WorldWideScience

Sample records for biological structure determination

  1. The potential for biological structure determination with pulsed neutrons

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-12-31

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

  2. 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.

  3. 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 ...

  4. What determines family structure?

    OpenAIRE

    Blau, David M.; van der Klaauw, Wilbert

    2010-01-01

    We estimate the effects of policy and labor market variables on the fertility, union formation and dissolution, type of union (cohabiting versus married), and partner choices of the NLSY79 cohort of women. These demographic behaviors interact to determine the family structure experienced by the children of these women: living with the biological mother and the married or cohabiting biological father, a married or cohabiting step father, or no man. We find that the average wage rates available...

  5. 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

  6. Determination of the Biological Activity and Structure Activity Relationships of Drugs Based on the Highly Cytotoxic Duocarmycins and CC-1065

    OpenAIRE

    2009-01-01

    The natural antibiotics CC‑1065 and the duocarmycins are highly cytotoxic compounds which however are not suitable for cancer therapy due to their general toxicity. We have developed glycosidic prodrugs of seco-analogues of these antibiotics for a selective cancer therapy using conjugates of glycohydrolases and tumour-selective monoclonal antibodies for the liberation of the drugs from the prodrugs predominantly at the tumour site. For the determination of structure activity relationships of ...

  7. [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.

  8. 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…

  9. 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...

  10. 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.

  11. Hierarchical structure of biological systems

    Science.gov (United States)

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

    2014-01-01

    A general theory of biological systems, based on few fundamental propositions, allows a generalization of both Wierner and Berthalanffy approaches to theoretical biology. Here, a biological system is defined as a set of self-organized, differentiated elements that interact pair-wise through various networks and media, isolated from other sets by boundaries. Their relation to other systems can be described as a closed loop in a steady-state, which leads to a hierarchical structure and functioning of the biological system. Our thermodynamical approach of hierarchical character can be applied to biological systems of varying sizes through some general principles, based on the exchange of energy information and/or mass from and within the systems. PMID:24145961

  12. [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.

  13. Isolation, structure determination and biological activity of 25-epi, 3{alpha}-carboxyacetylquercinic acid in daedalea dickinsii

    Energy Technology Data Exchange (ETDEWEB)

    Bae, Kang Gyu; Min, Tae Jin [Dongguk Univ., Seoul (Korea, Republic of)

    2000-02-01

    In order to develope bioactive substances, dried fruit body of Daedalea dickinsii collected from Taeback mountain was extracted with ethanol. The compounds 1 and 2 were purified by solvent extraction, silica gel column chromatography and recrystallization from the ethanol extracts. Melting point, molecular weight and molar extinction coefficient of the compound 1 were estimated to be 167{approx}168 .deg. C, 572 and 5,040 at 208 nm. The structure of this compound 1 has been elucidated to be 24S, 25S, 3{alpha}-carboxyacetylquercinic acid using spectroscopic properties. This compound showed antibiotic activities against fungi, yeasts and bacteria and it also showed anticancer activity(IC{sub 50}=64.5 {mu}M/ml) against Korean stomach cancer cell. Melting point, molecular weight and molar extinction coefficient of the compound 2 were estimated to be 233{approx}235 .deg. C, 572 and 5,080 at 208 nm. The structure of this compound was elucidated to be 24S, 25R, 3{alpha}-carboxyacetylquercinic acid. The compound 2 showed different antibiotic activities with the compound 1.

  14. [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.

  15. 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.

  16. 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.

  17. Structure Biology of Membrane Bound Enzymes

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-11-30

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

  18. 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.

  19. Estrogenic flavonoids: structural requirements for biological activity.

    Science.gov (United States)

    Miksicek, R J

    1995-01-01

    A systematic survey of polycyclic phenols has been performed to identify members of this chemical group with estrogenic activity. Twelve compounds were found to be able to stimulate the transcriptional activity of the human estrogen receptor expressed in cultured cells by transient transfection. These natural estrogens belong to several distinct, but chemically related classes including chalcones, flavanones, flavones, flavonols, and isoflavones. Selected examples of estrogenic flavonoids were further analyzed to determine their biological potencies and their relative affinities for binding to the estrogen receptor. These data are interpreted with respect to the molecular structure of polycyclic phenols required for hormonal activity as nonsteroidal estrogens.

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

    Science.gov (United States)

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

    2013-01-01

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

  1. Dissipative Structures and Biological Evolution

    Science.gov (United States)

    Brändas, E. J.

    This contribution celebrates Prof. Manuel G. Velarde's exceptional accomplishments in the science of Complex Systems and Non-Linear Dynamics in connection with his seventieth anniversary and subsequent retirement from the Instituto Pluridisciplinar de la Universidad Complutense de Madrid (UCM). In this commemoration I will discuss my provisional yet unique association with Manuel over the years. Although viewing scientific problems from differing ends of the micro-macro spectrum I believe our relationship has been mutually beneficial. In this account I will, in a few words, describe recent developments in our program to attack complicated issues on the borderline between physics and biology. Concrete overlapping interests incorporate problems related to strongly correlated systems like superconductivity as well as currently disputed issues pertaining to biological concepts and the unity of physical theory. In summary we will give examples of such wide-ranging proposals comprising potential avenues providing feasible platforms for the future.

  2. 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,...

  3. Structural Biology of Nuclear Auxin Action.

    Science.gov (United States)

    Dinesh, Dhurvas Chandrasekaran; Villalobos, Luz Irina A Calderón; Abel, Steffen

    2016-04-01

    Auxin coordinates plant development largely via hierarchical control of gene expression. During the past decades, the study of early auxin genes paired with the power of Arabidopsis genetics have unraveled key nuclear components and molecular interactions that perceive the hormone and activate primary response genes. Recent research in the realm of structural biology allowed unprecedented insight into: (i) the recognition of auxin-responsive DNA elements by auxin transcription factors; (ii) the inactivation of those auxin response factors by early auxin-inducible repressors; and (iii) the activation of target genes by auxin-triggered repressor degradation. The biophysical studies reviewed here provide an impetus for elucidating the molecular determinants of the intricate interactions between core components of the nuclear auxin response module.

  4. 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 ...

  5. 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,…

  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.

  7. 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.

  8. 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.

  9. Structural determination of argon trimer

    Directory of Open Access Journals (Sweden)

    Xiguo Xie

    2015-09-01

    Full Text Available Rare gas clusters are model systems to investigate structural properties at finite size. However, their structures are difficult to be determined with available experimental techniques because of the strong coupling between the vibration and the rotation. Here we experimentally investigated multiple ionization and fragmentation dynamics of argon trimer by ultrashort intense laser fields and reconstructed their structures with Coulomb explosion technique. The measured structure distribution was compared with our finite-temperature ab initio calculations and the discrepancy was discussed. The present study provides a guidance for the development of theoretical methods for exploring the geometric structure of rare gas clusters.

  10. Syntactic structures in languages and biology.

    Science.gov (United States)

    Horn, David

    2008-08-01

    Both natural languages and cell biology make use of one-dimensional encryption. Their investigation calls for syntactic deciphering of the text and semantic understanding of the resulting structures. Here we discuss recently published algorithms that allow for such searches: automatic distillation of structure (ADIOS) that is successful in discovering syntactic structures in linguistic texts and its motif extraction (MEX) component that can be used for uncovering motifs in DNA and protein sequences. The underlying principles of these syntactic algorithms and some of their results will be described.

  11. 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

  12. 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.

  13. Glycosides from marine sponges (Porifera, Demospongiae): structures, taxonomical distribution, biological activities and biological roles.

    Science.gov (United States)

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

    2012-08-01

    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.

  14. Exploiting structural biology in the fight against parasitic diseases.

    Science.gov (United States)

    Modis, Yorgo

    2012-04-01

    Despite spectacular advances in structural biology over the past half-century, only approximately 2% of the structures in the Protein Data Bank are from eukaryotic parasites and less than 0.5% are from multicellular parasites. Even when only major human pathogens are considered, 3D structures of parasites are vastly underrepresented. Yet approximately one-third of the global burden of human disease comes from parasites. It is time to divert greater effort and resources in structural biology to benefit the fight against parasitic diseases. Using as leverage recent technological and methodological advances, a concerted effort to determine macromolecular structures from parasite pathogens would provide invaluable mechanistic insights on vital processes of the parasites and would suggest novel strategies for inhibiting infection.

  15. Determinants and Polynomial Root Structure

    Science.gov (United States)

    De Pillis, L. G.

    2005-01-01

    A little known property of determinants is developed in a manner accessible to beginning undergraduates in linear algebra. Using the language of matrix theory, a classical result by Sylvester that describes when two polynomials have a common root is recaptured. Among results concerning the structure of polynomial roots, polynomials with pairs of…

  16. 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.

  17. 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.

  18. 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.

  19. 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...

  20. 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.

  1. Determinants of Glycosaminoglycan (GAG Structure

    Directory of Open Access Journals (Sweden)

    Kristian Prydz

    2015-08-01

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

  2. 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.

  3. 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.

  4. The structural biology of patellamide biosynthesis.

    Science.gov (United States)

    Koehnke, Jesko; Bent, Andrew F; Houssen, Wael E; Mann, Greg; Jaspars, Marcel; Naismith, James H

    2014-12-01

    The biosynthetic pathways for patellamide and related natural products have recently been studied by structural biology. These pathways produce molecules that have a complex framework and exhibit a diverse array of activity due to the variability of the amino acids that are found in them. As these molecules are difficult to synthesize chemically, exploitation of their properties has been modest. The patellamide pathway involves amino acid heterocyclization, peptide cleavage, peptide macrocyclization, heterocycle oxidation and epimerization; closely related products are also prenylated. Enzyme activities have been identified for all these transformations except epimerization, which may be spontaneous. This review highlights the recent structural and mechanistic work on amino acid heterocyclization, peptide cleavage and peptide macrocyclization. This work should help in using the enzymes to produce novel analogs of the natural products enabling an exploitation of their properties.

  5. 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.

  6. 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.

  7. Computing the structural influence matrix for biological systems.

    Science.gov (United States)

    Giordano, Giulia; Cuba Samaniego, Christian; Franco, Elisa; Blanchini, Franco

    2016-06-01

    We consider the problem of identifying structural influences of external inputs on steady-state outputs in a biological network model. We speak of a structural influence if, upon a perturbation due to a constant input, the ensuing variation of the steady-state output value has the same sign as the input (positive influence), the opposite sign (negative influence), or is zero (perfect adaptation), for any feasible choice of the model parameters. All these signs and zeros can constitute a structural influence matrix, whose (i, j) entry indicates the sign of steady-state influence of the jth system variable on the ith variable (the output caused by an external persistent input applied to the jth variable). Each entry is structurally determinate if the sign does not depend on the choice of the parameters, but is indeterminate otherwise. In principle, determining the influence matrix requires exhaustive testing of the system steady-state behaviour in the widest range of parameter values. Here we show that, in a broad class of biological networks, the influence matrix can be evaluated with an algorithm that tests the system steady-state behaviour only at a finite number of points. This algorithm also allows us to assess the structural effect of any perturbation, such as variations of relevant parameters. Our method is applied to nontrivial models of biochemical reaction networks and population dynamics drawn from the literature, providing a parameter-free insight into the system dynamics.

  8. Structural determinants of glomerular permeability.

    Science.gov (United States)

    Deen, W M; Lazzara, M J; Myers, B D

    2001-10-01

    Recent progress in relating the functional properties of the glomerular capillary wall to its unique structure is reviewed. The fenestrated endothelium, glomerular basement membrane (GBM), and epithelial filtration slits form a series arrangement in which the flow diverges as it enters the GBM from the fenestrae and converges again at the filtration slits. A hydrodynamic model that combines morphometric findings with water flow data in isolated GBM has predicted overall hydraulic permeabilities that are consistent with measurements in vivo. The resistance of the GBM to water flow, which accounts for roughly half that of the capillary wall, is strongly dependent on the extent to which the GBM surfaces are blocked by cells. The spatial frequency of filtration slits is predicted to be a very important determinant of the overall hydraulic permeability, in keeping with observations in several glomerular diseases in humans. Whereas the hydraulic resistances of the cell layers and GBM are additive, the overall sieving coefficient for a macromolecule (its concentration in Bowman's space divided by that in plasma) is the product of the sieving coefficients for the individual layers. Models for macromolecule filtration reveal that the individual sieving coefficients are influenced by one another and by the filtrate velocity, requiring great care in extrapolating in vitro observations to the living animal. The size selectivity of the glomerular capillary has been shown to be determined largely by the cellular layers, rather than the GBM. Controversial findings concerning glomerular charge selectivity are reviewed, and it is concluded that there is good evidence for a role of charge in restricting the transmural movement of albumin. Also discussed is an effect of albumin that has received little attention, namely, its tendency to increase the sieving coefficients of test macromolecules via steric interactions. Among the unresolved issues are the specific contributions of the

  9. Physics for Medicine and Biology: Determining Body Fat Content

    Science.gov (United States)

    Aaron, Ronald; Altman, Albert

    2011-04-01

    Hydrostatic weighing is a technique for determining body fat content that is based on Archimedes principle and varied applications of the ideal gas law. We use this procedure as an example of the types of physics material which should be presented in an introductory course for students that are interested in careers in biology and medicine.

  10. 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.

  11. J D Bernal and the genesis of structural biology

    Energy Technology Data Exchange (ETDEWEB)

    Caffrey, Martin [Department of Chemical and Environmental Sciences, University of Limerick, Limerick (Ireland)

    2007-02-02

    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.

  12. 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.

  13. 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.

  14. 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.

  15. 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...

  16. 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.

  17. 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.

  18. 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…

  19. 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…

  20. 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.

  1. 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...

  2. 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.

  3. 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…

  4. Sulfated oligosaccharide structures, as determined by NMR techniques

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-12-31

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

  5. Structure determination of enterovirus 71

    OpenAIRE

    Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G

    2012-01-01

    Determination of the orientation of the enterovirus 71 virions in the crystal required the calculation of a locked rotation function that included only icosahedral threefold and fivefold symmetry axes. Otherwise, misleading high rotation-function values were produced by accidental alignment of icosahedral and crystallographic twofold axes.

  6. STRUCTURE DETERMINATION OF SNZRS3

    NARCIS (Netherlands)

    MEETSMA, A; WIEGERS, GA; DEBOER, JL

    1993-01-01

    The structure of tin zirconium trisulfide is of the NH4CdCl3 type with double columns of edge-sharing Zr octahedra. These columns are linked together by Sn atoms. Sn is coordinated to three S atoms at 2 x 2.619 (2) and 2.765 (2) angstrom; a fourth S atom is at 3.065 (2) angstrom. The zirconium coord

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

    OpenAIRE

    Seebacher, Frank; Craig E. Franklin

    2012-01-01

    The emerging field of Conservation Physiology links environmental change and ecological success by the application of physiological theory, approaches and tools to elucidate and address conservation problems. Human activity has changed the natural environment to a point where the viability of many ecosystems is now under threat. There are already many descriptions of how changes in biological patterns are correlated with environmental changes. The next important step is to determine the causa...

  8. Image processing and computing in structural biology

    NARCIS (Netherlands)

    Jiang, Linhua

    2009-01-01

    With the help of modern techniques of imaging processing and computing, image data obtained by electron cryo-microscopy of biomolecules can be reconstructed to three-dimensional biological models at sub-nanometer resolution. These models allow answering urgent problems in life science, for instance,

  9. 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.

  10. Structure learning for Bayesian networks as models of biological networks.

    Science.gov (United States)

    Larjo, Antti; Shmulevich, Ilya; Lähdesmäki, Harri

    2013-01-01

    Bayesian networks are probabilistic graphical models suitable for modeling several kinds of biological systems. In many cases, the structure of a Bayesian network represents causal molecular mechanisms or statistical associations of the underlying system. Bayesian networks have been applied, for example, for inferring the structure of many biological networks from experimental data. We present some recent progress in learning the structure of static and dynamic Bayesian networks from data.

  11. 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.

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

    Science.gov (United States)

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

    2015-09-10

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

  13. Hierarchical structure of biological systems: A bioengineering approach

    OpenAIRE

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

    2013-01-01

    A general theory of biological systems, based on few fundamental propositions, allows a generalization of both Wierner and Berthalanffy approaches to theoretical biology. Here, a biological system is defined as a set of self-organized, differentiated elements that interact pair-wise through various networks and media, isolated from other sets by boundaries. Their relation to other systems can be described as a closed loop in a steady-state, which leads to a hierarchical structure and function...

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

    Science.gov (United States)

    Ramakrishnan, V

    2015-03-06

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

  15. 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.

  16. 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.

  17. The determinants of Dutch capital structure choice

    NARCIS (Netherlands)

    Chen, Linda H.; Jiang, George J.

    2001-01-01

    This paper uses the structural equation modeling (SEM) technique to empirically test the determinants of capital structure choice for Dutch firms. We include major factors identified by capital structure theories and construct proxies for these factors with consideration of specific institutional se

  18. Identifying and visualizing macromolecular flexibility in structural biology

    Directory of Open Access Journals (Sweden)

    Martina Palamini

    2016-09-01

    Full Text Available 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.

  19. Study of the structure and dynamics of complex biological networks

    Science.gov (United States)

    Samal, Areejit

    2008-12-01

    In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large scale metabolic networks inside three organisms, Escherichia coli, Saccharomyces cerevisiae and Staphylococcus aureus. We also study the dynamics of the large scale genetic network controlling E. coli metabolism. We have tried to explain the observed system level dynamical properties of these networks in terms of their underlying structure. Our studies of the system level dynamics of these large scale biological networks provide a different perspective on their functioning compared to that obtained from purely structural studies. Our study also leads to some new insights on features such as robustness, fragility and modularity of these large scale biological networks. We also shed light on how different networks inside the cell such as metabolic networks and genetic networks are interrelated to each other.

  20. 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.

  1. 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.

  2. 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...

  3. Genetic determinism in the Finnish upper secondary school biology textbooks

    Directory of Open Access Journals (Sweden)

    Tuomas Aivelo

    2015-05-01

    Full Text Available Genetics is a fast-developing field and it has been argued that genetics education is lagging behind. Genetics education has, for example, been suspected of indoctrinating strong genetic determinism. As the updating of the national upper secondary school curricula is about to start, we decided to study how the current curriculum manifests in Finnish biology textbooks. We studied the main four textbooks for historical gene models and definitions of genes using content analysis. Hybrid models were pervasive in textbooks. The textbooks expressed sometimes even strong genetic determinism, which might be linked to the dominance of older historical models in the textbooks. We also found instances of determinism which we call ‘weak determinism’: genes were depicted as more important factor than environment in relation to the expressed properties. Subsequently, there were no modern gene models found. We suggest gene models should be presented explicitly to reduce misconceptions about genes. We argue that genetics education needs to take more into account than environmental effects and there needs to be more emphasis on the temporal and developmental aspect of genotype-phenotype link. Specifically in Finland this could be done by a more explicit formulation of the national curriculum.

  4. 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

  5. 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 ...

  6. 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/.

  7. 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/.

  8. 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.

  9. In cellulo structure determination of a novel cypovirus polyhedrin

    Energy Technology Data Exchange (ETDEWEB)

    Axford, Danny [Diamond Light Source Ltd, Harwell Oxford, Didcot OX11 0DE (United Kingdom); Ji, Xiaoyun [University of Oxford, Oxford OX3 7BN (United Kingdom); Stuart, David I. [Diamond Light Source Ltd, Harwell Oxford, Didcot OX11 0DE (United Kingdom); University of Oxford, Oxford OX3 7BN (United Kingdom); Sutton, Geoff, E-mail: geoff@strubi.ox.ac.uk [University of Oxford, Oxford OX3 7BN (United Kingdom); Diamond Light Source Ltd, Harwell Oxford, Didcot OX11 0DE (United Kingdom)

    2014-05-01

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

  10. 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.

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

    Science.gov (United States)

    Cagua, E. F.; Berumen, M. L.; Tyler, E. H. M.

    2013-12-01

    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.

  12. Direct atomic structure determination by the inspection of structural phase.

    Science.gov (United States)

    Nakashima, Philip N H; Moodie, Alexander F; Etheridge, Joanne

    2013-08-27

    A century has passed since Bragg solved the first atomic structure using diffraction. As with this first structure, all atomic structures to date have been deduced from the measurement of many diffracted intensities using iterative and statistical methods. We show that centrosymmetric atomic structures can be determined without the need to measure or even record a diffracted intensity. Instead, atomic structures can be determined directly and quickly from the observation of crystallographic phases in electron diffraction patterns. Furthermore, only a few phases are required to achieve high resolution. This represents a paradigm shift in structure determination methods, which we demonstrate with the moderately complex α-Al2O3. We show that the observation of just nine phases enables the location of all atoms with a resolution of better than 0.1 Å. This level of certainty previously required the measurement of thousands of diffracted intensities.

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

  14. Simple approach for ranking structure determining residues

    Directory of Open Access Journals (Sweden)

    Oscar D. Luna-Martínez

    2016-06-01

    Full Text Available Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology.

  15. Simple approach for ranking structure determining residues.

    Science.gov (United States)

    Luna-Martínez, Oscar D; Vidal-Limón, Abraham; Villalba-Velázquez, Miryam I; Sánchez-Alcalá, Rosalba; Garduño-Juárez, Ramón; Uversky, Vladimir N; Becerril, Baltazar

    2016-01-01

    Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology.

  16. 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.

  17. 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

  18. Advances on surface structural determination by LEED.

    Science.gov (United States)

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

    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.

  19. 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)

  20. 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...

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

    Science.gov (United States)

    Stefanic, Peter; Dolenc, Marija Sollner

    2004-04-01

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

  2. 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

  3. 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.…

  4. Biology 23. Unit One -- The Cell: Structure and Physiology.

    Science.gov (United States)

    Nederland Independent School District, TX.

    GRADES OR AGES: Not given. SUBJECT MATTER: Biology, the structure and physiology of the cell. ORGANIZATION AND PHYSICAL APPEARANCE: There are four sections: a) objectives for the unit, b) bibliography, c) activities, and d) evaluation. The guide is directed to the student rather than the teacher. The guide is mimeographed and stapled, with no…

  5. 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.

  6. 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.

  7. 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.

  8. 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.

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

    Science.gov (United States)

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

    2016-06-17

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

  10. Crystal structure of meteoritic schreibersites: determination of absolute structure

    Science.gov (United States)

    Skála, Roman; Císařová, Ivana

    Minerals of the schreibersite nickelphosphide series (Fe,Ni)3P crystallize in the non-centrosymmetric space group Ibar 4. As a consequence, they can possess two different spatial arrangements of the constituting atoms within the unit cell, related by the inversion symmetry operation. Here, we present the crystal structure refinements from single crystal X-ray diffraction data for schreibersite grains from iron meteorites Acuña, Carlton, Hex River Mts. (three different crystals), Odessa (two different crystals), Sikhote Alin, and Toluca aiming for the determination of the absolute structure of the examined crystals. The crystals studied cover the composition range from 58 mol% to 80 mol% Fe3P end-member. Unit-cell parameter a and volume of the unit cell V, as well as certain topological structural parameters tightly correlate with Fe3P content. Unit-cell parameter c, on the other hand, does not show such strong correlation. Eight of the nine crystal structure refinements allowed unambiguous absolute structure assignment. The single crystal extracted from Toluca is, however, of poor quality and consequently the structure refinement did not provide as good results as the rest of the materials. Also, this crystal has only weak inversion distinguishing power to provide unequivocal absolute structure determination. Six of the eight unambiguous absolute structure determinations indicated inverted atomic arrangement compared to that reported in earlier structure refinements (here called standard). Only two grains, one taken from Odessa iron and the other from the Hex River Mts. meteorite, reveal the dominance of standard crystal structure setting.

  11. 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)

  12. 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.

  13. 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.

  14. 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.

  15. From electron microscopy to molecular cell biology, molecular genetics and structural biology: intracellular transport and kinesin superfamily proteins, KIFs: genes, structure, dynamics and functions.

    Science.gov (United States)

    Hirokawa, Nobutaka

    2011-01-01

    Cells transport and sort various proteins and lipids following synthesis as distinct types of membranous organelles and protein complexes to the correct destination at appropriate velocities. This intracellular transport is fundamental for cell morphogenesis, survival and functioning not only in highly polarized neurons but also in all types of cells in general. By developing quick-freeze electron microscopy (EM), new filamentous structures associated with cytoskeletons are uncovered. The characterization of chemical structures and functions of these new filamentous structures led us to discover kinesin superfamily molecular motors, KIFs. In this review, I discuss the identification of these new structures and characterization of their functions using molecular cell biology and molecular genetics. KIFs not only play significant roles by transporting various cargoes along microtubule rails, but also play unexpected fundamental roles on various important physiological processes such as learning and memory, brain wiring, development of central nervous system and peripheral nervous system, activity-dependent neuronal survival, development of early embryo, left-right determination of our body and tumourigenesis. Furthermore, by combining single-molecule biophysics with structural biology such as cryo-electrom microscopy and X-ray crystallography, atomic structures of KIF1A motor protein of almost all states during ATP hydrolysis have been determined and a common mechanism of motility has been proposed. Thus, this type of studies could be a good example of really integrative multidisciplinary life science in the twenty-first century.

  16. 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.

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

    Science.gov (United States)

    2010-01-01

    ... desiccated biological products. 113.29 Section 113.29 Animals and Animal Products ANIMAL AND PLANT HEALTH... biological products. Methods provided in this section must be used when a determination of moisture content in desiccated biological products is prescribed in an applicable Standard Requirement or in the...

  18. 21 CFR 601.26 - Reclassification procedures to determine that licensed biological products are safe, effective...

    Science.gov (United States)

    2010-04-01

    ... licensed biological products are safe, effective, and not misbranded under prescribed, recommended, or... Reclassification procedures to determine that licensed biological products are safe, effective, and not misbranded... for the reclassification of all biological products that have been classified into Category IIIA....

  19. 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......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 determinants of community structure. In this study, we first examined the relative importance of environmental gradients, microclimate, and food resources in driving spatial variation in the structure of detrital communities in forests of the southeastern USA. Then, in order to assess whether the determinants...... for the effect of climatic variation along the elevational gradient, food resource addition and microclimate alteration influenced the richness and abundance of some taxa. However, the effect of food resource addition and microclimate alteration on the richness and abundance of arthropods did not vary...

  20. 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.

  1. High Energy Density Nastic Structures Using Biological Transport Mechanisms

    Science.gov (United States)

    2007-02-28

    occur at the cell wall and membranes of inter-cellular organelles to transport nutrients in the plant. The concentration of ions from the active and... Planta , Vol. 179, June 1989, pp. 32–42. [4] Delrot, S., Atanassova, R., Gomes, E., and Thevenot, P., “Plasma Membrane Transporters : A Machinery...DATES COVERED Final Progress Report; 9/27/04 to 11/30/06 4. TITLE AND SUBTITLE High Energy Density Nastic Structures Using Biological Transport

  2. 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.

  3. Thermodynamic Rule Determining the Biological DNA Information Capacity

    CERN Document Server

    Widom, A; Srivastava, Y N; Sivasubramanian, S; Valenzi, V I

    2012-01-01

    A rigorous thermodynamic expression is derived for the total biological information capacity per unit length of a DNA molecule. The total information includes the usual four letter coding sequence information plus that excess information coding often erroneously referred to as "junk". We conclude that the currently understood human DNA code is about a hundred megabyte program written on a molecule with about a ten gigabyte memory. By far, most of the programing code is not presently understood.

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

    Science.gov (United States)

    Harris, J Robin

    2015-09-01

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

  5. The structural biology of enzymes involved in natural product glycosylation.

    Science.gov (United States)

    Singh, Shanteri; Phillips, George N; Thorson, Jon S

    2012-10-01

    The glycosylation of microbial natural products often dramatically influences the biological and/or pharmacological activities of the parental metabolite. Over the past decade, crystal structures of several enzymes involved in the biosynthesis and attachment of novel sugars found appended to natural products have emerged. In many cases, these studies have paved the way to a better understanding of the corresponding enzyme mechanism of action and have served as a starting point for engineering variant enzymes to facilitate to production of differentially-glycosylated natural products. This review specifically summarizes the structural studies of bacterial enzymes involved in biosynthesis of novel sugar nucleotides.

  6. 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)

  7. 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.

  8. A simple method of determination of partition coefficient for biologically active molecules.

    Science.gov (United States)

    Sersen, F

    1995-02-01

    A simple method is presented for the determination of partition coefficient of an effector between water environment and biological material, based on concentration-dependent effects. The method allows the determination of partition coefficients for biological objects such as algae, bacteria and other microorganisms.

  9. 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.

  10. The utility of structural biology in drug discovery.

    Science.gov (United States)

    Tari, Leslie W

    2012-01-01

    Access to detailed three-dimensional structural information on protein drug targets can streamline many aspects of drug discovery, from target selection and target product profile determination, to the discovery of novel molecular scaffolds that form the basis of potential drugs, to lead optimization. The information content of X-ray crystal structures, as well as the utility of structural methods in supporting the different phases of the drug discovery process, are described in this chapter.

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

    Science.gov (United States)

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

    2015-01-01

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

  12. 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.

  13. Superficial topography of wound: a determinant of underlying biological events?

    Science.gov (United States)

    Farahani, Ramin Mostofi Zadeh; Aminabadi, Naser Asl; Kloth, Luther C

    2008-01-01

    Three-dimensional configuration of wounds varies considerably according to the etiology. Wounding of skin is proceeded by release of dermal pretension. Subsequent disruption of physical equilibrium with resulting development of force vectors alters the primary shape of wound to maintain a new dynamic physical equilibrium. This leads to the development of stress-relaxation and stress-concentration areas throughout the wound milieu. Mechanical strain produces piezoelectric current which is maximal in stress-relaxation regions due to lower tissue stiffness and higher mobility. Early surge in the tissue level of TGF-beta would be exaggerated through synergistic interaction with piezoelectric current in stress-relaxation areas. Subsequently, fibroblasts migrate to these areas due to galvanotaxis. The gradual dissipation of tissue tension, due to irreversible loss of viscous strain, reduces the synergistic action of TGF-beta and piezoelectricity. However, a similar pattern of activity of TGF-beta due to the polarized migration of fibroblasts, which are the main source of TGF-beta during secondary surge, may be continued. It seems that a biological-mechanical continuum exists for wounds so that even the superficial topography of wounds may affect the underlying biological activity and final healing outcome during healing of dermal wounds.

  14. 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.

  15. 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.

  16. Structure of deviations from optimality in biological systems.

    Science.gov (United States)

    Pérez-Escudero, Alfonso; Rivera-Alba, Marta; de Polavieja, Gonzalo G

    2009-12-01

    Optimization theory has been used to analyze evolutionary adaptation. This theory has explained many features of biological systems, from the genetic code to animal behavior. However, these systems show important deviations from optimality. Typically, these deviations are large in some particular components of the system, whereas others seem to be almost optimal. Deviations from optimality may be due to many factors in evolution, including stochastic effects and finite time, that may not allow the system to reach the ideal optimum. However, we still expect the system to have a higher probability of reaching a state with a higher value of the proposed indirect measure of fitness. In systems of many components, this implies that the largest deviations are expected in those components with less impact on the indirect measure of fitness. Here, we show that this simple probabilistic rule explains deviations from optimality in two very different biological systems. In Caenorhabditis elegans, this rule successfully explains the experimental deviations of the position of neurons from the configuration of minimal wiring cost. In Escherichia coli, the probabilistic rule correctly obtains the structure of the experimental deviations of metabolic fluxes from the configuration that maximizes biomass production. This approach is proposed to explain or predict more data than optimization theory while using no extra parameters. Thus, it can also be used to find and refine hypotheses about which constraints have shaped biological structures in evolution.

  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. Fucoidans from brown alga Fucus evanescens: structure and biological activity

    Directory of Open Access Journals (Sweden)

    Roza Menshova

    2016-08-01

    Full Text Available Brown alga Fucus evanescens, widespread in the Far Eastern seas of Russia, is valuable source of sulfated polysaccharides – fucoidans with beneficial biological activities. The most homogenous fraction of fucoidan from F. evanescens was shown to be molecule containing linear main chain of alternating 2-sulfated 1,3- and 1,4-linked α-L-fucose residues. Few sulfate groups were found in position 4 of some 1,3-linked fucose residues. Acetyl groups occupied free C-3 of 1,4-linked residues and/or the C-4 of 1,3-linked fucose residues. Enzymatic hydrolysis, mild acid hydrolysis and autohydrolysis of native fucoidan were used for elucidation of the fine structural characteristics of fucoidan from F. evanescens. The aim of this review to summarize published data on biological activities of fucoidan from F. evanescens: antiviral, anticoagulant, thrombolytic, hepatoprotective, immunomodulatory, anticancer, and their practical application.

  19. 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

  20. Biological and behavioral determinants of fertility in Tierra del Fuego.

    Science.gov (United States)

    Pascual, J; García-Moro, C E; Hernández, M

    2005-05-01

    The reproductive history of 182 women in postreproductive life or near menopause from the Chilean part of Tierra del Fuego was traced back by means of familial interviews. These postmenopausal women represent the population since almost the beginning of the settlement, and their reproductive years were spent on the island. Path analysis was applied to analyze fertility determinants of these women and to propose a complex model of interconnections among factors. The reproductive history of these women is characterized by a long fertile span, a short childbearing period, and low fertility. Age at menarche is relatively late, and the age of the women at first birth is mainly determined by their late age at marriage. The use of contraception is related to both spacing and stopping behaviors. The late age of women at marriage, the rhythm of conception, and practices of contraception are proposed as the main determinants of fertility in Tierra del Fuego.

  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. 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

  3. 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'.

  4. Optoelectronic method for determining platinum in biological products

    Science.gov (United States)

    Radu, Simona; Ionicǎ, Mihai; Macovei, Radu Alexandru; Caragea, Genica; Forje, Mǎrgǎrita; Grecu, Iulia; Vlǎdescu, Marian; Viscol, Oana

    2016-12-01

    Of all platinum metals, platinum has the most uses and it's the most abundant and most easily to be processed. Its use in auto catalysts results in environmental contamination of crowded cities and high-traffic roads. In medicine, Pt is used as a cytostatic drug. In order to study the degree of contamination of the population with Pt or the correctness of treatment with Pt, it has been developed a method for its determination from urine or blood samples with a system Graphite Furnance - Atomic Absorption Spectrometer, (GF-AAS) Varian. There are presented the methods of sampling processing for blood or urine that followed the digest of the organic matrix. In the determination of the operating parameters for the system GF-AAS, was aimed the reducing of the nonanatomic absorbance by optimizing the drying temperatures, the calcination and atomization temperatures and the removal of the nonanatomic absorbance with D2 lamp. As a result of the use of the method are presented the concentrations of Pt in the blood or urine of a group of patients in Bucharest, a city with heavy traffic of vehicles. GF-AAS method presented is sensitive, reproducible, and relatively easy to apply with an acceptable cost. With this method, the concentration of Pt can be determined from blood and urine, both in order to establish the degree of contamination with Pt and for monitoring cancer therapy with platinum compounds.

  5. Determination of ferrous and ferric iron in aqueous biological solutions

    Energy Technology Data Exchange (ETDEWEB)

    Pepper, S.E. [Earth and Environmental Sciences Division, Los Alamos National Laboratory, 1400 University Drive, Carlsbad, NM 88220 (United States); Borkowski, M., E-mail: marian@lanl.gov [Earth and Environmental Sciences Division, Los Alamos National Laboratory, 1400 University Drive, Carlsbad, NM 88220 (United States); Richmann, M.K.; Reed, D.T. [Earth and Environmental Sciences Division, Los Alamos National Laboratory, 1400 University Drive, Carlsbad, NM 88220 (United States)

    2010-03-24

    A solvent extraction method was employed to determine ferrous and ferric iron in aqueous samples. Fe{sup 3+} is selectively extracted into the organic phase (n-heptane) using HDEHP (bis(2-ethylhexyl) hydrogen phosphate) and is then stripped using a strong acid. After separation, both oxidation states and the total iron content were determined directly by ICP-MS analysis. This extraction method was refined to allow determination of both iron oxidation states in the presence of strong complexing ligands, such as citrate, NTA and EDTA. The accuracy of the method was verified by crosschecking using a refinement of the ferrozine assay. Presented results demonstrate the ability of the extraction method to work in a microbiological system in the presence of strong chelating agents following the bioreduction of Fe{sup 3+} by the Shewanella alga BrY. Based on the results we report, a robust approach was defined to separately analyze Fe{sup 3+} and Fe{sup 2+} under a wide range of potential scenarios in subsurface environments where radionuclide/metal contamination may coexist with strongly complexing organic contaminants.

  6. 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 ...

  7. 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.

  8. Structural biology sheds light on the puzzle of genomic ORFans.

    Science.gov (United States)

    Siew, Naomi; Fischer, Daniel

    2004-09-10

    Genomic ORFans are orphan open reading frames (ORFs) with no significant sequence similarity to other ORFs. ORFans comprise 20-30% of the ORFs of most completely sequenced genomes. Because nothing can be learnt about ORFans via sequence homology, the functions and evolutionary origins of ORFans remain a mystery. Furthermore, because relatively few ORFans have been experimentally characterized, it has been suggested that most ORFans are not likely to correspond to functional, expressed proteins, but rather to spurious ORFs, pseudo-genes or to rapidly evolving proteins with non-essential roles. As a snapshot view of current ORFan structural studies, we searched for ORFans among proteins whose three-dimensional structures have been recently determined. We find that functional and structural studies of ORFans are not as underemphasized as previously suggested. These recently determined structures correspond to ORFans from all Kingdoms of life, and include proteins that have previously been functionally characterized, as well as structural genomics targets of unknown function labeled as "hypothetical proteins". This suggests that many of the ORFans in the databases are likely to correspond to expressed, functional (and even essential) proteins. Furthermore, the recently determined structures include examples of the various types of ORFans, suggesting that the functions and evolutionary origins of ORFans are diverse. Although this survey sheds some light on the ORFan mystery, further experimental studies are required to gain a better understanding of the role and origins of the tens of thousands of ORFans awaiting characterization.

  9. 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.

  10. 21 CFR 601.25 - Review procedures to determine that licensed biological products are safe, effective, and not...

    Science.gov (United States)

    2010-04-01

    ... biological products are safe, effective, and not misbranded under prescribed, recommended, or suggested... determine that licensed biological products are safe, effective, and not misbranded under prescribed, recommended, or suggested conditions of use. For purposes of reviewing biological products that have...

  11. 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)

  12. 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.

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

    Science.gov (United States)

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

    2010-01-01

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

  14. Biological mechanisms determining the success of RNA interference in insects.

    Science.gov (United States)

    Wynant, Niels; Santos, Dulce; Vanden Broeck, Jozef

    2014-01-01

    Insects constitute the largest group of animals on this planet, having a huge impact on our environment, as well as on our quality of life. RNA interference (RNAi) is a posttranscriptional gene silencing mechanism triggered by double-stranded (ds)RNA fragments. This process not only forms the basis of a widely used reverse genetics research method in many different eukaryotes but also holds great promise to contribute to the species-specific control of agricultural pests and to combat viral infections in beneficial and disease vectoring insects. However, in many economically important insect species, such as flies, mosquitoes, and caterpillars, systemic delivery of naked dsRNA does not trigger effective gene silencing. Although many components of the RNAi pathway have initially been deciphered in the fruit fly, Drosophila melanogaster, it will be of major importance to investigate this process in a wider variety of species, including dsRNA-sensitive insects such as locusts and beetles, to elucidate the factors responsible for the remarkable variability in RNAi efficiency, as observed in different insects. In this chapter, we review the current knowledge on the RNAi pathway, as well as the most recent insights into the mechanisms that might determine successful RNAi in insects.

  15. Coenzyme Q10 analytical determination in biological matrices and pharmaceuticals.

    Science.gov (United States)

    Lucangioli, Silvia; Martinefski, Manuela; Tripodi, Valeria

    2016-06-01

    In recent years, the analytical determination of coenzyme Q10 (CoQ10) has gained importance in clinical diagnosis and in pharmaceutical quality control. CoQ10 is an important cofactor in the mitochondrial respiratory chain and a potent endogenous antioxidant. CoQ10 deficiency is often associated with numerous diseases and patients with these conditions may benefit from administration of supplements of CoQ10. In this regard, it has been observed that the best benefits are obtained when CoQ10 deficiency is diagnosed and treated early. Therefore, it is of great value to develop analytical methods for the detection and quantification of CoQ10 in this type of disease. The methods above mentioned should be simple enough to be used in routine clinical laboratories as well as in quality control of pharmaceutical formulations containing CoQ10. Here, we discuss the advantages and disadvantages of different methods of CoQ10 analysis.

  16. Determining biomass in biological processes. Methods for wastewater biological treatment; Determinacion de la biomasa en procesos biologicos

    Energy Technology Data Exchange (ETDEWEB)

    Arnaiz, C.; Isaac, L.; Lebrato, J. [Universidad Politecnica de Sevilla (Spain)

    2000-07-01

    Biomass concentration and activity are two important parameters for the successful design and control of biological processes in wastewater treatment. Widely used parameter for biomass characterization is dry weight concentration. This parameter is, however, not sufficient to describe biomass activity. Improved analytical methods are needed in order to understand the physiological behaviour of the biomass. In this work, conventional and advanced analytical methods for biomass determination in wastewater treatment are reviewed. (Author) 27 refs.

  17. Structural and Biological Assessment of Zinc Doped Hydroxyapatite Nanoparticles

    Directory of Open Access Journals (Sweden)

    Cristina Liana Popa

    2016-01-01

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

  18. 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”.

  19. Data acquisition and analysis at the Structural Biology Center

    Energy Technology Data Exchange (ETDEWEB)

    Westbrook, M.L.; Coleman, T.A.; Daly, R.T. [Argonne National Lab., IL (United States); Pflugrath, J.W. [Molecular Structure Corp., The Woodlands, TX (United States)

    1996-12-31

    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.

  20. 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.

  1. The Plant Polyester Cutin: Biosynthesis, Structure, and Biological Roles.

    Science.gov (United States)

    Fich, Eric A; Segerson, Nicholas A; Rose, Jocelyn K C

    2016-04-29

    Cutin, a polyester composed mostly of oxygenated fatty acids, serves as the framework of the plant cuticle. The same types of cutin monomers occur across most plant lineages, although some evolutionary trends are evident. Additionally, cutins from some species have monomer profiles that are characteristic of the related polymer suberin. Compositional differences likely have profound structural consequences, but little is known about cutin's molecular organization and architectural heterogeneity. Its biological importance is suggested by the wide variety of associated mutants and gene-silencing lines that show a disruption of cuticular integrity, giving rise to numerous physiological and developmental abnormalities. Mapping and characterization of these mutants, along with suppression of gene paralogs through RNA interference, have revealed much of the biosynthetic pathway and several regulatory factors; however, the mechanisms of cutin polymerization and its interactions with other cuticle and cell wall components are only now beginning to be resolved.

  2. Studies on chemical modification and biology of a natural product, gambogic acid (III): determination of the essential pharmacophore for biological activity.

    Science.gov (United States)

    Wang, Xiaojian; Lu, Na; Yang, Qian; Gong, Dandan; Lin, Changjun; Zhang, Shenglie; Xi, Meiyang; Gao, Yuan; Wei, Libing; Guo, Qinglong; You, Qidong

    2011-04-01

    Caged 4-oxa-tricyclo[4.3.1.0(3,7)]dec-2-one structural motifs are found in Garcinia natural products that demonstrate anti-tumor activity. Gambogic acid (GA, 1), the most abundant caged Garcinia xanthones, has been reported to be a promising anti-cancer agent. To identify the essential pharmacophore for its anti-tumor activity, a series of GA analogues that address potential key structural features for biological activity were synthesized, among which compound 11a displayed comparable in vitro anti-tumor activity as GA. Mechanistic studies on 11a determined that the compound induces apoptosis as well as arrests the G2/M phase of the cell cycle in HepG2 cells. The determination of the essential part of the scaffold found in GA to maintain anti-tumor effects, and the SAR based on the caged pharmacophore are reported and will provide key information for future anti-cancer drug development studies.

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

  5. 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...

  6. 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.

  7. 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.

  8. 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.

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

    Science.gov (United States)

    Rzepecka-Stojko, Anna; Stojko, Jerzy; Kurek-Górecka, Anna; Górecki, Michał; Kabała-Dzik, Agata; Kubina, Robert; Moździerz, Aleksandra; Buszman, Ewa

    2015-12-04

    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.

  10. Structural diversity of biologically interesting datasets: a scaffold analysis approach

    Directory of Open Access Journals (Sweden)

    Khanna Varun

    2011-08-01

    Full Text Available Abstract Background The recent public availability of the human metabolome and natural product datasets has revitalized "metabolite-likeness" and "natural product-likeness" as a drug design concept to design lead libraries targeting specific pathways. Many reports have analyzed the physicochemical property space of biologically important datasets, with only a few comprehensively characterizing the scaffold diversity in public datasets of biological interest. With large collections of high quality public data currently available, we carried out a comparative analysis of current day leads with other biologically relevant datasets. Results In this study, we note a two-fold enrichment of metabolite scaffolds in drug dataset (42% as compared to currently used lead libraries (23%. We also note that only a small percentage (5% of natural product scaffolds space is shared by the lead dataset. We have identified specific scaffolds that are present in metabolites and natural products, with close counterparts in the drugs, but are missing in the lead dataset. To determine the distribution of compounds in physicochemical property space we analyzed the molecular polar surface area, the molecular solubility, the number of rings and the number of rotatable bonds in addition to four well-known Lipinski properties. Here, we note that, with only few exceptions, most of the drugs follow Lipinski's rule. The average values of the molecular polar surface area and the molecular solubility in metabolites is the highest while the number of rings is the lowest. In addition, we note that natural products contain the maximum number of rings and the rotatable bonds than any other dataset under consideration. Conclusions Currently used lead libraries make little use of the metabolites and natural products scaffold space. We believe that metabolites and natural products are recognized by at least one protein in the biosphere therefore, sampling the fragment and scaffold

  11. 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.

  12. Determining crystal structures through crowdsourcing and coursework

    Science.gov (United States)

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Silveira Belo Nascimento Roque, Paulo Sergio; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K.; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

    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.

  13. Determining crystal structures through crowdsourcing and coursework

    OpenAIRE

    2016-01-01

    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 pla...

  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

    2013-05-01

    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.

  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.

    2013-01-01

    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

  16. DETERMINING PUBLIC STRUCTURE CROWD EVACUATION CAPACITY

    Directory of Open Access Journals (Sweden)

    Pejman Kamkarian

    2013-11-01

    Full Text Available This paper explores a strategy for determining public space safety. Due to varied purposes and locations, each public space has architecture as well as facilities. A generalized analysis of capacities for public spaces is essential. The method we propose is to examine a public space with a given architecture. We used Bayesian Belief Network to determine the level of safety and identify points of weakness in public spaces.

  17. DETERMINING PUBLIC STRUCTURE CROWD EVACUATION CAPACITY

    OpenAIRE

    Pejman Kamkarian; Henry Hexmoor

    2013-01-01

    This paper explores a strategy for determining public space safety. Due to varied purposes and locations, each public space has architecture as well as facilities. A generalized analysis of capacities for public spaces is essential. The method we propose is to examine a public space with a given architecture. We used Bayesian Belief Network to determine the level of safety and identify points of weakness in public spaces.

  18. Insights from the sea: structural biology of marine polyketide synthases.

    Science.gov (United States)

    Akey, David L; Gehret, Jennifer J; Khare, Dheeraj; Smith, Janet L

    2012-10-01

    The world's oceans are a rich source of natural products with extremely interesting chemistry. Biosynthetic pathways have been worked out for a few, and the story is being enriched with crystal structures of interesting pathway enzymes. By far, the greatest number of structural insights from marine biosynthetic pathways has originated with studies of curacin A, a poster child for interesting marine chemistry with its cyclopropane and thiazoline rings, internal cis double bond, and terminal alkene. Using the curacin A pathway as a model, structural details are now available for a novel loading enzyme with remarkable dual decarboxylase and acetyltransferase activities, an Fe(2+)/α-ketoglutarate-dependent halogenase that dictates substrate binding order through conformational changes, a decarboxylase that establishes regiochemistry for cyclopropane formation, and a thioesterase with specificity for β-sulfated substrates that lead to terminal alkene offloading. The four curacin A pathway dehydratases reveal an intrinsic flexibility that may accommodate bulky or stiff polyketide intermediates. In the salinosporamide A pathway, active site volume determines the halide specificity of a halogenase that catalyzes for the synthesis of a halogenated building block. Structures of a number of putative polyketide cyclases may help in understanding reaction mechanisms and substrate specificities although their substrates are presently unknown.

  19. Comparative structural biology of eubacterial and archaeal oligosaccharyltransferases.

    Science.gov (United States)

    Maita, Nobuo; Nyirenda, James; Igura, Mayumi; Kamishikiryo, Jun; Kohda, Daisuke

    2010-02-12

    Oligosaccharyltransferase (OST) catalyzes the transfer of an oligosaccharide from a lipid donor to an asparagine residue in nascent polypeptide chains. In the bacterium Campylobacter jejuni, a single-subunit membrane protein, PglB, catalyzes N-glycosylation. We report the 2.8 A resolution crystal structure of the C-terminal globular domain of PglB and its comparison with the previously determined structure from the archaeon Pyrococcus AglB. The two distantly related oligosaccharyltransferases share unexpected structural similarity beyond that expected from the sequence comparison. The common architecture of the putative catalytic sites revealed a new catalytic motif in PglB. Site-directed mutagenesis analyses confirmed the contribution of this motif to the catalytic function. Bacterial PglB and archaeal AglB constitute a protein family of the catalytic subunit of OST along with STT3 from eukaryotes. A structure-aided multiple sequence alignment of the STT3/PglB/AglB protein family revealed three types of OST catalytic centers. This novel classification will provide a useful framework for understanding the enzymatic properties of the OST enzymes from Eukarya, Archaea, and Bacteria.

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

    Science.gov (United States)

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

    2014-11-01

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

  1. Determination of cadmium and lead in human biological samples by spectrometric techniques: a review.

    Science.gov (United States)

    Lemos, Valfredo Azevedo; de Carvalho, Anaildes Lago

    2010-12-01

    The analysis of human biological samples, such as blood, urine, nails, and hair, is generally used for the verification of human exposure to toxic metals. In this review, various spectrometric methods for the determination of cadmium and lead in biological samples are discussed and compared. Several spectrometric techniques are presented and discussed with respect to various characteristics such as sensitivity, selectivity, and cost. Special attention is drawn to the procedures for digestion prior to the determination of cadmium and lead in hair, nails, blood, and urine.

  2. Strategies for structuring interdisciplinary education in Systems Biology

    DEFF Research Database (Denmark)

    Cvijovic, Marija; Höfer, Thomas; Aćimović, Jure

    2016-01-01

    and example curricula. As university education at the Bachelor’s level is traditionally built upon disciplinary degrees, we believe that the most effective way to implement education in Systems Biology would be at the Master’s level, as it offers a more flexible framework. Our team of experts and active......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...... function by employing experimental data, mathematical models and computational simulations. As Systems Biology is inherently multidisciplinary, education within this field meets numerous hurdles including departmental barriers, availability of all required expertise locally, appropriate teaching material...

  3. Electron Diffraction Determination of Nanoscale Structures

    Energy Technology Data Exchange (ETDEWEB)

    Parks, Joel H

    2013-03-01

    Dominant research results on adsorption on gold clusters are reviewed, including adsorption of H{sub 2}O and O{sub 2} on gold cluster cations and anions, kinetics of CO adsorption to middle sized gold cluster cations, adsorption of CO on Au{sub n}{sup +} with induced changes in structure, and H{sub 2}O enhancement of CO adsorption.

  4. 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

  5. Determination of micro structural corrosion by BN

    Energy Technology Data Exchange (ETDEWEB)

    Zergoug, M.; Kamel, G.; Benchaala, A. [Laboratoire d' Electronique et d' Electrotechnique, Centre de soudage et de controle, Route de Dely Ibrahim, B.P:64, Cheraga (Algeria)

    2004-07-01

    The quality control of industrial components requires adaptation and the development of new material characterization and particular non destructive testing techniques. To characterize steel, it would be useful to know its chemical composition, physic-chemical constitution, metallurgical state (annealed, hammered) and other parameters (superficial and chemical processing, etc.). The testing method using Barkhausen noise (B.N.) is a particular method, which can be applied on ferromagnetic materials. It is a magnetic non destructive evaluation (NDE) method and can provide very important information about the material microstructure. The work here presented documents the ability to determine the metallurgical state of steel submitted to the corrosive attack by electrochemical process. The samples are characterized by Barkhausen noise as non destructive methods and are compared with methods as metallography, micro hardness measurement, and toughness determination. (authors)

  6. The Determination and Development of Sectoral Structure

    OpenAIRE

    1998-01-01

    The development over time of sectors in terms of value added and employment has common characteristics in all economies. We develop a simple Ricardian multi-sector general equilibrium model that allows for (i) non-unitary income elasticities, (ii) different paces of technological progress per sector, and (iii) endogenously determined technological progress per sector. A model with these ingredients allows us to replicate the sectoral developments that are found empirically, and which are show...

  7. 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

  8. 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.

  9. 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.

  10. 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

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

    Science.gov (United States)

    Castera, Jeremy; Bruguiere, Catherine; Clement, Pierre

    2008-01-01

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

  12. 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...

  13. 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.

  14. 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.

  15. Structural determinants of MALT1 protease activity.

    Science.gov (United States)

    Wiesmann, Christian; Leder, Lukas; Blank, Jutta; Bernardi, Anna; Melkko, Samu; Decock, Arnaud; D'Arcy, Allan; Villard, Frederic; Erbel, Paulus; Hughes, Nicola; Freuler, Felix; Nikolay, Rainer; Alves, Juliano; Bornancin, Frederic; Renatus, Martin

    2012-05-25

    The formation of the CBM (CARD11-BCL10-MALT1) complex is pivotal for antigen-receptor-mediated activation of the transcription factor NF-κB. Signaling is dependent on MALT1 (mucosa-associated lymphoid tissue lymphoma translocation protein 1), which not only acts as a scaffolding protein but also possesses proteolytic activity mediated by its caspase-like domain. It remained unclear how the CBM activates MALT1. Here, we provide biochemical and structural evidence that MALT1 activation is dependent on its dimerization and show that mutations at the dimer interface abrogate activity in cells. The unliganded protease presents itself in a dimeric yet inactive state and undergoes substantial conformational changes upon substrate binding. These structural changes also affect the conformation of the C-terminal Ig-like domain, a domain that is required for MALT1 activity. Binding to the active site is coupled to a relative movement of caspase and Ig-like domains. MALT1 binding partners thus may have the potential of tuning MALT1 protease activity without binding directly to the caspase domain.

  16. 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...

  17. 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.

  18. 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.

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

    Directory of Open Access Journals (Sweden)

    Theis Fabian J

    2010-10-01

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

  20. 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.

  1. Sensitive force technique to probe molecular adhesion and structural linkages at biological interfaces.

    OpenAIRE

    Evans, E; Ritchie, K; Merkel, R.

    1995-01-01

    Adhesion and cytoskeletal structure are intimately related in biological cell function. Even with the vast amount of biological and biochemical data that exist, little is known at the molecular level about physical mechanisms involved in attachments between cells or about consequences of adhesion on the material structure. To expose physical actions at soft biological interfaces, we have combined an ultrasensitive transducer and reflection interference microscopy to image submicroscopic displ...

  2. 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.

  3. Determination of atomic cluster structure with cluster fusion algorithm

    DEFF Research Database (Denmark)

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

    2005-01-01

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

  4. 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.

  5. 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.

  6. The relationship between molecular structure and biological activity of alkali metal salts of vanillic acid: Spectroscopic, theoretical and microbiological studies

    Science.gov (United States)

    Świsłocka, Renata; Piekut, Jolanta; Lewandowski, Włodzimierz

    In this paper we investigate the relationship between molecular structure of alkali metal vanillate molecules and their antimicrobial activity. To this end FT-IR, FT-Raman, UV absorption and 1H, 13C NMR spectra for lithium, sodium, potassium, rubidium and caesium vanillates in solid state were registered, assigned and analyzed. Microbial activity of studied compounds was tested against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Proteus vulgaris, Bacillus subtilis and Candida albicans. In order to evaluate the dependence between chemical structure and biological activity of alkali metal vanillates the statistical analysis was performed for selected wavenumbers from FT-IR spectra and parameters describing microbial activity of vanillates. The geometrical structures of the compounds studied were optimized and the structural characteristics were determined by density functional theory (DFT) using at B3LYP method with 6-311++G** as basis set. The obtained statistical equations show the existence of correlation between molecular structure of vanillates and their biological properties.

  7. Syntheses and Structure Determinations of Calcium Thiolates.

    Science.gov (United States)

    Chadwick, Scott; Englich, Ulrich; Noll, Bruce; Ruhlandt-Senge, Karin

    1998-09-07

    The exploration of synthetic methodologies toward heavy alkaline-earth chalcogenolates resulted in the preparation and structural characterization of a family of calcium thiolates, including [Ca(SC(6)F(5))(2)(py)(4)], 1 (py = pyridine), the separated ion-triple [Ca(18-crown-6)(NH(3))(3))][SMes](2).2THF, 2 (Mes = 2,4,6-tBu(3)C(6)H(2)), and the contact triple [Ca(18-crown-6)(SMes)(2)].THF, 3. Compound 1 was prepared by treating [Ca(N(SiMe(3))(2))(2)](2) with 4 equiv of HSC(6)F(5) under addition of pyridine. The thiolates 2 and 3 were synthesized by treatment of calcium metal dissolved in dry, liquid NH(3) under addition of 2 equiv of HSMes and crown ether or, alternatively, by the reduction of MesSSMes with calcium metal in dry, liquid ammonia. We also report two reaction products isolated during attempted calcium thiolate syntheses: [CaBr(4)(THF)(2)(&mgr;(2)-Li)(2)(THF)(4)], 4, isolated as the product of a salt elimination reaction between CaBr(2) and 2 equiv of [Li(THF)(n)()S-2,4,6-(i)()Pr(3)C(6)H(2)](m)(). [(NH(4))(py)(SC(6)F(5))], 5, was obtained as the sole product in the reaction of metallic calcium with HSC(6)F(5) in liquid ammonia under addition of pyridine. All compounds were characterized by single-crystal X-ray crystallography in addition to IR and NMR spectroscopy.

  8. 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.

  9. Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane

    Energy Technology Data Exchange (ETDEWEB)

    Lieberman, R.L.; Rosenzweig, A.C. (NWU)

    2010-03-08

    Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that catalyses the conversion of methane to methanol. Knowledge of how pMMO performs this extremely challenging chemistry may have an impact on the use of methane as an alternative energy source by facilitating the development of new synthetic catalysts. We have determined the structure of pMMO from the methanotroph Methylococcus capsulatus (Bath) to a resolution of 2.8 {angstrom}. The enzyme is a trimer with an {alpha}{sub 3}{beta}{sub 3}{gamma}{sub 3} polypeptide arrangement. Two metal centres, modelled as mononuclear copper and dinuclear copper, are located in soluble regions of each pmoB subunit, which resembles cytochrome c oxidase subunit II. A third metal centre, occupied by zinc in the crystal, is located within the membrane. The structure provides new insight into the molecular details of biological methane oxidation.

  10. 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.

  11. The structural biology of the FGF19 subfamily.

    Science.gov (United States)

    Beenken, Andrew; Mohammadi, Moosa

    2012-01-01

    The ability of the Fibroblast Growth Factor (FGF) 19 subfamily to signal in an endocrine fashion sets this subfamily apart from the remaining five FGF subfamilies known for their paracrine functions during embryonic development. Compared to the members of paracrine FGF subfamiles, the three members of the FGF19 subfamily, namely FGF19, FGF21 and FGF23, have poor affinity for heparan sulfate (HS) and therefore can diffuse freely in the HS-rich extracellular matrix to enter into the bloodstream. In further contrast to paracrine FGFs, FGF19 subfamily members have unusually poor affinity for their cognate FGF receptors (FGFRs) and therefore cannot bind and activate them in a solely HS-dependent fashion. As a result, the FGF19 subfamily requires α/βklotho coreceptor proteins in order to bind, dimerize and activate their cognate FGFRs. This klotho-dependency also determines the tissue specificity of endocrine FGFs. Recent structural and biochemical studies have begun to shed light onto the molecular basis for the klotho-dependent endocrine mode of action of the FGF19 subfamily. Crystal structures of FGF19 and FGF23 show that the topology of the HS binding site (HBS) of FGF19 subfamily members deviates drastically from the common topology adopted by the paracrine FGFs. The distinct topologies of the HBS of FGF19 and FGF23 prevent HS from direct hydrogen bonding with the backbone atoms of the HBS of these ligands and accordingly decrease the HS binding affinity of this subfamily. Recent biochemical data reveal that the ?klotho ectodomain binds avidly to the ectodomain of FGFR1c, the main cognate FGFR of FGF23, creating a de novo high affinity binding site for the C-terminal tail of FGF23. The isolated FGF23 C-terminus can be used to effectively inhibit the formation of the FGF23-FGFR1c-αklotho complex and alleviate hypophosphatemia in renal phosphate disorders due to elevated levels of FGF23.

  12. 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.

  13. 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.

  14. Determination of Cu, Zn, and Se in microvolumes of liquid biological samples

    Science.gov (United States)

    Shaban, H. A.; Shaltout, A. A.; Abdou, M.; Al Ashker, E. A.; Elgohary, M.

    2011-01-01

    Cu, Zn, and Se were successfully determined in a few microliters (<100 μl) of biological samples using discrete injection atomic absorption spectrometry. Different factors were investigated in order to obtain a biological sample volume which is valid for analysis. Among them are the effect of microsampling volume variations (starting from 40 to 200 μl), nebulization efficiency, detection limits, precision, and finally the calibration and sensitivity of the proposed method. It was found that 60 μl of the biological sample was adequate for the quantitative analysis with reasonable precision. The advantages of the proposed method are not only rapidity, simplicity, sensitivity, and good precision, but also, contrary to conventional flame atomic absorption spectrometry, the capability of analyzing microvolumes of samples.

  15. Recent developments in fatty acids profile determination in biological samples - a review

    Directory of Open Access Journals (Sweden)

    Tiuca Ioana

    2015-12-01

    Full Text Available The present paper is a literature review of the recent years dealing with the most important separation techniques of fatty acids in biological samples. Our aim was to make a synthesis of the analytical methods used, to note the most used ones, but also to mention other methods that are less utilized, which can have important advantages (such as less time consuming, greener reagents, etc.. Gas-chromatographic separation methods were described and compared to liquid chromatographic separations of fatty acids in different types of biological samples. In the same time, the importance of determining fatty acids profiles in biological samples was revealed, pointing out the possible implications in diagnostics of different types of disorders or remarking different profiles compared to healthy states.

  16. 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.

  17. A round-robin determination of boron in botanical and biological samples.

    Science.gov (United States)

    Downing, R G; Strong, P L

    1998-01-01

    The accurate determination of boron (B) at trace and ultratrace concentrations is an important step toward establishing the role of B in biological functions. However, low-level B concentrations are difficult to determine accurately, especially for many botanical and biological matrices. A round-robin study was conducted to assess analytical agreement for low-level B determinations. Ten experienced research groups from analytical laboratories extending across Europe, Asia, and the US participated in this study. These groups represent a cross-section of academic, commercial, and government facilities. The researchers employed both ion-coupled plasma and neutron techniques in the study. Results from this round-robin study indicate good agreement between participating laboratories at the mg/kg level, but at the lowest levels, microg/kg, only three laboratories participated, and agreement was poor. By encouraging discussion among scientists over these data, the secondary goal of this round-robin study is to stimulate continued improvement in analytical procedures and techniques for accurate low-level B determinations. Furthermore, it is intended to encourage the development of a variety of low-level (low mg/kg and microg/kg) B certified reference samples in biological and botanical matrices. The results from the round-robin analyses were compiled and are summarized in this article.

  18. 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

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

    Science.gov (United States)

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

    2015-09-04

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

  20. Toward a structure determination method for biomineral-associated protein using combined solid- state NMR and computational structure prediction.

    Science.gov (United States)

    Masica, David L; Ash, Jason T; Ndao, Moise; Drobny, Gary P; Gray, Jeffrey J

    2010-12-08

    Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the structure of biomineral-associated proteins cannot be determined by X-ray crystallography or solution nuclear magnetic resonance (NMR). Here we report a method for determining the structure of biomineral-associated proteins. The method combines solid-state NMR (ssNMR) and ssNMR-biased computational structure prediction. In addition, the algorithm is able to identify lattice geometries most compatible with ssNMR constraints, representing a quantitative, novel method for investigating crystal-face binding specificity. We use this method to determine most of the structure of human salivary statherin interacting with the mineral phase of tooth enamel. Computation and experiment converge on an ensemble of related structures and identify preferential binding at three crystal surfaces. The work represents a significant advance toward determining structure of biomineral-adsorbed protein using experimentally biased structure prediction. This method is generally applicable to proteins that can be chemically synthesized.

  1. Target selection and determination of function in structural genomics.

    Science.gov (United States)

    Watson, James D; Todd, Annabel E; Bray, James; Laskowski, Roman A; Edwards, Aled; Joachimiak, Andrzej; Orengo, Christine A; Thornton, Janet M

    2003-01-01

    The first crucial step in any structural genomics project is the selection and prioritization of target proteins for structure determination. There may be a number of selection criteria to be satisfied, including that the proteins have novel folds, that they be representatives of large families for which no structure is known, and so on. The better the selection at this stage, the greater is the value of the structures obtained at the end of the experimental process. This value can be further enhanced once the protein structures have been solved if the functions of the given proteins can also be determined. Here we describe the methods used at either end of the experimental process: firstly, sensitive sequence comparison techniques for selecting a high-quality list of target proteins, and secondly the various computational methods that can be applied to the eventual 3D structures to determine the most likely biochemical function of the proteins in question.

  2. 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

  3. Determination of cobalt and nickel in biological materials using catalytic adsorptive stripping voltammetry

    OpenAIRE

    Bobrowski, Andrzej; Zarębski, Jerzy; Królicka, Agnieszka

    2012-01-01

    The paper discusses the utilisation of the catalytic adsorptive stripping voltammetric method for the simultaneous determination of Co and Ni in biological materials such as hair, oyster tissue, bovine liver and oriental tobacco leaves. For this purpose the most sensitive and selective catalytic-adsorptive system with nioxime and nitrite has been selected. The optimal parameters, including concentration of the supporting electrolyte, pH and accumulation time and potential, have be...

  4. 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.

  5. 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.

  6. In vivo and in vitro techniques to determine the biological activity of food allergens

    DEFF Research Database (Denmark)

    Poulsen, Lars K.

    2001-01-01

    Methods for determination of the biological activity of food allergens comprise both determination of the allergenic potency, i.e. the capability to elicit an allergic reaction in an already sensitized individual, and the allergenic potential, i.e. the risk for sensitizing a hitherto non-allergic......Methods for determination of the biological activity of food allergens comprise both determination of the allergenic potency, i.e. the capability to elicit an allergic reaction in an already sensitized individual, and the allergenic potential, i.e. the risk for sensitizing a hitherto non......-allergic individual. Several methods are discussed for determination of potency including the double-blinded placebo-controlled food challenge, skin testing, in vitro effector cell assays such as basophil histamine release, and IgE-based techniques such as RAST and RAST inhibition. No reliable methods have yet been...... developed which can predict the allergenic potential of a food or a food allergen. The progress in the areas of stability studies and animal models for food allergy are discussed....

  7. 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.

  8. 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.

  9. 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 )

  10. 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

  11. 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.

  12. 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.

  13. Synthesis, Structure and Biological Activities of Novel Triazole Compounds Containing N,N-Dialkyldithiocarbamate Moiety

    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); SUN,Ping-Ping(孙萍萍); JIAO,Kui(焦奎)

    2004-01-01

    The two compounds, 2,2-dimethyl-4-S-(N,N-dimethyldithiocarbamato)-5-(1,2,4-triazol-1-yl)-propione (1) and 2,2-dimethyl-4-S-(N,N-diethyldithiocarbamato)-5-(1,2,4-triazol-1-yl)-3-propione (2), were prepared by reacting N,N-dialkyldithiocarbamate sodium with 2,2-dimethyl-4-bromo-5-(1,2,4-triazol-1-yl)-propione. Their structures were identified by elemental analysis, IR and 1H NMR spectroscopy. The structure of 1 has been determined by X-ray single crystal structure analysis. It crystallizes in monoclinic system with space group P21/c, a= 1.2315(3)nm, b =1.2057(2) nm, c=1.2532(3) nm, β=118.55(3)° Z=4, V= 1.6345(6) nm3, Dc= 1.221 g/cm3, μ=0.324 mm -1, F(000)=640, final R1 =0.0449. There is obvious potentially weak C-H…N intermolecular interaction in the crystal, which stabilizes the crystal structure. The result of the biological test showed that the two compounds have fungistasis and plant growth regulating activities.

  14. 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.

  15. 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.

  16. 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)

  17. 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…

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

    OpenAIRE

    Heider, Florian; Gropp, Reint

    2008-01-01

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

  19. 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.)

  20. 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.

  1. Problems in obtaining perfect images by single-particle electron cryomicroscopy of biological structures in amorphous ice

    OpenAIRE

    Henderson, Richard; McMullan, Greg

    2013-01-01

    Theoretical considerations together with simulations of single-particle electron cryomicroscopy images of biological assemblies in ice demonstrate that atomic structures should be obtainable from images of a few thousand asymmetric units, provided the molecular weight of the whole assembly being studied is greater than the minimum needed for accurate position and orientation determination. However, with present methods of specimen preparation and current microscope and detector...

  2. 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.

  3. 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.

  4. Cold Spring Harbor symposia on quantitative biology. Volume XLVII, Part 2. Structures of DNA

    Energy Technology Data Exchange (ETDEWEB)

    1983-01-01

    This is Volume 2 of the proceedings of the 1982 Cold Springs Harbor Symposium on Quantitative Biology. The volume contains papers on DNA methylation, DNA replication, gene recombination, organization of genes along DNA, molecular structure and enzymology of DNA.

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

    Science.gov (United States)

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

    2015-03-01

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

  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. 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.

  8. 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

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

    OpenAIRE

    2013-01-01

    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...

  10. 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

  11. Determination of steroid hormones in biological and environmental samples using green microextraction techniques: an overview.

    Science.gov (United States)

    Aufartová, Jana; Mahugo-Santana, Cristina; Sosa-Ferrera, Zoraida; Santana-Rodríguez, José Juan; Nováková, Lucie; Solich, Petr

    2011-10-17

    Residues of steroid hormones have become a cause for concern because they can affect the biological activity of non-target organisms. Steroid hormones are a potential risk for wildlife and humans through the consumption of contaminated food or water. Their determination requires extraction and clean-up steps, prior to detection, to reach low concentration levels. In recent years, a great effort has been made to develop new analytical methodologies, such as microextraction techniques, that reduce environmental pollution. Researchers have modified old methods to incorporate procedures that use less-hazardous chemicals or that use smaller amounts of them. They are able to do direct analysis using miniaturised equipment and reduced amounts of solvents and wastes. These accomplishments are the main objectives of green analytical chemistry. In this overview, we focus on microextraction techniques for the determination of steroid hormones in biological (e.g., human urine, human serum, fish, shrimp and prawn tissue and milk) and environmental (e.g., wastewaters, surface waters, tap waters, river waters, sewage sludges, marine sediments and river sediments) samples. We comment on the most recent applications in sorptive-microextraction modes, such as solid phase microextraction (SPME) with molecularly imprinted polymers (MIPs), in-tube solid-phase microextraction (IT-SPME), stir-bar sorptive extraction (SBSE) and microextraction in packed sorbent (MEPS). We also describe liquid-phase microextraction (LPME) approaches reported in the literature that are applied to the determination of steroid hormones.

  12. SiBr4--prediction and determination of crystal structures.

    Science.gov (United States)

    Wolf, Alexandra K; Glinnemann, Jürgen; Schmidt, Martin U; Tong, Jianwei; Dinnebier, Robert E; Simon, Arndt; Köhler, Jürgen

    2009-06-01

    For SiBr4 no crystal structures have been reported yet. In this work the crystal structures of SiBr4 were predicted by global lattice-energy minimizations using force-field methods. Over an energy range of 5 kJ mol(-1) above the global minimum ten possible structures were found. Two of these structures were experimentally determined from X-ray synchrotron powder diffraction data: The low-temperature beta phase crystallizes in P2(1)/c, the high-temperature alpha phase in Pa3. Temperature-dependant X-ray powder diffraction shows that the phase transition occurs at 168 K.

  13. SiBr4 - Prediction and Determination of Crystal Structures

    Energy Technology Data Exchange (ETDEWEB)

    Wolf, A.; Glinnemann, J; Schmidt, M; Tong, J; Dinnebier, R; Simon, A; Kohler, J

    2009-01-01

    For SiBr4 no crystal structures have been reported yet. In this work the crystal structures of SiBr4 were predicted by global lattice-energy minimizations using force-field methods. Over an energy range of 5 kJ mol-1 above the global minimum ten possible structures were found. Two of these structures were experimentally determined from X-ray synchrotron powder diffraction data: The low-temperature [beta] phase crystallizes in P21/c, the high-temperature [alpha] phase in Pa overline3. Temperature-dependant X-ray powder diffraction shows that the phase transition occurs at 168 K.

  14. Spectroscopic study of molecular structure, antioxidant activity and biological effects of metal hydroxyflavonol complexes

    Science.gov (United States)

    Samsonowicz, Mariola; Regulska, Ewa

    2017-02-01

    Flavonols with varied hydroxyl substitution can act as strong antioxidants. Thanks to their ability to chelate metals as well as to donate hydrogen atoms they have capacity to scavenge free radicals. Their metal complexes are often more active in comparison with free ligands. They exhibit interesting biological properties, e.g. anticancer, antiphlogistic and antibacterial. The relationship between molecular structure and their biological properties was intensively studied using spectroscopic methods (UV-Vis, IR, Raman, NMR, ESI-MS). The aim of this paper is review on spectroscopic analyses of molecular structure and biological activity of hydroxyflavonol metal complexes.

  15. Biological age as a basis for determining prenozological states in elementary school-age children.

    Directory of Open Access Journals (Sweden)

    Omelchenko T.G.

    2011-08-01

    Full Text Available The necessity of determining the biological age (BA in elementary school-age children as an important criterion for prenozological diagnostics is justified from the theoretical as well as practical prospective. The classification of prenozological states based on the BA is presented. The experiment features data of 159 children aged 7-10 years. Analyses of the obtained mean functional age (FA data shows deviation from the calendar age (CA in all age and gender groups which enables to diagnose prenozological state of elementary school-age children.

  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.

  18. 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.

  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. Improved FIA-ABTS method for antioxidant capacity determination in different biological samples.

    Science.gov (United States)

    Bompadre, Stefano; Leone, Luciana; Politi, Alessia; Battino, Maurizio

    2004-08-01

    In order to evaluate the actual antioxidant features of foods, beverages and also plasma from patients, a number of assays have been developed in the last few years to determine the so called total antioxidant activity (TAA), intended as the cumulative capacity of a biological sample to scavenge free radicals. Most of the assays partially failed in obtaining a good reproducibility when using plasma because it is composed of a large number of substances, some of which are present at very high concentrations and possess masking features. For these reasons we have improved the widely known ABTS method by means of a FIA system where both temperature and dispersion of sample and reagent were strictly controlled. We found that temperature may be a critical aspect in the measurement of plasma TAA whilst its influence may be less important in the assay of non-complex biological samples. We demonstrated that also the reaction time may be critical, depending on the nature of the substance employed. Data confirmed the high TAA of a methylsalicylate-containing mouthrinse as well as the negligible TAA offered by the chlorhexidine containing one. White wines (Verdicchio) also displayed interesting TAA values. The improved method was useful to screen rapidly, without dilution, with very limited handling of the sample and with high repeatability the TAA of plasma in addition to chemical products, beverages and non-complex biological mixtures.

  1. 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.

  2. Piezo impedance sensors to monitor degradation of biological structure

    Science.gov (United States)

    Annamdas, Kiran Kishore Kumar; Annamdas, Venu Gopal Madhav

    2010-04-01

    In some countries it is common to have wooden structures in their homes, especially Japan. However, metals and its alloys are the most widely used engineering materials in construction of any military or civil structure. Re-visiting natural disasters like the recent Haiti earthquake (12 Jan 2010) or Katrina (cyclones) reminds the necessity to have better housing infrastructure with robust monitoring systems. Traditionally wood (green material) was accepted as excellent rehabilitation material, after any disaster. In recent times, the recycling materials extracted from inorganic, biodegradable wastes are converted into blocks or sheets, and are also used to assist public in rehabilitation camps. The key issue which decreases the life of these rehabilitated structure including green materials (like wood) is unnecessary degradation or deterioration over time due to insect or acid attack or rain/ice fall. The recycling material also needs monitoring to protect them against acid or rain/ice attacks. Thus, a few health monitoring techniques have emerged in the recent past. Electromechanical Impedance technique is one such technique, which is simple but robust to detect variations in the integrity of structures. In this paper, impedance based piezoceramic sensor was bonded on wooden sample, which was subjected to degradation in presence of acids. Variations in mass of plank are studied.

  3. Impedance based sensor technology to monitor stiffness of biological structures

    Science.gov (United States)

    Annamdas, Venu Gopal Madhav; Annamdas, Kiran Kishore Kumar

    2010-04-01

    In countries like USA or Japan it is not so uncommon to have wooden structures in their homes. However, metals and its alloys are the most widely used engineering materials in construction of any military or civil structure. Revisiting natural disasters like the recent Haiti earthquake (12 Jan 2010) or Katrina (cyclones) reminds the necessity to have better housing infrastructure with robust monitoring systems. Traditionally wood is accepted as excellent rehabilitation material, after any disaster. The recycling materials extracted from in-organic, biodegradable wastes, also can be used for rehabilitation. The key issue which dampens the life of these rehabilitated structure including green materials (like wood) is unnecessary deposits (nails, screws, bolts etc)/damages due to insect attack. Thus, a few health monitoring techniques have emerged in the recent past. Electromechanical Impedance technique is one such technique, which is simple but robust to detect variations in the integrity of structures. In this paper, impedance based piezoceramic sensor was bonded on wooden sample, which was used to study changes due to metallic (steel nails) deposits at various locations. A study of weight deposits on aluminum plate was used for comparisons.

  4. 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.

  5. 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…

  6. 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

  7. 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

  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. 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.

  10. Biologic and structural differences of thrombopoietic growth factors.

    Science.gov (United States)

    Begley, C G; Basser, R L

    2000-04-01

    The search for a thrombopoietic agent has resulted in the identification of numerous cytokines and growth factors with thrombopoietic activity. However, with the exception of interleukin (IL)-11 and thrombopoietin (TPO), the megakaryopoietic activity of most of these molecules has not produced clearly identifiable clinical benefits. Despite the relatively modest effect of IL-11 on megakaryocyte and platelet production in vitro and in vivo, it does reduce the need for platelet transfusions in specialized clinical settings. In contrast, the c-Mpl ligand TPO has been shown to be a potent stimulator of megakaryocyte and platelet production both in vitro and in vivo. Clinical studies are being conducted with two different preparations of the c-Mpl ligand: recombinant human thrombopoietin (rhTPO) and pegylated recombinant human megakaryocyte growth and development factor (PEG-rHuMGDF). A recombinant form of the complete human molecule, rhTPO is glycosylated and produced in mammalian cells. PEG-rHuMGDF consists of only the receptor-binding domain linked to a polyethylene glycol (PEG) moiety and is generated in Escherichia coil. Although c-Mpl ligands are still being evaluated, preliminary evidence indicates that these molecules can elevate platelet counts and may be useful in a range of clinical contexts. This report discusses aspects of the biology behind the clinical actions of IL-11 and the c-Mpl ligands.

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

    Science.gov (United States)

    Sosa-Ferrera, Zoraida; Mahugo-Santana, Cristina; Santana-Rodríguez, José Juan

    2013-01-01

    Endocrine-disruptor compounds (EDCs) can mimic natural hormones and produce adverse effects in the endocrine functions by interacting with estrogen receptors. EDCs include both natural and synthetic chemicals, such as hormones, personal care products, surfactants, and flame retardants, among others. EDCs are characterised by their ubiquitous presence at trace-level concentrations and their wide diversity. Since the discovery of the adverse effects of these pollutants on wildlife and human health, analytical methods have been developed for their qualitative and quantitative determination. In particular, mass-based analytical methods show excellent sensitivity and precision for their quantification. This paper reviews recently published analytical methodologies for the sample preparation and for the determination of these compounds in different environmental and biological matrices by liquid chromatography coupled with mass spectrometry. The various sample preparation techniques are compared and discussed. In addition, recent developments and advances in this field are presented. PMID:23738329

  12. Analytical methodologies for the determination of endocrine disrupting compounds in biological and environmental samples.

    Science.gov (United States)

    Sosa-Ferrera, Zoraida; Mahugo-Santana, Cristina; Santana-Rodríguez, José Juan

    2013-01-01

    Endocrine-disruptor compounds (EDCs) can mimic natural hormones and produce adverse effects in the endocrine functions by interacting with estrogen receptors. EDCs include both natural and synthetic chemicals, such as hormones, personal care products, surfactants, and flame retardants, among others. EDCs are characterised by their ubiquitous presence at trace-level concentrations and their wide diversity. Since the discovery of the adverse effects of these pollutants on wildlife and human health, analytical methods have been developed for their qualitative and quantitative determination. In particular, mass-based analytical methods show excellent sensitivity and precision for their quantification. This paper reviews recently published analytical methodologies for the sample preparation and for the determination of these compounds in different environmental and biological matrices by liquid chromatography coupled with mass spectrometry. The various sample preparation techniques are compared and discussed. In addition, recent developments and advances in this field are presented.

  13. Determination of Sodium Cromoglycate by a New Kinetic Spectrophotometric Method in Biological Samples

    Directory of Open Access Journals (Sweden)

    Mohsen Keyvanfard

    2013-01-01

    Full Text Available A new kinetic spectrophotometric method is described for the determination of ultratrace amounts of sodium cromoglycate (SCG. The method based on catalytic action of SCG on the oxidation of amaranth with periodate in acidic and micellar medium. The reaction was monitored spectrophotometrically by measuring the decrease in absorbance of the amaranth at 518 nm, for the first 4 min from initiation of the reaction. Calibration curve was linear in the range of 4.0−36.0 ng mL−1 SCG. The limit of detection is 2.7 ng mL−1 SCG. The relative standard deviation (RSD for ten replicate analyses of 12, 20, and 28 ng mL−1 SCG was 0.40%, 0.32%, and 0.53%, respectively. The proposed method was used for the determination of SCG in biological samples.

  14. 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.

  15. 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.).

  16. Spectrofluorimetric determination of certain biologically active phenothiazines in commercial dosage forms and human plasma.

    Science.gov (United States)

    Mohamed, Abdel-Maaboud I; Abdelmageed, Osama H; Salem, Hesham; Nagy, Dalia M; Omar, Mahmoud A

    2013-01-01

    A validated simple and sensitive spectrofluorimetric method was developed for the determination of chlorpromazine hydrochloride, promethazine hydrochloride, trifluperazine hydrochloride, thioridazine hydrochloride, perazine maleate and oxomemazine. The method was based on condensation of malonic acid/acetic anhydride (MAA) under the catalytic effect of the tertiary amine moiety of the studied phenothiazines to provide a deep yellow to brown colour with green fluorescence. Relative fluorescence intensity of the products was measured at λ exc 398 nm and λ em 432 nm. Different variables affecting the reaction were studied and optimized. The method was successfully applied for the determination of the studied drugs in commercial dosage forms. The lower detection limits allowed the application of this method for the determination of the compounds in plasma as an example of a biological fluid. In addition, the method was considered specific for the determination of tertiary amines in the presence of primary and secondary amines; as a result, it was deemed suitable for the determination of the cited drugs in the presence of their degradation products resulting from N-dealkylation or oxidation of the corresponding sulphoxides or sulphones.

  17. Structural and biological study of carboxymethylated Phellinus linteus polysaccharides.

    Science.gov (United States)

    Shin, Ji-Yoon; Lee, Suyong; Bae, In Young; Yoo, Sang-Ho; Lee, Hyeon Gyu

    2007-05-02

    Polysaccharides isolated from Phellinus linteus were chemically modified by carboxymethylation, and the structural and physiological properties of the derivative were investigated. 13C NMR spectroscopy showed that the polysaccharides extracted from P. linteus contained (1-3)-beta-glucans with a (1-6)-linkage. The carboxymetehylation of the P. linteus polysaccharides was confirmed by Fourier transform infrared spectroscopy, and the degree of substitution was obtained by the potentiometric titration, which was calculated to be 0.63. The bronchoalveolar lavage experiments showed that the carboxymethylated derivative raised the nitric oxide production. In addition, the carboxymethylation stimulated in vitro cytotoxic activity against the HT1080 cell line. Thus, the derivative exhibited the enhanced activity of immune systems, which would be explained by the improved water solubility and structural changes by carboxymethylation. However, a slight decrease in the 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity of the derivative was observed.

  18. Evaluation of flow injection analysis for determination of cholinesterase activities in biological material.

    Science.gov (United States)

    Cabal, Jiri; Bajgar, Jiri; Kassa, Jiri

    2010-09-06

    The method for automatic continual monitoring of acetylcholinesterase (AChE) activity in biological material is described. It is based on flexible system of plastic pipes mixing samples of biological material with reagents for enzyme determination; reaction product penetrates through the semipermeable membrane and it is spectrophotometrically determined (Ellman's method). It consists of sampling (either in vitro or in vivo), adding the substrate and flowing to dialyzer; reaction product (thiocholine) is dialyzed and mixed with 5,5'-dithio-bis-2-nitrobenzoic acid (DTNB) transported to flow spectrophotometer. Flowing of all materials is realised using peristaltic pump. The method was validated: time for optimal hydratation of the cellophane membrane; type of the membrane; type of dialyzer; conditions for optimal permeation of reaction components; optimization of substrate and DTNB concentrations (linear dependence); efficacy of peristaltic pump; calibration of analytes after permeation through the membrane; excluding of the blood permeation through the membrane. Some examples of the evaluation of the effects of AChE inhibitors are described. It was demonstrated very good uniformity of peaks representing the enzyme activity (good reproducibility); time dependence of AChE inhibition caused by VX in vitro in the rat blood allowing to determine the half life of inhibition and thus, bimolecular rate constants of inhibition; reactivation of inhibited AChE by some reactivators, and continual monitoring of the activity in the whole blood in vivo in intact and VX-intoxicated rats. The method is simple and not expensive, allowing automatic determination of AChE activity in discrete or continual samples in vitro or in vivo. It will be evaluated for further research of cholinesterase inhibitors.

  19. 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

  20. Applications of a DAD-HPLC method for determination of loratadine on biological samples

    Directory of Open Access Journals (Sweden)

    Pavalache Georgeta

    2015-06-01

    Full Text Available The aim of research is to assess the active substance by a HPLC method for the separation and quantitative determination of loratadine. The method has been developed and validated on the standard solutions, in previous research. The current study was undertaken to present the results obtained from loratadine determination in biological samples (human serum, urine and breast milk. These results may be applicable on patients with different physiological conditions (aging, pregnancy or recently giving birth, etc. and pathological conditions which may interfere with the metabolism of loratadine. The used HPLC method detected loratadine concentrations in human serum samples, respectively urine samples, at 2 hours after drug administration. The method detected traces of loratadine which passed into breast milk, as well. Data were statistically interpreted using MED CALC 10.2 software. These results show that the applied method can be used for quantitative analysis of loratadine in biological fluids (all permissible limits of quality specifications being in the range 95- 105%.

  1. 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.

  2. 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.

  3. Determinants of Market Structure and the Airline Industry

    Science.gov (United States)

    Raduchel, W.

    1972-01-01

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

  4. In silico determination of intracellular glycosylation and phosphorylation sites in human selectins: Implications for biological function

    DEFF Research Database (Denmark)

    Ahmad, I.; Hoessli, D.C.; Gupta, Ramneek

    2007-01-01

    Post-translational modifications provide the proteins with the possibility to perform functions in addition to those determined by their primary sequence. However, analysis of multifunctional protein structures in the environment of cells and body fluids is made especially difficult by the presence...

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

    CERN Document Server

    Foda, O

    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.

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

    Science.gov (United States)

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

    2016-01-01

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

  7. 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...

  8. 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.

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

    OpenAIRE

    He, M-f; Wang, S.; Wang, Y; Wang, X-N.

    2013-01-01

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

  10. High-resolution protein structure determination by serial femtosecond crystallography.

    Science.gov (United States)

    Boutet, Sébastien; Lomb, Lukas; Williams, Garth J; Barends, Thomas R M; Aquila, Andrew; Doak, R Bruce; Weierstall, Uwe; DePonte, Daniel P; Steinbrener, Jan; Shoeman, Robert L; Messerschmidt, Marc; Barty, Anton; White, Thomas A; Kassemeyer, Stephan; Kirian, Richard A; Seibert, M Marvin; Montanez, Paul A; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M; Philipp, Hugh T; Tate, Mark W; Hromalik, Marianne; Koerner, Lucas J; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y; Hunter, Mark S; Johansson, Linda C; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C H; Chapman, Henry N; Schlichting, Ilme

    2012-07-20

    Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.

  11. Structural diversity and biological importance of ABO, H, Lewis and secretor histo-blood group carbohydrates.

    Science.gov (United States)

    de Mattos, Luiz Carlos

    ABO, H, secretor and Lewis histo-blood system genes control the expression of part of the carbohydrate repertoire present in areas of the body occupied by microorganisms. These carbohydrates, besides having great structural diversity, act as potential receptors for pathogenic and non-pathogenic microorganisms influencing susceptibility and resistance to infection and illness. Despite the knowledge of some structural variability of these carbohydrate antigens and their polymorphic levels of expression in tissue and exocrine secretions, little is known about their biological importance and potential applications in medicine. This review highlights the structural diversity, the biological importance and potential applications of ABO, H, Lewis and secretor histo-blood carbohydrates.

  12. Structural Equation Modeling: Applications in ecological and evolutionary biology research

    Science.gov (United States)

    Pugesek, Bruce H.; von Eye, Alexander; Tomer, Adrian

    2003-01-01

    This book presents an introduction to the methodology of structural equation modeling, illustrates its use, and goes on to argue that it has revolutionary implications for the study of natural systems. A major theme of this book is that we have, up to this point, attempted to study systems primarily using methods (such as the univariate model) that were designed only for considering individual processes. Understanding systems requires the capacity to examine simultaneous influences and responses. Structural equation modeling (SEM) has such capabilities. It also possesses many other traits that add strength to its utility as a means of making scientific progress. In light of the capabilities of SEM, it can be argued that much of ecological theory is currently locked in an immature state that impairs its relevance. It is further argued that the principles of SEM are capable of leading to the development and evaluation of multivariate theories of the sort vitally needed for the conservation of natural systems. Supplementary information can be found at the authors website, http://www.jamesbgrace.com/. • Details why multivariate analyses should be used to study ecological systems • Exposes unappreciated weakness in many current popular analyses • Emphasizes the future methodological developments needed to advance our understanding of ecological systems.

  13. Novel genetic algorithm search procedure for LEED surface structure determination.

    Science.gov (United States)

    Viana, M L; dos Reis, D D; Soares, E A; Van Hove, M A; Moritz, W; de Carvalho, V E

    2014-06-04

    Low Energy Electron Diffraction (LEED) is one of the most powerful experimental techniques for surface structure analysis but until now only a trial-and-error approach has been successful. So far, fitting procedures developed to optimize structural and nonstructural parameters-by minimization of the R-factor-have had a fairly small convergence radius, suitable only for local optimization. However, the identification of the global minimum among the several local minima is essential for complex surface structures. Global optimization methods have been applied to LEED structure determination, but they still require starting from structures that are relatively close to the correct one, in order to find the final structure. For complex systems, the number of trial structures and the resulting computation time increase so rapidly that the task of finding the correct model becomes impractical using the present methodologies. In this work we propose a new search method, based on Genetic Algorithms, which is able to determine the correct structural model starting from completely random structures. This method-called here NGA-LEED for Novel Genetic Algorithm for LEED-utilizes bond lengths and symmetry criteria to select reasonable trial structures before performing LEED calculations. This allows a reduction of the parameter space and, consequently of the calculation time, by several orders of magnitude. A refinement of the parameters by least squares fit of simulated annealing is performed only at some intermediate stages and in the final step. The method was successfully tested for two systems, Ag(1 1 1)(4 × 4)-O and Au(1 1 0)-(1 × 2), both in theory versus theory and in theory versus experiment comparisons. Details of the implementation as well as the results for these two systems are presented.

  14. Determining the Cognitive Structures of Geography Teacher Candidates on "Earthquake"

    Science.gov (United States)

    Kaya, Bastürk; Aladag, Caner

    2017-01-01

    The objective of this study is to determine the cognitive structures of the students of geography teaching department by identifying their conceptual frameworks about the concept of earthquake. A case study design from qualitative research approaches was used in this research. Sample group of the study constitutes 155 students from the Department…

  15. 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.

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

    Science.gov (United States)

    White, Bernard J.; Robyt, John F.

    1988-01-01

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

  17. 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…

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

    DEFF Research Database (Denmark)

    Olsson, Simon; Boomsma, Wouter; Frellsen, Jes

    2011-01-01

    rigorous approach was developed which treats structure determination as a problem of Bayesian inference. In this case, the forcefields are brought in as a prior distribution in the form of a Boltzmann factor. Due to high computational cost, the approach has been only sparsely applied in practice. Here, we...

  19. 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.

  20. 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.

  1. 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

  2. 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.

  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. Consequences of Persistent Small-Scale Biological Structure on Upper Ocean Trophic Processes

    Science.gov (United States)

    2016-06-14

    Consequences Of Persistent Small-Scale Biological Structure On Upper Ocean Trophic Processes Timothy J. Cowles College of Oceanic and Atmospheric... Sciences 104 Oceanography Admin Bldg Oregon State University Corvallis, OR 97331-5503 Office: (541) 737-3966 FAX: (541) 737-2064 email: cowles...interactions between small-scale biological and physical processes in the upper ocean. This project addresses that goal by examining the coherence in

  5. 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...

  6. 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.

  7. 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

  8. 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.

  9. Influence of the structure of ceftazidime on obtaining biologically active cellulosic bandage

    Directory of Open Access Journals (Sweden)

    Rodić-Grabovac Branka B.

    2017-01-01

    Full Text Available Biologically active fibers as drug carriers have improved characteristics in comparison with conventional medical therapies. Cellulosic fibers as hydrophilic and biocompatible, nontoxic and eco-friendly make a good polymer matrix for obtaining biologically active fibers. Current investigations in this area show that the features of these fibers depend on the type of carrier as well as the drug structure. Loading drugs on the fiber carrier is accomplished by ionic bonding between ionized drugs and the groups fixed on the fiber (by ion exchange or loosely adsorption on the fiber through hydrophobic interactions. These interactions can be achieved between hydrophobic parts of the drug and the fiber carrier or among the hydrophobic drugs bonded on the fiber. Prevailing mechanism of ionized drug bonding on the carrier is ionic, although different hydrophobic interactions can contribute the drug loading to varying degrees. In this paper oxidized cellulose (OC with different carboxylic group content is obtained by selective oxidation and used for chemical bonding of antibiotic ceftazidime. In its structure this antibiotic has aminothiazole ring and pyridine ring in the side chains of cephem nucleus. Ceftazidime has two carboxylic groups and also great number of electron donors and acceptors. Due to these groups and structures ceftazidime is able to form multiple chemical bonds i. e. interactions with oxidized cellulosic bandage. The bonding was performed in antibiotic water solution concentration of c=3,4∙10-3 mol/L at room temperature (22 ± 1°C, while desorption was performed in physiological solution. The amounts of bonded and released antibiotic were determined spectrophotometrically in UV range. Maximum amount of bound drug (0,0243 mg/g was obtained during the sorption on the oxidized bandage with 2,276 mmol/g COOH and the maximum amount of released drug was 0,0238 mmol/g. Antimicrobial activity of the samples with bonded ceftazidime was tested

  10. 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

  11. 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

  12. Towards the Structure Determination of a Modulated Protein Crystal: The Semicrystalline State of Profilin:Actin

    Science.gov (United States)

    Borgstahl, G.; Lovelace, J.; Snell, E. H.; Bellamy, H.

    2003-01-01

    One of the remaining challenges to structural biology is the solution of modulated structures. While small molecule crystallographers have championed this type of structure, to date, no modulated macromolecular structures have been determined. Modulation of the molecular structures within the crystal can produce satellite reflections or a superlattice of reflections in reciprocal space. We have developed the data collection methods and strategies that are needed to collect and analyze these data. If the macromolecule's crystal lattice is composed of physiologically relevant packing contacts, structural changes induced under physiological conditions can cause distortion relevant to the function and biophysical processes of the molecule making up the crystal. By careful measurement of the distortion, and the corresponding three-dimensional structure of the distorted molecule, we will visualize the motion and mechanism of the biological macromolecule(s). We have measured the modulated diffraction pattern produced by the semicrystalline state of profilin:actin crystals using highly parallel and highly monochromatic synchrotron radiation coupled with fine phi slicing (0.001-0.010 degrees) for structure determination. These crystals present these crystals present a unique opportunity to address an important question in structural biology. The modulation is believed to be due to the formation of actin helical filaments from the actin beta ribbon upon the pH-induced dissociation of profilin. To date, the filamentous state of actin has resisted crystallization and no detailed structures are available. The semicrystalline state profilin:actin crystals provides a unique opportunity to understand the many conformational states of actin. This knowledge is essential for understanding the dynamics underlying shape changes and motility of eukaryotic cells. Many essential processes, such as cytokinesis, phagocytosis, and cellular migration depend upon the capacity of the actin

  13. 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.

  14. [Determination of ethylene glycol in biological fluids--propylene glycol interferences].

    Science.gov (United States)

    Gomółka, Ewa; Cudzich-Czop, Sylwia; Sulka, Adrianna

    2013-01-01

    Many laboratories in Poland do not use gas chromatography (GC) method for determination of ethylene glycol (EG) and methanol in blood of poisoned patients, they use non specific spectrophotometry methods. One of the interfering substances is propylene glycol (PG)--compound present in many medical and cosmetic products: drops, air freshens, disinfectants, electronic cigarettes and others. In Laboratory of Analytical Toxicology and Drug Monitoring in Krakow determination of EG is made by GC method. The method enables to distinguish and make resolution of (EG) and (PG) in biological samples. In the years 2011-2012 in several serum samples from diagnosed patients PG was present in concentration from several to higher than 100 mg/dL. The aim of the study was to estimate PG interferences of serum EG determination by spectrophotometry method. Serum samples containing PG and EG were used in the study. The samples were analyzed by two methods: GC and spectrophotometry. Results of serum samples spiked with PG with no EG analysed by spectrophotometry method were improper ("false positive"). The results were correlated to PG concentration in samples. Calculated cross-reactivity of PG in the method was 42%. Positive results of EG measured by spectrophotometry method must be confirmed by reference GC method. Spectrophotometry method shouldn't be used for diagnostics and monitoring of patients poisoned by EG.

  15. Determination of phenolic compounds derived from hydrolysable tannins in biological matrices by RP-HPLC.

    Science.gov (United States)

    Díez, María Teresa; García del Moral, Pilar; Resines, José Antonio; Arín, María Jesús

    2008-08-01

    An RP-HPLC method for the determination of four phenolic compounds: gallic acid (GA), pyrogallol (PY), resorcinol (RE) and ellagic acid (EA), derived from hydrolysable tannins is reported. Separation was achieved on a SunFire C18 (250 x 4.6 mm id, 5 microm) column at 40 degrees C with gradient elution. UV detection at 280 nm was applied. The developed method was validated in terms of linearity, accuracy and precision. Satisfactory repeatability and between day precision were noticed with RSD values lower than 3%. Recoveries from different biological samples ranged from 91.50 to 105.25%. The LODs were estimated as 1.70 mg/L for PY, 1.68 mg/L for GA, 1.52 mg/L for RE and 0.98 mg/L for EA with a 20 microL injection volume. The method was applied for the determination of these compounds in oak leaves and in ruminal fluid and urine samples taken from beef cattle fed with oak leaves. The proposed method could be used in ruminant nutrition studies to verify the effect that a diet rich in tannins have on ruminal fermentation and to determine the toxicity of these compounds.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. A novel derivatization reagent possessing a bromoquinolinium structure for biological carboxylic acids in HPLC-ESI-MS/MS.

    Science.gov (United States)

    Mochizuki, Yuko; Inagaki, Shinsuke; Suzuki, Mayu; Min, Jun Zhe; Inoue, Koichi; Todoroki, Kenichiro; Toyo'oka, Toshimasa

    2013-06-01

    A novel bromoquinolinium reagent, i.e. 1-(3-aminopropyl)-3-bromoquinolinium bromide (APBQ), was synthesized for the analysis of carboxylic acids. A simple and practical precolumn derivatization procedure using the APBQ in RP chromatography and MS (HPLC-MS) has been developed using bile acids and free fatty acids, as the representative carboxylic acids in biological samples. The APBQ efficiently reacted with carboxylic acids at 60°C for 60 min in the presence of N,N-dicyclohexylcarbodiimide and pyridine as the activation reagents. Because the APBQ possesses a bromine atom in the structure, the identification of a series of carboxylic acids was easily achieved due to the characteristic bromine isotope pattern in the mass spectra. The APBQ also has a quaternary amine structure, thus the positively charged derivatives are predominate for the highly sensitive detection of carboxylic acids. The APBQ was successfully applied to the selective determination of biological carboxylic acids in human plasma. The bile acids (chenodeoxycholic acid and deoxycholic acid) and several saturated (stearic acid and palmitic acid) and unsaturated free fatty acids (oleic acid and linoleic acid) were reasonably determined by HPLC-MS under the proposed procedure. Based on the results of analyses of human plasma and saliva, the proposed procedure using APBQ seems to be applicable for the qualitative and quantitative analyses of a series of carboxylic acids in biological samples.

  1. 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

  2. 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

  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.

    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.

    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

  5. 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

  6. Eu(III)-Sensitized Luminescence Probe for Determination of Tolnaftate in Pharmaceuticals and Biological Fluids.

    Science.gov (United States)

    Alarfaj, Nawal A; El-Tohamy, Maha F

    2016-01-01

    A highly selective, sensitive, accurate, and reproducible luminescence procedure for determination of antifungal drug tolnaftate was developed. The introduced method was based on the formation of Europa Universalis III (Eu(III))-tolnaftate complex using sodium sulfite as a deoxygenated agent in the presence of acetate buffer (pH = 6) and micellar solution of anionic surfactant sodium dodecyl sulfate. The optimum conditions (effect of pH, buffer, surfactant, Eu(III), and sodium sulfite concentrations) for the luminescence signal were investigated and optimized. The luminescence signals were recorded at λex = 270 nm and λem = 460 nm. The method has a good linear response (0.2-130 μg/mL(-1)) between the luminescence intensity and the concentrations of the drug (r = 0.999), with a LOD 0.07 μg/mL(-1) and LOQ 0.2 μg/mL(-1). The luminescence signals of Eu (III)-tolnaftate-sodium dodecyl sulfate were found to be 200-fold more sensitive without the presence of micelle solution. The interferences of some additives, metals, amino acids, sugars, and other related pharmacological action drugs were examined and no interference was recorded. The proposed method was used for quick and simple determination of tolnaftate in its pharmaceuticals and biological fluids.

  7. 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.

  8. Cyclopentanone thiosemicarbazone, a new complexing agent for copper determination in biological samples by adsorptive stripping voltammetry.

    Science.gov (United States)

    Mahajan, Rakesh Kumar; Walia, T P S; Sumanjit; Lobana, T S

    2006-03-01

    A selective and sensitive stripping voltammetric method for the determination of trace amounts of copper(II) with cyclopentanone thiosemicarbazone (CPTSC) is presented. The method is based on the adsorptive accumulation of the resulting copper-CPTSC complex on a hanging mercury drop electrode, followed by the stripping voltammetric measurements at the reduction current of the adsorbed complex at -0.37 V vs. Ag/AgCl. The optimal conditions for the stripping analysis of copper include pH 9.3, deposition time of 120 s, and a deposition potential of -0.1 V (vs. Ag/AgCl). The peak current is linearly proportional to the copper concentration over a range 3.14 x 10(-9) M to 1.57 x 10(-6) M with a limit of detection of 1.57 x 10(-9) M. The technique has been applied to the determination of copper in biological samples, like urine and whole blood.

  9. MOTIVATION INTERNALIZATION AND SIMPLEX STRUCTURE IN SELF-DETERMINATION THEORY.

    Science.gov (United States)

    Ünlü, Ali; Dettweiler, Ulrich

    2015-12-01

    Self-determination theory, as proposed by Deci and Ryan, postulated different types of motivation regulation. As to the introjected and identified regulation of extrinsic motivation, their internalizations were described as "somewhat external" and "somewhat internal" and remained undetermined in the theory. This paper introduces a constrained regression analysis that allows these vaguely expressed motivations to be estimated in an "optimal" manner, in any given empirical context. The approach was even generalized and applied for simplex structure analysis in self-determination theory. The technique was exemplified with an empirical study comparing science teaching in a classical school class versus an expeditionary outdoor program. Based on a sample of 84 German pupils (43 girls, 41 boys, 10 to 12 years old), data were collected using the German version of the Academic Self-Regulation Questionnaire. The science-teaching format was seen to not influence the pupils' internalization of identified regulation. The internalization of introjected regulation differed and shifted more toward the external pole in the outdoor teaching format. The quantification approach supported the simplex structure of self-determination theory, whereas correlations may disconfirm the simplex structure.

  10. 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.

  11. Recursively partitioned mixture model clustering of DNA methylation data using biologically informed correlation structures.

    Science.gov (United States)

    Koestler, Devin C; Christensen, Brock C; Marsit, Carmen J; Kelsey, Karl T; Houseman, E Andres

    2013-03-05

    DNA methylation is a well-recognized epigenetic mechanism that has been the subject of a growing body of literature typically focused on the identification and study of profiles of DNA methylation and their association with human diseases and exposures. In recent years, a number of unsupervised clustering algorithms, both parametric and non-parametric, have been proposed for clustering large-scale DNA methylation data. However, most of these approaches do not incorporate known biological relationships of measured features, and in some cases, rely on unrealistic assumptions regarding the nature of DNA methylation. Here, we propose a modified version of a recursively partitioned mixture model (RPMM) that integrates information related to the proximity of CpG loci within the genome to inform correlation structures from which subsequent clustering analysis is based. Using simulations and four methylation data sets, we demonstrate that integrating biologically informative correlation structures within RPMM resulted in improved goodness-of-fit, clustering consistency, and the ability to detect biologically meaningful clusters compared to methods which ignore such correlation. Integrating biologically-informed correlation structures to enhance modeling techniques is motivated by the rapid increase in resolution of DNA methylation microarrays and the increasing understanding of the biology of this epigenetic mechanism.

  12. 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.

  13. Structure determines medication errors in nursing units: a mechanistic approach.

    Science.gov (United States)

    Hung, Chang-Chiao; Lee, Bih-O; Tsai, Shu-Ling; Tseng, Yun Shan; Chang, Chia-Hao

    2015-03-01

    Medication errors have long been considered critical in global health care systems. However, few studies have been conducted to explore the effects of nursing unit structure on medication errors. The purpose of this study, therefore, was to determine the effects of structural factors on medication errors in nursing units. A total of 977 staff nurses and 62 head nurses participated in this cross-sectional design study. The findings show that professional autonomy (β = .53, t = 6.03, p nursing experts (β = .52, t = 5.99, p medication error rates. This study shows that the structural factors influence medication administration and the mechanistic approach is specifically in relation of low medication error rates. The author suggests that head nurses should consider strategies that require adjustments to unit control mechanisms.

  14. 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.

  15. A comprehensive experiment for molecular biology: Determination of single nucleotide polymorphism in human REV3 gene using PCR-RFLP.

    Science.gov (United States)

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

    2017-02-01

    Laboratory exercise is helpful for medical students to understand the basic principles of molecular biology and to learn about the practical applications of molecular biology. We have designed a lab course on molecular biology about the determination of single nucleotide polymorphism (SNP) in human REV3 gene, the product of which is a subunit of DNA polymerase ζ and SNPs in this gene are associated with altered susceptibility to cancer. This newly designed experiment is composed of three parts, including genomic DNA extraction, gene amplification by PCR, and genotyping by RFLP. By combining these activities, the students are not only able to learn a series of biotechniques in molecular biology, but also acquire the ability to link the learned knowledge with practical applications. This comprehensive experiment will help the medical students improve the conceptual understanding of SNP and the technical understanding of SNP detection. © 2017 by The International Union of Biochemistry and Molecular Biology, 2017.

  16. Method for the determination of cobalt from biological products with graphite furnace atomic absorption spectrometer

    Science.gov (United States)

    Zamfir, Oana-Liliana; Ionicǎ, Mihai; Caragea, Genica; Radu, Simona; Vlǎdescu, Marian

    2016-12-01

    Cobalt is a chemical element with symbol Co and atomic number 27 and atomic weight 58.93. 59 Co is the only stable cobalt isotope and the only isotope to exist naturally on Earth. Cobalt is the active center of coenzymes called cobalamin or cyanocobalamin the most common example of which is vitamin B12. Vitamin B12 deficiency can potentially cause severe and irreversible damage, especially to the brain and nervous system in the form of fatigue, depression and poor memory or even mania and psychosis. In order to study the degree of deficiency of the population with Co or the correctness of treatment with vitamin B12, a modern optoelectronic method for the determination of metals and metalloids from biological samples has been developed, Graphite Furnace - Atomic Absorption Spectrometer (GF- AAS) method is recommended. The technique is based on the fact that free atoms will absorb light at wavelengths characteristic of the element of interest. Free atoms of the chemical element can be produced from samples by the application of high temperatures. The system GF-AAS Varian used as biological samples, blood or urine that followed the digest of the organic matrix. For the investigations was used a high - performance GF-AAS with D2 - background correction system and a transversely heated graphite atomizer. As result of the use of the method are presented the concentration of Co in the blood or urine of a group of patient in Bucharest. The method is sensitive, reproducible relatively easy to apply, with a moderately costs.

  17. Simple Sensitive Spectrophotometric Determination of Vanadium in Biological and Environmental Samples

    Directory of Open Access Journals (Sweden)

    B. Krishna Priya

    2006-01-01

    Full Text Available Novel, rapid, highly sensitive and selective spectrophotometric method for the determination of traces of vanadium (V in environmental and biological samples, pharmaceutical and steel samples was studied. The method is based on oxidation of 2,4- dinitro phenyl hydrazine(2,4-DNPH by vanadium (V followed by coupling reaction with N-(1-naphthalene-1-ylethane-1,2-diamine-dihydrochloride (NEDA in acidic medium to give red colored derivative or on oxidation of 4-Amino Pyridine by vanadium (V followed by coupling reaction with NEDA in basic medium to give pink colored derivative. The red colored derivative having an λmax 495 nm which is stable for 8 days and the pink colored derivative with 525 nm is stable for more than 7 days at 350C. Beer's law is obeyed for vanadium (V in the concentration range of 0.02 - 3.5 μg mL–1 (red derivative and 0.03 – 4.5 μg mL–1 (pink derivative at the wave length of maximum absorption. The optimum reaction conditions and other analytical parameters were investigated to enhance the sensitivity of the present method. The detailed study of various interferences made the method more selective. The proposed method was successfully applied to the analysis of vanadium in natural water samples, plant material, soil samples, synthetic mixtures, pharmaceutical samples and biological samples. The results obtained were agreed with the reported methods at the 95 % confidence level. The performance of proposed method was evaluated in terms of Student's t-test and Variance ratio f-test which indicates the significance of proposed method over reported method.

  18. Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental (129) Xe NMR Spectroscopy.

    Science.gov (United States)

    Selent, Marcin; Nyman, Jonas; Roukala, Juho; Ilczyszyn, Marek; Oilunkaniemi, Raija; Bygrave, Peter J; Laitinen, Risto; Jokisaari, Jukka; Day, Graeme M; Lantto, Perttu

    2017-01-23

    An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o- and m-fluorophenol, whose previously unknown clathrate structures have been studied by (129) Xe NMR spectroscopy. The high sensitivity of the (129) Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures.

  19. Personal remarks on the future of protein crystallography and structural biology.

    Science.gov (United States)

    Jaskolski, Mariusz

    2010-01-01

    Protein crystallography, the main experimental method of structural biology, has undergone in the recent past three revolutionary changes leading to its unexpected renaissance. They were connected with (i) the introduction of synchrotron radiation sources for X-ray diffraction experiments, (ii) implementation of Se-Met multiwavelength anomalous diffraction (MAD) for phasing, and (iii) initiation of structural genomics (SG) programs. It can be foreseen that in the next 10-15 years protein crystallography will continue to be in this revolutionary phase. We can expect not only an avalanche of protein crystal structures from SG centers, but also attacking of more demanding projects, such as the structure of membrane proteins and of very large macromolecular complexes. On the technological front, the introduction of X-ray radiation from free-electron lasers will revolutionize the experimental possibilities, making feasible even the imaging of single molecules and of intact biological cells.

  20. 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...

  1. 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.)

  2. 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.

  3. Structural, spectroscopic and biological investigation of copper oxides nanoparticles with various capping agents

    Energy Technology Data Exchange (ETDEWEB)

    Nowak, A., E-mail: ana.maria.nowak@gmail.com [A. Chelkowski Institute of Physics, University of Silesia, Katowice (Poland); Szade, J.; Talik, E.; Ratuszna, A. [A. Chelkowski Institute of Physics, University of Silesia, Katowice (Poland); Ostafin, M. [Agricultural University of Cracow, Department of Microbiology, Krakow (Poland); Peszke, J. [A. Chelkowski Institute of Physics, University of Silesia, Katowice (Poland)

    2014-06-01

    Powder composed of copper oxides nanoparticles with various capping agents has been synthesized and characterized with the use of X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and X-ray diffraction (XRD). Polyvinyl alcohol (PVA), glycol propylene, glycerin and glycerin plus ammonia were used as capping agents. The scanning electron microscopy (SEM) studies showed that nanoparticles form agglomerates with the size from 80 to 120 nm while particles size determined from the XRD experiment was in the range from 7 to 21 nm. XPS and XRD experiments revealed that depending on capping and reducing agents used in the synthesis nanoparticles are composed of Cu{sub 2}O, CuO or a mixture of them. The biological activity test performed for a selected sample where the capping agent was glycerin plus ammonia has shown promising killing/inhibiting behavior, very effective especially for Gram negatives bacteria. - Highlights: • We obtained copper oxide nanoparticles in a powder form. • Several capping agents were tested. • Structural and chemical tests showed that the main component were Cu{sub 2}O and CuO. • The size of nanoparticles was in the range 7–21 nm. • Nanoparticles with glycerin and ammonia capping agent showed good antibacterial properties.

  4. 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.

  5. Investigating the role that the Southern Ocean biological pump plays in determining global ocean oxygen concentrations and deoxygenation

    OpenAIRE

    Keller, David; Oschlies, Andreas

    2013-01-01

    Global ocean circulation connects marine biogeochemical cycles through the long-range transport of nutrients and oxygen with the Southern Ocean (SO) acting as a water mass crossroads. The biological pump in the SO has been shown to play an important role in these dynamics and the amount of export production is known to have a large impact on remote deep ocean nutrients and dissolved inorganic carbon. However, the role that the SO biological pump plays in determining ocean oxygen concentration...

  6. The roles of biological interactions and pollutant contamination in shaping microbial benthic community structure

    OpenAIRE

    Louati, H.; Ben Said, O.; A. Soltani; Got, P; Mahmoudi, E.; Cravo-Laureau, C.; Duran, R.; Aissa, P.; Pringault, Olivier

    2013-01-01

    Biological interactions between metazoans and the microbial community play a major role in structuring food webs in aquatic sediments. Pollutants can also strongly affect the structure of meiofauna and microbial communities. This study aims investigating, in a non-contaminated sediment, the impact of meiofauna on bacteria facing contamination by a mixture of three PAHs (fluoranthene, phenanthrene and pyrene). Sediment microcosms were incubated in the presence or absence of meiofauna during 30...

  7. 75 FR 33312 - Indexing Structured Product Labeling for Human Prescription Drug and Biological Products; Request...

    Science.gov (United States)

    2010-06-11

    ... HUMAN SERVICES Food and Drug Administration Indexing Structured Product Labeling for Human Prescription... Evaluation and Research (CDER) and Center for Biologics Evaluation and Research (CBER) are indexing certain... class as a top priority for indexing of product labeling information. FDA is now announcing that...

  8. 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...

  9. 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

  10. Applications of nonlinear microscopy for studying the structure and dynamics in biological systems

    Science.gov (United States)

    Prent, Nicole; Cisek, Richard; Greenhalgh, Catherine; Sparrow, Raymond; Rohitlall, Neeresh; Milkereit, Maike-Svenja; Green, Chantal; Barzda, Virginijus

    2005-09-01

    Laser scanning nonlinear optical microscopy is used to study structure and dynamics of cellular and sub-cellular structures in vivo. Under tight focusing conditions with a high numerical aperture objective, nonlinear optical signals such as third harmonic generation (THG), second harmonic generation (SHG), and multiphoton excitation fluorescence (MPF) are simultaneously produced. MPF is extensively used in biological imaging. Unfortunately, fluorescence is accompanied by heat dissipation in the sample and photobleaching effects. On the other hand, parametric processes such as SHG and THG are free of photobleaching since they involve only virtual electronic states where there is no transfer of energy into the medium. There are many naturally occurring structures that exhibit harmonic generation effects, and hence, do not require dyes that can potentially disrupt the normal functionality of the system. SHG is efficiently generated in non-centrosymmetric media, such as chiral structures and interfaces. The THG signal is generated due to a break in symmetry at interfaces and can be enhanced by the presence of multilamellar structures, as in the mitochondria or chloroplasts. Many interesting biological processes, such as signal transduction in neurons or ATP synthesis in mitochondria, involve the movement of ions across membranes. THG and SHG are sensitive to changing electric potential gradients, and hence are ideally suited for dynamical investigations of these biological processes. The present work will expose the structural factors and conditions that influence THG and SHG generation efficiencies in biological samples. Examples of visualizing chloroplasts and mitochondria will illustrate the advantages of harmonic generation microscopy for studying structural and functional properties of the in vivo systems.

  11. Electromagnetic fields as structure-function zeitgebers in biological systems: environmental orchestrations of morphogenesis and consciousness.

    Science.gov (United States)

    Rouleau, Nicolas; Dotta, Blake T

    2014-01-01

    Within a cell system structure dictates function. Any interaction between cells, or a cell and its environment, has the potential to have long term implications on the function of a given cell and emerging cell aggregates. The structure and function of cells are continuously subjected to modification by electrical and chemical stimuli. However, biological systems are also subjected to an ever-present influence: the electromagnetic (EM) environment. Biological systems have the potential to be influenced by subtle energies which are exchanged at atomic and subatomic scales as EM phenomena. These energy exchanges have the potential to manifest at higher orders of discourse and affect the output (behavior) of a biological system. Here we describe theoretical and experimental evidence of EM influence on cells and the integration of whole systems. Even weak interactions between EM energies and biological systems display the potential to affect a developing system. We suggest the growing literature of EM effects on biological systems has significant implications to the cell and its functional aggregates.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. Determination of sulpiride in pharmaceutical preparations and biological fluids using a Cr (III) enhanced chemiluminescence method.

    Science.gov (United States)

    Khan, Muhammad Naeem; Jan, Muhammad Rasul; Shah, Jasmin; Lee, Sang Hak; Kim, Young Ho

    2013-01-01

    A highly sensitive and simple method for identifying sulpiride in pharmaceutical formulations and biological fluids is presented. The method is based on increased chemiluminescence (CL) intensity of a luminol-H2O2 system in response to the addition of Cr (III) under alkaline conditions. The CL intensity of the luminol-H2O2-Cr (III) system was greatly enhanced by the addition of sulpiride and the CL intensity was proportional to the concentration of sulpiride in a sample solution. Various parameters affecting the CL intensity were systematically investigated and optimized for determination of the sulpiride in a sample. Under the optimum conditions, the CL intensity was proportional to the concentration of sulpiride in the range of 0.068-4.0 µg/mL, with a good correlation coefficient of 0.997. The limit of detection (LOD) and limit of quantification (LOQ) were found to be 8.50 × 10(-6) µg/mL and 2.83 × 10(-5) µg/mL, respectively. The method presented here produced good reproducibility with a relative standard deviation (RSD) of 2.70% (n = 7). The effects of common excipients and metal ions were studied for their interference effect. The method was validated statistically through recovery studies and successfully applied for the determination of sulpiride in pure form, pharmaceutical preparations and spiked human plasma samples. The percentage recoveries were found to range from 99.10 to 100.05% for pure form, 98.12 to 100.18% for pharmaceutical preparations and 97.9 to 101.4% for spiked human plasma.

  17. Biological determinants of photobioreactor design. Final report, September 1, 1993--August 31, 1995

    Energy Technology Data Exchange (ETDEWEB)

    Palsson, B.; Brown, G.G.

    1997-04-01

    Microalgae is being considered for the 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. The effect of various light compositions on the culture kinetics was studied. To determine the optimal composition, six wavelengths 470, 555, 560, 570, 580 and 605 nm, each supplemented with 680 nm of red light, 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 maximum capacity.

  18. 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.

  19. 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.

  20. Structural diversity and biological importance of ABO, H, Lewis and secretor histo-blood group carbohydrates

    Directory of Open Access Journals (Sweden)

    Luiz Carlos de Mattos

    Full Text Available ABSTRACT ABO, H, secretor and Lewis histo-blood system genes control the expression of part of the carbohydrate repertoire present in areas of the body occupied by microorganisms. These carbohydrates, besides having great structural diversity, act as potential receptors for pathogenic and non-pathogenic microorganisms influencing susceptibility and resistance to infection and illness. Despite the knowledge of some structural variability of these carbohydrate antigens and their polymorphic levels of expression in tissue and exocrine secretions, little is known about their biological importance and potential applications in medicine. This review highlights the structural diversity, the biological importance and potential applications of ABO, H, Lewis and secretor histo-blood carbohydrates.

  1. 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

    2016-09-01

    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.

  2. 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...

  3. Structure determination of spider silk from X-ray images

    Energy Technology Data Exchange (ETDEWEB)

    Ulrich, Stephan; Zippelius, Annette [Universitaet Goettingen, Institut fuer Theoretische Physik (Germany); Meling, Martin [Max-Planck-Institut fuer biophysikalische Chemie, Goettingen (Germany); Glisovic, Anja; Salditt, Tim [Universitaet Goettingen, Institut fuer Roentgenphysik (Germany)

    2008-07-01

    Spider silk consists of interconnected crystallites, which are typically aligned along the fiber axis. We present a method to systematically determine the structure of these crystallites. Hereby we introduce a model that calculates the scattering function G(q) which is fitted to the measured X-ray image (silk from nephila clavipes). With it, the crystallites' size, the constitution and dimensions of their unit cell, as well as their tilt with respect to the fiber axis is identified, and furthermore the effect of coherent scattering from different crystallites is investigated. The shown methods and the presented model can easily be generalized to a wide class of composite materials.

  4. 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.

  5. 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

  6. 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.

  7. Structural determinants of tobacco vein mottling virus protease substrate specificity.

    Science.gov (United States)

    Sun, Ping; Austin, Brian P; Tözsér, József; Waugh, David S

    2010-11-01

    Tobacco vein mottling virus (TVMV) is a member of the Potyviridae, one of the largest families of plant viruses. The TVMV genome is translated into a single large polyprotein that is subsequently processed by three virally encoded proteases. Seven of the nine cleavage events are carried out by the NIa protease. Its homolog from the tobacco etch virus (TEV) is a widely used reagent for the removal of affinity tags from recombinant proteins. Although TVMV protease is a close relative of TEV protease, they exhibit distinct sequence specificities. We report here the crystal structure of a catalytically inactive mutant TVMV protease (K65A/K67A/C151A) in complex with a canonical peptide substrate (Ac-RETVRFQSD) at 1.7-Å resolution. As observed in several crystal structures of TEV protease, the C-terminus (∼20 residues) of TVMV protease is disordered. Unexpectedly, although deleting the disordered residues from TEV protease reduces its catalytic activity by ∼10-fold, an analogous truncation mutant of TVMV protease is significantly more active. Comparison of the structures of TEV and TVMV protease in complex with their respective canonical substrate peptides reveals that the S3 and S4 pockets are mainly responsible for the differing substrate specificities. The structure of TVMV protease suggests that it is less tolerant of variation at the P1' position than TEV protease. This conjecture was confirmed experimentally by determining kinetic parameters k(cat) and K(m) for a series of oligopeptide substrates. Also, as predicted by the cocrystal structure, we confirm that substitutions in the P6 position are more readily tolerated by TVMV than TEV protease.

  8. 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.

  9. Shifting to structures in physics and biology: a prophylactic for promiscuous realism.

    Science.gov (United States)

    French, Steven

    2011-06-01

    Within the philosophy of science, the realism debate has been revitalised by the development of forms of structural realism. These urge a shift in focus from the object oriented ontologies that come and go through the history of science to the structures that remain through theory change. Such views have typically been elaborated in the context of theories of physics and are motivated by, first of all, the presence within such theories of mathematical equations that allow straightforward representation of the relevant structures; and secondly, the implications of such theories for the individuality and identity of putative objects. My aim in this paper is to explore the possibility of extending such views to biological theories. An obvious concern is that within the context of the latter it is typically insisted that we cannot find the kinds of highly mathematised structures that structural realism can point to in physics. I shall indicate how the model-theoretic approach to theories might help allay such concerns. Furthermore, issues of identity and individuality also arise within biology. Thus Dupré has recently noted that there exists a 'General Problem of Biological Individuality' which relates to the issue of how one divides 'massively integrated and interconnected' systems into discrete components. In response Dupré advocates a form of 'Promiscuous Realism' that holds, for example, that there is no unique way of dividing the phylogenetic tree into kinds. Instead I shall urge serious consideration of those aspects of the work of Dupré and others that lean towards a structuralist interpretation. By doing so I hope to suggest possible ways in which a structuralist stance might be extended to biology.

  10. 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.

  11. The Vibration Impact Determination of the Helicopter Structural Components

    Directory of Open Access Journals (Sweden)

    Khaksar Zeinab

    2017-01-01

    Full Text Available This paper presents the determination of the vibration impact of the helicopter structural components and skin repairs in terms of frequency characteristics. To address this issue, a 3D Finite Element Method (FEM model of 349 Gazelle helicopter has been developed in ABAQUS and the frequency analysis is conducted. The results on the natural frequencies of the full structure reasonably match with the literature giving confidence in the baseline model. The main advantage of this FEM model is that, it can be used to predict the natural frequencies of the full structure, precisely. In addition, the material properties and conditions of the components can be updated based on the applied conditions during the repair and maintenance period. Thus, the model gives a comprehensive design tool for analysing the frequencies of the helicopter with differing components. The effective variations in the frequency changes due to repair are predicted numerically. The discussion of these results helps in developing leads to improved selection of replacement materials and their properties.

  12. 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.

  13. 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

  14. A method for the determination of D-kynurenine in biological tissues.

    Science.gov (United States)

    Wang, Xiao-Dan; Horning, Kyle J; Notarangelo, Francesca M; Schwarcz, Robert

    2013-12-01

    D-kynurenine (D-KYN), a metabolite of D-tryptophan, can serve as the bioprecursor of kynurenic acid (KYNA) and 3-hydroxykynurenine, two neuroactive compounds that are believed to play a role in the pathophysiology of several neurological and psychiatric diseases. In order to investigate the possible presence of D-KYN in biological tissues, we developed a novel assay based on the conversion of D-KYN to KYNA by purified D-amino acid oxidase (D-AAO). Samples were incubated with D-AAO under optimal conditions for measuring D-AAO activity (100 mM borate buffer, pH 9.0), and newly produced KYNA was detected by high-performance liquid chromatography (HPLC) with fluorimetric detection. The detection limit for D-KYN was 300 fmol, and linearity of the assay was ascertained up to 300 pmol. No assay interference was noted when other D-amino acids, including D-serine and D-aspartate, were present in the incubation mixture at 50-fold higher concentrations than D-KYN. Using this new method, D-KYN was readily detected in the brain, liver, and plasma of mice treated systemically with D-KYN (300 mg/kg). In these experiments, enantioselectivity was confirmed by determining total kynurenine levels in the same samples using a conventional HPLC assay. Availability of a sensitive, specific, and simple method for D-KYN measurement will be instrumental for evaluating whether D-KYN should be considered for a role in physiology and pathology.

  15. 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.

  16. Habitat characteristics for different freshwater snail species as determined biologically through macroinvertebrate information.

    Science.gov (United States)

    El-Khayat, Hanaa M M; Mahmoud, Kadria M A; Mostafa, Bayomy B; Tantawy, Ahmad A; El-Deeb, Fatma A; Ragb, Fawzy M; Ismail, Nahed M; El-Said, Kalil M; Taleb, Hoda M Abu

    2011-12-01

    Macro-invertebrates including freshwater snails collected from 643 sites over 8 successive seasons among the River Nile, branches, main canals and certain drains in eight Egyptian Governorates. Thirteen snail species and one bivalve species were identified. The most distributed were Lanistus carinatus and Physa acuta while the most abundant were Cleopatra bulimoides and Physa acuta during the whole study. The sites that harbored each snail species in all the examined water-courses were grouped seasonally and their biological assessment was determined by their minimum and maximum total point similarity percentage to that of the corresponded reference site and mean of the total points. Habitats for most snail species attained minimum total point's similarity percentage less than 21% (very poor habitat) during autumn and winter then spring while during summer very poor habitat was harbored by only few snail species. P. acuta was the only survived snails in habitat which attained 0 as a minimum total point's similarity percentage during two seasons and L. carinatus and Succinea cleopatra during one season. With respect to medically important snails very poor sites constituted 23% of Biomphalaria alexandrina sites, 14% of Lymnaea natalensis and 9.4% of Bulinus truncatus sites. The studied macroinvertebrate matrices, total number of organisms, taxa richness, the Ephemeroptera, Plecoptera, and Trichoptera (EPT) index, ratio of EPT index to chironomidae, ratio of scraper to filtering collector, contribution of dominant macroinvertebrate major group, comparison revealed descending tolerances from B. alexanrina followed by L. natalensis then B. truncates, but Hilsenhoff Biotic Index (HBI) showed the same tolerance to organic pollution.

  17. 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

  18. 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.

  19. 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}.

  20. 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…

  1. Nanoscale structural features determined by AFM for single virus particles.

    Science.gov (United States)

    Chen, Shu-wen W; Odorico, Michael; Meillan, Matthieu; Vellutini, Luc; Teulon, Jean-Marie; Parot, Pierre; Bennetau, Bernard; Pellequer, Jean-Luc

    2013-11-21

    In this work, we propose "single-image analysis", as opposed to multi-image averaging, for extracting valuable information from AFM images of single bio-particles. This approach allows us to study molecular systems imaged by AFM under general circumstances without restrictions on their structural forms. As feature exhibition is a resolution correlation, we have performed AFM imaging on surfaces of tobacco mosaic virus (TMV) to demonstrate variations of structural patterns with probing resolution. Two AFM images were acquired with the same tip at different probing resolutions in terms of pixel width, i.e., 1.95 and 0.49 nm per pixel. For assessment, we have constructed an in silico topograph based on the three-dimensional crystal structure of TMV as a reference. The prominent artifacts observed in the AFM-determined shape of TMV were attributed to tip convolutions. The width of TMV rod was systematically overestimated by ~10 nm at both probing resolutions of AFM. Nevertheless, the effects of tip convolution were less severe in vertical orientation so that the estimated height of TMV by AFM imaging was in close agreement with the in silico X-ray topograph. Using dedicated image processing algorithms, we found that at low resolution (i.e., 1.95 nm per pixel), the extracted surface features of TMV can be interpreted as a partial or full helical repeat (three complete turns with ~7.0 nm in length), while individual protein subunits (~2.5 nm) were perceivable only at high resolution. The present study shows that the scales of revealed structural features in AFM images are subject to both probing resolution and processing algorithms for image analysis.

  2. Development of a radioimmunoassay for the determination of buprenorphine in biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Debrabandere, L.; Boven, M. Van; Daenens, P. (Louvain Univ. (Belgium))

    1993-02-01

    The development of a specific and sensitive radioimmunoassay for the detection of buprenorphine in urine samples is described. With minor adjustments, the assay was also applied to the analysis for buprenorphine in plasma samples. The 2-diazobenzoic acid derivative of buprenorphine has been prepared as a hapten. The immunization of rabbits with the hapten-bovine serum albumin conjugate resulted in the production of antibodies, which cross-reacted with N-dealkylbuprenophine up to about the 90% level. The antibodies showed very low cross-reactivities with the 3-O-glucuronides and with the structural analogue etorphine. The assay was mainly used to prescreen for buprenorphine in urine samples of persons suspected of Temgesic misuse and to determine buprenorphine in plasma samples. A linear calibration graph for buprenorphine was obtained after logit-log regression. The spiking recovery study showed a linear regression. Intra-and inter-assay relative standard deviations were < 4.35 and < 6.36%, respectively. A comparison study of the high-performance liquid chromatographic determination (X) to the radioimmunoassay (Y) resulted in the following regression equation for the urine samples: Y = 1.44 + 1.64 X (n = 32; r 0.910) and Y = 0.007 + 1.58 X (n = 10; r = 0.930) for plasma specimens. The minimum detectable dose of the immunoassay was calculated to be 10 pg ml[sup -1] (Student's t-distribution, p 0.01, degrees of freedom = 8). (Author).

  3. Towards Systems Biology of Heterosis: A Hypothesis about Molecular Network Structure Applied for the Arabidopsis Metabolome

    Directory of Open Access Journals (Sweden)

    Gärtner Tanja

    2009-01-01

    Full Text Available We propose a network structure-based model for heterosis, and investigate it relying on metabolite profiles from Arabidopsis. A simple feed-forward two-layer network model (the Steinbuch matrix is used in our conceptual approach. It allows for directly relating structural network properties with biological function. Interpreting heterosis as increased adaptability, our model predicts that the biological networks involved show increasing connectivity of regulatory interactions. A detailed analysis of metabolite profile data reveals that the increasing-connectivity prediction is true for graphical Gaussian models in our data from early development. This mirrors properties of observed heterotic Arabidopsis phenotypes. Furthermore, the model predicts a limit for increasing hybrid vigor with increasing heterozygosity—a known phenomenon in the literature.

  4. 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.

  5. Heteroaryl chalcones: design, synthesis, X-ray crystal structures and biological evaluation.

    Science.gov (United States)

    Kumar, C S Chidan; Loh, Wan-Sin; Ooi, Chin Wei; Quah, Ching Kheng; Fun, Hoong-Kun

    2013-10-15

    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.

  6. 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.

  7. 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.

  8. 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

  9. Relevant uses of surface proteins – display on self‐organized biological structures

    OpenAIRE

    Jahns, Anika C.; Rehm, Bernd H. A.

    2012-01-01

    Summary Proteins are often found attached to surfaces of self‐assembling biological units such as whole microbial cells or subcellular structures, e.g. intracellular inclusions. In the last two decades surface proteins were identified that could serve as anchors for the display of foreign protein functions. Extensive protein engineering based on structure–function data enabled efficient display of technically and/or medically relevant protein functions. Small size, diversity of the anchor pro...

  10. Nanoelectromechanics of Inorganic and Biological Systems: From Structural Imaging to Local Functionalities

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez, Brian [University College, Dublin; Kalinin, Sergei V [ORNL; Jesse, Stephen [ORNL; Thompson, G. L. [Clemson University; Vertegel, Alexey [ORNL; Hohlbauch, Sophia [Asylum Research, Santa Barbara, CA; Proksch, Roger [Asylum Research, Santa Barbara, CA

    2008-01-01

    Coupling between electrical and mechanical phenomena is extremely common in inorganic materials, and nearly ubiquitous in biological systems, underpinning phenomena and devices ranging from SONAR to cardiac activity and hearing. This paper briefly summarizes the Scanning Probe Microscopy (SPM) approach, referred to as Piezoresponse Force Microscopy (PFM), for probing electromechanical coupling on the nanometer scales, and delineates some existing and emerging applications to probe local structure and functionality in inorganic ferroelectrics, calcified and connective tissues, and complex biosystems based on electromechanical detection.

  11. Cold Spring Harbor symposia on quantitative biology. Volume XLVII, Part 1. Structures of DNA

    Energy Technology Data Exchange (ETDEWEB)

    1983-01-01

    The proceedings for the 47th Annual Cold Spring Harbor Symposia on Quantitative Biology are presented. This symposium focused on the Structure of DNA. Topics presented covered research in the handedness of DNA, conformational analysis, chemically modified DNA, chemical synthesis of DNA, DNA-protein interactions, DNA within nucleosomes, DNA methylation, DNA replication, gyrases and topoisomerases, recombining and mutating DNA, transcription of DNA and its regulation, the organization of genes along DNA, repetitive DNA and pseudogenes, and origins of replication, centromeres, and teleomeres.

  12. How useful is ion mobility mass spectrometry for structural biology? The relationship between protein crystal structures and their collision cross sections in the gas phase.

    Science.gov (United States)

    Jurneczko, Ewa; Barran, Perdita E

    2011-01-07

    The technique of ion mobility mass spectrometry (IM-MS) has become of increasing interest for rapid analysis of the conformations adopted by biological macromolecules. It is currently used routinely for analysis of explosives and illegal substances in airport and military security. In biophysical research, it can be used to determine the temperature dependent rotationally averaged collision cross section of gas-phase ions of proteins and nucleic acids along with their mass to charge ratios. Nanoelectrospray ionisation allows the gentle transfer of intact biomolecules from solutions in which the native form(s) are present, into the solvent free environment of a mass spectrometer. It is believed by many researchers that the experimental collision cross sections of these molecules should have some relationship to crystal structure coordinates. In this review we outline the different experimental methods that can be used to measure ion mobility; we also describe methods used to calculate collision cross sections from input coordinates. Following this survey of the methodological approaches to IM-MS, we then summarise IM-MS data published to date for some monomeric peptides and small soluble proteins, along with collision cross sections calculated from their crystal structure coordinates. Finally we consider the relationship between experimental gas-phase conformations and those adopted in crystals and give an outlook on the application of IM-MS as a tool for structural biology.

  13. 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.

  14. 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)

  15. 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.

  16. Determinants of capital structure: New evidence from Portuguese small firms

    Directory of Open Access Journals (Sweden)

    Zélia Serrasqueiro

    2016-11-01

    Full Text Available This paper studies the determinants of capital structure of 2,329 Portuguese small firms, decomposing total liabilities in long and short-term debt. The results of 2007-2011 panel data suggest that information asymmetry and agency problems seem to be important for small firms in accessing long-term debt. Greater size and a higher level of collateral are quite important in accessing long-term debt. Liquidity is positively associated with long-term debt, although it is negatively related to short-term debt. Higher profitability is related to lower levels of debt. When internal finance is insufficient, these firms seem to be strongly dependent on short-term debt, due to the difficulties in accessing long-term. The main conclusion of the current study is that the predicitons of POT and TOT are followed by small firms in their capital structure, which is in accordance with the results of previous studies focusing on SMEs.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Chemical cross-linking and native mass spectrometry: A fruitful combination for structural biology.

    Science.gov (United States)

    Sinz, Andrea; Arlt, Christian; Chorev, Dror; Sharon, Michal

    2015-08-01

    Mass spectrometry (MS) is becoming increasingly popular in the field of structural biology for analyzing protein three-dimensional-structures and for mapping protein-protein interactions. In this review, the specific contributions of chemical crosslinking and native MS are outlined to reveal the structural features of proteins and protein assemblies. Both strategies are illustrated based on the examples of the tetrameric tumor suppressor protein p53 and multisubunit vinculin-Arp2/3 hybrid complexes. We describe the distinct advantages and limitations of each technique and highlight synergistic effects when both techniques are combined. Integrating both methods is especially useful for characterizing large protein assemblies and for capturing transient interactions. We also point out the future directions we foresee for a combination of in vivo crosslinking and native MS for structural investigation of intact protein assemblies.

  3. 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.

  4. 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

  5. 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

  6. Paradigms in the structural biology of the mitogenic ternary complex FGF:FGFR:heparin.

    Science.gov (United States)

    Pomin, Vitor H

    2016-08-01

    The main achievements regarding the molecular interaction involving fibroblast growth factors (FGFs), canonical receptors (FGFRs) and the glycosaminoglycans (GAGs) heparan sulfate (HS)/heparin (Hp) are overviewed. Despite the recent works concerning the subject, conflicting paradigms in the structural biology of the resultant ternary complex FGF:FGFR:HS/Hp seem to persist up to these days. The principal dilemma, centered on the functional intermolecular complex of mitogenesis and angiogenesis, has been lasting for approximately a decade and a half since the publications of the two contradicting crystal structures, the asymmetric 2:2:1 versus the symmetric 2:2:2 complex model. When the principal results regarding this ternary complex are analyzed as a whole and through an impartial manner, conclusion heavily and reliably supports the existence and activity of both complex models. Selection of each complex is driven by multiple factors of different degrees of impact. Specificity in protein-binding motifs in ligands (although the minimal binding sequences are yet controversial), slight differences on the structure of the GAG-binding sites of FGF and of FGFR isoforms as well as on the possible ligand-induced conformational changes of FGFR are examples of these factors. Here, the structural biology of the mitogenic FGF:FGFR:HS/Hp ternary complex is revisited. Discussion is focused on the major attributes of this intermolecular complex including the existing conflicts about the righter biologically active model and information regarding ligand structure, conformation and minimal length required for binding to the growth factors and receptors. This review is very timely in light of the 100(th) anniversary of the discovery of Hp.

  7. 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

  8. 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.

  9. Role of zooplankton in determining the efficiency of the biological carbon pump

    Science.gov (United States)

    Cavan, Emma L.; Henson, Stephanie A.; Belcher, Anna; Sanders, Richard

    2017-01-01

    The efficiency of the ocean's biological carbon pump (BCPeff - here the product of particle export and transfer efficiencies) plays a key role in the air-sea partitioning of CO2. Despite its importance in the global carbon cycle, the biological processes that control BCPeff are poorly known. We investigate the potential role that zooplankton play in the biological carbon pump using both in situ observations and model output. Observed and modelled estimates of fast, slow, and total sinking fluxes are presented from three oceanic sites: the Atlantic sector of the Southern Ocean, the temperate North Atlantic, and the equatorial Pacific oxygen minimum zone (OMZ). We find that observed particle export efficiency is inversely related to primary production likely due to zooplankton grazing, in direct contrast to the model estimates. The model and observations show strongest agreement in remineralization coefficients and BCPeff at the OMZ site where zooplankton processing of particles in the mesopelagic zone is thought to be low. As the model has limited representation of zooplankton-mediated remineralization processes, we suggest that these results point to the importance of zooplankton in setting BCPeff, including particle grazing and fragmentation, and the effect of diel vertical migration. We suggest that improving parameterizations of zooplankton processes may increase the fidelity of biogeochemical model estimates of the biological carbon pump. Future changes in climate such as the expansion of OMZs may decrease the role of zooplankton in the biological carbon pump globally, hence increasing its efficiency.

  10. 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.

  11. 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.

  12. Sulfated fucans, fresh perspectives: structures, functions, and biological properties of sulfated fucans and an overview of enzymes active toward this class of polysaccharide.

    Science.gov (United States)

    Berteau, Olivier; Mulloy, Barbara

    2003-06-01

    Sulfated fucans, frequently referred to simply as fucans, constitute a class of polysaccharides first isolated in 1913. For many years fucans were regarded only as a potential source of l-fucose, although their anticoagulant activity was known. Even as the potent effects of fucans on physiological systems have become better characterized, structural studies have lagged behind. Recently the search for new drugs has raised increased interest in sulfated fucans. In the past few years, several structures of algal and invertebrate fucans have been solved, and many aspects of their biological activity have been elucidated. From this work emerges a more interesting picture of this class of polysaccharides than was previously suspected. The availability of purified fucans and fucan fractions with simple, but varied structures, in conjunction with the development of new enzymatic tools, demonstrate that the biological properties of sulfated fucans are not only a simple function of their charge density but also are determined by detailed structural features.

  13. Cruciform structures are a common DNA feature important for regulating biological processes

    Directory of Open Access Journals (Sweden)

    Arrowsmith Cheryl

    2011-08-01

    Full Text Available Abstract DNA cruciforms play an important role in the regulation of natural processes involving DNA. These structures are formed by inverted repeats, and their stability is enhanced by DNA supercoiling. Cruciform structures are fundamentally important for a wide range of biological processes, including replication, regulation of gene expression, nucleosome structure and recombination. They also have been implicated in the evolution and development of diseases including cancer, Werner's syndrome and others. Cruciform structures are targets for many architectural and regulatory proteins, such as histones H1 and H5, topoisomerase IIβ, HMG proteins, HU, p53, the proto-oncogene protein DEK and others. A number of DNA-binding proteins, such as the HMGB-box family members, Rad54, BRCA1 protein, as well as PARP-1 polymerase, possess weak sequence specific DNA binding yet bind preferentially to cruciform structures. Some of these proteins are, in fact, capable of inducing the formation of cruciform structures upon DNA binding. In this article, we review the protein families that are involved in interacting with and regulating cruciform structures, including (a the junction-resolving enzymes, (b DNA repair proteins and transcription factors, (c proteins involved in replication and (d chromatin-associated proteins. The prevalence of cruciform structures and their roles in protein interactions, epigenetic regulation and the maintenance of cell homeostasis are also discussed.

  14. 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.

  15. Sensitive force technique to probe molecular adhesion and structural linkages at biological interfaces.

    Science.gov (United States)

    Evans, E; Ritchie, K; Merkel, R

    1995-06-01

    Adhesion and cytoskeletal structure are intimately related in biological cell function. Even with the vast amount of biological and biochemical data that exist, little is known at the molecular level about physical mechanisms involved in attachments between cells or about consequences of adhesion on the material structure. To expose physical actions at soft biological interfaces, we have combined an ultrasensitive transducer and reflection interference microscopy to image submicroscopic displacements of probe contact with a test surface under minuscule forces. The transducer is a cell-size membrane capsule pressurized by micropipette suction where displacement normal to the membrane under tension is proportional to the applied force. Pressure control of the tension tunes the sensitivity in operation over four orders of magnitude through a range of force from 0.01 pN up to the strength of covalent bonds (approximately 1000 pN)! As the surface probe, a microscopic bead is biochemically glued to the transducer with a densely-bound ligand that is indifferent to the test surface. Movements of the probe under applied force are resolved down to an accuracy of approximately 5 nm from the interference fringe pattern created by light reflected from the bead. With this arrangement, we show that local mechanical compliance of a cell surface can be measured at a displacement resolution set by structural fluctuations. When desired, a second ligand is bound sparsely to the probe for focal adhesion to specific receptors in the test surface. We demonstrate that monitoring fluctuations in probe position at low transducer stiffness enhances detection of molecular adhesion and activation of cytoskeletal structure. Subsequent loading of an attachment tests mechanical response of the receptor-substrate linkage throughout the force-driven process of detachment.

  16. 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.

  17. 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

  18. Determination of biological activity of gonadotropins hCG and FSH by Förster resonance energy transfer based biosensors

    Science.gov (United States)

    Mazina, Olga; Allikalt, Anni; Tapanainen, Juha S.; Salumets, Andres; Rinken, Ago

    2017-01-01

    Determination of biological activity of gonadotropin hormones is essential in reproductive medicine and pharmaceutical manufacturing of the hormonal preparations. The aim of the study was to adopt a G-protein coupled receptor (GPCR)-mediated signal transduction pathway based assay for quantification of biological activity of gonadotropins. We focussed on studying human chorionic gonadotropin (hCG) and follicle-stimulating hormone (FSH), as these hormones are widely used in clinical practice. Receptor-specific changes in cellular cyclic adenosine monophosphate (cAMP, second messenger in GPCR signalling) were monitored by a Förster resonance energy transfer (FRET) biosensor protein TEpacVV in living cells upon activation of the relevant gonadotropin receptor. The BacMam gene delivery system was used for biosensor protein expression in target cells. In the developed assay only biologically active hormones initiated GPCR-mediated cellular signalling. High assay sensitivities were achieved for detection of hCG (limit of detection, LOD: 5 pM) and FSH (LOD: 100 pM). Even the small-scale conformational changes caused by thermal inactivation and reducing the biological activity of the hormones were registered. In conclusion, the proposed assay is suitable for quantification of biological activity of gonadotropins and is a good alternative to antibody- and animal-testing-based assays used in pharmaceutical industry and clinical research. PMID:28181555

  19. Determination of biological activity of gonadotropins hCG and FSH by Förster resonance energy transfer based biosensors.

    Science.gov (United States)

    Mazina, Olga; Allikalt, Anni; Tapanainen, Juha S; Salumets, Andres; Rinken, Ago

    2017-02-09

    Determination of biological activity of gonadotropin hormones is essential in reproductive medicine and pharmaceutical manufacturing of the hormonal preparations. The aim of the study was to adopt a G-protein coupled receptor (GPCR)-mediated signal transduction pathway based assay for quantification of biological activity of gonadotropins. We focussed on studying human chorionic gonadotropin (hCG) and follicle-stimulating hormone (FSH), as these hormones are widely used in clinical practice. Receptor-specific changes in cellular cyclic adenosine monophosphate (cAMP, second messenger in GPCR signalling) were monitored by a Förster resonance energy transfer (FRET) biosensor protein (T)Epac(VV) in living cells upon activation of the relevant gonadotropin receptor. The BacMam gene delivery system was used for biosensor protein expression in target cells. In the developed assay only biologically active hormones initiated GPCR-mediated cellular signalling. High assay sensitivities were achieved for detection of hCG (limit of detection, LOD: 5 pM) and FSH (LOD: 100 pM). Even the small-scale conformational changes caused by thermal inactivation and reducing the biological activity of the hormones were registered. In conclusion, the proposed assay is suitable for quantification of biological activity of gonadotropins and is a good alternative to antibody- and animal-testing-based assays used in pharmaceutical industry and clinical research.

  20. 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.

  1. 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.

  2. Two-dimensional imaging detectors for structural biology with X-ray lasers.

    Science.gov (United States)

    Denes, Peter

    2014-07-17

    Our ability to harness the advances in microelectronics over the past decade(s) for X-ray detection has resulted in significant improvements in the state of the art. Biology with X-ray free-electron lasers present daunting detector challenges: all of the photons arrive at the same time, and individual high peak power pulses must be read out shot-by-shot. Direct X-ray detection in silicon pixel detectors--monolithic or hybrid--are the standard for XFELs today. For structural biology, improvements are needed for today's 10-100 Hz XFELs, and further improvements are required for tomorrow's 10+ kHz XFELs. This article will discuss detector challenges, why they arise and ways to overcome them, along with the current state of the art.

  3. 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.

  4. [Theory of long-distance electron transfer in nanoscale biological structures].

    Science.gov (United States)

    Krasil'nikov, P M

    2011-01-01

    Macromolecular biological systems accomplishing the directed electron transfer are nano-sized structures. The distance between carrier molecules (cofactors), which represent practically isolated electron localization centers, reaches tens of angstroms. The electron transfer theory based on the concept of delocalized electron states, which is conventionally used in biophysics, is unable to adequately interpret the results of concrete observations in many cases. On the basis of the theory of electronic transitions in the case of localized states, developed in the physics of disorder matter, a mechanism of long distance electron transfer in biological systems is suggested. The molecular relaxation of the microenvironment of electron localization centers that accompanies the electron transfer process is also considered.

  5. 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.

  6. 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...

  7. 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...

  8. 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...

  9. 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…

  10. Structure-based design, synthesis, and biological evaluation of irreversible human rhinovirus 3C protease inhibitors. 2. Peptide structure-activity studies.

    Science.gov (United States)

    Dragovich, P S; Webber, S E; Babine, R E; Fuhrman, S A; Patick, A K; Matthews, D A; Reich, S H; Marakovits, J T; Prins, T J; Zhou, R; Tikhe, J; Littlefield, E S; Bleckman, T M; Wallace, M B; Little, T L; Ford, C E; Meador, J W; Ferre, R A; Brown, E L; Binford, S L; DeLisle, D M; Worland, S T

    1998-07-16

    The structure-based design, chemical synthesis, and biological evaluation of various peptide-derived human rhinovirus (HRV) 3C protease (3CP) inhibitors are described. These compounds are comprised of an ethyl propenoate Michael acceptor moiety and a tripeptidyl binding determinant. The systematic modification of each amino acid residue present in the binding determinant as well as the N-terminal functionality is described. Such modifications are shown to provide irreversible HRV-14 3CP inhibitors with anti-3CP activities (kobs/[I]) ranging from 60 to 280 000 M-1 s-1 and antiviral EC50's which approach 0.15 microM. An optimized inhibitor which incorporates several improvements identified by the structure-activity studies is also described. This molecule displays very rapid irreversible inhibition of HRV-14 3CP (kobs/[I] = 800 000 M-1 s-1) and potent antiviral activity against HRV-14 in cell culture (EC50 = 0.056 microM). A 1.9 A crystal structure of an S-alkylthiocarbamate-containing inhibitor complexed with HRV-2 3CP is also detailed.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. Track Structure and the Biological Effectiveness of Accelerated Particles for the Induction of Chromosome Damage

    Science.gov (United States)

    George, K.; Hada, M.; Chappell, L.; Cucinotta, F. A.

    2011-01-01

    Track structure models predict that at a fixed value of LET, particles with lower charge number, Z will have a higher biological effectiveness compared to particles with a higher Z. In this report we investigated how track structure effects induction of chromosomal aberration in human cells. Human lymphocytes were irradiated in vitro with various energies of accelerated iron, silicon, neon, or titanium ions and chromosome damage was assessed in using three color FISH chromosome painting in chemically induced PCC samples collected a first cell division post irradiation. The LET values for these ions ranged from 30 to195 keV/micron. Of the particles studied, Neon ions have the highest biological effectiveness for induction of total chromosome damage, which is consistent with track structure model predictions. For complex-type exchanges 64 MeV/ u Neon and 450 MeV/u Iron were equally effective and induced the most complex damage. In addition we present data on chromosomes exchanges induced by six different energies of protons (5 MeV/u to 2.5 GeV/u). The linear dose response term was similar for all energies of protons suggesting that the effect of the higher LET at low proton energies is balanced by the production of nuclear secondaries from the high energy protons.

  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. Deciphering molecular determinants of chemotherapy in gastrointestinal malignancy using systems biology approaches.

    Science.gov (United States)

    Lin, Li-Ling; Huang, Hsuan-Cheng; Juan, Hsueh-Fen

    2014-09-01

    Gastrointestinal cancers are asymptomatic in early tumor development, leading to high mortality rates. Peri- or postoperative chemotherapy is a common strategy used to prolong the life expectancy of patients with these diseases. Understanding the molecular mechanisms by which anticancer drugs exert their effect is crucial to the development of anticancer therapies, especially when drug resistance occurs and an alternative drug is needed. By integrating high-throughput techniques and computational modeling to explore biological systems at different levels, from gene expressions to networks, systems biology approaches have been successfully applied in various fields of cancer research. In this review, we highlight chemotherapy studies that reveal potential signatures using microarray analysis, next-generation sequencing (NGS), proteomic and metabolomic approaches for the treatment of gastrointestinal cancers.

  18. A Method for Determining the Content of Glycoproteins in Biological Samples

    Directory of Open Access Journals (Sweden)

    Yang Gao

    2016-11-01

    Full Text Available The glycoprotein purified from the mycelium extract of Tremella fuciformis was marked with iodine through the iodine substitution reaction. The content of iodine, which is indicative of the amount of the marked tremella glycoprotein (ITG, was detected with Inductively coupled plasma mass spectrometry (ICP-MS. The method was found to be stable, sensitive, and accurate at detecting the content of iodine-substituted glycoprotein, and was used in the quantitative analysis of biological samples, including blood and organs. Different biological samples were collected from rats after oral administration of ITG, and were tested for iodine content by ICP-MS to calculate the amount of ITG in the samples. The results suggested that ICP-MS is a sensitive, stable, and accurate method for detection of iodinated glycoproteins in blood and organs.

  19. 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.

  20. Fluconazol method validation by RP-HPLC for determination in biological skin matrices.

    Science.gov (United States)

    Ayub, Alessandra C; Vianna-Soares, Cristina D; Ferreira, Lucas A M

    2007-01-01

    The bis-triazole antifungal fluconazole (FCZ) is used in the systemic treatment of superficial mycoses. The inconvenience of drug interactions and incidence of adverse reactions occurs in approximately 16% of patients, despite several advantages against systemic fungal infections. Because its pharmacokinetics profile is favorable to cutaneous accumulation, it presents a prominent importance in the treatment of superficial mycoses. This study shows FCZ method validation by reversed-phase high-performance liquid chromatography in the linear range of 2 to 32 microg/mL, which suitable for application in biological matrices after topical permeation studies. The method is tested in simulated FCZ alcoholic solution applied to skin extracts after in vitro permeation studies using Franz cells. Recovery shows good results (in the range 75.0% +/- 4.1% to 82.0% +/- 6.6%) regarding the biological matrices.

  1. 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.

  2. Structure determination of bisacetylenic oxylipins in carrots (Daucus carota L.) and enantioselective synthesis of falcarindiol.

    Science.gov (United States)

    Schmiech, Ludger; Alayrac, Carole; Witulski, Bernhard; Hofmann, Thomas

    2009-11-25

    Although bisacetylenic oxylipins have been demonstrated to exhibit diverse biological activities, the chemical structures of many representatives of this class of phytochemicals still remain elusive. As carrots play an important role in our daily diet and are known as a source of bisacetylenes, an extract made from Daucus carota L. was screened for bisacetylenic oxylipins, and, after isolation, their structures were determined by means of LC-MS and 1D/2D NMR spectroscopy. Besides the previously reported falcarinol, falcarindiol, and falcarindiol 3-acetate, nine additional bisacetylenes were identified, among which six derivatives are reported for the first time in literature and three compounds were previously not identified in carrots. To determine the absolute stereochemistry of falcarindiol in carrots, the (3R,8R)-, (3R,8S)-, (3S,8R)-, and (3S,8S)-stereoisomers of falcarindiol were synthesized according to a novel 10-step total synthesis involving a Cadiot-Chodkiewicz cross-coupling reaction of (S)- and (R)-trimethylsilanyl-4-dodecen-1-yn-3-ol and (R)- and (S)-5-bromo-1-penten-4-yn-3-ol, respectively. Comparative chiral HPLC analysis of the synthetic stereoisomers with the isolated phytochemical led to the unequivocal assignment of the (Z)-(3R,8S)-configuration for falcarindiol in carrot extracts from Daucus carota L.

  3. 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...

  4. Critical comparison of radiometric and mass spectrometric methods for the determination of radionuclides in environmental, biological and nuclear waste samples

    DEFF Research Database (Denmark)

    Hou, Xiaolin; Roos, Per

    2008-01-01

    spectrometry, and glow discharge mass spectrometry are reviewed for the determination of radionuclides. These methods are critically compared for the determination of long-lived radionuclides important for radiation protection, decommissioning of nuclear facilities, repository of nuclear waste, tracer...... application in the environmental and biological researches, these radionuclides include H-3, C-14, Cl-36, Ca-41 Ni-59,Ni-63, Sr-89,Sr-90, Tc-99, I-129, Cs-135,Cs-137, Pb-210, Ra-226,Ra-228, Np-237, Am-241, and isotopes of thorium, uranium and plutonium. The application of on-line methods (flow injection...

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

    Science.gov (United States)

    Finnerty, Justin John; Peyser, Alexander; Carloni, Paolo

    2015-01-01

    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.

  6. 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.

  7. The terminal structure plays an important role in the biological activity of cecropin CMIV

    Institute of Scientific and Technical Information of China (English)

    窦非; 谢维; 董雪吟; 徐贤秀

    1999-01-01

    Antibacterial peptides have received increasing attention as a new pharmaceutical substance. But the molecular mechanism of lysis is still poorly understood. CMIV gene and mutant CMIV gene in GST fusion system were expressed. After cleaving with different cleavage reagents, the peptide with an excess of N-terminus and with an un-amidated C-terminus stopped the activity while the peptide with an excess Asn at the C-terminus had the activity level the same as natural CMIV. The results showed that the terminal structure of cecropin CMIV played an important role in its biological activity.

  8. Diversity of Pyrrolizidine Alkaloids in the Boraginaceae Structures, Distribution, and Biological Properties

    Directory of Open Access Journals (Sweden)

    Assem El-Shazly

    2014-04-01

    Full Text Available Among the diversity of secondary metabolites which are produced by plants as means of defence against herbivores and microbes, pyrrolizidine alkaloids (PAs are common in Boraginaceae, Asteraceae and some other plant families. Pyrrolizidine alkaloids are infamous as toxic compounds which can alkylate DNA und thus cause mutations and even cancer in herbivores and humans. Almost all genera of the family Boraginaceae synthesize and store this type of alkaloids. This review reports the available information on the present status (literature up to early 2014 of the pyrrolizidine alkaloids in the Boraginaceae and summarizes the topics structure, distribution, chemistry, chemotaxonomic significance, and biological properties.

  9. 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.

  10. Dielectric relaxation time and structure of bound water in biological materials

    Energy Technology Data Exchange (ETDEWEB)

    Mashimo, S.; Kuwabara, S.; Yagihara, S.; Higasi, K.

    1987-12-03

    The dielectric behavior of living tissues and a number of biological materials was examined by new equipment of the time domain reflectometry method in a wide frequency range of 10/sup 7/-10/sup 10/ Hz. The authors found two peaks of Debye absorption around 100 MHz and 20 GHz for all the materials. The low-frequency absorption is probably due to bound water while the high-frequency absorption to free water. From the observed relaxation times of bound water a hypothesis is ventured on the structure of bound water and its relaxation mechanism.

  11. 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.

  12. Determinants of biological drug survival in rheumatoid arthritis: evidence from a Hungarian rheumatology center over 8 years of retrospective data

    Science.gov (United States)

    Brodszky, Valentin; Bíró, Anikó; Szekanecz, Zoltán; Soós, Boglárka; Baji, Petra; Rencz, Fanni; Tóthfalusi, László; Gulácsi, László; Péntek, Márta

    2017-01-01

    Objective To compare drug survival of biological therapies in patients with rheumatoid arthritis (RA), and analyze the determinants of discontinuation probabilities and switches to other biological therapies. Materials and methods Consecutive RA patients initiating first biological treatment in one rheumatology center between 2006 and 2013 were included. Log-rank test was used to analyze the differences between the survival curves of different biological drugs. Cox regression was applied to analyze the discontinuation due to inefficacy, the occurrence of adverse events, or to any reasons. Results A total of 540 patients were included in the analysis. The most frequently used first-line biological treatments were infliximab (N=176, 33%), adalimumab (N=150, 28%), and etanercept (N=132, 24%). Discontinuation of first tumor necrosis factor-alpha (TNF-α) treatment was observed for 347 (64%) patients, due to inefficacy (n=209, 60%), adverse events (n=103, 30%), and other reasons (n=35, 10%). Drug survival rates for TNF-α and non-TNF-α therapies were significantly different, and were in favor of non-TNF-α therapies. Every additional number of treatment significantly increased the risk of inefficacy by 27% (ptreatment, switching to rituximab and tocilizumab was associated with significantly longer treatment duration than switching to a second TNF-α. The non-TNF-α therapies resulted in significantly longer treatment duration, due to both less adverse events and longer maintenance of effectiveness. Conclusion Non-TNF-α therapies resulted in significantly longer treatment duration, and lost their effectiveness later. Increase in the number of switches significantly increased the risk of discontinuation of any biological therapy.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. Practical Method for Determining Free Erythrocyte Protoporphyrin as a Biological Marker of Exposure to Inorganic Lead

    OpenAIRE

    Gloria Marilé Ávalos Ávalos

    2014-01-01

    Background: there are various exposure biomarkers for assessing occupational exposure to inorganic lead including the determination of blood lead levels and free erythrocyte protoporphyrin. Objective: to determine the practical and comparative reliability of a simple spectrophotometric method for determining free erythrocyte protoporphyrin as a biomarker of inorganic lead exposure. Methods: a group of 40 lead-exposed workers with different levels of exposure was studied. A blood sample was co...

  18. Structure-based design, synthesis, and biological evaluation of irreversible human rhinovirus 3C protease inhibitors. 3. Structure-activity studies of ketomethylene-containing peptidomimetics.

    Science.gov (United States)

    Dragovich, P S; Prins, T J; Zhou, R; Fuhrman, S A; Patick, A K; Matthews, D A; Ford, C E; Meador, J W; Ferre, R A; Worland, S T

    1999-04-08

    The structure-based design, chemical synthesis, and biological evaluation of various ketomethylene-containing human rhinovirus (HRV) 3C protease (3CP) inhibitors are described. These compounds are comprised of a peptidomimetic binding determinant and an ethyl propenoate Michael acceptor moiety which forms an irreversible covalent adduct with the active site cysteine residue of the 3C enzyme. The ketomethylene-containing inhibitors typically display slightly reduced 3CP inhibition activity relative to the corresponding peptide-derived molecules, but they also exhibit significantly improved antiviral properties. Optimization of the ketomethylene-containing compounds is shown to provide several highly active 3C protease inhibitors which function as potent antirhinoviral agents (EC90 = <1 microM) against multiple virus serotypes in cell culture.

  19. 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

  20. 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.

  1. Mapping the structural topology of IRS family cascades through computational biology.

    Science.gov (United States)

    Chakraborty, Chiranjib; Doss, C George Priya; Bandyopadhyay, Sanghamitra; Sarkar, Bimal Kumar; Haneef, S A Syed

    2013-01-01

    Structural topologies of proteins play significant roles in analyzing their biological functions. Converting the amino acid data in a protein sequence into structural information to outline the function of a protein is a major challenge in post-genome research which can add an extra room in understanding the protein sequence-structure-function relationships. In this study, we performed a comprehensive bioinformatics analysis of structural topology of the IRS family members such as IRS-1, IRS-2, IRS-3, IRS-4, IRS-5 and IRS-6. Based on this assessment, we found that IRS-2 encloses the highest number of α helices, β sheets and β turns in the secondary structure topology compared to IRS-1 and IRS-6. IRS family members are rich in serine or leucine residues. Among the IRS family members, the highest percentage of serine and leucine was observed in IRS-1 (15%) and IRS-5 (10%), respectively. Notably, the highest number of disulphide bonds was observed in IRS-1 (10) which is responsible for structural stability of the protein. Hydrogen bond pattern in α helices and β sheet was recorded in IRS-1, IRS-2 and IRS-6. By conservation analysis, the longest protein IRS-3 was found to be highly conserved among the IRS family members. The cluster of sequence logo present in the N terminus of these cascades was noted, and highly conserved residues in N-terminal region help in the formation of the two highly conserved domains such as PH domain and PTB domain. Results generated from this analysis will be more beneficial to researchers in understanding more about insulin signalling mechanism(s) as well as insulin resistance pathway. We discuss here that bioinformatics tools utilized in this study can play a vital role in addressing the complexity of structural topology to understand structure-function relationships in insulin signalling cascades.

  2. Current and Future Perspectives on the Structural Identification of Small Molecules in Biological Systems

    Directory of Open Access Journals (Sweden)

    Daniel A. Dias

    2016-12-01

    Full Text Available Although significant advances have been made in recent years, the structural elucidation of small molecules continues to remain a challenging issue for metabolite profiling. Many metabolomic studies feature unknown compounds; sometimes even in the list of features identified as “statistically significant” in the study. Such metabolic “dark matter” means that much of the potential information collected by metabolomics studies is lost. Accurate structure elucidation allows researchers to identify these compounds. This in turn, facilitates downstream metabolite pathway analysis, and a better understanding of the underlying biology of the system under investigation. This review covers a range of methods for the structural elucidation of individual compounds, including those based on gas and liquid chromatography hyphenated to mass spectrometry, single and multi-dimensional nuclear magnetic resonance spectroscopy, and high-resolution mass spectrometry and includes discussion of data standardization. Future perspectives in structure elucidation are also discussed; with a focus on the potential development of instruments and techniques, in both nuclear magnetic resonance spectroscopy and mass spectrometry that, may help solve some of the current issues that are hampering the complete identification of metabolite structure and function.

  3. 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.

  4. Structural study and preliminary biological evaluation on the collagen hydrogel crosslinked by γ-irradiation.

    Science.gov (United States)

    Zhang, Xiangmei; Xu, Ling; Huang, Xin; Wei, Shicheng; Zhai, Maolin

    2012-11-01

    Under γ-irradiation, concentrated collagen solutions yielded collagen hydrogels and liquid products. The molecular structure of collagen hydrogels and the source of the liquid products were studied. Furthermore, preliminary biological properties of the hydrogels were investigated. The results revealed that crosslinking occurred to form collagen hydrogel and the crosslinking density increased with the increasing of the absorbed dose, and the collagen hydrogels showed enhanced mechanical properties. Meanwhile, collagen underwent radiation degradation and water was squeezed out from hydrogel by contraction of hydrogel, yielding liquid products. Collagen hydrogels induced by γ-irradiation maintained the backbone structure of collagen, and tyrosine partially involved in crosslinking. The irradiated collagen hydrogels have higher denatured temperature, can promote fibroblasts proliferation, and their degradation rate in vivo depended on the absorbed dose. The comprehensive results suggested that the collagen hydrogels prepared by radiation crosslinking preserved the triple helical conformation, possessed improved thermal stability and mechanical properties, excellent biocompatibility, which is expected to favor its application as biomaterials.

  5. N-Hexyl-4-aminobutyl glycosides for investigating structures and biological functions of carbohydrates.

    Science.gov (United States)

    Suzuki, Katsuhiko; Tobe, Akifumi; Adachi, Shin; Daikoku, Shusaku; Hasegawa, Yasuko; Shioiri, Yuki; Kobayashi, Mariko; Kanie, Osamu

    2009-11-21

    The potential applications of N-hexyl-4-aminobutyl glycosides in the mass spectrometric investigation of glycan structure and in the investigation of glycan functions were studied. Under collision-induced dissociation (CID) conditions, sodiated glycosides carrying N-hexyl-4-aminobutyl groups effectively produced a hemiacetal species (C-ions), which is important in mass-spectrometry-based structural investigation. The usefulness of N-hexyl-4-aminobutyl glycosides in biological analysis was also confirmed by obtaining a binding constant for the binding of dipyrrometheneboron difluoride C3-labeled N-hexyl-4-aminobutyl beta-lactoside with an Erythrina cristagalli lectin, and by visualizing cellular organelles using a more hydrophobic BODIPY-labeled compound.

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

    Energy Technology Data Exchange (ETDEWEB)

    Samsahl, K.

    1966-02-15

    An anion-exchange method based on fast selective sorption steps from mixtures of sulfuric, hydrobromic, and hydrochloric acid solutions has been developed for the separation of five different groups of radioactive trace elements in neutron-irradiated biological material. The separations are performed automatically with a simple proportioning pump apparatus. The apparatus allows the exact adjustment of influent solutions to the series of ion-exchange columns. The practical application of the method is described in detail. The successful use of the method is practically independent on the level of Na activity present in the sample.

  7. Determination of Different Biological Factors on the Base of Dried Blood Spot Technology

    CERN Document Server

    Bozhenko, V K; Mishchenko, A S; Tuzhilin, A A; Shishkin, A M

    2011-01-01

    It is well-known that distinct biological indices (analytes) have distinct variability. We try to use some mathematical algorithms to pick out a set of blood parameters which give an opportunity to retrieve the initial volume of the blood spotted, and use it to calculate exact concentrations of analyts interesting to a physician. For our analysis we used the database of biochemical blood parameters obtained in Russian Scientific Center of Roentgen-Radiology during 1995-2000, which includes more than 30000 of patients.

  8. 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.

  9. 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.

  10. The effect of a biologically produced structure on the benthic copepods of a deep-sea site

    Science.gov (United States)

    Thistle, David; Eckman, James E.

    1990-04-01

    In deep-sea soft bottoms, a variety of organisms produce structures that persist for long periods, even after the structures are vacated. It has been hypothesized that these structures are a major source of patchiness in these communities and are important in maintaining the high diversities that characterize the deep sea. Although several studies have shown species' abundances to be correlated with structures, the mechanisms underlying the associations are not known. We attempted to discover these mechanisms, focusing on the responses of benthic copepods to mudballs made by the polychaete Tharyx luticastellus at a site at 1050 m depth in San Diego Trough (32° 52.4'N, 117°45.5'W). It was found that seven out of 40 species responded. Four were more abundant around the structure only when the worm was in residence. These species apparently benefit from some consequences of the worm's presence. Given that bacterial abundance is higher about occupied Tharyx mudballs than nearby controls, it may be that the attractiveness occupied Tharyx mudballs arises from the provision of food. Three species responded to unoccupied mudballs. We measured responses to various types of mudball mimics to determine whether responses were to a habitat provided by the mudball, to a refuge from predation in its vicinity, or to hydrodynamically mediated increases in local food availability. Two of the species appeared to use the mudball as a habitat, the third as a refuge from infaunal predators. The results indicate that biologically produced structures can persist long enough to be viewed as habitat heterogeneity by other species in the community and that this source of patchiness is important to deep-sea species.

  11. 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.

  12. Structural and biological mimicry of protein surface recognition by [alpha/beta]-peptide foldamers

    Energy Technology Data Exchange (ETDEWEB)

    Horne, W. Seth; Johnson, Lisa M.; Ketas, Thomas J.; Klasse, Per Johan; Lu, Min; Moore, John P.; Gellman, Samuel H.; (Cornell); (UW)

    2009-10-05

    Unnatural oligomers that can mimic protein surfaces offer a potentially useful strategy for blocking biomedically important protein-protein interactions. Here we evaluate an approach based on combining {alpha}- and {beta}-amino acid residues in the context of a polypeptide sequence from the HIV protein gp41, which represents an excellent testbed because of the wealth of available structural and biological information. We show that {alpha}/{beta}-peptides can mimic structural and functional properties of a critical gp41 subunit. Physical studies in solution, crystallographic data, and results from cell-fusion and virus-infectivity assays collectively indicate that the gp41-mimetic {alpha}/{beta}-peptides effectively block HIV-cell fusion via a mechanism comparable to that of gp41-derived {alpha}-peptides. An optimized {alpha}/{beta}-peptide is far less susceptible to proteolytic degradation than is an analogous {alpha}-peptide. Our findings show how a two-stage design approach, in which sequence-based {alpha} {yields} {beta} replacements are followed by site-specific backbone rigidification, can lead to physical and biological mimicry of a natural biorecognition process.

  13. Three-dimensional structure and cyanobacterial activity within a desert biological soil crust.

    Science.gov (United States)

    Raanan, Hagai; Felde, Vincent J M N L; Peth, Stephan; Drahorad, Sylvie; Ionescu, Danny; Eshkol, Gil; Treves, Haim; Felix-Henningsen, Peter; Berkowicz, Simon M; Keren, Nir; Horn, Rainer; Hagemann, Martin; Kaplan, Aaron

    2016-02-01

    Desert biological soil crusts (BSCs) are formed by adhesion of soil particles to polysaccharides excreted by filamentous cyanobacteria, the pioneers and main producers in this habitat. Biological soil crust destruction is a central factor leading to land degradation and desertification. We study the effect of BSC structure on cyanobacterial activity. Micro-scale structural analysis using X-ray microtomography revealed a vesiculated layer 1.5-2.5 mm beneath the surface in close proximity to the cyanobacterial location. Light profiles showed attenuation with depth of 1%-5% of surface light within 1 mm but also revealed the presence of 'light pockets', coinciding with the vesiculated layer, where the irradiance was 10-fold higher than adjacent crust parts at the same depth. Maximal photosynthetic activity, examined by O2 concentration profiles, was observed 1 mm beneath the surface and another peak in association with the 'light pockets'. Thus, photosynthetic activity may not be visible to currently used remote sensing techniques, suggesting that BSCs' contribution to terrestrial productivity is underestimated. Exposure to irradiance higher than 10% full sunlight diminished chlorophyll fluorescence, whereas O2 evolution and CO2 uptake rose, indicating that fluorescence did not reflect cyanobacterial photosynthetic activity. Our data also indicate that although resistant to high illumination, the BSC-inhabiting cyanobacteria function as 'low-light adapted' organisms.

  14. Determining sexual dimorphism in frog measurement data: integration of statistical significance, measurement error, effect size and biological significance

    Directory of Open Access Journals (Sweden)

    Hayek Lee-Ann C.

    2005-01-01

    Full Text Available Several analytic techniques have been used to determine sexual dimorphism in vertebrate morphological measurement data with no emergent consensus on which technique is superior. A further confounding problem for frog data is the existence of considerable measurement error. To determine dimorphism, we examine a single hypothesis (Ho = equal means for two groups (females and males. We demonstrate that frog measurement data meet assumptions for clearly defined statistical hypothesis testing with statistical linear models rather than those of exploratory multivariate techniques such as principal components, correlation or correspondence analysis. In order to distinguish biological from statistical significance of hypotheses, we propose a new protocol that incorporates measurement error and effect size. Measurement error is evaluated with a novel measurement error index. Effect size, widely used in the behavioral sciences and in meta-analysis studies in biology, proves to be the most useful single metric to evaluate whether statistically significant results are biologically meaningful. Definitions for a range of small, medium, and large effect sizes specifically for frog measurement data are provided. Examples with measurement data for species of the frog genus Leptodactylus are presented. The new protocol is recommended not only to evaluate sexual dimorphism for frog data but for any animal measurement data for which the measurement error index and observed or a priori effect sizes can be calculated.

  15. Synthesis and structure determination of uranyl peroxide nanospheres in the presence of organic structure directing agents

    Science.gov (United States)

    Forbes, T. Z.; Burns, P. C.

    2007-12-01

    Recently, actinyl peroxide nanoclusters containing 20, 24, 28, or 32 actinyl polyhedra have been synthesized and their structures identified with single crystal X-ray diffraction [1]. Most nanomaterials are composed of main group elements or transition metals, therefore, these actinyl nanospheres may display vastly different chemical and physical properties due to the presence of filled f-orbitals. A major goal of our research group is to create novel actinyl materials, focusing on nano- and mesoporous materials. The original nanosphere syntheses were limited to inorganic crystallization agents, such as monovalent cations. Over the last decade, the use of organic compounds and surfactants have received increased attention as structure-directing agents for the generation of novel inorganic materials. Using structure-directing organic amines we have successfully synthesized and determined the structures of uranyl nanospheres containing 40 and 50 uranyl polyhedra. The topology of the skeletal U-50 nanosphere is identical to the C50Cl10 fullerene [2]. The topographical relationship between the actinyl nanospheres and fullerene or fullerene-like material may provide additional insight into stable configurations for lower fullerenes. [1] Burns et al., Actinyl peroxide nanospheres. Angewandte Chemie, International Edition, 2005. 44(14): p. 2135. [2] Xie et al., Capturing the Labile Fullerene[50] as C50Cl10. Science, (2004) 305(5671): p. 699.

  16. An overview of the analytical methods for the determination of organic ultraviolet filters in biological fluids and tissues

    Energy Technology Data Exchange (ETDEWEB)

    Chisvert, Alberto, E-mail: alberto.chisvert@uv.es [Departamento de Quimica Analitica, Facultad de Quimica, Universitat de Valencia, Doctor Moliner St. 50, 46100 Burjassot, Valencia (Spain); Leon-Gonzalez, Zacarias [Unidad Analitica, Instituto de Investigacion Sanitaria Fundacion Hospital La Fe, 46009 Valencia (Spain); Tarazona, Isuha; Salvador, Amparo [Departamento de Quimica Analitica, Facultad de Quimica, Universitat de Valencia, Doctor Moliner St. 50, 46100 Burjassot, Valencia (Spain); Giokas, Dimosthenis [Laboratory of Analytical Chemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina (Greece)

    2012-11-08

    Highlights: Black-Right-Pointing-Pointer Papers describing the determination of UV filters in fluids and tissues are reviewed. Black-Right-Pointing-Pointer Matrix complexity and low amounts of analytes require effective sample treatments. Black-Right-Pointing-Pointer The published papers do not cover the study of all the substances allowed as UV filters. Black-Right-Pointing-Pointer New analytical methods for UV filters determination in these matrices are encouraged. - Abstract: Organic UV filters are chemical compounds added to cosmetic sunscreen products in order to protect users from UV solar radiation. The need of broad-spectrum protection to avoid the deleterious effects of solar radiation has triggered a trend in the cosmetic market of including these compounds not only in those exclusively designed for sun protection but also in all types of cosmetic products. Different studies have shown that organic UV filters can be absorbed through the skin after topical application, further metabolized in the body and eventually excreted or bioaccumulated. These percutaneous absorption processes may result in various adverse health effects, such as genotoxicity caused by the generation of free radicals, which can even lead to mutagenic or carcinogenic effects, and estrogenicity, which is associated with the endocrine disruption activity caused by some of these compounds. Due to the absence of official monitoring protocols, there is a demand for analytical methods that enable the determination of UV filters in biological fluids and tissues in order to retrieve more information regarding their behavior in the human body and thus encourage the development of safer cosmetic formulations. In view of this demand, there has recently been a noticeable increase in the development of sensitive and selective analytical methods for the determination of UV filters and their metabolites in biological fluids (i.e., urine, plasma, breast milk and semen) and tissues. The complexity of

  17. Modeling LIDAR Detection of Biological Aerosols to Determine Optimum Implementation Strategy

    Energy Technology Data Exchange (ETDEWEB)

    Sheen, David M.; Aker, Pam M.

    2007-09-19

    This report summarizes work performed for a larger multi-laboratory project named the Background Interferent Measurement and Standards project. While originally tasked to develop algorithms to optimize biological warfare agent detection using UV fluorescence LIDAR, the current uncertainties in the reported fluorescence profiles and cross sections the development of any meaningful models. It was decided that a better approach would be to model the wavelength-dependent elastic backscattering from a number of ambient background aerosol types, and compare this with that generated from representative sporulated and vegetative bacterial systems. Calculations in this report show that a 266, 355, 532 and 1064 nm elastic backscatter LIDAR experiment will allow an operator to immediately recognize when sulfate, VOC-based or road dust (silicate) aerosols are approaching, independent of humidity changes. It will be more difficult to distinguish soot aerosols from biological aerosols, or vegetative bacteria from sporulated bacteria. In these latter cases, the elastic scattering data will most likely have to be combined with UV fluorescence data to enable a more robust categorization.

  18. 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.

  19. Structure, function and management of semi-natural habitats for conservation biological control

    NARCIS (Netherlands)

    Holland, John M.; Bianchi, Felix J.J.A.; Entling, Martin H.; Moonen, Anna Camilla; Smith, Barbara M.; Jeanneret, Philippe

    2016-01-01

    Different semi-natural habitats occur on farmland, and it is the vegetation's traits and structure that subsequently determine their ability to support natural enemies and their associated contribution to conservation biocontrol. New habitats can be created and existing ones improved with agri-en

  20. 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.

  1. Critical comparison of radiometric and mass spectrometric methods for the determination of radionuclides in environmental, biological and nuclear waste samples.

    Science.gov (United States)

    Hou, Xiaolin; Roos, Per

    2008-02-11

    The radiometric methods, alpha (alpha)-, beta (beta)-, gamma (gamma)-spectrometry, and mass spectrometric methods, inductively coupled plasma mass spectrometry, accelerator mass spectrometry, thermal ionization mass spectrometry, resonance ionization mass spectrometry, secondary ion mass spectrometry, and glow discharge mass spectrometry are reviewed for the determination of radionuclides. These methods are critically compared for the determination of long-lived radionuclides important for radiation protection, decommissioning of nuclear facilities, repository of nuclear waste, tracer application in the environmental and biological researches, these radionuclides include (3)H, (14)C, (36)Cl, (41)Ca, (59,63)Ni, (89,90)Sr, (99)Tc, (129)I, (135,137)Cs, (210)Pb, (226,228)Ra, (237)Np, (241)Am, and isotopes of thorium, uranium and plutonium. The application of on-line methods (flow injection/sequential injection) for separation of radionuclides and automated determination of radionuclides is also discussed.

  2. Relevant uses of surface proteins--display on self-organized biological structures.

    Science.gov (United States)

    Jahns, Anika C; Rehm, Bernd H A

    2012-03-01

    Proteins are often found attached to surfaces of self-assembling biological units such as whole microbial cells or subcellular structures, e.g. intracellular inclusions. In the last two decades surface proteins were identified that could serve as anchors for the display of foreign protein functions. Extensive protein engineering based on structure-function data enabled efficient display of technically and/or medically relevant protein functions. Small size, diversity of the anchor protein as well as support structure, genetic manipulability and controlled cultivation of phages, bacterial cells and yeasts contributed to the establishment of designed and specifically functionalized tools for applications as sensors, catalysis, biomedicine, vaccine development and library-based screening technologies. Traditionally, phage display is employed for library screening but applications in biomedicine and vaccine development are also perceived. For some diagnostic purposes phages are even too small in size so other carrier materials where needed and gave way for cell and yeast display. Only recently, intracellular inclusions such as magnetosomes, polyhydroxyalkanoate granules and lipid bodies were conceived as stable subcellular structures enabling the display of foreign protein functions and showing potential as specific and tailor-made devices for medical and biotechnological applications.

  3. 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.

  4. Environmental conditions and community evenness determine the outcome of biological invasion.

    Science.gov (United States)

    De Roy, Karen; Marzorati, Massimo; Negroni, Andrea; Thas, Olivier; Balloi, Annalisa; Fava, Fabio; Verstraete, Willy; Daffonchio, Daniele; Boon, Nico

    2013-01-01

    Biological invasion is widely studied, however, conclusions on the outcome of this process mainly originate from observations in systems that leave a large number of experimental variables uncontrolled. Here using a fully controlled system consisting of assembled bacterial communities, we evaluate the degree of invasion and the effect on the community functionality in relation to the initial community evenness under specific environmental stressors. We show that evenness influences the level of invasion and that the introduced species can promote functionality under stress. The evenness-invasibility relationship is negative in the absence and neutral in the presence of stress. Under these conditions, the introduced species is able to maintain the functionality of uneven communities. These results indicate that communities, initially having the same genetic background, in the presence of the same invader, react in a different way with respect to invasibility and functionality depending on specific environmental conditions and community evenness.

  5. Determining Chemical Reactivity Driving Biological Activity from SMILES Transformations: The Bonding Mechanism of Anti-HIV Pyrimidines

    Directory of Open Access Journals (Sweden)

    Mihai V. Putz

    2013-07-01

    Full Text Available Assessing the molecular mechanism of a chemical-biological interaction and bonding stands as the ultimate goal of any modern quantitative structure-activity relationship (QSAR study. To this end the present work employs the main chemical reactivity structural descriptors (electronegativity, chemical hardness, chemical power, electrophilicity to unfold the variational QSAR though their min-max correspondence principles as applied to the Simplified Molecular Input Line Entry System (SMILES transformation of selected uracil derivatives with anti-HIV potential with the aim of establishing the main stages whereby the given compounds may inhibit HIV infection. The bonding can be completely described by explicitly considering by means of basic indices and chemical reactivity principles two forms of SMILES structures of the pyrimidines, the Longest SMILES Molecular Chain (LoSMoC and the Branching SMILES (BraS, respectively, as the effective forms involved in the anti-HIV activity mechanism and according to the present work, also necessary intermediates in molecular pathways targeting/docking biological sites of interest.

  6. 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.

  7. Synthesis, Crystal Structure, Spectroscopic Properties and Potential Biological Activities of Salicylate‒Neocuproine Ternary Copper(II Complexes

    Directory of Open Access Journals (Sweden)

    Lenka Kucková

    2015-01-01

    Full Text Available Mixed ligand copper(II complexes containing derivatives of salicylic acid and heterocyclic ligands with nitrogen donor atoms have been the subject of various studies and reviews. In this paper, synthesis and characterization of the ternary copper(II complexes of neocuproine (2,9-dimethyl-1,10-phenanthroline, Neo and salicylate ligands (Sal are reported. In addition, the crystal structures of ([Cu(H2O(5-Cl-Sal(Neo] (1, [Cu(μ-Sal(Neo]2 (2, Cu2(μ-5-Cl-Sal(5-Cl-HSal2(Neo2]·EtOH (3 were determined. In order to compare structural and biological properties of the prepared complexes, spectroscopic and biological studies were performed. Results of X-ray diffraction show that prepared complexes form three types of crystal structures in a given system: monomeric, dimeric and dinuclear complex. The preliminary study on the DNA cleavage activity has shown that the complexes under study behave as the chemical nucleases in the presence of added hydrogen peroxide with slight differences in the activity (1 > 2 > 3. The complexes 1 and 2 exhibited nuclease activity itself indicating the interaction of complexes with the DNA. It has been proposed that the enhanced destructive effect of the complexes 1 and 2 on the DNA is a result of two possible mechanisms of action: (i the conversion of closed circular DNA (form I to the nicked DNA (form II caused by the copper complex itself and (ii damage of DNA by Reactive Oxygen Species (ROS—products of the interaction of copper with hydrogen peroxide by means of Fenton reaction (hydroxyl radicals. Thus the biological activity of the prepared Cu(II complexes containing derivatives of salicylic acid and phenanthroline molecules is substantiated by two independent mechanisms. While derivatives of salicylic acids in the coordination sphere of copper complexes are responsible for radical-scavenging activity (predominantly towards superoxide radical anion, the presence of chelating ligand 2,9-dimethyl-1,10-phenanthroline

  8. Protein Structure Determination by Assembling Super-Secondary Structure Motifs Using Pseudocontact Shifts.

    Science.gov (United States)

    Pilla, Kala Bharath; Otting, Gottfried; Huber, Thomas

    2017-03-07

    Computational and nuclear magnetic resonance hybrid approaches provide efficient tools for 3D structure determination of small proteins, but currently available algorithms struggle to perform with larger proteins. Here we demonstrate a new computational algorithm that assembles the 3D structure of a protein from its constituent super-secondary structural motifs (Smotifs) with the help of pseudocontact shift (PCS) restraints for backbone amide protons, where the PCSs are produced from different metal centers. The algorithm, DINGO-PCS (3D assembly of Individual Smotifs to Near-native Geometry as Orchestrated by PCSs), employs the PCSs to recognize, orient, and assemble the constituent Smotifs of the target protein without any other experimental data or computational force fields. Using a universal Smotif database, the DINGO-PCS algorithm exhaustively enumerates any given Smotif. We benchmarked the program against ten different protein targets ranging from 100 to 220 residues with different topologies. For nine of these targets, the method was able to identify near-native Smotifs.

  9. Determination of trace lead in biological and water samples with dispersive liquid-liquid microextraction preconcentration.

    Science.gov (United States)

    Liang, Pei; Sang, Hongbo

    2008-09-01

    A new method for the determination of trace lead was developed by dispersive liquid-liquid microextraction preconcentration and graphite furnace atomic absorption spectrometry. In the proposed approach, 1-phenyl-3-methyl-4-benzoyl-5-pyrazolone (PMBP) was used as a chelating agent, and carbon tetrachloride and ethanol were selected as extraction and dispersive solvents. Some factors influencing the extraction efficiency of lead and its subsequent determination, including extraction and dispersive solvent type and volume, pH of sample solution, concentration of the chelating agent, and extraction time, were studied and optimized. Under the optimum conditions, the enrichment factor of this method for lead was reached at 78. The detection limit for lead was 39 ng L(-1) (3 sigma), and the relative standard deviation (RSD) was 3.2% (n=7, c=10 ng mL(-1)). The method was successfully applied to the determination of trace amounts of lead in human urine and water samples.

  10. Kinetic spectrophotometric method for the determination of morphine in biological samples

    Science.gov (United States)

    Sheibani, A.; Shishehbore, M. Reza; Mirparizi, E.

    2010-10-01

    In this paper a simple, selective and inexpensive kinetic method was developed for the determination of morphine based on its inhibitory effect on the Janus green-bromate system in sulfuric acid media. The reaction was monitored spectrophotometrically at 618 nm by a fixed time method. The effect of different parameters such as concentration of reactants and temperature on the rate of reaction was investigated and optimum conditions were obtained. The calibration curve was linear in the concentration range 0.07-7.98 mg L -1 of morphine, and detection limit of the method was 3.0 × 10 -2 mg L -1. The relative standard deviation for five determinations of 3.74 mg L -1 of morphine was 0.57%. Finally, the proposed method was successfully applied to the determination of morphine in human urine and serum as real samples.

  11. Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser.

    Science.gov (United States)

    Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr; Bunker, Richard D; Stellato, Francesco; Chiu, Elaine; Yeh, Shin-Mei; Aquila, Andrew; Basu, Shibom; Bean, Richard; Beyerlein, Kenneth R; Botha, Sabine; Boutet, Sébastien; DePonte, Daniel P; Doak, R Bruce; Fromme, Raimund; Galli, Lorenzo; Grotjohann, Ingo; James, Daniel R; Kupitz, Christopher; Lomb, Lukas; Messerschmidt, Marc; Nass, Karol; Rendek, Kimberly; Shoeman, Robert L; Wang, Dingjie; Weierstall, Uwe; White, Thomas A; Williams, Garth J; Zatsepin, Nadia A; Fromme, Petra; Spence, John C H; Goldie, Kenneth N; Jehle, Johannes A; Metcalf, Peter; Barty, Anton; Chapman, Henry N

    2017-02-28

    To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm(3) in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm(3) in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.

  12. Development of a mild mercaptoethanol extraction method for determination of mercury species in biological samples by HPLC-ICP-MS.

    Science.gov (United States)

    Wang, Meng; Feng, Weiyue; Shi, Junwen; Zhang, Fang; Wang, Bing; Zhu, Motao; Li, Bai; Zhao, Yuliang; Chai, Zhifang

    2007-03-30

    A mild, efficient and convenient extraction method of using 2-mercaptoethanol contained extractant solution combined with an incubator shaker for determination of mercury species in biological samples by HPLC-ICP-MS has been developed. The effects of the concentration of 2-mercaptoethanol, the composition of the extractant solution and the shaking time on the efficiency of mercury extraction were evaluated. The optimization experiments indicated that the quantitative extraction of mercury species from biological samples could be achieved by using 0.1% (v/v) HCl, 0.1% (v/v) 2-mercapoethanol and 0.15% (m/v) KCl extractant solution in an incubator shaker for shaking overnight (about 12h) at room temperature. The established method was validated by analysis of various biological certified reference materials, including NRCC DOLT-3 (dogfish liver), IAEA 436 (tuna fish), IAEA MA-B-3/TM (garfish filet), IAEA MA-M-2/TM (mussel tissue), GBW 08193 (bovine liver) and GBW 08572 (prawn). The analytical results of the reference materials were in good agreement with the certified or reference values of both methyl and total mercury, indicating that no distinguishable transformation between mercury species had occurred during the extraction and determination procedures. The limit of detection (LOD) for methyl (CH(3)Hg(+)) and inorganic mercury (Hg(2+)) by the method are both as 0.2microg L(-1). The relative standard deviation (R.S.D.s) for CH(3)Hg(+) and Hg(2+) are 3.0% and 5.8%, respectively. The advantages of the developed extraction method are that (1) it is easy to operate in HPLC-ICP-MS for mercury species determination since the extracted solution can be directly injected into the HPLC column without pH adjustment and (2) the memory effect of mercury in the ICP-MS measurement system can be reduced.

  13. WHAT DETERMINES THE CAPITAL STRUCTURE OF LISTED FIRMS IN ROMANIA

    Directory of Open Access Journals (Sweden)

    Floriniţa Duca

    2012-10-01

    Full Text Available This paper examines the relative importance of four factors in the capital structure decisions of Romanian listed firms. The existing empirical research on capital structure has been largely confined to developed countries. The Romanian Financial Market has been developing at an exponential rate and dedicated research in the field is required. We used 100 firms listed in 2010 at the Bucharest Stock Exchange. The objective of this paper is to build on previous studies model all the important factors affecting capital structure decisions. We find that factors such as tangibility of assets, firm size, liquidity, and profitability have significant influences on the leverage structure chosen by firms.These results are believed to have significant implications for the theory of finance and to be of importance to the corporate treasure in choice of new financing and to the financial analyst.

  14. Crystal Structure of Mitochondrial Respiratory Membrane Protein Complex Ⅱ Determined

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ Scientists at the CAS Institute of Biophysics (IBP) and Tsinghua University have gained new insights into the mechanism of mitochondria, the subcellular structures which generate energy for living cells.

  15. Structural determinants of Smad function in TGF-β signaling.

    Science.gov (United States)

    Macias, Maria J; Martin-Malpartida, Pau; Massagué, Joan

    2015-06-01

    Smad transcription factors are central to the signal transduction pathway that mediates the numerous effects of the transforming growth factor β (TGF-β) superfamily of cytokines in metazoan embryo development as well as in adult tissue regeneration and homeostasis. Although Smad proteins are conserved, recent genome-sequencing projects have revealed their sequence variation in metazoan evolution, human polymorphisms, and cancer. Structural studies of Smads bound to partner proteins and target DNA provide a framework for understanding the significance of these evolutionary and pathologic sequence variations. We synthesize the extant mutational and structural data to suggest how genetic variation in Smads may affect the structure, regulation, and function of these proteins. We also present a web application that compares Smad sequences and displays Smad protein structures and their disease-associated variants.

  16. Strategies for structuring interdisciplinary education in Systems Biology: an European perspective

    NARCIS (Netherlands)

    Cvijovic, Marija; Höfer, Thomas; Acimovic, Jure; Alberghina, Lilia; Almaas, Eivind; Besozzi, Daniela; Blomberg, Anders; Bretschneider, Till; Cascante, Marta; Collin, Olivier; Atauri, de Pedro; Depner, Cornelia; Dickinson, Robert; Dobrzynski, Maciej; Fleck, C.; Garcia-Ojalvo, Jordi; Gonze, Didier; Hahn, Jens; Hess, Heide Marie; Hollmann, Susanne; Krantz, Marcus; Kummer, Ursula; Lundh, Torbjörn; Martial, Gifta; Martins dos Santos, V.A.P.; Mauer-Oberthür, Angela; Regierer, Babette; Skene, Barbara; Stalidzans, Egils; Stelling, Jörg; Teusink, Bas; Workman, Christopher T.; Hohmann, Stefan

    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 funct

  17. Biological and spatial structure of an early classic period cemetery at Charco Redondo, Oaxaca.

    Science.gov (United States)

    Paul, Kathleen S; Stojanowski, Christopher M; Butler, Michelle M

    2013-10-01

    This article presents an analysis of biological and spatial patterning of an Early Classic (A.D. 250-500) Chatino cemetery at the archaeological site of Charco Redondo, located in the lower Río Verde Valley, Oaxaca, Mexico. The Early Classic was a time of political instability positioned between two phases of state-level centralization within the coastal valley. The communal cemetery at Charco Redondo adds significantly to the inventory of excavated graves from this time period and provides novel data on mortuary practices during a critical phase in the development of state level polities in the region. Cluster analysis of mortuary data is combined with intracemetery biodistance approaches to reconstruct how the Charco Redondo cemetery was organized with respect to biological relationships. Cluster analysis of mortuary data identified three groupings of burials. Multidimensional scaling of Euclidean distances and Gower coefficients based on 45 odontometric and 13 dental morphological variables suggests a strong relationship between grave characteristics and locations and phenotypic variation. In other words, the cemetery at Charco Redondo appears biologically kin-structured. The communal nature of the cemetery conflicts with the assumed "household" burial model for this time period. We propose the observed combination of features represents a transitional practice in which aspects of community, kin, and individual identity were signaled simultaneously within the funerary environment during a time of political transition in the Valley. This article highlights the utility of intracemetery biodistance analyses for examining dimensions of kinship, "house," and community throughout Mesoamerica where overarching models often mask regional variability.

  18. Improving the chances of successful protein structure determination with a random forest classifier

    Energy Technology Data Exchange (ETDEWEB)

    Jahandideh, Samad [Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92307 (United States); Joint Center for Structural Genomics, (United States); Jaroszewski, Lukasz; Godzik, Adam, E-mail: adam@burnham.org [Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92307 (United States); Joint Center for Structural Genomics, (United States); University of California, San Diego, La Jolla, California (United States)

    2014-03-01

    Using an extended set of protein features calculated separately for protein surface and interior, a new version of XtalPred based on a random forest classifier achieves a significant improvement in predicting the success of structure determination from the primary amino-acid sequence. Obtaining diffraction quality crystals remains one of the major bottlenecks in structural biology. The ability to predict the chances of crystallization from the amino-acid sequence of the protein can, at least partly, address this problem by allowing a crystallographer to select homologs that are more likely to succeed and/or to modify the sequence of the target to avoid features that are detrimental to successful crystallization. In 2007, the now widely used XtalPred algorithm [Slabinski et al. (2007 ▶), Protein Sci.16, 2472–2482] was developed. XtalPred classifies proteins into five ‘crystallization classes’ based on a simple statistical analysis of the physicochemical features of a protein. Here, towards the same goal, advanced machine-learning methods are applied and, in addition, the predictive potential of additional protein features such as predicted surface ruggedness, hydrophobicity, side-chain entropy of surface residues and amino-acid composition of the predicted protein surface are tested. The new XtalPred-RF (random forest) achieves significant improvement of the prediction of crystallization success over the original XtalPred. To illustrate this, XtalPred-RF was tested by revisiting target selection from 271 Pfam families targeted by the Joint Center for Structural Genomics (JCSG) in PSI-2, and it was estimated that the number of targets entered into the protein-production and crystallization pipeline could have been reduced by 30% without lowering the number of families for which the first structures were solved. The prediction improvement depends on the subset of targets used as a testing set and reaches 100% (i.e. twofold) for the top class of predicted

  19. Sex determination of Joseon people skeletons based on anatomical, cultural and molecular biological clues.

    Science.gov (United States)

    Kim, Yi-Suk; Oh, Chang Seok; Lee, Sang Jun; Park, Jun Bum; Kim, Myeung Ju; Shin, Dong Hoon

    2011-12-20

    Sex determination is very integral to examinations conducted by anatomists on human skeletons discovered in the archaeological field. In Korea, as in other countries, cultural or anatomical information has been the tool of first resort in making such determinations. In cases in which anatomical examination has revealed only borderline characteristics, PCR-based analysis of X/Y-chromosome genes has been employed. Even so, there are as yet very few reports on how accurately the respective results correspond with each other. In this study on 34 examined medieval Korean skeletons, 11 (32.3%) showed perfectly matching results for the three methods of sex determination. In the cases in which the cultural and anatomical findings were discordant, the amelogenin assay corroborated either the former or the latter. Although we must admit the relatively limited role of aDNA analysis, when only very small amounts of amplifiable DNA remain, we believe that the amelogenin assay can be very meaningful to Korean anatomists when employed in adjunct to conventional anatomically or culturally based sex determination.

  20. Determining Enzyme Kinetics for Systems Biology with Nuclear Magnetic Resonance Spectroscopy

    Directory of Open Access Journals (Sweden)

    Johann J. Eicher

    2012-11-01

    Full Text Available Enzyme kinetics for systems biology should ideally yield information about the enzyme’s activity under in vivo conditions, including such reaction features as substrate cooperativity, reversibility and allostery, and be applicable to enzymatic reactions with multiple substrates. A large body of enzyme-kinetic data in the literature is based on the uni-substrate Michaelis–Menten equation, which makes unnatural assumptions about enzymatic reactions (e.g., irreversibility, and its application in systems biology models is therefore limited. To overcome this limitation, we have utilised NMR time-course data in a combined theoretical and experimental approach to parameterize the generic reversible Hill equation, which is capable of describing enzymatic reactions in terms of all the properties mentioned above and has fewer parameters than detailed mechanistic kinetic equations; these parameters are moreover defined operationally. Traditionally, enzyme kinetic data have been obtained from initial-rate studies, often using assays coupled to NAD(PH-producing or NAD(PH-consuming reactions. However, these assays are very labour-intensive, especially for detailed characterisation of multi-substrate reactions. We here present a cost-effective and relatively rapid method for obtaining enzyme-kinetic parameters from metabolite time-course data generated using NMR spectroscopy. The method requires fewer runs than traditional initial-rate studies and yields more information per experiment, as whole time-courses are analyzed and used for parameter fitting. Additionally, this approach allows real-time simultaneous quantification of all metabolites present in the assay system (including products and allosteric modifiers, which demonstrates the superiority of NMR over traditional spectrophotometric coupled enzyme assays. The methodology presented is applied to the elucidation of kinetic parameters for two coupled glycolytic enzymes from Escherichia coli