WorldWideScience

Sample records for dynamic studies biological

  1. 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.

  2. Nonlinear dynamics in biological systems

    CERN Document Server

    Carballido-Landeira, Jorge

    2016-01-01

    This book presents recent research results relating to applications of nonlinear dynamics, focusing specifically on four topics of wide interest: heart dynamics, DNA/RNA, cell mobility, and proteins. The book derives from the First BCAM Workshop on Nonlinear Dynamics in Biological Systems, held in June 2014 at the Basque Center of Applied Mathematics (BCAM). At this international meeting, researchers from different but complementary backgrounds, including molecular dynamics, physical chemistry, bio-informatics and biophysics, presented their most recent results and discussed the future direction of their studies using theoretical, mathematical modeling and experimental approaches. Such was the level of interest stimulated that the decision was taken to produce this publication, with the organizers of the event acting as editors. All of the contributing authors are researchers working on diverse biological problems that can be approached using nonlinear dynamics. The book will appeal especially to applied math...

  3. Evolutionary Dynamics of Biological Games

    Science.gov (United States)

    Nowak, Martin A.; Sigmund, Karl

    2004-02-01

    Darwinian dynamics based on mutation and selection form the core of mathematical models for adaptation and coevolution of biological populations. The evolutionary outcome is often not a fitness-maximizing equilibrium but can include oscillations and chaos. For studying frequency-dependent selection, game-theoretic arguments are more appropriate than optimization algorithms. Replicator and adaptive dynamics describe short- and long-term evolution in phenotype space and have found applications ranging from animal behavior and ecology to speciation, macroevolution, and human language. Evolutionary game theory is an essential component of a mathematical and computational approach to biology.

  4. Evolutionary Dynamics of Biological Games

    OpenAIRE

    Nowak, M. A.; Sigmund, K.

    2004-01-01

    Darwinian dynamics based on mutation and selection from the core of mathematical models for adaptation and coevolution of biological populations. The evolutionary outcome is often not a fitness-maximizing equilibrium but can include oscillations and chaos. For studying frequency-dependent selection, game-theoretic arguments are more appropriate than optimization algorithms. Replicator and adaptive dynamics describe short-and long-term evolution in phenotype space and have found applications r...

  5. 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.

  6. Molecular dynamics study of accelerated ion-induced shock waves in biological media

    CERN Document Server

    de Vera, Pablo; Currell, Fred J; Solov'yov, Andrey V

    2016-01-01

    We present a molecular dynamics study of the effects of carbon- and iron-ion induced shock waves in DNA duplexes in liquid water. We use the CHARMM force field implemented within the MBN Explorer simulation package to optimize and equilibrate DNA duplexes in liquid water boxes of different sizes and shapes. The translational and vibrational degrees of freedom of water molecules are excited according to the energy deposited by the ions and the subsequent shock waves in liquid water are simulated. The pressure waves generated are studied and compared with an analytical hydrodynamics model which serves as a benchmark for evaluating the suitability of the simulation boxes. The energy deposition in the DNA backbone bonds is also monitored as an estimation of biological damage, something which lies beyond the possibilities of the analytical model.

  7. Study on the Dynamic Biological Characteristics of Sca-1+ Hematopoietic Stem and Progenitor Cell Senescence

    Directory of Open Access Journals (Sweden)

    Shan Geng

    2015-01-01

    Full Text Available The researches in the dynamic changes of the progress of HSCs aging are very limited and necessary. In this study, male C57BL/6 mice were divided into 5 groups by age. We found that the superoxide damage of HSPCs started to increase from the middle age (6 months old, with notably reduced antioxidation ability. In accordance with that, the senescence of HSPCs also started from the middle age, since the self-renewal and differentiation ability remarkably decreased, and senescence-associated markers SA-β-GAL increased in the 6-month-old and the older groups. Interestingly, the telomere length and telomerase activity increased to a certain degree in the 6-month-old group. It suggested an intrinsic spontaneous ability of HSPCs against aging. It may provide a theoretical and experimental foundation for better understanding the senescence progress of HSPCs. And the dynamic biological characteristics of HSPCs senescence may also contribute to the clinical optimal time for antiaging drug intervention.

  8. Network dynamics and systems biology

    Science.gov (United States)

    Norrell, Johannes A.

    The physics of complex systems has grown considerably as a field in recent decades, largely due to improved computational technology and increased availability of systems level data. One area in which physics is of growing relevance is molecular biology. A new field, systems biology, investigates features of biological systems as a whole, a strategy of particular importance for understanding emergent properties that result from a complex network of interactions. Due to the complicated nature of the systems under study, the physics of complex systems has a significant role to play in elucidating the collective behavior. In this dissertation, we explore three problems in the physics of complex systems, motivated in part by systems biology. The first of these concerns the applicability of Boolean models as an approximation of continuous systems. Studies of gene regulatory networks have employed both continuous and Boolean models to analyze the system dynamics, and the two have been found produce similar results in the cases analyzed. We ask whether or not Boolean models can generically reproduce the qualitative attractor dynamics of networks of continuously valued elements. Using a combination of analytical techniques and numerical simulations, we find that continuous networks exhibit two effects---an asymmetry between on and off states, and a decaying memory of events in each element's inputs---that are absent from synchronously updated Boolean models. We show that in simple loops these effects produce exactly the attractors that one would predict with an analysis of the stability of Boolean attractors, but in slightly more complicated topologies, they can destabilize solutions that are stable in the Boolean approximation, and can stabilize new attractors. Second, we investigate ensembles of large, random networks. Of particular interest is the transition between ordered and disordered dynamics, which is well characterized in Boolean systems. Networks at the

  9. Dynamical systems in population biology

    CERN Document Server

    Zhao, Xiao-Qiang

    2017-01-01

    This research monograph provides an introduction to the theory of nonautonomous semiflows with applications to population dynamics. It develops dynamical system approaches to various evolutionary equations such as difference, ordinary, functional, and partial differential equations, and pays more attention to periodic and almost periodic phenomena. The presentation includes persistence theory, monotone dynamics, periodic and almost periodic semiflows, basic reproduction ratios, traveling waves, and global analysis of prototypical population models in ecology and epidemiology. Research mathematicians working with nonlinear dynamics, particularly those interested in applications to biology, will find this book useful. It may also be used as a textbook or as supplementary reading for a graduate special topics course on the theory and applications of dynamical systems. Dr. Xiao-Qiang Zhao is a University Research Professor at Memorial University of Newfoundland, Canada. His main research interests involve applied...

  10. Abstracting the dynamics of biological pathways using information theory: a case study of apoptosis pathway.

    Science.gov (United States)

    Palaniappan, Sucheendra K; Bertaux, François; Pichené, Matthieu; Fabre, Eric; Batt, Gregory; Genest, Blaise

    2017-07-01

    Quantitative models are increasingly used in systems biology. Usually, these quantitative models involve many molecular species and their associated reactions. When simulating a tissue with thousands of cells, using these large models becomes computationally and time limiting. In this paper, we propose to construct abstractions using information theory notions. Entropy is used to discretize the state space and mutual information is used to select a subset of all original variables and their mutual dependencies. We apply our method to an hybrid model of TRAIL-induced apoptosis in HeLa cell. Our abstraction, represented as a Dynamic Bayesian Network (DBN), reduces the number of variables from 92 to 10, and accelerates numerical simulation by an order of magnitude, yet preserving essential features of cell death time distributions. This approach is implemented in the tool DBNizer, freely available at http://perso.crans.org/genest/DBNizer . gregory.batt@inria.fr or bgenest@irisa.fr. Supplementary data are available at Bioinformatics online.

  11. Indirect biological measures of consciousness from field studies of brains as dynamical systems.

    Science.gov (United States)

    Freeman, Walter J

    2007-11-01

    Consciousness fully supervenes when the 1.5 kgm mass of protoplasm in the head directs the body into material and social environments and engages in reciprocity. While consciousness is not susceptible to direct measurement, a limited form exercised in animals and pre-lingual children can be measured indirectly with biological assays of arousal, intention and attention. In this essay consciousness is viewed as operating simultaneously in a field at all levels ranging from subatomic to social. The relations and transpositions between levels require sophisticated mathematical treatments that are largely still to be devised. In anticipation of those developments the available experimental data are reviewed concerning the state variables in several levels that collectively constitute the substrate of biological consciousness. The basic metaphors are described that represent the neural machinery of transposition in consciousness. The processes are sketched by which spatiotemporal neural activity patterns emerge as fields that may represent the contents of consciousness. The results of dynamical analysis are discussed in terms serving to distinguish between the neural point processes dictated by the neuron doctrine vs. continuously variable neural fields generated by neural masses in cortex.

  12. Life at extreme conditions: Neutron scattering studies of biological molecules suggest that evolution selected dynamics

    Indian Academy of Sciences (India)

    Joseph (Giuseppe) Zaccai

    2008-10-01

    The short review concentrates on recent work performed at the neutrons in biology laboratories of the Institut Laue Langevin and Institut de Biologie Structurale in Grenoble. Extremophile organisms have been discovered that require extreme conditions of temperature, pressure or solvent environment for survival. The existence of such organisms poses a significant challenge in understanding the physical chemistry of their proteins, in view of the great sensitivity of protein structure and stability to the aqueous environment and to external conditions in general. Results of neutron scattering measurements on the dynamics of proteins from extremophile organisms, in vitro as well as in vivo, indicated remarkably how adaptation to extreme conditions involves forces and fluctuation amplitudes that have been selected specifically, suggesting that evolutionary macromolecular selection proceeded via dynamics. The experiments were performed on a halophilic protein, and membrane adapted to high salt, a thermophilic enzyme adapted to high temperature and its mesophilic (adapted to 37°C) homologue; and in vivo for psychrophilic, mesophilic, thermophilic and hyperthermophilic bacteria, adapted respectively to temperatures of 4°C, 37°C, 75°C and 85°C. Further work demonstrated the existence of a water component of exceptionally low mobility in an extreme halophile from the Dead Sea, which is not present in mesophile bacterial cells.

  13. Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology

    CERN Document Server

    Sushko, Gennady B; Verkhovtsev, Alexey V; Volkov, Sergey N; Solov'yov, Andrey V

    2015-01-01

    The concept of molecular mechanics force field has nowadays been widely accepted for studying various processes in biomolecular systems. In this paper we suggest a modification for the standard CHARMM force field, that permits simulations of systems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popular program MBN Explorer, and, to support the development, in this paper we provide several case studies where dynamical topology is necessary. In particular, it is shown, that the modified molecular mechanics force field can be applied for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation or collision induced damage, transformation and fragmentation processes involving biomolecular systems.

  14. BETAview: a digital {beta}-imaging system for dynamic studies of biological phenomena

    Energy Technology Data Exchange (ETDEWEB)

    Bertolucci, E.; Conti, M.; Mettivier, G.; Montesi, M.C. E-mail: montesi@na.infn.it; Russo, P

    2002-02-01

    We present a digital autoradiography (DAR) system, named BETAview, based on semiconductor pixel detectors and a single particle counting chip, for quantitative analysis of {beta}-emitting radioactive tracers in biological samples. The system is able to perform a real time monitoring of time-dependent biological phenomena. BETAview could be equipped either with GaAs or with Si semiconductor pixellated detectors. In this paper, we describe the results obtained with an assembly based on a Si detector, 300 {mu}m thick, segmented into 64x64 170 {mu}m size square pixels. The detector is bump-bonded to the low threshold, single particle counting chip named Medipix1, developed by a CERN-based European collaboration. The sensitive area is about 1 cm{sup 2}. Studies of background noise and detection efficiency have been performed. Moreover, time-resolved cellular uptake studies with radiolabelled molecules have been monitored. Specifically, we have followed in vivo and in real time, the [{sup 14}C]L-leucine amino acid uptake by eggs of Octopus vulgaris confirming the preliminary results of a previous paper. This opens the field of biomolecular kynetic studies with this new class of semiconductor DAR systems, whose evolution (using the Medipix2 chip, 256x256 pixels, 55 {mu}m pixel size) is soon to come.

  15. An optimization framework of biological dynamical systems.

    Science.gov (United States)

    Horie, Ryota

    2008-07-07

    Different biological dynamics are often described by different mathematical equations. On the other hand, some mathematical models describe many biological dynamics universally. Here, we focus on three biological dynamics: the Lotka-Volterra equation, the Hopfield neural networks, and the replicator equation. We describe these three dynamical models using a single optimization framework, which is constructed with employing the Riemannian geometry. Then, we show that the optimization structures of these dynamics are identical, and the differences among the three dynamics are only in the constraints of the optimization. From this perspective, we discuss the unified view for biological dynamics. We also discuss the plausible categorizations, the fundamental nature, and the efficient modeling of the biological dynamics, which arise from the optimization perspective of the dynamical systems.

  16. Molecular dynamics modeling the synthetic and biological polymers interactions pre-studied via docking

    Science.gov (United States)

    Tsvetkov, Vladimir B.; Serbin, Alexander V.

    2014-06-01

    In previous works we reported the design, synthesis and in vitro evaluations of synthetic anionic polymers modified by alicyclic pendant groups (hydrophobic anchors), as a novel class of inhibitors of the human immunodeficiency virus type 1 ( HIV-1) entry into human cells. Recently, these synthetic polymers interactions with key mediator of HIV-1 entry-fusion, the tri-helix core of the first heptad repeat regions [ HR1]3 of viral envelope protein gp41, were pre-studied via docking in terms of newly formulated algorithm for stepwise approximation from fragments of polymeric backbone and side-group models toward real polymeric chains. In the present article the docking results were verified under molecular dynamics ( MD) modeling. In contrast with limited capabilities of the docking, the MD allowed of using much more large models of the polymeric ligands, considering flexibility of both ligand and target simultaneously. Among the synthesized polymers the dinorbornen anchors containing alternating copolymers of maleic acid were selected as the most representative ligands (possessing the top anti-HIV activity in vitro in correlation with the highest binding energy in the docking). To verify the probability of binding of the polymers with the [HR1]3 in the sites defined via docking, various starting positions of polymer chains were tried. The MD simulations confirmed the main docking-predicted priority for binding sites, and possibilities for axial and belting modes of the ligands-target interactions. Some newly MD-discovered aspects of the ligand's backbone and anchor units dynamic cooperation in binding the viral target clarify mechanisms of the synthetic polymers anti-HIV activity and drug resistance prevention.

  17. Biologic response of inguinal hernia prosthetics: a comparative study of conventional static meshes versus 3D dynamic implants.

    Science.gov (United States)

    Amato, Giuseppe; Romano, Giorgio; Agrusa, Antonino; Marasa, Salvatore; Cocorullo, Gianfranco; Gulotta, Gaspare; Goetze, Thorsten; Puleio, Roberto

    2015-01-01

    Despite improvements in prosthetics and surgical techniques, the rate of complications following inguinal hernia repair remains high. Among these, discomfort and chronic pain have become a source of increasing concern among surgeons. Poor quality of tissue ingrowth, such as thin scar plates or shrinking scars-typical results with conventional static implants and plugs-may contribute to these adverse events. Recently, a new type of 3D dynamically responsive implant was introduced to the market. This device, designed to be placed fixation-free, seems to induce ingrowth of viable and structured tissue instead of regressive fibrotic scarring. To elucidate the differences in biologic response between the conventional static meshes and this 3D dynamically responsive implant, a histological comparison was planned. The aim of this study was to determine the quality of tissue incorporation in both types of implants excised after short, medium, and long periods post-implantation. The results showed large differences in the biologic responses between the two implant types. Histologically, the 3D dynamic implant showed development of tissue elements more similar to natural abdominal wall structures, such as the ingrowth of loose and well-hydrated connective tissue, well-formed vascular structures, elastic fibers, and mature nerves, with negligible or absent inflammatory response. All these characteristics were completely absent in the conventional static implants, where a persistent inflammatory reaction was associated with thin, hardened, and shrunken fibrotic scar formation. Consequently, as herniation is a degenerative process, the 3D dynamic implants, which induce regeneration of the typical groin components, seem to address its pathogenesis.

  18. Elaboration of station DICSI at KCSR and NT for studies on structural dynamics of biological objects

    Energy Technology Data Exchange (ETDEWEB)

    Korneev, V.N. [Institute of Cell Biophysics, RAS, 142290 Pushchino (Russian Federation)]. E-mail: korneev@icb.psn.ru; Shlektarev, V.A. [Institute of Theoretical and Experimental Biophysics, RAS, Institutskaya ul. 3, 142290 Pushchino (Russian Federation); Zabelin, A.V. [FSI, RRC ' Kurchatov Institute' , 123182 Moscow (Russian Federation); Medvedev, B.I. [Institute of Theoretical and Experimental Biophysics, RAS, Institutskaya ul. 3, 142290 Pushchino (Russian Federation); Sharafutdinov, M.R. [Institute of Solid State Chemistry and Mechanochemistry of SB, RAS, 630090 Novosibirsk (Russian Federation); Tolochko, V.P. [Institute of Solid State Chemistry and Mechanochemistry of SB, RAS, 630090 Novosibirsk (Russian Federation); Sheromov, M.A. [Budker Institute of Nuclear Physics of SB RAS, 630090 Novosibirsk (Russian Federation); Kondratyev, V.I. [Budker Institute of Nuclear Physics of SB RAS, 630090 Novosibirsk (Russian Federation); Umnov, A.I. [Institute of Cell Biophysics, RAS, 142290 Pushchino (Russian Federation); Vazina, A.A. [Institute of Theoretical and Experimental Biophysics, RAS, Institutskaya ul. 3, 142290 Pushchino (Russian Federation)

    2007-05-21

    In this article, the results of the experimental and theoretical developments for equipping the station 'DICSI', created on channel K1.3 (a) of the (Siberia-2) storage ring of the Kurchatov Centre for Synchrotron Radiation and Nanotechnology are considered. Argumentation for the basic parameters of the X-ray optical systems is given, photos and the schemes of created equipments are presented, in addition, the results of the test experiments with the biological objects are considered.

  19. Application of Wavelet-Based Tools to Study the Dynamics of Biological Processes

    DEFF Research Database (Denmark)

    Pavlov, A. N.; Makarov, V. A.; Mosekilde, Erik

    2006-01-01

    The article makes use of three different examples (sensory information processing in the rat trigeminal complex, intracellular interaction in snail neurons and multimodal dynamics in nephron autoregulation) to demonstrate how modern approaches to time-series analysis based on the wavelet...

  20. Green Algae as Model Organisms for Biological Fluid Dynamics.

    Science.gov (United States)

    Goldstein, Raymond E

    2015-01-01

    In the past decade the volvocine green algae, spanning from the unicellular Chlamydomonas to multicellular Volvox, have emerged as model organisms for a number of problems in biological fluid dynamics. These include flagellar propulsion, nutrient uptake by swimming organisms, hydrodynamic interactions mediated by walls, collective dynamics and transport within suspensions of microswimmers, the mechanism of phototaxis, and the stochastic dynamics of flagellar synchronization. Green algae are well suited to the study of such problems because of their range of sizes (from 10 μm to several millimetres), their geometric regularity, the ease with which they can be cultured and the availability of many mutants that allow for connections between molecular details and organism-level behavior. This review summarizes these recent developments and highlights promising future directions in the study of biological fluid dynamics, especially in the context of evolutionary biology, that can take advantage of these remarkable organisms.

  1. Dynamics of biomolecules, ligand binding & biological functions

    Science.gov (United States)

    Yi, Myunggi

    Proteins are flexible and dynamic. One static structure alone does not often completely explain biological functions of the protein, and some proteins do not even have high resolution structures. In order to provide better understanding to the biological functions of nicotinic acetylcholine receptor, Diphtheria toxin repressor and M2 proton channel, the dynamics of these proteins are investigated using molecular modeling and molecular dynamics (MD) simulations. With absence of high resolution structure of alpha7 receptor, the homology models of apo and cobra toxin bound forms have been built. From the MD simulations of these model structures, we observed one subunit of apo simulation moved away from other four subunits. With local movement of flexible loop regions, the whole subunit tilted clockwise. These conformational changes occurred spontaneously, and were strongly correlated with the conformational change when the channel is activated by agonists. Unlike other computational studies, we directly compared our model of open conformation with the experimental data. However, the subunits of toxin bound form were stable, and conformational change is restricted by the bound cobra toxin. These results provide activation and inhibition mechanisms of alpha7 receptors and a possible explanation for intermediate conductance of the channel. Intramolecular complex of SH3-like domain with a proline-rich (Pr) peptide segment in Diphtheria toxin repressor (DtxR) is stabilized in inactive state. Upon activation of DtxR by transition metal binding, this intramolecular complex should be dissociated. The dynamics of this intramolecular complex is investigated using MD simulations and NMR spectroscopy. We observed spontaneous opening and closing motions of the Pr segment binding pockets in both Pr-SH3 and SH3 simulations. The MD simulation results and NMR relaxation data suggest that the Pr segment exhibits a binding ↔ unbinding equilibrium. Despite a wealth of experimental

  2. Molecular Dynamics Simulations of DNA Translocation through a biological Nanopore

    OpenAIRE

    Barder, Simen Eidsmo

    2012-01-01

    Experimental and simulation studies of nucleic acid transport through nanosized channels, both biological and synthetic, has become a rapidly growing research area over the last decade. While the utilization of the alpha-hemolysin channel as a sequencing device is soon to be realized, other biological nanochannels may hold advantages that are yet unknown. Motivated by this, the first reported molecular dynamics simulations of DNA translocation through a connexon 26 channel were accomplished, ...

  3. From Coupled Dynamical Systems to Biological Irreversibility

    OpenAIRE

    Kaneko, Kunihiko

    2002-01-01

    In the first half of the paper, some recent advances in coupled dynamical systems, in particular, a globally coupled map are surveyed. First, dominance of Milnor attractors in partially ordered phase is demonstrated. Second, chaotic itinerancy in high-dimensional dynamical systems is briefly reviewed, with discussion on a possible connection with a Milnor attractor network. Third, infinite-dimensional collective dynamics is studied, in the thermodynamic limit of the globally coupled map, wher...

  4. Relevance of Dynamic Clustering to Biological Networks

    CERN Document Server

    Kaneko, K

    1993-01-01

    Abstract Network of nonlinear dynamical elements often show clustering of synchronization by chaotic instability. Relevance of the clustering to ecological, immune, neural, and cellular networks is discussed, with the emphasis of partially ordered states with chaotic itinerancy. First, clustering with bit structures in a hypercubic lattice is studied. Spontaneous formation and destruction of relevant bits are found, which give self-organizing, and chaotic genetic algorithms. When spontaneous changes of effective couplings are introduced, chaotic itinerancy of clusterings is widely seen through a feedback mechanism, which supports dynamic stability allowing for complexity and diversity, known as homeochaos. Second, synaptic dynamics of couplings is studied in relation with neural dynamics. The clustering structure is formed with a balance between external inputs and internal dynamics. Last, an extension allowing for the growth of the number of elements is given, in connection with cell differentiation. Effecti...

  5. A population dynamics approach to biological aging

    Science.gov (United States)

    de Almeida, R. M. C.

    A dynamical model for aging in biological population is discussed where asexual reproduction is considered. The maximum life span is inherited from parent to offspring with some random mutations described by a transition matrix, and the fertile period begins at a defined age R. The intra species competition is modeled through a Verhulst-like factor. Discrete time evolution equations are iterated and the transient and asymptotic solutions are obtained. When only bad mutations are taken into account, the stationary solutions are obtained analytically. The results are applied to the Penna model.

  6. Enhanced sampling techniques in molecular dynamics simulations of biological systems.

    Science.gov (United States)

    Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus

    2015-05-01

    Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. From total suspended solids to molecular biology tools--a personal view of biological wastewater treatment process population dynamics.

    Science.gov (United States)

    Jenkins, David

    2008-08-01

    The development of the tools needed to study the population dynamics of biological wastewater treatment processes is traced from its beginnings in the early 1900s to today's use of molecular biology tools (Oerther and Love, 2003). Examples of the benefits of population dynamics research in improving the performance and aiding the design and operation of biological wastewater treatment processes are given. Some thoughts on future areas of study are presented.

  8. Biological studies of dysthymia.

    Science.gov (United States)

    Howland, R H; Thase, M E

    1991-08-01

    Dysthymic disorder (DD) is a chronic subsyndromal depressive condition that has generated increasing interest since its formal introduction into the psychiatric nomenclature in 1980. Although DD was included among the affective disorders in DSM-III, this classification was controversial. Some clinical and family studies support an association between DD and major depression disorder (MDD), but there has been little additional research firmly establishing the diagnostic validity of DD or clarifying its relation to MDD and to personality disorders. In this article, the literature on the biology of DD is reviewed. Studies of rapid eye movement (REM) latency, electrodermal activity, and the thyroid axis show similarities between DD and MDD, but the findings are mixed. Other investigations, including the Dexamethasone Suppression Test (DST), catecholamines, and several other electroencephalogram (EEG) sleep variables, show more consistent differences between DD and MDD. These findings suggest that DD manifests primarily trait characteristics of depression, thus differentiating it from the state characteristics of MDD. The methodological problems and implications of these studies, and suggestions for future research, are discussed.

  9. Activating and inhibiting connections in biological network dynamics

    Directory of Open Access Journals (Sweden)

    Knight Rob

    2008-12-01

    Full Text Available Abstract Background Many studies of biochemical networks have analyzed network topology. Such work has suggested that specific types of network wiring may increase network robustness and therefore confer a selective advantage. However, knowledge of network topology does not allow one to predict network dynamical behavior – for example, whether deleting a protein from a signaling network would maintain the network's dynamical behavior, or induce oscillations or chaos. Results Here we report that the balance between activating and inhibiting connections is important in determining whether network dynamics reach steady state or oscillate. We use a simple dynamical model of a network of interacting genes or proteins. Using the model, we study random networks, networks selected for robust dynamics, and examples of biological network topologies. The fraction of activating connections influences whether the network dynamics reach steady state or oscillate. Conclusion The activating fraction may predispose a network to oscillate or reach steady state, and neutral evolution or selection of this parameter may affect the behavior of biological networks. This principle may unify the dynamics of a wide range of cellular networks. Reviewers Reviewed by Sergei Maslov, Eugene Koonin, and Yu (Brandon Xia (nominated by Mark Gerstein. For the full reviews, please go to the Reviewers' comments section.

  10. Developmental dynamics: toward a biologically plausible evolutionary psychology.

    Science.gov (United States)

    Lickliter, Robert; Honeycutt, Hunter

    2003-11-01

    There has been a conceptual revolution in the biological sciences over the past several decades. Evidence from genetics, embryology, and developmental biology has converged to offer a more epigenetic, contingent, and dynamic view of how organisms develop. Despite these advances, arguments for the heuristic value of a gene-centered, predeterministic approach to the study of human behavior and development have become increasingly evident in the psychological sciences during this time. In this article, the authors review recent advances in genetics, embryology, and developmental biology that have transformed contemporary developmental and evolutionary theory and explore how these advances challenge gene-centered explanations of human behavior that ignore the complex, highly coordinated system of regulatory dynamics involved in development and evolution.

  11. In-silico screening for DNA-dependent protein kinase (DNA-PK) inhibitors: Combined homology modeling, docking, molecular dynamic study followed by biological investigation.

    Science.gov (United States)

    Tarazi, Hamadeh; Saleh, Ekram; El-Awady, Raafat

    2016-10-01

    DNA-dependent protein kinase (DNA-PK) is a key enzyme in non-homologous DNA end joining (NHEJ) repair pathway. The targeted inhibition of such enzyme would furnish a valuable option for cancer treatment. In this study we report the development of validation of enzyme homology model, and the subsequent use of this model to perform docking-based virtual screening against a database of FDA-approved drugs. The nominated highest ranking hits (Praziquantel and Dutasteride) were subjected to biological investigation. Additionally, molecular dynamic study was carried-out for binding mode exploration. Results of the biological evaluation revealed that both compounds inhibit the DNA-PK enzymatic activity at relatively high concentration levels with an IC50 of 17.3μM for praziquantel and >20μM for dutasteride. Furthermore, both agents enhanced the anti-proliferative effects of doxorubicin and cisplatin on breast cancer (MCF7) and lung cancer (A549) cell lines. This result indicates that these two hits are good candidate as DNA-PK inhibitors and worth further structural modifications to enhance their enzyme inhibitory effects. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  12. Mammalian synthetic biology for studying the cell.

    Science.gov (United States)

    Mathur, Melina; Xiang, Joy S; Smolke, Christina D

    2017-01-02

    Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology. © 2017 Mathur et al.

  13. Introduction to focus issue: dynamics in systems biology.

    Science.gov (United States)

    Brackley, Chris A; Ebenhöh, Oliver; Grebogi, Celso; Kurths, Jürgen; de Moura, Alessandro; Romano, M Carmen; Thiel, Marco

    2010-12-01

    The methods of nonlinear systems form an extensive toolbox for the study of biology, and systems biology provides a rich source of motivation for the development of new mathematical techniques and the furthering of understanding of dynamical systems. This Focus Issue collects together a large variety of work which highlights the complementary nature of these two fields, showing what each has to offer the other. While a wide range of subjects is covered, the papers often have common themes such as "rhythms and oscillations," "networks and graph theory," and "switches and decision making." There is a particular emphasis on the links between experimental data and modeling and mathematical analysis.

  14. Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data.

    Science.gov (United States)

    Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H L; Onami, Shuichi

    2015-04-01

    Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  15. Dynamics of mathematical models in biology bringing mathematics to life

    CERN Document Server

    Zazzu, Valeria; Guarracino, Mario

    2016-01-01

    This volume focuses on contributions from both the mathematics and life science community surrounding the concepts of time and dynamicity of nature, two significant elements which are often overlooked in modeling process to avoid exponential computations. The book is divided into three distinct parts: dynamics of genomes and genetic variation, dynamics of motifs, and dynamics of biological networks. Chapters included in dynamics of genomes and genetic variation analyze the molecular mechanisms and evolutionary processes that shape the structure and function of genomes and those that govern genome dynamics. The dynamics of motifs portion of the volume provides an overview of current methods for motif searching in DNA, RNA and proteins, a key process to discover emergent properties of cells, tissues, and organisms. The part devoted to the dynamics of biological networks covers networks aptly discusses networks in complex biological functions and activities that interpret processes in cells. Moreover, chapters i...

  16. Sensitivity analysis of dynamic biological systems with time-delays.

    Science.gov (United States)

    Wu, Wu Hsiung; Wang, Feng Sheng; Chang, Maw Shang

    2010-10-15

    Mathematical modeling has been applied to the study and analysis of complex biological systems for a long time. Some processes in biological systems, such as the gene expression and feedback control in signal transduction networks, involve a time delay. These systems are represented as delay differential equation (DDE) models. Numerical sensitivity analysis of a DDE model by the direct method requires the solutions of model and sensitivity equations with time-delays. The major effort is the computation of Jacobian matrix when computing the solution of sensitivity equations. The computation of partial derivatives of complex equations either by the analytic method or by symbolic manipulation is time consuming, inconvenient, and prone to introduce human errors. To address this problem, an automatic approach to obtain the derivatives of complex functions efficiently and accurately is necessary. We have proposed an efficient algorithm with an adaptive step size control to compute the solution and dynamic sensitivities of biological systems described by ordinal differential equations (ODEs). The adaptive direct-decoupled algorithm is extended to solve the solution and dynamic sensitivities of time-delay systems describing by DDEs. To save the human effort and avoid the human errors in the computation of partial derivatives, an automatic differentiation technique is embedded in the extended algorithm to evaluate the Jacobian matrix. The extended algorithm is implemented and applied to two realistic models with time-delays: the cardiovascular control system and the TNF-α signal transduction network. The results show that the extended algorithm is a good tool for dynamic sensitivity analysis on DDE models with less user intervention. By comparing with direct-coupled methods in theory, the extended algorithm is efficient, accurate, and easy to use for end users without programming background to do dynamic sensitivity analysis on complex biological systems with time-delays.

  17. Dynamical Systems and Control Theory Inspired by Molecular Biology

    Science.gov (United States)

    2014-10-02

    in both bacterial and eukaryotic signaling pathways. A common theme in the systems biology literature is that certain systems whose output variables...AFRL-OSR-VA-TR-2014-0282 DYNAMICAL SYSTEMS AND CONTROL THEORY INSPIRED BY MOLECULAR BIOLOGY Eduardo Sontag RUTGERS THE STATE UNIVERSITY OF NEW JERSEY...Standard Form 298 (Re . 8-98) v Prescribed by ANSI Std. Z39.18 DYNAMICAL SYSTEMS AND CONTROL THEORY INSPIRED BY MOLECULAR BIOLOGY AFOSR FA9550-11-1-0247

  18. 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.

  19. Case Studies in Biology.

    Science.gov (United States)

    Zeakes, Samuel J.

    1989-01-01

    A case study writing exercise used in a course on parasitology was found to be a powerful learning experience for students because it involved discipline-based technical writing and terminology, brought the students in as evaluators, applied current learning, caused interaction among all students, and simulated real professional activities. (MSE)

  20. Dynamic properties of network motifs contribute to biological network organization.

    Directory of Open Access Journals (Sweden)

    Robert J Prill

    2005-11-01

    Full Text Available Biological networks, such as those describing gene regulation, signal transduction, and neural synapses, are representations of large-scale dynamic systems. Discovery of organizing principles of biological networks can be enhanced by embracing the notion that there is a deep interplay between network structure and system dynamics. Recently, many structural characteristics of these non-random networks have been identified, but dynamical implications of the features have not been explored comprehensively. We demonstrate by exhaustive computational analysis that a dynamical property--stability or robustness to small perturbations--is highly correlated with the relative abundance of small subnetworks (network motifs in several previously determined biological networks. We propose that robust dynamical stability is an influential property that can determine the non-random structure of biological networks.

  1. Biological Sampling Variability Study

    Energy Technology Data Exchange (ETDEWEB)

    Amidan, Brett G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hutchison, Janine R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-11-08

    There are many sources of variability that exist in the sample collection and analysis process. This paper addresses many, but not all, sources of variability. The main focus of this paper was to better understand and estimate variability due to differences between samplers. Variability between days was also studied, as well as random variability within each sampler. Experiments were performed using multiple surface materials (ceramic and stainless steel), multiple contaminant concentrations (10 spores and 100 spores), and with and without the presence of interfering material. All testing was done with sponge sticks using 10-inch by 10-inch coupons. Bacillus atrophaeus was used as the BA surrogate. Spores were deposited using wet deposition. Grime was coated on the coupons which were planned to include the interfering material (Section 3.3). Samples were prepared and analyzed at PNNL using CDC protocol (Section 3.4) and then cultured and counted. Five samplers were trained so that samples were taken using the same protocol. Each sampler randomly sampled eight coupons each day, four coupons with 10 spores deposited and four coupons with 100 spores deposited. Each day consisted of one material being tested. The clean samples (no interfering materials) were run first, followed by the dirty samples (coated with interfering material). There was a significant difference in recovery efficiency between the coupons with 10 spores deposited (mean of 48.9%) and those with 100 spores deposited (mean of 59.8%). There was no general significant difference between the clean and dirty (containing interfering material) coupons or between the two surface materials; however, there was a significant interaction between concentration amount and presence of interfering material. The recovery efficiency was close to the same for coupons with 10 spores deposited, but for the coupons with 100 spores deposited, the recovery efficiency for the dirty samples was significantly larger (65

  2. Dynamic heterogeneity controls diffusion and viscosity near biological interfaces

    Science.gov (United States)

    Pronk, Sander; Lindahl, Erik; Kasson, Peter M.

    2014-01-01

    At a nanometre scale, the behaviour of biological fluids is largely governed by interfacial physical chemistry. This may manifest as slowed or anomalous diffusion. Here we describe how measures developed for studying glassy systems allow quantitative measurement of interfacial effects on water dynamics, showing that correlated motions of particles near a surface result in a viscosity greater than anticipated from individual particle motions. This effect arises as a fundamental consequence of spatial heterogeneity on nanometre length scales and applies to any fluid near any surface. Increased interfacial viscosity also causes the classic finding that large solutes such as proteins diffuse much more slowly than predicted in bulk water. This has previously been treated via an empirical correction to the solute size: the hydrodynamic radius. Using measurements of quantities from theories of glass dynamics, we can now calculate diffusion constants from molecular details alone, eliminating the empirical correction factor.

  3. Process-based design of dynamical biological systems

    Science.gov (United States)

    Tanevski, Jovan; Todorovski, Ljupčo; Džeroski, Sašo

    2016-09-01

    The computational design of dynamical systems is an important emerging task in synthetic biology. Given desired properties of the behaviour of a dynamical system, the task of design is to build an in-silico model of a system whose simulated be- haviour meets these properties. We introduce a new, process-based, design methodology for addressing this task. The new methodology combines a flexible process-based formalism for specifying the space of candidate designs with multi-objective optimization approaches for selecting the most appropriate among these candidates. We demonstrate that the methodology is general enough to both formulate and solve tasks of designing deterministic and stochastic systems, successfully reproducing plausible designs reported in previous studies and proposing new designs that meet the design criteria, but have not been previously considered.

  4. Towards a Population Dynamics Theory for Evolutionary Computing: Learning from Biological Population Dynamics in Nature

    Science.gov (United States)

    Ma, Zhanshan (Sam)

    In evolutionary computing (EC), population size is one of the critical parameters that a researcher has to deal with. Hence, it was no surprise that the pioneers of EC, such as De Jong (1975) and Holland (1975), had already studied the population sizing from the very beginning of EC. What is perhaps surprising is that more than three decades later, we still largely depend on the experience or ad-hoc trial-and-error approach to set the population size. For example, in a recent monograph, Eiben and Smith (2003) indicated: "In almost all EC applications, the population size is constant and does not change during the evolutionary search." Despite enormous research on this issue in recent years, we still lack a well accepted theory for population sizing. In this paper, I propose to develop a population dynamics theory forEC with the inspiration from the population dynamics theory of biological populations in nature. Essentially, the EC population is considered as a dynamic system over time (generations) and space (search space or fitness landscape), similar to the spatial and temporal dynamics of biological populations in nature. With this conceptual mapping, I propose to 'transplant' the biological population dynamics theory to EC via three steps: (i) experimentally test the feasibility—whether or not emulating natural population dynamics improves the EC performance; (ii) comparatively study the underlying mechanisms—why there are improvements, primarily via statistical modeling analysis; (iii) conduct theoretical analysis with theoretical models such as percolation theory and extended evolutionary game theory that are generally applicable to both EC and natural populations. This article is a summary of a series of studies we have performed to achieve the general goal [27][30]-[32]. In the following, I start with an extremely brief introduction on the theory and models of natural population dynamics (Sections 1 & 2). In Sections 4 to 6, I briefly discuss three

  5. Modelling biological pathway dynamics with Timed Automata

    NARCIS (Netherlands)

    Schivo, Stefano; Scholma, Jetse; Wanders, B.; Urquidi Camacho, R.A.; van der Vet, P.E.; Karperien, Hermanus Bernardus Johannes; Langerak, Romanus; van de Pol, Jan Cornelis; Post, Janine Nicole

    2012-01-01

    When analysing complex interaction networks occurring in biological cells, a biologist needs computational support in order to understand the effects of signalling molecules (e.g. growth factors, drugs). ANIMO (Analysis of Networks with Interactive MOdelling) is a tool that allows the user to create

  6. Scaling for Dynamical Systems in Biology.

    Science.gov (United States)

    Ledder, Glenn

    2017-09-22

    Asymptotic methods can greatly simplify the analysis of all but the simplest mathematical models and should therefore be commonplace in such biological areas as ecology and epidemiology. One essential difficulty that limits their use is that they can only be applied to a suitably scaled dimensionless version of the original dimensional model. Many books discuss nondimensionalization, but with little attention given to the problem of choosing the right scales and dimensionless parameters. In this paper, we illustrate the value of using asymptotics on a properly scaled dimensionless model, develop a set of guidelines that can be used to make good scaling choices, and offer advice for teaching these topics in differential equations or mathematical biology courses.

  7. Dynamic analysis of higher order biological systems.

    Science.gov (United States)

    Sato, K

    1981-01-01

    Humans and animals consist of a variety of bio-systems exhibiting various bio-phenomena over the course of time, from the past to the present and into future, up to just before their death. Each state of a bio-phenomenon at any time is related in stochastic fashion not only to its past history, but those of many other bio- and natural phenomena, enormous in number, in their internal and external environments. Most states of these bio-phenomena sway more or less around respective averages, which suggest their levels of homeostasis, essentially important for maintaining life. In the above past history of sway was hidden an essential characteristic, i.e., dynamic higher-order activity, of the bio-system, whereas the bio- and natural phenomena in the environments act to drive, i.e., stimulate, as an ensemble, the bio-system to exhibit the bio-phenomena as its responses. From this new point of view, mono- and multivariate dynamic stimulation-system (activity)-response relations in stochastic fashion can be seen as an extension leading from of one of the most fundamental static laws of excitability, that is the threshold stimulus-excitability-unit response relation in physiology. The dynamic mono- and multivariate higher-order activities, each of which consisted of some first- and second-order component activities, can be described in the frequency and time-patterns as the power spectral densities or frequency responses and (unit) impulse responses, respectively. Some of these "dynamic activities" were manifested in the brain system of humans and cats, the human "posture holding system," "the pressure regulatory system" in the human pulmonary circulation and the "glucoregulatory system" of dogs, respectively.

  8. Dynamic programming algorithms for biological sequence comparison.

    Science.gov (United States)

    Pearson, W R; Miller, W

    1992-01-01

    Efficient dynamic programming algorithms are available for a broad class of protein and DNA sequence comparison problems. These algorithms require computer time proportional to the product of the lengths of the two sequences being compared [O(N2)] but require memory space proportional only to the sum of these lengths [O(N)]. Although the requirement for O(N2) time limits use of the algorithms to the largest computers when searching protein and DNA sequence databases, many other applications of these algorithms, such as calculation of distances for evolutionary trees and comparison of a new sequence to a library of sequence profiles, are well within the capabilities of desktop computers. In particular, the results of library searches with rapid searching programs, such as FASTA or BLAST, should be confirmed by performing a rigorous optimal alignment. Whereas rapid methods do not overlook significant sequence similarities, FASTA limits the number of gaps that can be inserted into an alignment, so that a rigorous alignment may extend the alignment substantially in some cases. BLAST does not allow gaps in the local regions that it reports; a calculation that allows gaps is very likely to extend the alignment substantially. Although a Monte Carlo evaluation of the statistical significance of a similarity score with a rigorous algorithm is much slower than the heuristic approach used by the RDF2 program, the dynamic programming approach should take less than 1 hr on a 386-based PC or desktop Unix workstation. For descriptive purposes, we have limited our discussion to methods for calculating similarity scores and distances that use gap penalties of the form g = rk. Nevertheless, programs for the more general case (g = q+rk) are readily available. Versions of these programs that run either on Unix workstations, IBM-PC class computers, or the Macintosh can be obtained from either of the authors.

  9. Biological studies of radiation effects

    Energy Technology Data Exchange (ETDEWEB)

    Lawrence, J.H.

    1949-11-16

    This paper discusses procedures for research on biological effects of radiation, using mouse tissue: activation trace analysis including methods and proceedures for handling samples before during and after irradiation; methods and procedures for ion exchange study; method of separation and recovery of copper, iron, zinc, cobalt, pubidium and cesium. Also included are studies of trace elements with radioactive isotopes: the distribution of cobalt 60, zinc 65, and copper 64 in the cytoplasm and nuclei of normal mice and those with tumors. 16 figs., 2 tabs.

  10. Applications of dynamical systems in biology and medicine

    CERN Document Server

    Radunskaya, Ami

    2015-01-01

    This volume highlights problems from a range of biological and medical applications that can be interpreted as questions about system behavior or control.  Topics include drug resistance in cancer and malaria, biological fluid dynamics, auto-regulation in the kidney, anti-coagulation therapy, evolutionary diversification and photo-transduction.  Mathematical techniques used to describe and investigate these biological and medical problems include ordinary, partial and stochastic differentiation equations, hybrid discrete-continuous approaches, as well as 2 and 3D numerical simulation. .

  11. Integrating Biological Systems in the Process Dynamics and Control Curriculum

    Science.gov (United States)

    Parker, Robert S.; Doyle, Francis J.; Henson, Michael A.

    2006-01-01

    The evolution of the chemical engineering discipline motivates a re-evaluation of the process dynamics and control curriculum. A key requirement of future courses will be the introduction of theoretical concepts and application examples relevant to emerging areas, notably complex biological systems. We outline the critical concepts required to…

  12. Quantum Processes and Dynamic Networks in Physical and Biological Systems.

    Science.gov (United States)

    Dudziak, Martin Joseph

    Quantum theory since its earliest formulations in the Copenhagen Interpretation has been difficult to integrate with general relativity and with classical Newtonian physics. There has been traditionally a regard for quantum phenomena as being a limiting case for a natural order that is fundamentally classical except for microscopic extrema where quantum mechanics must be applied, more as a mathematical reconciliation rather than as a description and explanation. Macroscopic sciences including the study of biological neural networks, cellular energy transports and the broad field of non-linear and chaotic systems point to a quantum dimension extending across all scales of measurement and encompassing all of Nature as a fundamentally quantum universe. Theory and observation lead to a number of hypotheses all of which point to dynamic, evolving networks of fundamental or elementary processes as the underlying logico-physical structure (manifestation) in Nature and a strongly quantized dimension to macroscalar processes such as are found in biological, ecological and social systems. The fundamental thesis advanced and presented herein is that quantum phenomena may be the direct consequence of a universe built not from objects and substance but from interacting, interdependent processes collectively operating as sets and networks, giving rise to systems that on microcosmic or macroscopic scales function wholistically and organically, exhibiting non-locality and other non -classical phenomena. The argument is made that such effects as non-locality are not aberrations or departures from the norm but ordinary consequences of the process-network dynamics of Nature. Quantum processes are taken to be the fundamental action-events within Nature; rather than being the exception quantum theory is the rule. The argument is also presented that the study of quantum physics could benefit from the study of selective higher-scale complex systems, such as neural processes in the brain

  13. Self-Organized Biological Dynamics and Nonlinear Control

    Science.gov (United States)

    Walleczek, Jan

    2006-04-01

    The frontiers and challenges of biodynamics research Jan Walleczek; Part I. Nonlinear Dynamics in Biology and Response to Stimuli: 1. External signals and internal oscillation dynamics - principal aspects and response of stimulated rhythmic processes Friedemann Kaiser; 2. Nonlinear dynamics in biochemical and biophysical systems: from enzyme kinetics to epilepsy Raima Larter, Robert Worth and Brent Speelman; 3. Fractal mechanisms in neural control: human heartbeat and gait dynamics in health and disease Chung-Kang Peng, Jeffrey M. Hausdorff and Ary L. Goldberger; 4. Self-organising dynamics in human coordination and perception Mingzhou Ding, Yanqing Chen, J. A. Scott Kelso and Betty Tuller; 5. Signal processing in biochemical reaction networks Adam P. Arkin; Part II. Nonlinear Sensitivity of Biological Systems to Electromagnetic Stimuli: 6. Electrical signal detection and noise in systems with long-range coherence Paul C. Gailey; 7. Oscillatory signals in migrating neutrophils: effects of time-varying chemical and electrical fields Howard R. Petty; 8. Enzyme kinetics and nonlinear biochemical amplification in response to static and oscillating magnetic fields Jan Walleczek and Clemens F. Eichwald; 9. Magnetic field sensitivity in the hippocampus Stefan Engström, Suzanne Bawin and W. Ross Adey; Part III. Stochastic Noise-Induced Dynamics and Transport in Biological Systems: 10. Stochastic resonance: looking forward Frank Moss; 11. Stochastic resonance and small-amplitude signal transduction in voltage-gated ion channels Sergey M. Bezrukov and Igor Vodyanoy; 12. Ratchets, rectifiers and demons: the constructive role of noise in free energy and signal transduction R. Dean Astumian; 13. Cellular transduction of periodic and stochastic energy signals by electroconformational coupling Tian Y. Tsong; Part IV. Nonlinear Control of Biological and Other Excitable Systems: 14. Controlling chaos in dynamical systems Kenneth Showalter; 15. Electromagnetic fields and biological

  14. Structural Studies of Biological Solids Using NMR

    Science.gov (United States)

    Ramamoorthy, Ayyalusamy

    2011-03-01

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

  15. Peroxisystem: harnessing systems cell biology to study peroxisomes.

    Science.gov (United States)

    Schuldiner, Maya; Zalckvar, Einat

    2015-04-01

    In recent years, high-throughput experimentation with quantitative analysis and modelling of cells, recently dubbed systems cell biology, has been harnessed to study the organisation and dynamics of simple biological systems. Here, we suggest that the peroxisome, a fascinating dynamic organelle, can be used as a good candidate for studying a complete biological system. We discuss several aspects of peroxisomes that can be studied using high-throughput systematic approaches and be integrated into a predictive model. Such approaches can be used in the future to study and understand how a more complex biological system, like a cell and maybe even ultimately a whole organism, works. © 2015 Société Française des Microscopies and Société de Biologie Cellulaire de France. Published by John Wiley & Sons Ltd.

  16. Logical and symbolic analysis of robust biological dynamics.

    Science.gov (United States)

    Glass, Leon; Siegelmann, Hava T

    2010-12-01

    Logical models provide insight about key control elements of biological networks. Based solely on the logical structure, we can determine state transition diagrams that give the allowed possible transitions in a coarse grained phase space. Attracting pathways and stable nodes in the state transition diagram correspond to robust attractors that would be found in several different types of dynamical systems that have the same logical structure. Attracting nodes in the state transition diagram correspond to stable steady states. Furthermore, the sequence of logical states appearing in biological networks with robust attracting pathways would be expected to appear also in Boolean networks, asynchronous switching networks, and differential equations having the same underlying structure. This provides a basis for investigating naturally occurring and synthetic systems, both to predict the dynamics if the structure is known, and to determine the structure if the transitions are known.

  17. Nanodomain stabilization dynamics in plasma membranes of biological cells

    Science.gov (United States)

    Das, Tamal; Maiti, Tapas K.; Chakraborty, Suman

    2011-02-01

    We discover that a synergistically amplifying role of stabilizing membrane proteins and continuous lipid recycling can explain the physics governing the stability, polydispersity, and dynamics of lipid raft domains in plasma membranes of biological cells. We establish the conjecture using a generalized order parameter based on theoretical formalism, endorsed by detailed scaling arguments and domain mapping. Quantitative agreements with morphological distributions of raft complexes, as obtained from Förster resonance energy transfer based visualization, support the present theoretical conjecture.

  18. Market study: Biological isolation garment

    Science.gov (United States)

    1975-01-01

    The biological isolation garment was originally designed for Apollo astronauts to wear upon their return to earth from the moon to avoid the possibility of their contaminating the environment. The concept has been adapted for medical use to protect certain patients from environmental contamination and the risk of infection. The nature and size of the anticipated market are examined with certain findings and conclusions relative to clinical acceptability and potential commercial viability of the biological isolation garment.

  19. Molecular dynamics modeling the synthetic and biological polymers interactions pre-studied via docking: anchors modified polyanions interference with the HIV-1 fusion mediator.

    Science.gov (United States)

    Tsvetkov, Vladimir B; Serbin, Alexander V

    2014-06-01

    In previous works we reported the design, synthesis and in vitro evaluations of synthetic anionic polymers modified by alicyclic pendant groups (hydrophobic anchors), as a novel class of inhibitors of the human immunodeficiency virus type 1 (HIV-1) entry into human cells. Recently, these synthetic polymers interactions with key mediator of HIV-1 entry-fusion, the tri-helix core of the first heptad repeat regions [HR1]3 of viral envelope protein gp41, were pre-studied via docking in terms of newly formulated algorithm for stepwise approximation from fragments of polymeric backbone and side-group models toward real polymeric chains. In the present article the docking results were verified under molecular dynamics (MD) modeling. In contrast with limited capabilities of the docking, the MD allowed of using much more large models of the polymeric ligands, considering flexibility of both ligand and target simultaneously. Among the synthesized polymers the dinorbornen anchors containing alternating copolymers of maleic acid were selected as the most representative ligands (possessing the top anti-HIV activity in vitro in correlation with the highest binding energy in the docking). To verify the probability of binding of the polymers with the [HR1]3 in the sites defined via docking, various starting positions of polymer chains were tried. The MD simulations confirmed the main docking-predicted priority for binding sites, and possibilities for axial and belting modes of the ligands-target interactions. Some newly MD-discovered aspects of the ligand's backbone and anchor units dynamic cooperation in binding the viral target clarify mechanisms of the synthetic polymers anti-HIV activity and drug resistance prevention.

  20. Information-theoretic analysis of the dynamics of an executable biological model.

    Directory of Open Access Journals (Sweden)

    Avital Sadot

    Full Text Available To facilitate analysis and understanding of biological systems, large-scale data are often integrated into models using a variety of mathematical and computational approaches. Such models describe the dynamics of the biological system and can be used to study the changes in the state of the system over time. For many model classes, such as discrete or continuous dynamical systems, there exist appropriate frameworks and tools for analyzing system dynamics. However, the heterogeneous information that encodes and bridges molecular and cellular dynamics, inherent to fine-grained molecular simulation models, presents significant challenges to the study of system dynamics. In this paper, we present an algorithmic information theory based approach for the analysis and interpretation of the dynamics of such executable models of biological systems. We apply a normalized compression distance (NCD analysis to the state representations of a model that simulates the immune decision making and immune cell behavior. We show that this analysis successfully captures the essential information in the dynamics of the system, which results from a variety of events including proliferation, differentiation, or perturbations such as gene knock-outs. We demonstrate that this approach can be used for the analysis of executable models, regardless of the modeling framework, and for making experimentally quantifiable predictions.

  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. Identification of curcumin derivatives as human glyoxalase I inhibitors: A combination of biological evaluation, molecular docking, 3D-QSAR and molecular dynamics simulation studies.

    Science.gov (United States)

    Yuan, Minggui; Luo, Minxian; Song, Yao; Xu, Qiu; Wang, Xiaofeng; Cao, Yi; Bu, Xianzhang; Ren, Yanliang; Hu, Xiaopeng

    2011-02-01

    Several recent developments suggest that the human glyoxalase I (GLO I) is a potential target for anti-tumor drug development. In present study, a series of curcumin derivatives with high inhibitory activity against human GLO I were discovered. Inhibition constant (K(i)) values of compounds 8, 9, 10, 11 and 13 to GLO I are 4.600μM, 2.600μM, 3.200μM, 3.600μM and 3.600μM, respectively. To elucidate the structural features of potent inhibitors, docking-based three-dimensional structure-activity relationship (3D-QSAR) analyses were performed. Satisfactory agreement between experiment and theory suggests that comparative molecular similarity index analysis (CoMSIA) modeling exhibit much better correlation and predictive power. The cross-validated q(2) value is 0.638 while no-validation r(2) value is 0.930. Integrated with docking-based 3D-QSAR CoMSIA modeling, molecular surface property (electrostatic and steric) mapping and molecular dynamics simulation, a set of receptor-ligand binding models and bio-affinity predictive models for rational design of more potent inhibitors of GLO I are established.

  3. Female juvenile murderers: Biological and psychological dynamics leading to homicide.

    Science.gov (United States)

    Heide, Kathleen M; Solomon, Eldra P

    2009-01-01

    The increasing involvement of girls under 18 in violent crime has been a matter of growing concern in the United States in recent years. This article reviews the arrests of female juveniles for violent crime and then focuses specifically on their involvement in homicide. Arrests of girls for murder, unlike arrests for assault, have not risen over the last 30 years, suggesting that the dynamics that propel female juveniles to engage in lethal violence differ from those contributing to assaultive behavior by this same group. A review of the literature indicates that theories as to why female adolescents kill do not take into account recent scientific findings on brain development and the biological effects of early trauma in explaining serious violent behavior by girls. Three cases, evaluated by the authors, involving female adolescents charged with murder or attempted murder, are presented. The authors focus on the biological and psychological dynamics that help explain their violent behavior. They discuss the effects of insecure attachment and child maltreatment, and trace a critical pathway between these early experiences and future risk of violent behavior. The dynamics of child maltreatment in fostering rage and violence are discussed thereafter in terms of offender accountability. The article concludes with a discussion of treatment and recommendations for future research.

  4. Cryo-electron microscopy for structural analysis of dynamic biological macromolecules.

    Science.gov (United States)

    Murata, Kazuyoshi; Wolf, Matthias

    2017-07-27

    Since the introduction of what became today's standard for cryo-embedding of biological macromolecules at native conditions more than 30years ago, techniques and equipment have been drastically improved and the structure of biomolecules can now be studied at near atomic resolution by cryo-electron microscopy (cryo-EM) while capturing multiple dynamic states. Here we review the recent progress in cryo-EM for structural studies of dynamic biological macromolecules. We provide an overview of the cryo-EM method and introduce contemporary studies to investigate biomolecular structure and dynamics, including examples from the recent literature. Cryo-EM is a powerful tool for the investigation of biological macromolecular structures including analysis of their dynamics by using advanced image-processing algorithms. The method has become even more widely applicable with present-day single particle analysis and electron tomography. The cryo-EM method can be used to determine the three-dimensional structure of biomacromolecules in near native condition at close to atomic resolution, and has the potential to reveal conformations of dynamic molecular complexes. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  5. Photonic engineering for biological study

    Science.gov (United States)

    Wu, Fei

    My dissertation focuses on designing and developing prototypes of optical tools in the laboratory that can facilitate practical medical therapies. More specifically, this dissertation examines two novel biophotonic techniques: (1) a frequency multiplexed confocal microscope with the potential to provide rational therapy of congestive heart failure (CHF), and (2) the "optical comb" with the potential to improve results of retina reattachment surgery and accelerate post surgical recovery. Next, I will discuss the background, design and initial experimental results of each study individually. Part I: The Frequency Multiplexed Confocal Microscope. To overcome the limitations of existing confocal microscope technology, this dissertation proposes a non-scanning, real-time, high resolution technique (a multi-point frequency multiplexed confocal microscope) to measure 3-D intracellular calcium ion concentration in a living cardiac myocyte. This method can be also applied to measure the intracellular sodium ion concentration, or other ions in which high quantum-yield fluorescent probes are available. The novelty of the proposed research lies in the introduction of carrier frequency multiplexing techniques which can differentiate fluorescence emitted at different spatial locations in cardiac myocyte by their modulated frequency. It therefore opens the possibility to visualize the transient dynamics of intracellular dynamics at multiple locations in cells simultaneously, which will shine a new light on our understanding of CHF. The procedure for frequency multiplexing proposed is described below. Multiple incident laser beams are focused onto different locations in an isolated rat cardiac myocyte with each beam modulated at a different carrier frequency. The fluorescence emission at each location therefore bears the same modulated frequency as the stimulation laser beam. Each fluorescence signal is sent to the photo multiplier tube (PMT) after being spatially filtered by a

  6. Nonlinear dynamics in the study of birdsong

    Science.gov (United States)

    Mindlin, Gabriel B.

    2017-09-01

    Birdsong, a rich and complex behavior, is a stellar model to understand a variety of biological problems, from motor control to learning. It also enables us to study how behavior emerges when a nervous system, a biomechanical device and the environment interact. In this review, I will show that many questions in the field can benefit from the approach of nonlinear dynamics, and how birdsong can inspire new directions for research in dynamics.

  7. Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems

    Directory of Open Access Journals (Sweden)

    Banga Julio R

    2006-11-01

    Full Text Available Abstract Background We consider the problem of parameter estimation (model calibration in nonlinear dynamic models of biological systems. Due to the frequent ill-conditioning and multi-modality of many of these problems, traditional local methods usually fail (unless initialized with very good guesses of the parameter vector. In order to surmount these difficulties, global optimization (GO methods have been suggested as robust alternatives. Currently, deterministic GO methods can not solve problems of realistic size within this class in reasonable computation times. In contrast, certain types of stochastic GO methods have shown promising results, although the computational cost remains large. Rodriguez-Fernandez and coworkers have presented hybrid stochastic-deterministic GO methods which could reduce computation time by one order of magnitude while guaranteeing robustness. Our goal here was to further reduce the computational effort without loosing robustness. Results We have developed a new procedure based on the scatter search methodology for nonlinear optimization of dynamic models of arbitrary (or even unknown structure (i.e. black-box models. In this contribution, we describe and apply this novel metaheuristic, inspired by recent developments in the field of operations research, to a set of complex identification problems and we make a critical comparison with respect to the previous (above mentioned successful methods. Conclusion Robust and efficient methods for parameter estimation are of key importance in systems biology and related areas. The new metaheuristic presented in this paper aims to ensure the proper solution of these problems by adopting a global optimization approach, while keeping the computational effort under reasonable values. This new metaheuristic was applied to a set of three challenging parameter estimation problems of nonlinear dynamic biological systems, outperforming very significantly all the methods previously

  8. Weak Solution to a Parabolic Nonlinear System Arising in Biological Dynamic in the Soil

    Directory of Open Access Journals (Sweden)

    Côme Goudjo

    2011-01-01

    Full Text Available We study a nonlinear parabolic system governing the biological dynamic in the soil. We prove global existence (in time and uniqueness of weak and positive solution for this reaction-diffusion semilinear system in a bounded domain, completed with homogeneous Neumann boundary conditions and positive initial conditions.

  9. Dynamic light scattering with applications to chemistry, biology, and physics

    CERN Document Server

    Berne, Bruce J

    2000-01-01

    Lasers play an increasingly important role in a variety of detection techniques, making inelastic light scattering a tool of growing value in the investigation of dynamic and structural problems in chemistry, biology, and physics. Until the initial publication of this work, however, no monograph treated the principles behind current developments in the field.This volume presents a comprehensive introduction to the principles underlying laser light scattering, focusing on the time dependence of fluctuations in fluid systems; it also serves as an introduction to the theory of time correlation f

  10. Synthesis, Molecular Docking, Molecular Dynamics Studies, and Biological Evaluation of 4H-Chromone-1,2,3,4-tetrahydropyrimidine-5-carboxylate Derivatives as Potential Antileukemic Agents.

    Science.gov (United States)

    Dolatkhah, Zahra; Javanshir, Shahrzad; Sadr, Ahmad Shahir; Hosseini, Jaber; Sardari, Soroush

    2017-06-26

    A series of 4H-chromone-1,2,3,4-tetrahydropyrimidine-5-carboxylates derivatives were synthesized via a three component one-pot condensation of chromone-3-carbaldehyde, alkyl acetoacetate, and urea or thiourea, using MCM-41-SO3H as efficient nanocatalysts and evaluated for their anticancer activity using a combined in silico docking and molecular dynamics protocol to estimate the binding affinity of the title compounds with the Bcr-Abl oncogene. Two programs, AutoDock 4 and AutoDock Vina software were applied to dock the target protein with synthesized compounds and ATP. AutoDock runs resulted in binding energy scores from -7.8 to -10.16 kcal/mol for AutoDock 4 and -6.9 to -8.5 (kcal/mol) for AutoDock Vina. Furthermore, molecular dynamics (MD) simulations are performed using Gromacs for up to 20 ns simulation time investigating the stability of a ligand-protein complex. Finally, a theoretical experiment using MD simulation for 10 ns was performed without defining the initial coordinates, and the affinity binding of ligand to receptors was directly studied, which revealed that the ligand approaches the active sites. The relative free binding energy for the structure 06 (S06), which has the highest binding energy in Autodock 4 and Autodock Vina (-10.10 and -8.5 kcal/mol, respectively), was also evaluated by molecular mechanics (MM) with Poisson-Boltzmann (PB) and a surface area solvation (MM-PBSA) method using g_mmpbsa tools for the last 15 ns MD. On the basis of binding energy scores, a negative binding energy value of 73.6 kcal/mol, S06, was recognized as the dominant potential inhibitors. The cytotoxic properties of S06 was evaluated against three cell lines, acute T cell leukemia (Jurkat), human chronic myelogenous leukemia, (K562) and human foreskin fibroblast (Hu02) using the microculture tetrazolium test MTT assay. Cisplatin was used as the reference agent. The results indicated that S06 has a higher safety index (SI = 0.73, IC50 = 152.64 μg/mL for Jurkat and

  11. Biology as population dynamics: heuristics for transmission risk.

    Science.gov (United States)

    Keebler, Daniel; Walwyn, David; Welte, Alex

    2013-02-01

    Population-type models, accounting for phenomena such as population lifetimes, mixing patterns, recruitment patterns, genetic evolution and environmental conditions, can be usefully applied to the biology of HIV infection and viral replication. A simple dynamic model can explore the effect of a vaccine-like stimulus on the mortality and infectiousness, which formally looks like fertility, of invading virions; the mortality of freshly infected cells; and the availability of target cells, all of which impact on the probability of infection. Variations on this model could capture the importance of the timing and duration of different key events in viral transmission, and hence be applied to questions of mucosal immunology. The dynamical insights and assumptions of such models are compatible with the continuum of between- and within-individual risks in sexual violence and may be helpful in making sense of the sparse data available on the association between HIV transmission and sexual violence. © 2012 John Wiley & Sons A/S.

  12. Dynamical model for biological functions of DNA molecules

    Institute of Scientific and Technical Information of China (English)

    PANGXiao-fengI; YANGYao

    2004-01-01

    We proposed a dynamic model of DNA to study its nonlinear excitation and duplication and transcription in the basis of molecular structure and changes of conformation of DNA under influence of bioenergy.

  13. Quantum Dynamics of Biological Plasma in the External Coulomb Field

    Science.gov (United States)

    Lasukov, V. V.; Lasukova, T. V.; Lasukova, O. V.

    2013-10-01

    A quantum solution to the truncated Fisher-Kolmogorov-Petrovskii-Piskunov equation with Coulomb convection and linear diffusion is derived. The quantum radiation of biological systems, individual microorganisms (cells, bacteria), and dust plasma particles in the Coulomb field is studied using the foregoing solution.

  14. Chemical biology approaches for studying posttranslational modifications.

    Science.gov (United States)

    Yang, Aerin; Cho, Kyukwang; Park, Hee-Sung

    2017-09-13

    Posttranslational modification (PTM) is a key mechanism for regulating diverse protein functions, and thus critically affects many essential biological processes. Critical for systematic study of the effects of PTMs is the ability to obtain recombinant proteins with defined and homogenous modifications. To this end, various synthetic and chemical biology approaches, including genetic code expansion and protein chemical modification methods, have been developed. These methods have proven effective for generating site-specific authentic modifications or structural mimics, and have demonstrated their value for in vitro and in vivo functional studies of diverse PTMs. This review will discuss recent advances in chemical biology strategies and their application to various PTM studies.

  15. Protein electron transfer: is biology (thermo)dynamic?

    Science.gov (United States)

    Matyushov, Dmitry V.

    2015-12-01

    Simple physical mechanisms are behind the flow of energy in all forms of life. Energy comes to living systems through electrons occupying high-energy states, either from food (respiratory chains) or from light (photosynthesis). This energy is transformed into the cross-membrane proton-motive force that eventually drives all biochemistry of the cell. Life’s ability to transfer electrons over large distances with nearly zero loss of free energy is puzzling and has not been accomplished in synthetic systems. The focus of this review is on how this energetic efficiency is realized. General physical mechanisms and interactions that allow proteins to fold into compact water-soluble structures are also responsible for a rugged landscape of energy states and a broad distribution of relaxation times. Specific to a protein as a fluctuating thermal bath is the protein-water interface, which is heterogeneous both dynamically and structurally. The spectrum of interfacial fluctuations is a consequence of protein’s elastic flexibility combined with a high density of surface charges polarizing water dipoles into surface nanodomains. Electrostatics is critical to the protein function and the relevant questions are: (i) What is the spectrum of interfacial electrostatic fluctuations? (ii) Does the interfacial biological water produce electrostatic signatures specific to proteins? (iii) How is protein-mediated chemistry affected by electrostatics? These questions connect the fluctuation spectrum to the dynamical control of chemical reactivity, i.e. the dependence of the activation free energy of the reaction on the dynamics of the bath. Ergodicity is often broken in protein-driven reactions and thermodynamic free energies become irrelevant. Continuous ergodicity breaking in a dense spectrum of relaxation times requires using dynamically restricted ensembles to calculate statistical averages. When applied to the calculation of the rates, this formalism leads to the nonergodic

  16. Diffusion of innovations dynamics, biological growth and catenary function

    Science.gov (United States)

    Guseo, Renato

    2016-12-01

    The catenary function has a well-known role in determining the shape of chains and cables supported at their ends under the force of gravity. This enables design using a specific static equilibrium over space. Its reflected version, the catenary arch, allows the construction of bridges and arches exploiting the dual equilibrium property under uniform compression. In this paper, we emphasize a further connection with well-known aggregate biological growth models over time and the related diffusion of innovation key paradigms (e.g., logistic and Bass distributions over time) that determine self-sustaining evolutionary growth dynamics in naturalistic and socio-economic contexts. Moreover, we prove that the 'local entropy function', related to a logistic distribution, is a catenary and vice versa. This special invariance may be explained, at a deeper level, through the Verlinde's conjecture on the origin of gravity as an effect of the entropic force.

  17. Extension of dynamics of granular flow methodology to cell biology

    Science.gov (United States)

    Kummer, A.; Ocone, R.

    2003-04-01

    In a previous paper (J. Non-Newtonian Fluid Mech. 76 (1998) 5), the analogy between the methodology typical of the dynamics of polymeric liquids and those used in granular flow theory was investigated. It was shown that such a methodology could be successfully extended to granular flow, and then it was speculated on the possibility of extending it to diverse areas. In this paper two important conclusions are reached. Firstly we show that the methodology behind the statistical theories (which starting from the microstructural element eventually leads to the formulation of constitutive equations (AICHE Symposium Series, Vol. 93, 1997, p. 103)) can be extended to an apparently completely different field, namely cell biology. We then show that classical thermodynamics, as applied to epigenetic systems, presents limitations which can be overcome following an axiomatic thermodynamic route (J. Rheol. 37 (1993) 727).

  18. Lessons Learned from Quantitative Dynamical Modeling in Systems Biology

    Science.gov (United States)

    Bachmann, Julie; Matteson, Andrew; Schelke, Max; Kaschek, Daniel; Hug, Sabine; Kreutz, Clemens; Harms, Brian D.; Theis, Fabian J.; Klingmüller, Ursula; Timmer, Jens

    2013-01-01

    Due to the high complexity of biological data it is difficult to disentangle cellular processes relying only on intuitive interpretation of measurements. A Systems Biology approach that combines quantitative experimental data with dynamic mathematical modeling promises to yield deeper insights into these processes. Nevertheless, with growing complexity and increasing amount of quantitative experimental data, building realistic and reliable mathematical models can become a challenging task: the quality of experimental data has to be assessed objectively, unknown model parameters need to be estimated from the experimental data, and numerical calculations need to be precise and efficient. Here, we discuss, compare and characterize the performance of computational methods throughout the process of quantitative dynamic modeling using two previously established examples, for which quantitative, dose- and time-resolved experimental data are available. In particular, we present an approach that allows to determine the quality of experimental data in an efficient, objective and automated manner. Using this approach data generated by different measurement techniques and even in single replicates can be reliably used for mathematical modeling. For the estimation of unknown model parameters, the performance of different optimization algorithms was compared systematically. Our results show that deterministic derivative-based optimization employing the sensitivity equations in combination with a multi-start strategy based on latin hypercube sampling outperforms the other methods by orders of magnitude in accuracy and speed. Finally, we investigated transformations that yield a more efficient parameterization of the model and therefore lead to a further enhancement in optimization performance. We provide a freely available open source software package that implements the algorithms and examples compared here. PMID:24098642

  19. Lessons learned from quantitative dynamical modeling in systems biology.

    Directory of Open Access Journals (Sweden)

    Andreas Raue

    Full Text Available Due to the high complexity of biological data it is difficult to disentangle cellular processes relying only on intuitive interpretation of measurements. A Systems Biology approach that combines quantitative experimental data with dynamic mathematical modeling promises to yield deeper insights into these processes. Nevertheless, with growing complexity and increasing amount of quantitative experimental data, building realistic and reliable mathematical models can become a challenging task: the quality of experimental data has to be assessed objectively, unknown model parameters need to be estimated from the experimental data, and numerical calculations need to be precise and efficient. Here, we discuss, compare and characterize the performance of computational methods throughout the process of quantitative dynamic modeling using two previously established examples, for which quantitative, dose- and time-resolved experimental data are available. In particular, we present an approach that allows to determine the quality of experimental data in an efficient, objective and automated manner. Using this approach data generated by different measurement techniques and even in single replicates can be reliably used for mathematical modeling. For the estimation of unknown model parameters, the performance of different optimization algorithms was compared systematically. Our results show that deterministic derivative-based optimization employing the sensitivity equations in combination with a multi-start strategy based on latin hypercube sampling outperforms the other methods by orders of magnitude in accuracy and speed. Finally, we investigated transformations that yield a more efficient parameterization of the model and therefore lead to a further enhancement in optimization performance. We provide a freely available open source software package that implements the algorithms and examples compared here.

  20. [From physics to biology: the intrinsic dynamics of the cosmos].

    Science.gov (United States)

    González de Posada, Francisco

    2003-01-01

    The History of Universe is described in an extremely summarized manner through the use of graphics, from Big bang until today. This is done according to the most recent standard models of Cosmology and Physics of elementary particles; in other words, according to those fields in Physics of a presupposed universal reference. The History of Life is immersed in this universal physical context, in a frame where our knowledge from Geology and Biology can be only terrestrial. The underlying ideas we try to arise are: 1) the transition from a relatively elementary structure to a posterior and a relatively more complex one requires some very special "environmental" conditions; and 2) the new structure can not be described only through its materic constituents, because in cosmic dynamicity new structures and new relationships (of intrinsic respectivity) arise, together with new laws (of extrinsic respectivity). Consequently and as an objective, physical knowledge (for example, elementary particles or atoms) alone in no way can explain biological reality (for example, cell or man).

  1. Dynamic processes in biological membrane mimics revealed by quasielastic neutron scattering.

    Science.gov (United States)

    Lautner, Lisa; Pluhackova, Kristyna; Barth, Nicolai K H; Seydel, Tilo; Lohstroh, Wiebke; Böckmann, Rainer A; Unruh, Tobias

    2017-08-01

    Neutron scattering is a powerful tool to study relaxation processes in biological membrane mimics in space and time. Combining different inelastic and quasielastic neutron scattering techniques, a large dynamic range can be covered: from atomic to mesoscopic lengths and from femto- to some hundreds of nanoseconds in time. This allows studies on e.g. the diffusion of lipids, the membrane undulation motions, the dispersion of sound waves in membranes as well as the mutual interactions of membrane constituents such as lipids, proteins, and additives. In particular, neutron scattering provides a quite direct experimental approach to the inter-atomic and inter-molecular potentials on length and time scales which are perfectly accessible by molecular dynamics (MD) simulations. Neutron scattering experiments may thus substantially support the further refinement of biomolecular force fields for MD simulations by supplying structural and dynamical information with high spatial and temporal resolution. In turn, MD simulations support the interpretation of neutron scattering data. The combination of both, neutron scattering experiments and MD simulations, yields an unprecedented insight into the molecular interactions governing the structure and dynamics of biological membranes. This review provides an overview of the molecular dynamics in biological membrane mimics as revealed by neutron scattering. It focuses on the latest findings such as the fundamental molecular mechanism of lateral lipid diffusion as well as the influence of additives and proteins on the short-time dynamics of lipids. Special emphasis is placed on the comparison of recent neutron scattering and MD simulation data with respect to molecular membrane dynamics on the pico- to nanosecond time scale. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Study of complex molecules of biological interest with synchrotron radiation

    Energy Technology Data Exchange (ETDEWEB)

    Prince, K.C. [Elettra-Sincrotrone Trieste, Strada Statale 14–km 163,5 in AREA Science Park, I-34149 Trieste (Italy); Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche, in Area Science Park, I-34149 Trieste (Italy); Molecular Model Discovery Laboratory, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Melbourne, Victoria, 3122 (Australia); Bolognesi, P., E-mail: paola.bolognesi@cnr.it [CNR-ISM, Area della Ricerca di Roma 1, Via Salaria Km. 29,300, Monterotondo (Roma) (Italy); Feyer, V. [Elettra-Sincrotrone Trieste, Strada Statale 14–km 163,5 in AREA Science Park, I-34149 Trieste (Italy); Research Center Jülich, Peter Grünberg Institute (PGI-6), 52425 Jülich (Germany); Plekan, O. [Elettra-Sincrotrone Trieste, Strada Statale 14–km 163,5 in AREA Science Park, I-34149 Trieste (Italy); Avaldi, L. [CNR-ISM, Area della Ricerca di Roma 1, Via Salaria Km. 29,300, Monterotondo (Roma) (Italy)

    2015-10-15

    Synchrotron radiation and synchrotron based spectroscopic techniques have found important applications in the study of isolated molecular species of biological interest. In this paper, some examples of spectroscopic and dynamic studies of amino acids and small peptides, nucleobases and pharmaceuticals are reviewed. Opportunities offered by the advent of new radiation sources combined with novel methods for the production of beams of these molecules are also discussed.

  3. Algebraic Systems Biology: A Case Study for the Wnt Pathway.

    Science.gov (United States)

    Gross, Elizabeth; Harrington, Heather A; Rosen, Zvi; Sturmfels, Bernd

    2016-01-01

    Steady-state analysis of dynamical systems for biological networks gives rise to algebraic varieties in high-dimensional spaces whose study is of interest in their own right. We demonstrate this for the shuttle model of the Wnt signaling pathway. Here, the variety is described by a polynomial system in 19 unknowns and 36 parameters. It has degree 9 over the parameter space. This case study explores multistationarity, model comparison, dynamics within regions of the state space, identifiability, and parameter estimation, from a geometric point of view. We employ current methods from computational algebraic geometry, polyhedral geometry, and combinatorics.

  4. OFFl Models: Novel Schema for Dynamical Modeling of Biological Systems.

    Science.gov (United States)

    Ogbunugafor, C Brandon; Robinson, Sean P

    2016-01-01

    Flow diagrams are a common tool used to help build and interpret models of dynamical systems, often in biological contexts such as consumer-resource models and similar compartmental models. Typically, their usage is intuitive and informal. Here, we present a formalized version of flow diagrams as a kind of weighted directed graph which follow a strict grammar, which translate into a system of ordinary differential equations (ODEs) by a single unambiguous rule, and which have an equivalent representation as a relational database. (We abbreviate this schema of "ODEs and formalized flow diagrams" as OFFL.) Drawing a diagram within this strict grammar encourages a mental discipline on the part of the modeler in which all dynamical processes of a system are thought of as interactions between dynamical species that draw parcels from one or more source species and deposit them into target species according to a set of transformation rules. From these rules, the net rate of change for each species can be derived. The modeling schema can therefore be understood as both an epistemic and practical heuristic for modeling, serving both as an organizational framework for the model building process and as a mechanism for deriving ODEs. All steps of the schema beyond the initial scientific (intuitive, creative) abstraction of natural observations into model variables are algorithmic and easily carried out by a computer, thus enabling the future development of a dedicated software implementation. Such tools would empower the modeler to consider significantly more complex models than practical limitations might have otherwise proscribed, since the modeling framework itself manages that complexity on the modeler's behalf. In this report, we describe the chief motivations for OFFL, carefully outline its implementation, and utilize a range of classic examples from ecology and epidemiology to showcase its features.

  5. OFFl Models: Novel Schema for Dynamical Modeling of Biological Systems

    Science.gov (United States)

    2016-01-01

    Flow diagrams are a common tool used to help build and interpret models of dynamical systems, often in biological contexts such as consumer-resource models and similar compartmental models. Typically, their usage is intuitive and informal. Here, we present a formalized version of flow diagrams as a kind of weighted directed graph which follow a strict grammar, which translate into a system of ordinary differential equations (ODEs) by a single unambiguous rule, and which have an equivalent representation as a relational database. (We abbreviate this schema of “ODEs and formalized flow diagrams” as OFFL.) Drawing a diagram within this strict grammar encourages a mental discipline on the part of the modeler in which all dynamical processes of a system are thought of as interactions between dynamical species that draw parcels from one or more source species and deposit them into target species according to a set of transformation rules. From these rules, the net rate of change for each species can be derived. The modeling schema can therefore be understood as both an epistemic and practical heuristic for modeling, serving both as an organizational framework for the model building process and as a mechanism for deriving ODEs. All steps of the schema beyond the initial scientific (intuitive, creative) abstraction of natural observations into model variables are algorithmic and easily carried out by a computer, thus enabling the future development of a dedicated software implementation. Such tools would empower the modeler to consider significantly more complex models than practical limitations might have otherwise proscribed, since the modeling framework itself manages that complexity on the modeler’s behalf. In this report, we describe the chief motivations for OFFL, carefully outline its implementation, and utilize a range of classic examples from ecology and epidemiology to showcase its features. PMID:27270918

  6. OFFl Models: Novel Schema for Dynamical Modeling of Biological Systems.

    Directory of Open Access Journals (Sweden)

    C Brandon Ogbunugafor

    Full Text Available Flow diagrams are a common tool used to help build and interpret models of dynamical systems, often in biological contexts such as consumer-resource models and similar compartmental models. Typically, their usage is intuitive and informal. Here, we present a formalized version of flow diagrams as a kind of weighted directed graph which follow a strict grammar, which translate into a system of ordinary differential equations (ODEs by a single unambiguous rule, and which have an equivalent representation as a relational database. (We abbreviate this schema of "ODEs and formalized flow diagrams" as OFFL. Drawing a diagram within this strict grammar encourages a mental discipline on the part of the modeler in which all dynamical processes of a system are thought of as interactions between dynamical species that draw parcels from one or more source species and deposit them into target species according to a set of transformation rules. From these rules, the net rate of change for each species can be derived. The modeling schema can therefore be understood as both an epistemic and practical heuristic for modeling, serving both as an organizational framework for the model building process and as a mechanism for deriving ODEs. All steps of the schema beyond the initial scientific (intuitive, creative abstraction of natural observations into model variables are algorithmic and easily carried out by a computer, thus enabling the future development of a dedicated software implementation. Such tools would empower the modeler to consider significantly more complex models than practical limitations might have otherwise proscribed, since the modeling framework itself manages that complexity on the modeler's behalf. In this report, we describe the chief motivations for OFFL, carefully outline its implementation, and utilize a range of classic examples from ecology and epidemiology to showcase its features.

  7. Studying cell biology in the skin

    Science.gov (United States)

    Morrow, Angel; Lechler, Terry

    2015-01-01

    Advances in cell biology have often been driven by studies in diverse organisms and cell types. Although there are technical reasons for why different cell types are used, there are also important physiological reasons. For example, ultrastructural studies of vesicle transport were aided by the use of professional secretory cell types. The use of tissues/primary cells has the advantage not only of using cells that are adapted to the use of certain cell biological machinery, but also of highlighting the physiological roles of this machinery. Here we discuss advantages of the skin as a model system. We discuss both advances in cell biology that used the skin as a driving force and future prospects for use of the skin to understand basic cell biology. A unique combination of characteristics and tools makes the skin a useful in vivo model system for many cell biologists. PMID:26564861

  8. Overshoot in biological systems modelled by Markov chains: a non-equilibrium dynamic phenomenon.

    Science.gov (United States)

    Jia, Chen; Qian, Minping; Jiang, Daquan

    2014-08-01

    A number of biological systems can be modelled by Markov chains. Recently, there has been an increasing concern about when biological systems modelled by Markov chains will perform a dynamic phenomenon called overshoot. In this study, the authors found that the steady-state behaviour of the system will have a great effect on the occurrence of overshoot. They showed that overshoot in general cannot occur in systems that will finally approach an equilibrium steady state. They further classified overshoot into two types, named as simple overshoot and oscillating overshoot. They showed that except for extreme cases, oscillating overshoot will occur if the system is far from equilibrium. All these results clearly show that overshoot is a non-equilibrium dynamic phenomenon with energy consumption. In addition, the main result in this study is validated with real experimental data.

  9. Salinity fluctuation influencing biological adaptation: growth dynamics and Na(+) /K(+) -ATPase activity in a euryhaline bacterium.

    Science.gov (United States)

    Yang, Hao; Meng, Yang; Song, Youxin; Tan, Yalin; Warren, Alan; Li, Jiqiu; Lin, Xiaofeng

    2017-07-01

    Although salinity fluctuation is a prominent characteristic of many coastal ecosystems, its effects on biological adaptation have not yet been fully recognized. To test the salinity fluctuations on biological adaptation, population growth dynamics and Na(+) /K(+) -ATPase activity were investigated in the euryhaline bacterium Idiomarina sp. DYB, which was acclimated at different salinity exposure levels, exposure times, and shifts in direction of salinity. Results showed: (1) bacterial population growth dynamics and Na(+) /K(+) -ATPase activity changed significantly in response to salinity fluctuation; (2) patterns of variation in bacterial growth dynamics were related to exposure times, levels of salinity, and shifts in direction of salinity change; (3) significant tradeoffs were detected between growth rate (r) and carrying capacity (K) on the one hand, and Na(+) /K(+) -ATPase activity on the other; and (4) beneficial acclimation was confirmed in Idiomarina sp. DYB. In brief, this study demonstrated that salinity fluctuation can change the population growth dynamics, Na(+) /K(+) -ATPase activity, and tradeoffs between r, K, and Na(+) /K(+) -ATPase activity, thus facilitating bacterial adaption in a changing environment. These findings provide constructive information for determining biological response patterns to environmental change. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Polarised neutron scattering from dynamic polarised targets in biology

    Science.gov (United States)

    Knop, W.; Hirai, M.; Olah, G.; Meerwinck, W.; Schink, H.-J.; Stuhrman, H. B.; Wagner, R.; Wenkow-EsSouni, M.; Zhao, J.; Schärpf, O.; Crichton, R. R.; Krumpolc, M.; Nierhaus, K. H.; Niinikoski, T. O.; Rijllart, A.

    1991-10-01

    The contrast giving rise to neutron small-angle scattering can be enhanced considerably by polarisation of the hydrogen nuclei [J. des Coizeaux and G. Jannink, Les Polymères en Solution, Les Editions de Physique, F-91944 Les Ulis, France (1987)]. Using polarised neutrons the scattering from protonated labels in a deuterated matrix will increase by an order of magnitude. This is the basis of nuclear spin contrast variation, a method which is of particular interest for the in situ structure determination of macromolecular components. A new polarised target for neutron scattering has been designed by CERN and tested successfully at FRG-1 of the GKSS research centre. For the purpose of thermal-neutron scattering the frozen solutions of biomolecules are immersed in liquid helium 4, which is thermally coupled to the cooling mixture of helium 3/helium 4 of the dilution refrigerator. The nuclear spins are aligned with respect to the external magnetic field-parallel or antiparallel-by dynamic nuclear polarisation (DNP). The gain in neutron scattering compared to earlier experiments using direct cooling of the sample by helium 3 is a factor of 30. Another factor of 30 arises from the installation of the cold source and the beryllium reflector in FRG-1 [W. Knop et al., J. Appl. Cryst. 22 (1989) 352]. Pure nuclear spin targets are produced from dynamic polarised targets by selective depolarisation. In biological material only the hydrogen isotopes contribute significantly to polarised neutron scattering. Thus, saturation of the proton NMR yields a deuteron target, provided the target material has been enriched by the latter isotope. A proton target is obtained from the dynamic polarised target by saturation of deuteron NMR. This leads to six additional scattering functions reflecting the proton and deuteron spin densities and the correlations between the polarised isotopes. Polarised neutron scattering from nuclear spin targets of apoferritin and various derivatives of the

  11. [Biocenotic dynamics of liquid sewage in the process of its biological purification at aeration stations].

    Science.gov (United States)

    Kalina, G P; Vinogradova, L A; Gipp, E K

    1975-08-01

    A study was made of biological purification of sewage at the aeration stations on the quantitative composition of the main indicator microbes--of bacteria of the coliform group and of the fecal coliform bacilli, enterococci, Proteus, and also pathogenic enterobacteria. There was found a difference in the behaviour of different species of Proteus, i.e. reduction in the process of purification in the numbers of Pr. mirabilis, and a sharp elevation of Pr. morganii content. There was noted an insignificant amount of Pr. vulgaris both before and after the biological purification. It was found that dynamics of biocenosis was influenced by air temperature at the time of collection of the samples. A possibility of reproduction of coliform bacilli serving as one of the factors of autopurification of sewage during the biological purification was confirmed.

  12. Dynamical systems an introduction with applications in economics and biology

    CERN Document Server

    Tu, Pierre N V

    1994-01-01

    The favourable reception of the first edition and the encouragement received from many readers have prompted the author to bring out this new edition. This provides the opportunity for correcting a number of errors, typographical and others, contained in the first edition and making further improvements. This second edition has a new chapter on simplifying Dynamical Systems covering Poincare map, Floquet theory, Centre Manifold Theorems, normal forms of dynamical systems, elimination of passive coordinates and Liapunov-Schmidt reduction theory. It would provide a gradual transition to the study of Bifurcation, Chaos and Catastrophe in Chapter 10. Apart from this, most others - in fact all except the first three and last chapters - have been revised and enlarged to bring in some new materials, elaborate some others, especially those sections which many readers felt were rather too concise in the first edition, by providing more explana­ tion, examples and applications. Chapter 11 provides some good examples o...

  13. Toxicity Studies on "840 Biologic Pesticide"

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    [Objective] "840 Biologic Pesticide" is a very effective biologic pesticide. It consists of Abamectin and celastrus angulatus. Toxicity study was aimed to provide scientific toxicological basis. [Methods] The acute toxicity test,Ames test,micronucleus test and testicle chromosome aberration test were done. [Results] The acute toxicity of single dose of "840 Biologic Pesticide" showed that acute oral LD50 for female and male rats are 4 300 and 4 280 mg/kg,and for female and male mice are 2 330 and 5 110 mg/kg,respectively. The dermal LD50 was >2 000 mg/kg for female and male rats. The mutagenesis studies indicated that Ames test,micronucleus test and testicle chromosome aberration test were negative. [Conclusion] Tested pesticidc belongs to low toticity grade.

  14. Studying cell biology in the skin.

    Science.gov (United States)

    Morrow, Angel; Lechler, Terry

    2015-11-15

    Advances in cell biology have often been driven by studies in diverse organisms and cell types. Although there are technical reasons for why different cell types are used, there are also important physiological reasons. For example, ultrastructural studies of vesicle transport were aided by the use of professional secretory cell types. The use of tissues/primary cells has the advantage not only of using cells that are adapted to the use of certain cell biological machinery, but also of highlighting the physiological roles of this machinery. Here we discuss advantages of the skin as a model system. We discuss both advances in cell biology that used the skin as a driving force and future prospects for use of the skin to understand basic cell biology. A unique combination of characteristics and tools makes the skin a useful in vivo model system for many cell biologists. © 2015 Morrow and Lechler. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  15. Experimental Approaches to Studying Biological Electron Transfer.

    Science.gov (United States)

    Scott, Robert A.; And Others

    1985-01-01

    Provides an overview on biological electron-transfer reactions, summarizing what is known about how distance, spatial organization, medium, and other factors affect electron transfer. Experimental approaches, including studies of bimolecular electron transfer reactions (electrostatic effects and precursor complexes), are considered. (JN)

  16. On the accurate molecular dynamics analysis of biological molecules

    Science.gov (United States)

    Yamashita, Takefumi

    2016-12-01

    As the evolution of computational technology has now enabled long molecular dynamics (MD) simulation, the evaluation of many physical properties shows improved convergence. Therefore, we can examine the detailed conditions of MD simulations and perform quantitative MD analyses. In this study, we address the quantitative and accuracy aspects of MD simulations using two example systems. First, it is found that several conditions of the MD simulations influence the area/lipid of the lipid bilayer. Second, we successfully detect the small but important differences in antibody motion between the antigen-bound and unbound states.

  17. II. Biological studies of radiation effects

    Energy Technology Data Exchange (ETDEWEB)

    Lawrence, J.H.

    1948-05-24

    With the completion of the 184 inch cyclotron in Berkeley and the successful construction of a deflector system, it was possible to bring the 190 Mev deuteron and the 380 Mev alpha beams out into the air and to begin a study of the effects of high-energy deuteron beams by direct irradiation of biological specimens. The direct biological use of deuteron beams was attempted earlier in Berkeley by Marshak, MacLeish, and Walker in 1940. These and other investigators have been aware for some time of the potential usefulness of high energy particle beams for radio-biological studies and their suitability for biological investigations. R.R. Wilson advanced the idea of using fast proton beams to deliver radiation and intervening tissues. R.E. Zirkle pointed out that such particle beams may be focused or screened until a cross-section of the beam is small enough to study effects of irradiation under the microscope on single cells or on parts of single cells. This article gives an overview of the radiological use of high energy deuteron beams, including the following topics: potential uses of high energy particle beams; experiments on the physical properties of the beam; lethal effect of the deuteron beam on mice.

  18. Agent-oriented modeling of the dynamics of complex biological processes I: single agent models

    NARCIS (Netherlands)

    Jonker, C.M.; Treur, J.

    2008-01-01

    In the pair of papers of which this is Part I, the agent-oriented modeling perspective to cope with biological complexity is discussed. Three levels of dynamics are distinguished and related to each other: dynamics of externally observable agent behavior, dynamics of internal agent processes, and dy

  19. Integration in biology: Philosophical perspectives on the dynamics of interdisciplinarity.

    Science.gov (United States)

    Brigandt, Ingo

    2013-12-01

    This introduction to the special section on integration in biology provides an overview of the different contributions. In addition to motivating the philosophical significance of analyzing integration and interdisciplinary research, I lay out common themes and novel insights found among the special section contributions, and indicate how they exhibit current trends in the philosophical study of integration. One upshot of the contributed papers is that there are different aspects to and kinds of integration, so that rather than attempting to offer a universal construal of what integrations is, philosophers have to analyze in concrete cases in what respects particular aspects of scientific theorizing and/or practice are 'integrative' and how this instance of integration works and was achieved.

  20. Space Biology Initiative. Trade Studies, volume 2

    Science.gov (United States)

    1989-01-01

    The six studies which are the subjects of this report are entitled: Design Modularity and Commonality; Modification of Existing Hardware (COTS) vs. New Hardware Build Cost Analysis; Automation Cost vs. Crew Utilization; Hardware Miniaturization versus Cost; Space Station Freedom/Spacelab Modules Compatibility vs. Cost; and Prototype Utilization in the Development of Space Hardware. The product of these six studies was intended to provide a knowledge base and methodology that enables equipment produced for the Space Biology Initiative program to meet specific design and functional requirements in the most efficient and cost effective form consistent with overall mission integration parameters. Each study promulgates rules of thumb, formulas, and matrices that serves as a handbook for the use and guidance of designers and engineers in design, development, and procurement of Space Biology Initiative (SBI) hardware and software.

  1. Space Biology Initiative. Trade Studies, volume 1

    Science.gov (United States)

    1989-01-01

    The six studies which are addressed are entitled: Design Modularity and Commonality; Modification of Existing Hardware (COTS) vs. New Hardware Build Cost Analysis; Automation Cost vs. Crew Utilization; Hardware Miniaturization versus Cost; Space Station Freedom/Spacelab Modules Compatibility vs. Cost; and Prototype Utilization in the Development of Space Hardware. The product of these six studies was intended to provide a knowledge base and methodology that enables equipment produced for the Space Biology Initiative program to meet specific design and functional requirements in the most efficient and cost effective form consistent with overall mission integration parameters. Each study promulgates rules of thumb, formulas, and matrices that serves has a handbook for the use and guidance of designers and engineers in design, development, and procurement of Space Biology Initiative (SBI) hardware and software.

  2. Chimeric alignment by dynamic programming: Algorithm and biological uses

    Energy Technology Data Exchange (ETDEWEB)

    Komatsoulis, G.A.; Waterman, M.S. [Univ. of Southern California, Los Angeles, CA (United States)

    1997-12-01

    A new nearest-neighbor method for detecting chimeric 16S rRNA artifacts generated during PCR amplification from mixed populations has been developed. The method uses dynamic programming to generate an optimal chimeric alignment, defined as the highest scoring alignment between a query and a concatenation of a 5{prime} and a 3{prime} segment from two separate entries from a database of related sequences. Chimeras are detected by studying the scores and form of the chimeric and global sequence alignments. The chimeric alignment method was found to be marginally more effective than k-tuple based nearest-neighbor methods in simulation studies, but its most effective use is in concert with k-tuple methods. 15 refs., 3 figs., 1 tab.

  3. Studying Dynamics in Business Networks

    DEFF Research Database (Denmark)

    Andersen, Poul Houman; Anderson, Helen; Havila, Virpi;

    1998-01-01

    This paper develops a theory on network dynamics using the concepts of role and position from sociological theory. Moreover, the theory is further tested using case studies from Denmark and Finland...

  4. Quantum dynamics of biological systems and dust plasma nanoparticles

    Science.gov (United States)

    Lasukov, V. V.; Lasukova, T. V.; Lasukova, O. V.

    2012-12-01

    A quantum solution of the Fisher-Kolmogorov-Petrovskii-Piskunov equation with convection and linear diffusion is obtained which can provide the basis for the quantum biology and quantum microphysics equation. On this basis, quantum emission of biological systems, separate microorganisms (cells or bacteria), and dust plasma particles is investigated.

  5. Applications of Discrete Molecular Dynamics in biology and medicine.

    Science.gov (United States)

    Proctor, Elizabeth A; Dokholyan, Nikolay V

    2016-04-01

    Discrete Molecular Dynamics (DMD) is a physics-based simulation method using discrete energetic potentials rather than traditional continuous potentials, allowing microsecond time scale simulations of biomolecular systems to be performed on personal computers rather than supercomputers or specialized hardware. With the ongoing explosion in processing power even in personal computers, applications of DMD have similarly multiplied. In the past two years, researchers have used DMD to model structures of disease-implicated protein folding intermediates, study assembly of protein complexes, predict protein-protein binding conformations, engineer rescue mutations in disease-causative protein mutants, design a protein conformational switch to control cell signaling, and describe the behavior of polymeric dispersants for environmental cleanup of oil spills, among other innovative applications.

  6. Biological Studies of Posttraumatic Stress Disorder

    Science.gov (United States)

    Pitman, Roger K.; Rasmusson, Ann M.; Koenen, Karestan C.; Shin, Lisa M.; Orr, Scott P.; Gilbertson, Mark W.; Milad, Mohammed R.; Liberzon, Israel

    2016-01-01

    Preface Posttraumatic stress disorder (PTSD) is the only major mental disorder for which a cause is considered to be known, viz., an event that involves threat to the physical integrity of oneself or others and induces a response of intense fear, helplessness, or horror. Although PTSD is still largely regarded as a psychological phenomenon, over the past three decades the growth of the biological PTSD literature has been explosive, and thousands of references now exist. Ultimately, the impact of an environmental event, such as a psychological trauma, must be understood at organic, cellular, and molecular levels. The present review attempts to present the current state of this understanding, based upon psychophysiological, structural and functional neuroimaging, endocrinological, genetic, and molecular biological studies in humans and in animal models. PMID:23047775

  7. A Real-Time and Dynamic Biological Information Retrieval and Analysis System (BIRAS)

    Institute of Scientific and Technical Information of China (English)

    Qi Zhou; Hong Zhang; Meiying Geng; Chenggang Zhang

    2003-01-01

    The aim of this study is to design a biological information retrieval and analysis system (BIRAS) based on the Internet. Using the specific network protocol, BIRAS system could send and receive information from the Entrez search and retrieval system maintained by National Center for Biotechnology Information (NCBI) in USA. The literatures, nucleotide sequence, protein sequences, and other resources according to the user-defined term could then be retrieved and sent to the user by pop up message or by E-mail informing automatically using BIRAS system.All the information retrieving and analyzing processes are done in real-time. As a robust system for intelligently and dynamically retrieving and analyzing on the user-defined information, it is believed that BIRAS would be extensively used to retrieve specific information from large amount of biological databases in now days.The program is available on request from the corresponding author.

  8. A Real—Time and Dynamic Biological Information Retrieval and Analysis System(BIRAS)

    Institute of Scientific and Technical Information of China (English)

    QiZhou; HongZhang; MeiyingGeng; ChenggangZhang

    2003-01-01

    The aim of this study is to design a biological information retrieval and analysis system(BIRAS) based on the Internet.Using the specific network protocol,BIRAS system could send and receive information from the Entrez search and retrieval system maintained by National Center for Biotechnology Information(NCBI)in USA.The literatures,nucleotide sequence,protein sequences,and other resources according to the user-defined term could then be retrieved and sent to the user by pop up message or by E-amil informing automatically using BIRAS system.All the information retrieving and analyzing processes are done in real-time.As a robust system for intelligently and dynamically retrieving and analyzing on the user-defined information,it is believed that BIRAS would be extensively used to retrieve specific information from large amount of biological databases in now days.The program is available on request from the corresponding author.

  9. Dynamics of marine ecosystems: biological-physical interactions in the oceans

    National Research Council Canada - National Science Library

    Mann, K.H; Lazier, J.R.N

    2006-01-01

    .... Dynamics of Marine Ecosystems considers the influence of physical forcing on biological processes in a wide range of marine habitats including coastal estuaries, shelf-break fronts, major ocean gyres...

  10. Ancestor of the new archetypal biology: Goethe's dynamic typology as a model for contemporary evolutionary developmental biology.

    Science.gov (United States)

    Riegner, Mark F

    2013-12-01

    As understood historically, typological thinking has no place in evolutionary biology since its conceptual framework is viewed as incompatible with population thinking. In this article, I propose that what I describe as dynamic typological thinking has been confused with, and has been overshadowed by, a static form of typological thinking. This conflation results from an inability to grasp dynamic typological thinking due to the overlooked requirement to engage our cognitive activity in an unfamiliar way. Thus, analytical thinking alone is unsuited to comprehend the nature of dynamic typological thinking. Over 200 years ago, J. W. von Goethe, in his Metamorphosis of Plants (1790) and other writings, introduced a dynamic form of typological thinking that has been traditionally misunderstood and misrepresented. I describe in detail Goethe's phenomenological methodology and its contemporary value in understanding morphological patterns in living organisms. Furthermore, contrary to the implications of static typological thinking, dynamic typological thinking is perfectly compatible with evolutionary dynamics and, if rightly understood, can contribute significantly to the still emerging field of evolutionary developmental biology (evo-devo).

  11. Age Dimension Homeostasis of Physiological Systems, a Slow Dynamics Model in Biology

    Science.gov (United States)

    Kurachi, K.; Yasui, M.; Isobe, T.; Suenaga, E.; Kurachi, S.

    2006-05-01

    Throughout the life span, complex physiological systems are regulated by specific age related mechanisms, thus maintaining the age axis homeostasis. Our efforts for understanding the underlying mechanisms began about a decade ago, successfully discovering the very fist such a mechanism, we called the ASE/AIE-mediated age-related regulatory mechanism of gene expression. This mechanism can explain the major feature of the age-related increase profile of blood coagulation activity. Global analyses of the mouse liver genes and proteins revealed heir highly dynamic and complex age-related regulation, suggesting the existence of several major phases over the life span. These studies facilitate a systematic investigation into the regulatory mechanisms of age-axis homeostasis, a slow dynamics system of the complex biological systems.

  12. Systems biology strategies to study lipidomes in health and disease.

    Science.gov (United States)

    Hyötyläinen, Tuulia; Orešič, Matej

    2014-07-01

    Lipids are a diverse group of metabolites that have many key biological functions, acting as structural components of cell membranes, energy storage sources and intermediates in signaling pathways. Due to their importance lipids are under tight homeostatic control and exhibit spatial and dynamic complexity at multiple levels. It is thus not surprising that altered lipid metabolism plays important roles in the pathogenesis of most of the common diseases. Lipidomics emerged as a discipline which is dedicated to global study of lipidomes, including pathways and networks of lipids in biological systems. When studying the lipidomes at a systems level, one of the key challenges is how to address the lipid functionality at many physiological levels, from metabolic and signaling pathways to spatial systems such as cellular membranes and lipoprotein particles. Besides the better analytical techniques to study lipids, computational techniques have started to emerge which enable modeling of lipidomes in their spatial and dynamic context. Together, the recent methodological advances in lipidomics have a potential to open novel avenues for predictive and preventive medicine. This review focuses on progress in systems approaches to study lipids in health and disease, with specific emphasis on clinical applications.

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

    CERN Document Server

    Chung, Shin-Ho; Krishnamurthy, Vikram

    2007-01-01

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

  14. A physical-biological coupled model for algal dynamics in lakes.

    Science.gov (United States)

    Franke, U; Hutter, K; Jöhnk, K

    1999-03-01

    A coupled model is presented for simulating physical and biological dynamics in fresh water lakes. The physical model rests upon the assumption that the turbulent kinetic energy in a water column of the lake is fully contained in a mixed layer of variable depth. Below this layer the mechanical energy content is assumed to vanish. Additionally, the horizontal currents are ignored. This one-dimensional two-layered model describes the internal conversion of the mechanical and thermal energy input from the atmosphere into an evolution of the mixed layer depth by entrainment and detrainment mechanisms. It is supposed to form the physical domain in which the simulation of the biological processes takes place. The biological model describes mathematically the typical properties of phyto- and zooplankton, their interactions and their response to the physical environment. This description then allows the study of the behaviour of Lagrangian clusters of virtual plankton that are subjected to such environments. The essence of the model is the dynamical simulation of an arbitrary number of nutrient limited phytoplankton species and one species of zooplankton. The members of the food web above and below affect the model only statically. The model is able to reproduce the typical progression of a predator-prey interaction between phyto- and zooplankton as well as the exploitative competition for nutrients between two phytoplankton species under grazing pressure of Daphnia. It suggests that the influence of the biological system on the physical system results in a weak increase of the surface temperature for coupled simulations, but a considerably higher seasonal thermocline in spring and a lower one in autumn.

  15. ANIMO: a tool for modeling biological pathway dynamics

    NARCIS (Netherlands)

    Schivo, S.; Scholma, J.; Karperien, M.; Langerak, R.; Pol, van de J.; Post, J.N.

    2014-01-01

    Introduction: Computational methods are applied with increasing success to the analysis of complex biological systems. However, their adoption is sometimes made difficult by requiring prior knowledge about the foundations of such methods, which often come from a different branch of science. The soft

  16. ANIMO: a tool for modeling biological pathway dynamics

    NARCIS (Netherlands)

    Schivo, Stefano; Scholma, Jetse; Karperien, Hermanus Bernardus Johannes; Langerak, Romanus; van de Pol, Jan Cornelis; Post, Janine Nicole

    2014-01-01

    Introduction Computational methods are applied with increasing success to the analysis of complex biological systems. However, their adoption is sometimes made difficult by requiring prior knowledge about the foundations of such methods, which often come from a different branch of science. The

  17. Cell biology and functional dynamics of the mammalian sperm surface

    NARCIS (Netherlands)

    Gadella, B.M.; Luna, C.

    2014-01-01

    Theriogenology has now a 40-year rich history on covering sperm biological aspects with a special emphasis on farm and husbandry animals. The major and most influential of these contributions will be placed into an evolutionary perspective of ongoing and intriguing progresses made in this field. Alt

  18. Biology and population dynamics of the cactus moth, Cactoblastis cactorum

    Science.gov (United States)

    The cactus moth, Cactoblastis cactorum, was a successful biological control agent against prickly pear cacti in Australia in the 1920’s. Since then, it was introduced to other countries including the Carribean islands. In 1989, the cactus moth was reported in Florida and has continued to spread nort...

  19. History of migration studies in biological anthropology.

    Science.gov (United States)

    Mascie-Taylor, C G Nicholas; Little, Michael A

    2004-01-01

    The earliest studies of human biological factors in migration in which a clear research design was employed date back to the early 20th century in the United States. Maurice Fishberg's study of Jewish migrants, published in 1905, antedated the classic study of Franz Boas initiated in 1908. There have been two main approaches. The first approach examined the impact of migration in relation to changing environment and the importance of environmental plasticity. For example, Fishberg reported that migrants had offspring different in stature from themselves and with differences thought to be due to improvements in the environment, although some selection of genetically determined traits was suggested. Subsequently, a number of research designs have been used, ranging from Boas's simple design of sedente (nonmigrant) adults and children compared with first- and second-generation migrants; Shapiro's extension of this study in Japanese migrants to Hawai'i; Goldstein's four-fold comparison of Mexican sedentes and their offspring in Mexico, and migrants to the USA and their offspring in the USA; and Lasker's extension of Goldstein's Mexican study by including comparison of sedentes with returning emigrants. More sophisticated designs were used by Harrison and Baker in examining altitude effects and changes in subsistence and lifestyle during the 1960s through to the 1980s. The second approach has focused on the effect of migration on gene flow. For example, the clinal variation of ABO blood groups in Europe and Australia is generally purported to result from past migration, although increasing random migration for blood groups is likely to eliminate clinal variation. Migration has usually been considered from a spatial (geographic) perspective, but more recent studies have also investigated the impact of social or occupational movement (social mobility) alone, or in combination with geographic migration, and tested whether such movements are selective or random for a number

  20. Theoretical studies of combustion dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Bowman, J.M. [Emory Univ., Atlanta, GA (United States)

    1993-12-01

    The basic objectives of this research program are to develop and apply theoretical techniques to fundamental dynamical processes of importance in gas-phase combustion. There are two major areas currently supported by this grant. One is reactive scattering of diatom-diatom systems, and the other is the dynamics of complex formation and decay based on L{sup 2} methods. In all of these studies, the authors focus on systems that are of interest experimentally, and for which potential energy surfaces based, at least in part, on ab initio calculations are available.

  1. 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.

  2. Extended inclusive fitness theory: synergy and assortment drives the evolutionary dynamics in biology and economics.

    Science.gov (United States)

    Jaffe, Klaus

    2016-01-01

    W.D. Hamilton's Inclusive Fitness Theory explains the conditions that favor the emergence and maintenance of social cooperation. Today we know that these include direct and indirect benefits an agent obtains by its actions, and through interactions with kin and with genetically unrelated individuals. That is, in addition to kin-selection, assortation or homophily, and social synergies drive the evolution of cooperation. An Extended Inclusive Fitness Theory (EIFT) synthesizes the natural selection forces acting on biological evolution and on human economic interactions by assuming that natural selection driven by inclusive fitness produces agents with utility functions that exploit assortation and synergistic opportunities. This formulation allows to estimate sustainable cost/benefit threshold ratios of cooperation among organisms and/or economic agents, using existent analytical tools, illuminating our understanding of the dynamic nature of society, the evolution of cooperation among kin and non-kin, inter-specific cooperation, co-evolution, symbioses, division of labor and social synergies. EIFT helps to promote an interdisciplinary cross fertilization of the understanding of synergy by, for example, allowing to describe the role for division of labor in the emergence of social synergies, providing an integrated framework for the study of both, biological evolution of social behavior and economic market dynamics. Another example is a bio-economic understanding of the motivations of terrorists, which identifies different forms of terrorism.

  3. dNSP: a biologically inspired dynamic Neural network approach to Signal Processing.

    Science.gov (United States)

    Cano-Izquierdo, José Manuel; Ibarrola, Julio; Pinzolas, Miguel; Almonacid, Miguel

    2008-09-01

    The arriving order of data is one of the intrinsic properties of a signal. Therefore, techniques dealing with this temporal relation are required for identification and signal processing tasks. To perform a classification of the signal according with its temporal characteristics, it would be useful to find a feature vector in which the temporal attributes were embedded. The correlation and power density spectrum functions are suitable tools to manage this issue. These functions are usually defined with statistical formulation. On the other hand, in biology there can be found numerous processes in which signals are processed to give a feature vector; for example, the processing of sound by the auditory system. In this work, the dNSP (dynamic Neural Signal Processing) architecture is proposed. This architecture allows representing a time-varying signal by a spatial (thus statical) vector. Inspired by the aforementioned biological processes, the dNSP performs frequency decomposition using an analogical parallel algorithm carried out by simple processing units. The architecture has been developed under the paradigm of a multilayer neural network, where the different layers are composed by units whose activation functions have been extracted from the theory of Neural Dynamic [Grossberg, S. (1988). Nonlinear neural networks principles, mechanisms and architectures. Neural Networks, 1, 17-61]. A theoretical study of the behavior of the dynamic equations of the units and their relationship with some statistical functions allows establishing a parallelism between the unit activations and correlation and power density spectrum functions. To test the capabilities of the proposed approach, several testbeds have been employed, i.e. the frequencial study of mathematical functions. As a possible application of the architecture, a highly interesting problem in the field of automatic control is addressed: the recognition of a controlled DC motor operating state.

  4. Dynamic statistical models of biological cognition: insights from communications theory

    Science.gov (United States)

    Wallace, Rodrick

    2014-10-01

    Maturana's cognitive perspective on the living state, Dretske's insight on how information theory constrains cognition, the Atlan/Cohen cognitive paradigm, and models of intelligence without representation, permit construction of a spectrum of dynamic necessary conditions statistical models of signal transduction, regulation, and metabolism at and across the many scales and levels of organisation of an organism and its context. Nonequilibrium critical phenomena analogous to physical phase transitions, driven by crosstalk, will be ubiquitous, representing not only signal switching, but the recruitment of underlying cognitive modules into tunable dynamic coalitions that address changing patterns of need and opportunity at all scales and levels of organisation. The models proposed here, while certainly providing much conceptual insight, should be most useful in the analysis of empirical data, much as are fitted regression equations.

  5. Biologically plausible learning in recurrent neural networks reproduces neural dynamics observed during cognitive tasks.

    Science.gov (United States)

    Miconi, Thomas

    2017-02-23

    Neural activity during cognitive tasks exhibits complex dynamics that flexibly encode task-relevant variables. Chaotic recurrent networks, which spontaneously generate rich dynamics, have been proposed as a model of cortical computation during cognitive tasks. However, existing methods for training these networks are either biologically implausible, and/or require a continuous, real-time error signal to guide learning. Here we show that a biologically plausible learning rule can train such recurrent networks, guided solely by delayed, phasic rewards at the end of each trial. Networks endowed with this learning rule can successfully learn nontrivial tasks requiring flexible (context-dependent) associations, memory maintenance, nonlinear mixed selectivities, and coordination among multiple outputs. The resulting networks replicate complex dynamics previously observed in animal cortex, such as dynamic encoding of task features and selective integration of sensory inputs. We conclude that recurrent neural networks offer a plausible model of cortical dynamics during both learning and performance of flexible behavior.

  6. Development of a General Modeling Framework for Investigating Complex Interactions among Biological and Physical Ecosystem Dynamics

    Science.gov (United States)

    Bennett, C.; Poole, G. C.; Kimball, J. S.; Stanford, J. A.; O'Daniel, S. J.; Mertes, L. A.

    2005-05-01

    Historically, physical scientists have developed models with highly accurate governing equations, while biologists have excelled at abstraction (the strategic simplification of system complexity). These different modeling paradigms yield biological (e.g. food web) and physical (e.g. hydrologic) models that can be difficult to integrate. Complex biological dynamics may be impossible to represent with governing equations. Conversely, physical processes may be oversimplified in biological models. Using agent-based modeling, a technique applied widely in social sciences and economics, we are developing a general modeling system to integrate accurate representations of physical dynamics such as water and heat flux with abstracted biological processes such as nutrient transformations. The modeling system represents an ecosystem as a complex integrated network of intelligent physical and biological "agents" that store, transform, and trade ecosystem resources (e.g., water, heat, nutrients, carbon) using equations that describe either abstracted concepts and/or physical laws. The modular design of the system allows resource submodels to be developed independently and installed into the simulation architecture. The modeling system provides a useful heuristic tool to support integrated physical and biological research topics, such as the influence of hydrologic dynamics and spatio-temporal physical heterogeneity on trophic (food web) dynamics and/or nutrient cycling.

  7. SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena.

    Science.gov (United States)

    Tohsato, Yukako; Ho, Kenneth H L; Kyoda, Koji; Onami, Shuichi

    2016-11-15

    Rapid advances in live-cell imaging analysis and mathematical modeling have produced a large amount of quantitative data on spatiotemporal dynamics of biological objects ranging from molecules to organisms. There is now a crucial need to bring these large amounts of quantitative biological dynamics data together centrally in a coherent and systematic manner. This will facilitate the reuse of this data for further analysis. We have developed the Systems Science of Biological Dynamics database (SSBD) to store and share quantitative biological dynamics data. SSBD currently provides 311 sets of quantitative data for single molecules, nuclei and whole organisms in a wide variety of model organisms from Escherichia coli to Mus musculus The data are provided in Biological Dynamics Markup Language format and also through a REST API. In addition, SSBD provides 188 sets of time-lapse microscopy images from which the quantitative data were obtained and software tools for data visualization and analysis. SSBD is accessible at http://ssbd.qbic.riken.jp CONTACT: sonami@riken.jp. © The Author 2016. Published by Oxford University Press.

  8. Dynamics of problem setting and framing in citizen discussions on synthetic biology.

    Science.gov (United States)

    Betten, Afke Wieke; Broerse, Jacqueline E W; Kupper, Frank

    2017-06-01

    Synthetic biology is an emerging scientific field where engineers and biologists design and build biological systems for various applications. Developing synthetic biology responsibly in the public interest necessitates a meaningful societal dialogue. In this article, we argue that facilitating such a dialogue requires an understanding of how people make sense of synthetic biology. We performed qualitative research to unravel the underlying dynamics of problem setting and framing in citizen discussions on synthetic biology. We found that most people are not inherently for or against synthetic biology as a technology or development in itself, but that their perspectives are framed by core values about our relationships with science and technology and that sensemaking is much dependent on the context and general feelings of (dis)content. Given that there are many assumptions focused on a more binary idea of the public's view, we emphasize the need for frame awareness and understanding in a meaningful dialogue.

  9. NMR Dynamic Studies in Living Systems

    Institute of Scientific and Technical Information of China (English)

    闫永彬; 范明杰; 罗雪春; 张日清

    2002-01-01

    Nuclear magnetic resonance (NMR) can noninvasively monitor the intracellular concentrations and kinetic properties of numerous inorganic and organic compounds. These characteristics have made NMR a useful tool for dynamic studies of living systems. Applications of NMR to living systems have successfully extended to many areas, including studies of metabolic regulation, ion transport, and intracellular reaction rates in vivo. The major purpose of this review is to summarize the results that can be obtained by modern NMR techniques in living systems. With the advances of new techniques, NMR measurements of various nuclides have been performed for specific physiological purposes. Although some technical problems still remain and there are still discrepancies between NMR and traditional biochemical results, the abundant and unique information obtained from NMR spectra suggests that NMR will be more extensively applied in future studies of living systems. The fast development of these new techniques is providing many new NMR applications in living systems, as well as in structural biology.

  10. Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations.

    Science.gov (United States)

    Lin, Yao-Cheng; Boone, Morgane; Meuris, Leander; Lemmens, Irma; Van Roy, Nadine; Soete, Arne; Reumers, Joke; Moisse, Matthieu; Plaisance, Stéphane; Drmanac, Radoje; Chen, Jason; Speleman, Frank; Lambrechts, Diether; Van de Peer, Yves; Tavernier, Jan; Callewaert, Nico

    2014-09-03

    The HEK293 human cell lineage is widely used in cell biology and biotechnology. Here we use whole-genome resequencing of six 293 cell lines to study the dynamics of this aneuploid genome in response to the manipulations used to generate common 293 cell derivatives, such as transformation and stable clone generation (293T); suspension growth adaptation (293S); and cytotoxic lectin selection (293SG). Remarkably, we observe that copy number alteration detection could identify the genomic region that enabled cell survival under selective conditions (i.c. ricin selection). Furthermore, we present methods to detect human/vector genome breakpoints and a user-friendly visualization tool for the 293 genome data. We also establish that the genome structure composition is in steady state for most of these cell lines when standard cell culturing conditions are used. This resource enables novel and more informed studies with 293 cells, and we will distribute the sequenced cell lines to this effect.

  11. Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.

    Science.gov (United States)

    Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji

    2016-07-01

    This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

  12. Biological vs. physical mixing effects on benthic food web dynamics.

    Directory of Open Access Journals (Sweden)

    Ulrike Braeckman

    Full Text Available Biological particle mixing (bioturbation and solute transfer (bio-irrigation contribute extensively to ecosystem functioning in sediments where physical mixing is low. Macrobenthos transports oxygen and organic matter deeper into the sediment, thereby likely providing favourable niches to lower trophic levels (i.e., smaller benthic animals such as meiofauna and bacteria and thus stimulating mineralisation. Whether this biological transport facilitates fresh organic matter assimilation by the metazoan lower part of the food web through niche establishment (i.e., ecosystem engineering or rather deprives them from food sources, is so far unclear. We investigated the effects of the ecosystem engineers Lanice conchilega (bio-irrigator and Abra alba (bioturbator compared to abiotic physical mixing events on survival and food uptake of nematodes after a simulated phytoplankton bloom. The (13C labelled diatom Skeletonema costatum was added to 4 treatments: (1 microcosms containing the bioturbator, (2 microcosms containing the bio-irrigator, (3 control microcosms and (4 microcosms with abiotic manual surface mixing. Nematode survival and subsurface peaks in nematode density profiles were most pronounced in the bio-irrigator treatment. However, nematode specific uptake (Δδ(13C of the added diatoms was highest in the physical mixing treatment, where macrobenthos was absent and the diatom (13C was homogenised. Overall, nematodes fed preferentially on bulk sedimentary organic material rather than the added diatoms. The total C budget (µg C m(-2, which included TO(13C remaining in the sediment, respiration, nematode and macrobenthic uptake, highlighted the limited assimilation by the metazoan benthos and the major role of bacterial respiration. In summary, bioturbation and especially bio-irrigation facilitated the lower trophic levels mainly over the long-term through niche establishment. Since the freshly added diatoms represented only a limited food

  13. Study on Biological Characteristics of Livestock Eperythrozoon

    Institute of Scientific and Technical Information of China (English)

    Peng Haisheng; Xie Minghua; Mu Qionghua

    2015-01-01

    Based on the study of infection and morphological characteristics of 12 kinds of livestock Eperythrozoon,disinfection test by drugs in vitro,disinfection test by ultraviolet light,Eperythrozoon survival test at different times and temperatures,drug sensitivity test and clinical treatment of infected swines were carried out on Eperythrozoon suis and Eperythrozoon wenyonii to further study the biological characteristics. Test results showed that infection level of livestock Eperythrozoon was high,while morbidity was low. Eperythrozoon suis and Eperythrozoon wenyonii could survive for 1 year at 3- 5 ℃,180 d at 16- 26 ℃ and 30 min at- 20 ℃,while which died instantly at 65 ℃. Eperythrozoon was sensitive to general chemical disinfection drugs,while not sensitive to ultraviolet light disinfection. Transmission of Eperythrozoon mainly included contagious transmission and vertical transmission. Results of drug sensitivity test showed that Eperythrozoon was sensitive to Tetracycline and antigen insect drugs. Sizes and shapes of different livestock Eperythrozoon were different. The study provided a scientific basis for the effective prevention and treatment of livestock Eperythrozoonosis.

  14. Phytochemical and biological studies of Agave attenuata.

    Science.gov (United States)

    Rizwan, Komal; Zubair, Muhammad; Rasool, Nasir; Riaz, Muhammad; Zia-Ul-Haq, Muhammad; de Feo, Vincenzo

    2012-01-01

    The present study was conducted to examine various biological activities of a methanol extract of Agave attenuata leaves. GC-MS analysis of the n-hexane fraction from the extract revealed the presence of 31 compounds, with mono-2-ethylhexyl phthalate (11.37%), 1,2-benzenedicarboxylic acid (6.33%), n-docosane (6.30%) and eicosane (6.02%) as the major components. The leaves contained appreciable levels of total phenolic contents (10.541-39.35 GAE, mg/100 g) and total flavonoid contents (43.35-304.8 CE, mg/100 g). The extract and some of its fractions showed moderate antimicrobial effects. Leaves extract and fractions also exhibited a good antioxidant potential when measured by DPPH radical scavenging activity and inhibition of lipid peroxidation assays. The hemolytic effect of the plant was found to be in a range of 1.01%-2.64%. From the present study it is concluded that this plant could be used as a source of natural antioxidants and functional food nutraceutical applications.

  15. Novel nuclear magnetic resonance techniques for studying biological molecules

    Energy Technology Data Exchange (ETDEWEB)

    Laws, David D.

    2000-06-01

    Over the fifty-five year history of Nuclear Magnetic Resonance (NMR), considerable progress has been made in the development of techniques for studying the structure, function, and dynamics of biological molecules. The majority of this research has involved the development of multi-dimensional NMR experiments for studying molecules in solution, although in recent years a number of groups have begun to explore NMR methods for studying biological systems in the solid-state. Despite this new effort, a need still exists for the development of techniques that improve sensitivity, maximize information, and take advantage of all the NMR interactions available in biological molecules. In this dissertation, a variety of novel NMR techniques for studying biomolecules are discussed. A method for determining backbone ({phi}/{psi}) dihedral angles by comparing experimentally determined {sup 13}C{sub a}, chemical-shift anisotropies with theoretical calculations is presented, along with a brief description of the theory behind chemical-shift computation in proteins and peptides. The utility of the Spin-Polarization Induced Nuclear Overhauser Effect (SPINOE) to selectively enhance NMR signals in solution is examined in a variety of systems, as are methods for extracting structural information from cross-relaxation rates that can be measured in SPINOE experiments. Techniques for the production of supercritical and liquid laser-polarized xenon are discussed, as well as the prospects for using optically pumped xenon as a polarizing solvent. In addition, a detailed study of the structure of PrP 89-143 is presented. PrP 89-143 is a 54 residue fragment of the prion proteins which, upon mutation and aggregation, can induce prion diseases in transgenic mice. Whereas the structure of the wild-type PrP 89-143 is a generally unstructured mixture of {alpha}-helical and {beta}-sheet conformers in the solid state, the aggregates formed from the PrP 89-143 mutants appear to be mostly {beta}-sheet.

  16. Galectin-9: From cell biology to complex disease dynamics

    Indian Academy of Sciences (India)

    SEBASTIAN JOHN; RASHMI MISHRA

    2016-09-01

    Galectins is a family of non-classically secreted, β-galactoside-binding proteins that has recently received considerableattention in the spatio-temporal regulation of surface ‘signal lattice’ organization, membrane dynamics, cell-adhesionand disease therapeutics. Galectin-9 is a unique member of this family, with two non-homologous carbohydraterecognition domains joined by a linker peptide sequence of variable lengths, generating isoforms with distinctproperties and functions in both physiological and pathological settings, such as during development, immunereaction, neoplastic transformations and metastasis. In this review, we summarize the latest knowledge on thestructure, receptors, cellular targets, trafficking pathways and functional properties of galectin-9 and discuss howgalectin-9-mediated signalling cascades can be exploited in cancers and immunotherapies.

  17. Diffusion in crowded biological environments: applications of Brownian dynamics

    Directory of Open Access Journals (Sweden)

    Długosz Maciej

    2011-03-01

    Full Text Available Abstract Biochemical reactions in living systems occur in complex, heterogeneous media with total concentrations of macromolecules in the range of 50 - 400 mgml. Molecular species occupy a significant fraction of the immersing medium, up to 40% of volume. Such complex and volume-occupied environments are generally termed 'crowded' and/or 'confined'. In crowded conditions non-specific interactions between macromolecules may hinder diffusion - a major process determining metabolism, transport, and signaling. Also, the crowded media can alter, both qualitatively and quantitatively, the reactions in vivo in comparison with their in vitro counterparts. This review focuses on recent developments in particle-based Brownian dynamics algorithms, their applications to model diffusive transport in crowded systems, and their abilities to reproduce and predict the behavior of macromolecules under in vivo conditions.

  18. Galectin-9: From cell biology to complex disease dynamics.

    Science.gov (United States)

    John, Sebastian; Mishra, Rashmi

    2016-09-01

    Galectins is a family of non-classically secreted, beta-galactoside-binding proteins that has recently received considerable attention in the spatio-temporal regulation of surface 'signal lattice' organization, membrane dynamics, cell-adhesion and disease therapeutics. Galectin-9 is a unique member of this family, with two non-homologous carbohydrate recognition domains joined by a linker peptide sequence of variable lengths, generating isoforms with distinct properties and functions in both physiological and pathological settings, such as during development, immune reaction, neoplastic transformations and metastasis. In this review, we summarize the latest knowledge on the structure, receptors, cellular targets, trafficking pathways and functional properties of galectin-9 and discuss how galectin-9-mediated signalling cascades can be exploited in cancers and immunotherapies.

  19. Circulatory bubble dynamics: from physical to biological aspects.

    Science.gov (United States)

    Papadopoulou, Virginie; Tang, Meng-Xing; Balestra, Costantino; Eckersley, Robert J; Karapantsios, Thodoris D

    2014-04-01

    Bubbles can form in the body during or after decompression from pressure exposures such as those undergone by scuba divers, astronauts, caisson and tunnel workers. Bubble growth and detachment physics then becomes significant in predicting and controlling the probability of these bubbles causing mechanical problems by blocking vessels, displacing tissues, or inducing an inflammatory cascade if they persist for too long in the body before being dissolved. By contrast to decompression induced bubbles whose site of initial formation and exact composition are debated, there are other instances of bubbles in the bloodstream which are well-defined. Gas emboli unwillingly introduced during surgical procedures and ultrasound microbubbles injected for use as contrast or drug delivery agents are therefore also discussed. After presenting the different ways that bubbles can end up in the human bloodstream, the general mathematical formalism related to the physics of bubble growth and detachment from decompression is reviewed. Bubble behavior in the bloodstream is then discussed, including bubble dissolution in blood, bubble rheology and biological interactions for the different cases of bubble and blood composition considered.

  20. Population dynamics in biological treatment process. ; Population dynamics of bacteria for biological phosphorus removal. Population dynamics to kankyo joka. ; Datsurin kin gun no population dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Okada, M. (Hiroshima Univ., Hiroshima (Japan). Faculty of Engineering)

    1992-09-10

    The microbial industry can easily cultivate only the specific microorganism by introducing the closed reaction system and the sterile operation. When the superior bacteria is selected or it is created by the gene manipulation, therefore, it is not so much difficult that it is utilized for production. Since the water treatment is an open reaction system many microorganisms can join, however, it becomes to be important that how the necessary microorganisms, for example, the dephosphorylation bacteria etc. out of them are let fixed in the reaction system, and win in a competition with the other microorganisms, and in addition, are let display their functions stably for a long period. In this regard, in this paper, concerning to the issues that whether the dephosphorylation bacteria exists or not, how the behavior of dephosphorylation bacteria in the activated sludge should be clarified, what kind of behavior the dephosphorylation bacteria shows in the dephosphorylation activated sludge and so forth, grasping the population dynamics of microorganism, and furthermore, including the methodology to control it, is outlined. 31 refs., 2 figs., 1 tab.

  1. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

    DEFF Research Database (Denmark)

    Papaleo, Elena

    2015-01-01

    In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the pos......In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

  2. Single-molecule conformational dynamics of a biologically functional hydroxocobalamin riboswitch.

    Science.gov (United States)

    Holmstrom, Erik D; Polaski, Jacob T; Batey, Robert T; Nesbitt, David J

    2014-12-03

    Riboswitches represent a family of highly structured regulatory elements found primarily in the leader sequences of bacterial mRNAs. They function as molecular switches capable of altering gene expression; commonly, this occurs via a conformational change in a regulatory element of a riboswitch that results from ligand binding in the aptamer domain. Numerous studies have investigated the ligand binding process, but little is known about the structural changes in the regulatory element. A mechanistic description of both processes is essential for deeply understanding how riboswitches modulate gene expression. This task is greatly facilitated by studying all aspects of riboswitch structure/dynamics/function in the same model system. To this end, single-molecule fluorescence resonance energy transfer (smFRET) techniques have been used to directly observe the conformational dynamics of a hydroxocobalamin (HyCbl) binding riboswitch (env8HyCbl) with a known crystallographic structure.1 The single-molecule RNA construct studied in this work is unique in that it contains all of the structural elements both necessary and sufficient for regulation of gene expression in a biological context. The results of this investigation reveal that the undocking rate constant associated with the disruption of a long-range kissing-loop (KL) interaction is substantially decreased when the ligand is bound to the RNA, resulting in a preferential stabilization of the docked conformation. Notably, the formation of this tertiary KL interaction directly sequesters the Shine-Dalgarno sequence (i.e., the ribosome binding site) via base-pairing, thus preventing translation initiation. These results reveal that the conformational dynamics of this regulatory switch are quantitatively described by a four-state kinetic model, whereby ligand binding promotes formation of the KL interaction. The results of complementary cell-based gene expression experiments conducted in Escherichia coli are highly

  3. Advanced models of neural networks nonlinear dynamics and stochasticity in biological neurons

    CERN Document Server

    Rigatos, Gerasimos G

    2015-01-01

    This book provides a complete study on neural structures exhibiting nonlinear and stochastic dynamics, elaborating on neural dynamics by introducing advanced models of neural networks. It overviews the main findings in the modelling of neural dynamics in terms of electrical circuits and examines their stability properties with the use of dynamical systems theory. It is suitable for researchers and postgraduate students engaged with neural networks and dynamical systems theory.

  4. Phytochemical and biological studies of bryophytes.

    Science.gov (United States)

    Asakawa, Yoshinori; Ludwiczuk, Agnieszka; Nagashima, Fumihiro

    2013-07-01

    The bryophytes contain the Marchantiophyta (liverworts), Bryophyta (mosses) and Anthocerotophyta (hornworts). Of these, the Marchantiophyta have a cellular oil body which produce a number of mono-, sesqui- and di-terpenoids, aromatic compounds like bibenzyl, bis-bibenzyls and acetogenins. Most sesqui- and di-terpenoids obtained from liverworts are enantiomers of those found in higher plants. Many of these compounds display a characteristic odor, and can have interesting biological activities. These include: allergenic contact dermatitis, antimicrobial, antifungal and antiviral, cytotoxic, insecticidal, insect antifeedant, superoxide anion radical release, 5-lipoxygenase, calmodulin, hyaluronidase, cyclooxygenase, DNA polymerase β, and α-glucosidase and NO production inhibitory, antioxidant, piscicidal, neurotrophic and muscle relaxing activities among others. Each liverwort biosynthesizes unique components, which are valuable for their chemotaxonomic classification. Typical chemical structures and biological activity of the selected liverwort constituents as well as the hemi- and total synthesis of some biologically active compounds are summarized.

  5. A systems biology approach to cancer: fractals, attractors, and nonlinear dynamics.

    Science.gov (United States)

    Dinicola, Simona; D'Anselmi, Fabrizio; Pasqualato, Alessia; Proietti, Sara; Lisi, Elisabetta; Cucina, Alessandra; Bizzarri, Mariano

    2011-03-01

    Cancer begins to be recognized as a highly complex disease, and advanced knowledge of the carcinogenic process claims to be acquired by means of supragenomic strategies. Experimental data evidence that tumor emerges from disruption of tissue architecture, and it is therefore consequential that the tissue level should be considered the proper level of observation for carcinogenic studies. This paradigm shift imposes to move from a reductionistic to a systems biology approach. Indeed, cell phenotypes are emergent modes arising through collective nonlinear interactions among different cellular and microenvironmental components, generally described by a phase space diagram, where stable states (attractors) are embedded into a landscape model. Within this framework cell states and cell transitions are generally conceived as mainly specified by the gene-regulatory network. However, the system's dynamics cannot be reduced to only the integrated functioning of the genome-proteome network, and the cell-stroma interacting system must be taken into consideration in order to give a more reliable picture. As cell form represents the spatial geometric configuration shaped by an integrated set of cellular and environmental cues participating in biological functions control, it is conceivable that fractal-shape parameters could be considered as "omics" descriptors of the cell-stroma system. Within this framework it seems that function follows form, and not the other way around.

  6. Yeast Population Dynamics during the Fermentation and Biological Aging of Sherry Wines

    Science.gov (United States)

    Esteve-Zarzoso, B.; Peris-Torán, M. J.; García-Maiquez, E.; Uruburu, F.; Querol, A.

    2001-01-01

    Molecular and physiological analyses were used to study the evolution of the yeast population, from alcoholic fermentation to biological aging in the process of “fino” sherry wine making. The four races of “flor” Saccharomyces cerevisiae (beticus, cheresiensis, montuliensis, and rouxii) exhibited identical restriction patterns for the region spanning the internal transcribed spacers 1 and 2 (ITS-1 and ITS-2) and the 5.8S rRNA gene, but this pattern was different, from those exhibited by non-flor S. cerevisiae strains. This flor-specific pattern was detected only after wines were fortified, never during alcoholic fermentation, and all the strains isolated from the velum exhibited the typical flor yeast pattern. By restriction fragment length polymorphism of mitochondrial DNA and karyotyping, we showed that (i) the native strain is better adapted to fermentation conditions than commercial strains; (ii) two different populations of S. cerevisiae strains are involved in the process of elaboration, of fino sherry wine, one of which is responsible for must fermentation and the other, for wine aging; and (iii) one strain was dominant in the flor population integrating the velum from sherry wines produced in González Byass wineries, although other authors have described a succession of races of flor S. cerevisiae during wine aging. Analyzing all these results together, we conclude that yeast population dynamics during biological aging is a complex phenomenon and differences between yeast populations from different wineries can be observed. PMID:11319081

  7. Polyketide stereocontrol: a study in chemical biology

    Science.gov (United States)

    2017-01-01

    The biosynthesis of reduced polyketides in bacteria by modular polyketide synthases (PKSs) proceeds with exquisite stereocontrol. As the stereochemistry is intimately linked to the strong bioactivity of these molecules, the origins of stereochemical control are of significant interest in attempts to create derivatives of these compounds by genetic engineering. In this review, we discuss the current state of knowledge regarding this key aspect of the biosynthetic pathways. Given that much of this information has been obtained using chemical biology tools, work in this area serves as a showcase for the power of this approach to provide answers to fundamental biological questions.

  8. Task Dynamics in a College Biology Course for Prospective Elementary Teachers.

    Science.gov (United States)

    Moscovici, Hedy

    2001-01-01

    Explores the dynamic profile of a task as interpreted by a group of six prospective elementary teachers enrolled in a college biology course. Describes the shift from a planned task to a transitional task and finally an enacted task. (Author/MM)

  9. Assessing Students' Ability to Trace Matter in Dynamic Systems in Cell Biology

    Science.gov (United States)

    Wilson, Christopher D.; Anderson, Charles W.; Heidemann, Merle; Merrill, John E.; Merritt, Brett W.; Richmond, Gail; Sibley, Duncan F.; Parker, Joyce M.

    2006-01-01

    College-level biology courses contain many complex processes that are often taught and learned as detailed narratives. These processes can be better understood by perceiving them as dynamic systems that are governed by common fundamental principles. Conservation of matter is such a principle, and thus tracing matter is an essential step in…

  10. Task Dynamics in a College Biology Course for Prospective Elementary Teachers.

    Science.gov (United States)

    Moscovici, Hedy

    2001-01-01

    Explores the dynamic profile of a task as interpreted by a group of six prospective elementary teachers enrolled in a college biology course. Describes the shift from a planned task to a transitional task and finally an enacted task. (Author/MM)

  11. Missile Studies with a Biological Target

    Science.gov (United States)

    1961-01-23

    Biology and Medicine of the U. S. Atomic Energy Commission and to the Office of Civil Defense and Mobilization (formerly the Federal Civil Defense...None Ear. left, laceration severed a peripheral blood vessel. 4P3A 4 1 Shoulder, left, 14 mm deep to scapular spine with small "nick" fracture

  12. Study of biocompatible and biological materials

    CERN Document Server

    Pecheva, Emilia

    2017-01-01

    The book gives an overview on biomineralization, biological, biocompatible and biomimetic materials. It reveals the use of biomaterials alone or in composites, how their performance can be improved by tailoring their surface properties by external factors and how standard surface modification techniques can be applied in the area of biomaterials to beneficially influence their growth on surfaces.

  13. Pharmacovigilance of biologicals : dynamics in post-approval safety learning

    NARCIS (Netherlands)

    Vermeer, N.S.

    2015-01-01

    Regulatory decisions to allow new drugs on the market by definition have to accept a certain level of uncertainty about the full benefit-risk balance. Pre-approval studies typically provide information on a limited number of patients over a relative short follow-up period, and handle strict inclusio

  14. Exploring the free-energy landscapes of biological systems with steered molecular dynamics.

    Science.gov (United States)

    Chen, L Y

    2011-04-01

    We perform steered molecular dynamics (SMD) simulations and use the Brownian dynamics fluctuation-dissipation-theorem (BD-FDT) to accurately compute the free-energy profiles for several biophysical processes of fundamental importance: hydration of methane and cations, binding of benzene to T4-lysozyme L99A mutant, and permeation of water through aquaglyceroporin. For each system, the center-of-mass of the small molecule (methane, ion, benzene, and water, respectively) is steered (pulled) at a given speed over a period of time, during which the system transitions from one macroscopic state/conformation (State A) to another one (State B). The mechanical work of pulling the system is measured during the process, sampling a forward pulling path. Then the reverse pulling is conducted to sample a reverse path from B back to A. Sampling a small number of forward and reverse paths, we are able to accurately compute the free-energy profiles for all the afore-listed systems that represent various important aspects of biological physics. The numerical results are in excellent agreement with the experimental data and/or other computational studies available in the literature.

  15. Teacher's Study Guide on the Biology of Human Populations: Africa.

    Science.gov (United States)

    United Nations Educational, Scientific, and Cultural Organization, Paris (France).

    This teacher's guide is designed to give background information on current biological subjects not usually treated in student texts. The book is divided into five parts, each representing one of the following topics: (1) evolution of human populations; (2) environment of human populations; (3) dynamics of human populations; (4) reproduction in…

  16. DOTcvpSB, a software toolbox for dynamic optimization in systems biology

    Directory of Open Access Journals (Sweden)

    Balsa-Canto Eva

    2009-06-01

    Full Text Available Abstract Background Mathematical optimization aims to make a system or design as effective or functional as possible, computing the quality of the different alternatives using a mathematical model. Most models in systems biology have a dynamic nature, usually described by sets of differential equations. Dynamic optimization addresses this class of systems, seeking the computation of the optimal time-varying conditions (control variables to minimize or maximize a certain performance index. Dynamic optimization can solve many important problems in systems biology, including optimal control for obtaining a desired biological performance, the analysis of network designs and computer aided design of biological units. Results Here, we present a software toolbox, DOTcvpSB, which uses a rich ensemble of state-of-the-art numerical methods for solving continuous and mixed-integer dynamic optimization (MIDO problems. The toolbox has been written in MATLAB and provides an easy and user friendly environment, including a graphical user interface, while ensuring a good numerical performance. Problems are easily stated thanks to the compact input definition. The toolbox also offers the possibility of importing SBML models, thus enabling it as a powerful optimization companion to modelling packages in systems biology. It serves as a means of handling generic black-box models as well. Conclusion Here we illustrate the capabilities and performance of DOTcvpSB by solving several challenging optimization problems related with bioreactor optimization, optimal drug infusion to a patient and the minimization of intracellular oscillations. The results illustrate how the suite of solvers available allows the efficient solution of a wide class of dynamic optimization problems, including challenging multimodal ones. The toolbox is freely available for academic use.

  17. Chemical approaches to studying stem cell biology

    Institute of Scientific and Technical Information of China (English)

    Wenlin Li; Kai Jiang; Wanguo Wei; Yan Shi; Sheng Ding

    2013-01-01

    Stem cells,including both pluripotent stem cells and multipotent somatic stem cells,hold great potential for interrogating the mechanisms of tissue development,homeostasis and pathology,and for treating numerous devastating diseases.Establishment of in vitro platforms to faithfully maintain and precisely manipulate stem cell fates is essential to understand the basic mechanisms of stem cell biology,and to translate stem cells into regenerative medicine.Chemical approaches have recently provided a number of small molecules that can be used to control cell selfrenewal,lineage differentiation,reprogramming and regeneration.These chemical modulators have been proven to be versatile tools for probing stem cell biology and manipulating cell fates toward desired outcomes.Ultimately,this strategy is promising to be a new frontier for drug development aimed at endogenous stem cell modulation.

  18. Gravitational studies in cellular and developmental biology

    Science.gov (United States)

    Spooner, B. S.

    1992-01-01

    The paucity of data on the role of gravity in cellular and developmental biology has been examined, and a hypothesis has been generated that unifies potential gravity sensitivity in both plant and animal systems. This hypothesis considers the macromolecular order and functional importance of the extracellular matrix compartment, the intracellular cytoskeleton compartment, and the connecting plasma membrane-signal transduction compartment of plant and animal systems as potentially sensitive to alterations in the unit gravity environment in which they evolved.

  19. Dynamic transcriptional signatures and network responses for clinical symptoms in influenza-infected human subjects using systems biology approaches.

    Science.gov (United States)

    Linel, Patrice; Wu, Shuang; Deng, Nan; Wu, Hulin

    2014-10-01

    Recent studies demonstrate that human blood transcriptional signatures may be used to support diagnosis and clinical decisions for acute respiratory viral infections such as influenza. In this article, we propose to use a newly developed systems biology approach for time course gene expression data to identify significant dynamically response genes and dynamic gene network responses to viral infection. We illustrate the methodological pipeline by reanalyzing the time course gene expression data from a study with healthy human subjects challenged by live influenza virus. We observed clear differences in the number of significant dynamic response genes (DRGs) between the symptomatic and asymptomatic subjects and also identified DRG signatures for symptomatic subjects with influenza infection. The 505 common DRGs shared by the symptomatic subjects have high consistency with the signature genes for predicting viral infection identified in previous works. The temporal response patterns and network response features were carefully analyzed and investigated.

  20. Structural and dynamical characterization of a biologically active unfolded fibronectin-binding protein from Staphylococcus aureus.

    Science.gov (United States)

    Penkett, C J; Redfield, C; Jones, J A; Dodd, I; Hubbard, J; Smith, R A; Smith, L J; Dobson, C M

    1998-12-01

    A 130-residue fragment (D1-D4) taken from a fibronectin-binding protein of Staphylococcus aureus, which contains four fibronectin-binding repeats and is unfolded but biologically active at neutral pH, has been studied extensively by NMR spectroscopy. Using heteronuclear multidimensional techniques, the conformational properties of D1-D4 have been defined at both a global and a local level. Diffusion studies give an average effective radius of 26.2 +/- 0.1 A, approximately 75% larger than that expected for a globular protein of this size. Analysis of chemical shift, 3JHNalpha coupling constant, and NOE data show that the experimental parameters agree well overall with values measured in short model peptides and with predictions from a statistical model for a random coil. Sequences where specific features give deviations from these predictions for a random coil have however been identified. These arise from clustering of hydrophobic side chains and electrostatic interactions between charged groups. 15N relaxation studies demonstrate that local fluctuations of the chain are the dominant motional process that gives rise to relaxation of the 15N nuclei, with a persistence length of approximately 7-10 residues for the segmental motion. The consequences of the structural and dynamical properties of this unfolded protein for its biological role of binding to fibronectin have been considered. It is found that the regions of the sequence involved in binding have a high propensity for populating extended conformations, a feature that would allow a number of both charged and hydrophobic groups to be presented to fibronectin for highly specific binding.

  1. Quasi-elastic neutron scattering studies of protein dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Rorschach, H.E.

    1991-03-20

    The techniques of X-ray and neutron scattering that have been so successfully applied to the study of the structure of biological macromolecules have in recent years been also used for the study of the thermal motion of these molecules. The diffraction of X-rays has been widely used to investigate the high-frequency motion of the heavy-atom residues of proteins. In these studies, the mean-square thermal amplitudes can be determined from the intensities of the sharp structural lines obtained from single crystals of the hydrated proteins. Similar information can be obtained on lighter atoms from the study of the neutron scattering from single crystals. The results of these measurements are coupled closely to the rapidly developing field of theoretical molecular dynamics which is now being applied to study the dynamics of large biological molecules. This report discusses research in this area.

  2. Bayesian networks: a powerful tool for systems biology study

    Institute of Scientific and Technical Information of China (English)

    Xiu-Jie WANG

    2010-01-01

    @@ Higher Education Press and Springer-Verlag Berlin Heidelberg 2010The wide application of omics research approaches caused a burst of biological data in the past decade, and also promoted the growth of systems biology, a research field that studies biological questions from a genome-wide point of view. One feature of systems biology study is to integrate and identify. Not only experiments are carried out at whole-genome scales, but also data from various resources, such as genomics, transcriptomics, proteomics,and metabolics data, need to be integrated to identify correlations among targeted entities. Therefore, plenty amounts of experimental data, robust statistical methods, and reliable network construction models are indispensable for systems biology study. Among the available network construction models, Bayesian network is considered as one of the most effective methods available so far for biological network predictions (Pe'er, 2005).

  3. Dynamic optimization of distributed biological systems using robust and efficient numerical techniques

    Directory of Open Access Journals (Sweden)

    Vilas Carlos

    2012-07-01

    Full Text Available Abstract Background Systems biology allows the analysis of biological systems behavior under different conditions through in silico experimentation. The possibility of perturbing biological systems in different manners calls for the design of perturbations to achieve particular goals. Examples would include, the design of a chemical stimulation to maximize the amplitude of a given cellular signal or to achieve a desired pattern in pattern formation systems, etc. Such design problems can be mathematically formulated as dynamic optimization problems which are particularly challenging when the system is described by partial differential equations. This work addresses the numerical solution of such dynamic optimization problems for spatially distributed biological systems. The usual nonlinear and large scale nature of the mathematical models related to this class of systems and the presence of constraints on the optimization problems, impose a number of difficulties, such as the presence of suboptimal solutions, which call for robust and efficient numerical techniques. Results Here, the use of a control vector parameterization approach combined with efficient and robust hybrid global optimization methods and a reduced order model methodology is proposed. The capabilities of this strategy are illustrated considering the solution of a two challenging problems: bacterial chemotaxis and the FitzHugh-Nagumo model. Conclusions In the process of chemotaxis the objective was to efficiently compute the time-varying optimal concentration of chemotractant in one of the spatial boundaries in order to achieve predefined cell distribution profiles. Results are in agreement with those previously published in the literature. The FitzHugh-Nagumo problem is also efficiently solved and it illustrates very well how dynamic optimization may be used to force a system to evolve from an undesired to a desired pattern with a reduced number of actuators. The presented

  4. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.

    Science.gov (United States)

    Papaleo, Elena

    2015-01-01

    In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

  5. System chemical biology studies of endocrine disruptors

    DEFF Research Database (Denmark)

    Taboureau, Olivier; Oprea, Tudor I.

    Endocrine disrupting chemicals (EDCs) alter hormonal balance and other physiological systems through inappropriate developmental or adult exposure, perturbing the reproductive function of further generations. While disruption of key receptors (e.g., estrogen, androgen, and thyroid) at the ligand...... binding domain (LBD) has been associated with EDCs, a significant number of EDCs do not appear to influence the LBDs of these receptors. Therefore, we evaluated the potential biological effects of EDCs in humans with the aim to rationalize the etiology of certain disorders associated with the reproductive...

  6. A Linked Physical and Biological Framework to Assess Biogeochemical Dynamics in a Shallow Estuarine Ecosystem

    Science.gov (United States)

    Buzzelli, C. P.; Wetzel, R. L.; Meyers, M. B.

    1999-12-01

    The littoral zone of Chesapeake Bay contains a mosaic of shallow vegetated and nonvegetated habitats with biotic components that are sensitive to changes in biological and physical driving factors. Static and dynamic modelling frameworks provide an integrative way to study complex hydrodynamic and biogeochemical processes in linked estuarine habitats. In this study we describe a spatial simulation model developed and calibrated relative to a specific littoral zone, estuarine ecosystem. The model consisted of four distinct habitats that contained phytoplankton, sediment microalgae, Zostera marina (eelgrass), and Spartina alterniflora. There was tidal exchange of phytoplankton, particulate and dissolved organic carbon and dissolved inorganic nitrogen between the littoral zone ecosystem and the offshore channel. Physical exchange and biogeochemical transformations within the habitats determined water column concentrations in each habitat. Predicted subtidal water column concentrations and Z. marina and S. alterniflora biomass were within the variability of validation data and the predicted annual rates of net primary production were similar to measured rates. Phytoplankton accounted for 17%, sediment microalgae 46%, the Z. marina community 24% and S. alterniflora 13% of the annual littoral zone primary production. The linked habitat model provided insights into producer, habitat and ecosystem carbon and nitrogen properties that might not have been evident with stand-alone models. Although it was an intra-ecosystem sink for particulate carbon, the seagrass habitat was a DOC source and responsible for over 30% of the littoral zone carbon and nitrogen primary production. The model predicted that the Goodwin Islands littoral zone was a sink of channel derived POC, but a source of DOC to the surrounding estuary. The framework created in this study of estuarine ecosystem dynamics is applicable to many different aquatic systems over a range of spatial and temporal scales.

  7. Biologically inspired design framework for Robot in Dynamic Environments using Framsticks

    CERN Document Server

    S., Raja Mohamed

    2012-01-01

    Robot design complexity is increasing day by day especially in automated industries. In this paper we propose biologically inspired design framework for robots in dynamic world on the basis of Co-Evolution, Virtual Ecology, Life time learning which are derived from biological creatures. We have created a virtual khepera robot in Framsticks and tested its operational credibility in terms hardware and software components by applying the above suggested techniques. Monitoring complex and non complex behaviors in different environments and obtaining the parameters that influence software and hardware design of the robot that influence anticipated and unanticipated failures, control programs of robot generation are the major concerns of our techniques.

  8. Novel nuclear magnetic resonance techniques for studying biological molecules

    Energy Technology Data Exchange (ETDEWEB)

    Laws, David Douglas [Univ. of California, Berkeley, CA (United States)

    2000-06-01

    Over the fifty-five year history of Nuclear Magnetic Resonance (NMR), considerable progress has been made in the development of techniques for studying the structure, function, and dynamics of biological molecules. The majority of this research has involved the development of multi-dimensional NMR experiments for studying molecules in solution, although in recent years a number of groups have begun to explore NMR methods for studying biological systems in the solid-state. Despite this new effort, a need still exists for the development of techniques that improve sensitivity, maximize information, and take advantage of all the NMR interactions available in biological molecules. In this dissertation, a variety of novel NMR techniques for studying biomolecules are discussed. A method for determining backbone (Φ/Ψ) dihedral angles by comparing experimentally determined 13Ca, chemical-shift anisotropies with theoretical calculations is presented, along with a brief description of the theory behind chemical-shift computation in proteins and peptides. The utility of the Spin-Polarization Induced Nuclear Overhauser Effect (SPINOE) to selectively enhance NMR signals in solution is examined in a variety of systems, as are methods for extracting structural information from cross-relaxation rates that can be measured in SPINOE experiments. Techniques for the production of supercritical and liquid laser-polarized xenon are discussed, as well as the prospects for using optically pumped xenon as a polarizing solvent. In addition, a detailed study of the structure of PrP 89-143 is presented. PrP 89-143 is a 54 residue fragment of the prion proteins which, upon mutation and aggregation, can induce prion diseases in transgenic mice. Whereas the structure of the wild-type PrP 89-143 is a generally unstructured mixture of α-helical and β-sheet conformers in the solid state, the aggregates formed from the PrP 89-143 mutants appear to be mostly β-sheet.

  9. New advances in pollination biology and the studies in China

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Pollination biology is the study of the various biological features in relation to the event of pollen transfer. It is one of the central concerns of plant reproductive ecology and evolutionary biology. In this paper, we attempt to introduce the main advances and some new interests in pollination biology and make a brief review of the research work that has been done in China in recent years. We also give some insights into the study that we intend to carry out in this field in the future.

  10. Stochastic Dynamics of Proteins and the Action of Biological Molecular Machines

    Directory of Open Access Journals (Sweden)

    Michal Kurzynski

    2014-04-01

    Full Text Available It is now well established that most if not all enzymatic proteins display a slow stochastic dynamics of transitions between a variety of conformational substates composing their native state. A hypothesis is stated that the protein conformational transition networks, as just as higher-level biological networks, the protein interaction network, and the metabolic network, have evolved in the process of self-organized criticality. Here, the criticality means that all the three classes of networks are scale-free and, moreover, display a transition from the fractal organization on a small length-scale to the small-world organization on the large length-scale. Good mathematical models of such networks are stochastic critical branching trees extended by long-range shortcuts. Biological molecular machines are proteins that operate under isothermal conditions and hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free energy-donating (input reaction and the free energy-accepting (output one. The far-from-equilibrium degree of coupling between the output and the input reaction fluxes have been studied both theoretically and by means of the Monte Carlo simulations on model networks. For single input and output gates the degree of coupling cannot exceed unity. Study simulations of random walks on model networks involving more extended gates indicate that the case of the degree of coupling value higher than one is realized on the mentioned above critical branching trees extended by long-range shortcuts.

  11. Bio-logic builder: a non-technical tool for building dynamical, qualitative models.

    Directory of Open Access Journals (Sweden)

    Tomáš Helikar

    Full Text Available Computational modeling of biological processes is a promising tool in biomedical research. While a large part of its potential lies in the ability to integrate it with laboratory research, modeling currently generally requires a high degree of training in mathematics and/or computer science. To help address this issue, we have developed a web-based tool, Bio-Logic Builder, that enables laboratory scientists to define mathematical representations (based on a discrete formalism of biological regulatory mechanisms in a modular and non-technical fashion. As part of the user interface, generalized "bio-logic" modules have been defined to provide users with the building blocks for many biological processes. To build/modify computational models, experimentalists provide purely qualitative information about a particular regulatory mechanisms as is generally found in the laboratory. The Bio-Logic Builder subsequently converts the provided information into a mathematical representation described with Boolean expressions/rules. We used this tool to build a number of dynamical models, including a 130-protein large-scale model of signal transduction with over 800 interactions, influenza A replication cycle with 127 species and 200+ interactions, and mammalian and budding yeast cell cycles. We also show that any and all qualitative regulatory mechanisms can be built using this tool.

  12. Phytochemical and biological studies of Ochna species.

    Science.gov (United States)

    Bandi, Anil Kumar Reddy; Lee, Dong-Ung; Tih, Raphaël Ghogomu; Gunasekar, Duvvuru; Bodo, Bernard

    2012-02-01

    The genus Ochna L. (Gr, Ochne; wild pear), belonging to the Ochnaceae family, includes ca. 85 species of evergreen trees, shrubs, and shrublets, distributed in tropical Asia, Africa, and America. Several members of this genus have long been used in folk medicine for treatment of various ailments, such as asthma, dysentery, epilepsy, gastric disorders, menstrual complaints, lumbago, ulcers, as an abortifacient, and as antidote against snake bites. Up to now, ca. 111 constituents, viz. flavonoids (including bi-, tri-, and pentaflavonoids), anthranoids, triterpenes, steroids, fatty acids, and a few others have been identified in the genus. Crude extracts and isolated compounds have been found to exhibit analgesic, anti-HIV-1, anti-inflammatory, antimalarial, antimicrobial, and cytotoxic activities, lending support to the rationale behind several of its traditional uses. The present review compiles the informations concerning the traditional uses, phytochemistry, and biological activities of Ochna.

  13. Multi-objective evolutionary optimization of biological pest control with impulsive dynamics in soybean crops.

    Science.gov (United States)

    Cardoso, Rodrigo T N; da Cruz, André R; Wanner, Elizabeth F; Takahashi, Ricardo H C

    2009-08-01

    The biological pest control in agriculture, an environment-friendly practice, maintains the density of pests below an economic injury level by releasing a suitable quantity of their natural enemies. This work proposes a multi-objective numerical solution to biological pest control for soybean crops, considering both the cost of application of the control action and the cost of economic damages. The system model is nonlinear with impulsive control dynamics, in order to cope more effectively with the actual control action to be applied, which should be performed in a finite number of discrete time instants. The dynamic optimization problem is solved using the NSGA-II, a fast and trustworthy multi-objective genetic algorithm. The results suggest a dual pest control policy, in which the relative price of control action versus the associated additional harvest yield determines the usage of either a low control action strategy or a higher one.

  14. Biological Motion Preference in Humans at Birth: Role of Dynamic and Configural Properties

    Science.gov (United States)

    Bardi, Lara; Regolin, Lucia; Simion, Francesca

    2011-01-01

    The present study addresses the hypothesis that detection of biological motion is an intrinsic capacity of the visual system guided by a non-species-specific predisposition for the pattern of vertebrate movement and investigates the role of global vs. local information in biological motion detection. Two-day-old babies exposed to a biological…

  15. Systems biology studies of Aspergilli - from sequence to science

    DEFF Research Database (Denmark)

    Andersen, Mikael Rørdam

    2008-01-01

    The recent dawn of the new biological mindset called systems biology has put forth a new way of analyzing and understanding biology. Carried by the notion that no element of a cell is an island, systems biology takes a holistic approach, and attempts to understand life as systems that have co...... a few. The recent publication of the genome sequences of several filamentous fungi of the Aspergillus species (Aspergilli), has, along with the accumulation of years of reductionist studies, been a catalyst for the application of systems biology to this interesting group of fungi. Among the genome...... biology approach has been applied to a wide range of issues. These tools include the compilation of data from literature on A. niger enzymes to form a re-constructed metabolic network and model of metabolism, allowing assessment of the industrial production potential of metabolites from this fungus. Based...

  16. 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

  17. 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 &

  18. [Preliminary study on pollination biology of Tulipa edulis].

    Science.gov (United States)

    Wu, Zhengjun; Zhu, Zaibiao; Guo, Qiaosheng; Xu, Hongjian; Ma, Hongliang; Miao, Yuanyuan

    2012-02-01

    Current study on the pollination biology of Tulipa edulis was conducted to investigate its pollination characteristics and to provide references for artificial domestication and breeding of T. edulis. Flowering dynamics, pollinators, morphology and structure of flower were observed. Different methods were adopted to evaluate the pollen vitality, and benzidine-H2O2 method was used for estimation of the stigma receptivity. Breeding system was evaluated based on out-crossing index (OCI) , pollen-ovule ratio (P/O) and the results of emasculation, bagging and artificial pollination studies. The flower of T. edulis showed typical characteristics of Liliaceae. The pollen remained viable to some extent during all the anthesis and peaked within three days after blossoming. Stigma acceptability peaked in the first day of blossom and dwindled away in the next four days. The type of breeding system of T. edulis was facultative xenogamy, three species of Halictus are the main pollination insects. The type of breeding system of T. edulis was facultative xenogamy, withal cross-pollination give priority to self-pollination, and the insects play a main role on the pollination of T. edulis, further validation are needed to judge if the wind is helpful to pollination.

  19. Microbubble generation by piezotransducer for biological studies

    Science.gov (United States)

    Zhu, W.; Alkhazal, M.; Cho, M.; Xiao, S.

    2015-12-01

    Bubbles induced by blast waves or shocks are speculated to be the major cause of damages in biological cells in mild traumatic brain injuries. Microbubble collapse was found to induce noticeable cell detachment from the cell substrate, changes in focal adhesion and biomechanics. To better understand the bubble mechanism, we would like to construct a system, which allows us to clearly differentiate the impact of bubbles from that of shocks. Such a generator needs to be low profile in order to place under a microscope. A piezoelectric transducer system was designed to meet the need. The system uses either a flat or a spherical focusing piezoelectric transducer to produce microbubbles in a cuvette loaded with cell-culture medium. The transducer is placed on the side of the cuvette with its axis lining horizontally. A cover slip is placed on the top of the cuvette. The impact of the waves to the cells is minimized as the cover slip is parallel to the direction of the wave. Only bubbles from the medium reach the cover slip and interact with cells. The effect of bubbles therefore can be separated that of pressure waves. The bubbles collected on a cover slip range in size from 100 μm to 10 μm in radius, but the dominant size is 20-30 μm.

  20. Atomic dynamics of alumina melt: A molecular dynamics simulation study

    Directory of Open Access Journals (Sweden)

    S.Jahn

    2008-03-01

    Full Text Available The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the spectra up to momentum transfers, Q, close to the principal peaks of partial static structure factors. The broadening of the Brillouin line widths is discussed in terms of a frequency dependent viscosity η(ω.

  1. Diversity, Stability, Recursivity, and Rule Generation in Biological System Intra-inter Dynamics Approach

    CERN Document Server

    Kaneko, K

    1998-01-01

    Basic problems for the construction of a scenario for the Life are discussed. To study the problems in terms of dynamical systems theory, a scheme of intra-inter dynamics is presented. It consists of internal dynamics of a unit, interaction among the units, and the dynamics to change the dynamics itself, for example by replication (and death) of units according to their internal states. Applying the dynamics to cell differentiation, isologous diversification theory is proposed. According to it, orbital instability leads to diversified cell behaviors first. At the next stage, several cell types are formed, first triggered by clustering of oscillations, and then as attracting states of internal dynamics stabilized by the cell-to-cell interaction. At the third stage, the differentiation is determined as a recursive state by cell division. At the last stage, hierarchical differentiation proceeds, with the emergence of stochastic rule for the differentiation to sub-groups, where regulation of the probability for t...

  2. Population dynamics of bacteria involved in enhanced biological phosphorus removal in Danish wastewater treatment plants.

    Science.gov (United States)

    Mielczarek, Artur Tomasz; Nguyen, Hien Thi Thu; Nielsen, Jeppe Lund; Nielsen, Per Halkjær

    2013-03-15

    The enhanced biological phosphorus removal (EBPR) process is increasingly popular as a sustainable method for removal of phosphorus (P) from wastewater. This study consisted of a comprehensive three-year investigation of the identity and population dynamics of polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) in 28 Danish municipal wastewater treatment plants with nutrient removal. Fluorescence in situ hybridization was applied to quantify ten probe-defined populations of PAO and GAO that in total constituted a large fraction (30% on average) of the entire microbial community targeted by the EUBmix probes. Two PAO genera, Accumulibacter and Tetrasphaera, were very abundant in all EBPR plants (average of 3.7% and 27% of all bacteria, respectively), and their abundance was relatively stable in the Danish full-scale plants without clear temporal variations. GAOs were occasionally present in some plants (Competibacter in 11 plants, Defluviicoccus in 6 plants) and were consistent in only a few plants. This shows that these were not core species in the EBPR communities. The total GAO abundance was always lower than that of Accumulibacter. In plants without EBPR design, the abundance of PAO and GAO was significantly lower. Competibacter correlated in general with high fraction of industrial wastewater. In specific plants Accumulibacter correlated with high C/P ratio of the wastewater and Tetrasphaera with high organic loading. Interestingly, the relative microbial composition of the PAO/GAO species was unique to each plant over time, which gives a characteristic plant-specific "fingerprint".

  3. Bacterial community dynamics in a rotating biological contactor treating 2-fluorophenol-containing wastewater.

    Science.gov (United States)

    Duque, Anouk F; Bessa, Vânia S; Castro, Paula M L

    2014-01-01

    One of the main factors affecting the performance of rotating biological contactors (RBC) is the biofilm characteristics. Therefore, a deep understanding of the microbial population dynamics and structure of the biofilm is mandatory if optimization of organic matter and nutrients removal is targeted. This study focused on the effects of organic shock loads of 2-fluorophenol (2-FP) on the microbial diversity present in an RBC biofilm. The RBC was seeded with activated sludge from a conventional wastewater treatment plant and was operated during 496 days. During the first 126 days, the RBC was subjected to intermittent 2-FP shocks of 25 mg l(-1) and no degradation occurred. Therefore, the reactor was subsequently augmented with a 2-FP-degrading strain (FP1). Afterwards, the RBC had a stable performance when subjected to 2-FP shocks up to 50 mg l(-1) and to a starvation period, as indicated by removal of the compound. Denaturing gradient gel electrophoresis (DGGE) revealed large shifts in microbial communities present in the first and fifth stages, although no clear relation between the sample collection time and spatial factor was found. Phylogenetic affiliation of some predominant members was assessed by direct sequencing of correspondent DGGE bands. Affiliations to α-, β- and δ-Proteobacteria were found. Several bacterial strains isolated from the reactor showed capacity for 2-FP degradation. Strain FP1 was successfully recovered from the biofilm by plating and by DGGE, reinforcing that bioaugmentation was successfully achieved.

  4. Chemical and biological activity in open flows: A dynamical system approach

    Energy Technology Data Exchange (ETDEWEB)

    Tel, Tamas [Institute for Theoretical Physics, Eoetvoes University, P.O. Box 32, H-1518, Budapest (Hungary); Moura, Alessandro de [Instituto de Fisica, Universidade de Sao Paulo, Caixa Postal 66318, 05315-970, Sao Paulo, SP (Brazil); Grebogi, Celso [Instituto de Fisica, Universidade de Sao Paulo, Caixa Postal 66318, 05315-970, Sao Paulo, SP (Brazil) and Max-Plank-Institute for the Physics of Complex Systems, Noethnitzer Str. 38, D-01187 Dresden (Germany)]. E-mail: grebogi@if.usp.br; Karolyi, Gyoergy [Center for Applied Mathematics and Computational Physics, and Department of Structural Mechanics, Budapest University of Technology and Economics, Mueegyetem rkp. 3, H-1521, Budapest (Hungary)

    2005-07-01

    Chemical and biological processes often take place in fluid flows. Many of them, like environmental or microfluidical ones, generate filamentary patterns which have a fractal structure, due to the presence of chaos in the underlying advection dynamics. In such cases, hydrodynamical stirring strongly couples to the reactivity of the advected species: the outcome of the reaction is then typically different from that of the same reaction taking place in a well-mixed environment. Here we review recent progress in this field, which became possible due to the application of methods taken from dynamical system theory. We place special emphasis on the derivation of effective rate equations which contain singular terms expressing the fact that the reaction takes place on a moving fractal catalyst, on the unstable foliation of the reaction free advection dynamics.

  5. Evolutionary game theory for physical and biological scientists. I. Training and validating population dynamics equations.

    Science.gov (United States)

    Liao, David; Tlsty, Thea D

    2014-08-06

    Failure to understand evolutionary dynamics has been hypothesized as limiting our ability to control biological systems. An increasing awareness of similarities between macroscopic ecosystems and cellular tissues has inspired optimism that game theory will provide insights into the progression and control of cancer. To realize this potential, the ability to compare game theoretic models and experimental measurements of population dynamics should be broadly disseminated. In this tutorial, we present an analysis method that can be used to train parameters in game theoretic dynamics equations, used to validate the resulting equations, and used to make predictions to challenge these equations and to design treatment strategies. The data analysis techniques in this tutorial are adapted from the analysis of reaction kinetics using the method of initial rates taught in undergraduate general chemistry courses. Reliance on computer programming is avoided to encourage the adoption of these methods as routine bench activities.

  6. Dynamics of biological water: insights from molecular modeling of light scattering in aqueous trehalose solutions.

    Science.gov (United States)

    Lupi, Laura; Comez, Lucia; Paolantoni, Marco; Fioretto, Daniele; Ladanyi, Branka M

    2012-06-28

    Extended depolarized light scattering (EDLS) measurements have been recently employed to investigate the dynamics of water solvating biological molecules, giving evidence of the presence of two different dynamical regimes among water molecules. An interpretation of EDLS has been proposed that provides an independent estimate of the retardation factor of slowdown with respect to fast water molecules and of the number of solvent molecules affected by this slowing down. Nevertheless this measure is an inherently complex one, due to the collective nature of the physical property probed. In the present work a molecular dynamics (MD) approach has been used to more deeply understand experimental results. Time correlation functions of the collective polarizability anisotropy have been calculated for the prototype disaccharide trehalose in aqueous solutions as a function of concentration. The unique capability of MD to disentangle the contributions to the dynamics arising from solute, solvent, and cross terms between the two allowed us to check the reliability of an interpretation that assumes a spectral separation of water and sugar dynamics, as well as to highlight the very presence of two distinct relaxation processes in water. The two processes have been attributed to the dynamics of bulk and hydration water, respectively. A retardation factor of ~5 and concentration dependent hydration numbers have been observed, in good agreement with experimental results [Paolantoni, M.; et al. J. Phys. Chem. B 2009, 113, 7874-7878].

  7. Reverse engineering dynamic temporal models of biological processes and their relationships.

    Science.gov (United States)

    Ramakrishnan, Naren; Tadepalli, Satish; Watson, Layne T; Helm, Richard F; Antoniotti, Marco; Mishra, Bud

    2010-07-13

    Biological processes such as circadian rhythms, cell division, metabolism, and development occur as ordered sequences of events. The synchronization of these coordinated events is essential for proper cell function, and hence the determination of critical time points in biological processes is an important component of all biological investigations. In particular, such critical time points establish logical ordering constraints on subprocesses, impose prerequisites on temporal regulation and spatial compartmentalization, and situate dynamic reorganization of functional elements in preparation for subsequent stages. Thus, building temporal phenomenological representations of biological processes from genome-wide datasets is relevant in formulating biological hypotheses on: how processes are mechanistically regulated; how the regulations vary on an evolutionary scale, and how their inadvertent disregulation leads to a diseased state or fatality. This paper presents a general framework (GOALIE) to reconstruct temporal models of cellular processes from time-course gene expression data. We mathematically formulate the problem as one of optimally segmenting datasets into a succession of "informative" windows such that time points within a window expose concerted clusters of gene action whereas time points straddling window boundaries constitute points of significant restructuring. We illustrate here how GOALIE successfully brings out the interplay between multiple yeast processes, inferred from combined experimental datasets for the cell cycle and the metabolic cycle.

  8. Bio-Logic Builder: A Non-Technical Tool for Building Dynamical, Qualitative Models

    Science.gov (United States)

    Helikar, Tomáš; Kowal, Bryan; Madrahimov, Alex; Shrestha, Manish; Pedersen, Jay; Limbu, Kahani; Thapa, Ishwor; Rowley, Thaine; Satalkar, Rahul; Kochi, Naomi; Konvalina, John; Rogers, Jim A.

    2012-01-01

    Computational modeling of biological processes is a promising tool in biomedical research. While a large part of its potential lies in the ability to integrate it with laboratory research, modeling currently generally requires a high degree of training in mathematics and/or computer science. To help address this issue, we have developed a web-based tool, Bio-Logic Builder, that enables laboratory scientists to define mathematical representations (based on a discrete formalism) of biological regulatory mechanisms in a modular and non-technical fashion. As part of the user interface, generalized “bio-logic” modules have been defined to provide users with the building blocks for many biological processes. To build/modify computational models, experimentalists provide purely qualitative information about a particular regulatory mechanisms as is generally found in the laboratory. The Bio-Logic Builder subsequently converts the provided information into a mathematical representation described with Boolean expressions/rules. We used this tool to build a number of dynamical models, including a 130-protein large-scale model of signal transduction with over 800 interactions, influenza A replication cycle with 127 species and 200+ interactions, and mammalian and budding yeast cell cycles. We also show that any and all qualitative regulatory mechanisms can be built using this tool. PMID:23082121

  9. Networks and their applications to biological systems: From ecological dynamics to gene regulation

    Science.gov (United States)

    Sevim, Volkan

    In this dissertation, we study three biological applications of networks. The first one is a biological coevolution model, in which a species is defined by a genome in the form of a finite bitstring and the interactions between species are given by a fixed matrix with randomly distributed elements. Here we study a version of the model, in which the matrix elements are correlated to a controllable degree by means of an averaging scheme. This method allows creation of mutants resembling their ancestors (wildtype). We compare long kinetic Monte Carlo simulations of models with uncorrelated and correlated interactions. We find that while there are quantitative differences, most qualitative features, such as 1/f behavior in power spectral densities for the diversity indices and the power-law distribution of species lifetimes, are not significantly affected by the correlations in the interaction matrix. The second application is the growth of a directed network, in which the growth is constrained by the cost of adding links to the existing nodes. This is a new preferential-attachment scheme, in which a new node attaches to an existing node i with probability pi(k i, k'i ) ∝ ( k'i /ki)gamma, where ki and k'i are the number of outgoing and incoming links at i, respectively, and gamma is a constant. First, we calculate the degree distribution for the outgoing links for a simplified form of this function, pi( ki) ∝ k-1i , both analytically and by Monte Carlo simulations. The distribution decays like kmuk/Gamma(k) for large k, where mu is a constant. We relate this mechanism to simple food-web models by implementing it in the cascade model. We also study the generalized case, pi(ki, k'i ) ∝ ( k'i /ki)gamma, by simulations. The third application is the evolution of robustness to mutations and noise in gene regulatory networks. It has been shown that robustness to mutations and noise can evolve through stabilizing selection for optimal phenotypes in model gene regulatory

  10. On the structural affinity of macromolecules with different biological properties: Molecular dynamics simulations of a series of TEM-1 mutants

    Energy Technology Data Exchange (ETDEWEB)

    Giampaolo, Alessia Di [Dipartimento di Scienze Fisiche e Chimiche, Universita’ degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy); Mazza, Fernando [Department of Health Sciences, Univ. of L’Aquila, 67010 L’Aquila (Italy); Daidone, Isabella [Dipartimento di Scienze Fisiche e Chimiche, Universita’ degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy); Amicosante, Gianfranco; Perilli, Mariagrazia [Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy); Aschi, Massimiliano, E-mail: massimiliano.aschi@univaq.it [Dipartimento di Scienze Fisiche e Chimiche, Universita’ degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy)

    2013-07-12

    Highlights: •We have performed molecular dynamics simulations of TEM-1 mutants. •Mutations effects on the mechanical properties are considered. •Mutants do not significantly alter the average enzymes structure. •Mutants produce sharp alterations in enzyme conformational repertoire. •Mutants also produce changes in the active site volume. -- Abstract: Molecular Dynamics simulations have been carried out in order to provide a molecular rationalization of the biological and thermodynamic differences observed for a class of TEM β-lactamases. In particular we have considered the TEM-1(wt), the single point mutants TEM-40 and TEM-19 representative of IRT and ESBL classes respectively, and TEM-1 mutant M182T, TEM-32 and TEM-20 which differ from the first three for the additional of M182T mutation. Results indicate that most of the thermodynamic, and probably biological behaviour of these systems arise from subtle effects which, starting from the alterations of the local interactions, produce drastic modifications of the conformational space spanned by the enzymes. The present study suggests that systems showing essentially the same secondary and tertiary structure may differentiate their chemical–biological activity essentially (and probably exclusively) on the basis of the thermal fluctuations occurring in their physiological environment.

  11. Negotiating the dynamics of uncomfortable knowledge: The case of dual use and synthetic biology

    Science.gov (United States)

    Marris, Claire; Jefferson, Catherine; Lentzos, Filippa

    2014-01-01

    Institutions need to ignore some knowledge in order to function. This is “uncomfortable knowledge” because it undermines the ability of those institutions to pursue their goals (Rayner, 2012). We identify three bodies of knowledge that are relevant to understandings of the dual use threat posed by synthetic biology but are excluded from related policy discussions. We demonstrate how these “unknown knowns” constitute uncomfortable knowledge because they disrupt the simplified worldview that underpins contemporary discourse on the potential misuse of synthetic biology by malign actors. We describe how these inconvenient truths have been systematically ignored and argue that this is because they are perceived as a threat by organisations involved in the promotion of synthetic biology as well as by those involved in managing biosecurity risks. This has led to a situation where concerns about the biosecurity threat posed by synthetic biology are not only exaggerated, but are, more importantly, misplaced. This, in turn, means that related policies are misdirected and unlikely to have much impact. We focus on the dynamics of discussions about synthetic biology and dual use to demonstrate how the same “knowns” that are denied or dismissed as “unknown knowns” in certain circumstances are sometimes mobilised as “known knowns” by the same category of actors in a different context, when this serves to sustain the goals of the individuals and institutions involved. Based on our own experience, we argue that negotiating the dynamics of uncomfortable knowledge is a difficult, but necessary, component of meaningful transdisciplinary collaborations. PMID:25484910

  12. Fluorescence spectroscopic studies of DNA dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Scalettar, B.A.

    1987-04-01

    Random solvent induced motions of DNA are manifest as nanosecond torsional oscillations of the helix backbone, nanosecond through millisecond bending deformations and overall rotational and translational diffusion of the polymer. Fluorescence spectroscopy is used to study this spectrum of DNA motions while ethidium monoazide was covalently bounded. The steady state fluorescence depolarization data indicate that the covalent monoazide/DNA complex exhibits internal motions characterized by an average angular amplitude of 26 degrees confirming reports of fast torsional oscillations in noncovalent ethidium bromide/DNA systems. Data obtained by use of a new polarized photobleaching recovery technique (FPR) reflect both the rotational dynamics of the polymer and the reversible photochemistry of the dye. To isolate the reorientational motion of the DNA, the FPR experiments were ran in two modes that differ only in the polarization of the bleaching light. A quotient function constructed from the data obtained in these two modes monitors only the rotational component of the FPR recovery. In specific applications those bending deformations of long DNA molecules that have characteristic relaxation times on the order of 100 microseconds have been resolved. A fluorescence correlation technique that relates fluctuations in particle number to center-of-mass motion was used to measure translational diffusion on coefficients of the plasmid PBR322 and a short oligomeric DNA. A theory that describes angular correlation in systems exhibiting cyclic, biologically directed reorientation and random Brownian rotation is developed.

  13. In vitro study of biofilm growth on biologic prosthetics.

    Science.gov (United States)

    Bellows, Charles; Smith, Alison

    2014-01-01

    Biologic prosthetics are increasingly used for the repair of abdominal wall hernia defects but can become infected as a result of peri- or early post-operative bacterial contamination. Data evaluating biofilm formation on biologic prosthetics is lacking. The aim of this study was to investigate the influence of different biologic prosthetics on the growth behavior of two different bacterial species and their ability to form biofilms. Methicillin resistant Staphylococcus aureus (MRSA) or Pseudomrnonas aeruginosa were incubated on disks of two biologic prosthetics-human acellular dermis (ADM), and porcine small intestinal submucosa (SIS). The bacteria were allowed to attach to the prosthetics and propagate into mature biofilms for 24 hours at 370C. Images of biofilms were obtained using confocal microscopy and scanning electron microscopy (SEM). The number of viable cells and the biofilm biomass were quantified by colony forming units (CFUs) and crystal violet staining respectively. Analysis of variance was performed to compare the mean values for the different prosthetics. Each biologic matrix had a distinct surface characteristic. SEM visualized mature biofilms characterized by highly organized multi-cellular structures on surface of both biologic prosthetics. Quantification of bacterial growth over time showed that ADM had the lowest CFUs and biofilm biomass at 24 hours post-inoculation compared to SIS for both bacterial strains. MRSA and P. aeruginosa can form mature biofilms on biologic prosthetics but the relative abundance of the biofilm varies on different prosthetic constructs. Biologic material composition and manufacturing methods may influence bacterial adherence.

  14. Biologic Discontinuations Studies: A Systematic Review of Methods

    Science.gov (United States)

    Yoshida, Kazuki; Sung, Yoon-Kyoung; Kavanaugh, Arthur; Bae, Sang-Cheol; Weinblatt, Michael E.; Kishimoto, Mitsumasa; Matsui, Kazuo; Tohma, Shigeto; Solomon, Daniel H.

    2016-01-01

    Objectives We conducted a systematic review to assess the design and “failure definition” in studies of biologic discontinuation in rheumatoid arthritis (RA). Methods We found 403 studies on PubMed, and included 9 published papers and 5 abstracts from scientific meetings. We used a structured extraction form to collect information regarding study design and outcome (failure) definition. Results Three types of studies were found: randomized controlled trials, long-term extension studies of clinical trials, and prospective discontinuation studies. The largest study had 196 subjects in the discontinuation arm. Most studies allowed concomitant use of non-biologic drugs at biologic discontinuation. Heterogeneity was also found in the failure definition. Although all studies used measures of disease activity, the threshold for failure and the time point of assessment differed among studies. Few studies incorporated changing use of non-biologic drugs or glucocorticoids into the failure definition. Conclusions Although many studies have examined the outcome of biologic discontinuation, they have all been relatively small. Typical practice studies from registries may add important information, but will likely need to rely on a broader failure definition. PMID:23723316

  15. Biological - Elwha River Dam Removal Study

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This study examines the ecosystem response of the Elwha River to the removal of the Elwha River dams. We will measure the following attributes of ecosystem response:...

  16. Toward Chemically Resolved Computer Simulations of Dynamics and Remodeling of Biological Membranes.

    Science.gov (United States)

    Soares, Thereza A; Vanni, Stefano; Milano, Giuseppe; Cascella, Michele

    2017-08-03

    Cellular membranes are fundamental constituents of living organisms. Apart from defining the boundaries of the cells, they are involved in a wide range of biological functions, associated with both their structural and the dynamical properties. Biomembranes can undergo large-scale transformations when subject to specific environmental changes, including gel-liquid phase transitions, change of aggregation structure, formation of microtubules, or rupture into vesicles. All of these processes are dependent on a delicate interplay between intermolecular forces, molecular crowding, and entropy, and their understanding requires approaches that are able to capture and rationalize the details of all of the involved interactions. Molecular dynamics-based computational models at atom-level resolution are, in principle, the best way to perform such investigations. Unfortunately, the relevant spatial and time dimensionalities involved in membrane remodeling phenomena would require computational costs that are today unaffordable on a routinely basis. Such hurdles can be removed by coarse-graining the representations of the individual molecular components of the systems. This procedure anyway reduces the possibility of describing the chemical variations in the lipid mixtures composing biological membranes. New hybrid particle field multiscale approaches offer today a promising alternative to the more traditional particle-based simulations methods. By combining chemically distinguishable molecular representations with mesoscale-based computationally affordable potentials, they appear as one of the most promising ways to keep an accurate description of the chemical complexity of biological membranes and, at the same time, cover the required scales to describe remodeling events.

  17. 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.

  18. Biological soil crusts on initial soils: organic carbon dynamics and chemistry under temperate climatic conditions

    Directory of Open Access Journals (Sweden)

    A. Dümig

    2013-01-01

    Full Text Available Numerous studies have been carried out on the community structure and diversity of biological soil crusts (BSCs as well as their important functions on ecosystem processes. However, the amount of BSC-derived organic carbon (OC input into soils and its chemical composition under natural conditions has rarely been investigated. In this study, different development stages of algae- and moss-dominated BSCs were investigated on a~natural (<17 yr old BSCs and experimental sand dune (<4 yr old BSCs in northeastern Germany. We determined the OC accumulation in BSC-layers and the BSC-derived OC input into the underlying substrates for bulk materials and fractions <63 μm. The chemical composition of OC was characterized by applying solid-state 13C NMR spectroscopy and analysis of the carbohydrate-C signature.14C contents were used to assess the origin and dynamic of OC in BSCs and underlying substrates. Our results indicated a rapid BSC establishment and development from algae- to moss-dominated BSCs within only 4 yr under this temperate climate. The distribution of BSC types was presumably controlled by the surface stability according to the position in the slope. We found no evidence that soil properties influenced the BSC distribution on both sand dunes. 14C contents clearly indicated the existence of two OC pools in BSCs and substrates, recent BSC-derived OC and lignite-derived "old" OC (biologically refractory. The input of recent BSC-derived OC strongly decreased the mean residence time of total OC. The downward translocation of OC into the underlying substrates was only found for moss-dominated BSCs at the natural sand dune which may accelerate soil formation at these spots. BSC-derived OC mainly comprised O-alkyl C (carbohydrate-C and to a lesser extent also alkyl C and N-alkyl C in varying compositions. Accumulation of alkyl C was only detected in BSCs at the experimental dune which may induce a~lower water

  19. In Vivo Models to Study Chemokine Biology.

    Science.gov (United States)

    Amaral, F A; Boff, D; Teixeira, M M

    2016-01-01

    Chemokines are essential mediators of leukocyte movement in vivo. In vitro assays of leukocyte migration cannot mimic the complex interactions with other cell types and matrix needed for cells to extravasate and migrate into tissues. Therefore, in vivo strategies to study the effects and potential relevance of chemokines for the migration of particular leukocyte subsets are necessary. Here, we describe methods to study the effects and endogenous role of chemokine in mice. Advantages and pitfalls of particular models are discussed and we focus on description in model's joint and pleural cavity inflammation and the effects and relevance of CXCR2 and CCR2 ligands on cell migration.

  20. iBET: Immersive visualization of biological electron-transfer dynamics.

    Science.gov (United States)

    Nakano, C Masato; Moen, Erick; Byun, Hye Suk; Ma, Heng; Newman, Bradley; McDowell, Alexander; Wei, Tao; El-Naggar, Mohamed Y

    2016-04-01

    Recently, we presented a computational framework named VizBET to simulate and visualize biological electron-transfer (ET) dynamics. The visualization process was encapsulated as a plugin to the Visual Molecular Dynamics (VMD) software. However, the user's ability to understand complex, multidimensional ET pathways was severely limited when visualized in 2D on traditional computer monitors. To provide a more accurate representation with enhanced depth perception, we here present an extension of VizBET named iBET to render the VMD model of ET dynamics in a commodity virtual reality (VR) platform. The paper describes detailed procedures to export VMD models into the Unity game engine and render it in an Oculus Rift head mounted display. With the increasing availability of low-cost VR systems like the Rift and rich programmability of game engines, the iBET framework provides a powerful means to explore and understand not only biological ET processes but also a unique experiential tool for broad scientific communities. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Biological oscillations for learning walking coordination: dynamic recurrent neural network functionally models physiological central pattern generator.

    Science.gov (United States)

    Hoellinger, Thomas; Petieau, Mathieu; Duvinage, Matthieu; Castermans, Thierry; Seetharaman, Karthik; Cebolla, Ana-Maria; Bengoetxea, Ana; Ivanenko, Yuri; Dan, Bernard; Cheron, Guy

    2013-01-01

    The existence of dedicated neuronal modules such as those organized in the cerebral cortex, thalamus, basal ganglia, cerebellum, or spinal cord raises the question of how these functional modules are coordinated for appropriate motor behavior. Study of human locomotion offers an interesting field for addressing this central question. The coordination of the elevation of the 3 leg segments under a planar covariation rule (Borghese et al., 1996) was recently modeled (Barliya et al., 2009) by phase-adjusted simple oscillators shedding new light on the understanding of the central pattern generator (CPG) processing relevant oscillation signals. We describe the use of a dynamic recurrent neural network (DRNN) mimicking the natural oscillatory behavior of human locomotion for reproducing the planar covariation rule in both legs at different walking speeds. Neural network learning was based on sinusoid signals integrating frequency and amplitude features of the first three harmonics of the sagittal elevation angles of the thigh, shank, and foot of each lower limb. We verified the biological plausibility of the neural networks. Best results were obtained with oscillations extracted from the first three harmonics in comparison to oscillations outside the harmonic frequency peaks. Physiological replication steadily increased with the number of neuronal units from 1 to 80, where similarity index reached 0.99. Analysis of synaptic weighting showed that the proportion of inhibitory connections consistently increased with the number of neuronal units in the DRNN. This emerging property in the artificial neural networks resonates with recent advances in neurophysiology of inhibitory neurons that are involved in central nervous system oscillatory activities. The main message of this study is that this type of DRNN may offer a useful model of physiological central pattern generator for gaining insights in basic research and developing clinical applications.

  2. Biological oscillations for learning walking coordination: dynamic recurrent neural network functionally models physiological central pattern generator

    Directory of Open Access Journals (Sweden)

    Thomas eHoellinger

    2013-05-01

    Full Text Available The existence of dedicated neuronal modules such as those organized in the cerebral cortex, thalamus, basal ganglia, cerebellum or spinal cord raises the question of how these functional modules are coordinated for appropriate motor behavior. Study of human locomotion offers an interesting field for addressing this central question. The coordination of the elevation of the 3 leg segments under a planar covariation rule (Borghese et al., 1996 was recently modeled (Barliya et al., 2009 by phase-adjusted simple oscillators shedding new light on the understanding of the central pattern generator processing relevant oscillation signals. We describe the use of a dynamic recurrent neural network (DRNN mimicking the natural oscillatory behavior of human locomotion for reproducing the planar covariation rule in both legs at different walking speeds. Neural network learning was based on sinusoid signals integrating frequency and amplitude features of the first three harmonics of the sagittal elevation angles of the thigh, shank and foot of each lower limb. We verified the biological plausibility of the neural networks. Best results were obtained with oscillations extracted from the first three harmonics in comparison to oscillations outside the harmonic frequency peaks. Physiological replication steadily increased with the number of neuronal units from 1 to 80, where similarity index reached 0.99. Analysis of synaptic weighting showed that the proportion of inhibitory connections consistently increased with the number of neuronal units in the DRNN. This emerging property in the artificial neural networks resonates with recent advances in neurophysiology of inhibitory neurons that are involved in central nervous system oscillatory activities. The main message of this study is that this type of DRNN may offer a useful model of physiological central pattern generator for gaining insights in basic research and developing clinical applications.

  3. DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models.

    Directory of Open Access Journals (Sweden)

    Alex Greenfield

    Full Text Available BACKGROUND: Current technologies have lead to the availability of multiple genomic data types in sufficient quantity and quality to serve as a basis for automatic global network inference. Accordingly, there are currently a large variety of network inference methods that learn regulatory networks to varying degrees of detail. These methods have different strengths and weaknesses and thus can be complementary. However, combining different methods in a mutually reinforcing manner remains a challenge. METHODOLOGY: We investigate how three scalable methods can be combined into a useful network inference pipeline. The first is a novel t-test-based method that relies on a comprehensive steady-state knock-out dataset to rank regulatory interactions. The remaining two are previously published mutual information and ordinary differential equation based methods (tlCLR and Inferelator 1.0, respectively that use both time-series and steady-state data to rank regulatory interactions; the latter has the added advantage of also inferring dynamic models of gene regulation which can be used to predict the system's response to new perturbations. CONCLUSION/SIGNIFICANCE: Our t-test based method proved powerful at ranking regulatory interactions, tying for first out of methods in the DREAM4 100-gene in-silico network inference challenge. We demonstrate complementarity between this method and the two methods that take advantage of time-series data by combining the three into a pipeline whose ability to rank regulatory interactions is markedly improved compared to either method alone. Moreover, the pipeline is able to accurately predict the response of the system to new conditions (in this case new double knock-out genetic perturbations. Our evaluation of the performance of multiple methods for network inference suggests avenues for future methods development and provides simple considerations for genomic experimental design. Our code is publicly available at http://err.bio.nyu.edu/inferelator/.

  4. Quantum Information Biology: From Theory of Open Quantum Systems to Adaptive Dynamics

    Science.gov (United States)

    Asano, Masanari; Basieva, Irina; Khrennikov, Andrei; Ohya, Masanori; Tanaka, Yoshiharu; Yamato, Ichiro

    This chapter reviews quantum(-like) information biology (QIB). Here biology is treated widely as even covering cognition and its derivatives: psychology and decision making, sociology, and behavioral economics and finances. QIB provides an integrative description of information processing by bio-systems at all scales of life: from proteins and cells to cognition, ecological and social systems. Mathematically QIB is based on the theory of adaptive quantum systems (which covers also open quantum systems). Ideologically QIB is based on the quantum-like (QL) paradigm: complex bio-systems process information in accordance with the laws of quantum information and probability. This paradigm is supported by plenty of statistical bio-data collected at all bio-scales. QIB re ects the two fundamental principles: a) adaptivity; and, b) openness (bio-systems are fundamentally open). In addition, quantum adaptive dynamics provides the most generally possible mathematical representation of these principles.

  5. Principal manifolds and graphs in practice: from molecular biology to dynamical systems

    CERN Document Server

    Gorban, A N

    2010-01-01

    We present several applications of non-linear data modeling, using principal manifolds and principal graphs constructed using the metaphor of elasticity (elastic principal graph approach). These approaches are generalizations of the Kohonen's self-organizing maps, a class of artificial neural networks. On several examples we show advantages of using non-linear objects for data approximation in comparison to the linear ones. We propose four numerical criteria for comparing linear and non-linear mappings of datasets into the spaces of lower dimension. The examples are taken from comparative political science, from analysis of high-throughput data in molecular biology, from analysis of dynamical systems.

  6. Molecular dynamics studies of entangled polymer chains

    NARCIS (Netherlands)

    Bulacu, Monica Iulia

    2008-01-01

    The thesis presents three molecular dynamics studies of polymeric ensembles in which the chain entanglement plays the major role in the internal dynamics of the system. A coarse-grained model is used for representing the polymer chains as strings of beads connected by finite-extensible springs. In a

  7. Nanog Dynamics in Mouse Embryonic Stem Cells: Results from Systems Biology Approaches

    Directory of Open Access Journals (Sweden)

    Lucia Marucci

    2017-01-01

    Full Text Available Mouse embryonic stem cells (mESCs, derived from the inner cell mass of the blastocyst, are pluripotent stem cells having self-renewal capability and the potential of differentiating into every cell type under the appropriate culture conditions. An increasing number of reports have been published to uncover the molecular mechanisms that orchestrate pluripotency and cell fate specification using combined computational and experimental methodologies. Here, we review recent systems biology approaches to describe the causes and functions of gene expression heterogeneity and complex temporal dynamics of pluripotency markers in mESCs under uniform culture conditions. In particular, we focus on the dynamics of Nanog, a key regulator of the core pluripotency network and of mESC fate. We summarize the strengths and limitations of different experimental and modeling approaches and discuss how various strategies could be used.

  8. Phytoplankton biomass dynamics and environmental variables around the Rocas Atoll Biological Reserve, South Atlantic

    Directory of Open Access Journals (Sweden)

    Marina Cavalcanti Jales

    2015-12-01

    Full Text Available Abstract The Rocas Atoll Biological Reserve is located in the Atlantic Ocean, at 3º 51' S and 33º 49' W. It lies 143 nautical miles from the City of Natal, Rio Grande do Norte (Brazil. The purpose of this study was to analyze the hydrology, water masses, currents and chlorophyll a content to determine the dynamics of phytoplankton biomass around the Rocas Atoll. Samples were collected in July 2010 in the area around the Atoll, using the Research Vessel Cruzeiro do Sul of the Brazilian Navy. Two transects were established according to the surface currents, one of which at the southeast of the Atoll (SE and the other at norwest (NW. Three collection points were determined on each of these transects. Samples were collected at different depths (surface and DCM - Deep Chlorophyll Maximum and different times (day and night. According to PCA (Principal Component Analysis, the nutrients analyzed, DIN (dissolved inorganic nitrogen, DIP (dissolved inorganic phosphorus and silicate, were inversely correlated with temperature and dissolved oxygen. Most environmental variables showed a significant increase due to the turbulence on the Northwest transect. There was an increase in the concentration of chlorophyll a and nutrients when the temperature and oxygen in the mixed layer was reduced due to the influence of the SACW (South Atlantic Central Water. Despite the increase observed in some variables such as nutrient salts and chlorophyll a, the temperature in the mixed layer attained a mean value of 23.23 ºC due to the predominance of Tropical Water. The increase of the phytoplankton biomass on the NW transect was, therefore, caused by the "island effect" and not by upwelling.

  9. Insights from Systems Biology in Physiological Studies: Learning from Context

    Directory of Open Access Journals (Sweden)

    Pedro Henrique Imenez Silva

    2017-06-01

    Full Text Available Systems biology presents an integrated view of biological systems, focusing on the relations between elements, whether functional or evolutionary, and providing a rich framework for the comprehension of life. At the same time, many low-throughput experimental studies are performed without influence from this integrated view, whilst high-throughput experiments use low-throughput results in their validation and interpretation. We propose an inversion in this logic, and ask which benefits could be obtained from a holistic view coming from high-throughput studies―and systems biology in particular―in interpreting and designing low-throughput experiments. By exploring some key examples from the renal and adrenal physiology, we try to show that network and modularity theory, along with observed patterns of association between elements in a biological system, can have profound effects on our ability to draw meaningful conclusions from experiments.

  10. The Panel Study of Income Dynamics (PSID)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Panel Study of Income Dynamics (PSID) began in 1968 with a nationally representative sample of over 18,000 individuals living in 5,000 families in the United...

  11. Making the right connections: Network biology and plant immune system dynamics

    Directory of Open Access Journals (Sweden)

    Maggie E. McCormack

    2016-04-01

    Full Text Available Network analysis has been a recent focus in biological sciences due to its ability to synthesize global visualizations of cellular processes and predict functions based on inferences from network properties. A protein–protein interaction network, or interactome, captures the emergent cellular states from gene regulation and environmental conditions. Given that proteins are involved in extensive local and systemic molecular interactions such as signaling and metabolism, understanding protein functions and interactions are essential for a systems view of biology. However, in plant sciences these network-based approaches to data integration have been few and far between due to limited data, especially protein–protein interaction data. In this review, we cover network construction from experimental data, network analysis based on topological properties, and finally we discuss advances in networks in plants and other organisms in a comparative approach. We focus on applications of network biology to discover the dynamics of host–pathogen interactions as these have potential agricultural uses in improving disease resistance in commercial crops.

  12. Quantitative and dynamic measurements of biological fresh samples with X-ray phase contrast tomography

    Energy Technology Data Exchange (ETDEWEB)

    Hoshino, Masato, E-mail: hoshino@spring8.or.jp; Uesugi, Kentaro [Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan); Tsukube, Takuro [Japanese Red Cross Kobe Hospital, 1-3-1 Wakinohamakaigandori, Chuo-ku, Kobe, Hyogo 651-0073 (Japan); Yagi, Naoto [Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan)

    2014-10-08

    Quantitative measurements of biological fresh samples based on three-dimensional densitometry using X-ray phase contrast tomography are presented. X-ray phase contrast tomography using a Talbot grating interferometer was applied to biological fresh samples which were not fixed by any fixatives. To achieve a high-throughput measurement for the fresh samples the X-ray phase contrast tomography measurement procedure was improved. The three-dimensional structure of a fresh mouse fetus was clearly depicted as a mass density map using X-ray phase contrast tomography. The mouse fetus measured in the fresh state was then fixed by formalin and measured in the fixed state. The influence of the formalin fixation on soft tissue was quantitatively evaluated by comparing the fresh and fixed samples. X-ray phase contrast tomography was also applied to the dynamic measurement of a biological fresh sample. Morphological changes of a ring-shaped fresh pig aorta were measured tomographically under different degrees of stretching.

  13. Directing experimental biology: a case study in mitochondrial biogenesis.

    Science.gov (United States)

    Hibbs, Matthew A; Myers, Chad L; Huttenhower, Curtis; Hess, David C; Li, Kai; Caudy, Amy A; Troyanskaya, Olga G

    2009-03-01

    Computational approaches have promised to organize collections of functional genomics data into testable predictions of gene and protein involvement in biological processes and pathways. However, few such predictions have been experimentally validated on a large scale, leaving many bioinformatic methods unproven and underutilized in the biology community. Further, it remains unclear what biological concerns should be taken into account when using computational methods to drive real-world experimental efforts. To investigate these concerns and to establish the utility of computational predictions of gene function, we experimentally tested hundreds of predictions generated from an ensemble of three complementary methods for the process of mitochondrial organization and biogenesis in Saccharomyces cerevisiae. The biological data with respect to the mitochondria are presented in a companion manuscript published in PLoS Genetics (doi:10.1371/journal.pgen.1000407). Here we analyze and explore the results of this study that are broadly applicable for computationalists applying gene function prediction techniques, including a new experimental comparison with 48 genes representing the genomic background. Our study leads to several conclusions that are important to consider when driving laboratory investigations using computational prediction approaches. While most genes in yeast are already known to participate in at least one biological process, we confirm that genes with known functions can still be strong candidates for annotation of additional gene functions. We find that different analysis techniques and different underlying data can both greatly affect the types of functional predictions produced by computational methods. This diversity allows an ensemble of techniques to substantially broaden the biological scope and breadth of predictions. We also find that performing prediction and validation steps iteratively allows us to more completely characterize a biological

  14. Directing experimental biology: a case study in mitochondrial biogenesis.

    Directory of Open Access Journals (Sweden)

    Matthew A Hibbs

    2009-03-01

    Full Text Available Computational approaches have promised to organize collections of functional genomics data into testable predictions of gene and protein involvement in biological processes and pathways. However, few such predictions have been experimentally validated on a large scale, leaving many bioinformatic methods unproven and underutilized in the biology community. Further, it remains unclear what biological concerns should be taken into account when using computational methods to drive real-world experimental efforts. To investigate these concerns and to establish the utility of computational predictions of gene function, we experimentally tested hundreds of predictions generated from an ensemble of three complementary methods for the process of mitochondrial organization and biogenesis in Saccharomyces cerevisiae. The biological data with respect to the mitochondria are presented in a companion manuscript published in PLoS Genetics (doi:10.1371/journal.pgen.1000407. Here we analyze and explore the results of this study that are broadly applicable for computationalists applying gene function prediction techniques, including a new experimental comparison with 48 genes representing the genomic background. Our study leads to several conclusions that are important to consider when driving laboratory investigations using computational prediction approaches. While most genes in yeast are already known to participate in at least one biological process, we confirm that genes with known functions can still be strong candidates for annotation of additional gene functions. We find that different analysis techniques and different underlying data can both greatly affect the types of functional predictions produced by computational methods. This diversity allows an ensemble of techniques to substantially broaden the biological scope and breadth of predictions. We also find that performing prediction and validation steps iteratively allows us to more completely

  15. Psychological and biological foundations of time preference: evidence from a day reconstruction study with biological tracking

    OpenAIRE

    Daly, Michael; Delaney, Liam; Harmon, Colm

    2008-01-01

    This paper considers the relationship between the economic concept of time preference and relevant concepts from psychology and biology. Using novel data from a time diary study conducted in Ireland that combined detailed psychometric testing with medical testing and real-time bio-tracking, we examine the distribution of a number of psychometric measures linked to the economic concept of time preferences and test the extent to which these measures form coherent clusters and the degree to whic...

  16. Experiment design through dynamical characterisation of non-linear systems biology models utilising sparse grids.

    Science.gov (United States)

    Donahue, M M; Buzzard, G T; Rundell, A E

    2010-07-01

    The sparse grid-based experiment design algorithm sequentially selects an experimental design point to discriminate between hypotheses for given experimental conditions. Sparse grids efficiently screen the global uncertain parameter space to identify acceptable parameter subspaces. Clustering the located acceptable parameter vectors by the similarity of the simulated model trajectories characterises the data-compatible model dynamics. The experiment design algorithm capitalizes on the diversity of the experimentally distinguishable system output dynamics to select the design point that best discerns between competing model-structure and parameter-encoded hypotheses. As opposed to designing the experiments to explicitly reduce uncertainty in the model parameters, this approach selects design points to differentiate between dynamical behaviours. This approach further differs from other experimental design methods in that it simultaneously addresses both parameter- and structural-based uncertainty that is applicable to some ill-posed problems where the number of uncertain parameters exceeds the amount of data, places very few requirements on the model type, available data and a priori parameter estimates, and is performed over the global uncertain parameter space. The experiment design algorithm is demonstrated on a mitogen-activated protein kinase cascade model. The results show that system dynamics are highly uncertain with limited experimental data. Nevertheless, the algorithm requires only three additional experimental data points to simultaneously discriminate between possible model structures and acceptable parameter values. This sparse grid-based experiment design process provides a systematic and computationally efficient exploration over the entire uncertain parameter space of potential model structures to resolve the uncertainty in the non-linear systems biology model dynamics.

  17. Detection of biological objects using dynamic characteristics of double-walled carbon nanotubes

    Science.gov (United States)

    Patel, Ajay M.; Joshi, Anand Y.

    2015-08-01

    This study explores double-walled carbon nanotubes as the sensing devices for biological objects including viruses and bacteria. The biological objects studied include alanine with amino terminal residue, deoxyadenosine with free residue, Coronaviridae and Bartonella bacilliformis. An expression has been articulated to identify the mass of biological objects from the shift of frequency. Sensitivity of the sensor has been calculated when subjected to such biological objects. Molecular structural mechanics approach has been used for investigating the vibrational responses of zigzag and armchair double-walled carbon nanotube-based nano biosensors. The elastic properties of beam element are calculated by considering mechanical characteristics of covalent bonds between the carbon atoms in the hexagonal lattice. Spring elements are used to describe the interlayer interactions between the inner and outer tubes caused due to the van der Waals forces. The mass of each beam element is assumed as point mass at nodes coinciding with carbon atoms at inner and outer wall of DWCNT. Based on the sensitivity and the frequency shift it can be concluded that cantilever zigzag DWCNTs are better candidates for detecting the biological objects.

  18. Modelling biological behaviours with the unified modelling language: an immunological case study and critique.

    Science.gov (United States)

    Read, Mark; Andrews, Paul S; Timmis, Jon; Kumar, Vipin

    2014-10-01

    We present a framework to assist the diagrammatic modelling of complex biological systems using the unified modelling language (UML). The framework comprises three levels of modelling, ranging in scope from the dynamics of individual model entities to system-level emergent properties. By way of an immunological case study of the mouse disease experimental autoimmune encephalomyelitis, we show how the framework can be used to produce models that capture and communicate the biological system, detailing how biological entities, interactions and behaviours lead to higher-level emergent properties observed in the real world. We demonstrate how the UML can be successfully applied within our framework, and provide a critique of UML's ability to capture concepts fundamental to immunology and biology more generally. We show how specialized, well-explained diagrams with less formal semantics can be used where no suitable UML formalism exists. We highlight UML's lack of expressive ability concerning cyclic feedbacks in cellular networks, and the compounding concurrency arising from huge numbers of stochastic, interacting agents. To compensate for this, we propose several additional relationships for expressing these concepts in UML's activity diagram. We also demonstrate the ambiguous nature of class diagrams when applied to complex biology, and question their utility in modelling such dynamic systems. Models created through our framework are non-executable, and expressly free of simulation implementation concerns. They are a valuable complement and precursor to simulation specifications and implementations, focusing purely on thoroughly exploring the biology, recording hypotheses and assumptions, and serve as a communication medium detailing exactly how a simulation relates to the real biology.

  19. Bioorthogonal chemistry:a covalent strategy for the study of biological systems

    Institute of Scientific and Technical Information of China (English)

    LIM; Reyna; K.V.

    2010-01-01

    The development of genetically encoded,wavelength-tunable fluorescent proteins has provided a powerful imaging tool to the study of protein dynamics and functions in cellular and organismal biology.However,many biological functions are not directly encoded in the protein primary sequence,e.g.,dynamic regulation afforded by protein posttranslational modifications such as phosphorylation.To meet this challenge,an emerging field of bioorthogonal chemistry has promised to offer a versatile strategy to selectively label a biomolecule of interest and track their dynamic regulations in its native habitat.This strategy has been successfully applied to the studies of all classes of biomolecules in living systems,including proteins,nucleic acids,carbohydrates,and lipids.Whereas the incorporation of a bioorthogonal reporter site-selectively into a biomolecule through either genetic or metabolic approaches has been well established,the development of bioorthogonal reactions that allow fast ligation of exogenous chemical probes with the bioorthogonal reporter in living systems remains in its early stage.Here,we review the recent development of bioorthogonal reactions and their applications in various biological systems,with a detailed discussion about our own work―the development of the tetrazole-based,photoinducible 1,3-dipolar cycloaddition reaction.

  20. AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology

    Science.gov (United States)

    Balsa-Canto, Eva; Henriques, David; Gábor, Attila; Banga, Julio R.

    2016-01-01

    Motivation: Many problems of interest in dynamic modeling and control of biological systems can be posed as non-linear optimization problems subject to algebraic and dynamic constraints. In the context of modeling, this is the case of, e.g. parameter estimation, optimal experimental design and dynamic flux balance analysis. In the context of control, model-based metabolic engineering or drug dose optimization problems can be formulated as (multi-objective) optimal control problems. Finding a solution to those problems is a very challenging task which requires advanced numerical methods. Results: This work presents the AMIGO2 toolbox: the first multiplatform software tool that automatizes the solution of all those problems, offering a suite of state-of-the-art (multi-objective) global optimizers and advanced simulation approaches. Availability and Implementation: The toolbox and its documentation are available at: sites.google.com/site/amigo2toolbox. Contact: ebalsa@iim.csic.es Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27378288

  1. Seasonal bacterial community dynamics in a full-scale enhanced biological phosphorus removal plant.

    Science.gov (United States)

    Flowers, Jason J; Cadkin, Tracey A; McMahon, Katherine D

    2013-12-01

    Activated sludge is one of the most abundant and effective wastewater treatment process used to treat wastewater, and has been used in developed countries for nearly a century. In all that time, several hundreds of studies have explored the bacterial communities responsible for treatment, but most studies were based on a handful of samples and did not consider temporal dynamics. In this study, we used the DNA fingerprinting technique called automated ribosomal intergenic spacer region analysis (ARISA) to study bacterial community dynamics over a two-year period in two different treatment trains. We also used quantitative PCR to measure the variation of five phylogenetically-defined clades within the Accumulibacter lineage, which is a model polyphosphate accumulating organism. The total bacterial community exhibited seasonal patterns of change reminiscent of those observed in lakes and oceans. Surprisingly, all five Accumulibacter clades were present throughout the study, and the total Accumulibacter community was relatively stable. However, the abundance of each clade did fluctuate through time. Clade IIA dynamics correlated positively with temperature (ρ = 0.65, p < 0.05) while Clade IA dynamics correlated negatively with temperature (ρ = -0.35, p < 0.05). This relationship with temperature hints at the mechanisms that may be driving the seasonal patterns in overall bacterial community dynamics and provides further evidence for ecological differentiation among clades within the Accumulibacter lineage. This work provides a valuable baseline for activated sludge bacterial community variation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Dynamic study of milling low depth channels

    Directory of Open Access Journals (Sweden)

    Rosca Dorin Mircea

    2017-01-01

    Full Text Available This paper presents a study of dynamic aspects of the milling cutters used in particular case of low depth channels. A new calculation method was developed, taking into account the high variations of cutting forces during milling small depth channels with peripheral cutting tools. A new formula was established for the minimal value of channel depth that allows cutting process to be performed in conditions of dynamic stability.

  3. Cine CT technique for dynamic airway studies

    Energy Technology Data Exchange (ETDEWEB)

    Ell, S.R.; Jolles, H.; Keyes, W.D.; Galvin, J.R.

    1985-07-01

    The advent of cine CT scanning with its 50-msec data acquisition time promises a much wider range of dynamic CT studies. The authors describe a method for dynamic evaluation of the extrathoracic airway, which they believe has considerable potential application in nonfixed upper-airway disease, such as sleep apnea and stridor of unknown cause. Conventional CT is limited in such studies by long data acquisition time and can be used to study only prolonged maneuvers such as phonation. Fluoroscopy and digital subtraction studies are limited by relatively high radiation dose and inability to image all wall motions simultaneously.

  4. Vitamin D biology and heart failure : Clinical and experimental studies

    NARCIS (Netherlands)

    Meems, Laura

    2015-01-01

    In the last decade, vitamin D biology has been studied more extensively than ever before.. The use of vitamin D supplements is common, and so is determination of plasma vitamin D status. Besides its role in bone homeostasis, vitamin D is thought to be an important player in the development and treat

  5. Stable isotope methods in biological and ecological studies of arthropods

    NARCIS (Netherlands)

    Hood-Nowotny, R.C.; Knols, B.G.J.

    2007-01-01

    This is an eclectic review and analysis of contemporary and promising stable isotope methodologies to study the biology and ecology of arthropods. It is augmented with literature from other disciplines, indicative of the potential for knowledge transfer. It is demonstrated that stable isotopes can

  6. Subject Didactic Studies of Research Training in Biology and Physics.

    Science.gov (United States)

    Lybeck, Leif

    1984-01-01

    The objectives and design of a 3-year study of research training and supervision in biology and physics are discussed. Scientific problems arising from work on the thesis will be a focus for the postgraduate students and their supervisors. Attention will be focused on supervisors' and students' conceptions of science, subject range, research,…

  7. Vitamin D biology and heart failure : Clinical and experimental studies

    NARCIS (Netherlands)

    Meems, Laura

    2015-01-01

    In the last decade, vitamin D biology has been studied more extensively than ever before.. The use of vitamin D supplements is common, and so is determination of plasma vitamin D status. Besides its role in bone homeostasis, vitamin D is thought to be an important player in the development and

  8. Considerations for clinical pharmacology studies for biologics in emerging markets.

    Science.gov (United States)

    Damle, Bharat; White, Robert; Wang, Huifen Faye

    2015-03-01

    Registration of innovative biologics in Emerging Markets (EMs) poses many opportunities and challenges. The BRIC-MT countries (Brazil, Russia, India, China, Mexico, and Turkey) that are the fastest growing markets and regulators in these countries have imposed certain requirements, including the need for local clinical studies, for registration of biologics. The regulatory landscape in these countries is rapidly evolving, which necessitates an up-to-date understanding of such requirements. There is growing evidence which suggests that race, after accounting for body weight differences, may not influence the pharmacokinetics of biologics to the same extent that it does for small molecules. Thus, the requirements for clinical pharmacology trials in EMs are driven mainly by regulatory needs set forth by local Ministry of Health. In addition to the clinical Phase I to III studies done in the global program that supports registration in large geographies, countries such as China require local single and multiple dose Phase I studies. Participating in global studies with clinical sites within their country may be sufficient for some markets, while other regulators may be satisfied with a Certificate of Pharmaceutical Product. This paper discusses the current requirements for registration of innovative biologics in key EMs.

  9. Learning Experiences of University Biology Faculty: A Qualitative Pilot Study

    Science.gov (United States)

    Kusch, Jennifer

    2016-01-01

    The study described in this article incorporates qualitative research through in-depth, individual, structured interviews with 12 biology faculty from two Midwestern universities to explore perceptions about how they have learned to teach and how they work to improve their skills.

  10. Large scale molecular dynamics study of polymer-surfactant complex

    Science.gov (United States)

    Goswami, Monojoy; Sumpter, Bobby

    2012-02-01

    In this work, we study the self-assembly of cationic polyelectrolytes mediated by anionic surfactants in dilute or semi-dilute and gel states. The understanding of the dilute system is a requirement for the understanding of gel states. The importance of polyelectrolyte with oppositely charged colloidal particles can be found in biological systems, such as immobilization of enzymes in polyelectrolyte complexes or nonspecific association of DNA with protein. With the same understanding, interaction of surfactants with polyelectrolytes shows intriguing phenomena that are important for both in academic research as well as industrial applications. Many useful properties of PE surfactant complexes come from the highly ordered structures of surfactant self-assembly inside the PE aggregate. We do large scale molecular dynamics simulation using LAMMPS to understand the structure and dynamics of PE-surfactant systems. Our investigation shows highly ordered ring-string structures that have been observed experimentally in biological systems. We will investigate many different properties of PE-surfactant complexation which will be helpful for pharmaceutical, engineering and biological applications.

  11. The role of transient dynamics in biological pest control: insights from a host-parasitoid community.

    Science.gov (United States)

    Kidd, David; Amarasekare, Priyanga

    2012-01-01

    1. Identifying natural enemies that can maintain pests at low abundances is a priority in biological control. Here, we show that experiments combined with models generate new insights into identifying effective control agents prior to their release in the field. Using a host-parasitoid community (the harlequin bug and its egg parasitoids) as a model system, we report three key findings. 2. The interplay between the host's self-limitation and the parasitoids' saturating functional response causes the long-term (steady-state) outcomes for pest suppression to differ from those of short-term (transient) dynamics. When the bug's self-limitation is moderately strong, the parasitoid with the higher attack rate and conversion efficiency (Ooencyrtus) achieves greater host suppression in the long term, but its longer handling time causes long periods of transient dynamics during which the bug can reach high abundances; when the bug's self-limitation is weak, host fluctuations amplify over time and Ooencyrtus fails at host suppression altogether. In contrast, the parasitoid with the lower attack rate and conversion efficiency but the shorter handling time (Trissolcus) induces only weak transient fluctuations of short duration and can maintain the host at low abundances regardless of the strength of the bug's self-limitation. 3. Release of multiple enemy species can compromise host suppression if an enemy that induces stronger transient fluctuations excludes one that induces weaker fluctuations. For instance, Ooencyrtus excludes Trissolcus despite having a longer handling time because of its higher conversion efficiency. The model correctly predicts the time to exclusion observed in experiments, suggesting that it captures the key biological features of the host-parasitoid interaction. 4. Intraspecific interference reduces long-term pest suppression but improves short-term pest control by reducing the magnitude and duration of transient fluctuations. 5. These results highlight

  12. Novel recurrent neural network for modelling biological networks: oscillatory p53 interaction dynamics.

    Science.gov (United States)

    Ling, Hong; Samarasinghe, Sandhya; Kulasiri, Don

    2013-12-01

    Understanding the control of cellular networks consisting of gene and protein interactions and their emergent properties is a central activity of Systems Biology research. For this, continuous, discrete, hybrid, and stochastic methods have been proposed. Currently, the most common approach to modelling accurate temporal dynamics of networks is ordinary differential equations (ODE). However, critical limitations of ODE models are difficulty in kinetic parameter estimation and numerical solution of a large number of equations, making them more suited to smaller systems. In this article, we introduce a novel recurrent artificial neural network (RNN) that addresses above limitations and produces a continuous model that easily estimates parameters from data, can handle a large number of molecular interactions and quantifies temporal dynamics and emergent systems properties. This RNN is based on a system of ODEs representing molecular interactions in a signalling network. Each neuron represents concentration change of one molecule represented by an ODE. Weights of the RNN correspond to kinetic parameters in the system and can be adjusted incrementally during network training. The method is applied to the p53-Mdm2 oscillation system - a crucial component of the DNA damage response pathways activated by a damage signal. Simulation results indicate that the proposed RNN can successfully represent the behaviour of the p53-Mdm2 oscillation system and solve the parameter estimation problem with high accuracy. Furthermore, we presented a modified form of the RNN that estimates parameters and captures systems dynamics from sparse data collected over relatively large time steps. We also investigate the robustness of the p53-Mdm2 system using the trained RNN under various levels of parameter perturbation to gain a greater understanding of the control of the p53-Mdm2 system. Its outcomes on robustness are consistent with the current biological knowledge of this system. As more

  13. Prospect of detection and recognition of single biological molecules using ultrafast coherent dynamics in quantum dot-metallic nanoparticle systems

    Science.gov (United States)

    Sadeghi, S. M.

    2015-08-01

    Conventional plasmonic sensors are based on the intrinsic resonances of metallic nanoparticles. In such sensors wavelength shift of such resonances are used to detect biological molecules. Recently we introduced ultra-sensitive timedomain nanosensors based on the way variations in the environmental conditions influence coherent dynamics of hybrid systems consisting of metallic nanoparticles and quantum dots. Such dynamics are generated via interaction of these systems with a laser field, generating quantum coherence and coherent exciton-plasmon coupling. These sensors are based on impact of variations of the refractive index of the environment on such dynamics, generating time-dependent changes in the emission of the QDs. In this paper we study the impact of material properties of the metallic nanoparticles on this process and demonstrate the key role played by the design of the quantum dots. We show that Ag nanoparticles, even in a simple spherical shape, may allow these sensors to operate at room temperature, owing to the special properties of quantum dot-metallic nanoparticle systems that may allow coherent effects utilized in such sensors happen in the presence of the ultrafast polarization dephasing of quantum dots.

  14. Bacterial community dynamics over successional stages of Australian biological soil crusts

    Science.gov (United States)

    Chilton, Angela; Woodhouse, Jason; Neilan, Brett

    2015-04-01

    A key aspect for successful ecological rehabilitation is understanding the naturally occurring ecosystem and landscape function which is to be restored. This allows for recovery indicators to be identified and criteria to be developed to assess progress and outcomes. In arid rangelands, environmental stresses result in characteristically heterogeneous landscapes where biological soil crusts (BSCs) cover large expanses of inter-plant areas. Here, BSCs perform crucial roles in nutrient cycling and re-distribution, affect hydrological patterns and stabilise the soil surface. They also serve as a large reservoir of microbial and avascular plant biodiversity. The recognition of these important roles has resulted in increased global arid rehabilitation efforts employing BSCs. Within Australia, research has focused on the macro components of BSCs including lichens and mosses, however, there have been insufficient studies examining the BSC bacterial communities and their dynamics over different successional stages. This project surveyed the bacterial community of crust-free soil and three successional stages of undisturbed BSCs from New South Wales (NSW), Australia, in order to provide reference standards of naturally occurring Australian BSCs. Visual assessments were conducted and BSCs were categorised as Early, Mid or Late stage depending on colour, thickness, topography and presence of lichens and mosses. The crust-free soil and different stages were sampled within three 50 m2 plots of the same edaphic conditions near the town of Cobar, NSW. High throughput sequencing using the Illumina MiSeq platform was performed targeting the V2 region of the 16S rRNA gene. Preliminary analysis has revealed a clear distinction between the crust-free and crusted soil while Canonical Analysis of Principal Co-ordinates (CAP) suggests the presence of two distinct BSC microbial communities despite three stages being sampled. Across all sample types, the dominant phyla were Actinobacteria

  15. Structural dynamics in complex liquids studied with multidimensional vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Tokmakoff, Andrei [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

    2013-08-31

    The development of new sustainable energy sources is linked to our understanding of the molecular properties of water and aqueous solutions. Energy conversion, storage, and transduction processes, particularly those that occur in biology, fuel cells, and batteries, make use of water for the purpose of moving energy in the form of charges and mediating the redox chemistry that allows this energy to be stored as and released from chemical bonds. To build our fundamental knowledge in this area, this project supports work in the Tokmakoff group to investigate the molecular dynamics of water’s hydrogen bond network, and how these dynamics influence its solutes and the mechanism of proton transport in water. To reach the goals of this grant, we developed experiments to observe molecular dynamics in water as directly as possible, using ultrafast multidimensional vibrational spectroscopy. We excite and probe broad vibrational resonances of water, molecular solutes, and protons in water. By correlating how molecules evolve from an initial excitation frequency to a final frequency, we can describe the underlying molecular dynamics. Theoretical modeling of the data with the help of computational spectroscopy coupled with molecular dynamics simulations provided the atomistic insight in these studies.

  16. Dynamics of Intracellular Polymers in Enhanced Biological Phosphorus Removal Processes under Different Organic Carbon Concentrations

    Directory of Open Access Journals (Sweden)

    Lizhen Xing

    2013-01-01

    Full Text Available Enhanced biological phosphorus removal (EBPR may deteriorate or fail during low organic carbon loading periods. Polyphosphate accumulating organisms (PAOs in EBPR were acclimated under both high and low organic carbon conditions, and then dynamics of polymers in typical cycles, anaerobic conditions with excess organic carbons, and endogenous respiration conditions were examined. After long-term acclimation, it was found that organic loading rates did not affect the yield of PAOs and the applied low organic carbon concentrations were advantageous for the enrichment of PAOs. A low influent organic carbon concentration induced a high production of extracellular carbohydrate. During both anaerobic and aerobic endogenous respirations, when glycogen decreased to around 80 ± 10 mg C per gram of volatile suspended solids, PAOs began to utilize polyphosphate significantly. Regressed by the first-order reaction model, glycogen possessed the highest degradation rate and then was followed by polyphosphate, while biomass decay had the lowest degradation rate.

  17. Dynamics of intracellular polymers in enhanced biological phosphorus removal processes under different organic carbon concentrations.

    Science.gov (United States)

    Xing, Lizhen; Ren, Li; Tang, Bo; Wu, Guangxue; Guan, Yuntao

    2013-01-01

    Enhanced biological phosphorus removal (EBPR) may deteriorate or fail during low organic carbon loading periods. Polyphosphate accumulating organisms (PAOs) in EBPR were acclimated under both high and low organic carbon conditions, and then dynamics of polymers in typical cycles, anaerobic conditions with excess organic carbons, and endogenous respiration conditions were examined. After long-term acclimation, it was found that organic loading rates did not affect the yield of PAOs and the applied low organic carbon concentrations were advantageous for the enrichment of PAOs. A low influent organic carbon concentration induced a high production of extracellular carbohydrate. During both anaerobic and aerobic endogenous respirations, when glycogen decreased to around 80 ± 10 mg C per gram of volatile suspended solids, PAOs began to utilize polyphosphate significantly. Regressed by the first-order reaction model, glycogen possessed the highest degradation rate and then was followed by polyphosphate, while biomass decay had the lowest degradation rate.

  18. Effects of dynamic operating conditions on nitrification in biological rapid sand filters for drinking water treatment

    DEFF Research Database (Denmark)

    Lee, Carson Odell; Boe-Hansen, Rasmus; Musovic, Sanin

    2014-01-01

    Biological rapid sand filters are often used to remove ammonium from groundwater for drinking water supply. They often operate under dynamic substrate and hydraulic loading conditions, which can lead to increased levels of ammonium and nitrite in the effluent. To determine the maximum nitrification...... operating conditions. The ammonium removal rate of the filter was determined by the ammonium loading rate, but was independent of both the flow and influent ammonium concentration individually. Ammonia-oxidizing bacteria and archaea were almost equally abundant in the filter. Both ammonium removal...... rates and safe operating windows of rapid sand filters, a pilot scale rapid sand filter was used to test short-term increased ammonium loads, set by varying either influent ammonium concentrations or hydraulic loading rates. Ammonium and iron (flock) removal were consistent between the pilot...

  19. "Gestaltomics": Systems Biology Schemes for the Study of Neuropsychiatric Diseases.

    Science.gov (United States)

    Gutierrez Najera, Nora A; Resendis-Antonio, Osbaldo; Nicolini, Humberto

    2017-01-01

    The integration of different sources of biological information about what defines a behavioral phenotype is difficult to unify in an entity that reflects the arithmetic sum of its individual parts. In this sense, the challenge of Systems Biology for understanding the "psychiatric phenotype" is to provide an improved vision of the shape of the phenotype as it is visualized by "Gestalt" psychology, whose fundamental axiom is that the observed phenotype (behavior or mental disorder) will be the result of the integrative composition of every part. Therefore, we propose the term "Gestaltomics" as a term from Systems Biology to integrate data coming from different sources of information (such as the genome, transcriptome, proteome, epigenome, metabolome, phenome, and microbiome). In addition to this biological complexity, the mind is integrated through multiple brain functions that receive and process complex information through channels and perception networks (i.e., sight, ear, smell, memory, and attention) that in turn are programmed by genes and influenced by environmental processes (epigenetic). Today, the approach of medical research in human diseases is to isolate one disease for study; however, the presence of an additional disease (co-morbidity) or more than one disease (multimorbidity) adds complexity to the study of these conditions. This review will present the challenge of integrating psychiatric disorders at different levels of information (Gestaltomics). The implications of increasing the level of complexity, for example, studying the co-morbidity with another disease such as cancer, will also be discussed.

  20. Toward total synthesis of cell function: Reconstituting cell dynamics with synthetic biology.

    Science.gov (United States)

    Kim, Allen K; DeRose, Robert; Ueno, Tasuku; Lin, Benjamin; Komatsu, Toru; Nakamura, Hideki; Inoue, Takanari

    2016-02-09

    Biological phenomena, such as cellular differentiation and phagocytosis, are fundamental processes that enable cells to fulfill important physiological roles in multicellular organisms. In the field of synthetic biology, the study of these behaviors relies on the use of a broad range of molecular tools that enable the real-time manipulation and measurement of key components in the underlying signaling pathways. This Review will focus on a subset of synthetic biology tools known as bottom-up techniques, which use technologies such as optogenetics and chemically induced dimerization to reconstitute cellular behavior in cells. These techniques have been crucial not only in revealing causal relationships within signaling networks but also in identifying the minimal signaling components that are necessary for a given cellular function. We discuss studies that used these systems in a broad range of cellular and molecular phenomena, including the time-dependent modulation of protein activity in cellular proliferation and differentiation, the reconstitution of phagocytosis, the reconstitution of chemotaxis, and the regulation of actin reorganization. Finally, we discuss the potential contribution of synthetic biology to medicine.

  1. A novel approach to neutron scattering instrumentation for probing multiscale dynamics in soft and biological matter

    Science.gov (United States)

    Mamontov, Eugene

    2016-09-01

    We present a concept and ray-tracing simulation of a mechanical device that will enable inelastic neutron scattering measurements where the data at energy transfers from a few μeV to several hundred meV can be collected in a single, gapless spectrum. Besides covering 5 orders of magnitude on the energy (time) scale, the device provides data over 2 orders of magnitude on the scattering momentum (length) scale in a single measurement. Such capabilities are geared primarily toward soft and biological matter, where the broad dynamical features of relaxation origin largely overlap with vibration features, thus necessitating gapless spectral coverage over several orders of magnitude in time and space. Furthermore, neutron scattering experiments with such a device are performed with a fixed neutron final energy, which enables measurements, with neutron energy loss in the sample, at arbitrarily low temperatures over the same broad spectral range. This capability is also invaluable in biological and soft matter research, as the variable temperature dependence of different relaxation components allows their separation in the scattering spectra as a function of temperature.

  2. Biological sulphide removal from anaerobically treated domestic sewage: reactor performance and microbial community dynamics.

    Science.gov (United States)

    Garcia, Graziella Patrício Pereira; Diniz, Renata Côrtes Oliveira; Bicalho, Sarah Kinaip; Franco, Vitor Araujo de Souza; Gontijo, Eider Max de Oliveira; Toscano, Rodrigo Argolo; Canhestro, Kenia Oliveira; Santos, Merly Rita Dos; Carmo, Ana Luiza Rodrigues Dias; Lobato, Livia Cristina S; Brandt, Emanuel Manfred F; Chernicharo, Carlos A L; Calabria de Araujo, Juliana

    2015-01-01

    We developed a biological sulphide oxidation system and evaluated two reactors (shaped similar to the settler compartment of an up-flow anaerobic sludge blanket [UASB] reactor) with different support materials for biomass retention: polypropylene rings and polyurethane foam. The start-up reaction was achieved using microorganisms naturally occurring on the open surface of UASB reactors treating domestic wastewater. Sulphide removal efficiencies of 65% and 90% were achieved with hydraulic retention times (HRTs) of 24 and 12 h, respectively, in both reactors. However, a higher amount of elemental sulphur was formed and accumulated in the biomass from reactor 1 (20 mg S(0) g(-1) VTS) than in that from reactor 2 (2.9 mg S(0) g(-1) VTS) with an HRT of 24 h. Denaturing gradient gel electrophoresis (DGGE) results revealed that the the pink and green biomass that developed in both reactors comprised a diverse bacterial community and had sequences related to phototrophic green and purple-sulphur bacteria such as Chlorobium sp., Chloronema giganteum, and Chromatiaceae. DGGE band patterns also demonstrated that bacterial community was dynamic over time within the same reactor and that different support materials selected for distinct bacterial communities. Taken together, these results indicated that sulphide concentrations of 1-6 mg L(-1) could be efficiently removed from the effluent of a pilot-scale UASB reactor in two sulphide biological oxidation reactors at HRTs of 12 and 24 h, showing the potential for sulphur recovery from anaerobically treated domestic wastewater.

  3. An empirical study of dynamic graph algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Alberts, D. [Freie Universitaet Berlin (Germany); Cattaneo, G. [Universita di Salerno (Italy); Italiano, G.F. [Universita Ca Forscari di Venezia (Italy)

    1996-12-31

    We conduct an empirical study on some dynamic graph algorithms which where developed recently. The following implementations were tested and compared with simple algorithms: dynamic connectivity, and dynamic minimum 1 spanning tree based on sparsification by Eppstein et al.; dynamic connectivity based on a very recent paper by Henzinger and King. In our experiments, we considered both random and non-random inputs. Moreover, we present a simplified variant of the algorithm by Henzinger and King, which for random inputs was always faster than the original implementation. Indeed, this variant was among the fastest implementations for random inputs. For non-random inputs, sparsification was the fastest algorithm for small sequences of updates; for medium and large sequences of updates, the original algorithm by Henzinger and King was faster. Perhaps one of the main practical results of this paper is that our implementations of the sophisticated dynamic graph algorithms were faster than simpler algorithms for most practical values of the graph parameters, and competitive with simpler algorithms even in case of very small graphs (say graphs with less than a dozen vertices and edges). From the theoretical point of view, we analyze the average case running time of sparsification and prove that the logarithmic overhead for simple sparsification vanishes for dynamic random graphs.

  4. NMR studies of nucleic acid dynamics

    Science.gov (United States)

    Al-Hashimi, Hashim M.

    2013-12-01

    Nucleic acid structures have to satisfy two diametrically opposite requirements; on one hand they have to adopt well-defined 3D structures that can be specifically recognized by proteins; on the other hand, their structures must be sufficiently flexible to undergo very large conformational changes that are required during key biochemical processes, including replication, transcription, and translation. How do nucleic acids introduce flexibility into their 3D structure without losing biological specificity? Here, I describe the development and application of NMR spectroscopic techniques in my laboratory for characterizing the dynamic properties of nucleic acids that tightly integrate a broad set of NMR measurements, including residual dipolar couplings, spin relaxation, and relaxation dispersion with sample engineering and computational approaches. This approach allowed us to obtain fundamental new insights into directional flexibility in nucleic acids that enable their structures to change in a very specific functional manner.

  5. Center of cancer systems biology second annual workshop--tumor metronomics: timing and dose level dynamics.

    Science.gov (United States)

    Hahnfeldt, Philip; Hlatky, Lynn; Klement, Giannoula Lakka

    2013-05-15

    Metronomic chemotherapy, the delivery of doses in a low, regular manner so as to avoid toxic side effects, was introduced over 12 years ago in the face of substantial clinical and preclinical evidence supporting its tumor-suppressive capability. It constituted a marked departure from the classic maximum-tolerated dose (MTD) strategy, which, given its goal of rapid eradication, uses dosing sufficiently intense to require rest periods between cycles to limit toxicity. Even so, upfront tumor eradication is frequently not achieved with MTD, whereupon a de facto goal of longer-term tumor control is often pursued. As metronomic dosing has shown tumor control capability, even for cancers that have become resistant to the same drug delivered under MTD, the question arises whether it may be a preferable alternative dosing approach from the outset. To date, however, our knowledge of the coupled dynamics underlying metronomic dosing is neither sufficiently well developed nor widely enough disseminated to establish its actual potential. Meeting organizers thus felt the time was right, armed with new quantitative approaches, to call a workshop on "Tumor Metronomics: Timing and Dose Level Dynamics" to explore prospects for gaining a deeper, systems-level appreciation of the metronomics concept. The workshop proved to be a forum in which experts from the clinical, biologic, mathematical, and computational realms could work together to clarify the principles and underpinnings of metronomics. Among other things, the need for significant shifts in thinking regarding endpoints to be used as clinical standards of therapeutic progress was recognized.

  6. Equivalences in Biological and Economical Systems: Peloton Dynamics and the Rebound Effect.

    Science.gov (United States)

    Trenchard, Hugh; Perc, Matjaz

    2016-01-01

    An interdisciplinary bridge is proposed between principles of collective behavior in biological systems, particularly bicycle pelotons, and the economic phenomenon called the rebound effect. Two main equivalencies are proposed between aspects of peloton dynamics and aspects of energy service efficiencies and the rebound effect. Firstly, a threshold whereby weaker cyclists, up to maximal capacities, sustain speeds of pacesetters by drafting; equivalent to a threshold whereby consumers will not exceed maximum allocated budgets for energy services, costs for which are externally determined. Secondly, a threshold of peloton dynamics whereby, below this threshold, weaker cyclists share costly non-drafting positions, whereas above this threshold cyclists cannot share these positions but can sustain pacesetter speeds. This is in turn equivalent to the threshold in the context of energy service efficiency, whereby consumers will increase spending to the limit indicated by the rebound magnitude but not to their maximum allocated budgets. These thresholds are a consequence of the model equations, and the latter threshold is explained by consumer apprehension that existing energy efficiencies could disappear or be negative, when consumers would be over budget. This partly explains long term rebound increase, whereby consumers increase consumption as confidence rises that cost savings due to energy service efficiency is stable.

  7. Suppressing and enhancing effects of mesoscale dynamics on biological production in the Mozambique Channel

    Science.gov (United States)

    José, Y. S.; Penven, P.; Aumont, O.; Machu, E.; Moloney, C. L.; Shillington, F.; Maury, O.

    2016-06-01

    We used a coupled physical-biogeochemical model to investigate how the strong eddy activity typical of the Mozambique Channel affects biological production. A numerical experiment was carried out, in which mesoscale dynamics were suppressed by cancelling the nonlinear terms for horizontal momentum in the Naviers-Stokes equation. Mesoscale dynamics were found to be responsible for (1) increased offshore production in the Mozambique Channel as a result of net eddy-induced offshore transport of nutrient-rich coastal waters; (2) decreased shelf production along the central Mozambican and south-west Madagascar coast caused by a reduction in nutrient availability related to the net eddy-induced lateral transport of nutrients; (3) increased coastal production along the northern Mozambican coast caused by eddy-induced nutrient supply. The model results also showed an intensification and shallowing of the subsurface production, related to increased upper layer nutrient concentrations caused by eddy activity. In addition, by driving the detachment of the East Madagascar Current at the southern tip of the island, inertial processes intensify the southern Madagascar upwelling and causes offshore diffusion of the upwelled waters. These results emphasize the complex role played by eddy activity and, more generally, inertial processes on marine ecosystems in this region.

  8. VUV studies of molecular photofragmentation dynamics

    Energy Technology Data Exchange (ETDEWEB)

    White, M.G. [Brookhaven National Laboratory, Upton, NY (United States)

    1993-12-01

    State-resolved, photoion and photoelectron methods are used to study the neutral fragmentation and ionization dynamics of small molecules relevant to atmospheric and combustion chemistry. Photodissociation and ionization are initiated by coherent VUV radiation and the fragmentation dynamics are extracted from measurements of product rovibronic state distributions, kinetic energies and angular distributions. The general aim of these studies is to investigate the multichannel interactions between the electronic and nuclear motions which determine the evolution of the photoexcited {open_quotes}complex{close_quotes} into the observed asymptotic channels.

  9. In vivo Dynamic Studies of Brain Metabolism

    Institute of Scientific and Technical Information of China (English)

    LUO Xuechun; JIANG Yufeng; ZHANG Riqing

    2005-01-01

    Nuclear magnetic resonance (NMR) can noninvasively monitor intracellular concentrations and kinetic properties of numerous inorganic and organic compounds. A 31P NMR surface coil was used in vivo to dynamically measure phosphocreatine (PCr), adenosine triphosphate (ATP), and intracellular inorganic phosphate (Pi) levels in mouse brain during ischemia-reperfusion to study the damage of cerebral tissues caused by ischemia and effects of herbs on cerebral energy metabolism during ischemia-reperfusion. The study provides dynamic brain energy metabolism data during different periods. The data show that some herbs more rapidly increase the PCr level during the recovery phase than in the control group.

  10. 2nd International Symposium "Atomic Cluster Collisions : Structure and Dynamics from the Nuclear to the Biological Scale"

    CERN Document Server

    Solov'yov, Andrey; ISACC 2007; Latest advances in atomic cluster collisions

    2008-01-01

    This book presents a 'snapshot' of the most recent and significant advances in the field of cluster physics. It is a comprehensive review based on contributions by the participants of the 2nd International Symposium on Atomic Cluster Collisions (ISACC 2007) held in July 19-23, 2007 at GSI, Darmstadt, Germany. The purpose of the Symposium is to promote the growth and exchange of scientific information on the structure and properties of nuclear, atomic, molecular, biological and complex cluster systems studied by means of photonic, electronic, heavy particle and atomic collisions. Particular attention is devoted to dynamic phenomena, many-body effects taking place in cluster systems of a different nature - these include problems of fusion and fission, fragmentation, collective electron excitations, phase transitions, etc.Both the experimental and theoretical aspects of cluster physics, uniquely placed between nuclear physics on the one hand and atomic, molecular and solid state physics on the other, are discuss...

  11. Biological soil crusts across disturbance-recovery scenarios: effect of grazing regime on community dynamics

    Science.gov (United States)

    Concostrina-Zubiri, L.; Huber-Sannwald, E.; Martínez, I.; Flores Flores, J. L.; Reyes-Agüero, J. A.; Escudero, A.; Belnap, Jayne

    2014-01-01

    Grazing represents one of the most common disturbances in drylands worldwide, affecting both ecosystem structure and functioning. Despite the efforts to understand the nature and magnitude of grazing effects on ecosystem components and processes, contrasting results continue to arise. This is particularly remarkable for the biological soil crust (BSC) communities (i.e., cyanobacteria, lichens, and bryophytes), which play an important role in soil dynamics. Here we evaluated simultaneously the effect of grazing impact on BSC communities (resistance) and recovery after livestock exclusion (resilience) in a semiarid grassland of Central Mexico. In particular, we examined BSC species distribution, species richness, taxonomical group cover (i.e., cyanobacteria, lichen, bryophyte), and composition along a disturbance gradient with different grazing regimes (low, medium, high impact) and along a recovery gradient with differently aged livestock exclosures (short-, medium-, long-term exclusion). Differences in grazing impact and time of recovery from grazing both resulted in slight changes in species richness; however, there were pronounced shifts in species composition and group cover. We found we could distinguish four highly diverse and dynamic BSC species groups: (1) species with high resistance and resilience to grazing, (2) species with high resistance but low resilience, (3) species with low resistance but high resilience, and (4) species with low resistance and resilience. While disturbance resulted in a novel diversity configuration, which may profoundly affect ecosystem functioning, we observed that 10 years of disturbance removal did not lead to the ecosystem structure found after 27 years of recovery. These findings are an important contribution to our understanding of BCS dynamics from a species and community perspective placed in a land use change context.

  12. Dynamic CT head phantom for perfusion and angiography studies

    Science.gov (United States)

    Russell, K.; Blazeski, A.; Dannecker, K.; Lee, Q. Y.; Holscher, C.; Donahue, C.; van Kampen, W.

    2010-03-01

    Contrast imaging is a compelling enhancement for the portable, flat panel-based brain CT scanner currently under development at Xoran. Due to the relative low temporal resolution of flat panel detectors, enabling tomographic imaging on such platform requires optimizing the imaging and injection protocols. A dynamic CT head phantom was designed to facilitate this task. The Dynamic Perfusion and Angiography Model (PAM), mimics tissue attenuation in CT images, provides physiological timing for angiography and perfusion studies, and moves fluid with properties similar to those of blood. The design consists of an arterial system, which contains bifurcating vessels that feed into perfusion chambers, mimicking blood flow through capillaries and smaller vessels, and a venous system, which is symmetrical to the arterial side and drains the perfusion chambers. The variation of geometry and flow rate in the phantom provides the physiological total time that fluid spends in the head, and the difference in material densities correlates to CT numbers for biological tissues. This paper discusses the design of Dynamic PAM and shows experimental results demonstrating its ability to realistically simulate blood flow. Results of dynamic imaging studies of the phantom are also presented.

  13. Dynamics on and of complex networks applications to biology, computer science, and the social sciences

    CERN Document Server

    Ganguly, Niloy; Mukherjee, Animesh

    2009-01-01

    This self-contained book systematically explores the statistical dynamics on and of complex networks having relevance across a large number of scientific disciplines. The theories related to complex networks are increasingly being used by researchers for their usefulness in harnessing the most difficult problems of a particular discipline. The book is a collection of surveys and cutting-edge research contributions exploring the interdisciplinary relationship of dynamics on and of complex networks. Towards this goal, the work is thematically organized into three main sections: Part I studies th

  14. Biological control of harmful algal blooms: A modelling study

    Science.gov (United States)

    Solé, Jordi; Estrada, Marta; Garcia-Ladona, Emilio

    2006-07-01

    A multispecies dynamic simulation model (ERSEM) was used to examine the influence of allelopathic and trophic interactions causing feeding avoidance by predators, on the formation of harmful algal blooms, under environmental scenarios typical of a Mediterranean harbour (Barcelona). The biological state variables of the model included four functional groups of phytoplankton (diatoms, toxic and non-toxic flagellates and picophytoplankton), heterotrophic flagellates, micro- and mesozooplankton and bacteria. The physical-chemical forcing (irradiance, temperature and major nutrient concentrations) was based on an actual series of measurements taken along a year cycle in the Barcelona harbour. In order to evaluate potential effects of advection, some runs were repeated after introducing a biomass loss term. Numerical simulations showed that allelopathic effects of a toxic alga on a non-toxic but otherwise similar competitor did not have appreciable influence on the dynamics of the system. However, induction of avoidance of the toxic alga by predators, which resulted on increased predation pressure on other algal groups had a significant effect on the development of algal and predator populations. The presence of advection overrided the effect of these interactions and only allowed organisms with sufficiently high potential growth rates to thrive.

  15. Contributions to the Study of Dynamic Absorbers, a Case Study

    Directory of Open Access Journals (Sweden)

    Monica Balcau

    2012-01-01

    Full Text Available Dynamic absorbers are used to reduce torsional vibrations. This paper studies the effect of a dynamic absorber attached to a mechanical system formed of three reduced masses which are acted on by one, two or three order x harmonics of a disruptive force.

  16. Current status of the studies of biological objects by the time-resolved X-ray diffraction technique

    Energy Technology Data Exchange (ETDEWEB)

    Aul' chenko, V.M. [Budker Institute of Nuclear Physics, Siberian Division of the Russian Academy of Sciences, Novosibirsk (Russian Federation); Bukin, M.A. [Budker Institute of Nuclear Physics, Siberian Division of the Russian Academy of Sciences, Novosibirsk (Russian Federation); Vazina, A.A. [Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino (Russian Federation); Gadzhiev, A.M. [Karaev Institute of Physiology, National Academy of Sciences of Azerbaijan, AzNas, 2, Sharifzade str., Baku, AZ1100 Azerbaijan (Azerbaijan)]. E-mail: agadzhiev@bakinter.net; Korneev, B.N. [Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino (Russian Federation); Sergienko, P.M. [Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino (Russian Federation); Titov, V.M. [Budker Institute of Nuclear Physics, Siberian Division of the Russian Academy of Sciences, Novosibirsk (Russian Federation); Tolochko, B.P. [Institute of Solid State Chemistry and Mechanochemistry, Siberian Division of the Russian Academy of Sciences, Novosibirsk (Russian Federation); Sheromov, M.A. [Budker Institute of Nuclear Physics, Siberian Division of the Russian Academy of Sciences, Novosibirsk (Russian Federation)

    2005-05-01

    The methodological and technical aspects of the biological objects study by the time-resolved X-ray diffraction technique are described with reference to muscle contraction. The results of relevant investigations into the structural dynamics of a living muscle during its contraction are presented.

  17. Dynamic study of synchronous machine electric drive

    Directory of Open Access Journals (Sweden)

    Dimitar Spirov

    2005-10-01

    Full Text Available The dynamic behaviour of the fan blower synchoronous machine drive have been studied in the paper. The equations for the voltages of the synchoronous machine windings are presented in a coordinate system which rotates at the angular speed of the rotor. The mechanical equipment is presented by means of a single-mass dynamic model. The derived system of differential equations is transformed and solved using suitable software product. The results obtained for rotation frequency and electromagnetic torque motor in the courses of different values of rated supply voltage and of different initial resistant moment of the mechanism have been graphically presented. Conclusions from the results obtained have been done.

  18. Molecular Dynamics Studies of Matrix Metalloproteases.

    Science.gov (United States)

    Díaz, Natalia; Suárez, Dimas

    2017-01-01

    Matrix metalloproteases are multidomain enzymes with a remarkable proteolytic activity located in the extracellular environment. Their catalytic activity and structural properties have been intensively studied during the last few decades using both experimental and theoretical approaches, but many open questions still remain. Extensive molecular dynamics simulations enable the sampling of the configurational space of a molecular system, thus contributing to the characterization of the structure, dynamics, and ligand binding properties of a particular MMP. Based on previous computational experience, we provide in this chapter technical and methodological guidelines that may be useful to and stimulate other researchers to perform molecular dynamics simulations to help address unresolved questions concerning the molecular mode of action of MMPs.

  19. Cancer systems biology in the genome sequencing era: part 2, evolutionary dynamics of tumor clonal networks and drug resistance.

    Science.gov (United States)

    Wang, Edwin; Zou, Jinfeng; Zaman, Naif; Beitel, Lenore K; Trifiro, Mark; Paliouras, Miltiadis

    2013-08-01

    A tumor often consists of multiple cell subpopulations (clones). Current chemo-treatments often target one clone of a tumor. Although the drug kills that clone, other clones overtake it and the tumor recurs. Genome sequencing and computational analysis allows to computational dissection of clones from tumors, while singe-cell genome sequencing including RNA-Seq allows profiling of these clones. This opens a new window for treating a tumor as a system in which clones are evolving. Future cancer systems biology studies should consider a tumor as an evolving system with multiple clones. Therefore, topics discussed in Part 2 of this review include evolutionary dynamics of clonal networks, early-warning signals (e.g., genome duplication events) for formation of fast-growing clones, dissecting tumor heterogeneity, and modeling of clone-clone-stroma interactions for drug resistance. The ultimate goal of the future systems biology analysis is to obtain a 'whole-system' understanding of a tumor and therefore provides a more efficient and personalized management strategies for cancer patients. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

  20. A Molecular Dynamics Study of the Structural and Dynamical Properties of Putative Arsenic Substituted Lipid Bilayers

    Directory of Open Access Journals (Sweden)

    Ratna Juwita

    2013-04-01

    Full Text Available Cell membranes are composed mainly of phospholipids which are in turn, composed of five major chemical elements: carbon, hydrogen, nitrogen, oxygen, and phosphorus. Recent studies have suggested the possibility of sustaining life if the phosphorus is substituted by arsenic. Although this issue is still controversial, it is of interest to investigate the properties of arsenated-lipid bilayers to evaluate this possibility. In this study, we simulated arsenated-lipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-arsenocholine (POAC, lipid bilayers using all-atom molecular dynamics to understand basic structural and dynamical properties, in particular, the differences from analogous 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, (POPC lipid bilayers. Our simulations showed that POAC lipid bilayers have distinct structural and dynamical properties from those of native POPC lipid bilayers. Relative to POPC lipid bilayers, POAC lipid bilayers have a more compact structure with smaller lateral areas and greater order. The compact structure of POAC lipid bilayers is due to the fact that more inter-lipid salt bridges are formed with arsenate-choline compared to the phosphate-choline of POPC lipid bilayers. These inter-lipid salt bridges bind POAC lipids together and also slow down the head group rotation and lateral diffusion of POAC lipids. Thus, it would be anticipated that POAC and POPC lipid bilayers would have different biological implications.

  1. Nonequilibrium dynamics of active matter with correlated noise: A dynamical renormalization group study

    Science.gov (United States)

    Kachan, Devin; Levine, Alex; Bruinsma, Robijn

    2014-03-01

    Biology is rife with examples of active materials - soft matter systems driven into nonequilibrium steady states by energy input at the micro scale. For example, solutions of active micron scale swimmers produce active fluids showing phenomena reminiscent of turbulent convection at low Reynolds number; cytoskeletal networks driven by endogenous molecular motors produce active solids whose mechanics and low frequency strain fluctuations depend sensitively on motor activity. One hallmark of these systems is that they are driven at the micro scale by temporally correlated forces. In this talk, we study how correlated noise at the micro scale leads to novel long wavelength and long time scale dynamics at the macro scale in a simple model system. Specifically, we study the fluctuations of a ϕ4 scalar field obeying model A dynamics and driven by noise with a finite correlation time τ. We show that the effective dynamical system at long length and time scales is driven by white noise with a renormalized amplitude and renormalized transport coefficients. We discuss the implications of this result for a broad class of active matter systems driven at the micro scale by colored noise.

  2. Dynamic Study of Bicycle Frame Structure

    Science.gov (United States)

    Sani, M. S. M.; Nazri, N. A.; Zahari, S. N.; Abdullah, N. A. Z.; Priyandoko, G.

    2016-11-01

    Bicycle frames have to bear variety of loads and it is needed to ensure the frame can withstand dynamic loads to move. This paper focusing on dynamic study for bicycle frame structure with a purpose to avoid the problem regarding loads on the structure and to ensure the structure is safe when multiple loads are applied on it. The main objectives of dynamic study are to find the modal properties using two method; finite element analysis (FEA) and experimental modal analysis (EMA). The correlation between two studies will be obtained using percentage error. Firstly, 3D model of mountain bike frame structure has been draw using computer-aided design (CAD) software and normal mode analysis using MSC Nastran Patran was executed for numerical method meanwhile modal testing using impact hammer was performed for experimental counterpart. From the correlation result, it show that percentage error between FEA and EMA were below 10% due to noise, imperfect experiment setup during perform EMA and imperfect modeling of mountain bike frame structure in CAD software. Small percentage error differences makes both of the method can be applied to obtain the dynamic characteristic of structure. It is essential to determine whether the structure is safe or not. In conclusion, model updating method is required to reduce more percentage error between two results.

  3. Population dynamics in wastewater treatment plants with enhanced biological phosphorus removal operated with and without nitrogen removal

    DEFF Research Database (Denmark)

    Lee, N.; Jansen, J.l.C.; Aspegren, H.

    2002-01-01

    The population dynamics of activated sludge in a pilot plant with two activated sludge systems, both designed for enhanced biological phosphorus removal (EBPR), but one of them with (BNP) and the other without (BP) nitrogen removal, was monitored during a period of 2.5 years. The influent water...

  4. A Non-Homogeneous Dynamic Bayesian Network with Sequentially Coupled Interaction Parameters for Applications in Systems and Synthetic Biology

    NARCIS (Netherlands)

    Grzegorczyk, Marco; Husmeier, Dirk

    2012-01-01

    An important and challenging problem in systems biology is the inference of gene regulatory networks from short non-stationary time series of transcriptional profiles. A popular approach that has been widely applied to this end is based on dynamic Bayesian networks (DBNs), although traditional homog

  5. A Non-Homogeneous Dynamic Bayesian Network with Sequentially Coupled Interaction Parameters for Applications in Systems and Synthetic Biology

    NARCIS (Netherlands)

    Grzegorczyk, Marco; Husmeier, Dirk

    2012-01-01

    An important and challenging problem in systems biology is the inference of gene regulatory networks from short non-stationary time series of transcriptional profiles. A popular approach that has been widely applied to this end is based on dynamic Bayesian networks (DBNs), although traditional

  6. Studying chemical reactions in biological systems with MBN Explorer

    DEFF Research Database (Denmark)

    Sushko, Gennady B.; Solov'yov, Ilia A.; Verkhovtsev, Alexey V.

    2016-01-01

    The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations of systems with dynamically changing molecular topologies....... for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation- or collision-induced damage, and also in transformation and fragmentation processes involving biomolecular systems....

  7. Unmanned Aircraft Systems complement biologging in spatial ecology studies.

    Science.gov (United States)

    Mulero-Pázmány, Margarita; Barasona, Jose Ángel; Acevedo, Pelayo; Vicente, Joaquín; Negro, Juan José

    2015-11-01

    The knowledge about the spatial ecology and distribution of organisms is important for both basic and applied science. Biologging is one of the most popular methods for obtaining information about spatial distribution of animals, but requires capturing the animals and is often limited by costs and data retrieval. Unmanned Aircraft Systems (UAS) have proven their efficacy for wildlife surveillance and habitat monitoring, but their potential contribution to the prediction of animal distribution patterns and abundance has not been thoroughly evaluated. In this study, we assess the usefulness of UAS overflights to (1) get data to model the distribution of free-ranging cattle for a comparison with results obtained from biologged (GPS-GSM collared) cattle and (2) predict species densities for a comparison with actual density in a protected area. UAS and biologging derived data models provided similar distribution patterns. Predictions from the UAS model overestimated cattle densities, which may be associated with higher aggregated distributions of this species. Overall, while the particular researcher interests and species characteristics will influence the method of choice for each study, we demonstrate here that UAS constitute a noninvasive methodology able to provide accurate spatial data useful for ecological research, wildlife management and rangeland planning.

  8. Study of β-NMR for Liquid Biological Samples

    CERN Document Server

    Beattie, Caitlin

    2017-01-01

    β-NMR is an exotic form of NMR spectroscopy that allows for the characterization of matter based on the anisotropic β-decay of radioactive probe nuclei. This has been shown to be an effective spectroscopic technique for many different compounds, but its use for liquid biological samples is relatively unexplored. The work at the VITO line of ISOLDE seeks to employ this technique to study such samples. Currently, preparations are being made for an experiment to characterize DNA G-quadruplexes and their interactions with stabilizing cations. More specifically, the work in which I engaged as a summer student focused on the experiment’s liquid handling system and the stability of the relevant biological samples under vacuum.

  9. Biological studies of post-traumatic stress disorder.

    Science.gov (United States)

    Pitman, Roger K; Rasmusson, Ann M; Koenen, Karestan C; Shin, Lisa M; Orr, Scott P; Gilbertson, Mark W; Milad, Mohammed R; Liberzon, Israel

    2012-11-01

    Post-traumatic stress disorder (PTSD) is the only major mental disorder for which a cause is considered to be known: that is, an event that involves threat to the physical integrity of oneself or others and induces a response of intense fear, helplessness or horror. Although PTSD is still largely regarded as a psychological phenomenon, over the past three decades the growth of the biological PTSD literature has been explosive, and thousands of references now exist. Ultimately, the impact of an environmental event, such as a psychological trauma, must be understood at organic, cellular and molecular levels. This Review attempts to present the current state of this understanding on the basis of psychophysiological, structural and functional neuroimaging, and endocrinological, genetic and molecular biological studies in humans and in animal models.

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

    Science.gov (United States)

    Boseman, Adam J.

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

  11. Evolutionary game theory for physical and biological scientists. II. Population dynamics equations can be associated with interpretations.

    Science.gov (United States)

    Liao, David; Tlsty, Thea D

    2014-08-01

    The use of mathematical equations to analyse population dynamics measurements is being increasingly applied to elucidate complex dynamic processes in biological systems, including cancer. Purely 'empirical' equations may provide sufficient accuracy to support predictions and therapy design. Nevertheless, interpretation of fitting equations in terms of physical and biological propositions can provide additional insights that can be used both to refine models that prove inconsistent with data and to understand the scope of applicability of models that validate. The purpose of this tutorial is to assist readers in mathematically associating interpretations with equations and to provide guidance in choosing interpretations and experimental systems to investigate based on currently available biological knowledge, techniques in mathematical and computational analysis and methods for in vitro and in vivo experiments.

  12. Dynamic mixtures and combinatorial libraries: imines as probes for molecular evolution at the interface between chemistry and biology.

    Science.gov (United States)

    Herrmann, Andreas

    2009-08-21

    In analogy to evolution in biological processes, "molecular evolution", based on the reversible formation of imines, has successfully been explored for drug discovery, receptor design and as a controlled-release vehicle. Multicomponent systems composed of amines and carbonyl compounds generate structural diversity by reversible reaction of the different components to form equilibrated dynamic mixtures or combinatorial libraries (DCLs). Under thermodynamic control and in the presence of an external factor which influences the equilibrium, these systems evolve by selective adaptation to the changing external conditions. This concept allows the casting of biologically or catalytically active substrates and the molding of receptors from DCLs which are composed of smaller non-active amine and carbonyl moieties. Similarly, if the amine or carbonyl compounds are the biologically active compounds of interest, the corresponding dynamic mixtures are found to be efficient delivery systems, allowing their controlled release over time.

  13. Studies about space radiation promote new fields in radiation biology.

    Science.gov (United States)

    Ohnishi, Takeo; Takahashi, Akihisa; Ohnishi, Ken

    2002-12-01

    Astronauts are constantly exposed to space radiation of various types of energy with a low dose-rate during long-term stays in space. Therefore, it is important to determine correctly the biological effects of space radiation on human health. Studies about biological the effects at a low dose and a low dose-rate include various aspects of microbeams, bystander effects, radioadaptive responses and hormesis which are important fields in radiation biology. In addition, space radiations contain high linear energy transfer (LET) particles. In particular, neutrons may cause reverse effectiveness at a low dose-rate in comparison to ionizing radiation. We are also interested in p53-centered signal transduction pathways involved in the cell cycle, DNA repair and apoptosis induced by space radiations. We must also study whether the relative biological effectiveness (RBE) of space radiation is affected by microgravity which is another typical component in space. To confirm this, we must prepare centrifuge systems in an International Space Station (ISS). In addition, we must prepare many types of equipment for space experiments in an ISS, because we cannot use conventional equipment from our laboratories. Furthermore, the research for space radiation might give us valuable information about the birth and evolution of life on the Earth. We can also realize the importance of preventing the ozone layer from depletion by the use of exposure equipment to sunlight in an ISS. For these reasons, we desire to educate space researchers of the next generation based on the consideration of the preservation of the Earth from research about space radiation.

  14. LOW-x Dynamics Through Jet Studies

    Science.gov (United States)

    Ferencei, Jozef; H1; ZEUS Collaborations

    One of the most challenging aspects of low x proton structure is the study of QCD dynamics - the evolution of partons between different kinematic regimes. In electron-proton deep-inelastic scattering, this can be investigated by studying processes in the target region of the proton - forward going jets. In this paper various measurements made at HERA by the H1 and ZEUS experiments are presented and compared to Monte Carlo models and fixed-order QCD calculations.

  15. Study of Nanowires Using Molecular Dynamics Simulations

    OpenAIRE

    Monk, Joshua D

    2007-01-01

    In this dissertation I present computational studies that focus on the unique characteristics of metallic nanowires. We generated virtual nanowires of nanocrystalline nickel (nc-Ni) and single crystalline silver (Ag) in order to investigate particular nanoscale effects. Three-dimensional atomistic molecular dynamics studies were performed for each sample using the super computer System X located at Virginia Tech. Thermal grain growth simulations were performed on 4 nm grain size nc-Ni by o...

  16. Molecularly engineered surfaces for cell biology: from static to dynamic surfaces.

    Science.gov (United States)

    Gooding, J Justin; Parker, Stephen G; Lu, Yong; Gaus, Katharina

    2014-04-01

    Surfaces with a well-defined presentation of ligands for receptors on the cell membrane can serve as models of the extracellular matrix for studying cell adhesion or as model cell surfaces for exploring cell-cell contacts. Because such surfaces can provide exquisite control over, for example, the density of these ligands or when the ligands are presented to the cell, they provide a very precise strategy for understanding the mechanisms by which cells respond to external adhesive cues. In the present feature article, we present an overview of the basic biology of cell adhesion before discussing surfaces that have a static presentation of immobile ligands. We outline the biological information that such surfaces have given us, before progressing to recently developed switchable surfaces and surfaces that mimic the lipid bilayer, having adhesive ligands that can move around the membrane and be remodeled by the cell. Finally, the feature article closes with some of the biological information that these new types of surfaces could provide.

  17. Assessment of biological activity in RAW 264.7 cell line stimulated with lipopolysaccharide using dynamic laser speckle

    Science.gov (United States)

    González-Peña, Rolando J.; Pérez-Montoyo, Héctor; Braga, Roberto A.; Viana, Dimitri Campos

    2016-11-01

    Dynamic laser speckle (DLS) technique or biospeckle is a noninvasive approach that can sensitively monitor the dynamics of a biological material such as the metabolism of cells. In turn, stimulation of cell activity is widely used in microbiology: it can be done by means of many agents, such as lipopolysaccharide (LPS), which is the most common component within the cell wall of Gram-negative bacteria, and it has been extensively used in in vitro models studying inflammation. The main challenge is to monitor the change of behavior inside the cells during their stimulation. This work tested the viability of the BSL to monitor the change in the metabolism of RAW cells when LPS is applied. The results show different answers of cells to distinct concentrations of LPS, and the inflammatory process promoted by the LPS could be best distinguished from the RAW cells alone in a concentration of 10 ng/mL. This proved the ability of the DLS to monitor the agent stimulus.

  18. Morphological and Biological Study of Sanguisorba Officinalis Germination

    Directory of Open Access Journals (Sweden)

    Alexandra Sh. Dodonova

    2013-01-01

    Full Text Available This work deals with the study of influence of terms and storage conditions on Sanguisorba officinalis seed material quality, put into various containers (paper, plastic, fabric, glass, in the different temperature conditions, light and dark grown. The morphology, biology of Sanguisorba officinalis seeds was described and experiments on cryopreservation were made. Basing on the study, we recommend to store Sanguisorba officinalis seed material within 3 months at a temperature of +4˚С in glass container, use plastic container for cryopreservation and to defreeze seeds by double boiling.

  19. Caenorhabditis elegans - A model system for space biology studies

    Science.gov (United States)

    Johnson, Thomas E.; Nelson, Gregory A.

    1991-01-01

    The utility of the nematode Caenorhabditis elegans in studies spanning aspects of development, aging, and radiobiology is reviewed. These topics are interrelated via cellular and DNA repair processes especially in the context of oxidative stress and free-radical metabolism. The relevance of these research topics to problems in space biology is discussed and properties of the space environment are outlined. Exposure to the space-flight environment can induce rapid changes in living systems that are similar to changes occurring during aging; manipulation of these environmental parameters may represent an experimental strategy for studies of development and senescence. The current and future opportunities for such space-flight experimentation are presented.

  20. Study on the biological characteristics of Homalotglus flaminus

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Homalotglus flaminus (Dalman) is an important natural enemy of the Chilocorus kuwanae. Its biological characteristic, life history, the action style on hosts were studied at Hongqi Forest Farm, Daqing City, Heilongjiang Province from June 1998 to October 2000, in order to control H. flaminus and raise the control ability of Chilocorus kuwanae to Quadraspidiotus gigas pest. The observed results indicated that H. flaminus has two generation one year in study area, the pupating span is 12.7 d, life span of females and males is 17.6 d and 10.8 d respectively, egg span is 10 d, and the sex ratio of females to males is 1:3.

  1. Genome-wide studies of telomere biology in budding yeast

    Directory of Open Access Journals (Sweden)

    Yaniv Harari

    2014-03-01

    Full Text Available Telomeres are specialized DNA-protein structures at the ends of eukaryotic chromosomes. Telomeres are essential for chromosomal stability and integrity, as they prevent chromosome ends from being recognized as double strand breaks. In rapidly proliferating cells, telomeric DNA is synthesized by the enzyme telomerase, which copies a short template sequence within its own RNA moiety, thus helping to solve the “end-replication problem”, in which information is lost at the ends of chromosomes with each DNA replication cycle. The basic mechanisms of telomere length, structure and function maintenance are conserved among eukaryotes. Studies in the yeast Saccharomyces cerevisiae have been instrumental in deciphering the basic aspects of telomere biology. In the last decade, technical advances, such as the availability of mutant collections, have allowed carrying out systematic genome-wide screens for mutants affecting various aspects of telomere biology. In this review we summarize these efforts, and the insights that this Systems Biology approach has produced so far.

  2. Estimation of instantaneous complex dynamics through Lyapunov exponents: a study on heartbeat dynamics.

    Science.gov (United States)

    Valenza, Gaetano; Citi, Luca; Barbieri, Riccardo

    2014-01-01

    Measures of nonlinearity and complexity, and in particular the study of Lyapunov exponents, have been increasingly used to characterize dynamical properties of a wide range of biological nonlinear systems, including cardiovascular control. In this work, we present a novel methodology able to effectively estimate the Lyapunov spectrum of a series of stochastic events in an instantaneous fashion. The paradigm relies on a novel point-process high-order nonlinear model of the event series dynamics. The long-term information is taken into account by expanding the linear, quadratic, and cubic Wiener-Volterra kernels with the orthonormal Laguerre basis functions. Applications to synthetic data such as the Hénon map and Rössler attractor, as well as two experimental heartbeat interval datasets (i.e., healthy subjects undergoing postural changes and patients with severe cardiac heart failure), focus on estimation and tracking of the Instantaneous Dominant Lyapunov Exponent (IDLE). The novel cardiovascular assessment demonstrates that our method is able to effectively and instantaneously track the nonlinear autonomic control dynamics, allowing for complexity variability estimations.

  3. Fabrication of dynamic self-assembled monolayers for cell migration and adhesion studies.

    Science.gov (United States)

    Westcott, Nathan P; Yousaf, Muhammad N

    2011-01-01

    How cells interact with the extracellular matrix (ECM) is important for a number of fundamental -processes in cell biology. However, the ECM is highly complex and in order to simplify the matrix for cell biological studies, it has been modeled with self-assembled monolayers (SAMs) of alkanethiolates on gold substrates. In this chapter, we outline procedures to create dynamic surfaces by functionalizing SAMs. SAMs based on quinone, oxyamine, and alcohol-terminated thiols were used to immobilize cell adhesive peptides with spatial control. Cells were seeded to these surfaces to provide cell co-culture -patterns suitable for biological studies.

  4. Developing a press for static and dynamic testing of orthopedic devices and biological tissue

    Directory of Open Access Journals (Sweden)

    Arlex Leyton Virgen

    2010-05-01

    Full Text Available This paper describes designing and constructing a test machine having a 1,800 N capacity and maximum 3 Hz frequency which will be used in static and dynamic testing of biological tissues and orthopedic devices such as external fixers. It consists of an oc-tagonal base with 500 mm distance between faces and a crosshead which slides between two columns (useful 350 mm opening thus allowing changing the height (maximum 600 mm according to the size of the specimen to be tested. A ball screw actuator is mounted over the crosshead which transforms a servomotor’s rotating movement into a lineal movement (maximum 150 mm stroke. First validations indicated that the machine performed within the design parameters. This project shows that the techno-logy required for supporting research is possible in developing countries thereby avoiding dependence on foreign companies for supporting, maintaining and updating equipment. Some conditions were also produced for the evolution of mechanical engi-neering in Colombia.

  5. Modeling systems-level dynamics: Understanding without mechanistic explanation in integrative systems biology.

    Science.gov (United States)

    MacLeod, Miles; Nersessian, Nancy J

    2015-02-01

    In this paper we draw upon rich ethnographic data of two systems biology labs to explore the roles of explanation and understanding in large-scale systems modeling. We illustrate practices that depart from the goal of dynamic mechanistic explanation for the sake of more limited modeling goals. These processes use abstract mathematical formulations of bio-molecular interactions and data fitting techniques which we call top-down abstraction to trade away accurate mechanistic accounts of large-scale systems for specific information about aspects of those systems. We characterize these practices as pragmatic responses to the constraints many modelers of large-scale systems face, which in turn generate more limited pragmatic non-mechanistic forms of understanding of systems. These forms aim at knowledge of how to predict system responses in order to manipulate and control some aspects of them. We propose that this analysis of understanding provides a way to interpret what many systems biologists are aiming for in practice when they talk about the objective of a "systems-level understanding."

  6. The force generated by biological membranes on a polymer rod and its response: Statics and dynamics

    Science.gov (United States)

    Daniels, D. R.; Turner, M. S.

    2004-10-01

    We propose a theory for the force exerted by a fluctuating membrane on a polymer rod tip. Using statistical mechanical methods, the expression for the generated force is written in terms of the distance of the rod tip from the membrane "frame." We apply the theory in calculating the stall force and membrane displacement required to cease the growth of a growing fiber induced by membrane fluctuations, as well as the membrane force and membrane displacement required for rod/fiber buckling. We also consider the dynamics of a growing fiber tip under the influence of a fluctuation-induced membrane force. We discuss the importance of our results in various biological contexts. Finally, we present a method to simultaneously extract both the rigidity of the semiflexible rod and the force applied by, e.g., the membrane from the measurements of the bending fluctuations of the rod. Such a measurement of the force would give information about the thermodynamics of the rod polymerization that involves the usual Brownian ratchet mechanism.

  7. Biological conversion of synthesis gas. Topical report: Bioreactor studies

    Energy Technology Data Exchange (ETDEWEB)

    Basu, R.; Klasson, K.T.; Clausen, E.C.; Gaddy, J.L.

    1993-09-01

    The purpose of the proposed research is to develop a technically and economically feasible process for biologically producing H{sub 2} from synthesis gas while, at the same time, removing harmful sulfur gas compounds. Six major tasks are being studied: culture development, where the best cultures are selected and conditions optimized for simultaneous hydrogen production and sulfur gas removal; mass transfer and kinetic studies in which equations necessary for process design are developed; bioreactor design studies, where the cultures chosen in Task 1 are utilized in continuous reaction vessels to demonstrate process feasibility and define operating conditions; evaluation of biological synthesis gas conversion under limiting conditions in preparation for industrial demonstration studies; process scale-up where laboratory data are scaled to larger-size units in preparation for process demonstration in a pilot-scale unit; and economic evaluation, where process simulations are used to project process economics and identify high cost areas during sensitivity analyses. The purpose of this report is to present results from bioreactor studies involving H{sub 2} production by water gas shift and H{sub 2}S removal to produce elemental sulfur. Many of the results for H{sub 2} production by Rhodospirillum rubrum have been presented during earlier contracts. Thus, this report concentrates mainly on H{sub 2}S conversion to elemental sulfur by R. rubrum.

  8. Dynamic optimization case studies in DYNOPT tool

    Science.gov (United States)

    Ozana, Stepan; Pies, Martin; Docekal, Tomas

    2016-06-01

    Dynamic programming is typically applied to optimization problems. As the analytical solutions are generally very difficult, chosen software tools are used widely. These software packages are often third-party products bound for standard simulation software tools on the market. As typical examples of such tools, TOMLAB and DYNOPT could be effectively applied for solution of problems of dynamic programming. DYNOPT will be presented in this paper due to its licensing policy (free product under GPL) and simplicity of use. DYNOPT is a set of MATLAB functions for determination of optimal control trajectory by given description of the process, the cost to be minimized, subject to equality and inequality constraints, using orthogonal collocation on finite elements method. The actual optimal control problem is solved by complete parameterization both the control and the state profile vector. It is assumed, that the optimized dynamic model may be described by a set of ordinary differential equations (ODEs) or differential-algebraic equations (DAEs). This collection of functions extends the capability of the MATLAB Optimization Tool-box. The paper will introduce use of DYNOPT in the field of dynamic optimization problems by means of case studies regarding chosen laboratory physical educational models.

  9. Dynamics in natural history collections: Decapod Crustaceans in Biological Reference Collections

    OpenAIRE

    Duró, Alícia; Pérez, Félix; Olivas, Francisco J.; Villanueva, Roger; Lombarte, Antoni; Abelló, Pere, 1959-

    2013-01-01

    One of the main goals of natural history collections is to preserve for a long term the specimens used for describing and naming new species for science. In this sense, the Biological Reference Collections (CBR) at the Institut de Ciències del Mar of the Consejo Superior de Investigaciones Científicas are a key site for the study and research on marine biodiversity since they act as a scientific marine reference facility. The concept of natural history collections is not dead. On the cont...

  10. Molecular dynamics study of naturally existing cavity couplings in proteins.

    Science.gov (United States)

    Barbany, Montserrat; Meyer, Tim; Hospital, Adam; Faustino, Ignacio; D'Abramo, Marco; Morata, Jordi; Orozco, Modesto; de la Cruz, Xavier

    2015-01-01

    Couplings between protein sub-structures are a common property of protein dynamics. Some of these couplings are especially interesting since they relate to function and its regulation. In this article we have studied the case of cavity couplings because cavities can host functional sites, allosteric sites, and are the locus of interactions with the cell milieu. We have divided this problem into two parts. In the first part, we have explored the presence of cavity couplings in the natural dynamics of 75 proteins, using 20 ns molecular dynamics simulations. For each of these proteins, we have obtained two trajectories around their native state. After applying a stringent filtering procedure, we found significant cavity correlations in 60% of the proteins. We analyze and discuss the structure origins of these correlations, including neighbourhood, cavity distance, etc. In the second part of our study, we have used longer simulations (≥100 ns) from the MoDEL project, to obtain a broader view of cavity couplings, particularly about their dependence on time. Using moving window computations we explored the fluctuations of cavity couplings along time, finding that these couplings could fluctuate substantially during the trajectory, reaching in several cases correlations above 0.25/0.5. In summary, we describe the structural origin and the variations with time of cavity couplings. We complete our work with a brief discussion of the biological implications of these results.

  11. Dynamic MRI study for breast tumors

    Energy Technology Data Exchange (ETDEWEB)

    Seki, Tsuneaki (Kyorin Univ., Mitaka, Tokyo (Japan). School of Medicine)

    1990-10-01

    Application of MRI for diagnosis of breast tumors was retrospectively examined in 103 consecutive cases. Contrast enhancement, mostly by dynamic study, was performed in 83 cases using Gd-DTPA and 0.5 T superconductive apparatus. Results were compared to those of mammography and sonography. On dynamic study, carcinoma showed abrupt rise of signal intensity with clear-cut peak formation in early phase, while benign fibroadenoma showed slow rise of signal intensity and prolonged enhancement without peak formation. In 12 of 33 carcinomas (33%), peripheral ring enhancement was noted reflecting vascular stroma of histologic sections. All fibroadenomas showed homogenous enhancement without peripheral ring. In MRI, sensitivity, specificity, and accuracy were 86%, 96%, 91%. In mammography 82%, 95%, 87% and in ultrasonography 91%, 95%, 93%. Although MRI should not be regarded as routine diagnostic procedure because of expense and limited availability, it may afford useful additional information when standard mammographic findings are not conclusive. (author).

  12. Dynamic inventory models: an illustrative case study

    Directory of Open Access Journals (Sweden)

    Adendorff, Kris

    2014-10-01

    Full Text Available The study revisits the subject matter of inventory control, a continual part of the activities of wide-ranging organisations internationally. The mathematical model is presented of a particular situation that deals with the regular acquisition of a material required for a production process in a volatile environment of varying demand and fluctuating price. The usual process dynamics are demonstrated against a background of diverse choices of probability density function. The model makes use of Normal and Weibull distributions.

  13. 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.

  14. Theoretical studies of chemical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Schatz, G.C. [Argonne National Laboratory, IL (United States)

    1993-12-01

    This collaborative program with the Theoretical Chemistry Group at Argonne involves theoretical studies of gas phase chemical reactions and related energy transfer and photodissociation processes. Many of the reactions studied are of direct relevance to combustion; others are selected they provide important examples of special dynamical processes, or are of relevance to experimental measurements. Both classical trajectory and quantum reactive scattering methods are used for these studies, and the types of information determined range from thermal rate constants to state to state differential cross sections.

  15. Osmosis : a molecular dynamics computer simulation study

    Science.gov (United States)

    Lion, Thomas

    Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..

  16. DMPD: Lysophospholipid receptors: signaling and biology. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 15189145 Lysophospholipid receptors: signaling and biology. Ishii I, Fukushima N, Y...e X, Chun J. Annu Rev Biochem. 2004;73:321-54. (.png) (.svg) (.html) (.csml) Show Lysophospholipid receptors: signaling and biology.... PubmedID 15189145 Title Lysophospholipid receptors: signaling and biology. Authors

  17. DMPD: Type I interferon receptors: biochemistry and biological functions. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 17502368 Type I interferon receptors: biochemistry and biological functions. de Wee...(.html) (.csml) Show Type I interferon receptors: biochemistry and biological functions. PubmedID 17502368 T...itle Type I interferon receptors: biochemistry and biological functions. Authors

  18. Biological Oceanography

    Science.gov (United States)

    Dyhrman, Sonya

    2004-10-01

    The ocean is arguably the largest habitat on the planet, and it houses an astounding array of life, from microbes to whales. As a testament to this diversity and its importance, the discipline of biological oceanography spans studies of all levels of biological organization, from that of single genes, to organisms, to their population dynamics. Biological oceanography also includes studies on how organisms interact with, and contribute to, essential global processes. Students of biological oceanography are often as comfortable looking at satellite images as they are electron micrographs. This diversity of perspective begins the textbook Biological Oceanography, with cover graphics including a Coastal Zone Color Scanner image representing chlorophyll concentration, an electron micrograph of a dinoflagellate, and a photograph of a copepod. These images instantly capture the reader's attention and illustrate some of the different scales on which budding oceanographers are required to think. Having taught a core graduate course in biological oceanography for many years, Charlie Miller has used his lecture notes as the genesis for this book. The text covers the subject of biological oceanography in a manner that is targeted to introductory graduate students, but it would also be appropriate for advanced undergraduates.

  19. A Friendly-Biological Reactor SIMulator (BioReSIM for studying biological processes in wastewater treatment processes

    Directory of Open Access Journals (Sweden)

    Raul Molina

    2014-12-01

    Full Text Available Biological processes for wastewater treatments are inherently dynamic systems because of the large variations in the influent wastewater flow rate, concentration composition and the adaptive behavior of the involved microorganisms. Moreover, the sludge retention time (SRT is a critical factor to understand the bioreactor performances when changes in the influent or in the operation conditions take place. Since SRT are usually in the range of 10-30 days, the performance of biological reactors needs a long time to be monitored in a regular laboratory demonstration, limiting the knowledge that can be obtained in the experimental lab practice. In order to overcome this lack, mathematical models and computer simulations are useful tools to describe biochemical processes and predict the overall performance of bioreactors under different working operation conditions and variations of the inlet wastewater composition. The mathematical solution of the model could be difficult as numerous biochemical processes can be considered. Additionally, biological reactors description (mass balance, etc. needs models represented by partial or/and ordinary differential equations associated to algebraic expressions, that require complex computational codes to obtain the numerical solutions. Different kind of software for mathematical modeling can be used, from large degree of freedom simulators capable of free models definition (as AQUASIM, to closed predefined model structure programs (as BIOWIN. The first ones usually require long learning curves, whereas the second ones could be excessively rigid for specific wastewater treatment systems. As alternative, we present Biological Reactor SIMulator (BioReSIM, a MATLAB code for the simulation of sequencing batch reactors (SBR and rotating biological contactors (RBC as biological systems of suspended and attached biomass for wastewater treatment, respectively. This BioReSIM allows the evaluation of simple and complex

  20. Solar dynamic power system definition study

    Science.gov (United States)

    Wallin, Wayne E.; Friefeld, Jerry M.

    1988-01-01

    The solar dynamic power system design and analysis study compared Brayton, alkali-metal Rankine, and free-piston Stirling cycles with silicon planar and GaAs concentrator photovoltaic power systems for application to missions beyond the Phase 2 Space Station level of technology for all power systems. Conceptual designs for Brayton and Stirling power systems were developed for 35 kWe and 7 kWe power levels. All power systems were designed for 7-year end-of-life conditions in low Earth orbit. LiF was selected for thermal energy storage for the solar dynamic systems. Results indicate that the Stirling cycle systems have the highest performance (lowest weight and area) followed by the Brayton cycle, with photovoltaic systems considerably lower in performance. For example, based on the performance assumptions used, the planar silicon power system weight was 55 to 75 percent higher than for the Stirling system. A technology program was developed to address areas wherein significant performance improvements could be realized relative to the current state-of-the-art as represented by Space Station. In addition, a preliminary evaluation of hardenability potential found that solar dynamic systems can be hardened beyond the hardness inherent in the conceptual designs of this study.

  1. Student perception of relevance of biology content to everyday life: A study in higher education biology courses

    Science.gov (United States)

    Himschoot, Agnes Rose

    The purpose of this mixed method case study was to examine the effects of methods of instruction on students' perception of relevance in higher education non-biology majors' courses. Nearly ninety percent of all students in a liberal arts college are required to take a general biology course. It is proposed that for many of those students, this is the last science course they will take for life. General biology courses are suspected of discouraging student interest in biology with large enrollment, didactic instruction, covering a huge amount of content in one semester, and are charged with promoting student disengagement with biology by the end of the course. Previous research has been aimed at increasing student motivation and interest in biology as measured by surveys and test results. Various methods of instruction have been tested and show evidence of improved learning gains. This study focused on students' perception of relevance of biology content to everyday life and the methods of instruction that increase it. A quantitative survey was administered to assess perception of relevance pre and post instruction over three topics typically taught in a general biology course. A second quantitative survey of student experiences during instruction was administered to identify methods of instruction used in the course lecture and lab. While perception of relevance dropped in the study, qualitative focus groups provided insight into the surprising results by identifying topics that are more relevant than the ones chosen for the study, conveying the affects of the instructor's personal and instructional skills on student engagement, explanation of how active engagement during instruction promotes understanding of relevance, the roll of laboratory in promoting students' understanding of relevance as well as identifying external factors that affect student engagement. The study also investigated the extent to which gender affected changes in students' perception of

  2. Molecular biology in studies of oceanic primary production

    Energy Technology Data Exchange (ETDEWEB)

    LaRoche, J.; Falkowski, P.G. [Brookhaven National Lab., Upton, NY (United States); Geider, R. [Delaware Univ., Lewes, DE (United States). Coll. of Marine Studies

    1992-07-01

    Remote sensing and the use of moored in situ instrumentation has greatly improved our ability to measure phytoplankton chlorophyll and photosynthesis on global scales with high temporal resolution. However, the interpretation of these measurements and their significance with respect to the biogeochemical cycling of carbon relies on their relationship with physiological and biochemical processes in phytoplankton. For example, the use of satellite images of surface chlorophyll to estimate primary production is often based on the functional relationship between photosynthesis and irradiance. A variety of environmental factors such as light, temperature, nutrient availability affect the photosynthesis/irradiance (P vs I) relationship in phytoplankton. We present three examples showing how molecular biology can be used to provide basic insight into the factors controlling primary productivity at three different levels of complexity: 1. Studies of light intensity regulation in unicellular alga show how molecular biology can help understand the processing of environmental cues leading to the regulation of photosynthetic gene expression. 2. Probing of the photosynthetic apparatus using molecular techniques can be used to test existing mechanistic models derived from the interpretation of physiological and biophysical measurements. 3. Exploratory work on the expression of specific proteins during nutrient-limited growth of phytoplankton may lead to the identification and production of molecular probes for field studies.

  3. Molecular biology in studies of oceanic primary production

    Energy Technology Data Exchange (ETDEWEB)

    LaRoche, J.; Falkowski, P.G. (Brookhaven National Lab., Upton, NY (United States)); Geider, R. (Delaware Univ., Lewes, DE (United States). Coll. of Marine Studies)

    1992-01-01

    Remote sensing and the use of moored in situ instrumentation has greatly improved our ability to measure phytoplankton chlorophyll and photosynthesis on global scales with high temporal resolution. However, the interpretation of these measurements and their significance with respect to the biogeochemical cycling of carbon relies on their relationship with physiological and biochemical processes in phytoplankton. For example, the use of satellite images of surface chlorophyll to estimate primary production is often based on the functional relationship between photosynthesis and irradiance. A variety of environmental factors such as light, temperature, nutrient availability affect the photosynthesis/irradiance (P vs I) relationship in phytoplankton. We present three examples showing how molecular biology can be used to provide basic insight into the factors controlling primary productivity at three different levels of complexity: 1. Studies of light intensity regulation in unicellular alga show how molecular biology can help understand the processing of environmental cues leading to the regulation of photosynthetic gene expression. 2. Probing of the photosynthetic apparatus using molecular techniques can be used to test existing mechanistic models derived from the interpretation of physiological and biophysical measurements. 3. Exploratory work on the expression of specific proteins during nutrient-limited growth of phytoplankton may lead to the identification and production of molecular probes for field studies.

  4. Spectroscopic studies of silica nanoparticles: Magnetic resonance and nanomaterial-biological interactions

    Science.gov (United States)

    Lehman, Sean E.

    Primarily concerned with manipulation and study of matter at the nanoscale, the concept of nanoscience encompasses ideas such as nanomaterial synthesis, characterization, and applications to modern scientific and societal problems. These problems encompass a broad range of issues such as energy storage and conversion, medical diagnostics and treatment, environmental remediation and detection, carbon economy and as well as many others. Silica nanoparticles of porous morphology have broad application to many of these issues. In particular, the utility of silica nanoparticles is facilitated by their large intrinsic surface area, tunable surface chemistry, and synthetic variability in both their size and morphology. This facilitates applications to these problems. However, extensive characterization and deeper understanding is needed before full implementation in key applications can be realized. The work described in this thesis aims to explore fundamental and applied characterization of silica nanoparticles that might be used in biomedical and environmental applications. Fundamental studies of functionalized nanomaterials using NMR spectroscopy reveal complex, dynamic phenomena related to-and ultimately deriving from-the intrinsic and/or modified surface chemistry. Applied studies of nanomaterial-biological interfaces demonstrate free radical chemistry as dominating the toxic response of the materials when exposed to biological systems of interest. Characterization of protein adsorbed on the interface reinforces the ubiquitous nature of protein adsorption on nanomaterial surface in biological and environmental media. Overall, this work illuminates and highlights complex changes that take place in aqueous solution for silica nanoparticles of varied morphology and surface chemistry.

  5. Somatostatin, somatostatin analogs and somatostatin receptor dynamics in the biology of cancer progression.

    Science.gov (United States)

    Ruscica, M; Arvigo, M; Steffani, L; Ferone, D; Magni, P

    2013-05-01

    The pharmacological effects (i.e., inhibition of endocrine secretion and cell proliferation) mediated by the hormone somatostatin (SRIF) are derived from its universal high-affinity binding to five different G proteincoupled receptors (GPCRs), named sst1-5. However, SRIF has a half-life of less than 3 min, whereas the available mono- and bi-specific SRIF preferential analogs show prolonged half-life and increased potency. These compounds may control tumor development, cell proliferation and metastatization by direct actions, including cell division arrest in G0/G1 phase (i.e., induction of cyclin-dependent kinase inhibitor p27(kip1) or p21(Cip1)), induction of apoptosis (i.e., induction of p53 and Bax) and suppression of cell invasion. Along with these direct actions on the biology of cancer progression, in vivo SRIF analogs may also regulate tumor growth through indirect actions, by suppressing the secretion of growth-promoting hormones and growth factors and angiogenesis. Interestingly, when ssts are co-expressed, they may interact forming homo- or heterodimers, also with other GPCRs such as type 2 dopamine receptor and the μ-opioid receptor 1, altering their original pharmacological and functional properties. Dimers can be not only constitutive, but perhaps also ligandpromoted: hence, compounds with high affinity for different ssts isoforms may be used to achieve effects elicited by specific dimers. Future developments in the knowledge of ssts dynamics upon SRIF and SRIF analogs binding in neoplastic tissues may allow the full elucidation of the pathophysiological role of this system and the exploitation of the therapeutic potential of its modulation.

  6. Twenty years of protein interaction studies for biological function deciphering.

    Science.gov (United States)

    Legrain, Pierre; Rain, Jean-Christophe

    2014-07-31

    Intensive methodological developments and technology innovation have been devoted to protein-protein interaction studies over 20years. Genetic indirect assays and sophisticated large scale biochemical analyses have jointly contributed to the elucidation of protein-protein interactions, still with a lot of drawbacks despite heavy investment in human resources and technologies. With the most recent developments in mass spectrometry and computational tools for studying protein content of complex samples, the initial goal of deciphering molecular bases of biological functions is now within reach. Here, we described the various steps of this process and gave examples of key milestones in this scientific story line. This article is part of a Special Issue entitled: 20years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini, Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.

  7. Chemical Biology Studies on Molecular Diversity of Annonaceous Acetogenins

    Institute of Scientific and Technical Information of China (English)

    Yao Zhu-Jun

    2004-01-01

    Annonaceous acetogenins, isolated from the Annonaceae plants, have been attracting worldwide attention in recent years due to their biological activities, especially as growth inhibitors of certain tumor ceils [ 1 ]. They have been shown to function by blocking complex I in mitochondria [2] as well as ubiquinone-linked NADPH oxidase in the cells of specific tumor cell lines, including some multidrug-resistant ones [3]. These features make these acetogenins excellent leads for the new antitumor agents. In our previous work, the compounds 1a to 1d (Figure 1), which relies on structure simplification while maintaining all essential functionalities of the acetogenins, was in vitro tested against several human solid tumor cell lines and showed interesting cell selectivity [4]. All four analogues show remarkable activity against the HCT-8 and HT-29 cell lines, while compound 1c was found the best [4bi. In order to further investigate the effects of key structural features, a convergent parallel fragments assembly strategy was developed [4e]. In addition, the biological relevancies of typical annonaceous acetogenin mimetics were also studied [4f].

  8. The emerging molecular biology toolbox for the study of long noncoding RNA biology.

    Science.gov (United States)

    Fok, Ezio T; Scholefield, Janine; Fanucchi, Stephanie; Mhlanga, Musa M

    2017-09-06

    Long noncoding RNAs (lncRNAs) have been implicated in many biological processes. However, due to the unique nature of lncRNAs and the consequential difficulties associated with their characterization, there is a growing disparity between the rate at which lncRNAs are being discovered and the assignment of biological function to these transcripts. Here we present a molecular biology toolbox equipped to help dissect aspects of lncRNA biology and reveal functionality. We outline an approach that begins with a broad survey of genome-wide, high-throughput datasets to identify potential lncRNA candidates and then narrow the focus on specific methods that are well suited to interrogate the transcripts of interest more closely. This involves the use of imaging-based strategies to validate these candidates and observe the behaviors of these transcripts at single molecule resolution in individual cells. We also describe the use of gene editing tools and interactome capture techniques to interrogate functionality and infer mechanism, respectively. With the emergence of lncRNAs as important molecules in healthy and diseased cellular function, it remains crucial to deepen our understanding of their biology.

  9. On the study of nonlinear dynamics of complex chemical reaction systems

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    With ever-increasing attentions being paid to complex systems such as the life system, soft matter, and nano-systems, theoretical studies of non-equilibrium nonlinear problems involved in chemical dynamics are now of general interest. In this mini-review, we mainly give a brief introduction to some frontier topics in this field, namely, nonlinear state-state dynamics, nonlinear chemical dynamics on complex networks, and nonlinear dynamics in mesoscopic chemical reaction systems. Deep study of these topics will make great contribution to discovering new laws of chemical dynamics, to exploring new control methods of complex chemical processes, to figuring out the very roles of chemical processes in the life system, and to crosslinking the scientific study of chemistry, physics and biology.

  10. THE DYNAMICS OF IN VITRO DEGRADATION OF NON-WOVEN POLYLACTIDE MATRICES IN MODEL BIOLOGICAL LIQUID

    Directory of Open Access Journals (Sweden)

    I. A. Khlusov

    2013-01-01

    Full Text Available The weekly in vitro degradation of fibrous-porous non-woven polylactide scaffolds made by aerodynamic formation in a turbulent gas flow has been studied with 37 °С in model RPMI-1640 medium imitated body fluid of organism. Lactate monomers released into solution exponentially and reached slowly a maximum value the end of the observation (5th week of dissolution. At the same time, reducing the concentrations of calcium and inorganic phosphorus ions in solutions contacted with tested samples (10×10×1 mm2 testified about chemical elements adsorption on artificial material. Ions exchange with biological fluids may be a basis of regulated bioactivity of fibrous-porous non-woven biodegradable material in application to intercellular matrix bioengineering for regenerative medicine

  11. Biodynsensing: Sensing Through Dynamics of Hybrid Affinity/Cellular Platforms; Towards Appraisal of Environmental and Biological Risks of Nanobiotechnology

    Science.gov (United States)

    Gheorghiu, E.; Gheorghiu, M.; David, S.; Polonschii, C.

    Chemical cues and nano-topographies present on the surface or in the extracellular medium strongly influence the fate and adhesion of biological cells. Careful tuning of cell—matrix interaction via engineered surfaces, either attractive or repulsive, require non-invasive, long time monitoring capabilities and lay the foundation of sensing platforms for risk assessment. Aiming to assess changes underwent by biointerfaces due to cell—environment interaction (in particular nanotechnology products), we have developed hybrid cellular platforms allowing for time based dual assays, i.e., impedance/dielectric spectroscopy (IS) and Surface Plasmon Resonance (SPR). Such platforms comprising Flow Injection Analysis (FIA) have been advanced to assess the interaction between selected (normal and malignant) cells and nano-patterned and/or chemically modified surfaces, as well as the impact of engineered nanoparticles, revealed by the related changes exhibited by cell membrane, morphology, adhesion and monolayer integrity. Besides experimental aspects dealing with measurement set-up, we will emphasize theoretical aspects related to: dielectric modeling. Aiming for a quantitative approach, microscopic models on dielectric behavior of ensembles of interconnected cells have been developed and their capabilities will be outlined within the presentation. Assessment of affinity reactions as revealed by dielectric/impedance assays of biointerfaces. Modeling the dynamics of the impedance in relation to the “quality” of cell layer and sensor's active surface, this study presents further developments of our approach described in Analytical Chemistry, 2002. Data analysis. This issue is related to the following basic question: Are there “simple” Biosensing Platforms? When coping with cellular platforms, either in suspension or immobilized (on filters, adhered on surfaces or entrapped, e.g., on using set-ups) there is an intrinsic nonlinear behavior of biological systems related

  12. Biological Properties and Organic Matter Dynamics of Soil in Pasture and Natural Regeneration Areas in the Atlantic Forest Biome

    Directory of Open Access Journals (Sweden)

    Leandro Ribeiro Nogueira

    Full Text Available ABSTRACT The removal of original vegetation for crops and pasture production and then followed by natural regeneration is a standard practice in the Atlantic Forest, which has produced patches with different degrees of degradation and regeneration across the landscape. The aim of this study was to evaluate the effects of replacement of native forest by pasture and natural regeneration of vegetation on soil and on soil organic matter (SOM dynamics in the dry and rainy season in an Atlantic Forest fragment in Passa Vinte, Minas Gerais (MG, Brazil. Soil samples were collected in the rainy and dry season, at a depth of 0.00-0.05 m. The variables determined were total organic carbon (TOC and particle-size fractions of SOM [particulate organic carbon (POC and mineral-associated organic carbon (MOC]; microbial activity by basal respiration (BR and microbial biomass carbon (MBC; species richness (SR and spore abundance (SA of arbuscular mycorrhizal fungi (AMF; and total and easily extractable glomalin-related soil protein (T-GRSP and EE-GRSP, respectively. The conversion of native forest into pasture reduced TOC, POC, MOC, AMF-SA, T-GRSP, and EE-GRSP. However, it did not reduce MBC and BR. The fallow period in the area under natural regeneration was not long enough to restore soil TOC, POC, MOC, BR, MBC, T-GRSP, and EE-GRSP to levels approaching those observed in the forest area. Nevertheless, natural regeneration of vegetation stimulated the production of seedlings (spores of arbuscular mycorrhizal fungi, which are important for the establishment of plant species and advance of ecological succession. Seasonality affected some of the biological soil properties and SOM dynamics.

  13. Bacterial Community and “Candidatus Accumulibacter” Population Dynamics in Laboratory-Scale Enhanced Biological Phosphorus Removal Reactors ▿ †

    Science.gov (United States)

    He, Shaomei; Bishop, Forrest I.; McMahon, Katherine D.

    2010-01-01

    “Candidatus Accumulibacter” and total bacterial community dynamics were studied in two lab-scale enhanced biological phosphorus removal (EBPR) reactors by using a community fingerprint technique, automated ribosomal intergenic spacer analysis (ARISA). We first evaluated the quantitative capability of ARISA compared to quantitative real-time PCR (qPCR). ARISA and qPCR provided comparable relative quantification of the two dominant “Ca. Accumulibacter” clades (IA and IIA) detected in our reactors. The quantification of total “Ca. Accumulibacter” 16S rRNA genes relative to that from the total bacterial community was highly correlated, with ARISA systematically underestimating “Ca. Accumulibacter” abundance, probably due to the different normalization techniques applied. During 6 months of normal (undisturbed) operation, the distribution of the two clades within the total “Ca. Accumulibacter” population was quite stable in one reactor while comparatively dynamic in the other reactor. However, the variance in the clade distribution did not appear to affect reactor performance. Instead, good EBPR activity was positively associated with the abundance of total “Ca. Accumulibacter.” Therefore, we concluded that the different clades in the system provided functional redundancy. We disturbed the reactor operation by adding nitrate together with acetate feeding in the anaerobic phase to reach initial reactor concentrations of 10 mg/liter NO3-N for 35 days. The reactor performance deteriorated with a concomitant decrease in the total “Ca. Accumulibacter” population, suggesting that a population shift was the cause of performance upset after a long exposure to nitrate in the anaerobic phase. PMID:20601516

  14. Allosteric dynamics of SAMHD1 studied by molecular dynamics simulations

    Science.gov (United States)

    Patra, K. K.; Bhattacharya, A.; Bhattacharya, S.

    2016-10-01

    SAMHD1 is a human cellular enzyme that blocks HIV-1 infection in myeloid cells and non-cycling CD4+T cells. The enzyme is an allosterically regulated triphosphohydrolase that modulates the level of cellular dNTP. The virus restriction is attributed to the lowering of the pool of dNTP in the cell to a point where reverse-transcription is impaired. Mutations in SAMHD1 are also implicated in Aicardi-Goutieres syndrome. A mechanistic understanding of the allosteric activation of the enzyme is still elusive. We have performed molecular dynamics simulations to examine the allosteric site dynamics of the protein and to examine the connection between the stability of the tetrameric complex and the Allosite occupancy.

  15. Simulation of Interval Censored Data in Medical and Biological Studies

    Science.gov (United States)

    Kiani, Kaveh; Arasan, Jayanthi

    This research looks at the simulation of interval censored data when the survivor function of the survival time is known and attendance probability of the subjects for follow-ups can take any number between 0 to 1. Interval censored data often arise in the medical and biological follow-up studies where the event of interest occurs somewhere between two known times. Regardless of the methods used to analyze these types of data, simulation of interval censored data is an important and challenging step toward model building and prediction of survival time. The simulation itself is rather tedious and very computer intensive due to the interval monitoring of subjects at prescheduled times and subject's incomplete attendance to follow-ups. In this paper the simulated data by the proposed method were assessed using the bias, standard error and root mean square error (RMSE) of the parameter estimates where the survival time T is assumed to follow the Gompertz distribution function.

  16. Visual Literacy in Preservice Teachers: a Case Study in Biology

    Science.gov (United States)

    Ruiz-Gallardo, José Reyes; García Fernández, Beatriz; Mateos Jiménez, Antonio

    2017-07-01

    In this study, we explore the competence of preservice teachers (n = 161) in labelling and creating new cross-sectional human diagrams, based on anatomy knowledge depicted in longitudinal sections. Using educational standards to assess visual literacy and ad hoc open questions, results indicate limited skills for both tasks. However, their competence is particularly poor creating diagrams, where shortcomings were observed not only in visual literacy but in content knowledge. We discuss the misconceptions detected during these assessments. Visual literacy training should be strengthened for these students, as it is a skill that is especially important for future teachers to use in learning, assessing, and reflecting on content in science education. This is particularly important in preservice teachers since they should be fluent in the use of visual teaching tools in teaching anatomy and other content in the biology curriculum.

  17. Current studies on physiological functions and biological production of lactosucrose.

    Science.gov (United States)

    Mu, Wanmeng; Chen, Qiuming; Wang, Xiao; Zhang, Tao; Jiang, Bo

    2013-08-01

    Lactosucrose (O-β-D-galactopyranosyl-(1,4)-O-α-D-glucopyranosyl-(1,2)-β-D-fructofuranoside) is a trisaccharide formed from lactose and sucrose by enzymatic transglycosylation. This rare trisaccharide is a kind of indigestible carbohydrate, has good prebiotic effect, and promotes intestinal mineral absorption. It has been used as a functional ingredient in a range of food products which are approved as foods for specified health uses in Japan. Using lactose and sucrose as substrates, lactosucrose can be produced through transfructosylation by β-fructofuranosidase from Arthrobacter sp. K-1 or a range of levansucrases, or through transgalactosylation by β-galactosidase from Bacillus circulans. This article presented a review of recent studies on the physiological functions of lactosucrose and the biological production from lactose and sucrose by different enzymes.

  18. MODERN TECHNOLOGIES AND APPROACHES TO APOPTOSIS STUDIES IN EXPERIMENTAL BIOLOGY

    Directory of Open Access Journals (Sweden)

    I. V. Kudriavtsev

    2012-01-01

    Full Text Available Abstract. This review is focused on analysis of currently used flow cytometric methods designed foridentifying apoptotic cells in various invertebrate and vertebrate species. Apoptosis can be characterized by stage-specific morphological and biochemical changes that are typical to all kinds of eukaryotic cells. In this article, we consider different techniques of apoptosis detection based on assessment of cellular morphology and plasma membrane alterations, activation of intracellular enzymes and components of a caspase cascade, as well as DNA fragmentation and failure of mitochondrial transmembrane potential, as assessed in various animal groups. Apoptosis recognized as a key mechanism aiming at maintenance of cellular homeostasis in multicellular organisms, and such investigations represent a necessary component of fundamental and applied studies in diverse fields of experimental biology and immunology. A broad spectrum of apoptosis markers isused, and the preference is given to optimal approaches, as determined by experimental tasks, and technical opportunities of the laboratory.

  19. Stability studies of Solar Optical Telescope dynamics

    Science.gov (United States)

    Gullapalli, Sarma N.; Pal, Parimal K.; Ruthven, Gregory P.

    1987-01-01

    The Solar Optical Telescope (SOT) is designed to operate as an attached payload mounted on the Instrument Pointing System (IPS) in the cargo bay of the Shuttle Orbiter. Pointing and control of SOT is accomplished by an active Articulated Primary Mirror (APM), an active Tertiary Mirror (TM), an elaborate set of optical sensors, electromechanical actuators and programmable controllers. The structural interactions of this complex control system are significant factors in the stability of the SOT. The preliminary stability study results of the SOT dynamical system are presented. Structural transfer functions obtained from the NASTRAN model of the structure were used. These studies apply to a single degree of freedom (elevation). Fully integrated model studies will be conducted in the future.

  20. Experimental study on dynamic gas adsorption

    Institute of Scientific and Technical Information of China (English)

    Qin Yueping; Wang Yaru; Yang Xiaobin; Liu Wei; Luo Wei

    2012-01-01

    In order to predict the actual adsorption amount as gas adsorption reaches the equilibrium,this research designed a dynamic gas adsorption experiment under constant temperature and pressure,and also studied the isopiestic adsorption characteristics of coal samples with same quality but different sizes.Through the experiment,the study found the adsorption-time changing relationships under different pressures of four different size samples.After regression analysis,we obtained the functional relationship between adsorption and time.According to this,the research resulted in the actual adsorption amount when gas adsorption reaches the equilibrium.In addition,the current study obtained the relationship between adsorption and pressure as well as the effect of the coal size to the adsorption rate.These results have great theoretical and practical significance for the prediction of gas amount in coal seam and gas adsorption process.

  1. Molecular Dynamics Studies of Nanofluidic Devices

    DEFF Research Database (Denmark)

    Zambrano Rodriguez, Harvey Alexander

    in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate...... in transport caused by the walls become more dominant and the fluid consists of fewer molecules. Carbon nanotubes are tubular graphite molecules which can be imagined to function as nanoscale pipes or conduits. Another important material for nanofluidics applications is silica. Nowadays, silica nanochannels...... of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism...

  2. Systems biology studies of Aspergilli - from sequence to science

    OpenAIRE

    Andersen, Mikael Rørdam; Nielsen, Jens; Nielsen, Michael Lynge

    2008-01-01

    The recent dawn of the new biological mindset called systems biology has put forth a new way of analyzing and understanding biology. Carried by the notion that no element of a cell is an island, systems biology takes a holistic approach, and attempts to understand life as systems that have co-evolved and not as a haphazardly compiled list of parts. This has been made possible by the socalled genomic revolution — the sequencing of the genomic DNA of a rapidly increasing number of organisms — a...

  3. Magnetoencephalography in the study of brain dynamics.

    Science.gov (United States)

    Pizzella, Vittorio; Marzetti, Laura; Della Penna, Stefania; de Pasquale, Francesco; Zappasodi, Filippo; Romani, Gian Luca

    2014-01-01

    To progress toward understanding of the mechanisms underlying the functional organization of the human brain, either a bottom-up or a top-down approach may be adopted. The former starts from the study of the detailed functioning of a small number of neuronal assemblies, while the latter tries to decode brain functioning by considering the brain as a whole. This review discusses the top-down approach and the use of magnetoencephalography (MEG) to describe global brain properties. The main idea behind this approach is that the concurrence of several areas is required for the brain to instantiate a specific behavior/functioning. A central issue is therefore the study of brain functional connectivity and the concept of brain networks as ensembles of distant brain areas that preferentially exchange information. Importantly, the human brain is a dynamic device, and MEG is ideally suited to investigate phenomena on behaviorally relevant timescales, also offering the possibility of capturing behaviorally-related brain connectivity dynamics.

  4. Dynamical Study of 3D Boson Stars

    Science.gov (United States)

    Choi, Dae-Il; Choptuik, M. W.

    1998-10-01

    We study the dynamical evolution of ``boson stars'' in 3D numerical relativity. Boson stars are equilibrium states of a self-gravitating, complex Klein-Gordon field: a resurgence of interest in scalar fields in the context of astroparticle physics and quantum cosmology has prompted investigation of their dynamics, particularly since they are possible dark matter candidates. In addition, even though any direct physical relevance has yet to be demonstrated, boson star systems provide excellent numerical laboratories in which to study strong gravitational fields. Specifically, the boson star model provides an ideal vehicle with which to implement and evaluate (1) various coordinate conditions in the context of the ADM formalism, and (2) multi-dimensional adaptive mesh refinement techniques which appear crucial for many problems in 3D numerical relativity. We first consider boson stars in the Newtonian regime, where the (numerical) stability of single stars is shown and the interaction of multiple-star-systems is simulated. We also discuss issues which hamper progress towards a stable evolution of general relativistic boson stars, and then show some preliminary results for the general relativistic case.

  5. PANET: a GPU-based tool for fast parallel analysis of robustness dynamics and feed-forward/feedback loop structures in large-scale biological networks.

    Science.gov (United States)

    Trinh, Hung-Cuong; Le, Duc-Hau; Kwon, Yung-Keun

    2014-01-01

    It has been a challenge in systems biology to unravel relationships between structural properties and dynamic behaviors of biological networks. A Cytoscape plugin named NetDS was recently proposed to analyze the robustness-related dynamics and feed-forward/feedback loop structures of biological networks. Despite such a useful function, limitations on the network size that can be analyzed exist due to high computational costs. In addition, the plugin cannot verify an intrinsic property which can be induced by an observed result because it has no function to simulate the observation on a large number of random networks. To overcome these limitations, we have developed a novel software tool, PANET. First, the time-consuming parts of NetDS were redesigned to be processed in parallel using the OpenCL library. This approach utilizes the full computing power of multi-core central processing units and graphics processing units. Eventually, this made it possible to investigate a large-scale network such as a human signaling network with 1,609 nodes and 5,063 links. We also developed a new function to perform a batch-mode simulation where it generates a lot of random networks and conducts robustness calculations and feed-forward/feedback loop examinations of them. This helps us to determine if the findings in real biological networks are valid in arbitrary random networks or not. We tested our plugin in two case studies based on two large-scale signaling networks and found interesting results regarding relationships between coherently coupled feed-forward/feedback loops and robustness. In addition, we verified whether or not those findings are consistently conserved in random networks through batch-mode simulations. Taken together, our plugin is expected to effectively investigate various relationships between dynamics and structural properties in large-scale networks. Our software tool, user manual and example datasets are freely available at http://panet-csc.sourceforge.net/.

  6. PANET: a GPU-based tool for fast parallel analysis of robustness dynamics and feed-forward/feedback loop structures in large-scale biological networks.

    Directory of Open Access Journals (Sweden)

    Hung-Cuong Trinh

    Full Text Available It has been a challenge in systems biology to unravel relationships between structural properties and dynamic behaviors of biological networks. A Cytoscape plugin named NetDS was recently proposed to analyze the robustness-related dynamics and feed-forward/feedback loop structures of biological networks. Despite such a useful function, limitations on the network size that can be analyzed exist due to high computational costs. In addition, the plugin cannot verify an intrinsic property which can be induced by an observed result because it has no function to simulate the observation on a large number of random networks. To overcome these limitations, we have developed a novel software tool, PANET. First, the time-consuming parts of NetDS were redesigned to be processed in parallel using the OpenCL library. This approach utilizes the full computing power of multi-core central processing units and graphics processing units. Eventually, this made it possible to investigate a large-scale network such as a human signaling network with 1,609 nodes and 5,063 links. We also developed a new function to perform a batch-mode simulation where it generates a lot of random networks and conducts robustness calculations and feed-forward/feedback loop examinations of them. This helps us to determine if the findings in real biological networks are valid in arbitrary random networks or not. We tested our plugin in two case studies based on two large-scale signaling networks and found interesting results regarding relationships between coherently coupled feed-forward/feedback loops and robustness. In addition, we verified whether or not those findings are consistently conserved in random networks through batch-mode simulations. Taken together, our plugin is expected to effectively investigate various relationships between dynamics and structural properties in large-scale networks. Our software tool, user manual and example datasets are freely available at http://panet-csc.sourceforge.net/.

  7. Translational systems biology using an agent-based approach for dynamic knowledge representation: An evolutionary paradigm for biomedical research.

    Science.gov (United States)

    An, Gary C

    2010-01-01

    The greatest challenge facing the biomedical research community is the effective translation of basic mechanistic knowledge into clinically effective therapeutics. This challenge is most evident in attempts to understand and modulate "systems" processes/disorders, such as sepsis, cancer, and wound healing. Formulating an investigatory strategy for these issues requires the recognition that these are dynamic processes. Representation of the dynamic behavior of biological systems can aid in the investigation of complex pathophysiological processes by augmenting existing discovery procedures by integrating disparate information sources and knowledge. This approach is termed Translational Systems Biology. Focusing on the development of computational models capturing the behavior of mechanistic hypotheses provides a tool that bridges gaps in the understanding of a disease process by visualizing "thought experiments" to fill those gaps. Agent-based modeling is a computational method particularly well suited to the translation of mechanistic knowledge into a computational framework. Utilizing agent-based models as a means of dynamic hypothesis representation will be a vital means of describing, communicating, and integrating community-wide knowledge. The transparent representation of hypotheses in this dynamic fashion can form the basis of "knowledge ecologies," where selection between competing hypotheses will apply an evolutionary paradigm to the development of community knowledge.

  8. Coupling Lattice Boltzmann with Atomistic Dynamics for the multiscale simulation of nano-biological flows

    CERN Document Server

    Fyta, Maria; Kaxiras, Efthimios; Succi, Sauro

    2007-01-01

    We describe a recent multiscale approach based on the concurrent coupling of constrained molecular dynamics for long biomolecules with a mesoscopic lattice Boltzmann treatment of solvent hydrodynamics. The multiscale approach is based on a simple scheme of exchange of space-time information between the atomistic and mesoscopic scales and is capable of describing self-consistent hydrodynamic effects on molecular motion at a computational cost which scales linearly with both solute size and solvent volume. For an application of our multiscale method, we consider the much studied problem of biopolymer translocation through nanopores: we find that the method reproduces with remarkable accuracy the statistical scaling behavior of the translocation process and provides valuable insight into the cooperative aspects of biopolymer and hydrodynamic motion.

  9. Tools for the study of dynamical spacetimes

    Science.gov (United States)

    Zhang, Fan

    This thesis covers a range of topics in numerical and analytical relativity, centered around introducing tools and methodologies for the study of dynamical spacetimes. The scope of the studies is limited to classical (as opposed to quantum) vacuum spacetimes described by Einstein's general theory of relativity. The numerical works presented here are carried out within the Spectral Einstein Code (SpEC) infrastructure, while analytical calculations extensively utilize Wolfram's Mathematica program. We begin by examining highly dynamical spacetimes such as binary black hole mergers, which can be investigated using numerical simulations. However, there are difficulties in interpreting the output of such simulations. One difficulty stems from the lack of a canonical coordinate system (henceforth referred to as gauge freedom) and tetrad, against which quantities such as Newman-Penrose Psi4 (usually interpreted as the gravitational wave part of curvature) should be measured. We tackle this problem in Chapter 2 by introducing a set of geometrically motivated coordinates that are independent of the simulation gauge choice, as well as a quasi-Kinnersley tetrad, also invariant under gauge changes in addition to being optimally suited to the task of gravitational wave extraction. Another difficulty arises from the need to condense the overwhelming amount of data generated by the numerical simulations. In order to extract physical information in a succinct and transparent manner, one may define a version of gravitational field lines and field strength using spatial projections of the Weyl curvature tensor. Introduction, investigation and utilization of these quantities will constitute the main content in Chapters 3 through 6. For the last two chapters, we turn to the analytical study of a simpler dynamical spacetime, namely a perturbed Kerr black hole. We will introduce in Chapter 7 a new analytical approximation to the quasi-normal mode (QNM) frequencies, and relate various

  10. Molecular beam studies of reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.

  11. Ultrasonic Study of Dislocation Dynamics in Lithium -

    Science.gov (United States)

    Han, Myeong-Deok

    1987-09-01

    Experimental studies of dislocation dynamics in LiF single crystals, using ultrasonic techniques combined with dynamic loading, were performed to investigate the time evolution of the plastic deformation process under a short stress pulse at room temperature, and the temperature dependence of the dislocation damping mechanism in the temperature range 25 - 300(DEGREES)K. From the former, the time dependence of the ultrasonic attenuation was understood as resulting from dislocation multiplication followed by the evolution of mobile dislocations to immobile ones under large stress. From the latter, the temperature dependence of the ultrasonic attenuation was interpreted as due to the motion of the dislocation loops overcoming the periodic Peierls potential barrier in a manner analogous to the motion of a thermalized sine-Gordon chain under a small stress. The Peierls stress obtained from the experimental results by application of Seeger's relaxation model with exponential dislocation length distribution was 4.26MPa, which is consistent with the lowest stress for the linear relation between the dislocation velocity and stress observed by Flinn and Tinder.

  12. The Viable Mitral Annular Dynamics and Left Ventricular Function after Mitral Valve Repair by Biological Rings

    Directory of Open Access Journals (Sweden)

    Farideh Roshanali

    2012-12-01

    Full Text Available Objective: Considering the importance of annular dynamics in the valvular and ventricular function, we sought to evaluate the effects of treated pericardial annuloplasty rings on mitral annular dynamics and left-ventricular (LV function after mitral valve repair. The results were compared with the mitral annular dynamics and LV function in patients with rigid and flexible rings and also in those without any heart problems. Materials and Methods: One hundred and thirty-six consecutive patients with a myxomatous mitral valve and severe regurgitation were prospectively enrolled in this observational cohort study. The patients underwent comparable surgical mitral valve reconstruction; of these 100 received autologous pericardium rings (Group I, 20 were given flexible prosthetic rings (Group II, and 16 received rigid rings (Group III. Other repair modalities were also performed, depending on the involved segments. The patients were compared with 100 normal subjects in whom an evaluation of the coronary artery was not indicative of valvular or myocardial abnormalities (Group IV. At follow-up, LV systolic indices were assessed via two-dimensional echocardiography at rest and during dobutamine stress echocardiography. Mitral annular motion was examined through mitral annulus systolic excursion (MASE. Peak transmitral flow velocities (TMFV and mitral valve area (MVA were also evaluated by means of continuous-wave Doppler. Results: A postoperative echocardiographic study showed significant mitral regurgitation (>=2+ in one patient in Group I, one patient in Group II, and none in Group III. None of the patients died. There was a noteworthy increase in TMFV with stress in all the groups, the increase being more considerable in the prosthetic ring groups (Group I from 1.10 ± 0.08 to 1.36 ± 0.13 m/s, Group II from 1.30 ± 0.11 to 1.59 ± 0.19 m/s, Group III from 1.33 ± 0.09 to 1.69 ± 0.21 m/s, and Group IV from 1.08 ± 0.08 to 1.21 ± 0.12 m

  13. Recombinant human thrombopoietin: basic biology and evaluation of clinical studies.

    Science.gov (United States)

    Kuter, David J; Begley, C Glenn

    2002-11-15

    Thrombocytopenia is a common medical problem for which the main treatment is platelet transfusion. Given the increasing use of platelets and the declining donor population, identification of a safe and effective platelet growth factor could improve the management of thrombocytopenia. Thrombopoietin (TPO), the c-Mpl ligand, is the primary physiologic regulator of megakaryocyte and platelet development. Since the purification of TPO in 1994, 2 recombinant forms of the c-Mpl ligand--recombinant human thrombopoietin (rhTPO) and pegylated recombinant human megakaryocyte growth and development factor (PEG-rHuMGDF)--have undergone extensive clinical investigation. Both have been shown to be potent stimulators of megakaryocyte growth and platelet production and are biologically active in reducing the thrombocytopenia of nonmyeloablative chemotherapy. However, neither TPO has demonstrated benefit in stem cell transplantation or leukemia chemotherapy. Other clinical studies have investigated the use of TPO in treating chronic nonchemotherapy-induced thrombocytopenia associated with myelodysplastic syndromes, idiopathic thrombocytopenic purpura, thrombocytopenia due to human immunodeficiency virus, and liver disease. Based solely on animal studies, TPO may be effective in reducing surgical thrombocytopenia and bleeding, ex vivo expansion of pluripotent stem cells, and as a radioprotectant. Ongoing and future studies will help define the clinical role of recombinant TPO and TPO mimetics in the treatment of chemotherapy- and nonchemotherapy-induced thrombocytopenia.

  14. A quantum molecular dynamics study of aqueous solvation dynamics

    Science.gov (United States)

    Videla, Pablo E.; Rossky, Peter J.; Laria, D.

    2013-10-01

    Ring polymer molecular dynamics experiments have been carried out to examine effects derived from nuclear quantum fluctuations at ambient conditions on equilibrium and non-equilibrium dynamical characteristics of charge solvation by a popular simple, rigid, water model, SPC/E, and for a more recent, and flexible, q-TIP4P/F model, to examine the generality of conclusions. In particular, we have recorded the relaxation of the solvent energy gap following instantaneous, ±e charge jumps in an initially uncharged Lennard-Jones-like solute. In both charge cases, quantum effects are reflected in sharper decays at the initial stages of the relaxation, which produce up to a ˜20% reduction in the characteristic timescales describing the solvation processes. For anionic solvation, the magnitude of polarization fluctuations controlling the extent of the water proton localization in the first solvation shell is somewhat more marked than for cations, bringing the quantum solvation process closer to the classical case. Effects on the solvation response from the explicit incorporation of flexibility in the water Hamiltonian are also examined. Predictions from linear response theories for the overall relaxation profile and for the corresponding characteristic timescales are reasonably accurate for the solvation of cations, whereas we find that they are much less satisfactory for the anionic case.

  15. Molecular dynamics studies of aromatic hydrocarbon liquids

    Energy Technology Data Exchange (ETDEWEB)

    McLaughlin, E.; Gupta, S.

    1990-01-01

    This project mainly involves a molecular dynamics and Monte Carlo study of the effect of molecular shape on thermophysical properties of bulk fluids with an emphasis on the aromatic hydrocarbon liquids. In this regard we have studied the modeling, simulation methodologies, and predictive and correlating methods for thermodynamic properties of fluids of nonspherical molecules. In connection with modeling we have studied the use of anisotropic site-site potentials, through a modification of the Gay-Berne Gaussian overlap potential, to successfully model the aromatic rings after adding the necessary electrostatic moments. We have also shown these interaction sites should be located at the geometric centers of the chemical groups. In connection with predictive methods, we have shown two perturbation type theories to work well for fluids modeled using one-center anisotropic potentials and the possibility exists for extending these to anisotropic site-site models. In connection with correlation methods, we have studied, through simulations, the effect of molecular shape on the attraction term in the generalized van der Waals equation of state for fluids of nonspherical molecules and proposed a possible form which is to be studied further. We have successfully studied the vector and parallel processing aspects of molecular simulations for fluids of nonspherical molecules.

  16. COMPUTATIONAL METHODS FOR STUDYING THE INTERACTION BETWEEN POLYCYCLIC AROMATIC HYDROCARBONS AND BIOLOGICAL MACROMOLECULES

    Science.gov (United States)

    Computational Methods for Studying the Interaction between Polycyclic Aromatic Hydrocarbons and Biological Macromolecules .The mechanisms for the processes that result in significant biological activity of PAHs depend on the interaction of these molecules or their metabol...

  17. Estudo comparativo das características fluidodinâmicas de próteses valvulares biológicas de pericárdio bovino de perfil alto e baixo Comparative study of fluid dynamic characteristics in high and low biological prosthetic heart valves from bovine pericardium

    Directory of Open Access Journals (Sweden)

    Aron J. P Andrade

    1989-12-01

    Full Text Available O comportamento fluidodinâmico e a vida útil média de uma prótese valvular cardíaca são características muito importantes na escolha do modelo de prótese a ser implantada em um determinado paciente. Por esse motivo, foi realizado um estudo comparativo entre as válvulas biológicas de perfil alto e baixo, para se verificarem possíveis alterações na vida média, gradiente de pressão e refluxo, causadas pela diminuição do perfil dessas próteses. Com o auxílio de um duplicador de pulso, foram analisadas cinco próteses de perfil alto e cinco de perfil baixo, todas tamanho 29, fabricadas no Instituto Dante Pazzanese de Cardiologia (IDPC. Mantendo-se a freqüência de batimentos em 100 bpm e a diferença de pressão em 1000 mmHg, verificou-se que a vida útil média da válvula de perfil baixo permaneceu equivalente à de perfil alto. Em outro equipamento, denominado simulador cardíaco, as próteses foram submetidas a condições semelhantes às condições fisiológicas de funcionamento para uma freqüência cardíaca de 75 bpm. Os resultados mostraram que o volume de retorno necessário para fechamento (refluxo, nas válvulas de perfil baixo, é menor do que nas de perfil alto. Isso traz um melhor aproveitamento do efeito de bombeamento do coração. As perdas de carga das válvulas foram comparadas através dos gradientes máximos de pressão visibilizados com a sobreposição dos sinais de pressão. Observou-se que as válvulas de perfil baixo oferecem menos resistência ao fluxo; assim, quando são implantadas, possibilitam uma passagem mais livre e desobstruída do sangue.The fluid dynamic performance and lifetime of a prosthetic heart valve are one of the most important characteristics to determine the choice of what prosthesis must be applied to a patient. Because of this, two different biological prosthetic heart valves profiles (one high profile and other low profile were studied, to verify possible alterations of working

  18. Dynamic speckle study of microbial growth

    Science.gov (United States)

    Vincitorio, F. M.; Mulone, C.; Marcuzzi, P. A.; Budini, N.; Freyre, C.; Lopez, A. J.; Ramil, A.

    2015-08-01

    In this work we present a characterization of yeast dynamic speckle activity during growth in an isolated agar culture medium. We found that it is possible to detect the growth of the microorganisms even before they turn out to be visible. By observing the time evolution of the speckle activity at different regions of the culture medium we could extract a map of the growth process, which served to analyze how the yeast develops and spreads over the agar's medium. An interesting point of this study concerns with the influence of the laser light on the yeast growth rate. We have found that yeast finds hard to develop at regions with higher laser light illumination, although we used a synchronous system to capture the speckle pattern. The results obtained in this work would serve us as a starting point to fabricate a detector of growing microorganism colonies, with obvious interesting applications in diverse areas.

  19. Monte Carlo study of real time dynamics

    CERN Document Server

    Alexandru, Andrei; Bedaque, Paulo F; Vartak, Sohan; Warrington, Neill C

    2016-01-01

    Monte Carlo studies involving real time dynamics are severely restricted by the sign problem that emerges from highly oscillatory phase of the path integral. In this letter, we present a new method to compute real time quantities on the lattice using the Schwinger-Keldysh formalism via Monte Carlo simulations. The key idea is to deform the path integration domain to a complex manifold where the phase oscillations are mild and the sign problem is manageable. We use the previously introduced "contraction algorithm" to create a Markov chain on this alternative manifold. We substantiate our approach by analyzing the quantum mechanical anharmonic oscillator. Our results are in agreement with the exact ones obtained by diagonalization of the Hamiltonian. The method we introduce is generic and in principle applicable to quantum field theory albeit very slow. We discuss some possible improvements that should speed up the algorithm.

  20. Molecular dynamics study of ice structural evolution

    Institute of Scientific and Technical Information of China (English)

    Wang Yan; Dong Shun-Le

    2008-01-01

    Molecular dynamics simulation is employed to study the structural evolution of low density amorphous ice during its compression from one atmosphere to 2.5 GPa. Calculated results show that high density amorphous ice is formed at an intermediate pressure of~1.0GPa; the O-O-O bond angle ranges from 83° to 113°, and the O-H...O bond is bent from 112° to 160°. Very high density amorphous ice is obtained by quenching to 80K and decompressing the ice to ambient pressure from 160 K/1.3 GPa or 160 K/1.7 GPa; and the next-nearest O-O length is found to be 0.310 nm, just 0.035 nm beyond the nearest O-O distance of 0.275 nm.

  1. Comparing protein VEGF inhibitors: In vitro biological studies

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Lanlan; Liang, Xiao Huan [Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080 (United States); Ferrara, Napoleone, E-mail: nf@gene.com [Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080 (United States)

    2011-05-06

    Highlights: {yields} VEGF is a mediator of angiogenesis. {yields} VEGF inhibitors have clinical applications in cancer and eye disorders. {yields} Five protein VEGF inhibitors were compared for their ability to inhibit. {yields} VEGF-induced activities in cultured endothelial cells. -- Abstract: VEGF inhibitors are widely used as a therapy for tumors and intravascular neovascular disorders, but limited and conflicting data regarding their relative biological potencies are available. The purpose of the study is to compare different protein VEGF inhibitors for their ability to inhibit VEGF-stimulated activities. We tested ranibizumab, the full-length variant of ranibizumab (Mab Y0317), bevacizumab, the VEGF-TrapR1R2 and Flt(1-3)-IgG in bioassays measuring VEGF-stimulated proliferation of bovine retinal microvascular endothelial cells or chemotaxis of human umbilical vein endothelial cells (HUVEC). The inhibitors were also compared for their ability to inhibit MAP kinase activation in HUVECs following VEGF addition. Ranibizumab, VEGF-TrapR1R2 and Flt(1-3)-IgG had very similar potencies in the bioassays tested. Bevacizumab was over 10-fold less potent than these molecules. Mab Y0317 was over 30-fold more potent than bevacizumab. The findings reported in this manuscript describe important intrinsic characteristics of several VEGF inhibitors that may be useful to design and interpret preclinical or clinical studies.

  2. Oxidation dynamics of nanophase aluminum clusters : a molecular dynamics study.

    Energy Technology Data Exchange (ETDEWEB)

    Ogata, S.

    1998-01-27

    Oxidation of an aluminum nanocluster (252,158 atoms) of radius 100{angstrom} placed in gaseous oxygen (530,727 atoms) is investigated by performing molecular-dynamics simulations on parallel computers. The simulation takes into account the effect of charge transfer between Al and O based on the electronegativity equalization principles. We find that the oxidation starts at the surface of the cluster and the oxide layer grows to a thickness of {approximately}28{angstrom}. Evolutions of local temperature and densities of Al and O are investigated. The surface oxide melts because of the high temperature resulting from the release of energy associated with Al-O bondings. Amorphous surface-oxides are obtained by quenching the cluster. Vibrational density-of-states for the surface oxide is analyzed through comparisons with those for crystalline Al, Al nanocluster, and {alpha}-Al{sub 2}O{sub 3}.

  3. Long-term population dynamics and in situ physiology in activated sludge systems with enhanced biological phosphorus removal operated with and without nitrogen removal

    DEFF Research Database (Denmark)

    Lee, N.; Nielsen, P.H.; Aspegren, H.

    2003-01-01

    Quantitative fluorescence in situ hybridization (FISH) and the combination of FISH with microautoradiography (MAR) were used in order to study the long-term population dynamics (2.5 years) and the in situ physiology in two parallel activated sludge pilot systems with enhanced biological phosphorus...... removal (EBPR). The two systems received the same influent wastewater, but were differently operated (with and without nitrogen removal, respectively). Both systems showed a significant P removal that increased when different substrates (phosphorus (P), acetate and glucose, respectively) were added...

  4. The Impact of Ozone Treatment in Dynamic Bed Parameters on Changes in Biologically Active Substances of Juniper Berries.

    Science.gov (United States)

    Brodowska, Agnieszka Joanna; Śmigielski, Krzysztof; Nowak, Agnieszka; Czyżowska, Agata; Otlewska, Anna

    2015-01-01

    The development of the parameters of ozone decontamination method assuring the least possible losses of biologically active substances (essential oils and polyphenols) and their activity in common juniper (Juniperus communis (L.)) berries was studied. Ozone treatment in dynamic bed was conducted 9 times. The process was conducted under different ozone concentrations (100.0; 130.0; 160.0 g O3/m3) and times (30, 60, 90 min). After each decontamination, the microbiological profile of the juniper berries was studied, and the contaminating microflora was identified. Next to the microbiological profile, the phenolic profile, as well as antioxidant activity of extracts and essential oils were determined. The total polyphenol content (TPC), composition of essential oils, free radical-scavenging capacity, total antioxidant capacity, ferric-reducing antioxidant power (FRAP), beta-carotene bleaching test (BCB) and LC-MS polyphenol analysis were carried out. The study reveals that during short ozone contact times, higher amounts of TPC, 15.47 and 12.91 mg CE/g of extract, for samples 100/30 and 130/30, respectively, were demonstrated. Whereas samples 100/60, 130/60, 100/90, and 160/90 exhibited the lowest amount of phenolics. The highest antioxidant activity was found in the methanol extract obtained from ozonated berries which exhibited the lowest IC50 in all the antioxidant assays, such as DPPH, FRAP, and BCB assays. Ozone treatment showed noteworthy potential and its usage in food manufacturing and as an alternative decontamination method should be considered.

  5. The Impact of Ozone Treatment in Dynamic Bed Parameters on Changes in Biologically Active Substances of Juniper Berries.

    Directory of Open Access Journals (Sweden)

    Agnieszka Joanna Brodowska

    Full Text Available The development of the parameters of ozone decontamination method assuring the least possible losses of biologically active substances (essential oils and polyphenols and their activity in common juniper (Juniperus communis (L. berries was studied. Ozone treatment in dynamic bed was conducted 9 times. The process was conducted under different ozone concentrations (100.0; 130.0; 160.0 g O3/m3 and times (30, 60, 90 min. After each decontamination, the microbiological profile of the juniper berries was studied, and the contaminating microflora was identified. Next to the microbiological profile, the phenolic profile, as well as antioxidant activity of extracts and essential oils were determined. The total polyphenol content (TPC, composition of essential oils, free radical-scavenging capacity, total antioxidant capacity, ferric-reducing antioxidant power (FRAP, beta-carotene bleaching test (BCB and LC-MS polyphenol analysis were carried out. The study reveals that during short ozone contact times, higher amounts of TPC, 15.47 and 12.91 mg CE/g of extract, for samples 100/30 and 130/30, respectively, were demonstrated. Whereas samples 100/60, 130/60, 100/90, and 160/90 exhibited the lowest amount of phenolics. The highest antioxidant activity was found in the methanol extract obtained from ozonated berries which exhibited the lowest IC50 in all the antioxidant assays, such as DPPH, FRAP, and BCB assays. Ozone treatment showed noteworthy potential and its usage in food manufacturing and as an alternative decontamination method should be considered.

  6. Quantifying biologically and physically induced flow and tracer dynamics in permeable sediments

    Directory of Open Access Journals (Sweden)

    F. J. R. Meysman

    2007-08-01

    Full Text Available Insight in the biogeochemistry and ecology of sandy sediments crucially depends on a quantitative description of pore water flow and the associated transport of various solutes and particles. We show that widely different problems can be modelled by the same flow and tracer equations. The principal difference between model applications concerns the geometry of the sediment-water interface and the pressure conditions that are specified along this boundary. We illustrate this commonality with four different case studies. These include biologically and physically induced pore water flows, as well as simplified laboratory set-ups versus more complex field-like conditions: [1] lugworm bio-irrigation in laboratory set-up, [2] interaction of bio-irrigation and groundwater seepage on a tidal flat, [3] pore water flow induced by rotational stirring in benthic chambers, and [4] pore water flow induced by unidirectional flow over a ripple sequence. The same two example simulations are performed in all four cases: (a the time-dependent spreading of an inert tracer in the pore water, and (b the computation of the steady-state distribution of oxygen in the sediment. Overall, our model comparison indicates that model development for sandy sediments is promising, but within an early stage. Clear challenges remain in terms of model development, model validation, and model implementation.

  7. Recent excitements in protein NMR: Large proteins and biologically relevant dynamics

    Indian Academy of Sciences (India)

    SAI CHAITANYA CHILIVERI; MANDAR V DESHMUKH

    2016-12-01

    The advent of Transverse Relaxation Optimized SpectroscopY (TROSY) and perdeuteration allowed biomolecularNMR spectroscopists to overcome the size limitation barrier (~20 kDa) in de novo structure determination of proteins.The utility of these techniques was immediately demonstrated on large proteins and protein complexes (e.g. GroELGroES,ClpP protease, Hsp90-p53, 20S proteasome, etc.). Further, recent methodological developments such asResidual Dipolar Couplings and Paramagnetic Relaxation Enhancement allowed accurate measurement of long-rangestructural restraints. Additionally, Carr-Purcell-Meiboom-Gill (CPMG), rotating frame relaxation experiments (R1ρ)and saturation transfer experiments (CEST and DEST) created never-before accessibility to the μs–ms timescaledynamic parameters that led to the deeper understanding of biological processes. Meanwhile, the excitement in thefield continued with a series of developments in the fast data acquisition methods allowing rapid structural studies onless stable proteins. This review aims to discuss important developments in the field of biomolecular NMRspectroscopy in the recent past, i.e., in the post TROSY era. These developments not only gave access to the structuralstudies of large protein assemblies, but also revolutionized tools in the arsenal of today’s biomolecular NMR and pointto a bright future of biomolecular NMR spectroscopy.

  8. Energy efficient walking with central pattern generators: from passive dynamic walking to biologically inspired control

    NARCIS (Netherlands)

    Verdaasdonk, B.W.; Koopman, H.F.J.M.; Van der Helm, F.C.T.

    2009-01-01

    Like human walking, passive dynamic walking—i.e. walking down a slope with no actuation except gravity—is energy efficient by exploiting the natural dynamics. In the animal world, neural oscillators termed central pattern generators (CPGs) provide the basic rhythm for muscular activity in

  9. Energy efficient walking with central pattern generators: from passive dynamic walking to biologically inspired control

    NARCIS (Netherlands)

    Verdaasdonk, B.W.; Koopman, H.F.J.M.; Van der Helm, F.C.T.

    2009-01-01

    Like human walking, passive dynamic walking—i.e. walking down a slope with no actuation except gravity—is energy efficient by exploiting the natural dynamics. In the animal world, neural oscillators termed central pattern generators (CPGs) provide the basic rhythm for muscular activity in locomotion

  10. Biological factors underlying regularity and chaos in aquatic ecosystems: Simple models of complex dynamics

    Indian Academy of Sciences (India)

    A B Medvinsky; S V Petrovskii; D A Tikhonov; I A Tikhonova; G R Ivanitsky; E Venturino; H Malchow

    2001-03-01

    This work is focused on the processes underlying the dynamics of spatially inhomogeneous plankton communities. We demonstrate that reaction—diffusion mathematical models are an appropriate tool for searching and understanding basic mechanisms of complex spatio-temporal plankton dynamics and fractal properties of planktivorous fish school walks.

  11. Cahaba River: Biological and Water Quality Studies, Birmingham, AL,

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Excessive sedimentation and nutrient enrichment are affecting the biology of the Cahaba Riverwatershed. Deleterious effects of sediment deposition on the fish and...

  12. Application of Bioinformatics and Systems Biology in Medicinal Plant Studies

    Institute of Scientific and Technical Information of China (English)

    DENG You-ping; AI Jun-mei; XIAO Pei-gen

    2010-01-01

    One important purpose to investigate medicinal plants is to understand genes and enzymes that govern the biological metabolic process to produce bioactive compounds.Genome wide high throughput technologies such as genomics,transcriptomics,proteomics and metabolomics can help reach that goal.Such technologies can produce a vast amount of data which desperately need bioinformatics and systems biology to process,manage,distribute and understand these data.By dealing with the"omics"data,bioinformatics and systems biology can also help improve the quality of traditional medicinal materials,develop new approaches for the classification and authentication of medicinal plants,identify new active compounds,and cultivate medicinal plant species that tolerate harsh environmental conditions.In this review,the application of bioinformatics and systems biology in medicinal plants is briefly introduced.

  13. Study of the biology of Trichogramma chilonis Ishii (Hymenoptera ...

    African Journals Online (AJOL)

    user1

    KEYWORDS: Trichogramma chilonis, Maruca vitrata, biology, Plutella xylostella ... Egg parasitoids play an important role in the control of lepidopterous pests. (Li, 1994). ..... I am also grateful to Mr D. Abeeluck, Principal Research Scientist of.

  14. Dynamic infrared imaging for biological and medical applications in Boron neutron capture therapy

    Science.gov (United States)

    Santa Cruz, Gustavo A.; González, Sara J.; Dagrosa, Alejandra; Schwint, Amanda E.; Carpano, Marina; Trivillin, Verónica A.; Boggio, Esteban F.; Bertotti, José; Marín, Julio; Monti Hughes, Andrea; Molinari, Ana J.; Albero, Miguel

    2011-05-01

    Boron Neutron Capture Therapy (BNCT) is a treatment modality, currently focused on the treatment of cancer, which involves a tumor selective 10B compound and a specially tuned neutron beam to produce a lethal nuclear reaction. BNCT kills target cells with microscopic selectivity while sparing normal tissues from potentially lethal doses of radiation. In the context of the Argentine clinical and research BNCT projects at the National Atomic Energy Commission and in a strong collaboration with INVAP SE, we successfully implemented Dynamic Infrared Imaging (DIRI) in the clinical setting for the observation of cutaneous melanoma patients and included DIRI as a non invasive methodology in several research protocols involving small animals. We were able to characterize melanoma lesions in terms of temperature and temperature rate-of-recovery after applying a mild cold thermal stress, distinguishing melanoma from other skin pigmented lesions. We observed a spatial and temporal correlation between skin acute reactions after irradiation, the temperature pattern and the dose distribution. We studied temperature distribution as a function of tumor growth in mouse xenografts, observing a significant correlation between tumor temperature and drug uptake; we investigated temperature evolution in the limbs of Wistar rats for a protocol of induced rheumatoid arthritis (RA), DIRI being especially sensitive to RA induction even before the development of clinical signs and studied surface characteristics of tumors, precancerous and normal tissues in a model of oral cancer in the hamster cheek pouch.

  15. Gold complexes with benzimidazole derivatives: synthesis, characterization and biological studies.

    Science.gov (United States)

    Mota, Vinicius Zamprogno; de Carvalho, Gustavo Senra Gonçalves; da Silva, Adilson David; Costa, Luiz Antônio Sodré; de Almeida Machado, Patrícia; Coimbra, Elaine Soares; Ferreira, Carmen Veríssima; Shishido, Silvia Mika; Cuin, Alexandre

    2014-02-01

    Synthesis, characterization, DFT studies and biological assays of new gold(I) and gold(III) complexes of benzimidazole are reported. Molecular and structural characterizations of the compounds were based on elemental (C, H and N) and thermal (TG-DTA) analyses, and FT-IR and UV-Visible spectroscopic measurements. The structures of complexes were proposed based DFT calculations. The benzimidazole compounds (Lig1 and Lig2) and the gold complexes were tested against three Leishmania species related to cutaneous manifestations of leishmaniasis. The free benzimidazole compounds showed no leishmanicidal activity. On the other hand, the gold(I and III) complexes have shown to possess significant activity against Leishmania in both stages of parasite, and the gold(III) complex with Lig2 exhibited expressive leishmanicidal activity with IC50 values below 5.7 μM. Also, the gold complexes showed high leishmania selectivity. The gold(I) complex with Lig1, for example, is almost 50 times more toxic for the parasite than for macrophages. Besides the leishmanicidal activity, all complexes exhibited toxic effect against SK-Mel 103 and Balb/c 3T3, cancer cells.

  16. Biological studies on Brazilian plants used in wound healing.

    Science.gov (United States)

    Schmidt, C; Fronza, M; Goettert, M; Geller, F; Luik, S; Flores, E M M; Bittencourt, C F; Zanetti, G D; Heinzmann, B M; Laufer, S; Merfort, I

    2009-04-21

    n-Hexanic and ethanolic extracts from twelve plants (Brugmansia suaveolens Brecht. et Presl., Eupatorium laevigatum Lam., Galinsoga parviflora Cav., Iresine herbstii Hook., Kalanchöe tubiflora Hamet-Ahti, Petiveria alliacea L., Pluchea sagittalis (Lam.) Cabrera, Piper regnellii DC., Schinus molle L., Sedum dendroideum Moç et Sessé ex DC., Waltheria douradinha St. Hill., Xanthium cavanillesii Schouw.) used in traditional South Brazilian medicine as wound healing agents were investigated in various biological assays, targeting different aspects in this complex process. The extracts were investigated on NF-kappaB DNA binding, p38alpha MAPK, TNF-alpha release, direct elastase inhibition and its release as well as on caspase-3. Fibroblasts migration to and proliferation into the wounded monolayers were evaluated in the scratch assay, the agar diffusion test for antibacterial and the MTT assay for cytotoxic effects. The hydrophilic extracts from Galinsoga parviflora, Petiveria alliacea, Schinus molle, Waltheria douradinha and Xanthium cavanillesii as well as the lipophilic extract of Waltheria douradinha turned out to be the most active ones. These results increase our knowledge on the wound healing effects of the investigated medicinal plants. Further studies are necessary to find out the effective secondary metabolites responsible for the observed effects.

  17. Biological conversion of synthesis gas. Mass transfer/kinetic studies

    Energy Technology Data Exchange (ETDEWEB)

    Klasson, K.T.; Basu, R.; Johnson, E.R.; Clausen, E.C.; Gaddy, J.L.

    1992-03-01

    Mass transfer and kinetic studies were carried out for the Rhodospirillum rubrum and Chlorobium thiosulfatophilum bacterial systems. R. rubrum is a photosynthetic anaerobic bacterium which catalyzes the biological water gas shift reaction: CO + H{sub 2}0 {yields} CO{sub 2} + H{sub 2}. C. thiosulfatophilum is also a H{sub 2}S and COS to elemental sulfur. The growth of R. rubrum may be satisfactorily carried out at 25{degree} and 30{degree}C, while CO uptake and thus the conversion of CO best occurs at temperatures of either 30{degree}, 32{degree} or 34{degree}C. The rate of conversion of COs and H{sub 2}O to CO{sub 2} and H{sub 2}S may be modeled by a first order rate expression. The rate constant at 30{degree}C was found to be 0.243 h{sup {minus}1}. The growth of C. thiosulfatophilum may be modeled in terms of incoming light intensity using a Monod equation: {mu} = {sub 351} + I{sub o}/{sup 0.152}I{sub o}. Comparisons of the growth of R. rubrum and C. thiosulfatophilum shows that the specific growth rate of C. thiosulfatophilum is much higher at a given light intensity.

  18. Seasonal nutrient and plankton dynamics in a physical-biological model of Crater Lake

    Science.gov (United States)

    Fennel, K.; Collier, R.; Larson, G.; Crawford, G.; Boss, E.

    2007-01-01

    A coupled 1D physical-biological model of Crater Lake is presented. The model simulates the seasonal evolution of two functional phytoplankton groups, total chlorophyll, and zooplankton in good quantitative agreement with observations from a 10-year monitoring study. During the stratified period in summer and early fall the model displays a marked vertical structure: the phytoplankton biomass of the functional group 1, which represents diatoms and dinoflagellates, has its highest concentration in the upper 40 m; the phytoplankton biomass of group 2, which represents chlorophyta, chrysophyta, cryptomonads and cyanobacteria, has its highest concentrations between 50 and 80 m, and phytoplankton chlorophyll has its maximum at 120 m depth. A similar vertical structure is a reoccurring feature in the available data. In the model the key process allowing a vertical separation between biomass and chlorophyll is photoacclimation. Vertical light attenuation (i.e., water clarity) and the physiological ability of phytoplankton to increase their cellular chlorophyll-to-biomass ratio are ultimately determining the location of the chlorophyll maximum. The location of the particle maxima on the other hand is determined by the balance between growth and losses and occurs where growth and losses equal. The vertical particle flux simulated by our model agrees well with flux measurements from a sediment trap. This motivated us to revisit a previously published study by Dymond et al. (1996). Dymond et al. used a box model to estimate the vertical particle flux and found a discrepancy by a factor 2.5-10 between their model-derived flux and measured fluxes from a sediment trap. Their box model neglected the exchange flux of dissolved and suspended organic matter, which, as our model and available data suggests is significant for the vertical exchange of nitrogen. Adjustment of Dymond et al.'s assumptions to account for dissolved and suspended nitrogen yields a flux estimate that is

  19. Biology and cytotoxicity of dental materials: an in vitro study.

    Science.gov (United States)

    Gociu, M; Pătroi, D; Prejmerean, Cristina; Păstrăv, O; Boboia, Stanca; Prodan, Doina; Moldovan, Marioara

    2013-01-01

    The purpose of the experiment was to determine the degree of biocompatibility of a sealer (RO, laboratory made product) dental material in terms of cytotoxicity and animal tests. In the present study, the biological compatibility of eight experimental composite materials was examined by in vitro methods. The bio-composites used for the cytotoxicity test were placed into direct contact with normal human fibroblasts in a cell-culture dish. After fibroblast bioassay was performed, a duplicate sample of biomaterial was placed in each well, and then the fibroblasts were incubated for 48 hours at 37°C and 5% carbon dioxide. Local reactions after the implantation of the material regarding preclinical evaluation have been carried out within the Biobase Laboratory of the "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania. The biocompatibility was studied using the tolerance test by the subcutaneous and intramuscular implantation of the cured specimens. The sealant C3 scored the highest value to the cell viability. The results of the present study showed that different dental materials had different effects on cells. The resin monomer TEGDMA, present in the sealer's composition, increased the amount of intracellular reactive oxygen species. Resin-based composites are cytotoxic before polymerization and immediately thereafter, whereas already set specimens cause almost no reaction. The test of tolerance showed that the composite materials do not contain any toxic, irritant substances or destructive ones for the living cells or tissues. The tests with experimental composite materials revealed that they are not cytotoxic for the living cells, in all versions of the materials used. All the samples of composite materials have maintained their integrity during the experiment, allowing the testing together with the embedded cells, which proved good viability, so they are suitable for dentistry use.

  20. Molecular Dynamics Study of Helicobacter pylori Urease.

    Science.gov (United States)

    Minkara, Mona S; Ucisik, Melek N; Weaver, Michael N; Merz, Kenneth M

    2014-05-13

    Helicobacter pylori have been implicated in an array of gastrointestinal disorders including, but not limited to, gastric and duodenal ulcers and adenocarcinoma. This bacterium utilizes an enzyme, urease, to produce copious amounts of ammonia through urea hydrolysis in order to survive the harsh acidic conditions of the stomach. Molecular dynamics (MD) studies on the H. pylori urease enzyme have been employed in order to study structural features of this enzyme that may shed light on the hydrolysis mechanism. A total of 400 ns of MD simulation time were collected and analyzed in this study. A wide-open flap state previously observed in MD simulations on Klebsiella aerogenes [Roberts et al. J. Am. Chem. Soc.2012, 134, 9934] urease has been identified in the H. pylori enzyme that has yet to be experimentally observed. Critical distances between residues on the flap, contact points in the closed state, and the separation between the active site Ni(2+) ions and the critical histidine α322 residue were used to characterize flap motion. An additional flap in the active site was elaborated upon that we postulate may serve as an exit conduit for hydrolysis products. Finally we discuss the internal hollow cavity and present analysis of the distribution of sodium ions over the course of the simulation.

  1. Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations

    Directory of Open Access Journals (Sweden)

    Kleessen Sabrina

    2012-03-01

    Full Text Available Abstract Background Flux balance analysis (FBA together with its extension, dynamic FBA, have proven instrumental for analyzing the robustness and dynamics of metabolic networks by employing only the stoichiometry of the included reactions coupled with adequately chosen objective function. In addition, under the assumption of minimization of metabolic adjustment, dynamic FBA has recently been employed to analyze the transition between metabolic states. Results Here, we propose a suite of novel methods for analyzing the dynamics of (internally perturbed metabolic networks and for quantifying their robustness with limited knowledge of kinetic parameters. Following the biochemically meaningful premise that metabolite concentrations exhibit smooth temporal changes, the proposed methods rely on minimizing the significant fluctuations of metabolic profiles to predict the time-resolved metabolic state, characterized by both fluxes and concentrations. By conducting a comparative analysis with a kinetic model of the Calvin-Benson cycle and a model of plant carbohydrate metabolism, we demonstrate that the principle of regulatory on/off minimization coupled with dynamic FBA can accurately predict the changes in metabolic states. Conclusions Our methods outperform the existing dynamic FBA-based modeling alternatives, and could help in revealing the mechanisms for maintaining robustness of dynamic processes in metabolic networks over time.

  2. Recommendations for designing and conducting veterinary clinical pathology biologic variation studies

    DEFF Research Database (Denmark)

    Freeman, Kathleen P; Baral, Randolph M; Dhand, Navneet K

    2017-01-01

    The recent creation of a veterinary clinical pathology biologic variation website has highlighted the need to provide recommendations for future studies of biologic variation in animals in order to help standardize and improve the quality of published information and to facilitate review and sele......). These recommendations provide a valuable resource for clinicians, laboratorians, and researchers interested in conducting studies of biologic variation and in determining the quality of studies of biologic variation in veterinary laboratory testing.......The recent creation of a veterinary clinical pathology biologic variation website has highlighted the need to provide recommendations for future studies of biologic variation in animals in order to help standardize and improve the quality of published information and to facilitate review...... and selection of publications as standard references. The following recommendations are provided in the format and order commonly found in veterinary publications. A checklist is provided to aid in planning, implementing, and evaluating veterinary studies on biologic variation (Appendix S1...

  3. Teaching Biochemestry in Biology and Microbiology in the Faculty of Biology, University of Havana, in Studies Plan D

    Directory of Open Access Journals (Sweden)

    Jorge Oscar González Bacerio

    2014-04-01

    Full Text Available In this work, a review of the contents traditionally studied on Biochemistry I and II courses for Biology and Microbiology careers, at the Faculty of Biology, University of Havana, is realized. This analysis was done taking into account the agreement of contents with the Knowledge and Skills Systems recognized in the current Study Plan D. From this analysis, compa-rative with the equivalent courses on Biochemistry and Molecular Biology career, a redesign of the studied contents is presented. According to this, these con-tents were displaced, when was possible and conve-nient, from the classical mammal model to the study objects of these professionals: the living world in all its diversity, for biologists, and microorganisms and viru-ses, for microbiologists. In this manner, we use on Bio-chemistry I lectures specific examples of structure-function relationship of biomolecules from models of organisms more appropriated for the two careers. Similarly, we exploit on Biochemistry II the extraordi-nary metabolic diversity that is present in different groups of living organisms, as well as we introduced the teaching of other metabolic routes, characteristic of each group or which constitute variations of classi-cal mammalian pathways. These modifications could make easier the teaching and learning of Biochemistry for biologists and microbiologists, as well as could increase the contribution of these courses to the for-mation of professionals in these domains of Biological Sciences.

  4. A case study of species assessment in invasion biology: the Village Weaverbird Ploceus cucullatus

    Directory of Open Access Journals (Sweden)

    Lahti, D. C.

    2003-01-01

    Full Text Available Application of recent insights gained in invasion biology to particular species may aid in addressing a central problem of the field, that of prediction of the dynamics of future introduction and invasion. The Village Weaverbird (Ploceus cucullatus is concluded to be a potential invader of concern in several regions, especially the Mediterranean, Caribbean, and southeastern United States. This conclusion is supported by the introduction and invasion history of the species, factors concluded in recent reviews and quantitative studies to correlate with introduction success or invasiveness in birds, the species' agricultural pest status in its current range, and a published rating system. A proactive stance is recommended since control efforts have met with little success, but certain characteristics of the Village Weaver may provide opportunities for management.

  5. Structural dynamics and aerodynamics measurements of biologically inspired flexible flapping wings

    Energy Technology Data Exchange (ETDEWEB)

    Wu, P; Stanford, B K; Ifju, P G [Department of Mechanical and Aerospace Engineering, MAE-A 231, University of Florida, Gainesville, FL 32611 (United States); Saellstroem, E; Ukeiley, L, E-mail: diccidwp@ufl.edu [Department of Mechanical and Aerospace Engineering, University of Florida, Shalimar, FL 32579 (United States)

    2011-03-15

    Flapping wing flight as seen in hummingbirds and insects poses an interesting unsteady aerodynamic problem: coupling of wing kinematics, structural dynamics and aerodynamics. There have been numerous studies on the kinematics and aerodynamics in both experimental and computational cases with both natural and artificial wings. These studies tend to ignore wing flexibility; however, observation in nature affirms that passive wing deformation is predominant and may be crucial to the aerodynamic performance. This paper presents a multidisciplinary experimental endeavor in correlating a flapping micro air vehicle wing's aeroelasticity and thrust production, by quantifying and comparing overall thrust, structural deformation and airflow of six pairs of hummingbird-shaped membrane wings of different properties. The results show that for a specific spatial distribution of flexibility, there is an effective frequency range in thrust production. The wing deformation at the thrust-productive frequencies indicates the importance of flexibility: both bending and twisting motion can interact with aerodynamic loads to enhance wing performance under certain conditions, such as the deformation phase and amplitude. By measuring structural deformations under the same aerodynamic conditions, beneficial effects of passive wing deformation can be observed from the visualized airflow and averaged thrust. The measurements and their presentation enable observation and understanding of the required structural properties for a thrust effective flapping wing. The intended passive responses of the different wings follow a particular pattern in correlation to their aerodynamic performance. Consequently, both the experimental technique and data analysis method can lead to further studies to determine the design principles for micro air vehicle flapping wings.

  6. Unravelling novel synergies between organometallic and biological partners: a quantum mechanics/molecular mechanics study of an artificial metalloenzyme.

    Science.gov (United States)

    Ortega-Carrasco, Elisabeth; Lledós, Agustí; Maréchal, Jean-Didier

    2014-07-06

    In recent years, the design of artificial metalloenzymes obtained by the insertion of homogeneous catalysts into biological macromolecules has become a major field of research. These hybrids, and the corresponding X-ray structures of several of them, are offering opportunities to better understand the synergy between organometallic and biological subsystems. In this work, we investigate the resting state and activation process of a hybrid inspired by an oxidative haemoenzyme but presenting an unexpected reactivity and structural features. An extensive series of quantum mechanics/molecular mechanics calculations show that the resting state and the activation processes of the novel enzyme differ from naturally occurring haemoenzymes in terms of the electronic state of the metal, participation of the first coordination sphere of the metal and the dynamic process. This study presents novel insights into the sensitivity of the association between organometallic and biological partners and illustrates the molecular challenge that represents the design of efficient enzymes based on this strategy.

  7. Real-time neutron scattering investigations of biological signal transduction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    May, Roland [Institut Laue-Langevinx, Grenoble Cedex (France); Hendriks, Johnny [Vrije Universiteit Amsterdam, Amsterdam (Netherlands); Crielaard, Wim [Swammerdam Institute for Life Sciences and Academic Center for Dentistry, University of Amsterdam, Amsterdam (Netherlands)

    2005-07-01

    During their catalytic cycle, proteins involved in biological signal transduction undergo unexpectedly large conformational changes, which are at the core of their biological functioning. Until now it has been extremely difficult to obtain experimental insight into the nature of these conformational changes. Mathematical modeling and time-resolved X-ray crystallography have resulted in probable routes along which these conformational changes may take place, but so far this fundamental biological phenomenon has hardly been tackled experimentally. Here, we report on an attempt to observe structural changes in Photoactive Yellow Protein with time-resolved small-angle neutron scattering using diffractometer D22 at the high-flux reactor of the Institut Laue-Langevin, Grenoble, France.

  8. Bioreactor Studies and Computational Fluid Dynamics

    Science.gov (United States)

    Singh, H.; Hutmacher, D. W.

    The hydrodynamic environment “created” by bioreactors for the culture of a tissue engineered construct (TEC) is known to influence cell migration, proliferation and extra cellular matrix production. However, tissue engineers have looked at bioreactors as black boxes within which TECs are cultured mainly by trial and error, as the complex relationship between the hydrodynamic environment and tissue properties remains elusive, yet is critical to the production of clinically useful tissues. It is well known in the chemical and biotechnology field that a more detailed description of fluid mechanics and nutrient transport within process equipment can be achieved via the use of computational fluid dynamics (CFD) technology. Hence, the coupling of experimental methods and computational simulations forms a synergistic relationship that can potentially yield greater and yet, more cohesive data sets for bioreactor studies. This review aims at discussing the rationale of using CFD in bioreactor studies related to tissue engineering, as fluid flow processes and phenomena have direct implications on cellular response such as migration and/or proliferation. We conclude that CFD should be seen by tissue engineers as an invaluable tool allowing us to analyze and visualize the impact of fluidic forces and stresses on cells and TECs.

  9. Biophysically realistic filament bending dynamics in agent-based biological simulation.

    Science.gov (United States)

    Alberts, Jonathan B

    2009-01-01

    An appealing tool for study of the complex biological behaviors that can emerge from networks of simple molecular interactions is an agent-based, computational simulation that explicitly tracks small-scale local interactions--following thousands to millions of states through time. For many critical cell processes (e.g. cytokinetic furrow specification, nuclear centration, cytokinesis), the flexible nature of cytoskeletal filaments is likely to be critical. Any computer model that hopes to explain the complex emergent behaviors in these processes therefore needs to encode filament flexibility in a realistic manner. Here I present a numerically convenient and biophysically realistic method for modeling cytoskeletal filament flexibility in silico. Each cytoskeletal filament is represented by a series of rigid segments linked end-to-end in series with a variable attachment point for the translational elastic element. This connection scheme allows an empirically tuning, for a wide range of segment sizes, viscosities, and time-steps, that endows any filament species with the experimentally observed (or theoretically expected) static force deflection, relaxation time-constant, and thermal writhing motions. I additionally employ a unique pair of elastic elements--one representing the axial and the other the bending rigidity- that formulate the restoring force in terms of single time-step constraint resolution. This method is highly local -adjacent rigid segments of a filament only interact with one another through constraint forces-and is thus well-suited to simulations in which arbitrary additional forces (e.g. those representing interactions of a filament with other bodies or cross-links / entanglements between filaments) may be present. Implementation in code is straightforward; Java source code is available at www.celldynamics.org.

  10. Biophysically realistic filament bending dynamics in agent-based biological simulation.

    Directory of Open Access Journals (Sweden)

    Jonathan B Alberts

    Full Text Available An appealing tool for study of the complex biological behaviors that can emerge from networks of simple molecular interactions is an agent-based, computational simulation that explicitly tracks small-scale local interactions--following thousands to millions of states through time. For many critical cell processes (e.g. cytokinetic furrow specification, nuclear centration, cytokinesis, the flexible nature of cytoskeletal filaments is likely to be critical. Any computer model that hopes to explain the complex emergent behaviors in these processes therefore needs to encode filament flexibility in a realistic manner. Here I present a numerically convenient and biophysically realistic method for modeling cytoskeletal filament flexibility in silico. Each cytoskeletal filament is represented by a series of rigid segments linked end-to-end in series with a variable attachment point for the translational elastic element. This connection scheme allows an empirically tuning, for a wide range of segment sizes, viscosities, and time-steps, that endows any filament species with the experimentally observed (or theoretically expected static force deflection, relaxation time-constant, and thermal writhing motions. I additionally employ a unique pair of elastic elements--one representing the axial and the other the bending rigidity- that formulate the restoring force in terms of single time-step constraint resolution. This method is highly local -adjacent rigid segments of a filament only interact with one another through constraint forces-and is thus well-suited to simulations in which arbitrary additional forces (e.g. those representing interactions of a filament with other bodies or cross-links / entanglements between filaments may be present. Implementation in code is straightforward; Java source code is available at www.celldynamics.org.

  11. Biology, literacy, and the African American voice: A case study of meaningful learning in the biology classroom

    Science.gov (United States)

    Reese, Keturah

    Under the direction of Sharon Murphy Augustine, Ph.D./Ph.D Curriculum and Instruction There was a substantial performance gap among African Americans and other ethnic groups. Additionally, African American students in a Title I school were at a significantly high risk of not meeting or exceeding on performance tests in science. Past reports have shown average gains in some subject areas, and declines in others (NCES, 2011; GADOE, 2012). Current instructional strategies and the lack of literacy within the biology classroom created a problem for African American high school students on national and state assessments. The purpose of this study was to examine the perceptions of African American students and teachers in the context of literacy and biology through the incorporation of an interactive notebook and other literacy strategies. The data was collected three ways: field notes for a two week observation period within the biology classroom, student and teacher interviews, and student work samples. During the observations, student work collection, and interviews, I looked for the following codes: active learning, constructive learning, collaborative learning, authentic learning, and intentional learning. In the process of coding for the pre-determined codes, three more codes emerged. The three codes that emerged were organization, studying/student ownership, and student teacher relationships. Students and teachers both solidified the notion that literacy and biology worked well together. The implemented literacy strategies were something that both teachers and students appreciated in their learning of biology. Overall students and teachers perceived that the interactive notebook along Cornell notes, Thinking maps, close reads, writing, lab experiments, and group work created meaningful learning experiences within the biology classroom.

  12. A novel comprehensive learning artificial bee colony optimizer for dynamic optimization biological problems

    Directory of Open Access Journals (Sweden)

    Weixing Su

    2017-03-01

    Full Text Available There are many dynamic optimization problems in the real world, whose convergence and searching ability is cautiously desired, obviously different from static optimization cases. This requires an optimization algorithm adaptively seek the changing optima over dynamic environments, instead of only finding the global optimal solution in the static environment. This paper proposes a novel comprehensive learning artificial bee colony optimizer (CLABC for optimization in dynamic environments problems, which employs a pool of optimal foraging strategies to balance the exploration and exploitation tradeoff. The main motive of CLABC is to enrich artificial bee foraging behaviors in the ABC model by combining Powell’s pattern search method, life-cycle, and crossover-based social learning strategy. The proposed CLABC is a more bee-colony-realistic model that the bee can reproduce and die dynamically throughout the foraging process and population size varies as the algorithm runs. The experiments for evaluating CLABC are conducted on the dynamic moving peak benchmarks. Furthermore, the proposed algorithm is applied to a real-world application of dynamic RFID network optimization. Statistical analysis of all these cases highlights the significant performance improvement due to the beneficial combination and demonstrates the performance superiority of the proposed algorithm.

  13. Theoretical studies of lipid bilayer electroporation using molecular dynamics simulations

    Science.gov (United States)

    Levine, Zachary Alan

    Computer simulations of physical, chemical, and biological systems have improved tremendously over the past five decades. From simple studies of liquid argon in the 1960s to fully atomistic simulations of entire viruses in the past few years, recent advances in high-performance computing have continuously enabled simulations to bridge the gap between scientific theory and experiment. Molecular dynamics simulations in particular have allowed for the direct observation of spatial and temporal events which are at present inaccessible to experiments. For this dissertation I employ all-atom molecular dynamics simulations to study the transient, electric field-induced poration (or electroporation) of phospholipid bilayers at MV/m electric fields. Phospholipid bilayers are the dominant constituents of cell membranes and act as both a barrier and gatekeeper to the cell interior. This makes their structural integrity and susceptibility to external perturbations an important topic for study, especially as the density of electromagnetic radiation in our environment is increasing steadily. The primary goal of this dissertation is to understand the specific physical and biological mechanisms which facilitate electroporation, and to connect our simulated observations to experiments with live cells and to continuum models which seek to describe the underlying biological processes of electroporation. In Chapter 1 I begin with a brief introduction to phospholipids and phospholipid bilayers, followed by an extensive overview of electroporation and atomistic molecular dynamics simulations. The following chapters will then focus on peer-reviewed and published work we performed, or on existing projects which are currently being prepared for submission. Chapter 2 looks at how external electric fields affect both oxidized and unoxidized lipid bilayers as a function of oxidation concentration and oxidized lipid type. Oxidative damage to cell membranes represents a physiologically relevant

  14. Perspective: On the relevance of slower-than-femtosecond time scales in chemical structural-dynamics studies

    Directory of Open Access Journals (Sweden)

    Philip Coppens

    2015-03-01

    Full Text Available A number of examples illustrate structural-dynamics studies of picosecond and slower photo-induced processes. They include molecular rearrangements and excitations. The information that can be obtained from such studies is discussed. The results are complementary to the information obtained from femtosecond studies. The point is made that all pertinent time scales should be covered to obtain comprehensive insight in dynamic processes of chemical and biological importance.

  15. International Biological Engagement Programs Facilitate Newcastle Disease Epidemiological Studies

    Science.gov (United States)

    Miller, Patti J.; Dimitrov, Kiril M.; Williams-Coplin, Dawn; Peterson, Melanie P.; Pantin-Jackwood, Mary J.; Swayne, David E.; Suarez, David L.; Afonso, Claudio L.

    2015-01-01

    Infections of poultry species with virulent strains of Newcastle disease virus (NDV) cause Newcastle disease (ND), one of the most economically significant and devastating diseases for poultry producers worldwide. Biological engagement programs between the Southeast Poultry Research Laboratory (SEPRL) of the United States Department of Agriculture and laboratories from Russia, Pakistan, Ukraine, Kazakhstan, and Indonesia collectively have produced a better understanding of the genetic diversity and evolution of the viruses responsible for ND, which is crucial for the control of the disease. The data from Kazakhstan, Russia, and Ukraine identified possible migratory routes for birds that may carry both virulent NDV (vNDV) and NDV of low virulence into Europe. In addition, related NDV strains were isolated from wild birds in Ukraine and Nigeria, and from birds in continental USA, Alaska, Russia, and Japan, identifying wild birds as a possible mechanism of intercontinental spread of NDV of low virulence. More recently, the detection of new sub-genotypes of vNDV suggests that a new, fifth, panzootic of ND has already originated in Southeast Asia, extended to the Middle East, and is now entering into Eastern Europe. Despite expected challenges when multiple independent laboratories interact, many scientists from the collaborating countries have successfully been trained by SEPRL on molecular diagnostics, best laboratory practices, and critical biosecurity protocols, providing our partners the capacity to further train other employes and to identify locally the viruses that cause this OIE listed disease. These and other collaborations with partners in Mexico, Bulgaria, Israel, and Tanzania have allowed SEPRL scientists to engage in field studies, to elucidate more aspects of ND epidemiology in endemic countries, and to understand the challenges that the scientists and field veterinarians in these countries face on a daily basis. Finally, new viral characterization tools

  16. [Studies on acetylspiramycin. II. Biological activities of spiramycin components].

    Science.gov (United States)

    Kondo, A; Sato, K; Shuto, K; Yamashita, K; Ichikawa, S; Takahashi, K; Kita, K; Nishiie, Y; Sano, H; Yamaguchi, K

    1990-09-01

    Acetylspiramycin (ASPM) was fractionated using high performance liquid chromatography (HPLC). The peak fractions were named F1 to F7 successively in order of increasing retention times (Rt), i.e., increasing hydrophobicity, and studied for 1) antibacterial activities (MIC), 2) antibacterial potency against Bacillus subtilis ATCC 6633, 3) therapeutic effect on mice infected with Streptococcus pneumoniae III, Staphylococcus aureus Smith, 4) acute toxicity by i.p. administration to mice (LD50) and 5) cytotoxicities to fibroblasts derived from Chinese-hamster lung (CHL), cow pulmonary artery endothelial cells (CPAE) and rat hepatic cells. The results obtained are summarized below. 1. Components F1 and 4'-acetylspiramycin F2 had significantly different biological activities from those of other components: F1 showed the lowest antibacterial potency of 492 micrograms (potency)/mg, F2 showed the highest antibacterial potency of 2,040 micrograms (potency)/mg and correspondingly the lowest LD50 value of 692 mg/kg (the highest toxicity). The therapeutic effect of F2 on infections in mice was found to be the second smallest and was superior only to that of F1. The LD50 value of F1 was 1,200 mg/kg and similar to that of ASPM. 2. Antibacterial potencies of F3, F4, F5 and F6 were 1,165, 1,266, 1,374 and 1,530 micrograms (potency)/mg, respectively; fraction with the higher antibacterial activities corresponded to the longer retention times, i.e., the greater hydrophobicities. The most hydrophobic component, F7, 3-propionyl-3",4"-diacetylspiramycin, however, showed a low antibacterial potency of 1,085 micrograms (potency)/mg, next to the lowest one, F1, a fact which was in contradiction to with the sequential relation between hydrophobicities and potencies from F3 to F6.(ABSTRACT TRUNCATED AT 250 WORDS)

  17. Systems biology of persistent infection: tuberculosis as a case study.

    Science.gov (United States)

    Young, Douglas; Stark, Jaroslav; Kirschner, Denise

    2008-07-01

    The human immune response does an excellent job of clearing most of the pathogens that we encounter throughout our lives. However, some pathogens persist for the lifetime of the host. Despite many years of research, scientists have yet to determine the basis of persistence of most pathogens, and have therefore struggled to develop reliable prevention and treatment strategies. Systems biology provides a new and integrative tool that will help to achieve these goals. In this article, we use Mycobacterium tuberculosis as an example of how systems-biology approaches have begun to make strides in uncovering important facets of the host-pathogen interaction.

  18. Integrated perspectives on geological and biological dynamics in ancient Lake Ohrid

    Science.gov (United States)

    Wagner, Bernd; Wilke, Thomas; Krastel, Sebastian; Zanchetta, Giovanni; Leng, Melanie; Wonik, Thomas; Francke, Alexander; Leicher, Niklas; Just, Janna; Lacey, Jack; Baumgarten, Henrike; Levkov, Zlatko; Reed, Jane; Cvetkoska, Aleksandra; Vogel, Hendrik; Sadori, Laura

    2016-04-01

    Lake Ohrid on the Balkan Peninsula is one of the very few lakes in the world that provides a continuous and high-resolution record of environmental change of >1.2 Ma. The outstanding number of endemic taxa (>300 endemic taxa) in Lake Ohrid in combination with its long existence makes Lake Ohrid a unique target to study the drivers of speciation and endemism. For this purpose, a 569 m long sediment sequence was recovered from the central part of the lake in spring 2013 within the scope of the International Continental Scientific Drilling Program (ICDP) and the Scientific Collaboration on Past Speciation Conditions in Lake Ohrid (SCOPSCO) project. In January 2016, the lowermost core sections of the 569 m long sediment sequence were opened. Ongoing work comprises core correlation to a composite sequence and various geological and biological analyses on the sediment material. Here, we present the results of analyses of the upper 248 m of this sequence, which covers the last ca. 640 ka according to an age model based on tephrostratigraphy as well as tuning of in situ physical and biogeochemical proxy data to orbital parameters and supported by paleomagnetic studies. The sedimentological, physical, and geochemical data from the sediment sequence indicate changes in primary productivity, water column stratification, and water depth of the lake, and in weathering and erosion processes in the catchment. These changes can be clearly correlated with orbitally driven environmental change, such as the intensity of glacial and interglacial periods as well as stadials and interstadials. These long-term changes are interspersed by short-term events, such as the deposition of tephra horizons. More than 30 tephra layers were found in the upper 248 m. The comparison of long-term and short-term environmental changes with paleontological and molecular clock analyses indicates that catastrophic extinction events in the endemic species community did not occur over the last 640 ka in Lake

  19. Dynamics of crowd disasters: An empirical study

    Science.gov (United States)

    Helbing, Dirk; Johansson, Anders; Al-Abideen, Habib Zein

    2007-04-01

    Many observations of the dynamics of pedestrian crowds, including various self-organization phenomena, have been successfully described by simple many-particle models. For ethical reasons, however, there is a serious lack of experimental data regarding crowd panic. Therefore, we have analyzed video recordings of the crowd disaster in Mina/Makkah during the Hajj in 1426H on 12 January 2006. They reveal two subsequent, sudden transitions from laminar to stop-and-go and “turbulent” flows, which question many previous simulation models. While the transition from laminar to stop-and-go flows supports a recent model of bottleneck flows [D. Helbing , Phys. Rev. Lett. 97, 168001 (2006)], the subsequent transition to turbulent flow is not yet well understood. It is responsible for sudden eruptions of pressure release comparable to earthquakes, which cause sudden displacements and the falling and trampling of people. The insights of this study into the reasons for critical crowd conditions are important for the organization of safer mass events. In particular, they allow one to understand where and when crowd accidents tend to occur. They have also led to organizational changes, which have ensured a safe Hajj in 1427H.

  20. Single Molecule Studies on Dynamics in Liquid Crystals

    Directory of Open Access Journals (Sweden)

    Daniela Täuber

    2013-09-01

    Full Text Available Single molecule (SM methods are able to resolve structure related dynamics of guest molecules in liquid crystals (LC. Highly diluted small dye molecules on the one hand explore structure formation and LC dynamics, on the other hand they report about a distortion caused by the guest molecules. The anisotropic structure of LC materials is used to retrieve specific conformation related properties of larger guest molecules like conjugated polymers. This in particular sheds light on organization mechanisms within biological cells, where large molecules are found in nematic LC surroundings. This review gives a short overview related to the application of highly sensitive SM detection schemes in LC.

  1. Dynamics of Diffusion Flames in von Karman Swirling Flows Studied

    Science.gov (United States)

    Nayagam, Vedha; Williams, Forman A.

    2002-01-01

    Von Karman swirling flow is generated by the viscous pumping action of a solid disk spinning in a quiescent fluid media. When this spinning disk is ignited in an oxidizing environment, a flat diffusion flame is established adjacent to the disk, embedded in the boundary layer (see the preceding illustration). For this geometry, the conservation equations reduce to a system of ordinary differential equations, enabling researchers to carry out detailed theoretical models to study the effects of varying strain on the dynamics of diffusion flames. Experimentally, the spinning disk burner provides an ideal configuration to precisely control the strain rates over a wide range. Our original motivation at the NASA Glenn Research Center to study these flames arose from a need to understand the flammability characteristics of solid fuels in microgravity where slow, subbuoyant flows can exist, producing very small strain rates. In a recent work (ref. 1), we showed that the flammability boundaries are wider and the minimum oxygen index (below which flames cannot be sustained) is lower for the von Karman flow configuration in comparison to a stagnation-point flow. Adding a small forced convection to the swirling flow pushes the flame into regions of higher strain and, thereby, decreases the range of flammable strain rates. Experiments using downward facing, polymethylmethacrylate (PMMA) disks spinning in air revealed that, close to the extinction boundaries, the flat diffusion flame breaks up into rotating spiral flames (refs. 2 and 3). Remarkably, the dynamics of these spiral flame edges exhibit a number of similarities to spirals observed in biological systems, such as the electric pulses in cardiac muscles and the aggregation of slime-mold amoeba. The tail of the spiral rotates rigidly while the tip executes a compound, meandering motion sometimes observed in Belousov-Zhabotinskii reactions.

  2. Systems Biology based studies on anti-inflammatory compounds

    NARCIS (Netherlands)

    Verhoeckx, Kitty Catharina Maria

    2005-01-01

    The introduction of the ‘omics’ techniques (transcriptomics, proteomics, and metabolomics) and systems biology, has caused fundamental changes in the drug discovery process and many other fields in the life science area. In this thesis we explored the possibilities to apply these holistic technologi

  3. Teacher's Study Guide on the Biology of Human Populations: Asia.

    Science.gov (United States)

    United Nations Educational, Scientific, and Cultural Organization, Paris (France).

    Factual and conceptual information dealing with the biology of human populations is offered in this guide for secondary science teachers. Instructional approaches are reviewed and suggestions are offered for use of the problem method approach, the discussion technique, and the project option. Information is organized into an introduction and five…

  4. Study on Biological Characters of Asparagus macowanii Baker.

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    Asparagus macowanfi Baker, is a climbing herbaceous foliage species in genus Asparagus of Liliaceae, This paper summarized its multiple uses, morphologi- cal characteristics, biological habit, reproduction methods, management after cultiva- tion, prevention and control of pests and disease, as well as harvest and grading, with the objective to provide references for the exploitation and utilization of As- paragus macowanii Baker.

  5. Mössbauer study of some biological iron complexes

    Indian Academy of Sciences (India)

    Sikander Ali; Alimuddin; V R Reddy

    2005-12-01

    Some biological complexes containing iron are investigated experimentally at room temperature using the Mössbauer resonance. The complexes show quadrupole doublet and Kramer's degeneracy is found to exist. The electric field gradient, difference in -electron densities and quadrupole coupling constant have been calculated in each case. These parameters are used to obtain information on the surroundings of the Mössbauer atom.

  6. Studies of dynamical processes affecting global climate

    Energy Technology Data Exchange (ETDEWEB)

    Keller, C.; Cooper, D.; Eichinger, W. [and others

    1998-12-31

    This is the final report of a three-year, Laboratory Directed Research and Development project at the Los Alamos National Laboratory (LANL). The main objective was, by a combined theoretical and observational approach, to develop improved models of dynamic processes in the oceans and atmosphere and to incorporate them into large climate codes, chiefly in four main areas: numerical physics, chemistry, water vapor, and ocean-atmosphere interactions. Main areas of investigation included studies of: cloud parameterizations for global climate codes, Lidar and the planetary boundary layer, chemistry, climate variability using coupled ocean-atmospheric models, and numerical physical methods. This project employed a unique approach that included participation of a number of University of California faculty, postdoctoral fellows and graduate students who collaborated with Los Alamos research staff on specific tasks, thus greatly enhancing the research output. Overall accomplishments during the sensing of the atmospheric planetary were: (1) first two- and three-dimensional remote sensing of the atmospheric planetary boundary layer using Lidars, (2) modeling of 20-year cycle in both pressure and sea surface temperatures in North Pacific, (3) modeling of low frequency internal variability, (4) addition of aerosols to stratosphere to simulate Pinatubo effect on ozone, (5) development of fast, comprehensive chemistry in the troposphere for urban pollution studies, (6) new prognostic cloud parameterization in global atmospheric code remedied problems with North Pacific atmospheric circulation and excessive equatorial precipitation, (7) development of a unique aerosol analysis technique, the aerosol time-of-flight mass spectrometer (ATOFMS), which allows real-time analysis of the size and chemical composition of individual aerosol particles, and (8) numerical physics applying Approximate Inertial Manifolds to ocean circulation. 14 refs., 6 figs.

  7. Biological and physical influences on soil 14CO2 seasonal dynamics in a temperate hardwood forest

    Directory of Open Access Journals (Sweden)

    C. L. Phillips

    2013-07-01

    Full Text Available While radiocarbon (14C abundance in standing stocks of soil carbon has been used to evaluate rates of soil carbon turnover on timescales of several years to centuries, soil-respired 14CO2 measurements are an important tool for identifying more immediate responses to disturbance and climate change. Soil 14CO2 data are often temporally sparse, however, and could be interpreted better with more context for typical seasonal ranges and trends. We report on a semi-high-frequency sampling campaign to distinguish physical and biological drivers of soil 14CO2 at a temperate forest site in Northern Wisconsin, USA. We sampled 14CO2 profiles every three weeks during snow-free months through 2012, in three intact plots and one trenched plot that excluded roots. Respired 14CO2 declined through the summer in intact plots, shifting from an older C composition that contained more bomb 14C, to a younger composition more closely resembling present 14C levels in the atmosphere. In the trenched plot respired 14C was variable but remained comparatively higher than in intact plots, reflecting older bomb-enriched 14C sources. Although respired 14CO2 from intact plots correlated with soil moisture, related analyses did not support a clear cause-and-effect relationship with moisture. The initial decrease in 14CO2 from spring to midsummer could be explained by increases in 14C-deplete root respiration; however, 14CO2 continued to decline in late summer after root activity decreased. We also investigated whether soil moisture impacted vertical partitioning of CO2 production, but found this had little effect on respired 14CO2 because CO2 contained modern bomb-C at depth, even in the trenched plot. This surprising result contrasted with decades to centuries-old pre-bomb CO2 produced in lab incubations of the same soils. Our results suggest that root-derived C and other recent C sources had dominant impacts on 14CO2 in situ, even at depth. We propose that 14CO2 may have

  8. The silica dynamics of deforestation: new evidence for a biologically controlled Si cycle

    Science.gov (United States)

    Struyf, Eric; Smis, Adriaan; Clymans, Wim; Govers, Gerard; van Wesemael, Bas; Frot, Elisabeth; Batelaan, Okke; Goos, Peter; van Damme, Stefan; Meire, Patrick

    2010-05-01

    timeframes associated with all these stages are currently unknown. Our results emphasize the potential interference between changes in vegetation, either natural or though human intervention, and the silica-carbon pump in the ocean. Reduced Si fluxes as a result of deforestation could eventually lead to reduced carbon burial in the ocean. We can safely say that research on the silica cycle is currently on the verge of a new research era. The biological Si buffer is currently not incorporated in biogeochemical models. There are still major gaps in our fundamental understanding, and the integration of processes at different spatial and temporal scales is lacking. Addressing these knowledge gaps is essential and urgent. Their incorporation in future biogeochemical models might alter fundamental knowledge of the global silica cycle and all associated biogeochemical cycles. Our results show that land use is important to consider in models of continental silica fluxes, in addition to the traditionally studied effects of precipitation and bedrock lithology.

  9. Respectful Modeling: Addressing Uncertainty in Dynamic System Models for Molecular Biology.

    Science.gov (United States)

    Tsigkinopoulou, Areti; Baker, Syed Murtuza; Breitling, Rainer

    2017-06-01

    Although there is still some skepticism in the biological community regarding the value and significance of quantitative computational modeling, important steps are continually being taken to enhance its accessibility and predictive power. We view these developments as essential components of an emerging 'respectful modeling' framework which has two key aims: (i) respecting the models themselves and facilitating the reproduction and update of modeling results by other scientists, and (ii) respecting the predictions of the models and rigorously quantifying the confidence associated with the modeling results. This respectful attitude will guide the design of higher-quality models and facilitate the use of models in modern applications such as engineering and manipulating microbial metabolism by synthetic biology. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Nonlinear Effects of Nanoparticles: Biological Variability From Hormetic Doses, Small Particle Sizes, and Dynamic Adaptive Interactions

    OpenAIRE

    Bell, Iris R.; Ives, John A.; Wayne B. Jonas

    2013-01-01

    Researchers are increasingly focused on the nanoscale level of organization where biological processes take place in living systems. Nanoparticles (NPs, e.g., 1–100 nm diameter) are small forms of natural or manufactured source material whose properties differ markedly from those of the respective bulk forms of the “same” material. Certain NPs have diagnostic and therapeutic uses; some NPs exhibit low-dose toxicity; other NPs show ability to stimulate low-dose adaptive responses (hormesis). B...

  11. Study of the benzocaine transfer from aqueous solution to the interior of a biological membrane.

    Science.gov (United States)

    Porasso, Rodolfo D; Bennett, W F Drew; Oliveira-Costa, S D; López Cascales, J J

    2009-07-23

    The precise molecular mechanism of general anesthetics remains unknown. It is therefore important to understand where molecules with anesthetic properties localize within biological membranes. We have determined the free energy profile of a benzocaine molecule (BZC) across a biological membrane using molecular dynamics simulation. We use an asymmetric phospholipid bilayer with DPPS in one leaflet of a DPPC bilayer (Lopez Cascales et al. J. Phys. Chem. B 2006, 110, 2358-2363) to model a biological bilayer. From the free energy profile, we predict the zone of actuation of a benzocaine is located in the hydrocarbon region or at the end of the lipid head, depending of the presence of charged lipids (DPPS) in the leaflet. We observe a moderate increase in the disorder of the membrane and in particular an increase in the disorder of DPPS. Static and dynamic physicochemical properties of the benzocaine, such as its dipole orientation, translational diffusion coefficient, and rotational relaxation time were measured.

  12. Inference problems in structural biology

    DEFF Research Database (Denmark)

    Olsson, Simon

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

  13. 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...

  14. [Clinical, biochemical and anthropometric studies and determination of biological age in relation to body mass in a longitudinal study].

    Science.gov (United States)

    Hunecke, I; Reuter, W; Sauer, I; Ries, W

    1989-01-15

    On 46 adipose persons (25 males and 21 females) and 53 test persons with normal weight (35 males and 18 females) at the age of 25-40 years since 1976 clinical, biochemical and anthropometric investigations as well as the determination of the biological age have annually been performed. Several of the parameters established (e.g. cholesterol, triglycerides, fasting blood sugar, blood pressure among others) in the course of 9 years within the well-known normal regions draw towards the adequate valid limit value to the pathological entity. The results of the study distinctly show the central role of obesity for the development of risk factors. Despite the partly only with a certain tendency recognizable behaviour of single parameters after 9 years from our point of view the longitudinal method represents itself as a very well suitable method for establishing dynamic processes and risk factors of age.

  15. Energy efficient walking with central pattern generators: from passive dynamic walking to biologically inspired control.

    Science.gov (United States)

    Verdaasdonk, B W; Koopman, H F J M; van der Helm, F C T

    2009-07-01

    Like human walking, passive dynamic walking-i.e. walking down a slope with no actuation except gravity-is energy efficient by exploiting the natural dynamics. In the animal world, neural oscillators termed central pattern generators (CPGs) provide the basic rhythm for muscular activity in locomotion. We present a CPG model, which automatically tunes into the resonance frequency of the passive dynamics of a bipedal walker, i.e. the CPG model exhibits resonance tuning behavior. Each leg is coupled to its own CPG, controlling the hip moment of force. Resonance tuning above the endogenous frequency of the CPG-i.e. the CPG's eigenfrequency-is achieved by feedback of both limb angles to their corresponding CPG, while integration of the limb angles provides resonance tuning at and below the endogenous frequency of the CPG. Feedback of the angular velocity of both limbs to their corresponding CPG compensates for the time delay in the loop coupling each limb to its CPG. The resonance tuning behavior of the CPG model allows the gait velocity to be controlled by a single parameter, while retaining the energy efficiency of passive dynamic walking.

  16. Final report for NIF chamber dynamics studies

    Energy Technology Data Exchange (ETDEWEB)

    Burnham, A; Peterson, P F; Scott, J M

    1998-09-01

    The National Ignition Facility (NIF), a 1.8 MJ, 192 laser beam facility, will have anticipated fusion yields of up to 20 MJ from D-T pellets encased in a gold hohlraum target. The energy emitted from the target in the form of x rays, neutrons, target debris kinetic energy, and target shrapnel will be contained in a 5 m. radius spherical target chamber. various diagnostics will be stationed around the target at varying distances from the target. During each shot, the target will emit x rays that will vaporize nearby target facing surfaces including those of the diagnostics, the target positioner, and other chamber structures. This ablated vapor will be transported throughout the chamber, and will eventually condense and deposit on surfaces in the chamber, including the final optics debris shields. The research at the University of California at Berkeley relates primarily to the NIF chamber dynamics. The key design issues are the ablation of the chamber structures, transport of the vapor through the chamber and the condensation or deposition processes of those vaporized materials. An understanding of these processes is essential in developing a concept for protecting the fina optics debris shields from an excessive coating (> 10 A) of target debris and ablated material, thereby prolonging their lifetime between change-outs. At Berkeley, we have studied the physical issues of the ablation process and the effects of varying materials, the condensation process of the vaporized material, and design schemes that can lower the threat posed to the debris shields by these processes. The work or portions of the work completed this year have been published in several papers and a dissertation [l-5].

  17. Rotational coherence spectroscopy at FLASH. Toward dynamic studies in nanosuperfluids

    Energy Technology Data Exchange (ETDEWEB)

    Kickermann, Andreas

    2013-07-15

    The field of molecular physics, which is focusing on molecular motion in the transition states of physical, chemical, and biological changes, is a wide-spread research area. It strives to reveal the structural and functional properties of molecules, the chemical bonds between atoms and the time evolution. Many processes occurring in nature upon electronic excitation proceed on the ultrafast femtosecond timescale and can be triggered by modern ultrashort femtosecond-laser sources under laboratory conditions. In the present thesis pump-probe studies were performed to follow molecular motion using ultrashort light pulses in the nanometer wavelength range provided by an XUV freeelectron laser (FEL). In detail, alignment of molecular species in space under field-free conditions was investigated. In the specific case of rotational wave packets in molecules the rotational dynamics shows characteristic temporal features, which contain a wealth of information on molecular structure and give insight into molecular coupling mechanisms, i.e. rotational constants and transition frequencies. Within this thesis, Rotational Coherence Spectroscopy (RCS) reveals wave-packet motion observed by subsequent Coulomb explosion of Raman excited carbon monoxide, which results in a time-dependent asymmetry of spatial fragmentation patterns. With the method presented here, the time resolution to elucidate the fast dynamics of strong couplings can be pushed toward a single rotational period even for the fastest rotors. This is due to large pump-probe delays with small subpicosecond step size. This kind of spectroscopy can also be expanded to molecular species, which are not accessible by other powerful spectroscopic methods, such as Fourier-transform microwave spectroscopy (FTMW). Furthermore, it allows to measure weak molecular couplings on a long timescale (large pump-probe delays), e.g. couplings of molecules in a solution or molecules dissolved in quantum fluids. This is valuable to

  18. Hazardous wastes in aquatic environments: Biological uptake and metabolism studies

    Energy Technology Data Exchange (ETDEWEB)

    Barber, J.; Apblett, A.; Ensley, H. [and others

    1996-05-02

    The projects discussed in this article include the following: the uptake, accumulation, metabolism, toxicity and physiological effects of various environmentally-important contaminants, inorganic and organic, in several wetland species that are interrelated through food webs; and investigation of the potential for developing and linking chemical and biological methods of remediation so as to encapsulate bioaccummulated ions in stable wasteforms such as ceramics and/or zeolites. 24 refs.

  19. Presynaptic Neurotoxins: Biochemistry, Molecular Biology, Immunology and Other Exploratory Studies

    Science.gov (United States)

    1994-04-01

    residues are conserved in PLA2s that exist as aggregates (e.g. crotoxin, Mojave toxin, vipoxin from Vipera ammodytes , the complex from Pseudocerastes...success of others in using the site-directed polyclonal antibody approach to localize the toxic site in the ammodytoxins from the venom of Vipera ... ammodytes (Curin-Serbec et al, 1991). Molecular Biology. Descriptions of the organization of genomic presynaptic neurotoxin genes is presently in its

  20. Computational Fluid Dynamic Simulations of Maternal Circulation: Wall Shear Stress in the Human Placenta and Its Biological Implications

    Science.gov (United States)

    Lecarpentier, E.; Bhatt, M.; Bertin, G. I.; Deloison, B.; Salomon, L. J.; Deloron, P.; Fournier, T.; Barakat, A. I.; Tsatsaris, V.

    2016-01-01

    Introduction In the human placenta the maternal blood circulates in the intervillous space (IVS). The syncytiotrophoblast (STB) is in direct contact with maternal blood. The wall shear stress (WSS) exerted by the maternal blood flow on the STB has not been evaluated. Our objective was to determine the physiological WSS exerted on the surface of the STB during the third trimester of pregnancy. Material and Methods To gain insight into the shear stress levels that the STB is expected to experience in vivo, we have formulated three different computational models of varying levels of complexity that reflect different physical representations of the IVS. Computations of the flow fields in all models were performed using the CFD module of the finite element code COMSOL Multiphysics 4.4. The mean velocity of maternal blood in the IVS during the third trimester was measured in vivo with dynamic MRI (0.94±0.14 mm.s-1). To investigate if the in silico results are consistent with physiological observations, we studied the cytoadhesion of human parasitized (Plasmodium falciparum) erythrocytes to primary human STB cultures, in flow conditions with different WSS values. Results The WSS applied to the STB is highly heterogeneous in the IVS. The estimated average values are relatively low (0.5±0.2 to 2.3±1.1 dyn.cm-2). The increase of WSS from 0.15 to 5 dyn.cm-2 was associated with a significant decrease of infected erythrocyte cytoadhesion. No cytoadhesion of infected erythrocytes was observed above 5 dyn.cm-2 applied for one hour. Conclusion Our study provides for the first time a WSS estimation in the maternal placental circulation. In spite of high maternal blood flow rates, the average WSS applied at the surface of the chorionic villi is low (<5 dyn.cm-2). These results provide the basis for future physiologically-relevant in vitro studies of the biological effects of WSS on the STB. PMID:26815115

  1. Vortex Dynamics Studies in Type II Superconductors

    Science.gov (United States)

    Xu, Zhigang

    1993-03-01

    Vibrating reed, ac susceptibility and resistance measurements have been used to study the dynamics of vortices in type II superconductors. In Nb measurements, in spite of the low T _{c}'s and long coherence lengths compared to the high T_{c} superconductors, we find an extended region of temperature and field over which reversible flux line motion occurs when the Nb reed is oriented with its long dimension perpendicular to the applied field. We observe a strong, frequency-independent depression of the "irreversibility temperature" T _{Q}(H) below the resistively determined critical temperature T_{R}. The results of the ac susceptibility measurements also support these results. We concluded that observation of an extended region of magnetic reversibility is not restricted to high T_{c} or extremely anisotropic materials, and depends upon the geometry of samples with respect to the applied field direction. In NbSe_2 measurements, vibrating reed measurements were performed with the hexagonal c-axis approximately parallel or perpendicular to an applied magnetic field. Field-cooling data revealed an unusual peak in the frequency shift of the reed, accompanied by two peaks in reed dissipation. The upper peak occurs near the temperature where R~ 0, and the lower peak is very sample and amplitude dependent and hysteretic. The ac susceptibility results also show that corresponding features. The interplay of superconductivity and density waves were investigated by comparing data for NbSe _2 with the results for NbS_2 , which has a comparable superconducting T _{c } and crystal structure. In NbS_2 measurements, we did not see such a peak in the frequency shift nor the double peak feature in the dissipation in either vibrating reed measurements or ac susceptibility measurements. We have also studied the (Ba,K)BiO_3 system. It is cubic at its superconducting composition, but exhibits a moderately high T_{c }=30 K that is intermediate between conventional and high T_{rm c

  2. New Synthetic Biology Tools to Track Microbial Dynamics in the Earth System

    Science.gov (United States)

    Silberg, J. J.; Masiello, C. A.; Cheng, H. Y.

    2015-12-01

    Microbes drive processes in the Earth system far exceeding their physical scale, mediating significant fluxes in the global C and N cycles. The tools of synthetic biology have the potential to significantly improve our understanding of microbes' role in the Earth system; however, these tools have not yet seen wide laboratory use because synthetically "programmed" microbes typically report by fluorescing (expressing green fluorescent protein), making them challenging to deploy into many Earth materials, the majority of which are not transparent and are heterogeneous (soils, sediments, and biomass). We are developing a new suite of biosensors that report instead by releasing gases. We will provide an overview of the use of gas-reporting biosensors in biogeochemistry and will report the development of the systematics of these sensors. These sensors will make tractable the testing of gene expression hypotheses derived from metagenomics data. Examples of processes that could be tracked non-invasively with gas sensors include coordination of biofilm formation, nitrification, rhizobial infection of plant roots, and at least some forms of methanogenesis, all of which are managed by an easily-engineered cell-cell communication system. Another relatively simple process to track with gas sensors is horizontal gene transfer. Successful development of gas biosensors for Earth science applications will require addressing issues including: engineering the intensity and selectivity of microbial gas production to maximize the signal to noise using the tools of synthetic biology; normalizing the gas reporter signal to cell population size, since the number of cells and gene expression both contribute to gas production; managing gas diffusion effects on signal shape; and developing multiple gases that can be used in parallel to report on multiple biological processes in parallel. We will report on progress addressing each of these issues.

  3. Beam Dynamics Studies for the SPARC Project

    Energy Technology Data Exchange (ETDEWEB)

    Ferrario, M.; Biagini, Maria E.; Boscolo, M.; Fusco, V.; Guiducci, S.; Migliorati, M.; Serafini, L.; Vaccarezza, C.; Bartolini, R.; Giannessi, L.; Quattromini, M.; Ronsivalle, C.; Limborg, C.G.; /Unlisted /Unlisted /ENEA, Frascati /SLAC

    2008-03-17

    The aim of the SPARC project, is to promote an R&D activity oriented to the development of a high brightness photoinjector to drive SASE-FEL experiments. We discuss in this paper the status of the beam dynamics simulation activities.

  4. Future Directions of Nonlinear Dynamics in PhysicaL and Biological Systems,

    Science.gov (United States)

    1992-01-01

    CHARGE DENSITY WAVES, POLARONIC SPIN DENSITY WAVES AND HIGH Tc SUPERCONDUCTIVITY Serge Aubry* CNLS, Los Alamos National Laboratory Los Alamos, NM 87545...300 Jim). MODEL AND BASIC PROPERTIES The laser dynamics is described by the Lang and Kobayashi equations4 for the Future Directions of Nonlinear...LT-4, 1655 (1986). 4. R. Lang , and K. Kobayashi, IEEE J. Quantum Electron. QE-16, 347 (1980). 5. J. Mork, M. Semkow, and B. Tromborg, Electron. Lett

  5. DNAtraffic—a new database for systems biology of DNA dynamics during the cell life

    OpenAIRE

    Kuchta, Krzysztof; Barszcz, Daniela; Grzesiuk, Elzbieta; Pomorski, Pawel; Krwawicz, Joanna

    2011-01-01

    DNAtraffic (http://dnatraffic.ibb.waw.pl/) is dedicated to be a unique comprehensive and richly annotated database of genome dynamics during the cell life. It contains extensive data on the nomenclature, ontology, structure and function of proteins related to the DNA integrity mechanisms such as chromatin remodeling, histone modifications, DNA repair and damage response from eight organisms: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae,...

  6. Dynamics and thermodynamics in hierarchically organized systems applications in physics, biology and economics

    CERN Document Server

    Auger, P

    2013-01-01

    One of the most fundamental and efficient ways of conceptualizing complex systems is to organize them hierarchically. A hierarchically organized system is represented by a network of interconnected subsystems, each of which has its own network of subsystems, and so on, until some elementary subsystems are reached that are not further decomposed. This original and important book proposes a general mathematical theory of a hierarchical system and shows how it can be applied to very different topics such as physics (Hamiltonian systems), biology (coupling the molecular and the cellular levels), e

  7. Granger causality vs. dynamic Bayesian network inference: a comparative study

    Directory of Open Access Journals (Sweden)

    Feng Jianfeng

    2009-04-01

    Full Text Available Abstract Background In computational biology, one often faces the problem of deriving the causal relationship among different elements such as genes, proteins, metabolites, neurons and so on, based upon multi-dimensional temporal data. Currently, there are two common approaches used to explore the network structure among elements. One is the Granger causality approach, and the other is the dynamic Bayesian network inference approach. Both have at least a few thousand publications reported in the literature. A key issue is to choose which approach is used to tackle the data, in particular when they give rise to contradictory results. Results In this paper, we provide an answer by focusing on a systematic and computationally intensive comparison between the two approaches on both synthesized and experimental data. For synthesized data, a critical point of the data length is found: the dynamic Bayesian network outperforms the Granger causality approach when the data length is short, and vice versa. We then test our results in experimental data of short length which is a common scenario in current biological experiments: it is again confirmed that the dynamic Bayesian network works better. Conclusion When the data size is short, the dynamic Bayesian network inference performs better than the Granger causality approach; otherwise the Granger causality approach is better.

  8. Molecular Dynamics study on the Micellization of Rhamnolipids.

    Science.gov (United States)

    Munusamy, Elango; Schwartz, Steven D.

    2015-03-01

    Oil spills have become one of the most serious environmental and ecological problems owing to the growth of oil exploration, production and transportation. Millions of gallons of crude oil and refined products are spilled into marine waters worldwide each year. Large volumes of surfactants are applied to the ocean as a remediation strategy. Environmental and toxicity issues arise when such a voluminous amounts of chemical surfactants are applied. One prospective solution to this problem is to use greener surfactants that possess excellent biodegradation and toxicity characteristics relative to existing classes of commonly used surfactants. In this context, we are interested in designing and developing greener surfactants that are patterned after naturally occurring glycolipids. In the present work, we concentrate on one of the more commonly studied glycolipid, rhamnolipid (Rha1C10C10) . Despite the available experimental data, the molecular structure, shape and geometry of micelles formed by rhamnolipid is unknown. Molecular Dynamics (MD) simulations were performed to understand the aggregation behavior of rhamnolipids in aqueous solution and at air-water interface. All calculations were performed in NPT ensembles at 300 K using NAMD 2.8, a parallel code designed for high-performance simulation of large biological macromolecule using the CHARMM force field. The results obtained from MD simulations on the aggregation of rhamnolipids in water and at air-water interface will be presented.

  9. Anticipatory dynamics of biological systems: from molecular quantum states to evolution

    Science.gov (United States)

    Igamberdiev, Abir U.

    2015-08-01

    Living systems possess anticipatory behaviour that is based on the flexibility of internal models generated by the system's embedded description. The idea was suggested by Aristotle and is explicitly introduced to theoretical biology by Rosen. The possibility of holding the embedded internal model is grounded in the principle of stable non-equilibrium (Bauer). From the quantum mechanical view, this principle aims to minimize energy dissipation in expense of long relaxation times. The ideas of stable non-equilibrium were developed by Liberman who viewed living systems as subdivided into the quantum regulator and the molecular computer supporting coherence of the regulator's internal quantum state. The computational power of the cell molecular computer is based on the possibility of molecular rearrangements according to molecular addresses. In evolution, the anticipatory strategies are realized both as a precession of phylogenesis by ontogenesis (Berg) and as the anticipatory search of genetic fixation of adaptive changes that incorporates them into the internal model of genetic system. We discuss how the fundamental ideas of anticipation can be introduced into the basic foundations of theoretical biology.

  10. The relative contributions of biological and abiotic processes to carbon dynamics in subarctic sea ice

    DEFF Research Database (Denmark)

    Søgaard, Dorte Haubjerg; Thomas, David; Rysgaard, Søren

    2013-01-01

    Knowledge on the relative effects of biological activity and precipitation/dissolution of calcium carbonate (CaCO3) in influencing the air-ice CO2 exchange in sea-ice-covered season is currently lacking. Furthermore, the spatial and temporal occurrence of CaCO3 and other biogeochemical parameters...... of melting CaCO3-free sea ice. There was a considerable spatial and temporal variability of CaCO3 and the other biogeochemical parameters measured (dissolved organic and inorganic nutrients).......Knowledge on the relative effects of biological activity and precipitation/dissolution of calcium carbonate (CaCO3) in influencing the air-ice CO2 exchange in sea-ice-covered season is currently lacking. Furthermore, the spatial and temporal occurrence of CaCO3 and other biogeochemical parameters...... in sea ice are still not well described. Here we investigated autotrophic and heterotrophic activity as well as the precipitation/dissolution of CaCO3 in subarctic sea ice in South West Greenland. Integrated over the entire ice season (71 days), the sea ice was net autotrophic with a net carbon fixation...

  11. Utility Rate Equations of Group Population Dynamics in Biological and Social Systems

    CERN Document Server

    Yukalov, V I; Sornette, D

    2014-01-01

    We present a novel system of equations to describe the evolution of self-organized structured societies (biological or human) composed of several trait groups. The suggested approach is based on the combination of ideas employed in the theory of biological populations, system theory, and utility theory. The evolution equations are defined as utility rate equations, whose parameters are characterized by the utility of each group with respect to the society as a whole and by the mutual utilities of groups with respect to each other. We analyze in detail the cases of two groups (cooperators and defectors) and of three groups (cooperators, defectors, and regulators) and find that, in a self-organized society, neither defectors nor regulators can overpass the maximal fractions of about 10% each. This is in agreement with the data for bee and ant colonies. The classification of societies by their distance from equilibrium is proposed. We apply the formalism to rank the countries according to the introduced metric q...

  12. STRUCTURE AND DYNAMICS OF ALKALI BORATE GLASSES - A MOLECULAR-DYNAMICS STUDY

    NARCIS (Netherlands)

    VERHOEF, AH; DENHARTOG, HW

    1995-01-01

    Structural and dynamical properties of lithium, cesium and mixed alkali (i.e., lithium and cesium) borate glasses have been studied by the molecular dynamics method. The calculations yield glass structures consisting of planar BO3 triangles and BO4 tetrahedrons with no sixfold ring structures at all

  13. Incubation Station for the Bacterial Growth Study in Biological Samples

    Directory of Open Access Journals (Sweden)

    Carlos Rafael Duharte Rodríguez

    2015-12-01

    Full Text Available This work shows the designing and characterization of a prototype of laboratory incubator as support of Microbiology research, in particular for the research of the bacterial growth in biological samples through optic methods (Turbidimetry and electrometric measurements of bioimpedance. It shows the results of simulation and experimentation of the design proposed for the canals of measurement of the variables: temperature and humidity, with a high linearity from the adequate selection of the corresponding sensors and the analogue components of every canal, controlled with help of a microcontroller AT89C51 (ATMEL with adequate benefi ts for this type of application.

  14. Computational studies of gene regulatory networks: in numero molecular biology.

    Science.gov (United States)

    Hasty, J; McMillen, D; Isaacs, F; Collins, J J

    2001-04-01

    Remarkable progress in genomic research is leading to a complete map of the building blocks of biology. Knowledge of this map is, in turn, setting the stage for a fundamental description of cellular function at the DNA level. Such a description will entail an understanding of gene regulation, in which proteins often regulate their own production or that of other proteins in a complex web of interactions. The implications of the underlying logic of genetic networks are difficult to deduce through experimental techniques alone, and successful approaches will probably involve the union of new experiments and computational modelling techniques.

  15. Mesoscopic biology

    Indian Academy of Sciences (India)

    G V Shivashankar

    2002-02-01

    In this paper we present a qualitative outlook of mesoscopic biology where the typical length scale is of the order of nanometers and the energy scales comparable to thermal energy. Novel biomolecular machines, governed by coded information at the level of DNA and proteins, operate at these length scales in biological systems. In recent years advances in technology have led to the study of some of the design principles of these machines; in particular at the level of an individual molecule. For example, the forces that operate in molecular interactions, the stochasticity involved in these interactions and their spatio-temporal dynamics are beginning to be explored. Understanding such design principles is opening new possibilities in mesoscopic physics with potential applications.

  16. Dissolved Oxygen Dynamics in Coastal Pacific Northwest Rivers: Biological Controls and Management Options

    Science.gov (United States)

    Sobota, D. J.; Foster, E.; Michie, R.; Waltz, D.

    2014-12-01

    In Oregon's Central Coast Range (OCR), dissolved O2 concentrations in at least 10% of stream length frequently dip below state standards set to ensure survival and reproduction of native salmonids. We examined O2 dynamics on 12 OCR rivers during times of the year when standards had been violated. Continuous dissolved O2 data were collected 15 minutes apart over a 24-hour period during spring (May - June) or fall (September - November) 2008 on each river. We modeled O2 dynamics for each river with parameters describing O2 exchange with the atmosphere, production of O2 from gross primary production (GPP), and consumption of O2 by ecosystem respiration (ER) fit to observed data. Average nighttime atmospheric O2 exchange and ER were estimated by regressing interval changes in dissolved O2 concentrations between measurements with corresponding O2 saturation deficits. GPP for each daytime sampling interval was calculated as the difference between O2 saturation deficit and the sum of temperature-corrected reaeration and ecosystem respiration. All regression models developed for estimating night-time reaeration and ER were highly significant (pbiological processes) ranged from -11.64 to 3.75 mg O2 L-1 d-1 across all rivers and seasons. Increased aquatic productivity resulting from adjacent and upstream human activities likely altered dissolved O2 dynamics in these rivers. Through scenario analysis, we found that at one river (Alsea), GPP and ER would need to be reduced by 85 and 73%, respectively, to meet the state standard (95% saturation). Our modeling approach can be connected with management actions across a variety of spatial and temporal scales, ranging from local, riparian-scale manipulations of shading and organic matter input to watershed and regional nutrient and temperature management.

  17. Dynamic impact indentation of hydrated biological tissues and tissue surrogate gels

    Science.gov (United States)

    Ilke Kalcioglu, Z.; Qu, Meng; Strawhecker, Kenneth E.; Shazly, Tarek; Edelman, Elazer; VanLandingham, Mark R.; Smith, James F.; Van Vliet, Krystyn J.

    2011-03-01

    For both materials engineering research and applied biomedicine, a growing need exists to quantify mechanical behaviour of tissues under defined hydration and loading conditions. In particular, characterisation under dynamic contact-loading conditions can enable quantitative predictions of deformation due to high rate 'impact' events typical of industrial accidents and ballistic insults. The impact indentation responses were examined of both hydrated tissues and candidate tissue surrogate materials. The goals of this work were to determine the mechanical response of fully hydrated soft tissues under defined dynamic loading conditions, and to identify design principles by which synthetic, air-stable polymers could mimic those responses. Soft tissues from two organs (liver and heart), a commercially available tissue surrogate gel (Perma-Gel™) and three styrenic block copolymer gels were investigated. Impact indentation enabled quantification of resistance to penetration and energy dissipative constants under the rates and energy densities of interest for tissue surrogate applications. These analyses indicated that the energy dissipation capacity under dynamic impact increased with increasing diblock concentration in the styrenic gels. Under the impact rates employed (2 mm/s to 20 mm/s, corresponding to approximate strain energy densities from 0.4 kJ/m3 to 20 kJ/m3), the energy dissipation capacities of fully hydrated soft tissues were ultimately well matched by a 50/50 triblock/diblock composition that is stable in ambient environments. More generally, the methodologies detailed here facilitate further optimisation of impact energy dissipation capacity of polymer-based tissue surrogate materials, either in air or in fluids.

  18. The biological traits of the large red scorpionfish, Scorpaena scrofa: Temporal and ontogenetic dynamics

    Science.gov (United States)

    Matić-Skoko, Sanja; Stagličić, Nika; Kraljević, Miro; Pallaoro, Armin; Dulčić, Jakov

    2015-01-01

    Large red scorpionfish, Scorpaena scrofa, is a prevalent, important and highly valued commercial species throughout the rocky coastal areas of the Mediterranean Sea. Despite this, there is a surprising scarcity of biological and ecological information for this species. As artisanal fisheries have a very long tradition in the whole Mediterranean, a considerable impact of continuous fishing pressure is expected on this valuable rockfish. To elucidate some biological parameters that indicate the status of S. scrofa in the Adriatic Sea and to show which consequences high fishery effort may have on its age, growth and reproduction, sampling was carried out in the middle Adriatic using trammel nets. Temporal trends in body size/weight of S. scrofa were also assessed using long-term data including specimens caught from 1960 to 2010. Temporal trends of S. scrofa in the middle Adriatic indicated significant decreases of 19% in length and 43% in total weight over time. In contrast, official landings for the last five years showed an increase of 13%. However, this increasing trend most likely reflects the continuous change in national policies for reporting the catches. Both catch data and landings statistics showed peak in catch per unit effort during summer which coincides with spawning period of S. scrofa. Length at first sexual maturity was observed at 29.0 cm for females and 24.9 cm for males. All specimens larger than 32 cm were mature. Age analysis revealed 15 age classes with a 25 year old female as the oldest specimen. However, age classes 3+ and 4+ were predominant in the total catch. The growth rate is relatively high during the first four years of life and afterwards it considerably slows down, with females growing at slightly slower rate and attaining slightly larger sizes than males. Given the identified biological implications that confirm our assumptions of inherent vulnerabilities and negative effects arising from continued artisanal fisheries practice

  19. Excess water dynamics in hydrotalcite: QENS study

    Indian Academy of Sciences (India)

    S Mitra; A Pramanik; D Chakrabarty; R Mukhopadhyay

    2004-08-01

    Results of the quasi-elastic neutron scattering (QENS) measurements on the dynamics of excess water in hydrotalcite sample with varied content of excess water are reported. Translational motion of excess water can be best described by random translational jump diffusion model. The observed increase in translational diffusivity with increase in the amount of excess water is attributed to the change in binding of the water molecules to the host layer.

  20. Molecular Biological and Biochemical Studies Reveal New Pathways Important for Cotton Fiber Development

    Institute of Scientific and Technical Information of China (English)

    Yu Xu; Hong-Bin Li; Yu-Xian Zhu

    2007-01-01

    As one of the longest single-celled seed trichomes, fibers provide an excellent model for studying fundamental biological processes such as cell differentiation, cell expansion, and cell wall biosynthesis. In this review, we summarize recent progress in cotton functional genomic studies that characterize the dynamic changes in the transcriptomes of fiber cells. Extensive expression profilings of cotton fiber transcriptomes have provided comprehensive information, as quite a number of transcription factors and enzyme-coding genes have been shown to express preferentially during the fiber elongation period. Biosynthesis of the plant hormone ethylene is found significantly upregulated during the fiber growth period as revealed by both microarray analysis and by biochemical and physiological studies. It is suggested that genetic engineering of the ethylene pathway may improve the quality and the productivity of cotton lint. Many metabolic pathways, such as biosynthesis of celiulose and matrix polysaccharides are preferentially expressed in actively growing fiber cells. Five gene families, including proline-rich proteins (PRP), arabinogalactan proteins (AGP), expansins, tubulins and lipid transfer proteins (LTP) are activated during early fiber development,indicating that they may also be needed for cell elongation. In conclusion, we identify a few areas of future research for cotton functional genomic studies.

  1. Multiscale Physical and Biological Dynamics in the Philippines Archipelago: Predictions and Processes

    Science.gov (United States)

    2011-01-01

    Sicily  Strait   (Lermusiaux,  1999;  Lermusiaux  and  Robinson,  2001...of  deep  convection  in  a  semi-­‐closed   tropical   marginal  basin:  Sulu  Sea.  Deep-­‐Sea  Res.,  54,  4–13...variability,   circulation  patterns  and  dynamics  in  the  Strait  of   Sicily .  Deep  Sea  Research,  (48),

  2. Application of biological design criteria and computational fluid dynamics to investigate fish survival in Kaplan turbines

    Energy Technology Data Exchange (ETDEWEB)

    Garrison, Laura A. [Voith Siemens Hydro Power Generation, Inc., York, PA (United States); Fisher, Jr., Richard K. [Voith Siemens Hydro Power Generation, Inc., York, PA (United States); Sale, Michael J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Cada, Glenn [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2002-07-01

    One of the contributing factors to fish injury in a turbine environment is shear stress. This paper presents the use of computational fluid dynamics (CFD) to display and quantify areas of elevated shear stress in the Wanapum Kaplan turbine operating at four different flow conditions over its operating range. CFD observations will be compared to field test observations at the same four flow conditions. Methods developed here could be used to facilitate the design of turbines and related water passages with lower risks of fish injury.

  3. A Study of the Probe Effect on the Apparent Image of Biological Atomic Force Microscopy

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The probe effect on the apparent image of biological atomic force microscopy was explored in this study, and the potential of AFM in conformational study of gene related biological processes was illustrated by the specific nanostructural information of a new antitumor drug binding to DNA.

  4. A systems biology study to tailored treatment in chronic heart failure

    NARCIS (Netherlands)

    Ouwerkerk, W.

    2017-01-01

    This thesis was part of the The BIOlogy STudy to TAilored Treatment in Chronic Heart Failure (BIOSTAT-CHF) project. BIOSTAT-CHF was a European, multicenter, multinational, prospective, observational study that was especially designed to find biological mechanisms involved with response to ESC

  5. Tribological Studies of Dynamic Thermal Seal Materials

    Science.gov (United States)

    DeMange, Jeffrey J.; Taylor, Shawn C.

    2016-01-01

    Thermal seals are required on high-speed vehicles in many dynamic applications such as variable inlets in propulsion systems and control surfaces. These seals, often referred to as dynamic thermal seals, must not only mitigate inboard heat transfer, but must also exhibit sufficient durability when scrubbed against mating surfaces. For high-temperature high-speed vehicle applications, the mating surfaces are often made from thermal protection system (TPS) materials, which are typically rougher and more abrasive than TPS materials used at lower temperatures. The high-temperature TPS materials used can include non-ablative (e.g., lightweight porous oxides, ceramic matrix composites) andor ablative systems (e.g., phenolic systems). Due to the increased need for durable high-temperature dynamic seals, researchers working with the NASA Glenn Research Center embarked on an effort to (a) characterize the tribological performance of state-of-the-art thermal seal materials against a variety of TPS materials and (b) develop approaches for improved wear resistance. Tests were conducted using a recently upgraded high-temperature tribometer to assess wear resistance for a variety of tribopairs under multiple conditions. This data will begin to frame the challenges of using these materials and eventually permit an improved ability to design and implement these critical TPS components.

  6. Models to Study NK Cell Biology and Possible Clinical Application.

    Science.gov (United States)

    Zamora, Anthony E; Grossenbacher, Steven K; Aguilar, Ethan G; Murphy, William J

    2015-08-03

    Natural killer (NK) cells are large granular lymphocytes of the innate immune system, responsible for direct targeting and killing of both virally infected and transformed cells. NK cells rapidly recognize and respond to abnormal cells in the absence of prior sensitization due to their wide array of germline-encoded inhibitory and activating receptors, which differs from the receptor diversity found in B and T lymphocytes that is due to the use of recombination-activation gene (RAG) enzymes. Although NK cells have traditionally been described as natural killers that provide a first line of defense prior to the induction of adaptive immunity, a more complex view of NK cells is beginning to emerge, indicating they may also function in various immunoregulatory roles and have the capacity to shape adaptive immune responses. With the growing appreciation for the diverse functions of NK cells, and recent technological advancements that allow for a more in-depth understanding of NK cell biology, we can now begin to explore new ways to manipulate NK cells to increase their clinical utility. In this overview unit, we introduce the reader to various aspects of NK cell biology by reviewing topics ranging from NK cell diversity and function, mouse models, and the roles of NK cells in health and disease, to potential clinical applications. © 2015 by John Wiley & Sons, Inc. Copyright © 2015 John Wiley & Sons, Inc.

  7. Atomic Force Microscopy Application in Biological Research: A Review Study

    Directory of Open Access Journals (Sweden)

    Surena Vahabi

    2013-06-01

    Full Text Available Atomic force microscopy (AFM is a three-dimensional topographic technique with a high atomic resolution to measure surface roughness. AFM is a kind of scanning probe microscope, and its near-field technique is based on the interaction between a sharp tip and the atoms of the sample surface. There are several methods and many ways to modify the tip of the AFM to investigate surface properties, including measuring friction, adhesion forces and viscoelastic properties as well as determining the Young modulus and imaging magnetic or electrostatic properties. The AFM technique can analyze any kind of samples such as polymers, adsorbed molecules, films or fibers, and powders in the air whether in a controlled atmosphere or in a liquid medium. In the past decade, the AFM has emerged as a powerful tool to obtain the nanostructural details and biomechanical properties of biological samples, including biomolecules and cells. The AFM applications, techniques, and -in particular- its ability to measure forces, are not still familiar to most clinicians. This paper reviews the literature on the main principles of the AFM modality and highlights the advantages of this technique in biology, medicine, and- especially- dentistry. This literature review was performed through E-resources, including Science Direct, PubMed, Blackwell Synergy, Embase, Elsevier, and Scholar Google for the references published between 1985 and 2010.

  8. Stochastic dynamics of magnetic nanoparticles and a mechanism of biological orientation in the geomagnetic field

    CERN Document Server

    Binhi, V N

    2004-01-01

    The rotations of microscopic magnetic particles, magnetosomes, embedded into the cytoskeleton are considered. A great number of magnetosomes are shown to possess two stable equilibrium positions, between which there occur transitions under the influence of thermal disturbances. The random rotations attain the value of order of radian. The rate of the transitions and the probability of magnetosomes to stay in the different states depend on magnetic field direction with respect to an averaged magnetosome's orientation. This effect explains the ability of migrant birds to faultless orientation in long-term passages in the absence of the direct visibility of optical reference points. The sensitivity to deviation from an `ideal' orientation is estimated to be 1-2 degrees. Possible participation of magnetosomes in biological effects caused by microwave electromagnetic fields is discussed.

  9. 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.

  10. Dynamic simulation and modeling of the motion modes produced during the 3D controlled manipulation of biological micro/nanoparticles based on the AFM.

    Science.gov (United States)

    Saraee, Mahdieh B; Korayem, Moharam H

    2015-08-01

    Determining the motion modes and the exact position of a particle displaced during the manipulation process is of special importance. This issue becomes even more important when the studied particles are biological micro/nanoparticles and the goals of manipulation are the transfer of these particles within body cells, repair of cancerous cells and the delivery of medication to damaged cells. However, due to the delicate nature of biological nanoparticles and their higher vulnerability, by obtaining the necessary force of manipulation for the considered motion mode, we can prevent the sample from interlocking with or sticking to the substrate because of applying a weak force or avoid damaging the sample due to the exertion of excessive force. In this paper, the dynamic behaviors and the motion modes of biological micro/nanoparticles such as DNA, yeast, platelet and bacteria due to the 3D manipulation effect have been investigated. Since the above nanoparticles generally have a cylindrical shape, the cylindrical contact models have been employed in an attempt to more precisely model the forces exerted on the nanoparticle during the manipulation process. Also, this investigation has performed a comprehensive modeling and simulation of all the possible motion modes in 3D manipulation by taking into account the eccentricity of the applied load on the biological nanoparticle. The obtained results indicate that unlike the macroscopic scale, the sliding of nanoparticle on substrate in nano-scale takes place sooner than the other motion modes and that the spinning about the vertical and transverse axes and the rolling of nanoparticle occur later than the other motion modes. The simulation results also indicate that the applied force necessary for the onset of nanoparticle movement and the resulting motion mode depend on the size and aspect ratio of the nanoparticle.

  11. DMSP and DMS dynamics during a mesoscale iron fertilization experiment in the Northeast Pacific Part II: Biological cycling

    Science.gov (United States)

    Merzouk, Anissa; Levasseur, Maurice; Scarratt, Michael G.; Michaud, Sonia; Rivkin, Richard B.; Hale, Michelle S.; Kiene, Ronald P.; Price, Neil M.; Li, William K. W.

    2006-10-01

    Dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS) biological cycling rates were determined during SERIES, a mesoscale iron-fertilization experiment conducted in the high-nutrient low-chlorophyll (HNLC) waters of the northeast subarctic Pacific. The iron fertilization resulted in the rapid development of a nanoplankton assemblage that persisted for 11 days before abruptly crashing. The nanoplankton bloom was followed by a diatom bloom, accompanied by an important increase in bacterial abundance and production. These iron-induced alterations of the plankton assemblage coincided with changes in the size and biological cycling of the DMSP and DMS pools. The initial nanoplankton bloom resulted in increases in particulate DMSP (DMSPp; 77-180 nmol L -1), dissolved DMSP (DMSPd; 1-24 nmol L -1), and biological gross (0.11-0.78 nmol L -1 h -1) and net (0.04-0.74 nmol L -1 h -1) DMS production rates. During the nanoplankton bloom, DMSPd consumption by bacteria exceeded their sulfur demand and the excess sulfur was probably released as DMS, consistent with the high gross DMS production rates observed during that period. The crash of the nanoplankton bloom was marked by the rapid decline of DMSPp, DMSPd, and gross DMS production to their initial values. Following the crash of the nanoplankton bloom, bacterial production and estimated sulfur demand reached transient maxima of 9.3 μg C L -1 d -1 and 14.2 nmol S L -1 d -1, respectively. During this period of high bacterial production, bacterial DMSPd consumption was also very high (6 nmol L -1 h -1), but none of the consumed DMSPd was converted into DMS and a net biological DMS consumption was measured. This transient period initiated a rapid decrease in DMS concentrations inside the iron-enriched patch, which persisted during the following diatom bloom due to low biological gross and net DMS production that prevented the replenishment of DMS. Our results show that the impact of Fe fertilization on DMS production in

  12. Autonomy and Fear of Synthetic Biology: How Can Patients' Autonomy Be Enhanced in the Field of Synthetic Biology? A Qualitative Study with Stable Patients.

    Science.gov (United States)

    Rakic, Milenko; Wienand, Isabelle; Shaw, David; Nast, Rebecca; Elger, Bernice S

    2017-04-01

    We analyzed stable patients' views regarding synthetic biology in general, the medical application of synthetic biology, and their potential participation in trials of synthetic biology in particular. The aim of the study was to find out whether patients' views and preferences change after receiving more detailed information about synthetic biology and its clinical applications. The qualitative study was carried out with a purposive sample of 36 stable patients, who suffered from diabetes or gout. Interviews were transcribed verbatim, translated and fully anonymized. Thematic analysis was applied in order to examine stable patients' attitudes towards synthetic biology, its medical application, and their participation in trials. When patients were asked about synthetic biology in general, most of them were anxious that something uncontrollable could be created. After a concrete example of possible future treatment options, patients started to see synthetic biology in a more positive way. Our study constitutes an important first empirical insight into stable patients' views on synthetic biology and into the kind of fears triggered by the term "synthetic biology." Our results show that clear and concrete information can change patients' initial negative feelings towards synthetic biology. Information should thus be transmitted with great accuracy and transparency in order to reduce irrational fears of patients and to minimize the risk that researchers present facts too positively for the purposes of persuading patients to participate in clinical trials. Potential participants need to be adequately informed in order to be able to autonomously decide whether to participate in human subject research involving synthetic biology.

  13. Study on Biological Control Of Rhizoctonia solani via Trichoderma

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Strain T02-25 was selected from approximately 30 rhizosphere isolates of Trichoderma species isolated from roots of crops. Its biological activity against Rhizoctonia solani was determined for the control efficacy to pepper seedling blight caused by R. solani in the field. The assay methods were treating R. solani sclerotia by Trichoderma conidial suspension (106cfu ml-1) and scattering Thichoderma rice bran over the pepper root medium. The results showed that T02-25 was active against R. solani in both ways, and its control efficacy was 82.7% and 78.0%, respectively. In addition to comparison of the efficacy of the two application methods, the relationship of different factors in the control efficacy of Trichoderma against R. solani was discussed.

  14. Combined Mechanical and Electrical Study of Polymers of Biological Origin

    Science.gov (United States)

    Zsoldos, G.; Szoda, K.; Marossy, K.

    2017-02-01

    Thermally Simulated Depolarization Current measurement is an excellent but not widely used method for identifying relaxation processes in polymers. The DMA method is used here to analyze the mechanical changes depend on temperature in biopolymers. The two techniques take advantage of the energy changes involved in the various phase transitions of certain polymer molecules. This allows for several properties of the material to be ascertained; melting points, enthalpies of melting, crystallization temperatures, glass transition temperatures and degradation temperatures. The examined biopolymer films are made from biological materials such as proteins and polysaccharides. These materials have gained wide usage in pharmaceutical, medical and food areas. The uses of biopolymer films depend on their structure and mechanical properties. This work is based on pectin and gelatin films. The films were prepared by casting. The casting technique used aqueous solutions in each case of sample preparation. The manufacturing process of the pectin and gelatin films was a single stage solving process.

  15. Biological studies of matrix metalloproteinase sensitive drug delivery systems

    DEFF Research Database (Denmark)

    Johansen, Pia Thermann

    due to severe side effects as a result of drug distribution to healthy tissues. To enhance ecacy of treatment and improve life quality of patients, tumor specific drug delivery strategies, such as liposome encapsulated drugs, which accumulate in tumor tissue, has gained increased attention. Several...... for delivery of drugs to specific tissues or cells utilizing biological knowledge of cancer tissue is getting increased attention. In this thesis a novel matrix metalloproteinase-2 (MMP-2) sensitive poly-ethylene glycol (PEG) coated liposomal drug delivery system for treatment of cancer was developed...... the use of MMP- 2 as a trigger for liposomal activation in tumor tissue. Thus, this new strategy provides a promising system for specific delivery of encapsulated drugs and controlled release in tumor tissues, resulting in enhanced drug bioavailability and decreased systemic side effects. In addition, we...

  16. A Comprehensive Systems Biology Approach to Studying Zika Virus

    Science.gov (United States)

    Relich, Ryan F.

    2016-01-01

    Zika virus (ZIKV) is responsible for an ongoing and intensifying epidemic in the Western Hemisphere. We examined the complete predicted proteomes, glycomes, and selectomes of 33 ZIKV strains representing temporally diverse members of the African lineage, the Asian lineage, and the current outbreak in the Americas. Derivation of the complete selectome is an ‘omics’ approach to identify distinct evolutionary pressures acting on different features of an organism. Employment of the M8 model did not show evidence of global diversifying selection acting on the ZIKV polyprotein; however, a mixed effect model of evolution showed strong evidence (P<0.05) for episodic diversifying selection acting on specific sites. Single nucleotide polymorphisms (SNPs) were predictably frequent across strains relative to the derived consensus sequence. None of the 9 published detection procedures utilize targets that share 100% identity across the 33 strains examined, indicating that ZIKV escape from molecular detection is predictable. The predicted O-linked glycome showed marked diversity across strains; however, the N-linked glycome was highly stable. All Asian and American strains examined were predicted to include glycosylation of E protein ASN154, a modification proposed to mediate neurotropism, whereas the modification was not predicted for African strains. SNP diversity, episodic diversifying selection, and differential glycosylation, particularly of ASN154, may have major biological implications for ZIKV disease. Taken together, the systems biology perspective of ZIKV indicates: a.) The recently emergent Asian/American N-glycotype is mediating the new and emerging neuropathogenic potential of ZIKV; and b.) further divergence at specific sites is predictable as endemnicity is established in the Americas. PMID:27584813

  17. Lattice dynamical studies of HTSC materials

    Energy Technology Data Exchange (ETDEWEB)

    Pintschovius, L.; Pyka, N.; Reichardt, W. (Kernforschungszentrum Karlsruhe, INFP (Germany)); Rumiantsev, A.Yu.; Mitrofanov, N.L.; Ivanov, A.S. (I.V. Kurchatov-Inst. of Atomic Energy, Moscow (USSR)); Collin, G.; Bourges, P. (Lab. Leon Brillouin, CEA-CNRS, CEN Saclay, 91 - Gif-sur-Yvette (France))

    1991-12-01

    A survey is presented on recent progress in the understanding of the lattice dynamics in Nd{sub 2}CuO{sub 4}, (La,Sr){sub 2}CuO{sub 4} and YBa{sub 2}Cu{sub 3}O{sub 6/7}. Classical anharmonicity and twinning were found to be major complications for the interpretation of the data. The lattice vibrations of the cuprates can now largely be described within the framework of shell models for strongly ionic compounds. Phonon anomalies inferred from a comparison of doped and undoped compounds resemble those found in classical superconductors. (orig.).

  18. From benchtop to raceway : spectroscopic signatures of dynamic biological processes in algal communities.

    Energy Technology Data Exchange (ETDEWEB)

    Trahan, Christine Alexandra; Garcia, Omar Fidel; Martino, Anthony A.; Raymer, Michelle; Collins, Aaron M.; Hanson, David T. (University of New Mexico, Albuquerque, NM); Turner, Tom (University of New Mexico, Albuquerque, NM); Powell, Amy Jo; James, Scott Carlton (Sandia National Laboratories, Livermore, CA); Timlin, Jerilyn Ann; Scholle, Steven (University of New Mexico, Albuquerque, NM); Dwyer, Brian P.; Ruffing, Anne; Jones, Howland D. T.; Ricken, James Bryce; Reichardt, Thomas A. (Sandia National Laboratories, Livermore, CA)

    2010-08-01

    The search is on for new renewable energy and algal-derived biofuel is a critical piece in the multi-faceted renewable energy puzzle. It has 30x more oil than any terrestrial oilseed crop, ideal composition for biodiesel, no competition with food crops, can be grown in waste water, and is cleaner than petroleum based fuels. This project discusses these three goals: (1) Conduct fundamental research into the effects that dynamic biotic and abiotic stressors have on algal growth and lipid production - Genomics/Transcriptomics, Bioanalytical spectroscopy/Chemical imaging; (2) Discover spectral signatures for algal health at the benchtop and greenhouse scale - Remote sensing, Bioanalytical spectroscopy; and (3) Develop computational model for algal growth and productivity at the raceway scale - Computational modeling.

  19. Hybrid grammar-based approach to nonlinear dynamical system identification from biological time series

    Science.gov (United States)

    McKinney, B. A.; Crowe, J. E., Jr.; Voss, H. U.; Crooke, P. S.; Barney, N.; Moore, J. H.

    2006-02-01

    We introduce a grammar-based hybrid approach to reverse engineering nonlinear ordinary differential equation models from observed time series. This hybrid approach combines a genetic algorithm to search the space of model architectures with a Kalman filter to estimate the model parameters. Domain-specific knowledge is used in a context-free grammar to restrict the search space for the functional form of the target model. We find that the hybrid approach outperforms a pure evolutionary algorithm method, and we observe features in the evolution of the dynamical models that correspond with the emergence of favorable model components. We apply the hybrid method to both artificially generated time series and experimentally observed protein levels from subjects who received the smallpox vaccine. From the observed data, we infer a cytokine protein interaction network for an individual’s response to the smallpox vaccine.

  20. Prospects for the study of biological systems with high power sources of terahertz radiation.

    Science.gov (United States)

    Weightman, Peter

    2012-10-01

    The emergence of intense sources of terahertz radiation based on lasers and electron accelerators has considerable potential for research on biological systems. This perspective gives a brief survey of theoretical work and the results of experiments on biological molecules and more complex biological systems. Evidence is accumulating that terahertz radiation influences biological systems and this needs to be clarified in order to establish safe levels of human exposure to this radiation. The use of strong sources of terahertz radiation may contribute to the resolution of controversies over the mechanism of biological organization. However the potential of these sources will only be realized if they are accompanied by the development of sophisticated pump-probe and multidimensional experimental techniques and by the study of biological systems in the controlled environments necessary for their maintenance and viability.

  1. Molecular-dynamic study of liquid ethylenediamine

    Science.gov (United States)

    Balabaev, N. K.; Kraevskii, S. V.; Rodnikova, M. N.; Solonina, I. A.

    2016-10-01

    Models of liquid ethylenediamine (ED) are built using the molecular dynamics approach at temperatures of 293-363 K and a size of 1000 molecules in a basic cell as a cuboid. The structural and dynamic characteristics of liquid ED versus temperature are derived. The gauche conformation of the ED molecule that is characteristic of the gas phase is shown to transition easily into the trans conformation of the molecules in the liquid. NH···N hydrogen bonds are analyzed in liquid ED. The number of H-bonds per ED molecule is found to vary from 5.02 at 293 K to 3.86 at 363 K. The lifetimes in the range of the temperatures and dissociation activation energy for several H-bonds in liquid ED are found to range from 0.574 to 4.524 ps at 293 K; the activation energies are 8.8 kJ/mol for 50% of the H-bonds and 16.3 kJ/mol for 6.25% of them. A weaker and more mobile spatial grid of H-bonds in liquid ED is observed, compared to data calculated earlier for monoethanolamine.

  2. Biological and physical induced oxygen dynamics in melting sea ice of the Fram Strait

    DEFF Research Database (Denmark)

    Glud, Ronnie; Rysgaard, Søren; Turner, Gavin

    2014-01-01

    We investigated the production, consumption, and exchange of O2 in melting sea ice to assess the biological- and physical-induced O2 turnover. The underside of the ice was covered with 5–20 cm3 large, buoyant algal aggregates. Their gross primary production amounted to 0.49 mmol C m−2 d−1, which...... that the aggregates were formed from agglutinated algae released from the melting ice. At the prevailing light conditions, the sea ice–encrusted communities were almost at metabolic balance, while the aggregates were net heterotrophic. Together, the two communities were responsible for an overall O2 consumption of 0.......32 mmol m−2 d−1. The sea ice–associated communities thereby represent a southward-drifting carbon source that is being exhausted by sea ice–affiliated food webs. The sea ice volume decreased rapidly, releasing meltwater at a rate 25 L m−2 d−1, but no surface melt ponds were formed. Aquatic eddy...

  3. A new fluid dynamics model to evaluate the contractile force of a biological spring, Vorticella convallaria

    Science.gov (United States)

    Ryu, Sangjin; Matsudaira, Paul

    2008-11-01

    Vorticella convallaria, a sessile peritrich having a body and spring-like stalk, is a model for a bioinspired actuator because of its remarkably fast (msec) and powerful contractions (nN). An example of a biological spring, the stalk converts biochemical energy to physical motion, but the mechanics of contraction are poorly understood. To evaluate contraction force, past models have assumed the body to be a sphere moving in quiescent water and have equated contraction force to drag force on the body described by Stokes' law. However, flow induced by contracting Vorticella does not satisfy conditions of Stokes' law because the flow is unsteady (Womersley number > 1) and bound with a solid substrate to which the cell is tethered. We develop a more rigorous model for contraction force evaluation by assuming the body to be a sphere unsteadily moving perpendicularly toward a solid surface. The model comprises quasi-steady drag force, added mass force and history force with wall effect correction terms for each force. Vorticella not only generates a maximum contraction force greater than Stokes' drag, but it also experiences drag force in the direction of contraction in the later stage of contraction due to the memory effect of water.

  4. Biological and physical induced oxygen dynamics in melting sea ice of the Fram Strait

    DEFF Research Database (Denmark)

    Glud, Ronnie; Rysgaard, Søren; Turner, Gavin

    2014-01-01

    We investigated the production, consumption, and exchange of O2 in melting sea ice to assess the biological- and physical-induced O2 turnover. The underside of the ice was covered with 5–20 cm3 large, buoyant algal aggregates. Their gross primary production amounted to 0.49 mmol C m−2 d−1, which...... that the aggregates were formed from agglutinated algae released from the melting ice. At the prevailing light conditions, the sea ice–encrusted communities were almost at metabolic balance, while the aggregates were net heterotrophic. Together, the two communities were responsible for an overall O2 consumption of 0.......32 mmol m−2 d−1. The sea ice–associated communities thereby represent a southward-drifting carbon source that is being exhausted by sea ice–affiliated food webs. The sea ice volume decreased rapidly, releasing meltwater at a rate 25 L m−2 d−1, but no surface melt ponds were formed. Aquatic eddy...

  5. Visualization in simulation tools: requirements and a tool specification to support the teaching of dynamic biological processes.

    Science.gov (United States)

    Jørgensen, Katarina M; Haddow, Pauline C

    2011-08-01

    Simulation tools are playing an increasingly important role behind advances in the field of systems biology. However, the current generation of biological science students has either little or no experience with such tools. As such, this educational glitch is limiting both the potential use of such tools as well as the potential for tighter cooperation between the designers and users. Although some simulation tool producers encourage their use in teaching, little attempt has hitherto been made to analyze and discuss their suitability as an educational tool for noncomputing science students. In general, today's simulation tools assume that the user has a stronger mathematical and computing background than that which is found in most biological science curricula, thus making the introduction of such tools a considerable pedagogical challenge. This paper provides an evaluation of the pedagogical attributes of existing simulation tools for cell signal transduction based on Cognitive Load theory. Further, design recommendations for an improved educational simulation tool are provided. The study is based on simulation tools for cell signal transduction. However, the discussions are relevant to a broader biological simulation tool set.

  6. Molecular Dynamics Studies of Energy Transfer Processes in Crystal Systems.

    Science.gov (United States)

    1984-11-30

    Computer molecular dynamics studies have been carried out on the problem of attaining a fundamental understanding of shock-induced initiation of...intramolecular energy exchange in shock-loaded systems are presented. Originator-supplied keywords include: Molecular dynamics , Energy transfer, Shock front, Shock wave, Explosives, Shock structure.

  7. First-principles studies of atomic dynamics in tetrahedrite thermoelectrics

    Science.gov (United States)

    Li, Junchao; Zhu, Mengze; Abernathy, Douglas L.; Ke, Xianglin; Morelli, Donald T.; Lai, Wei

    2016-10-01

    Cu12Sb4S13-based tetrahedrites are high-performance thermoelectrics that contain earth-abundant and environmentally friendly elements. At present, the mechanistic understanding of their low lattice thermal conductivity (applies first-principles molecular dynamics simulations, along with inelastic neutron scattering (INS) experiments, to study the incoherent and coherent atomic dynamics in Cu10.5NiZn0.5Sb4S13, in order to deepen our insight into mechanisms of anomalous dynamic behavior and low lattice thermal conductivity in tetrahedrites. Our study of incoherent dynamics reveals the anomalous "phonon softening upon cooling" behavior commonly observed in inelastic neutron scattering data. By examining the dynamic Cu-Sb distances inside the Sb[CuS3]Sb cage, we ascribe softening to the decreased anharmonic "rattling" of Cu in the cage. On the other hand, our study of coherent dynamics reveals that acoustic modes are confined in a small region of dynamic scattering space, which we hypothesize leads to a minimum phonon mean free path. By assuming a Debye model, we obtain a lattice minimum thermal conductivity value consistent with experiments. We believe this study furthers our understanding of the atomic dynamics of tetrahedrite thermoelectrics and will more generally help shed light on the origin of intrinsically low lattice thermal conductivity in these and other structurally similar materials.

  8. First-principles studies of atomic dynamics in tetrahedrite thermoelectrics

    Directory of Open Access Journals (Sweden)

    Junchao Li

    2016-10-01

    Full Text Available Cu12Sb4S13-based tetrahedrites are high-performance thermoelectrics that contain earth-abundant and environmentally friendly elements. At present, the mechanistic understanding of their low lattice thermal conductivity (<1 W m−1 K−1 at 300 K remains limited. This work applies first-principles molecular dynamics simulations, along with inelastic neutron scattering (INS experiments, to study the incoherent and coherent atomic dynamics in Cu10.5NiZn0.5Sb4S13, in order to deepen our insight into mechanisms of anomalous dynamic behavior and low lattice thermal conductivity in tetrahedrites. Our study of incoherent dynamics reveals the anomalous “phonon softening upon cooling” behavior commonly observed in inelastic neutron scattering data. By examining the dynamic Cu-Sb distances inside the Sb[CuS3]Sb cage, we ascribe softening to the decreased anharmonic “rattling” of Cu in the cage. On the other hand, our study of coherent dynamics reveals that acoustic modes are confined in a small region of dynamic scattering space, which we hypothesize leads to a minimum phonon mean free path. By assuming a Debye model, we obtain a lattice minimum thermal conductivity value consistent with experiments. We believe this study furthers our understanding of the atomic dynamics of tetrahedrite thermoelectrics and will more generally help shed light on the origin of intrinsically low lattice thermal conductivity in these and other structurally similar materials.

  9. Some case studies of random walks in dynamic random environments

    NARCIS (Netherlands)

    Soares dos Santos, Renato

    2012-01-01

    This thesis is dedicated to the study of random walks in dynamic random environments. These are models for the motion of a tracer particle in a disordered medium, which is called a static random environment if it stays constant in time, or dynamic otherwise. The evolution of the random walk is defi

  10. A non-homogeneous dynamic Bayesian network with sequentially coupled interaction parameters for applications in systems and synthetic biology.

    Science.gov (United States)

    Grzegorczyk, Marco; Husmeier, Dirk

    2012-07-12

    An important and challenging problem in systems biology is the inference of gene regulatory networks from short non-stationary time series of transcriptional profiles. A popular approach that has been widely applied to this end is based on dynamic Bayesian networks (DBNs), although traditional homogeneous DBNs fail to model the non-stationarity and time-varying nature of the gene regulatory processes. Various authors have therefore recently proposed combining DBNs with multiple changepoint processes to obtain time varying dynamic Bayesian networks (TV-DBNs). However, TV-DBNs are not without problems. Gene expression time series are typically short, which leaves the model over-flexible, leading to over-fitting or inflated inference uncertainty. In the present paper, we introduce a Bayesian regularization scheme that addresses this difficulty. Our approach is based on the rationale that changes in gene regulatory processes appear gradually during an organism's life cycle or in response to a changing environment, and we have integrated this notion in the prior distribution of the TV-DBN parameters. We have extensively tested our regularized TV-DBN model on synthetic data, in which we have simulated short non-homogeneous time series produced from a system subject to gradual change. We have then applied our method to real-world gene expression time series, measured during the life cycle of Drosophila melanogaster, under artificially generated constant light condition in Arabidopsis thaliana, and from a synthetically designed strain of Saccharomyces cerevisiae exposed to a changing environment.

  11. Systems biology, emergence and antireductionism.

    Science.gov (United States)

    Kesić, Srdjan

    2016-09-01

    This study explores the conceptual history of systems biology and its impact on philosophical and scientific conceptions of reductionism, antireductionism and emergence. Development of systems biology at the beginning of 21st century transformed biological science. Systems biology is a new holistic approach or strategy how to research biological organisms, developed through three phases. The first phase was completed when molecular biology transformed into systems molecular biology. Prior to the second phase, convergence between applied general systems theory and nonlinear dynamics took place, hence allowing the formation of systems mathematical biology. The second phase happened when systems molecular biology and systems mathematical biology, together, were applied for analysis of biological data. Finally, after successful application in science, medicine and biotechnology, the process of the formation of modern systems biology was completed. Systems and molecular reductionist views on organisms were completely opposed to each other. Implications of systems and molecular biology on reductionist-antireductionist debate were quite different. The analysis of reductionism, antireductionism and emergence issues, in the era of systems biology, revealed the hierarchy between methodological, epistemological and ontological antireductionism. Primarily, methodological antireductionism followed from the systems biology. Only after, epistemological and ontological antireductionism could be supported.

  12. Water Quality Monitoring: An Environmental Studies Unit for Biology 20/30. Student Manual.

    Science.gov (United States)

    Alberta Environment, Edmonton. Environmental Education Resources Branch.

    The objective of this environmental studies unit is to establish a water quality monitoring project for high school students in Alberta while simultaneously providing a unit which meets the objectives of the Biology 20 program (and which may also be used in Biology 10 and 30). Through this project, students assist in the collection,…

  13. Investigating Lebanese Grade Seven Biology Teachers Mathematical Knowledge and Skills: A Case Study

    Science.gov (United States)

    Raad, Nawal Abou; Chatila, Hanadi

    2016-01-01

    This paper investigates Lebanese grade 7 biology teachers' mathematical knowledge and skills, by exploring how they explain a visual representation in an activity depending on the mathematical concept "Function". Twenty Lebanese in-service biology teachers participated in the study, and were interviewed about their explanation for the…

  14. Biologically based neural circuit modelling for the study of fear learning and extinction

    Science.gov (United States)

    Nair, Satish S.; Paré, Denis; Vicentic, Aleksandra

    2016-11-01

    The neuronal systems that promote protective defensive behaviours have been studied extensively using Pavlovian conditioning. In this paradigm, an initially neutral-conditioned stimulus is paired with an aversive unconditioned stimulus leading the subjects to display behavioural signs of fear. Decades of research into the neural bases of this simple behavioural paradigm uncovered that the amygdala, a complex structure comprised of several interconnected nuclei, is an essential part of the neural circuits required for the acquisition, consolidation and expression of fear memory. However, emerging evidence from the confluence of electrophysiological, tract tracing, imaging, molecular, optogenetic and chemogenetic methodologies, reveals that fear learning is mediated by multiple connections between several amygdala nuclei and their distributed targets, dynamical changes in plasticity in local circuit elements as well as neuromodulatory mechanisms that promote synaptic plasticity. To uncover these complex relations and analyse multi-modal data sets acquired from these studies, we argue that biologically realistic computational modelling, in conjunction with experiments, offers an opportunity to advance our understanding of the neural circuit mechanisms of fear learning and to address how their dysfunction may lead to maladaptive fear responses in mental disorders.

  15. Dynamics of forest ecosystems regenerated on burned and harvested areas in mountain regions of Siberia: characteristics of biological diversity, structure and productivity

    Directory of Open Access Journals (Sweden)

    I. M. Danilin

    2016-12-01

    Full Text Available Complex estimation of forest ecosystems dynamics based on detailing characteristics of structure, growth and productivity of the stands and describing general geographical and biological management options for preserving their biodiversity and sustaining stability are discussed in the paper by describing examples of tree stands restored on burned and logged areas in mountain regions of Siberia. On vast areas in Siberia, characterized as sub-boreal, subarid and with a strongly continental climate, forests grow on seasonally frozen soils and in many cases are surrounded by vast steppe and forest-steppe areas and uplands. Developing criteria for sustainability of mountain forest ecosystems is necessary for forest resource management and conservation. It is therefore important to obtain complex biometric characteristics on forest stands and landscapes and to thoroughly study their structure, biological diversity and productivity. Morphometric methods, Weibull simulation and allometric equations were used to determine the dimensional hierarchies of coenopopulation individuals. Structure and productivity of the aboveground stand components were also studied.

  16. Systems approaches to study root architecture dynamics

    Directory of Open Access Journals (Sweden)

    Candela eCuesta

    2013-12-01

    Full Text Available The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation.Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how lateral roots and thereby root system architecture is established and developed.

  17. Fungal life-styles and ecosystem dynamics: biological aspects of plant pathogens, plant endophytes and saprophytes

    Science.gov (United States)

    Rodriguez, R.J.; Redman, R.S.

    1997-01-01

    This chapter discusses various biochemical, genetic, ecological, and evolutionary aspects of fungi that express either symbiotic or saprophytic life-styles. An enormous pool of potential pathogens exists in both agricultural and natural ecosystems, and virtually all plant species are susceptible to one or more fungal pathogens. Fungal pathogens have the potential to impact on the genetic structure of populations of individual plant species, the composition of plant communities and the process of plant succession. Endophytic fungi exist for at least part of their life cycles within the tissues of a plant host. This group of fungi is distinguished from plant pathogens because they do not elicit significant disease symptoms. However, endophytes do maintain the genetic and biochemical mechanisms required for infection and colonization of plant hosts. Fungi that obtain chemical nutrients from dead organic matter are known as saprophytes and are critical to the dynamics and resilience of ecosystems. There are two modes of saprophytic growth: one in which biomolecules that are amenable to transport across cell walls and membranes are directly absorbed, and another in which fungi must actively convert complex biopolymers into subunit forms amenable to transportation into cells. Regardless of life-style, fungi employ similar biochemical mechanisms for the acquisition and conversion of nutrients into complex biomolecules that are necessary for vegetative growth, production and dissemination of progeny, organismal competition, and survival during periods of nutrient deprivation or environmental inclemency.

  18. Studying of Phenomenon of Biological Adaptation to Heavy Water

    Directory of Open Access Journals (Sweden)

    Oleg Mosin

    2014-12-01

    Full Text Available Biological influence of deuterium on cells of various taxonomic groups of prokaryotic and eucaryotic microorganisms realizing methylotrophic, chemoheterotrophic, photo-organotrophic, and photosynthetic ways of assimilation of carbon substrates (methylotrophic bacteria Brevibacterium methylicum, chemoheterotrophic bacteria Bacillus subtilis, photo-organotrophic halobacteria Halobacterium halobium, and green micro algae Chlorella vulgaris was investigated at the growth on media with heavy water (2H2O. For investigated microorganisms are submitted the data on growth and adaptation on the growth media containing as sources of deuterated substrates 2H2O, [2H]methanol and hydrolisates of deutero-biomass of methylotrophic bacteria B. methylicum, obtained after multistage adaptation to 2H2O. The qualitative and quantitative composition of intra- and endocellular amino acids, proteins, carbohydrates and fatty acids in conditions of adaptation to 2H2O is investigated. It is shown, that the effects observed at adaptation to 2H2O, possess a complex multifactorial character and connected to cytological, morphological and physiological changes – the magnitude of the lag- period, time of cellular generation, output of biomass, a parity ratio of synthesized amino acids, proteins, carbohydrates and lipids, and also with an evolutionary level of the organization of the investigated object and the pathways of assimilation of carbon substrates as well.

  19. An ESR study on biological dosimeters: Human hair

    Energy Technology Data Exchange (ETDEWEB)

    Colak, Seyda, E-mail: seyda@hacettepe.edu.t [Hacettepe University, Physics Engineering Department, 06800 Ankara (Turkey); Ozbey, Turan [Hacettepe University, Physics Engineering Department, 06800 Ankara (Turkey)

    2011-05-15

    In the present work, characteristic features of the radicals found in untreated, gamma and UV-irradiated and mechanical damaged human hair samples were investigated by ESR spectroscopy. Heights of the resonance peaks measured with respect to the spectrum base line were used to monitor microwave power, dose-response, storage time and temperature dependent kinetic features of the radical species contributing to the formation of recorded experimental ESR spectra. Peak heights and g-values (2.0037-2.0052) determined from recorded spectra of hair were color dependent with {Delta}Hpp-0.47 mT. The act of cutting hair samples gene rates sulfur centered radicals which are found in the a-keratin structure of hair. The variations of the peak heights with temperature were related with the water content found in the hair samples. In the 6-1100 Gy dose range, a linear + quadratic dose-response curve was recorded for hair and the mean radiation yield (G{sub mean}) was calculated to be 0.4. The gamma radiation induced radicals were stable for a several hours at room temperature storage conditions. Based on these findings it was concluded that human hair samples could be used as biological/personnel dosimeters and that ESR spectroscopy could be successfully used as a potential technique for monitoring its dosimetric behaviours.

  20. Preliminary Study of Greywater Treatment through Rotating Biological Contactor

    Directory of Open Access Journals (Sweden)

    Ashfaq Ahmed Pathan

    2011-07-01

    Full Text Available The characteristics of the greywater vary from country to country and it depends upon the cultural and social behavior of the respective country. There was a considerable need to characterize and recycle the greywater. In this regard greywater was separated from the black water and analyzed for various physiochemical parameters. Among various greywater recycling treatment technologies, RBC (Rotating Biological Contactor is more effective treatment technique in reducing COD (Chemical Oxygen Demand and organic matters from the greywater. But this technology was not applied and tested in Pakistan. There was extensive need to investigate the RBC technology for greywater recycling at small scale before applying at mass scale. To treat the greywater, a single-stage RBC simulator was designed and developed at laboratory scale. An electric motor equipped with gear box to control the rotations of the disks was mounted on the tank. The simulator was run at the rate of 1.7 rpm. The disc area of the RBC was immersed about 40% in the greywater. Water samples were collected at each HRT (Hydraulic Retention Time and analyzed for the parameters such as pH, conductivity, TDS (Total Dissolved Solids, salinity, BOD5 (Biochemical Oxygen Demand, COD and suspended solids by using standard methods. The results are encouraging with percentage removal of BOD5 and COD being 53 and 60% respectively.

  1. Extraction, characterization and biological studies of phytochemicals from Mammea suriga

    Directory of Open Access Journals (Sweden)

    Mahesha M. Poojary

    2015-06-01

    Full Text Available The present work involves extraction of phytochemicals from the root bark of a well-known Indian traditional medicinal plant, viz. Mammea suriga, with various solvents and evaluation of their in vitro antimicrobial and antioxidant activities using standard methods. The phytochemical analysis indicates the presence of some interesting secondary metabolites like flavonoids, cardiac glycosides, alkaloids, saponins and tannins in the extracts. Also, the solvent extracts displayed promising antimicrobial activity against Staphylococcus aureus, Bacillus subtilis and Cryptococcus neoformans with inhibition zone in a range of 20–33 mm. Further, results of their antioxidant screening revealed that aqueous extract (with IC50 values of 111.51±1.03 and 31.05±0.92 μg/mL in total reducing power assay and DPHH radical scavenging assay, respectively and ethanolic extract (with IC50 values of 128.00±1.01 and 33.25±0.89 μg/mL in total reducing power assay and DPHH radical scavenging assay, respectively were better antioxidants than standard ascorbic acid. Interestingly, FT-IR analysis of each extract established the presence of various biologically active functional groups in it.

  2. Extraction, characterization and biological studies of phytochemicals from Mammea suriga

    Institute of Scientific and Technical Information of China (English)

    Mahesha M. Poojary; Kanivebagilu A.Vishnumurthy; Airody Vasudeva Adhikari

    2015-01-01

    The present work involves extraction of phytochemicals from the root bark of a well-known Indian traditional medicinal plant, viz. Mammea suriga, with various solvents and evaluation of their in vitro antimicrobial and antioxidant activities using standard methods. The phytochemical analysis indicates the presence of some interesting secondary metabolites like flavonoids, cardiac glycosides, alkaloids, saponins and tannins in the extracts. Also, the solvent extracts displayed promising anti-microbial activity against Staphylococcus aureus, Bacillus subtilis and Cryptococcus neoformans with inhibition zone in a range of 20–33 mm. Further, results of their antioxidant screening revealed that aqueous extract (with IC50 values of 111.51±1.03 and 31.05±0.92μg/mL in total reducing power assay and DPHH radical scavenging assay, respectively) and ethanolic extract (with IC50 values of 128.00±1.01 and 33.25±0.89μg/mL in total reducing power assay and DPHH radical scavenging assay, respectively) were better antioxidants than standard ascorbic acid. Interestingly, FT-IR analysis of each extract established the presence of various biologically active functional groups in it.

  3. Applied Bayesian statistical studies in biology and medicine

    CERN Document Server

    D’Amore, G; Scalfari, F

    2004-01-01

    It was written on another occasion· that "It is apparent that the scientific culture, if one means production of scientific papers, is growing exponentially, and chaotically, in almost every field of investigation". The biomedical sciences sensu lato and mathematical statistics are no exceptions. One might say then, and with good reason, that another collection of bio­ statistical papers would only add to the overflow and cause even more confusion. Nevertheless, this book may be greeted with some interest if we state that most of the papers in it are the result of a collaboration between biologists and statisticians, and partly the product of the Summer School th "Statistical Inference in Human Biology" which reaches its 10 edition in 2003 (information about the School can be obtained at the Web site http://www2. stat. unibo. itleventilSito%20scuolalindex. htm). is common experience - and not only This is rather important. Indeed, it in Italy - that encounters between statisticians and researchers are spora...

  4. Forest Biomass, Carbon Stocks, and Macrofungal Dynamics: A Case Study in Costa Rica

    Directory of Open Access Journals (Sweden)

    Carlos Rojas

    2014-01-01

    Full Text Available There are few published studies providing information about macrofungal biology in a context of forest dynamics in tropical areas. For this study, a characterization of above-ground standing tree biomass and carbon stocks was performed for four different forest subtypes within two life zones in Costa Rica. Fungal productivity and reproductive success were estimated and analyzed in the context of the forest systems studied and results showed fungal dynamics to be a complex and challenging topic. In the present study, fungal productivity was higher in forest patches with more tree density but independent from life zones, whereas fungal biomass was higher in premontane areas with ectomycorrhizal dominant trees. Even though some observed patterns could be explained in terms of climatic differences and biotic relationships, the high fungal productivity observed in dry forests was an interesting finding and represents a topic for further studies.

  5. Clinical study and numerical simulation of brain cancer dynamics under radiotherapy

    Science.gov (United States)

    Nawrocki, S.; Zubik-Kowal, B.

    2015-05-01

    We perform a clinical and numerical study of the progression of brain cancer tumor growth dynamics coupled with the effects of radiotherapy. We obtained clinical data from a sample of brain cancer patients undergoing radiotherapy and compare it to our numerical simulations to a mathematical model of brain tumor cell population growth influenced by radiation treatment. We model how the body biologically receives a physically delivered dose of radiation to the affected tumorous area in the form of a generalized LQ model, modified to account for the conversion process of sublethal lesions into lethal lesions at high radiation doses. We obtain good agreement between our clinical data and our numerical simulations of brain cancer progression given by the mathematical model, which couples tumor growth dynamics and the effect of irradiation. The correlation, spanning a wide dataset, demonstrates the potential of the mathematical model to describe the dynamics of brain tumor growth influenced by radiotherapy.

  6. IOM Review of FDA--approved biologics labeled or studied for pediatric use.

    Science.gov (United States)

    Field, Marilyn J; Ellinger, Lara K; Boat, Thomas F

    2013-02-01

    Studies have examined the extent to which public policies such as the Best Pharmaceuticals for Children Act have increased pediatric information in drug labeling. Little attention has focused on pediatric labeling of biologics. This analysis examines the extent to which biologics are labeled for pediatric use or have been studied in children. The analysis covers the 96 biologics (excluding vaccines) that were first licensed by the Food and Drug Administration between 1997 and 2010 and were still marketed as of 2010. Product labeling was consulted for information on approved pediatric uses, pediatric studies, or pediatric safety warnings based on analyses of adverse events. The online database ClinicalTrials.gov was searched for registered pediatric studies of these biologics. A separate analysis examined labeling and studies for 55 vaccines. For ∼60% of the 96 biologics, labeling shows approved pediatric use or pediatric study information or both. Approximately 85% of the biologics have ≥1 registered pediatric trial completed, underway, or planned. Overall, ∼90% are labeled for pediatric use, have pediatric information in the label, have a registered pediatric study, or have some combination of these characteristics. For the 55 analyzed vaccines, the corresponding figure is 95%. A majority of biologics approved in the past 15 years include some pediatric information in their labeling, and pediatric trials have been registered for a substantial majority of these products.

  7. Dynamic range studies and improvements for multiplexed photonic Doppler velocimetry

    Science.gov (United States)

    Miller, Edward Kirk; Lee, Kevin; Larson, Eric; Daykin, Edward

    2017-01-01

    We present studies of the dynamic range achievable with multiplexed photonic Doppler velocimetry (MPDV) measurements, and we demonstrate some techniques to extend the dynamic range. Improved dynamic range for MPDV measurements is needed in order to track the velocity of the free surface behind a cloud of ejecta, so we have undertaken theoretical and experimental studies of factors affecting dynamic range, particularly in cases where the large number of MPDV probe points precludes high illumination power on each channel. To quantify the potential dynamic range of a given MPDV configuration, we introduce a metric called the frequency-domain number of bits, FNOB, which is less stringent than the formally defined equivalent number of bits (ENOB). This new metric is simple to compute in the lab, and it is well suited to conventional PDV analysis, which does not require digitizer phase coherence beyond tens of nanoseconds.

  8. Social inclusion enhances biological motion processing: a functional near-infrared spectroscopy study.

    Science.gov (United States)

    Bolling, Danielle Z; Pelphrey, Kevin A; Kaiser, Martha D

    2013-04-01

    Humans are especially tuned to the movements of other people. Neural correlates of this social attunement have been proposed to lie in and around the right posterior superior temporal sulcus (STS) region, which robustly responds to biological motion in contrast to a variety of non-biological motions. This response persists even when no form information is provided, as in point-light displays (PLDs). The aim of the current study was to assess the ability of functional near-infrared spectroscopy (fNIRS) to reliably measure brain responses to PLDs of biological motion, and determine the sensitivity of these responses to interpersonal contextual factors. To establish reliability, we measured brain activation to biological motion with fNIRS and functional magnetic resonance imaging (fMRI) during two separate sessions in an identical group of 12 participants. To establish sensitivity, brain responses to biological motion measured with fNIRS were subjected to an additional social manipulation where participants were either socially included or excluded before viewing PLDs of biological motion. Results revealed comparable brain responses to biological motion using fMRI and fNIRS in the right supramarginal gyrus. Further, social inclusion increased brain responses to biological motion in right supramarginal gyrus and posterior STS. Thus, fNIRS can reliably measure brain responses to biological motion and can detect social experience-dependent modulations of these brain responses.

  9. Dynamics of biopolymers on nanomaterials studied by quasielastic neutron scattering and MD simulations

    Science.gov (United States)

    Dhindsa, Gurpreet K.

    Neutron scattering has been proved to be a powerful tool to study the dynamics of biological systems under various conditions. This thesis intends to utilize neutron scattering techniques, combining with MD simulations, to develop fundamental understanding of several biologically interesting systems. Our systems include a drug delivery system containing Nanodiamonds with nucleic acid (RNA), and two specific model proteins, beta-Casein and Inorganic Pyrophosphatase (IPPase). RNA and nanodiamond (ND) both are suitable for drug-delivery applications in nano-biotechnology. The architecturally flexible RNA with catalytic functionality forms nanocomposites that can treat life-threatening diseases. The non-toxic ND has excellent mechanical and optical properties and functionalizable high surface area, and thus actively considered for biomedical applications. In this thesis, we utilized two tools, quasielastic neutron scattering (QENS) and Molecular Dynamics Simulations to probe the effect of ND on RNA dynamics. Our work provides fundamental understanding of how hydrated RNA motions are affected in the RNA-ND nanocomposites. From the experimental and Molecular Dynamics Simulation (MD), we found that hydrated RNA motion is faster on ND surface than a freestanding one. MD Simulation results showed that the failure of Stokes Einstein relation results the presence of dynamic heterogeneities in the biomacromolecules. Radial pair distribution function from MD Simulation confirmed that the hydrophilic nature of ND attracts more water than RNA results the de-confinement of RNA on ND. Therefore, RNA exhibits faster motion in the presence of ND than freestanding RNA. In the second project, we studied the dynamics of a natively disordered protein beta-Casein which lacks secondary structures. In this study, the temperature and hydration effects on the dynamics of beta-Casein are explored by Quasielastic Neutron Scattering (QENS). We investigated the mean square displacement (MSD) of

  10. NATO Advanced Study Institute on Chaotic Dynamics : Theory and Practice

    CERN Document Server

    1992-01-01

    Many conferences, meetings, workshops, summer schools and symposia on nonlinear dynamical systems are being organized these days, dealing with a great variety of topics and themes -classical and quantum, theoretical and experimental. Some focus on integrability, or discuss the mathematical foundations of chaos. Others explore the beauty of fractals, or examine endless possibilities of applications to problems of physics, chemistry, biology and other sciences. A new scientific discipline has thus emerged, with its own distinct philosophical viewpoint and an impressive arsenal of new methods and techniques, which may be called Chaotic Dynamics. Perhaps its most outstanding achievement so far has been to shed new light on many long­ standing issues involving complicated, irregular or "chaotic" nonlinear phenomena. The concepts of randomness, complexity and unpredictability have been critically re-examined and the fundamental importance of scaling, self-similarity and sensitive dependence on parameters a...

  11. Studying Plant-Rhizobium Mutualism in the Biology Classroom: Connecting the Big Ideas in Biology through Inquiry

    Science.gov (United States)

    Suwa, Tomomi; Williamson, Brad

    2014-01-01

    We present a guided-inquiry biology lesson, using the plant-rhizobium symbiosis as a model system. This system provides a rich environment for developing connections between the big ideas in biology as outlined in the College Board's new AP Biology Curriculum. Students gain experience with the practice of scientific investigation, from…

  12. Studying Plant-Rhizobium Mutualism in the Biology Classroom: Connecting the Big Ideas in Biology through Inquiry

    Science.gov (United States)

    Suwa, Tomomi; Williamson, Brad

    2014-01-01

    We present a guided-inquiry biology lesson, using the plant-rhizobium symbiosis as a model system. This system provides a rich environment for developing connections between the big ideas in biology as outlined in the College Board's new AP Biology Curriculum. Students gain experience with the practice of scientific investigation, from…

  13. The pelagic ecosystem of the tropical Pacific Ocean: dynamic spatial modelling and biological consequences of ENSO

    Science.gov (United States)

    Lehodey, Patrick

    A feature of the central equatorial Pacific is a strong divergent equatorial upwelling called the cold tongue, which is favorable to the development of a large zonal band with high levels of primary production. Contiguous to the cold tongue, is the western Pacific warm pool, which is characterized by warmer water with lower levels of primary production. At the top of the food web, the tropical tunas are a major component of the pelagic ecosystem and have their maximum biomass in the warm pool. However, during ENSO (El Niño Southern Oscillation) events, variability is observed in both environmental factors and the spatial distribution of tuna. A Spatial Environmental Population Dynamics Model (SEPODYM) is used to assist in the analysis and interpretation of these fishery oceanographic observations. A modelling approach is described and applied to the population and fisheries of skipjack tuna, one of the top predator species with its greatest biomass in the tropical pelagic ecosystem. Environmental variables are used in the model for delineating the spawning area of skipjack, reproducing the transport of its larvae and juveniles, and simulating tuna forage. The forage production is deduced from a simple ecological transfer based on new primary production with biomass calculated as a single population. The model considers an interaction between predicted tuna density and forage density. A habitat index combining temperature preferences with forage distribution is used to constrain the movement of adult tuna. Results of the simulation allow realistic prediction of the large-scale distribution of the species. There is a remarkable out-of-phase pattern linked to ENSO between the western Pacific region and the cold tongue. This pattern is consistent with the observed movements of skipjack.

  14. Epigenetic phenomena, chromatin dynamics, and gene expression. New theoretical approaches in the study of living systems.

    Science.gov (United States)

    Boi, Luciano

    2008-01-01

    This paper is aimed at exploring the genome at the level beyond that of DNA sequence alone. We stress the fact that the level of genes is not the sole "reality" in the living world, for there are different epigenetic processes that profoundly affect change in living systems. Moreover, epigenetics very likely influences the course of evolution and the unfolding of life. We further attempt to investigate how the genome is dynamically organized into the nuclear space within the cell. We mainly focus on analyses of higher order nuclear architecture and the dynamic interactions of chromatin with other nuclear components. We especially want to know how epigenetic phenomena influences genes expression and chromosome functions. The proper understanding of these processes require new concepts and approaches be introduced and developed. In particular, we think that research in biology has to shift from only describing molecular and local features of living systems to studying the regulatory networks of interactions among gene pathways, the folding and dynamics of chromatin structure and how environmental factors affects the behavior of organisms. There are essential components of biological information on living organisms which cannot be portrayed in the DNA sequence alone. In a post-genomic era, the importance of chromatin/epigenetic interface has become increasingly apparent. One of the purposes of current research should be to highlight the enormous impact of chromatin organization and dynamics on epigenetic phenomena, and, conversely, to emphasize the important role that epigenetic phenomena play in gene expression and cell regulation.

  15. New sources and instrumentation for neutrons in biology

    DEFF Research Database (Denmark)

    Teixeira, S. C. M.; Zaccai, G.; Ankner, J.

    2008-01-01

    Neutron radiation offers significant advantages for the study of biological molecular structure and dynamics. A broad and significant effort towards instrumental and methodological development to facilitate biology experiments at neutron sources worldwide is reviewed.......Neutron radiation offers significant advantages for the study of biological molecular structure and dynamics. A broad and significant effort towards instrumental and methodological development to facilitate biology experiments at neutron sources worldwide is reviewed....

  16. New sources and instrumentation for neutrons in biology

    DEFF Research Database (Denmark)

    Teixeira, S. C. M.; Zaccai, G.; Ankner, J.;

    2008-01-01

    Neutron radiation offers significant advantages for the study of biological molecular structure and dynamics. A broad and significant effort towards instrumental and methodological development to facilitate biology experiments at neutron sources worldwide is reviewed.......Neutron radiation offers significant advantages for the study of biological molecular structure and dynamics. A broad and significant effort towards instrumental and methodological development to facilitate biology experiments at neutron sources worldwide is reviewed....

  17. Biological characterization of implant surfaces - in vitro study

    Directory of Open Access Journals (Sweden)

    Priscilla Barbosa Ferreira Soares

    Full Text Available AbstractObjectiveEvaluate the biological performance of titanium alloys grade IV under different surface treatments: sandblasting and double etching (Experimental surface 1; Exp1, NEODENT; surface with wettability increase (Experimental surface 2; Exp2, NEODENT on response of preliminary differentiation and cell maturation.Material and methodImmortalized osteoblast cells were plated on Exp1 and Exp2 titanium discs. The polystyrene plate surface without disc was used as control group (C. Cell viability was assessed by measuring mitochondrial activity (MTT at 4 and 24 h (n = 5, cell attachment was performed using trypan blue exclusion within 4 hours (n = 5, serum total protein and alkaline phosphatase normalization was performed at 4, 7 and 14 days (n = 5. Data were analyzed using one-way ANOVA and Tukey test.ResultThe values of cell viability were: 4h: C– 0.32±0.01A; Exp1– 0.34±0.08A; Exp2– 0.29±0.03A. 24h: C– 0.43±0.02A; Exp1– 0.39±0.01A; Exp2– 0.37±0.03A. The cell adhesion counting was: C– 85±10A; Exp1- 35±5B; Exp2– 20±2B. The amounts of serum total protein were 4d: C– 40±2B; Exp1– 120±10A; Exp2– 130±20A. 7d: C– 38±2B; Exp1– 75±4A; Exp2– 70±6A. 14 d: C– 100±3A; Exp1– 130±5A; Exp2– 137±9A. The values of alkaline phosphatase normalization were: 4d: C– 2.0±0.1C; Exp1– 5.1±0.8B; Exp2– 9.8±2.0A. 7d: C– 1.0±0.01C; Exp1– 5.3±0.5A; Exp2– 3.0±0.3B. 14 d: C– 4.1±0.3A; Exp1– 4.4±0.8A; Exp2– 2.2±0.2B. Different letters related to statistical differences.ConclusionThe surfaces tested exhibit different behavior at dosage of alkaline phosphatase normalization showing that the Exp2 is more associated with induction of cell differentiation process and that Exp1 is more related to the mineralization process.

  18. Transcription Adaptation during In Vitro Adipogenesis and Osteogenesis of Porcine Mesenchymal Stem Cells: Dynamics of Pathways, Biological Processes, Up-Stream Regulators, and Gene Networks.

    Science.gov (United States)

    Bionaz, Massimo; Monaco, Elisa; Wheeler, Matthew B

    2015-01-01

    The importance of mesenchymal stem cells (MSC) for bone regeneration is growing. Among MSC the bone marrow-derived stem cells (BMSC) are considered the gold standard in tissue engineering and regenerative medicine; however, the adipose-derived stem cells (ASC) have very similar properties and some advantages to be considered a good alternative to BMSC. The molecular mechanisms driving adipogenesis are relatively well-known but mechanisms driving osteogenesis are poorly known, particularly in pig. In the present study we have used transcriptome analysis to unravel pathways and biological functions driving in vitro adipogenesis and osteogenesis in BMSC and ASC. The analysis was performed using the novel Dynamic Impact Approach and functional enrichment analysis. In addition, a k-mean cluster analysis in association with enrichment analysis, networks reconstruction, and transcription factors overlapping analysis were performed in order to uncover the coordination of biological functions underlining differentiations. Analysis indicated a larger and more coordinated transcriptomic adaptation during adipogenesis compared to osteogenesis, with a larger induction of metabolism, particularly lipid synthesis (mostly triglycerides), and a larger use of amino acids for synthesis of feed-forward adipogenic compounds, larger cell signaling, lower cell-to-cell interactions, particularly for the cytoskeleton organization and cell junctions, and lower cell proliferation. The coordination of adipogenesis was mostly driven by Peroxisome Proliferator-activated Receptors together with other known adipogenic transcription factors. Only a few pathways and functions were more induced during osteogenesis compared to adipogenesis and some were more inhibited during osteogenesis, such as cholesterol and protein synthesis. Up-stream transcription factor analysis indicated activation of several lipid-related transcription regulators (e.g., PPARs and CEBPα) during adipogenesis but osteogenesis

  19. Laser-induced damage in biological tissue: Role of complex and dynamic optical properties of the medium

    Science.gov (United States)

    Ahmed, Elharith M.

    Since its invention in the early 1960's, the laser has been used as a tool for surgical, therapeutic, and diagnostic purposes. To achieve maximum effectiveness with the greatest margin of safety it is important to understand the mechanisms of light propagation through tissue and how that light affects living cells. Lasers with novel output characteristics for medical and military applications are too often implemented prior to proper evaluation with respect to tissue optical properties and human safety. Therefore, advances in computational models that describe light propagation and the cellular responses to laser exposure, without the use of animal models, are of considerable interest. Here, a physics-based laser-tissue interaction model was developed to predict the spatial and temporal temperature and pressure rise during laser exposure to biological tissues. Our new model also takes into account the dynamic nature of tissue optical properties and their impact on the induced temperature and pressure profiles. The laser-induced retinal damage is attributed to the formation of microbubbles formed around melanosomes in the retinal pigment epithelium (RPE) and the damage mechanism is assumed to be photo-thermal. Selective absorption by melanin creates these bubbles that expand and collapse around melanosomes, destroying cell membranes and killing cells. The Finite Element (FE) approach taken provides suitable ground for modeling localized pigment absorption which leads to a non-uniform temperature distribution within pigmented cells following laser pulse exposure. These hot-spots are sources for localized thermo-elastic stresses which lead to rapid localized expansions that manifest themselves as microbubbles and lead to microcavitations. Model predictions for the interaction of lasers at wavelengths of 193, 694, 532, 590, 1314, 1540, 2000, and 2940 nm with biological tissues were generated and comparisons were made with available experimental data for the retina

  20. Study Reveals Brain Biology behind Self-Control

    Science.gov (United States)

    Sparks, Sarah D.

    2011-01-01

    A new neuroscience twist on a classic psychology study offers some clues to what makes one student able to buckle down for hours of homework before a test while his classmates party. The study published in the September 2011 edition of "Proceedings of the National Academy of Science," suggests environmental cues may "hijack" the brain's mechanisms…

  1. Study Reveals Brain Biology behind Self-Control

    Science.gov (United States)

    Sparks, Sarah D.

    2011-01-01

    A new neuroscience twist on a classic psychology study offers some clues to what makes one student able to buckle down for hours of homework before a test while his classmates party. The study published in the September 2011 edition of "Proceedings of the National Academy of Science," suggests environmental cues may "hijack" the brain's mechanisms…

  2. 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.

  3. The Danish National Prescription Registry in studies of a biological pharmaceutical

    DEFF Research Database (Denmark)

    Haerskjold, Ann; Henriksen, Lonny; Way, Susanne

    2015-01-01

    BACKGROUND: National prescription databases are important tools in pharmacoepidemiological studies investigating potential long-term adverse events after drug use. Palivizumab is a biological pharmaceutical used as passive prophylaxis against severe infection with respiratory syncytial virus in h...

  4. Environmental Contaminants Monitoring in Selected Wetlands of Wyoming: Biologically Active Elements Study

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Sediment, water and biota were collected from selected wetlands in Wyoming for the Biologically Active Elements (BAE) Study in 1988, 1989 and 1990 to identify...

  5. Practical problems and their solutions in studying the biology of the ...

    African Journals Online (AJOL)

    Johnson

    their natural enemies from orchards regularly sprayed with insecticides, and combating vandalism in study orchards. ... biology and to determine its natural enemies. In this ... usually kept on twigs or leaves in dark containers and the emerging ...

  6. Boolean network model for GPR142 against Type 2 diabetes and relative dynamic change ratio analysis using systems and biological circuits approach.

    Science.gov (United States)

    Kaushik, Aman Chandra; Sahi, Shakti

    2015-06-01

    Systems biology addresses challenges in the analysis of genomics data, especially for complex genes and protein interactions using Meta data approach on various signaling pathways. In this paper, we report systems biology and biological circuits approach to construct pathway and identify early gene and protein interactions for predicting GPR142 responses in Type 2 diabetes. The information regarding genes, proteins and other molecules involved in Type 2 diabetes were retrieved from literature and kinetic simulation of GPR142 was carried out in order to determine the dynamic interactions. The major objective of this work was to design a GPR142 biochemical pathway using both systems biology as well as biological circuits synthetically. The term 'synthetically' refers to building biological circuits for cell signaling pathway especially for hormonal pathway disease. The focus of the paper is on logical components and logical circuits whereby using these applications users can create complex virtual circuits. Logic gates process represents only true or false and investigates whether biological regulatory circuits are active or inactive. The basic gates used are AND, NAND, OR, XOR and NOT gates and Integrated circuit composition of many such basic gates and some derived gates. Biological circuits may have a futuristic application in biomedical sciences which may involve placing a micro chip in human cells to modulate the down or up regulation of hormonal disease.

  7. Applying systems biology methods to the study of human physiology in extreme environments.

    Science.gov (United States)

    Edwards, Lindsay M; Thiele, Ines

    2013-03-22

    Systems biology is defined in this review as 'an iterative process of computational model building and experimental model revision with the aim of understanding or simulating complex biological systems'. We propose that, in practice, systems biology rests on three pillars: computation, the omics disciplines and repeated experimental perturbation of the system of interest. The number of ethical and physiologically relevant perturbations that can be used in experiments on healthy humans is extremely limited and principally comprises exercise, nutrition, infusions (e.g. Intralipid), some drugs and altered environment. Thus, we argue that systems biology and environmental physiology are natural symbionts for those interested in a system-level understanding of human biology. However, despite excellent progress in high-altitude genetics and several proteomics studies, systems biology research into human adaptation to extreme environments is in its infancy. A brief description and overview of systems biology in its current guise is given, followed by a mini review of computational methods used for modelling biological systems. Special attention is given to high-altitude research, metabolic network reconstruction and constraint-based modelling.

  8. A Multicolor Single-Molecule FRET Approach to Study Protein Dynamics and Interactions Simultaneously.

    Science.gov (United States)

    Götz, M; Wortmann, P; Schmid, S; Hugel, T

    2016-01-01

    Single-molecule Förster resonance energy transfer (smFRET) is a versatile tool for studying biomolecules in a quantitative manner. Multiple conformations within and interactions between biomolecules can be detected and their kinetics can be determined. Thus, smFRET has become an essential tool in enzymology. Ordinary two-color smFRET experiments can provide only limited insight into the function of biological systems, which commonly consist of more than two components. A complete understanding of complex multicomponent biological systems requires correlated information on conformational rearrangements on the one hand and transient interactions with binding partners on the other. Multicolor smFRET experiments enable the direct observation of such correlated dynamics and interactions. Here we demonstrate the power and limitations of multicolor smFRET experiments including the description of a multicolor smFRET setup and data analysis. A general analytical procedure for multicolor smFRET data is presented and applied to the multicomponent heat shock protein 90 system. This allows us to identify microscopic states in transient complexes. Conformational dynamics and nucleotide binding are simultaneously detected, which is impossible using two-color smFRET. Additionally, their correlation is quantified using 3D ensemble hidden Markov analysis, in and out of equilibrium. This method is perfectly suited for protein systems that are much more sophisticated than previously studied DNA-based systems. By extending the application to biologically relevant systems, multicolor smFRET comes of age and provides a unique mechanistic insight into protein machines.

  9. The rise in computational systems biology approaches for understanding NF-κB signaling dynamics.

    Science.gov (United States)

    Williams, Richard A; Timmis, Jon; Qwarnstrom, Eva E

    2015-07-14

    A study by Cheng et al. in this issue of Science Signaling highlights the distinct single-cell signaling characteristics conferred by pathways mediated by the adaptor proteins MyD88 and TRIF in the TLR4-dependent activation of the transcription factor nuclear factor κB (NF-κB).

  10. Carbon dynamics modelization and biological community sensitivity to temperature in an oligotrophic freshwater Antarctic lake

    DEFF Research Database (Denmark)

    Antonio Villaescusa, Juan; Jorgensen, Sven Erik; Rochera, Carlos

    2016-01-01

    Lake Limnopolar, located in one of the areas on Earth experiencing the strongest local warming, has been studied as a maritime Antarctic lake model by the Limnopolar Research Team during the last decade. Data collected during this period revealed the existence of an important meteorological inter...

  11. Carbonate chemistry dynamics and biological processes along a river-sea gradient (Gulf of Trieste, northern Adriatic Sea)

    Science.gov (United States)

    Ingrosso, Gianmarco; Giani, Michele; Cibic, Tamara; Karuza, Ana; Kralj, Martina; Del Negro, Paola

    2016-03-01

    In this paper we investigated, for two years and with a bi-monthly frequency, how physical, chemical, and biological processes affect the marine carbonate system in a coastal area characterized by high alkalinity riverine discharge (Gulf of Trieste, northern Adriatic Sea, Mediterranean Sea). By combining synoptic measurements of the carbonate system with in situ determinations of the primary production (14C incorporation technique) and secondary prokaryotic carbon production (3H-leucine incorporation) along a river-sea gradient, we showed that the conservative mixing between river endmember and off-shore waters was the main driver of the dissolved inorganic carbon (DIC) distribution and seasonal variation. However, during spring and summer seasons also the influence of biological uptake and release of DIC was significant. In the surface water of June 2012, the spreading and persistence of nutrient-rich freshwater stimulated the primary production (3.21 μg C L- 1 h- 1) and net biological DIC decrease (- 100 μmol kg- 1), reducing the dissolved CO2 concentration and increasing the pHT. Below the pycnocline of August 2012, instead, an elevated bacterial carbon production rate (0.92 μg C L- 1 h- 1) was related with net DIC increase (92 μmol kg- 1), low dissolved oxygen concentration, and strong pHT reduction, suggesting the predominance of bacterial heterotrophic respiration over primary production. The flux of carbon dioxide estimated at the air-sea interface exerted a low influence on the seasonal variation of the carbonate system. A complex temporal and spatial dynamic of the air-sea CO2 exchange was also detected, due to the combined effects of seawater temperature, river discharge, and water circulation. On annual scale the system was a sink of atmospheric CO2. However, in summer and during elevated riverine discharges, the area close to the river's mouth acted as a source of carbon dioxide. Also the wind speed was crucial in controlling the air-sea CO2

  12. Dynamic Relationship Between Biologically Active Soil Organic Carbon and Aggregate Stability in Long-Term Organically Fertilized Soils

    Institute of Scientific and Technical Information of China (English)

    LI Cheng-Liang; XU Jiang-Bing; HE Yuan-Qiu; LIU Yan-Li; FAN Jian-Bo

    2012-01-01

    Biologically active soil organic carbon (BASOC) is an important fraction of soil organic carbon (SOC),but our understanding of the correlation between BASOC and soil aggregate stability is limited.At an ecological experimental station (28° 04′-28° 37′ N,116°41′-117° 09′ E) in Yujiang County,Jiangxi Province,China,we analyzed the dynamic relationship between soil aggregate stability and BASOC content over time in the red soil (Udic Ferrosols) fertilized with a nitrogen-phosphorus-potassium chemical fertilizer (NPK)without manure or with NPK plus livestock manure or green manure.The dynamics of BASOC was evaluated using CO2 efflux,and soil aggregates were separated according to size using a wet-sieving technique.The soils fertilized with NPK plus livestock manure had a significantly higher content of BASOC and an improved aggregate stability compared to the soils fertilized with NPK plus green manure or NPK alone The BASOC contents in all fertilized soils decreased over time The contents of large aggregates (800-2000μm) dramatically decreased over the first 7 d of incubation,but the contents of small aggregates (< 800.μm) either remained the same or increased,depending on the incubation time and specific aggregate sizes.The aggregate stability did not differ significantly at the beginning and end of incubation,but the lowest stability inall fertilized soils occurred in the middle of the incubation,which implied that the soils had a strong resilience for aggregate stability.The change in BASOC content was only correlated with aggregate stability during the first 27 d of incubation.

  13. A Trade Study of Two Membrane-Aerated Biological Water Processors

    Science.gov (United States)

    Allada, Ram; Lange, Kevin; Vega. Leticia; Roberts, Michael S.; Jackson, Andrew; Anderson, Molly; Pickering, Karen

    2011-01-01

    Biologically based systems are under evaluation as primary water processors for next generation life support systems due to their low power requirements and their inherent regenerative nature. This paper will summarize the results of two recent studies involving membrane aerated biological water processors and present results of a trade study comparing the two systems with regards to waste stream composition, nutrient loading and system design. Results of optimal configurations will be presented.

  14. Electron Transfer Studies of Ruthenium(II) Complexes with Biologically Important Phenolic Acids and Tyrosine.

    Science.gov (United States)

    Rajeswari, Angusamy; Ramdass, Arumugam; Muthu Mareeswaran, Paulpandian; Rajagopal, Seenivasan

    2016-03-01

    The ruthenium(II) complexes having 2,2'-bipyridine and phenanthroline derivatives are synthesized and characterized. The photophysical properties of these complexes at pH 12.5 are studied. The electron transfer reaction of biologically important phenolic acids and tyrosine are studied using absorption, emission and transient absorption spectral techniques. Semiclassical theory is applied to calculate the rate of electron transfer between ruthenium(II) complexes and biologically important phenolic acids.

  15. Northeast Cooperative Research Study Fleet (SF) Program Biological Sampling Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Northeast Cooperative Research Study Fleet (SF) Program partners with a subset of commercial fishermen to collect high quality, high resolution, haul by haul...

  16. Biological characteristics as a part of pollution monitoring studies

    Digital Repository Service at National Institute of Oceanography (India)

    Nair, V.R.; Govindan, K.

    Ecosystem modifications can be considered as an integral part of any pollution monitoring studies and in such cases community structure/diversity is of prime importance. Considering this advantage of aquatic life, pelagic and benthic communities...

  17. The dynamic range of biologic functions and variation of many environmental cues may be declining in the modern age: implications for diseases and therapeutics.

    Science.gov (United States)

    Yun, Anthony J; Bazar, Kimberly A; Gerber, Anthony; Lee, Patrick Y; Daniel, Stephanie M

    2005-01-01

    We hypothesize that declining dynamic range and variation of environmental cues may contribute to health dysfunctions, and that judicious expansion of biologic dynamic ranges may be beneficial. Three disparate examples involving the endocrine, autonomic, and musculoskeletal systems are discussed. Daytime sheltering, optical shading, and nighttime use of artificial light may reduce circadian luminal variation. The resulting melatonin alterations may contribute to systemic dysfunctions. Loss of temporal variation of other hormones may contribute to biologic dysfunctions, especially those involving the hypothalamic-pituitary axis. Reduced variation of physical exertion, environmental stressors, and thermal gradients that characterize modern lifestyles may reduce the autonomic dynamic range resulting in lowered heart rate variability and a myriad of systemic dysfunctions. The health benefits of activities such as exercise, meditation, acupuncture, coitus, and laughter may operate through increasing autonomic variability. Reduced physical exertion also accounts for declining dynamic range of musculoskeletal function. The resulting muscle atrophy, fat infiltration, and sarcomere shortening may not only have deleterious local effects, but may also be involved in systemic metabolic dysfunctions such as insulin resistance. The extent to which our endogenous systems rely on environmental variation for self-tuning and the impact that under-utilization of compensatory mechanisms has on biologic function are not well understood. Modern therapeutic approaches generally result in reversion to the mean of physiologic functions and may buffer against variation. For example, beta-blockers are given to reduce adrenergic excess, insulin to treat insulin insufficiency, serotonin-reuptake inhibitors for depression, and refractive lenses for myopia. By undermining the demand for native compensatory functions, such therapeutic strategies may actually impair future ability to respond to

  18. Femtosecond photodissociation dynamics of I studied by ion imaging

    DEFF Research Database (Denmark)

    Larsen, J.J.; Bjerre, N.; Mørkbak, N.J.

    1998-01-01

    on imaging is employed to analyze the fragments from timed Coulomb explosion studies of femtosecond (fs) molecular dynamics. The technique provides high detection efficiency and direct recording of the two-dimensional velocity of all ionized fragments. We illustrate the approach by studying photo...... agreement with quantum mechanical wave packet simulations. We discuss the perspectives for extending the studies to photochemical reactions of small polyatomic molecules......on imaging is employed to analyze the fragments from timed Coulomb explosion studies of femtosecond (fs) molecular dynamics. The technique provides high detection efficiency and direct recording of the two-dimensional velocity of all ionized fragments. We illustrate the approach by studying...

  19. Placenta-on-a-chip: a novel platform to study the biology of the human placenta.

    Science.gov (United States)

    Lee, Ji Soo; Romero, Roberto; Han, Yu Mi; Kim, Hee Chan; Kim, Chong Jai; Hong, Joon-Seok; Huh, Dongeun

    2016-01-01

    Studying the biology of the human placenta represents a major experimental challenge. Although conventional cell culture techniques have been used to study different types of placenta-derived cells, current in vitro models have limitations in recapitulating organ-specific structure and key physiological functions of the placenta. Here we demonstrate that it is possible to leverage microfluidic and microfabrication technologies to develop a microengineered biomimetic model that replicates the architecture and function of the placenta. A "Placenta-on-a-Chip" microdevice was created by using a set of soft elastomer-based microfabrication techniques known as soft lithography. This microsystem consisted of two polydimethylsiloxane (PDMS) microfluidic channels separated by a thin extracellular matrix (ECM) membrane. To reproduce the placental barrier in this model, human trophoblasts (JEG-3) and human umbilical vein endothelial cells (HUVECs) were seeded onto the opposite sides of the ECM membrane and cultured under dynamic flow conditions to form confluent epithelial and endothelial layers in close apposition. We tested the physiological function of the microengineered placental barrier by measuring glucose transport across the trophoblast-endothelial interface over time. The permeability of the barrier study was analyzed and compared to that obtained from acellular devices and additional control groups that contained epithelial or endothelial layers alone. Our microfluidic cell culture system provided a tightly controlled fluidic environment conducive to the proliferation and maintenance of JEG-3 trophoblasts and HUVECs on the ECM scaffold. Prolonged culture in this model produced confluent cellular monolayers on the intervening membrane that together formed the placental barrier. This in vivo-like microarchitecture was also critical for creating a physiologically relevant effective barrier to glucose transport. Quantitative investigation of barrier function was

  20. 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 ​Other Fact Sheets What is structural biology? Structural biology is the study of how biological ...