found more sensitive and selective for steroid determination. Conducting polymer modified bio-sensors and microchip devices are suggested as possible future prospects for the ultra sensitive and simultaneous determination of steroids and their metabolites in various samples.

  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. PMID:18351053

  18. Determination of uranium in seawater, biological samples and sediments using laser induced fluorescence spectrometry

    International Nuclear Information System (INIS)

    Uranium has been determined in seawater, biological samples and sediments using laser induced fluorescence spectrometry (LIFS). The biological samples and sediments are digested with a mixture of HNO3, HClO4 and HF. The conductivity of the seawater should be below 5.0 mS and the pH of the sample should be in the range 6.5-9.0. The volume of the reagent used to enhance the fluorescence intensity was 0.5 ml. Comparison with other methods was favorable, LIFS being rapid, simple and sensitive, and well suited to environmental monitoring. (author)

  19. Analytical methods for vancomycin determination in biological fluids and in pharmaceuticals

    Directory of Open Access Journals (Sweden)

    Marta Maria Duarte Carvalho Vila

    2007-04-01

    Full Text Available Vancomycin is a glycopeptide antibiotic employed in the treatment of infections caused by certain methicillin-resistant staphylococci. It is indicated also for patients allergic to penicillin or when there is no response to penicillins or cephalosporins. The adequate vancomycin concentration levels in blood serum lies between 5 and 10 mg/L. Higher values are toxic, causing mainly nephrotoxicity and ototoxicity. Various analytical methods are described in the literature: spectrophotometric, immunologic, biologic and chromatographic methods. This paper reviews the main analytical methods for vancomycin determination in biological fluids and in pharmaceutical preparations.

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

    International Nuclear Information System (INIS)

    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 18F, a pure positron emitter which is the product of the photonuclear reaction 19F(γ, n)18F. The simultaneous formation of some additional positron emitters, particularly 45Ti and 34mCl, 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. 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

  2. Polysaccharides of higher fungi: Biological role, structure, and antioxidative activity

    OpenAIRE

    Kozarski Maja S.; Klaus Anita S.; Nikšić Miomir P.; van Griensven Leo J.L.D.; Vrvić Miroslav M.; Jakovljević Dragica M.

    2014-01-01

    Fungal polysaccharides attract a lot of attention due to their multiple challenging biological properties, such as: anti-tumor, anti-viral, anticomplementary, anticoagulant, hypolipidemic and immunomodulatory and immune-stimulatory activities, which all together make them suitable for application in many quite distinctive areas, such as food industry, biomedicine, cosmetology, agriculture, environmental protection and waste water management. This article pr...

  3. 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.

  4. Structural Determinants of Sleeping Beauty Transposase Activity.

    Science.gov (United States)

    Abrusán, György; Yant, Stephen R; Szilágyi, András; Marsh, Joseph A; Mátés, Lajos; Izsvák, Zsuzsanna; Barabás, Orsolya; Ivics, Zoltán

    2016-08-01

    Transposases are important tools in genome engineering, and there is considerable interest in engineering more efficient ones. Here, we seek to understand the factors determining their activity using the Sleeping Beauty transposase. Recent work suggests that protein coevolutionary information can be used to classify groups of physically connected, coevolving residues into elements called "sectors", which have proven useful for understanding the folding, allosteric interactions, and enzymatic activity of proteins. Using extensive mutagenesis data, protein modeling and analysis of folding energies, we show that (i) The Sleeping Beauty transposase contains two sectors, which span across conserved domains, and are enriched in DNA-binding residues, indicating that the DNA binding and endonuclease functions of the transposase coevolve; (ii) Sector residues are highly sensitive to mutations, and most mutations of these residues strongly reduce transposition rate; (iii) Mutations with a strong effect on free energy of folding in the DDE domain of the transposase significantly reduce transposition rate. (iv) Mutations that influence DNA and protein-protein interactions generally reduce transposition rate, although most hyperactive mutants are also located on the protein surface, including residues with protein-protein interactions. This suggests that hyperactivity results from the modification of protein interactions, rather than the stabilization of protein fold.

  5. Structural Determinants of Sleeping Beauty Transposase Activity.

    Science.gov (United States)

    Abrusán, György; Yant, Stephen R; Szilágyi, András; Marsh, Joseph A; Mátés, Lajos; Izsvák, Zsuzsanna; Barabás, Orsolya; Ivics, Zoltán

    2016-08-01

    Transposases are important tools in genome engineering, and there is considerable interest in engineering more efficient ones. Here, we seek to understand the factors determining their activity using the Sleeping Beauty transposase. Recent work suggests that protein coevolutionary information can be used to classify groups of physically connected, coevolving residues into elements called "sectors", which have proven useful for understanding the folding, allosteric interactions, and enzymatic activity of proteins. Using extensive mutagenesis data, protein modeling and analysis of folding energies, we show that (i) The Sleeping Beauty transposase contains two sectors, which span across conserved domains, and are enriched in DNA-binding residues, indicating that the DNA binding and endonuclease functions of the transposase coevolve; (ii) Sector residues are highly sensitive to mutations, and most mutations of these residues strongly reduce transposition rate; (iii) Mutations with a strong effect on free energy of folding in the DDE domain of the transposase significantly reduce transposition rate. (iv) Mutations that influence DNA and protein-protein interactions generally reduce transposition rate, although most hyperactive mutants are also located on the protein surface, including residues with protein-protein interactions. This suggests that hyperactivity results from the modification of protein interactions, rather than the stabilization of protein fold. PMID:27401040

  6. Determination of Ice Characteristics for Marine Hydroengineering Structures

    Energy Technology Data Exchange (ETDEWEB)

    Kantarzhi, I. G., E-mail: kantardgi@yandex.ru [Moscow State University of Civil Engineering (MSGU) (Russian Federation); Maderich, V. S., E-mail: vladmad@gmail.com; Koshebutskii, V. I., E-mail: koshik1@gmail.com [Ukrainian Center of Environmental and Water Projects (UTsÉVP) (Ukraine)

    2016-01-15

    Problems and potential approaches to determining ice characteristics for sea hydroengineering structures design are considered. A system for numerical modeling of ice dynamics is presented. The system may be used to define ice characteristics on approaches to structures with due regard for local hydrometeorological conditions and ice loads on structures. System application examples are presented for determining computational scenarios for ice loads at structures of the Pevek floating nuclear power plant (FNPP), as well as for the breakwater pier under reconstruction in Vanino. A scenario approach is used to determined ice loads.

  7. The methodology of determining the corrosion of steel structures

    OpenAIRE

    S.D. Fedotov; A.V. Ulybin; N.N. Shabrov

    2013-01-01

    The problems of determining the corrosive wear of steel structures are considered. The results of applying ultrasonic method to determine the remaining profile of the structure are described. The main advantages and disadvantages of ultrasonic thickness meters comparing to mechanical devices are given. Low reliability of the method based on evaluating the thickness of the corrosion oxides is substantiated. The problems of determining the original section of the elements are outlined. The alg...

  8. Audit Fee Determinants in different Ownership Structures : The Swedish Setting

    OpenAIRE

    Ask, Joakim; LJ Holm, Mattias

    2013-01-01

    The aim of this study is to test the audit fee determinants for companies listed on Nasdaq OMX Stockholm Stock Exchange and to examine whether the audit fee determinants diverge for ownership structures. By testing the audit fee determinants in a Swedish setting the study contributes to the research body in two ways; by testing a previously sparsely researched setting and examining the monitoring need for different ownership structures. The results indicate that audit fees are explained to a ...

  9. Ab initio structure determination via powder X-ray diffraction

    Indian Academy of Sciences (India)

    Digamber G Porob; T N Guru Row

    2001-10-01

    Structure determination by powder X-ray diffraction data has gone through a recent surge since it has become important to get to the structural information of materials which do not yield good quality single crystals. Although the method of structure completion when once the starting model is provided is facile through the Rietveld refinement technique, the structure solution ab initio os still not push-button technology. In this article a survey of the recent development in this area is provided with an illustration of the structure determination of -NaBi3V2O10.

  10. 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.

  11. The determination of retainable phosphorus, relative biological availability, and relative biological value of phosphorus sources for broilers.

    Science.gov (United States)

    Coon, C N; Seo, S; Manangi, M K

    2007-05-01

    A 10- to 21-d chick bioassay was conducted to determine the absolute retention value (ARV) for 2 different defluorinated phosphates (DF-1 and DF-2) and a reagent grade dicalcium phosphate (DCP). The total and test P in excreta regressed on feed P levels were subjected to general straight-line (linear), 1-slope broken-line, 2-slope broken-line, and polynomial regression methods to find the best analysis model. The relative biological availability (RBA) and relative biological value (RBV) for P from the 2 different defluorinated phosphates (DF-1 and DF-2) were obtained by the slope ratio method using 3 different bone measurements (% tibia ash, tibia breaking force, tibia weight) and RBV calculated using percentage tibia ash, weight gain, and feed/gain. The DCP was used as reference standard for RBA and RBV. The ARV measured at the breakpoints for test P by 2-slope analysis were determined to be 82.99% for DCP, 76.34% for DF-1, and 70.30% for DF-2. The ARV of test P determined at 0.45% NPP was 62.41% for DCP, 63.58% for DF-1, and 59.25% for DF-2. The relationship of ARV and RBA were similar in that DCP was 6% higher in ARV at the breakpoint compared with DF-1 and the RBA of DF-1 was 71 and 91% from tibia weight and tibia breaking force, respectively, compared with the bone parameters from chicks fed DCP. The DF-1 phosphate had 3 and 7% higher ARV at the breakpoint and 0.45% NPP, respectively, compared with DF-2. The RBA of DF-2 was 59 and 80% from tibia weight and bone-breaking force. The ARV of phosphate sources were independent of an arbitrary reference. The ARV for P sources provide retainable P information for industry-based feed formulation that can reduce excess P in poultry waste. The excreta P data from broilers fed increasing levels of DCP indicates that the data are best described statistically with a 1-slope broken-line regression, 2-slope broken-line regression, or polynomial regression.

  12. Structural characteristics and biological functions of the HIV-1 gp120 V3 region

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Recent studies demonstrate that the V3 loop of HIV-1 gp120 plays an important role in the attachment of HIV-1 to the target cells. Several amino acids in this domain are involved in the interaction of gp120 with the co-receptors. The V3 loop elicits one of the earliest antiviral antibody responses in HIV-1 infection and has been identified as the principal neutralizing determinant (PND). A subset of antibodies to V3 loop show a broad range of neutralizing activity. Unfortunately, this loop undergoes broad mutation and is one of the hypervariable regions. Mutations of some amino acids in this PND could affect syncytium formation, virus infectivity and neutralization. Knowing the structural characteristics and biological functions of the V3 region could help us to understand mechanism of HIV infection and to develop new strategy against HIV-1. In this review, the structural characteristics, variation and biological functions of the V3 loop as well as immunological responses to the V3 loop are discussed.

  13. Polycyclic Xanthone Natural Products: Structure, Biological Activity and Chemical Synthesis

    OpenAIRE

    Winter, Dana K.; Sloman, David L.; Porco, John A.

    2013-01-01

    Polycyclic xanthone natural products are a family of polyketides which are characterized by highly oxygenated, angular hexacyclic frameworks. In the last decade, this novel class of molecules has attracted noticeable attention from the synthetic and biological communities due to emerging reports of their potential use as antitumour agents. The aim of this article is to highlight the most recent developments of this subset of the xanthone family by detailing the innate challenges of the constr...

  14. Qualitative analysis of biological oscillators as processing structures

    OpenAIRE

    Bordon, Jure

    2011-01-01

    Recently there is a certain tendency in the field of computer science to find alternative processing platforms, which would replace the conventional ones that are starting to reach their limits in the meaning of components' size and speed. Computer science is trying to avoid its dependency on traditional electronic components. One of such alternatives is also processing in biological systems. Whatever the future processing platform might be, computer science will most likely always need a com...

  15. Polarized Neutron in Structural Biology Present and Future Outlook

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Jinkui [ORNL; Robertson, Lee [ORNL; Herwig, Kenneth W [ORNL; Crabb, Don [University of Virginia

    2013-01-01

    Hydrogen has a strong polarization-dependent neutron scattering cross section. This property has been exploited in the study of soft matters, especially biological macromolecules. When a polarized neutron beam is scattered off a polarized hydrogenous sample, the otherwise large hydrogen incoherent cross section is drastically reduced while the coherent signal is significantly increased. Past experiments have demonstrated the potentials and benefits of polarized neutron scattering from soft materials. The main technical challenge of polarized neutron scattering from biological matters lies at sample polarization. Dynamic nuclear polarization is a proven yet rather sophisticated technique. Its complexity is one of the main reasons for the technique's slow adoption. The future of polarized neutron scattering in biology may rest largely in neutron protein crystallography. Polarization of protein crystals is much easier to accomplish, since protein crystals are typically rather small (<<1 mm) and only require small and easy- to-operate polarization apparatuses. In addition, the high resolution nature of neutron protein crystallography means that we will be able to study individual atoms using the polarized neutron scattering technique.

  16. Determination of selenium in biological samples with an energy-dispersive X-ray fluorescence spectrometer.

    Science.gov (United States)

    Li, Xiaoli; Yu, Zhaoshui

    2016-05-01

    Selenium is both a nutrient and a toxin. Selenium-especially organic selenium-is a core component of human nutrition. Thus, it is very important to measure selenium in biological samples. The limited sensitivity of conventional XRF hampers its widespread use in biological samples. Here, we describe the use of high-energy (100kV, 600W) linearly polarized beam energy-dispersive X-Ray fluorescence spectroscopy (EDXRF) in tandem with a three-dimensional optics design to determine 0.1-5.1μgg(-1) levels of selenium in biological samples. The effects of various experimental parameters such as applied voltage, acquisition time, secondary target and various filters were thoroughly investigated. The detection limit of selenium in biological samples via high-energy (100kV, 600W) linearly polarized beam energy-dispersive X-ray fluorescence spectroscopy was decreased by one order of magnitude versus conventional XRF (Paltridge et al., 2012) and found to be 0.1μg/g. To the best of our knowledge, this is the first report to describe EDXRF measurements of Se in biological samples with important implications for the nutrition and analytical chemistry communities. PMID:26922394

  17. 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.

  18. Gyroid cuticular structures in butterfly wing scales: biological photonic crystals

    OpenAIRE

    Michielsen, K.; Stavenga, D.G.

    2007-01-01

    We present a systematic study of the cuticular structure in the butterfly wing scales of some papilionids (Parides sesostris and Teinopalpus imperialis) and lycaenids (Callophrys rubi, Cyanophrys remus, Mitoura gryneus and Callophrys dumetorum). Using published scanning and transmission electron microscopy (TEM) images, analytical modelling and computer-generated TEM micrographs, we find that the three-dimensional cuticular structures can be modelled by gyroid structures with various filling ...

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

    International Nuclear Information System (INIS)

    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

  20. Determination of 36Cl in biological shield concrete using pyrohydrolysis and liquid scintillation counting.

    Science.gov (United States)

    Itoh, Mitsuo; Watanabe, Kazuo; Hatakeyama, Mutsuo; Tachibana, Mitsuo

    2002-07-01

    A method for the determination of 36Cl in biological shield concrete of nuclear reactors was developed. Cl in the concrete sample was extracted quantitatively by pyrohydrolysis at 900 degrees C and recovered in Na2CO3 solution for subsequent measurement of 36Cl by liquid scintillation counting. WO3 was used as an accelerator in the pyrohydrolysis. The Cl extraction procedure was optimized by investigating experimental conditions with the use of ion chromatography and its recovery was evaluated by the analysis of the geochemical reference samples. The detection limit of 36Cl was 0.02 Bq g(-1) for a sample weight of 2 g. The relative standard deviation was 3-7% for the samples containing 0.5 Bq g(-1) levels of 36Cl. The method was applied to determine 36Cl in biological shield concrete of the Japan Power Demonstration Reactor. PMID:12173658

  1. Facilitating best practices in collecting anomalous scattering data for de novo structure solution at the ESRF Structural Biology Beamlines

    Science.gov (United States)

    de Sanctis, Daniele; Oscarsson, Marcus; Popov, Alexander; Svensson, Olof; Leonard, Gordon

    2016-01-01

    The constant evolution of synchrotron structural biology beamlines, the viability of screening protein crystals for a wide range of heavy-atom derivatives, the advent of efficient protein labelling and the availability of automatic data-processing and structure-solution pipelines have combined to make de novo structure solution in macromolecular crystallography a less arduous task. Nevertheless, the collection of diffraction data of sufficient quality for experimental phasing is still a difficult and crucial step. Here, some examples of good data-collection practice for projects requiring experimental phasing are presented and recent developments at the ESRF Structural Biology beamlines that have facilitated these are illustrated. PMID:26960128

  2. Structural and Computational Biology in the Design of Immunogenic Vaccine Antigens

    Directory of Open Access Journals (Sweden)

    Lassi Liljeroos

    2015-01-01

    Full Text Available Vaccination is historically one of the most important medical interventions for the prevention of infectious disease. Previously, vaccines were typically made of rather crude mixtures of inactivated or attenuated causative agents. However, over the last 10–20 years, several important technological and computational advances have enabled major progress in the discovery and design of potently immunogenic recombinant protein vaccine antigens. Here we discuss three key breakthrough approaches that have potentiated structural and computational vaccine design. Firstly, genomic sciences gave birth to the field of reverse vaccinology, which has enabled the rapid computational identification of potential vaccine antigens. Secondly, major advances in structural biology, experimental epitope mapping, and computational epitope prediction have yielded molecular insights into the immunogenic determinants defining protective antigens, enabling their rational optimization. Thirdly, and most recently, computational approaches have been used to convert this wealth of structural and immunological information into the design of improved vaccine antigens. This review aims to illustrate the growing power of combining sequencing, structural and computational approaches, and we discuss how this may drive the design of novel immunogens suitable for future vaccines urgently needed to increase the global prevention of infectious disease.

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

    International Nuclear Information System (INIS)

    The distribution of induced 15O and 11C 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 15O activity proves to be a valid means of beam localization

  4. Voltammetric and amperometric determination of biologically active organic compounds using various types of silver amalgam electrodes

    OpenAIRE

    Barek, Jiří; Fischer, Jan; Moreira, Josino C.; Wang, Joseph

    2014-01-01

    In this paper, possibilities of various types of silver amalgam electrodes for determination of micromolar and submicromolar concentrations of various electrochemically reducible biologically active organic compounds are reviewed. Attention is paid to the use of polished and mercury meniscus modified silver solid amalgam electrodes, silver amalgam paste electrodes both with and without pasting liquids, single crystal silver amalgam electrodes, composite silver amalgam electrodes, and porous s...

  5. Optimization and validation of spectrophotometric methods for determination of finasteride in dosage and biological forms

    OpenAIRE

    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 de...

  6. Sex determination meltdown upon biological control introduction of the parasitoid Cotesia rubecula?

    OpenAIRE

    Boer; Kuijper, B.; Heimpel, G.E.; Beukeboom, L. W.

    2012-01-01

    Natural enemies may go through genetic bottlenecks during the process of biological control introductions. Such bottlenecks are expected to be particularly detrimental in parasitoid Hymenoptera that exhibit complementary sex determination (CSD). CSD is associated with a severe form of inbreeding depression because homozygosity at one or multiple sex loci leads to the production of diploid males that are typically unviable or sterile. We observed that diploid males occur at a relatively high r...

  7. 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…

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

    International Nuclear Information System (INIS)

    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 HNO3 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 00C 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)

  9. 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.)

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

    International Nuclear Information System (INIS)

    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.)

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

    International Nuclear Information System (INIS)

    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

  12. 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.

  13. Insights into IL-23 biology: From structure to function.

    Science.gov (United States)

    Floss, Doreen M; Schröder, Jutta; Franke, Manuel; Scheller, Jürgen

    2015-10-01

    Interleukin (IL-)23 is a central cytokine controlling TH17 development. Overshooting IL-23 signaling contribute to autoimmune diseases. Moreover, GWAS studies have identified several SNPs within the IL-23 receptor, which are associated with autoimmune diseases. IL-23 is a member of the IL-12-type cytokine family and consists of IL-23p19 and p40. Within the IL-12 family, IL-12 and IL-23 share the p40 cytokine subunit and the IL-12Rβ1 as one chain of the receptor complex. For signaling, IL-23 triggers heterodimerization of IL-12Rβ1 and the IL-23R. Subsequently, signal transduction pathways including JAK/STAT, MAPK and PI3K are activated. Most studies have investigated the biological relevance of IL-23 in the development of TH17 cells and autoimmunity, whereas less is known about the molecular context of IL-23 biology. Therefore, we focused on IL-23 receptor complex assembly, signal transduction and functional relevance of IL-23R SNPs in the context of IL-23-inhibitory principles.

  14. 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.

  15. 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.

  16. Gyroid cuticular structures in butterfly wing scales : biological photonic crystals

    NARCIS (Netherlands)

    Michielsen, K.; Stavenga, D. G.

    2008-01-01

    We present a systematic study of the cuticular structure in the butterfly wing scales of some papilionids (Parides sesostris and Teinopalpus imperialis) and lycaenids (Callophrys rubi, Cyanophrys remus, Mitoura gryneus and Callophrys dumetorum). Using published scanning and transmission electron mic

  17. 3-D Structure of Molecules of Biological Significance

    Science.gov (United States)

    Bennett, Alice S.; Schwenk, Karl

    1974-01-01

    Describes how to use the distinctive properties of osazone formation in conjunction with molecular model construction to demonstrate the relationship between the three-dimensional structures of simple sugars and the shapes of crystals they form. (BR)

  18. Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli

    OpenAIRE

    Chang, Roger L.; Andrews, Kathleen; Kim, Donghyuk; Li, Zhanwen; Godzik, Adam; Palsson, Bernhard Ø.

    2013-01-01

    Genome scale network reconstruction has enabled predictive modeling of metabolism for many systems. Traditionally, protein structural information has not been represented in such reconstructions. Expanding a genome-scale model of Escherichia coli metabolism by including experimental and predicted protein structures enabled the analysis of protein thermostability in a network context, allowing prediction of protein activities that limit network function at super-optimal temperature and mechani...

  19. Structure and Cell Biology of Archaeal Virus STIV

    OpenAIRE

    Fu, Chi-yu; Johnson, John E.

    2012-01-01

    Recent investigations of archaeal viruses have revealed novel features of their structures and life cycles when compared to eukaryotic and bacterial viruses, yet there are structure-based unifying themes suggesting common ancestral relationships among dsDNA viruses in the three kingdoms of life. Sulfolobus solfataricus and the infecting virus Sulfolobus turreted icosahedral virus (STIV) is one of the well-established model systems to study archaeal virus replication and viral-host interaction...

  20. Synthesis of a new group of aliphatic hydrazide derivatives and the correlations between their molecular structure and biological activity.

    Science.gov (United States)

    Kostecka, Małgorzata

    2012-01-01

    In view of the growing demand for new compounds showing biological activity against pathogenic microorganisms, such as pathogenic and phytopathogenic fungi, the objective of this study was to synthesize a new group of aliphatic and aromatic derivatives of hydrazide. In consequence of the reactions observed during synthesis, the resulting compounds retained their linear structure. Their structure and lipophilicity, measured by high-performance liquid chromatography (HPLC), were analyzed. Correlations were determined between the compounds' molecular parameters and biological activity against Fusarium solani and Fusarium oxysporum fungi. The investigated compounds were also examined for their antifungal activity against Aspergillus fumigatus. The obtained results indicate that compounds with fluorine-containing substituents penetrate the cell structure more effectively and are characterized by higher antifungal potential than analogues with different substituents. PMID:22441334

  1. Synthesis of a New Group of Aliphatic Hydrazide Derivatives and the Correlations between Their Molecular Structure and Biological Activity

    Directory of Open Access Journals (Sweden)

    Małgorzata Kostecka

    2012-03-01

    Full Text Available In view of the growing demand for new compounds showing biological activity against pathogenic microorganisms, such as pathogenic and phytopathogenic fungi, the objective of this study was to synthesize a new group of aliphatic and aromatic derivatives of hydrazide. In consequence of the reactions observed during synthesis, the resulting compounds retained their linear structure. Their structure and lipophilicity, measured by high-performance liquid chromatography (HPLC, were analyzed. Correlations were determined between the compounds’ molecular parameters and biological activity against Fusarium solani and Fusarium oxysporum fungi. The investigated compounds were also examined for their antifungal activity against Aspergillus fumigatus. The obtained results indicate that compounds with fluorine-containing substituents penetrate the cell structure more effectively and are characterized by higher antifungal potential than analogues with different substituents.

  2. Determination of macrolides in biological matrices by high-performance liquid chromatography with electrochemical detection.

    Science.gov (United States)

    Kees, F; Spangler, S; Wellenhofer, M

    1998-07-01

    A liquid chromatographic method for the determination of macrolide antibiotics is described using a cyanopropyl column which proved to be as efficient or superior to the normally used apolar reversed-phase columns. The recovery of the macrolides from water and plasma was 80-90%. Using 0.5 ml of plasma, 30 ng/ml of clarithromycin, 50 ng/ml of roxithromycin and 10 ng/ml of azithromycin could be determined with acceptable precision and accuracy. The method has been employed in pharmacokinetic studies in humans for the determination of roxithromycin, clarithromycin and azithromycin in plasma, serum and other biological matrices. The particular selectivity of the cyanopropyl phase may also allow the simultaneous determination of erythromycin and its prodrug esters. PMID:9691325

  3. CONCIDERING OF FUNDATION SLOPE TO DETERMINE THE ENGENEERING STRUCTURE HEIGHT

    OpenAIRE

    Zubko, Z.

    2005-01-01

    The article considers some aspects of determining of engineering structure height. It proposes the technique for terrain slope consideration in the course of base adjustment under difficult conditions of geodetic surveying.

  4. Structural Investigation of Biological and Semiconductor Nanostructures with Nonlinear Multicontrast Microscopy

    Science.gov (United States)

    Cisek, Richard

    Physical and functional properties of advanced nano-composite materials and biological structures are determined by self-organized atoms and molecules into nanostructures and in turn by microscopic organization of the nanostructures into assemblies of higher structural complexity. Therefore, microscopes are indispensable tools for structural investigations at various levels of organization. In this work, novel nonlinear optical microscopy methods were developed to non-invasively study structural organization at the nanoscopic and microscopic levels. Atomic organization of semiconductor nanowires, molecular organization of amylose biocrystallites in starch granules, and microscopic organization of several photosynthetic organisms was elucidated. The structure of ZnSe nanowires, key components in many modern nanodevices, was investigated using polarization harmonic generation microscopy. Based on nonlinear optical properties of the different crystal lattices, zinc blende and wurtzite nanowires were differentiated, and the three-dimensional orientation of the zinc blende nanowires could be found. The structure of starch granules, a model biocrystal, important in food as well as health sciences, was also investigated using polarization harmonic microscopy. The study was combined with ab initio calculations using the crystal structures of amylose A and B, revealing that second harmonic signals originate from the hydroxide and hydrogen bonds in the starch granules. Visualization of several photosynthetic organisms including the green algae, Chlamydomonas reinhardtii, two species of cyanobacteria, Leptolyngbya sp. and Anabaena sp., aggregates of light-harvesting pigment-protein complexes as well as chloroplasts from green plants were also explored, revealing that future nonlinear microscopy applications could include structural studies of cell walls, the Chlamydomonas eyespot, and photosynthetic membranes. In this study, several nonlinear optical microscopy modalities

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

    Science.gov (United States)

    Barthlott, W; Mail, M; Neinhuis, C

    2016-08-01

    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

  6. Crystallization and Structure Determination of Superantigens and Immune Receptor Complexes.

    Science.gov (United States)

    Rödström, Karin E J; Lindkvist-Petersson, Karin

    2016-01-01

    Structure determination of superantigens and the complexes they form with immune receptors have over the years provided insight in their modes of action. This technique requires growing large and highly ordered crystals of the superantigen or receptor-superantigen complex, followed by exposure to X-ray radiation and data collection. Here, we describe methods for crystallizing superantigens and superantigen-receptor complexes using the vapor diffusion technique, how the crystals may be optimized, and lastly data collection and structure determination.

  7. NMRFAM-SDF: a protein structure determination framework

    Energy Technology Data Exchange (ETDEWEB)

    Dashti, Hesam; Lee, Woonghee; Tonelli, Marco; Cornilescu, Claudia C.; Cornilescu, Gabriel; Assadi-Porter, Fariba M.; Westler, William M.; Eghbalnia, Hamid R.; Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison, Biochemistry Department (United States)

    2015-08-15

    The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMR—from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website ( http://nmrfam.wisc.edu/software.htm http://nmrfam.wisc.edu/software.htm )

  8. Sperm chromatin structure and male fertility: biological and clinical aspects

    Institute of Scientific and Technical Information of China (English)

    J. Erenpreiss; M. Spano; J. Erenpreisa; M. Bungum; A. Giwercman

    2006-01-01

    Aim: Sperm chromatin/DNA integrity is essential for the accurate transmission of paternal genetic information, and normal sperm chromatin structure is important for sperm fertilizing ability. The routine examination of semen, which includes sperm concentration, motility and morphology, does not identify defects in sperm chromatin structure. The origin of sperm DNA damage and a variety of methods for its assessment are described. Evaluation of sperm DNA damage appears to be a useful tool for assessing male fertility potential both in vivo and in vitro. The possible impact of sperm DNA defects on the offspring is also discussed.

  9. Molecular subtype analysis determines the association of advanced breast cancer in Egypt with favorable biology

    Directory of Open Access Journals (Sweden)

    DuQuette Rachelle A

    2011-09-01

    Full Text Available Abstract Background Prognostic markers and molecular breast cancer subtypes reflect underlying biological tumor behavior and are important for patient management. Compared to Western countries, women in North Africa are less likely to be prognosticated and treated based on well-characterized markers such as the estrogen receptor (ER, progesterone receptor (PR and Her2. We conducted this study to determine the prevalence of breast cancer molecular subtypes in the North African country of Egypt as a measure of underlying biological characteristics driving tumor manifestations. Methods To determine molecular subtypes we characterized over 200 tumor specimens obtained from Egypt by performing ER, PR, Her2, CK5/6, EGFR and Ki67 immunohistochemistry. Results Our study demonstrated that the Luminal A subtype, associated with favorable prognosis, was found in nearly 45% of cases examined. However, the basal-like subtype, associated with poor prognosis, was found in 11% of cases. These findings are in sharp contrast to other parts of Africa in which the basal-like subtype is over-represented. Conclusions Egyptians appear to have favorable underlying biology, albeit having advanced disease at diagnosis. These data suggest that Egyptians would largely profit from early detection of their disease. Intervention at the public health level, including education on the benefits of early detection is necessary and would likely have tremendous impact on breast cancer outcome in Egypt.

  10. Application of source-receptor models to determine source areas of biological components (pollen and butterflies

    Directory of Open Access Journals (Sweden)

    M. Alarcón

    2010-01-01

    Full Text Available The source-receptor models allow the establishment of relationships between a receptor point (sampling point and the probable source areas (regions of emission through the association of concentration values at the receptor point with the corresponding atmospheric back-trajectories, and, together with other techniques, to interpret transport phenomena on a synoptic scale. These models are generally used in air pollution studies to determine the areas of origin of chemical compounds measured at a sampling point, and thus be able to target actions to reduce pollutants. However, until now, few studies have applied these types of models to describe the source areas of biological organisms. In Catalonia there are very complete records of pollen (data from the Xarxa Aerobiològica de Catalunya, Aerobiology Network of Catalonia and butterflies (data from the Catalan Butterfly Monitoring Scheme, a biological material that is also liable to be transported long distances and whose areas of origin could be interesting to know. This work presents the results of the use of the Seibert et al. model applied to the study of the source regions of: (1 certain pollen of an allergic nature, observed in Catalonia and the Canary Islands, and (2 the migratory butterfly Vanessa cardui, observed in Catalonia. Based on the results obtained we can corroborate the suitability of these models to determine the area of origin of several species, both chemical and biological, therefore expanding the possibilities of applying the original model to the wider field of Aerobiology.

  11. Determination of absolute structure using Bayesian statistics on Bijvoet differences

    NARCIS (Netherlands)

    Hooft, R.W.W.; Straver, L.H.; Spek, A.L.

    2008-01-01

    A new probabilistic approach is introduced for the determination of the absolute structure of a compound which is known to be enantiopure based on Bijvoet-pair intensity differences. The new method provides relative probabilities for different models of the chiral composition of the structure. The o

  12. China Takes the Lead in the Structural Determination of Lumbrokinase

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    @@ After five years of arduous work, CAS scientists re cently succeeded in determining the structure of lumbrokinase (earthworm fibrinolytic enzyme),shedding light on the understanding of this drug at the molecular level and laying a foundation for drug design based on its structure.

  13. 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.

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

    DEFF Research Database (Denmark)

    Olsson, Simon; Boomsma, Wouter; Frellsen, Jes;

    2011-01-01

    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 theoretical...

  15. 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)

  16. Determinants of euro term structure of credit spreads

    OpenAIRE

    Astrid Van Landschoot

    2004-01-01

    In this paper, we investigate the determinants of the Euro term structure of credit spreads. More specifically, we analyze whether the sensitivity of credit spread changes to financial and macroeconomic variables depends on bond characteristics such as rating and maturity. According to the structural models and empirical evidence on credit spreads, we find that changes in the level and the slope of the default-free term structure, the market return, implied volatility, and liquidity risk sign...

  17. 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…

  18. Structure and cell biology of archaeal virus STIV.

    Science.gov (United States)

    Fu, Chi-yu; Johnson, Johnson E

    2012-04-01

    Recent investigations of archaeal viruses have revealed novel features of their structures and life cycles when compared to eukaryotic and bacterial viruses, yet there are structure-based unifying themes suggesting common ancestral relationships among dsDNA viruses in the three kingdoms of life. Sulfolobus solfataricus and the infecting virus Sulfolobus turreted icosahedral virus (STIV) is one of the well-established model systems to study archaeal virus replication and viral-host interactions. Reliable laboratory conditions to propagate STIV and available genetic tools allowed structural characterization of the virus and viral components that lead to the proposal of common capsid ancestry with PRD1 (bacteriophage), Adenovirus (eukaryotic virus) and PBCV (chlorellavirus). Microarray and proteomics approaches systematically analyzed viral replication and the corresponding host responses. Cellular cryo-electron tomography and thin-section EM studies uncovered the assembly and maturation pathway of STIV and revealed dramatic cellular ultra-structure changes upon infection. The viral-induced pyramid-like protrusions on cell surfaces represent a novel viral release mechanism and previously uncharacterized functions in viral replication. PMID:22482708

  19. Family structure and wellbeing of out-of-wedlock children: The significance of the biological parents' relationship

    Directory of Open Access Journals (Sweden)

    Shirley H. Liu

    2006-09-01

    Full Text Available This study examines the role of the relationship between the biological parents in determining child wellbeing using longitudinal data from the Fragile Families and Child Wellbeing Study (FFCWS. We extend prior research by considering children born to unmarried parents in an investigation of the effect of the relationship structure between the biological parents on infant health and behavior. The main findings are that children born to cohabiting biological parents (i realize better outcomes, on average, than those born to mothers who are less involved with the child's biological father, and (ii whose parents marry within a year after childbirth do not display significantly better outcomes than children of parents who continue to cohabit. Furthermore, children born to cohabiting or visiting biological parents who end their relationship within the first year of the child's life are up to 9 percent more likely to have asthma compared to children whose biological parents remain (romantically involved. The results are robust to a rich set of controls for socioeconomic status, health endowments, home investments, and relationship characteristics.

  20. Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements

    Science.gov (United States)

    Fernandez-Chamorro, Javier; Lozano, Gloria; Garcia-Martin, Juan Antonio; Ramajo, Jorge; Dotu, Ivan; Clote, Peter; Martinez-Salas, Encarnacion

    2016-04-01

    The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin inactivates IRES activity, since the stronger the stability of the hairpin the higher the inhibition of protein synthesis. Destabilization of the stem-loop immediately upstream of the pyrimidine-tract also decreases IRES activity. Our work introduces a hybrid computational/experimental method to determine the importance of structural motifs for biological function. Specifically, we show the feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function.

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

    International Nuclear Information System (INIS)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    Eisenberg, David S.

    2008-07-15

    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

  3. Determination of acrylamide in local and commercial cultivar of potatoes from biological farm.

    Science.gov (United States)

    Marchettini, Nadia; Focardi, Silvia; Guarnieri, Massimo; Guerranti, Cristiana; Perra, Guido

    2013-02-15

    This paper reports the results of a preliminary study on the characterization of parameters influencing formation of acrylamide in fried potatoes, from biological cultivation. The formation of acrylamide was investigated in relation to frying in biological extra virgin olive oil and commercial seed oil. Three different cultivars (Rossa di Colfiorito, Quarantina bianca genovese and Kennebec) were chosen. Asparagine, glucose, fructose and sucrose concentrations were determined in potato slice before frying, while acrylamide content was analysed by LC-ESI-MS/MS in the slices fried in seed and extra virgin olive oil. The Kennebec cultivar showed differences in its potential for acrylamide formation, which was primarily related to its relatively high asparagine and reducing sugars contents, respect the other local cultivars (particulary Quarantina). Values of acrylamide below detection limit (LOD) were found in Quarantina bianca genovese cultivar samples fried in extra virgin olive oil and peanuts seed oil and higher in peanuts seed oil fried potatoes of Kennebec cultivar.

  4. A new era for GPCR research: structures, biology anddrug discovery

    Institute of Scientific and Technical Information of China (English)

    H Eric XU; Rui-ping XIAO

    2012-01-01

    Cells in a living organism must communicate with each other through continuously sending and receiving messages.G-protein coupled receptors (GPCRs) are the largest family of communicating molecules at the cell surface.They transmit diverse extracellular signals,ranging from light and small chemical hormones to large peptide and protein hormones,and as such they play crucial roles in numerous physiological and pathological processes.More importantly,GPCRsare the most successful class of drug targets that are relevant to many major diseases,including cancer,heart failure,and inflammatory diseases.Over 50% of currently used drugs are targeted to GPCRs.However,these drugs target only 50-60 GPCRs,leaving the majority of human GPCRs,exceeding 800,unexplored for drug discovery.Given the prominent roles of GPCRs in biology and their successful track records as drug targets,GPCRs have become a hot frontier in basic research of life science and therapeutic discovery of translational medicines.

  5. Integral membrane protein structure determination using pseudocontact shifts

    International Nuclear Information System (INIS)

    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

  6. 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.

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

    International Nuclear Information System (INIS)

    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 99Tc values had previously been determined suggest possible competition between Re and Tc in the accumulation process. (author)

  8. Nanotwin-governed toughening mechanism in hierarchically structured biological materials

    Science.gov (United States)

    Shin, Yoon Ah; Yin, Sheng; Li, Xiaoyan; Lee, Subin; Moon, Sungmin; Jeong, Jiwon; Kwon, Minhyug; Yoo, Seung Jo; Kim, Young-Min; Zhang, Teng; Gao, Huajian; Oh, Sang Ho

    2016-02-01

    As a natural biocomposite, Strombus gigas, commonly known as the giant pink queen conch shell, exhibits outstanding mechanical properties, especially a high fracture toughness. It is known that the basic building block of conch shell contains a high density of growth twins with average thickness of several nanometres, but their effects on the mechanical properties of the shell remain mysterious. Here we reveal a toughening mechanism governed by nanoscale twins in the conch shell. A combination of in situ fracture experiments inside a transmission electron microscope, large-scale atomistic simulations and finite element modelling show that the twin boundaries can effectively block crack propagation by inducing phase transformation and delocalization of deformation around the crack tip. This mechanism leads to an increase in fracture energy of the basic building block by one order of magnitude, and contributes significantly to that of the overall structure via structural hierarchy.

  9. Structural determination of intact proteins using mass spectrometry

    Science.gov (United States)

    Kruppa, Gary; Schoeniger, Joseph S.; Young, Malin M.

    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.

  10. Higher order chromatin structure: bridging physics and biology

    OpenAIRE

    Fudenberg, Geoffrey; Mirny, Leonid A.

    2012-01-01

    Recent advances in microscopy and genomic techniques have provided new insight into spatial chromatin organization inside of the nucleus. In particular, chromosome conformation capture data has highlighted the relevance of polymer physics for high-order chromatin organization. In this context, we review basic polymer states, discuss how an appropriate polymer model can be determined from experimental data, and examine the success and limitations of various polymer models of high-order interph...

  11. Two-photon excited fluorescent chemosensor for homogeneous determination of copper(II) in aqueous media and complicated biological matrix.

    Science.gov (United States)

    Liu, Lingzhi; Dong, Xiaohu; Xiao, Yan; Lian, Wenlong; Liu, Zhihong

    2011-05-21

    In the present work, a two-photon excited fluorescent chemosensor for Cu(2+) was prepared. The probe was constructed on the basis of internal charge transfer (ICT) principle with macrocyclic dioxotetraamine as the Cu(2+) receptor. The good water-solubility of the molecule enabled recognition and assay of Cu(2+) ions in biological media. The photophysical properties of the chemosensor were investigated in detail, exhibiting favorable fluorescence quantum yield and moderate two-photon absorption cross-section. The studies on binding thermodynamics demonstrated the formation of 1 : 1 complex between the chemosensor and Cu(2+) and an association constant of ca. 1.04 × 10(5) M(-1). Due to the rational design of the molecular structure, the sensor was highly specific to Cu(2+), which ensured high selectivity in Cu(2+) determination. Upon Cu(2+) binding, the intramolecular charge-transfer extent within the chromophore was weakened resulting in a remarkable quenching of fluorescence, based on which quantitative determination of Cu(2+) was performed. Good linearity was obtained between the fluorescence quenching value and Cu(2+) concentration ranging from 0.04 to 2.0 μM in aqueous solution. Benefiting from the merits of two-photon excitation, the chemosensor was free of interference from background luminescence in serum. A homogeneous quantitative determination of Cu(2+) was achieved in the serum medium with a linear range of 0.04 to 2.0 μM. Considering the structural flexibility of the sensor, this work also opens up the possibility to construct other two-photon excited chemosensors for direct homogeneous assay of various molecules/ions in complicated biological sample matrices. PMID:21416097

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

    OpenAIRE

    He, M-f; S. Wang; 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. Molecular structure and biological function of proliferating cell nuclear antigen

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Proliferating cell nuclear antigen (PCNA) is the core component of replication complex in eukaryote.As a processive factor of DNA polymerase delta, PCNA coordinates the replication process by interacting with various replication proteins. PCNA appears to play an essential role in many cell events, such as DNA damage repair, cell cycle regulation, and apoptosis, through the coordination or organization of different partners. PCNA is an essential factor in cell proliferation, and has clinical significance in tumor research. In this article we review the functional structure of PCNA, which acts as a function switch in different cell events.

  14. Structural biology of starch-degrading enzymes and their regulation

    DEFF Research Database (Denmark)

    Møller, Marie Sofie; Svensson, Birte

    2016-01-01

    Starch is a major energy source for all domains of life. Recent advances in structures of starch-degrading enzymes encompass the substrate complex of starch debranching enzyme, the function of surface binding sites in plant isoamylase, details on individual steps in the mechanism of plant...... disproportionating enzyme and a self-stabilised conformation of amylose accommodated in the active site of plant α-glucosidase. Important inhibitor complexes include a flavonol glycoside, montbretin A, binding at the active site of human pancreatic α-amylase and barley limit dextrinase inhibitor binding...... to the debranching enzyme, limit dextrinase using a new binding mode for cereal protein inhibitors....

  15. Structure of Biologically Active Organotin(IV) Dithiocarbamates

    Science.gov (United States)

    Farina, Y.; Sanuddin, M.; Yamin, B. M.

    2008-03-01

    The diorganotin(IV) complexes of dithiocarbamates derived from from N-ethyl-n-propylamine (EtPrdtc), 2-dimethylaminoethylamine (Me2Etdtc), 3-dimethlyamino-1-propylamine (Me2Prdtc), p-tolylmethanamine (TylMetdtc) and N-methyl-1-phenylmethanamine (MePhMetdtc) have been synthesized and characterized. Single crystal X-ray diffraction studies on Ph3Sn(EtPrdtc), Me2Sn(MePhMetdtc)2 and Bu2Sn(MePhMetdtc)2 showed that the complexes adopted a monoclinic system with space group P(2)/n, P21/n and C2/c, respectively. The Ph3Sn(EtPrdtc) complex adopted a trigonal pyramidal structure while the Me2Sn(MePhMetdtc)2 and Bu2Sn(MePhMetdtc)2 complexes displayed structures which may be described as distorted octahedrons. Cytotoxicity test using HL60 cells (human promyelocytic leukemic) showed that only Me2Sn(Me2Etdtc), Me2Sn(MePhMetdtc)2 and Bu2Sn(MePhMetdtc)2 complexes were active. The rest of the complexes did not show cytotoxicity behaviour towards HL60 cells.

  16. 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....

  17. Biological psychological and social determinants of old age: bio-psycho-social aspects of human aging.

    Science.gov (United States)

    Dziechciaż, Małgorzata; Filip, Rafał

    2014-01-01

    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. PMID:25528930

  18. Spatio-structural granularity of biological material entities

    Directory of Open Access Journals (Sweden)

    Vogt Lars

    2010-05-01

    Full Text Available Abstract Background With the continuously increasing demands on knowledge- and data-management that databases have to meet, ontologies and the theories of granularity they use become more and more important. Unfortunately, currently used theories and schemes of granularity unnecessarily limit the performance of ontologies due to two shortcomings: (i they do not allow the integration of multiple granularity perspectives into one granularity framework; (ii they are not applicable to cumulative-constitutively organized material entities, which cover most of the biomedical material entities. Results The above mentioned shortcomings are responsible for the major inconsistencies in currently used spatio-structural granularity schemes. By using the Basic Formal Ontology (BFO as a top-level ontology and Keet's general theory of granularity, a granularity framework is presented that is applicable to cumulative-constitutively organized material entities. It provides a scheme for granulating complex material entities into their constitutive and regional parts by integrating various compositional and spatial granularity perspectives. Within a scale dependent resolution perspective, it even allows distinguishing different types of representations of the same material entity. Within other scale dependent perspectives, which are based on specific types of measurements (e.g. weight, volume, etc., the possibility of organizing instances of material entities independent of their parthood relations and only according to increasing measures is provided as well. All granularity perspectives are connected to one another through overcrossing granularity levels, together forming an integrated whole that uses the compositional object perspective as an integrating backbone. This granularity framework allows to consistently assign structural granularity values to all different types of material entities. Conclusions The here presented framework provides a spatio-structural

  19. 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.

  20. Synthesis, Structure and Biological Activity of Zn(II) Complex with Tris(benzimidazol-2-yl-methyl)amine Ligand

    Institute of Scientific and Technical Information of China (English)

    LIU,Xiao-Lan(刘小兰); ZHAO,Ru(赵茹); LIU,Xiao-Hong(刘晓红); YUE,Jun-Jie(岳俊杰); YIN,Yu-Xin(尹宇新); SUN,Yun(孙云); SUN,Ming(孙命)

    2004-01-01

    A new Zn(II) mononuclear complex with tris(benzimidazol-2-yl-methyl)amine (NTB) was synthesized with stoichiometry of [Zn(NTB)NO3]NO3·DIPY·DMF (DIPY∶4,4'-dipyridyl). The complex was characterized by elemental analysis, UV and IR spectra. The crystal structure was determined by using X-ray diffraction analysis. The crystal structure indicates that four N atoms and one O atom coordinate to zinc ion to construct a distorted trigonal-dipyramid configuration. Three nonprotonated N atoms from imidazole groups are in the equatorial plane, one alkylamino N atom and one O atom from in the axial directions. The biological activity assay shows that this complex presents certain biological activity by means of pyrogallol autoxidation and it can be called a model compound of superoxide dismutase (SOD).

  1. Structural Biology of CI from Phage TP901-1

    DEFF Research Database (Denmark)

    Rasmussen, Kim Krighaar

    bacteriophage 901-1 (TP901-1) hosts a genetic switch, which is until present unique in many aspects compared to other investigated genetic switches such as those found in λ - and 186 bacteriophage. In TP901-1 the genetic switch consists of Clear I repressor (CI), the antirepressor Modulator Of Repression (MOR......), three Operator sites, Right, Left and Distance (OR, OL and OD) and two Promoters, Right and Left (PR and PL). The CI repressor is generally the major regulator of temperate bacteriophages genetic switches. In general CI repressors consist of two domains, the N-Terminal Domain (NTD) and C-Terminal Domain...... (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...

  2. Emergence, self-organization and morphogenesis in biological structures.

    Science.gov (United States)

    Dobrescu, R; Purcarea, V I

    2011-01-01

    The paper discusses the connection between emergence, pattern formation and nonlinear dynamics, focusing on the similarity between discrete patterns and fractal structures, and then describes different solutions to model reaction-diffusion systems as representative processes in morphogenesis. A specific example is the diffusion limited aggregation growth process, illustrated by the simulation of the evolution of a bacterial colony that shows the roles of instability and sensitivity in non-equilibrium pattern formation. Based on this particular case, it is shown how self-organization could be achieved from non-organized agglomeration of separate entities, in a region of space. We conclude with some brief remarks about universality, predictability and long-term prospects for this field of research. PMID:21505578

  3. Packing regularities in biological structures relate to their dynamics.

    Science.gov (United States)

    Jernigan, Robert L; Kloczkowski, Andrzej

    2007-01-01

    The high packing density inside proteins leads to certain geometric regularities and also is one of the most important contributors to the high extent of cooperativity manifested by proteins in their cohesive domain motions. The orientations between neighboring nonbonded residues in proteins substantially follow the similar geometric regularities, regardless of whether the residues are on the surface or buried, a direct result of hydrophobicity forces. These orientations are relatively fixed and correspond closely to small deformations from those of the face-centered cubic lattice, which is the way in which identical spheres pack at the highest density. Packing density also is related to the extent of conservation of residues, and we show this relationship for residue packing densities by averaging over a large sample or residue packings. There are three regimes: (1) over a broad range of packing densities the relationship between sequence entropy and inverse packing density is nearly linear, (2) over a limited range of low packing densities the sequence entropy is nearly constant, and (3) at extremely low packing densities the sequence entropy is highly variable. These packing results provide important justification for the simple elastic network models that have been shown for a large number of proteins to represent protein dynamics so successfully, even when the models are extremely coarse grained. Elastic network models for polymeric chains are simple and could be combined with these protein elastic networks to represent partially denatured parts of proteins. Finally, we show results of applications of the elastic network model to study the functional motions of the ribosome, based on its known structure. These results indicate expected correlations among its components for the step-wise processing steps in protein synthesis, and suggest ways to use these elastic network models to develop more detailed mechanisms, an important possibility because most

  4. Magnetic stimulation for non-homogeneous biological structures

    Directory of Open Access Journals (Sweden)

    Papazov Sava P

    2002-09-01

    Full Text Available Abstract Background Magnetic stimulation has gained relatively wide application in studying nervous system structures. This technology has the advantage of reduced excitation of sensory nerve endings, and hence results in quasi-painless action. It has become clinically accepted modality for brain stimulation. However, theoretical and practical solutions for assessment of induced current distribution need more detailed and accurate consideration. Some possible analyses are proposed for distribution of the current induced from excitation current contours of different shape and disposition. Relatively non-difficult solutions are shown, applicable for two- and three-dimensional analysis. Methods The boundary conditions for field analysis by the internal Dirichlet problem are introduced, based on the vector potential field excited by external current coils. The feedback from the induced eddy currents is neglected. Finite element modeling is applied for obtaining the electromagnetic fields distribution in a non-homogeneous domain. Results The distributions were obtained in a non-homogeneous structure comprised of homogeneous layers. A tendency was found of the induced currents to follow paths in lower resistivity layers, deviating from the expected theoretical course for a homogeneous domain. Current density concentrations occur at the boundary between layers, suggesting the possibility for focusing on, or predicting of, a zone of stimulation. Conclusion The theoretical basis and simplified approach for generation of 3D FEM networks for magnetic stimulation analysis are presented, applicable in non-homogeneous and non-linear media. The inconveniences of introducing external excitation currents are avoided. Thus, the possibilities are improved for analysis of distributions induced by time-varying currents from contours of various geometry and position with respect to the medium.

  5. Physical-chemical determinant properties of biological communities in continental semi-arid waters.

    Science.gov (United States)

    da Rocha, Francisco Cleiton; de Andrade, Eunice Maia; Lopes, Fernando Bezerra; de Paula Filho, Francisco José; Filho, José Hamilton Costa; da Silva, Merivalda Doroteu

    2016-08-01

    Throughout human history, water has undergone changes in quality. This problem is more serious in dry areas, where there is a natural water deficit due to climatic factors. The aims of this study, therefore, were (i) to verify correlations between physical attributes, chemical attributes and biological metrics and (ii) from the biological attributes, to verify the similarity between different points of a body of water in a tropical semi-arid region. Samples were collected every 2 months, from July 2009 to July 2011, at seven points. Four physical attributes, five chemical attributes and four biological metrics were investigated. To identify the correlations between the physicochemical properties and the biological metrics, hierarchical cluster analysis (HCA) and canonical correlation analysis (CCA) were applied. Nine classes of phytoplankton were identified, with the predominance of species of cyanobacteria, and ten families of macroinvertebrates. The use of HCA resulted in the formation of three similar groups, showing that it was possible to reduce the number of sampling points when monitoring water quality with a consequent reduction in cost. Group I was formed from the waters at the high end of the reservoir (points P1, P2 and P3), group II by the waters from the middle third (points P4 and P5), and group III by the waters from the lower part of the reservoir (points P6 and P7). Richness of the phytoplanktons Cyanophyceae, Chorophyceae and Bacillariophyceae was the attribute which determined dissimilarity in water quality. Using CCA, it was possible to identify the spatial variability of the physicochemical attributes (TSS, TKN, nitrate and total phosphorus) that most influence the metrics of the macroinvertebrates and phytoplankton present in the water. Low macroinvertebrate diversity, with a predominance of indicator families for deterioration in water quality, and the composition of phytoplankton showing a predominance of cyanobacteria, suggests greater

  6. Physical-chemical determinant properties of biological communities in continental semi-arid waters.

    Science.gov (United States)

    da Rocha, Francisco Cleiton; de Andrade, Eunice Maia; Lopes, Fernando Bezerra; de Paula Filho, Francisco José; Filho, José Hamilton Costa; da Silva, Merivalda Doroteu

    2016-08-01

    Throughout human history, water has undergone changes in quality. This problem is more serious in dry areas, where there is a natural water deficit due to climatic factors. The aims of this study, therefore, were (i) to verify correlations between physical attributes, chemical attributes and biological metrics and (ii) from the biological attributes, to verify the similarity between different points of a body of water in a tropical semi-arid region. Samples were collected every 2 months, from July 2009 to July 2011, at seven points. Four physical attributes, five chemical attributes and four biological metrics were investigated. To identify the correlations between the physicochemical properties and the biological metrics, hierarchical cluster analysis (HCA) and canonical correlation analysis (CCA) were applied. Nine classes of phytoplankton were identified, with the predominance of species of cyanobacteria, and ten families of macroinvertebrates. The use of HCA resulted in the formation of three similar groups, showing that it was possible to reduce the number of sampling points when monitoring water quality with a consequent reduction in cost. Group I was formed from the waters at the high end of the reservoir (points P1, P2 and P3), group II by the waters from the middle third (points P4 and P5), and group III by the waters from the lower part of the reservoir (points P6 and P7). Richness of the phytoplanktons Cyanophyceae, Chorophyceae and Bacillariophyceae was the attribute which determined dissimilarity in water quality. Using CCA, it was possible to identify the spatial variability of the physicochemical attributes (TSS, TKN, nitrate and total phosphorus) that most influence the metrics of the macroinvertebrates and phytoplankton present in the water. Low macroinvertebrate diversity, with a predominance of indicator families for deterioration in water quality, and the composition of phytoplankton showing a predominance of cyanobacteria, suggests greater

  7. Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data

    International Nuclear Information System (INIS)

    The X-ray free-electron laser (XFEL) allows the analysis of small weakly diffracting protein crystals, but has required very many crystals to obtain good data. Here we use an XFEL to determine the room temperature atomic structure for the smallest cytoplasmic polyhedrosis virus polyhedra yet characterized, which we failed to solve at a synchrotron. These protein microcrystals, roughly a micron across, accrue within infected cells. We use a new physical model for XFEL diffraction, which better estimates the experimental signal, delivering a high-resolution XFEL structure (1.75 Å), using fewer crystals than previously required for this resolution. The crystal lattice and protein core are conserved compared with a polyhedrin with less than 10% sequence identity. We explain how the conserved biological phenotype, the crystal lattice, is maintained in the face of extreme environmental challenge and massive evolutionary divergence. Our improved methods should open up more challenging biological samples to XFEL analysis

  8. 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.

  9. Synthesis, Structure and Biological Activities of Novel Triazole Compounds Containing Thioamide Group

    Institute of Scientific and Technical Information of China (English)

    刘法谦; 秦永其; 许良忠; 陆路德; 杨绪杰; 汪信

    2005-01-01

    Two compounds 2-benzoyl-N-phenyl-2-( 1,2,4-triazol- 1-yl)thioacetamide (1) and 2-(4-chlorobenzoyl)-N-phenyl-2-(1,2,4-triazol-1-yl)thioacetamide (2) were synthesized from substituted acetophenone, triazole and phenyl isothiocyanate by several step reactions. The structure of compound 1 was determined by single-crystal X-ray diffraction analysis. It crystallizes in monoclinic system with space group P21/c, a =0.8806(2) nm, b= 1.2097(2) nm, c= 1.4809(3) nm, β=105.88°, Z=4, V=1.5173(6) nm3, Dc= 1.411 Mg/m3, μ=0.22 mm-1, F(000)=672, final R1=0.040 and Rw=0.103. There is obvious potentially weak C—H…N intermolecular interaction in the crystal, which stabilizes the structure. The results of biological test show that the two compounds have antifungal and plant growth regulating activities.

  10. 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. PMID:26857446

  11. Enzymatic determination of carbon-14 labeled L-alanine in biological samples

    International Nuclear Information System (INIS)

    A method for determination of L-alanine-specific radioactivity in biological samples is presented. This method is based on the specific enzymatic transformation of L-alanine to pyruvic acid hydrazone catalyzed by the enzyme L-alanine dehydrogenase, formation of the pyruvic acid 2,4-dinitrophenylhydrazone derivative, and quantitative trapping in Amberlite XAD-7 columns, followed by radioactivity counting of the lipophilic eluate. No interferences from other 14C-labeled materials such as D-glucose, glycerol, L-lactate, L-serine, L-glutamate, L-phenylalanine, glycine, L-leucine, and L-arginine were observed. This inexpensive and high-speed method is applicable to the simultaneous determination of L-alanine-specific radioactivity for a large number of samples

  12. Enzymatic determination of carbon-14 labeled L-alanine in biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Serra, F.; Palou, A.; Pons, A.

    1987-07-15

    A method for determination of L-alanine-specific radioactivity in biological samples is presented. This method is based on the specific enzymatic transformation of L-alanine to pyruvic acid hydrazone catalyzed by the enzyme L-alanine dehydrogenase, formation of the pyruvic acid 2,4-dinitrophenylhydrazone derivative, and quantitative trapping in Amberlite XAD-7 columns, followed by radioactivity counting of the lipophilic eluate. No interferences from other UC-labeled materials such as D-glucose, glycerol, L-lactate, L-serine, L-glutamate, L-phenylalanine, glycine, L-leucine, and L-arginine were observed. This inexpensive and high-speed method is applicable to the simultaneous determination of L-alanine-specific radioactivity for a large number of samples.

  13. 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.

  14. Selective spectrofluorimetric determination of zinc in biological samples by Flow Injection Analysis (FIA)

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez, P.; Perez Conde, C.; Gutierrez, A.; Camara, C. (Universidad Complutense, Madrid (Spain). Dept. de Quimica Analitica)

    1992-03-01

    The automatization of a spectrofluorimetric method for the determination of zinc at trace level is described. It is based on the formation of the fluorescent complex Zn(II)-5,7-dibromo-8-quinolinol (Zn(II)-DBQ) followed by extraction into diethylether using flow injection analysis. The optimum fluorescent emission is reached in hexamethylenetetramine (H{sub 2}MTA{sup +}/HMTA) buffer pH 6.0. A membrane phase separator was used. The calibration graph is linear up to 1.5 {mu}g/ml of Zn(II). The proposed method (detection limit 3 ng/ml) is very selective and has been successfully applied to determine Zn(II) in biological samples, tap waters and various food items. (orig.).

  15. Activation analytical determination of essential and toxic trace elements in biological material

    International Nuclear Information System (INIS)

    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 10-8g, 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)

  16. [Dialectic of the interrelationship between structure and function in biology and medicine].

    Science.gov (United States)

    Strukov, A I; Kakturskiĭ, L V

    1977-01-01

    The paper deals with some aspects of the dialectics of structure and function relationships in biological objects normally and pathologically. Idealistic and metaphysical concepts of the structure-function relationships (morphological idealism, holism, physiological idealism, functionalism) are critisized, and historical premises of these concepts are characterized. The principle of indissoluble unity and interconnection of changes in structure and function is emphasized, while the thesis of the primacy of function in the shaping of the form and the concept of functional diseases are rejected. Much attention is paid to the methodological principles of the study of structure and function based on the systemic approach to the investigation of biological objects from the point of view of structural levels and integratism. The groundlessness of the principles of reductionism and organicism in the solution of this problem is indicated. The connection of the concepts of structure and function with categories and laws of materialistic dialectics is dwelt on. PMID:880057

  17. Structure and Biological Roles of Sinorhizobium fredii HH103 Exopolysaccharide

    Science.gov (United States)

    Acosta-Jurado, Sebastián; Soto, María J.; Margaret, Isabel; Crespo-Rivas, Juan C.; Sanjuan, Juan; Temprano, Francisco; Gil-Serrano, Antonio; Ruiz-Sainz, José E.; Vinardell, José M.

    2014-01-01

    Here we report that the structure of the Sinorhizobium fredii HH103 exopolysaccharide (EPS) is composed of glucose, galactose, glucuronic acid, pyruvic acid, in the ratios 5∶2∶2∶1 and is partially acetylated. A S. fredii HH103 exoA mutant (SVQ530), unable to produce EPS, not only forms nitrogen fixing nodules with soybean but also shows increased competitive capacity for nodule occupancy. Mutant SVQ530 is, however, less competitive to nodulate Vigna unguiculata. Biofilm formation was reduced in mutant SVQ530 but increased in an EPS overproducing mutant. Mutant SVQ530 was impaired in surface motility and showed higher osmosensitivity compared to its wild type strain in media containing 50 mM NaCl or 5% (w/v) sucrose. Neither S. fredii HH103 nor 41 other S. fredii strains were recognized by soybean lectin (SBL). S. fredii HH103 mutants affected in exopolysaccharides (EPS), lipopolysaccharides (LPS), cyclic glucans (CG) or capsular polysaccharides (KPS) were not significantly impaired in their soybean-root attachment capacity, suggesting that these surface polysaccharides might not be relevant in early attachment to soybean roots. These results also indicate that the molecular mechanisms involved in S. fredii attachment to soybean roots might be different to those operating in Bradyrhizobium japonicum. PMID:25521500

  18. Neutron diffractometers for structural biology at spallation neutron sources

    International Nuclear Information System (INIS)

    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 3He 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

  19. Structure and biological roles of Sinorhizobium fredii HH103 exopolysaccharide.

    Science.gov (United States)

    Rodríguez-Navarro, Dulce N; Rodríguez-Carvajal, Miguel A; Acosta-Jurado, Sebastián; Soto, María J; Margaret, Isabel; Crespo-Rivas, Juan C; Sanjuan, Juan; Temprano, Francisco; Gil-Serrano, Antonio; Ruiz-Sainz, José E; Vinardell, José M

    2014-01-01

    Here we report that the structure of the Sinorhizobium fredii HH103 exopolysaccharide (EPS) is composed of glucose, galactose, glucuronic acid, pyruvic acid, in the ratios 5∶2∶2∶1 and is partially acetylated. A S. fredii HH103 exoA mutant (SVQ530), unable to produce EPS, not only forms nitrogen fixing nodules with soybean but also shows increased competitive capacity for nodule occupancy. Mutant SVQ530 is, however, less competitive to nodulate Vigna unguiculata. Biofilm formation was reduced in mutant SVQ530 but increased in an EPS overproducing mutant. Mutant SVQ530 was impaired in surface motility and showed higher osmosensitivity compared to its wild type strain in media containing 50 mM NaCl or 5% (w/v) sucrose. Neither S. fredii HH103 nor 41 other S. fredii strains were recognized by soybean lectin (SBL). S. fredii HH103 mutants affected in exopolysaccharides (EPS), lipopolysaccharides (LPS), cyclic glucans (CG) or capsular polysaccharides (KPS) were not significantly impaired in their soybean-root attachment capacity, suggesting that these surface polysaccharides might not be relevant in early attachment to soybean roots. These results also indicate that the molecular mechanisms involved in S. fredii attachment to soybean roots might be different to those operating in Bradyrhizobium japonicum. PMID:25521500

  20. Study of structural model of biological membranes by synchrotron radiation

    CERN Document Server

    Cavalcanti, L P

    2001-01-01

    The objective of this work has been to study, from the structural point of view, the process of incorporation of various types of hydrophobic compounds into the lamellar phase of liposomes and multilayers of the zwitterionic phospholipid DPPC. X-ray diffraction and scattering techniques using synchrotron radiation, have been used to monitor changes of several bilayer systems. Thermotropic phase transitions as well as the order of the lamellar packing were studied in situ experiments. The behavior of the L beta' and L alpha phases was followed as a function of the water content in dispersions of DPPC multi lamellar vesicles with the addition of the alkaloid Ellipticine in several concentrations. The results showed a decrease in the temperature of the pre-transition as well as that of the main transition (P beta' ->L alpha). The decrease of the lamellar spacing as a function of temperature in the liquid crystalline phase leads to the description of the thermal compression coefficient in the L alpha phase. It wa...

  1. Normal and aging hair biology and structure 'aging and hair'.

    Science.gov (United States)

    Goodier, Molly; Hordinsky, Maria

    2015-01-01

    Much like an individual's hairstyle, hair fibers along the scalp see a number of changes over the course of one's lifetime. As the decades pass, the shine and volume synonymous with youthful hair may give way to thin, dull, and brittle hair commonly associated with aging. These changes are a result of a compilation of genetic and environmental elements influencing the cells of the hair follicle, specifically the hair follicle stem cells and melanocytes. Telomere shortening, decrease in cell numbers, and particular transcription factors have all been implicated in this process. In turn, these molecular alterations lead to structural modifications of the hair fiber, decrease in melanin production, and lengthening of the telogen phase of the hair cycle. Despite this inevitable progression with aging, there exists an array of treatments such as light therapy, minoxidil, and finasteride which have been designed to mitigate the effects of aging, particularly balding and thinning hair. Although each works through a different mechanism, all aim to maintain or potentially restore the youthful quality of hair. PMID:26370639

  2. 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.

  3. Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures.

    Science.gov (United States)

    Koehler, Jacob; Rawlings, Chris; Verrier, Paul; Mitchell, Rowan; Skusa, Andre; Ruegg, Alexander; Philippi, Stephan

    2005-01-01

    The structure of a closely integrated data warehouse is described that is designed to link different types and varying numbers of biological networks, sequence analysis methods and experimental results such as those coming from microarrays. The data schema is inspired by a combination of graph based methods and generalised data structures and makes use of ontologies and meta-data. The core idea is to consider and store biological networks as graphs, and to use generalised data structures (GDS) for the storage of further relevant information. This is possible because many biological networks can be stored as graphs: protein interactions, signal transduction networks, metabolic pathways, gene regulatory networks etc. Nodes in biological graphs represent entities such as promoters, proteins, genes and transcripts whereas the edges of such graphs specify how the nodes are related. The semantics of the nodes and edges are defined using ontologies of node and relation types. Besides generic attributes that most biological entities possess (name, attribute description), further information is stored using generalised data structures. By directly linking to underlying sequences (exons, introns, promoters, amino acid sequences) in a systematic way, close interoperability to sequence analysis methods can be achieved. This approach allows us to store, query and update a wide variety of biological information in a way that is semantically compact without requiring changes at the database schema level when new kinds of biological information is added. We describe how this datawarehouse is being implemented by extending the text-mining framework ONDEX to link, support and complement different bioinformatics applications and research activities such as microarray analysis, sequence analysis and modelling/simulation of biological systems. The system is developed under the GPL license and can be downloaded from http://sourceforge.net/projects/ondex/

  4. 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.

  5. Determination of gadolinium-based MRI contrast agents in biological and environmental samples: A review

    Energy Technology Data Exchange (ETDEWEB)

    Telgmann, Lena [University of Münster, Institute of Inorganic and Analytical Chemistry, Münster (Germany); Sperling, Michael [University of Münster, Institute of Inorganic and Analytical Chemistry, Münster (Germany); European Virtual Institute for Speciation Analysis (EVISA), Münster (Germany); Karst, Uwe, E-mail: uk@uni-muenster.de [University of Münster, Institute of Inorganic and Analytical Chemistry, Münster (Germany)

    2013-02-18

    Highlights: ► All major methods for the analysis of Gd-based MRI contrast agents are discussed. ► Biological and environmental samples are covered. ► Pharmacokinetics and species transformation can be investigated. ► The figures of merit as limit of detection and analysis time are described. -- Abstract: The development of analytical methods and strategies to determine gadolinium and its complexes in biological and environmental matrices is evaluated in this review. Gadolinium (Gd) chelates are employed as contrast agents for magnetic resonance imaging (MRI) since the 1980s. In general they were considered as safe and well-tolerated, when in 2006, the disease nephrogenic systemic fibrosis (NSF) was connected to the administration of MRI contrast agents based on Gd. Pathogenesis and etiology of NSF are yet unclear and called for the development of several analytical methods to obtain elucidation in this field. Determination of Gd complex stability in vitro and in vivo, as well as the quantification of Gd in body fluids like blood and urine was carried out. Separation of the Gd chelates was achieved with high performance liquid chromatography (HPLC) and capillary electrophoresis (CE). For detection, various methods were employed, including UV–vis absorbance and fluorescence spectroscopy, electrospray ionization mass spectrometry (ESI-MS) and inductively coupled plasma mass spectrometry (ICP-MS). A second challenge for analysts was the discovery of high concentrations of anthropogenic Gd in surface waters draining populated areas. The source could soon be determined to be the increasing administration of Gd complexes during MRI examinations. Identification and quantification of the contrast agents was carried out in various surface and groundwater samples to determine the behavior and fate of the Gd chelates in the environment. The improvement of limits of detection (LOD) and limits of quantification (LOQ) was and still is the goal of past and ongoing

  6. Potentiometric detection in UPLC as an easy alternative to determine cocaine in biological samples.

    Science.gov (United States)

    Daems, Devin; van Nuijs, Alexander L N; Covaci, Adrian; Hamidi-Asl, Ezat; Van Camp, Guy; Nagels, Luc J

    2015-07-01

    The analytical methods which are often used for the determination of cocaine in complex biological matrices are a prescreening immunoassay and confirmation by chromatography combined with mass spectrometry. We suggest an ultra-high-pressure liquid chromatography combined with a potentiometric detector, as a fast and practical method to detect and quantify cocaine in biological samples. An adsorption/desorption model was used to investigate the usefulness of the potentiometric detector to determine cocaine in complex matrices. Detection limits of 6.3 ng mL(-1) were obtained in plasma and urine, which is below the maximum residue limit (MRL) of 25 ng mL(-1). A set of seven plasma samples and 10 urine samples were classified identically by both methods as exceeding the MRL or being inferior to it. The results obtained with the UPLC/potentiometric detection method were compared with the results obtained with the UPLC/MS method for samples spiked with varying cocaine concentrations. The intraclass correlation coefficient was 0.997 for serum (n =7) and 0.977 for urine (n =8). As liquid chromatography is an established technique, and as potentiometry is very simple and cost-effective in terms of equipment, we believe that this method is potentially easy, inexpensive, fast and reliable.

  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. Ambient and biological monitoring of cokeoven workers: determinants of the internal dose of polycyclic aromatic hydrocarbons.

    Science.gov (United States)

    Jongeneelen, F J; van Leeuwen, F E; Oosterink, S; Anzion, R B; van der Loop, F; Bos, R P; van Veen, H G

    1990-07-01

    Polycyclic aromatic hydrocarbons (PAH) were measured in the breathing zone air of 56 battery workers at two cokeovens during three consecutive days. The concentration of total PAH ranged up to 186 micrograms/m3. Preshift and end of shift urine samples were collected to determine 1-hydroxypyrene, a metabolite of pyrene. Control urine samples were available from 44 workers in the shipping yard of a hot rolling mill. The median values of 1-hydroxypyrene in urine of smoking and non-smoking controls were 0.51 and 0.17 mumol/mol creatinine, respectively. Concentrations of 1-hydroxypyrene up to 11.2 mumol/mol were found in the urine of the cokeoven workers. At the start of the three day working period after 32 hours off work, the 1-hydroxypyrene concentrations were four times higher and at the end of the working period 10 times higher compared with control concentrations. Excretion of 1-hydroxypyrene occurred with a half life of 6-35 hours. Both the ambient air monitoring data and the biological monitoring data showed that the topside workers were the heaviest exposed workers. The relation between air monitoring data and biological monitoring data was not strong. Multiple regression analysis was performed to identify determinants of the internal dose. The combination of exposure and smoking amplify each other and the use of a protective airstream helmet decreases the internal dose. An effect of alcohol consumption and the use of medication on the toxicokinetics of pyrene was not found.

  9. Determinants of capital structure: Evidence from Istanbul stock exchange

    OpenAIRE

    Samery, Mohammad

    2013-01-01

    ABSTRACT: This thesis aims to explain determinants of capital structure evidence from istanbul stock exchange from three companies (Turkcell ,Vodafone and Deutesche Telekom).The two main theories used are for trade-off theory and pecking order theory. The essential of the pecking order is the manager's of capital structure decision are influenced by the market perception of manager's superior information. The trade-off theory provides support for manager's trade-off between benefits and costs...

  10. The beamlines of ELETTRA and their application to structural biology.

    Science.gov (United States)

    Zanini, F; Lausi, A; Savoia, A

    1999-01-01

    sample crystal in order to reduce the radiation damage. SAXS is an experimental technique used to derive structural information about supra-molecular assemblies, amorphous materials and partly ordered systems (e.g. size and shape of large molecules). The high-flux SAXS beamline at ELETTRA is mainly intended for time-resolved studies on fast structural transitions in the sub-millisecond time region in solutions and in partly ordered systems, triggered by external or process parameters, with a SAXS resolution between 10 and 1400 A in real space. The source is the already mentioned 57-pole and the SAXS beamline accepts three discrete energies of its spectrum, namely 5.4, 8 and 16 keV. The beamline optics consists of a flat double-crystal monochromator and a double focusing toroidal mirror. A multi-purpose sample stage, movable along an optical table in order to optimise the sample to detect distance, allows to perform fast time-resolved relaxation studies based on temperature- or pressure-jumps as well as stopped flow experiments. Moreover, the users have option to install their own specialised sample surrounding equipment. The optimisation of the beamline with respect to high-flux and consequently high-flux density, allows to perform the following experiments: low contrast solution scattering, grazing incidence surface diffraction, micro-spot scanning, X-ray fluorescence analysis, time-resolved studies > or = 11 microseconds, simultaneous small- and wide-angle measurements on gels, liquid crystals, biopolymers, amorphous materials, muscles. PMID:10710723

  11. Slavnov determinants, Yang-Mills structure constants, and discrete KP

    OpenAIRE

    Foda, O.; Wheeler, M.

    2012-01-01

    Using Slavnov's scalar product of a Bethe eigenstate and a generic state in closed XXZ spin-1/2 chains, with possibly twisted boundary conditions, we obtain determinant expressions for tree-level structure constants in 1-loop conformally-invariant sectors in various planar (super) Yang-Mills theories. When certain rapidity variables are allowed to be free rather than satisfy Bethe equations, these determinants become discrete KP tau-functions.

  12. A Biological Condition Gradient Model for Historical Assessment of Estuarine Habitat Structure

    Science.gov (United States)

    Shumchenia, Emily J.; Pelletier, Marguerite C.; Cicchetti, Giancarlo; Davies, Susan; Pesch, Carol E.; Deacutis, Christopher F.; Pryor, Margherita

    2015-01-01

    Coastal ecosystems are affected by ever-increasing natural and human pressures. Because the physical, chemical, and biological characteristics unique to estuarine ecosystems control the ways that biological resources respond to ecosystem stressors, we present a flexible and adaptable biological assessment method for estuaries. The biological condition gradient (BCG) is a scientific framework of biological response to increasing anthropogenic stress that is comprehensive and ecosystem based and evaluates environmental conditions and the status of ecosystem services in order to identify, communicate, and prioritize management action. Using existing data, we constructed the first estuarine BCG framework that examines changes in habitat structure through time. Working in a New England (U.S.) estuary with a long history of human influence, we developed an approach to define a reference level, which we described as a "minimally disturbed" range of conditions for the ecosystem, anchored by observations before 1850 AD. Like many estuaries in the U.S., the relative importance of environmental stressors changed over time, but even qualitative descriptions of the biological indicators' status provided useful information for defining condition levels. This BCG demonstrated that stressors rarely acted alone and that declines in one biological indicator influenced the declines of others. By documenting the biological responses to cumulative stressors, the BCG inherently suggests an ecosystem-based approach to management. Additionally, the BCG process initiates thinking over long time scales and can be used to inspire scientists, managers, and the public toward environmental action.

  13. In search of a reliable technique for the determination of the biological stability of the organic matter in the mechanical-biological treated waste.

    Science.gov (United States)

    Barrena, Raquel; d'Imporzano, Giuliana; Ponsá, Sergio; Gea, Teresa; Artola, Adriana; Vázquez, Felícitas; Sánchez, Antoni; Adani, Fabrizio

    2009-03-15

    The biological stability determines the extent to which readily biodegradable organic matter has decomposed. In this work, a massive estimation of indices suitable for the measurement of biological stability of the organic matter content in solid waste samples has been carried out. Samples from different stages in a mechanical-biological treatment (MBT) plant treating municipal solid wastes (MSW) were selected as examples of different stages of organic matter stability in waste biological treatment. Aerobic indices based on respiration techniques properly reflected the process of organic matter biodegradation. Static and dynamic respirometry showed similar values in terms of aerobic biological activity (expressed as oxygen uptake rate, OUR), whereas cumulative oxygen consumption was a reliable method to express the biological stability of organic matter in solid samples. Methods based on OUR and cumulative oxygen consumption were positively correlated. Anaerobic methods based on biogas production (BP) tests also reflected well the degree of biological stability, although significant differences were found in solid and liquid BP assays. A significant correlation was found between cumulative oxygen consumption and ultimate biogas production. The results obtained in this study can be a basis for the quantitative measurement of the efficiency in the stabilization of organic matter in waste treatment plants, including MBT plants, anaerobic digestion of MSW and composting plants. PMID:18606494

  14. Capital Structure of Agricultural Businesses and its Determinants

    Directory of Open Access Journals (Sweden)

    R. Aulová

    2013-06-01

    Full Text Available The article deals with the analysis of the capital structure of agricultural businesses of legal entities and its determinants. It discusses the effect of selected determinants on the capital structure of businesses, expressed by way of three categories of indebtedness. The analysis of the determinants of capital structure is conducted by way of multiple linear regression. Also being verified is the hypothesis of whether the effect of individual determinants of capital structure is in accordance with the theoretical assumptions of conditional theories of capital structure and empirical studies.The panel data for the article were acquired from the Albertina database, provided by the company Soliditet, s.r.o. Specifically, the data used were those from accounting statements for the years 2004 – 2010 for the agricultural businesses of legal entities. In total, the object of examination was 16075 businesses, which were divided up according to legal forms (joint stock company, cooperative, and limited liability company and subsequently the relevant size group. In total, 18 groups of businesses were created, whereby the average balance and profit and loss account were drawn up for each group, on the basis of which the relevant calculations were conducted. The article is a part of the grant project IGA 20121069 “Identification of the main determinants of the result of economic activity of agricultural businesses of legal entities and the determination of their specifics” and of the institutional research intentions MSM 6046070906 „Economics sources of Czech agriculture and their efficient use in the context of multifunctional agri-food systems“.

  15. Biological Determinism and the Narrative of Adjustment: The High School Biology Textbooks of Truman Jesse Moon, c. 1921-1963

    Science.gov (United States)

    Selden, Steven

    2007-01-01

    While the mainline eugenics movement in early 20th century was closely associated with racism and the European Holocaust and was present in biology textbooks in the early 20th century, the following article finds that a transformed eugenics could be found the U.S. science curriculum by mid-century. The following article analyzes the content of 73…

  16. 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.

  17. Benzenediol lactones: a class of fungal metabolites with diverse structural features and biological activities.

    Science.gov (United States)

    Shen, Weiyun; Mao, Hongqiang; Huang, Qian; Dong, Jinyan

    2015-06-01

    Benzenediol lactones are a structurally variable family of fungal polyketide metabolites possessing a macrolide core structure fused into a resorcinol aromatic ring. These compounds are widespread in fungi mainly in the genera such as Aigialus, Cochliobolus, Curvularia, Fusarium, Humicola, Lasiodiplodia, Penicillium and Pochonia etc. Most of these fungal metabolites were reported to possess several interesting biological activities, such as cytotoxicities, nematicidal properties, inhibition of various kinases, receptor agonists, anti-inflammatory activities, heat shock response and immune system modulatory activities etc. This review summarizes the research on the isolation, structure elucidation, and biological activities of the benzenediol lactones, along with some available structure-activity relationships, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structure or stereochemistry, published up to the year of 2014. More than 190 benzenediol lactones are described, and over 300 references cited. PMID:25559850

  18. 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…

  19. Synthesis and structure determination of novel hexasubstituted cyclohexadienes

    Institute of Scientific and Technical Information of China (English)

    Hong Mei Qu; Xin Hui Niu; Juan Li; Jun Liu; Li Li Jiang; Jian Ke Tang; Li Shan Zhou

    2012-01-01

    The linear trienes were obtained in high yields by copper-mediated cycloaddition of 2,5-bis(trimethylsilyl)zirconacyclopentadienes with dimethyl acetylenedicarboxylate (DMAD) which can be quantitatively converted to novel asymmetric hexasubstituted cyclohexadienes with high (E)-stereoselectivity.The structure of cyclohexadienes was determined via X-ray analysis.

  20. 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

  1. 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.

  2. The use of self-determination theory to foster environmental motivation in an environmental biology course

    Science.gov (United States)

    Darner, Rebekka

    A scientifically literate person is one who understands the nature of science, its processes, products, and their appropriate application to decision-making contexts. The impetus to make informed decisions about environmental issues is environmental motivation. I examined students' environmental motivation, its relationship to scientific knowledge, and how environmental motivation can be fostered in a science classroom. This study took place in a college-level environmental biology course in which the instructor attempted to support students' basic psychological needs, as defined by self-determination theory (SDT). The first question was to what extent does an SDT-guided environmental biology course differ from a non-SDT-guided course in the degree to which it fostered self-determined motivation toward the environment. The administration of a well-validated scale to two sections before, after, and six months following the end of the course indicated that SDT-guided instruction is a plausible way to foster environmental motivation in the classroom. The second question was what are the multiple influences on fostering self-determined motivation toward the environment in an SDT-guided course. Path analysis indicated that environmental motivation can be partially accomplished in an environmental biology course by conveying to students that they are cared for, are connected to others, and can trust others while solving environmental problems. The third question sought to characterize students' scientific conceptualizations as they solve environmental problems and the extent to which their conceptualizations relate to the satisfaction of their need for competence. Students were videotaped during in-class problem-solving, after which stimulated-recall interviews were conducted. Grounded theory and an established coding scheme were combined to analyze these data, which resulted in three grounded hypotheses about what characterizes students' scientific knowledge when they

  3. The Widespread Prevalence and Functional Significance of Silk-Like Structural Proteins in Metazoan Biological Materials.

    Science.gov (United States)

    McDougall, Carmel; Woodcroft, Ben J; Degnan, Bernard M

    2016-01-01

    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 construction of

  4. 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

  5. The Widespread Prevalence and Functional Significance of Silk-Like Structural Proteins in Metazoan Biological Materials

    Science.gov (United States)

    McDougall, Carmel; Woodcroft, Ben J.

    2016-01-01

    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 construction of

  6. Determination of zinc stable isotopes in biological materials using isotope dilution inductively coupled plasma mass spectrometry

    International Nuclear Information System (INIS)

    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

  7. The challenge of determining the need for remediation following a wide-area biological release.

    Science.gov (United States)

    Raber, Ellen

    2011-09-01

    Recovering from a biological attack is a complex process requiring the successful resolution of numerous challenges. The Interagency Biological Restoration Demonstration program is one of the first multiagency efforts to develop strategies and tools that could be effective following a wide-area release of B. anthracis spores. Nevertheless, several key policy issues and associated science and technology issues still need to be addressed. For example, more refined risk assessment and management approaches are needed to help evaluate "true" public health risk. Once the risk is understood, that information can be considered along with the types of characterization activities deemed necessary to determine whether the cost and time of decontamination are actually warranted. This commentary offers 5 recommendations associated with decision making regarding decontamination and clearance options that should accompany a comprehensive risk analysis leading to more effective risk management decisions. It summarizes some of the most important technological gaps that still need to be addressed to help decision makers in their objective of reducing health risks to an acceptable level. The risk management approach described should enable decision makers to improve credibility and gain public acceptance, especially when an adequate science and technology base is available to support the required decisions. PMID:21882967

  8. WHOLE CELL TOMOGRAPHY/MOLECULAR BIOLOGY/STRUCTURAL BIOLOGY: Affordable x-ray microscopy with nanoscale resolution

    Energy Technology Data Exchange (ETDEWEB)

    Evans, James E.; Blackborow, Paul; Horne, Stephen J.; Gelb, Jeff

    2013-03-01

    Biological research spans 10 orders of magnitude from angstroms to meters. While electron microscopy can reveal structural details at most of these spatial length scales, transmission electron tomography only reliably reconstructs three-dimensional (3-D) volumes of cellular material with a spatial resolution between 1-5 nm from samples less than 500 nm thick1. Most biological cells are 2-30 times thicker than this threshold, which means that a cell must be cut into consecutive slices with each slice reconstructed individually in order to approximate the contextual information of the entire cell. Fortunately, due to a larger penetration depth2, X-ray computed tomography bypasses the need to physically section a cell and enables imaging of intact cells and tissues on the micrometer or larger scale with tens to hundreds of nanometer spatial resolution. While the technique of soft x-ray microscopy has been extensively developed in synchrotron facilities, advancements in laboratory x-ray source designs now increase its accessibility by supporting commercial systems suitable for a standard laboratory. In this paper, we highlight a new commercial compact cryogenic soft x-ray microscope designed for a standard laboratory setting and explore its capabilities for mesoscopic investigations of intact prokaryotic and eukaryotic cells.

  9. 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 t

  10. The ALOUD Study: Adult Learning Open University Determinants Study - Influence of biological and psychological determinants on study success in formal lifelong learning in adults

    NARCIS (Netherlands)

    Gijselaers, Jérôme; Neroni, Joyce; De Groot, Renate; Kirschner, Paul A.

    2011-01-01

    Gijselaers, H. J. M., Neroni, J., De Groot, R. H. M., & Kirschner, P. A. (2011, September). The ALOUD Study: Adult Learning Open University Determinants Study - Influence of biological and psychological determinants on study success in formal lifelong learning in adults. Presentation given for visit

  11. Methylmercury determination in biological samples using electrothermal atomic absorption spectrometry after acid leaching extraction

    Energy Technology Data Exchange (ETDEWEB)

    Saber-Tehrani, Mohammad; Hashemi-Moghaddam, Hamid; Givianrad, Mohammad Hadi; Abroomand-Azar, Parviz [Islamic Azad University, Department of Chemistry, Science and Research Branch, Tehran (Iran)

    2006-11-15

    An efficient and sensitive method for the determination of methylmercury in biological samples was developed based on acid leaching extraction of methylmercury into toluene. Methylmercury in the organic phase was determined by electrothermal atomic absorption spectrometry (ETAAS). The methylmercury signal was enhanced and the reproducibility increased by formation of certain complexes and addition of Pd-DDC modifier. The complex of methylmercury with DDC produced the optimum analytical signal in terms of sensitivity and reproducibility compared to complexes with dithizone, cysteine, 1,10-phenanthroline, and diethyldithiocarbamate. Method performance was optimized by modifying parameters such as temperature of mineralization, atomization, and gas flow rate. The limit of detection for methylmercury determination was 0.015 {mu}g g{sup -1} and the RSD of the whole procedure was 12% for human teeth samples (n=5) and 15.8% for hair samples (n=5). The method's accuracy was investigated by using NIES-13 and by spiking the samples with different amounts of methylmercury. The results were in good agreement with the certified values and the recoveries were 88-95%. (orig.)

  12. 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.

  13. A simple kinetic spectrophotometric method for the determination of oxamniquine in formulations and spiked biological fluids.

    Science.gov (United States)

    Rizk, M; Belal, F; Ibrahim, F; Ahmed, S M; El-Enany, N M

    2000-08-15

    A simple and sensitive kinetic method for the determination of oxamniquine in pharmaceutical preparations and biological fluids was developed. The procedure is based upon a kinetic investigation of the oxidation reaction of the drug with alkaline potassium permanganate at room temperature for a fixed time of 20 min. The absorbance of the colored manganate ions was measured at 610 nm. Alternatively, the decrease in the absorbance of potassium permanganate after addition of the drug was measured at 525 nm. The absorbance concentration plots in both procedures were rectilinear over the range 0.5-4 microg ml(-1). The concentration of oxamniquine is calculated using the corresponding calibration equation for the fixed-time method. The determination of oxamniquine by fixed-concentration and rate-constant methods was feasible with the calibration equations obtained but the fixed time method had been found to be more applicable. Both procedures were applied to the determination of oxamniquine in formulations. The results obtained were in good agreement with those obtained using the official method. The fixed time method of 20 min was further applied to spiked human urine and plasma, the recoveries (%) were 100.94 +/- 0.57 and 98.07 +/- 0.88 for urine and plasma, respectively, at 610 nm, and 97.51 +/- 1.27 and 95.69 +/- 1.23 for urine and plasma, respectively, at 525 nm. PMID:10933544

  14. 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.

  15. 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. PMID:25585870

  16. 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.

  17. 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, E-mail: chatake@rri.kyoto-u.ac.jp [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.

  18. 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...

  19. NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology.

    Science.gov (United States)

    Romano, Paolo; Cordero, Francesca

    2016-03-02

    The fourteenth NETTAB workshop, NETTAB 2014, was devoted to a range of disciplines going from structural bioinformatics, to proteomics and to integrative systems biology. The topics of the workshop were centred around bioinformatics methods, tools, applications, and perspectives for models, standards and management of high-throughput biological data, structural bioinformatics, functional proteomics, mass spectrometry, drug discovery, and systems biology.43 scientific contributions were presented at NETTAB 2014, including keynote, special guest and tutorial talks, oral communications, and posters. Full papers from some of the best contributions presented at the workshop were later submitted to a special Call for this Supplement.Here, we provide an overview of the workshop and introduce manuscripts that have been accepted for publication in this Supplement.

  20. Flowering biology and structure of floral nectaries in Galanthus nivalis L.

    Directory of Open Access Journals (Sweden)

    Elżbieta Weryszko-Chmielewska

    2016-03-01

    Full Text Available In Poland Galanthus nivalis L. is partially protected. The flowers of this species are one of the first sources of nectar and pollen for insects from February to April. The aim of this study was to present the flowering biology as well as the topography, anatomical, and ultrastructural features of the floral nectary. The flower lifespan, the breeding system, and the mass of pollen and nectar produced by the flowers were determined. Examination of the nectary structure was performed using light, fluorescence, scanning and transmission electron microscopy. The flower of G. nivalis lives for about 30 days. The stamens and pistils mature simultaneously and during this time nectar is secreted. The anthers of one flower produced the large amount of pollen (4 mg. The breeding system of G. nivalis was found to be characterized by partial self-compatibility, outcrossing, and xenogamy. The nectary is located at the top of the inferior ovary. The nectary epidermal cells are characterized by striated cuticular ornamentation. Initially, the secreted nectar formed vesicle-like protuberances under the cuticle. The epidermal and parenchymal cells contain numerous plastids, mitochondria, dictyosomes, ER cisterns, and vesicles fused with the plasmalemma, which indicates granulocrine nectar secretion.

  1. 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.

  2. 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. PMID:27596431

  3. X-ray structure determination at low resolution

    International Nuclear Information System (INIS)

    Refinement is meaningful even at 4 Å or lower, but with present methodologies it should start from high-resolution crystal structures whenever possible. As an example of structure determination in the 3.5–4.5 Å resolution range, crystal structures of the ATPase p97/VCP, consisting of an N-terminal domain followed by a tandem pair of ATPase domains (D1 and D2), are discussed. The structures were originally solved by molecular replacement with the high-resolution structure of the N-D1 fragment of p97/VCP, whereas the D2 domain was manually built using its homology to the D1 domain as a guide. The structure of the D2 domain alone was subsequently solved at 3 Å resolution. The refined model of D2 and the high-resolution structure of the N-D1 fragment were then used as starting models for re-refinement against the low-resolution diffraction data for full-length p97. The re-refined full-length models showed significant improvement in both secondary structure and R values. The free R values dropped by as much as 5% compared with the original structure refinements, indicating that refinement is meaningful at low resolution and that there is information in the diffraction data even at ∼4 Å resolution that objectively assesses the quality of the model. It is concluded that de novo model building is problematic at low resolution and refinement should start from high-resolution crystal structures whenever possible

  4. Can OCT be sensitive to nanoscale structural alterations in biological tissue?

    OpenAIRE

    Yi, Ji; Radosevich, Andrew J.; Rogers, Jeremy D.; Norris, Sam C.P.; Çapoğlu, İlker R.; Taflove, Allen; Backman, Vadim

    2013-01-01

    Exploration of nanoscale tissue structures is crucial in understanding biological processes. Although novel optical microscopy methods have been developed to probe cellular features beyond the diffraction limit, nanometer-scale quantification remains still inaccessible for in situ tissue. Here we demonstrate that, without actually resolving specific geometrical feature, OCT can be sensitive to tissue structural properties at the nanometer length scale. The statistical mass-density distributio...

  5. Breaking Frontiers: Submicron Structures in Physics and Biology - 52 Zakopane School of Physics

    International Nuclear Information System (INIS)

    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

  6. Observation and Structure Determination of an Oxide Quasicrystal Approximant.

    Science.gov (United States)

    Förster, S; Trautmann, M; Roy, S; Adeagbo, W A; Zollner, E M; Hammer, R; Schumann, F O; Meinel, K; Nayak, S K; Mohseni, K; Hergert, W; Meyerheim, H L; Widdra, W

    2016-08-26

    We report on the first observation of an approximant structure to the recently discovered two-dimensional oxide quasicrystal. Using scanning tunneling microscopy, low-energy electron diffraction, and surface x-ray diffraction in combination with ab initio calculations, the atomic structure and the bonding scheme are determined. The oxide approximant follows a 3^{2}.4.3.4 Archimedean tiling. Ti atoms reside at the corners of each tiling element and are threefold coordinated to oxygen atoms. Ba atoms separate the TiO_{3} clusters, leading to a fundamental edge length of the tiling 6.7 Å. PMID:27610863

  7. Music structure determines heart rate variability of singers

    Science.gov (United States)

    Vickhoff, Björn; Malmgren, Helge; Åström, Rickard; Nyberg, Gunnar; Ekström, Seth-Reino; Engwall, Mathias; Snygg, Johan; Nilsson, Michael; Jörnsten, Rebecka

    2013-01-01

    Choir singing is known to promote wellbeing. One reason for this may be that singing demands a slower than normal respiration, which may in turn affect heart activity. Coupling of heart rate variability (HRV) to respiration is called Respiratory sinus arrhythmia (RSA). This coupling has a subjective as well as a biologically soothing effect, and it is beneficial for cardiovascular function. RSA is seen to be more marked during slow-paced breathing and at lower respiration rates (0.1 Hz and below). In this study, we investigate how singing, which is a form of guided breathing, affects HRV and RSA. The study comprises a group of healthy 18 year olds of mixed gender. The subjects are asked to; (1) hum a single tone and breathe whenever they need to; (2) sing a hymn with free, unguided breathing; and (3) sing a slow mantra and breathe solely between phrases. Heart rate (HR) is measured continuously during the study. The study design makes it possible to compare above three levels of song structure. In a separate case study, we examine five individuals performing singing tasks (1–3). We collect data with more advanced equipment, simultaneously recording HR, respiration, skin conductance and finger temperature. We show how song structure, respiration and HR are connected. Unison singing of regular song structures makes the hearts of the singers accelerate and decelerate simultaneously. Implications concerning the effect on wellbeing and health are discussed as well as the question how this inner entrainment may affect perception and behavior. PMID:23847555

  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.

    Science.gov (United States)

    Ventegodt, Søren; Hermansen, Tyge Dahl; Flensborg-Madsen, Trine; Rald, Erik; Nielsen, Maj Lyck; Merrick, Joav

    2006-01-01

    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. PMID:17115083

  9. How Events at the Nano/Bio Interface Determine Good and Adverse Biological Outcomes

    Science.gov (United States)

    Nel, Andre

    2014-03-01

    We have come to recognize that much of biology is executed at the nanoscale level, therefore providing a rational approach to using discovery about the structure and function of engineered nanomaterials (ENMs) at the nano/bio interface for interrogation of disease, diagnosis, treatment, and imaging at levels of sophistication not possible before. Moreover, the behavior of ENM's at the nano/bio interface also constitutes the basis for hazard generation and is therefore key for understanding the safety assessment and safer design of nanomaterials. In this overview, I will discuss how discovery at the molecular, cellular, organ and systemic nano/bio interfaces has helped us to my progress progress in the fields of nanomedicine and nanotoxicology. I will explain how the physicochemical properties of nanomaterials relate to nanoscale interactions at the membrane, intracellular organelles, tissues and organs in response to exposure to a variety of commercial ENMs as well as for therapeutic nanocarriers. I will delineate how the use of high throughput screening to establish structure-activity relationships can be used for the design of improved nanocarriers for cancer treatment as well as hazard and risk ranking of large categories of commercial ENMs on their way to the marketplace.

  10. Silica-titania xerogel for solid phase spectrophotometric determination of salicylate and its derivatives in biological liquids and pharmaceuticals

    OpenAIRE

    Morosanova, Maria A.; Morosanova, Elena I.

    2015-01-01

    Background Salicylic acid and its derivatives are widely used drugs with potential toxicity. The main areas of salicylate derivatives determination are biological liquids and pharmaceuticals analysis. Results Silica-titania xerogel has been used for solid phase spectrophotometric determination of various salicylate derivatives (salicylate, salicylamide, methylsalicylate). The reaction conditions influence on the interaction of salicylate derivatives with silica-titania xerogels has been inves...

  11. Empirical Analysis of the Determinants of Marketing Contract Structures

    OpenAIRE

    Paulson, Nicholas D.; Katchova, Ani L.; Sergio H. Lence

    2008-01-01

    Initial draft replaced by updated/revised version. This is an electronic version of a journal article, please cite as: Paulson, N.D., A.L. Katchova, and S.H. Lence. “An Empirical Analysis of the Determinants of Marketing Contract Structures for Corn and Soybeans.” Journal of Agricultural and Food Industrial Organization 8(2010), 4: 1-23.

  12. 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.

  13. Structural Determination and Daily Variations of Porcine Milk Oligosaccharides

    OpenAIRE

    Tao, Nannan; Ochonicky, Karen L.; German, J Bruce; Donovan, Sharon M.; Lebrilla, Carlito B.

    2010-01-01

    Free milk oligosaccharides (OS) is a major component of mammalian milk. Swine are important agricultural species and biomedical models. Despite their importance, little is known of the OS profile of porcine milk. Herein, the porcine milk glycome was elucidated and monitored over the entire lactation period by liquid chromatography profiling and structural determination with mass spectrometry. Milk was collected from second parity sows (n=3) at farrowing and on days 1, 4, 7 and 24 of lactation...

  14. Regional Mechanics Determine Collagen Fiber Structure in Healing Myocardial Infarcts

    OpenAIRE

    Fomovsky, Gregory M.; Rouillard, Andrew D.; Holmes, Jeffrey W.

    2012-01-01

    Following myocardial infarction, the mechanical properties of the healing infarct are an important determinant of heart function and the risk of progression to heart failure. In particular, mechanical anisotropy (having different mechanical properties in different directions) in the healing infarct can preserve pump function of the heart. Based on reports of different collagen structures and mechanical properties in various animal models, we hypothesized that differences in infarct size, shap...

  15. Determination of polycyclic aromatic compounds and heavy metals in sludges from biological sewage treatment plants.

    Science.gov (United States)

    Bodzek, D; Janoszka, B; Dobosz, C; Warzecha, L; Bodzek, M

    1997-07-11

    The procedure of the analysis of polycyclic aromatic hydrocarbons (PAHs) and their derivatives in the sludges from biological sewage treatment plants has been worked out. The analysis included isolation of organic matter from sludges, separation of the extract into fractions of similar chemical character, qualitative-quantitative analysis of individual PAHs and their nitrogenated and oxygenated derivatives. Liquid-solid chromatography, solid-phase extraction and semipreparative band thin-layer chromatography techniques were used for the separation. Capillary gas chromatography-mass spectrometry analysis of the separated fractions enabled identification of more than 21 PAHs, including hydrocarbons which contained 2-6 aromatic rings as well as their alkyl derivatives, 10 oxygen derivatives, 9 nitroarenes, aminoarenes and over 20 azaarenes and carbazoles. Using the capillary gas chromatography-flame ionization detection technique the content of 17 dominant PAHs was determined. The content of heavy metals was determined in investigated sludges with the use of atomic absorption spectrometry. The concentrations of the respective metals could be ranked in the order Cd coal mine wastes, taking into consideration the contents of toxic organic pollutants and heavy metals. PMID:9253190

  16. A new kinetic spectrophotometric method for the determination of major metabolite of heroin in biological samples

    Institute of Scientific and Technical Information of China (English)

    M. Reza Shishehbore; Ali Sheibani; Ehsan Mirparizi

    2012-01-01

    This study describes a simple,rapid and selective catalytic kinetic spectrophotometric method for the determination of 6-monoacetylmorphine (6-MAM) as major metabolite of heroin in biological samples.The method is based upon the catalytic effect of 6-MAM on the oxidation of Janus Green by bromate in acid media.The reaction was followed spectrophotometrically by measuring the decrease in absorbance of Janus Green at 618 nm.The dependence of sensitivity on the reaction variables was studied.Under optimum conditions,two linear calibration curves over the range 0.1-1.0 μg mL-1 and 1.0-34.0 μg mL-1 of 6-MAM were obtained.The detection limit was 1.2 × 10-2 μg mL-1 of 6-MAM.The relative standard deviations for six replicate determinations of 0.8 and 5.0 μg mL 1 of 6-MAM were 1.4 and 1.1% respectively.The effect of various species commonly associated with heroin in real samples was also investigated.The proposed method was successfully applied in human urine and serum samples with satisfactory results.

  17. 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.

  18. 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. PMID:26595290

  19. 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.

  20. Electron Crystallographic Study on Structure Determination for Minute Crystals

    Institute of Scientific and Technical Information of China (English)

    LI Fanghua; FAN Haifu; WAN Zhenghua; HU Jianjun; TANG Dong

    2007-01-01

    @@ In the 1970s the development of high-resolution electron microscopy (HREM) provided a new approach to structure determination for minute crystals, which is thoroughly different from the diffraction methods.However, the previous method of trial and error has its own limits, such as some preliminary structural information must be known in advance; the crystals must be sufficient strong under the electron beam irradiation;and not all atoms can be seen in the image. Two ideas were proposed to initiate the present research project:one is to transform an arbitrary image into the crystal structure map, and the other is to enhance the image resolution by combining the information contained in the image and the corresponding electron diffraction pattern. These ideas have been realized via the combination of electron microscopy and diffraction crystallography.

  1. Local magnetic structure determination using polarized neutron holography

    Energy Technology Data Exchange (ETDEWEB)

    Szakál, Alex, E-mail: szakal.alex@wigner.mta.hu; Markó, Márton, E-mail: marko.marton@wigner.mta.hu; Cser, László, E-mail: cser.laszlo@wigner.mta.hu [Wigner Research Centre for Physics, Konkoly Thege M. út 29-33, H-1121 Budapest (Hungary)

    2015-05-07

    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.

  2. Determination of the stretch tensor for structural transformations

    Science.gov (United States)

    Chen, Xian; Song, Yintao; Tamura, Nobumichi; James, Richard D.

    2016-08-01

    Structural transformations in crystalline solids are increasingly the basis of the functional behavior of materials. Recently, in diverse alloy systems, both low hysteresis and reversibility of phase transformations have been linked to the satisfaction of the nongeneric conditions of compatibility between phases. According to the Cauchy-Born rule, these conditions are expressed as properties of transformation stretch tensor. The transformation stretch tensor is difficult to measure directly due to the lack of knowledge about the exact transforming pathway during the structural change, and the complicating effects of microstructure. In this paper we give a rigorous algorithmic approach for determining the transformation stretch tensor from X-ray measurements of structure and lattice parameters. For some traditional and emerging phase transformations, the results given by the algorithm suggest unexpected transformation mechanisms.

  3. Method and apparatus for determining material structural integrity

    Science.gov (United States)

    Pechersky, Martin

    1996-01-01

    A non-destructive method and apparatus for determining the structural integrity of materials by combining laser vibrometry with damping analysis techniques to determine the damping loss factor of a material. The method comprises the steps of vibrating the area being tested over a known frequency range and measuring vibrational force and velocity as a function of time over the known frequency range. Vibrational velocity is preferably measured by a laser vibrometer. Measurement of the vibrational force depends on the vibration method. If an electromagnetic coil is used to vibrate a magnet secured to the area being tested, then the vibrational force is determined by the amount of coil current used in vibrating the magnet. If a reciprocating transducer is used to vibrate a magnet secured to the area being tested, then the vibrational force is determined by a force gauge in the reciprocating transducer. Using known vibrational analysis methods, a plot of the drive point mobility of the material over the preselected frequency range is generated from the vibrational force and velocity measurements. The damping loss factor is derived from a plot of the drive point mobility over the preselected frequency range using the resonance dwell method and compared with a reference damping loss factor for structural integrity evaluation.

  4. 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.

  5. Entity grammar systems: a grammatical tool for studying the hierarchical structures of biological systems.

    Science.gov (United States)

    Wang, Yun

    2004-05-01

    The hierarchical structures of biological systems are the typical complex hierarchical dynamical structures in the physical world, the effective investigations on which could not be performed with the existing formal grammar systems. To meet the needs of the investigation on these kinds of systems, especially the emerging field of system biology, a grammatical tool was proposed in the present article. Because the grammatical tool mainly deals with the systems composed of structured entities, they are called entity grammar systems (EGSs). The structure of entities in EGSs have the general form of the objects in the physical world, which means EGSs could be used as a tool to study the complex system composed of many objects with different structures, just like the biological systems. The article contains the formal definition of EGSs and the hierarchy of EGSs, which is congruent with the Chomsky hierarchy. The relationship between EGSs and array grammar systems, graph grammar systems, tree grammar systems, multi-set grammar systems are discussed to show the generative power of EGSs. At the end of the present article, the steps to define new grammar systems with the form of EGS are provided and the possible applicable fields of EGSs are discussed. PMID:15006443

  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

    2016-01-01

    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-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. PMID:26902326

  7. Form and function: Perspectives on structural biology and resources for the future

    International Nuclear Information System (INIS)

    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

  8. 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.

  9. Chemical modifiers in arsenic determination in biological materials by tungsten coil electrothermal atomic absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Bruhn, C.G.; Huerta, V.N.; Neira, J.Y. [Departamento de Analisis Instrumental, Facultad de Farmacia, Universidad de Concepcion, P.O. Box 237, Concepcion (Chile)

    2004-01-01

    Palladium, iridium, and rhodium are evaluated as possible chemical modifiers in the determination of As in digest solutions of biological materials (human hair and clam) by tungsten coil electrothermal atomic absorption spectrophotometry (TCA-AAS). The modifier in solution was applied onto the coil and thermally pre-reduced; the pre-reduction conditions, the amount of modifier, and the thermal program were optimized. Palladium was not satisfactory, whereas Ir and Rh were effective modifiers and rendered better relative sensitivity for As by a factor of 1.4 and 1.9, respectively compared to the case without modifier. Upon optimization of thermal conditions for As in pre-reduced Ir (2.0 {mu}g) and Rh (2.0 {mu}g) modifiers and in the digest solutions of the study matrices, Rh (2.0 {mu}g) was more effective modifier and was selected as such. The mean within-day repeatability was 2.8% in consecutive measurements (25-100 {mu}g L{sup -1}) (3 cycles, each of n=6) and confirmed good short-term stability of the absorbance measurements. The mean reproducibility was 4.4% (n=20 in a 3-day period) and the detection limit (3{sigma}{sub blank}/slope) was 29 pg (n=15). The useful coil lifetime in Rh modifier was extended to 300-400 firings. Validation was by determination of As in the certified reference material (CRM) of ''Oyster tissue'' solution with a percentage relative error (E{sub rel}%) of 2% and percentage relative standard deviation (RSD%) of 3% (n=4), and by analytical recovery of As spiked in CRM of human hair [94{+-}8% (n=4)]. The methodology is simple, fast (sample readout frequency 21 h{sup -1}), reliable, of low cost, and was applied to the determination of As in hair samples of exposed and unexposed workers. (orig.)

  10. 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

  11. Three-dimensional printing of complex biological structures by freeform reversible embedding of suspended hydrogels.

    Science.gov (United States)

    Hinton, Thomas J; Jallerat, Quentin; Palchesko, Rachelle N; Park, Joon Hyung; Grodzicki, Martin S; Shue, Hao-Jan; Ramadan, Mohamed H; Hudson, Andrew R; Feinberg, Adam W

    2015-10-01

    We demonstrate the additive manufacturing of complex three-dimensional (3D) biological structures using soft protein and polysaccharide hydrogels that are challenging or impossible to create using traditional fabrication approaches. These structures are built by embedding the printed hydrogel within a secondary hydrogel that serves as a temporary, thermoreversible, and biocompatible support. This process, termed freeform reversible embedding of suspended hydrogels, enables 3D printing of hydrated materials with an elastic modulus hardware and software tools. Proof-of-concept structures based on femurs, branched coronary arteries, trabeculated embryonic hearts, and human brains were mechanically robust and recreated complex 3D internal and external anatomical architectures. PMID:26601312

  12. Synthesis, Dimeric Crystal Structure, and Biological Activities of N-(4-Methyl-6-oxo-1,6-dihydro-pyrimidin-2-yl)-N-(2-trifluoromethyl-phenyl)-guanidine

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The title compound, N-(4-methyl-6-oxo-1,6-dihydro-pyrimidin-2-yl)-N′-(2-trifluoromethyl-phenyl)-guanidine, was synthesized and its structure was confirmed by using IR, MS, 1H NMR, and elemental analysis. The single crystal structure of the title compound was determined by X-ray diffraction. The preliminary biological test showed that the synthesized compound has a weak herbicidal activity.

  13. Determination of organic crystal structures by X ray powder diffraction

    CERN Document Server

    McBride, L

    2000-01-01

    The crystal structure of Ibuprofen has been solved from synchrotron X-ray powder diffraction data using a genetic algorithm (GA). The performance of the GA is improved by incorporating prior chemical information in the form of hard limits on the values that can be taken by the flexible torsion angles within the molecule. Powder X-ray diffraction data were collected for the anti-convulsant compounds remacemide, remacemide nitrate and remacemide acetate at 130 K on BM 16 at the X-ray European Synchrotron Radiation Facility (ESRF) at Grenoble. High quality crystal structures were obtained using data collected to a resolution of typically 1.5 A. The structure determinations were performed using a simulated annealing (SA) method and constrained Rietveld refinements for the structures converged to chi sup 2 values of 1.64, 1.84 and 1.76 for the free base, nitrate and acetate respectively. The previously unknown crystal structure of the drug famotidine Form B has been solved using X-ray powder diffraction data colle...

  14. Ab initio determination of dark structures in radiationless transitions for aromatic carbonyl compounds.

    Science.gov (United States)

    Fang, Wei-Hai

    2008-03-01

    Mechanistic photodissociation of a polyatomic molecule has long been regarded as an intellectually challenging area of chemical physics, the results of which are relevant to atmospheric chemistry, biological systems, and many application fields. Carbonyl compounds play a unique role in the development of our understanding of the spectroscopy, photochemistry, and photophysics of polyatomic molecules and their photodissociation has been the subject of numerous studies over many decades. Upon irradiation, a molecule can undergo internal conversion (IC) and intersystem crossing (ISC) processes, besides photochemical and other photophysical processes. Transient intermediates formed in the IC and ISC radiationless processes, which are termed "dark", are not amenable to detection by conventional light absorption or emission. However, these dark intermediates play critical roles in IC and ISC processes and thus are essential to understanding mechanistic photochemistry of a polyatomic molecule. We have applied the multiconfiguration complete active space self-consistent field (CASSCF) method to determine the dark transient structures involved in radiationless processes for acetophenone and the related aromatic carbonyl compounds. The electronic and geometric structures predicted for the dark states are in a good agreement with those determined by ultrafast electron diffraction experiments. Intersection structure of different electronic states provides a very efficient "funnel" for the IC or ISC process. However, experimental determination of the intersection structure involved in radiationless transitions of a polyatomic molecule is impossible at present. We have discovered a minimum energy crossing point among the three potential energy surfaces (S1, T1, and T2) that appears to be common to a wide variety of aromatic carbonyl compounds with a constant structure. This new type of crossing point holds the key to understanding much about radiationless processes after

  15. 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.

  16. Synthesis and Structural Determination of Temocapril Sulfoxide Hydrochlorides

    Energy Technology Data Exchange (ETDEWEB)

    Seong, Seok Bong; Moon, Jong Taik; Kim, Jung Ahn; Choo, Dong Joon; Lee, Jae Yeol [Kyung Hee Univ., Seoul (Korea, Republic of)

    2012-10-15

    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.

  17. Velocity Structure Determination Through Seismic Waveform Modeling and Time Deviations

    Science.gov (United States)

    Savage, B.; Zhu, L.; Tan, Y.; Helmberger, D. V.

    2001-12-01

    Through the use of seismic waveforms recorded by TriNet, a dataset of earthquake focal mechanisms and deviations (time shifts) relative to a standard model facilitates the investigation of the crust and uppermost mantle of southern California. The CAP method of focal mechanism determination, in use by TriNet on a routine basis, provides time shifts for surface waves and Pnl arrivals independently relative to the reference model. These shifts serve as initial data for calibration of local and regional seismic paths. Time shifts from the CAP method are derived by splitting the Pnl section of the waveform, the first arriving Pn to just before the arrival of the S wave, from the much slower surface waves then cross-correlating the data with synthetic waveforms computed from a standard model. Surface waves interact with the entire crust, but the upper crust causes the greatest effect. Whereas, Pnl arrivals sample the deeper crust, upper mantle, and source region. This natural division separates the upper from lower crust for regional calibration and structural modeling and allows 3-D velocity maps to be created using the resulting time shifts. Further examination of Pnl and other arrivals which interact with the Moho illuminate the complex nature of this boundary. Initial attempts at using the first 10 seconds of the Pnl section to determine upper most mantle structure have proven insightful. Two large earthquakes north of southern California in Nevada and Mammoth Lakes, CA allow the creation of record sections from 200 to 600 km. As the paths swing from east to west across southern California, simple 1-D models turn into complex structure, dramatically changing the waveform character. Using finite difference models to explain the structure, we determine that a low velocity zone is present at the base of the crust and extends to 100 km in depth. Velocity variations of 5 percent of the mantle in combination with steeply sloping edges produces complex waveform variations

  18. 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.

  19. Mercury speciation and total trace element determination of low-biomass biological samples.

    Science.gov (United States)

    Taylor, Vivien F; Jackson, Brian P; Chen, Celia Y

    2008-12-01

    Current approaches to mercury speciation and total trace element analysis require separate extraction/digestions of the sample. Ecologically important aquatic organisms--notably primary consumers such as zooplankton, polychaetes and amphipods--usually yield very low biomass for analysis, even with significant compositing of multiple organisms. Individual organisms in the lower aquatic food chains (mussels, snails, oysters, silversides, killifish) can also have very low sample mass, and analysis of whole single organisms is important to metal uptake studies. A method for the determination of both methyl Hg and total heavy metal concentrations (Zn, As, Se, Cd, Hg, Pb) in a single, low-mass sample of aquatic organisms was developed. Samples (2 to 50 mg) were spiked with enriched with (201)MeHg and (199)Hg, then leached in 4 M HNO(3) at 55 degrees C for extraction of MeHg. After 16 h, an aliquot (0.05 mL) was removed to determine mercury species (methyl and inorganic Hg) by isotope dilution gas chromatography inductively coupled plasma mass spectrometry (ICP-MS). The leachate was then acidified to 9 M HNO(3) and digested in a microwave at 150 degrees C for 10 min, and total metal concentrations were determined by collision cell ICP-MS. The method was validated by analyzing five biological certified reference materials. Average percent recoveries for Zn, As, Se, Cd, MeHg, Hg(total) and Pb were 99.9%, 103.5%, 100.4%, 103.3%, 101%, 97.7%, and 97.1%, respectively. The correlation between the sum of MeHg and inorganic Hg from the speciation analysis and total Hg by conventional digestion of the sample was determined for a large sample set of aquatic invertebrates (n = 285). Excellent agreement between the two measured values was achieved. This method is advantageous in situations where sample size is limited, and where correlations between Hg species and other metals are required in the same sample. The method also provides further validation of speciation data, by

  20. Separation Scheme for the Determination of Nine Elements in Biological Material

    International Nuclear Information System (INIS)

    A separation scheme is presented for the determination of nine trace elements in biological samples that give rise to long-lived gamma-emitting isotopes by neutron irradiation, namely silver, molybdenum, mercury, gold, chromium, cobalt, selenium, iron and zinc. The organic material is destroyed by combustion with oxygen in a flask according to Schöniger in the presence of 100 μg of carrier of each element. The ignition is electrical and provides an easy and safe method for burning the samples and avoiding losses of volatile elements. The combustion products are collected in HNO3-H2O2 - solution. Carrier yields of at least 98% were obtained in tracer experiments, except for gold and silver. At high temperatures these elements apparently form an Au-Pt and Ag-Pt alloy with the platinum combustion catalyst. Boiling the platinum sample holder with a few millilitres of aqua regia results in a quantitative recovery of both elements. The HNO3-H2O2 solution is evaporated to dryness and re dissolved in 2N HF. A number of trace elements are adsorbed on a Dowex 1-X8 column and eluted successively with 9N HCl, 1.2N HCl, 8N HNO3 + 4N NH4NO3 and 10% thiourea. A quantitative séparation is thus obtained of Ag, Mo, Hg and Au. Cr, Co, Se, Fe and Zn are not absorbed in 2N HF. This eluate is adsorbed on a second Dowex 1-X8 column in ION HCl and eluated successively with ION HCl, 3N HCl, 0.4N HCl and H2O. Fractions of Cr, Co + Se, Fe and Zn are obtained. A quantitative separation of Co from Se can be achieved on Dowex 50W-X4 in HCl. The volumes in which the individual elements are quantitatively collected are smaller than 30 ml. Consequently a relatively high counting efficiency can be achieved in a 25-ml well-type crystal. Quantitative recovery for all elements is obtained except for mercury and gold. Mercury losses occur on evaporating the HNO3-H2O2 mixture. As a suitable method for the determination of the mercury yield, dithizone titration was chosen. The yield of gold is

  1. INFLUENCE OF BIOLOGICALLY ACTIVE AGENTS ON A STRUCTURAL STATE AND THE ENZYMATIC ACTIVITY OF BLACK ORDINARY CARBONATED SOIL

    Directory of Open Access Journals (Sweden)

    Lychman V. A.

    2014-04-01

    Full Text Available The results of a long-term research of the influence of various biologically active agents (a humic preparation Lignogumat and microbiological Baikal EM fertilizer on a structural state and the enzymatic activity of ordinary carbonated black soil are presented. It has been established that biologically active substances contribute to increased enzymatic activity, humus and improve the soil structure

  2. 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

  3. Determination of hydroxyurea in capsules and biological fluids by ion-selective potentiometry and fluorimetry.

    Science.gov (United States)

    El-Kosasy, Amira M

    2003-01-01

    Two hydroxyurea selective electrodes were investigated with beta-cyclodextrin used as ionophore and either tetrakis (p-chlorophenyl) borate (electrode 1), or tetrakis [3,4-bis (trifluoromethyl) phenyl] borate (electrode 2), as a fixed anionic site in a polymeric matrix of carboxylated polyvinyl chloride. Linear responses of hydroxyurea within a concentration range of 10(-5)-10(-)3 M with slopes of 51.2 and 58.6 mV/decade with pH 3-6 were obtained by using electrodes 1 and 2, respectively. Two spectrofluorimetric methods involving the formation of drug-AI(III) complex (method 3) and drug-Mg(II) complex (method 4) at pH 5 were also investigated. These complexes emit fluorescence at wavelengths of 380 and 355 nm, after excitation at 305 nm, for AI and Mg complexes, respectively. The calibration graphs were rectilinear from 0.5 to 2.5 microg/mL for the AI complex and 1 to 5 microg/mL for the Mg complex. The 4 proposed methods display useful analytical characteristics for determination of hydroxyurea, with average recoveries of 100.2 +/- 0.83 and 99.4 +/- 1.81% in capsules and 99.7 +/- 0.70 and 99.4 +/- 1.25% in biological fluids for the potentiometric and fluorimetric methods, respectively. Results obtained by the proposed procedures were statistically analyzed and compared with those obtained by the U.S. Pharmacopeial method. The 4 proposed procedures were also used to determine the stability of the drug in the presence of its degradate, hydroxylamine.

  4. Biological determinants of photobioreactor design. 1st Quarterly report, September 1, 1993--November 30, 1993

    Energy Technology Data Exchange (ETDEWEB)

    Palsson, B.O.; Brown, G.G.

    1994-05-01

    Microalgae is being considered for capture and sequestration Of CO{sub 2} from power-plant flue-gases. High productivity of microalgae is necessary to make this process cost effective compared to the conventional methods used for reducing CO{sub 2} levels in the atmosphere. This obviates the need for large-scale cultivation technologies and proper photobioreactor technology. The physical factors that influence the performance of a photoautotrophic microalgal culture are the quality and composition of light, inlet carbon dioxide concentration, nutrients, and secondary metabolites at high cell densities. In developing photobioreactor technology, balancing of biological processes to the physical rate process becomes important. In this first quarterly report, the effect of various light compositions on the culture kinetics is studied. To determine the optimal composition, six wavelengths 470, 555, 560, 570, 580 and 605, each supplemented with 680 nm were used to cultivate cultures. Based on the results obtained it is concluded that a monochromatic red light of 680 nm is sufficient to obtain the maximum capacity.

  5. 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.

  6. Two-Dimensional Flow Nanometry of Biological Nanoparticles for Accurate Determination of Their Size and Emission Intensity

    CERN Document Server

    Block, Stephan; Lundgren, Anders; Zhdanov, Vladimir P; Höök, Fredrik

    2016-01-01

    Biological nanoparticles (BNPs) are of high interest due to their key role in various biological processes and use as biomarkers. BNP size and molecular composition are decisive for their functions, but simultaneous determination of both properties with high accuracy remains challenging, which is a severe limitation. Surface-sensitive microscopy allows one to precisely determine fluorescence or scattering intensity, but not the size of individual BNPs. The latter is better determined by tracking their random motion in bulk, but the limited illumination volume for tracking this motion impedes reliable intensity determination. We here show that attaching BNPs (specifically, vesicles and functionalized gold NPs) to a supported lipid bilayer, subjecting them to a hydrodynamic flow, and tracking their motion via surface-sensitive imaging enable to determine their diffusion coefficients and flow-induced drift velocities and to accurately quantify both BNP size and emission intensity. For vesicles, the high accuracy...

  7. Structure Determination of Natural Products by Nuclear Magnetic Resonance Spectroscopy

    Science.gov (United States)

    Li, Du.

    High-field NMR experiments were used to determine the full structures of six new natural products extracted from plants. These are: four saponins (PT-2, P1, P2 and P3) from the plant Alphitonia zizyphoides found in Samoa; one sesquiterpene (DF-4) from Douglas fir and one diterpene derivative (E-2) from a Chinese medicinal herb. By concerted use of various 1D and 2D NMR techniques, the structures of the above compounds were established and complete resonance assignments were achieved. The 2D INADEQUATE technique coupled with a computerized spectral analysis was extensively used. When carried out on concentrations as low as 60 mg of sample, this technique provided absolute confirmation of the assignments for 35 of the possible 53 C-C bonds for PT-2. On 30 mg of sample of E-21, it revealed 22 of 28 possible C-C bonds.

  8. The determinants of health: structure, context and agency.

    Science.gov (United States)

    Williams, Gareth H

    2003-01-01

    The concept of social structure is one of the main building blocks of the social sciences, but it lacks any precise technical definition within general sociological theory. This paper reviews the way in which the concept has been deployed within medical sociology, arguing that in recent times it has been used primarily as a frame for the sociological interpretation of health inequalities and their social determinants. It goes on to examine the contribution that medical sociologists have made to the debate over health inequalities, giving particular attention to contributions to Sociology of Health and Illness. These have often provided a focus for discussions outside or critical of the mainstream debates that have been driven primarily by epidemiologists. The paper reviews some of the main points of criticism of epidemiological approaches, focusing in particular on the methodological constraints that limit the capacity of epidemiologists to develop more theoretically satisfactory accounts of the inter-relationships of social structure, context and agency in their impact on health and well being. Some recent examples from the Journal of more theoretically innovative and analytically fine-grained approaches to understanding the impact of social structure on health are then explored. The paper concludes with an argument for a more historically-informed analysis of the relationships between social structure and health, using the knowledgeable narratives of people in places as a window onto those relationships. PMID:14498934

  9. Crystal structure determination of anti-DNA Fab A52.

    Science.gov (United States)

    Stanfield, Robyn L; Eilat, Dan

    2014-08-01

    A52 is a murine monoclonal antibody isolated from autoimmune New Zealand Black/New Zealand White F1 mice that recognizes single and double stranded DNA. This mouse strain spontaneously develops systemic lupus erythematosus-like symptoms and has served as a model for that disease for many years. The 1.62 Å crystal structure of the A52 Fab fragment reveals an H3 complementarity determining region with four closely spaced arginine residues, creating a positively charged surface to accommodate bound DNA.

  10. Spatial structure characteristic analysis of corn stover during alkali and biological co-pretreatment using XRD.

    Science.gov (United States)

    Tianxue, Yang; Li, Yun; Haobo, Hou; Beidou, Xi; Liansheng, He; Xiaowei, Wang; Caihong, Huang; Kun, Wu; Ying, Zhao; Bin, Chen

    2014-07-01

    Dynamic variation in the spatial structure of corn stover during alkali and biological co-pretreatment was investigated by X-ray diffraction. The result for crystallinity and microcrystalline size of cellulose showed periodic changes during the pretreatment process. The dominant destruction periods of crystalline areas were mainly located at 3-5d and 7-17d, and prevailing destroyed amorphous areas mainly occurred at 0-2d and 5-7d. On day 7, the relative crystallinity and microcrystalline size reached 52.81% and 8.56 nm, respectively, which were the maximum and minimum values during the whole co-pretreatment. The results indicated that spatial structure change was not uniform with pretreatment time, and this was contributed to explore the vital time point of destruction during the alkali-biological pretreatment.

  11. Heteroaryl Chalcones: Design, Synthesis, X-ray Crystal Structures and Biological Evaluation

    Directory of Open Access Journals (Sweden)

    Hoong-Kun Fun

    2013-10-01

    Full Text Available Chalcone derivatives have attracted increasing attention due to their numerous pharmacological activities. Changes in their structures have displayed high degree of diversity that has proven to result in a broad spectrum of biological activities. The present study highlights the synthesis of some halogen substituted chalcones 3(a–i containing the 5-chlorothiophene moiety, their X-ray crystal structures and the evaluation of possible biological activities such as antibacterial, antifungal and reducing power abilities. The results indicate the tested compounds show a varied range of inhibition values against all the tested microbial strains. Compound 3c with a p-fluoro substituent on the phenyl ring exhibits elevated antimicrobial activity, whereas the compounds 3e and 3f displayed the least antimicrobial activities. The compounds 3d, 3e, 3f and 3i showed good ferric and cupric reducing abilities, and the compounds 3b and 3c showed the weakest reducing power in the series.

  12. 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.

  13. Population structure and biological characteristics of Siriella gracilis (Mysida) from the Exclusive Economic Zone of India

    Digital Repository Service at National Institute of Oceanography (India)

    Biju, A.; Honey, U.K.; Kusum, K.K.; Jagadeesan, L.

    per females and maternal size of Siriella gracilis. UN CO RR EC TE D PR OO F CRUS [1.110] 2013/02/12 9:37; Prn:15/03/2013; 9:13 F:crus3198.tex; p. 17 (1041-1074) POPULATION STRUCTURE AND BIOLOGY OF SIRIELLA GRACILIS 17 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8...

  14. MetalPDB: a database of metal sites in biological macromolecular structures

    OpenAIRE

    C. Andreini; Cavallaro, G.; Lorenzini, S.; Rosato, A.

    2013-01-01

    We present here MetalPDB (freely accessible at http://metalweb.cerm.unifi.it), a novel resource aimed at conveying the information available on the three-dimensional (3D) structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal-binding sites in proteins and nucleic acids by way of Minimal Functional Sites (MFSs). MFSs are 3D templates that describe the local environment around the ...

  15. Influence of Lipid Oxidization on Structures and Functions of Biological Membranes

    OpenAIRE

    Korytowski, Agatha Anna

    2016-01-01

    The primary aim of this thesis is to clarify how the structures and functions of biological membranes are influenced by the oxidative damage mediated by free radicals. As a precisely defined model systems, artificially reconstituted lipid membranes (Langmuir monolayers, vesicles, supported membranes, multilamellar membranes) incorporating two oxidized phospholipids bearing aldehyde or carboxyl groups at the end of truncated sn-2 acyl chains were fabricated. By the combination of various exper...

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

    OpenAIRE

    Shah Parantu K; Wattarujeekrit Tuangthong; Collier Nigel

    2004-01-01

    Abstract Background The exploitation of information extraction (IE), a technology aiming to provide instances of structured representations from free-form text, has been rapidly growing within the molecular biology (MB) research community to keep track of the latest results reported in literature. IE systems have traditionally used shallow syntactic patterns for matching facts in sentences but such approaches appear inadequate to achieve high accuracy in MB event extraction due to complex sen...

  17. Determining the Structure of Biomaterials Interfaces using Synchrotron-based X-ray Diffraction

    Energy Technology Data Exchange (ETDEWEB)

    McBride, M

    2002-01-24

    The purpose of this project is to explore the feasibility of using surface X-ray diffraction (SXRD) to determine the structure of biomineral surfaces in electrolyte solutions and of the adsorbed layer of acidic amino acids that are believed to play a central role in the control of biomineral formation and function. The work is a critical component in the development of an integrated picture of the physical and chemical basis for deposition and dissolution at solid-liquid interfaces in biological systems, and brings a new and very powerful surface-sensitive capability to LLNL. We have chosen as our model systems calcium carbonate and calcium phosphate in aspartic and glutamic acid-bearing solutions. The calcium compounds are ubiquitous among biomineral structures, both those that are beneficial such as bones and teeth, and those that are pathological such as kidney stones, while the two acidic amino acids--both as simple and poly-amino acids--are the dominant constituents of protein mixtures implicated in the control of biomineralization. The goals of the work are: (1) to determine the surface structure of pure calcium phosphate and calcium carbonate surfaces in aqueous solution using SXRD; (2) to determine how those surfaces are modified by the presence of aspartic and glutamic acid, both as the simple amino acids and as poly-aspartate and poly-glutamate and (3) to model the interactions of acidic amino acids with calcite.

  18. 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)

  19. Biological structure and health implications from tooth size at Mission San Luis de Apalachee.

    Science.gov (United States)

    Stojanowski, Christopher M; Larsen, Clark S; Tung, Tiffiny A; McEwan, Bonnie G

    2007-02-01

    This study analyzes dental metric variation to examine the biological structure of the native population at Mission San Luis de Apalachee, a late 17th century mission located in the Apalachee Province of Spanish colonial Florida. Three topics are addressed: (1) comparison of tooth sizes among adult and subadults, (2) analysis of the bio-spatial structure of skeletons within the church area, and (3) comparison of phenotypic profiles of individuals interred within coffins in the ritual nucleus of the church: the altar region. Analyses indicate that subadults had smaller average tooth sizes than adults for the posterior dentition that was particularly evident in mandibular nonpolar molars and premolars. This disparity, also documented in two other mission populations, likely represents ontogenetic stress and resulting increased mortality among those most at risk for early death. Analysis of the spatial structure of graves failed to document biological structuring by side of the aisle or by burial row, although some gross differences were evident when front, middle, and rear church burials were compared. Individuals buried in coffins within the same row were phenotypically similar to one another. However, inter-row comparisons indicated lack of phenotypic similarity among all coffin interments. These analyses suggest maintenance of kin-structured burial for elites alone within the San Luis community.

  20. The Structure of a Gene Co-Expression Network Reveals Biological Functions Underlying eQTLs

    Science.gov (United States)

    Villa-Vialaneix, Nathalie; Liaubet, Laurence; Laurent, Thibault; Cherel, Pierre; Gamot, Adrien; SanCristobal, Magali

    2013-01-01

    What are the commonalities between genes, whose expression level is partially controlled by eQTL, especially with regard to biological functions? Moreover, how are these genes related to a phenotype of interest? These issues are particularly difficult to address when the genome annotation is incomplete, as is the case for mammalian species. Moreover, the direct link between gene expression and a phenotype of interest may be weak, and thus difficult to handle. In this framework, the use of a co-expression network has proven useful: it is a robust approach for modeling a complex system of genetic regulations, and to infer knowledge for yet unknown genes. In this article, a case study was conducted with a mammalian species. It showed that the use of a co-expression network based on partial correlation, combined with a relevant clustering of nodes, leads to an enrichment of biological functions of around 83%. Moreover, the use of a spatial statistics approach allowed us to superimpose additional information related to a phenotype; this lead to highlighting specific genes or gene clusters that are related to the network structure and the phenotype. Three main results are worth noting: first, key genes were highlighted as a potential focus for forthcoming biological experiments; second, a set of biological functions, which support a list of genes under partial eQTL control, was set up by an overview of the global structure of the gene expression network; third, pH was found correlated with gene clusters, and then with related biological functions, as a result of a spatial analysis of the network topology. PMID:23577081

  1. Modern methods for vancomycin determination in biological fluids by methods based on high-performance liquid chromatography--A review.

    Science.gov (United States)

    Javorska, Lenka; Krcmova, Lenka Kujovska; Solichova, Dagmar; Solich, Petr; Kaska, Milan

    2016-01-01

    Vancomycin is a glycopeptide antibiotic used in the therapy of severe bacterial infection. The monitoring of vancomycin levels is recommended because of its narrow therapeutic index and toxicity. This measurement is especially appropriate in patients with unstable renal functions, who receive high doses of vancomycin or present serious bacterial infections accompanied by important sequestration of liquids when it could be difficult to achieve the optimal therapeutic dose. Most of the methods for vancomycin determination in routine practice are immunoassays. However, chromatography-based techniques in combination with UV or mass spectrometry detection provide results with greater accuracy and precision also in complicated biological matrices. This review provides a detailed overview of modern approaches for the chromatographic separation of vancomycin in various biological samples and useful sample preparation procedures for vancomycin determination in various biological fluids.

  2. In Situ Cryo-Electron Tomography: A Post-Reductionist Approach to Structural Biology.

    Science.gov (United States)

    Asano, Shoh; Engel, Benjamin D; Baumeister, Wolfgang

    2016-01-29

    Cryo-electron tomography is a powerful technique that can faithfully image the native cellular environment at nanometer resolution. Unlike many other imaging approaches, cryo-electron tomography provides a label-free method of detecting biological structures, relying on the intrinsic contrast of frozen cellular material for direct identification of macromolecules. Recent advances in sample preparation, detector technology, and phase plate imaging have enabled the structural characterization of protein complexes within intact cells. Here, we review these technical developments and outline a detailed computational workflow for in situ structural analysis. Two recent studies are described to illustrate how this workflow can be adapted to examine both known and unknown cellular complexes. The stage is now set to realize the promise of visual proteomics--a complete structural description of the cell's native molecular landscape.

  3. Recent advances in the structural molecular biology of Ets transcription factors: interactions, interfaces and inhibition.

    Science.gov (United States)

    Cooper, Christopher D O; Newman, Joseph A; Gileadi, Opher

    2014-02-01

    The Ets family of eukaryotic transcription factors is based around the conserved Ets DNA-binding domain. Although their DNA-binding selectivity is biochemically and structurally well characterized, structures of homodimeric and ternary complexes point to Ets domains functioning as versatile protein-interaction modules. In the present paper, we review the progress made over the last decade to elucidate the structural mechanisms involved in modulation of DNA binding and protein partner selection during dimerization. We see that Ets domains, although conserved around a core architecture, have evolved to utilize a variety of interaction surfaces and binding mechanisms, reflecting Ets domains as dynamic interfaces for both DNA and protein interaction. Furthermore, we discuss recent advances in drug development for inhibition of Ets factors, and the roles structural biology can play in their future.

  4. Using a commodity high-definition television for collaborative structural biology.

    Science.gov (United States)

    Yennamalli, Ragothaman; Arangarasan, Raj; Bryden, Aaron; Gleicher, Michael; Phillips, George N

    2014-06-01

    Visualization of protein structures using stereoscopic systems is frequently needed by structural biologists working to understand a protein's structure-function relationships. Often several scientists are working as a team and need simultaneous interaction with each other and the graphics representations. Most existing molecular visualization tools support single-user tasks, which are not suitable for a collaborative group. Expensive caves, domes or geowalls have been developed, but the availability and low cost of high-definition televisions (HDTVs) and game controllers in the commodity entertainment market provide an economically attractive option to achieve a collaborative environment. This paper describes a low-cost environment, using standard consumer game controllers and commercially available stereoscopic HDTV monitors with appropriate signal converters for structural biology collaborations employing existing binary distributions of commonly used software packages like Coot, PyMOL, Chimera, VMD, O, Olex2 and others. PMID:24904249

  5. 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}.

  6. Ecological and biological determinants of methylmercury accumulation in tropical coastal fish.

    Science.gov (United States)

    Seixas, Tércia G; Moreira, Isabel; Malm, Olaf; Kehrig, Helena A

    2013-02-01

    This research investigated whether environmental conditions, biological fish characteristics and anthropogenic impacts influenced mercury (Hg) assimilation into the muscle tissue of two fish species from two Brazilian bays, Ilha Grande Bay and Guanabara Bay. Fish and superficial water were collected in different periods. Hg was determined by CV-AAS. Methylmercury (MeHg) was identified and quantified by ECD-GC. Chlorophyll a concentrations in the water column indicated that Ilha Grande Bay and Guanabara Bay were oligotrophic and eutrophic, respectively. Hg in fish ranged from 2.10 to 870.17 μg kg(-1) dry wt. in Ilha Grande Bay and 40.90 to 809.24 μg kg(-1) dry wt. in Guanabara Bay. Slight differences were found between the length-normalized Hg concentrations and its percent of Hg in a voracious predator from the bays. In Guanabara Bay, where the presence of a chlor-alkali plant causes Hg input, the iliophagous fish species showed the highest length-normalized Hg concentrations and the voracious predator the lowest. Iliophagous fish is consumed by voracious predator and, consequently, acts as their MeHg food supply. Iliophagous fish from Ilha Grande Bay presented a higher percent of MeHg (80.0 %) than specimens from Guanabara Bay (54.5 %). This fact suggests that more MeHg was transferred from iliophagous fish to voracious predator in Ilha Grande Bay. At Guanabara Bay, the bioproduction is greater than that at Ilha Grande Bay, presenting the highest biomass in it ecosystem, which may subsequently dilute Hg and reduce its availability to the biota; i.e., influencing in Hg and MeHg availability throughout the food chain. Consequently, more MeHg is available in the aquatic environment of Ilha Grande Bay.

  7. Biological Macromolecule Crystallization Database

    Science.gov (United States)

    SRD 21 Biological Macromolecule Crystallization Database (Web, free access)   The Biological Macromolecule Crystallization Database and NASA Archive for Protein Crystal Growth Data (BMCD) contains the conditions reported for the crystallization of proteins and nucleic acids used in X-ray structure determinations and archives the results of microgravity macromolecule crystallization studies.

  8. Structure-property relationship of quinuclidinium surfactants--Towards multifunctional biologically active molecules.

    Science.gov (United States)

    Skočibušić, Mirjana; Odžak, Renata; Štefanić, Zoran; Križić, Ivana; Krišto, Lucija; Jović, Ozren; Hrenar, Tomica; Primožič, Ines; Jurašin, Darija

    2016-04-01

    Motivated by diverse biological and pharmacological activity of quinuclidine and oxime compounds we have synthesized and characterized novel class of surfactants, 3-hydroxyimino quinuclidinium bromides with different alkyl chains lengths (CnQNOH; n=12, 14 and 16). The incorporation of non conventional hydroxyimino quinuclidinium headgroup and variation in alkyl chain length affects hydrophilic-hydrophobic balance of surfactant molecule and thereby physicochemical properties important for its application. Therefore, newly synthesized surfactants were characterized by the combination of different experimental techniques: X-ray analysis, potentiometry, electrical conductivity, surface tension and dynamic light scattering measurements, as well as antimicrobial susceptibility tests. Comprehensive investigation of CnQNOH surfactants enabled insight into structure-property relationship i.e., way in which the arrangement of surfactant molecules in the crystal phase correlates with their solution behavior and biologically activity. The synthesized CnQNOH surfactants exhibited high adsorption efficiency and relatively low critical micelle concentrations. In addition, all investigated compounds showed very potent and promising activity against Gram-positive and clinically relevant Gram-negative bacterial strains compared to conventional antimicrobial agents: tetracycline and gentamicin. The overall results indicate that bicyclic headgroup with oxime moiety, which affects both hydrophilicity and hydrophobicity of CnQNOH molecule in addition to enabling hydrogen bonding, has dominant effect on crystal packing and physicochemical properties. The unique structural features of cationic surfactants with hydroxyimino quinuclidine headgroup along with diverse biological activity have made them promising structures in novel drug discovery. Obtained fundamental understanding how combination of different functionalities in a single surfactant molecule affects its physicochemical

  9. Spectrophotometric Determination of Thioridazine Hydrochloride in Tablets and Biological Fluids by Ion-Pair and Oxidation Reactions

    OpenAIRE

    El-Didamony, Akram; Hafeez, Sameh

    2012-01-01

    Two simple, sensitive and selective spectrophotometric methods have been described for the determination of the psychoactive drug, thioridazine HCl in tablets and in biological fluids. The first method is based on the oxidation of thioridazine HCl with measured excess of KMnO4 under acidic conditions followed by the determination of unreacted oxidant using indigo carmine and methyl orange. The second method is based on the formation of ion-pair complexes with the acidic sulphophthalein dyes s...

  10. Determination of Nitric Oxide-Derived Nitrite and Nitrate in Biological Samples by HPLC Coupled to Nitrite Oxidation

    OpenAIRE

    Wu, Anguo; Duan, Tingting; Tang, Dan; Xu, Youhua; Feng, Liang; Zheng, Zhaoguang; Zhu, Jiaxiao; Wang, Rushang; Zhu, Quan

    2013-01-01

    Nitrite and nitrate are main stable products of nitric oxide, a pivotal cellular signaling molecule, in biological fluids. Therefore, accurate measurement of the two ions is profoundly important. Nitrite is difficult to be determined for a larger number of interferences and unstable in the presence of oxygen. In this paper, a simple, cost-effective and accurate HPLC method for the determination of nitrite and nitrate was developed. On the basis of the reaction that nitrite is oxidized rapidly...

  11. Two Methods of Determining Total Phenolic Content of Foods and Juices in a General, Organic, and Biological (GOB) Chemistry Lab

    Science.gov (United States)

    Shaver, Lee Alan; Leung, Sam H.; Puderbaugh, Amy; Angel, Stephen A.

    2011-01-01

    The determination of total phenolics in foods and fruit juices was used successfully as a laboratory experiment in our undergraduate general, organic, and biological (GOB) chemistry course. Two different colorimetric methods were used over three years and comparative student results indicate that a ferrous ammonium sulfate (FAS) indicator…

  12. Ultra high performance liquid chromatography tandem mass spectrometry determination and profiling of prohibited steroids in human biological matrices. A review.

    Science.gov (United States)

    Gosetti, Fabio; Mazzucco, Eleonora; Gennaro, Maria Carla; Marengo, Emilio

    2013-05-15

    The use of doping agents, once restricted to professional athletes, has nowadays become a problem of public health, since it also concerns young people and non-competing amateurs in different sports. The use is also diffused in social life for improving physical appearance and enhancing performance and even dietary supplements assumed to improve performance often contain anabolic steroids. While decades ago the so-called "classical doping agents" (like stimulants and narcotics) were used, to-day anabolic steroids are more widely diffused. Anabolic steroids are synthetic substances prepared by introducing modifications in the molecular structure of testosterone, the main natural androgenic anabolic steroid that forms in testes interstitial cells. The first report concerning the use of anabolic steroids by an athlete who searched for increased weight and power dates 1954. In 1974 the misuse of anabolic steroids in sports was banned by the International Olympic Committee and control tests were implemented in 1976 Montreal Olympic Games through radioimmunoassay analysis: the technique, however, only allows for unspecific detection of a limited number of exogenous steroids. Over the years, always new doping substances are synthesized and, as a consequence, the list of prohibited compounds is continuously updated and new suitable analytical methods for their detection and determination in biological matrices are continuously required. In doping control analysis the knowledge of steroid metabolism pathway in human body is of primary importance and the analytical methods must permit the simultaneous detection and determination not only of the forbidden precursor agents but also of their metabolites. In addition, the potential presence and amount in the biological samples of species that can interfere in the analysis should be evaluated. Also the several anabolic steroids, specifically designed to circumvent doping control, put on the market have been incorporated in the

  13. 3D structure determination of protein using TEM single particle analysis.

    Science.gov (United States)

    Sato, Chikara; Mio, Kazuhiro; Kawata, Masaaki; Ogura, Toshihiko

    2014-11-01

    Proteins play important roles in cell functions such as enzymes, cell trafficking, neurotransmission, muscle contraction and hormone secretion. However, some proteins are very difficult to be crystallized and their structures are undetermined. Several techniques have been developed to elucidate the structure of macromolecules; X-ray or electron crystallography, nuclear magnetic resonance spectroscopy, and high-resolution electron microscopy. Among them, electron microscopy based single particle reconstruction (SPA) technique is a computer-aided structure determination method. This method reconstructs the 3D structure from projection images of dispersed protein. A large number of two-dimensional particle images are picked up from EM films, aligned and classified to generate 2D averages, and used to reconstruct the 3D structure by assigning the Euler angle of each 2D average. Due to the necessity of elaborate collaboration between the classical biology and the innovative information technology including parallel computing, scientists needed to break unseen barriers to get a start of this analysis. However, recent progresses in electron microscopes, mathematical algorithms, and computational abilities greatly reduced the height of barriers and expanded targets that are considered to be primarily addressable using single particle analysis. Membrane proteins are one of these targets to which the single particle analysis is successfully applied for the understanding of their 3D structures. For this purpose, we have developed various SPA methods [1-5] and applied them to different proteins [6-8].Here, we introduce reconstructed proteins, and discuss the availability of this technique. The intramembrane-cleaving proteases (I-CLiPs) that sever the transmembrane domains of their substrates have been identified in a range of organisms and play a variety of roles in biological conditions. I-CLiPs have been classified into three groups: serine-, aspartyl- and metalloprotease

  14. Crystal Structure of Escherichia coli L-Arabinose Isomerase (ECAI), The Putative Target of Biological Tagatose Production

    Energy Technology Data Exchange (ETDEWEB)

    Manjasetty,B.; Chance, M.

    2006-01-01

    Escherichia coli L-arabinose isomerase (ECAI; EC 5.3.1.4) catalyzes the isomerization of L-arabinose to L-ribulose in vivo. This enzyme is also of commercial interest as it catalyzes the conversion of D-galactose to D-tagatose in vitro. The crystal structure of ECAI was solved and refined at 2.6 Angstroms resolution. The subunit structure of ECAI is organized into three domains: an N-terminal, a central and a C-terminal domain. It forms a crystallographic trimeric architecture in the asymmetric unit. Packing within the crystal suggests the idea that ECAI can form a hexameric assembly. Previous electron microscopic and biochemical studies supports that ECAI is hexameric in solution. A comparison with other known structures reveals that ECAI adopts a protein fold most similar to E. coli fucose isomerase (ECFI) despite very low sequence identity 9.7%. The structural similarity between ECAI and ECFI with regard to number of domains, overall fold, biological assembly, and active site architecture strongly suggests that the enzymes have functional similarities. Further, the crystal structure of ECAI forms a basis for identifying molecular determinants responsible for isomerization of arabinose to ribulose in vivo and galactose to tagatose in vitro.

  15. A biologically inspired modular structure to control the sit-to-stand transfer of a biped robot.

    Science.gov (United States)

    Andani, M Emadi; Bahrami, F; Maralani, P Jabedar

    2007-01-01

    In this study, a biologically inspired control structure to control the sit-to-stand (STS) transfer from a chair is developed and simulated. STS movement is consisted of two main phases. First phase of the movement is before leaving the seat (seat-off moment). In this phase seat reactions forces act on the body parts which are in contact with the seat. The second phase is after seat-off, where the only external forces acting on the body are ground reaction forces. A proper control algorithm of the STS transfer needs to consider switching between these two phases, which correspond to two different dynamical structures. The control structure developed and discussed in this work is based on the MOSAIC structure, proposed first by Wolpert and Kawato [1]. Original MOSAIC structure has a modular architecture which is based on multiple pairs of forward and inverse models of the dynamical system to be controlled, and each module is trained separately to learn one part of a given task. The number of effective modules is predetermined. We have developed a new method to train all modules simultaneously. This method is based on reinforcement and cooperative competitive learning, and the number of effective modules is determined automatically. In this study, the simulation was begun with four modules. Our results showed that only two modules out of four were selected to control the STS task. Responsibility of controlling the task was switched between the two modules around the seat-off moment.

  16. 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.

  17. Adapting federated cyberinfrastructure for shared data collection facilities in structural biology

    International Nuclear Information System (INIS)

    It has been difficult, historically, to manage and maintain early-stage experimental data collected by structural biologists in synchrotron facilities. This work describes a prototype system that adapts existing federated cyberinfrastructure technology and techniques to manage collected data at synchrotrons and to facilitate the efficient and secure transfer of data to the owner's home institution. 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

  18. I love you with all my brain: laying aside the intellectually dull sword of biological determinism

    OpenAIRE

    Woodson, James C.

    2012-01-01

    Background: By organizing and activating our passions with both hormones and experiences, the heart and mind of sexual behavior, sexual motivation, and sexual preference is the brain, the organ of learning. Despite decades of progress, this incontrovertible truth is somehow lost in the far-too-often biologically deterministic interpretation of genetic, hormonal, and anatomical scientific research into the biological origins of sexual motivation. Simplistic and polarized arguments are used in ...

  19. Structural Determinants of Clostridium difficile Toxin A Glucosyltransferase Activity

    Energy Technology Data Exchange (ETDEWEB)

    Pruitt, Rory N.; Chumbler, Nicole M.; Rutherford, Stacey A.; Farrow, Melissa A.; Friedman, David B.; Spiller, Ben; Lacy, D. Borden (Vanderbilt)

    2012-03-28

    The principle virulence factors in Clostridium difficile pathogenesis are TcdA and TcdB, homologous glucosyltransferases capable of inactivating small GTPases within the host cell. We present crystal structures of the TcdA glucosyltransferase domain in the presence and absence of the co-substrate UDP-glucose. Although the enzymatic core is similar to that of TcdB, the proposed GTPase-binding surface differs significantly. We show that TcdA is comparable with TcdB in its modification of Rho family substrates and that, unlike TcdB, TcdA is also capable of modifying Rap family GTPases both in vitro and in cells. The glucosyltransferase activities of both toxins are reduced in the context of the holotoxin but can be restored with autoproteolytic activation and glucosyltransferase domain release. These studies highlight the importance of cellular activation in determining the array of substrates available to the toxins once delivered into the cell.

  20. Medicinal properties of mangiferin, structural features, derivative synthesis, pharmacokinetics and biological activities.

    Science.gov (United States)

    Benard, Outhiriaradjou; Chi, Yuling

    2015-01-01

    The identification of biologically active and potentially therapeutically useful pharmacophores from natural products has been a long-term focus in the pharmaceutical industry. The recent emergence of a worldwide obesity and Type II diabetes epidemic has increased focus upon small molecules that can modulate energy metabolism, insulin sensitivity and fat biology. Interesting preliminary work done on mangiferin (MGF), the predominant constituent of extracts of the mango plant Mangifera indica L., portends potential for this pharmacophore as a novel parent compound for treating metabolic disorders. MGF is comprised of a C-glucosylated xanthone. Owing to the xanthone chemical structure, MGF has a redox active aromatic system and has antioxidant properties. MGF exerts varied and impressive metabolic effects in animals, improving metabolic disorders. For example we have discovered that MGF is a novel activator of the mammalian pyruvate dehydrogenase complex, leading to enhancement of carbohydrate utilization in oxidative metabolism, and leading to increased insulin sensitivity in animal models of obesity and insulin resistance. In addition, recent unbiased proteomics studies revealed that MGF upregulates proteins pivotal for mitochondrial bioenergetics and downregulates proteins controlling de novo lipogenesis in liver, helping to explain protective effects of MGF in prevention of liver steatosis. Several chemical studies have achieved synthesis of MGF, suggesting possible synthetic strategies to alter its chemical structure for development of structure-activity relationship (SAR) information. Ultimately, chemical derivatization studies could lead to the eventual development of novel therapeutics based upon the parent pharmacophore structure. Here we provide comprehensive review on chemical features of MGF, synthesis of its derivatives, its pharmacokinetics and biological activities. PMID:25827900

  1. Encoding of Primary Structures of Biological Macromolecules Within a Data Mining Perspective

    Institute of Scientific and Technical Information of China (English)

    Mondher Maddouri; Mourad Elloumi

    2004-01-01

    An encoding method has a direct effect on the quality and the representation of the discovered knowledge in data mining systems. Biological macromolecules are encoded by strings of characters, called primary structures. Knowing that data mining systems usually use relational tables to encode data, we have then to reencode these strings and transform them into relational tables. In this paper, we do a comparative study of the existing static encoding methods, that are based on the Biologist know-how, and our new dynamic encoding one,that is based on the construction of Discriminant and Minimal Substrings (DMS). Different classification methods are used to do this study. The experimental results show that our dynamic encoding method is more efficient than the static ones, to encode biological macromolecules within a data mining perspective.

  2. The Google matrix controls the stability of structured ecological and biological networks

    Science.gov (United States)

    Stone, Lewi

    2016-09-01

    May's celebrated theoretical work of the 70's contradicted the established paradigm by demonstrating that complexity leads to instability in biological systems. Here May's random-matrix modelling approach is generalized to realistic large-scale webs of species interactions, be they structured by networks of competition, mutualism or both. Simple relationships are found to govern these otherwise intractable models, and control the parameter ranges for which biological systems are stable and feasible. Our analysis of model and real empirical networks is only achievable on introducing a simplifying Google-matrix reduction scheme, which in the process, yields a practical ecological eigenvalue stability index. These results provide an insight into how network topology, especially connectance, influences species stable coexistence. Constraints controlling feasibility (positive equilibrium populations) in these systems are found more restrictive than those controlling stability, helping explain the enigma of why many classes of feasible ecological models are nearly always stable.

  3. Visual analysis of transcriptome data in the context of anatomical structures and biological networks

    Directory of Open Access Journals (Sweden)

    Astrid eJunker

    2012-11-01

    Full Text Available The complexity and temporal as well as spatial resolution of transcriptome datasets is constantly increasing due to extensive technological developments. Here we present methods for advanced visualization and intuitive exploration of transcriptomics data as necessary prerequisites in order to facilitate the gain of biological knowledge. Color-coding of structural images based on the expression level enables a fast visual data analysis in the background of the examined biological system. The network-based exploration of these visualizations allows for comparative analysis of genes with specific transcript patterns and supports the extraction of functional relationships even from large datasets. In order to illustrate the presented methods, the tool HIVE was applied for visualization and exploration of database-retrieved expression data for master regulators of Arabidopsis thaliana flower and seed development in the context of corresponding tissue-specific regulatory networks.

  4. On the remote interaction of biological objects with identical genetic structures

    CERN Document Server

    Berkovich, S Y

    2002-01-01

    The paper puts forward an unusual prediction that cultivating a clone can curtail the lifespan of the clone donor. Neither the arrangement of this suggested empirical study nor the analyses of the anticipated outcomes rely on the accompanying theoretical contemplations. This prediction has come from the interpretation of the genome as a "barcode". The genome is considered as an identification label rather than a repository of control information, so living beings are portrayed as a community of users on the "Internet of the physical Universe". Thus, biological objects with identical (or nearly identical) DNA structures can interfere, and the surmised remote impact appears tangible. The effect of clone-donor interaction leads to a decisive Experimentum Crucis that can reject the common view on the organization of biological information processing. Exploitation of this effect can be potentially dangerous.

  5. Integrated analysis of multiple data sources reveals modular structure of biological networks

    International Nuclear Information System (INIS)

    It has been a challenging task to integrate high-throughput data into investigations of the systematic and dynamic organization of biological networks. Here, we presented a simple hierarchical clustering algorithm that goes a long way to achieve this aim. Our method effectively reveals the modular structure of the yeast protein-protein interaction network and distinguishes protein complexes from functional modules by integrating high-throughput protein-protein interaction data with the added subcellular localization and expression profile data. Furthermore, we take advantage of the detected modules to provide a reliably functional context for the uncharacterized components within modules. On the other hand, the integration of various protein-protein association information makes our method robust to false-positives, especially for derived protein complexes. More importantly, this simple method can be extended naturally to other types of data fusion and provides a framework for the study of more comprehensive properties of the biological network and other forms of complex networks

  6. A review of chromatographic methods for the determination of water- and fat-soluble vitamins in biological fluids.

    Science.gov (United States)

    Karaźniewicz-Łada, Marta; Główka, Anna

    2016-01-01

    Vitamins are an essential element of nutrition and thus contribute to human health. Vitamins catalyze many biochemical reactions and their lack or excess can cause health problems. Therefore, monitoring vitamin concentrations in plasma or other biological fluids may be useful in the diagnosis of various disorders as well as in the treatment process. Several chromatographic methods have been developed for the determination of these compounds in biological samples, including high-performance liquid chromatography with UV and fluorescence detection. Recently, high-performance liquid chromatography with tandem mass spectrometry methods have been widely used for the determination of vitamins in complex matrices because of their high sensitivity and selectivity. This method requires preconditioning of samples for analysis, including protein precipitation and/or various extraction techniques. The choice of method may depend on the desired cost, convenience, turnaround time, specificity, and accuracy of the information to be obtained. This article reviews the recently reported chromatographic methods used for determination of vitamins in biological fluids. Relevant papers published mostly during the last 5 years were identified by an extensive PubMed search using appropriate keywords. Particular attention was given to the preparation steps and extraction techniques. This report may be helpful in the selection of procedures that are appropriate for certain types of biological materials and analytes. PMID:26503668

  7. The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype-phenotype maps.

    Science.gov (United States)

    Greenbury, S F; Ahnert, S E

    2015-12-01

    Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype-phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into 'constrained' and 'unconstrained' sequences, in the broadest possible sense. As 'constrained' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. 'Unconstrained' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with 'coding' and 'non-coding' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps. PMID:26609063

  8. The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype-phenotype maps.

    Science.gov (United States)

    Greenbury, S F; Ahnert, S E

    2015-12-01

    Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype-phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into 'constrained' and 'unconstrained' sequences, in the broadest possible sense. As 'constrained' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. 'Unconstrained' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with 'coding' and 'non-coding' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps.

  9. The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype–phenotype maps

    Science.gov (United States)

    Greenbury, S. F.; Ahnert, S. E.

    2015-01-01

    Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype–phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into ‘constrained' and ‘unconstrained' sequences, in the broadest possible sense. As ‘constrained' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. ‘Unconstrained' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with ‘coding' and ‘non-coding' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps. PMID:26609063

  10. The determinants of capital structure choice: Evidence from Western Europe

    Directory of Open Access Journals (Sweden)

    Ana Mugosa

    2015-07-01

    Full Text Available This paper examines corporate leverage and its determinants on panel of 921 large Western European companies from 2003 to 2010. The results proved a substantial influence of estimated variables on changes in target debt or leverage ratio. Apart of the determinants from the “core” model, I test the influence of stock price variations on changes in capital structure to conclude if companies “time” the market. The estimation procedure of target debt ratio was performed using Fixed-Effect and FGLS methods. The results were compared to the results of often used methodology in previous research – OLS and Tobit regression. I found statistically significant and negative correlation between target leverage ratio and tangibility, market to book, profitability, product uniqueness and total return (average stock return and statistically significant and positive correlation between target leverage ratio and size. The results suggest the mix of trade-off and pecking order theory predictions and are consistent with findings of previous studies. Future research should focus on impact of leverage deficit (deviations from target leverage ratio on corporate decisions in Europe.

  11. The Detection of Structural Deformation Errors in Attitude Determination

    Institute of Scientific and Technical Information of China (English)

    M. J. Moore; C. Rizos; J. Wang

    2003-01-01

    In the determination of the attitude parameters from a multi-antenna GPS array, one of the major assumptions is that the body frame is rigid at all times. If this assumption is not true then the derived attitude parameters will be in error. It is well known that in airborne platforms the wings often experience some displacement during flight, especially during periods of initializing maneouvres, such as taking off, landing,and banking. Often it is at these points in time that it is most critical to have the most precise attitude parameters.There are a number of techniques available for the detection of modeling errors.The CUSUM algorithm has successfully been implemented in the past to detect small persistent changes. In this paper the authors investigate different methods of generating the residuals, to be tested by the CUSUM algorithm, in an effort to determine which technique is best suited for the detection of structural deformation of an airborne platform. The methods investigated include monitoring the mean of the residuals generated from the difference between the known body frame coordinates, and those calculated from the derived attitude parameters. The generated residuals are then passed to a CUSUM algorithm to detect any small persistent changes. An alternative method involves transforming the generated residuals into the frequency domain through the use of the Fast Fourier Transform. The CUSUM algorithm is then used to detect any frequency changes. The final technique investigated involves transforming the generated residuals using the Haar wavelet. The wavelet coefficients are then monitored by the CUSUM algorithm in order to detect any significant change to the rigidity of the body frame.Detecting structural deformation, and quantifying the degree of deformation, during flight will ensure that these effects can be removed from the system, thus ensuring the most precise and reliable attitude parameter solutions. This paper, through a series

  12. Spectrophotometric determination of copper(II) in pharmaceutical, biological and water samples by 4-(2'-benzothiazolylazo)-salicylic acid

    Science.gov (United States)

    Hashem, E. Y.; Seleim, M. M.; El-Zohry, A. M.

    2011-09-01

    A highly sensitive method is proposed to determine copper(II) ions by forming a stable complex through their interaction with 4-(2'-benzothiazolylazo)-salicylic acid (BTAS) at room temperature and pH of about 5.0. The complex gave a maximum absorption at λ = 485 nm with a molar absorptivity coefficient of 2.35·104 l/(mol·cm). The linear range for the copper determination is 0.63-5.04 mg/l. The method can be applied to determine copper ions in different biological specimens like some drugs and water samples.

  13. Chemical Structure-Biological Activity Models for Pharmacophores' 3D-Interactions.

    Science.gov (United States)

    Putz, Mihai V; Duda-Seiman, Corina; Duda-Seiman, Daniel; Putz, Ana-Maria; Alexandrescu, Iulia; Mernea, Maria; Avram, Speranta

    2016-01-01

    Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners' (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions. PMID:27399692

  14. Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions

    Directory of Open Access Journals (Sweden)

    Mihai V. Putz

    2016-07-01

    Full Text Available Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding and quantitative (for predicting mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD as the revived precursor for comparative molecular field analyses (CoMFA and comparative molecular similarity indices analysis (CoMSIA; all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy-methyl]-6-(phenylthiothymine congeners’ (HEPT ligands antiviral activity against Human Immunodeficiency Virus of first type (HIV-1 and new pharmacophores in treating severe genetic disorders (like depression and psychosis, respectively, all involving 3D pharmacophore interactions.

  15. Three-dimensional visualisation of soft biological structures by X-ray computed micro-tomography.

    Science.gov (United States)

    Shearer, Tom; Bradley, Robert S; Hidalgo-Bastida, L Araida; Sherratt, Michael J; Cartmell, Sarah H

    2016-07-01

    Whereas the two-dimensional (2D) visualisation of biological samples is routine, three-dimensional (3D) imaging remains a time-consuming and relatively specialised pursuit. Current commonly adopted techniques for characterising the 3D structure of non-calcified tissues and biomaterials include optical and electron microscopy of serial sections and sectioned block faces, and the visualisation of intact samples by confocal microscopy or electron tomography. As an alternative to these approaches, X-ray computed micro-tomography (microCT) can both rapidly image the internal 3D structure of macroscopic volumes at sub-micron resolutions and visualise dynamic changes in living tissues at a microsecond scale. In this Commentary, we discuss the history and current capabilities of microCT. To that end, we present four case studies to illustrate the ability of microCT to visualise and quantify: (1) pressure-induced changes in the internal structure of unstained rat arteries, (2) the differential morphology of stained collagen fascicles in tendon and ligament, (3) the development of Vanessa cardui chrysalises, and (4) the distribution of cells within a tissue-engineering construct. Future developments in detector design and the use of synchrotron X-ray sources might enable real-time 3D imaging of dynamically remodelling biological samples. PMID:27278017

  16. Structural identifiability of systems biology models: a critical comparison of methods.

    Directory of Open Access Journals (Sweden)

    Oana-Teodora Chis

    Full Text Available Analysing the properties of a biological system through in silico experimentation requires a satisfactory mathematical representation of the system including accurate values of the model parameters. Fortunately, modern experimental techniques allow obtaining time-series data of appropriate quality which may then be used to estimate unknown parameters. However, in many cases, a subset of those parameters may not be uniquely estimated, independently of the experimental data available or the numerical techniques used for estimation. This lack of identifiability is related to the structure of the model, i.e. the system dynamics plus the observation function. Despite the interest in knowing a priori whether there is any chance of uniquely estimating all model unknown parameters, the structural identifiability analysis for general non-linear dynamic models is still an open question. There is no method amenable to every model, thus at some point we have to face the selection of one of the possibilities. This work presents a critical comparison of the currently available techniques. To this end, we perform the structural identifiability analysis of a collection of biological models. The results reveal that the generating series approach, in combination with identifiability tableaus, offers the most advantageous compromise among range of applicability, computational complexity and information provided.

  17. Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions

    Science.gov (United States)

    Putz, Mihai V.; Duda-Seiman, Corina; Duda-Seiman, Daniel; Putz, Ana-Maria; Alexandrescu, Iulia; Mernea, Maria; Avram, Speranta

    2016-01-01

    Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners’ (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions. PMID:27399692

  18. Anthraquinones and Derivatives from Marine-Derived Fungi: Structural Diversity and Selected Biological Activities.

    Science.gov (United States)

    Fouillaud, Mireille; Venkatachalam, Mekala; Girard-Valenciennes, Emmanuelle; Caro, Yanis; Dufossé, Laurent

    2016-04-01

    Anthraquinones and their derivatives constitute a large group of quinoid compounds with about 700 molecules described. They are widespread in fungi and their chemical diversity and biological activities recently attracted attention of industries in such fields as pharmaceuticals, clothes dyeing, and food colorants. Their positive and/or negative effect(s) due to the 9,10-anthracenedione structure and its substituents are still not clearly understood and their potential roles or effects on human health are today strongly discussed among scientists. As marine microorganisms recently appeared as producers of an astonishing variety of structurally unique secondary metabolites, they may represent a promising resource for identifying new candidates for therapeutic drugs or daily additives. Within this review, we investigate the present knowledge about the anthraquinones and derivatives listed to date from marine-derived filamentous fungi's productions. This overview highlights the molecules which have been identified in microorganisms for the first time. The structures and colors of the anthraquinoid compounds come along with the known roles of some molecules in the life of the organisms. Some specific biological activities are also described. This may help to open doors towards innovative natural substances. PMID:27023571

  19. Anthraquinones and Derivatives from Marine-Derived Fungi: Structural Diversity and Selected Biological Activities

    Directory of Open Access Journals (Sweden)

    Mireille Fouillaud

    2016-03-01

    Full Text Available Anthraquinones and their derivatives constitute a large group of quinoid compounds with about 700 molecules described. They are widespread in fungi and their chemical diversity and biological activities recently attracted attention of industries in such fields as pharmaceuticals, clothes dyeing, and food colorants. Their positive and/or negative effect(s due to the 9,10-anthracenedione structure and its substituents are still not clearly understood and their potential roles or effects on human health are today strongly discussed among scientists. As marine microorganisms recently appeared as producers of an astonishing variety of structurally unique secondary metabolites, they may represent a promising resource for identifying new candidates for therapeutic drugs or daily additives. Within this review, we investigate the present knowledge about the anthraquinones and derivatives listed to date from marine-derived filamentous fungi′s productions. This overview highlights the molecules which have been identified in microorganisms for the first time. The structures and colors of the anthraquinoid compounds come along with the known roles of some molecules in the life of the organisms. Some specific biological activities are also described. This may help to open doors towards innovative natural substances.

  20. Variability of Biological Degradation of Aromatic Hydrocarbons in an Aerobic Aquifer Determined by Laboratory Batch Experiments

    DEFF Research Database (Denmark)

    Nielsen, Per Henning; Christensen, Thomas Højlund

    1994-01-01

    The biological aerobic degradation of 7 aromatic hydrocarbons (benzene, toluene, o-xylene, p-dichlorobenzene, o-dichlorobenzene, naphthalene and biphenyl) was studied for 149 days in replicate laboratory batch experiments with groundwater and sediment from 8 localities representing a 15 m × 30 m...... section of an aerobic aquifer. Compared to biologically deactivated control experiments all compounds were biologically degraded. Degradation curves were very reproducible for some compounds (benzene, toluene, o-xylene, o-dichlorobenzene and p-dichlorobenzene) and less reproducible for other (naphthalene...... and biphenyl). Based on observed length of lag phases, length of the degradation periods and percent degradation, the variation among the 8 localities appears to be modest. However, detailed examination of the degradation rates revealed statistically significant variation among localities for benzene, toluene...

  1. Synthesis, Crystal Structure and Biological Activities of Novel Anthranilic(Isophthalic) Acid Esters

    Institute of Scientific and Technical Information of China (English)

    YAN Tao; YU Guan-ping; LIU Peng-fei; XIONG Li-xia; YU Shu-jing; LI Zheng-ming

    2012-01-01

    In search of environmentally benign insecticides with high activity,low toxicity and low resistance,a series of novel anthranilic(isophthalic) acid esters was designed and synthesized based on the structure of ryanodine modulating agent.All the compounds were characterized by 1H NMR spectra,elemental analysis or high resolution mass spectrometry(HRMS).The preliminary results of biological activity assessment indicate that some of the title compounds exhibit certain but unremarkable insecticidal activity against Mythimna separata Walker at 200 mg/L and fungicidal activities against five funguses at 50 mg/L.

  2. Simple synthesis and biological evaluation of flocoumafen and its structural isomers

    Indian Academy of Sciences (India)

    Jae-Chul Jung; Soyong Jang; Seikwan Oh; Oee-Sook Park

    2010-11-01

    Simple synthesis and biological properties of flocoumafen 1 and its structural isomers are described. The key synthetic strategies involve Knoevenagel condensation, Grignard reaction, intramolecular ring cyclization and coupling reaction. Flocoumafen 1 was easily separated into cis and trans forms using flash column chromatography. They were then evaluated for suppression of LPS-induced NO generation and anti-excitotoxicity in vitro. It was found that the trans-flocoumafen was potent suppressor of NO generation with the concentration of 10 M in vitro, while no significant effect for neurotoxicity in cultured cortical neurons.

  3. Cation Selectivity in Biological Cation Channels Using Experimental Structural Information and Statistical Mechanical Simulation.

    Directory of Open Access Journals (Sweden)

    Justin John Finnerty

    Full Text Available Cation selective channels constitute the gate for ion currents through the cell membrane. Here we present an improved statistical mechanical model based on atomistic structural information, cation hydration state and without tuned parameters that reproduces the selectivity of biological Na+ and Ca2+ ion channels. The importance of the inclusion of step-wise cation hydration in these results confirms the essential role partial dehydration plays in the bacterial Na+ channels. The model, proven reliable against experimental data, could be straightforwardly used for designing Na+ and Ca2+ selective nanopores.

  4. Automatic Structure Determination of Organic Molecules: Principle and Implementation of the LSD Program

    Institute of Scientific and Technical Information of China (English)

    NUZILLARD,Jean-Marc

    2003-01-01

    The LSD (Logic for Structure Determination) program generates organic molecular structures from 1D and 2D NMR data without resorting to chemical shift databases. Its use in the resolution of natural product structure determination problems has been already reported in the literature. This paper describes how data and structures are internally represented and processed by LSD to build solution structures.

  5. Towards an integrative structural biology approach: combining Cryo-TEM, X-ray crystallography, and NMR.

    Science.gov (United States)

    Lengyel, Jeffrey; Hnath, Eric; Storms, Marc; Wohlfarth, Thomas

    2014-09-01

    Cryo-transmission electron microscopy (Cryo-TEM) and particularly single particle analysis is rapidly becoming the premier method for determining the three-dimensional structure of protein complexes, and viruses. In the last several years there have been dramatic technological improvements in Cryo-TEM, such as advancements in automation and use of improved detectors, as well as improved image processing techniques. While Cryo-TEM was once thought of as a low resolution structural technique, the method is currently capable of generating nearly atomic resolution structures on a routine basis. Moreover, the combination of Cryo-TEM and other methods such as X-ray crystallography, nuclear magnetic resonance spectroscopy, and molecular dynamics modeling are allowing researchers to address scientific questions previously thought intractable. Future technological developments are widely believed to further enhance the method and it is not inconceivable that Cryo-TEM could become as routine as X-ray crystallography for protein structure determination.

  6. Biological activity of Bt proteins expressed in different structures of transgenic corn against Spodoptera frugiperda

    Directory of Open Access Journals (Sweden)

    Daniel Bernardi

    2016-06-01

    Full Text Available ABSTRACT: Spodoptera frugiperda (J. E. Smith is the main target pest of Bt corn technologies, such as YieldGard VT PRO(tm (Cry1A.105/Cry2Ab2 and PowerCore(tm (Cry1A.105/Cry2Ab2/Cry1F. In this study, it was evaluated the biological activity of Bt proteins expressed in different plant structures of YieldGard VT PRO(tm and PowerCore(tm corn against S. frugiperda . Complete mortality of S. frugiperda neonates was observed on leaf-disc of both Bt corn technologies. However, the mortality in silks and grains was lower than 50 and 6%, respectively. In addition, more than 49% of the surviving larvae in silks and grains completed the biological cycle. However, all life table parameters were negatively affected in insects that developed in silks and grains of both Bt corn events. In summary, the low biological activity of Bt proteins expressed on silks and grains of YieldGard VT PRO(tm and PowerCore(tm corn can contribute to the resistance evolution in S. frugiperda populations.

  7. Curcumin and Its Carbocyclic Analogs: Structure-Activity in Relation to Antioxidant and Selected Biological Properties

    Directory of Open Access Journals (Sweden)

    H. P. Vasantha Rupasinghe

    2013-05-01

    Full Text Available Curcumin is the major phenolic compound present in turmeric (Curcuma longa L.. Curcumin and 15 novel analogs were investigated for their antioxidant and selected biological activities. Strong relationships between the structure and evaluated activity revealed that the compounds with specific functional groups and carbon skeleton had specific biological profiles. Among the compounds tested, the derivatives (E-2-(3,4-dimethoxybenzylidene-5-((E-3-(3,4-dimethoxyphenylacryloylcyclopentanone (3e, and (E-2-(4-hydroxy-3-methoxybenzylidene-5-((E-3-(4-hydroxy-3-methoxyphenylacryloyl-cyclopentanone (3d and the parent compound curcumin exhibited the strongest free radical scavenging and antioxidant capacity. Concerning the other biological activities studied the compound (E-2-(4-hydroxy-3-methoxybenzylidene-5-((E-3-(4-hydroxy-3-methoxy-phenyl-acryloylcyclopentanone (3d was the most potent angiotensin converting enzyme (ACE inhibitor, while the derivatives (E-2-(4-hydroxybenzylidene-6-((E-3-(4-hydroxyphenylacryloylcyclohexanone (2b, (E-2-(3,4-dimethoxybenzylidene-6-((E-3-(3,4-dimethoxyphenylacryloylcyclohexanone (2e and (E-2-(3,4-dimethoxybenzylidene-5-((E-3-(3,4-dimethoxyphenylacryloylcyclopentanone (3e exhibited strong tyrosinase inhibition. Moreover, (E-2-(3,4-dimethoxybenzylidene-6-((E-3-(3,4-dimethoxyphenyl-acryloylcyclohexanone (2e was also found to be the strongest human HIV-1 protease inhibitor in vitro among the tested compounds. Cytotoxicity studies using normal human lung cells revealed that the novel curcumin as well as its carbocyclic analogs are not toxic.

  8. Use of novel silver nanoparticles with Hyaluronan as potential biological labels for determining the quality of embryos development

    Science.gov (United States)

    Syrvatka, Vasyl J.; Slyvchuk, Yurij I.; Rozgoni, Ivan I.; Hevkan, Ivan I.; Bilyi, Oleksandr I.; Osypchuk, Oleksandr S.; Zyuzyun, Aza B.

    2013-09-01

    In reproductive medicine it is important to determine the quality of embryo development without interference in their function and viability. The surface plasmon resonance of silver nanoparticles makes them promising candidates for optical sensing, molecular labeling and imaging applications. Furthermore unique optical properties of silver nanoparticles provide an opportunity to use them as real time analytic tools in living state especially for observation of dynamic processes in gametes and embryos. The main aim of the study was to investigate the physicochemical properties and biological activities of novel silver nanoparticles with prospect of their use for the determining the quality of embryo development. For this purpose, we investigated the optical properties of new silver nanoparticles in biological mediums during cultivation and their influence on rabbit's embryos development in vitro. The physicochemical and biological properties of novel silver nanoparticles were compared with silver nanoparticles identical in size and shapes but with different chemical surfaces modifications by polyvinylpyrrolidone and bovine serum albumin. The results suggest that silver nanoparticles with hyaluronic acid were disintegrated with the formation of new complexes with proteins in biological mediums. This property with strong optical surface plasmon resonance of novel silver nanoparticles with hyaluronan makes them promising candidates in diagnostic area and gives reasons to explore them as biomarkers of target molecules. Nevertheless novel silver nanoparticles with hyaluronan at the concentrations of 0.1-1 μg/ml have no toxic effect on rabbit's embryos development and can be successfully applied in reproductive medicine.

  9. Elements determination of clinical relevance in biological tissues Dmdmdx/J dystrophic mice strains investigated by NAA

    International Nuclear Information System (INIS)

    In this work the determination of chemistry elements in biological tissues (whole blood, bones and organs) of dystrophic mice, used as animal model of Duchenne Muscular Dystrophy (DMD), was performed using analytical nuclear technique. The aim of this work was to determine reference values of elements of clinical (Ca, Cl, K, Mg, Na) and nutritional (Br and S) relevance in whole blood, tibia, quadriceps and hearts from Dmdmdx/J (10 males and 10 females) dystrophic mice and C57BL/6J (10 males) control group mice, using Neutron Activation Analysis technique (NAA). To show in more details the alterations that this disease may cause in these biological tissues, correlations matrixes of the DMDmdx/J mouse strain were generated and compared with C57BL/6J control group. For this study 119 samples of biological tissue were irradiated in the IEA-R1 nuclear reactor at IPEN (Sao Paulo, Brazil). The concentrations of these elements in biological tissues of Dmdmdx/J and C57B/6J mice are the first indicative interval for reference values. Moreover, the alteration in some correlation coefficients data among the elements in the health status and in the diseased status indicates a connection between these elements in whole blood, tibia, quadriceps and heart. These results may help the researchers to evaluate the efficiency of new treatments and to compare the advantages of different treatment approaches before performing tests in patients with muscular dystrophy. (author)

  10. Determining the impacts of trawling on benthic function in European waters : a biological traits approach

    DEFF Research Database (Denmark)

    Bolam, Stefan; Kenny, Andrew; Garcia, Clement;

    on benthic ecosystem functioning over much larger spatial scales than previously undertaken. Biological traits information from 887 stations across European waters (Norwegian, UK, Belgian, Dutch, Danish waters, the Mediterranean and Black Sea) were analysed to: i) quantify the relationships between infaunal...

  11. Incorporating Biological Mass Spectrometry into Undergraduate Teaching Labs, Part 2: Peptide Identification via Molecular Mass Determination

    Science.gov (United States)

    Arnquist, Isaac J.; Beussman, Douglas J.

    2009-01-01

    Mass spectrometry has become a routine analytical tool in the undergraduate curriculum in the form of GC-MS. While relatively few undergraduate programs have incorporated biological mass spectrometry into their programs, the importance of these techniques, as demonstrated by their recognition with the 2002 Nobel Prize, will hopefully lead to…

  12. Moooving forward on determining biologically active compounds in milk and their impact on health

    Science.gov (United States)

    Recent studies have demonstrated that some of the lesser studied components in milk, known as biologically active compounds (BACs), may provide potential benefits to human health. The added health-value of raw milk and milk from organic and grass-fed herds is strongly debated because of limited, an...

  13. Determination of the Biologically Relevant Sampling Depth for Terrestrial and Aquatic Ecological Risk Assessments (Final Report)

    Science.gov (United States)

    This technical paper provides defensible approximations for what the depth of the biologically active zone, or “biotic zone” is within certain environments. The methods used in this study differ somewhat between Part 1 (Terrestrial Biotic Zone) and Part 2 (Aquatic Biotic Zone). ...

  14. Crystal and molecular structures of some organophosphorus insecticides and computer methods for structure determination. [Dissertation

    Energy Technology Data Exchange (ETDEWEB)

    Lapp, R.L.

    1979-01-01

    Molecular structure investigations of a set of organophosphorus insecticides have been carried out in order to acquire the data base to develop correlations between such parameters and their toxicities. The crystal and molecular structures of dimethoate (LD/sub 50/ (rats) = 600 mg/kg), IPAT, and leptophos (LD/sub 50/ (rats) = 90 mg/kg) have been determined via three-dimensional x-ray analysis. The crystal and molecular structure of (-)-..cap alpha..-phenylethylammonium (-)-0-methyl-phenylphosphonothioate was solved by conventional Patterson and Fourier techniques to a final R value of 0.057. The crystal and molecular structures of two crystalline forms of calcium formate were determined. A new least-squares refinement program was written which is much more general and efficient than any previous program. In particular, a new block-diagonal approximation has been devised which is much more economical than full-matrix refinement and appears to work much better than previous block-diagonal methods. A Howells, Phillips and Rogers test for a center of symmetry and a Wilson plot have been programmed into the data collection algorithm. Some approximations and special problems are discussed relative to implementing these routines in a real-time mode on a minicomputer. A mathematical background and program description are included for each program.

  15. DNA-Protein Cross-Links: Formation, Structural Identities, and Biological Outcomes.

    Science.gov (United States)

    Tretyakova, Natalia Y; Groehler, Arnold; Ji, Shaofei

    2015-06-16

    Noncovalent DNA-protein interactions are at the heart of normal cell function. In eukaryotic cells, genomic DNA is wrapped around histone octamers to allow for chromosomal packaging in the nucleus. Binding of regulatory protein factors to DNA directs replication, controls transcription, and mediates cellular responses to DNA damage. Because of their fundamental significance in all cellular processes involving DNA, dynamic DNA-protein interactions are required for cell survival, and their disruption is likely to have serious biological consequences. DNA-protein cross-links (DPCs) form when cellular proteins become covalently trapped on DNA strands upon exposure to various endogenous, environmental and chemotherapeutic agents. DPCs progressively accumulate in the brain and heart tissues as a result of endogenous exposure to reactive oxygen species and lipid peroxidation products, as well as normal cellular metabolism. A range of structurally diverse DPCs are found following treatment with chemotherapeutic drugs, transition metal ions, and metabolically activated carcinogens. Because of their considerable size and their helix-distorting nature, DPCs interfere with the progression of replication and transcription machineries and hence hamper the faithful expression of genetic information, potentially contributing to mutagenesis and carcinogenesis. Mass spectrometry-based studies have identified hundreds of proteins that can become cross-linked to nuclear DNA in the presence of reactive oxygen species, carcinogen metabolites, and antitumor drugs. While many of these proteins including histones, transcription factors, and repair proteins are known DNA binding partners, other gene products with no documented affinity for DNA also participate in DPC formation. Furthermore, multiple sites within DNA can be targeted for cross-linking including the N7 of guanine, the C-5 methyl group of thymine, and the exocyclic amino groups of guanine, cytosine, and adenine. This structural

  16. Beyond terrestrial biology: charting the chemical universe of α-amino acid structures.

    Science.gov (United States)

    Meringer, Markus; Cleaves, H James; Freeland, Stephen J

    2013-11-25

    α-Amino acids are fundamental to biochemistry as the monomeric building blocks with which cells construct proteins according to genetic instructions. However, the 20 amino acids of the standard genetic code represent a tiny fraction of the number of α-amino acid chemical structures that could plausibly play such a role, both from the perspective of natural processes by which life emerged and evolved, and from the perspective of human-engineered genetically coded proteins. Until now, efforts to describe the structures comprising this broader set, or even estimate their number, have been hampered by the complex combinatorial properties of organic molecules. Here, we use computer software based on graph theory and constructive combinatorics in order to conduct an efficient and exhaustive search of the chemical structures implied by two careful and precise definitions of the α-amino acids relevant to coded biological proteins. Our results include two virtual libraries of α-amino acid structures corresponding to these different approaches, comprising 121 044 and 3 846 structures, respectively, and suggest a simple approach to exploring much larger, as yet uncomputed, libraries of interest.

  17. Determination of thorium and uranium in biological samples by inductively coupled plasma mass spectrometry using internal standardisation

    International Nuclear Information System (INIS)

    The Th and U contents of six typical biological samples (for example US NIST SRMs and Japan NIES CRMs) were determined by inductively coupled plasma mass spectrometry (ICP-MS). The internal standardisation method was adopted to compensate for non-spectroscopic interferences arising from matrix elements in the sample solution. Bismuth and Tl were chosen as the internal standards, and the effect of the matrix on the behaviour of their signals was monitored by adding several elements to the NIST human lung sample. It would appear that elements of similar mass give similar signal responses, thus In is unsuitable as the internal standard in this instance. After correction by either Bi or Tl internal standardisation, the results for the Th and U concentrations agreed well with literature values, showing that both are applicable for the determination of Th and U in biological samples. (author)

  18. An analysis of the structure of the compound biological effectiveness factor

    Science.gov (United States)

    Ono, Koji

    2016-01-01

    This report is an analysis of the structure of the compound biological effectiveness (CBE) factor. The value of the CBE factor previously reported was revalued for the central nervous system, skin and lung. To describe the structure, the following terms are introduced: the vascular CBE (v-CBE), intraluminal CBE (il-CBE), extraluminal CBE (el-CBE) and non-vascular CBE (nv-CBE) factors and the geometric biological factor (GBF), i.e. the contributions that are derived from the total dose to the vasculature, each dose to vasculature from the intraluminal side and the extraluminal side, the dose to the non-vascular tissue and the factor to calculate el-CBE from il-CBE, respectively. The el-CBE factor element was also introduced to relate il-CBE to el-CBE factors. A CBE factor of 0.36 for disodium mercaptoundecahydrododecaborate (BSH) for the CNS was independent of the 10B level in the blood; however, that for p-Boron-L-phenylalanine (BPA) increased with the 10B level ratio of the normal tissue to the blood (N/B). The CBE factor was expressed as follows: factor = 0.32 + N/B × 1.65. The factor of 0.32 at 0 of N/B was close to the CBE factor for BSH. GBFs had similar values, between BSH and BPA, 1.39 and 1.52, respectively. The structure of the CBE factor for BPA to the lung was also elucidated based on this idea. The factor is described as follows: CBE factor = 0.32 + N/B × 1.80. By this elucidation of the structure of the CBE factor, it is expected that basic and clinical research into boron neutron capture therapy will progress. PMID:27021218

  19. Quantification of layered patterns with structural anisotropy: a comparison of biological and geological systems.

    Science.gov (United States)

    Smolyar, I; Bromage, T; Wikelski, M

    2016-03-01

    Large-scale patterns evident from satellite images of aeolian landforms on Earth and other planets; those of intermediate scale in marine and terrestrial sand ripples and sediment profiles; and small-scale patterns such as lamellae in the bones of vertebrates and annuli in fish scales are each represented by layers of different thicknesses and lengths. Layered patterns are important because they form a record of the state of internal and external factors that regulate pattern formation in these geological and biological systems. It is therefore potentially possible to recognize trends, periodicities, and events in the history of the formation of these systems among the incremental sequences. Though the structures and sizes of these 2-D patterns are typically scale-free, they are also characteristically anisotropic; that is, the number of layers and their absolute thicknesses vary significantly during formation. The aim of the present work is to quantify the structure of layered patterns and to reveal similarities and differences in the processing and interpretation of layered landforms and biological systems. To reach this goal we used N-partite graph and Boolean functions to quantify the structure of layers and plot charts for "layer thickness vs. layer number" and "layer area vs. layer number". These charts serve as a source of information about events in the history of formation of layered systems. The concept of synchronization of layer formation across a 2-D plane is introduced to develop the procedure for plotting "layer thickness vs. layer number" and "layer area vs. layer number", which takes into account the structural anisotropy of layered patterns and increase signal-to-noise ratio in charts. Examples include landforms on Mars and Earth and incremental layers in human and iguana bones. PMID:27441261

  20. Report on intercomparison run SNR-1 for the determination of trace elements in synthetic resin simulating biological material

    International Nuclear Information System (INIS)

    A synthetic resin, SNR-1, simulating biological material and containing homogeneously distributed trace amounts of As, Au, Br, Cr, Cs, Hg, La, Mn, Rb, Sb, Se and Sr, was made available to 16 laboratories in the form of 50 mg - pellets. Various methods for the quantitative determination of these elements (and, in some cases, also of impurities) including neutron activation analysis, and neutron activation analysis with radio-chemical analysis were used in an interlaboratory comparative study. The results are tabulated

  1. Determination of selenium in biological materials by flow injection hydride generation atomic absorption spectrometry (FI-HG-AAS)

    OpenAIRE

    Galgan, Vera

    2007-01-01

    The selenium (Se) poor environment in the Scandinavian countries focused the interest on the development of an analytical method with high capacity, sensitivity, low limit of detection, including automated wet digestion, automated analysis and computer aided calculation. To facilitate the choice of an appropriate analytical method, procedures for determination in biological materials were discussed. The most frequently used sample-preparation procedures and various analytical techniques were ...

  2. Dynamic neuronal ensembles: Issues in representing structure change in object-oriented, biologically-based brain models

    Energy Technology Data Exchange (ETDEWEB)

    Vahie, S.; Zeigler, B.P.; Cho, H. [Univ. of Arizona, Tucson, AZ (United States)

    1996-12-31

    This paper describes the structure of dynamic neuronal ensembles (DNEs). DNEs represent a new paradigm for learning, based on biological neural networks that use variable structures. We present a computational neural element that demonstrates biological neuron functionality such as neurotransmitter feedback absolute refractory period and multiple output potentials. More specifically, we will develop a network of neural elements that have the ability to dynamically strengthen, weaken, add and remove interconnections. We demonstrate that the DNE is capable of performing dynamic modifications to neuron connections and exhibiting biological neuron functionality. In addition to its applications for learning, DNEs provide an excellent environment for testing and analysis of biological neural systems. An example of habituation and hyper-sensitization in biological systems, using a neural circuit from a snail is presented and discussed. This paper provides an insight into the DNE paradigm using models developed and simulated in DEVS.

  3. GC-MS and LC-MS approaches for determination of tocopherols and tocotrienols in biological and food matrices.

    Science.gov (United States)

    Bartosińska, E; Buszewska-Forajta, M; Siluk, D

    2016-08-01

    Tocopherols and tocotrienols, widely described as vitamin E derivatives, have been proven to take part in a number of important biological functions. Among them, antioxidant properties had been investigated and documented in the literature. Since tocochromanols have revealed their plausible beneficial impact on several pathological processes, such as cancerogenesis or cognitive impairment diseases, there is a growing interest in quantitative determination of these compounds in biological fluids, tissues and plant organs. However, due to vitamin E chemical features, such as lipophilic and non-polar characteristics, quantitative determination of the compounds seems to be problematic. In this paper we present current analytical approaches in tocopherols and tocotrienols determination in biological and food matrices with the use of chromatographic techniques, especially gas chromatography (GC) and high performance liquid chromatography (HPLC) coupled with mass spectrometry. Derivatization techniques applied for GC-MS analysis in the case of tocol derivatives, especially silylation and acylation, are described. Significant attention is paid to ionization process of tocopherols and tocotrienols. PMID:26964480

  4. Allergen structures and biologic functions: the cutting edge of allergy research.

    Science.gov (United States)

    Pomés, Anna

    2008-09-01

    Studies of structure and function of allergens using state-of-the-art technologies have led to a better understanding of allergenicity, including aspects related to cross-reactivity, allergen nomenclature, and the identification of antigenic determinants. This information is being applied to the design and production of allergy vaccines, some of which already have proven efficacy and safety in clinical trials.

  5. Determination of Strong Acidic Drugs in Biological Matrices: A Review of Separation Methods

    Directory of Open Access Journals (Sweden)

    Lingli Mu

    2014-01-01

    Full Text Available Strong acidic drugs are a class of chemical compounds that normally have high hydrophilicity and large negative charges, such as organophosphatic compounds and organosulphonic compounds. This review focuses on sample preparation and separation methods for this group of compounds in biological matrices in recent years. A wide range of separation techniques, especially chromatographic method, are presented and critically discussed, which include liquid chromatography (e.g., ion-pair and ion-exchange chromatography, capillary electrophoresis (CE, and other types. Due to the extremely low concentration level of target analytes as well as the complexity of biological matrices, sample pretreatment methods, such as dilute and shoot methods, protein precipitation (PP, liquid-liquid extraction (LLE, solid-phase extraction (SPE, degradation, and derivatization strategy, also play important roles for the development of successful analytical methods and thus are also discussed.

  6. Electroanalytical Determination of Danofloxacin in Biological Samples Using Square Wave Voltammetry

    Directory of Open Access Journals (Sweden)

    Chirley Vanessa Boone

    2014-10-01

    Full Text Available The voltammetric behavior of danofloxacin (DFX has been studied, in aqueous solution, on a glassy carbon electrode using square wave voltammetry (SWV as electroanalytical technique. After optimization of the experimental conditions, DFX was analyzed in spiked biologic samples using a Britton-Robinson buffer with pH = 5.0 as the supporting electrolyte. Oxidation occurs at 0.98 V vs. Ag/AgCl in a two-electron process controlled by adsorption of the electrogenerated products on the electrode surface. A acceptable recovery was obtained for assay of spiked biologic samples, with value of 98.7% for the swine urine and 95.3 % for the bovine urine.

  7. Synthesis, Structure and Biological Activities of Novel Triazole Compounds Containing 4,6-Dimethyl-pyrimidin-2-ylthio Group

    Institute of Scientific and Technical Information of China (English)

    XU, Liang-Zhong(许良忠); JIAN, Fang-Fang(建方方); SHI, Jian-Gang(时建刚); LI, Lin(李琳)

    2004-01-01

    Four compounds were prepared by reacting 4,6-dimethyl-2-mercaptopyrimidine with α-bromo-α-(1,2,4-triazol-1-yl)-substituted acetylbenzene. Their structures were identified by means of elemental analysis, IR, and 1H NMR spectra. The single crystal structure of 2- [ 1 -(1,2,4-triazol- 1-yl)- 1-p-methoxyphenylcarbonylmethylthio] -4,6-dimethyl-pyrimidine was also determined. It crystallizes in monoclinic system, space group P21/c, a=0.8016(2) nm, b=1.2462(3) nm, c= 1.7824(4) nm,β=99.89(3)°, Z=4, V=1.7540(7) nm3, Dc=1.346 g/cm3, μ=0.205 mm-1, F(000)=744, final R1=0.0452. There is obviously potentially weak C-H…N intermolecular interaction between the molecules in the crystal lattice, which stabilizes the crystal structure. The result of the biological test showed that the four compounds all have some fungicidal and plant growth regulating activities.

  8. Reproductive biology and age determination of Garra rufa Heckel, 1843 (Actinopterygii: Cyprinidae) in central Iran

    OpenAIRE

    ABEDI, Masoud; SHIVA, Amir Houshang; Mohammadi, Hamid; MALEKPOUR, Rokhsareh

    2011-01-01

    Some aspects of the reproductive biology of Garra rufa Heckel, 1843, a native cyprinid fish species from the Armand stream in Chaharmahal-o-Bakhtiari province, central Iran, were investigated by regular monthly collections throughout 1 year. A significant relationship between length and weight and the isometric growth pattern were observed in this fish. There were no significant differences in the total number of male and female specimens. The population of this cyprinid fish had a narrow age...

  9. Biological monitoring to determine worker dose in a butadiene processing plant

    Energy Technology Data Exchange (ETDEWEB)

    Bechtold, W.E.; Hayes, R.B. [National Cancer Inst., Bethesda, MD (United States)

    1995-12-01

    Butadiene (BD) is a reactive gas used extensively in the rubber industry and is also found in combustion products. Although BD is genotoxic and acts as an animal carcinogen, the evidence for carcinogenicity in humans is limited. Extrapolation from animal studies on BD carcinogenicity to risk in humans has been controversial because of uncertainties regarding relative biologic exposure and related effects in humans vs. experimental animals. To reduce this uncertainty, a study was designed to characterize exposure to BD at a polymer production facility and to relate this exposure to mutational and cytogenetic effects. Biological monitoring was used to better assess the internal dose of BD received by the workers. Measurement of 1,2-dihydroxy-4-(N-acetylcysteinyl) butane (M1) in urine served as the biomarker in this study. M1 has been shown to correlate with area monitoring in previous studies. Most studies that relate exposure to a toxic chemical with its biological effects rely on exposure concentration as the dose metric; however, exposure concentration may or may not reflect the actual internal dose of the chemical.

  10. Two-dimensional flow nanometry of biological nanoparticles for accurate determination of their size and emission intensity

    Science.gov (United States)

    Block, Stephan; Fast, Björn Johansson; Lundgren, Anders; Zhdanov, Vladimir P.; Höök, Fredrik

    2016-01-01

    Biological nanoparticles (BNPs) are of high interest due to their key role in various biological processes and use as biomarkers. BNP size and composition are decisive for their functions, but simultaneous determination of both properties with high accuracy remains challenging. Optical microscopy allows precise determination of fluorescence/scattering intensity, but not the size of individual BNPs. The latter is better determined by tracking their random motion in bulk, but the limited illumination volume for tracking this motion impedes reliable intensity determination. Here, we show that by attaching BNPs to a supported lipid bilayer, subjecting them to hydrodynamic flows and tracking their motion via surface-sensitive optical imaging enable determination of their diffusion coefficients and flow-induced drifts, from which accurate quantification of both BNP size and emission intensity can be made. For vesicles, the accuracy of this approach is demonstrated by resolving the expected radius-squared dependence of their fluorescence intensity for radii down to 15 nm. PMID:27658367

  11. Use of cloud-point preconcentration for spectrophotometric determination of trace amounts of antimony in biological and environmental samples.

    Science.gov (United States)

    El-Sharjawy, Abdel-Azeem M; Amin, Alaa S

    2016-01-01

    This work presents a cloud-point extraction process using the micelle-mediated extraction method for simultaneous preconcentration and determination of Sb(III) and Sb(V) species in biological and environmental samples as a prior preconcentration step to their spectrophotometric determination. The analytical system is based on the selective reaction between Sb(III) and 3-dichloro-6-(3-carboxy-2-hydroxy-1-naphthylazo)quinoxaline (DCHNAQ) in the presence of cetyltrimethylammonium bromide (CTAB) and potassium iodide at pH 4.5. Total Sb concentration was determined after reduction of Sb(V) to Sb(III) in the presence of potassium iodide and ascorbic acid. The optimal reaction conditions and extraction were studied, and the analytical characteristics of the method (e.g., limits of detection and quantification, linear range, preconcentration, improvement factors) were obtained. Linearity for Sb(III) was obeyed in the range of 0.2-20 ng ml(-1). The detection and quantification limits for the determination of Sb(III) were 0.055 and 0.185 ng ml(-1), respectively. The method has a lower detection limit and wider linear range, inexpensive instrument, and low cost, and is more sensitive compared with most other methods. The interference effect of some anions and cations was also studied. The method was applied to the determination of Sb(III) in the presence of Sb(V) and total antimony in blood plasma, urine, biological, and water samples.

  12. The structural determinants of insulin-like peptide 3 activity

    Directory of Open Access Journals (Sweden)

    Ross AD Bathgate

    2012-02-01

    Full Text Available INSL3 is a hormone and/or paracrine factor which is a member of the relaxin peptide family. It has key roles as a fertility regulator in both males and females. The receptor for INSL3 is the leucine rich repeat (LRR containing G-protein coupled receptor 8 (LGR8 which is now known as relaxin family peptide receptor 2 (RXFP2. Receptor activation by INSL3 involves binding to the LRRs in the large ectodomain of RXFP2 by residues within the B-chain of INSL3 as well as an interaction with the transmembrane exoloops of the receptor. Although the binding to the LRRs is well characterized the features of the peptide and receptor involved in the exoloop interaction are currently unknown. This study was designed to determine the key INSL3 determinants for RXFP2 activation. A chimeric peptide approach was first utilized to demonstrate that the A-chain is critical for receptor activation. Replacement of the INSL3 A-chain with that from the related peptides INSL5 and INSL6 resulted in complete loss of activity despite only minor changes in binding affinity. Subsequent replacement of specific A-chain residues with those from the INSL5 peptide highlighted that the N-terminus of the A-chain of INSL3 is critical for its activity. Remarkably, replacement of the entire N-terminus with four or five alanine residues resulted in peptides with near native activity suggesting that specific residues are not necessary for activity. Additionally removal of two amino acids at the C-terminus of the A-chain and mutation of Lys-8 in the B-chain also resulted in minor decreases in peptide activity. Therefore we have demonstrated that the activity of the INSL3 peptide is driven predominantly by residues 5-9 in the A-chain, with minor additional contributions from the two C-terminal A-chain residues and Lys-8 in the B-chain. Using this new knowledge, we were able to produce a truncated INSL3 peptide structure which retained native activity, despite having 14 fewer residues than

  13. The formation, function and regulation of amyloids: insights from structural biology.

    Science.gov (United States)

    Landreh, M; Sawaya, M R; Hipp, M S; Eisenberg, D S; Wüthrich, K; Hartl, F U

    2016-08-01

    Amyloid diseases are characterized by the accumulation of insoluble, β-strand-rich aggregates. The underlying structural conversions are closely associated with cellular toxicity, but can also drive the formation of functional protein assemblies. In recent years, studies in the field of structural studies have revealed astonishing insights into the origins, mechanisms and implications of amyloid formation. Notably, high-resolution crystal structures of peptides in amyloid-like fibrils and prefibrillar oligomers have become available despite their challenging chemical nature. Nuclear magnetic resonance spectroscopy has revealed that dynamic local polymorphisms in the benign form of the prion protein affect the transformation into amyloid fibrils and the transmissibility of prion diseases. Studies of the structures and interactions of chaperone proteins help us to understand how the cellular proteostasis network is able to recognize different stages of aberrant protein folding and prevent aggregation. In this review, we will focus on recent developments that connect the different aspects of amyloid biology and discuss how understanding the process of amyloid formation and the associated defence mechanisms can reveal targets for pharmacological intervention that may become the first steps towards clinically viable treatment strategies. PMID:27237473

  14. Membrane protein structural biology using X-ray free electron lasers.

    Science.gov (United States)

    Neutze, Richard; Brändén, Gisela; Schertler, Gebhard F X

    2015-08-01

    Membrane protein structural biology has benefitted tremendously from access to micro-focus crystallography at synchrotron radiation sources. X-ray free electron lasers (XFELs) are linear accelerator driven X-ray sources that deliver a jump in peak X-ray brilliance of nine orders of magnitude and represent a disruptive technology with potential to dramatically change the field. Membrane proteins were amongst the first macromolecules to be studied with XFEL radiation and include proof-of-principle demonstrations of serial femtosecond crystallography (SFX), the observation that XFEL data can deliver damage free crystallographic structures, initial experiments towards recording structural information from 2D arrays of membrane proteins, and time-resolved SFX, time-resolved wide angle X-ray scattering and time-resolved X-ray emission spectroscopy studies. Conversely, serial crystallography methods are now being applied using synchrotron radiation. We believe that a context dependent choice of synchrotron or XFEL radiation will accelerate progress towards novel insights in understanding membrane protein structure and dynamics.

  15. Development of standards for chemical and biological decontamination of buildings and structures affected by terrorism

    Energy Technology Data Exchange (ETDEWEB)

    Lumley, T.C.; Volchek, K.; Fingas, M. [Environment Canada, Ottawa, ON (Canada). Emergencies Science and Technology Division, Environmental Technology Centre, Science and Technology Branch; Hay, A.W.M. [Leeds Univ., Leeds (United Kingdom)

    2006-07-01

    Currently, there are no suitable standards for determining levels of safety when reoccupying a building that has been recommissioned following a biological or chemical attack. For that reason, this study focused on developing clean-up standards for decontaminating buildings and construction materials after acts of terrorism. Several parameters must be assessed when determining the course of action to decontaminate toxic agents and to rehabilitate facilities. First, the hazardous substance must be positively identified along with the degree of contamination and information on likely receptors. Potential exposure route is also a key consideration in the risk assessment process. A key objective of the study was to develop specific guidelines for ascertaining and defining clean. In particular, standards for chemical and biological agents that pose a real or potential risk for use as agents of terrorism will be developed. The selected agents for standards development were ammonia, fentanyl, malathion, mustard gas, potassium cyanide, ricin, sarin, hepatitis A virus, and bacillus anthracis. The standards will be developed by establishing the relationship between the amount of exposure and expected health effects; assessing real and potential risks by identifying individuals at risk and consideration of all exposure routes; and, characterizing the risk to determine the potential for toxicity or infectivity. For non-carcinogens, this was done through the analysis of other known guidelines. Cancer-slope factors will be considered for carcinogens. The standards will be assessed in the laboratory using animal models. The guidelines and standards are intended for first-responders and are scheduled for development by the end of 2006. 15 refs., 3 tabs.

  16. Market power versus capital structure determinants: Do they impact leverage?

    Directory of Open Access Journals (Sweden)

    Agha Jahanzeb

    2015-12-01

    Full Text Available The purpose of this study is to investigate the association between market power and capital structure. This study will further provide a logical explanation towards the factors affecting capital structure. This study analysed 176 non-financial Pakistani companies listed on Karachi Stock Exchange over the period of 2003–2012. Capital structure has been tried to investigate with a different perspective by investigating its association with market power. It has been seen that there is a significant and positive relation between market power and capital structure. Size and liquidity remained significantly negative with capital structure, whereas profitability and dividend payout remained significantly positive with capital structure. To the best of authors’ knowledge, this is the first study that investigates the relationship between market power and capital structure in any developing economy by employing the data of non-financial Pakistani firms.

  17. Analytical methods for determination of terbinafine hydrochloride in pharmaceuticals and biological materials$

    Institute of Scientific and Technical Information of China (English)

    Basavaiah Kanakapura n; Vamsi Krishna Penmatsa

    2016-01-01

    Terbinafine is a new powerful antifungal agent indicated for both oral and topical treatment of myco-sessince. It is highly effective in the treatment of determatomycoses. The chemical and pharmaceutical analysis of the drug requires effective analytical methods for quality control and pharmacodynamic and pharmacokinetic studies. Ever since it was introduced as an effective antifungal agent, many methods have been developed and validated for its assay in pharmaceuticals and biological materials. This article reviews the various methods reported during the last 25 years.

  18. Separation Technique for the Determination of Highly Polar Metabolites in Biological Samples

    Directory of Open Access Journals (Sweden)

    Yusuke Iwasaki

    2012-08-01

    Full Text Available Metabolomics is a new approach that is based on the systematic study of the full complement of metabolites in a biological sample. Metabolomics has the potential to fundamentally change clinical chemistry and, by extension, the fields of nutrition, toxicology, and medicine. However, it can be difficult to separate highly polar compounds. Mass spectrometry (MS, in combination with capillary electrophoresis (CE, gas chromatography (GC, or high performance liquid chromatography (HPLC is the key analytical technique on which emerging "omics" technologies, namely, proteomics, metabolomics, and lipidomics, are based. In this review, we introduce various methods for the separation of highly polar metabolites.

  19. Biological determination of the variation of fast-neutron field quality with depth, RBE, and OER

    International Nuclear Information System (INIS)

    The biological effectiveness of two cyclotron-produced fast neutron fields (E/sub n/ approximately 3.5 and 7 MeV) has been studied as a function of depth within a water phantom. Aerobic and hypoxic HeLa S3 cell survival data were obtained at depths of 2 and 12 cm and compared with those measured in a 60Co gamma ray field. Although the resulting survival curves show a small decrease in sensitivity with increasing depth, the oxygen enhancement ratio remains constant and has a value of 1.8 +- 0.1 in both fields. (U.S.)

  20. Gender differences in stress response: Role of developmental and biological determinants

    Directory of Open Access Journals (Sweden)

    Rohit Verma

    2011-01-01

    Full Text Available Stress response is associated with manifestations of various psychosomatic and psychiatric disorders. Hence, it is important to understand the underlying mechanisms that influence this association. Moreover, men and women tend to react differently with stress-both psychologically and biologically. These differences also need to be studied in order to have a better understanding in the gender difference observed for many disorders, which are likely to be contributed by the gender difference in stress reactivity and responses. Such an understanding would have a significant impact on our understanding about how adult health is set during early life and how adult disease could be prevented in men and women.